njahn82/dvcs_epmc_md.csv

## dvcs_epmc_md.csv
"","id","source","pmid","DOI","title","authorString","journalTitle","pubYear","journalIssn","pubType","isOpenAccess","inEPMC","inPMC","citedByCount","hasReferences","hasTextMinedTerms","hasDbCrossReferences","hasLabsLinks","hasTMAccessionNumbers","luceneScore","issue","journalVolume","pageInfo","pmcid","tmAccessionTypeList","dbCrossReferenceList","dvcs"
"1","25577191","MED","25577191","10.1093/molbev/msu411","CodABC: A Computational Framework to Coestimate Recombination, Substitution and Molecular Adaptation rates by approximate Bayesian computation.","Arenas M, Lopes JS, Beaumont MA, Posada D.","Mol Biol Evol","2015","0737-4038","journal article","N","N","N","0","N","N","N","N","N","719.82654",NA,NA,NA,NA,NA,NA,"code.google.com"
"2","25217575","MED","25217575","10.1093/bioinformatics/btu609","EUROCarbDB(CCRC): a EUROCarbDB node for storing glycomics standard data.","Al Jadda K, Porterfield MP, Bridger R, Heiss C, Tiemeyer M, Wells L, Miller JA, York WS, Ranzinger R.","Bioinformatics","2015","1367-4803","journal article","N","N","N","0","N","N","N","N","N","719.82654","2","31","242-245",NA,NA,NA,"code.google.com"
"3","25265629","MED","25265629","10.1109/tmi.2014.2360496","Exact confidence intervals for channelized hotelling observer performance in image quality studies.","Wunderlich A, Noo F, Gallas BD, Heilbrun ME.","IEEE Trans Med Imaging","2015","0278-0062","journal article","N","N","N","0","N","N","N","N","N","719.82654","2","34","453-464",NA,NA,NA,"code.google.com"
"4","25223640","MED","25223640","10.1093/bioinformatics/btu568","JAMM: a peak finder for joint analysis of NGS replicates.","Ibrahim MM, Lacadie SA, Ohler U.","Bioinformatics","2015","1367-4803","journal article","N","N","N","0","N","N","N","N","N","718.1179","1","31","48-55",NA,NA,NA,"code.google.com"
"5","25282642","MED","25282642","10.1093/bioinformatics/btu652","LocalAli: an evolutionary-based local alignment approach to identify functionally conserved modules in multiple networks.","Hu J, Reinert K.","Bioinformatics","2015","1367-4803","journal article","N","N","N","0","N","N","N","N","N","718.1179","3","31","363-372",NA,NA,NA,"code.google.com"
"6","25209223","MED","25209223","10.1093/sysbio/syu062","ModelOMatic: fast and automated model selection between RY, nucleotide, amino acid, and codon substitution models.","Whelan S, Allen JE, Blackburne BP, Talavera D.","Syst Biol","2015","1063-5157","journal article; research support, non-u.s. gov't","N","N","N","0","N","N","N","Y","N","716.4093","1","64","42-55",NA,NA,NA,"code.google.com"
"7","25589474","MED","25589474","10.1038/srep07813","qPMS9: An Efficient Algorithm for Quorum Planted Motif Search.","Nicolae M, Rajasekaran S.","Sci Rep","2015","2045-2322","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","710.99023",NA,"5","7813","PMC4295094",NA,NA,"code.google.com"
"8","25625228","MED","25625228","10.3201/eid2102.140290","Potentially novel ehrlichia species in horses, nicaragua.","O'Nion VL, Montilla HJ, Qurollo BA, Maggi RG, Hegarty BC, Tornquist SJ, Breitschwerdt EB.","Emerg Infect Dis","2015","1080-6040","journal article; brief-report","Y","Y","N","0","N","Y","N","N","Y","710.4291","2","21","335-338","PMC4313632","gen",NA,"code.google.com"
"9","25260700","MED","25260700","10.1093/bioinformatics/btu638","HTSeq-a Python framework to work with high-throughput sequencing data.","Anders S, Pyl PT, Huber W.","Bioinformatics","2015","1367-4803","journal article; research-article","Y","Y","N","6","Y","Y","N","N","N","709.57477","2","31","166-169","PMC4287950",NA,NA,"code.google.com"
"10","25505034","MED","25505034","10.1093/pcp/pcu188","Plant Omics Data Center: An Integrated Web Repository for Interspecies Gene Expression Networks with NLP-Based Curation.","Ohyanagi H, Takano T, Terashima S, Kobayashi M, Kanno M, Morimoto K, Kanegae H, Sasaki Y, Saito M, Asano S, Ozaki S, Kudo T, Yokoyama K, Aya K, Suwabe K, Suzuki G, Aoki K, Kubo Y, Watanabe M, Matsuoka M, Yano K.","Plant Cell Physiol","2015","0032-0781","journal article; research-article","Y","Y","N","0","N","Y","N","N","N","709.14764","1","56","e9","PMC4301748",NA,NA,"code.google.com"
"11","25568947","MED","25568947","10.1371/journal.pone.0117075","Variable Frequency of Plastid RNA Editing among Ferns and Repeated Loss of Uridine-to-Cytidine Editing from Vascular Plants.","Guo W, Grewe F, Mower JP.","PLoS One","2015","1932-6203","journal article; research-article","Y","Y","N","0","Y","Y","N","N","Y","708.7205","1","10","e0117075","PMC4287625","gen",NA,"code.google.com"
"12","25129841","MED","25129841","10.1007/s12021-014-9240-7","IT Infrastructure to Support the Secondary Use of Routinely Acquired Clinical Imaging Data for Research.","Leung KY, van der Lijn F, Vrooman HA, Sturkenboom MC, Niessen WJ.","Neuroinformatics","2015","1539-2791","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","708.29333","1","13","65-81","PMC4303741",NA,NA,"code.google.com"
"13","24115168","MED","24115168","10.1093/bioinformatics/btt582","orthAgogue: an agile tool for the rapid prediction of orthology relations.","Ekseth OK, Kuiper M, Mironov V.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","1","Y","N","N","Y","N","335.79907","5","30","734-736",NA,NA,NA,"code.google.com"
"14","24453188","MED","24453188","10.1002/pmic.201300281","The jmzQuantML programming interface and validator for the mzQuantML data standard.","Qi D, Krishna R, Jones AR.","Proteomics","2014","1615-9853","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","N","N","N","334.21185","6","14","685-688","PMC4016760",NA,NA,"code.google.com"
"15","24170401","MED","24170401","10.1007/978-1-62703-646-7_10","Phylogeny-aware alignment with PRANK.","LÃ¶ytynoja A.","Methods Mol Biol","2014","1064-3745","journal article","N","N","N","2","N","N","N","N","N","334.09042",NA,"1079","155-170",NA,NA,NA,"code.google.com"
"16","24356218","MED","24356218","10.1016/j.aca.2013.11.032","A strategy that iteratively retains informative variables for selecting optimal variable subset in multivariate calibration.","Yun YH, Wang WT, Tan ML, Liang YZ, Li HD, Cao DS, Lu HM, Xu QS.","Anal Chim Acta","2014","0003-2670","journal article; research support, non-u.s. gov't","N","N","N","0","Y","N","N","N","N","334.09042",NA,"807","36-43",NA,NA,NA,"code.google.com"
"17","24336806","MED","24336806","10.1093/bioinformatics/btt715","NetCoffee: a fast and accurate global alignment approach to identify functionally conserved proteins in multiple networks.","Hu J, Kehr B, Reinert K.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","1","Y","N","N","N","N","334.09042","4","30","540-548",NA,NA,NA,"code.google.com"
"18","24604165","MED","24604165","10.1007/s00726-014-1697-z","Selection of relevant features from amino acids enables development of robust classifiers.","Das Roy R, Dash D.","Amino Acids","2014","0939-4451","evaluation studies; journal article; research support, non-u.s. gov't","N","N","N","3","Y","N","N","N","N","334.09042","5","46","1343-1351",NA,NA,NA,"code.google.com"
"19","25424913","MED","25424913","10.2478/s11658-014-0221-5","FunPred-1: Protein function prediction from a protein interaction network using neighborhood analysis.","Saha S, Chatterjee P, Basu S, Kundu M, Nasipuri M.","Cell Mol Biol Lett","2014","1425-8153","journal article","N","N","N","0","N","N","N","N","N","334.09042","4","19","675-691",NA,NA,NA,"code.google.com"
"20","24153413","MED","24153413","10.1016/j.jbi.2013.10.002","Identifying non-elliptical entity mentions in a coordinated NP with ellipses.","Chae J, Jung Y, Lee T, Jung S, Huh C, Kim G, Kim H, Oh H.","J Biomed Inform","2014","1532-0464","journal article; research support, non-u.s. gov't","N","N","N","0","Y","N","N","N","N","332.3818",NA,"47","139-152",NA,NA,NA,"code.google.com"
"21","24680097","MED","24680097","10.1016/j.artmed.2014.02.002","Statistical parsing of varieties of clinical Finnish.","Laippala V, Viljanen T, Airola A, Kanerva J, SalanterÃ¤ S, Salakoski T, Ginter F.","Artif Intell Med","2014","0933-3657","journal article; research support, non-u.s. gov't","N","N","N","0","N","N","N","N","N","332.3818","3","61","131-136",NA,NA,NA,"code.google.com"
"22","24894502","MED","24894502","10.1093/bioinformatics/btu372","PePr: a peak-calling prioritization pipeline to identify consistent or differential peaks from replicated ChIP-Seq data.","Zhang Y, Lin YH, Johnson TD, Rozek LS, Sartor MA.","Bioinformatics","2014","1367-4803","journal article; research support, n.i.h., extramural","N","N","N","0","Y","N","N","N","N","332.3818","18","30","2568-2575",NA,NA,NA,"code.google.com"
"23","24659499","MED","24659499","10.1002/pmic.201300560","jmzTab: a java interface to the mzTab data standard.","Xu QW, Griss J, Wang R, Jones AR, Hermjakob H, VizcaÃno JA.","Proteomics","2014","1615-9853","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","2","Y","Y","N","N","N","331.68158","11","14","1328-1332","PMC4230411",NA,NA,"code.google.com"
"24","24078714","MED","24078714","10.1093/bioinformatics/btt567","A C library for retrieving specific reactions from the BioModels database.","Neal ML, Galdzicki M, Gallimore JT, Sauro HM.","Bioinformatics","2014","1367-4803","journal article; research support, n.i.h., extramural; research-article","N","Y","N","1","Y","Y","N","N","N","331.00833","1","30","129-130","PMC3866552",NA,NA,"code.google.com"
"25","25505091","MED","25505091",NA,"JEPEG: a summary statistics based tool for gene-level joint testing of functional variants.","Lee D, Williamson VS, Bigdeli TB, Riley BP, Fanous AH, Vladimirov VI, Bacanu SA.","Bioinformatics","2014","1367-4803","journal article","N","N","N","0","N","N","N","N","N","330.6732",NA,NA,NA,NA,NA,NA,"code.google.com"
"26","24876376","MED","24876376","10.1093/bioinformatics/btu360","Reference-free prediction of rearrangement breakpoint reads.","Wijaya E, Shimizu K, Asai K, Hamada M.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","0","Y","N","N","N","N","330.6732","18","30","2559-2567",NA,NA,NA,"code.google.com"
"27","25481010","MED","25481010","10.1093/bioinformatics/btu804","SNPlice: Variants that Modulate Intron-retention from RNA-sequencing Data.","Mudvari P, Movassagh M, Kowsari K, Seyfi A, Kokkinaki M, Edwards NJ, Golestaneh N, Horvath A.","Bioinformatics","2014","1367-4803","journal article","N","N","N","0","N","N","N","N","N","330.6732",NA,NA,NA,NA,NA,NA,"code.google.com"
"28","24771516","MED","24771516","10.1093/bioinformatics/btu202","ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging.","OvesnÃ½ M, KÅÃÅ¾ek P, Borkovec J, Svindrych Z, Hagen GM.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","329.37918","16","30","2389-2390","PMC4207427",NA,NA,"code.google.com"
"29","25099149","MED","25099149","10.1371/journal.pone.0102623","The GBIF integrated publishing toolkit: facilitating the efficient publishing of biodiversity data on the internet.","Robertson T, DÃ¶ring M, Guralnick R, Bloom D, Wieczorek J, Braak K, Otegui J, Russell L, Desmet P.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","Y","329.37918","8","9","e102623","PMC4123864","doi",NA,"code.google.com"
"30","24045775","MED","24045775","10.1093/bioinformatics/btt539","Pattern search in BioPAX models.","Babur Ã, Aksoy BA, Rodchenkov I, SÃ¼mer SO, Sander C, Demir E.","Bioinformatics","2014","1367-4803","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","1","Y","Y","N","N","N","329.37918","1","30","139-140","PMC3866551",NA,NA,"code.google.com"
"31","25052702","MED","25052702","10.1093/database/bau075","Standardized description of scientific evidence using the Evidence Ontology (ECO).","Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M.","Database (Oxford)","2014","1758-0463","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","1","Y","Y","N","N","N","329.37918",NA,"2014",NA,"PMC4105709",NA,NA,"code.google.com"
"32","25089276","MED","25089276","10.1155/2014/742482","SSFinder: high throughput CRISPR-Cas target sites prediction tool.","Upadhyay SK, Sharma S.","Biomed Res Int","2014","2314-6133","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","329.37918",NA,"2014","742482","PMC4095993",NA,NA,"code.google.com"
"33","24336645","MED","24336645","10.1093/bioinformatics/btt682","PhenoMan: phenotypic data exploration, selection, management and quality control for association studies of rare and common variants.","Li B, Wang G, Leal SM.","Bioinformatics","2014","1367-4803","journal article; research support, n.i.h., extramural; research-article","N","Y","N","0","Y","Y","N","N","N","329.37918","3","30","442-444","PMC3904519",NA,NA,"code.google.com"
"34","24557445","MED","24557445","10.1093/molbev/msu078","Simulation of genome-wide evolution under heterogeneous substitution models and complex multispecies coalescent histories.","Arenas M, Posada D.","Mol Biol Evol","2014","0737-4038","journal article; research support, non-u.s. gov't; letter","Y","Y","Y","0","Y","Y","N","N","N","328.9646","5","31","1295-1301","PMC3995339",NA,NA,"code.google.com"
"35","24604644","MED","24604644","10.1128/genomea.00116-14","Genome Sequence of a Bacillus anthracis Outbreak Strain from Zambia, 2011.","Ohnishi N, Maruyama F, Ogawa H, Kachi H, Yamada S, Fujikura D, Nakagawa I, Hang'ombe MB, Thomas Y, Mweene AS, Higashi H.","Genome Announc","2014","2169-8287","journal article; brief-report","Y","Y","Y","1","Y","Y","N","N","N","328.9646","2","2",NA,"PMC3945500",NA,NA,"code.google.com"
"36","24831140","MED","24831140","10.1128/genomea.00368-14","Draft Genome Sequence of Pseudomonas aeruginosa Strain RB, a Bacterium Capable of Synthesizing Cadmium Selenide Nanoparticles.","Ayano H, Kuroda M, Soda S, Ike M.","Genome Announc","2014","2169-8287","journal article; brief-report","Y","Y","Y","0","Y","Y","N","N","Y","328.9646","3","2",NA,"PMC4022804","gen",NA,"code.google.com"
"37","25031571","MED","25031571","10.5808/gi.2014.12.2.76","SFannotation: A Simple and Fast Protein Function Annotation System.","Yu DS, Kim BK.","Genomics Inform","2014","1598-866x","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","328.9646","2","12","76-78","PMC4099352",NA,NA,"code.google.com"
"38","24482511","MED","24482511","10.1128/genomea.01203-13","Draft Genome Sequence of the Gammaproteobacterial Strain MOLA455, a Representative of a Ubiquitous Proteorhodopsin-Producing Group in the Ocean.","Courties A, Riedel T, Jarek M, Papadatou M, Intertaglia L, Lebaron P, Suzuki MT.","Genome Announc","2014","2169-8287","journal article; brief-report","Y","Y","Y","0","Y","Y","Y","N","N","328.9646","1","2",NA,"PMC3907726",NA,"EMBLUNIPROT","code.google.com"
"39","25414506","MED","25414506","10.1128/genomea.01208-14","Genome Sequence of Gammaproteobacterial Pseudohaliea rubra Type Strain DSM 19751, Isolated from Coastal Seawater of the Mediterranean Sea.","Spring S, Fiebig A, Riedel T, GÃ¶ker M, Klenk HP.","Genome Announc","2014","2169-8287","journal article; brief-report","Y","Y","N","0","Y","Y","Y","N","N","328.9646","6","2",NA,"PMC4239361",NA,"EMBLUNIPROT","code.google.com"
"40","25077800","MED","25077800","10.1371/journal.pone.0103441","Fast and sensitive alignment of microbial whole genome sequencing reads to large sequence datasets on a desktop PC: application to metagenomic datasets and pathogen identification.","Pongor LS, Vera R, Ligeti B.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","328.91098","7","9","e103441","PMC4117525",NA,NA,"code.google.com"
"41","25417797","MED","25417797","10.3201/eid2012.140184","Mycobacterium species related to M. leprae and M. lepromatosis from cows with bovine nodular thelitis.","Pin D, GuÃ©rin-FaublÃ©e V, Garreau V, Breysse F, Dumitrescu O, Flandrois JP, Lina G.","Emerg Infect Dis","2014","1080-6040","journal article; research support, non-u.s. gov't; brief-report","Y","Y","N","0","Y","Y","N","N","N","328.171","12","20","2111-2114","PMC4257800",NA,NA,"code.google.com"
"42","24292941","MED","24292941","10.1093/bioinformatics/btt693","AISAIC: a software suite for accurate identification of significant aberrations in cancers.","Zhang B, Hou X, Yuan X, Shih IeM, Zhang Z, Clarke R, Wang RR, Fu Y, Madhavan S, Wang Y, Yu G.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","N","0","Y","Y","N","N","N","328.171","3","30","431-433","PMC3904524",NA,NA,"code.google.com"
"43","24999329","MED","24999329","10.3389/fninf.2014.00062","Interdisciplinary perspectives on the development, integration, and application of cognitive ontologies.","Hastings J, Frishkoff GA, Smith B, Jensen M, Poldrack RA, Lomax J, Bandrowski A, Imam F, Turner JA, Martone ME.","Front Neuroinform","2014","1662-5196","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","328.1103",NA,"8","62","PMC4064452",NA,NA,"code.google.com"
"44","25494997","MED","25494997","10.1186/s12859-014-0382-2","Masking as an effective quality control method for next-generation sequencing data analysis.","Yun S, Yun S.","BMC Bioinformatics","2014","1471-2105","journal article; research support, n.i.h., intramural; research-article","Y","Y","N","0","Y","Y","N","N","N","328.04892","1","15","382","PMC4268903",NA,NA,"code.google.com"
"45","25209025","MED","25209025","10.1093/database/bau084","Unsupervised gene function extraction using semantic vectors.","Emadzadeh E, Nikfarjam A, Ginn RE, Gonzalez G.","Database (Oxford)","2014","1758-0463","journal article; research support, n.i.h., extramural; research-article","Y","Y","N","0","Y","Y","N","N","N","328.04892",NA,"2014",NA,"PMC4160099",NA,NA,"code.google.com"
"46","24214537","MED","24214537","10.1093/molbev/mst221","A guide for the design of evolve and resequencing studies.","Kofler R, SchlÃ¶tterer C.","Mol Biol Evol","2014","0737-4038","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","N","N","N","327.861","2","31","474-483","PMC3907048",NA,NA,"code.google.com"
"47","24624052","MED","24624052","10.3389/fnins.2014.00015","Connexel visualization: a software implementation of glyphs and edge-bundling for dense connectivity data using brainGL.","BÃ¶ttger J, Schurade R, Jakobsen E, Schaefer A, Margulies DS.","Front Neurosci","2014","1662-4548","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","327.78085",NA,"8","15","PMC3941704",NA,NA,"code.google.com"
"48","24465198","MED","24465198","10.1371/journal.pcbi.1003441","VBA: a probabilistic treatment of nonlinear models for neurobiological and behavioural data.","Daunizeau J, Adam V, Rigoux L.","PLoS Comput Biol","2014","1553-734x","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","4","Y","Y","N","N","N","327.36166","1","10","e1003441","PMC3900378",NA,NA,"code.google.com"
"49","25086704","MED","25086704","10.1186/1471-2164-15-642","Integrating biological pathways and genomic profiles with ChiBE 2.","Babur Ã, Dogrusoz U, ÃakÄ±r M, Aksoy BA, Schultz N, Sander C, Demir E.","BMC Genomics","2014","1471-2164","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","327.30908","1","15","642","PMC4131037",NA,NA,"code.google.com"
"50","24438387","MED","24438387","10.1186/2041-1480-5-4","The epidemiology ontology: an ontology for the semantic annotation of epidemiological resources.","Pesquita C, Ferreira JD, Couto FM, Silva MJ.","J Biomed Semantics","2014","2041-1480","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","327.30908","1","5","4","PMC3926306",NA,NA,"code.google.com"
"51","25276334","MED","25276334","10.1186/2041-1480-5-39","The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology.","Thacker RW, DÃaz MC, Kerner A, Vignes-Lebbe R, Segerdell E, Haendel MA, Mungall CJ.","J Biomed Semantics","2014","2041-1480","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","327.30908","1","5","39","PMC4177528",NA,NA,"code.google.com"
"52","23584085","MED","23584085","10.1016/j.bbapap.2013.04.004","A tutorial for software development in quantitative proteomics using PSI standard formats.","Gonzalez-Galarza FF, Qi D, Fan J, Bessant C, Jones AR.","Biochim Biophys Acta","2014","0006-3002","journal article; review; research support, non-u.s. gov't; review-article","Y","Y","Y","1","Y","Y","N","N","N","327.30908","1 pt a","1844","88-97","PMC4008935",NA,NA,"code.google.com"
"53","24760958","MED","24760958","10.1074/mcp.m113.035907","qcML: an exchange format for quality control metrics from mass spectrometry experiments.","Walzer M, Pernas LE, Nasso S, Bittremieux W, Nahnsen S, Kelchtermans P, Pichler P, van den Toorn HW, Staes A, Vandenbussche J, Mazanek M, Taus T, Scheltema RA, Kelstrup CD, Gatto L, van Breukelen B, Aiche S, Valkenborg D, Laukens K, Lilley KS, Olsen JV, Heck AJ, Mechtler K, Aebersold R, Gevaert K, VizcaÃno JA, Hermjakob H, Kohlbacher O, Martens L.","Mol Cell Proteomics","2014","1535-9476","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","327.30908","8","13","1905-1913","PMC4125725",NA,NA,"code.google.com"
"54","24706872","MED","24706872","10.1073/pnas.1314447111","Two-photon excitation improves multifocal structured illumination microscopy in thick scattering tissue.","Ingaramo M, York AG, Wawrzusin P, Milberg O, Hong A, Weigert R, Shroff H, Patterson GH.","Proc Natl Acad Sci U S A","2014","0027-8424","journal article; research support, n.i.h., intramural; research-article","N","Y","N","1","Y","Y","N","N","N","327.25595","14","111","5254-5259","PMC3986197",NA,NA,"code.google.com"
"55","24451626","MED","24451626","10.1093/bioinformatics/btu031","InterProScan 5: genome-scale protein function classification.","Jones P, Binns D, Chang HY, Fraser M, Li W, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G, Pesseat S, Quinn AF, Sangrador-Vegas A, Scheremetjew M, Yong SY, Lopez R, Hunter S.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","20","Y","Y","N","N","N","326.9628","9","30","1236-1240","PMC3998142",NA,NA,"code.google.com"
"56","24757667","MED","24757667","10.1155/2014/248505","Development and evaluation of an open-source software package ""CGITA"" for quantifying tumor heterogeneity with molecular images.","Fang YH, Lin CY, Shih MJ, Wang HM, Ho TY, Liao CT, Yen TC.","Biomed Res Int","2014","2314-6133","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","326.56924",NA,"2014","248505","PMC3976812",NA,NA,"code.google.com"
"57","25474441","MED","25474441","10.1186/1471-2105-15-s15-s7","EasyCluster2: an improved tool for clustering and assembling long transcriptome reads.","Bevilacqua V, Pietroleonardo N, Giannino E, Stroppa F, Simone D, Pesole G, Picardi E.","BMC Bioinformatics","2014","1471-2105","journal article; research support, non-u.s. gov't; abstract","Y","Y","N","0","Y","Y","N","N","N","326.56924","Suppl 15","15 Suppl 15","s7","PMC4271567",NA,NA,"code.google.com"
"58","25346941","MED","25346941",NA,"M2Lite: An Open-source, Light-weight, Pluggable and Fast Proteome Discoverer MSF to mzIdentML Tool.","Aiyetan P, Zhang B, Chen L, Zhang Z, Zhang H.","J Bioinform","2014","2373-0188","journal article; research-article","N","Y","N","1","Y","Y","N","N","N","326.4016","2","1","40-49","PMC4206089",NA,NA,"code.google.com"
"59","24434814","MED","24434814","10.1038/srep03745","Identification of three novel mutations in the FRMD7 gene for X-linked idiopathic congenital nystagmus.","Zhang X, Ge X, Yu Y, Zhang Y, Wu Y, Luan Y, Sun J, Qu J, Jin ZB, Gu F.","Sci Rep","2014","2045-2322","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","326.4016",NA,"4","3745","PMC3894538",NA,NA,"code.google.com"
"60","25095880","MED","25095880","10.1093/bioinformatics/btu531","AliView: a fast and lightweight alignment viewer and editor for large datasets.","Larsson A.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","326.4016","22","30","3276-3278","PMC4221126",NA,NA,"code.google.com"
"61","25344399","MED","25344399","10.1261/rna.046532.114","Distinctive profiles of small RNA couple inverted repeat-induced post-transcriptional gene silencing with endogenous RNA silencing pathways in Arabidopsis.","Wroblewski T, Matvienko M, Piskurewicz U, Xu H, Martineau B, Wong J, Govindarajulu M, Kozik A, Michelmore RW.","RNA","2014","1355-8382","journal article; research support, u.s. gov't, non-p.h.s.; research-article","N","Y","N","0","Y","Y","N","N","N","326.4016","12","20","1987-1999","PMC4238362",NA,NA,"code.google.com"
"62","24786953","MED","24786953","10.1128/genomea.00348-14","High-Quality Draft Whole-Genome Sequences of 162 Salmonella enterica subsp. enterica Serovar Enteritidis Strains Isolated from Diverse Sources in Canada.","Rehman MA, Ziebell K, Nash JH, Kropinski AM, Zong Z, Nafziger E, Boerlin P, Chui L, Devenish J, Bekal S, Graham M, Johnson RP.","Genome Announc","2014","2169-8287","journal article; brief-report","Y","Y","Y","0","Y","Y","N","N","N","326.4016","2","2",NA,"PMC4007988",NA,NA,"code.google.com"
"63","24948611","MED","24948611","10.1093/nar/gku517","Lynx web services for annotations and systems analysis of multi-gene disorders.","Sulakhe D, Taylor A, Balasubramanian S, Feng B, Xie B, BÃ¶rnigen D, Dave UJ, Foster IT, Gilliam TC, Maltsev N.","Nucleic Acids Res","2014","0305-1048","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","N","0","Y","Y","N","N","N","326.4016","web server issue","42","w473-7","PMC4086124",NA,NA,"code.google.com"
"64","25165537","MED","25165537","10.12688/f1000research.4492.1","Cytoscape: the network visualization tool for GenomeSpace workflows.","Demchak B, Hull T, Reich M, Liefeld T, Smoot M, Ideker T, Mesirov JP.","F1000Res","2014","2046-1402","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","Y","326.4016",NA,"3","151","PMC4133763","doi",NA,"code.google.com"
"65","24751287","MED","24751287","10.3201/eid2005.131088","Rickettsia spp. in seabird ticks from western Indian Ocean islands, 2011-2012.","Dietrich M, Lebarbenchon C, Jaeger A, Le Rouzic C, Bastien M, Lagadec E, McCoy KD, Pascalis H, Le Corre M, Dellagi K, Tortosa P.","Emerg Infect Dis","2014","1080-6040","journal article; research support, non-u.s. gov't; brief-report","Y","Y","Y","3","Y","Y","Y","N","N","326.4016","5","20","838-842","PMC4012800",NA,"EMBLUNIPROT","code.google.com"
"66","24856088","MED","24856088","10.3201/eid2006.130635","Identification of possible virulence marker from Campylobacter jejuni isolates.","Harrison JW, Dung TT, Siddiqui F, Korbrisate S, Bukhari H, Tra MP, Hoang NV, Carrique-Mas J, Bryant J, Campbell JI, Studholme DJ, Wren BW, Baker S, Titball RW, Champion OL.","Emerg Infect Dis","2014","1080-6040","journal article; research support, non-u.s. gov't; brief-report","Y","Y","Y","0","Y","Y","Y","N","N","326.4016","6","20","1026-1029","PMC4036754",NA,"EMBLUNIPROT","code.google.com"
"67","24895686","MED","24895686","10.1155/2014/982569","Modeling and simulation of network-on-chip systems with DEVS and DEUS.","Amoretti M.","ScientificWorldJournal","2014","2356-6140","journal article; research-article","Y","Y","Y","0","N","Y","N","N","N","326.3587",NA,"2014","982569","PMC4032749",NA,NA,"code.google.com"
"68","24634649","MED","24634649","10.3389/fnhum.2014.00121","MoBILAB: an open source toolbox for analysis and visualization of mobile brain/body imaging data.","Ojeda A, Bigdely-Shamlo N, Makeig S.","Front Hum Neurosci","2014","1662-5161","journal article; research-article","Y","Y","Y","2","Y","Y","N","N","N","326.3587",NA,"8","121","PMC3942646",NA,NA,"code.google.com"
"69","25144530","MED","25144530","10.1371/journal.pone.0105348","A survey of overlooked viral infections in biological experiment systems.","Wang Y, Wang H, Xu K, Ni P, Zhang H, Ma J, Yang H, Xu F.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","326.3587","8","9","e105348","PMC4140767",NA,NA,"code.google.com"
"70","24648555","MED","24648555","10.1128/jcm.00029-14","Deriving group A Streptococcus typing information from short-read whole-genome sequencing data.","Athey TB, Teatero S, Li A, Marchand-Austin A, Beall BW, Fittipaldi N.","J Clin Microbiol","2014","0095-1137","evaluation studies; journal article; research support, non-u.s. gov't; research-article","N","Y","N","1","Y","Y","N","N","N","326.3587","6","52","1871-1876","PMC4042799",NA,NA,"code.google.com"
"71","24904398","MED","24904398","10.3389/fninf.2014.00052","A simple tool for neuroimaging data sharing.","Haselgrove C, Poline JB, Kennedy DN.","Front Neuroinform","2014","1662-5196","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","326.3587",NA,"8","52","PMC4033259",NA,NA,"code.google.com"
"72","25541944","MED","25541944","10.1371/journal.pone.0115740","Allele workbench: transcriptome pipeline and interactive graphics for allele-specific expression.","Soderlund CA, Nelson WM, Goff SA.","PLoS One","2014","1932-6203","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","325.82938","12","9","e115740","PMC4277417",NA,NA,"code.google.com"
"73","24753423","MED","24753423","10.1093/nar/gku323","TEMP: a computational method for analyzing transposable element polymorphism in populations.","Zhuang J, Wang J, Theurkauf W, Weng Z.","Nucleic Acids Res","2014","0305-1048","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","2","Y","Y","N","Y","N","325.82938","11","42","6826-6838","PMC4066757",NA,NA,"code.google.com"
"74","25393544","MED","25393544","10.1371/journal.pone.0112774","Negation's not solved: generalizability versus optimizability in clinical natural language processing.","Wu S, Miller T, Masanz J, Coarr M, Halgrim S, Carrell D, Clark C.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","325.82938","11","9","e112774","PMC4231086",NA,NA,"code.google.com"
"75","24595056","MED","24595056","10.1371/journal.pone.0089606","Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies.","Walls RL, Deck J, Guralnick R, Baskauf S, Beaman R, Blum S, Bowers S, Buttigieg PL, Davies N, Endresen D, Gandolfo MA, Hanner R, Janning A, Krishtalka L, Matsunaga A, Midford P, Morrison N, Ã Tuama Ã, Schildhauer M, Smith B, Stucky BJ, Thomer A, Wieczorek J, Whitacre J, Wooley J.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","2","Y","Y","N","Y","N","325.82938","3","9","e89606","PMC3940615",NA,NA,"code.google.com"
"76","25540777","MED","25540777","10.3389/fbioe.2014.00069","Comprehensive reconstruction and visualization of non-coding regulatory networks in human.","Bonnici V, Russo F, Bombieri N, Pulvirenti A, Giugno R.","Front Bioeng Biotechnol","2014","2296-4185","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","325.7546",NA,"2","69","PMC4261811",NA,NA,"code.google.com"
"77","24979410","MED","24979410","10.1371/journal.pone.0101144","WImpiBLAST: web interface for mpiBLAST to help biologists perform large-scale annotation using high performance computing.","Sharma P, Mantri SS.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.7546","6","9","e101144","PMC4076281",NA,NA,"code.google.com"
"78","25260792","MED","25260792","10.1186/preaccept-3452801621370693","Dynamic evolution of clonal epialleles revealed by methclone.","Li S, Garrett-Bakelman F, Perl AE, Luger SM, Zhang C, To BL, Lewis ID, Brown AL, D Andrea RJ, Ross M, Levine R, Carroll M, Melnick A, Mason CE.","Genome Biol","2014","1465-6906","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","325.7546","9","15","472","PMC4242486",NA,NA,"code.google.com"
"79","24393219","MED","24393219","10.1186/1471-2229-14-4","Genome-wide expression analysis of reactive oxygen species gene network in Mizuna plants grown in long-term spaceflight.","Sugimoto M, Oono Y, Gusev O, Matsumoto T, Yazawa T, Levinskikh MA, Sychev VN, Bingham GE, Wheeler R, Hummerick M.","BMC Plant Biol","2014","1471-2229","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.7546",NA,"14","4","PMC3927260",NA,NA,"code.google.com"
"80","24449909","MED","24449909","10.1073/pnas.1319703111","Essential role of poly(ADP-ribosyl)ation in cocaine action.","Scobie KN, Damez-Werno D, Sun H, Shao N, Gancarz A, Panganiban CH, Dias C, Koo J, Caiafa P, Kaufman L, Neve RL, Dietz DM, Shen L, Nestler EJ.","Proc Natl Acad Sci U S A","2014","0027-8424","journal article; research-article","N","Y","Y","1","Y","Y","Y","N","N","325.7546","5","111","2005-2010","PMC3918779",NA,"ARXPR","code.google.com"
"81","24634472","MED","24634472","10.1093/database/bau017","Linking tissues to phenotypes using gene expression profiles.","Oellrich A, Sanger Mouse Genetics Project, Smedley D.","Database (Oxford)","2014","1758-0463","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.7546",NA,"2014","bau017","PMC3982582",NA,NA,"code.google.com"
"82","24898977","MED","24898977","10.1007/s00439-014-1454-0","A single codon insertion in PICALM is associated with development of familial subvalvular aortic stenosis in Newfoundland dogs.","Stern JA, White SN, Lehmkuhl LB, Reina-Doreste Y, Ferguson JL, Nascone-Yoder NM, Meurs KM.","Hum Genet","2014","0340-6717","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","Y","N","Y","325.7546","9","133","1139-1148","PMC4148152","gen","OMIM","code.google.com"
"83","24076470","MED","24076470","10.1016/j.ijpsycho.2013.09.003","Imaging natural cognition in action.","Gramann K, Ferris DP, Gwin J, Makeig S.","Int J Psychophysiol","2014","0167-8760","journal article; review; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","N","2","Y","Y","N","N","N","325.7546","1","91","22-29","PMC3983402",NA,NA,"code.google.com"
"84","24787444","MED","24787444","10.1371/journal.pone.0093769","An ontology-based, mobile-optimized system for pharmacogenomic decision support at the point-of-care.","MiÃ±arro-GimÃ©nez JA, Blagec K, Boyce RD, Adlassnig KP, Samwald M.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","Y","325.7546","5","9","e93769","PMC4008421","refsnp",NA,"code.google.com"
"85","25465054","MED","25465054","10.1186/s12859-014-0389-8","VTBuilder: a tool for the assembly of multi isoform transcriptomes.","Archer JP, Whiteley G, Casewell NR, Harrison RA, Wagstaff SC.","BMC Bioinformatics","2014","1471-2105","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","325.7546","1","15","389","PMC4260244",NA,NA,"code.google.com"
"86","25106482","MED","25106482","10.1186/1756-0500-7-509","Illumina sequencing of 15 deafness genes using fragmented amplicons.","Van Nieuwerburgh F, De Keulenaer S, De Schrijver J, Vandesompele J, Van Criekinge W, Coucke PJ, Deforce D.","BMC Res Notes","2014","1756-0500","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","325.54733","1","7","509","PMC4266979",NA,NA,"code.google.com"
"87","25520780","MED","25520780","10.12688/f1000research.5263.1","Using Twitter to investigate opinions about multiple sclerosis treatments: a descriptive, exploratory study.","Ramagopalan S, Wasiak R, Cox AP.","F1000Res","2014","2046-1402","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","325.54733",NA,"3","216","PMC4264640",NA,NA,"code.google.com"
"88","24137012","MED","24137012","10.1093/nar/gkt928","The Global Genome Biodiversity Network (GGBN) Data Portal.","Droege G, Barker K, Astrin JJ, Bartels P, Butler C, Cantrill D, Coddington J, Forest F, Gemeinholzer B, Hobern D, Mackenzie-Dodds J, Ã Tuama Ã, Petersen G, Sanjur O, Schindel D, Seberg O.","Nucleic Acids Res","2014","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.54733","database issue","42","d607-12","PMC3965106",NA,NA,"code.google.com"
"89","25421430","MED","25421430","10.1186/1756-0500-7-830","A review of software for analyzing molecular sequences.","Nilakanta H, Drews KL, Firrell S, Foulkes MA, Jablonski KA.","BMC Res Notes","2014","1756-0500","journal article; research support, n.i.h., extramural; case-report","Y","Y","N","0","Y","Y","N","N","N","325.54733","1","7","830","PMC4258797",NA,NA,"code.google.com"
"90","25231498","MED","25231498","10.1093/database/bau095","WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions.","Karr JR, Phillips NC, Covert MW.","Database (Oxford)","2014","1758-0463","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","N","0","Y","Y","N","N","N","325.54733",NA,"2014",NA,"PMC4165886",NA,NA,"code.google.com"
"91","24447135","MED","24447135","10.2144/000114123","Quantitative analysis of colony morphology in yeast.","Ruusuvuori P, Lin J, Scott AC, Tan Z, Sorsa S, Kallio A, Nykter M, Yli-Harja O, Shmulevich I, Dudley AM.","Biotechniques","2014","0736-6205","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","1","Y","Y","N","N","N","325.54733","1","56","18-27","PMC3996921",NA,NA,"code.google.com"
"92","24377763","MED","24377763","10.3201/eid2001.121024","Dobrava-Belgrade virus in Apodemus flavicollis and A. uralensis mice, Turkey.","Oktem IM, Uyar Y, Dincer E, Gozalan A, Schlegel M, Babur C, Celebi B, Sozen M, Karatas A, Ozkazanc NK, Matur F, Korukluoglu G, Ulrich RG, Ertek M, Ozkul A.","Emerg Infect Dis","2014","1080-6040","journal article; brief-report","Y","Y","Y","0","Y","Y","Y","N","Y","325.54733","1","20","121-125","PMC3887490","gen","UNIPROT","code.google.com"
"93","24901218","MED","24901218","10.1371/journal.pone.0098635","Gene expression profiling analysis of bisphenol A-induced perturbation in biological processes in ER-negative HEK293 cells.","Yin R, Gu L, Li M, Jiang C, Cao T, Zhang X.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.54733","6","9","e98635","PMC4047077",NA,NA,"code.google.com"
"94","24729964","MED","24729964","10.1155/2014/240403","Evaluating word representation features in biomedical named entity recognition tasks.","Tang B, Cao H, Wang X, Chen Q, Xu H.","Biomed Res Int","2014","2314-6133","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.54733",NA,"2014","240403","PMC3963372",NA,NA,"code.google.com"
"95","24961236","MED","24961236","10.1093/database/bau059","BioC implementations in Go, Perl, Python and Ruby.","Liu W, Islamaj DoÄan R, Kwon D, Marques H, Rinaldi F, Wilbur WJ, Comeau DC.","Database (Oxford)","2014","1758-0463","journal article; research support, n.i.h., intramural; research-article","Y","Y","Y","1","Y","Y","N","N","N","325.54733",NA,"2014",NA,"PMC4067548",NA,NA,"code.google.com"
"96","25136372","MED","25136372","10.1155/2014/601064","Treatment of acute lymphoblastic leukemia from traditional chinese medicine.","Hsiao YL, Chang PC, Huang HJ, Kuo CC, Chen CY.","Evid Based Complement Alternat Med","2014","1741-427x","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","Y","325.54733",NA,"2014","601064","PMC4055129","pdb",NA,"code.google.com"
"97","25374051","MED","25374051","10.1038/srep06936","A recurrent deletion mutation in OPA1 causes autosomal dominant optic atrophy in a Chinese family.","Zhang L, Shi W, Song L, Zhang X, Cheng L, Wang Y, Ge X, Li W, Zhang W, Min Q, Jin ZB, Qu J, Gu F.","Sci Rep","2014","2045-2322","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","325.54733",NA,"4","6936","PMC4221781",NA,NA,"code.google.com"
"98","25418838","MED","25418838","10.3201/eid2012.140765","Circulation of reassortant influenza A(H7N9) viruses in poultry and humans, Guangdong Province, China, 2013.","Ke C, Lu J, Wu J, Guan D, Zou L, Song T, Yi L, Zeng X, Liang L, Ni H, Kang M, Zhang X, Zhong H, He J, Lin J, Smith D, Burke D, Fouchier RA, Koopmans M, Zhang Y.","Emerg Infect Dis","2014","1080-6040","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","325.54733","12","20","2034-2040","PMC4257815",NA,NA,"code.google.com"
"99","25566532","MED","25566532","10.3389/fbioe.2014.00065","Synthetic RNAs for Gene Regulation: Design Principles and Computational Tools.","LaganÃ  A, Shasha D, Croce CM.","Front Bioeng Biotechnol","2014","2296-4185","journal article; review; review-article","Y","Y","N","0","Y","Y","N","N","N","325.54733",NA,"2","65","PMC4263176",NA,NA,"code.google.com"
"100","25110940","MED","25110940","10.1371/journal.pone.0104984","Solving the problem of comparing whole bacterial genomes across different sequencing platforms.","Kaas RS, Leekitcharoenphon P, Aarestrup FM, Lund O.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","325.54733","8","9","e104984","PMC4128722",NA,NA,"code.google.com"
"101","25364938","MED","25364938","10.1371/journal.pone.0111613","A bridge role metric model for nodes in software networks.","Li B, Feng Y, Ge S, Li D.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","325.54733","11","9","e111613","PMC4218783",NA,NA,"code.google.com"
"102","24870228","MED","24870228","10.1038/nature13420","Targeted genome editing in human repopulating haematopoietic stem cells.","Genovese P, Schiroli G, Escobar G, Di Tomaso T, Firrito C, Calabria A, Moi D, Mazzieri R, Bonini C, Holmes MC, Gregory PD, van der Burg M, Gentner B, Montini E, Lombardo A, Naldini L.","Nature","2014","0028-0836","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","4","Y","Y","N","N","N","325.15054","7504","510","235-240","PMC4082311",NA,NA,"code.google.com"
"103","25063469","MED","25063469","10.1186/s13059-014-0410-6","Corset: enabling differential gene expression analysis for de novo assembled transcriptomes.","Davidson NM, Oshlack A.","Genome Biol","2014","1465-6906","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","325.15054","7","15","410","PMC4165373",NA,NA,"code.google.com"
"104","24565500","MED","24565500","10.1186/gb-2014-15-2-r38","MOABS: model based analysis of bisulfite sequencing data.","Sun D, Xi Y, Rodriguez B, Park HJ, Tong P, Meong M, Goodell MA, Li W.","Genome Biol","2014","1465-6906","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","4","Y","Y","N","N","N","325.15054","2","15","r38","PMC4054608",NA,NA,"code.google.com"
"105","25122667","MED","25122667","10.1534/g3.114.012526","Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing.","Devisetty UK, Covington MF, Tat AV, Lekkala S, Maloof JN.","G3 (Bethesda)","2014","2160-1836","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","325.15054","11","4","2065-2078","PMC4232532",NA,NA,"code.google.com"
"106","24391153","MED","24391153","10.1093/gbe/evt206","Assessing the state of substitution models describing noncoding RNA evolution.","Allen JE, Whelan S.","Genome Biol Evol","2014","1759-6653","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.15054","1","6","65-75","PMC3914692",NA,NA,"code.google.com"
"107","24940543","MED","24940543","10.1364/boe.5.001822","Image simulation for biological microscopy: microlith.","Mehta SB, Oldenbourg R.","Biomed Opt Express","2014","2156-7085","journal article; research-article","N","Y","Y","0","Y","Y","N","N","N","325.15054","6","5","1822-1838","PMC4052850",NA,NA,"code.google.com"
"108","25055743","MED","25055743","10.1186/s12862-014-0163-6","Novel non-parametric models to estimate evolutionary rates and divergence times from heterochronous sequence data.","Fourment M, Holmes EC.","BMC Evol Biol","2014","1471-2148","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","N","0","Y","Y","N","N","N","325.15054",NA,"14","163","PMC4222489",NA,NA,"code.google.com"
"109","24172133","MED","24172133","10.1534/genetics.113.157172","Inference of the properties of the recombination process from whole bacterial genomes.","Ansari MA, Didelot X.","Genetics","2014","0016-6731","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","325.15054","1","196","253-265","PMC3872189",NA,NA,"code.google.com"
"110","24037521","MED","24037521","10.1002/bit.25115","Automated method for the rapid and precise estimation of adherent cell culture characteristics from phase contrast microscopy images.","Jaccard N, Griffin LD, Keser A, Macown RJ, Super A, Veraitch FS, Szita N.","Biotechnol Bioeng","2014","0006-3592","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","1","Y","Y","N","N","N","325.15054","3","111","504-517","PMC4260842",NA,NA,"code.google.com"
"111","24177718","MED","24177718","10.1093/bioinformatics/btt622","EXPANDS: expanding ploidy and allele frequency on nested subpopulations.","Andor N, Harness JV, MÃ¼ller S, Mewes HW, Petritsch C.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","4","Y","Y","N","Y","N","325.15054","1","30","50-60","PMC3866558",NA,NA,"code.google.com"
"112","24948510","MED","24948510","10.1093/database/bau057","A novel multi-alignment pipeline for high-throughput sequencing data.","Huang S, Holt J, Kao CY, McMillan L, Wang W.","Database (Oxford)","2014","1758-0463","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","1","Y","Y","N","N","N","325.15054",NA,"2014",NA,"PMC4062837",NA,NA,"code.google.com"
"113","24270360","MED","24270360","10.1038/ng.2836","Large conserved domains of low DNA methylation maintained by Dnmt3a.","Jeong M, Sun D, Luo M, Huang Y, Challen GA, Rodriguez B, Zhang X, Chavez L, Wang H, Hannah R, Kim SB, Yang L, Ko M, Chen R, GÃ¶ttgens B, Lee JS, Gunaratne P, Godley LA, Darlington GJ, Rao A, Li W, Goodell MA.","Nat Genet","2014","1061-4036","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","21","Y","Y","Y","N","N","325.15054","1","46","17-23","PMC3920905",NA,"UNIPROTARXPR","code.google.com"
"114","24735413","MED","24735413","10.1186/1471-2164-15-284","ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases.","Shen L, Shao N, Liu X, Nestler E.","BMC Genomics","2014","1471-2164","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; product-review","Y","Y","Y","5","Y","Y","N","N","N","325.15054",NA,"15","284","PMC4028082",NA,NA,"code.google.com"
"115","25270054","MED","25270054","10.1186/1755-8794-7-57","Identification of co-expression gene networks, regulatory genes and pathways for obesity based on adipose tissue RNA Sequencing in a porcine model.","Kogelman LJ, Cirera S, Zhernakova DV, Fredholm M, Franke L, Kadarmideen HN.","BMC Med Genomics","2014","1755-8794","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","Y","N","N","325.15054",NA,"7","57","PMC4183073",NA,"ARXPR","code.google.com"
"116","25286837","MED","25286837","10.1107/s1399004714016174","Operation of the Australian Store.Synchrotron for macromolecular crystallography.","Meyer GR, AragÃ£o D, Mudie NJ, Caradoc-Davies TT, McGowan S, Bertling PJ, Groenewegen D, Quenette SM, Bond CS, Buckle AM, Androulakis S.","Acta Crystallogr D Biol Crystallogr","2014","0907-4449","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","N","Y","N","N","N","325.15054","pt 10","70","2510-2519","PMC4187999",NA,NA,"code.google.com"
"117","24722143","MED","24722143","10.1371/journal.pone.0094697","Use of targeted exome sequencing in genetic diagnosis of Chinese familial hypercholesterolemia.","Wu WF, Sun LY, Pan XD, Yang SW, Wang LY.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","Y","325.12018","4","9","e94697","PMC3983231","refseq",NA,"code.google.com"
"118","25329610","MED","25329610","10.1371/journal.pone.0109293","Self-organization on social media: endo-exo bursts and baseline fluctuations.","Oka M, Hashimoto Y, Ikegami T.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","325.12018","10","9","e109293","PMC4199606",NA,NA,"code.google.com"
"119","25250654","MED","25250654","10.1371/journal.pone.0106491","Diversity and community composition of methanogenic archaea in the rumen of Scottish upland sheep assessed by different methods.","Snelling TJ, GenÃ§ B, McKain N, Watson M, Waters SM, Creevey CJ, Wallace RJ.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","Y","325.12018","9","9","e106491","PMC4175461","gen",NA,"code.google.com"
"120","24270789","MED","24270789","10.1093/nar/gkt1173","Protein Ontology: a controlled structured network of protein entities.","Natale DA, Arighi CN, Blake JA, Bult CJ, Christie KR, Cowart J, D'Eustachio P, Diehl AD, Drabkin HJ, Helfer O, Huang H, Masci AM, Ren J, Roberts NV, Ross K, Ruttenberg A, Shamovsky V, Smith B, Yerramalla MS, Zhang J, AlJanahi A, Ãelen I, Gan C, Lv M, Schuster-Lezell E, Wu CH.","Nucleic Acids Res","2014","0305-1048","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","1","Y","Y","N","N","Y","325.12018","database issue","42","d415-21","PMC3964965","sprot",NA,"code.google.com"
"121","25516833","MED","25516833","10.1016/j.ijpddr.2014.10.004","Automated, high-throughput, motility analysis in Caenorhabditis elegans and parasitic nematodes: Applications in the search for new anthelmintics.","Buckingham SD, Partridge FA, Sattelle DB.","Int J Parasitol Drugs Drug Resist","2014","2211-3207","journal article; review; review-article","Y","Y","N","0","Y","Y","N","N","N","325.12018","3","4","226-232","PMC4266775",NA,NA,"code.google.com"
"122","24406431","MED","24406431","10.1038/srep03623","Aberrant CDK4 amplification in refractory rhabdomyosarcoma as identified by genomic profiling.","Park S, Lee J, Do IG, Jang J, Rho K, Ahn S, Maruja L, Kim SJ, Kim KM, Mao M, Oh E, Kim YJ, Kim J, Choi YL.","Sci Rep","2014","2045-2322","journal article; case reports; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.12018",NA,"4","3623","PMC3887377",NA,NA,"code.google.com"
"123","24447369","MED","24447369","10.1186/1471-2105-15-23","Gene expression and nucleotide composition are associated with genic methylation level in Oryza sativa.","Elhaik E, Pellegrini M, Tatarinova TV.","BMC Bioinformatics","2014","1471-2105","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.12018",NA,"15","23","PMC3903047",NA,NA,"code.google.com"
"124","24600334","MED","24600334",NA,"Fluorescence microscopy gets faster and clearer: roles of photochemistry and selective illumination.","Wolenski JS, Julich D.","Yale J Biol Med","2014","0044-0086","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.12018","1","87","21-32","PMC3941456",NA,NA,"code.google.com"
"125","25144201","MED","25144201","10.1371/journal.pone.0105592","Development of a prokaryotic universal primer for simultaneous analysis of Bacteria and Archaea using next-generation sequencing.","Takahashi S, Tomita J, Nishioka K, Hisada T, Nishijima M.","PLoS One","2014","1932-6203","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.12018","8","9","e105592","PMC4140814",NA,NA,"code.google.com"
"126","24554752","MED","24554752","10.1128/jcm.03554-13","Characterization of invasive group B streptococcus strains from the greater Toronto area, Canada.","Teatero S, McGeer A, Low DE, Li A, Demczuk W, Martin I, Fittipaldi N.","J Clin Microbiol","2014","0095-1137","journal article; research support, non-u.s. gov't; research-article","N","Y","N","0","Y","Y","N","N","N","325.12018","5","52","1441-1447","PMC3993709",NA,NA,"code.google.com"
"127","25408696","MED","25408696","10.3389/fpls.2014.00598","Integrated network analysis and effective tools in plant systems biology.","Fukushima A, Kanaya S, Nishida K.","Front Plant Sci","2014","1664-462x","journal article; review; review-article","Y","Y","N","0","Y","Y","N","N","N","325.12018",NA,"5","598","PMC4219401",NA,NA,"code.google.com"
"128","24899907","MED","24899907","10.1155/2014/364819","Ligand-based and structure-based investigation for Alzheimer's disease from traditional chinese medicine.","Liao KH, Chen KB, Lee WY, Sun MF, Lee CC, Chen CY.","Evid Based Complement Alternat Med","2014","1741-427x","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","Y","325.12018",NA,"2014","364819","PMC4034731","pdb",NA,"code.google.com"
"129","24605066","MED","24605066","10.1155/2014/860170","Video conferences through the internet: how to survive in a hostile environment.","FernÃ¡ndez C, Saldana J, FernÃ¡ndez-Navajas J, Sequeira L, Casadesus L.","ScientificWorldJournal","2014","2356-6140","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","N","Y","N","N","N","325.12018",NA,"2014","860170","PMC3926290",NA,NA,"code.google.com"
"130","24678985","MED","24678985","10.1186/1746-4811-10-8","ClearedLeavesDB: an online database of cleared plant leaf images.","Das A, Bucksch A, Price CA, Weitz JS.","Plant Methods","2014","1746-4811","journal article; research-article","Y","Y","Y","2","Y","Y","N","N","N","325.12018","1","10","8","PMC3986656",NA,NA,"code.google.com"
"131","24725334","MED","24725334","10.1186/1471-2164-15-279","The miRNAome of the postpartum dairy cow liver in negative energy balance.","Fatima A, Lynn DJ, O'Boyle P, Seoighe C, Morris D.","BMC Genomics","2014","1471-2164","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.12018",NA,"15","279","PMC4023597",NA,NA,"code.google.com"
"132","24910613","MED","24910613","10.3389/fnagi.2014.00105","Aging Influence on Gray Matter Structural Associations within the Default Mode Network Utilizing Bayesian Network Modeling.","Wang Y, Chen K, Zhang J, Yao L, Li K, Jin Z, Ye Q, Guo X.","Front Aging Neurosci","2014","1663-4365","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","325.12018",NA,"6","105","PMC4038778",NA,NA,"code.google.com"
"133","25061474","MED","25061474","10.1186/1748-7188-9-16","Enumerating all maximal frequent subtrees in collections of phylogenetic trees.","Deepak A, FernÃ¡ndez-Baca D.","Algorithms Mol Biol","2014","1748-7188","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.12018",NA,"9","16","PMC4085724",NA,NA,"code.google.com"
"134","24263086","MED","24263086","10.2967/jnumed.112.116715","The effect of small tumor volumes on studies of intratumoral heterogeneity of tracer uptake.","Brooks FJ, Grigsby PW.","J Nucl Med","2014","0161-5505","journal article; research support, n.i.h., extramural; research-article","N","Y","N","1","Y","Y","N","N","N","325.12018","1","55","37-42","PMC4017737",NA,NA,"code.google.com"
"135","24763286","MED","24763286","10.1371/journal.pone.0095528","Molecular diagnosis of putative Stargardt disease by capture next generation sequencing.","Zhang X, Ge X, Shi W, Huang P, Min Q, Li M, Yu X, Wu Y, Zhao G, Tong Y, Jin ZB, Qu J, Gu F.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","Y","325.12018","4","9","e95528","PMC3999032","sprot",NA,"code.google.com"
"136","24215457","MED","24215457","10.1111/1755-0998.12201","Development of a Nasonia vitripennis outbred laboratory population for genetic analysis.","van de Zande L, Ferber S, de Haan A, Beukeboom LW, van Heerwaarden J, Pannebakker BA.","Mol Ecol Resour","2014","1755-098x","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","Y","Y","325.12018","3","14","578-587","PMC4260118","doi",NA,"code.google.com"
"137","24415924","MED","24415924","10.1371/journal.pbio.1001745","Best practices for scientific computing.","Wilson G, Aruliah DA, Brown CT, Chue Hong NP, Davis M, Guy RT, Haddock SH, Huff KD, Mitchell IM, Plumbley MD, Waugh B, White EP, Wilson P.","PLoS Biol","2014","1544-9173","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","5","Y","Y","N","N","N","325.12018","1","12","e1001745","PMC3886731",NA,NA,"code.google.com"
"138","24336318","MED","24336318","10.1038/nbt.2778","Reduced local mutation density in regulatory DNA of cancer genomes is linked to DNA repair.","Polak P, Lawrence MS, Haugen E, Stoletzki N, Stojanov P, Thurman RE, Garraway LA, Mirkin S, Getz G, Stamatoyannopoulos JA, Sunyaev SR.","Nat Biotechnol","2014","1087-0156","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","2","Y","Y","N","N","N","325.12018","1","32","71-75","PMC4116484",NA,NA,"code.google.com"
"139","24217912","MED","24217912","10.1093/nar/gkt1026","The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data.","KÃ¶hler S, Doelken SC, Mungall CJ, Bauer S, Firth HV, Bailleul-Forestier I, Black GC, Brown DL, Brudno M, Campbell J, FitzPatrick DR, Eppig JT, Jackson AP, Freson K, Girdea M, Helbig I, Hurst JA, JÃ¤hn J, Jackson LG, Kelly AM, Ledbetter DH, Mansour S, Martin CL, Moss C, Mumford A, Ouwehand WH, Park SM, Riggs ER, Scott RH, Sisodiya S, Van Vooren S, Wapner RJ, Wilkie AO, Wright CF, Vulto-van Silfhout AT, de Leeuw N, de Vries BB, Washingthon NL, Smith CL, Westerfield M, Schofield P, Ruef BJ, Gkoutos GV, Haendel M, Smedley D, Lewis SE, Robinson PN.","Nucleic Acids Res","2014","0305-1048","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","19","Y","Y","N","N","N","325.12018","database issue","42","d966-74","PMC3965098",NA,NA,"code.google.com"
"140","24389049","MED","24389049","10.1101/gr.163832.113","Simultaneous identification and prioritization of variants in familial, de novo, and somatic genetic disorders with VariantMaster.","Santoni FA, Makrythanasis P, Nikolaev S, Guipponi M, Robyr D, Bottani A, Antonarakis SE.","Genome Res","2014","1088-9051","journal article; research support, non-u.s. gov't; research-article","N","Y","Y","8","Y","Y","N","Y","N","325.12018","2","24","349-355","PMC3912425",NA,NA,"code.google.com"
"141","24950227","MED","24950227","10.1371/journal.pone.0099439","The ""grep"" command but not FusionMap, FusionFinder or ChimeraScan captures the CIC-DUX4 fusion gene from whole transcriptome sequencing data on a small round cell tumor with t(4;19)(q35;q13).","Panagopoulos I, Gorunova L, Bjerkehagen B, Heim S.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","Y","N","N","325.12018","6","9","e99439","PMC4064965",NA,"EMBLUNIPROT","code.google.com"
"142","25203398","MED","25203398","10.1371/journal.pone.0106900","De Novo characterization of a Cephalotaxus hainanensis transcriptome and genes related to paclitaxel biosynthesis.","Qiao F, Cong H, Jiang X, Wang R, Yin J, Qian D, Wang Z, Nick P.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","Y","N","N","325.12018","9","9","e106900","PMC4159234",NA,"EMBL","code.google.com"
"143","24392128","MED","24392128","10.1371/journal.pone.0084348","Comparison of metatranscriptomic samples based on k-tuple frequencies.","Wang Y, Liu L, Chen L, Chen T, Sun F.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.0895","1","9","e84348","PMC3879298",NA,NA,"code.google.com"
"144","24550818","MED","24550818","10.3389/fninf.2014.00002","A versatile software package for inter-subject correlation based analyses of fMRI.","Kauppi JP, Pajula J, Tohka J.","Front Neuroinform","2014","1662-5196","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.0895",NA,"8","2","PMC3907702",NA,NA,"code.google.com"
"145","25309417","MED","25309417","10.3389/fninf.2014.00074","Cyberinfrastructure for the digital brain: spatial standards for integrating rodent brain atlases.","Zaslavsky I, Baldock RA, Boline J.","Front Neuroinform","2014","1662-5196","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","325.0895",NA,"8","74","PMC4162418",NA,NA,"code.google.com"
"146","25349885","MED","25349885","10.1186/1471-2105-15-s11-s10","SeqAssist: a novel toolkit for preliminary analysis of next-generation sequencing data.","Peng Y, Maxwell AS, Barker ND, Laird JG, Kennedy AJ, Wang N, Zhang C, Gong P.","BMC Bioinformatics","2014","1471-2105","journal article; research support, u.s. gov't, non-p.h.s.; abstract","Y","Y","N","1","Y","Y","N","N","N","324.69302","Suppl 11","15 Suppl 11","s10","PMC4251038",NA,NA,"code.google.com"
"147","25350391","MED","25350391","10.1186/1471-2105-15-s11-s7","Trends in the production of scientific data analysis resources.","Hennessey J, Georgescu C, Wren JD.","BMC Bioinformatics","2014","1471-2105","journal article; research support, u.s. gov't, non-p.h.s.; abstract","Y","Y","N","1","Y","Y","N","N","N","324.69302","Suppl 11","15 Suppl 11","s7","PMC4251054",NA,NA,"code.google.com"
"148","24856417","MED","24856417","10.3201/eid2006.131438","Rapid spread and diversification of respiratory syncytial virus genotype ON1, Kenya.","Agoti CN, Otieno JR, Gitahi CW, Cane PA, Nokes DJ.","Emerg Infect Dis","2014","1080-6040","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","3","Y","Y","Y","N","Y","324.69302","6","20","950-959","PMC4036793","gen","UNIPROT","code.google.com"
"149","24609361","MED","24609361","10.1038/nchembio.1475","G quadruplexes are genomewide targets of transcriptional helicases XPB and XPD.","Gray LT, Vallur AC, Eddy J, Maizels N.","Nat Chem Biol","2014","1552-4450","journal article; research support, n.i.h., extramural; research-article","Y","Y","N","5","Y","Y","Y","N","N","324.69302","4","10","313-318","PMC4006364",NA,"UNIPROTARXPR","code.google.com"
"150","24454815","MED","24454815","10.1371/journal.pone.0085182","A snapshot of a coral ""holobiont"": a transcriptome assembly of the scleractinian coral, porites, captures a wide variety of genes from both the host and symbiotic zooxanthellae.","Shinzato C, Inoue M, Kusakabe M.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","3","Y","Y","N","N","Y","324.69302","1","9","e85182","PMC3893191","gen",NA,"code.google.com"
"151","25177549","MED","25177549","10.3389/fcimb.2014.00108","Functional expression of dental plaque microbiota.","Peterson SN, Meissner T, Su AI, Snesrud E, Ong AC, Schork NJ, Bretz WA.","Front Cell Infect Microbiol","2014","2235-2988","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.69302",NA,"4","108","PMC4132376",NA,NA,"code.google.com"
"152","25346182","MED","25346182","10.1186/1756-0500-7-761","Expression level of a flavonoid 3'-hydroxylase gene determines pathogen-induced color variation in sorghum.","Mizuno H, Yazawa T, Kasuga S, Sawada Y, Ogata J, Ando T, Kanamori H, Yonemaru J, Wu J, Hirai MY, Matsumoto T, Kawahigashi H.","BMC Res Notes","2014","1756-0500","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","Y","324.69302","1","7","761","PMC4219097","gen",NA,"code.google.com"
"153","24549172","MED","24549172","10.3390/ijms15022672","Paclitaxel induces apoptosis in breast cancer cells through different calcium--regulating mechanisms depending on external calcium conditions.","Pan Z, Avila A, Gollahon L.","Int J Mol Sci","2014","1422-0067","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.69302","2","15","2672-2694","PMC3958875",NA,NA,"code.google.com"
"154","25516834","MED","25516834","10.1016/j.ijpddr.2014.08.003","Utilization of computer processed high definition video imaging for measuring motility of microscopic nematode stages on a quantitative scale: ""The Worminator"".","Storey B, Marcellino C, Miller M, Maclean M, Mostafa E, Howell S, Sakanari J, Wolstenholme A, Kaplan R.","Int J Parasitol Drugs Drug Resist","2014","2211-3207","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.69302","3","4","233-243","PMC4266792",NA,NA,"code.google.com"
"155","24743145","MED","24743145","10.1172/jci70577","Cardiac fibroblast-derived microRNA passenger strand-enriched exosomes mediate cardiomyocyte hypertrophy.","Bang C, Batkai S, Dangwal S, Gupta SK, Foinquinos A, Holzmann A, Just A, Remke J, Zimmer K, Zeug A, Ponimaskin E, Schmiedl A, Yin X, Mayr M, Halder R, Fischer A, Engelhardt S, Wei Y, Schober A, Fiedler J, Thum T.","J Clin Invest","2014","0021-9738","journal article; research support, non-u.s. gov't; research-article","N","Y","Y","10","Y","Y","N","N","N","324.69302","5","124","2136-2146","PMC4001534",NA,NA,"code.google.com"
"156","25056908","MED","25056908","10.1038/srep05756","Decipher the dynamic coordination between enzymatic activity and structural modulation at focal adhesions in living cells.","Lu S, Seong J, Wang Y, Chang SC, Eichorst JP, Ouyang M, Li JY, Chien S, Wang Y.","Sci Rep","2014","2045-2322","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.69302",NA,"4","5756","PMC4108961",NA,NA,"code.google.com"
"157","24947819","MED","24947819","10.1038/srep05371","Epigenetic regulation by chromatin activation mark H3K4me3 in primate progenitor cells within adult neurogenic niche.","Sandstrom RS, Foret MR, Grow DA, Haugen E, Rhodes CT, Cardona AE, Phelix CF, Wang Y, Berger MS, Lin CH.","Sci Rep","2014","2045-2322","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","1","Y","Y","N","N","N","324.69302",NA,"4","5371","PMC4064326",NA,NA,"code.google.com"
"158","25437873","MED","25437873","10.1371/journal.pone.0113838","The connectome visualization utility: software for visualization of human brain networks.","LaPlante RA, Douw L, Tang W, Stufflebeam SM.","PLoS One","2014","1932-6203","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.69302","12","9","e113838","PMC4250035",NA,NA,"code.google.com"
"159","25294186","MED","25294186","10.1186/1471-2164-15-875","Cohen's h for detection of disease association with rare genetic variants.","Wen SH, Yeh JI.","BMC Genomics","2014","1471-2164","journal article; research-article","Y","Y","N","0","Y","Y","N","N","Y","324.69302","1","15","875","PMC4198687","refsnp",NA,"code.google.com"
"160","25229475","MED","25229475","10.1371/journal.pone.0107909","Effect of oral administration of metronidazole or prednisolone on fecal microbiota in dogs.","Igarashi H, Maeda S, Ohno K, Horigome A, Odamaki T, Tsujimoto H.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","324.69302","9","9","e107909","PMC4168260",NA,NA,"code.google.com"
"161","25081493","MED","25081493","10.1186/1471-2164-15-s5-s2","RandAL: a randomized approach to aligning DNA sequences to reference genomes.","Vo NS, Tran Q, Niraula N, Phan V.","BMC Genomics","2014","1471-2164","journal article; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.69302","Suppl 5","15 Suppl 5","s2","PMC4120144",NA,NA,"code.google.com"
"162","25173757","MED","25173757","10.1093/gbe/evu175","Genomic signatures of distributive conjugal transfer among mycobacteria.","Mortimer TD, Pepperell CS.","Genome Biol Evol","2014","1759-6653","journal article; research support, n.i.h., extramural; research-article","Y","Y","N","0","Y","Y","N","N","N","324.69302","9","6","2489-2500","PMC4202316",NA,NA,"code.google.com"
"163","24742282","MED","24742282","10.1186/1471-2229-14-101","RNA sequencing-mediated transcriptome analysis of rice plants in endoplasmic reticulum stress conditions.","Wakasa Y, Oono Y, Yazawa T, Hayashi S, Ozawa K, Handa H, Matsumoto T, Takaiwa F.","BMC Plant Biol","2014","1471-2229","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.69302",NA,"14","101","PMC4021347",NA,NA,"code.google.com"
"164","24834107","MED","24834107","10.1155/2014/293980","Modeling and visualizing cell type switching.","Ghaffarizadeh A, Podgorski GJ, Flann NS.","Comput Math Methods Med","2014","1748-670x","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.69302",NA,"2014","293980","PMC4009162",NA,NA,"code.google.com"
"165","25505842","MED","25505842","10.1590/s1415-47572014005000020","Identification of novel and conserved microRNAs in Coffea canephora and Coffea arabica.","Loss-Morais G, Ferreira DC, Margis R, Alves-Ferreira M, CorrÃªa RL.","Genet Mol Biol","2014","1415-4757","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.69302","4","37","671-682","PMC4261967",NA,NA,"code.google.com"
"166","24172151","MED","24172151","10.1128/jcm.02680-13","Genotypic and epidemiologic trends of norovirus outbreaks in the United States, 2009 to 2013.","Vega E, Barclay L, Gregoricus N, Shirley SH, Lee D, VinjÃ© J.","J Clin Microbiol","2014","0095-1137","journal article; research support, u.s. gov't, non-p.h.s.; research support, u.s. gov't, p.h.s.; research-article","N","Y","Y","10","Y","Y","N","N","Y","324.69302","1","52","147-155","PMC3911414","gen",NA,"code.google.com"
"167","25227120","MED","25227120","10.1186/1471-2164-15-798","Next-generation sequencing identifies equine cartilage and subchondral bone miRNAs and suggests their involvement in osteochondrosis physiopathology.","Desjardin C, Vaiman A, Mata X, Legendre R, Laubier J, Kennedy SP, Laloe D, Barrey E, Jacques C, Cribiu EP, Schibler L.","BMC Genomics","2014","1471-2164","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","Y","324.69302","1","15","798","PMC4190437","arrayexpress",NA,"code.google.com"
"168","25502423","MED","25502423","10.1371/journal.pone.0114901","Diagnostics of primary immunodeficiency diseases: a sequencing capture approach.","Moens LN, Falk-SÃ¶rqvist E, Asplund AC, Bernatowska E, Smith CI, Nilsson M.","PLoS One","2014","1932-6203","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.69302","12","9","e114901","PMC4263707",NA,NA,"code.google.com"
"169","25063298","MED","25063298","10.1093/nar/gku631","The multiMiR R package and database: integration of microRNA-target interactions along with their disease and drug associations.","Ru Y, Kechris KJ, Tabakoff B, Hoffman P, Radcliffe RA, Bowler R, Mahaffey S, Rossi S, Calin GA, Bemis L, Theodorescu D.","Nucleic Acids Res","2014","0305-1048","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","N","0","Y","Y","N","N","Y","324.69302","17","42","e133","PMC4176155","arrayexpress",NA,"code.google.com"
"170","24336765","MED","24336765","10.1101/gr.159608.113","Principles of nucleation of H3K27 methylation during embryonic development.","van Heeringen SJ, Akkers RC, van Kruijsbergen I, Arif MA, Hanssen LL, Sharifi N, Veenstra GJ.","Genome Res","2014","1088-9051","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","5","Y","Y","N","N","N","324.69302","3","24","401-410","PMC3941105",NA,NA,"code.google.com"
"171","24409309","MED","24409309","10.1371/journal.pone.0084785","Assessment of whole genome amplification for sequence capture and massively parallel sequencing.","Hasmats J, GrÃ©en H, Orear C, Validire P, Huss M, KÃ¤ller M, Lundeberg J.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","Y","N","324.69302","1","9","e84785","PMC3883664",NA,NA,"code.google.com"
"172","24489891","MED","24489891","10.1371/journal.pone.0087289","The feeding tube of cyst nematodes: characterisation of protein exclusion.","Eves-van den Akker S, Lilley CJ, Ault JR, Ashcroft AE, Jones JT, Urwin PE.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","Y","324.69302","1","9","e87289","PMC3905015","pdb",NA,"code.google.com"
"173","24519333","MED","24519333","10.1007/s13361-013-0796-5","BRAIN 2.0: time and memory complexity improvements in the algorithm for calculating the isotope distribution.","Dittwald P, Valkenborg D.","J Am Soc Mass Spectrom","2014","1044-0305","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.69302","4","25","588-594","PMC3953541",NA,NA,"code.google.com"
"174","24568354","MED","24568354","10.4155/bio.13.348","Stable isotope-labeling studies in metabolomics: new insights into structure and dynamics of metabolic networks.","Chokkathukalam A, Kim DH, Barrett MP, Breitling R, Creek DJ.","Bioanalysis","2014","1757-6180","journal article; review; research support, non-u.s. gov't; research-article","N","Y","Y","2","Y","Y","N","N","N","324.69302","4","6","511-524","PMC4048731",NA,NA,"code.google.com"
"175","24602515","MED","24602515","10.1186/2041-1480-5-13","Panacea, a semantic-enabled drug recommendations discovery framework.","Doulaverakis C, Nikolaidis G, Kleontas A, Kompatsiaris I.","J Biomed Semantics","2014","2041-1480","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.69302","1","5","13","PMC3975719",NA,NA,"code.google.com"
"176","24621103","MED","24621103","10.1186/1471-2105-15-69","MAAMD: a workflow to standardize meta-analyses and comparison of affymetrix microarray data.","Gan Z, Wang J, Salomonis N, Stowe JC, Haddad GG, McCulloch AD, Altintas I, Zambon AC.","BMC Bioinformatics","2014","1471-2105","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; product-review","Y","Y","Y","0","Y","Y","N","Y","N","324.69302",NA,"15","69","PMC3975178",NA,NA,"code.google.com"
"177","25144537","MED","25144537","10.1371/journal.pone.0104579","Choice of reference sequence and assembler for alignment of Listeria monocytogenes short-read sequence data greatly influences rates of error in SNP analyses.","Pightling AW, Petronella N, Pagotto F.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","324.69302","8","9","e104579","PMC4140716",NA,NA,"code.google.com"
"178","24489671","MED","24489671","10.1371/journal.pone.0085777","Powerlaw: a Python package for analysis of heavy-tailed distributions.","Alstott J, Bullmore E, Plenz D.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research support, n.i.h., intramural; research-article","Y","Y","Y","4","Y","Y","N","N","N","324.69302","1","9","e85777","PMC3906378",NA,NA,"code.google.com"
"179","25057252","MED","25057252","10.3897/bdj.2.e1114","Symbiota - A virtual platform for creating voucher-based biodiversity information communities.","Gries C, Gilbert EE, Franz NM.","Biodivers Data J","2014","1314-2828","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","324.69302","2",NA,"e1114","PMC4092327",NA,NA,"code.google.com"
"180","24694083","MED","24694083","10.1186/1471-2105-15-95","A local average distance descriptor for flexible protein structure comparison.","Wang HW, Chu CH, Wang WC, Pai TW.","BMC Bioinformatics","2014","1471-2105","journal article; research support, non-u.s. gov't; comparative study; research-article","Y","Y","Y","0","Y","Y","N","N","Y","324.69302",NA,"15","95","PMC3992163","pdb",NA,"code.google.com"
"181","24725457","MED","24725457","10.1186/1559-0275-11-15","Glycoproteomic and glycomic databases.","Baycin Hizal D, Wolozny D, Colao J, Jacobson E, Tian Y, Krag SS, Betenbaugh MJ, Zhang H.","Clin Proteomics","2014","1542-6416","journal article; review; review-article","Y","Y","Y","2","Y","Y","N","N","N","324.69302","1","11","15","PMC3996109",NA,NA,"code.google.com"
"182","24782889","MED","24782889","10.3389/fgene.2014.00075","Impact of artifact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data.","Carroll TS, Liang Z, Salama R, Stark R, de Santiago I.","Front Genet","2014","1664-8021","journal article; research-article","Y","Y","Y","2","Y","Y","N","N","N","324.69302",NA,"5","75","PMC3989762",NA,NA,"code.google.com"
"183","24917877","MED","24917877","10.3389/fgene.2014.00153","Copy number variants and selective sweeps in natural populations of the house mouse (Mus musculus domesticus).","Bryk J, Tautz D.","Front Genet","2014","1664-8021","journal article; review; review-article","Y","Y","Y","1","Y","Y","N","N","N","324.69302",NA,"5","153","PMC4042557",NA,NA,"code.google.com"
"184","24925680","MED","24925680","10.1186/1471-2105-15-182","Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads.","Jiang H, Lei R, Ding SW, Zhu S.","BMC Bioinformatics","2014","1471-2105","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.69302",NA,"15","182","PMC4074385",NA,NA,"code.google.com"
"185","25024921","MED","25024921","10.7717/peerj.453","scikit-image: image processing in Python.","van der Walt S, SchÃ¶nberger JL, Nunez-Iglesias J, Boulogne F, Warner JD, Yager N, Gouillart E, Yu T, scikit-image contributors.","PeerJ","2014","2167-8359","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","324.69302",NA,"2","e453","PMC4081273",NA,NA,"code.google.com"
"186","25078021","MED","25078021","10.1186/1471-2105-15-s7-s7","Multistable switches and their role in cellular differentiation networks.","Ghaffarizadeh A, Flann NS, Podgorski GJ.","BMC Bioinformatics","2014","1471-2105","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","Y","N","Y","324.69302","Suppl 7","15 Suppl 7","s7","PMC4110729","arrayexpress","ARXPR","code.google.com"
"187","25295024","MED","25295024","10.3389/fpsyg.2014.01080","Evidence of weak conscious experiences in the exclusion task.","Sandberg K, Del Pin SH, Bibby BM, Overgaard M.","Front Psychol","2014","1664-1078","journal article; research-article","Y","Y","N","1","Y","Y","N","N","N","324.69302",NA,"5","1080","PMC4172090",NA,NA,"code.google.com"
"188","25324771","MED","25324771","10.3389/fncom.2014.00122","Characterizing structural association alterations within brain networks in normal aging using Gaussian Bayesian networks.","Guo X, Wang Y, Chen K, Wu X, Zhang J, Li K, Jin Z, Yao L.","Front Comput Neurosci","2014","1662-5188","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.69302",NA,"8","122","PMC4179716",NA,NA,"code.google.com"
"189","24884487","MED","24884487","10.1186/1471-2148-14-102","Reconstructing the age and historical biogeography of the ancient flowering-plant family Hydatellaceae (Nymphaeales).","Iles WJ, Lee C, Sokoloff DD, Remizowa MV, Yadav SR, Barrett MD, Barrett RL, Macfarlane TD, Rudall PJ, Graham SW.","BMC Evol Biol","2014","1471-2148","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","Y","N","Y","324.69302",NA,"14","102","PMC4030046","gen","EMBLUNIPROT","code.google.com"
"190","24942165","MED","24942165","10.1186/1471-2164-15-484","Next-generation sequencing of small RNAs from inner ear sensory epithelium identifies microRNAs and defines regulatory pathways.","Rudnicki A, Isakov O, Ushakov K, Shivatzki S, Weiss I, Friedman LM, Shomron N, Avraham KB.","BMC Genomics","2014","1471-2164","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","Y","N","N","324.69302","1","15","484","PMC4073505",NA,"UNIPROT","code.google.com"
"191","24379390","MED","24379390","10.1073/pnas.1314561111","Recursive genomewide recombination and sequencing reveals a key refinement step in the evolution of a metabolic innovation in Escherichia coli.","Quandt EM, Deatherage DE, Ellington AD, Georgiou G, Barrick JE.","Proc Natl Acad Sci U S A","2014","0027-8424","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","Y","4","Y","Y","N","N","N","324.69302","6","111","2217-2222","PMC3926077",NA,NA,"code.google.com"
"192","24319317","MED","24319317","10.1016/j.ijar.2013.03.013","Bayesian network models in brain functional connectivity analysis.","Ide JS, Zhang S, Li CS.","Int J Approx Reason","2014","0888-613x","journal article; research-article","N","Y","N","0","Y","Y","N","N","N","324.69302","1 pt 1","56",NA,"PMC3848787",NA,NA,"code.google.com"
"193","25295002","MED","25295002","10.3389/fninf.2014.00080","SIMA: Python software for analysis of dynamic fluorescence imaging data.","Kaifosh P, Zaremba JD, Danielson NB, Losonczy A.","Front Neuroinform","2014","1662-5196","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.69302",NA,"8","80","PMC4172099",NA,NA,"code.google.com"
"194","24834071","MED","24834071","10.3389/fgene.2014.00111","Quality control of next-generation sequencing data without a reference.","Trivedi UH, CÃ©zard T, Bridgett S, Montazam A, Nichols J, Blaxter M, Gharbi K.","Front Genet","2014","1664-8021","journal article; research-article","Y","Y","Y","2","Y","Y","N","N","N","324.69302",NA,"5","111","PMC4018527",NA,NA,"code.google.com"
"195","25333065","MED","25333065","10.1002/mgg3.81","Identification of three novel FGF16 mutations in X-linked recessive fusion of the fourth and fifth metacarpals and possible correlation with heart disease.","Laurell T, Nilsson D, Hofmeister W, Lindstrand A, Ahituv N, Vandermeer J, Amilon A, AnnerÃ©n G, Arner M, Pettersson M, JÃ¤ntti N, Rosberg HE, Cattini PA, NordenskjÃ¶ld A, MÃ¤kitie O, Grigelioniene G, Nordgren A.","Mol Genet Genomic Med","2014","2324-9269","journal article; research-article","Y","Y","N","0","Y","Y","Y","N","Y","324.69302","5","2","402-411","PMC4190875","refseq","UNIPROT","code.google.com"
"196","24733896","MED","24733896","10.1073/pnas.1403138111","Evolutionary pathway to increased virulence and epidemic group A Streptococcus disease derived from 3,615 genome sequences.","Nasser W, Beres SB, Olsen RJ, Dean MA, Rice KA, Long SW, Kristinsson KG, Gottfredsson M, Vuopio J, Raisanen K, Caugant DA, Steinbakk M, Low DE, McGeer A, Darenberg J, Henriques-Normark B, Van Beneden CA, Hoffmann S, Musser JM.","Proc Natl Acad Sci U S A","2014","0027-8424","journal article; research support, non-u.s. gov't; research-article","N","Y","Y","5","Y","Y","Y","N","Y","324.69302","17","111","e1768-76","PMC4035937","gen","EMBLUNIPROT","code.google.com"
"197","25510865","MED","25510865","10.1038/ncomms6495","Transposable element islands facilitate adaptation to novel environments in an invasive species.","Schrader L, Kim JW, Ence D, Zimin A, Klein A, Wyschetzki K, Weichselgartner T, Kemena C, StÃ¶kl J, Schultner E, Wurm Y, Smith CD, Yandell M, Heinze J, Gadau J, Oettler J.","Nat Commun","2014","2041-1723","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.69302",NA,"5","5495","PMC4284661",NA,NA,"code.google.com"
"198","25002514","MED","25002514","10.1073/pnas.1319778111","Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses.","Hurwitz BL, Westveld AH, Brum JR, Sullivan MB.","Proc Natl Acad Sci U S A","2014","0027-8424","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; comparative study; research-article","N","Y","Y","3","Y","Y","N","N","N","324.69302","29","111","10714-10719","PMC4115555",NA,NA,"code.google.com"
"199","25443390","MED","25443390","10.1186/1471-2164-15-1049","Diversity, expression and mRNA targeting abilities of Argonaute-targeting miRNAs among selected vascular plants.","Jagtap S, Shivaprasad PV.","BMC Genomics","2014","1471-2164","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","324.69302","1","15","1049","PMC4300679",NA,NA,"code.google.com"
"200","25134978","MED","25134978","10.1016/j.neuroimage.2014.08.019","Optimising beamformer regions of interest analysis.","Oswal A, Litvak V, Brown P, Woolrich M, Barnes G.","Neuroimage","2014","1053-8119","journal article; research support, non-u.s. gov't; brief-report","Y","Y","N","0","Y","Y","N","N","N","324.69302",NA,"102 Pt 2","945-954","PMC4229504",NA,NA,"code.google.com"
"201","24814343","MED","24814343","10.1038/nature13261","CFIm25 links alternative polyadenylation to glioblastoma tumour suppression.","Masamha CP, Xia Z, Yang J, Albrecht TR, Li M, Shyu AB, Li W, Wagner EJ.","Nature","2014","0028-0836","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","N","0","Y","Y","Y","N","N","324.69302","7505","510","412-416","PMC4128630",NA,"OMIMARXPR","code.google.com"
"202","24673816","MED","24673816","10.1186/1471-2164-15-241","De novo transcriptome assembly reveals sex-specific selection acting on evolving neo-sex chromosomes in Drosophila miranda.","Kaiser VB, Bachtrog D.","BMC Genomics","2014","1471-2164","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","Y","Y","N","324.69302",NA,"15","241","PMC3986819",NA,"EMBL","code.google.com"
"203","25058586","MED","25058586","10.1371/journal.pgen.1004501","Determinative developmental cell lineages are robust to cell deaths.","Yang JR, Ruan S, Zhang J.","PLoS Genet","2014","1553-7390","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.54645","7","10","e1004501","PMC4110091",NA,NA,"code.google.com"
"204","24699269","MED","24699269","10.1371/journal.pcbi.1003544","Exact hybrid particle/population simulation of rule-based models of biochemical systems.","Hogg JS, Harris LA, Stover LJ, Nair NS, Faeder JR.","PLoS Comput Biol","2014","1553-734x","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","2","Y","Y","N","N","N","324.54645","4","10","e1003544","PMC3974646",NA,NA,"code.google.com"
"205","25474312","MED","25474312","10.1371/journal.pgen.1004813","Genetic analysis of the cardiac methylome at single nucleotide resolution in a model of human cardiovascular disease.","Johnson MD, Mueller M, Adamowicz-Brice M, Collins MJ, Gellert P, Maratou K, Srivastava PK, Rotival M, Butt S, Game L, Atanur SS, Silver N, Norsworthy PJ, Langley SR, Petretto E, Pravenec M, Aitman TJ.","PLoS Genet","2014","1553-7390","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","Y","N","Y","324.54645","12","10","e1004813","PMC4256262","arrayexpress","ARXPR","code.google.com"
"206","24470219","MED","24470219","10.1534/g3.113.009936","MicroRNA regulation of bovine monocyte inflammatory and metabolic networks in an in vivo infection model.","Lawless N, Reinhardt TA, Bryan K, Baker M, Pesch B, Zimmerman D, Zuelke K, Sonstegard T, O'Farrelly C, Lippolis JD, Lynn DJ.","G3 (Bethesda)","2014","2160-1836","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","1","Y","Y","Y","N","N","324.54645","6","4","957-971","PMC4065264",NA,"ARXPR","code.google.com"
"207","25025130","MED","25025130","10.1371/journal.pone.0100855","OMIT: dynamic, semi-automated ontology development for the microRNA domain.","Huang J, Dang J, Borchert GM, Eilbeck K, Zhang H, Xiong M, Jiang W, Wu H, Blake JA, Natale DA, Tan M.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.26587","7","9","e100855","PMC4099014",NA,NA,"code.google.com"
"208","24448446","MED","24448446","10.1261/rna.041657.113","Fast-evolving microRNAs are highly expressed in the early embryo of Drosophila virilis.","Ninova M, Ronshaugen M, Griffiths-Jones S.","RNA","2014","1355-8382","journal article; research support, non-u.s. gov't; research-article","N","Y","Y","3","Y","Y","N","Y","N","324.26587","3","20","360-372","PMC3923130",NA,NA,"code.google.com"
"209","25057768","MED","25057768","10.1371/journal.pone.0102968","Role of polycomb group proteins in the DNA damage response--a reassessment.","Chandler H, Patel H, Palermo R, Brookes S, Matthews N, Peters G.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","Y","N","N","324.26587","7","9","e102968","PMC4109945",NA,"ARXPR","code.google.com"
"210","24706719","MED","24706719","10.1093/jxb/eru148","Fruit load induces changes in global gene expression and in abscisic acid (ABA) and indole acetic acid (IAA) homeostasis in citrus buds.","Shalom L, Samuels S, Zur N, Shlizerman L, Doron-Faigenboim A, Blumwald E, Sadka A.","J Exp Bot","2014","0022-0957","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","324.26587","12","65","3029-3044","PMC4071824",NA,NA,"code.google.com"
"211","24916072","MED","24916072","10.1093/jxb/eru218","A broad survey of hydraulic and mechanical safety in the xylem of conifers.","Bouche PS, Larter M, Domec JC, Burlett R, Gasson P, Jansen S, Delzon S.","J Exp Bot","2014","0022-0957","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.26587","15","65","4419-4431","PMC4112641",NA,NA,"code.google.com"
"212","25337713","MED","25337713","10.1371/journal.pone.0111089","Unisexual reproduction of Cryptococcus gattii.","Phadke SS, Feretzaki M, Clancey SA, Mueller O, Heitman J.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","N","0","Y","Y","N","N","N","324.26587","10","9","e111089","PMC4206507",NA,NA,"code.google.com"
"213","25279728","MED","25279728","10.1371/journal.pone.0108550","A comparison of next generation sequencing technologies for transcriptome assembly and utility for RNA-Seq in a non-model bird.","Finseth FR, Harrison RG.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","N","0","Y","Y","N","N","N","324.26587","10","9","e108550","PMC4184788",NA,NA,"code.google.com"
"214","25142519","MED","25142519","10.1098/rsif.2014.0535","Progressive promoter element combinations classify conserved orthogonal plant circadian gene expression modules.","Smieszek SP, Yang H, Paccanaro A, Devlin PF.","J R Soc Interface","2014","1742-5689","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","324.26587","99","11",NA,"PMC4233729",NA,NA,"code.google.com"
"215","25290450","MED","25290450","10.1371/journal.pone.0109831","A transcriptome for the study of early processes of retinal regeneration in the adult newt, Cynops pyrrhogaster.","Nakamura K, Islam MR, Takayanagi M, Yasumuro H, Inami W, Kunahong A, Casco-Robles RM, Toyama F, Chiba C.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","Y","N","N","324.26587","10","9","e109831","PMC4188609",NA,"UNIPROT","code.google.com"
"216","25411636","MED","25411636","10.1186/2049-2618-2-39","Comparison of assembly algorithms for improving rate of metatranscriptomic functional annotation.","Celaj A, Markle J, Danska J, Parkinson J.","Microbiome","2014","2049-2618","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.26587",NA,"2","39","PMC4236897",NA,NA,"code.google.com"
"217","25185836","MED","25185836","10.1186/1471-2164-15-756","Transcriptional profiles of bovine in vivo pre-implantation development.","Jiang Z, Sun J, Dong H, Luo O, Zheng X, Obergfell C, Tang Y, Bi J, O'Neill R, Ruan Y, Chen J, Tian XC.","BMC Genomics","2014","1471-2164","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","N","0","Y","Y","Y","N","N","324.26587","1","15","756","PMC4162962",NA,"ARXPR","code.google.com"
"218","24945156","MED","24945156","10.1371/journal.pone.0100250","Novel method for analysis of allele specific expression in triploid Oryzias latipes reveals consistent pattern of allele exclusion.","Garcia TI, Matos I, Shen Y, Pabuwal V, Coelho MM, Wakamatsu Y, Schartl M, Walter RB.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","0","N","Y","N","N","N","324.26587","6","9","e100250","PMC4063754",NA,NA,"code.google.com"
"219","24727652","MED","24727652","10.1038/nmeth.2924","Multiscale representation of genomic signals.","Knijnenburg TA, Ramsey SA, Berman BP, Kennedy KA, Smit AF, Wessels LF, Laird PW, Aderem A, Shmulevich I.","Nat Methods","2014","1548-7091","journal article; research support, n.i.h., extramural; research-article","Y","Y","N","1","Y","Y","N","N","N","324.26587","6","11","689-694","PMC4040162",NA,NA,"code.google.com"
"220","24625827","MED","24625827","10.1371/journal.pone.0090943","Lateralized readiness potentials reveal properties of a neural mechanism for implementing a decision threshold.","van Vugt MK, Simen P, Nystrom L, Holmes P, Cohen JD.","PLoS One","2014","1932-6203","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","1","Y","Y","N","N","N","324.26587","3","9","e90943","PMC3953213",NA,NA,"code.google.com"
"221","24453971","MED","24453971","10.1371/journal.ppat.1003877","Alphavirus mutator variants present host-specific defects and attenuation in mammalian and insect models.","Rozen-Gagnon K, Stapleford KA, Mongelli V, Blanc H, Failloux AB, Saleh MC, Vignuzzi M.","PLoS Pathog","2014","1553-7366","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","5","Y","Y","N","Y","N","324.26587","1","10","e1003877","PMC3894214",NA,NA,"code.google.com"
"222","25404915","MED","25404915","10.3389/fneng.2014.00040","Real-time in vivo optogenetic neuromodulation and multielectrode electrophysiologic recording with NeuroRighter.","Laxpati NG, Mahmoudi B, Gutekunst CA, Newman JP, Zeller-Townson R, Gross RE.","Front Neuroeng","2014","1662-6443","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.26587",NA,"7","40","PMC4217045",NA,NA,"code.google.com"
"223","24573331","MED","24573331","10.1098/rsif.2013.1106","Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth-death SIR model.","KÃ¼hnert D, Stadler T, Vaughan TG, Drummond AJ.","J R Soc Interface","2014","1742-5689","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","5","Y","Y","N","N","N","324.26587","94","11","20131106","PMC3973358",NA,NA,"code.google.com"
"224","24714079","MED","24714079","10.1093/molbev/msu121","Bayesian inference of infectious disease transmission from whole-genome sequence data.","Didelot X, Gardy J, Colijn C.","Mol Biol Evol","2014","0737-4038","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","5","Y","Y","N","N","N","324.26587","7","31","1869-1879","PMC4069612",NA,NA,"code.google.com"
"225","24347632","MED","24347632","10.1534/g3.113.008680","Large-scale quality analysis of published ChIP-seq data.","Marinov GK, Kundaje A, Park PJ, Wold BJ.","G3 (Bethesda)","2014","2160-1836","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","3","Y","Y","N","N","N","324.26587","2","4","209-223","PMC3931556",NA,NA,"code.google.com"
"226","24369422","MED","24369422","10.1093/nar/gkt1317","SUMOylation of the polycomb group protein L3MBTL2 facilitates repression of its target genes.","Stielow C, Stielow B, Finkernagel F, Scharfe M, Jarek M, Suske G.","Nucleic Acids Res","2014","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","Y","N","Y","324.26587","5","42","3044-3058","PMC3950706","arrayexpress","ARXPR","code.google.com"
"227","24431433","MED","24431433","10.1523/jneurosci.0352-13.2014","Mental action simulation synchronizes action-observation circuits across individuals.","Nummenmaa L, Smirnov D, Lahnakoski JM, Glerean E, JÃ¤Ã¤skelÃ¤inen IP, Sams M, Hari R.","J Neurosci","2014","0270-6474","journal article; randomized controlled trial; research support, non-u.s. gov't; research-article","N","Y","Y","3","Y","Y","N","N","N","324.26587","3","34","748-757","PMC3891955",NA,NA,"code.google.com"
"228","24478635","MED","24478635","10.3389/fncir.2014.00001","N2A: a computational tool for modeling from neurons to algorithms.","Rothganger F, Warrender CE, Trumbo D, Aimone JB.","Front Neural Circuits","2014","1662-5110","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.26587",NA,"8","1","PMC3901007",NA,NA,"code.google.com"
"229","25157851","MED","25157851","10.1371/journal.pone.0103963","Transcriptome wide identification and validation of calcium sensor gene family in the developing spikes of finger millet genotypes for elucidating its role in grain calcium accumulation.","Singh UM, Chandra M, Shankhdhar SC, Kumar A.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.26587","8","9","e103963","PMC4144799",NA,NA,"code.google.com"
"230","24927774","MED","24927774","10.1186/1471-2164-15-471","Allele-specific expression and eQTL analysis in mouse adipose tissue.","Hasin-Brumshtein Y, Hormozdiari F, Martin L, van Nas A, Eskin E, Lusis AJ, Drake TA.","BMC Genomics","2014","1471-2164","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.26587","1","15","471","PMC4089026",NA,NA,"code.google.com"
"231","25144184","MED","25144184","10.1371/journal.pone.0103997","A new method to infer causal phenotype networks using QTL and phenotypic information.","Wang H, van Eeuwijk FA.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.26587","8","9","e103997","PMC4140682",NA,NA,"code.google.com"
"232","24789338","MED","24789338","10.1371/journal.pone.0096434","Ontology for the asexual development and anatomy of the colonial chordate Botryllus schlosseri.","Manni L, Gasparini F, Hotta K, Ishizuka KJ, Ricci L, Tiozzo S, Voskoboynik A, Dauga D.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","2","Y","Y","N","N","N","324.26587","5","9","e96434","PMC4006837",NA,NA,"code.google.com"
"233","24793089","MED","24793089","10.1534/genetics.114.161299","A Bayesian approach to inferring the phylogenetic structure of communities from metagenomic data.","O'Brien JD, Didelot X, Iqbal Z, Amenga-Etego L, Ahiska B, Falush D.","Genetics","2014","0016-6731","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.26587","3","197","925-937","PMC4096371",NA,NA,"code.google.com"
"234","23990268","MED","23990268","10.1093/bib/bbt054","A comprehensive overview of Infinium HumanMethylation450 data processing.","Dedeurwaerder S, Defrance M, Bizet M, Calonne E, Bontempi G, Fuks F.","Brief Bioinform","2014","1467-5463","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","324.26587","6","15","929-941","PMC4239800",NA,NA,"code.google.com"
"235","24626288","MED","24626288","10.1534/g3.114.010249","Bioinformatics analysis of alternative polyadenylation in green alga Chlamydomonas reinhardtii using transcriptome sequences from three different sequencing platforms.","Zhao Z, Wu X, Kumar PK, Dong M, Ji G, Li QQ, Liang C.","G3 (Bethesda)","2014","2160-1836","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.26587","5","4","871-883","PMC4025486",NA,NA,"code.google.com"
"236","24753410","MED","24753410","10.1093/nar/gku303","The histone variant H2A.Bbd is enriched at sites of DNA synthesis.","Sansoni V, Casas-Delucchi CS, Rajan M, Schmidt A, BÃ¶nisch C, Thomae AW, Staege MS, Hake SB, Cardoso MC, Imhof A.","Nucleic Acids Res","2014","0305-1048","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","324.26587","10","42","6405-6420","PMC4041467",NA,NA,"code.google.com"
"237","25159725","MED","25159725","10.1007/s00335-014-9540-0","Responsiveness of cardiometabolic-related microbiota to diet is influenced by host genetics.","O'Connor A, Quizon PM, Albright JE, Lin FT, Bennett BJ.","Mamm Genome","2014","0938-8990","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.26587","11-12","25","583-599","PMC4239785",NA,NA,"code.google.com"
"238","25192061","MED","25192061","10.1371/journal.pone.0106649","Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies.","Card DC, Schield DR, Reyes-Velasco J, Fujita MK, Andrew AL, Oyler-McCance SJ, Fike JA, Tomback DF, Ruggiero RP, Castoe TA.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","Y","N","324.26587","9","9","e106649","PMC4156343",NA,NA,"code.google.com"
"239","24676052","MED","24676052","10.1371/journal.pcbi.1003529","Comparative analysis of the macroscale structural connectivity in the macaque and human brain.","Goulas A, Bastiani M, Bezgin G, Uylings HB, Roebroeck A, Stiers P.","PLoS Comput Biol","2014","1553-734x","journal article; comparative study; research-article","Y","Y","Y","2","Y","Y","N","N","N","324.26587","3","10","e1003529","PMC3967942",NA,NA,"code.google.com"
"240","24682735","MED","24682735","10.1093/database/bau027","The eGenVar data management system--cataloguing and sharing sensitive data and metadata for the life sciences.","Razick S, MoÄnik R, Thomas LF, Ryeng E, DrablÃ¸s F, SÃ¦trom P.","Database (Oxford)","2014","1758-0463","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.26587",NA,"2014","bau027","PMC4030636",NA,NA,"code.google.com"
"241","24713319","MED","24713319","10.1128/mbio.00074-14","Noncanonical microRNA (miRNA) biogenesis gives rise to retroviral mimics of lymphoproliferative and immunosuppressive host miRNAs.","Kincaid RP, Chen Y, Cox JE, Rethwilm A, Sullivan CS.","MBio","2014","2150-7511","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","2","Y","Y","N","N","N","324.26587","2","5","e00074","PMC3993851",NA,NA,"code.google.com"
"242","24884572","MED","24884572","10.1186/1471-2148-14-103","Molecular evolution accompanying functional divergence of duplicated genes along the plant starch biosynthesis pathway.","NouguÃ© O, Corbi J, Ball SG, Manicacci D, Tenaillon MI.","BMC Evol Biol","2014","1471-2148","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","Y","Y","324.26587",NA,"14","103","PMC4041918","doi",NA,"code.google.com"
"243","24963371","MED","24963371","10.1186/2041-1480-5-19","The ontology of genetic susceptibility factors (OGSF) and its application in modeling genetic susceptibility to vaccine adverse events.","Lin Y, He Y.","J Biomed Semantics","2014","2041-1480","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","Y","324.26587",NA,"5","19","PMC4068904","refsnp",NA,"code.google.com"
"244","25009539","MED","25009539","10.3389/fmicb.2014.00311","A dual-species co-cultivation system to study the interactions between Roseobacters and dinoflagellates.","Wang H, Tomasch J, Jarek M, Wagner-DÃ¶bler I.","Front Microbiol","2014","1664-302x","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.26587",NA,"5","311","PMC4069834",NA,NA,"code.google.com"
"245","25093019","MED","25093019","10.1186/s13637-014-0010-5","Learning restricted Boolean network model by time-series data.","Ouyang H, Fang J, Shen L, Dougherty ER, Liu W.","EURASIP J Bioinform Syst Biol","2014","1687-4145","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.26587","1","2014","10","PMC4107581",NA,NA,"code.google.com"
"246","25140222","MED","25140222","10.1186/2041-1480-5-34","Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology.","Dahdul WM, Cui H, Mabee PM, Mungall CJ, Osumi-Sutherland D, Walls RL, Haendel MA.","J Biomed Semantics","2014","2041-1480","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.26587",NA,"5","34","PMC4137724",NA,NA,"code.google.com"
"247","24904260","MED","24904260","10.3389/fnins.2014.00116","Online tracking of the contents of conscious perception using real-time fMRI.","Reichert C, Fendrich R, Bernarding J, Tempelmann C, Hinrichs H, Rieger JW.","Front Neurosci","2014","1662-4548","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","324.26587",NA,"8","116","PMC4033165",NA,NA,"code.google.com"
"248","25538569","MED","25538569","10.3389/fnana.2014.00138","Statistical analysis and data mining of digital reconstructions of dendritic morphologies.","Polavaram S, Gillette TA, Parekh R, Ascoli GA.","Front Neuroanat","2014","1662-5129","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.26587",NA,"8","138","PMC4255610",NA,NA,"code.google.com"
"249","25565969","MED","25565969","10.3389/fncel.2014.00437","Gene regulatory network analysis reveals differences in site-specific cell fate determination in mammalian brain.","Ertaylan G, Okawa S, Schwamborn JC, Del Sol A.","Front Cell Neurosci","2014","1662-5102","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.26587",NA,"8","437","PMC4270183",NA,NA,"code.google.com"
"250","24150038","MED","24150038","10.1093/molbev/mst203","Reconciling phylodynamics with epidemiology: the case of dengue virus in southern Vietnam.","Rasmussen DA, Boni MF, Koelle K.","Mol Biol Evol","2014","0737-4038","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","5","Y","Y","N","N","N","324.26587","2","31","258-271","PMC3907054",NA,NA,"code.google.com"
"251","25517905","MED","25517905","10.1371/journal.pone.0113652","IMOS National Reference Stations: A Continental-Wide Physical, Chemical and Biological Coastal Observing System.","Lynch TP, Morello EB, Evans K, Richardson AJ, Rochester W, Steinberg CR, Roughan M, Thompson P, Middleton JF, Feng M, Sherrington R, Brando V, Tilbrook B, Ridgway K, Allen S, Doherty P, Hill K, Moltmann TC.","PLoS One","2014","1932-6203","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.26587","12","9","e113652","PMC4269483",NA,NA,"code.google.com"
"252","25390365","MED","25390365","10.1371/journal.pone.0112265","Adaptive robotic control driven by a versatile spiking cerebellar network.","Casellato C, Antonietti A, Garrido JA, Carrillo RR, Luque NR, Ros E, Pedrocchi A, D'Angelo E.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","324.26587","11","9","e112265","PMC4229206",NA,NA,"code.google.com"
"253","25120271","MED","25120271","10.1093/nar/gku712","The bone-specific Runx2-P1 promoter displays conserved three-dimensional chromatin structure with the syntenic Supt3h promoter.","Barutcu AR, Tai PW, Wu H, Gordon JA, Whitfield TW, Dobson JR, Imbalzano AN, Lian JB, van Wijnen AJ, Stein JL, Stein GS.","Nucleic Acids Res","2014","0305-1048","journal article; research support, n.i.h., extramural; research-article","Y","Y","N","0","Y","Y","N","N","N","324.26587","16","42","10360-10372","PMC4176362",NA,NA,"code.google.com"
"254","25381880","MED","25381880","10.1038/ncomms6269","Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution.","Geering AD, Maumus F, Copetti D, Choisne N, Zwickl DJ, Zytnicki M, McTaggart AR, Scalabrin S, Vezzulli S, Wing RA, Quesneville H, Teycheney PY.","Nat Commun","2014","2041-1723","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","Y","324.26587",NA,"5","5269","PMC4241990","gen",NA,"code.google.com"
"255","24816929","MED","24816929","10.1371/journal.pone.0096946","Genome-wide transcriptome analysis reveals that cadmium stress signaling controls the expression of genes in drought stress signal pathways in rice.","Oono Y, Yazawa T, Kawahara Y, Kanamori H, Kobayashi F, Sasaki H, Mori S, Wu J, Handa H, Itoh T, Matsumoto T.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","Y","324.26587","5","9","e96946","PMC4016200","pfam",NA,"code.google.com"
"256","24465193","MED","24465193","10.1371/journal.pcbi.1003416","Immune-mediated competition in rodent malaria is most likely caused by induced changes in innate immune clearance of merozoites.","Santhanam J, RÃ¥berg L, Read AF, Savill NJ.","PLoS Comput Biol","2014","1553-734x","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.26587","1","10","e1003416","PMC3900382",NA,NA,"code.google.com"
"257","24627184","MED","24627184","10.1093/sysbio/syu015","Inferring heterogeneous evolutionary processes through time: from sequence substitution to phylogeography.","Bielejec F, Lemey P, Baele G, Rambaut A, Suchard MA.","Syst Biol","2014","1063-5157","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","Y","Y","324.26587","4","63","493-504","PMC4055869","doi",NA,"code.google.com"
"258","24699266","MED","24699266","10.1371/journal.pone.0092644","The draft genome sequence of European pear (Pyrus communis L. 'Bartlett').","ChagnÃ© D, Crowhurst RN, Pindo M, Thrimawithana A, Deng C, Ireland H, Fiers M, Dzierzon H, Cestaro A, Fontana P, Bianco L, Lu A, Storey R, KnÃ¤bel M, Saeed M, Montanari S, Kim YK, Nicolini D, Larger S, Stefani E, Allan AC, Bowen J, Harvey I, Johnston J, Malnoy M, Troggio M, Perchepied L, Sawyer G, Wiedow C, Won K, Viola R, Hellens RP, Brewer L, Bus VG, Schaffer RJ, Gardiner SE, Velasco R.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","324.26587","4","9","e92644","PMC3974708",NA,NA,"code.google.com"
"259","25398475","MED","25398475","10.1186/1471-2164-15-969","MaxSSmap: a GPU program for mapping divergent short reads to genomes with the maximum scoring subsequence.","Turki T, Roshan U.","BMC Genomics","2014","1471-2164","journal article; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","N","0","Y","Y","N","N","N","324.26587","1","15","969","PMC4289234",NA,NA,"code.google.com"
"260","25009735","MED","25009735","10.1186/2041-1480-5-21","Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon.","Haendel MA, Balhoff JP, Bastian FB, Blackburn DC, Blake JA, Bradford Y, Comte A, Dahdul WM, Dececchi TA, Druzinsky RE, Hayamizu TF, Ibrahim N, Lewis SE, Mabee PM, Niknejad A, Robinson-Rechavi M, Sereno PC, Mungall CJ.","J Biomed Semantics","2014","2041-1480","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","324.26587",NA,"5","21","PMC4089931",NA,NA,"code.google.com"
"261","24489818","MED","24489818","10.1371/journal.pone.0086976","Transcriptomic analysis of flower development in wintersweet (Chimonanthus praecox).","Liu D, Sui S, Ma J, Li Z, Guo Y, Luo D, Yang J, Li M.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","N","N","N","324.26587","1","9","e86976","PMC3906103",NA,NA,"code.google.com"
"262","24277029","MED","24277029","10.1128/aac.02183-13","Phosphate-containing polyethylene glycol polymers prevent lethal sepsis by multidrug-resistant pathogens.","Zaborin A, Defazio JR, Kade M, Kaiser BL, Belogortseva N, Camp DG 2nd, Smith RD, Adkins JN, Kim SM, Alverdy A, Goldfeld D, Firestone MA, Collier JH, Jabri B, Tirrell M, Zaborina O, Alverdy JC.","Antimicrob Agents Chemother","2014","0066-4804","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","Y","2","Y","Y","N","N","N","324.26587","2","58","966-977","PMC3910877",NA,NA,"code.google.com"
"263","24705617","MED","24705617","10.1371/journal.pone.0093975","A framework phylogeny of the American oak clade based on sequenced RAD data.","Hipp AL, Eaton DA, Cavender-Bares J, Fitzek E, Nipper R, Manos PS.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","3","Y","Y","N","Y","Y","324.26587","4","9","e93975","PMC3976371","doi",NA,"code.google.com"
"264","24442674","MED","24442674","10.1093/nar/gkt1386","Comparative ribosome profiling reveals extensive translational complexity in different Trypanosoma brucei life cycle stages.","Vasquez JJ, Hon CC, Vanselow JT, Schlosser A, Siegel TN.","Nucleic Acids Res","2014","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","4","Y","Y","N","N","N","324.26587","6","42","3623-3637","PMC3973304",NA,NA,"code.google.com"
"265","24909122","MED","24909122","10.1038/ncomms4979","Long non-coding RNAs and enhancer RNAs regulate the lipopolysaccharide-induced inflammatory response in human monocytes.","IIott NE, Heward JA, Roux B, Tsitsiou E, Fenwick PS, Lenzi L, Goodhead I, Hertz-Fowler C, Heger A, Hall N, Donnelly LE, Sims D, Lindsay MA.","Nat Commun","2014","2041-1723","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","6","Y","Y","N","N","Y","324.26587",NA,"5","3979","PMC4061460","arrayexpress",NA,"code.google.com"
"266","24586134","MED","24586134","10.1371/journal.pcbi.1003483","Pathway thermodynamics highlights kinetic obstacles in central metabolism.","Noor E, Bar-Even A, Flamholz A, Reznik E, Liebermeister W, Milo R.","PLoS Comput Biol","2014","1553-734x","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","4","Y","Y","N","N","N","324.26587","2","10","e1003483","PMC3930492",NA,NA,"code.google.com"
"267","24758272","MED","24758272","10.1186/1471-2164-15-305","A house finch (Haemorhous mexicanus) spleen transcriptome reveals intra- and interspecific patterns of gene expression, alternative splicing and genetic diversity in passerines.","Zhang Q, Hill GE, Edwards SV, BackstrÃ¶m N.","BMC Genomics","2014","1471-2164","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","N","0","Y","Y","N","N","N","324.26587",NA,"15","305","PMC4235107",NA,NA,"code.google.com"
"268","24722556","MED","24722556","10.1371/journal.pone.0094651","Transcriptomic analysis of Petunia hybrida in response to salt stress using high throughput RNA sequencing.","Villarino GH, Bombarely A, Giovannoni JJ, Scanlon MJ, Mattson NS.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","324.26587","4","9","e94651","PMC3983219",NA,NA,"code.google.com"
"269","25071822","MED","25071822","10.3389/fgene.2014.00192","Identification of structural variation in mouse genomes.","Keane TM, Wong K, Adams DJ, Flint J, Reymond A, Yalcin B.","Front Genet","2014","1664-8021","journal article; review; review-article","Y","Y","Y","1","Y","Y","N","N","N","324.26587",NA,"5","192","PMC4079067",NA,NA,"code.google.com"
"270","24787735","MED","24787735","10.1371/journal.pone.0096105","Patterns of genome-wide VDR locations.","TuoresmÃ¤ki P, VÃ¤isÃ¤nen S, Neme A, Heikkinen S, Carlberg C.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","6","Y","Y","Y","N","N","324.26587","4","9","e96105","PMC4005760",NA,"ARXPR","code.google.com"
"271","24400075","MED","24400075","10.1371/journal.pone.0083675","Exploring candidate genes for pericarp russet pigmentation of sand pear (Pyrus pyrifolia) via RNA-Seq data in two genotypes contrasting for pericarp color.","Wang YZ, Dai MS, Zhang SJ, Shi ZB.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","Y","N","Y","324.26587","1","9","e83675","PMC3882208","gen","EMBL","code.google.com"
"272","24559402","MED","24559402","10.1186/1471-2164-15-148","Improving transcriptome construction in non-model organisms: integrating manual and automated gene definition in Emiliania huxleyi.","Feldmesser E, Rosenwasser S, Vardi A, Ben-Dor S.","BMC Genomics","2014","1471-2164","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","Y","N","N","324.26587",NA,"15","148","PMC4028052",NA,"EMBLUNIPROT","code.google.com"
"273","24438054","MED","24438054","10.1186/1471-2164-15-45","The transcriptome of the NZ endemic sea urchin Kina (Evechinus chloroticus).","Gillard GB, Garama DJ, Brown CM.","BMC Genomics","2014","1471-2164","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","Y","N","Y","324.26587",NA,"15","45","PMC3898728","pfam","EMBL","code.google.com"
"274","24427303","MED","24427303","10.1371/journal.pone.0085368","Population history and pathways of spread of the plant pathogen Phytophthora plurivora.","Schoebel CN, Stewart J, Gruenwald NJ, Rigling D, Prospero S.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","Y","N","Y","324.26587","1","9","e85368","PMC3888410","gen","EMBLUNIPROT","code.google.com"
"275","24809511","MED","24809511","10.1371/journal.pgen.1004355","A lack of parasitic reduction in the obligate parasitic green alga Helicosporidium.","Pombert JF, Blouin NA, Lane C, Boucias D, Keeling PJ.","PLoS Genet","2014","1553-7390","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","Y","N","N","324.26587","5","10","e1004355","PMC4014436",NA,"EMBLUNIPROT","code.google.com"
"276","25474637","MED","25474637","10.1371/journal.pcbi.1003992","The social Bayesian brain: does mentalizing make a difference when we learn?","Devaine M, Hollard G, Daunizeau J.","PLoS Comput Biol","2014","1553-734x","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","323.8387","12","10","e1003992","PMC4256068",NA,NA,"code.google.com"
"277","24555784","MED","24555784","10.1186/1745-6150-9-4","A survey of motif finding Web tools for detecting binding site motifs in ChIP-Seq data.","Tran NT, Huang CH.","Biol Direct","2014","1745-6150","evaluation studies; journal article; review; research support, u.s. gov't, non-p.h.s.; review-article","Y","Y","Y","1","Y","Y","N","N","N","323.8387",NA,"9","4","PMC4022013",NA,NA,"code.google.com"
"278","24393330","MED","24393330","10.1186/1479-5876-12-3","Methods and matrices: approaches to identifying miRNAs for nasopharyngeal carcinoma.","Plieskatt JL, Rinaldi G, Feng Y, Levine PH, Easley S, Martinez E, Hashmi S, Sadeghi N, Brindley PJ, Bethony JM, Mulvenna JP.","J Transl Med","2014","1479-5876","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","Y","N","N","323.8387",NA,"12","3","PMC3895762",NA,"ARXPR","code.google.com"
"279","25255432","MED","25255432","10.1371/journal.pone.0108466","Formal modelling of toll like receptor 4 and JAK/STAT signalling pathways: insight into the roles of SOCS-1, interferon-Î² and proinflammatory cytokines in sepsis.","Paracha RZ, Ahmad J, Ali A, Hussain R, Niazi U, Tareen SH, Aslam B.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","323.8387","9","9","e108466","PMC4185881",NA,NA,"code.google.com"
"280","25192015","MED","25192015","10.1371/journal.pone.0106795","The expression pattern of microRNAs in granulosa cells of subordinate and dominant follicles during the early luteal phase of the bovine estrous cycle.","Salilew-Wondim D, Ahmad I, Gebremedhn S, Sahadevan S, Hossain MD, Rings F, Hoelker M, Tholen E, Neuhoff C, Looft C, Schellander K, Tesfaye D.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","323.8387","9","9","e106795","PMC4156418",NA,NA,"code.google.com"
"281","25485311","MED","25485311",NA,"Breaking and Fixing Origin-Based Access Control in Hybrid Web/Mobile Application Frameworks.","Georgiev M, Jana S, Shmatikov V.","NDSS symposium","2014",NA,"journal article; research-article","N","Y","N","0","N","Y","N","N","N","323.8387",NA,"2014","1-15","PMC4254737",NA,NA,"code.google.com"
"282","25538939","MED","25538939","10.3389/fbioe.2014.00061","Improving collaboration by standardization efforts in systems biology.","DrÃ¤ger A, Palsson BÃ.","Front Bioeng Biotechnol","2014","2296-4185","journal article; review; review-article","Y","Y","N","0","Y","Y","N","N","N","323.8387",NA,"2","61","PMC4259112",NA,NA,"code.google.com"
"283","24743590","MED","24743590","10.1371/journal.pcbi.1003570","Phylodynamic inference for structured epidemiological models.","Rasmussen DA, Volz EM, Koelle K.","PLoS Comput Biol","2014","1553-734x","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","3","Y","Y","N","N","N","323.8387","4","10","e1003570","PMC3990497",NA,NA,"code.google.com"
"284","24743711","MED","24743711","10.1371/journal.pcbi.1003584","How the brain decides when to work and when to rest: dissociation of implicit-reactive from explicit-predictive computational processes.","Meyniel F, Safra L, Pessiglione M.","PLoS Comput Biol","2014","1553-734x","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","323.8387","4","10","e1003584","PMC3990494",NA,NA,"code.google.com"
"285","25313861","MED","25313861","10.1371/journal.pbio.1001969","A conserved endoplasmic reticulum membrane protein complex (EMC) facilitates phospholipid transfer from the ER to mitochondria.","Lahiri S, Chao JT, Tavassoli S, Wong AK, Choudhary V, Young BP, Loewen CJ, Prinz WA.","PLoS Biol","2014","1544-9173","journal article; research support, non-u.s. gov't; research support, n.i.h., intramural; research-article","Y","Y","N","0","Y","Y","Y","N","N","323.8387","10","12","e1001969","PMC4196738",NA,"UNIPROT","code.google.com"
"286","24678134","MED","24678134","10.1080/01621459.2013.869222","Some Statistical Strategies for DAE-seq Data Analysis: Variable Selection and Modeling Dependencies among Observations.","Rashid NU, Sun W, Ibrahim JG.","J Am Stat Assoc","2014","0162-1459","journal article; research-article","N","Y","N","0","Y","Y","N","N","N","323.8387","505","109","78-94","PMC3963211",NA,NA,"code.google.com"
"287","24441104","MED","24441104","10.1093/molbev/msu048","The power to detect quantitative trait loci using resequenced, experimentally evolved populations of diploid, sexual organisms.","Baldwin-Brown JG, Long AD, Thornton KR.","Mol Biol Evol","2014","0737-4038","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","1","Y","Y","N","N","N","323.8387","4","31","1040-1055","PMC3969567",NA,NA,"code.google.com"
"288","24842994","MED","24842994","10.7554/elife.02105","Tyrosine phosphorylation of RNA polymerase II CTD is associated with antisense promoter transcription and active enhancers in mammalian cells.","Descostes N, Heidemann M, Spinelli L, SchÃ¼ller R, Maqbool MA, Fenouil R, Koch F, Innocenti C, Gut M, Gut I, Eick D, Andrau JC.","Elife","2014","2050-084x","journal article; research-article","Y","Y","Y","1","Y","Y","Y","N","N","323.8387",NA,"3","e02105","PMC4042876",NA,"ARXPR","code.google.com"
"289","24911316","MED","24911316","10.1371/journal.pone.0099334","Predicting epileptic seizures in advance.","Moghim N, Corne DW.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","323.8387","6","9","e99334","PMC4049812",NA,NA,"code.google.com"
"290","24788524","MED","24788524","10.1371/journal.ppat.1004088","Dual-site phosphorylation of the control of virulence regulator impacts group a streptococcal global gene expression and pathogenesis.","Horstmann N, SaldaÃ±a M, Sahasrabhojane P, Yao H, Su X, Thompson E, Koller A, Shelburne SA 3rd.","PLoS Pathog","2014","1553-7366","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","323.8387","5","10","e1004088","PMC4006921",NA,NA,"code.google.com"
"291","24507381","MED","24507381","10.1186/1752-0509-8-13","Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach.","Meyer P, Cokelaer T, Chandran D, Kim KH, Loh PR, Tucker G, Lipson M, Berger B, Kreutz C, Raue A, Steiert B, Timmer J, Bilal E, Dream Six and Seven Parameter Estimation Consortium, Sauro HM, Stolovitzky G, Saez-Rodriguez J.","BMC Syst Biol","2014","1752-0509","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","323.8387",NA,"8","13","PMC3927870",NA,NA,"code.google.com"
"292","24782528","MED","24782528","10.1093/nar/gku312","The interaction of MYC with the trithorax protein ASH2L promotes gene transcription by regulating H3K27 modification.","Ullius A, LÃ¼scher-Firzlaff J, Costa IG, Walsemann G, Forst AH, Gusmao EG, Kapelle K, Kleine H, Kremmer E, Vervoorts J, LÃ¼scher B.","Nucleic Acids Res","2014","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","323.8387","11","42","6901-6920","PMC4066752",NA,NA,"code.google.com"
"293","24963381","MED","24963381","10.1002/ece3.1068","A multiscale analysis of gene flow for the New England cottontail, an imperiled habitat specialist in a fragmented landscape.","Fenderson LE, Kovach AI, Litvaitis JA, O'Brien KM, Boland KM, Jakubas WJ.","Ecol Evol","2014","2045-7758","journal article; research-article","Y","Y","Y","0","Y","Y","N","Y","N","323.8387","10","4","1853-1875","PMC4063480",NA,NA,"code.google.com"
"294","25152673","MED","25152673","10.3897/zookeys.433.7054","The type material of Mantodea (praying mantises) deposited in the National Museum of Natural History, Smithsonian Institution, USA.","Svenson GJ.","Zookeys","2014","1313-2989","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","323.8387","433",NA,"31-75","PMC4141179",NA,NA,"code.google.com"
"295","25101664","MED","25101664","10.1371/journal.pgen.1004526","Asymmetric division and differential gene expression during a bacterial developmental program requires DivIVA.","Eswaramoorthy P, Winter PW, Wawrzusin P, York AG, Shroff H, Ramamurthi KS.","PLoS Genet","2014","1553-7390","journal article; research support, n.i.h., extramural; research support, n.i.h., intramural; research-article","Y","Y","Y","1","Y","Y","N","N","N","323.8387","8","10","e1004526","PMC4125091",NA,NA,"code.google.com"
"296","25380807","MED","25380807","10.1186/1471-2164-15-966","A novel approach for multi-domain and multi-gene family identification provides insights into evolutionary dynamics of disease resistance genes in core eudicot plants.","Hofberger JA, Zhou B, Tang H, Jones JD, Schranz ME.","BMC Genomics","2014","1471-2164","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","Y","323.8387","1","15","966","PMC4289383","pfam",NA,"code.google.com"
"297","25031397","MED","25031397","10.1523/jneurosci.0712-14.2014","Natural whisker-guided behavior by head-fixed mice in tactile virtual reality.","Sofroniew NJ, Cohen JD, Lee AK, Svoboda K.","J Neurosci","2014","0270-6474","journal article; research support, non-u.s. gov't; research-article","N","Y","N","1","Y","Y","N","N","N","323.8387","29","34","9537-9550","PMC4099538",NA,NA,"code.google.com"
"298","24722003","MED","24722003","10.1371/journal.pone.0094249","Analysis, optimization and verification of Illumina-generated 16S rRNA gene amplicon surveys.","Nelson MC, Morrison HG, Benjamino J, Grim SL, Graf J.","PLoS One","2014","1932-6203","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","3","Y","Y","N","N","N","323.8387","4","9","e94249","PMC3983156",NA,NA,"code.google.com"
"299","25485284","MED","25485284","10.1080/2326263x.2013.876724","Workshops of the Fifth International Brain-Computer Interface Meeting: Defining the Future.","Huggins JE, Guger C, Allison B, Anderson CW, Batista A, Brouwer AM, Brunner C, Chavarriaga R, Fried-Oken M, Gunduz A, Gupta D, KÃ¼bler A, Leeb R, Lotte F, Miller LE, MÃ¼ller-Putz G, Rutkowski T, Tangermann M, Thompson DE.","Brain Comput Interfaces (Abingdon)","2014","2326-263x","journal article; research-article","N","Y","N","0","Y","Y","N","N","N","323.8387","1","1","27-49","PMC4255956",NA,NA,"code.google.com"
"300","25610393","MED","25610393","10.3389/fninf.2014.00088","The Decoding Toolbox (TDT): a versatile software package for multivariate analyses of functional imaging data.","Hebart MN, GÃ¶rgen K, Haynes JD.","Front Neuroinform","2014","1662-5196","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","323.8387",NA,"8","88","PMC4285115",NA,NA,"code.google.com"
"301","24425782","MED","24425782","10.1093/molbev/msu037","A high-definition view of functional genetic variation from natural yeast genomes.","BergstrÃ¶m A, Simpson JT, Salinas F, BarrÃ© B, Parts L, Zia A, Nguyen Ba AN, Moses AM, Louis EJ, Mustonen V, Warringer J, Durbin R, Liti G.","Mol Biol Evol","2014","0737-4038","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","9","Y","Y","Y","N","Y","323.8387","4","31","872-888","PMC3969562","gen","UNIPROT","code.google.com"
"302","25063321","MED","25063321","10.1186/1471-2164-15-628","The genome and occlusion bodies of marine Penaeus monodon nudivirus (PmNV, also known as MBV and PemoNPV) suggest that it should be assigned to a new nudivirus genus that is distinct from the terrestrial nudiviruses.","Yang YT, Lee DY, Wang Y, Hu JM, Li WH, Leu JH, Chang GD, Ke HM, Kang ST, Lin SS, Kou GH, Lo CF.","BMC Genomics","2014","1471-2164","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","Y","N","Y","323.8387","1","15","628","PMC4132918","gen","EMBLUNIPROT","code.google.com"
"303","24497547","MED","24497547","10.7554/elife.01914","Integrating influenza antigenic dynamics with molecular evolution.","Bedford T, Suchard MA, Lemey P, Dudas G, Gregory V, Hay AJ, McCauley JW, Russell CA, Smith DJ, Rambaut A.","Elife","2014","2050-084x","journal article; research-article","Y","Y","Y","9","Y","Y","N","Y","Y","323.8387",NA,"3","e01914","PMC3909918","doi",NA,"code.google.com"
"304","24967076","MED","24967076","10.1002/ece3.1042","Selection and demographic history shape the molecular evolution of the gamete compatibility protein bindin in Pisaster sea stars.","Popovic I, Marko PB, Wares JP, Hart MW.","Ecol Evol","2014","2045-7758","journal article; research-article","Y","Y","Y","0","Y","Y","Y","N","Y","323.8387","9","4","1567-1588","PMC4063459","gen","EMBL","code.google.com"
"305","24391515","MED","24391515","10.1371/journal.pgen.1004046","The SPF27 homologue Num1 connects splicing and kinesin 1-dependent cytoplasmic trafficking in Ustilago maydis.","Kellner N, Heimel K, Obhof T, Finkernagel F, KÃ¤mper J.","PLoS Genet","2014","1553-7390","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","Y","N","Y","323.62515","1","10","e1004046","PMC3879195","arrayexpress","ARXPR","code.google.com"
"306","24843027","MED","24843027","10.7554/elife.02407","Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons.","Jonkers I, Kwak H, Lis JT.","Elife","2014","2050-084x","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","323.62515",NA,"3","e02407","PMC4001325",NA,NA,"code.google.com"
"307","23742983","MED","23742983","10.1093/bioinformatics/btt287","REDItools: high-throughput RNA editing detection made easy.","Picardi E, Pesole G.","Bioinformatics","2013","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","2","Y","N","N","N","N","294.0518","14","29","1813-1814",NA,NA,NA,"code.google.com"
"308","23547006","MED","23547006",NA,"A Graph-Theoretical Approach to the Selection of the Minimum Tiling Path from a Physical Map.","Bozdag S, Close TJ, Lonardi S.","IEEE/ACM Trans Comput Biol Bioinform","2013","1545-5963","journal article","N","N","N","0","N","N","N","N","N","290.63458",NA,NA,NA,NA,NA,NA,"code.google.com"
"309","23479353","MED","23479353","10.1093/bioinformatics/btt122","JAWAMix5: an out-of-core HDF5-based java implementation of whole-genome association studies using mixed models.","Long Q, Zhang Q, Vilhjalmsson BJ, Forai P, Seren Ã, Nordborg M.","Bioinformatics","2013","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","2","Y","N","N","N","N","290.63458","9","29","1220-1222",NA,NA,NA,"code.google.com"
"310","23493324","MED","23493324","10.1093/bioinformatics/btt105","ChemoPy: freely available python package for computational biology and chemoinformatics.","Cao DS, Xu QS, Hu QN, Liang YZ.","Bioinformatics","2013","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","2","Y","N","N","N","N","290.63458","8","29","1092-1094",NA,NA,NA,"code.google.com"
"311","23129296","MED","23129296","10.1093/bioinformatics/bts649","PBSIM: PacBio reads simulator--toward accurate genome assembly.","Ono Y, Asai K, Hamada M.","Bioinformatics","2013","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","7","Y","N","N","N","N","290.63455","1","29","119-121",NA,NA,NA,"code.google.com"
"312","23778299","MED","23778299","10.1039/c3an00743j","Morphological weighted penalized least squares for background correction.","Li Z, Zhan DJ, Wang JJ, Huang J, Xu QS, Zhang ZM, Zheng YB, Liang YZ, Wang H.","Analyst","2013","0003-2654","journal article; research support, non-u.s. gov't","N","N","N","2","Y","N","N","N","N","290.63455","16","138","4483-4492",NA,NA,NA,"code.google.com"
"313","23842806","MED","23842806","10.1093/bioinformatics/btt398","BioSmalltalk: a pure object system and library for bioinformatics.","Morales HF, Giovambattista G.","Bioinformatics","2013","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","0","Y","N","N","N","N","290.63455","18","29","2355-2356",NA,NA,NA,"code.google.com"
"314","23602956","MED","23602956","10.1016/j.saa.2013.03.083","An efficient method of wavelength interval selection based on random frog for multivariate spectral calibration.","Yun YH, Li HD, Wood LR, Fan W, Wang JJ, Cao DS, Xu QS, Liang YZ.","Spectrochim Acta A Mol Biomol Spectrosc","2013","1386-1425","journal article; research support, non-u.s. gov't","N","N","N","2","Y","N","N","N","N","290.63455",NA,"111","31-36",NA,NA,NA,"code.google.com"
"315","22798331","MED","22798331","10.1093/sysbio/sys063","From trajectories to averages: an improved description of the heterogeneity of substitution rates along lineages.","Guindon S.","Syst Biol","2013","1063-5157","journal article; research support, non-u.s. gov't","N","N","N","2","Y","N","N","N","N","288.92593","1","62","22-34",NA,NA,NA,"code.google.com"
"316","23413436","MED","23413436","10.1093/bioinformatics/btt071","SPINAL: scalable protein interaction network alignment.","Aladag AE, Erten C.","Bioinformatics","2013","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","7","Y","N","N","N","N","288.92593","7","29","917-924",NA,NA,NA,"code.google.com"
"317","23426256","MED","23426256","10.1093/bioinformatics/btt072","propy: a tool to generate various modes of Chou's PseAAC.","Cao DS, Xu QS, Liang YZ.","Bioinformatics","2013","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","37","Y","N","N","N","N","288.92593","7","29","960-962",NA,NA,NA,"code.google.com"
"318","23032169","MED","23032169","10.1177/2211068212460237","Clarity: an open-source manager for laboratory automation.","Delaney NF, Rojas Echenique JI, Marx CJ.","J Lab Autom","2013","2211-0682","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural","N","N","N","4","N","N","N","N","N","288.92593","2","18","171-177",NA,NA,NA,"code.google.com"
"319","23929859","MED","23929859","10.1109/tcbb.2013.26","A graph-theoretical approach to the selection of the minimum tiling path from a physical map.","Bozdag S, Close TJ, Lonardi S.","IEEE/ACM Trans Comput Biol Bioinform","2013","1545-5963","journal article; research support, u.s. gov't, non-p.h.s.","N","N","N","1","N","N","N","N","N","288.92593","2","10","352-360",NA,NA,NA,"code.google.com"
"320","24184705","MED","24184705","10.1016/j.compbiolchem.2013.09.002","Prediction of protein modification sites of gamma-carboxylation using position specific scoring matrices based evolutionary information.","Gao J, Zhang N, Ruan J.","Comput Biol Chem","2013","1476-9271","journal article; research support, non-u.s. gov't","N","N","N","0","Y","N","N","N","N","288.9259",NA,"47","215-220",NA,NA,NA,"code.google.com"
"321","24209380","MED","24209380","10.1016/j.talanta.2013.07.070","Selective of informative metabolites using random forests based on model population analysis.","Huang JH, Yan J, Wu QH, Duarte Ferro M, Yi LZ, Lu HM, Xu QS, Liang YZ.","Talanta","2013","0039-9140","journal article; research support, non-u.s. gov't","N","N","N","0","Y","N","N","N","N","288.9259",NA,"117","549-555",NA,NA,NA,"code.google.com"
"322","23793106","MED","23793106","10.1007/s00251-013-0715-8","An automated algorithm for extracting functional immunologic V-genes from genomes in jawed vertebrates.","Olivieri D, Faro J, von Haeften B, SÃ¡nchez-Espinel C, GambÃ³n-Deza F.","Immunogenetics","2013","0093-7711","journal article; research support, non-u.s. gov't","N","N","N","2","Y","N","N","N","N","288.9259","9","65","691-702",NA,NA,NA,"code.google.com"
"323","23846744","MED","23846744","10.1093/bioinformatics/btt397","An integrated toolkit for accurate prediction and analysis of cis-regulatory motifs at a genome scale.","Ma Q, Liu B, Zhou C, Yin Y, Li G, Xu Y.","Bioinformatics","2013","1367-4803","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.","N","N","N","4","Y","N","N","N","N","288.9259","18","29","2261-2268",NA,NA,NA,"code.google.com"
"324","23671334","MED","23671334","10.1093/nar/gkt392","A new reference implementation of the PSICQUIC web service.","del-Toro N, Dumousseau M, Orchard S, Jimenez RC, Galeota E, Launay G, Goll J, Breuer K, Ono K, Salwinski L, Hermjakob H.","Nucleic Acids Res","2013","0305-1048","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","7","Y","Y","N","N","N","287.77185","web server issue","41","w601-6","PMC3977660",NA,NA,"code.google.com"
"325","23846595","MED","23846595","10.1093/database/bat051","JBioWH: an open-source Java framework for bioinformatics data integration.","Vera R, Perez-Riverol Y, Perez S, Ligeti B, KertÃ©sz-Farkas A, Pongor S.","Database (Oxford)","2013","1758-0463","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","Y","287.7465",NA,"2013","bat051","PMC3708619","sprot",NA,"code.google.com"
"326","24095682","MED","24095682","10.1016/j.mimet.2013.09.017","ApicoAMP: the first computational model for identifying apicoplast-targeted transmembrane proteins in Apicomplexa.","Cilingir G, Lau AO, Broschat SL.","J Microbiol Methods","2013","0167-7012","journal article","N","N","N","1","Y","N","N","N","N","287.21732","3","95","313-319",NA,NA,NA,"code.google.com"
"327","22595284","MED","22595284","10.1016/j.ijmedinf.2012.04.006","Detecting temporal expressions in medical narratives.","Reeves RM, Ong FR, Matheny ME, Denny JC, Aronsky D, Gobbel GT, Montella D, Speroff T, Brown SH.","Int J Med Inform","2013","1386-5056","journal article; research support, non-u.s. gov't","N","N","N","2","N","N","N","N","N","287.2173","2","82","118-127",NA,NA,NA,"code.google.com"
"328","23435069","MED","23435069","10.1093/bioinformatics/btt100","BioJS: an open source JavaScript framework for biological data visualization.","GÃ³mez J, GarcÃa LJ, Salazar GA, Villaveces J, Gore S, GarcÃa A, MartÃn MJ, Launay G, AlcÃ¡ntara R, Del-Toro N, Dumousseau M, Orchard S, Velankar S, Hermjakob H, Zong C, Ping P, Corpas M, JimÃ©nez RC.","Bioinformatics","2013","1367-4803","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","16","Y","Y","N","Y","N","285.42285","8","29","1103-1104","PMC3624812",NA,NA,"code.google.com"
"329","23559752","MED","23559752","10.6026/97320630009325","PyPLIF: Python-based Protein-Ligand Interaction Fingerprinting.","Radifar M, Yuniarti N, Istyastono EP.","Bioinformation","2013","0973-2063","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","284.21466","6","9","325-328","PMC3607193",NA,NA,"code.google.com"
"330","23958730","MED","23958730","10.1093/bioinformatics/btt483","HippDB: a database of readily targeted helical protein-protein interactions.","Bergey CM, Watkins AM, Arora PS.","Bioinformatics","2013","1367-4803","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","N","1","Y","Y","N","N","N","284.21466","21","29","2806-2807","PMC3799476",NA,NA,"code.google.com"
"331","23782611","MED","23782611","10.1093/bioinformatics/btt343","GAT: a simulation framework for testing the association of genomic intervals.","Heger A, Webber C, Goodson M, Ponting CP, Lunter G.","Bioinformatics","2013","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","6","Y","Y","N","N","N","284.21466","16","29","2046-2048","PMC3722528",NA,NA,"code.google.com"
"332","23574737","MED","23574737","10.1093/bioinformatics/btt159","Biographer: web-based editing and rendering of SBGN compliant biochemical networks.","Krause F, Schulz M, Ripkens B, FlÃ¶ttmann M, Krantz M, Klipp E, Handorf T.","Bioinformatics","2013","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","4","Y","Y","N","N","N","284.21466","11","29","1467-1468","PMC3661053",NA,NA,"code.google.com"
"333","23930018","MED","23930018","10.6026/97320630009673","Molecular distribution of amino acid substitutions on neuraminidase from the 2009 (H1N1) human influenza pandemic virus.","Quiliano M, Valdivia-Olarte H, Olivares C, Requena D, GutiÃ©rrez AH, Reyes-Loyola P, Tolentino-Lopez LE, Sheen P, Briz V, MuÃ±oz-FernÃ¡ndez MA, Correa-Basurto J, Zimic M.","Bioinformation","2013","0973-2063","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","Y","283.8001","13","9","673-679","PMC3732439","pdb",NA,"code.google.com"
"334","24009693","MED","24009693","10.1371/journal.pone.0072614","DistMap: a toolkit for distributed short read mapping on a Hadoop cluster.","Pandey RV, SchlÃ¶tterer C.","PLoS One","2013","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","4","Y","Y","N","Y","N","283.8001","8","8","e72614","PMC3751911",NA,NA,"code.google.com"
"335","23203882","MED","23203882","10.1093/nar/gks1262","The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013.","VizcaÃno JA, CÃ´tÃ© RG, Csordas A, Dianes JA, Fabregat A, Foster JM, Griss J, Alpi E, Birim M, Contell J, O'Kelly G, Schoenegger A, Ovelleiro D, PÃ©rez-Riverol Y, Reisinger F, RÃos D, Wang R, Hermjakob H.","Nucleic Acids Res","2013","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","244","Y","Y","N","Y","N","283.8001","database issue","41","d1063-9","PMC3531176",NA,NA,"code.google.com"
"336","24356832","MED","24356832","10.1128/genomea.01062-13","Genome Sequence of Strain MOLA814, a Proteorhodopsin-Containing Representative of the Betaproteobacteria Common in the Ocean.","Courties A, Riedel T, Jarek M, Intertaglia L, Lebaron P, Suzuki MT.","Genome Announc","2013","2169-8287","journal article; brief-report","Y","Y","Y","0","Y","Y","Y","N","N","283.80008","6","1",NA,"PMC3868856",NA,"EMBLUNIPROT","code.google.com"
"337","23661681","MED","23661681","10.1093/nar/gkt377","STRAW: Species TRee Analysis Web server.","Shaw TI, Ruan Z, Glenn TC, Liu L.","Nucleic Acids Res","2013","0305-1048","journal article; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","10","Y","Y","N","N","N","283.00653","web server issue","41","w238-41","PMC3692081",NA,NA,"code.google.com"
"338","24064417","MED","24064417","10.1093/bioinformatics/btt548","BSeQC: quality control of bisulfite sequencing experiments.","Lin X, Sun D, Rodriguez B, Zhao Q, Sun H, Zhang Y, Li W.","Bioinformatics","2013","1367-4803","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","N","2","Y","Y","N","N","N","283.00653","24","29","3227-3229","PMC3842756",NA,NA,"code.google.com"
"339","23990413","MED","23990413","10.1093/bioinformatics/btt500","DIST: direct imputation of summary statistics for unmeasured SNPs.","Lee D, Bigdeli TB, Riley BP, Fanous AH, Bacanu SA.","Bioinformatics","2013","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","283.00653","22","29","2925-2927","PMC3810851",NA,NA,"code.google.com"
"340","23935862","MED","23935862","10.1371/journal.pone.0068358","Improved inference of gene regulatory networks through integrated Bayesian clustering and dynamic modeling of time-course expression data.","Godsey B.","PLoS One","2013","1932-6203","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","282.94577","7","8","e68358","PMC3720774",NA,NA,"code.google.com"
"341","24358873","MED","24358873","10.12688/f1000research.2-30.v2","Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research.","KÃ¶hler S, Doelken SC, Ruef BJ, Bauer S, Washington N, Westerfield M, Gkoutos G, Schofield P, Smedley D, Lewis SE, Robinson PN, Mungall CJ.","F1000Res","2013","2046-1402","journal article; research-article","Y","Y","Y","5","Y","Y","N","N","N","282.94577",NA,"2","30","PMC3799545",NA,NA,"code.google.com"
"342","23390980","MED","23390980","10.1186/1471-2105-14-45","Snpdat: easy and rapid annotation of results from de novo snp discovery projects for model and non-model organisms.","Doran AG, Creevey CJ.","BMC Bioinformatics","2013","1471-2105","journal article; research support, non-u.s. gov't; product-review","Y","Y","Y","2","Y","Y","N","Y","N","282.88446",NA,"14","45","PMC3574845",NA,NA,"code.google.com"
"343","23077130","MED","23077130","10.1136/amiajnl-2012-001350","Knowledge-based biomedical word sense disambiguation: an evaluation and application to clinical document classification.","Garla VN, Brandt C.","J Am Med Inform Assoc","2013","1067-5027","evaluation studies; journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","Y","1","Y","Y","N","N","N","282.88443","5","20","882-886","PMC3756260",NA,NA,"code.google.com"
"344","23829206","MED","23829206","10.1186/1471-2105-14-215","Gel2DE - a software tool for correlation analysis of 2D gel electrophoresis data.","Ãye OK, JÃ¸rgensen KM, Hjelle SM, Sulen A, Ulvang DM, Gjertsen BT.","BMC Bioinformatics","2013","1471-2105","journal article; research support, non-u.s. gov't; product-review","Y","Y","Y","0","Y","Y","N","N","N","282.88443",NA,"14","215","PMC3710208",NA,NA,"code.google.com"
"345","24273510","MED","24273510","10.3389/fninf.2013.00026","Spyke Viewer: a flexible and extensible platform for electrophysiological data analysis.","PrÃ¶pper R, Obermayer K.","Front Neuroinform","2013","1662-5196","journal article; research-article","Y","Y","Y","6","Y","Y","N","N","N","282.1446",NA,"7","26","PMC3822898",NA,NA,"code.google.com"
"346","23295781","MED","23295781","10.1097/mpa.0b013e318264cea5","A resequence analysis of genomic loci on chromosomes 1q32.1, 5p15.33, and 13q22.1 associated with pancreatic cancer risk.","Parikh H, Jia J, Zhang X, Chung CC, Jacobs KB, Yeager M, Boland J, Hutchinson A, Burdett L, Hoskins J, Risch HA, Stolzenberg-Solomon RZ, Chanock SJ, Wolpin BM, Petersen GM, Fuchs CS, Hartge P, Amundadottir L.","Pancreas","2013","0885-3177","journal article; research support, n.i.h., intramural; comparative study; research-article","N","Y","Y","2","Y","Y","N","N","Y","282.1446","2","42","209-215","PMC3618611","refsnp",NA,"code.google.com"
"347","23658422","MED","23658422","10.1093/bioinformatics/btt266","FYPO: the fission yeast phenotype ontology.","Harris MA, Lock A, BÃ¤hler J, Oliver SG, Wood V.","Bioinformatics","2013","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","6","Y","Y","N","N","N","282.1446","13","29","1671-1678","PMC3694669",NA,NA,"code.google.com"
"348","22877769","MED","22877769","10.1093/bib/bbs044","Application of next generation sequencing to human gene fusion detection: computational tools, features and perspectives.","Wang Q, Xia J, Jia P, Pao W, Zhao Z.","Brief Bioinform","2013","1467-5463","journal article; review; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","6","Y","Y","N","N","N","282.0915","4","14","506-519","PMC3713712",NA,NA,"code.google.com"
"349","23044549","MED","23044549","10.1093/bioinformatics/bts567","MGAviewer: a desktop visualization tool for analysis of metagenomics alignment data.","Zhu Z, Niu B, Chen J, Wu S, Sun S, Li W.","Bioinformatics","2013","1367-4803","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","3","Y","Y","N","N","N","282.0915","1","29","122-123","PMC3530914",NA,NA,"code.google.com"
"350","24139062","MED","24139062","10.1186/2041-1480-4-32","The Drosophila anatomy ontology.","Costa M, Reeve S, Grumbling G, Osumi-Sutherland D.","J Biomed Semantics","2013","2041-1480","journal article; research-article","Y","Y","Y","4","Y","Y","N","Y","N","282.0915","1","4","32","PMC4015547",NA,NA,"code.google.com"
"351","23505292","MED","23505292","10.1093/bioinformatics/btt109","Brain: biomedical knowledge manipulation.","Croset S, Overington JP, Rebholz-Schuhmann D.","Bioinformatics","2013","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","N","N","N","282.09146","9","29","1238-1239","PMC3634181",NA,NA,"code.google.com"
"352","23314324","MED","23314324","10.1093/bioinformatics/bts731","NGSUtils: a software suite for analyzing and manipulating next-generation sequencing datasets.","Breese MR, Liu Y.","Bioinformatics","2013","1367-4803","journal article; research support, n.i.h., extramural; research-article","N","Y","Y","9","Y","Y","N","Y","N","282.09146","4","29","494-496","PMC3570212",NA,NA,"code.google.com"
"353","24008420","MED","24008420","10.1093/bioinformatics/btt514","OntoQuery: easy-to-use web-based OWL querying.","Tudose I, Hastings J, Muthukrishnan V, Owen G, Turner S, Dekker A, Kale N, Ennis M, Steinbeck C.","Bioinformatics","2013","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","N","N","N","282.09146","22","29","2955-2957","PMC3810857",NA,NA,"code.google.com"
"354","23630176","MED","23630176","10.1093/bioinformatics/btt199","BioBlend: automating pipeline analyses within Galaxy and CloudMan.","Sloggett C, Goonasekera N, Afgan E.","Bioinformatics","2013","1367-4803","journal article; research support, non-u.s. gov't; research-article","N","Y","N","2","Y","Y","N","N","N","282.09146","13","29","1685-1686","PMC4288140",NA,NA,"code.google.com"
"355","23580546","MED","23580546","10.1093/nar/gkt228","Reflex: intramolecular barcoding of long-range PCR products for sequencing multiple pooled DNAs.","Casbon JA, Slatter AF, Musgrave-Brown E, Osborne RJ, Lichtenstein CP, Brenner S.","Nucleic Acids Res","2013","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","281.7983","10","41","e112","PMC3664814",NA,NA,"code.google.com"
"356","23042674","MED","23042674","10.1093/nar/gks915","LNCipedia: a database for annotated human lncRNA transcript sequences and structures.","Volders PJ, Helsens K, Wang X, Menten B, Martens L, Gevaert K, Vandesompele J, Mestdagh P.","Nucleic Acids Res","2013","0305-1048","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","38","Y","Y","N","N","N","281.7983","database issue","41","d246-51","PMC3531107",NA,NA,"code.google.com"
"357","23533138","MED","23533138","10.1002/pmic.201200514","From Peptidome to PRIDE: public proteomics data migration at a large scale.","Csordas A, Wang R, RÃos D, Reisinger F, Foster JM, Slotta DJ, VizcaÃno JA, Hermjakob H.","Proteomics","2013","1615-9853","journal article; research support, non-u.s. gov't; research support, n.i.h., intramural; research-article","Y","Y","Y","2","Y","Y","N","N","N","281.79828","10-11","13","1692-1695","PMC3717177",NA,NA,"code.google.com"
"358","24564169","MED","24564169","10.1186/1471-2105-14-s11-s1","Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives.","Zhao M, Wang Q, Wang Q, Jia P, Zhao Z.","BMC Bioinformatics","2013","1471-2105","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","3","Y","Y","N","N","N","281.74136","Suppl 11","14 Suppl 11","s1","PMC3846878",NA,NA,"code.google.com"
"359","24278254","MED","24278254","10.1371/journal.pone.0080156","PD5: a general purpose library for primer design software.","Riley MC, Aubrey W, Young M, Clare A.","PLoS One","2013","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","281.40472","11","8","e80156","PMC3836914",NA,NA,"code.google.com"
"360","24279920","MED","24279920","10.1186/2041-1480-4-40","The Ontology of Vaccine Adverse Events (OVAE) and its usage in representing and analyzing adverse events associated with US-licensed human vaccines.","Marcos E, Zhao B, He Y.","J Biomed Semantics","2013","2041-1480","journal article; research-article","Y","Y","N","5","Y","Y","N","Y","N","281.40472","1","4","40","PMC4177204",NA,NA,"code.google.com"
"361","24391582","MED","24391582","10.3389/fninf.2013.00036","Hardware-accelerated interactive data visualization for neuroscience in Python.","Rossant C, Harris KD.","Front Neuroinform","2013","1662-5196","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","281.4047",NA,"7","36","PMC3867689",NA,NA,"code.google.com"
"362","25473124","MED","25473124","10.1109/tmag.2013.2239621","Size-Dependent Relaxation Properties of Monodisperse Magnetite Nanoparticles Measured Over Seven Decades of Frequency by AC Susceptometry.","Ferguson RM, Khandhar AP, Jonasson C, Blomgren J, Johansson C, Krishnan KM.","IEEE Trans Magn","2013","0018-9464","journal article; research-article","N","Y","N","0","Y","Y","N","N","N","281.23715","7","49","3441-3444","PMC4248603",NA,NA,"code.google.com"
"363","23295477","MED","23295477","10.1107/s1744309112048890","Structure determination of LpxD from the lipopolysaccharide-synthesis pathway of Acinetobacter baumannii.","Badger J, Chie-Leon B, Logan C, Sridhar V, Sankaran B, Zwart PH, Nienaber V.","Acta Crystallogr Sect F Struct Biol Cryst Commun","2013","1744-3091","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","Y","0","N","Y","Y","N","Y","281.23715","pt 1","69","6-9","PMC3539694","pdb; sprot","PDBUNIPROT","code.google.com"
"364","23620816","MED","23620816","10.1371/journal.pone.0062249","Conformational B-cell epitope prediction on antigen protein structures: a review of current algorithms and comparison with common binding site prediction methods.","Yao B, Zheng D, Liang S, Zhang C.","PLoS One","2013","1932-6203","journal article; research support, non-u.s. gov't; comparative study; research-article","Y","Y","Y","8","Y","Y","N","N","Y","281.23715","4","8","e62249","PMC3631208","pdb",NA,"code.google.com"
"365","23828721","MED","23828721","10.1109/mic.2013.38","The AppScale Cloud Platform: Enabling Portable, Scalable Web Application Deployment.","Krintz C.","IEEE Internet Comput","2013","1089-7801","journal article; research-article","N","Y","Y","0","N","Y","N","N","N","281.23712","2","17","72-75","PMC3698982",NA,NA,"code.google.com"
"366","23093603","MED","23093603","10.1093/nar/gks998","The Online Protein Processing Resource (TOPPR): a database and analysis platform for protein processing events.","Colaert N, Maddelein D, Impens F, Van Damme P, Plasman K, Helsens K, Hulstaert N, Vandekerckhove J, Gevaert K, Martens L.","Nucleic Acids Res","2013","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","3","Y","Y","N","N","N","281.23712","database issue","41","d333-7","PMC3531153",NA,NA,"code.google.com"
"367","24314207","MED","24314207","10.1186/2041-1480-4-42","The neurological disease ontology.","Jensen M, Cox AP, Chaudhry N, Ng M, Sule D, Duncan W, Ray P, Weinstock-Guttman B, Smith B, Ruttenberg A, Szigeti K, Diehl AD.","J Biomed Semantics","2013","2041-1480","journal article; research-article","Y","Y","Y","1","Y","Y","N","Y","N","281.19424","1","4","42","PMC4028878",NA,NA,"code.google.com"
"368","23558168","MED","23558168","10.1136/amiajnl-2013-001622","Comprehensive temporal information detection from clinical text: medical events, time, and TLINK identification.","Sohn S, Wagholikar KB, Li D, Jonnalagadda SR, Tao C, Komandur Elayavilli R, Liu H.","J Am Med Inform Assoc","2013","1067-5027","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","Y","1","Y","Y","N","N","N","281.19424","5","20","836-842","PMC3756269",NA,NA,"code.google.com"
"369","23667450","MED","23667450","10.1371/journal.pone.0061951","LipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics.","Foster JM, Moreno P, Fabregat A, Hermjakob H, Steinbeck C, Apweiler R, Wakelam MJ, VizcaÃno JA.","PLoS One","2013","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","5","Y","Y","N","N","N","281.19424","5","8","e61951","PMC3646891",NA,NA,"code.google.com"
"370","24358278","MED","24358278","10.1371/journal.pone.0083356","SoftSearch: integration of multiple sequence features to identify breakpoints of structural variations.","Hart SN, Sarangi V, Moore R, Baheti S, Bhavsar JD, Couch FJ, Kocher JP.","PLoS One","2013","1932-6203","journal article; validation studies; research-article","Y","Y","Y","1","Y","Y","N","N","N","281.1942","12","8","e83356","PMC3865185",NA,NA,"code.google.com"
"371","23735126","MED","23735126","10.1186/1471-2105-14-s5-s10","An optimized algorithm for detecting and annotating regional differential methylation.","Li S, Garrett-Bakelman FE, Akalin A, Zumbo P, Levine R, To BL, Lewis ID, Brown AL, D'Andrea RJ, Melnick A, Mason CE.","BMC Bioinformatics","2013","1471-2105","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; abstract","Y","Y","Y","3","Y","Y","N","N","N","281.1942","Suppl 5","14 Suppl 5","s10","PMC3622633",NA,NA,"code.google.com"
"372","23193274","MED","23193274","10.1093/nar/gks1172","ENCODE data in the UCSC Genome Browser: year 5 update.","Rosenbloom KR, Sloan CA, Malladi VS, Dreszer TR, Learned K, Kirkup VM, Wong MC, Maddren M, Fang R, Heitner SG, Lee BT, Barber GP, Harte RA, Diekhans M, Long JC, Wilder SP, Zweig AS, Karolchik D, Kuhn RM, Haussler D, Kent WJ.","Nucleic Acids Res","2013","0305-1048","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","91","Y","Y","N","N","N","281.1942","database issue","41","d56-63","PMC3531152",NA,NA,"code.google.com"
"373","23550116","MED","23550116","10.1534/g3.112.004929","An Ultra High-Density, Transcript-Based, Genetic Map of Lettuce.","Truco MJ, Ashrafi H, Kozik A, van Leeuwen H, Bowers J, Reyes Chin Wo S, Stoffel K, Xu H, Hill T, Van Deynze A, Michelmore RW.","G3 (Bethesda)","2013","2160-1836","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","Y","280.6649","4","3",NA,"PMC3618349","gen",NA,"code.google.com"
"374","23729008","MED","23729008","10.1007/s00894-013-1886-9","PPIcons: identification of protein-protein interaction sites in selected organisms.","Sriwastava BK, Basu S, Maulik U, Plewczynski D.","J Mol Model","2013","1610-2940","journal article; research support, non-u.s. gov't; case-report","Y","Y","Y","1","Y","Y","N","N","N","280.6649","9","19","4059-4070","PMC3744667",NA,NA,"code.google.com"
"375","23842810","MED","23842810","10.1093/bioinformatics/btt375","A comparative analysis of algorithms for somatic SNV detection in cancer.","Roberts ND, Kortschak RD, Parker WT, Schreiber AW, Branford S, Scott HS, Glonek G, Adelson DL.","Bioinformatics","2013","1367-4803","journal article; research support, non-u.s. gov't; comparative study; review-article","Y","Y","Y","13","Y","Y","N","N","N","280.59015","18","29","2223-2230","PMC3753564",NA,NA,"code.google.com"
"376","23211964","MED","23211964","10.1038/jcbfm.2012.175","Spontaneous calcium waves in Bergman glia increase with age and hypoxia and may reduce tissue oxygen.","Mathiesen C, Brazhe A, Thomsen K, Lauritzen M.","J Cereb Blood Flow Metab","2013","0271-678x","journal article; research support, non-u.s. gov't; research-article","N","Y","Y","10","Y","Y","N","N","N","280.59015","2","33","161-169","PMC3564203",NA,NA,"code.google.com"
"377","22965123","MED","22965123","10.1093/nar/gks830","FadE: whole genome methylation analysis for multiple sequencing platforms.","Souaiaia T, Zhang Z, Chen T.","Nucleic Acids Res","2013","0305-1048","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","Y","N","280.59015","1","41","e14","PMC3592442",NA,NA,"code.google.com"
"378","23479348","MED","23479348","10.1093/bioinformatics/btt113","EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats.","Ison J, Kalas M, Jonassen I, Bolser D, Uludag M, McWilliam H, Malone J, Lopez R, Pettifer S, Rice P.","Bioinformatics","2013","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","4","Y","Y","N","N","N","280.59015","10","29","1325-1332","PMC3654706",NA,NA,"code.google.com"
"379","23104886","MED","23104886","10.1093/bioinformatics/bts635","STAR: ultrafast universal RNA-seq aligner.","Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR.","Bioinformatics","2013","1367-4803","evaluation studies; journal article; research support, n.i.h., extramural; research-article","N","Y","Y","104","Y","Y","N","Y","N","280.59015","1","29","15-21","PMC3530905",NA,NA,"code.google.com"
"380","23418788","MED","23418788","10.1186/1471-2148-13-44","Simulating gene trees under the multispecies coalescent and time-dependent migration.","Heled J, Bryant D, Drummond AJ.","BMC Evol Biol","2013","1471-2148","evaluation studies; journal article; research support, non-u.s. gov't; product-review","Y","Y","Y","3","Y","Y","N","N","N","280.59015",NA,"13","44","PMC3646706",NA,NA,"code.google.com"
"381","23175756","MED","23175756","10.1093/bioinformatics/bts680","A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data.","Teschendorff AE, Marabita F, Lechner M, Bartlett T, Tegner J, Gomez-Cabrero D, Beck S.","Bioinformatics","2013","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","31","Y","Y","N","Y","N","280.59015","2","29","189-196","PMC3546795",NA,NA,"code.google.com"
"382","24957991","MED","24957991","10.3390/metabo3020259","Getting your peaks in line: a review of alignment methods for NMR spectral data.","Vu TN, Laukens K.","Metabolites","2013","2218-1989","journal article; review-article","Y","Y","Y","0","Y","Y","N","N","N","280.59015","2","3","259-276","PMC3901265",NA,NA,"code.google.com"
"383","23995392","MED","23995392","10.1093/bioinformatics/btt512","PyroHMMvar: a sensitive and accurate method to call short indels and SNPs for Ion Torrent and 454 data.","Zeng F, Jiang R, Chen T.","Bioinformatics","2013","1367-4803","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","N","0","Y","Y","N","N","N","280.59012","22","29","2859-2868","PMC3888126",NA,NA,"code.google.com"
"384","24376861","MED","24376861","10.1371/journal.pone.0085024","An extensive evaluation of read trimming effects on Illumina NGS data analysis.","Del Fabbro C, Scalabrin S, Morgante M, Giorgi FM.","PLoS One","2013","1932-6203","evaluation studies; journal article; research support, non-u.s. gov't; comparative study; research-article","Y","Y","Y","3","Y","Y","N","N","N","280.59012","12","8","e85024","PMC3871669",NA,NA,"code.google.com"
"385","23746447","MED","23746447","10.1016/j.celrep.2013.05.005","NDUFA4 mutations underlie dysfunction of a cytochrome c oxidase subunit linked to human neurological disease.","Pitceathly RD, Rahman S, Wedatilake Y, Polke JM, Cirak S, Foley AR, Sailer A, Hurles ME, Stalker J, Hargreaves I, Woodward CE, Sweeney MG, Muntoni F, Houlden H, Taanman JW, Hanna MG, UK10K Consortium.","Cell Rep","2013","2211-1247","journal article; research support, non-u.s. gov't; brief-report","Y","Y","Y","2","Y","Y","Y","N","Y","280.59012","6","3","1795-1805","PMC3701321","omim","UNIPROT","code.google.com"
"386","23462292","MED","23462292","10.1093/hmg/ddt109","Testicular germ cell tumor susceptibility associated with the UCK2 locus on chromosome 1q23.","Schumacher FR, Wang Z, Skotheim RI, Koster R, Chung CC, Hildebrandt MA, Kratz CP, Bakken AC, Bishop DT, Cook MB, Erickson RL, FossÃ¥ SD, Greene MH, Jacobs KB, Kanetsky PA, Kolonel LN, Loud JT, Korde LA, Le Marchand L, Lewinger JP, Lothe RA, Pike MC, Rahman N, Rubertone MV, Schwartz SM, Siegmund KD, Skinner EC, Turnbull C, Van Den Berg DJ, Wu X, Yeager M, Nathanson KL, Chanock SJ, Cortessis VK, McGlynn KA.","Hum Mol Genet","2013","0964-6906","journal article; meta-analysis; research support, non-u.s. gov't; research support, n.i.h., extramural; research support, n.i.h., intramural; research-article","N","Y","Y","8","Y","Y","Y","N","Y","280.38284","13","22","2748-2753","PMC3674801","refsnp","UNIPROT","code.google.com"
"387","24499624","MED","24499624","10.1186/2046-1682-6-5","Time-resolved force distribution analysis.","Costescu BI, GrÃ¤ter F.","BMC Biophys","2013","2046-1682","journal article; research-article","Y","Y","Y","3","Y","Y","N","N","N","280.38284","1","6","5","PMC3669045",NA,NA,"code.google.com"
"388","24303273","MED","24303273",NA,"An ontology-based method for secondary use of electronic dental record data.","Schleyer TK, Ruttenberg A, Duncan W, Haendel M, Torniai C, Acharya A, Song M, Thyvalikakath TP, Liu K, Hernandez P.","AMIA Jt Summits Transl Sci Proc","2013","2153-4063","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","280.38284",NA,"2013","234-238","PMC3845770",NA,NA,"code.google.com"
"389","23920642","MED","23920642",NA,"Extending the NegEx lexicon for multiple languages.","Chapman WW, Hillert D, Velupillai S, Kvist M, Skeppstedt M, Chapman BE, Conway M, Tharp M, Mowery DL, Deleger L.","Stud Health Technol Inform","2013","0926-9630","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","1","Y","Y","N","N","N","280.38284",NA,"192","677-681","PMC3923890",NA,NA,"code.google.com"
"390","24308566","MED","24308566","10.1186/1756-0500-6-511","OGA: an ontological tool of human phenotypes with genetic associations.","Herrera-Galeano JE, Hirschberg DL, Mokashi V, Solka J.","BMC Res Notes","2013","1756-0500","journal article; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","N","0","Y","Y","N","N","N","280.38284",NA,"6","511","PMC4234991",NA,NA,"code.google.com"
"391","23972281","MED","23972281","10.1186/2041-1480-4-15","EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update.","Hayamizu TF, Wicks MN, Davidson DR, Burger A, Ringwald M, Baldock RA.","J Biomed Semantics","2013","2041-1480","journal article; brief-report","Y","Y","Y","4","Y","Y","N","N","N","280.38284","1","4","15","PMC3851555",NA,NA,"code.google.com"
"392","24551367","MED","24551367",NA,"Using hierarchical mixture of experts model for fusion of outbreak detection methods.","Jafarpour N, Precup D, Izadi M, Buckeridge D.","AMIA Annu Symp Proc","2013","1942-597x","journal article; research-article","N","Y","Y","0","Y","Y","N","N","N","280.38284",NA,"2013","663-669","PMC3900208",NA,NA,"code.google.com"
"393","24551417","MED","24551417",NA,"Apollo: giving application developers a single point of access to public health models using structured vocabularies and Web services.","Wagner MM, Levander JD, Brown S, Hogan WR, Millett N, Hanna J.","AMIA Annu Symp Proc","2013","1942-597x","journal article; research support, n.i.h., extramural; research-article","N","Y","Y","0","Y","Y","N","N","N","280.38284",NA,"2013","1415-1424","PMC3900155",NA,NA,"code.google.com"
"394","23175606","MED","23175606","10.1093/nar/gks1108","WholeCellKB: model organism databases for comprehensive whole-cell models.","Karr JR, Sanghvi JC, Macklin DN, Arora A, Covert MW.","Nucleic Acids Res","2013","0305-1048","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","6","Y","Y","N","N","N","280.38284","database issue","41","d787-92","PMC3531061",NA,NA,"code.google.com"
"395","23535375","MED","23535375","10.1016/j.bbrc.2013.03.046","Interleukin-27 treated human macrophages induce the expression of novel microRNAs which may mediate anti-viral properties.","Swaminathan S, Hu X, Zheng X, Kriga Y, Shetty J, Zhao Y, Stephens R, Tran B, Baseler MW, Yang J, Lempicki RA, Huang D, Lane HC, Imamichi T.","Biochem Biophys Res Commun","2013","0006-291x","journal article; research support, n.i.h., extramural; research-article","N","Y","Y","4","Y","Y","Y","N","N","280.38284","2","434","228-234","PMC3700531",NA,"EMBL","code.google.com"
"396","23587045","MED","23587045","10.1186/1756-0500-6-145","Treetrimmer: a method for phylogenetic dataset size reduction.","Maruyama S, Eveleigh RJ, Archibald JM.","BMC Res Notes","2013","1756-0500","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","280.38284",NA,"6","145","PMC3637088",NA,NA,"code.google.com"
"397","23161688","MED","23161688","10.1093/nar/gks1059","SwissBioisostere: a database of molecular replacements for ligand design.","Wirth M, Zoete V, Michielin O, Sauer WH.","Nucleic Acids Res","2013","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","3","Y","Y","N","N","N","280.38284","database issue","41","d1137-43","PMC3531158",NA,NA,"code.google.com"
"398","23402499","MED","23402499","10.1186/1746-1596-8-22","Open source tools for management and archiving of digital microscopy data to allow integration with patient pathology and treatment information.","Khushi M, Edwards G, de Marcos DA, Carpenter JE, Graham JD, Clarke CL.","Diagn Pathol","2013","1746-1596","journal article; product-review","Y","Y","Y","1","Y","Y","N","N","N","280.38284",NA,"8","22","PMC3575263",NA,NA,"code.google.com"
"399","23737954","MED","23737954","10.1371/journal.pone.0063832","Targeted exome sequencing identified novel USH2A mutations in Usher syndrome families.","Huang XF, Xiang P, Chen J, Xing DJ, Huang N, Min Q, Gu F, Tong Y, Pang CP, Qu J, Jin ZB.","PLoS One","2013","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","9","Y","Y","Y","N","N","280.38284","5","8","e63832","PMC3667821",NA,"UNIPROT","code.google.com"
"400","23203888","MED","23203888","10.1093/nar/gks1215","Interferome v2.0: an updated database of annotated interferon-regulated genes.","Rusinova I, Forster S, Yu S, Kannan A, Masse M, Cumming H, Chapman R, Hertzog PJ.","Nucleic Acids Res","2013","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","25","Y","Y","N","N","N","280.38284","database issue","41","d1040-6","PMC3531205",NA,NA,"code.google.com"
"401","23554109","MED","23554109","10.1002/pds.3418","Natural Language Processing to identify pneumonia from radiology reports.","Dublin S, Baldwin E, Walker RL, Christensen LM, Haug PJ, Jackson ML, Nelson JC, Ferraro J, Carrell D, Chapman WW.","Pharmacoepidemiol Drug Saf","2013","1053-8569","journal article; validation studies; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","4","Y","Y","N","N","N","280.38284","8","22","834-841","PMC3811072",NA,NA,"code.google.com"
"402","23977187","MED","23977187","10.1371/journal.pone.0071956","The genetic diversity of the Nguni breed of African Cattle (Bos spp.): complete mitochondrial genomes of haplogroup T1.","Horsburgh KA, Prost S, Gosling A, Stanton JA, Rand C, Matisoo-Smith EA.","PLoS One","2013","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","Y","N","Y","280.38284","8","8","e71956","PMC3747060","gen","EMBLUNIPROT","code.google.com"
"403","24715956","MED","24715956","10.12688/f1000research.2-192.v1","Cyrface: An interface from Cytoscape to R that provides a user interface to R packages.","GonÃ§alves E, Saez-Rodriguez J.","F1000Res","2013","2046-1402","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","280.3828",NA,"2","192","PMC3962008",NA,NA,"code.google.com"
"404","23727862","MED","23727862","10.1038/ng.2645","Genome-wide association study identifies two susceptibility loci for osteosarcoma.","Savage SA, Mirabello L, Wang Z, Gastier-Foster JM, Gorlick R, Khanna C, Flanagan AM, Tirabosco R, Andrulis IL, Wunder JS, Gokgoz N, PatiÃ±o-Garcia A, SierrasesÃºmaga L, Lecanda F, Kurucu N, Ilhan IE, Sari N, Serra M, Hattinger C, Picci P, Spector LG, Barkauskas DA, Marina N, de Toledo SR, Petrilli AS, Amary MF, Halai D, Thomas DM, Douglass C, Meltzer PS, Jacobs K, Chung CC, Berndt SI, Purdue MP, Caporaso NE, Tucker M, Rothman N, Landi MT, Silverman DT, Kraft P, Hunter DJ, Malats N, Kogevinas M, Wacholder S, Troisi R, Helman L, Fraumeni JF Jr, Yeager M, Hoover RN, Chanock SJ.","Nat Genet","2013","1061-4036","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research support, n.i.h., intramural; research-article","Y","Y","Y","21","Y","Y","N","Y","Y","280.3828","7","45","799-803","PMC3910497","refsnp",NA,"code.google.com"
"405","24198712","MED","24198712","10.3897/phytokeys.25.3100","Database of Vascular Plants of Canada (VASCAN): a community contributed taxonomic checklist of all vascular plants of Canada, Saint Pierre andÂ Miquelon, and Greenland.","Desmet P, Brouillet L.","PhytoKeys","2013","1314-2011","journal article; research-article","Y","Y","Y","3","N","Y","N","N","Y","280.3828","25",NA,"55-67","PMC3819130","doi",NA,"code.google.com"
"406","23803001","MED","23803001","10.1186/1471-2105-14-209","GenPhyloData: realistic simulation of gene family evolution.","SjÃ¶strand J, Arvestad L, Lagergren J, Sennblad B.","BMC Bioinformatics","2013","1471-2105","journal article; research support, non-u.s. gov't; product-review","Y","Y","Y","1","Y","Y","N","N","N","280.3828",NA,"14","209","PMC3703295",NA,NA,"code.google.com"
"407","23193294","MED","23193294","10.1093/nar/gks1165","CTCFBSDB 2.0: a database for CTCF-binding sites and genome organization.","Ziebarth JD, Bhattacharya A, Cui Y.","Nucleic Acids Res","2013","0305-1048","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","9","Y","Y","N","Y","N","280.3828","database issue","41","d188-94","PMC3531215",NA,NA,"code.google.com"
"408","23155061","MED","23155061","10.1093/nar/gks1052","RNApathwaysDB--a database of RNA maturation and decay pathways.","Milanowska K, Mikolajczak K, Lukasik A, Skorupski M, Balcer Z, Machnicka MA, Nowacka M, Rother KM, Bujnicki JM.","Nucleic Acids Res","2013","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","N","N","N","280.3828","database issue","41","d268-72","PMC3531052",NA,NA,"code.google.com"
"409","23794914","MED","23794914","10.3897/zookeys.305.5438","A specialist's audit of aggregated occurrence records: An 'aggregator's' perspective.","Belbin L, Daly J, Hirsch T, Hobern D, Salle JL.","Zookeys","2013","1313-2989","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","280.3828","305",NA,"67-76","PMC3689094",NA,NA,"code.google.com"
"410","23843771","MED","23843771","10.5808/gi.2013.11.2.60","Human Transcriptome and Chromatin Modifications: An ENCODE Perspective.","Shen L, Choi I, Nestler EJ, Won KJ.","Genomics Inform","2013","1598-866x","journal article; review-article","Y","Y","Y","1","Y","Y","N","N","N","280.3828","2","11","60-67","PMC3704928",NA,NA,"code.google.com"
"411","22790250","MED","22790250","10.3174/ajnr.a3197","Alterations of directional connectivity among resting-state networks in Alzheimer disease.","Li R, Wu X, Chen K, Fleisher AS, Reiman EM, Yao L.","AJNR Am J Neuroradiol","2013","0195-6108","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","5","Y","Y","N","N","N","280.3828","2","34","340-345","PMC4097966",NA,NA,"code.google.com"
"412","23335781","MED","23335781","10.1093/nar/gkt006","CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model.","Wang L, Park HJ, Dasari S, Wang S, Kocher JP, Li W.","Nucleic Acids Res","2013","0305-1048","evaluation studies; journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","23","Y","Y","N","N","N","280.3828","6","41","e74","PMC3616698",NA,NA,"code.google.com"
"413","23615333","MED","23615333","10.1111/1755-0998.12110","Allelic imbalance metre (Allim), a new tool for measuring allele-specific gene expression with RNA-seq data.","Pandey RV, Franssen SU, Futschik A, SchlÃ¶tterer C.","Mol Ecol Resour","2013","1755-098x","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","4","Y","Y","N","N","N","280.3828","4","13","740-745","PMC3739924",NA,NA,"code.google.com"
"414","24182195","MED","24182195","10.1186/1752-0509-7-118","Identification of direction in gene networks from expression and methylation.","Simcha DM, Younes L, Aryee MJ, Geman D.","BMC Syst Biol","2013","1752-0509","journal article; research support, n.i.h., extramural; research-article","Y","Y","N","0","Y","Y","N","N","N","279.98605",NA,"7","118","PMC4228359",NA,NA,"code.google.com"
"415","24376455","MED","24376455","10.3389/fgene.2013.00272","Validation of gene regulatory network inference based on controllability.","Qian X, Dougherty ER.","Front Genet","2013","1664-8021","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","279.98605",NA,"4","272","PMC3860259",NA,NA,"code.google.com"
"416","23841592","MED","23841592","10.1021/ac401145q","Optimized nonlinear gradients for reversed-phase liquid chromatography in shotgun proteomics.","Moruz L, Pichler P, Stranzl T, Mechtler K, KÃ¤ll L.","Anal Chem","2013","0003-2700","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","3","Y","Y","N","N","N","279.98605","16","85","7777-7785","PMC3805310",NA,NA,"code.google.com"
"417","24074221","MED","24074221","10.1021/pr400705q","Mass fingerprinting of complex mixtures: protein inference from high-resolution peptide masses and predicted retention times.","Moruz L, Hoopmann MR, Rosenlund M, Granholm V, Moritz RL, KÃ¤ll L.","J Proteome Res","2013","1535-3893","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research support, american recovery and reinvestment act; research-article","N","Y","N","0","Y","Y","N","N","N","279.98605","12","12","5730-5741","PMC3860378",NA,NA,"code.google.com"
"418","23517579","MED","23517579","10.1186/1756-0500-6-107","Estimating the similarity of alternative Affymetrix probe sets using transcriptional networks.","Bellis M.","BMC Res Notes","2013","1756-0500","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","279.98605",NA,"6","107","PMC3630002",NA,NA,"code.google.com"
"419","23663436","MED","23663436","10.1186/1471-2164-14-322","Transcription profile of soybean-root-knot nematode interaction reveals a key role of phythormones in the resistance reaction.","Beneventi MA, da Silva OB Jr, de SÃ¡ ME, Firmino AA, de Amorim RM, Albuquerque EV, da Silva MC, da Silva JP, Campos Mde A, Lopes MJ, Togawa RC, Pappas GJ Jr, Grossi-de-Sa MF.","BMC Genomics","2013","1471-2164","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","Y","279.98605",NA,"14","322","PMC3701510","pfam",NA,"code.google.com"
"420","23700313","MED","23700313","10.1093/nar/gkt372","PyroHMMsnp: an SNP caller for Ion Torrent and 454 sequencing data.","Zeng F, Jiang R, Chen T.","Nucleic Acids Res","2013","0305-1048","evaluation studies; journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","2","Y","Y","N","N","Y","279.98605","13","41","e136","PMC3711422","refsnp",NA,"code.google.com"
"421","23812978","MED","23812978","10.1093/bioinformatics/btt235","CAMPways: constrained alignment framework for the comparative analysis of a pair of metabolic pathways.","Abaka G, BÄ±yÄ±koÄlu T, Erten C.","Bioinformatics","2013","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","279.98605","13","29","i145-53","PMC3694646",NA,NA,"code.google.com"
"422","23954162","MED","23954162","10.1016/j.ajhg.2013.07.003","DrGaP: a powerful tool for identifying driver genes and pathways in cancer sequencing studies.","Hua X, Xu H, Yang Y, Zhu J, Liu P, Lu Y.","Am J Hum Genet","2013","0002-9297","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","2","Y","Y","N","N","N","279.98605","3","93","439-451","PMC3769934",NA,NA,"code.google.com"
"423","24305553","MED","24305553","10.1186/1471-2105-14-354","Balony: a software package for analysis of data generated by synthetic genetic array experiments.","Young BP, Loewen CJ.","BMC Bioinformatics","2013","1471-2105","journal article; research support, non-u.s. gov't; product-review","Y","Y","N","3","Y","Y","N","Y","N","279.98605",NA,"14","354","PMC4234492",NA,NA,"code.google.com"
"424","24367249","MED","24367249","10.1371/journal.pcbi.1003397","Inferring the source of transmission with phylogenetic data.","Volz EM, Frost SD.","PLoS Comput Biol","2013","1553-734x","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","4","Y","Y","N","N","N","279.98605","12","9","e1003397","PMC3868546",NA,NA,"code.google.com"
"425","24367263","MED","24367263","10.1371/journal.ppat.1003818","A human torque teno virus encodes a microRNA that inhibits interferon signaling.","Kincaid RP, Burke JM, Cox JC, de Villiers EM, Sullivan CS.","PLoS Pathog","2013","1553-7366","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","3","Y","Y","N","N","N","279.98605","12","9","e1003818","PMC3868544",NA,NA,"code.google.com"
"426","23268448","MED","23268448","10.1093/nar/gks1299","TEAK: topology enrichment analysis framework for detecting activated biological subpathways.","Judeh T, Johnson C, Kumar A, Zhu D.","Nucleic Acids Res","2013","0305-1048","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","2","Y","Y","Y","N","N","279.98605","3","41","1425-1437","PMC3561980",NA,"UNIPROT","code.google.com"
"427","23652347","MED","23652347","10.1093/sysbio/syt028","A semantic model for species description applied to the ensign wasps (hymenoptera: evaniidae) of New Caledonia.","Balhoff JP, MikÃ³ I, Yoder MJ, Mullins PL, Deans AR.","Syst Biol","2013","1063-5157","journal article; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","4","Y","Y","N","Y","Y","279.98605","5","62","639-659","PMC3739881","doi",NA,"code.google.com"
"428","23198894","MED","23198894","10.1162/jocn_a_00305","Decoding attended information in short-term memory: an EEG study.","LaRocque JJ, Lewis-Peacock JA, Drysdale AT, Oberauer K, Postle BR.","J Cogn Neurosci","2013","0898-929x","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","14","Y","Y","N","N","N","279.98605","1","25","127-142","PMC3775605",NA,NA,"code.google.com"
"429","23379779","MED","23379779","10.1186/1471-2164-14-77","Characterisation of the wheat (Triticum aestivum L.) transcriptome by de novo assembly for the discovery of phosphate starvation-responsive genes: gene expression in Pi-stressed wheat.","Oono Y, Kobayashi F, Kawahara Y, Yazawa T, Handa H, Itoh T, Matsumoto T.","BMC Genomics","2013","1471-2164","journal article; research-article","Y","Y","Y","10","Y","Y","N","N","Y","279.98605",NA,"14","77","PMC3598684","gen",NA,"code.google.com"
"430","24103098","MED","24103098","10.1186/2041-1480-4-25","Using ontologies to study cell transitions.","Fuellen G, Jansen L, Leser U, Kurtz A.","J Biomed Semantics","2013","2041-1480","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","279.95572","1","4","25","PMC4128511",NA,NA,"code.google.com"
"431","24191249","MED","24191249","10.1155/2013/687607","Computer-assisted system with multiple feature fused support vector machine for sperm morphology diagnosis.","Tseng KK, Li Y, Hsu CY, Huang HN, Zhao M, Ding M.","Biomed Res Int","2013","2314-6133","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","279.95572",NA,"2013","687607","PMC3803132",NA,NA,"code.google.com"
"432","24194707","MED","24194707","10.3389/fnhum.2013.00692","Emotional expressions evoke a differential response in the fusiform face area.","Harry B, Williams MA, Davis C, Kim J.","Front Hum Neurosci","2013","1662-5161","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","279.95572",NA,"7","692","PMC3809557",NA,NA,"code.google.com"
"433","24294142","MED","24294142","10.1155/2013/935026","Lateral inhibition in accumulative computation and fuzzy sets for human fall pattern recognition in colour and infrared imagery.","FernÃ¡ndez-Caballero A, Sokolova MV, Serrano-Cuerda J.","ScientificWorldJournal","2013","2356-6140","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","279.95572",NA,"2013","935026","PMC3833320",NA,NA,"code.google.com"
"434","24320447","MED","24320447","10.1118/1.4824926","CONRAD--a software framework for cone-beam imaging in radiology.","Maier A, Hofmann HG, Berger M, Fischer P, Schwemmer C, Wu H, MÃ¼ller K, Hornegger J, Choi JH, Riess C, Keil A, Fahrig R.","Med Phys","2013","0094-2405","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","N","0","Y","Y","N","N","N","279.95572","11","40","111914","PMC3820625",NA,NA,"code.google.com"
"435","23794735","MED","23794735","10.1093/database/bat044","The CARLSBAD database: a confederated database of chemical bioactivities.","Mathias SL, Hines-Kay J, Yang JJ, Zahoransky-Kohalmi G, Bologa CG, Ursu O, Oprea TI.","Database (Oxford)","2013","1758-0463","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","279.95572",NA,"2013","bat044","PMC3689437",NA,NA,"code.google.com"
"436","23620360","MED","23620360","10.1093/bioinformatics/btt183","Shimmer: detection of genetic alterations in tumors using next-generation sequence data.","Hansen NF, Gartner JJ, Mei L, Samuels Y, Mullikin JC.","Bioinformatics","2013","1367-4803","journal article; research support, n.i.h., intramural; research-article","N","Y","Y","5","Y","Y","N","N","N","279.95572","12","29","1498-1503","PMC3673219",NA,NA,"code.google.com"
"437","23696889","MED","23696889","10.1371/journal.pone.0064393","Comparison of microRNA deep sequencing of matched formalin-fixed paraffin-embedded and fresh frozen cancer tissues.","Meng W, McElroy JP, Volinia S, Palatini J, Warner S, Ayers LW, Palanichamy K, Chakravarti A, Lautenschlaeger T.","PLoS One","2013","1932-6203","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; in vitro; research-article","Y","Y","Y","7","Y","Y","N","N","N","279.95572","5","8","e64393","PMC3655971",NA,NA,"code.google.com"
"438","23762401","MED","23762401","10.1371/journal.pone.0065617","Quantifying disorder through conditional entropy: an application to fluid mixing.","Brandani GB, Schor M, Macphee CE, GrubmÃ¼ller H, Zachariae U, Marenduzzo D.","PLoS One","2013","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","279.95572","6","8","e65617","PMC3677935",NA,NA,"code.google.com"
"439","23350031","MED","23350031","10.1038/srep01124","Citrullination as early-stage indicator of cell response to single-walled carbon nanotubes.","Mohamed BM, Movia D, Knyazev A, Langevin D, Davies AM, Prina-Mello A, Volkov Y.","Sci Rep","2013","2045-2322","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","279.95572",NA,"3","1124","PMC3554256",NA,NA,"code.google.com"
"440","23875683","MED","23875683","10.1186/1471-2164-14-494","Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE.","Trinh QM, Jen FY, Zhou Z, Chu KM, Perry MD, Kephart ET, Contrino S, Ruzanov P, Stein LD.","BMC Genomics","2013","1471-2164","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; product-review","Y","Y","Y","3","Y","Y","N","Y","N","279.95572",NA,"14","494","PMC3734164",NA,NA,"code.google.com"
"441","23991150","MED","23991150","10.1371/journal.pone.0072781","Genome-wide SNP and STR discovery in the Japanese crested ibis and genetic diversity among founders of the Japanese population.","Taniguchi Y, Matsuda H, Yamada T, Sugiyama T, Homma K, Kaneko Y, Yamagishi S, Iwaisaki H.","PLoS One","2013","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","279.95572","8","8","e72781","PMC3749161",NA,NA,"code.google.com"
"442","23441864","MED","23441864","10.1186/1471-2105-14-65","FAVR (Filtering and Annotation of Variants that are Rare): methods to facilitate the analysis of rare germline genetic variants from massively parallel sequencing datasets.","Pope BJ, Nguyen-Dumont T, Odefrey F, Hammet F, Bell R, Tao K, Tavtigian SV, Goldgar DE, Lonie A, Southey MC, Park DJ.","BMC Bioinformatics","2013","1471-2105","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","2","Y","Y","N","N","N","279.95572",NA,"14","65","PMC3599469",NA,NA,"code.google.com"
"443","23633588","MED","23633588","10.1107/s0907444913001984","AutoDrug: fully automated macromolecular crystallography workflows for fragment-based drug discovery.","Tsai Y, McPhillips SE, GonzÃ¡lez A, McPhillips TM, Zinn D, Cohen AE, Feese MD, Bushnell D, Tiefenbrunn T, Stout CD, Ludaescher B, Hedman B, Hodgson KO, Soltis SM.","Acta Crystallogr D Biol Crystallogr","2013","0907-4449","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","Y","2","N","Y","N","N","N","279.95572","pt 5","69","796-803","PMC3640469",NA,NA,"code.google.com"
"444","23702683","MED","23702683","10.1038/leu.2013.117","Detailed molecular characterisation of acute myeloid leukaemia with a normal karyotype using targeted DNA capture.","Conte N, Varela I, Grove C, Manes N, Yusa K, Moreno T, Segonds-Pichon A, Bench A, Gudgin E, Herman B, Bolli N, Ellis P, Haddad D, Costeas P, Rad R, Scott M, Huntly B, Bradley A, Vassiliou GS.","Leukemia","2013","0887-6924","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","3","Y","Y","N","N","N","279.95572","9","27","1820-1825","PMC3768109",NA,NA,"code.google.com"
"445","23577015","MED","23577015","10.3389/fpls.2013.00073","Recent progress in the development of metabolome databases for plant systems biology.","Fukushima A, Kusano M.","Front Plant Sci","2013","1664-462x","journal article; review-article","Y","Y","Y","7","Y","Y","N","N","N","279.95572",NA,"4","73","PMC3616245",NA,NA,"code.google.com"
"446","23940738","MED","23940738","10.1371/journal.pone.0071305","Population level inference for multivariate MEG analysis.","Jafarpour A, Barnes G, Fuentemilla L, Duzel E, Penny WD.","PLoS One","2013","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","279.95572","8","8","e71305","PMC3734032",NA,NA,"code.google.com"
"447","23349661","MED","23349661","10.1371/journal.pone.0048156","De novo transcriptome assembly in chili pepper (Capsicum frutescens) to identify genes involved in the biosynthesis of capsaicinoids.","Liu S, Li W, Wu Y, Chen C, Lei J.","PLoS One","2013","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","16","Y","Y","N","N","N","279.95572","1","8","e48156","PMC3551913",NA,NA,"code.google.com"
"448","23630246","MED","23630246","10.1093/database/bat029","The MetaboLights repository: curation challenges in metabolomics.","Salek RM, Haug K, Conesa P, Hastings J, Williams M, Mahendraker T, Maguire E, GonzÃ¡lez-BeltrÃ¡n AN, Rocca-Serra P, Sansone SA, Steinbeck C.","Database (Oxford)","2013","1758-0463","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","4","Y","Y","N","Y","N","279.95572",NA,"2013","bat029","PMC3638156",NA,NA,"code.google.com"
"449","23748742","MED","23748742","10.1093/icb/ict071","Nearly complete 28S rRNA gene sequences confirm new hypotheses of sponge evolution.","Thacker RW, Hill AL, Hill MS, Redmond NE, Collins AG, Morrow CC, Spicer L, Carmack CA, Zappe ME, Pohlmann D, Hall C, Diaz MC, Bangalore PV.","Integr Comp Biol","2013","1540-7063","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","Y","4","Y","Y","Y","N","Y","279.95572","3","53","373-387","PMC3744897","gen","EMBL","code.google.com"
"450","23847424","MED","23847424","10.4137/bii.s11664","Using empirically constructed lexical resources for named entity recognition.","Jonnalagadda S, Cohen T, Wu S, Liu H, Gonzalez G.","Biomed Inform Insights","2013","1178-2226","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","279.95572","suppl 1","6","17-27","PMC3702195",NA,NA,"code.google.com"
"451","24386226","MED","24386226","10.1371/journal.pone.0083547","Intra-specific regulatory variation in Drosophila pseudoobscura.","Suvorov A, Nolte V, Pandey RV, Franssen SU, Futschik A, SchlÃ¶tterer C.","PLoS One","2013","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","Y","Y","279.9557","12","8","e83547","PMC3873948","arrayexpress",NA,"code.google.com"
"452","24551366","MED","24551366",NA,"Desiderata for healthcare integrated data repositories based on architectural comparison of three public repositories.","Huser V, Cimino JJ.","AMIA Annu Symp Proc","2013","1942-597x","journal article; research support, n.i.h., intramural; comparative study; research-article","N","Y","Y","0","Y","Y","N","N","N","279.9557",NA,"2013","648-656","PMC3900207",NA,NA,"code.google.com"
"453","24207125","MED","24207125","10.1016/j.str.2013.09.006","Transient protein states in designing inhibitors of the MDM2-p53 interaction.","Bista M, Wolf S, Khoury K, Kowalska K, Huang Y, Wrona E, Arciniega M, Popowicz GM, Holak TA, DÃ¶mling A.","Structure","2013","0969-2126","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","N","3","Y","Y","Y","N","Y","279.9557","12","21","2143-2151","PMC4104591","pdb","PDBUNIPROT","code.google.com"
"454","25279136","MED","25279136",NA,"Easy-DHPSF open-source software for three-dimensional localization of single molecules with precision beyond the optical diffraction limit.","Lew MD, von Diezmann AR, Moerner WE.","Protoc exch","2013","2043-0116","journal article; research-article","N","Y","N","0","Y","Y","N","N","N","279.9557",NA,"2013",NA,"PMC4180084",NA,NA,"code.google.com"
"455","23666239","MED","23666239","10.1038/ng.2634","Meta-analysis identifies four new loci associated with testicular germ cell tumor.","Chung CC, Kanetsky PA, Wang Z, Hildebrandt MA, Koster R, Skotheim RI, Kratz CP, Turnbull C, Cortessis VK, Bakken AC, Bishop DT, Cook MB, Erickson RL, FossÃ¥ SD, Jacobs KB, Korde LA, Kraggerud SM, Lothe RA, Loud JT, Rahman N, Skinner EC, Thomas DC, Wu X, Yeager M, Schumacher FR, Greene MH, Schwartz SM, McGlynn KA, Chanock SJ, Nathanson KL.","Nat Genet","2013","1061-4036","journal article; meta-analysis; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","14","Y","Y","N","Y","Y","279.9557","6","45","680-685","PMC3723930","refsnp; omim",NA,"code.google.com"
"456","23536290","MED","23536290","10.1073/pnas.1216863110","Structure of the rare archaeal biosphere and seasonal dynamics of active ecotypes in surface coastal waters.","Hugoni M, Taib N, Debroas D, Domaizon I, Jouan Dufournel I, Bronner G, Salter I, AgoguÃ© H, Mary I, Galand PE.","Proc Natl Acad Sci U S A","2013","0027-8424","journal article; research support, non-u.s. gov't; research-article","N","Y","Y","5","Y","Y","N","Y","Y","279.9557","15","110","6004-6009","PMC3625260","doi",NA,"code.google.com"
"457","23836170","MED","23836170","10.1128/aac.01030-13","Genetic basis for in vitro and in vivo resistance to lincosamides, streptogramins A, and pleuromutilins (LSAP phenotype) in Enterococcus faecium.","Isnard C, Malbruny B, Leclercq R, Cattoir V.","Antimicrob Agents Chemother","2013","0066-4804","journal article; research support, non-u.s. gov't; research-article","N","Y","Y","4","Y","Y","Y","N","Y","279.9557","9","57","4463-4469","PMC3754343","gen","EMBLUNIPROT","code.google.com"
"458","23770754","MED","23770754","10.1038/nmeth.2522","Genome-wide profiling of human cap-independent translation-enhancing elements.","Wellensiek BP, Larsen AC, Stephens B, Kukurba K, Waern K, Briones N, Liu L, Snyder M, Jacobs BL, Kumar S, Chaput JC.","Nat Methods","2013","1548-7091","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","2","Y","Y","N","N","N","279.9557","8","10","747-750","PMC3731418",NA,NA,"code.google.com"
"459","23763826","MED","23763826","10.1186/1471-2105-14-191","KNODWAT: a scientific framework application for testing knowledge discovery methods for the biomedical domain.","Holzinger A, Zupan M.","BMC Bioinformatics","2013","1471-2105","journal article; product-review","Y","Y","Y","2","Y","Y","N","N","N","279.9557",NA,"14","191","PMC3691758",NA,NA,"code.google.com"
"460","23793153","MED","23793153","10.1107/s0907444913000863","New Python-based methods for data processing.","Sauter NK, Hattne J, Grosse-Kunstleve RW, Echols N.","Acta Crystallogr D Biol Crystallogr","2013","0907-4449","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","8","N","Y","Y","N","N","279.9557","pt 7","69","1274-1282","PMC3689530",NA,"PDBUNIPROT","code.google.com"
"461","23819435","MED","23819435","10.1186/1755-8794-6-s2-s5","Diplotyper: diplotype-based association analysis.","Kim S, Park K, Shin C, Cho NH, Ko JJ, Koh I, Kwack K.","BMC Med Genomics","2013","1755-8794","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","N","N","Y","279.9557","Suppl 2","6 Suppl 2","s5","PMC3654869","refsnp",NA,"code.google.com"
"462","24273734","MED","24273734","10.1016/j.nicl.2013.10.010","Prolonged febrile seizures cause reversible reductions in white matter integrity.","Yoong M, Seunarine K, Martinos M, Chin RF, Clark CA, Scott RC.","Neuroimage Clin","2013","2213-1582","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","279.9557",NA,"3","515-521","PMC3830064",NA,NA,"code.google.com"
"463","24033628","MED","24033628","10.1111/acem.12174","Automated outcome classification of emergency department computed tomography imaging reports.","Yadav K, Sarioglu E, Smith M, Choi HA.","Acad Emerg Med","2013","1069-6563","journal article; research support, n.i.h., extramural; research-article","N","Y","Y","2","Y","Y","N","N","N","279.9557","8","20","848-854","PMC3898888",NA,NA,"code.google.com"
"464","23967013","MED","23967013","10.3389/fgene.2013.00153","MicroRNA expression profiles in avian haemopoietic cells.","Yao Y, Charlesworth J, Nair V, Watson M.","Front Genet","2013","1664-8021","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","279.9557",NA,"4","153","PMC3743212",NA,NA,"code.google.com"
"465","23535838","MED","23535838","10.1038/srep01569","Long-term strain improvements accumulate mutations in regulatory elements responsible for hyper-production of cellulolytic enzymes.","Liu G, Zhang L, Qin Y, Zou G, Li Z, Yan X, Wei X, Chen M, Chen L, Zheng K, Zhang J, Ma L, Li J, Liu R, Xu H, Bao X, Fang X, Wang L, Zhong Y, Liu W, Zheng H, Wang S, Wang C, Xun L, Zhao GP, Wang T, Zhou Z, Qu Y.","Sci Rep","2013","2045-2322","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","11","Y","Y","Y","N","N","279.9557",NA,"3","1569","PMC3610096",NA,"EMBL","code.google.com"
"466","24204918","MED","24204918","10.1371/journal.pone.0077686","Identification of cichlid fishes from Lake Malawi using computer vision.","Joo D, Kwan YS, Song J, Pinho C, Hey J, Won YJ.","PLoS One","2013","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","Y","279.92502","10","8","e77686","PMC3808401","gen",NA,"code.google.com"
"467","23409088","MED","23409088","10.1371/journal.pone.0055913","Consequences of normalizing transcriptomic and genomic libraries of plant genomes using a duplex-specific nuclease and tetramethylammonium chloride.","Matvienko M, Kozik A, Froenicke L, Lavelle D, Martineau B, Perroud B, Michelmore R.","PLoS One","2013","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","4","Y","Y","N","N","Y","279.92502","2","8","e55913","PMC3568094","gen; pfam",NA,"code.google.com"
"468","24098570","MED","24098570","10.1371/journal.pone.0076925","Application of genotyping-by-sequencing on semiconductor sequencing platforms: a comparison of genetic and reference-based marker ordering in barley.","Mascher M, Wu S, Amand PS, Stein N, Poland J.","PLoS One","2013","1932-6203","journal article; research support, non-u.s. gov't; comparative study; research-article","Y","Y","Y","8","Y","Y","N","N","N","279.52853","10","8","e76925","PMC3789676",NA,NA,"code.google.com"
"469","24167551","MED","24167551","10.1371/journal.pone.0076911","GRAPES: a software for parallel searching on biological graphs targeting multi-core architectures.","Giugno R, Bonnici V, Bombieri N, Pulvirenti A, Ferro A, Shasha D.","PLoS One","2013","1932-6203","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","1","Y","Y","N","N","N","279.52853","10","8","e76911","PMC3805575",NA,NA,"code.google.com"
"470","24191891","MED","24191891","10.1186/1471-2105-14-317","Automated analysis of phylogenetic clusters.","Ragonnet-Cronin M, Hodcroft E, HuÃ© S, Fearnhill E, Delpech V, Brown AJ, Lycett S, UK HIV Drug Resistance Database.","BMC Bioinformatics","2013","1471-2105","journal article; research support, non-u.s. gov't; product-review","Y","Y","N","4","Y","Y","N","N","Y","279.52853",NA,"14","317","PMC4228337","gen",NA,"code.google.com"
"471","24204225","MED","24204225","10.1371/journal.pcbi.1003273","Molecular mechanical differences between isoforms of contractile actin in the presence of isoforms of smooth muscle tropomyosin.","Hilbert L, Bates G, Roman HN, Blumenthal JL, Zitouni NB, Sobieszek A, Mackey MC, Lauzon AM.","PLoS Comput Biol","2013","1553-734x","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","279.52853","10","9","e1003273","PMC3812040",NA,NA,"code.google.com"
"472","24240121","MED","24240121",NA,"Computational methods for detecting copy number variations in cancer genome using next generation sequencing: principles and challenges.","Liu B, Morrison CD, Johnson CS, Trump DL, Qin M, Conroy JC, Wang J, Liu S.","Oncotarget","2013","1949-2553","journal article; review; research support, n.i.h., extramural; review-article","Y","Y","Y","3","Y","Y","N","N","N","279.52853","11","4","1868-1881","PMC3875755",NA,NA,"code.google.com"
"473","24282601","MED","24282601","10.1371/journal.pone.0081502","The origin of the RB1 imprint.","Kanber D, Buiting K, Roos C, Gromoll J, Kaya S, Horsthemke B, Lohmann D.","PLoS One","2013","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","279.52853","11","8","e81502","PMC3839921",NA,NA,"code.google.com"
"474","23630264","MED","23630264","10.1073/pnas.1215283110","Glycolytic strategy as a tradeoff between energy yield and protein cost.","Flamholz A, Noor E, Bar-Even A, Liebermeister W, Milo R.","Proc Natl Acad Sci U S A","2013","0027-8424","journal article; research support, non-u.s. gov't; research-article","N","Y","Y","23","Y","Y","N","N","N","279.52853","24","110","10039-10044","PMC3683749",NA,NA,"code.google.com"
"475","25285051","MED","25285051",NA,"Using Visualizations to Explore Network Dynamics.","Chu KH, Wipfli H, Valente TW.","J Soc Struct","2013","1529-1227","journal article; research-article","N","Y","N","0","Y","Y","N","N","N","279.52853",NA,"14",NA,"PMC4184104",NA,NA,"code.google.com"
"476","24244136","MED","24244136","10.1371/journal.pcbi.1003326","Practical guidelines for the comprehensive analysis of ChIP-seq data.","Bailey T, Krajewski P, Ladunga I, Lefebvre C, Li Q, Liu T, Madrigal P, Taslim C, Zhang J.","PLoS Comput Biol","2013","1553-734x","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","8","Y","Y","N","N","N","279.52853","11","9","e1003326","PMC3828144",NA,NA,"code.google.com"
"477","24376708","MED","24376708","10.1371/journal.pone.0083489","An efficient immunization strategy for community networks.","Gong K, Tang M, Hui PM, Zhang HF, Younghae D, Lai YC.","PLoS One","2013","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","279.52853","12","8","e83489","PMC3869806",NA,NA,"code.google.com"
"478","23663776","MED","23663776","10.1016/j.cell.2013.04.030","Reprogramming the maternal zebrafish genome after fertilization to match the paternal methylation pattern.","Potok ME, Nix DA, Parnell TJ, Cairns BR.","Cell","2013","0092-8674","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","32","Y","Y","N","N","N","279.52853","4","153","759-772","PMC4030421",NA,NA,"code.google.com"
"479","24349421","MED","24349421","10.1371/journal.pone.0083016","Gathering and exploring scientific knowledge in pharmacovigilance.","Lopes P, Nunes T, Campos D, Furlong LI, Bauer-Mehren A, Sanz F, Carrascosa MC, Mestres J, Kors J, Singh B, van Mulligen E, Van der Lei J, Diallo G, Avillach P, Ahlberg E, Boyer S, Diaz C, Oliveira JL.","PLoS One","2013","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","279.52853","12","8","e83016","PMC3859628",NA,NA,"code.google.com"
"480","23658117","MED","23658117","10.1098/rsif.2013.0246","Unravelling daily human mobility motifs.","Schneider CM, Belik V, CouronnÃ© T, Smoreda Z, GonzÃ¡lez MC.","J R Soc Interface","2013","1742-5689","journal article; research support, non-u.s. gov't; research-article","N","Y","Y","5","Y","Y","N","N","N","279.52853","84","10","20130246","PMC3673164",NA,NA,"code.google.com"
"481","24088188","MED","24088188","10.1186/1471-2164-14-674","V-Phaser 2: variant inference for viral populations.","Yang X, Charlebois P, Macalalad A, Henn MR, Zody MC.","BMC Genomics","2013","1471-2164","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","1","Y","Y","N","Y","N","279.52853",NA,"14","674","PMC3907024",NA,NA,"code.google.com"
"482","24564884","MED","24564884","10.1186/1753-6561-7-s7-s2","Conceptualization of molecular findings by mining gene annotations.","Chen V, Lu X.","BMC Proc","2013","1753-6561","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","279.52853","suppl 7","7","s2","PMC4042834",NA,NA,"code.google.com"
"483","24205174","MED","24205174","10.1371/journal.pone.0078264","Emergent group level navigation: an agent-based evaluation of movement patterns in a folivorous primate.","Bonnell TR, CampennÃ¬ M, Chapman CA, Gogarten JF, Reyna-Hurtado RA, Teichroeb JA, Wasserman MD, Sengupta R.","PLoS One","2013","1932-6203","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","1","Y","Y","N","N","N","279.52853","10","8","e78264","PMC3804626",NA,NA,"code.google.com"
"484","24348509","MED","24348509","10.3389/fgene.2013.00237","Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots.","Kumar S, Jones M, Koutsovoulos G, Clarke M, Blaxter M.","Front Genet","2013","1664-8021","journal article; research-article","Y","Y","Y","5","Y","Y","N","N","N","279.52853",NA,"4","237","PMC3843372",NA,NA,"code.google.com"
"485","24205931","MED","24205931","10.1021/ac4033615","""Retention projection"" enables reliable use of shared gas chromatographic retention data across laboratories, instruments, and methods.","Barnes BB, Wilson MB, Carr PW, Vitha MF, Broeckling CD, Heuberger AL, Prenni J, Janis GC, Corcoran H, Snow NH, Chopra S, Dhandapani R, Tawfall A, Sumner LW, Boswell PG.","Anal Chem","2013","0003-2700","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; comparative study; research-article","N","Y","N","1","Y","Y","N","N","N","279.52853","23","85","11650-11657","PMC3962126",NA,NA,"code.google.com"
"486","24723764","MED","24723764","10.3897/bdj.1.e968","The BioCASe Monitor Service - A tool for monitoring progress and quality of data provision through distributed data networks.","GlÃ¶ckler F, Hoffmann J, Theeten F.","Biodivers Data J","2013","1314-2828","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","279.52853","1",NA,"e968","PMC3964725",NA,NA,"code.google.com"
"487","23483880","MED","23483880","10.1371/journal.pone.0056776","Estimating at-sea mortality of marine turtles from stranding frequencies and drifter experiments.","Koch V, Peckham H, Mancini A, Eguchi T.","PLoS One","2013","1932-6203","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","2","Y","Y","N","N","N","279.52853","2","8","e56776","PMC3577704",NA,NA,"code.google.com"
"488","23508232","MED","23508232","10.3389/fninf.2013.00004","Accelerating compartmental modeling on a graphical processing unit.","Ben-Shalom R, Liberman G, Korngreen A.","Front Neuroinform","2013","1662-5196","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","279.52853",NA,"7","4","PMC3600538",NA,NA,"code.google.com"
"489","23523638","MED","23523638","10.1016/j.jprot.2013.02.033","Proteomic survey of the Streptomyces coelicolor nucleoid.","Bradshaw E, Saalbach G, McArthur M.","J Proteomics","2013","1874-3919","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","279.52853","100","83","37-46","PMC3784963",NA,NA,"code.google.com"
"490","23568264","MED","23568264","10.1038/srep01630","An integrative network algorithm identifies age-associated differential methylation interactome hotspots targeting stem-cell differentiation pathways.","West J, Beck S, Wang X, Teschendorff AE.","Sci Rep","2013","2045-2322","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","9","Y","Y","N","N","N","279.52853",NA,"3","1630","PMC3620664",NA,NA,"code.google.com"
"491","23574621","MED","23574621","10.1186/1471-2164-14-240","Reevaluation of the evolutionary events within recA/RAD51 phylogeny.","Chintapalli SV, Bhardwaj G, Babu J, Hadjiyianni L, Hong Y, Todd GK, Boosalis CA, Zhang Z, Zhou X, Ma H, Anishkin A, van Rossum DB, Patterson RL.","BMC Genomics","2013","1471-2164","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","279.52853",NA,"14","240","PMC3637515",NA,NA,"code.google.com"
"492","23593277","MED","23593277","10.1371/journal.pone.0060667","MrBayes tgMCÂ³: a tight GPU implementation of MrBayes.","Ling C, Hamada T, Bai J, Li X, Chesters D, Zheng W, Shi W.","PLoS One","2013","1932-6203","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","279.52853","4","8","e60667","PMC3621901",NA,NA,"code.google.com"
"493","23599001","MED","23599001","10.1093/nar/gkt261","Computational analyses of transcriptomic data reveal the dynamic organization of the Escherichia coli chromosome under different conditions.","Ma Q, Yin Y, Schell MA, Zhang H, Li G, Xu Y.","Nucleic Acids Res","2013","0305-1048","journal article; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","0","Y","Y","N","N","N","279.52853","11","41","5594-5603","PMC3675479",NA,NA,"code.google.com"
"494","23628075","MED","23628075","10.1186/2045-8118-10-17","Quantitative proteomics comparison of arachnoid cyst fluid and cerebrospinal fluid collected perioperatively from arachnoid cyst patients.","Berle M, Kroksveen AC, Garberg H, Aarhus M, Haaland OA, Wester K, Ulvik RJ, Helland C, Berven F.","Fluids Barriers CNS","2013","2045-8118","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","279.52853","1","10","17","PMC3641952",NA,NA,"code.google.com"
"495","23636795","MED","23636795","10.1007/s10822-013-9646-6","Cheminformatics aspects of high throughput screening: from robots to models: symposium summary.","Jane Tseng Y, Martin E, G Bologa C, Shelat AA.","J Comput Aided Mol Des","2013","0920-654x","congresses; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","N","0","Y","Y","N","N","N","279.52853","5","27","443-453","PMC4205101",NA,NA,"code.google.com"
"496","23269663","MED","23269663","10.1101/gr.146985.112","CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize.","Gent JI, Ellis NA, Guo L, Harkess AE, Yao Y, Zhang X, Dawe RK.","Genome Res","2013","1088-9051","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","Y","10","Y","Y","N","N","N","279.52853","4","23","628-637","PMC3613580",NA,NA,"code.google.com"
"497","23408860","MED","23408860","10.1093/nar/gkt084","The structural basis of actinomycin D-binding induces nucleotide flipping out, a sharp bend and a left-handed twist in CGG triplet repeats.","Lo YS, Tseng WH, Chuang CY, Hou MH.","Nucleic Acids Res","2013","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","Y","N","Y","279.52853","7","41","4284-4294","PMC3627577","pdb","PDB","code.google.com"
"498","23470999","MED","23470999","10.1093/nar/gkt141","A high-throughput and quantitative method to assess the mutagenic potential of translesion DNA synthesis.","Taggart DJ, Camerlengo TL, Harrison JK, Sherrer SM, Kshetry AK, Taylor JS, Huang K, Suo Z.","Nucleic Acids Res","2013","0305-1048","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","1","Y","Y","N","N","N","279.52853","8","41","e96","PMC3632128",NA,NA,"code.google.com"
"499","22989579","MED","22989579","10.1093/cercor/bhs289","Coding of melodic gestalt in human auditory cortex.","Schindler A, Herdener M, Bartels A.","Cereb Cortex","2013","1047-3211","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","3","Y","Y","N","N","N","279.52853","12","23","2987-2993","PMC3827712",NA,NA,"code.google.com"
"500","23777293","MED","23777293","10.1186/1471-2148-13-125","Dispersing away from bad genotypes: the evolution of Fitness-Associated Dispersal (FAD) in homogeneous environments.","Gueijman A, Ayali A, Ram Y, Hadany L.","BMC Evol Biol","2013","1471-2148","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","0","Y","Y","N","N","N","279.52853",NA,"13","125","PMC3704926",NA,NA,"code.google.com"
"501","23835289","MED","23835289","10.1186/1752-0509-7-58","Reaction-contingency based bipartite Boolean modelling.","FlÃ¶ttmann M, Krause F, Klipp E, Krantz M.","BMC Syst Biol","2013","1752-0509","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","279.52853",NA,"7","58","PMC3710479",NA,NA,"code.google.com"
"502","23840783","MED","23840783","10.1371/journal.pone.0067885","HLA haplotyping from RNA-seq data using hierarchical read weighting.","Kim HJ, Pourmand N.","PLoS One","2013","1932-6203","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","1","Y","Y","N","N","N","279.52853","6","8","e67885","PMC3696101",NA,NA,"code.google.com"
"503","23894653","MED","23894653","10.1371/journal.pone.0070412","Detection of deregulated modules using deregulatory linked path.","Hu Y, Gao L, Shi K, Chiu DK.","PLoS One","2013","1932-6203","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","0","Y","Y","N","N","N","279.52853","7","8","e70412","PMC3722188",NA,NA,"code.google.com"
"504","23919725","MED","23919725","10.1021/pr4003883","ISPTM: an iterative search algorithm for systematic identification of post-translational modifications from complex proteome mixtures.","Huang X, Huang L, Peng H, Guru A, Xue W, Hong SY, Liu M, Sharma S, Fu K, Caprez AP, Swanson DR, Zhang Z, Ding SJ.","J Proteome Res","2013","1535-3893","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","1","Y","Y","N","N","N","279.52853","9","12","3831-3842","PMC3786209",NA,NA,"code.google.com"
"505","23956693","MED","23956693","10.1155/2013/386180","PRESEE: an MDL/MML algorithm to time-series stream segmenting.","Xu K, Jiang Y, Tang M, Yuan C, Tang C.","ScientificWorldJournal","2013","2356-6140","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","0","N","Y","N","N","N","279.52853",NA,"2013","386180","PMC3706014",NA,NA,"code.google.com"
"506","24019480","MED","24019480","10.1073/pnas.1309697110","Coalescence and genetic diversity in sexual populations under selection.","Neher RA, Kessinger TA, Shraiman BI.","Proc Natl Acad Sci U S A","2013","0027-8424","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","Y","2","Y","Y","N","N","N","279.52853","39","110","15836-15841","PMC3785765",NA,NA,"code.google.com"
"507","22723502","MED","22723502","10.1093/biostatistics/kxs020","ROC curve estimation under test-result-dependent sampling.","Wang X, Ma J, George SL.","Biostatistics","2013","1465-4644","journal article; research support, n.i.h., extramural; comparative study; research-article","N","Y","Y","0","Y","Y","N","N","N","279.52853","1","14","160-172","PMC3577107",NA,NA,"code.google.com"
"508","23437348","MED","23437348","10.1371/journal.pone.0057233","Identification and characterization of miRNA transcriptome in potato by high-throughput sequencing.","Zhang R, Marshall D, Bryan GJ, Hornyik C.","PLoS One","2013","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","7","Y","Y","Y","N","N","279.52853","2","8","e57233","PMC3578796",NA,"ARXPR","code.google.com"
"509","24093729","MED","24093729","10.1186/1471-2105-14-301","afterParty: turning raw transcriptomes into permanent resources.","Jones M, Blaxter M.","BMC Bioinformatics","2013","1471-2105","journal article; research support, non-u.s. gov't; product-review","Y","Y","Y","1","Y","Y","N","N","N","279.52853",NA,"14","301","PMC3856601",NA,NA,"code.google.com"
"510","24097271","MED","24097271","10.1038/nmeth.2687","Instant super-resolution imaging in live cells and embryos via analog image processing.","York AG, Chandris P, Nogare DD, Head J, Wawrzusin P, Fischer RS, Chitnis A, Shroff H.","Nat Methods","2013","1548-7091","journal article; research support, n.i.h., extramural; research support, n.i.h., intramural; research-article","Y","Y","Y","8","Y","Y","N","N","N","279.52853","11","10","1122-1126","PMC3898876",NA,NA,"code.google.com"
"511","23576735","MED","23576735","10.1073/pnas.1219992110","Genome-wide reprogramming of the chromatin landscape underlies endocrine therapy resistance in breast cancer.","Magnani L, Stoeck A, Zhang X, LÃ¡nczky A, Mirabella AC, Wang TL, Gyorffy B, Lupien M.","Proc Natl Acad Sci U S A","2013","0027-8424","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","12","Y","Y","Y","N","N","279.52853","16","110","e1490-9","PMC3631697",NA,"UNIPROTARXPR","code.google.com"
"512","23895341","MED","23895341","10.1186/1471-2164-14-513","Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology.","Hill DP, Adams N, Bada M, Batchelor C, Berardini TZ, Dietze H, Drabkin HJ, Ennis M, Foulger RE, Harris MA, Hastings J, Kale NS, de Matos P, Mungall CJ, Owen G, Roncaglia P, Steinbeck C, Turner S, Lomax J.","BMC Genomics","2013","1471-2164","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","6","Y","Y","N","N","N","279.52853",NA,"14","513","PMC3733925",NA,NA,"code.google.com"
"513","23650393","MED","23650393","10.1073/pnas.1222722110","Lymphatic abnormalities are associated with RASA1 gene mutations in mouse and man.","Burrows PE, Gonzalez-Garay ML, Rasmussen JC, Aldrich MB, Guilliod R, Maus EA, Fife CE, Kwon S, Lapinski PE, King PD, Sevick-Muraca EM.","Proc Natl Acad Sci U S A","2013","0027-8424","clinical trial; journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","10","Y","Y","Y","N","N","279.52853","21","110","8621-8626","PMC3666675",NA,"UNIPROT","code.google.com"
"514","23660285","MED","23660285","10.1093/database/bat025","PhenoDigm: analyzing curated annotations to associate animal models with human diseases.","Smedley D, Oellrich A, KÃ¶hler S, Ruef B, Sanger Mouse Genetics Project, Westerfield M, Robinson P, Lewis S, Mungall C.","Database (Oxford)","2013","1758-0463","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","9","Y","Y","N","N","N","279.52853",NA,"2013","bat025","PMC3649640",NA,NA,"code.google.com"
"515","23807872","MED","23807872","10.3233/sw-2012-0057","WebProtÃ©gÃ©: A Collaborative Ontology Editor and Knowledge Acquisition Tool for the Web.","Tudorache T, Nyulas C, Noy NF, Musen MA.","Semant Web","2013","1570-0844","journal article; research-article","N","Y","Y","3","Y","Y","N","N","N","279.52853","1","4","89-99","PMC3691821",NA,NA,"code.google.com"
"516","23663384","MED","23663384","10.1186/1471-2164-14-320","Sequencing platform and library preparation choices impact viral metagenomes.","Solonenko SA, Ignacio-Espinoza JC, Alberti A, Cruaud C, Hallam S, Konstantinidis K, Tyson G, Wincker P, Sullivan MB.","BMC Genomics","2013","1471-2164","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","11","Y","Y","N","N","N","279.52853",NA,"14","320","PMC3655917",NA,NA,"code.google.com"
"517","24450540","MED","24450540","10.1186/2049-2618-1-12","Comparative meta-RNA-seq of the vaginal microbiota and differential expression by Lactobacillus iners in health and dysbiosis.","Macklaim JM, Fernandes AD, Di Bella JM, Hammond JA, Reid G, Gloor GB.","Microbiome","2013","2049-2618","journal article; research-article","Y","Y","Y","10","Y","Y","N","N","N","279.52853","1","1","12","PMC3971606",NA,NA,"code.google.com"
"518","23468974","MED","23468974","10.1371/journal.pone.0057355","The Pacific Ocean virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology.","Hurwitz BL, Sullivan MB.","PLoS One","2013","1932-6203","journal article; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","21","Y","Y","N","N","N","279.52853","2","8","e57355","PMC3585363",NA,NA,"code.google.com"
"519","24315375","MED","24315375","10.1016/j.cmet.2013.11.013","SIRT5 regulates the mitochondrial lysine succinylome and metabolic networks.","Rardin MJ, He W, Nishida Y, Newman JC, Carrico C, Danielson SR, Guo A, Gut P, Sahu AK, Li B, Uppala R, Fitch M, Riiff T, Zhu L, Zhou J, Mulhern D, Stevens RD, Ilkayeva OR, Newgard CB, Jacobson MP, Hellerstein M, Goetzman ES, Gibson BW, Verdin E.","Cell Metab","2013","1550-4131","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","N","11","Y","Y","Y","N","N","279.52853","6","18","920-933","PMC4105152",NA,"UNIPROT","code.google.com"
"520","23535733","MED","23535733","10.1038/ng.2561","Genome-wide association studies identify four ER negative-specific breast cancer risk loci.","Garcia-Closas M, Couch FJ, Lindstrom S, Michailidou K, Schmidt MK, Brook MN, Orr N, Rhie SK, Riboli E, Feigelson HS, Le Marchand L, Buring JE, Eccles D, Miron P, Fasching PA, Brauch H, Chang-Claude J, Carpenter J, Godwin AK, Nevanlinna H, Giles GG, Cox A, Hopper JL, Bolla MK, Wang Q, Dennis J, Dicks E, Howat WJ, Schoof N, Bojesen SE, Lambrechts D, Broeks A, Andrulis IL, GuÃ©nel P, Burwinkel B, Sawyer EJ, Hollestelle A, Fletcher O, Winqvist R, Brenner H, Mannermaa A, Hamann U, Meindl A, Lindblom A, Zheng W, Devillee P, Goldberg MS, Lubinski J, Kristensen V, Swerdlow A, Anton-Culver H, DÃ¶rk T, Muir K, Matsuo K, Wu AH, Radice P, Teo SH, Shu XO, Blot W, Kang D, Hartman M, Sangrajrang S, Shen CY, Southey MC, Park DJ, Hammet F, Stone J, Veer LJ, Rutgers EJ, Lophatananon A, Stewart-Brown S, Siriwanarangsan P, Peto J, Schrauder MG, Ekici AB, Beckmann MW, Dos Santos Silva I, Johnson N, Warren H, Tomlinson I, Kerin MJ, Miller N, Marme F, Schneeweiss A, Sohn C, Truong T, Laurent-Puig P, Kerbrat P, Nordestgaard BG, Nielsen SF, Flyger H, Milne RL, Perez JI, MenÃ©ndez P, MÃ¼ller H, Arndt V, Stegmaier C, Lichtner P, Lochmann M, Justenhoven C, Ko YD, Gene ENvironmental Interaction and breast CAncer (GENICA) Network, Muranen TA, AittomÃ¤ki K, Blomqvist C, Greco D, Heikkinen T, Ito H, Iwata H, Yatabe Y, Antonenkova NN, Margolin S, Kataja V, Kosma VM, Hartikainen JM, Balleine R, kConFab Investigators, Tseng CC, Berg DV, Stram DO, Neven P, DieudonnÃ© AS, Leunen K, Rudolph A, Nickels S, Flesch-Janys D, Peterlongo P, Peissel B, Bernard L, Olson JE, Wang X, Stevens K, Severi G, Baglietto L, McLean C, Coetzee GA, Feng Y, Henderson BE, Schumacher F, Bogdanova NV, LabrÃ¨che F, Dumont M, Yip CH, Taib NA, Cheng CY, Shrubsole M, Long J, PylkÃ¤s K, Jukkola-Vuorinen A, Kauppila S, Knight JA, Glendon G, Mulligan AM, Tollenaar RA, Seynaeve CM, Kriege M, Hooning MJ, van den Ouweland AM, van Deurzen CH, Lu W, Gao YT, Cai H, Balasubramanian SP, Cross SS, Reed MW, Signorello L, Cai Q, Shah M, Miao H, Chan CW, Chia KS, Jakubowska A, Jaworska K, Durda K, Hsiung CN, Wu PE, Yu JC, Ashworth A, Jones M, Tessier DC, GonzÃ¡lez-Neira A, Pita G, Alonso MR, Vincent D, Bacot F, Ambrosone CB, Bandera EV, John EM, Chen GK, Hu JJ, Rodriguez-Gil JL, Bernstein L, Press MF, Ziegler RG, Millikan RM, Deming-Halverson SL, Nyante S, Ingles SA, Waisfisz Q, Tsimiklis H, Makalic E, Schmidt D, Bui M, Gibson L, MÃ¼ller-Myhsok B, Schmutzler RK, Hein R, Dahmen N, Beckmann L, Aaltonen K, Czene K, Irwanto A, Liu J, Turnbull C, Familial Breast Cancer Study (FBCS), Rahman N, Meijers-Heijboer H, Uitterlinden AG, Rivadeneira F, Australian Breast Cancer Tissue Bank (ABCTB) Investigators, Olswold C, Slager S, Pilarski R, Ademuyiwa F, Konstantopoulou I, Martin NG, Montgomery GW, Slamon DJ, Rauh C, Lux MP, Jud SM, Bruning T, Weaver J, Sharma P, Pathak H, Tapper W, Gerty S, Durcan L, Trichopoulos D, Tumino R, Peeters PH, Kaaks R, Campa D, Canzian F, Weiderpass E, Johansson M, Khaw KT, Travis R, Clavel-Chapelon F, Kolonel LN, Chen C, Beck A, Hankinson SE, Berg CD, Hoover RN, Lissowska J, Figueroa JD, Chasman DI, Gaudet MM, Diver WR, Willett WC, Hunter DJ, Simard J, Benitez J, Dunning AM, Sherman ME, Chenevix-Trench G, Chanock SJ, Hall P, Pharoah PD, Vachon C, Easton DF, Haiman CA, Kraft P.","Nat Genet","2013","1061-4036","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","50","Y","Y","N","Y","Y","279.52853","4","45","392-8, 398e1-2","PMC3771695","refsnp",NA,"code.google.com"
"521","24138933","MED","24138933","10.1186/2041-1480-4-30","The Drosophila phenotype ontology.","Osumi-Sutherland D, Marygold SJ, Millburn GH, McQuilton PA, Ponting L, Stefancsik R, Falls K, Brown NH, Gkoutos GV.","J Biomed Semantics","2013","2041-1480","journal article; research-article","Y","Y","Y","2","Y","Y","N","Y","N","279.52853","1","4","30","PMC3816596",NA,NA,"code.google.com"
"522","23626672","MED","23626672","10.1371/journal.pone.0060847","Systematic analysis of experimental phenotype data reveals gene functions.","Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV.","PLoS One","2013","1932-6203","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","3","Y","Y","N","Y","N","279.52853","4","8","e60847","PMC3628905",NA,NA,"code.google.com"
"523","23998490","MED","23998490","10.1111/tpj.12319","Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ).","Mascher M, Muehlbauer GJ, Rokhsar DS, Chapman J, Schmutz J, Barry K, MuÃ±oz-AmatriaÃn M, Close TJ, Wise RP, Schulman AH, Himmelbach A, Mayer KF, Scholz U, Poland JA, Stein N, Waugh R.","Plant J","2013","0960-7412","journal article; validation studies; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","N","12","Y","Y","N","N","N","279.52853","4","76","718-727","PMC4298792",NA,NA,"code.google.com"
"524","23525074","MED","23525074","10.1038/ng.2585","Genomics of Loa loa, a Wolbachia-free filarial parasite of humans.","Desjardins CA, Cerqueira GC, Goldberg JM, Dunning Hotopp JC, Haas BJ, Zucker J, Ribeiro JM, Saif S, Levin JZ, Fan L, Zeng Q, Russ C, Wortman JR, Fink DL, Birren BW, Nutman TB.","Nat Genet","2013","1061-4036","journal article; research support, n.i.h., extramural; research support, n.i.h., intramural; research-article","Y","Y","N","26","Y","Y","Y","N","N","279.52853","5","45","495-500","PMC4238225",NA,"EMBL","code.google.com"
"525","23331995","MED","23331995","10.1186/1471-2164-14-41","De novo transcriptome characterization of Vitis vinifera cv. Corvina unveils varietal diversity.","Venturini L, Ferrarini A, Zenoni S, Tornielli GB, Fasoli M, Dal Santo S, Minio A, Buson G, Tononi P, Zago ED, Zamperin G, Bellin D, Pezzotti M, Delledonne M.","BMC Genomics","2013","1471-2164","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","9","Y","Y","Y","N","N","279.52853",NA,"14","41","PMC3556335",NA,"EMBL","code.google.com"
"526","24090403","MED","24090403","10.1186/1471-2164-14-675","Efficient and accurate whole genome assembly and methylome profiling of E. coli.","Powers JG, Weigman VJ, Shu J, Pufky JM, Cox D, Hurban P.","BMC Genomics","2013","1471-2164","journal article; research-article","Y","Y","Y","4","Y","Y","N","N","Y","279.38196","1","14","675","PMC4046830","gen",NA,"code.google.com"
"527","23547856","MED","23547856","10.1186/1471-2164-14-212","Species and condition specific adaptation of the transcriptional landscapes in Candida albicans and Candida dubliniensis.","Grumaz C, Lorenz S, Stevens P, Lindemann E, SchÃ¶ck U, Retey J, Rupp S, Sohn K.","BMC Genomics","2013","1471-2164","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","Y","N","N","279.38196",NA,"14","212","PMC3626586",NA,"ARXPR","code.google.com"
"528","23935467","MED","23935467","10.1371/journal.pcbi.1003126","Reconstruction and validation of a genome-scale metabolic model for the filamentous fungus Neurospora crassa using FARM.","Dreyfuss JM, Zucker JD, Hood HM, Ocasio LR, Sachs MS, Galagan JE.","PLoS Comput Biol","2013","1553-734x","journal article; validation studies; research support, n.i.h., extramural; research-article","Y","Y","Y","3","Y","Y","N","N","N","279.38196","7","9","e1003126","PMC3730674",NA,NA,"code.google.com"
"529","23220694","MED","23220694","10.1093/pcp/pcs163","The plant ontology as a tool for comparative plant anatomy and genomic analyses.","Cooper L, Walls RL, Elser J, Gandolfo MA, Stevenson DW, Smith B, Preece J, Athreya B, Mungall CJ, Rensing S, Hiss M, Lang D, Reski R, Berardini TZ, Li D, Huala E, Schaeffer M, Menda N, Arnaud E, Shrestha R, Yamazaki Y, Jaiswal P.","Plant Cell Physiol","2013","0032-0781","journal article; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","14","Y","Y","Y","N","N","279.38196","2","54","e1","PMC3583023",NA,"UNIPROT","code.google.com"
"530","24086243","MED","24086243","10.1371/journal.pone.0069446","Embedding and publishing interactive, 3-dimensional, scientific figures in Portable Document Format (PDF) files.","Barnes DG, Vidiassov M, Ruthensteiner B, Fluke CJ, Quayle MR, McHenry CR.","PLoS One","2013","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","N","N","N","279.38193","9","8","e69446","PMC3783416",NA,NA,"code.google.com"
"531","23935484","MED","23935484","10.1371/journal.ppat.1003503","Genomic analysis of the Kiwifruit pathogen Pseudomonas syringae pv. actinidiae provides insight into the origins of an emergent plant disease.","McCann HC, Rikkerink EH, Bertels F, Fiers M, Lu A, Rees-George J, Andersen MT, Gleave AP, Haubold B, Wohlers MW, Guttman DS, Wang PW, Straub C, Vanneste JL, Rainey PB, Templeton MD.","PLoS Pathog","2013","1553-7366","journal article; research support, non-u.s. gov't; comparative study; research-article","Y","Y","Y","9","Y","Y","Y","N","N","279.38193","7","9","e1003503","PMC3723570",NA,"EMBLUNIPROT","code.google.com"
"532","24067240","MED","24067240","10.1093/database/bat066","Capturing cooperative interactions with the PSI-MI format.","Van Roey K, Orchard S, Kerrien S, Dumousseau M, Ricard-Blum S, Hermjakob H, Gibson TJ.","Database (Oxford)","2013","1758-0463","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","N","N","Y","279.1014",NA,"2013","bat066","PMC3782717","pdb",NA,"code.google.com"
"533","24073207","MED","24073207","10.1371/journal.pone.0074304","Metaphor interpretation using paraphrases extracted from the web.","Bollegala D, Shutova E.","PLoS One","2013","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","N","Y","N","N","N","279.1014","9","8","e74304","PMC3779216",NA,NA,"code.google.com"
"534","24224019","MED","24224019","10.1371/journal.pone.0079909","Genome-wide identification of regulatory elements and reconstruction of gene regulatory networks of the green alga Chlamydomonas reinhardtii under carbon deprivation.","Winck FV, Arvidsson S, RiaÃ±o-PachÃ³n DM, Hempel S, Koseska A, Nikoloski Z, Urbina Gomez DA, Rupprecht J, Mueller-Roeber B.","PLoS One","2013","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","279.1014","11","8","e79909","PMC3816576",NA,NA,"code.google.com"
"535","24263090","MED","24263090","10.1038/nprot.2013.150","Target analysis by integration of transcriptome and ChIP-seq data with BETA.","Wang S, Sun H, Ma J, Zang C, Wang C, Wang J, Tang Q, Meyer CA, Zhang Y, Liu XS.","Nat Protoc","2013","1754-2189","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","0","Y","Y","N","Y","N","279.1014","12","8","2502-2515","PMC4135175",NA,NA,"code.google.com"
"536","24303057","MED","24303057","10.1371/journal.pone.0081606","Transcriptional reprogramming of wheat and the hemibiotrophic pathogen Septoria tritici during two phases of the compatible interaction.","Yang F, Li W, JÃ¸rgensen HJ.","PLoS One","2013","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","N","N","N","279.1014","11","8","e81606","PMC3841193",NA,NA,"code.google.com"
"537","24266939","MED","24266939","10.1186/1471-2164-14-s4-s5","How reliable is the linear noise approximation of gene regulatory networks?","Thomas P, Matuschek H, Grima R.","BMC Genomics","2013","1471-2164","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","279.1014","Suppl 4","14 Suppl 4","s5","PMC3849541",NA,NA,"code.google.com"
"538","24349131","MED","24349131","10.1371/journal.pone.0081809","Next generation sequencing analysis of human platelet PolyA+ mRNAs and rRNA-depleted total RNA.","Kissopoulou A, Jonasson J, Lindahl TL, Osman A.","PLoS One","2013","1932-6203","journal article; research-article","Y","Y","Y","2","Y","Y","N","Y","N","279.1014","12","8","e81809","PMC3859545",NA,NA,"code.google.com"
"539","23187890","MED","23187890","10.1101/gr.142331.112","Genome-wide mapping of human DNA-replication origins: levels of transcription at ORC1 sites regulate origin selection and replication timing.","Dellino GI, Cittaro D, Piccioni R, Luzi L, Banfi S, Segalla S, Cesaroni M, Mendoza-Maldonado R, Giacca M, Pelicci PG.","Genome Res","2013","1088-9051","journal article; research support, non-u.s. gov't; research-article","N","Y","Y","18","Y","Y","Y","N","N","279.1014","1","23","1-11","PMC3530669",NA,"UNIPROTARXPR","code.google.com"
"540","23193179","MED","23193179","10.1101/gr.142067.112","DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing.","Chen K, Xi Y, Pan X, Li Z, Kaestner K, Tyler J, Dent S, He X, Li W.","Genome Res","2013","1088-9051","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","11","Y","Y","N","N","N","279.1014","2","23","341-351","PMC3561875",NA,NA,"code.google.com"
"541","23518479","MED","23518479","10.1111/rssc.12001","A model-based framework for air quality indices and population risk evaluation, with an application to the analysis of Scottish air quality data.","Finazzi F, Scott EM, FassÃ² A.","J R Stat Soc Ser C Appl Stat","2013","0035-9254","journal article; research-article","Y","Y","Y","0","N","Y","N","N","N","279.1014","2","62","287-308","PMC3600869",NA,NA,"code.google.com"
"542","23578051","MED","23578051","10.1186/1478-811x-11-24","Light microscopy applications in systems biology: opportunities and challenges.","Antony PM, Trefois C, Stojanovic A, Baumuratov AS, Kozak K.","Cell Commun Signal","2013","1478-811x","journal article; review-article","Y","Y","Y","1","Y","Y","N","N","N","279.1014","1","11","24","PMC3627909",NA,NA,"code.google.com"
"543","23678114","MED","23678114","10.1523/jneurosci.5565-12.2013","Strengthened effective connectivity underlies transfer of working memory training to tests of short-term memory and attention.","Kundu B, Sutterer DW, Emrich SM, Postle BR.","J Neurosci","2013","0270-6474","journal article; research support, n.i.h., extramural; research-article","N","Y","Y","15","Y","Y","N","N","N","279.1014","20","33","8705-8715","PMC3758887",NA,NA,"code.google.com"
"544","23552814","MED","23552814","10.4161/viru.24041","Mathematical modeling of infectious disease dynamics.","Siettos CI, Russo L.","Virulence","2013","2150-5594","journal article; review; review-article","Y","Y","Y","0","Y","Y","N","N","N","279.1014","4","4","295-306","PMC3710332",NA,NA,"code.google.com"
"545","23505522","MED","23505522","10.1371/journal.pone.0058505","PSimScan: algorithm and utility for fast protein similarity search.","Kaznadzey A, Alexandrova N, Novichkov V, Kaznadzey D.","PLoS One","2013","1932-6203","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","279.1014","3","8","e58505","PMC3591303",NA,NA,"code.google.com"
"546","23509072","MED","23509072","10.1083/jcb.201301120","A novel single-cell screening platform reveals proteome plasticity during yeast stress responses.","Breker M, Gymrek M, Schuldiner M.","J Cell Biol","2013","0021-9525","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","14","Y","Y","Y","N","N","279.1014","6","200","839-850","PMC3601363",NA,"UNIPROT","code.google.com"
"547","23516585","MED","23516585","10.1371/journal.pone.0058950","Phylogenetic affiliation of SSU rRNA genes generated by massively parallel sequencing: new insights into the freshwater protist diversity.","Taib N, Mangot JF, Domaizon I, Bronner G, Debroas D.","PLoS One","2013","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","3","Y","Y","N","Y","N","279.1014","3","8","e58950","PMC3597552",NA,NA,"code.google.com"
"548","23520388","MED","23520388","10.1101/gr.146886.112","Widespread and extensive lengthening of 3' UTRs in the mammalian brain.","Miura P, Shenker S, Andreu-Agullo C, Westholm JO, Lai EC.","Genome Res","2013","1088-9051","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","24","Y","Y","N","N","N","279.1014","5","23","812-825","PMC3638137",NA,NA,"code.google.com"
"549","23555213","MED","23555213","10.1371/journal.pcbi.1002976","Automated analysis of a diverse synapse population.","Busse B, Smith S.","PLoS Comput Biol","2013","1553-734x","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","1","Y","Y","N","N","N","279.1014","3","9","e1002976","PMC3610606",NA,NA,"code.google.com"
"550","23550763","MED","23550763","10.1111/evo.12009","An evaluation of the hybrid speciation hypothesis for Xiphophorus clemenciae based on whole genome sequences.","Schumer M, Cui R, Boussau B, Walter R, Rosenthal G, Andolfatto P.","Evolution","2013","0014-3820","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research support, american recovery and reinvestment act; research-article","N","Y","Y","3","Y","Y","N","Y","Y","279.1014","4","67","1155-1168","PMC3621027","gen; doi",NA,"code.google.com"
"551","23597283","MED","23597283","10.1186/1751-0473-8-11","BioPatRec: A modular research platform for the control of artificial limbs based on pattern recognition algorithms.","Ortiz-Catalan M, BrÃ¥nemark R, HÃ¥kansson B.","Source Code Biol Med","2013","1751-0473","journal article; research-article","Y","Y","Y","2","Y","Y","N","N","N","279.1014","1","8","11","PMC3669028",NA,NA,"code.google.com"
"552","23646200","MED","23646200","10.1371/journal.pone.0063219","CNVrd, a read-depth algorithm for assigning copy-number at the FCGR locus: population-specific tagging of copy number variation at FCGR3B.","tan Nguyen H, Merriman TR, Black MA.","PLoS One","2013","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","Y","279.1014","4","8","e63219","PMC3640002","refsnp",NA,"code.google.com"
"553","23658738","MED","23658738","10.1371/journal.pone.0062522","Estrogen-dependent dynamic profile of eNOS-DNA associations in prostate cancer.","Nanni S, Aiello A, Re A, Guffanti A, Benvenuti V, Colussi C, Castro-Vega LJ, Felsani A, Londono-Vallejo A, Capogrossi MC, Bacchetti S, Gaetano C, Pontecorvi A, Farsetti A.","PLoS One","2013","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","Y","N","Y","279.1014","5","8","e62522","PMC3643940","arrayexpress","ARXPR","code.google.com"
"554","23736102","MED","23736102","10.1093/sysbio/syt040","Bayesian analysis of biogeography when the number of areas is large.","Landis MJ, Matzke NJ, Moore BR, Huelsenbeck JP.","Syst Biol","2013","1063-5157","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","N","5","Y","Y","N","Y","Y","279.1014","6","62","789-804","PMC4064008","doi",NA,"code.google.com"
"555","23307945","MED","23307945","10.1194/jlr.m031195","Structural and functional analysis of APOA5 mutations identified in patients with severe hypertriglyceridemia.","Mendoza-BarberÃ¡ E, Julve J, Nilsson SK, Lookene A, MartÃn-Campos JM, Roig R, Lechuga-Sancho AM, Sloan JH, Fuentes-Prior P, Blanco-Vaca F.","J Lipid Res","2013","0022-2275","journal article; research support, non-u.s. gov't; research-article","N","Y","Y","3","Y","Y","Y","N","Y","279.1014","3","54","649-661","PMC3617940","refsnp","UNIPROT","code.google.com"
"556","23349711","MED","23349711","10.1371/journal.pone.0053437","Solving hard computational problems efficiently: asymptotic parametric complexity 3-coloring algorithm.","MartÃn H JA.","PLoS One","2013","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","279.1014","1","8","e53437","PMC3544923",NA,NA,"code.google.com"
"557","23362319","MED","23362319","10.1128/mbio.00524-12","Quantifying pathogen surveillance using temporal genomic data.","Chan JM, Rabadan R.","MBio","2013","2150-7511","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","1","Y","Y","N","N","N","279.1014","1","4","e00524-12","PMC3560527",NA,NA,"code.google.com"
"558","23427646","MED","23427646","10.1603/me12169","Ontology for vector surveillance and management.","Lozano-Fuentes S, Bandyopadhyay A, Cowell LG, Goldfain A, Eisen L.","J Med Entomol","2013","0022-2585","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","2","Y","Y","N","N","N","279.1014","1","50","1-14","PMC3695545",NA,NA,"code.google.com"
"559","23441908","MED","23441908","10.1186/1471-2105-14-67","A hybrid short read mapping accelerator.","Chen Y, Schmidt B, Maskell DL.","BMC Bioinformatics","2013","1471-2105","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","279.1014",NA,"14","67","PMC3598928",NA,NA,"code.google.com"
"560","23447050","MED","23447050","10.1039/c3np20111b","A global approach to analysis and interpretation of metabolic data for plant natural product discovery.","Hur M, Campbell AA, Almeida-de-Macedo M, Li L, Ransom N, Jose A, Crispin M, Nikolau BJ, Wurtele ES.","Nat Prod Rep","2013","0265-0568","journal article; review; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","Y","12","Y","Y","N","N","N","279.1014","4","30","565-583","PMC3629923",NA,NA,"code.google.com"
"561","23453054","MED","23453054","10.1186/1752-0509-7-18","BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats.","Bonnet E, Calzone L, Rovera D, Stoll G, Barillot E, Zinovyev A.","BMC Syst Biol","2013","1752-0509","journal article; research support, non-u.s. gov't; product-review","Y","Y","Y","3","Y","Y","N","Y","N","279.1014",NA,"7","18","PMC3646686",NA,NA,"code.google.com"
"562","23124522","MED","23124522","10.1101/gr.141952.112","Stabilization of the promoter nucleosomes in nucleosome-free regions by the yeast Cyc8-Tup1 corepressor.","Chen K, Wilson MA, Hirsch C, Watson A, Liang S, Lu Y, Li W, Dent SY.","Genome Res","2013","1088-9051","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","3","Y","Y","Y","N","N","279.1014","2","23","312-322","PMC3561872",NA,"UNIPROT","code.google.com"
"563","23819467","MED","23819467","10.1186/1755-8794-6-s2-s6","BioBin: a bioinformatics tool for automating the binning of rare variants using publicly available biological knowledge.","Moore CB, Wallace JR, Frase AT, Pendergrass SA, Ritchie MD.","BMC Med Genomics","2013","1755-8794","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","2","Y","Y","N","N","Y","279.1014","Suppl 2","6 Suppl 2","s6","PMC3654874","omim",NA,"code.google.com"
"564","23874343","MED","23874343","10.3389/fpls.2013.00170","Automated conserved non-coding sequence (CNS) discovery reveals differences in gene content and promoter evolution among grasses.","Turco G, Schnable JC, Pedersen B, Freeling M.","Front Plant Sci","2013","1664-462x","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","279.1014",NA,"4","170","PMC3708275",NA,NA,"code.google.com"
"565","23925128","MED","23925128","10.1093/nar/gkt698","Direct assessment of transcription fidelity by high-resolution RNA sequencing.","Imashimizu M, Oshima T, Lubkowska L, Kashlev M.","Nucleic Acids Res","2013","0305-1048","journal article; research support, non-u.s. gov't; research support, n.i.h., intramural; research-article","Y","Y","Y","3","Y","Y","Y","N","N","279.1014","19","41","9090-9104","PMC3799451",NA,"ARXPR","code.google.com"
"566","23943281","MED","23943281","10.1007/s12021-013-9199-9","3D brain atlas reconstructor service--online repository of three-dimensional models of brain structures.","Majka P, Kowalski JM, Chlodzinska N, WÃ³jcik DK.","Neuroinformatics","2013","1539-2791","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","279.1014","4","11","507-518","PMC3824210",NA,NA,"code.google.com"
"567","23967161","MED","23967161","10.1371/journal.pone.0071152","Identification and characterization of long non-coding RNAs related to mouse embryonic brain development from available transcriptomic data.","Lv J, Cui W, Liu H, He H, Xiu Y, Guo J, Liu H, Liu Q, Zeng T, Chen Y, Zhang Y, Wu Q.","PLoS One","2013","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","3","Y","Y","N","N","N","279.1014","8","8","e71152","PMC3743905",NA,NA,"code.google.com"
"568","23233462","MED","23233462","10.1093/molbev/mss258","Bayesian selection of nucleotide substitution models and their site assignments.","Wu CH, Suchard MA, Drummond AJ.","Mol Biol Evol","2013","0737-4038","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","10","Y","Y","N","N","N","279.1014","3","30","669-688","PMC3563969",NA,NA,"code.google.com"
"569","23382430","MED","23382430","10.1098/rstb.2012.0208","Modelling tree shape and structure in viral phylodynamics.","Frost SD, Volz EM.","Philos Trans R Soc Lond B Biol Sci","2013","0962-8436","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","7","Y","Y","N","N","N","279.1014","1614","368","20120208","PMC3678332",NA,NA,"code.google.com"
"570","23632988","MED","23632988","10.1007/s00424-013-1286-0","Regulation of ClC-2 gating by intracellular ATP.","StÃ¶lting G, Teodorescu G, Begemann B, Schubert J, Nabbout R, Toliat MR, Sander T, NÃ¼rnberg P, Lerche H, Fahlke C.","Pflugers Arch","2013","0031-6768","journal article; research-article","Y","Y","Y","2","Y","Y","N","N","N","279.1014","10","465","1423-1437","PMC3778897",NA,NA,"code.google.com"
"571","23653593","MED","23653593","10.3389/fncir.2013.00069","MANTA--an open-source, high density electrophysiology recording suite for MATLAB.","Englitz B, David SV, Sorenson MD, Shamma SA.","Front Neural Circuits","2013","1662-5110","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","3","Y","Y","N","N","N","279.1014",NA,"7","69","PMC3644699",NA,NA,"code.google.com"
"572","23625862","MED","23625862","10.1002/sim.5817","Large-scale parametric survival analysis.","Mittal S, Madigan D, Cheng JQ, Burd RS.","Stat Med","2013","0277-6715","journal article; research support, n.i.h., extramural; research-article","N","Y","N","0","Y","Y","N","N","N","279.1014","23","32","3955-3971","PMC3796130",NA,NA,"code.google.com"
"573","24278038","MED","24278038","10.1371/journal.pgen.1003972","Whole genome, whole population sequencing reveals that loss of signaling networks is the major adaptive strategy in a constant environment.","Kvitek DJ, Sherlock G.","PLoS Genet","2013","1553-7390","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","3","Y","Y","N","N","N","279.1014","11","9","e1003972","PMC3836717",NA,NA,"code.google.com"
"574","22875861","MED","22875861","10.1093/cercor/bhs227","The development of hub architecture in the human functional brain network.","Hwang K, Hallquist MN, Luna B.","Cereb Cortex","2013","1047-3211","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","N","12","Y","Y","N","N","N","279.1014","10","23","2380-2393","PMC3767958",NA,NA,"code.google.com"
"575","24349502","MED","24349502","10.1371/journal.pone.0083383","New rRNA gene-based phylogenies of the Alphaproteobacteria provide perspective on major groups, mitochondrial ancestry and phylogenetic instability.","Ferla MP, Thrash JC, Giovannoni SJ, Patrick WM.","PLoS One","2013","1932-6203","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","4","Y","Y","N","N","N","279.1014","12","8","e83383","PMC3859672",NA,NA,"code.google.com"
"576","23497037","MED","23497037","10.1186/1471-2164-14-148","Dissecting structural and nucleotide genome-wide variation in inbred Iberian pigs.","Esteve-Codina A, Paudel Y, Ferretti L, Raineri E, Megens HJ, SiliÃ³ L, RodrÃguez MC, Groenen MA, Ramos-Onsins SE, PÃ©rez-Enciso M.","BMC Genomics","2013","1471-2164","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","6","Y","Y","N","N","N","279.1014",NA,"14","148","PMC3601988",NA,NA,"code.google.com"
"577","23819870","MED","23819870","10.1186/1471-2164-14-s3-s3","Identifying Mendelian disease genes with the variant effect scoring tool.","Carter H, Douville C, Stenson PD, Cooper DN, Karchin R.","BMC Genomics","2013","1471-2164","evaluation studies; journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; comparative study; research-article","Y","Y","Y","7","Y","Y","N","N","N","279.1014","Suppl 3","14 Suppl 3","s3","PMC3665549",NA,NA,"code.google.com"
"578","23404334","MED","23404334","10.1093/brain/awt010","Congenital myasthenic syndromes due to mutations in ALG2 and ALG14.","Cossins J, Belaya K, Hicks D, Salih MA, Finlayson S, Carboni N, Liu WW, Maxwell S, Zoltowska K, Farsani GT, Laval S, Seidhamed MZ, WGS500 Consortium, Donnelly P, Bentley D, McGowan SJ, MÃ¼ller J, Palace J, LochmÃ¼ller H, Beeson D.","Brain","2013","0006-8950","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","8","Y","Y","Y","N","Y","279.1014","pt 3","136","944-956","PMC3580273","omim; refseq","UNIPROT","code.google.com"
"579","24107992","MED","24107992","10.1038/nature12598","DNMT1-interacting RNAs block gene-specific DNA methylation.","Di Ruscio A, Ebralidze AK, Benoukraf T, Amabile G, Goff LA, Terragni J, Figueroa ME, De Figueiredo Pontes LL, Alberich-Jorda M, Zhang P, Wu M, D'AlÃ² F, Melnick A, Leone G, Ebralidze KK, Pradhan S, Rinn JL, Tenen DG.","Nature","2013","0028-0836","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","28","Y","Y","Y","N","N","279.1014","7476","503","371-376","PMC3870304",NA,"OMIMUNIPROT","code.google.com"
"580","23382690","MED","23382690","10.1371/journal.pgen.1003219","Unlocking the bottleneck in forward genetics using whole-genome sequencing and identity by descent to isolate causative mutations.","Bull KR, Rimmer AJ, Siggs OM, Miosge LA, Roots CM, Enders A, Bertram EM, Crockford TL, Whittle B, Potter PK, Simon MM, Mallon AM, Brown SD, Beutler B, Goodnow CC, Lunter G, Cornall RJ.","PLoS Genet","2013","1553-7390","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","7","Y","Y","Y","N","N","279.1014","1","9","e1003219","PMC3561070",NA,"UNIPROT","code.google.com"
"581","24058483","MED","24058483","10.1371/journal.pone.0073674","SNP discovery by illumina-based transcriptome sequencing of the olive and the genetic characterization of Turkish olive genotypes revealed by AFLP, SSR and SNP markers.","Kaya HB, Cetin O, Kaya H, Sahin M, Sefer F, Kahraman A, Tanyolac B.","PLoS One","2013","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","4","Y","Y","N","N","N","279.1014","9","8","e73674","PMC3772808",NA,NA,"code.google.com"
"582","24290377","MED","24290377","10.1016/j.ajhg.2013.11.005","Whole-exome sequencing of 2,000 Danish individuals and the role of rare coding variants in type 2 diabetes.","Lohmueller KE, SparsÃ¸ T, Li Q, Andersson E, Korneliussen T, Albrechtsen A, Banasik K, Grarup N, Hallgrimsdottir I, Kiil K, KilpelÃ¤inen TO, Krarup NT, Pers TH, Sanchez G, Hu Y, Degiorgio M, JÃ¸rgensen T, SandbÃ¦k A, Lauritzen T, Brunak S, Kristiansen K, Li Y, Hansen T, Wang J, Nielsen R, Pedersen O.","Am J Hum Genet","2013","0002-9297","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","N","Y","Y","11","Y","Y","N","N","N","279.1014","6","93","1072-1086","PMC3852935",NA,NA,"code.google.com"
"583","24098590","MED","24098590","10.1371/journal.pone.0077594","Population differentiation and species formation in the deep sea: the potential role of environmental gradients and depth.","Jennings RM, Etter RJ, Ficarra L.","PLoS One","2013","1932-6203","journal article; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","0","Y","Y","Y","N","Y","279.1014","10","8","e77594","PMC3788136","gen","EMBLUNIPROT","code.google.com"
"584","24151245","MED","24151245","10.1152/physiolgenomics.00136.2013","Genome-wide analysis of the rat colon reveals proximal-distal differences in histone modifications and proto-oncogene expression.","Triff K, Konganti K, Gaddis S, Zhou B, Ivanov I, Chapkin RS.","Physiol Genomics","2013","1094-8341","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","N","1","Y","Y","N","N","N","279.10138","24","45","1229-1243","PMC3882682",NA,NA,"code.google.com"
"585","24066147","MED","24066147","10.1371/journal.pone.0074570","A novel electronic data collection system for large-scale surveys of neglected tropical diseases.","King JD, Buolamwini J, Cromwell EA, Panfel A, Teferi T, Zerihun M, Melak B, Watson J, Tadesse Z, Vienneau D, Ngondi J, Utzinger J, Odermatt P, Emerson PM.","PLoS One","2013","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","4","Y","Y","N","N","N","279.10138","9","8","e74570","PMC3774718",NA,NA,"code.google.com"
"586","24106471","MED","24106471","10.3389/fnhum.2013.00633","Exploring the brains of Baduk (Go) experts: gray matter morphometry, resting-state functional connectivity, and graph theoretical analysis.","Jung WH, Kim SN, Lee TY, Jang JH, Choi CH, Kang DH, Kwon JS.","Front Hum Neurosci","2013","1662-5161","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","279.10138",NA,"7","633","PMC3788340",NA,NA,"code.google.com"
"587","24260313","MED","24260313","10.1371/journal.pone.0079871","Compression of structured high-throughput sequencing data.","Campagne F, Dorff KC, Chambwe N, Robinson JT, Mesirov JP.","PLoS One","2013","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","279.10138","11","8","e79871","PMC3832420",NA,NA,"code.google.com"
"588","23390601","MED","23390601","10.1534/g3.112.005314","Origin and evolution of dishevelled.","Dillman AR, Minor PJ, Sternberg PW.","G3 (Bethesda)","2013","2160-1836","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","4","Y","Y","N","Y","N","279.10138","2","3","251-262","PMC3564985",NA,NA,"code.google.com"
"589","24532991","MED","24532991","10.1021/cg3016029","Real-Time Protein Crystallization Image Acquisition and Classification System.","Sigdel M, Pusey ML, Aygun RS.","Cryst Growth Des","2013","1528-7483","journal article; research-article","N","Y","Y","0","Y","Y","N","N","N","279.10138","7","13","2728-2736","PMC3921687",NA,NA,"code.google.com"
"590","24660019","MED","24660019","10.1088/1742-5468/2013/01/p01010","Mathematical modeling of escape of HIV from cytotoxic T lymphocyte responses.","Ganusov VV, Neher RA, Perelson AS.","J Stat Mech","2013","1742-5468","journal article; research-article","N","Y","Y","3","Y","Y","N","N","N","279.10138",NA,"2013","p01010","PMC3961578",NA,NA,"code.google.com"
"591","23874469","MED","23874469","10.1371/journal.pone.0067932","Activating and relaxing music entrains the speed of beat synchronized walking.","Leman M, Moelants D, Varewyck M, Styns F, van Noorden L, Martens JP.","PLoS One","2013","1932-6203","journal article; randomized controlled trial; research support, non-u.s. gov't; research-article","Y","Y","Y","8","Y","Y","N","N","N","279.10138","7","8","e67932","PMC3707869",NA,NA,"code.google.com"
"592","23433509","MED","23433509","10.1186/1752-0509-7-15","Precise generation of systems biology models from KEGG pathways.","Wrzodek C, BÃ¼chel F, Ruff M, DrÃ¤ger A, Zell A.","BMC Syst Biol","2013","1752-0509","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","10","Y","Y","N","N","N","279.10138",NA,"7","15","PMC3623889",NA,NA,"code.google.com"
"593","24373163","MED","24373163","10.1186/1471-2229-13-228","Comparative analyses of two Geraniaceae transcriptomes using next-generation sequencing.","Zhang J, Ruhlman TA, Mower JP, Jansen RK.","BMC Plant Biol","2013","1471-2229","journal article; research support, u.s. gov't, non-p.h.s.; comparative study; research-article","Y","Y","Y","2","Y","Y","N","N","N","279.10138",NA,"13","228","PMC3880972",NA,NA,"code.google.com"
"594","22965131","MED","22965131","10.1093/nar/gks836","From next-generation sequencing alignments to accurate comparison and validation of single-nucleotide variants: the pibase software.","Forster M, Forster P, Elsharawy A, Hemmrich G, Kreck B, Wittig M, Thomsen I, Stade B, Barann M, Ellinghaus D, Petersen BS, May S, Melum E, Schilhabel MB, Keller A, Schreiber S, Rosenstiel P, Franke A.","Nucleic Acids Res","2013","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","7","Y","Y","N","N","N","279.10138","1","41","e16","PMC3592472",NA,NA,"code.google.com"
"595","23467472","MED","23467472","10.1136/amiajnl-2012-001607","An end-to-end system to identify temporal relation in discharge summaries: 2012 i2b2 challenge.","Xu Y, Wang Y, Liu T, Tsujii J, Chang EI.","J Am Med Inform Assoc","2013","1067-5027","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","3","Y","Y","N","N","N","279.10138","5","20","849-858","PMC3756267",NA,NA,"code.google.com"
"596","23762400","MED","23762400","10.1371/journal.pone.0065598","diffReps: detecting differential chromatin modification sites from ChIP-seq data with biological replicates.","Shen L, Shao NY, Liu X, Maze I, Feng J, Nestler EJ.","PLoS One","2013","1932-6203","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","5","Y","Y","N","N","N","279.10138","6","8","e65598","PMC3677880",NA,NA,"code.google.com"
"597","22884549","MED","22884549","10.1016/j.neurobiolaging.2012.07.010","CREB-binding protein levels in the rat hippocampus fail to predict chronological or cognitive aging.","TomÃ¡s Pereira I, Coletta CE, Perez EV, Kim DH, Gallagher M, Goldberg IG, Rapp PR.","Neurobiol Aging","2013","0197-4580","journal article; research support, non-u.s. gov't; research support, n.i.h., intramural; research-article","N","Y","Y","1","Y","Y","Y","N","N","279.10138","3","34","832-844","PMC3518677",NA,"UNIPROT","code.google.com"
"598","23818839","MED","23818839","10.1371/journal.pcbi.1003100","Integrative analysis of deep sequencing data identifies estrogen receptor early response genes and links ATAD3B to poor survival in breast cancer.","Ovaska K, Matarese F, Grote K, Charapitsa I, Cervera A, Liu C, Reid G, Seifert M, Stunnenberg HG, Hautaniemi S.","PLoS Comput Biol","2013","1553-734x","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","279.10138","6","9","e1003100","PMC3688481",NA,NA,"code.google.com"
"599","23840385","MED","23840385","10.1371/journal.pone.0065986","Multicellular computing using conjugation for wiring.","GoÃ±i-Moreno A, Amos M, de la Cruz F.","PLoS One","2013","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","4","Y","Y","N","N","N","279.10138","6","8","e65986","PMC3688716",NA,NA,"code.google.com"
"600","23857470","MED","23857470","10.1007/s11103-013-0106-4","Diversity in the complexity of phosphate starvation transcriptomes among rice cultivars based on RNA-Seq profiles.","Oono Y, Kawahara Y, Yazawa T, Kanamori H, Kuramata M, Yamagata H, Hosokawa S, Minami H, Ishikawa S, Wu J, Antonio B, Handa H, Itoh T, Matsumoto T.","Plant Mol Biol","2013","0167-4412","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","N","N","N","279.10138","6","83","523-537","PMC3830200",NA,NA,"code.google.com"
"601","24204733","MED","24204733","10.1371/journal.pone.0077053","A high-content small molecule screen identifies sensitivity of glioblastoma stem cells to inhibition of polo-like kinase 1.","Danovi D, Folarin A, Gogolok S, Ender C, Elbatsh AM, EngstrÃ¶m PG, Stricker SH, Gagrica S, Georgian A, Yu D, U KP, Harvey KJ, Ferretti P, Paddison PJ, Preston JE, Abbott NJ, Bertone P, Smith A, Pollard SM.","PLoS One","2013","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","279.10138","10","8","e77053","PMC3813721",NA,NA,"code.google.com"
"602","24265601","MED","24265601","10.1371/journal.pmed.1001551","Role of DNA methylation and epigenetic silencing of HAND2 in endometrial cancer development.","Jones A, Teschendorff AE, Li Q, Hayward JD, Kannan A, Mould T, West J, Zikan M, Cibula D, Fiegl H, Lee SH, Wik E, Hadwin R, Arora R, Lemech C, Turunen H, Pakarinen P, Jacobs IJ, Salvesen HB, Bagchi MK, Bagchi IC, Widschwendter M.","PLoS Med","2013","1549-1277","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","1","Y","Y","Y","N","N","279.10138","11","10","e1001551","PMC3825654",NA,"UNIPROT","code.google.com"
"603","24009507","MED","24009507","10.1371/journal.ppat.1003579","Functional specialization of the small interfering RNA pathway in response to virus infection.","Marques JT, Wang JP, Wang X, de Oliveira KP, Gao C, Aguiar ER, Jafari N, Carthew RW.","PLoS Pathog","2013","1553-7366","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","3","Y","Y","Y","Y","N","279.10138","8","9","e1003579","PMC3757037",NA,"UNIPROT","code.google.com"
"604","23874174","MED","23874174","10.1371/journal.pcbi.1003130","Hierarchical modeling for rare event detection and cell subset alignment across flow cytometry samples.","Cron A, Gouttefangeas C, Frelinger J, Lin L, Singh SK, Britten CM, Welters MJ, van der Burg SH, West M, Chan C.","PLoS Comput Biol","2013","1553-734x","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","5","Y","Y","N","N","N","279.10138","7","9","e1003130","PMC3708855",NA,NA,"code.google.com"
"605","24109446","MED","24109446","10.3389/fnhum.2013.00623","Physiological noise in brainstem FMRI.","Brooks JC, Faull OK, Pattinson KT, Jenkinson M.","Front Hum Neurosci","2013","1662-5161","journal article; research-article","Y","Y","Y","3","Y","Y","N","N","N","279.10138",NA,"7","623","PMC3790256",NA,NA,"code.google.com"
"606","23206254","MED","23206254","10.1111/mec.12111","The influence of the arid Andean high plateau on the phylogeography and population genetics of guanaco (Lama guanicoe) in South America.","Marin JC, GonzÃ¡lez BA, Poulin E, Casey CS, Johnson WE.","Mol Ecol","2013","0962-1083","journal article; research support, non-u.s. gov't; research-article","N","Y","Y","2","Y","Y","Y","Y","Y","279.10138","2","22","463-482","PMC3549358","gen; doi","EMBL","code.google.com"
"607","23656624","MED","23656624","10.1186/1472-6947-13-57","Applying representational state transfer (REST) architecture to archetype-based electronic health record systems.","Sundvall E, NystrÃ¶m M, Karlsson D, Eneling M, Chen R, Ãrman H.","BMC Med Inform Decis Mak","2013","1472-6947","journal article; research support, non-u.s. gov't; product-review","Y","Y","Y","0","Y","Y","N","Y","N","279.07993",NA,"13","57","PMC3694512",NA,NA,"code.google.com"
"608","23499722","MED","23499722","10.1016/j.neuropsychologia.2013.02.017","Moderate levels of activation lead to forgetting in the think/no-think paradigm.","Detre GJ, Natarajan A, Gershman SJ, Norman KA.","Neuropsychologia","2013","0028-3932","journal article; research support, n.i.h., extramural; research-article","N","Y","N","7","Y","Y","N","N","N","279.07993","12","51","2371-2388","PMC3702674",NA,NA,"code.google.com"
"609","23741616","MED","23741616","10.7554/elife.00425","Decoding the neural mechanisms of human tool use.","Gallivan JP, McLean DA, Valyear KF, Culham JC.","Elife","2013","2050-084x","journal article; research-article","Y","Y","Y","8","Y","Y","N","N","N","278.67426",NA,"2","e00425","PMC3667577",NA,NA,"code.google.com"
"610","23577233","MED","23577233","10.7554/elife.00367","Improved use of a public good selects for the evolution of undifferentiated multicellularity.","Koschwanez JH, Foster KR, Murray AW.","Elife","2013","2050-084x","journal article; research-article","Y","Y","Y","7","Y","Y","Y","N","N","278.67426",NA,"2","e00367","PMC3614033",NA,"UNIPROT","code.google.com"
"611","24015111","MED","24015111","10.1371/journal.pbio.1001643","Comparative sex chromosome genomics in snakes: differentiation, evolutionary strata, and lack of global dosage compensation.","Vicoso B, Emerson JJ, Zektser Y, Mahajan S, Bachtrog D.","PLoS Biol","2013","1544-9173","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","16","Y","Y","N","N","N","278.67426","8","11","e1001643","PMC3754893",NA,NA,"code.google.com"
"612","23521852","MED","23521852","10.1186/1471-2164-14-202","The genome and transcriptome of perennial ryegrass mitochondria.","Islam MS, Studer B, Byrne SL, Farrell JD, Panitz F, Bendixen C, MÃ¸ller IM, Asp T.","BMC Genomics","2013","1471-2164","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","Y","N","Y","278.67426",NA,"14","202","PMC3664089","gen","EMBLUNIPROT","code.google.com"
"613","23587327","MED","23587327","10.1186/1752-0509-7-33","A metabolite-centric view on flux distributions in genome-scale metabolic models.","Riemer SA, Rex R, Schomburg D.","BMC Syst Biol","2013","1752-0509","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","278.67426",NA,"7","33","PMC3644240",NA,NA,"code.google.com"
"614","23593040","MED","23593040","10.1371/journal.pgen.1003460","Continent-wide decoupling of Y-chromosomal genetic variation from language and geography in native South Americans.","Roewer L, Nothnagel M, GusmÃ£o L, Gomes V, GonzÃ¡lez M, Corach D, Sala A, Alechine E, Palha T, Santos N, Ribeiro-Dos-Santos A, Geppert M, Willuweit S, Nagy M, Zweynert S, Baeta M, NÃºÃ±ez C, MartÃnez-Jarreta B, GonzÃ¡lez-Andrade F, Fagundes de Carvalho E, da Silva DA, Builes JJ, TurbÃ³n D, Lopez Parra AM, Arroyo-Pardo E, Toscanini U, Borjas L, Barletta C, Ewart E, Santos S, Krawczak M.","PLoS Genet","2013","1553-7390","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","4","Y","Y","N","N","N","278.67426","4","9","e1003460","PMC3623769",NA,NA,"code.google.com"
"615","23635285","MED","23635285","10.1118/1.4801895","Monte Carlo study of the effects of system geometry and antiscatter grids on cone-beam CT scatter distributions.","Sisniega A, Zbijewski W, Badal A, Kyprianou IS, Stayman JW, Vaquero JJ, Siewerdsen JH.","Med Phys","2013","0094-2405","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","5","Y","Y","N","N","N","278.67426","5","40","051915","PMC3651212",NA,NA,"code.google.com"
"616","23717278","MED","23717278","10.3389/fninf.2013.00007","A knowledge based approach to matching human neurodegenerative disease and animal models.","Maynard SM, Mungall CJ, Lewis SE, Imam FT, Martone ME.","Front Neuroinform","2013","1662-5196","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","278.67426",NA,"7","7","PMC3653101",NA,NA,"code.google.com"
"617","23717647","MED","23717647","10.1371/journal.pone.0064656","SEARCH: Spatially Explicit Animal Response to Composition of Habitat.","Pauli BP, McCann NP, Zollner PA, Cummings R, Gilbert JH, Gustafson EJ.","PLoS One","2013","1932-6203","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","0","Y","Y","N","N","N","278.67426","5","8","e64656","PMC3661500",NA,NA,"code.google.com"
"618","23398688","MED","23398688","10.1186/1471-2105-14-47","A survey of protein interaction data and multigenic inherited disorders.","Mora A, Michalickova K, Donaldson IM.","BMC Bioinformatics","2013","1471-2105","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","Y","278.67426",NA,"14","47","PMC3598893","omim",NA,"code.google.com"
"619","22875859","MED","22875859","10.1093/cercor/bhs229","Category-specific neural oscillations predict recall organization during memory search.","Morton NW, Kahana MJ, Rosenberg EA, Baltuch GH, Litt B, Sharan AD, Sperling MR, Polyn SM.","Cereb Cortex","2013","1047-3211","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","N","3","Y","Y","N","N","N","278.67426","10","23","2407-2422","PMC3767960",NA,NA,"code.google.com"
"620","23883524","MED","23883524","10.1093/molbev/mst129","Abundance and distribution of transposable elements in two Drosophila QTL mapping resources.","Cridland JM, Macdonald SJ, Long AD, Thornton KR.","Mol Biol Evol","2013","0737-4038","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","9","Y","Y","Y","Y","N","278.67426","10","30","2311-2327","PMC3773372",NA,"UNIPROT","code.google.com"
"621","23637635","MED","23637635","10.1371/journal.pgen.1003470","Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs.","Kapusta A, Kronenberg Z, Lynch VJ, Zhuo X, Ramsay L, Bourque G, Yandell M, Feschotte C.","PLoS Genet","2013","1553-7390","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","37","Y","Y","N","N","N","278.67426","4","9","e1003470","PMC3636048",NA,NA,"code.google.com"
"622","23410887","MED","23410887","10.1101/gr.143677.112","Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms.","Malhotra A, Lindberg M, Faust GG, Leibowitz ML, Clark RA, Layer RM, Quinlan AR, Hall IM.","Genome Res","2013","1088-9051","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","22","Y","Y","N","N","N","278.67426","5","23","762-776","PMC3638133",NA,NA,"code.google.com"
"623","23555231","MED","23555231","10.1371/journal.pcbi.1003000","Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.","FranzÃ©n O, JerlstrÃ¶m-Hultqvist J, Einarsson E, Ankarklev J, Ferella M, Andersson B, SvÃ¤rd SG.","PLoS Comput Biol","2013","1553-734x","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","5","Y","Y","N","N","N","278.67426","3","9","e1003000","PMC3610916",NA,NA,"code.google.com"
"624","23792673","MED","23792673","10.1152/ajpheart.00919.2012","Unchanged mitochondrial organization and compartmentation of high-energy phosphates in creatine-deficient GAMT-/- mouse hearts.","Branovets J, Sepp M, Kotlyarova S, Jepihhina N, Sokolova N, Aksentijevic D, Lygate CA, Neubauer S, Vendelin M, Birkedal R.","Am J Physiol Heart Circ Physiol","2013","0363-6135","journal article; research support, non-u.s. gov't; research-article","N","Y","Y","3","Y","Y","Y","N","N","278.67426","4","305","h506-20","PMC3891243",NA,"UNIPROT","code.google.com"
"625","23093607","MED","23093607","10.1093/nar/gks959","Chromatin acetylation at transcription start sites and vitamin D receptor binding regions relates to effects of 1Î±,25-dihydroxyvitamin D3 and histone deacetylase inhibitors on gene expression.","Seuter S, Heikkinen S, Carlberg C.","Nucleic Acids Res","2013","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","11","Y","Y","Y","N","N","278.67426","1","41","110-124","PMC3592476",NA,"ARXPR","code.google.com"
"626","23471366","MED","23471366","10.1016/j.jss.2012.09.037","A posteriori operation detection in evolving software models.","Langer P, Wimmer M, Brosch P, HerrmannsdÃ¶rfer M, Seidl M, Wieland K, Kappel G.","J Syst Softw","2013","0164-1212","journal article; research-article","Y","Y","Y","0","N","Y","N","N","N","278.67422","2","86","551-566","PMC3587339",NA,NA,"code.google.com"
"627","23843979","MED","23843979","10.1371/journal.pone.0067019","ANOVA-like differential expression (ALDEx) analysis for mixed population RNA-Seq.","Fernandes AD, Macklaim JM, Linn TG, Reid G, Gloor GB.","PLoS One","2013","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","6","Y","Y","N","N","N","278.67422","7","8","e67019","PMC3699591",NA,NA,"code.google.com"
"628","23805099","MED","23805099","10.3389/fncom.2013.00079","A musculoskeletal model of human locomotion driven by a low dimensional set of impulsive excitation primitives.","Sartori M, Gizzi L, Lloyd DG, Farina D.","Front Comput Neurosci","2013","1662-5188","journal article; research-article","Y","Y","Y","3","Y","Y","N","N","N","278.67422",NA,"7","79","PMC3693080",NA,NA,"code.google.com"
"629","23356439","MED","23356439","10.1111/cmi.12116","Perturbations of Plasmodium Puf2 expression and RNA-seq of Puf2-deficient sporozoites reveal a critical role in maintaining RNA homeostasis and parasite transmissibility.","Lindner SE, Mikolajczak SA, Vaughan AM, Moon W, Joyce BR, Sullivan WJ Jr, Kappe SH.","Cell Microbiol","2013","1462-5814","journal article; research support, n.i.h., extramural; research-article","N","Y","Y","6","Y","Y","Y","N","N","278.67422","7","15","1266-1283","PMC3815636",NA,"ARXPR","code.google.com"
"630","23785273","MED","23785273","10.1371/journal.pcbi.1003104","Neuronal functional connection graphs among multiple areas of the rat somatosensory system during spontaneous and evoked activities.","Zippo AG, Storchi R, Nencini S, Caramenti GC, Valente M, Biella GE.","PLoS Comput Biol","2013","1553-734x","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","278.67422","6","9","e1003104","PMC3681651",NA,NA,"code.google.com"
"631","23816990","MED","23816990","10.1074/mcp.m112.026476","The Rhesus macaque (Macaca mulatta) sperm proteome.","Skerget S, Rosenow M, Polpitiya A, Petritis K, Dorus S, Karr TL.","Mol Cell Proteomics","2013","1535-9476","journal article; research-article","N","Y","N","5","Y","Y","N","N","N","278.67422","11","12","3052-3067","PMC3820923",NA,NA,"code.google.com"
"632","23853079","MED","23853079","10.1002/0471142905.hg0126s78","Identifying rare variants associated with complex traits via sequencing.","Li B, Liu DJ, Leal SM.","Curr Protoc Hum Genet","2013","1934-8266","journal article; review; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","0","Y","Y","N","N","N","278.67422",NA,"Chapter 1","unit 1.26","PMC3830981",NA,NA,"code.google.com"
"633","23668630","MED","23668630","10.1186/1471-2105-14-158","Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient.","Stoltzfus A, Lapp H, Matasci N, Deus H, Sidlauskas B, Zmasek CM, Vaidya G, Pontelli E, Cranston K, Vos R, Webb CO, Harmon LJ, Pirrung M, O'Meara B, Pennell MW, Mirarab S, Rosenberg MS, Balhoff JP, Bik HM, Heath TA, Midford PE, Brown JW, McTavish EJ, Sukumaran J, Westneat M, Alfaro ME, Steele A, Jordan G.","BMC Bioinformatics","2013","1471-2105","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; product-review","Y","Y","Y","2","Y","Y","N","N","N","278.67422",NA,"14","158","PMC3669619",NA,NA,"code.google.com"
"634","24209455","MED","24209455","10.1186/1471-2105-14-320","Design of RNA splicing analysis null models for post hoc filtering of Drosophila head RNA-Seq data with the splicing analysis kit (Spanki).","Sturgill D, Malone JH, Sun X, Smith HE, Rabinow L, Samson ML, Oliver B.","BMC Bioinformatics","2013","1471-2105","journal article; research support, non-u.s. gov't; research support, n.i.h., intramural; research-article","Y","Y","Y","3","Y","Y","Y","Y","N","278.67422",NA,"14","320","PMC3827500",NA,"UNIPROT","code.google.com"
"635","24133250","MED","24133250","10.1523/jneurosci.2625-13.2013","Frontal and parietal cortical interactions with distributed visual representations during selective attention and action selection.","Nelissen N, Stokes M, Nobre AC, Rushworth MF.","J Neurosci","2013","0270-6474","journal article; research support, non-u.s. gov't; research-article","N","Y","Y","5","Y","Y","N","N","N","278.67422","42","33","16443-16458","PMC3797369",NA,NA,"code.google.com"
"636","24136347","MED","24136347","10.1038/nprot.2013.133","Selective ribosome profiling as a tool for studying the interaction of chaperones and targeting factors with nascent polypeptide chains and ribosomes.","Becker AH, Oh E, Weissman JS, Kramer G, Bukau B.","Nat Protoc","2013","1754-2189","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","N","1","Y","Y","N","N","N","278.46066","11","8","2212-2239","PMC4001812",NA,NA,"code.google.com"
"637","23865810","MED","23865810","10.1186/1471-2105-14-226","Fast online and index-based algorithms for approximate search of RNA sequence-structure patterns.","Meyer F, Kurtz S, Beckstette M.","BMC Bioinformatics","2013","1471-2105","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","278.46066",NA,"14","226","PMC3765529",NA,NA,"code.google.com"
"638","24385918","MED","24385918","10.1371/journal.pgen.1003993","Quantifying missing heritability at known GWAS loci.","Gusev A, Bhatia G, Zaitlen N, Vilhjalmsson BJ, Diogo D, Stahl EA, Gregersen PK, Worthington J, Klareskog L, Raychaudhuri S, Plenge RM, Pasaniuc B, Price AL.","PLoS Genet","2013","1553-7390","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","4","Y","Y","N","N","N","278.46066","12","9","e1003993","PMC3873246",NA,NA,"code.google.com"
"639","23795297","MED","23795297","10.7554/elife.00808","Condensin controls recruitment of RNA polymerase II to achieve nematode X-chromosome dosage compensation.","Kruesi WS, Core LJ, Waters CT, Lis JT, Meyer BJ.","Elife","2013","2050-084x","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","10","Y","Y","Y","Y","N","278.2471",NA,"2","e00808","PMC3687364",NA,"ARXPR","code.google.com"
"640","22635606","MED","22635606","10.1093/bioinformatics/bts315","Gowinda: unbiased analysis of gene set enrichment for genome-wide association studies.","Kofler R, SchlÃ¶tterer C.","Bioinformatics","2012","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","7","Y","Y","N","N","N","218.2545","15","28","2084-2085","PMC3400962",NA,NA,"code.google.com"
"641","22113082","MED","22113082","10.1093/bioinformatics/btr646","GenomicTools: a computational platform for developing high-throughput analytics in genomics.","Tsirigos A, Haiminen N, Bilal E, Utro F.","Bioinformatics","2012","1367-4803","journal article","N","N","N","4","Y","N","N","Y","N","214.92291","2","28","282-283",NA,NA,NA,"code.google.com"
"642","22238261","MED","22238261","10.1093/bioinformatics/bts017","SSuMMo: rapid analysis, comparison and visualization of microbial communities.","Leach AL, Chong JP, Redeker KR.","Bioinformatics","2012","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","1","Y","N","N","N","N","214.92291","5","28","679-686",NA,NA,NA,"code.google.com"
"643","23148880","MED","23148880","10.2144/000113953","prfectBLAST: a platform-independent portable front end for the command terminal BLAST+ stand-alone suite.","Santiago-Sotelo P, Ramirez-Prado JH.","Biotechniques","2012","0736-6205","journal article; research support, non-u.s. gov't","N","N","N","3","N","N","N","N","N","214.92291","5","53","299-300",NA,NA,NA,"code.google.com"
"644","22581177","MED","22581177","10.1093/bioinformatics/bts274","Exhaustive database searching for amino acid mutations in proteomes.","Hyatt D, Pan C.","Bioinformatics","2012","1367-4803","journal article; research support, u.s. gov't, non-p.h.s.","N","N","N","2","Y","N","N","N","N","214.92291","14","28","1895-1901",NA,NA,NA,"code.google.com"
"645","22730435","MED","22730435","10.1093/bioinformatics/bts355","DySC: software for greedy clustering of 16S rRNA reads.","Zheng Z, Kramer S, Schmidt B.","Bioinformatics","2012","1367-4803","journal article; comparative study","N","N","N","2","Y","N","N","Y","N","214.92291","16","28","2182-2183",NA,NA,NA,"code.google.com"
"646","22796954","MED","22796954","10.1093/bioinformatics/bts429","Gene and translation initiation site prediction in metagenomic sequences.","Hyatt D, LoCascio PF, Hauser LJ, Uberbacher EC.","Bioinformatics","2012","1367-4803","journal article; research support, u.s. gov't, non-p.h.s.","N","N","N","8","Y","N","N","N","N","214.92291","17","28","2223-2230",NA,NA,NA,"code.google.com"
"647","22199382","MED","22199382","10.1093/bioinformatics/btr697","Modeling mechanistic biological networks: an advanced Boolean approach.","Handorf T, Klipp E.","Bioinformatics","2012","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","6","Y","N","N","N","N","214.92291","4","28","557-563",NA,NA,NA,"code.google.com"
"648","22222564","MED","22222564","10.1016/j.chroma.2011.12.047","Multiscale peak alignment for chromatographic datasets.","Zhang ZM, Liang YZ, Lu HM, Tan BB, Xu XN, Ferro M.","J Chromatogr A","2012","0021-9673","journal article; research support, non-u.s. gov't","N","N","N","5","N","N","N","N","N","214.92291",NA,"1223","93-106",NA,NA,NA,"code.google.com"
"649","22954626","MED","22954626","10.1093/bioinformatics/bts524","HighSSR: high-throughput SSR characterization and locus development from next-gen sequencing data.","Churbanov A, Ryan R, Hasan N, Bailey D, Chen H, Milligan B, Houde P.","Bioinformatics","2012","1367-4803","evaluation studies; journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.","N","N","N","3","Y","N","N","Y","N","213.2143","21","28","2797-2803",NA,NA,NA,"code.google.com"
"650","22982573","MED","22982573","10.1093/bioinformatics/bts548","DLRS: gene tree evolution in light of a species tree.","SjÃ¶strand J, Sennblad B, Arvestad L, Lagergren J.","Bioinformatics","2012","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","8","Y","N","N","N","N","213.2143","22","28","2994-2995",NA,NA,NA,"code.google.com"
"651","22623287","MED","22623287","10.1002/pmic.201200029","Software for analysing ion mobility mass spectrometry data to improve peptide identification.","Xia D, Ghali F, Gaskell SJ, O'Cualain R, Sims PF, Jones AR.","Proteomics","2012","1615-9853","journal article; research support, non-u.s. gov't","N","N","N","0","Y","N","N","N","N","213.2143","12","12","1912-1916",NA,NA,NA,"code.google.com"
"652","22743226","MED","22743226","10.1093/bioinformatics/bts356","RSeQC: quality control of RNA-seq experiments.","Wang L, Wang S, Li W.","Bioinformatics","2012","1367-4803","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.","N","N","N","35","Y","N","N","Y","N","213.2143","16","28","2184-2185",NA,NA,NA,"code.google.com"
"653","22689389","MED","22689389","10.1093/bioinformatics/bts339","BatMis: a fast algorithm for k-mismatch mapping.","Tennakoon C, Purbojati RW, Sung WK.","Bioinformatics","2012","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","2","Y","N","N","N","N","213.2143","16","28","2122-2128",NA,NA,NA,"code.google.com"
"654","22806579","MED","22806579","10.1002/jcc.23066","DataPipeline: automated importing and fitting of large amounts of biophysical data.","Farrell D, Nielsen JE.","J Comput Chem","2012","0192-8651","journal article; research support, non-u.s. gov't","N","N","N","0","Y","N","N","N","N","213.2143","29","33","2357-2362",NA,NA,NA,"code.google.com"
"655","22840646","MED","22840646","10.1016/j.aca.2012.06.031","Random frog: an efficient reversible jump Markov Chain Monte Carlo-like approach for variable selection with applications to gene selection and disease classification.","Li HD, Xu QS, Liang YZ.","Anal Chim Acta","2012","0003-2670","journal article; research support, non-u.s. gov't","N","N","N","6","N","N","N","N","N","213.2143",NA,"740","20-26",NA,NA,NA,"code.google.com"
"656","22539430","MED","22539430","10.1002/pmic.201100578","jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats.","Griss J, Reisinger F, Hermjakob H, VizcaÃno JA.","Proteomics","2012","1615-9853","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","9","Y","Y","N","N","N","212.5554","6","12","795-798","PMC3472022",NA,NA,"code.google.com"
"657","22492642","MED","22492642","10.1093/bioinformatics/bts175","GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies.","Gritsenko AA, Nijkamp JF, Reinders MJ, de Ridder D.","Bioinformatics","2012","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","5","Y","N","N","Y","N","211.50566","11","28","1429-1437",NA,NA,NA,"code.google.com"
"658","22695796","MED","22695796","10.1093/nar/gks576","EvolView, an online tool for visualizing, annotating and managing phylogenetic trees.","Zhang H, Gao S, Lercher MJ, Hu S, Chen WH.","Nucleic Acids Res","2012","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","15","Y","Y","N","N","N","209.79706","web server issue","40","w569-72","PMC3394307",NA,NA,"code.google.com"
"659","22576172","MED","22576172","10.1093/bioinformatics/bts277","BEDOPS: high-performance genomic feature operations.","Neph S, Kuehn MS, Reynolds AP, Haugen E, Thurman RE, Johnson AK, Rynes E, Maurano MT, Vierstra J, Thomas S, Sandstrom R, Humbert R, Stamatoyannopoulos JA.","Bioinformatics","2012","1367-4803","journal article; research support, n.i.h., extramural; research-article","N","Y","Y","14","Y","Y","N","Y","N","209.71118","14","28","1919-1920","PMC3389768",NA,NA,"code.google.com"
"660","22846423","MED","22846423","10.1186/1751-0473-7-8","JobCenter: an open source, cross-platform, and distributed job queue management system optimized for scalability and versatility.","Jaschob D, Riffle M.","Source Code Biol Med","2012","1751-0473","journal article; product-review","Y","Y","Y","0","Y","Y","N","N","N","208.89513","1","7","8","PMC3494518",NA,NA,"code.google.com"
"661","22611296","MED","22611296","10.1074/mcp.o111.015149","A mass spectrometry proteomics data management platform.","Sharma V, Eng JK, Maccoss MJ, Riffle M.","Mol Cell Proteomics","2012","1535-9476","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","2","Y","Y","N","N","N","208.57814","9","11","824-831","PMC3434774",NA,NA,"code.google.com"
"662","22375074","MED","22375074","10.1074/mcp.m111.014381","The mzIdentML data standard for mass spectrometry-based proteomics results.","Jones AR, Eisenacher M, Mayer G, Kohlbacher O, Siepen J, Hubbard SJ, Selley JN, Searle BC, Shofstahl J, Seymour SL, Julian R, Binz PA, Deutsch EW, Hermjakob H, Reisinger F, Griss J, VizcaÃno JA, Chambers M, Pizarro A, Creasy D.","Mol Cell Proteomics","2012","1535-9476","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","19","Y","Y","N","N","N","208.57814","7","11","m111.014381","PMC3394945",NA,NA,"code.google.com"
"663","22155865","MED","22155865","10.1093/bioinformatics/btr660","B-SOLANA: an approach for the analysis of two-base encoding bisulfite sequencing data.","Kreck B, Marnellos G, Richter J, Krueger F, Siebert R, Franke A.","Bioinformatics","2012","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","5","Y","Y","N","N","N","208.503","3","28","428-429","PMC3268236",NA,NA,"code.google.com"
"664","22954633","MED","22954633","10.1093/bioinformatics/bts536","Mendel-GPU: haplotyping and genotype imputation on graphics processing units.","Chen GK, Wang K, Stram AH, Sobel EM, Lange K.","Bioinformatics","2012","1367-4803","journal article; research support, n.i.h., extramural; research-article","N","Y","Y","3","Y","Y","N","N","N","208.503","22","28","2979-2980","PMC3634317",NA,NA,"code.google.com"
"665","22640904","MED","22640904","10.1186/1751-0473-7-7","Layout-aware text extraction from full-text PDF of scientific articles.","Ramakrishnan C, Patnia A, Hovy E, Burns GA.","Source Code Biol Med","2012","1751-0473","journal article; product-review","Y","Y","Y","2","Y","Y","N","Y","N","208.03484","1","7","7","PMC3441580",NA,NA,"code.google.com"
"666","22238653","MED","22238653","10.1371/journal.pone.0029788","SASqPCR: robust and rapid analysis of RT-qPCR data in SAS.","Ling D.","PLoS One","2012","1932-6203","journal article; validation studies; research-article","Y","Y","Y","5","Y","Y","N","N","N","207.93999","1","7","e29788","PMC3253109",NA,NA,"code.google.com"
"667","22383735","MED","22383735","10.1093/bioinformatics/bts099","GENI-DB: a database of global events for epidemic intelligence.","Collier N, Doan S.","Bioinformatics","2012","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","4","Y","Y","N","N","N","207.29483","8","28","1186-1188","PMC3324518",NA,NA,"code.google.com"
"668","23451295","MED","23451295","10.4056/sigs.3166513","Meeting Report: Hackathon-Workshop on Darwin Core and MIxS Standards Alignment (February 2012).","Tuama EÃ, Deck J, DrÃ¶ge G, DÃ¶ring M, Field D, Kottmann R, Ma J, Mori H, Morrison N, Sterk P, Sugawara H, Wieczorek J, Wu L, Yilmaz P.","Stand Genomic Sci","2012","1944-3277","journal article; research-article","Y","Y","Y","2","Y","Y","N","N","N","207.29483","1","7","166-170","PMC3570805",NA,NA,"code.google.com"
"669","22305525","MED","22305525","10.3201/eid1802.111403","Shuni virus as cause of neurologic disease in horses.","van Eeden C, Williams JH, Gerdes TG, van Wilpe E, Viljoen A, Swanepoel R, Venter M.","Emerg Infect Dis","2012","1080-6040","journal article; case reports; research support, non-u.s. gov't; brief-report","Y","Y","Y","4","Y","Y","Y","N","N","207.29483","2","18","318-321","PMC3310469",NA,"EMBLUNIPROT","code.google.com"
"670","22238263","MED","22238263","10.1093/bioinformatics/bts012","MetExtract: a new software tool for the automated comprehensive extraction of metabolite-derived LC/MS signals in metabolomics research.","Bueschl C, Kluger B, Berthiller F, Lirk G, Winkler S, Krska R, Schuhmacher R.","Bioinformatics","2012","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","12","Y","Y","N","N","N","207.29483","5","28","736-738","PMC3289915",NA,NA,"code.google.com"
"671","22888986","MED","22888986","10.1089/omi.2012.0042","A software toolkit and interface for performing stable isotope labeling and top3 quantification using Progenesis LC-MS.","Qi D, Brownridge P, Xia D, Mackay K, Gonzalez-Galarza FF, Kenyani J, Harman V, Beynon RJ, Jones AR.","OMICS","2012","1536-2310","journal article; research support, non-u.s. gov't; research-article","N","Y","Y","6","Y","Y","N","N","N","207.23412","9","16","489-495","PMC3437041",NA,NA,"code.google.com"
"672","22718978","MED","22718978","10.1093/nar/gks531","Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools.","Ham TS, Dmytriv Z, Plahar H, Chen J, Hillson NJ, Keasling JD.","Nucleic Acids Res","2012","0305-1048","journal article; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","7","Y","Y","N","N","N","207.23412","18","40","e141","PMC3467034",NA,NA,"code.google.com"
"673","22754383","MED","22754383","10.7171/jbt.2012-2302-001","ArrayOU: a web application for microarray data analysis and visualization.","Shen K, Wyatt SE, Nadella V.","J Biomol Tech","2012","1524-0215","journal article; research-article","N","Y","Y","0","Y","Y","N","N","N","207.23412","2","23","37-39","PMC3378286",NA,NA,"code.google.com"
"674","22238640","MED","22238640","10.1371/journal.pone.0029715","Darwin Core: an evolving community-developed biodiversity data standard.","Wieczorek J, Bloom D, Guralnick R, Blum S, DÃ¶ring M, Giovanni R, Robertson T, Vieglais D.","PLoS One","2012","1932-6203","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","21","Y","Y","N","N","N","206.98483","1","7","e29715","PMC3253084",NA,NA,"code.google.com"
"675","22102570","MED","22102570","10.1093/nar/gkr1022","ProPortal: a resource for integrated systems biology of Prochlorococcus and its phage.","Kelly L, Huang KH, Ding H, Chisholm SW.","Nucleic Acids Res","2012","0305-1048","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., intramural; research-article","Y","Y","Y","9","Y","Y","N","Y","N","206.43294","database issue","40","d632-40","PMC3245167",NA,NA,"code.google.com"
"676","23148484","MED","23148484","10.1186/1471-2105-13-297","Oculus: faster sequence alignment by streaming read compression.","Veeneman BA, Iyer MK, Chinnaiyan AM.","BMC Bioinformatics","2012","1471-2105","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; product-review","Y","Y","Y","1","Y","Y","N","N","N","206.43294",NA,"13","297","PMC3534618",NA,NA,"code.google.com"
"677","22992255","MED","22992255","10.1186/1471-2105-13-239","SNP calling by sequencing pooled samples.","Raineri E, Ferretti L, Esteve-Codina A, Nevado B, Heath S, PÃ©rez-Enciso M.","BMC Bioinformatics","2012","1471-2105","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","5","Y","Y","N","N","N","206.43294",NA,"13","239","PMC3475117",NA,NA,"code.google.com"
"678","22914216","MED","22914216","10.1093/bioinformatics/bts499","SimRare: a program to generate and analyze sequence-based data for association studies of quantitative and qualitative traits.","Li B, Wang G, Leal SM.","Bioinformatics","2012","1367-4803","journal article; research support, n.i.h., extramural; research-article","N","Y","Y","7","Y","Y","N","Y","N","206.37982","20","28","2703-2704","PMC3467746",NA,NA,"code.google.com"
"679","23240016","MED","23240016","10.1371/journal.pone.0051359","Analysis of HIV using a high resolution melting (HRM) diversity assay: automation of HRM data analysis enhances the utility of the assay for analysis of HIV incidence.","Cousins MM, Swan D, Magaret CA, Hoover DR, Eshleman SH.","PLoS One","2012","1932-6203","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","6","Y","Y","N","N","N","206.37982","12","7","e51359","PMC3519891",NA,NA,"code.google.com"
"680","23097421","MED","23097421","10.1093/bioinformatics/bts633","FFPopSim: an efficient forward simulation package for the evolution of large populations.","Zanini F, Neher RA.","Bioinformatics","2012","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","6","Y","Y","N","N","N","206.37982","24","28","3332-3333","PMC3519462",NA,NA,"code.google.com"
"681","22834945","MED","22834945","10.1186/1752-0509-6-91","Condor-COPASI: high-throughput computing for biochemical networks.","Kent E, Hoops S, Mendes P.","BMC Syst Biol","2012","1752-0509","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; product-review","Y","Y","Y","7","Y","Y","N","N","N","206.37982",NA,"6","91","PMC3527284",NA,NA,"code.google.com"
"682","22844195","MED","22844195","10.4137/ebo.s9179","Reliable Phylogenetic Trees Building: A New Web Interface for FIGENIX.","Paganini J, Gouret P.","Evol Bioinform Online","2012","1176-9343","journal article; research-article","Y","Y","Y","3","Y","Y","N","N","N","206.37982",NA,"8","417-421","PMC3399708",NA,NA,"code.google.com"
"683","22155871","MED","22155871","10.1093/bioinformatics/btr668","RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing.","Xi Y, Bock C, MÃ¼ller F, Sun D, Meissner A, Li W.","Bioinformatics","2012","1367-4803","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","16","Y","Y","N","N","N","206.37982","3","28","430-432","PMC3268241",NA,NA,"code.google.com"
"684","22160811","MED","22160811","10.1007/s10858-011-9589-y","GUARDD: user-friendly MATLAB software for rigorous analysis of CPMG RD NMR data.","Kleckner IR, Foster MP.","J Biomol NMR","2012","0925-2738","journal article; research support, n.i.h., extramural; research-article","N","Y","Y","5","Y","Y","N","N","N","206.37982","1","52","11-22","PMC3593345",NA,NA,"code.google.com"
"685","22210867","MED","22210867","10.1093/bioinformatics/btr719","CytoSEED: a Cytoscape plugin for viewing, manipulating and analyzing metabolic models created by the Model SEED.","DeJongh M, Bockstege B, Frybarger P, Hazekamp N, Kammeraad J, McGeehan T.","Bioinformatics","2012","1367-4803","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","6","Y","Y","N","N","N","206.37982","6","28","891-892","PMC3307106",NA,NA,"code.google.com"
"686","22228834","MED","22228834","10.1093/nar/gkr1259","Correction of RT-qPCR data for genomic DNA-derived signals with ValidPrime.","Laurell H, Iacovoni JS, Abot A, Svec D, Maoret JJ, Arnal JF, Kubista M.","Nucleic Acids Res","2012","0305-1048","journal article; validation studies; research support, non-u.s. gov't; research-article","Y","Y","Y","7","Y","Y","N","Y","N","206.37982","7","40","e51","PMC3326333",NA,NA,"code.google.com"
"687","22434838","MED","22434838","10.1093/database/bas004","PRIDE: quality control in a proteomics data repository.","Csordas A, Ovelleiro D, Wang R, Foster JM, RÃos D, VizcaÃno JA, Hermjakob H.","Database (Oxford)","2012","1758-0463","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","10","Y","Y","N","N","N","206.08667",NA,"2012","bas004","PMC3308160",NA,NA,"code.google.com"
"688","23304327","MED","23304327",NA,"ClinData Express--a metadata driven clinical research data management system for secondary use of clinical data.","Li Z, Wen J, Zhang X, Wu C, Li Z, Liu L.","AMIA Annu Symp Proc","2012","1942-597x","journal article; research support, non-u.s. gov't; research-article","N","Y","Y","1","Y","Y","N","N","N","206.08667",NA,"2012","552-557","PMC3540469",NA,NA,"code.google.com"
"689","23304331","MED","23304331",NA,"Using SemRep to label semantic relations extracted from clinical text.","Liu Y, Bill R, Fiszman M, Rindflesch T, Pedersen T, Melton GB, Pakhomov SV.","AMIA Annu Symp Proc","2012","1942-597x","journal article; research support, n.i.h., intramural; research-article","N","Y","Y","0","Y","Y","N","N","N","206.08667",NA,"2012","587-595","PMC3540517",NA,NA,"code.google.com"
"690","22493575","MED","22493575","10.3389/fninf.2012.00007","The pipeline system for Octave and Matlab (PSOM): a lightweight scripting framework and execution engine for scientific workflows.","Bellec P, Lavoie-Courchesne S, Dickinson P, Lerch JP, Zijdenbos AP, Evans AC.","Front Neuroinform","2012","1662-5196","journal article; research-article","Y","Y","Y","9","Y","Y","N","Y","N","206.08667",NA,"6","7","PMC3318188",NA,NA,"code.google.com"
"691","22096229","MED","22096229","10.1093/nar/gkr948","InterPro in 2011: new developments in the family and domain prediction database.","Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S, de Castro E, Coggill P, Corbett M, Das U, Daugherty L, Duquenne L, Finn RD, Fraser M, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, McMenamin C, Mi H, Mutowo-Muellenet P, Mulder N, Natale D, Orengo C, Pesseat S, Punta M, Quinn AF, Rivoire C, Sangrador-Vegas A, Selengut JD, Sigrist CJ, Scheremetjew M, Tate J, Thimmajanarthanan M, Thomas PD, Wu CH, Yeats C, Yong SY.","Nucleic Acids Res","2012","0305-1048","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","310","Y","Y","N","Y","N","206.08667","database issue","40","d306-12","PMC3245097",NA,NA,"code.google.com"
"692","23028496","MED","23028496","10.1371/journal.pone.0044180","MyDas, an extensible Java DAS server.","Salazar GA, GarcÃa LJ, Jones P, Jimenez RC, Quinn AF, Jenkinson AM, Mulder N, Martin M, Hunter S, Hermjakob H.","PLoS One","2012","1932-6203","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","206.08667","9","7","e44180","PMC3441562",NA,NA,"code.google.com"
"693","25621316","MED","25621316",NA,"Read-mapping using personalized diploid reference genome for RNA sequencing data reduced bias for detecting allele-specific expression.","Yuan S, Qin Z.","IEEE International Conference on Bioinformatics and Biomedicine workshops IEEE International Conference on Bioinformatics and Biomedicine","2012",NA,"journal article; research-article","N","Y","N","0","N","Y","N","N","N","206.08667",NA,"2012","718-724","PMC4304670",NA,NA,"code.google.com"
"694","22580178","MED","22580178","10.1016/j.jbi.2012.04.010","Ontology-guided feature engineering for clinical text classification.","Garla VN, Brandt C.","J Biomed Inform","2012","1532-0464","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","Y","4","Y","Y","N","N","N","205.69308","5","45","992-998","PMC3431438",NA,NA,"code.google.com"
"695","23282411","MED","23282411","10.1186/1752-0509-6-s3-s7","Revealing functionally coherent subsets using a spectral clustering and an information integration approach.","Richards AJ, Schwacke JH, Rohrer B, Cowart LA, Lu X.","BMC Syst Biol","2012","1752-0509","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","1","Y","Y","N","N","N","205.69308","Suppl 3","6 Suppl 3","s7","PMC3542577",NA,NA,"code.google.com"
"696","22941959","MED","22941959","10.1093/bib/bbr067","Interfaces to PeptideAtlas: a case study of standard data access systems.","Killcoyne S, Handcock J, Robinson T, Deutsch EW, Boyle J.","Brief Bioinform","2012","1467-5463","journal article; research-article","N","Y","Y","0","Y","Y","N","N","N","205.69308","5","13","615-626","PMC3431717",NA,NA,"code.google.com"
"697","22719993","MED","22719993","10.1371/journal.pone.0038937","Improving disease gene prioritization by comparing the semantic similarity of phenotypes in mice with those of human diseases.","Oellrich A, Hoehndorf R, Gkoutos GV, Rebholz-Schuhmann D.","PLoS One","2012","1932-6203","journal article; research support, non-u.s. gov't; comparative study; research-article","Y","Y","Y","7","Y","Y","N","N","N","205.69308","6","7","e38937","PMC3375301",NA,NA,"code.google.com"
"698","23372966","MED","23372966","10.4103/2152-7806.104743","An open-source and cross-platform framework for Brain Computer Interface-guided robotic arm control.","Kubben PL, Pouratian N.","Surg Neurol Int","2012","2229-5097","journal article; other","Y","Y","Y","1","Y","Y","N","N","N","205.5255",NA,"3","149","PMC3551496",NA,NA,"code.google.com"
"699","23110314","MED","23110314","10.1186/1471-2164-13-571","De novo assembly of the pepper transcriptome (Capsicum annuum): a benchmark for in silico discovery of SNPs, SSRs and candidate genes.","Ashrafi H, Hill T, Stoffel K, Kozik A, Yao J, Chin-Wo SR, Van Deynze A.","BMC Genomics","2012","1471-2164","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","13","Y","Y","N","N","Y","205.5255",NA,"13","571","PMC3545863","gen",NA,"code.google.com"
"700","22689644","MED","22689644","10.1093/nar/gks552","MFEprimer-2.0: a fast thermodynamics-based program for checking PCR primer specificity.","Qu W, Zhou Y, Zhang Y, Lu Y, Wang X, Zhao D, Yang Y, Zhang C.","Nucleic Acids Res","2012","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","N","N","N","205.5255","web server issue","40","w205-8","PMC3394324",NA,NA,"code.google.com"
"701","22807455","MED","22807455","10.1002/pmic.201200003","Comparative phosphoproteomic analysis of neonatal and adult murine brain.","Goswami T, Li X, Smith AM, Luderowski EM, Vincent JJ, Rush J, Ballif BA.","Proteomics","2012","1615-9853","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; comparative study; research-article","N","Y","Y","10","Y","Y","Y","N","N","205.5255","13","12","2185-2189","PMC3816108",NA,"UNIPROT","code.google.com"
"702","22275265","MED","22275265","10.1002/lary.23209","Common genetic variants in the 8q24 region and risk of papillary thyroid cancer.","Neta G, Yu CL, Brenner A, Gu F, Hutchinson A, Pfeiffer R, Sturgis EM, Xu L, Linet MS, Alexander BH, Chanock S, Sigurdson AJ.","Laryngoscope","2012","0023-852x","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research support, n.i.h., intramural; comparative study; research-article","N","Y","Y","5","Y","Y","N","N","Y","205.5255","5","122","1040-1042","PMC3408055","refsnp",NA,"code.google.com"
"703","22238636","MED","22238636","10.1371/journal.pone.0029697","An analysis approach for high-field fMRI data from awake non-human primates.","Stoewer S, Goense J, Keliris GA, Bartels A, Logothetis NK, Duncan J, Sigala N.","PLoS One","2012","1932-6203","evaluation studies; journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","3","Y","Y","N","N","N","205.5255","1","7","e29697","PMC3253095",NA,NA,"code.google.com"
"704","23194264","MED","23194264","10.1586/epr.12.44","Cross-linking/mass spectrometry as a new field and the proteomics information mountain of tomorrow.","Rappsilber J.","Expert Rev Proteomics","2012","1478-9450","congresses; research support, non-u.s. gov't; research-article","N","Y","Y","2","Y","Y","N","N","N","205.5255","5","9","485-487","PMC3926187",NA,NA,"code.google.com"
"705","23001122","MED","23001122","10.1038/ng.2417","Genome-wide association study identifies a common variant in RAD51B associated with male breast cancer risk.","Orr N, Lemnrau A, Cooke R, Fletcher O, Tomczyk K, Jones M, Johnson N, Lord CJ, Mitsopoulos C, Zvelebil M, McDade SS, Buck G, Blancher C, KConFab Consortium, Trainer AH, James PA, Bojesen SE, Bokmand S, Nevanlinna H, Mattson J, Friedman E, Laitman Y, Palli D, Masala G, Zanna I, Ottini L, Giannini G, Hollestelle A, Ouweland AM, NovakoviÄ S, Krajc M, Gago-Dominguez M, Castelao JE, Olsson H, Hedenfalk I, Easton DF, Pharoah PD, Dunning AM, Bishop DT, Neuhausen SL, Steele L, Houlston RS, Garcia-Closas M, Ashworth A, Swerdlow AJ.","Nat Genet","2012","1061-4036","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","14","Y","Y","Y","Y","Y","205.5255","11","44","1182-1184","PMC3722904","refsnp","OMIMUNIPROT","code.google.com"
"706","22962475","MED","22962475","10.1093/bioinformatics/bts401","Random sampling of elementary flux modes in large-scale metabolic networks.","Machado D, Soons Z, Patil KR, Ferreira EC, Rocha I.","Bioinformatics","2012","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","6","Y","Y","N","N","N","205.48257","18","28","i515-i521","PMC3436828",NA,NA,"code.google.com"
"707","23226242","MED","23226242","10.1371/journal.pone.0050147","Accurate diagnostics for Bovine tuberculosis based on high-throughput sequencing.","Churbanov A, Milligan B.","PLoS One","2012","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","N","N","N","205.48257","11","7","e50147","PMC3511461",NA,NA,"code.google.com"
"708","22927906","MED","22927906","10.1371/journal.pone.0041224","Genometa--a fast and accurate classifier for short metagenomic shotgun reads.","Davenport CF, Neugebauer J, Beckmann N, Friedrich B, Kameri B, Kokott S, Paetow M, Siekmann B, Wieding-Drewes M, WienhÃ¶fer M, Wolf S, TÃ¼mmler B, Ahlers V, Sprengel F.","PLoS One","2012","1932-6203","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","6","Y","Y","N","Y","N","205.48257","8","7","e41224","PMC3424124",NA,NA,"code.google.com"
"709","22934238","MED","22934238","10.4103/2153-3539.98813","ImageJS: Personalized, participated, pervasive, and reproducible image bioinformatics in the web browser.","Almeida JS, Iriabho EE, Gorrepati VL, Wilkinson SR, GrÃ¼neberg A, Robbins DE, Hackney JR.","J Pathol Inform","2012","2229-5089","journal article; research-article","Y","Y","Y","2","Y","Y","N","N","N","205.48257",NA,"3","25","PMC3424663",NA,NA,"code.google.com"
"710","23072312","MED","23072312","10.1186/1471-2105-13-269","Gene Fusion Markup Language: a prototype for exchanging gene fusion data.","Kalyana-Sundaram S, Shanmugam A, Chinnaiyan AM.","BMC Bioinformatics","2012","1471-2105","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","205.48257",NA,"13","269","PMC3607969",NA,NA,"code.google.com"
"711","23034086","MED","23034086","10.1186/gb-2012-13-10-r87","methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles.","Akalin A, Kormaksson M, Li S, Garrett-Bakelman FE, Figueroa ME, Melnick A, Mason CE.","Genome Biol","2012","1465-6906","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; product-review","Y","Y","Y","35","Y","Y","N","N","N","205.48257","10","13","r87","PMC3491415",NA,NA,"code.google.com"
"712","22319561","MED","22319561","10.1371/journal.pone.0030126","Dirichlet multinomial mixtures: generative models for microbial metagenomics.","Holmes I, Harris K, Quince C.","PLoS One","2012","1932-6203","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","17","Y","Y","N","N","N","204.95322","2","7","e30126","PMC3272020",NA,NA,"code.google.com"
"713","22555647","MED","22555647","10.1007/s00726-012-1290-2","AMS 4.0: consensus prediction of post-translational modifications in protein sequences.","Plewczynski D, Basu S, Saha I.","Amino Acids","2012","0939-4451","journal article; research support, non-u.s. gov't; comparative study; research-article","Y","Y","Y","3","Y","Y","N","N","N","204.95322","2","43","573-582","PMC3397139",NA,NA,"code.google.com"
"714","22554190","MED","22554190","10.1186/1472-6750-12-16","Pattern analysis approach reveals restriction enzyme cutting abnormalities and other cDNA library construction artifacts using raw EST data.","Zhou S, Ji G, Liu X, Li P, Moler J, Karro JE, Liang C.","BMC Biotechnol","2012","1472-6750","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","204.95322",NA,"12","16","PMC3424822",NA,NA,"code.google.com"
"715","22859876","MED","22859876","10.3897/zookeys.209.3135","Five task clusters that enable efficient and effective digitization of biological collections.","Nelson G, Paul D, Riccardi G, Mast AR.","Zookeys","2012","1313-2989","journal article; research-article","Y","Y","Y","3","N","Y","N","N","N","204.95322","209",NA,"19-45","PMC3406464",NA,NA,"code.google.com"
"716","23046094","MED","23046094","10.1186/1471-2105-13-261","Semantic similarity in the biomedical domain: an evaluation across knowledge sources.","Garla VN, Brandt C.","BMC Bioinformatics","2012","1471-2105","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; comparative study; research-article","Y","Y","Y","2","Y","Y","N","N","N","204.95322",NA,"13","261","PMC3533586",NA,NA,"code.google.com"
"717","22685456","MED","22685456","10.1155/2012/391574","Applications of natural language processing in biodiversity science.","Thessen AE, Cui H, Mozzherin D.","Adv Bioinformatics","2012","1687-8027","journal article; review-article","Y","Y","Y","2","Y","Y","N","N","N","204.95322",NA,"2012","391574","PMC3364545",NA,NA,"code.google.com"
"718","22788675","MED","22788675","10.1186/1471-2105-13-163","A graph-based approach for designing extensible pipelines.","Rodrigues MR, MagalhÃ£es WC, Machado M, Tarazona-Santos E.","BMC Bioinformatics","2012","1471-2105","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","204.95322",NA,"13","163","PMC3496580",NA,NA,"code.google.com"
"719","22563066","MED","22563066","10.1093/bioinformatics/bts260","Identifying differentially expressed transcripts from RNA-seq data with biological variation.","Glaus P, Honkela A, Rattray M.","Bioinformatics","2012","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","20","Y","Y","N","N","N","204.8785","13","28","1721-1728","PMC3381971",NA,NA,"code.google.com"
"720","23189163","MED","23189163","10.1371/journal.pone.0049785","OTU analysis using metagenomic shotgun sequencing data.","Hao X, Chen T.","PLoS One","2012","1932-6203","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","2","Y","Y","N","N","N","204.8785","11","7","e49785","PMC3506635",NA,NA,"code.google.com"
"721","23049804","MED","23049804","10.1371/journal.pone.0045474","GlycReSoft: a software package for automated recognition of glycans from LC/MS data.","Maxwell E, Tan Y, Tan Y, Hu H, Benson G, Aizikov K, Conley S, Staples GO, Slysz GW, Smith RD, Zaia J.","PLoS One","2012","1932-6203","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","8","Y","Y","N","N","N","204.8785","9","7","e45474","PMC3458864",NA,NA,"code.google.com"
"722","22763442","MED","22763442","10.1038/nature11323","IDH1(R132H) mutation increases murine haematopoietic progenitors and alters epigenetics.","Sasaki M, Knobbe CB, Munger JC, Lind EF, Brenner D, BrÃ¼stle A, Harris IS, Holmes R, Wakeham A, Haight J, You-Ten A, Li WY, Schalm S, Su SM, Virtanen C, Reifenberger G, Ohashi PS, Barber DL, Figueroa ME, Melnick A, ZÃºÃ±iga-PflÃ¼cker JC, Mak TW.","Nature","2012","0028-0836","journal article; research support, non-u.s. gov't; research-article","N","Y","Y","89","Y","Y","Y","N","N","204.8785","7413","488","656-659","PMC4005896",NA,"OMIMUNIPROTARXPR","code.google.com"
"723","22645166","MED","22645166","10.1093/bioinformatics/bts317","An integrated open framework for thermodynamics of reactions that combines accuracy and coverage.","Noor E, Bar-Even A, Flamholz A, Lubling Y, Davidi D, Milo R.","Bioinformatics","2012","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","13","Y","Y","N","N","N","204.8785","15","28","2037-2044","PMC3400964",NA,NA,"code.google.com"
"724","22768292","MED","22768292","10.1371/journal.pone.0038586","Exposure render: an interactive photo-realistic volume rendering framework.","Kroes T, Post FH, Botha CP.","PLoS One","2012","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","204.8785","7","7","e38586","PMC3388083",NA,NA,"code.google.com"
"725","22961259","MED","22961259","10.1007/s00335-012-9421-3","The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data.","Smith CL, Eppig JT.","Mamm Genome","2012","0938-8990","journal article; research support, n.i.h., extramural; review-article","Y","Y","Y","16","Y","Y","N","N","N","204.8785","9-10","23","653-668","PMC3463787",NA,NA,"code.google.com"
"726","22531217","MED","22531217","10.1093/bioinformatics/bts198","Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm.","LÃ¶ytynoja A, Vilella AJ, Goldman N.","Bioinformatics","2012","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","17","Y","Y","N","N","N","204.8785","13","28","1684-1691","PMC3381962",NA,NA,"code.google.com"
"727","24187947","MED","24187947","10.1021/ac402731h","Comment on ""Computation of isotopic peak center-mass distribution by fourier transform"".","Hu H, Dittwald P, Zaia J, Valkenborg D.","Anal Chem","2013","0003-2700","comment; letter; research support, non-u.s. gov't; article-commentary","N","Y","N","0","Y","Y","N","N","N","204.69772","24","85","12189-12192","PMC4119064",NA,NA,"code.google.com"
"728","22075991","MED","22075991","10.1093/nar/gkr925","The Gene Wiki in 2011: community intelligence applied to human gene annotation.","Good BM, Clarke EL, de Alfaro L, Su AI.","Nucleic Acids Res","2012","0305-1048","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","12","Y","Y","N","N","N","204.6712","database issue","40","d1255-61","PMC3245148",NA,NA,"code.google.com"
"729","23046488","MED","23046488","10.1186/1687-4153-2012-15","Fastbreak: a tool for analysis and visualization of structural variations in genomic data.","Bressler R, Lin J, Eakin A, Robinson T, Kreisberg R, Rovira H, Knijnenburg T, Boyle J, Shmulevich I.","EURASIP J Bioinform Syst Biol","2012","1687-4145","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","204.6712","1","2012","15","PMC3605143",NA,NA,"code.google.com"
"730","21748797","MED","21748797","10.1002/mrm.23072","Complex and magnitude-only preprocessing of 2D and 3D BOLD fMRI data at 7 T.","Barry RL, Strother SC, Gore JC.","Magn Reson Med","2012","0740-3194","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","4","Y","Y","N","N","N","204.6712","3","67","867-871","PMC3193895",NA,NA,"code.google.com"
"731","22406831","MED","22406831","10.1093/nar/gks228","Novel insight into the non-coding repertoire through deep sequencing analysis.","Isakov O, Ronen R, Kovarsky J, Gabay A, Gan I, Modai S, Shomron N.","Nucleic Acids Res","2012","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","5","Y","Y","N","N","N","204.6712","11","40","e86","PMC3367215",NA,NA,"code.google.com"
"732","22425670","MED","22425670","10.1016/j.neuroimage.2012.03.016","Multivariate pattern analysis of fMRI: the early beginnings.","Haxby JV.","Neuroimage","2012","1053-8119","historical article; journal article; review; research-article","N","Y","Y","17","Y","Y","N","N","N","204.6712","2","62","852-855","PMC3389290",NA,NA,"code.google.com"
"733","22558468","MED","22558468","10.1371/journal.pone.0036456","Determining the repertoire of immunodominant proteins via whole-genome amplification of intracellular pathogens.","Dark MJ, Lundgren AM, Barbet AF.","PLoS One","2012","1932-6203","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","5","Y","Y","N","N","N","204.6712","4","7","e36456","PMC3340345",NA,NA,"code.google.com"
"734","22985071","MED","22985071","10.1021/ac302232c","Top-down approach for the direct characterization of low molecular weight heparins using LC-FT-MS.","Li L, Zhang F, Zaia J, Linhardt RJ.","Anal Chem","2012","0003-2700","journal article; research support, n.i.h., extramural; research-article","N","Y","Y","13","Y","Y","N","N","N","204.6712","20","84","8822-8829","PMC3479637",NA,NA,"code.google.com"
"735","23216909","MED","23216909","10.1186/1471-2105-13-324","Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework.","Lewis S, Csordas A, Killcoyne S, Hermjakob H, Hoopmann MR, Moritz RL, Deutsch EW, Boyle J.","BMC Bioinformatics","2012","1471-2105","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research support, american recovery and reinvestment act; product-review","Y","Y","Y","4","Y","Y","N","N","N","204.6712",NA,"13","324","PMC3538679",NA,NA,"code.google.com"
"736","21850031","MED","21850031","10.1038/gene.2011.56","Evidence for two independent associations with type 1 diabetes at the 12q13 locus.","Keene KL, Quinlan AR, Hou X, Hall IM, Mychaleckyj JC, Onengut-Gumuscu S, Concannon P.","Genes Immun","2012","1466-4879","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","5","Y","Y","N","N","Y","204.6712","1","13","66-70","PMC3285513","refsnp",NA,"code.google.com"
"737","22969026","MED","22969026","10.1002/pmic.201270126","Ten years of standardizing proteomic data: a report on the HUPO-PSI Spring Workshop: April 12-14th, 2012, San Diego, USA.","Orchard S, Binz PA, Borchers C, Gilson MK, Jones AR, Nicola G, Vizcaino JA, Deutsch EW, Hermjakob H.","Proteomics","2012","1615-9853","consensus development conference; historical article; journal article; research-article","N","Y","Y","5","Y","Y","N","N","N","204.6712","18","12","2767-2772","PMC3895333",NA,NA,"code.google.com"
"738","23189198","MED","23189198","10.1371/journal.pone.0050362","De-MetaST-BLAST: a tool for the validation of degenerate primer sets and data mining of publicly available metagenomes.","Gulvik CA, Effler TC, Wilhelm SW, Buchan A.","PLoS One","2012","1932-6203","journal article; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","0","Y","Y","N","N","N","204.6712","11","7","e50362","PMC3506598",NA,NA,"code.google.com"
"739","23192027","MED","23192027","10.1107/s174430911204571x","Structure determination of LpxA from the lipopolysaccharide-synthesis pathway of Acinetobacter baumannii.","Badger J, Chie-Leon B, Logan C, Sridhar V, Sankaran B, Zwart PH, Nienaber V.","Acta Crystallogr Sect F Struct Biol Cryst Commun","2012","1744-3091","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","Y","1","N","Y","Y","N","Y","204.6712","pt 12","68","1477-1481","PMC3509968","pdb","PDBUNIPROT","code.google.com"
"740","23275754","MED","23275754","10.3897/zookeys.247.3812","High mitochondrial DNA sequence divergence in New Guinea Carabdytes stream beetles and the taxonomist's dilemma when other evidence is kind of subtleâ¦ (andÂ collecting localities are far far away).","Skale A, TÃ¤nzler R, Hendrich L, Balke M.","Zookeys","2012","1313-2989","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","204.6712","247",NA,"31-43","PMC3520138",NA,NA,"code.google.com"
"741","23028371","MED","23028371","10.1371/journal.pgen.1002972","Tethering of the conserved piggyBac transposase fusion protein CSB-PGBD3 to chromosomal AP-1 proteins regulates expression of nearby genes in humans.","Gray LT, Fong KK, Pavelitz T, Weiner AM.","PLoS Genet","2012","1553-7390","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","9","Y","Y","Y","N","N","204.6712","9","8","e1002972","PMC3459987",NA,"ARXPR","code.google.com"
"742","23029292","MED","23029292","10.1371/journal.pone.0045879","Analyzing gene expression from whole tissue vs. different cell types reveals the central role of neurons in predicting severity of Alzheimer's disease.","Stempler S, Ruppin E.","PLoS One","2012","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","3","Y","Y","N","N","N","204.6712","9","7","e45879","PMC3461041",NA,NA,"code.google.com"
"743","23060432","MED","23060432","10.1093/database/bas033","The Units Ontology: a tool for integrating units of measurement in science.","Gkoutos GV, Schofield PN, Hoehndorf R.","Database (Oxford)","2012","1758-0463","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","6","Y","Y","N","N","N","204.6712",NA,"2012","bas033","PMC3468815",NA,NA,"code.google.com"
"744","22647087","MED","22647087","10.1186/1471-2105-13-115","PyMS: a Python toolkit for processing of gas chromatography-mass spectrometry (GC-MS) data. Application and comparative study of selected tools.","O'Callaghan S, De Souza DP, Isaac A, Wang Q, Hodkinson L, Olshansky M, Erwin T, Appelbe B, Tull DL, Roessner U, Bacic A, McConville MJ, LikiÄ VA.","BMC Bioinformatics","2012","1471-2105","journal article; research support, non-u.s. gov't; comparative study; product-review","Y","Y","Y","6","Y","Y","N","N","N","204.6712",NA,"13","115","PMC3533878",NA,NA,"code.google.com"
"745","22695947","MED","22695947","10.1007/s13244-012-0166-z","Stereology: a novel technique for rapid assessment of liver volume.","Torkzad MR, NorÃ©n A, Kullberg J.","Insights Imaging","2012","1869-4101","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","204.6712","4","3","387-393","PMC3481078",NA,NA,"code.google.com"
"746","22804230","MED","22804230","10.1089/omi.2011.0137","The effect of peptide identification search algorithms on MS2-based label-free protein quantification.","Degroeve S, Staes A, De Bock PJ, Martens L.","OMICS","2012","1536-2310","journal article; research support, non-u.s. gov't; research-article","N","Y","Y","0","Y","Y","N","N","N","204.6712","9","16","443-448","PMC3437043",NA,NA,"code.google.com"
"747","22224819","MED","22224819","10.1089/thy.2011.0309","Common genetic variants in sex hormone pathway genes and papillary thyroid cancer risk.","Schonfeld SJ, Neta G, Sturgis EM, Pfeiffer RM, Hutchinson AA, Xu L, Wheeler W, GuÃ©nel P, Rajaraman P, de Vathaire F, Ron E, Tucker MA, Chanock SJ, Sigurdson AJ, Brenner AV.","Thyroid","2012","1050-7256","journal article; research support, n.i.h., extramural; research support, n.i.h., intramural; research-article","N","Y","Y","3","Y","Y","N","N","Y","204.6712","2","22","151-156","PMC3271376","refsnp",NA,"code.google.com"
"748","22298319","MED","22298319","10.1002/jcc.22927","Exploring biological electron transfer pathway dynamics with the Pathways plugin for VMD.","Balabin IA, Hu X, Beratan DN.","J Comput Chem","2012","0192-8651","journal article; research support, n.i.h., extramural; research-article","N","Y","Y","5","Y","Y","N","N","Y","204.6712","8","33","906-910","PMC3288650","pdb",NA,"code.google.com"
"749","22301088","MED","22301088","10.1186/1758-2946-4-3","LICSS - a chemical spreadsheet in microsoft excel.","Lawson KR, Lawson J.","J Cheminform","2012","1758-2946","journal article; product-review","Y","Y","Y","2","Y","Y","N","N","N","204.6712","1","4","3","PMC3310842",NA,NA,"code.google.com"
"750","22319566","MED","22319566","10.1371/journal.pone.0030370","CAPRG: sequence assembling pipeline for next generation sequencing of non-model organisms.","Rawat A, Elasri MO, Gust KA, George G, Pham D, Scanlan LD, Vulpe C, Perkins EJ.","PLoS One","2012","1932-6203","evaluation studies; journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","4","Y","Y","N","N","N","204.6712","2","7","e30370","PMC3272009",NA,NA,"code.google.com"
"751","23346047","MED","23346047","10.3389/fncir.2012.00098","Closed-Loop, Multichannel Experimentation Using the Open-Source NeuroRighter Electrophysiology Platform.","Newman JP, Zeller-Townson R, Fong MF, Arcot Desai S, Gross RE, Potter SM.","Front Neural Circuits","2012","1662-5110","journal article; research-article","Y","Y","Y","10","Y","Y","N","N","N","204.6712",NA,"6","98","PMC3548271",NA,NA,"code.google.com"
"752","23046555","MED","23046555","10.1186/2041-1480-3-s2-s1","Quantitative comparison of mapping methods between Human and Mammalian Phenotype Ontology.","Oellrich A, Gkoutos GV, Hoehndorf R, Rebholz-Schuhmann D.","J Biomed Semantics","2012","2041-1480","journal article; research-article","Y","Y","Y","2","Y","Y","N","N","N","204.6712","Suppl 2","3 Suppl 2","s1","PMC3448526",NA,NA,"code.google.com"
"753","22693222","MED","22693222","10.1093/nar/gks514","BioMe: biologically relevant metals.","Tus A, Rakipovic A, Peretin G, Tomic S, Sikic M.","Nucleic Acids Res","2012","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","6","Y","Y","N","N","N","204.6712","web server issue","40","w352-7","PMC3394320",NA,NA,"code.google.com"
"754","22886559","MED","22886559","10.1007/s00439-012-1212-0","Genome-wide association study of glioma and meta-analysis.","Rajaraman P, Melin BS, Wang Z, McKean-Cowdin R, Michaud DS, Wang SS, Bondy M, Houlston R, Jenkins RB, Wrensch M, Yeager M, Ahlbom A, Albanes D, Andersson U, Freeman LE, Buring JE, Butler MA, Braganza M, Carreon T, Feychting M, Fleming SJ, Gapstur SM, Gaziano JM, Giles GG, Hallmans G, Henriksson R, Hoffman-Bolton J, Inskip PD, Johansen C, Kitahara CM, Lathrop M, Liu C, Le Marchand L, Linet MS, Lonn S, Peters U, Purdue MP, Rothman N, Ruder AM, Sanson M, Sesso HD, Severi G, Shu XO, Simon M, Stampfer M, Stevens VL, Visvanathan K, White E, Wolk A, Zeleniuch-Jacquotte A, Zheng W, Decker P, Enciso-Mora V, Fridley B, Gao YT, Kosel M, Lachance DH, Lau C, Rice T, Swerdlow A, Wiemels JL, Wiencke JK, Shete S, Xiang YB, Xiao Y, Hoover RN, Fraumeni JF Jr, Chatterjee N, Hartge P, Chanock SJ.","Hum Genet","2012","0340-6717","journal article; meta-analysis; research support, n.i.h., extramural; research support, n.i.h., intramural; research-article","N","Y","Y","36","Y","Y","N","Y","N","204.6712","12","131","1877-1888","PMC3761216",NA,NA,"code.google.com"
"755","22960999","MED","22960999","10.1038/ng.2411","Genome-wide association analyses of esophageal squamous cell carcinoma in Chinese identify multiple susceptibility loci and gene-environment interactions.","Wu C, Kraft P, Zhai K, Chang J, Wang Z, Li Y, Hu Z, He Z, Jia W, Abnet CC, Liang L, Hu N, Miao X, Zhou Y, Liu Z, Zhan Q, Liu Y, Qiao Y, Zhou Y, Jin G, Guo C, Lu C, Yang H, Fu J, Yu D, Freedman ND, Ding T, Tan W, Goldstein AM, Wu T, Shen H, Ke Y, Zeng Y, Chanock SJ, Taylor PR, Lin D.","Nat Genet","2012","1061-4036","journal article; research support, non-u.s. gov't; research support, n.i.h., intramural; research-article","N","Y","Y","37","Y","Y","Y","Y","Y","204.6712","10","44","1090-1097","PMC3513832","refsnp","OMIMUNIPROT","code.google.com"
"756","22684630","MED","22684630","10.1093/nar/gks540","RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics.","Lohse M, Bolger AM, Nagel A, Fernie AR, Lunn JE, Stitt M, Usadel B.","Nucleic Acids Res","2012","0305-1048","journal article; research-article","Y","Y","Y","141","Y","Y","N","Y","N","204.6712","web server issue","40","w622-7","PMC3394330",NA,NA,"code.google.com"
"757","22064852","MED","22064852","10.1093/nar/gkr874","eQuilibrator--the biochemical thermodynamics calculator.","Flamholz A, Noor E, Bar-Even A, Milo R.","Nucleic Acids Res","2012","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","16","Y","Y","N","Y","N","204.6712","database issue","40","d770-5","PMC3245061",NA,NA,"code.google.com"
"758","22121220","MED","22121220","10.1093/nar/gkr1088","The IntAct molecular interaction database in 2012.","Kerrien S, Aranda B, Breuza L, Bridge A, Broackes-Carter F, Chen C, Duesbury M, Dumousseau M, Feuermann M, Hinz U, Jandrasits C, Jimenez RC, Khadake J, Mahadevan U, Masson P, Pedruzzi I, Pfeiffenberger E, Porras P, Raghunath A, Roechert B, Orchard S, Hermjakob H.","Nucleic Acids Res","2012","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","202","Y","Y","N","Y","N","204.6712","database issue","40","d841-6","PMC3245075",NA,NA,"code.google.com"
"759","23304386","MED","23304386",NA,"Quality assurance in LOINC using Description Logic.","Adamusiak T, Bodenreider O.","AMIA Annu Symp Proc","2012","1942-597x","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., intramural; research-article","N","Y","Y","1","Y","Y","N","N","N","204.6712",NA,"2012","1099-1108","PMC3540427",NA,NA,"code.google.com"
"760","22023727","MED","22023727","10.1016/j.conb.2011.10.001","Towards reliable spike-train recordings from thousands of neurons with multielectrodes.","Einevoll GT, Franke F, Hagen E, Pouzat C, Harris KD.","Curr Opin Neurobiol","2012","0959-4388","journal article; review; research support, non-u.s. gov't; research-article","N","Y","Y","19","Y","Y","N","N","N","204.6712","1","22","11-17","PMC3314330",NA,NA,"code.google.com"
"761","22588877","MED","22588877","10.1158/2159-8290.cd-12-0095","The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data.","Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA, Jacobsen A, Byrne CJ, Heuer ML, Larsson E, Antipin Y, Reva B, Goldberg AP, Sander C, Schultz N.","Cancer Discov","2012","2159-8274","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","281","Y","Y","N","N","N","204.6712","5","2","401-404","PMC3956037",NA,NA,"code.google.com"
"762","23022100","MED","23022100","10.1016/j.ajhg.2012.08.021","Discovery and fine mapping of serum protein loci through transethnic meta-analysis.","Franceschini N, van Rooij FJ, Prins BP, Feitosa MF, Karakas M, Eckfeldt JH, Folsom AR, Kopp J, Vaez A, Andrews JS, Baumert J, Boraska V, Broer L, Hayward C, Ngwa JS, Okada Y, Polasek O, Westra HJ, Wang YA, Del Greco M F, Glazer NL, Kapur K, Kema IP, Lopez LM, Schillert A, Smith AV, Winkler CA, Zgaga L, LifeLines Cohort Study, Bandinelli S, Bergmann S, Boban M, Bochud M, Chen YD, Davies G, Dehghan A, Ding J, Doering A, Durda JP, Ferrucci L, Franco OH, Franke L, Gunjaca G, Hofman A, Hsu FC, Kolcic I, Kraja A, Kubo M, Lackner KJ, Launer L, Loehr LR, Li G, Meisinger C, Nakamura Y, Schwienbacher C, Starr JM, Takahashi A, Torlak V, Uitterlinden AG, Vitart V, Waldenberger M, Wild PS, Kirin M, Zeller T, Zemunik T, Zhang Q, Ziegler A, Blankenberg S, Boerwinkle E, Borecki IB, Campbell H, Deary IJ, Frayling TM, Gieger C, Harris TB, Hicks AA, Koenig W, O' Donnell CJ, Fox CS, Pramstaller PP, Psaty BM, Reiner AP, Rotter JI, Rudan I, Snieder H, Tanaka T, van Duijn CM, Vollenweider P, Waeber G, Wilson JF, Witteman JC, Wolffenbuttel BH, Wright AF, Wu Q, Liu Y, Jenny NS, North KE, Felix JF, Alizadeh BZ, Cupples LA, Perry JR, Morris AP.","Am J Hum Genet","2012","0002-9297","journal article; meta-analysis; research support, non-u.s. gov't; research support, n.i.h., extramural; research support, u.s. gov't, p.h.s.; brief-report","N","Y","Y","15","Y","Y","N","Y","Y","204.6712","4","91","744-753","PMC3484648","refsnp; refseq",NA,"code.google.com"
"763","22988083","MED","22988083","10.1073/pnas.1213621109","Hemisphere-scale differences in conifer evolutionary dynamics.","Leslie AB, Beaulieu JM, Rai HS, Crane PR, Donoghue MJ, Mathews S.","Proc Natl Acad Sci U S A","2012","0027-8424","journal article; research support, u.s. gov't, non-p.h.s.; research-article","N","Y","Y","11","Y","Y","Y","N","Y","204.6712","40","109","16217-16221","PMC3479534","gen","EMBLUNIPROT","code.google.com"
"764","22139937","MED","22139937","10.1093/nar/gkr1134","NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB.","Doreleijers JF, Vranken WF, Schulte C, Markley JL, Ulrich EL, Vriend G, Vuister GW.","Nucleic Acids Res","2012","0305-1048","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","9","Y","Y","N","Y","Y","204.6712","database issue","40","d519-24","PMC3245154","pdb",NA,"code.google.com"
"765","22457641","MED","22457641","10.1371/journal.pgen.1002599","Widespread site-dependent buffering of human regulatory polymorphism.","Maurano MT, Wang H, Kutyavin T, Stamatoyannopoulos JA.","PLoS Genet","2012","1553-7390","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","21","Y","Y","N","N","N","204.2744","3","8","e1002599","PMC3310774",NA,NA,"code.google.com"
"766","22496762","MED","22496762","10.1371/journal.pone.0033744","Functional annotation of hierarchical modularity.","Padmanabhan K, Wang K, Samatova NF.","PLoS One","2012","1932-6203","journal article; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","0","Y","Y","N","N","N","204.2744","4","7","e33744","PMC3319548",NA,NA,"code.google.com"
"767","22506001","MED","22506001","10.1371/journal.pone.0033384","Multi-dimensional, mesoscopic Monte Carlo simulations of inhomogeneous reaction-drift-diffusion systems on graphics-processing units.","Vigelius M, Meyer B.","PLoS One","2012","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","3","Y","Y","N","N","N","204.2744","4","7","e33384","PMC3323590",NA,NA,"code.google.com"
"768","23034162","MED","23034162","10.1186/gb-2012-13-10-r82","BatMeth: improved mapper for bisulfite sequencing reads on DNA methylation.","Lim JQ, Tennakoon C, Li G, Wong E, Ruan Y, Wei CL, Sung WK.","Genome Biol","2012","1465-6906","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","7","Y","Y","N","N","N","204.2744","10","13","r82","PMC3491410",NA,NA,"code.google.com"
"769","24704847","MED","24704847","10.3390/genes3010138","The genetics of symbiotic nitrogen fixation: comparative genomics of 14 rhizobia strains by resolution of protein clusters.","Black M, Moolhuijzen P, Chapman B, Barrero R, Howieson J, Hungria M, Bellgard M.","Genes (Basel)","2012","2073-4425","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","204.2744","1","3","138-166","PMC3899959",NA,NA,"code.google.com"
"770","23144830","MED","23144830","10.1371/journal.pone.0047836","The limits of de novo DNA motif discovery.","Simcha D, Price ND, Geman D.","PLoS One","2012","1932-6203","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","204.2744","11","7","e47836","PMC3492406",NA,NA,"code.google.com"
"771","22804616","MED","22804616","10.1089/omi.2012.0022","A critical appraisal of techniques, software packages, and standards for quantitative proteomic analysis.","Gonzalez-Galarza FF, Lawless C, Hubbard SJ, Fan J, Bessant C, Hermjakob H, Jones AR.","OMICS","2012","1536-2310","journal article; research support, non-u.s. gov't; review-article","N","Y","Y","10","Y","Y","N","N","N","204.2744","9","16","431-442","PMC3437040",NA,NA,"code.google.com"
"772","22574192","MED","22574192","10.1371/journal.pone.0036598","ApicoAP: the first computational model for identifying apicoplast-targeted proteins in multiple species of Apicomplexa.","Cilingir G, Broschat SL, Lau AO.","PLoS One","2012","1932-6203","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","6","Y","Y","N","N","N","204.2744","5","7","e36598","PMC3344922",NA,NA,"code.google.com"
"773","23189036","MED","23189036","10.3389/fnins.2012.00168","Reading visual braille with a retinal prosthesis.","Lauritzen TZ, Harris J, Mohand-Said S, Sahel JA, Dorn JD, McClure K, Greenberg RJ.","Front Neurosci","2012","1662-4548","journal article; research-article","Y","Y","Y","2","Y","Y","N","N","N","204.24405",NA,"6","168","PMC3504310",NA,NA,"code.google.com"
"774","22171334","MED","22171334","10.1093/bioinformatics/btr686","Detection of microRNAs in color space.","Marco A, Griffiths-Jones S.","Bioinformatics","2012","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","9","Y","Y","N","N","N","204.24405","3","28","318-323","PMC3268249",NA,NA,"code.google.com"
"775","22303493","MED","22303493","10.1371/journal.pntd.0001494","WormAssay: a novel computer application for whole-plate motion-based screening of macroscopic parasites.","Marcellino C, Gut J, Lim KC, Singh R, McKerrow J, Sakanari J.","PLoS Negl Trop Dis","2012","1935-2727","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","8","Y","Y","N","N","N","204.24405","1","6","e1494","PMC3269415",NA,NA,"code.google.com"
"776","22373327","MED","22373327","10.1186/1471-2105-13-s1-s2","SPARQL assist language-neutral query composer.","McCarthy L, Vandervalk B, Wilkinson M.","BMC Bioinformatics","2012","1471-2105","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","N","N","N","204.24405","Suppl 1","13 Suppl 1","s2","PMC3471353",NA,NA,"code.google.com"
"777","22415040","MED","22415040","10.1074/mcp.m111.016808","Retrieving backbone string neighbors provides insights into structural modeling of membrane proteins.","Sun JM, Li TH, Cong PS, Tang SN, Xiong WW.","Mol Cell Proteomics","2012","1535-9476","journal article; research support, non-u.s. gov't; research-article","N","Y","Y","0","Y","Y","N","N","Y","204.24405","7","11","m111.016808","PMC3394956","pdb",NA,"code.google.com"
"778","22434844","MED","22434844","10.1093/database/bas010","Argo: an integrative, interactive, text mining-based workbench supporting curation.","Rak R, Rowley A, Black W, Ananiadou S.","Database (Oxford)","2012","1758-0463","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","3","Y","Y","N","N","N","204.24405",NA,"2012","bas010","PMC3308166",NA,NA,"code.google.com"
"779","22468268","MED","22468268","10.1002/pros.21450","Comprehensive resequence analysis of a 123-kb region of chromosome 11q13 associated with prostate cancer.","Chung CC, Boland J, Yeager M, Jacobs KB, Zhang X, Deng Z, Matthews C, Berndt SI, Chanock SJ.","Prostate","2012","0270-4137","journal article; research support, n.i.h., intramural; research-article","N","Y","Y","2","Y","Y","N","N","Y","204.24405","5","72","476-486","PMC3325513","refsnp; refseq",NA,"code.google.com"
"780","22470575","MED","22470575","10.1371/journal.pone.0034484","When subterranean termites challenge the rules of fungal epizootics.","Chouvenc T, Su NY.","PLoS One","2012","1932-6203","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","5","Y","Y","N","N","N","204.24405","3","7","e34484","PMC3314638",NA,NA,"code.google.com"
"781","22504272","MED","22504272","10.1016/j.ygcen.2012.03.010","Conservation of the photoperiodic neuroendocrine axis among vertebrates: evidence from the teleost fish, Gasterosteus aculeatus.","O'Brien CS, Bourdo R, Bradshaw WE, Holzapfel CM, Cresko WA.","Gen Comp Endocrinol","2012","0016-6480","journal article; research support, u.s. gov't, non-p.h.s.; research-article","N","Y","Y","2","Y","Y","N","N","Y","204.24405","1","178","19-27","PMC3389224","ensembl",NA,"code.google.com"
"782","22522262","MED","22522262","10.1038/nchem.1299","Protein fold determined by paramagnetic magic-angle spinning solid-state NMR spectroscopy.","Sengupta I, Nadaud PS, Helmus JJ, Schwieters CD, Jaroniec CP.","Nat Chem","2012","1755-4330","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., intramural; research-article","Y","Y","Y","15","Y","Y","N","N","Y","204.24405","5","4","410-417","PMC3335742","pdb",NA,"code.google.com"
"783","22574135","MED","22574135","10.1371/journal.pone.0036060","GHOSTM: a GPU-accelerated homology search tool for metagenomics.","Suzuki S, Ishida T, Kurokawa K, Akiyama Y.","PLoS One","2012","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","204.24405","5","7","e36060","PMC3344842",NA,NA,"code.google.com"
"784","22829875","MED","22829875","10.1371/journal.pone.0040506","Using GFP video to track 3D movement and conditional gene expression in free-moving flies.","Ardekani R, Huang YM, Sancheti P, Stanciauskas R, TavarÃ© S, Tower J.","PLoS One","2012","1932-6203","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","1","Y","Y","Y","Y","N","204.24405","7","7","e40506","PMC3400653",NA,"UNIPROT","code.google.com"
"785","23189202","MED","23189202","10.1371/journal.pone.0050441","Multi-year lags between forest browning and soil respiration at high northern latitudes.","Bond-Lamberty B, Bunn AG, Thomson AM.","PLoS One","2012","1932-6203","journal article; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","3","Y","Y","N","N","N","204.24405","11","7","e50441","PMC3506603",NA,NA,"code.google.com"
"786","23320851","MED","23320851","10.1186/1471-2105-13-s13-s2","Graph-based signal integration for high-throughput phenotyping.","Herskovic JR, Subramanian D, Cohen T, Bozzo-Silva PA, Bearden CF, Bernstam EV.","BMC Bioinformatics","2012","1471-2105","evaluation studies; journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","1","Y","Y","N","N","N","204.24405","Suppl 13","13 Suppl 13","s2","PMC3426800",NA,NA,"code.google.com"
"787","22859875","MED","22859875","10.3897/zookeys.209.3313","Mass digitization of scientific collections: New opportunities to transform the use of biological specimens and underwrite biodiversity science.","Beaman RS, Cellinese N.","Zookeys","2012","1313-2989","journal article; research-article","Y","Y","Y","4","Y","Y","N","N","N","204.24405","209",NA,"7-17","PMC3406463",NA,NA,"code.google.com"
"788","22889144","MED","22889144","10.1186/1748-717x-7-139","Seminal vesicle interfraction displacement and margins in image guided radiotherapy for prostate cancer.","Mak D, Gill S, Paul R, Stillie A, Haworth A, Kron T, Cramb J, Knight K, Thomas J, Duchesne G, Foroudi F.","Radiat Oncol","2012","1748-717x","journal article; research-article","Y","Y","Y","4","Y","Y","N","N","N","204.24405",NA,"7","139","PMC3487760",NA,NA,"code.google.com"
"789","22955980","MED","22955980","10.1101/gr.136101.111","Widespread plasticity in CTCF occupancy linked to DNA methylation.","Wang H, Maurano MT, Qu H, Varley KE, Gertz J, Pauli F, Lee K, Canfield T, Weaver M, Sandstrom R, Thurman RE, Kaul R, Myers RM, Stamatoyannopoulos JA.","Genome Res","2012","1088-9051","journal article; research support, n.i.h., extramural; research-article","N","Y","Y","56","Y","Y","Y","N","N","204.24405","9","22","1680-1688","PMC3431485",NA,"ARXPR","code.google.com"
"790","22959976","MED","22959976","10.1016/j.arcmed.2012.08.005","Population-based risk factors for elevated alanine aminotransferase in a South Texas Mexican-American population.","Qu HQ, Li Q, Grove ML, Lu Y, Pan JJ, Rentfro AR, Bickel PE, Fallon MB, Hanis CL, Boerwinkle E, McCormick JB, Fisher-Hoch SP.","Arch Med Res","2012","0188-4409","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","1","Y","Y","N","N","Y","204.24405","6","43","482-488","PMC3590902","refsnp",NA,"code.google.com"
"791","23126499","MED","23126499","10.1186/1471-2105-13-288","PAnalyzer: a software tool for protein inference in shotgun proteomics.","Prieto G, Aloria K, Osinalde N, Fullaondo A, Arizmendi JM, Matthiesen R.","BMC Bioinformatics","2012","1471-2105","journal article; research support, non-u.s. gov't; product-review","Y","Y","Y","2","Y","Y","N","N","N","204.24405",NA,"13","288","PMC3548767",NA,NA,"code.google.com"
"792","22625207","MED","22625207","10.2217/nnm.11.177","Citrullination of proteins: a common post-translational modification pathway induced by different nanoparticles in vitro and in vivo.","Mohamed BM, Verma NK, Davies AM, McGowan A, Crosbie-Staunton K, Prina-Mello A, Kelleher D, Botting CH, Causey CP, Thompson PR, Pruijn GJ, Kisin ER, Tkach AV, Shvedova AA, Volkov Y.","Nanomedicine (Lond)","2012","1743-5889","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","8","Y","Y","N","N","N","204.24405","8","7","1181-1195","PMC3465773",NA,NA,"code.google.com"
"793","22630360","MED","22630360","10.1111/j.1471-1842.2012.00977.x","Dissemination of public health information: key tools utilised by the NECOBELAC network in Europe and Latin America.","De Castro P, Marsili D, Poltronieri E, CalderÃ³n CA.","Health Info Libr J","2012","1471-1834","journal article; research-article","Y","Y","Y","3","Y","Y","N","N","N","204.24405","2","29","119-130","PMC3440589",NA,NA,"code.google.com"
"794","22689768","MED","22689768","10.1093/bioinformatics/bts221","Improved synapse detection for mGRASP-assisted brain connectivity mapping.","Feng L, Zhao T, Kim J.","Bioinformatics","2012","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","N","N","N","204.24405","12","28","i25-31","PMC3371853",NA,NA,"code.google.com"
"795","22748135","MED","22748135","10.1186/1756-0500-5-337","AdapterRemoval: easy cleaning of next-generation sequencing reads.","Lindgreen S.","BMC Res Notes","2012","1756-0500","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","39","Y","Y","N","Y","N","204.24405",NA,"5","337","PMC3532080",NA,NA,"code.google.com"
"796","22779049","MED","22779049",NA,"Formal concept analysis of disease similarity.","Keller BJ, Eichinger F, Kretzler M.","AMIA Summits on Translational Science Proceedings","2012","2153-4063","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","204.24405",NA,"2012","42-51","PMC3392047",NA,NA,"code.google.com"
"797","22778781","MED","22778781","10.1155/2012/968083","Application of metabolomics in traditional chinese medicine differentiation of deficiency and excess syndromes in patients with diabetes mellitus.","Wu T, Yang M, Wei HF, He SH, Wang SC, Ji G.","Evid Based Complement Alternat Med","2012","1741-427x","journal article; research-article","Y","Y","Y","4","Y","Y","N","N","N","204.24405",NA,"2012","968083","PMC3384925",NA,NA,"code.google.com"
"798","22827772","MED","22827772","10.1186/1471-2164-13-340","How accurate can genetic predictions be?","Dreyfuss JM, Levner D, Galagan JE, Church GM, Ramoni MF.","BMC Genomics","2012","1471-2164","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","204.24405",NA,"13","340","PMC3534619",NA,NA,"code.google.com"
"799","22842118","MED","22842118","10.2390/biecoll-jib-2012-208","Coex-Rank: An approach incorporating co-expression information for combined analysis of microarray data.","Cai J, Keen HL, Sigmund CD, Casavant TL.","J Integr Bioinform","2012","1613-4516","journal article; research support, n.i.h., extramural; research-article","N","Y","Y","1","Y","Y","N","N","N","204.24405","1","9","208","PMC3482100",NA,NA,"code.google.com"
"800","22411907","MED","22411907","10.1002/cyto.a.22034","Enabling user-guided segmentation and tracking of surface-labeled cells in time-lapse image sets of living tissues.","Mashburn DN, Lynch HE, Ma X, Hutson MS.","Cytometry A","2012","1552-4922","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","Y","4","Y","Y","N","Y","N","204.24405","5","81","409-418","PMC3331924",NA,NA,"code.google.com"
"801","22945789","MED","22945789","10.1093/bioinformatics/bts525","JEnsembl: a version-aware Java API to Ensembl data systems.","Paterson T, Law A.","Bioinformatics","2012","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","Y","204.24405","21","28","2724-2731","PMC3476335","ensembl",NA,"code.google.com"
"802","22032952","MED","22032952","10.1016/j.ygeno.2011.09.003","Genome-wide transcriptome analysis in murine neural retina using high-throughput RNA sequencing.","Gamsiz ED, Ouyang Q, Schmidt M, Nagpal S, Morrow EM.","Genomics","2012","0888-7543","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","9","Y","Y","N","N","N","204.24405","1","99","44-51","PMC3392719",NA,NA,"code.google.com"
"803","22343411","MED","22343411","10.1093/hmg/dds055","Whole-genome sequencing reveals a coding non-pathogenic variant tagging a non-coding pathogenic hexanucleotide repeat expansion in C9orf72 as cause of amyotrophic lateral sclerosis.","Herdewyn S, Zhao H, Moisse M, Race V, Matthijs G, Reumers J, Kusters B, Schelhaas HJ, van den Berg LH, Goris A, Robberecht W, Lambrechts D, Van Damme P.","Hum Mol Genet","2012","0964-6906","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","11","Y","Y","Y","N","N","204.24405","11","21","2412-2419","PMC3349421",NA,"UNIPROT","code.google.com"
"804","23143601","MED","23143601","10.1038/ng.2456","Genome-wide association analysis identifies new lung cancer susceptibility loci in never-smoking women in Asia.","Lan Q, Hsiung CA, Matsuo K, Hong YC, Seow A, Wang Z, Hosgood HD 3rd, Chen K, Wang JC, Chatterjee N, Hu W, Wong MP, Zheng W, Caporaso N, Park JY, Chen CJ, Kim YH, Kim YT, Landi MT, Shen H, Lawrence C, Burdett L, Yeager M, Yuenger J, Jacobs KB, Chang IS, Mitsudomi T, Kim HN, Chang GC, Bassig BA, Tucker M, Wei F, Yin Z, Wu C, An SJ, Qian B, Lee VH, Lu D, Liu J, Jeon HS, Hsiao CF, Sung JS, Kim JH, Gao YT, Tsai YH, Jung YJ, Guo H, Hu Z, Hutchinson A, Wang WC, Klein R, Chung CC, Oh IJ, Chen KY, Berndt SI, He X, Wu W, Chang J, Zhang XC, Huang MS, Zheng H, Wang J, Zhao X, Li Y, Choi JE, Su WC, Park KH, Sung SW, Shu XO, Chen YM, Liu L, Kang CH, Hu L, Chen CH, Pao W, Kim YC, Yang TY, Xu J, Guan P, Tan W, Su J, Wang CL, Li H, Sihoe AD, Zhao Z, Chen Y, Choi YY, Hung JY, Kim JS, Yoon HI, Cai Q, Lin CC, Park IK, Xu P, Dong J, Kim C, He Q, Perng RP, Kohno T, Kweon SS, Chen CY, Vermeulen R, Wu J, Lim WY, Chen KC, Chow WH, Ji BT, Chan JK, Chu M, Li YJ, Yokota J, Li J, Chen H, Xiang YB, Yu CJ, Kunitoh H, Wu G, Jin L, Lo YL, Shiraishi K, Chen YH, Lin HC, Wu T, Wu YL, Yang PC, Zhou B, Shin MH, Fraumeni JF Jr, Lin D, Chanock SJ, Rothman N.","Nat Genet","2012","1061-4036","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research support, n.i.h., intramural; research-article","N","Y","N","38","Y","Y","N","Y","Y","204.24405","12","44","1330-1335","PMC4169232","refsnp",NA,"code.google.com"
"805","22581176","MED","22581176","10.1093/bioinformatics/bts270","Software support for SBGN maps: SBGN-ML and LibSBGN.","van Iersel MP, VillÃ©ger AC, Czauderna T, Boyd SE, Bergmann FT, Luna A, Demir E, Sorokin A, Dogrusoz U, Matsuoka Y, Funahashi A, Aladjem MI, Mi H, Moodie SL, Kitano H, Le NovÃ¨re N, Schreiber F.","Bioinformatics","2012","1367-4803","journal article; research support, non-u.s. gov't; research support, n.i.h., intramural; research-article","Y","Y","Y","13","Y","Y","N","N","N","204.24405","15","28","2016-2021","PMC3400951",NA,NA,"code.google.com"
"806","23260146","MED","23260146","10.1016/j.cell.2012.11.018","Foxa2 and H2A.Z mediate nucleosome depletion during embryonic stem cell differentiation.","Li Z, Gadue P, Chen K, Jiao Y, Tuteja G, Schug J, Li W, Kaestner KH.","Cell","2012","0092-8674","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","30","Y","Y","Y","N","N","204.24405","7","151","1608-1616","PMC3530164",NA,"INTACTUNIPROTARXPR","code.google.com"
"807","22426492","MED","22426492","10.1038/nmeth.1937","Unsupervised pattern discovery in human chromatin structure through genomic segmentation.","Hoffman MM, Buske OJ, Wang J, Weng Z, Bilmes JA, Noble WS.","Nat Methods","2012","1548-7091","journal article; research support, n.i.h., extramural; research-article","N","Y","Y","57","Y","Y","N","N","N","204.24405","5","9","473-476","PMC3340533",NA,NA,"code.google.com"
"808","22815713","MED","22815713","10.1371/journal.pone.0039740","CACTI: free, open-source software for the sequential coding of behavioral interactions.","Glynn LH, Hallgren KA, Houck JM, Moyers TB.","PLoS One","2012","1932-6203","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","7","Y","Y","N","N","N","204.24405","7","7","e39740","PMC3397966",NA,NA,"code.google.com"
"809","23212374","MED","23212374","10.1038/ncomms2266","Symptomatic atherosclerosis is associated with an altered gut metagenome.","Karlsson FH, FÃ¥k F, Nookaew I, Tremaroli V, Fagerberg B, Petranovic D, BÃ¤ckhed F, Nielsen J.","Nat Commun","2012","2041-1723","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","43","Y","Y","N","N","N","204.24405",NA,"3","1245","PMC3538954",NA,NA,"code.google.com"
"810","23991264","MED","23991264","10.4056/sigs.3907833","Clarifying concepts and terms in biodiversity informatics.","Deck J, Barker K, Beaman R, Buttigieg PL, DrÃ¶ge G, Guralnick R, Miller C, Tuama EÃ, Murrell Z, Parr C, Robbins B, Schigel D, Stucky B, Walls R, Wieczorek J, Morrison N, Wooley J.","Stand Genomic Sci","2013","1944-3277","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","204.057","2","8","352-359","PMC3746421",NA,NA,"code.google.com"
"811","21642352","MED","21642352","10.1093/scan/nsr036","The importance of actions and the worth of an object: dissociable neural systems representing core value and economic value.","Brosch T, Coppin G, Schwartz S, Sander D.","Soc Cogn Affect Neurosci","2012","1749-5016","journal article; research support, non-u.s. gov't; research-article","N","Y","Y","3","Y","Y","N","N","N","203.8169","5","7","497-505","PMC3375888",NA,NA,"code.google.com"
"812","22115774","MED","22115774","10.1016/j.jmb.2011.11.019","Mechanisms of allosteric gene regulation by NMR quantification of microsecond-millisecond protein dynamics.","Kleckner IR, Gollnick P, Foster MP.","J Mol Biol","2012","0022-2836","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","4","Y","Y","N","N","N","203.8169","2","415","372-381","PMC3258336",NA,NA,"code.google.com"
"813","22754559","MED","22754559","10.3389/fpls.2012.00140","Arabinogalactan-proteins and the research challenges for these enigmatic plant cell surface proteoglycans.","Tan L, Showalter AM, Egelund J, Hernandez-Sanchez A, Doblin MS, Bacic A.","Front Plant Sci","2012","1664-462x","journal article; research-article","Y","Y","Y","17","Y","Y","N","N","N","203.8169",NA,"3","140","PMC3384089",NA,NA,"code.google.com"
"814","22615686","MED","22615686","10.3389/fncir.2012.00029","Stimulus-evoked high frequency oscillations are present in neuronal networks on microelectrode arrays.","Hales CM, Zeller-Townson R, Newman JP, Shoemaker JT, Killian NJ, Potter SM.","Front Neural Circuits","2012","1662-5110","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","203.8169",NA,"6","29","PMC3351760",NA,NA,"code.google.com"
"815","23028432","MED","23028432","10.1371/journal.pone.0042304","An integrated pipeline for de novo assembly of microbial genomes.","Tritt A, Eisen JA, Facciotti MT, Darling AE.","PLoS One","2012","1932-6203","journal article; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","43","Y","Y","N","N","N","203.8169","9","7","e42304","PMC3441570",NA,NA,"code.google.com"
"816","22102698","MED","22102698","10.1093/carcin/bgr258","Genetic variation in nucleotide excision repair pathway genes, pesticide exposure and prostate cancer risk.","Barry KH, Koutros S, Andreotti G, Sandler DP, Burdette LA, Yeager M, Beane Freeman LE, Lubin JH, Ma X, Zheng T, Alavanja MC, Berndt SI.","Carcinogenesis","2012","0143-3334","journal article; research support, n.i.h., extramural; research support, n.i.h., intramural; research-article","N","Y","Y","8","Y","Y","N","N","Y","203.8169","2","33","331-337","PMC3271261","refsnp",NA,"code.google.com"
"817","22388958","MED","22388958","10.1038/nn.3060","Active dendrites support efficient initiation of dendritic spikes in hippocampal CA3 pyramidal neurons.","Kim S, Guzman SJ, Hu H, Jonas P.","Nat Neurosci","2012","1097-6256","journal article; research support, non-u.s. gov't; comparative study; research-article","N","Y","Y","12","Y","Y","N","N","N","203.8169","4","15","600-606","PMC3617474",NA,NA,"code.google.com"
"818","22438999","MED","22438999","10.1371/journal.pone.0033781","Host genetics and Chlamydia disease: prediction and validation of disease severity mechanisms.","Miyairi I, Ziebarth J, Laxton JD, Wang X, van Rooijen N, Williams RW, Lu L, Byrne GI, Cui Y.","PLoS One","2012","1932-6203","journal article; validation studies; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","7","Y","Y","N","N","N","203.8169","3","7","e33781","PMC3306297",NA,NA,"code.google.com"
"819","22529798","MED","22529798","10.3389/fncom.2012.00018","Learning from open source software projects to improve scientific review.","Ghosh SS, Klein A, Avants B, Millman KJ.","Front Comput Neurosci","2012","1662-5188","journal article; research-article","Y","Y","Y","7","Y","Y","N","N","N","203.8169",NA,"6","18","PMC3328792",NA,NA,"code.google.com"
"820","25285328","MED","25285328",NA,"Predicting accurate probabilities with a ranking loss.","Menon AK, Jiang XJ, Vembu S, Elkan C, Ohno-Machado L.","Mach Learn Int Conf Mach Learn","2012",NA,"journal article; research-article","N","Y","N","0","Y","Y","N","N","N","203.8169",NA,"2012","703-710","PMC4180410",NA,NA,"code.google.com"
"821","22387999","MED","22387999","10.1038/ng.1110","Ascorbic acid prevents loss of Dlk1-Dio3 imprinting and facilitates generation of all-iPS cell mice from terminally differentiated B cells.","Stadtfeld M, Apostolou E, Ferrari F, Choi J, Walsh RM, Chen T, Ooi SS, Kim SY, Bestor TH, Shioda T, Park PJ, Hochedlinger K.","Nat Genet","2012","1061-4036","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","56","Y","Y","Y","N","N","203.8169","4","44","398-405, s1-2","PMC3538378",NA,"UNIPROT","code.google.com"
"822","23197736","MED","23197736","10.1523/jneurosci.1357-12.2012","Morphine epigenomically regulates behavior through alterations in histone H3 lysine 9 dimethylation in the nucleus accumbens.","Sun H, Maze I, Dietz DM, Scobie KN, Kennedy PJ, Damez-Werno D, Neve RL, Zachariou V, Shen L, Nestler EJ.","J Neurosci","2012","0270-6474","journal article; research-article","N","Y","Y","16","Y","Y","N","N","N","203.8169","48","32","17454-17464","PMC3516048",NA,NA,"code.google.com"
"823","22545654","MED","22545654","10.1021/jp212541y","AWSEM-MD: protein structure prediction using coarse-grained physical potentials and bioinformatically based local structure biasing.","Davtyan A, Schafer NP, Zheng W, Clementi C, Wolynes PG, Papoian GA.","J Phys Chem B","2012","1520-6106","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","Y","14","Y","Y","N","N","N","203.8169","29","116","8494-8503","PMC3406225",NA,NA,"code.google.com"
"824","22904078","MED","22904078","10.1093/nar/gks754","Compression of next-generation sequencing reads aided by highly efficient de novo assembly.","Jones DC, Ruzzo WL, Peng X, Katze MG.","Nucleic Acids Res","2012","0305-1048","evaluation studies; journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","18","Y","Y","N","N","N","203.8169","22","40","e171","PMC3526293",NA,NA,"code.google.com"
"825","22271044","MED","22271044","10.1007/s00439-012-1139-5","Y chromosome haplogroups and prostate cancer in populations of European and Ashkenazi Jewish ancestry.","Wang Z, Parikh H, Jia J, Myers T, Yeager M, Jacobs KB, Hutchinson A, Burdett L, Ghosh A, Thun MJ, Gapstur SM, Ryan Diver W, Virtamo J, Albanes D, Cancel-Tassin G, Valeri A, Cussenot O, Offit K, Giovannucci E, Ma J, Stampfer MJ, Michael Gaziano J, Hunter DJ, Dutra-Clarke A, Kirchhoff T, Alavanja M, Freeman LB, Koutros S, Hoover R, Berndt SI, Hayes RB, Agalliu I, Burk RD, Wacholder S, Thomas G, Amundadottir L.","Hum Genet","2012","0340-6717","journal article; meta-analysis; research support, non-u.s. gov't; research support, n.i.h., intramural; research-article","Y","Y","Y","1","Y","Y","N","N","N","203.8169","7","131","1173-1185","PMC3374121",NA,NA,"code.google.com"
"826","21908399","MED","21908399","10.1093/nar/gkr723","Histone hypoacetylation is required to maintain late replication timing of constitutive heterochromatin.","Casas-Delucchi CS, van Bemmel JG, Haase S, Herce HD, Nowak D, Meilinger D, Stear JH, Leonhardt H, Cardoso MC.","Nucleic Acids Res","2012","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","9","Y","Y","N","N","N","203.8169","1","40","159-169","PMC3245938",NA,NA,"code.google.com"
"827","22902541","MED","22902541","10.1210/me.2012-1180","Minireview: progress and challenges in proteomics data management, sharing, and integration.","Becnel LB, McKenna NJ.","Mol Endocrinol","2012","0888-8809","journal article; review; research support, n.i.h., extramural; review-article","N","Y","Y","5","Y","Y","N","N","N","203.8169","10","26","1660-1674","PMC3458223",NA,NA,"code.google.com"
"828","23569631","MED","23569631","10.5210/ojphi.v4i1.3910","The Architecture of a Software System for Supporting Community-based Primary Health Care with Mobile Technology: The Mobile Technology for Community Health (MoTeCH) Initiative in Ghana.","Macleod B, Phillips J, Stone AE, Walji A, Awoonor-Williams JK.","Online J Public Health Inform","2012","1947-2579","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","203.8169","1","4","335-344","PMC3615808",NA,NA,"code.google.com"
"829","23194155","MED","23194155","10.1186/1471-2164-13-679","Multiple-omic data analysis of Klebsiella pneumoniae MGH 78578 reveals its transcriptional architecture and regulatory features.","Seo JH, Hong JS, Kim D, Cho BK, Huang TW, Tsai SF, Palsson BO, Charusanti P.","BMC Genomics","2012","1471-2164","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","7","Y","Y","N","N","Y","203.8169",NA,"13","679","PMC3536570","gen",NA,"code.google.com"
"830","23237380","MED","23237380","10.1186/1471-2105-13-331","Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study.","Sun L, Zhang Z, Bailey TL, Perkins AC, Tallack MR, Xu Z, Liu H.","BMC Bioinformatics","2012","1471-2105","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","10","Y","Y","N","N","N","203.8169",NA,"13","331","PMC3577497",NA,NA,"code.google.com"
"831","23251139","MED","23251139","10.3389/fgene.2012.00287","Bioinformatics of Cancer ncRNA in High Throughput Sequencing: Present State and Challenges.","Jorge NA, Ferreira CG, Passetti F.","Front Genet","2012","1664-8021","journal article; review-article","Y","Y","Y","0","Y","Y","N","N","N","203.8169",NA,"3","287","PMC3523245",NA,NA,"code.google.com"
"832","23300661","MED","23300661","10.1371/journal.pone.0052403","A comprehensive evaluation of alignment algorithms in the context of RNA-seq.","Lindner R, Friedel CC.","PLoS One","2012","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","8","Y","Y","N","N","N","203.8169","12","7","e52403","PMC3530550",NA,NA,"code.google.com"
"833","22876295","MED","22876295","10.1371/journal.pone.0041962","A new estimation of global soil greenhouse gas fluxes using a simple data-oriented model.","Hashimoto S.","PLoS One","2012","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","N","N","N","203.8169","8","7","e41962","PMC3410890",NA,NA,"code.google.com"
"834","22911539","MED","22911539","10.1109/tbme.2012.2208746","Modeling the human knee for assistive technologies.","Sartori M, Reggiani M, Pagello E, Lloyd DG.","IEEE Trans Biomed Eng","2012","0018-9294","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","2","Y","Y","N","N","N","203.8169","9","59","2642-2649","PMC3668098",NA,NA,"code.google.com"
"835","22916139","MED","22916139","10.1371/journal.pone.0042608","Abnormal neural responses to social exclusion in schizophrenia.","Gradin VB, Waiter G, Kumar P, Stickle C, Milders M, Matthews K, Reid I, Hall J, Steele JD.","PLoS One","2012","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","N","N","N","203.8169","8","7","e42608","PMC3420898",NA,NA,"code.google.com"
"836","22916302","MED","22916302","10.1371/journal.pone.0043762","Transcriptomics and comparative analysis of three antarctic notothenioid fishes.","Shin SC, Kim SJ, Lee JK, Ahn do H, Kim MG, Lee H, Lee J, Kim BK, Park H.","PLoS One","2012","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","5","Y","Y","N","N","N","203.8169","8","7","e43762","PMC3420891",NA,NA,"code.google.com"
"837","22927994","MED","22927994","10.1371/journal.pone.0043575","Computational prediction of conformational B-cell epitopes from antigen primary structures by ensemble learning.","Zhang W, Niu Y, Xiong Y, Zhao M, Yu R, Liu J.","PLoS One","2012","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","203.8169","8","7","e43575","PMC3424238",NA,NA,"code.google.com"
"838","23069247","MED","23069247","10.1016/j.jmb.2012.10.005","Nucleotide-resolution profiling of RNA recombination in the encapsidated genome of a eukaryotic RNA virus by next-generation sequencing.","Routh A, Ordoukhanian P, Johnson JE.","J Mol Biol","2012","0022-2836","evaluation studies; journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","4","Y","Y","N","N","N","203.8169","5","424","257-269","PMC3502730",NA,NA,"code.google.com"
"839","23092124","MED","23092124","10.1021/pr300702c","Mass spectrometry-based identification of native cardiac Nav1.5 channel Î± subunit phosphorylation sites.","Marionneau C, Lichti CF, Lindenbaum P, Charpentier F, Nerbonne JM, Townsend RR, MÃ©rot J.","J Proteome Res","2012","1535-3893","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","7","Y","Y","Y","N","N","203.8169","12","11","5994-6007","PMC3518584",NA,"UNIPROT","code.google.com"
"840","23097517","MED","23097517","10.1098/rspb.2012.1795","A congruent phylogenomic signal places eukaryotes within the Archaea.","Williams TA, Foster PG, Nye TM, Cox CJ, Embley TM.","Proc Biol Sci","2012","0962-8452","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","12","Y","Y","N","Y","N","203.8169","1749","279","4870-4879","PMC3497233",NA,NA,"code.google.com"
"841","22558107","MED","22558107","10.1371/journal.pone.0035003","High-throughput sequencing of mGluR signaling pathway genes reveals enrichment of rare variants in autism.","Kelleher RJ 3rd, GeigenmÃ¼ller U, Hovhannisyan H, Trautman E, Pinard R, Rathmell B, Carpenter R, Margulies D.","PLoS One","2012","1932-6203","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","25","Y","Y","Y","N","N","203.8169","4","7","e35003","PMC3338748",NA,"UNIPROT","code.google.com"
"842","22696444","MED","22696444","10.4049/jimmunol.1200245","In vivo VL-targeted microbial superantigen induced global shifts in the B cell repertoire.","GrÃ¶nwall C, Kosakovsky Pond SL, Young JA, Silverman GJ.","J Immunol","2012","0022-1767","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","2","Y","Y","N","N","N","203.8169","2","189","850-859","PMC3598568",NA,NA,"code.google.com"
"843","22723971","MED","22723971","10.1371/journal.pone.0039232","ccTSA: a coverage-centric threaded sequence assembler.","Ahn JH.","PLoS One","2012","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","N","Y","N","N","N","203.8169","6","7","e39232","PMC3378524",NA,NA,"code.google.com"
"844","22452920","MED","22452920","10.1186/1756-0500-5-164","Identifying microRNA/mRNA dysregulations in ovarian cancer.","Miles GD, Seiler M, Rodriguez L, Rajagopal G, Bhanot G.","BMC Res Notes","2012","1756-0500","journal article; research-article","Y","Y","Y","11","Y","Y","Y","N","N","203.8169",NA,"5","164","PMC3342161",NA,"UNIPROT","code.google.com"
"845","23251424","MED","23251424","10.1371/journal.pone.0051070","A unified anatomy ontology of the vertebrate skeletal system.","Dahdul WM, Balhoff JP, Blackburn DC, Diehl AD, Haendel MA, Hall BK, Lapp H, Lundberg JG, Mungall CJ, Ringwald M, Segerdell E, Van Slyke CE, Vickaryous MK, Westerfield M, Mabee PM.","PLoS One","2012","1932-6203","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","7","Y","Y","N","Y","Y","203.8169","12","7","e51070","PMC3519498","doi",NA,"code.google.com"
"846","22949509","MED","22949509","10.1074/mcp.o112.021543","The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium.","CÃ´tÃ© RG, Griss J, Dianes JA, Wang R, Wright JC, van den Toorn HW, van Breukelen B, Heck AJ, Hulstaert N, Martens L, Reisinger F, Csordas A, Ovelleiro D, Perez-Rivevol Y, Barsnes H, Hermjakob H, VizcaÃno JA.","Mol Cell Proteomics","2012","1535-9476","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","17","Y","Y","N","Y","N","203.8169","12","11","1682-1689","PMC3518121",NA,NA,"code.google.com"
"847","22581372","MED","22581372","10.1038/nmeth.2025","Resolution doubling in live, multicellular organisms via multifocal structured illumination microscopy.","York AG, Parekh SH, Dalle Nogare D, Fischer RS, Temprine K, Mione M, Chitnis AB, Combs CA, Shroff H.","Nat Methods","2012","1548-7091","journal article; research support, n.i.h., intramural; research-article","Y","Y","Y","27","Y","Y","N","N","N","203.8169","7","9","749-754","PMC3462167",NA,NA,"code.google.com"
"848","23064000","MED","23064000","10.1093/bioinformatics/bts580","A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection.","Lemey P, Minin VN, Bielejec F, Kosakovsky Pond SL, Suchard MA.","Bioinformatics","2012","1367-4803","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","Y","8","Y","Y","N","N","N","203.8169","24","28","3248-3256","PMC3579240",NA,NA,"code.google.com"
"849","22403703","MED","22403703","10.1371/journal.pone.0032749","Optimization of time-course experiments for kinetic model discrimination.","Lages NF, Cordeiro C, Sousa Silva M, Ponces Freire A, Ferreira AE.","PLoS One","2012","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","3","Y","Y","N","N","N","203.8169","3","7","e32749","PMC3293846",NA,NA,"code.google.com"
"850","22578020","MED","22578020","10.1111/j.1528-1167.2012.03464.x","Patterns of altered functional connectivity in mesial temporal lobe epilepsy.","Pittau F, Grova C, Moeller F, Dubeau F, Gotman J.","Epilepsia","2012","0013-9580","journal article; research-article","N","Y","Y","41","Y","Y","N","N","N","203.8169","6","53","1013-1023","PMC3767602",NA,NA,"code.google.com"
"851","22498630","MED","22498630","10.1038/nature10985","Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function.","Lickwar CR, Mueller F, Hanlon SE, McNally JG, Lieb JD.","Nature","2012","0028-0836","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research support, n.i.h., intramural; research-article","Y","Y","Y","54","Y","Y","Y","N","N","203.8169","7393","484","251-255","PMC3341663",NA,"UNIPROT","code.google.com"
"852","22559794","MED","22559794","10.1089/brain.2011.0068","Functional magnetic resonance imaging phase synchronization as a measure of dynamic functional connectivity.","Glerean E, Salmi J, Lahnakoski JM, JÃ¤Ã¤skelÃ¤inen IP, Sams M.","Brain Connect","2012","2158-0014","journal article; research support, non-u.s. gov't; research-article","N","Y","Y","8","Y","Y","N","N","N","203.8169","2","2","91-101","PMC3624768",NA,NA,"code.google.com"
"853","22724034","MED","22724034","10.1371/journal.pntd.0001694","Combined spatial prediction of schistosomiasis and soil-transmitted helminthiasis in Sierra Leone: a tool for integrated disease control.","Hodges MH, Soares MagalhÃ£es RJ, Paye J, Koroma JB, Sonnie M, Clements A, Zhang Y.","PLoS Negl Trop Dis","2012","1935-2727","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","6","Y","Y","N","N","N","203.8169","6","6","e1694","PMC3378624",NA,NA,"code.google.com"
"854","22955981","MED","22955981","10.1101/gr.134890.111","Personal and population genomics of human regulatory variation.","Vernot B, Stergachis AB, Maurano MT, Vierstra J, Neph S, Thurman RE, Stamatoyannopoulos JA, Akey JM.","Genome Res","2012","1088-9051","journal article; research support, n.i.h., extramural; research-article","N","Y","Y","32","Y","Y","N","N","N","203.8169","9","22","1689-1697","PMC3431486",NA,NA,"code.google.com"
"855","22726122","MED","22726122","10.1111/j.1365-294x.2012.05673.x","Adaptation of Drosophila to a novel laboratory environment reveals temporally heterogeneous trajectories of selected alleles.","Orozco-terWengel P, Kapun M, Nolte V, Kofler R, Flatt T, SchlÃ¶tterer C.","Mol Ecol","2012","0962-1083","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","23","Y","Y","N","Y","Y","203.8169","20","21","4931-4941","PMC3533796","doi",NA,"code.google.com"
"856","22609849","MED","22609849","10.1016/j.ygeno.2012.05.006","Relax with CouchDB--into the non-relational DBMS era of bioinformatics.","Manyam G, Payton MA, Roth JA, Abruzzo LV, Coombes KR.","Genomics","2012","0888-7543","journal article; research support, n.i.h., extramural; research-article","N","Y","Y","2","Y","Y","N","N","N","203.8169","1","100","1-7","PMC3383915",NA,NA,"code.google.com"
"857","22426077","MED","22426077","10.1038/ncb2466","Telomeric DNA damage is irreparable and causes persistent DNA-damage-response activation.","Fumagalli M, Rossiello F, Clerici M, Barozzi S, Cittaro D, Kaplunov JM, Bucci G, Dobreva M, Matti V, Beausejour CM, Herbig U, Longhese MP, d'Adda di Fagagna F.","Nat Cell Biol","2012","1465-7392","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","72","Y","Y","N","N","N","203.8169","4","14","355-365","PMC3717580",NA,NA,"code.google.com"
"858","22503634","MED","22503634","10.1016/j.ajhg.2012.03.014","Genetic adaptation of fatty-acid metabolism: a human-specific haplotype increasing the biosynthesis of long-chain omega-3 and omega-6 fatty acids.","Ameur A, Enroth S, Johansson A, Zaboli G, Igl W, Johansson AC, Rivas MA, Daly MJ, Schmitz G, Hicks AA, Meitinger T, Feuk L, van Duijn C, Oostra B, Pramstaller PP, Rudan I, Wright AF, Wilson JF, Campbell H, Gyllensten U.","Am J Hum Genet","2012","0002-9297","journal article; research support, non-u.s. gov't; research-article","N","Y","Y","10","Y","Y","Y","N","Y","203.8169","5","90","809-820","PMC3376635","refsnp","OMIM","code.google.com"
"859","22213709","MED","22213709","10.1093/sysbio/syr120","Pleistocene speciation in the genus Populus (salicaceae).","Levsen ND, Tiffin P, Olson MS.","Syst Biol","2012","1063-5157","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","Y","9","Y","Y","Y","Y","Y","203.8169","3","61","401-412","PMC3529545","gen; doi","EMBL","code.google.com"
"860","23055825","MED","23055825","10.1371/journal.pbio.1001400","Embryonic origin of olfactory circuitry in Drosophila: contact and activity-mediated interactions pattern connectivity in the antennal lobe.","Prieto-Godino LL, Diegelmann S, Bate M.","PLoS Biol","2012","1544-9173","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","Y","Y","N","203.6703","10","10","e1001400","PMC3462790",NA,"UNIPROT","code.google.com"
"861","22723865","MED","22723865","10.1371/journal.pone.0038518","Intrinsic noise analyzer: a software package for the exploration of stochastic biochemical kinetics using the system size expansion.","Thomas P, Matuschek H, Grima R.","PLoS One","2012","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","8","Y","Y","N","N","N","203.6703","6","7","e38518","PMC3373587",NA,NA,"code.google.com"
"862","22258828","MED","22258828","10.1007/s12021-012-9140-7","Using evolutionary algorithms for fitting high-dimensional models to neuronal data.","Svensson CM, Coombes S, Peirce JW.","Neuroinformatics","2012","1539-2791","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","N","N","N","203.6703","2","10","199-218","PMC3272374",NA,NA,"code.google.com"
"863","22901054","MED","22901054","10.1186/1471-2105-13-207","A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools.","Verspoor K, Cohen KB, Lanfranchi A, Warner C, Johnson HL, Roeder C, Choi JD, Funk C, Malenkiy Y, Eckert M, Xue N, Baumgartner WA Jr, Bada M, Palmer M, Hunter LE.","BMC Bioinformatics","2012","1471-2105","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","9","Y","Y","N","N","N","203.6703",NA,"13","207","PMC3483229",NA,NA,"code.google.com"
"864","22822389","MED","22822389","10.3389/fnins.2012.00106","EEG oscillations reveal neural correlates of evidence accumulation.","van Vugt MK, Simen P, Nystrom LE, Holmes P, Cohen JD.","Front Neurosci","2012","1662-4548","journal article; research-article","Y","Y","Y","8","Y","Y","N","N","N","203.38972",NA,"6","106","PMC3398314",NA,NA,"code.google.com"
"865","23056003","MED","23056003","10.3389/fpls.2012.00220","RNA-Seq Assembly - Are We There Yet?","Schliesky S, Gowik U, Weber AP, BrÃ¤utigam A.","Front Plant Sci","2012","1664-462x","journal article; review-article","Y","Y","Y","21","Y","Y","N","N","N","203.38972",NA,"3","220","PMC3457010",NA,NA,"code.google.com"
"866","22412892","MED","22412892","10.1371/journal.pone.0032587","Simulated impact of RTS,S/AS01 vaccination programs in the context of changing malaria transmission.","Brooks A, BriÃ«t OJ, Hardy D, Steketee R, Smith TA.","PLoS One","2012","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","6","Y","Y","N","N","N","203.38972","3","7","e32587","PMC3295753",NA,NA,"code.google.com"
"867","23145153","MED","23145153","10.1371/journal.pone.0049334","CREST--classification resources for environmental sequence tags.","LanzÃ©n A, JÃ¸rgensen SL, Huson DH, Gorfer M, Grindhaug SH, Jonassen I, ÃvreÃ¥s L, Urich T.","PLoS One","2012","1932-6203","journal article; validation studies; research support, non-u.s. gov't; research-article","Y","Y","Y","11","Y","Y","N","N","N","203.38972","11","7","e49334","PMC3493522",NA,NA,"code.google.com"
"868","22079099","MED","22079099","10.1016/j.molbiopara.2011.10.011","Mapping of VSG similarities in Trypanosoma brucei.","Weirather JL, Wilson ME, Donelson JE.","Mol Biochem Parasitol","2012","0166-6851","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","Y","2","Y","Y","N","N","N","203.38972","2","181","141-152","PMC3268917",NA,NA,"code.google.com"
"869","22412365","MED","22412365","10.1371/journal.pcbi.1002422","Ensemble models of neutrophil trafficking in severe sepsis.","Song SO, Hogg J, Peng ZY, Parker R, Kellum JA, Clermont G.","PLoS Comput Biol","2012","1553-734x","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","3","Y","Y","N","N","N","203.38972","3","8","e1002422","PMC3297568",NA,NA,"code.google.com"
"870","22434839","MED","22434839","10.1093/database/bas005","A hybrid human and machine resource curation pipeline for the Neuroscience Information Framework.","Bandrowski AE, Cachat J, Li Y, MÃ¼ller HM, Sternberg PW, Ciccarese P, Clark T, Marenco L, Wang R, Astakhov V, Grethe JS, Martone ME.","Database (Oxford)","2012","1758-0463","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","5","Y","Y","N","Y","N","203.38972",NA,"2012","bas005","PMC3308161",NA,NA,"code.google.com"
"871","22479409","MED","22479409","10.1371/journal.pone.0033532","Formal modeling and analysis of the MAL-associated biological regulatory network: insight into cerebral malaria.","Ahmad J, Niazi U, Mansoor S, Siddique U, Bibby J.","PLoS One","2012","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","N","N","N","203.38972","3","7","e33532","PMC3316585",NA,NA,"code.google.com"
"872","23166519","MED","23166519","10.1371/journal.pgen.1003075","A unified method for detecting secondary trait associations with rare variants: application to sequence data.","Liu DJ, Leal SM.","PLoS Genet","2012","1553-7390","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research support, n.i.h., intramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","203.38972","11","8","e1003075","PMC3499373",NA,NA,"code.google.com"
"873","22905239","MED","22905239","10.1371/journal.pone.0043245","A bioinformatic strategy for the detection, classification and analysis of bacterial autotransporters.","Celik N, Webb CT, Leyton DL, Holt KE, Heinz E, Gorrell R, Kwok T, Naderer T, Strugnell RA, Speed TP, Teasdale RD, LikiÄ VA, Lithgow T.","PLoS One","2012","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","11","Y","Y","N","N","Y","203.38972","8","7","e43245","PMC3419190","pdb; pfam",NA,"code.google.com"
"874","22848102","MED","22848102","10.1093/nar/gks692","Structural and functional analyses of the interaction of archaeal RNA polymerase with DNA.","Wojtas MN, Mogni M, Millet O, Bell SD, Abrescia NG.","Nucleic Acids Res","2012","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","3","Y","Y","Y","N","Y","203.38972","19","40","9941-9952","PMC3479171","pdb","PDBUNIPROT","code.google.com"
"875","22496632","MED","22496632","10.1371/journal.pcbi.1002457","Automatic filtering and substantiation of drug safety signals.","Bauer-Mehren A, van Mullingen EM, Avillach P, Carrascosa Mdel C, Garcia-Serna R, PiÃ±ero J, Singh B, Lopes P, Oliveira JL, Diallo G, Ahlberg Helgee E, Boyer S, Mestres J, Sanz F, Kors JA, Furlong LI.","PLoS Comput Biol","2012","1553-734x","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","8","Y","Y","N","N","N","203.38972","4","8","e1002457","PMC3320573",NA,NA,"code.google.com"
"876","22524202","MED","22524202","10.1111/j.1365-2958.2012.08059.x","The evolution of new lipoprotein subunits of the bacterial outer membrane BAM complex.","Anwari K, Webb CT, Poggio S, Perry AJ, Belousoff M, Celik N, Ramm G, Lovering A, Sockett RE, Smit J, Jacobs-Wagner C, Lithgow T.","Mol Microbiol","2012","0950-382x","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","6","Y","Y","N","N","Y","203.38972","5","84","832-844","PMC3359395","pdb",NA,"code.google.com"
"877","22976474","MED","22976474","10.1093/hmg/dds381","A meta-analysis of genome-wide association studies of breast cancer identifies two novel susceptibility loci at 6q14 and 20q11.","Siddiq A, Couch FJ, Chen GK, LindstrÃ¶m S, Eccles D, Millikan RC, Michailidou K, Stram DO, Beckmann L, Rhie SK, Ambrosone CB, AittomÃ¤ki K, Amiano P, Apicella C, Australian Breast Cancer Tissue Bank Investigators, Baglietto L, Bandera EV, Beckmann MW, Berg CD, Bernstein L, Blomqvist C, Brauch H, Brinton L, Bui QM, Buring JE, Buys SS, Campa D, Carpenter JE, Chasman DI, Chang-Claude J, Chen C, Clavel-Chapelon F, Cox A, Cross SS, Czene K, Deming SL, Diasio RB, Diver WR, Dunning AM, Durcan L, Ekici AB, Fasching PA, Familial Breast Cancer Study, Feigelson HS, Fejerman L, Figueroa JD, Fletcher O, Flesch-Janys D, Gaudet MM, GENICA Consortium, Gerty SM, Rodriguez-Gil JL, Giles GG, van Gils CH, Godwin AK, Graham N, Greco D, Hall P, Hankinson SE, Hartmann A, Hein R, Heinz J, Hoover RN, Hopper JL, Hu JJ, Huntsman S, Ingles SA, Irwanto A, Isaacs C, Jacobs KB, John EM, Justenhoven C, Kaaks R, Kolonel LN, Coetzee GA, Lathrop M, Le Marchand L, Lee AM, Lee IM, Lesnick T, Lichtner P, Liu J, Lund E, Makalic E, Martin NG, McLean CA, Meijers-Heijboer H, Meindl A, Miron P, Monroe KR, Montgomery GW, MÃ¼ller-Myhsok B, Nickels S, Nyante SJ, Olswold C, Overvad K, Palli D, Park DJ, Palmer JR, Pathak H, Peto J, Pharoah P, Rahman N, Rivadeneira F, Schmidt DF, Schmutzler RK, Slager S, Southey MC, Stevens KN, Sinn HP, Press MF, Ross E, Riboli E, Ridker PM, Schumacher FR, Severi G, Dos Santos Silva I, Stone J, Sund M, Tapper WJ, Thun MJ, Travis RC, Turnbull C, Uitterlinden AG, Waisfisz Q, Wang X, Wang Z, Weaver J, Schulz-Wendtland R, Wilkens LR, Van Den Berg D, Zheng W, Ziegler RG, Ziv E, Nevanlinna H, Easton DF, Hunter DJ, Henderson BE, Chanock SJ, Garcia-Closas M, Kraft P, Haiman CA, Vachon CM.","Hum Mol Genet","2012","0964-6906","journal article; meta-analysis; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research support, n.i.h., intramural; research-article","N","Y","Y","24","Y","Y","N","Y","Y","203.38972","24","21","5373-5384","PMC3510753","refsnp",NA,"code.google.com"
"878","23185239","MED","23185239","10.1371/journal.pone.0047450","Resolving discrepancy between nucleotides and amino acids in deep-level arthropod phylogenomics: differentiating serine codons in 21-amino-acid models.","Zwick A, Regier JC, Zwickl DJ.","PLoS One","2012","1932-6203","journal article; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","7","Y","Y","N","N","N","203.38972","11","7","e47450","PMC3502419",NA,NA,"code.google.com"
"879","23181553","MED","23181553","10.1186/1471-2105-13-316","TeraStitcher - a tool for fast automatic 3D-stitching of teravoxel-sized microscopy images.","Bria A, Iannello G.","BMC Bioinformatics","2012","1471-2105","journal article; research support, non-u.s. gov't; product-review","Y","Y","Y","7","Y","Y","N","N","N","203.38972",NA,"13","316","PMC3582611",NA,NA,"code.google.com"
"880","23236266","MED","23236266","10.1371/journal.pcbi.1002795","Sensitivity analysis of flux determination in heart by Hâ Â¹â¸O -provided labeling using a dynamic Isotopologue model of energy transfer pathways.","Schryer DW, Peterson P, Illaste A, Vendelin M.","PLoS Comput Biol","2012","1553-734x","journal article; validation studies; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","203.38972","12","8","e1002795","PMC3516558",NA,NA,"code.google.com"
"881","23281941","MED","23281941","10.1186/1471-2105-13-s17-s22","Personalized cloud-based bioinformatics services for research and education: use cases and the elasticHPC package.","El-Kalioby M, Abouelhoda M, KrÃ¼ger J, Giegerich R, Sczyrba A, Wall DP, Tonellato P.","BMC Bioinformatics","2012","1471-2105","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","203.38972","Suppl 17","13 Suppl 17","s22","PMC3521398",NA,NA,"code.google.com"
"882","22924089","MED","22924089","10.1371/journal.pone.0041196","Inter-subject correlation in fMRI: method validation against stimulus-model based analysis.","Pajula J, Kauppi JP, Tohka J.","PLoS One","2012","1932-6203","journal article; validation studies; research support, non-u.s. gov't; comparative study; research-article","Y","Y","Y","7","Y","Y","N","N","N","203.38972","8","7","e41196","PMC3414505",NA,NA,"code.google.com"
"883","22955985","MED","22955985","10.1101/gr.136366.111","Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements.","Kundaje A, Kyriazopoulou-Panagiotopoulou S, Libbrecht M, Smith CL, Raha D, Winters EE, Johnson SM, Snyder M, Batzoglou S, Sidow A.","Genome Res","2012","1088-9051","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","N","Y","Y","35","Y","Y","N","N","N","203.38972","9","22","1735-1747","PMC3431490",NA,NA,"code.google.com"
"884","22998945","MED","22998945","10.1186/1476-072x-11-41","Displaying R spatial statistics on Google dynamic maps with web applications created by Rwui.","Newton R, Deonarine A, Wernisch L.","Int J Health Geogr","2012","1476-072x","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","203.38972",NA,"11","41","PMC3548681",NA,NA,"code.google.com"
"885","23056299","MED","23056299","10.1371/journal.pone.0046401","GenoSets: visual analytic methods for comparative genomics.","Cain AA, Kosara R, Gibas CJ.","PLoS One","2012","1932-6203","journal article; research support, u.s. gov't, non-p.h.s.; comparative study; research-article","Y","Y","Y","2","Y","Y","N","N","N","203.38972","10","7","e46401","PMC3463605",NA,NA,"code.google.com"
"886","23139896","MED","23139896","10.3390/genes3030545","Next generation sequence analysis and computational genomics using graphical pipeline workflows.","Torri F, Dinov ID, Zamanyan A, Hobel S, Genco A, Petrosyan P, Clark AP, Liu Z, Eggert P, Pierce J, Knowles JA, Ames J, Kesselman C, Toga AW, Potkin SG, Vawter MP, Macciardi F.","Genes (Basel)","2012","2073-4425","journal article; research-article","Y","Y","Y","13","Y","Y","N","N","N","203.38972","3","3","545-575","PMC3490498",NA,NA,"code.google.com"
"887","23143274","MED","23143274","10.1038/emboj.2012.294","Transcriptional repression of the APC/C activator CCS52A1 promotes active termination of cell growth.","Breuer C, Morohashi K, Kawamura A, Takahashi N, Ishida T, Umeda M, Grotewold E, Sugimoto K.","EMBO J","2012","0261-4189","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","N","Y","Y","7","Y","Y","Y","N","N","203.38972","24","31","4488-4501","PMC3545286",NA,"UNIPROT","code.google.com"
"888","22595089","MED","22595089","10.1186/1472-6947-12-s1-s4","Detecting modification of biomedical events using a deep parsing approach.","Mackinlay A, Martinez D, Baldwin T.","BMC Med Inform Decis Mak","2012","1472-6947","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","203.38972","Suppl 1","12 Suppl 1","s4","PMC3339397",NA,NA,"code.google.com"
"889","22684502","MED","22684502","10.1093/nar/gks544","Genome-wide localization and expression profiling establish Sp2 as a sequence-specific transcription factor regulating vitally important genes.","Terrados G, Finkernagel F, Stielow B, Sadic D, Neubert J, Herdt O, Krause M, Scharfe M, Jarek M, Suske G.","Nucleic Acids Res","2012","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","4","Y","Y","Y","N","Y","203.38972","16","40","7844-7857","PMC3439921","arrayexpress","UNIPROTARXPR","code.google.com"
"890","22689778","MED","22689778","10.1093/bioinformatics/bts212","A single source k-shortest paths algorithm to infer regulatory pathways in a gene network.","Shih YK, Parthasarathy S.","Bioinformatics","2012","1367-4803","journal article; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","5","Y","Y","N","N","N","203.38972","12","28","i49-58","PMC3371844",NA,NA,"code.google.com"
"891","22729532","MED","22729532","10.1128/aem.01435-12","Pyrosequencing-derived bacterial, archaeal, and fungal diversity of spacecraft hardware destined for Mars.","La Duc MT, Vaishampayan P, Nilsson HR, Torok T, Venkateswaran K.","Appl Environ Microbiol","2012","0099-2240","journal article; research-article","N","Y","Y","9","Y","Y","N","N","N","203.38972","16","78","5912-5922","PMC3406123",NA,NA,"code.google.com"
"892","22733562","MED","22733562","10.1002/prot.24135","Event detection and sub-state discovery from biomolecular simulations using higher-order statistics: application to enzyme adenylate kinase.","Ramanathan A, Savol AJ, Agarwal PK, Chennubhotla CS.","Proteins","2012","0887-3585","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","0","Y","Y","N","N","N","203.38972","11","80","2536-2551","PMC3538151",NA,NA,"code.google.com"
"893","22805979","MED","22805979","10.1007/s10439-012-0611-7","Multiscale modeling and data integration in the virtual physiological rat project.","Beard DA, Neal ML, Tabesh-Saleki N, Thompson CT, Bassingthwaighte JB, Shimoyama M, Carlson BE.","Ann Biomed Eng","2012","0090-6964","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","10","Y","Y","N","N","N","203.38972","11","40","2365-2378","PMC3463790",NA,NA,"code.google.com"
"894","22815946","MED","22815946","10.1371/journal.pone.0041148","Fractal dimension and vessel complexity in patients with cerebral arteriovenous malformations.","Reishofer G, Koschutnig K, Enzinger C, Ebner F, Ahammer H.","PLoS One","2012","1932-6203","journal article; research-article","Y","Y","Y","5","Y","Y","N","N","N","203.38972","7","7","e41148","PMC3399805",NA,NA,"code.google.com"
"895","22844090","MED","22844090","10.1093/nar/gks701","A benchmark for chromatin binding measurements in live cells.","Mazza D, Abernathy A, Golob N, Morisaki T, McNally JG.","Nucleic Acids Res","2012","0305-1048","journal article; research support, non-u.s. gov't; research support, n.i.h., intramural; research-article","Y","Y","Y","25","Y","Y","N","N","N","203.38972","15","40","e119","PMC3424588",NA,NA,"code.google.com"
"896","22855212","MED","22855212","10.1038/ismej.2012.84","Significant and persistent impact of timber harvesting on soil microbial communities in Northern coniferous forests.","Hartmann M, Howes CG, VanInsberghe D, Yu H, Bachar D, Christen R, Henrik Nilsson R, Hallam SJ, Mohn WW.","ISME J","2012","1751-7362","journal article; research support, non-u.s. gov't; research-article","N","Y","Y","13","Y","Y","N","N","N","203.38972","12","6","2199-2218","PMC3504969",NA,NA,"code.google.com"
"897","22384239","MED","22384239","10.1371/journal.pone.0032394","pcaGoPromoter--an R package for biological and regulatory interpretation of principal components in genome-wide gene expression data.","Hansen M, Gerds TA, Nielsen OH, Seidelin JB, Troelsen JT, Olsen J.","PLoS One","2012","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","3","Y","Y","N","N","N","203.38972","2","7","e32394","PMC3288097",NA,NA,"code.google.com"
"898","22666382","MED","22666382","10.1371/journal.pone.0037694","Genus paracoccidioides: Species recognition and biogeographic aspects.","Theodoro RC, Teixeira Mde M, Felipe MS, Paduan Kdos S, Ribolla PM, San-Blas G, Bagagli E.","PLoS One","2012","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","13","Y","Y","N","N","Y","203.38972","5","7","e37694","PMC3364295","gen",NA,"code.google.com"
"899","22992491","MED","22992491","10.1016/j.neuroimage.2012.08.034","Rostral-caudal gradients of abstraction revealed by multi-variate pattern analysis of working memory.","Nee DE, Brown JW.","Neuroimage","2012","1053-8119","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","Y","10","Y","Y","N","N","N","203.38972","3","63","1285-1294","PMC3472084",NA,NA,"code.google.com"
"900","23251396","MED","23251396","10.1371/journal.pone.0050881","Using answer set programming to integrate RNA expression with signalling pathway information to infer how mutations affect ageing.","Papatheodorou I, Ziehm M, Wieser D, Alic N, Partridge L, Thornton JM.","PLoS One","2012","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","4","Y","Y","N","Y","N","203.38972","12","7","e50881","PMC3519537",NA,NA,"code.google.com"
"901","22936843","MED","22936843","10.1093/beheco/ars078","Wind selectivity and partial compensation for wind drift among nocturnally migrating passerines.","McLaren JD, Shamoun-Baranes J, Bouten W.","Behav Ecol","2012","1045-2249","journal article; research-article","Y","Y","Y","2","Y","Y","N","N","N","203.38972","5","23","1089-1101","PMC3431116",NA,NA,"code.google.com"
"902","22973268","MED","22973268","10.3389/fmicb.2012.00329","Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data.","Beerenwinkel N, GÃ¼nthard HF, Roth V, Metzner KJ.","Front Microbiol","2012","1664-302x","journal article; review-article","Y","Y","Y","33","Y","Y","N","N","N","203.38972",NA,"3","329","PMC3438994",NA,NA,"code.google.com"
"903","22794270","MED","22794270","10.1016/j.neuron.2012.05.010","Hippocampal and ventral medial prefrontal activation during retrieval-mediated learning supports novel inference.","Zeithamova D, Dominick AL, Preston AR.","Neuron","2012","0896-6273","journal article; randomized controlled trial; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","Y","26","Y","Y","N","N","N","203.38972","1","75","168-179","PMC3398403",NA,NA,"code.google.com"
"904","22984289","MED","22984289","10.1074/mcp.m112.021105","Intermembrane space proteome of yeast mitochondria.","VÃ¶gtle FN, Burkhart JM, Rao S, Gerbeth C, Hinrichs J, Martinou JC, Chacinska A, Sickmann A, Zahedi RP, Meisinger C.","Mol Cell Proteomics","2012","1535-9476","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","16","Y","Y","Y","N","N","203.38972","12","11","1840-1852","PMC3518125",NA,"UNIPROT","code.google.com"
"905","22926237","MED","22926237","10.1016/j.ymeth.2012.08.006","Genome-wide identification of miRNA targets by PAR-CLIP.","Hafner M, Lianoglou S, Tuschl T, Betel D.","Methods","2012","1046-2023","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","16","Y","Y","N","N","N","203.38972","2","58","94-105","PMC3508682",NA,NA,"code.google.com"
"906","23028512","MED","23028512","10.1371/journal.pone.0044272","Fast feedback in active sensing: touch-induced changes to whisker-object interaction.","Deutsch D, Pietr M, Knutsen PM, Ahissar E, Schneidman E.","PLoS One","2012","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","5","Y","Y","N","N","N","203.38972","9","7","e44272","PMC3445569",NA,NA,"code.google.com"
"907","22830651","MED","22830651","10.1186/gm359","Identifying disease mutations in genomic medicine settings: current challenges and how to accelerate progress.","Lyon GJ, Wang K.","Genome Med","2012","1756-994x","journal article; review; review-article","Y","Y","Y","15","Y","Y","N","N","N","203.38972","7","4","58","PMC3580414",NA,NA,"code.google.com"
"908","22292040","MED","22292040","10.1371/journal.pone.0030783","SurfaceSlide: a multitouch digital pathology platform.","Wang Y, Williamson KE, Kelly PJ, James JA, Hamilton PW.","PLoS One","2012","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","3","Y","Y","N","N","N","203.38972","1","7","e30783","PMC3264630",NA,NA,"code.google.com"
"909","22493576","MED","22493576","10.3389/fninf.2012.00009","Data sharing in neuroimaging research.","Poline JB, Breeze JL, Ghosh S, Gorgolewski K, Halchenko YO, Hanke M, Haselgrove C, Helmer KG, Keator DB, Marcus DS, Poldrack RA, Schwartz Y, Ashburner J, Kennedy DN.","Front Neuroinform","2012","1662-5196","journal article; review-article","Y","Y","Y","20","Y","Y","N","N","N","203.38972",NA,"6","9","PMC3319918",NA,NA,"code.google.com"
"910","21937730","MED","21937730","10.1074/mcp.m111.011429","A quantitative spatial proteomics analysis of proteome turnover in human cells.","Boisvert FM, Ahmad Y, GierliÅski M, CharriÃ¨re F, Lamont D, Scott M, Barton G, Lamond AI.","Mol Cell Proteomics","2012","1535-9476","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","13","Y","Y","N","N","N","203.38972","3","11","m111.011429","PMC3316722",NA,NA,"code.google.com"
"911","22986687","MED","22986687","10.1007/s10858-012-9669-7","CING: an integrated residue-based structure validation program suite.","Doreleijers JF, Sousa da Silva AW, Krieger E, Nabuurs SB, Spronk CA, Stevens TJ, Vranken WF, Vriend G, Vuister GW.","J Biomol NMR","2012","0925-2738","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","28","Y","Y","N","N","Y","203.38972","3","54","267-283","PMC3483101","pdb",NA,"code.google.com"
"912","22582004","MED","22582004","10.1016/j.jdeveco.2011.08.007","A Comparison of EPI Sampling, Probability Sampling, and Compact Segment Sampling Methods for Micro and Small Enterprises.","Chao LW, Szrek H, Peltzer K, Ramlagan S, Fleming P, Leite R, Magerman J, Ngwenya GB, Pereira NS, Behrman J.","J Dev Econ","2012","0304-3878","journal article; research-article","N","Y","Y","0","Y","Y","N","N","N","202.96257","1","98","94-107","PMC3347860",NA,NA,"code.google.com"
"913","22883141","MED","22883141","10.1016/j.ajhg.2012.06.013","Phasing of many thousands of genotyped samples.","Williams AL, Patterson N, Glessner J, Hakonarson H, Reich D.","Am J Hum Genet","2012","0002-9297","evaluation studies; journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; comparative study; research-article","N","Y","Y","16","Y","Y","N","N","N","202.96257","2","91","238-251","PMC3415548",NA,NA,"code.google.com"
"914","22514290","MED","22514290","10.1152/jn.00004.2012","Detection of tactile inputs in the rat vibrissa pathway.","Ollerenshaw DR, Bari BA, Millard DC, Orr LE, Wang Q, Stanley GB.","J Neurophysiol","2012","0022-3077","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","Y","1","Y","Y","N","N","N","202.96257","2","108","479-490","PMC3404799",NA,NA,"code.google.com"
"915","23201997","MED","23201997","10.3390/s121013295","WikiSensing: an online collaborative approach for sensor data management.","Silva D, Ghanem M, Guo Y.","Sensors (Basel)","2012","1424-8220","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","N","Y","N","N","N","202.96257","10","12","13295-13332","PMC3545568",NA,NA,"code.google.com"
"916","23316158","MED","23316158","10.3389/fninf.2012.00031","Increasing quality and managing complexity in neuroinformatics software development with continuous integration.","Zaytsev YV, Morrison A.","Front Neuroinform","2012","1662-5196","journal article; research-article","Y","Y","Y","2","Y","Y","N","N","N","202.96257",NA,"6","31","PMC3539731",NA,NA,"code.google.com"
"917","23144721","MED","23144721","10.1371/journal.pone.0048022","Transforming microbial genotyping: a robotic pipeline for genotyping bacterial strains.","O'Farrell B, Haase JK, Velayudhan V, Murphy RA, Achtman M.","PLoS One","2012","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","4","Y","Y","N","N","N","202.96257","10","7","e48022","PMC3483277",NA,NA,"code.google.com"
"918","22947175","MED","22947175","10.1186/1471-2164-13-454","Comparative genomics of Brachyspira pilosicoli strains: genome rearrangements, reductions and correlation of genetic compliment with phenotypic diversity.","Mappley LJ, Black ML, AbuOun M, Darby AC, Woodward MJ, Parkhill J, Turner AK, Bellgard MI, La T, Phillips ND, La Ragione RM, Hampson DJ.","BMC Genomics","2012","1471-2164","journal article; research support, non-u.s. gov't; comparative study; research-article","Y","Y","Y","6","Y","Y","Y","N","Y","202.96257",NA,"13","454","PMC3532143","gen","EMBLUNIPROT","code.google.com"
"919","22272189","MED","22272189","10.1371/journal.pmed.1001157","Ensemble modeling of the likely public health impact of a pre-erythrocytic malaria vaccine.","Smith T, Ross A, Maire N, Chitnis N, Studer A, Hardy D, Brooks A, Penny M, Tanner M.","PLoS Med","2012","1549-1277","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","22","Y","Y","N","N","N","202.96257","1","9","e1001157","PMC3260300",NA,NA,"code.google.com"
"920","22913798","MED","22913798","10.1111/j.1365-294x.2012.05731.x","Genome-wide patterns of latitudinal differentiation among populations of Drosophila melanogaster from North America.","Fabian DK, Kapun M, Nolte V, Kofler R, Schmidt PS, SchlÃ¶tterer C, Flatt T.","Mol Ecol","2012","0962-1083","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; comparative study; research-article","Y","Y","Y","22","Y","Y","Y","Y","N","202.96257","19","21","4748-4769","PMC3482935",NA,"UNIPROT","code.google.com"
"921","22583801","MED","22583801","10.1186/1471-2164-13-185","Development and application of a 6.5 million feature Affymetrix GenechipÂ® for massively parallel discovery of single position polymorphisms in lettuce (Lactuca spp.).","Stoffel K, van Leeuwen H, Kozik A, Caldwell D, Ashrafi H, Cui X, Tan X, Hill T, Reyes-Chin-Wo S, Truco MJ, Michelmore RW, Van Deynze A.","BMC Genomics","2012","1471-2164","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","5","Y","Y","N","N","N","202.96257",NA,"13","185","PMC3490809",NA,NA,"code.google.com"
"922","22838835","MED","22838835","10.1186/1471-2229-12-120","miRNA regulation in the early development of barley seed.","Curaba J, Spriggs A, Taylor J, Li Z, Helliwell C.","BMC Plant Biol","2012","1471-2229","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","8","Y","Y","N","N","N","202.96257",NA,"12","120","PMC3443071",NA,NA,"code.google.com"
"923","22272231","MED","22272231","10.1371/journal.pone.0029264","Generating adaptive behaviour within a memory-prediction framework.","Rawlinson D, Kowadlo G.","PLoS One","2012","1932-6203","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","202.96257","1","7","e29264","PMC3260147",NA,NA,"code.google.com"
"924","23087639","MED","23087639","10.3389/fncom.2012.00079","Open evaluation: a vision for entirely transparent post-publication peer review and rating for science.","Kriegeskorte N.","Front Comput Neurosci","2012","1662-5188","journal article; research-article","Y","Y","Y","5","Y","Y","N","N","N","202.96257",NA,"6","79","PMC3473231",NA,NA,"code.google.com"
"925","22912590","MED","22912590","10.1371/journal.pgen.1002867","Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling.","Kim D, Hong JS, Qiu Y, Nagarajan H, Seo JH, Cho BK, Tsai SF, Palsson BÃ.","PLoS Genet","2012","1553-7390","journal article; research support, non-u.s. gov't; comparative study; research-article","Y","Y","Y","20","Y","Y","Y","N","Y","202.96257","8","8","e1002867","PMC3415461","refseq","ARXPR","code.google.com"
"926","21955164","MED","21955164","10.1162/jocn_a_00140","Neural evidence for a distinction between short-term memory and the focus of attention.","Lewis-Peacock JA, Drysdale AT, Oberauer K, Postle BR.","J Cogn Neurosci","2012","0898-929x","journal article; research support, n.i.h., extramural; research-article","N","Y","Y","34","Y","Y","N","N","N","202.96257","1","24","61-79","PMC3222712",NA,NA,"code.google.com"
"927","22678431","MED","22678431","10.1038/nprot.2012.068","A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs.","Swain MT, Tsai IJ, Assefa SA, Newbold C, Berriman M, Otto TD.","Nat Protoc","2012","1754-2189","journal article; research support, non-u.s. gov't; research-article","N","Y","Y","37","Y","Y","N","N","N","202.96257","7","7","1260-1284","PMC3648784",NA,NA,"code.google.com"
"928","22291611","MED","22291611","10.1371/journal.pgen.1002487","Sequencing of pooled DNA samples (Pool-Seq) uncovers complex dynamics of transposable element insertions in Drosophila melanogaster.","Kofler R, Betancourt AJ, SchlÃ¶tterer C.","PLoS Genet","2012","1553-7390","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","25","Y","Y","N","Y","N","202.96257","1","8","e1002487","PMC3266889",NA,NA,"code.google.com"
"929","22955991","MED","22955991","10.1101/gr.136184.111","ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.","Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, Tolstorukov MY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M.","Genome Res","2012","1088-9051","journal article; research-article","N","Y","Y","129","Y","Y","N","N","N","202.96257","9","22","1813-1831","PMC3431496",NA,NA,"code.google.com"
"930","22955616","MED","22955616","10.1038/nature11247","An integrated encyclopedia of DNA elements in the human genome.","ENCODE Project Consortium.","Nature","2012","0028-0836","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research support, n.i.h., intramural; research support, american recovery and reinvestment act; research-article","Y","Y","Y","1408","Y","Y","N","N","N","202.96257","7414","489","57-74","PMC3439153",NA,NA,"code.google.com"
"931","22584621","MED","22584621","10.1093/nar/gks408","Prospects and limitations of full-text index structures in genome analysis.","Vyverman M, De Baets B, Fack V, Dawyndt P.","Nucleic Acids Res","2012","0305-1048","journal article; review; research support, non-u.s. gov't; research-article","Y","Y","Y","8","Y","Y","N","N","N","202.749","15","40","6993-7015","PMC3424560",NA,NA,"code.google.com"
"932","23028269","MED","23028269","10.1371/journal.pcbi.1002632","An online bioinformatics curriculum.","Searls DB.","PLoS Comput Biol","2012","1553-734x","journal article; research-article","Y","Y","Y","3","N","Y","N","N","N","202.749","9","8","e1002632","PMC3441465",NA,NA,"code.google.com"
"933","22616011","MED","22616011","10.1371/journal.pone.0037454","Mapping connectivity damage in the case of Phineas Gage.","Van Horn JD, Irimia A, Torgerson CM, Chambers MC, Kikinis R, Toga AW.","PLoS One","2012","1932-6203","biography; historical article; journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","11","Y","Y","N","N","N","202.749","5","7","e37454","PMC3353935",NA,NA,"code.google.com"
"934","22781312","MED","22781312","10.1186/1472-6947-12-67","A systematic review of healthcare applications for smartphones.","Mosa AS, Yoo I, Sheets L.","BMC Med Inform Decis Mak","2012","1472-6947","journal article; review; research-article","Y","Y","Y","38","Y","Y","N","N","N","202.749",NA,"12","67","PMC3534499",NA,NA,"code.google.com"
"935","22833496","MED","22833496","10.1093/bib/bbs018","Mining the pharmacogenomics literature--a survey of the state of the art.","Hahn U, Cohen KB, Garten Y, Shah NH.","Brief Bioinform","2012","1467-5463","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","8","Y","Y","N","N","N","202.749","4","13","460-494","PMC3404399",NA,NA,"code.google.com"
"936","PMC3970004","PMC",NA,NA,"The genome sequence and effector complement of the flax rust pathogen Melampsora lini.","Nemri A, Saunders DGO, Anderson C, Upadhyaya NM, Win J, Lawrence GJ, Jones DA, Kamoun S, Ellis JG, Dodds PN.","Frontiers in Plant Science","2014","1664-462x","journal article; research-article","Y","Y","Y","0","N","Y","N","N","N","202.57658",NA,"5",NA,"PMC3970004",NA,NA,"code.google.com"
"937","PMC3970055","PMC",NA,NA,"Self-Supervised Chinese Ontology Learning from Online Encyclopedias.","Hu F, Shao Z, Ruan T.","The Scientific World Journal","2014","1537-744x","journal article; research-article","Y","Y","Y","0","N","Y","N","N","N","202.57658",NA,"2014",NA,"PMC3970055",NA,NA,"code.google.com"
"938","PMC3970018","PMC",NA,NA,"Methodological aspects of EEG and body dynamics measurements during motion.","Reis PMR, Hebenstreit F, Gabsteiger F, von Tscharner V, Lochmann M.","Frontiers in Human Neuroscience","2014","1662-5161","journal article; research-article","Y","Y","Y","0","N","Y","N","N","N","202.2562",NA,"8",NA,"PMC3970018",NA,NA,"code.google.com"
"939","22318026","MED","22318026","10.1038/nbt.2112","PRIDE Inspector: a tool to visualize and validate MS proteomics data.","Wang R, Fabregat A, RÃos D, Ovelleiro D, Foster JM, CÃ´tÃ© RG, Griss J, Csordas A, Perez-Riverol Y, Reisinger F, Hermjakob H, Martens L, VizcaÃno JA.","Nat Biotechnol","2012","1087-0156","letter; research support, non-u.s. gov't; research-article","Y","Y","Y","28","Y","Y","N","Y","N","150.25925","2","30","135-137","PMC3277942",NA,NA,"code.google.com"
"940","22025480","MED","22025480","10.1093/bioinformatics/btr589","PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq).","Kofler R, Pandey RV, SchlÃ¶tterer C.","Bioinformatics","2011","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","35","Y","Y","N","Y","N","146.87057","24","27","3435-3436","PMC3232374",NA,NA,"code.google.com"
"941","21041879","MED","21041879","10.1109/tvcg.2010.240","Efficient sparse voxel octrees.","Laine S, Karras T.","IEEE Trans Vis Comput Graph","2011","1077-2626","journal article","N","N","N","0","N","N","N","N","N","140.70555","8","17","1048-1059",NA,NA,NA,"code.google.com"
"942","21478488","MED","21478488","10.1093/bioinformatics/btr178","Reliability-oriented bioinformatic networks visualization.","AladaÄ AE, Erten C, SÃ¶zdinler M.","Bioinformatics","2011","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","1","Y","N","N","N","N","140.70554","11","27","1583-1584",NA,NA,NA,"code.google.com"
"943","21813478","MED","21813478","10.1093/bioinformatics/btr457","GlobalMIT: learning globally optimal dynamic bayesian network with the mutual information test criterion.","Vinh NX, Chetty M, Coppel R, Wangikar PP.","Bioinformatics","2011","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","7","Y","N","N","N","N","140.70554","19","27","2765-2766",NA,NA,NA,"code.google.com"
"944","21998157","MED","21998157","10.1093/bioinformatics/btr574","BDTcomparator: a program for comparing binary classifiers.","Fijorek K, Fijorek D, Wisniowska B, Polak S.","Bioinformatics","2011","1367-4803","journal article","N","N","N","6","Y","N","N","N","N","140.70554","24","27","3439-3440",NA,NA,NA,"code.google.com"
"945","21123222","MED","21123222","10.1093/bioinformatics/btq663","Open source platform for the execution and analysis of mechanical refolding experiments.","Aioanei D, Brucale M, SamorÃ B.","Bioinformatics","2011","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","1","Y","N","N","N","N","140.70554","3","27","423-425",NA,NA,NA,"code.google.com"
"946","21984769","MED","21984769","10.1093/bioinformatics/btr560","KABOOM! A new suffix array based algorithm for clustering expression data.","Hazelhurst S, LiptÃ¡k Z.","Bioinformatics","2011","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","3","Y","N","N","N","N","138.99695","24","27","3348-3355",NA,NA,NA,"code.google.com"
"947","21339535","MED","21339535","10.1109/tcbb.2011.36","Recipe for uncovering predictive genes using support vector machines based on model population analysis.","Li HD, Liang YZ, Xu QS, Cao DS, Tan BB, Deng BC, Lin CC.","IEEE/ACM Trans Comput Biol Bioinform","2011","1545-5963","journal article; research support, non-u.s. gov't","N","N","N","2","N","N","N","N","N","138.99695","6","8","1633-1641",NA,NA,NA,"code.google.com"
"948","21728180","MED","21728180","10.1002/jcc.21874","MyMolDB: a micromolecular database solution with open source and free components.","Xia B, Tai ZF, Gu YC, Li BJ, Ding LS, Zhou Y.","J Comput Chem","2011","0192-8651","journal article; research support, non-u.s. gov't","N","N","N","2","Y","N","N","N","N","138.99693","13","32","2942-2948",NA,NA,NA,"code.google.com"
"949","21775305","MED","21775305","10.1093/bioinformatics/btr425","CalcTav--integration of a spreadsheet and Taverna workbench.","Sroka J, Krupa Å, Kierzek AM, Tyszkiewicz J.","Bioinformatics","2011","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","0","N","N","N","N","N","138.99693","18","27","2618-2619",NA,NA,NA,"code.google.com"
"950","21429144","MED","21429144","10.1111/j.1755-0998.2010.02925.x","DIM SUM: demography and individual migration simulated using a Markov chain.","Brown JM, Savidge K, McTavish EJ.","Mol Ecol Resour","2011","1755-098x","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.","N","N","N","0","N","N","N","N","N","138.99693","2","11","358-363",NA,NA,NA,"code.google.com"
"951","21442443","MED","21442443","10.2478/s11658-011-0008-x","PPI_SVM: prediction of protein-protein interactions using machine learning, domain-domain affinities and frequency tables.","Chatterjee P, Basu S, Kundu M, Nasipuri M, Plewczynski D.","Cell Mol Biol Lett","2011","1425-8153","journal article; research support, non-u.s. gov't","N","N","N","2","Y","N","N","N","N","138.99693","2","16","264-278",NA,NA,NA,"code.google.com"
"952","21215845","MED","21215845","10.1016/j.talanta.2010.08.008","Peak alignment using wavelet pattern matching and differential evolution.","Zhang ZM, Chen S, Liang YZ.","Talanta","2011","0039-9140","journal article; research support, non-u.s. gov't","N","N","N","10","Y","N","N","N","N","138.99693","4","83","1108-1117",NA,NA,NA,"code.google.com"
"953","21159624","MED","21159624","10.1093/bioinformatics/btq694","Automated analysis of information processing, kinetic independence and modular architecture in biochemical networks using MIDIA.","Bowsher CG.","Bioinformatics","2011","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","1","Y","N","N","N","N","137.2883","4","27","584-586",NA,NA,NA,"code.google.com"
"954","21798964","MED","21798964","10.1093/bioinformatics/btr433","Dasty3, a WEB framework for DAS.","Villaveces JM, Jimenez RC, Garcia LJ, Salazar GA, Gel B, Mulder N, Martin M, Garcia A, Hermjakob H.","Bioinformatics","2011","1367-4803","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","8","Y","Y","N","N","N","135.91486","18","27","2616-2617","PMC3167052",NA,NA,"code.google.com"
"955","21216779","MED","21216779","10.1093/bioinformatics/btq715","A Java API for working with PubChem datasets.","Southern MR, Griffin PR.","Bioinformatics","2011","1367-4803","journal article; research support, n.i.h., extramural; research-article","N","Y","Y","2","Y","Y","N","N","N","135.91484","5","27","741-742","PMC3105478",NA,NA,"code.google.com"
"956","21904437","MED","21904437","10.6026/97320630007038","ValFold: Program for the aptamer truncation process.","Akitomi J, Kato S, Yoshida Y, Horii K, Furuichi M, Waga I.","Bioinformation","2011","0973-2063","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","135.49384","1","7","38-40","PMC3163931",NA,NA,"code.google.com"
"957","21718534","MED","21718534","10.1186/1756-0500-4-227","CANGS DB: a stand-alone web-based database tool for processing, managing and analyzing 454 data in biodiversity studies.","Pandey RV, Nolte V, Boenigk J, SchlÃ¶tterer C.","BMC Res Notes","2011","1756-0500","journal article; research-article","Y","Y","Y","2","Y","Y","N","N","N","134.67776",NA,"4","227","PMC3146855",NA,NA,"code.google.com"
"958","22035155","MED","22035155","10.1186/1756-0500-4-462","Functional Genomics Assistant (FUGA): a toolbox for the analysis of complex biological networks.","Drozdov I, Ouzounis CA, Shah AM, Tsoka S.","BMC Res Notes","2011","1756-0500","journal article; research-article","Y","Y","Y","6","Y","Y","N","N","Y","134.43515",NA,"4","462","PMC3214203","arrayexpress",NA,"code.google.com"
"959","21149339","MED","21149339","10.1093/bioinformatics/btq658","MU2A--reconciling the genome and transcriptome to determine the effects of base substitutions.","Garla V, Kong Y, Szpakowski S, Krauthammer M.","Bioinformatics","2011","1367-4803","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","4","Y","Y","N","N","N","134.28564","3","27","416-418","PMC3031033",NA,NA,"code.google.com"
"960","21599881","MED","21599881","10.1186/1471-2105-12-178","TreeRipper web application: towards a fully automated optical tree recognition software.","Hughes J.","BMC Bioinformatics","2011","1471-2105","journal article; research support, non-u.s. gov't; product-review","Y","Y","Y","4","Y","Y","N","N","N","133.07748",NA,"12","178","PMC3111373",NA,NA,"code.google.com"
"961","21967198","MED","21967198","10.1021/pr200664h","jTraML: an open source Java API for TraML, the PSI standard for sharing SRM transitions.","Helsens K, Brusniak MY, Deutsch E, Moritz RL, Martens L.","J Proteome Res","2011","1535-3893","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; brief-report","Y","Y","Y","8","Y","Y","N","N","N","133.07747","11","10","5260-5263","PMC3208355",NA,NA,"code.google.com"
"962","21418653","MED","21418653","10.1186/1751-0473-6-5","Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format.","Webb RL, Ma'ayan A.","Source Code Biol Med","2011","1751-0473","journal article; product-review","Y","Y","Y","2","Y","Y","N","N","N","133.07747",NA,"6","5","PMC3071313",NA,NA,"code.google.com"
"963","21935468","MED","21935468","10.1371/journal.pone.0024797","CDinFusion--submission-ready, on-line integration of sequence and contextual data.","Hankeln W, Wendel NJ, Gerken J, Waldmann J, Buttigieg PL, Kostadinov I, Kottmann R, Yilmaz P, GlÃ¶ckner FO.","PLoS One","2011","1932-6203","journal article; research-article","Y","Y","Y","2","Y","Y","Y","N","Y","133.01677","9","6","e24797","PMC3172294","gen","EMBL","code.google.com"
"964","21533259","MED","21533259","10.1371/journal.pone.0018460","MartiTracks: a geometrical approach for identifying geographical patterns of distribution.","EcheverrÃa-LondoÃ±o S, Miranda-Esquivel DR.","PLoS One","2011","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","132.95543","4","6","e18460","PMC3075252",NA,NA,"code.google.com"
"965","21310746","MED","21310746","10.1093/bioinformatics/btr053","FISH Finder: a high-throughput tool for analyzing FISH images.","Shirley JW, Ty S, Takebayashi S, Liu X, Gilbert DM.","Bioinformatics","2011","1367-4803","evaluation studies; journal article; research support, n.i.h., extramural; research-article","N","Y","Y","7","Y","Y","N","N","N","132.21559","7","27","933-938","PMC3065689",NA,NA,"code.google.com"
"966","21305028","MED","21305028","10.1371/journal.pone.0016327","ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads.","Miller CA, Hampton O, Coarfa C, Milosavljevic A.","PLoS One","2011","1932-6203","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","30","Y","Y","N","N","N","132.21558","1","6","e16327","PMC3031566",NA,NA,"code.google.com"
"967","21846404","MED","21846404","10.1186/1471-2105-12-341","Prediction of conformational B-cell epitopes from 3D structures by random forests with a distance-based feature.","Zhang W, Xiong Y, Zhao M, Zou H, Ye X, Liu J.","BMC Bioinformatics","2011","1471-2105","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","14","Y","Y","N","N","N","132.16245",NA,"12","341","PMC3228550",NA,NA,"code.google.com"
"968","21984761","MED","21984761","10.1093/bioinformatics/btr554","Knime4Bio: a set of custom nodes for the interpretation of next-generation sequencing data with KNIME.","Lindenbaum P, Le Scouarnec S, Portero V, Redon R.","Bioinformatics","2011","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","4","Y","Y","N","Y","N","132.16245","22","27","3200-3201","PMC3208396",NA,NA,"code.google.com"
"969","22208765","MED","22208765","10.1186/1471-2105-12-493","A new strategy for better genome assembly from very short reads.","Ji Y, Shi Y, Ding G, Li Y.","BMC Bioinformatics","2011","1471-2105","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","4","Y","Y","N","N","N","132.16245",NA,"12","493","PMC3268122",NA,NA,"code.google.com"
"970","21636591","MED","21636591","10.1093/bioinformatics/btr336","PathVisio-MIM: PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs).","Luna A, Sunshine ML, van Iersel MP, Aladjem MI, Kohn KW.","Bioinformatics","2011","1367-4803","journal article; research support, non-u.s. gov't; research support, n.i.h., intramural; research-article","N","Y","Y","4","Y","Y","N","N","N","132.16245","15","27","2165-2166","PMC3137219",NA,NA,"code.google.com"
"971","21149340","MED","21149340","10.1093/bioinformatics/btq675","Cytoscape 2.8: new features for data integration and network visualization.","Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T.","Bioinformatics","2011","1367-4803","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","804","Y","Y","N","Y","N","132.16245","3","27","431-432","PMC3031041",NA,NA,"code.google.com"
"972","21512582","MED","21512582","10.1155/2011/406391","PyEEG: an open source Python module for EEG/MEG feature extraction.","Bao FS, Liu X, Zhang C.","Comput Intell Neurosci","2011","1687-5265","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","131.86931",NA,"2011","406391","PMC3070217",NA,NA,"code.google.com"
"973","21750706","MED","21750706","10.1371/journal.pone.0021270","GenExp: an interactive web-based genomic DAS client with client-side data rendering.","Gel Moreno B, Messeguer Peypoch X.","PLoS One","2011","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","131.86931","7","6","e21270","PMC3130039",NA,NA,"code.google.com"
"974","21501475","MED","21501475","10.1186/1471-2105-12-101","Implementation of force distribution analysis for molecular dynamics simulations.","Stacklies W, Seifert C, Graeter F.","BMC Bioinformatics","2011","1471-2105","journal article; research-article","Y","Y","Y","12","Y","Y","N","N","Y","131.86931",NA,"12","101","PMC3094238","pdb",NA,"code.google.com"
"975","22195200","MED","22195200",NA,"An OWL meta-ontology for representing the Clinical Element Model.","Tao C, Parker CG, Oniki TA, Pathak J, Huff SM, Chute CG.","AMIA Annu Symp Proc","2011","1942-597x","journal article; research support, u.s. gov't, non-p.h.s.; research support, u.s. gov't, p.h.s.; research-article","N","Y","Y","3","Y","Y","N","N","N","131.86931",NA,"2011","1372-1381","PMC3243162",NA,NA,"code.google.com"
"976","21705364","MED","21705364","10.1093/database/bar027","The Strategies WDK: a graphical search interface and web development kit for functional genomics databases.","Fischer S, Aurrecoechea C, Brunk BP, Gao X, Harb OS, Kraemer ET, Pennington C, Treatman C, Kissinger JC, Roos DS, Stoeckert CJ.","Database (Oxford)","2011","1758-0463","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","3","Y","Y","N","N","N","131.47574",NA,"2011","bar027","PMC3122067",NA,NA,"code.google.com"
"977","21531787","MED","21531787","10.1093/hmg/ddr189","Fine mapping of a region of chromosome 11q13 reveals multiple independent loci associated with risk of prostate cancer.","Chung CC, Ciampa J, Yeager M, Jacobs KB, Berndt SI, Hayes RB, Gonzalez-Bosquet J, Kraft P, Wacholder S, Orr N, Yu K, Hutchinson A, Boland J, Chen Q, Feigelson HS, Thun MJ, Diver WR, Albanes D, Virtamo J, Weinstein S, Schumacher FR, Cancel-Tassin G, Cussenot O, Valeri A, Andriole GL, Crawford ED, Haiman CA, Henderson BE, Kolonel L, Le Marchand L, Siddiq A, Riboli E, Key TJ, Kaaks R, Isaacs WB, Isaacs SD, GrÃ¶nberg H, Wiklund F, Xu J, Vatten LJ, Hveem K, Njolstad I, Gerhard DS, Tucker M, Hoover RN, Fraumeni JF Jr, Hunter DJ, Thomas G, Chatterjee N, Chanock SJ.","Hum Mol Genet","2011","0964-6906","journal article; multicenter study; research support, n.i.h., extramural; research support, n.i.h., intramural; research-article","N","Y","Y","12","Y","Y","N","N","Y","131.47572","14","20","2869-2878","PMC3118760","refsnp; gen",NA,"code.google.com"
"978","22039460","MED","22039460","10.1371/journal.pone.0026314","ConDeTri--a content dependent read trimmer for Illumina data.","Smeds L, KÃ¼nstner A.","PLoS One","2011","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","41","Y","Y","N","N","N","131.47572","10","6","e26314","PMC3198461",NA,NA,"code.google.com"
"979","21909385","MED","21909385","10.1371/journal.pone.0024230","Next generation sequencing provides rapid access to the genome of Puccinia striiformis f. sp. tritici, the causal agent of wheat stripe rust.","Cantu D, Govindarajulu M, Kozik A, Wang M, Chen X, Kojima KK, Jurka J, Michelmore RW, Dubcovsky J.","PLoS One","2011","1932-6203","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","28","Y","Y","Y","N","Y","131.47572","8","6","e24230","PMC3164196","gen","EMBLUNIPROT","code.google.com"
"980","21538880","MED","21538880","10.1002/pmic.201000256","Proteomic characterization of the major arthropod associates of the carnivorous pitcher plant Sarracenia purpurea.","Gotelli NJ, Smith AM, Ellison AM, Ballif BA.","Proteomics","2011","1615-9853","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","Y","2","Y","Y","N","N","N","131.30815","11","11","2354-2358","PMC3517077",NA,NA,"code.google.com"
"981","21624154","MED","21624154","10.1186/2041-1480-2-s2-i1","Selected papers from the 13th Annual Bio-Ontologies Special Interest Group Meeting.","Soldatova LN, Sansone SA, Stephens SM, Shah NH.","J Biomed Semantics","2011","2041-1480","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","131.30815","Suppl 2","2 Suppl 2","i1","PMC3102888",NA,NA,"code.google.com"
"982","21624891","MED","21624891","10.1093/nar/gkr433","GLAMM: Genome-Linked Application for Metabolic Maps.","Bates JT, Chivian D, Arkin AP.","Nucleic Acids Res","2011","0305-1048","journal article; research support, u.s. gov't, non-p.h.s.; research support, american recovery and reinvestment act; research-article","Y","Y","Y","8","Y","Y","N","N","N","131.30815","web server issue","39","w400-5","PMC3125797",NA,NA,"code.google.com"
"983","21712192","MED","21712192","10.1186/1479-7364-5-4-310","Pathway annotation and analysis with Reactome: the solute carrier class of membrane transporters.","Jassal B.","Hum Genomics","2011","1473-9542","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","131.30815","4","5","310-315","PMC3525243",NA,NA,"code.google.com"
"984","21059685","MED","21059685","10.1093/nar/gkq1120","AGRIS: the Arabidopsis Gene Regulatory Information Server, an update.","Yilmaz A, Mejia-Guerra MK, Kurz K, Liang X, Welch L, Grotewold E.","Nucleic Acids Res","2011","0305-1048","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","52","Y","Y","N","Y","N","131.30815","database issue","39","d1118-22","PMC3013708",NA,NA,"code.google.com"
"985","21285414","MED","21285414","10.1074/mcp.m110.006049","Quantitative tracking of isotope flows in proteomes of microbial communities.","Pan C, Fischer CR, Hyatt D, Bowen BP, Hettich RL, Banfield JF.","Mol Cell Proteomics","2011","1535-9476","journal article; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","5","Y","Y","N","N","N","131.30815","4","10","m110.006049","PMC3069347",NA,NA,"code.google.com"
"986","21569281","MED","21569281","10.1186/1471-2105-12-143","DAS writeback: a collaborative annotation system.","Salazar GA, Jimenez RC, Garcia A, Hermjakob H, Mulder N, Blake E.","BMC Bioinformatics","2011","1471-2105","journal article; research support, non-u.s. gov't; product-review","Y","Y","Y","1","Y","Y","N","N","N","131.26524",NA,"12","143","PMC3115852",NA,NA,"code.google.com"
"987","21244646","MED","21244646","10.1186/1471-2105-12-23","easyDAS: automatic creation of DAS servers.","Gel Moreno B, Jenkinson AM, Jimenez RC, Messeguer Peypoch X, Hermjakob H.","BMC Bioinformatics","2011","1471-2105","journal article; research support, non-u.s. gov't; product-review","Y","Y","Y","3","Y","Y","N","N","N","131.26524",NA,"12","23","PMC3031199",NA,NA,"code.google.com"
"988","21407812","MED","21407812","10.1371/journal.pone.0017636","A Java program for LRE-based real-time qPCR that enables large-scale absolute quantification.","Rutledge RG.","PLoS One","2011","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","8","Y","Y","N","N","N","131.26524","3","6","e17636","PMC3047581",NA,NA,"code.google.com"
"989","22024252","MED","22024252","10.1186/1471-2105-12-411","EPEPT: a web service for enhanced P-value estimation in permutation tests.","Knijnenburg TA, Lin J, Rovira H, Boyle J, Shmulevich I.","BMC Bioinformatics","2011","1471-2105","journal article; research support, n.i.h., extramural; product-review","Y","Y","Y","0","Y","Y","N","N","N","131.26523",NA,"12","411","PMC3277916",NA,NA,"code.google.com"
"990","21624159","MED","21624159","10.1186/2041-1480-2-s2-s4","An open annotation ontology for science on web 3.0.","Ciccarese P, Ocana M, Garcia Castro LJ, Das S, Clark T.","J Biomed Semantics","2011","2041-1480","journal article; research-article","Y","Y","Y","13","Y","Y","N","Y","N","130.73587","Suppl 2","2 Suppl 2","s4","PMC3102893",NA,NA,"code.google.com"
"991","22131910","MED","22131910","10.1371/journal.pcbi.1002284","Genome majority vote improves gene predictions.","Wall ME, Raghavan S, Cohn JD, Dunbar J.","PLoS Comput Biol","2011","1553-734x","journal article; research-article","Y","Y","Y","4","Y","Y","N","N","N","130.73587","11","7","e1002284","PMC3219611",NA,NA,"code.google.com"
"992","22054122","MED","22054122","10.1186/1471-2105-12-431","AIGO: towards a unified framework for the analysis and the inter-comparison of GO functional annotations.","Defoin-Platel M, Hindle MM, Lysenko A, Powers SJ, Habash DZ, Rawlings CJ, Saqi M.","BMC Bioinformatics","2011","1471-2105","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","N","N","N","130.73587",NA,"12","431","PMC3237112",NA,NA,"code.google.com"
"993","21545720","MED","21545720","10.1186/1752-0509-5-61","Inference of gene regulatory networks from time series by Tsallis entropy.","Lopes FM, de Oliveira EA, Cesar RM Jr.","BMC Syst Biol","2011","1752-0509","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","6","Y","Y","N","N","N","130.73586",NA,"5","61","PMC3117729",NA,NA,"code.google.com"
"994","21594694","MED","21594694","10.1007/s00894-011-1102-8","PSP_MCSVM: brainstorming consensus prediction of protein secondary structures using two-stage multiclass support vector machines.","Chatterjee P, Basu S, Kundu M, Nasipuri M, Plewczynski D.","J Mol Model","2011","1610-2940","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","4","Y","Y","N","N","N","130.73586","9","17","2191-2201","PMC3168739",NA,NA,"code.google.com"
"995","22102894","MED","22102894","10.1371/journal.pone.0027431","Extending transfer entropy improves identification of effective connectivity in a spiking cortical network model.","Ito S, Hansen ME, Heiland R, Lumsdaine A, Litke AM, Beggs JM.","PLoS One","2011","1932-6203","journal article; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","8","Y","Y","N","N","Y","130.73586","11","6","e27431","PMC3216957","doi",NA,"code.google.com"
"996","21477781","MED","21477781","10.1016/j.jgg.2011.02.003","The impact of next-generation sequencing on genomics.","Zhang J, Chiodini R, Badr A, Zhang G.","J Genet Genomics","2011","1673-8527","journal article; review; research support, non-u.s. gov't; research-article","N","Y","Y","66","Y","Y","N","N","N","130.73586","3","38","95-109","PMC3076108",NA,NA,"code.google.com"
"997","22014236","MED","22014236","10.1186/1471-2105-12-405","An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data.","Vu TN, Valkenborg D, Smets K, Verwaest KA, Dommisse R, LemiÃ¨re F, Verschoren A, Goethals B, Laukens K.","BMC Bioinformatics","2011","1471-2105","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","130.73586",NA,"12","405","PMC3217056",NA,NA,"code.google.com"
"998","21622934","MED","21622934","10.1136/amiajnl-2011-000093","The Yale cTAKES extensions for document classification: architecture and application.","Garla V, Lo Re V 3rd, Dorey-Stein Z, Kidwai F, Scotch M, Womack J, Justice A, Brandt C.","J Am Med Inform Assoc","2011","1067-5027","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","Y","7","Y","Y","N","N","N","130.66115","5","18","614-620","PMC3168305",NA,NA,"code.google.com"
"999","22132098","MED","22132098","10.1371/journal.pone.0027372","An open environment CT-US fusion for tissue segmentation during interventional guidance.","Caskey CF, Hlawitschka M, Qin S, Mahakian LM, Cardiff RD, Boone JM, Ferrara KW.","PLoS One","2011","1932-6203","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","5","Y","Y","N","N","N","130.66115","11","6","e27372","PMC3223172",NA,NA,"code.google.com"
"1000","21318478","MED","21318478","10.1007/s00439-011-0953-5","Fine mapping the KLK3 locus on chromosome 19q13.33 associated with prostate cancer susceptibility and PSA levels.","Parikh H, Wang Z, Pettigrew KA, Jia J, Daugherty S, Yeager M, Jacobs KB, Hutchinson A, Burdett L, Cullen M, Qi L, Boland J, Collins I, Albert TJ, Vatten LJ, Hveem K, NjÃ¸lstad I, Cancel-Tassin G, Cussenot O, Valeri A, Virtamo J, Thun MJ, Feigelson HS, Diver WR, Chatterjee N, Thomas G, Albanes D, Chanock SJ, Hunter DJ, Hoover R, Hayes RB, Berndt SI, Sampson J, Amundadottir L.","Hum Genet","2011","0340-6717","journal article; research support, non-u.s. gov't; research support, n.i.h., intramural; research-article","Y","Y","Y","6","Y","Y","N","N","Y","130.66115","6","129","675-685","PMC3092924","refsnp",NA,"code.google.com"
"1001","22053155","MED","22053155","10.3389/fninf.2011.00024","Knowledge synthesis with maps of neural connectivity.","Tallis M, Thompson R, Russ TA, Burns GA.","Front Neuroinform","2011","1662-5196","journal article; research-article","Y","Y","Y","2","Y","Y","N","N","N","130.66115",NA,"5","24","PMC3205380",NA,NA,"code.google.com"
"1002","21233169","MED","21233169","10.1093/bioinformatics/btq725","Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering.","Hao X, Jiang R, Chen T.","Bioinformatics","2011","1367-4803","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","27","Y","Y","N","Y","N","130.66115","5","27","611-618","PMC3042185",NA,NA,"code.google.com"
"1003","21586134","MED","21586134","10.1186/1471-2105-12-167","A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method.","Luna A, Karac EI, Sunshine M, Chang L, Nussinov R, Aladjem MI, Kohn KW.","BMC Bioinformatics","2011","1471-2105","journal article; research support, n.i.h., extramural; research support, n.i.h., intramural; research-article","Y","Y","Y","6","Y","Y","N","N","N","130.66113",NA,"12","167","PMC3118169",NA,NA,"code.google.com"
"1004","21609434","MED","21609434","10.1186/1471-2105-12-196","Acorn: a grid computing system for constraint based modeling and visualization of the genome scale metabolic reaction networks via a web interface.","Sroka J, Bieniasz-Krzywiec L, GwÃ³ÅºdÅº S, Leniowski D, LÄcki J, Markowski M, Avignone-Rossa C, Bushell ME, McFadden J, Kierzek AM.","BMC Bioinformatics","2011","1471-2105","journal article; research support, non-u.s. gov't; product-review","Y","Y","Y","4","Y","Y","N","N","N","130.66113",NA,"12","196","PMC3116490",NA,NA,"code.google.com"
"1005","22115278","MED","22115278","10.1186/1471-2105-12-456","Unintended consequences of existential quantifications in biomedical ontologies.","Boeker M, Tudose I, Hastings J, Schober D, Schulz S.","BMC Bioinformatics","2011","1471-2105","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","3","Y","Y","N","N","N","130.66113",NA,"12","456","PMC3280341",NA,NA,"code.google.com"
"1006","21253599","MED","21253599","10.1371/journal.pone.0015925","PoPoolation: a toolbox for population genetic analysis of next generation sequencing data from pooled individuals.","Kofler R, Orozco-terWengel P, De Maio N, Pandey RV, Nolte V, Futschik A, Kosiol C, SchlÃ¶tterer C.","PLoS One","2011","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","60","Y","Y","N","Y","N","130.66113","1","6","e15925","PMC3017084",NA,NA,"code.google.com"
"1007","21731423","MED","21731423","10.1080/13658810903214203","The GeoViz Toolkit: Using component-oriented coordination methods for geographic visualization and analysis.","Hardisty F, Robinson AC.","Int J Geogr Inf Sci","2011","1365-8816","journal article; research-article","N","Y","Y","5","Y","Y","N","N","N","130.66113","2","25","191-210","PMC3126618",NA,NA,"code.google.com"
"1008","21917716","MED","21917716","10.1126/scisignal.2001989","Systems biology--biomedical modeling.","Sobie EA, Lee YS, Jenkins SL, Iyengar R.","Sci Signal","2011","1937-9145","journal article; review; research support, n.i.h., extramural; research-article","N","Y","Y","2","Y","Y","N","N","N","130.45386","190","4","tr2","PMC3188945",NA,NA,"code.google.com"
"1009","21949660","MED","21949660","10.1371/journal.pgen.1002290","Genetic variants at chromosomes 2q35, 5p12, 6q25.1, 10q26.13, and 16q12.1 influence the risk of breast cancer in men.","Orr N, Cooke R, Jones M, Fletcher O, Dudbridge F, Chilcott-Burns S, Tomczyk K, Broderick P, Houlston R, Ashworth A, Swerdlow A.","PLoS Genet","2011","1553-7390","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","9","Y","Y","N","N","Y","130.45386","9","7","e1002290","PMC3174231","refsnp",NA,"code.google.com"
"1010","21602264","MED","21602264","10.1093/nar/gkr374","miRvestigator: web application to identify miRNAs responsible for co-regulated gene expression patterns discovered through transcriptome profiling.","Plaisier CL, Bare JC, Baliga NS.","Nucleic Acids Res","2011","0305-1048","journal article; research-article","Y","Y","Y","8","Y","Y","N","Y","N","130.45384","web server issue","39","w125-31","PMC3125776",NA,NA,"code.google.com"
"1011","21682879","MED","21682879","10.1186/1471-2105-12-243","RegNetB: predicting relevant regulator-gene relationships in localized prostate tumor samples.","Alvarez A, Woolf PJ.","BMC Bioinformatics","2011","1471-2105","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","2","Y","Y","N","N","N","130.45384",NA,"12","243","PMC3128037",NA,NA,"code.google.com"
"1012","21795786","MED","21795786","10.1107/s1744309111018811","The structure of LpxD from Pseudomonas aeruginosa at 1.3âÃ resolution.","Badger J, Chie-Leon B, Logan C, Sridhar V, Sankaran B, Zwart PH, Nienaber V.","Acta Crystallogr Sect F Struct Biol Cryst Commun","2011","1744-3091","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","Y","2","Y","Y","Y","N","Y","130.45384","pt 7","67","749-752","PMC3144788","pdb","PDBUNIPROT","code.google.com"
"1013","20953780","MED","20953780","10.1007/s00216-010-4235-1","Targeted analysis of glycomics liquid chromatography/mass spectrometry data.","Dreyfuss JM, Jacobs C, Gindin Y, Benson G, Staples GO, Zaia J.","Anal Bioanal Chem","2011","1618-2642","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","Y","6","Y","Y","N","N","N","130.45384","2","399","727-735","PMC3254673",NA,NA,"code.google.com"
"1014","21148691","MED","21148691","10.1128/aem.01733-10","mathFISH, a web tool that uses thermodynamics-based mathematical models for in silico evaluation of oligonucleotide probes for fluorescence in situ hybridization.","Yilmaz LS, Parnerkar S, Noguera DR.","Appl Environ Microbiol","2011","0099-2240","evaluation studies; journal article; research support, u.s. gov't, non-p.h.s.; research-article","N","Y","Y","9","Y","Y","N","N","N","130.45384","3","77","1118-1122","PMC3028703",NA,NA,"code.google.com"
"1015","21222473","MED","21222473","10.1021/pr101157s","FDRAnalysis: a tool for the integrated analysis of tandem mass spectrometry identification results from multiple search engines.","Wedge DC, Krishna R, Blackhurst P, Siepen JA, Jones AR, Hubbard SJ.","J Proteome Res","2011","1535-3893","evaluation studies; journal article; research support, non-u.s. gov't; research-article","N","Y","Y","8","Y","Y","N","N","N","130.45384","4","10","2088-2094","PMC3707089",NA,NA,"code.google.com"
"1016","21695082","MED","21695082","10.1371/journal.pone.0021041","The definition of insulin resistance using HOMA-IR for Americans of Mexican descent using machine learning.","Qu HQ, Li Q, Rentfro AR, Fisher-Hoch SP, McCormick JB.","PLoS One","2011","1932-6203","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","22","Y","Y","N","N","N","130.45384","6","6","e21041","PMC3114864",NA,NA,"code.google.com"
"1017","23275860","MED","23275860","10.1109/icra.2011.5980345","Handheld Micromanipulation with Vision-Based Virtual Fixtures.","Becker BC, Maclachlan RA, Hager GD, Riviere CN.","IEEE Int Conf Robot Autom","2011","2152-4092","journal article; research-article","N","Y","Y","5","Y","Y","N","N","N","130.45384",NA,"2011","4127-4132","PMC3531243",NA,NA,"code.google.com"
"1018","21071392","MED","21071392","10.1093/nar/gkq1039","Pathway Commons, a web resource for biological pathway data.","Cerami EG, Gross BE, Demir E, Rodchenkov I, Babur O, Anwar N, Schultz N, Bader GD, Sander C.","Nucleic Acids Res","2011","0305-1048","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","127","Y","Y","N","Y","N","130.45384","database issue","39","d685-90","PMC3013659",NA,NA,"code.google.com"
"1019","PMC4263484","PMC",NA,NA,"Friday 5 September, 0800â1000 Concurrent Session: Radiation Oncology Varian Prize.",NA,"Journal of Medical Radiation Sciences","2014","2051-3895","abstract","Y","Y","Y","0","N","Y","N","N","N","130.36368","suppl 1","61","63-112","PMC4263484",NA,NA,"code.google.com"
"1020","21459155","MED","21459155","10.1016/j.jbi.2011.03.011","Document-level classification of CT pulmonary angiography reports based on an extension of the ConText algorithm.","Chapman BE, Lee S, Kang HP, Chapman WW.","J Biomed Inform","2011","1532-0464","journal article; research support, n.i.h., extramural; research-article","N","Y","Y","6","Y","Y","N","N","N","130.05705","5","44","728-737","PMC3164892",NA,NA,"code.google.com"
"1021","21494330","MED","21494330","10.1371/journal.pone.0016835","Directed partial correlation: inferring large-scale gene regulatory network through induced topology disruptions.","Yuan Y, Li CT, Windram O.","PLoS One","2011","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","7","Y","Y","N","N","N","130.05705","4","6","e16835","PMC3071805",NA,NA,"code.google.com"
"1022","21859449","MED","21859449","10.1186/1471-2105-12-351","Knowledge engineering tools for reasoning with scientific observations and interpretations: a neural connectivity use case.","Russ TA, Ramakrishnan C, Hovy EH, Bota M, Burns GA.","BMC Bioinformatics","2011","1471-2105","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; product-review","Y","Y","Y","9","Y","Y","N","Y","N","130.05705",NA,"12","351","PMC3176268",NA,NA,"code.google.com"
"1023","21624155","MED","21624155","10.1186/2041-1480-2-s2-s1","The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside.","Luciano JS, Andersson B, Batchelor C, Bodenreider O, Clark T, Denney CK, Domarew C, Gambet T, Harland L, Jentzsch A, Kashyap V, Kos P, Kozlovsky J, Lebo T, Marshall SM, McCusker JP, McGuinness DL, Ogbuji C, Pichler E, Powers RL, Prud'hommeaux E, Samwald M, Schriml L, Tonellato PJ, Whetzel PL, Zhao J, Stephens S, Dumontier M.","J Biomed Semantics","2011","2041-1480","journal article; research-article","Y","Y","Y","8","Y","Y","N","N","N","130.05705","Suppl 2","2 Suppl 2","s1","PMC3102889",NA,NA,"code.google.com"
"1024","22165866","MED","22165866","10.1186/1471-2105-12-470","Algorithms, data structures, and numerics for likelihood-based phylogenetic inference of huge trees.","Izquierdo-Carrasco F, Smith SA, Stamatakis A.","BMC Bioinformatics","2011","1471-2105","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","3","Y","Y","N","N","N","130.05705",NA,"12","470","PMC3267785",NA,NA,"code.google.com"
"1025","21991315","MED","21991315","10.1371/journal.pone.0025513","The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web.","Hastings J, Chepelev L, Willighagen E, Adams N, Steinbeck C, Dumontier M.","PLoS One","2011","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","16","Y","Y","N","Y","N","130.05705","10","6","e25513","PMC3184996",NA,NA,"code.google.com"
"1026","21317909","MED","21317909","10.1038/nmeth.1571","Confined activation and subdiffractive localization enables whole-cell PALM with genetically expressed probes.","York AG, Ghitani A, Vaziri A, Davidson MW, Shroff H.","Nat Methods","2011","1548-7091","journal article; research support, n.i.h., intramural; research-article","Y","Y","Y","44","Y","Y","N","N","N","130.05705","4","8","327-333","PMC3073501",NA,NA,"code.google.com"
"1027","21619704","MED","21619704","10.1186/1471-2407-11-209","A comprehensive candidate gene approach identifies genetic variation associated with osteosarcoma.","Mirabello L, Yu K, Berndt SI, Burdett L, Wang Z, Chowdhury S, Teshome K, Uzoka A, Hutchinson A, Grotmol T, Douglass C, Hayes RB, Hoover RN, Savage SA, National Osteosarcoma Etiology Study Group.","BMC Cancer","2011","1471-2407","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., intramural; research support, u.s. gov't, p.h.s.; research-article","Y","Y","Y","16","Y","Y","N","N","Y","130.0267",NA,"11","209","PMC3138419","refsnp",NA,"code.google.com"
"1028","21658258","MED","21658258","10.1186/1748-717x-6-69","Current measures of metabolic heterogeneity within cervical cancer do not predict disease outcome.","Brooks FJ, Grigsby PW.","Radiat Oncol","2011","1748-717x","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","4","Y","Y","N","N","N","130.0267",NA,"6","69","PMC3130664",NA,NA,"code.google.com"
"1029","21915705","MED","21915705","10.1007/s12105-011-0300-0","The challenges of defining oral cancer: analysis of an ontological approach.","Tapia JL, Goldberg LJ.","Head Neck Pathol","2011","1936-055x","journal article; review; research-article","N","Y","Y","0","Y","Y","N","N","N","130.0267","4","5","376-384","PMC3210219",NA,NA,"code.google.com"
"1030","22105246","MED","22105246","10.3791/3307","Cross-modal multivariate pattern analysis.","Meyer K, Kaplan JT.","J Vis Exp","2011","1940-087x","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; video-audio media; research-article","Y","Y","Y","0","Y","Y","N","N","N","130.0267","57",NA,"13473-13474","PMC3308596",NA,NA,"code.google.com"
"1031","21901085","MED","21901085","10.1371/journal.pcbi.1002147","Biomedical cloud computing with Amazon Web Services.","Fusaro VA, Patil P, Gafni E, Wall DP, Tonellato PJ.","PLoS Comput Biol","2011","1553-734x","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","20","Y","Y","N","N","N","130.0267","8","7","e1002147","PMC3161908",NA,NA,"code.google.com"
"1032","21576123","MED","21576123","10.1093/hmg/ddr213","Large-scale fine mapping of the HNF1B locus and prostate cancer risk.","Berndt SI, Sampson J, Yeager M, Jacobs KB, Wang Z, Hutchinson A, Chung C, Orr N, Wacholder S, Chatterjee N, Yu K, Kraft P, Feigelson HS, Thun MJ, Diver WR, Albanes D, Virtamo J, Weinstein S, Schumacher FR, Cancel-Tassin G, Cussenot O, Valeri A, Andriole GL, Crawford ED, Haiman C, Henderson B, Kolonel L, Le Marchand L, Siddiq A, Riboli E, Travis RC, Kaaks R, Isaacs W, Isaacs S, Wiley KE, Gronberg H, Wiklund F, Stattin P, Xu J, Zheng SL, Sun J, Vatten LJ, Hveem K, NjÃ¸lstad I, Gerhard DS, Tucker M, Hayes RB, Hoover RN, Fraumeni JF Jr, Hunter DJ, Thomas G, Chanock SJ.","Hum Mol Genet","2011","0964-6906","journal article; research support, n.i.h., extramural; research support, n.i.h., intramural; research-article","N","Y","Y","6","Y","Y","Y","N","Y","130.02669","16","20","3322-3329","PMC3140817","refsnp","OMIM","code.google.com"
"1033","21750734","MED","21750734","10.1371/journal.pone.0021810","Integrated management and visualization of electronic tag data with Tagbase.","Lam CH, Tsontos VM.","PLoS One","2011","1932-6203","journal article; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","0","Y","Y","N","N","N","130.02669","7","6","e21810","PMC3130046",NA,NA,"code.google.com"
"1034","21963049","MED","21963049","10.1016/j.ajhg.2011.09.004","Adenosine kinase deficiency disrupts the methionine cycle and causes hypermethioninemia, encephalopathy, and abnormal liver function.","Bjursell MK, Blom HJ, Cayuela JA, Engvall ML, Lesko N, Balasubramaniam S, Brandberg G, Halldin M, Falkenberg M, Jakobs C, Smith D, Struys E, von DÃ¶beln U, Gustafsson CM, Lundeberg J, Wedell A.","Am J Hum Genet","2011","0002-9297","journal article; case reports; research support, non-u.s. gov't; research-article","N","Y","Y","19","Y","Y","Y","N","Y","130.02669","4","89","507-515","PMC3188832","refseq","OMIMUNIPROT","code.google.com"
"1035","21982236","MED","21982236","10.1016/j.stem.2011.07.018","Genome sequencing of mouse induced pluripotent stem cells reveals retroelement stability and infrequent DNA rearrangement during reprogramming.","Quinlan AR, Boland MJ, Leibowitz ML, Shumilina S, Pehrson SM, Baldwin KK, Hall IM.","Cell Stem Cell","2011","1934-5909","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","28","Y","Y","N","N","N","130.02669","4","9","366-373","PMC3975295",NA,NA,"code.google.com"
"1036","21415925","MED","21415925","10.3389/fnins.2011.00009","Fitting neuron models to spike trains.","Rossant C, Goodman DF, Fontaine B, Platkiewicz J, Magnusson AK, Brette R.","Front Neurosci","2011","1662-4548","journal article; research-article","Y","Y","Y","8","Y","Y","N","N","N","130.02669",NA,"5","9","PMC3051271",NA,NA,"code.google.com"
"1037","21087766","MED","21087766","10.1016/j.compbiomed.2010.10.008","A review of diffusion tensor magnetic resonance imaging computational methods and software tools.","Hasan KM, Walimuni IS, Abid H, Hahn KR.","Comput Biol Med","2011","0010-4825","journal article; review; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","13","Y","Y","N","N","N","130.02669","12","41","1062-1072","PMC3135778",NA,NA,"code.google.com"
"1038","21269474","MED","21269474","10.1186/1472-6920-11-4","Enhanced virtual microscopy for collaborative education.","Triola MM, Holloway WJ.","BMC Med Educ","2011","1472-6920","journal article; product-review","Y","Y","Y","14","Y","Y","N","N","N","130.02669",NA,"11","4","PMC3037351",NA,NA,"code.google.com"
"1039","22229055","MED","22229055","10.1371/journal.pone.0028747","Mutual information for the detection of crush.","Harding P, Gwynne S, Amos M.","PLoS One","2011","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","130.02669","12","6","e28747","PMC3244399",NA,NA,"code.google.com"
"1040","21824976","MED","21824976","10.1093/hmg/ddr342","A genome-wide association study of bladder cancer identifies a new susceptibility locus within SLC14A1, a urea transporter gene on chromosome 18q12.3.","Garcia-Closas M, Ye Y, Rothman N, Figueroa JD, Malats N, Dinney CP, Chatterjee N, Prokunina-Olsson L, Wang Z, Lin J, Real FX, Jacobs KB, Baris D, Thun M, De Vivo I, Albanes D, Purdue MP, Kogevinas M, Kamat AM, Lerner SP, Grossman HB, Gu J, Pu X, Hutchinson A, Fu YP, Burdett L, Yeager M, Tang W, TardÃ³n A, Serra C, Carrato A, GarcÃa-Closas R, Lloreta J, Johnson A, Schwenn M, Karagas MR, Schned A, Andriole G Jr, Grubb R 3rd, Black A, Jacobs EJ, Diver WR, Gapstur SM, Weinstein SJ, Virtamo J, Hunter DJ, Caporaso N, Landi MT, Fraumeni JF Jr, Silverman DT, Chanock SJ, Wu X.","Hum Mol Genet","2011","0964-6906","journal article; meta-analysis; research support, non-u.s. gov't; research support, n.i.h., extramural; research support, n.i.h., intramural; research-article","N","Y","Y","28","Y","Y","Y","Y","Y","130.02669","21","20","4282-4289","PMC3188994","refsnp","UNIPROT","code.google.com"
"1041","21565377","MED","21565377","10.1016/j.virol.2011.04.007","Metabolite profiles of human immunodeficiency virus infected CD4+ T cells and macrophages using LC-MS/MS analysis.","Hollenbaugh JA, Munger J, Kim B.","Virology","2011","0042-6822","evaluation studies; journal article; research support, n.i.h., extramural; research-article","N","Y","Y","8","Y","Y","N","N","N","130.02669","2","415","153-159","PMC3107887",NA,NA,"code.google.com"
"1042","21935457","MED","21935457","10.1371/journal.pone.0024756","iDNA-Prot: identification of DNA binding proteins using random forest with grey model.","Lin WZ, Fang JA, Xiao X, Chou KC.","PLoS One","2011","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","33","Y","Y","N","N","N","130.02669","9","6","e24756","PMC3174210",NA,NA,"code.google.com"
"1043","21597105","MED","21597105","10.1136/amiajnl-2011-000154","Hybrid methods for improving information access in clinical documents: concept, assertion, and relation identification.","Minard AL, Ligozat AL, Ben Abacha A, Bernhard D, Cartoni B, DelÃ©ger L, Grau B, Rosset S, Zweigenbaum P, Grouin C.","J Am Med Inform Assoc","2011","1067-5027","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","Y","12","Y","Y","N","N","N","130.02669","5","18","588-593","PMC3168313",NA,NA,"code.google.com"
"1044","21831268","MED","21831268","10.1186/1471-2105-12-333","Efficient counting of k-mers in DNA sequences using a bloom filter.","Melsted P, Pritchard JK.","BMC Bioinformatics","2011","1471-2105","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","15","Y","Y","N","Y","N","130.02669",NA,"12","333","PMC3166945",NA,NA,"code.google.com"
"1045","21596083","MED","21596083","10.1016/j.vaccine.2011.04.131","Multistrain genome analysis identifies candidate vaccine antigens of Anaplasma marginale.","Dark MJ, Al-Khedery B, Barbet AF.","Vaccine","2011","0264-410x","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","11","Y","Y","Y","N","Y","130.02669","31","29","4923-4932","PMC3133685","gen","EMBL","code.google.com"
"1046","21477364","MED","21477364","10.1186/1471-2288-11-43","Implementation of workflow engine technology to deliver basic clinical decision support functionality.","Huser V, Rasmussen LV, Oberg R, Starren JB.","BMC Med Res Methodol","2011","1471-2288","journal article; research support, n.i.h., extramural; product-review","Y","Y","Y","3","Y","Y","N","N","N","129.99602",NA,"11","43","PMC3079703",NA,NA,"code.google.com"
"1047","21682852","MED","21682852","10.1186/1471-2105-12-242","Querying large read collections in main memory: a versatile data structure.","Philippe N, Salson M, Lecroq T, LÃ©onard M, Commes T, Rivals E.","BMC Bioinformatics","2011","1471-2105","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","129.99602",NA,"12","242","PMC3163563",NA,NA,"code.google.com"
"1048","21729295","MED","21729295","10.1186/1471-2164-12-344","Comparative analysis of methods for detecting interacting loci.","Chen L, Yu G, Langefeld CD, Miller DJ, Guy RT, Raghuram J, Yuan X, Herrington DM, Wang Y.","BMC Genomics","2011","1471-2164","journal article; research support, n.i.h., extramural; comparative study; research-article","Y","Y","Y","10","Y","Y","N","N","N","129.99602",NA,"12","344","PMC3161015",NA,NA,"code.google.com"
"1049","21952134","MED","21952134","10.1038/msb.2011.64","A regression model approach to enable cell morphology correction in high-throughput flow cytometry.","Knijnenburg TA, Roda O, Wan Y, Nolan GP, Aitchison JD, Shmulevich I.","Mol Syst Biol","2011","1744-4292","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","5","Y","Y","Y","N","N","129.99602",NA,"7","531","PMC3202802",NA,"UNIPROT","code.google.com"
"1050","21981858","MED","21981858","10.1186/1471-2164-12-492","Effect of the down-regulation of the high Grain Protein Content (GPC) genes on the wheat transcriptome during monocarpic senescence.","Cantu D, Pearce SP, Distelfeld A, Christiansen MW, Uauy C, Akhunov E, Fahima T, Dubcovsky J.","BMC Genomics","2011","1471-2164","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","24","Y","Y","Y","N","Y","129.99602",NA,"12","492","PMC3209470","gen","EMBLARXPR","code.google.com"
"1051","21642358","MED","21642358","10.1093/carcin/bgr100","Common genetic variants related to genomic integrity and risk of papillary thyroid cancer.","Neta G, Brenner AV, Sturgis EM, Pfeiffer RM, Hutchinson AA, Aschebrook-Kilfoy B, Yeager M, Xu L, Wheeler W, Abend M, Ron E, Tucker MA, Chanock SJ, Sigurdson AJ.","Carcinogenesis","2011","0143-3334","journal article; research support, non-u.s. gov't; research support, n.i.h., intramural; comparative study; research-article","N","Y","Y","9","Y","Y","N","N","Y","129.59955","8","32","1231-1237","PMC3166197","refsnp",NA,"code.google.com"
"1052","21112962","MED","21112962","10.1093/molbev/msq319","Testing spatiotemporal hypothesis of bacterial evolution using methicillin-resistant Staphylococcus aureus ST239 genome-wide data within a bayesian framework.","Gray RR, Tatem AJ, Johnson JA, Alekseyenko AV, Pybus OG, Suchard MA, Salemi M.","Mol Biol Evol","2011","0737-4038","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","15","Y","Y","N","N","N","129.59955","5","28","1593-1603","PMC3115679",NA,NA,"code.google.com"
"1053","21951689","MED","21951689","10.1186/1741-7007-9-64","Double-strand break repair processes drive evolution of the mitochondrial genome in Arabidopsis.","Davila JI, Arrieta-Montiel MP, Wamboldt Y, Cao J, Hagmann J, Shedge V, Xu YZ, Weigel D, Mackenzie SA.","BMC Biol","2011","1741-7007","journal article; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","30","Y","Y","Y","N","Y","129.59955",NA,"9","64","PMC3193812","gen","UNIPROT","code.google.com"
"1054","22039405","MED","22039405","10.1371/journal.pone.0024982","SNPpy--database management for SNP data from genome wide association studies.","Mitha F, Herodotou H, Borisov N, Jiang C, Yoder J, Owzar K.","PLoS One","2011","1932-6203","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","129.59955","10","6","e24982","PMC3198468",NA,NA,"code.google.com"
"1055","22166341","MED","22166341","10.1186/2041-1480-2-s5-s1","Ontology design patterns to disambiguate relations between genes and gene products in GENIA.","Hoehndorf R, Ngonga Ngomo AC, Pyysalo S, Ohta T, Oellrich A, Rebholz-Schuhmann D.","J Biomed Semantics","2011","2041-1480","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","129.59955","Suppl 5","2 Suppl 5","s1","PMC3239299",NA,NA,"code.google.com"
"1056","21867511","MED","21867511","10.1186/1471-2105-12-354","Parallelized short read assembly of large genomes using de Bruijn graphs.","Liu Y, Schmidt B, Maskell DL.","BMC Bioinformatics","2011","1471-2105","journal article; research-article","Y","Y","Y","10","Y","Y","N","Y","N","129.59955",NA,"12","354","PMC3167803",NA,NA,"code.google.com"
"1057","21605356","MED","21605356","10.1186/1471-2105-12-187","Extracting scientific articles from a large digital archive: BioStor and the Biodiversity Heritage Library.","Page RD.","BMC Bioinformatics","2011","1471-2105","journal article; research-article","Y","Y","Y","3","Y","Y","N","N","N","129.59953",NA,"12","187","PMC3129327",NA,NA,"code.google.com"
"1058","21613275","MED","21613275","10.1093/cvr/cvr143","Recovery of cardiac calcium release is controlled by sarcoplasmic reticulum refilling and ryanodine receptor sensitivity.","Ramay HR, Liu OZ, Sobie EA.","Cardiovasc Res","2011","0008-6363","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","28","Y","Y","N","N","N","129.59953","4","91","598-605","PMC3156908",NA,NA,"code.google.com"
"1059","21619639","MED","21619639","10.1186/1752-0509-5-86","Partially observed bipartite network analysis to identify predictive connections in transcriptional regulatory networks.","Alvarez A, Woolf PJ.","BMC Syst Biol","2011","1752-0509","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","2","Y","Y","N","N","N","129.59953",NA,"5","86","PMC3117734",NA,NA,"code.google.com"
"1060","21396456","MED","21396456","10.1016/j.neuroimage.2011.03.010","Large-scale directional connections among multi resting-state neural networks in human brain: a functional MRI and Bayesian network modeling study.","Li R, Chen K, Fleisher AS, Reiman EM, Yao L, Wu X.","Neuroimage","2011","1053-8119","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","15","Y","Y","N","N","N","129.59953","3","56","1035-1042","PMC3319766",NA,NA,"code.google.com"
"1061","21736759","MED","21736759","10.1186/1471-2164-12-353","The differential disease regulome.","Sandve GK, Gundersen S, Rydbeck H, Glad IK, Holden L, Holden M, LiestÃ¸l K, Clancy T, DrablÃ¸s F, Ferkingstad E, Johansen M, Nygaard V, TÃ¸stesen E, Frigessi A, Hovig E.","BMC Genomics","2011","1471-2164","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","3","Y","Y","N","N","N","129.59953",NA,"12","353","PMC3160420",NA,NA,"code.google.com"
"1062","21851626","MED","21851626","10.1186/1751-0473-6-13","Nephele: genotyping via complete composition vectors and MapReduce.","Colosimo ME, Peterson MW, Mardis S, Hirschman L.","Source Code Biol Med","2011","1751-0473","journal article; product-review","Y","Y","Y","2","Y","Y","N","N","N","129.59953",NA,"6","13","PMC3182884",NA,NA,"code.google.com"
"1063","21862759","MED","21862759","10.1074/mcp.m111.008110","Proteomic and metabolomic profiling of a trait anxiety mouse model implicate affected pathways.","Zhang Y, Filiou MD, Reckow S, Gormanns P, Maccarrone G, Kessler MS, Frank E, Hambsch B, Holsboer F, Landgraf R, Turck CW.","Mol Cell Proteomics","2011","1535-9476","journal article; research support, non-u.s. gov't; research-article","N","Y","Y","6","Y","Y","N","N","N","129.59953","12","10","m111.008110","PMC3237072",NA,NA,"code.google.com"
"1064","21872852","MED","21872852","10.1016/j.compbiomed.2011.08.004","Simulating ventilation distribution in heterogenous lung injury using a binary tree data structure.","Colletti AA, Amini R, Kaczka DW.","Comput Biol Med","2011","0010-4825","journal article; research support, n.i.h., extramural; research-article","N","Y","Y","3","Y","Y","N","N","N","129.59953","10","41","936-945","PMC3177984",NA,NA,"code.google.com"
"1065","21984743","MED","21984743","10.1093/bib/bbr055","Tools and collaborative environments for bioinformatics research.","Romano P, Giugno R, Pulvirenti A.","Brief Bioinform","2011","1467-5463","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","6","Y","Y","N","N","N","129.59953","6","12","549-561","PMC3220874",NA,NA,"code.google.com"
"1066","20206294","MED","20206294","10.1016/j.jbi.2010.02.008","Towards an ontological representation of resistance: the case of MRSA.","Goldfain A, Smith B, Cowell LG.","J Biomed Inform","2011","1532-0464","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","3","Y","Y","N","N","N","129.59953","1","44","35-41","PMC2930208",NA,NA,"code.google.com"
"1067","21354348","MED","21354348","10.1016/j.jprot.2011.02.017","High throughput proteomic analysis of the secretome in an explant model of articular cartilage inflammation.","Clutterbuck AL, Smith JR, Allaway D, Harris P, Liddell S, Mobasheri A.","J Proteomics","2011","1874-3919","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","12","Y","Y","N","N","N","129.59953","5","74","704-715","PMC3078332",NA,NA,"code.google.com"
"1068","21249219","MED","21249219","10.1371/journal.pone.0015237","ePlant and the 3D data display initiative: integrative systems biology on the world wide web.","Fucile G, Di Biase D, Nahal H, La G, Khodabandeh S, Chen Y, Easley K, Christendat D, Kelley L, Provart NJ.","PLoS One","2011","1932-6203","journal article; research-article","Y","Y","Y","2","Y","Y","N","N","Y","129.59953","1","6","e15237","PMC3018417","pdb",NA,"code.google.com"
"1069","21304545","MED","21304545","10.1038/hdy.2011.4","Targeted resequencing of a genomic region influencing tameness and aggression reveals multiple signals of positive selection.","Albert FW, Hodges E, Jensen JD, Besnier F, Xuan Z, Rooks M, Bhattacharjee A, Brizuela L, Good JM, Green RE, Burbano HA, Plyusnina IZ, Trut L, Andersson L, SchÃ¶neberg T, Carlborg O, Hannon GJ, PÃ¤Ã¤bo S.","Heredity (Edinb)","2011","0018-067x","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","7","Y","Y","N","N","N","129.59953","3","107","205-214","PMC3183948",NA,NA,"code.google.com"
"1070","22166257","MED","22166257","10.1186/2041-1480-2-s5-s6","Coreference based event-argument relation extraction on biomedical text.","Yoshikawa K, Riedel S, Hirao T, Asahara M, Matsumoto Y.","J Biomed Semantics","2011","2041-1480","journal article; research-article","Y","Y","Y","2","Y","Y","N","N","N","129.59953","Suppl 5","2 Suppl 5","s6","PMC3239306",NA,NA,"code.google.com"
"1071","21436044","MED","21436044","10.1073/pnas.1016939108","Fidelity of neural reactivation reveals competition between memories.","Kuhl BA, Rissman J, Chun MM, Wagner AD.","Proc Natl Acad Sci U S A","2011","0027-8424","journal article; research support, n.i.h., extramural; research-article","N","Y","Y","29","Y","Y","N","N","N","129.59953","14","108","5903-5908","PMC3078372",NA,NA,"code.google.com"
"1072","22044581","MED","22044581","10.1186/1471-2105-12-426","A Bayesian model for gene family evolution.","Liu L, Yu L, Kalavacharla V, Liu Z.","BMC Bioinformatics","2011","1471-2105","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","5","Y","Y","N","N","N","129.59953",NA,"12","426","PMC3774087",NA,NA,"code.google.com"
"1073","21896751","MED","21896751","10.1073/pnas.1107906108","Inhibition of influenza virus replication via small molecules that induce the formation of higher-order nucleoprotein oligomers.","Gerritz SW, Cianci C, Kim S, Pearce BC, Deminie C, Discotto L, McAuliffe B, Minassian BF, Shi S, Zhu S, Zhai W, Pendri A, Li G, Poss MA, Edavettal S, McDonnell PA, Lewis HA, Maskos K, MÃ¶rtl M, Kiefersauer R, Steinbacher S, Baldwin ET, Metzler W, Bryson J, Healy MD, Philip T, Zoeckler M, Schartman R, Sinz M, Leyva-Grado VH, Hoffmann HH, Langley DR, Meanwell NA, Krystal M.","Proc Natl Acad Sci U S A","2011","0027-8424","journal article; research-article","N","Y","Y","24","Y","Y","Y","N","Y","129.59953","37","108","15366-15371","PMC3174639","pdb","PDBUNIPROT","code.google.com"
"1074","21538547","MED","21538547","10.1002/prot.23035","Crystal structure of a metal-dependent phosphoesterase (YP_910028.1) from Bifidobacterium adolescentis: Computational prediction and experimental validation of phosphoesterase activity.","Han GW, Ko J, Farr CL, Deller MC, Xu Q, Chiu HJ, Miller MD, Sefcikova J, Somarowthu S, Beuning PJ, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA, Ondrechen MJ.","Proteins","2011","0887-3585","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","Y","3","Y","Y","Y","N","Y","129.59953","7","79","2146-2160","PMC3115465","pfam; pdb; sprot; gen","PDBUNIPROT","code.google.com"
"1075","22172142","MED","22172142","10.1186/1752-0509-5-198","Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language.","Waltemath D, Adams R, Bergmann FT, Hucka M, Kolpakov F, Miller AK, Moraru II, Nickerson D, Sahle S, Snoep JL, Le NovÃ¨re N.","BMC Syst Biol","2011","1752-0509","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","18","Y","Y","N","Y","N","129.59953",NA,"5","198","PMC3292844",NA,NA,"code.google.com"
"1076","21816034","MED","21816034","10.1186/1471-2105-12-321","The volatile compound BinBase mass spectral database.","Skogerson K, Wohlgemuth G, Barupal DK, Fiehn O.","BMC Bioinformatics","2011","1471-2105","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","13","Y","Y","N","N","N","129.17238",NA,"12","321","PMC3199763",NA,NA,"code.google.com"
"1077","21349178","MED","21349178","10.1186/1475-2859-10-12","Multi-omics approach to study the growth efficiency and amino acid metabolism in Lactococcus lactis at various specific growth rates.","Lahtvee PJ, Adamberg K, Arike L, Nahku R, Aller K, Vilu R.","Microb Cell Fact","2011","1475-2859","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","11","Y","Y","N","N","N","129.17238",NA,"10","12","PMC3049130",NA,NA,"code.google.com"
"1078","21465547","MED","21465547","10.1002/gepi.20577","Genetic variance components estimation for binary traits using multiple related individuals.","Papachristou C, Ober C, Abney M.","Genet Epidemiol","2011","0741-0395","journal article; research support, n.i.h., extramural; research-article","N","Y","Y","0","Y","Y","N","N","N","129.17236","5","35","291-302","PMC3612980",NA,NA,"code.google.com"
"1079","21533090","MED","21533090","10.1371/journal.pone.0018880","Arabidopsis plasmodesmal proteome.","Fernandez-Calvino L, Faulkner C, Walshaw J, Saalbach G, Bayer E, Benitez-Alfonso Y, Maule A.","PLoS One","2011","1932-6203","journal article; validation studies; research support, non-u.s. gov't; research-article","Y","Y","Y","33","Y","Y","Y","N","N","129.17236","4","6","e18880","PMC3080382",NA,"UNIPROT","code.google.com"
"1080","21569231","MED","21569231","10.1186/1472-6750-11-47","Increasing gene dosage greatly enhances recombinant expression of aquaporins in Pichia pastoris.","NordÃ©n K, Agemark M, Danielson JÃ, Alexandersson E, Kjellbom P, Johanson U.","BMC Biotechnol","2011","1472-6750","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","12","Y","Y","N","N","N","129.17236",NA,"11","47","PMC3118338",NA,NA,"code.google.com"
"1081","21589869","MED","21589869","10.1371/journal.pone.0019470","RAD21 cooperates with pluripotency transcription factors in the maintenance of embryonic stem cell identity.","Nitzsche A, Paszkowski-Rogacz M, Matarese F, Janssen-Megens EM, Hubner NC, Schulz H, de Vries I, Ding L, Huebner N, Mann M, Stunnenberg HG, Buchholz F.","PLoS One","2011","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","29","Y","Y","Y","N","N","129.17236","5","6","e19470","PMC3093395",NA,"UNIPROTARXPR","code.google.com"
"1082","21712727","MED","21712727","10.231/jim.0b013e318224d8cc","Computational approaches for translational clinical research in disease progression.","McGuire MF, Iyengar MS, Mercer DW.","J Investig Med","2011","1081-5589","journal article; review; research support, n.i.h., extramural; research-article","N","Y","Y","4","Y","Y","N","N","N","129.17236","6","59","893-903","PMC3196807",NA,NA,"code.google.com"
"1083","21738630","MED","21738630","10.1371/journal.pone.0021293","Computational analysis of the spatiotemporal coordination of polarized PI3K and Rac1 activities in micro-patterned live cells.","Lu S, Kim TJ, Chen CE, Ouyang M, Seong J, Liao X, Wang Y.","PLoS One","2011","1932-6203","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","3","Y","Y","N","N","N","129.17236","6","6","e21293","PMC3124492",NA,NA,"code.google.com"
"1084","21767363","MED","21767363","10.1186/1471-2156-12-63","A strategy analysis for genetic association studies with known inbreeding.","Cabras S, Castellanos ME, Biino G, Persico I, Sassu A, Casula L, Del Giacco S, Bertolino F, Pirastu M, Pirastu N.","BMC Genet","2011","1471-2156","evaluation studies; journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","Y","129.17236",NA,"12","63","PMC3155486","refsnp",NA,"code.google.com"
"1085","21859805","MED","21859805","10.1093/gbe/evr087","Comparative analysis of chromosome counts infers three paleopolyploidies in the mollusca.","Hallinan NM, Lindberg DR.","Genome Biol Evol","2011","1759-6653","journal article; research support, non-u.s. gov't; comparative study; research-article","Y","Y","Y","1","Y","Y","N","N","N","129.17236",NA,"3","1150-1163","PMC3194838",NA,NA,"code.google.com"
"1086","21887219","MED","21887219","10.1371/journal.pone.0022483","Rec-DCM-Eigen: reconstructing a less parsimonious but more accurate tree in shorter time.","Kang S, Tang J, Schaeffer SW, Bader DA.","PLoS One","2011","1932-6203","journal article; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","0","Y","Y","N","N","N","129.17236","8","6","e22483","PMC3160844",NA,NA,"code.google.com"
"1087","21991246","MED","21991246","10.3389/fnsys.2011.00074","Minimal impairment in a rat model of duration discrimination following excitotoxic lesions of primary auditory and prefrontal cortices.","Pai S, Erlich JC, Kopec C, Brody CD.","Front Syst Neurosci","2011","1662-5137","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","129.17236",NA,"5","74","PMC3180561",NA,NA,"code.google.com"
"1088","22087219","MED","22087219","10.1371/journal.pone.0026054","Next-generation sequencing of apoptotic DNA breakpoints reveals association with actively transcribed genes and gene translocations.","Fullwood MJ, Lee J, Lin L, Li G, Huss M, Ng P, Sung WK, Shenolikar S.","PLoS One","2011","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","Y","N","N","129.17236","11","6","e26054","PMC3210745",NA,"ARXPR","code.google.com"
"1089","22102801","MED","22102801","10.1371/journal.pcbi.1002263","Computational modeling and analysis of insulin induced eukaryotic translation initiation.","Lequieu J, Chakrabarti A, Nayak S, Varner JD.","PLoS Comput Biol","2011","1553-734x","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","3","Y","Y","N","N","N","129.17236","11","7","e1002263","PMC3213178",NA,NA,"code.google.com"
"1090","22114666","MED","22114666","10.1371/journal.pone.0027080","CAGO: a software tool for dynamic visual comparison and correlation measurement of genome organization.","Chang YF, Chang CH.","PLoS One","2011","1932-6203","journal article; research support, non-u.s. gov't; comparative study; research-article","Y","Y","Y","0","Y","Y","N","N","N","129.17236","11","6","e27080","PMC3219657",NA,NA,"code.google.com"
"1091","21406390","MED","21406390","10.1074/mcp.m110.006866","Redox proteomics of protein-bound methionine oxidation.","GhesquiÃ¨re B, Jonckheere V, Colaert N, Van Durme J, Timmerman E, Goethals M, Schymkowitz J, Rousseau F, Vandekerckhove J, Gevaert K.","Mol Cell Proteomics","2011","1535-9476","journal article; research support, non-u.s. gov't; research-article","N","Y","Y","11","Y","Y","N","N","Y","129.17236","5","10","m110.006866","PMC3098596","pdb",NA,"code.google.com"
"1092","21437295","MED","21437295","10.1039/c0ib00141d","Modeling and analysis of retinoic acid induced differentiation of uncommitted precursor cells.","Tasseff R, Nayak S, Song SO, Yen A, Varner JD.","Integr Biol (Camb)","2011","1757-9694","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","Y","6","Y","Y","N","N","N","129.17236","5","3","578-591","PMC3685823",NA,NA,"code.google.com"
"1093","20709176","MED","20709176","10.1016/j.neuroimage.2010.07.074","Detecting stable distributed patterns of brain activation using Gini contrast.","Langs G, Menze BH, Lashkari D, Golland P.","Neuroimage","2011","1053-8119","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","Y","6","Y","Y","N","N","N","129.17236","2","56","497-507","PMC3960973",NA,NA,"code.google.com"
"1094","21232613","MED","21232613","10.1016/j.neuroimage.2010.12.086","Data-driven optimization and evaluation of 2D EPI and 3D PRESTO for BOLD fMRI at 7 Tesla: I. Focal coverage.","Barry RL, Strother SC, Gatenby JC, Gore JC.","Neuroimage","2011","1053-8119","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","10","Y","Y","N","N","N","129.17236","3","55","1034-1043","PMC3049844",NA,NA,"code.google.com"
"1095","21305044","MED","21305044","10.1371/journal.pone.0016499","Novel analysis of oceanic surface water metagenomes suggests importance of polyphosphate metabolism in oligotrophic environments.","Temperton B, Gilbert JA, Quinn JP, McGrath JW.","PLoS One","2011","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","13","Y","Y","N","N","Y","129.17236","1","6","e16499","PMC3030594","pfam",NA,"code.google.com"
"1096","22259303","MED","22259303","10.3897/zookeys.137.1786","Revision of Poliaspis (Hemiptera, Coccoidea, Diaspididae), with descriptions of 8 new species from Australia.","Hardy N, Henderson RC.","Zookeys","2011","1313-2989","journal article; research-article","Y","Y","Y","0","N","Y","N","N","N","129.17236","137",NA,"1-40","PMC3260887",NA,NA,"code.google.com"
"1097","21555742","MED","21555742","10.1182/blood-2010-10-315309","Structural basis of thrombin-mediated factor V activation: the Glu666-Glu672 sequence is critical for processing at the heavy chain-B domain junction.","Corral-RodrÃguez MÃ, Bock PE, HernÃ¡ndez-Carvajal E, GutiÃ©rrez-Gallego R, Fuentes-Prior P.","Blood","2011","0006-4971","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","3","Y","Y","Y","N","Y","129.17236","26","117","7164-7173","PMC3143557","pdb","PDBUNIPROT","code.google.com"
"1098","21529368","MED","21529368","10.1186/1759-8753-2-6","Prevalence of SOS-mediated control of integron integrase expression as an adaptive trait of chromosomal and mobile integrons.","Cambray G, Sanchez-Alberola N, Campoy S, Guerin E, Da Re S, GonzÃ¡lez-Zorn B, Ploy MC, BarbÃ© J, Mazel D, Erill I.","Mob DNA","2011","1759-8753","journal article; research-article","Y","Y","Y","20","Y","Y","N","Y","N","129.17236","1","2","6","PMC3108266",NA,NA,"code.google.com"
"1099","21737429","MED","21737429","10.1093/nar/gkr538","PhenomeNET: a whole-phenome approach to disease gene discovery.","Hoehndorf R, Schofield PN, Gkoutos GV.","Nucleic Acids Res","2011","0305-1048","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","48","Y","Y","N","Y","N","129.17236","18","39","e119","PMC3185433",NA,NA,"code.google.com"
"1100","21801388","MED","21801388","10.1186/1477-3155-9-29","Activation of stress-related signalling pathway in human cells upon SiO2 nanoparticles exposure as an early indicator of cytotoxicity.","Mohamed BM, Verma NK, Prina-Mello A, Williams Y, Davies AM, Bakos G, Tormey L, Edwards C, Hanrahan J, Salvati A, Lynch I, Dawson K, Kelleher D, Volkov Y.","J Nanobiotechnology","2011","1477-3155","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","17","Y","Y","N","N","N","129.17236",NA,"9","29","PMC3164618",NA,NA,"code.google.com"
"1101","21713110","MED","21713110","10.3389/fninf.2011.00003","The connectome viewer toolkit: an open source framework to manage, analyze, and visualize connectomes.","Gerhard S, Daducci A, Lemkaddem A, Meuli R, Thiran JP, Hagmann P.","Front Neuroinform","2011","1662-5196","journal article; research-article","Y","Y","Y","11","Y","Y","N","Y","N","129.17236",NA,"5","3","PMC3112315",NA,NA,"code.google.com"
"1102","21277996","MED","21277996","10.1016/j.jbi.2011.01.007","Learning relational policies from electronic health record access logs.","Malin B, Nyemba S, Paulett J.","J Biomed Inform","2011","1532-0464","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","Y","11","Y","Y","N","N","N","129.17236","2","44","333-342","PMC3063332",NA,NA,"code.google.com"
"1103","21645414","MED","21645414","10.1186/1471-2164-12-295","Characterization of killer immunoglobulin-like receptor genetics and comprehensive genotyping by pyrosequencing in rhesus macaques.","Moreland AJ, Guethlein LA, Reeves RK, Broman KW, Johnson RP, Parham P, O'Connor DH, Bimber BN.","BMC Genomics","2011","1471-2164","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","6","Y","Y","Y","N","N","129.17236",NA,"12","295","PMC3125267",NA,"EMBL","code.google.com"
"1104","21619640","MED","21619640","10.1186/1471-2105-12-214","Structator: fast index-based search for RNA sequence-structure patterns.","Meyer F, Kurtz S, Backofen R, Will S, Beckstette M.","BMC Bioinformatics","2011","1471-2105","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","8","Y","Y","N","N","N","128.74522",NA,"12","214","PMC3154205",NA,NA,"code.google.com"
"1105","21701575","MED","21701575","10.1371/journal.pone.0020642","Reconciling apparent conflicts between mitochondrial and nuclear phylogenies in African elephants.","Ishida Y, Oleksyk TK, Georgiadis NJ, David VA, Zhao K, Stephens RM, Kolokotronis SO, Roca AL.","PLoS One","2011","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","8","Y","Y","N","N","Y","128.74522","6","6","e20642","PMC3110795","gen",NA,"code.google.com"
"1106","21705473","MED","21705473","10.1093/gbe/evr063","Characterizing the influence of effective population size on the rate of adaptation: Gillespie's Darwin domain.","Jensen JD, Bachtrog D.","Genome Biol Evol","2011","1759-6653","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","12","Y","Y","N","Y","Y","128.74522",NA,"3","687-701","PMC3157839","gen",NA,"code.google.com"
"1107","22319486","MED","22319486","10.3389/fncom.2011.00052","A statistical description of neural ensemble dynamics.","Long JD 2nd, Carmena JM.","Front Comput Neurosci","2011","1662-5188","journal article; research-article","Y","Y","Y","2","Y","Y","N","N","N","128.74522",NA,"5","52","PMC3226070",NA,NA,"code.google.com"
"1108","22207805","MED","22207805","10.3897/zookeys.150.1766","Data issues in the life sciences.","Thessen AE, Patterson DJ.","Zookeys","2011","1313-2989","journal article; review-article","Y","Y","Y","7","Y","Y","N","N","N","128.74522","150",NA,"15-51","PMC3234430",NA,NA,"code.google.com"
"1109","21829512","MED","21829512","10.1371/journal.pone.0022780","Comprehensive phylogenetic reconstruction of amoebozoa based on concatenated analyses of SSU-rDNA and actin genes.","Lahr DJ, Grant J, Nguyen T, Lin JH, Katz LA.","PLoS One","2011","1932-6203","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; comparative study; research-article","Y","Y","Y","19","Y","Y","Y","N","N","128.74522","7","6","e22780","PMC3145751",NA,"EMBLUNIPROT","code.google.com"
"1110","21787385","MED","21787385","10.1186/gb-2011-12-7-r67","ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions.","Rashid NU, Giresi PG, Ibrahim JG, Sun W, Lieb JD.","Genome Biol","2011","1465-6906","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","36","Y","Y","N","Y","N","128.74521","7","12","r67","PMC3218829",NA,NA,"code.google.com"
"1111","22098775","MED","22098775","10.1186/1471-2202-12-119","TRENTOOL: a Matlab open source toolbox to analyse information flow in time series data with transfer entropy.","Lindner M, Vicente R, Priesemann V, Wibral M.","BMC Neurosci","2011","1471-2202","journal article; research support, non-u.s. gov't; product-review","Y","Y","Y","14","Y","Y","N","N","N","128.74521",NA,"12","119","PMC3287134",NA,NA,"code.google.com"
"1112","22444074","MED","22444074","10.1089/brain.2011.0065","Global and system-specific resting-state fMRI fluctuations are uncorrelated: principal component analysis reveals anti-correlated networks.","Carbonell F, Bellec P, Shmuel A.","Brain Connect","2011","2158-0014","journal article; research support, non-u.s. gov't; research-article","N","Y","Y","14","Y","Y","N","N","N","128.74521","6","1","496-510","PMC3604782",NA,NA,"code.google.com"
"1113","20858546","MED","20858546","10.1016/j.neuroimage.2010.09.034","Dimensionality estimation for optimal detection of functional networks in BOLD fMRI data.","Yourganov G, Chen X, Lukic AS, Grady CL, Small SL, Wernick MN, Strother SC.","Neuroimage","2011","1053-8119","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","16","Y","Y","N","N","N","128.74521","2","56","531-543","PMC3052418",NA,NA,"code.google.com"
"1114","22242142","MED","22242142","10.1371/journal.pone.0029731","Efficient maximum likelihood estimation of kinetic rate constants from macroscopic currents.","Stepanyuk AR, Borisyuk AL, Belan PV.","PLoS One","2011","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","128.74521","12","6","e29731","PMC3248447",NA,NA,"code.google.com"
"1115","22645531","MED","22645531","10.3389/fpls.2011.00034","The iPlant Collaborative: Cyberinfrastructure for Plant Biology.","Goff SA, Vaughn M, McKay S, Lyons E, Stapleton AE, Gessler D, Matasci N, Wang L, Hanlon M, Lenards A, Muir A, Merchant N, Lowry S, Mock S, Helmke M, Kubach A, Narro M, Hopkins N, Micklos D, Hilgert U, Gonzales M, Jordan C, Skidmore E, Dooley R, Cazes J, McLay R, Lu Z, Pasternak S, Koesterke L, Piel WH, Grene R, Noutsos C, Gendler K, Feng X, Tang C, Lent M, Kim SJ, Kvilekval K, Manjunath BS, Tannen V, Stamatakis A, Sanderson M, Welch SM, Cranston KA, Soltis P, Soltis D, O'Meara B, Ane C, Brutnell T, Kleibenstein DJ, White JW, Leebens-Mack J, Donoghue MJ, Spalding EP, Vision TJ, Myers CR, Lowenthal D, Enquist BJ, Boyle B, Akoglu A, Andrews G, Ram S, Ware D, Stein L, Stanzione D.","Front Plant Sci","2011","1664-462x","journal article; review-article","Y","Y","Y","23","Y","Y","N","N","N","128.74521",NA,"2","34","PMC3355756",NA,NA,"code.google.com"
"1116","21594144","MED","21594144","10.3897/zookeys.80.907","Revision of the Malagasy genus Trichoteleia Kieffer (Hymenoptera, Platygastroidea, Platygastridae).","Talamas EJ, Masner L, Johnson NF.","Zookeys","2011","1313-2989","journal article; research-article","Y","Y","Y","3","N","Y","N","N","N","128.10449","80",NA,"1-126","PMC3088049",NA,NA,"code.google.com"
"1117","PMC3478825","PMC",NA,NA,"Using SWE Standards for Ubiquitous Environmental Sensing: A Performance Analysis.","Tamayo A, Granell C, Huerta J.","Sensors (Basel)","2012","1424-8220","journal article; research-article","Y","Y","Y","0","N","Y","N","N","N","111.919464","9","12","12026-12051","PMC3478825",NA,NA,"code.google.com"
"1118","21569523","MED","21569523","10.1186/1758-2946-3-15","Resource description framework technologies in chemistry.","Willighagen EL, BrÃ¤ndle MP.","J Cheminform","2011","1758-2946","journal article; editorial","Y","Y","Y","4","Y","Y","N","N","N","92.250984","1","3","15","PMC3118380",NA,NA,"code.google.com"
"1119","18227120","MED","18227120","10.1093/bioinformatics/btm619","Phyutility: a phyloinformatics tool for trees, alignments and molecular data.","Smith SA, Dunn CW.","Bioinformatics","2008","1367-4803","journal article; research support, u.s. gov't, non-p.h.s.","N","N","N","70","Y","N","N","N","N","59.66761","5","24","715-716",NA,NA,NA,"code.google.com"
"1120","19336443","MED","19336443","10.1093/bioinformatics/btp180","Hooke: an open software platform for force spectroscopy.","Sandal M, Benedetti F, Brucale M, Gomez-Casado A, SamorÃ¬ B.","Bioinformatics","2009","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","7","Y","N","N","N","N","57.104675","11","25","1428-1430",NA,NA,NA,"code.google.com"
"1121","19639591","MED","19639591","10.1002/pmic.200900037","OMSSA Parser: an open-source library to parse and extract data from OMSSA MS/MS search results.","Barsnes H, Huber S, Sickmann A, Eidhammer I, Martens L.","Proteomics","2009","1615-9853","journal article; research support, non-u.s. gov't","N","N","N","18","N","N","N","N","N","57.104675","14","9","3772-3774",NA,NA,NA,"code.google.com"
"1122","20419267","MED","20419267","10.1039/b922045c","Baseline correction using adaptive iteratively reweighted penalized least squares.","Zhang ZM, Chen S, Liang YZ.","Analyst","2010","0003-2654","journal article; research support, non-u.s. gov't","N","N","N","16","Y","N","N","N","N","57.104675","5","135","1138-1146",NA,NA,NA,"code.google.com"
"1123","20141333","MED","20141333","10.1089/omi.2009.0083","ConsensusCluster: a software tool for unsupervised cluster discovery in numerical data.","Seiler M, Huang CC, Szalma S, Bhanot G.","OMICS","2010","1536-2310","journal article; research support, non-u.s. gov't","N","N","N","5","Y","N","N","N","N","57.104675","1","14","109-113",NA,NA,NA,"code.google.com"
"1124","19098028","MED","19098028","10.1093/bioinformatics/btn651","PuMA: Bayesian analysis of partitioned (and unpartitioned) model adequacy.","Brown JM, ElDabaje R.","Bioinformatics","2009","1367-4803","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.","N","N","N","9","Y","N","N","N","N","57.104675","4","25","537-538",NA,NA,NA,"code.google.com"
"1125","18711720","MED","18711720","10.1002/jcc.21088","MeTA studio: a cross platform, programmable IDE for computational chemist.","Ganesh V.","J Comput Chem","2009","0192-8651","journal article","N","N","N","5","Y","N","N","N","N","57.104675","4","30","661-672",NA,NA,NA,"code.google.com"
"1126","18801749","MED","18801749","10.1093/bioinformatics/btn496","A toolkit for capturing and sharing FuGE experiments.","Belhajjame K, Jones AR, Paton NW.","Bioinformatics","2008","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","6","Y","N","N","N","N","57.104675","22","24","2647-2649",NA,NA,NA,"code.google.com"
"1127","20703591","MED","20703591","10.1007/s10916-009-9335-0","A geographical information system using the Google Map API for guidance to referral hospitals.","Kobayashi S, Fujioka T, Tanaka Y, Inoue M, Niho Y, Miyoshi A.","J Med Syst","2010","0148-5598","journal article","N","N","N","1","Y","N","N","N","N","57.104675","6","34","1157-1160",NA,NA,NA,"code.google.com"
"1128","20709689","MED","20709689","10.1093/bioinformatics/btq443","QuantProReloaded: quantitative analysis of microspot immunoassays.","JÃ¶cker A, Sonntag J, Henjes F, GÃ¶tschel F, Tresch A, Beissbarth T, Wiemann S, Korf U.","Bioinformatics","2010","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","0","Y","N","N","N","N","57.104675","19","26","2480-2481",NA,NA,NA,"code.google.com"
"1129","21585724","MED","21585724","10.1111/j.1471-8286.2007.01884.x","msatcommander: detection of microsatellite repeat arrays and automated, locus-specific primer design.","Faircloth BC.","Mol Ecol Resour","2008","1755-098x","journal article","N","N","N","75","N","N","N","N","N","57.104675","1","8","92-94",NA,NA,NA,"code.google.com"
"1130","20493291","MED","20493291","10.1016/j.aca.2010.04.032","A novel storage method for near infrared spectroscopy chemometric models.","Zhang ZM, Chen S, Liang YZ.","Anal Chim Acta","2010","0003-2670","journal article; research support, non-u.s. gov't","N","N","N","0","N","N","N","N","N","55.82322","2","668","149-154",NA,NA,NA,"code.google.com"
"1131","20671150","MED","20671150","10.1093/bioinformatics/btq355","TreesimJ: a flexible, forward time population genetic simulator.","O'Fallon B.","Bioinformatics","2010","1367-4803","journal article; research support, u.s. gov't, non-p.h.s.","N","N","N","5","Y","N","N","N","N","55.82322","17","26","2200-2201",NA,NA,NA,"code.google.com"
"1132","19965880","MED","19965880","10.1093/bioinformatics/btp667","DataPflex: a MATLAB-based tool for the manipulation and visualization of multidimensional datasets.","Hendriks BS, Espelin CW.","Bioinformatics","2010","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","6","Y","N","N","N","N","55.82322","3","26","432-433",NA,NA,NA,"code.google.com"
"1133","19965885","MED","19965885","10.1093/bioinformatics/btp668","Protein complex prediction based on simultaneous protein interaction network.","Jung SH, Hyun B, Jang WH, Hur HY, Han DS.","Bioinformatics","2010","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","11","Y","N","N","N","N","55.82322","3","26","385-391",NA,NA,NA,"code.google.com"
"1134","20733062","MED","20733062","10.1093/bioinformatics/btq462","Annotare--a tool for annotating high-throughput biomedical investigations and resulting data.","Shankar R, Parkinson H, Burdett T, Hastings E, Liu J, Miller M, Srinivasa R, White J, Brazma A, Sherlock G, Stoeckert CJ Jr, Ball CA.","Bioinformatics","2010","1367-4803","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","4","Y","Y","N","N","N","54.54175","19","26","2470-2471","PMC2944206",NA,NA,"code.google.com"
"1135","20733064","MED","20733064","10.1093/bioinformatics/btq473","Improving performances of suboptimal greedy iterative biclustering heuristics via localization.","Erten C, SÃ¶zdinler M.","Bioinformatics","2010","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","2","Y","N","N","N","N","54.54175","20","26","2594-2600",NA,NA,NA,"code.google.com"
"1136","20975886","MED","20975886","10.6026/97320630004390","ExSer: A standalone tool to mine protein data bank (PDB) for secondary structural elements.","Vignesh D, Daniel P, Raja N, Balasubramanian P, Arul L.","Bioinformation","2010","0973-2063","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","54.102024","9","4","390-391","PMC2951642",NA,NA,"code.google.com"
"1137","18563730","MED","18563730","10.1002/pmic.200701126","OMSSAGUI: An open-source user interface component to configure and run the OMSSA search engine.","Tharakan R, Martens L, Van Eyk JE, Graham DR.","Proteomics","2008","1615-9853","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","4","Y","Y","N","N","N","53.51165","12","8","2376-2378","PMC2905866",NA,NA,"code.google.com"
"1138","17631616","MED","17631616","10.1093/nar/gkm384","REPK: an analytical web server to select restriction endonucleases for terminal restriction fragment length polymorphism analysis.","Collins RE, Rocap G.","Nucleic Acids Res","2007","0305-1048","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","13","Y","Y","N","N","N","52.40187","web server issue","35","w58-62","PMC1933217",NA,NA,"code.google.com"
"1139","21364786","MED","21364786","10.6026/97320630005085","SeqCalc: A portable bioinformatics software for sequence analysis.","Vignesh D, Parameswari P, Jin KH, Pyo LY.","Bioinformation","2010","0973-2063","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","52.28976","3","5","85-88","PMC3041003",NA,NA,"code.google.com"
"1140","18948277","MED","18948277","10.1093/nar/gkn729","The RNA virus database.","Belshaw R, de Oliveira T, Markowitz S, Rambaut A.","Nucleic Acids Res","2009","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","4","Y","Y","N","N","N","51.383625","database issue","37","d431-5","PMC2686580",NA,NA,"code.google.com"
"1141","20110278","MED","20110278","10.1093/bioinformatics/btq033","BEDTools: a flexible suite of utilities for comparing genomic features.","Quinlan AR, Hall IM.","Bioinformatics","2010","1367-4803","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; comparative study; research-article","Y","Y","Y","854","Y","Y","N","Y","N","51.383625","6","26","841-842","PMC2832824",NA,NA,"code.google.com"
"1142","19420054","MED","19420054","10.1093/bioinformatics/btp268","CycSim--an online tool for exploring and experimenting with genome-scale metabolic models.","Le FÃ¨vre F, Smidtas S, Combe C, Durot M, d'AlchÃ©-Buc F, Schachter V.","Bioinformatics","2009","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","8","Y","Y","N","N","N","51.338093","15","25","1987-1988","PMC2712333",NA,NA,"code.google.com"
"1143","20553619","MED","20553619","10.1186/1471-2105-11-329","permGPU: Using graphics processing units in RNA microarray association studies.","Shterev ID, Jung SH, George SL, Owzar K.","BMC Bioinformatics","2010","1471-2105","journal article; research support, n.i.h., extramural; product-review","Y","Y","Y","6","Y","Y","N","N","N","51.292088",NA,"11","329","PMC2910023",NA,NA,"code.google.com"
"1144","20113482","MED","20113482","10.1186/1471-2105-11-67","MLPAinter for MLPA interpretation: an integrated approach for the analysis, visualisation and data management of Multiplex Ligation-dependent Probe Amplification.","van Eijk R, Eilers PH, NattÃ© R, Cleton-Jansen AM, Morreau H, van Wezel T, Oosting J.","BMC Bioinformatics","2010","1471-2105","journal article; product-review","Y","Y","Y","5","Y","Y","N","N","N","50.737198",NA,"11","67","PMC3098110",NA,NA,"code.google.com"
"1145","19662629","MED","19662629","10.1002/pmic.200900402","A guide to the Proteomics Identifications Database proteomics data repository.","VizcaÃno JA, CÃ´tÃ© R, Reisinger F, Foster JM, Mueller M, Rameseder J, Hermjakob H, Martens L.","Proteomics","2009","1615-9853","journal article; research support, non-u.s. gov't; other","Y","Y","Y","119","Y","Y","N","Y","N","50.737198","18","9","4276-4283","PMC2970915",NA,NA,"code.google.com"
"1146","19897547","MED","19897547","10.1093/nar/gkp983","MINT, the molecular interaction database: 2009 update.","Ceol A, Chatr Aryamontri A, Licata L, Peluso D, Briganti L, Perfetto L, Castagnoli L, Cesareni G.","Nucleic Acids Res","2010","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","193","Y","Y","N","Y","N","50.737198","database issue","38","d532-9","PMC2808973",NA,NA,"code.google.com"
"1147","19809795","MED","19809795","10.1007/s10858-009-9378-z","The NMR restraints grid at BMRB for 5,266 protein and nucleic acid PDB entries.","Doreleijers JF, Vranken WF, Schulte C, Lin J, Wedell JR, Penkett CJ, Vuister GW, Vriend G, Markley JL, Ulrich EL.","J Biomol NMR","2009","0925-2738","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","10","Y","Y","N","N","Y","50.737198","4","45","389-396","PMC2777234","pdb",NA,"code.google.com"
"1148","21532902","MED","21532902",NA,"Epi Infoâ¢: Now an Open-source application that continues a long and productive ""life"" through CDC support and funding.","Nieves E, Jones J.","Pan Afr Med J","2009","1937-8688","journal article; research-article","Y","Y","Y","0","N","Y","N","N","N","50.697357",NA,"2","6","PMC2984269",NA,NA,"code.google.com"
"1149","20829444","MED","20829444","10.1093/bioinformatics/btq476","The Chemical Translation Service--a web-based tool to improve standardization of metabolomic reports.","Wohlgemuth G, Haldiya PK, Willighagen E, Kind T, Fiehn O.","Bioinformatics","2010","1367-4803","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","15","Y","Y","N","N","N","50.697357","20","26","2647-2648","PMC2951090",NA,NA,"code.google.com"
"1150","19734151","MED","19734151","10.1093/bioinformatics/btp523","Saint: a lightweight integration environment for model annotation.","Lister AL, Pocock M, Taschuk M, Wipat A.","Bioinformatics","2009","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","6","Y","Y","N","N","Y","50.697357","22","25","3026-3027","PMC2773255","sprot",NA,"code.google.com"
"1151","20423529","MED","20423529","10.1186/1471-2105-11-210","AMS 3.0: prediction of post-translational modifications.","Basu S, Plewczynski D.","BMC Bioinformatics","2010","1471-2105","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","10","Y","Y","N","N","N","50.697357",NA,"11","210","PMC2874555",NA,NA,"code.google.com"
"1152","20562413","MED","20562413","10.1093/bioinformatics/btq330","Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor.","McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, Cunningham F.","Bioinformatics","2010","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","195","Y","Y","N","Y","N","50.697357","16","26","2069-2070","PMC2916720",NA,NA,"code.google.com"
"1153","19789925","MED","19789925","10.1007/s10278-009-9242-4","Is android or iPhone the platform for innovation in imaging informatics.","Shih G, Lakhani P, Nagy P.","J Digit Imaging","2010","0897-1889","journal article; research-article","Y","Y","Y","3","N","Y","N","N","N","50.477497","1","23","2-7","PMC2809941",NA,NA,"code.google.com"
"1154","18480101","MED","18480101","10.1093/bioinformatics/btn203","An overview of the wcd EST clustering tool.","Hazelhurst S, Hide W, LiptÃ¡k Z, Nogueira R, Starfield R.","Bioinformatics","2008","1367-4803","journal article; review; research support, non-u.s. gov't; research-article","Y","Y","Y","16","Y","Y","N","N","N","50.477497","13","24","1542-1546","PMC2718666",NA,NA,"code.google.com"
"1155","20819865","MED","20819865","10.1136/jamia.2010.004077","Lancet: a high precision medication event extraction system for clinical text.","Li Z, Liu F, Antieau L, Cao Y, Yu H.","J Am Med Inform Assoc","2010","1067-5027","journal article; research support, n.i.h., extramural; research-article","N","Y","Y","14","Y","Y","N","N","N","50.477497","5","17","563-567","PMC2995682",NA,NA,"code.google.com"
"1156","20460470","MED","20460470","10.1093/nar/gkq352","VISIBIOweb: visualization and layout services for BioPAX pathway models.","Dilek A, Belviranli ME, Dogrusoz U.","Nucleic Acids Res","2010","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","6","Y","Y","N","N","N","50.05663","web server issue","38","w150-4","PMC2896092",NA,NA,"code.google.com"
"1157","20512790","MED","20512790","10.1002/pmic.201000039","Expanding the mouse embryonic stem cell proteome: combining three proteomic approaches.","Gundry RL, Tchernyshyov I, Sheng S, Tarasova Y, Raginski K, Boheler KR, Van Eyk JE.","Proteomics","2010","1615-9853","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research support, n.i.h., intramural; research-article","N","Y","Y","7","Y","Y","N","N","N","50.05663","14","10","2728-2732","PMC2934747",NA,NA,"code.google.com"
"1158","18561252","MED","18561252","10.1002/ajp.20581","Polymorphic microsatellite loci for the common marmoset (Callithrix jacchus) designed using a cost- and time-efficient method.","Raveendran M, Tardif S, Ross CN, Austad SN, Harris RA, Milosavljevic A, Rogers J.","Am J Primatol","2008","0275-2565","journal article; research support, n.i.h., extramural; research-article","N","Y","Y","3","Y","Y","N","N","N","50.05663","9","70","906-910","PMC2799112",NA,NA,"code.google.com"
"1159","20865558","MED","20865558","10.1007/978-1-4419-5913-3_79","Visual presentation as a welcome alternative to textual presentation of gene annotation information.","Desai J, Flatow JM, Song J, Zhu LJ, Du P, Huang CC, Lu H, Lin SM, Kibbe WA.","Adv Exp Med Biol","2010","0065-2598","journal article; research-article","N","Y","Y","1","Y","Y","N","N","N","50.05663",NA,"680","709-715","PMC3039430",NA,NA,"code.google.com"
"1160","20460452","MED","20460452","10.1093/nar/gkq331","The Ontology Lookup Service: bigger and better.","CÃ´tÃ© R, Reisinger F, Martens L, Barsnes H, Vizcaino JA, Hermjakob H.","Nucleic Acids Res","2010","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","18","Y","Y","N","N","N","50.05663","web server issue","38","w155-60","PMC2896109",NA,NA,"code.google.com"
"1161","21258498","MED","21258498","10.1364/boe.1.000658","Next-generation acceleration and code optimization for light transport in turbid media using GPUs.","Alerstam E, Lo WC, Han TD, Rose J, Andersson-Engels S, Lilge L.","Biomed Opt Express","2010","2156-7085","journal article; research-article","Y","Y","Y","15","Y","Y","N","N","N","50.05663","2","1","658-675","PMC3018007",NA,NA,"code.google.com"
"1162","20677327","MED","20677327","10.1002/pmic.201000120","The gel electrophoresis markup language (GelML) from the Proteomics Standards Initiative.","Gibson F, Hoogland C, Martinez-BartolomÃ© S, Medina-Aunon JA, Albar JP, Babnigg G, Wipat A, Hermjakob H, Almeida JS, Stanislaus R, Paton NW, Jones AR.","Proteomics","2010","1615-9853","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","10","Y","Y","N","N","N","50.02443","17","10","3073-3081","PMC3193076",NA,NA,"code.google.com"
"1163","20494977","MED","20494977","10.1093/nar/gkq430","THREaD Mapper Studio: a novel, visual web server for the estimation of genetic linkage maps.","Cheema J, Ellis TH, Dicks J.","Nucleic Acids Res","2010","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","50.02443","web server issue","38","w188-93","PMC2896177",NA,NA,"code.google.com"
"1164","20298554","MED","20298554","10.1186/1471-2105-11-141","YODA: software to facilitate high-throughput analysis of chronological life span, growth rate, and survival in budding yeast.","Olsen B, Murakami CJ, Kaeberlein M.","BMC Bioinformatics","2010","1471-2105","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; product-review","Y","Y","Y","10","Y","Y","N","N","N","50.02443",NA,"11","141","PMC2850362",NA,NA,"code.google.com"
"1165","20731383","MED","20731383","10.1021/pr1006685","Precursor charge state prediction for electron transfer dissociation tandem mass spectra.","Sharma V, Eng JK, Feldman S, von Haller PD, MacCoss MJ, Noble WS.","J Proteome Res","2010","1535-3893","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","3","Y","Y","N","N","N","50.02443","10","9","5438-5444","PMC2966942",NA,NA,"code.google.com"
"1166","19850723","MED","19850723","10.1093/nar/gkp878","The IntAct molecular interaction database in 2010.","Aranda B, Achuthan P, Alam-Faruque Y, Armean I, Bridge A, Derow C, Feuermann M, Ghanbarian AT, Kerrien S, Khadake J, Kerssemakers J, Leroy C, Menden M, Michaut M, Montecchi-Palazzi L, Neuhauser SN, Orchard S, Perreau V, Roechert B, van Eijk K, Hermjakob H.","Nucleic Acids Res","2010","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","276","Y","Y","N","Y","N","50.02443","database issue","38","d525-31","PMC2808934",NA,NA,"code.google.com"
"1167","19115005","MED","19115005","10.1371/journal.pone.0004076","Exploratory analysis of the copy number alterations in glioblastoma multiforme.","Freire P, Vilela M, Deus H, Kim YW, Koul D, Colman H, Aldape KD, Bogler O, Yung WK, Coombes K, Mills GB, Vasconcelos AT, Almeida JS.","PLoS One","2008","1932-6203","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; comparative study; research-article","Y","Y","Y","15","Y","Y","N","N","N","49.62742","12","3","e4076","PMC2605252",NA,NA,"code.google.com"
"1168","20923983","MED","20923983","10.1534/genetics.110.120121","Inference of homologous recombination in bacteria using whole-genome sequences.","Didelot X, Lawson D, Darling A, Falush D.","Genetics","2010","0016-6731","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","N","Y","Y","44","Y","Y","N","N","N","49.62742","4","186","1435-1449","PMC2998322",NA,NA,"code.google.com"
"1169","19212459","MED","19212459","10.3389/neuro.11.003.2009","PyMVPA: A Unifying Approach to the Analysis of Neuroscientific Data.","Hanke M, Halchenko YO, Sederberg PB, Olivetti E, FrÃ¼nd I, Rieger JW, Herrmann CS, Haxby JV, Hanson SJ, Pollmann S.","Front Neuroinform","2009","1662-5196","journal article; research-article","Y","Y","Y","16","Y","Y","N","Y","N","49.62742",NA,"3","3","PMC2638552",NA,NA,"code.google.com"
"1170","19675096","MED","19675096","10.1093/bioinformatics/btp486","PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds.","Chen Y, Souaiaia T, Chen T.","Bioinformatics","2009","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","32","Y","Y","N","Y","N","49.57136","19","25","2514-2521","PMC2752623",NA,NA,"code.google.com"
"1171","20554690","MED","20554690","10.1093/bioinformatics/btq309","A Poisson model for random multigraphs.","Ranola JM, Ahn S, Sehl M, Smith DJ, Lange K.","Bioinformatics","2010","1367-4803","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","4","Y","Y","N","N","N","49.57136","16","26","2004-2011","PMC3025746",NA,NA,"code.google.com"
"1172","20152048","MED","20152048","10.1186/1471-2148-10-42","SPRIT: Identifying horizontal gene transfer in rooted phylogenetic trees.","Hill T, NordstrÃ¶m KJ, Thollesson M, SÃ¤fstrÃ¶m TM, Vernersson AK, Fredriksson R, SchiÃ¶th HB.","BMC Evol Biol","2010","1471-2148","journal article; research support, non-u.s. gov't; product-review","Y","Y","Y","7","Y","Y","N","N","N","49.57136",NA,"10","42","PMC2829038",NA,NA,"code.google.com"
"1173","18218655","MED","18218655","10.1093/bioinformatics/btn018","Flexible informatics for linking experimental data to mathematical models via DataRail.","Saez-Rodriguez J, Goldsipe A, Muhlich J, Alexopoulos LG, Millard B, Lauffenburger DA, Sorger PK.","Bioinformatics","2008","1367-4803","evaluation studies; journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","32","Y","Y","N","N","N","49.57136","6","24","840-847","PMC2617752",NA,NA,"code.google.com"
"1174","20478825","MED","20478825","10.1093/nar/gkq392","DSAP: deep-sequencing small RNA analysis pipeline.","Huang PJ, Liu YC, Lee CC, Lin WC, Gan RR, Lyu PC, Tang P.","Nucleic Acids Res","2010","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","30","Y","Y","N","Y","N","49.415897","web server issue","38","w385-91","PMC2896168",NA,NA,"code.google.com"
"1175","20494971","MED","20494971","10.1261/rna.1996810","CORSEN, a new software dedicated to microscope-based 3D distance measurements: mRNA-mitochondria distance, from single-cell to population analyses.","Jourdren L, Delaveau T, Marquenet E, Jacq C, Garcia M.","RNA","2010","1355-8382","journal article; research support, non-u.s. gov't; research-article","N","Y","Y","5","Y","Y","N","N","N","49.415897","7","16","1301-1307","PMC2885679",NA,NA,"code.google.com"
"1176","20351818","MED","20351818",NA,"A multi-lingual web service for drug side-effect data.","Bedrick SD, Mauro A.","AMIA Annu Symp Proc","2009","1942-597x","evaluation studies; journal article; research support, n.i.h., extramural; research-article","N","Y","Y","0","Y","Y","N","N","N","49.415897",NA,"2009","34-38","PMC2815498",NA,NA,"code.google.com"
"1177","20386612","MED","20386612","10.1371/journal.pone.0010049","MrGrid: a portable grid based molecular replacement pipeline.","Schmidberger JW, Bate MA, Reboul CF, Androulakis SG, Phan JM, Whisstock JC, Goscinski WJ, Abramson D, Buckle AM.","PLoS One","2010","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","Y","49.415897","4","5","e10049","PMC2850370","pdb",NA,"code.google.com"
"1178","20504857","MED","20504857","10.1093/nar/gkq445","POLYVIEW-MM: web-based platform for animation and analysis of molecular simulations.","Porollo A, Meller J.","Nucleic Acids Res","2010","0305-1048","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","1","Y","Y","N","N","Y","49.415897","web server issue","38","w662-6","PMC2896192","pdb",NA,"code.google.com"
"1179","21063542","MED","21063542",NA,"A comparison of two approaches to text processing: facilitating chart reviews of radiology reports in electronic medical records.","Womack JA, Scotch M, Gibert C, Chapman W, Yin M, Justice AC, Brandt C.","Perspect Health Inf Manag","2010","1559-4122","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; comparative study; research-article","N","Y","Y","4","Y","Y","N","N","N","49.415897","Fall","7","1a","PMC2966352",NA,NA,"code.google.com"
"1180","21210985","MED","21210985","10.1186/1471-2105-11-s12-s6","WordSeeker: concurrent bioinformatics software for discovering genome-wide patterns and word-based genomic signatures.","Lichtenberg J, Kurz K, Liang X, Al-ouran R, Neiman L, Nau LJ, Welch JD, Jacox E, Bitterman T, Ecker K, Elnitski L, Drews F, Lee SS, Welch LR.","BMC Bioinformatics","2010","1471-2105","evaluation studies; journal article; research support, non-u.s. gov't; research support, n.i.h., intramural; research-article","Y","Y","Y","2","Y","Y","N","N","N","49.415897","Suppl 12","11 Suppl 12","s6","PMC3040532",NA,NA,"code.google.com"
"1181","20418944","MED","20418944","10.1371/journal.pone.0010071","BioTorrents: a file sharing service for scientific data.","Langille MG, Eisen JA.","PLoS One","2010","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","11","Y","Y","N","N","N","49.415897","4","5","e10071","PMC2854681",NA,NA,"code.google.com"
"1182","21603108","MED","21603108",NA,"PyMC: Bayesian Stochastic Modelling in Python.","Patil A, Huard D, Fonnesbeck CJ.","J Stat Softw","2010","1548-7660","journal article; research-article","N","Y","Y","62","Y","Y","N","N","N","49.207165","4","35","1-81","PMC3097064",NA,NA,"code.google.com"
"1183","20308636","MED","20308636","10.1101/gr.102970.109","Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome.","Quinlan AR, Clark RA, Sokolova S, Leibowitz ML, Zhang Y, Hurles ME, Mell JC, Hall IM.","Genome Res","2010","1088-9051","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","82","Y","Y","N","N","N","49.118294","5","20","623-635","PMC2860164",NA,NA,"code.google.com"
"1184","20805289","MED","20805289","10.1261/rna.2379610","Dynamic isomiR regulation in Drosophila development.","Fernandez-Valverde SL, Taft RJ, Mattick JS.","RNA","2010","1355-8382","journal article; research support, non-u.s. gov't; research-article","N","Y","Y","71","Y","Y","N","Y","N","49.095528","10","16","1881-1888","PMC2941097",NA,NA,"code.google.com"
"1185","19383797","MED","19383797","10.1073/pnas.0902104106","Fine mapping and functional analysis of a common variant in MSMB on chromosome 10q11.2 associated with prostate cancer susceptibility.","Lou H, Yeager M, Li H, Bosquet JG, Hayes RB, Orr N, Yu K, Hutchinson A, Jacobs KB, Kraft P, Wacholder S, Chatterjee N, Feigelson HS, Thun MJ, Diver WR, Albanes D, Virtamo J, Weinstein S, Ma J, Gaziano JM, Stampfer M, Schumacher FR, Giovannucci E, Cancel-Tassin G, Cussenot O, Valeri A, Andriole GL, Crawford ED, Anderson SK, Tucker M, Hoover RN, Fraumeni JF Jr, Thomas G, Hunter DJ, Dean M, Chanock SJ.","Proc Natl Acad Sci U S A","2009","0027-8424","journal article; research-article","N","Y","Y","42","Y","Y","Y","N","Y","49.095528","19","106","7933-7938","PMC2671324","refsnp; gen","OMIMUNIPROT","code.google.com"
"1186","19644707","MED","19644707","10.1007/s00439-009-0723-9","Comprehensive resequence analysis of a 97 kb region of chromosome 10q11.2 containing the MSMB gene associated with prostate cancer.","Yeager M, Deng Z, Boland J, Matthews C, Bacior J, Lonsberry V, Hutchinson A, Burdett LA, Qi L, Jacobs KB, Gonzalez-Bosquet J, Berndt SI, Hayes RB, Hoover RN, Thomas G, Hunter DJ, Dean M, Chanock SJ.","Hum Genet","2009","0340-6717","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","10","Y","Y","Y","N","Y","49.095528","6","126","743-750","PMC2778717","refsnp","OMIM","code.google.com"
"1187","24163721","MED","24163721","10.4018/jats.2010070102","SPARK: A Framework for Multi-Scale Agent-Based Biomedical Modeling.","Solovyev A, Mikheev M, Zhou L, Dutta-Moscato J, Ziraldo C, An G, Vodovotz Y, Mi Q.","Int J Agent Technol Syst","2010","1943-0744","journal article; research-article","N","Y","Y","2","Y","Y","N","N","N","49.095528","3","2","18-30","PMC3806198",NA,NA,"code.google.com"
"1188","19919683","MED","19919683","10.1186/1752-0509-3-109","DASMiner: discovering and integrating data from DAS sources.","Veiga DF, Deus HF, Akdemir C, Vasconcelos AT, Almeida JS.","BMC Syst Biol","2009","1752-0509","journal article; research support, non-u.s. gov't; product-review","Y","Y","Y","2","Y","Y","N","N","N","49.095528",NA,"3","109","PMC2789070",NA,NA,"code.google.com"
"1189","20449775","MED","20449775","10.1007/s12021-010-9072-z","Integrating clinical trial imaging data resources using service-oriented architecture and grid computing.","El-Ghatta SB, CladÃ© T, Snyder JC.","Neuroinformatics","2010","1539-2791","journal article; research-article","Y","Y","Y","1","N","Y","N","N","N","49.095528","4","8","251-259","PMC2974907",NA,NA,"code.google.com"
"1190","20494976","MED","20494976","10.1093/nar/gkq424","Discovering causal signaling pathways through gene-expression patterns.","Parikh JR, Klinger B, Xia Y, Marto JA, BlÃ¼thgen N.","Nucleic Acids Res","2010","0305-1048","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","5","Y","Y","N","N","N","49.095528","web server issue","38","w109-17","PMC2896193",NA,NA,"code.google.com"
"1191","20530236","MED","20530236","10.1093/carcin/bgq117","Genetic variation at chromosome 8q24 in osteosarcoma cases and controls.","Mirabello L, Berndt SI, Seratti GF, Burdett L, Yeager M, Chowdhury S, Teshome K, Uzoka A, Douglass C, Hayes RB, Hoover RN, Savage SA, National Osteosarcoma Etiology Study Group.","Carcinogenesis","2010","0143-3334","journal article; research support, n.i.h., extramural; research support, n.i.h., intramural; research-article","N","Y","Y","7","Y","Y","N","N","Y","49.095528","8","31","1400-1404","PMC2915635","refsnp",NA,"code.google.com"
"1192","20142480","MED","20142480","10.1073/pnas.0909672107","Phylogenetic analyses reveal the shady history of C4 grasses.","Edwards EJ, Smith SA.","Proc Natl Acad Sci U S A","2010","0027-8424","journal article; research-article","N","Y","Y","32","Y","Y","N","N","N","49.095528","6","107","2532-2537","PMC2823882",NA,NA,"code.google.com"
"1193","20174560","MED","20174560","10.1371/journal.pone.0009314","Application description and policy model in collaborative environment for sharing of information on epidemiological and clinical research data sets.","de Carvalho EC, Batilana AP, Simkins J, Martins H, Shah J, Rajgor D, Shah A, Rockart S, Pietrobon R.","PLoS One","2010","1932-6203","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","3","Y","Y","N","N","N","49.095528","2","5","e9314","PMC2824801",NA,NA,"code.google.com"
"1194","19900301","MED","19900301","10.1186/1471-2105-10-s14-s5","bioGUID: resolving, discovering, and minting identifiers for biodiversity informatics.","Page RD.","BMC Bioinformatics","2009","1471-2105","journal article; research-article","Y","Y","Y","6","Y","Y","N","N","Y","49.095528","Suppl 14","10 Suppl 14","s5","PMC2775151","gen",NA,"code.google.com"
"1195","19059333","MED","19059333","10.1016/j.ygeno.2008.11.004","An autosomal genetic linkage map of the domestic cat, Felis silvestris catus.","Menotti-Raymond M, David VA, SchÃ¤ffer AA, Tomlin JF, Eizirik E, Phillip C, Wells D, Pontius JU, Hannah SS, O'Brien SJ.","Genomics","2009","0888-7543","journal article; research support, n.i.h., extramural; research support, n.i.h., intramural; research-article","N","Y","Y","11","Y","Y","N","N","N","49.095528","4","93","305-313","PMC2656606",NA,NA,"code.google.com"
"1196","19823874","MED","19823874","10.1007/s00439-009-0751-5","A comprehensive resequence analysis of the KLK15-KLK3-KLK2 locus on chromosome 19q13.33.","Parikh H, Deng Z, Yeager M, Boland J, Matthews C, Jia J, Collins I, White A, Burdett L, Hutchinson A, Qi L, Bacior JA, Lonsberry V, Rodesch MJ, Jeddeloh JA, Albert TJ, Halvensleben HA, Harkins TT, Ahn J, Berndt SI, Chatterjee N, Hoover R, Thomas G, Hunter DJ, Hayes RB, Chanock SJ, Amundadottir L.","Hum Genet","2010","0340-6717","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","7","Y","Y","N","N","Y","49.095528","1","127","91-99","PMC2793378","refsnp",NA,"code.google.com"
"1197","20053928","MED","20053928","10.1093/carcin/bgp328","Common genetic variation in the sex hormone metabolic pathway and endometrial cancer risk: pathway-based evaluation of candidate genes.","Yang HP, Gonzalez Bosquet J, Li Q, Platz EA, Brinton LA, Sherman ME, Lacey JV Jr, Gaudet MM, Burdette LA, Figueroa JD, Ciampa JG, Lissowska J, Peplonska B, Chanock SJ, Garcia-Closas M.","Carcinogenesis","2010","0143-3334","journal article; research support, n.i.h., intramural; research-article","N","Y","Y","12","Y","Y","Y","N","Y","49.095528","5","31","827-833","PMC2864407","refsnp","UNIPROT","code.google.com"
"1198","20967209","MED","20967209","10.1371/journal.pone.0013336","Genetic admixture and population substructure in Guanacaste Costa Rica.","Wang Z, Hildesheim A, Wang SS, Herrero R, Gonzalez P, Burdette L, Hutchinson A, Thomas G, Chanock SJ, Yu K.","PLoS One","2010","1932-6203","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","5","Y","Y","N","N","Y","49.095528","10","5","e13336","PMC2954167","refsnp",NA,"code.google.com"
"1199","20939882","MED","20939882","10.1186/1471-2105-11-506","Geoseq: a tool for dissecting deep-sequencing datasets.","Gurtowski J, Cancio A, Shah H, Levovitz C, George A, Homann R, Sachidanandam R.","BMC Bioinformatics","2010","1471-2105","journal article; product-review","Y","Y","Y","1","Y","Y","N","N","N","49.095528",NA,"11","506","PMC2972303",NA,NA,"code.google.com"
"1200","20729852","MED","20729852","10.1038/ng.649","A shared susceptibility locus in PLCE1 at 10q23 for gastric adenocarcinoma and esophageal squamous cell carcinoma.","Abnet CC, Freedman ND, Hu N, Wang Z, Yu K, Shu XO, Yuan JM, Zheng W, Dawsey SM, Dong LM, Lee MP, Ding T, Qiao YL, Gao YT, Koh WP, Xiang YB, Tang ZZ, Fan JH, Wang C, Wheeler W, Gail MH, Yeager M, Yuenger J, Hutchinson A, Jacobs KB, Giffen CA, Burdett L, Fraumeni JF Jr, Tucker MA, Chow WH, Goldstein AM, Chanock SJ, Taylor PR.","Nat Genet","2010","1061-4036","journal article; research support, n.i.h., extramural; research support, n.i.h., intramural; research-article","Y","Y","Y","124","Y","Y","Y","Y","Y","49.095528","9","42","764-767","PMC2947317","refsnp","OMIMUNIPROT","code.google.com"
"1201","19635165","MED","19635165","10.1186/1471-2105-10-232","BSMAP: whole genome bisulfite sequence MAPping program.","Xi Y, Li W.","BMC Bioinformatics","2009","1471-2105","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","77","Y","Y","N","N","N","49.095528",NA,"10","232","PMC2724425",NA,NA,"code.google.com"
"1202","21293137","MED","21293137","10.1159/000323318","Genome-wide meta-analysis of joint tests for genetic and gene-environment interaction effects.","Aschard H, Hancock DB, London SJ, Kraft P.","Hum Hered","2010","0001-5652","journal article; validation studies; research support, n.i.h., extramural; research-article","N","Y","Y","11","Y","Y","N","N","Y","49.095528","4","70","292-300","PMC3085519","refsnp",NA,"code.google.com"
"1203","19330030","MED","19330030","10.1038/ng.353","A multistage genome-wide association study in breast cancer identifies two new risk alleles at 1p11.2 and 14q24.1 (RAD51L1).","Thomas G, Jacobs KB, Kraft P, Yeager M, Wacholder S, Cox DG, Hankinson SE, Hutchinson A, Wang Z, Yu K, Chatterjee N, Garcia-Closas M, Gonzalez-Bosquet J, Prokunina-Olsson L, Orr N, Willett WC, Colditz GA, Ziegler RG, Berg CD, Buys SS, McCarty CA, Feigelson HS, Calle EE, Thun MJ, Diver R, Prentice R, Jackson R, Kooperberg C, Chlebowski R, Lissowska J, Peplonska B, Brinton LA, Sigurdson A, Doody M, Bhatti P, Alexander BH, Buring J, Lee IM, Vatten LJ, Hveem K, Kumle M, Hayes RB, Tucker M, Gerhard DS, Fraumeni JF Jr, Hoover RN, Chanock SJ, Hunter DJ.","Nat Genet","2009","1061-4036","journal article; research support, n.i.h., extramural; research support, n.i.h., intramural; research-article","N","Y","Y","262","Y","Y","Y","Y","Y","49.095528","5","41","579-584","PMC2928646","refsnp","OMIMUNIPROT","code.google.com"
"1204","18981051","MED","18981051","10.1093/nar/gkn840","VIPERdb2: an enhanced and web API enabled relational database for structural virology.","Carrillo-Tripp M, Shepherd CM, Borelli IA, Venkataraman S, Lander G, Natarajan P, Johnson JE, Brooks CL 3rd, Reddy VS.","Nucleic Acids Res","2009","0305-1048","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","72","Y","Y","N","N","Y","49.095528","database issue","37","d436-42","PMC2686430","pdb",NA,"code.google.com"
"1205","20972438","MED","20972438","10.1038/ng.687","A multi-stage genome-wide association study of bladder cancer identifies multiple susceptibility loci.","Rothman N, Garcia-Closas M, Chatterjee N, Malats N, Wu X, Figueroa JD, Real FX, Van Den Berg D, Matullo G, Baris D, Thun M, Kiemeney LA, Vineis P, De Vivo I, Albanes D, Purdue MP, Rafnar T, Hildebrandt MA, Kiltie AE, Cussenot O, Golka K, Kumar R, Taylor JA, Mayordomo JI, Jacobs KB, Kogevinas M, Hutchinson A, Wang Z, Fu YP, Prokunina-Olsson L, Burdett L, Yeager M, Wheeler W, TardÃ³n A, Serra C, Carrato A, GarcÃa-Closas R, Lloreta J, Johnson A, Schwenn M, Karagas MR, Schned A, Andriole G Jr, Grubb R 3rd, Black A, Jacobs EJ, Diver WR, Gapstur SM, Weinstein SJ, Virtamo J, Cortessis VK, Gago-Dominguez M, Pike MC, Stern MC, Yuan JM, Hunter DJ, McGrath M, Dinney CP, Czerniak B, Chen M, Yang H, Vermeulen SH, Aben KK, Witjes JA, Makkinje RR, Sulem P, Besenbacher S, Stefansson K, Riboli E, Brennan P, Panico S, Navarro C, Allen NE, Bueno-de-Mesquita HB, Trichopoulos D, Caporaso N, Landi MT, Canzian F, Ljungberg B, Tjonneland A, Clavel-Chapelon F, Bishop DT, Teo MT, Knowles MA, Guarrera S, Polidoro S, Ricceri F, Sacerdote C, Allione A, Cancel-Tassin G, Selinski S, Hengstler JG, Dietrich H, Fletcher T, Rudnai P, Gurzau E, Koppova K, Bolick SC, Godfrey A, Xu Z, Sanz-Velez JI, D GarcÃa-Prats M, Sanchez M, Valdivia G, Porru S, Benhamou S, Hoover RN, Fraumeni JF Jr, Silverman DT, Chanock SJ.","Nat Genet","2010","1061-4036","journal article; research support, n.i.h., extramural; research support, n.i.h., intramural; research-article","Y","Y","Y","119","Y","Y","Y","Y","Y","49.095528","11","42","978-984","PMC3049891","refsnp","UNIPROT","code.google.com"
"1206","19242557","MED","19242557","10.3389/neuro.11.004.2009","Python for information theoretic analysis of neural data.","Ince RA, Petersen RS, Swan DC, Panzeri S.","Front Neuroinform","2009","1662-5196","journal article; research-article","Y","Y","Y","12","Y","Y","N","N","N","49.07253",NA,"3","4","PMC2647335",NA,NA,"code.google.com"
"1207","20807414","MED","20807414","10.1186/1741-7007-8-114","Bayesian random local clocks, or one rate to rule them all.","Drummond AJ, Suchard MA.","BMC Biol","2010","1741-7007","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","47","Y","Y","N","N","N","48.77516",NA,"8","114","PMC2949620",NA,NA,"code.google.com"
"1208","19450253","MED","19450253","10.1186/1471-2148-9-108","PhyloExplorer: a web server to validate, explore and query phylogenetic trees.","Ranwez V, Clairon N, Delsuc F, Pourali S, Auberval N, Diser S, Berry V.","BMC Evol Biol","2009","1471-2148","journal article; research support, non-u.s. gov't; product-review","Y","Y","Y","6","Y","Y","N","N","N","48.77516",NA,"9","108","PMC2695458",NA,NA,"code.google.com"
"1209","19750924","MED","19750924",NA,"Lucid dreaming: a state of consciousness with features of both waking and non-lucid dreaming.","Voss U, Holzmann R, Tuin I, Hobson JA.","Sleep","2009","0161-8105","journal article; research-article","N","Y","Y","53","Y","Y","N","N","N","48.77516","9","32","1191-1200","PMC2737577",NA,NA,"code.google.com"
"1210","19795424","MED","19795424","10.1002/pmic.200900216","Proteomics data repositories.","Riffle M, Eng JK.","Proteomics","2009","1615-9853","journal article; review; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","8","Y","Y","N","N","N","48.77516","20","9","4653-4663","PMC2908408",NA,NA,"code.google.com"
"1211","19907644","MED","19907644","10.1371/journal.pone.0007710","Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API.","Kono N, Arakawa K, Ogawa R, Kido N, Oshita K, Ikegami K, Tamaki S, Tomita M.","PLoS One","2009","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","19","Y","Y","N","N","N","48.77516","11","4","e7710","PMC2770834",NA,NA,"code.google.com"
"1212","19914901","MED","19914901","10.2196/jmir.1225","Use of live interactive webcasting for an international postgraduate module in ehealth: case study evaluation.","Jones RB, Maramba I, Boulos MN, Alexander T.","J Med Internet Res","2009","1439-4456","journal article; research-article","Y","Y","Y","4","Y","Y","N","N","N","48.77516","4","11","e46","PMC2802565",NA,NA,"code.google.com"
"1213","20571085","MED","20571085","10.1093/nar/gkq532","Identifying compositionally homogeneous and nonhomogeneous domains within the human genome using a novel segmentation algorithm.","Elhaik E, Graur D, JosiÄ K, Landan G.","Nucleic Acids Res","2010","0305-1048","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","6","Y","Y","N","N","N","48.77516","15","38","e158","PMC2926622",NA,NA,"code.google.com"
"1214","20639369","MED","20639369","10.1128/aem.03115-09","Response of porcine intestinal in vitro organ culture tissues following exposure to Lactobacillus plantarum JC1 and Salmonella enterica serovar Typhimurium SL1344.","Collins JW, Coldham NG, Salguero FJ, Cooley WA, Newell WR, Rastall RA, Gibson GR, Woodward MJ, La Ragione RM.","Appl Environ Microbiol","2010","0099-2240","journal article; research support, non-u.s. gov't; in vitro; research-article","N","Y","Y","2","Y","Y","N","N","N","48.77516","19","76","6645-6657","PMC2950466",NA,NA,"code.google.com"
"1215","20663193","MED","20663193","10.1186/1749-8546-5-27","Publishing Chinese medicine knowledge as Linked Data on the Web.","Zhao J.","Chin Med","2010","1749-8546","journal article; research-article","Y","Y","Y","2","Y","Y","N","N","N","48.77516",NA,"5","27","PMC2936390",NA,NA,"code.google.com"
"1216","20851208","MED","20851208","10.1016/j.jbi.2010.09.004","Exposing the cancer genome atlas as a SPARQL endpoint.","Deus HF, Veiga DF, Freire PR, Weinstein JN, Mills GB, Almeida JS.","J Biomed Inform","2010","1532-0464","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","8","Y","Y","N","N","N","48.77516","6","43","998-1008","PMC3071752",NA,NA,"code.google.com"
"1217","20200009","MED","20200009","10.1093/bioinformatics/btq099","Modeling sample variables with an Experimental Factor Ontology.","Malone J, Holloway E, Adamusiak T, Kapushesky M, Zheng J, Kolesnikov N, Zhukova A, Brazma A, Parkinson H.","Bioinformatics","2010","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","47","Y","Y","N","Y","N","48.77516","8","26","1112-1118","PMC2853691",NA,NA,"code.google.com"
"1218","19125200","MED","19125200","10.1371/journal.pone.0004128","Using pathway signatures as means of identifying similarities among microarray experiments.","Beltrame L, Rizzetto L, Paola R, Rocca-Serra P, Gambineri L, Battaglia C, Cavalieri D.","PLoS One","2009","1932-6203","evaluation studies; journal article; research-article","Y","Y","Y","11","Y","Y","Y","N","N","48.77516","1","4","e4128","PMC2610483",NA,"ARXPR","code.google.com"
"1219","20356373","MED","20356373","10.1186/1471-2105-11-163","New components of the Dictyostelium PKA pathway revealed by Bayesian analysis of expression data.","Parikh A, Huang E, Dinh C, Zupan B, Kuspa A, Subramanian D, Shaulsky G.","BMC Bioinformatics","2010","1471-2105","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","4","Y","Y","Y","N","N","48.77516",NA,"11","163","PMC2873529",NA,"UNIPROT","code.google.com"
"1220","18167549","MED","18167549","10.1371/journal.pone.0001390","High-resolution molecular epidemiology and evolutionary history of HIV-1 subtypes in Albania.","Salemi M, de Oliveira T, Ciccozzi M, Rezza G, Goodenow MM.","PLoS One","2008","1932-6203","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","33","Y","Y","N","N","N","48.77516","1","3","e1390","PMC2148102",NA,NA,"code.google.com"
"1221","20700438","MED","20700438","10.1371/journal.pgen.1001051","The 5p15.33 locus is associated with risk of lung adenocarcinoma in never-smoking females in Asia.","Hsiung CA, Lan Q, Hong YC, Chen CJ, Hosgood HD, Chang IS, Chatterjee N, Brennan P, Wu C, Zheng W, Chang GC, Wu T, Park JY, Hsiao CF, Kim YH, Shen H, Seow A, Yeager M, Tsai YH, Kim YT, Chow WH, Guo H, Wang WC, Sung SW, Hu Z, Chen KY, Kim JH, Chen Y, Huang L, Lee KM, Lo YL, Gao YT, Kim JH, Liu L, Huang MS, Jung TH, Jin G, Caporaso N, Yu D, Kim CH, Su WC, Shu XO, Xu P, Kim IS, Chen YM, Ma H, Shen M, Cha SI, Tan W, Chang CH, Sung JS, Zhang M, Yang TY, Park KH, Yuenger J, Wang CL, Ryu JS, Xiang Y, Deng Q, Hutchinson A, Kim JS, Cai Q, Landi MT, Yu CJ, Park JY, Tucker M, Hung JY, Lin CC, Perng RP, Boffetta P, Chen CY, Chen KC, Yang SY, Hu CY, Chang CK, Fraumeni JF Jr, Chanock S, Yang PC, Rothman N, Lin D.","PLoS Genet","2010","1553-7390","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research support, n.i.h., intramural; research-article","Y","Y","Y","22","Y","Y","N","Y","Y","48.77516","8","6","861-864","PMC2916850","refsnp",NA,"code.google.com"
"1222","20730105","MED","20730105","10.3389/neuro.01.011.2010","Open source tools for the information theoretic analysis of neural data.","Ince RA, Mazzoni A, Petersen RS, Panzeri S.","Front Neurosci","2010","1662-4548","journal article; research-article","Y","Y","Y","2","Y","Y","N","N","N","48.77516",NA,"4",NA,"PMC2891486",NA,NA,"code.google.com"
"1223","19420069","MED","19420069","10.1093/bioinformatics/btp142","DASMI: exchanging, annotating and assessing molecular interaction data.","Blankenburg H, Finn RD, PrliÄ A, Jenkinson AM, RamÃrez F, Emig D, Schelhorn SE, BÃ¼ch J, Lengauer T, Albrecht M.","Bioinformatics","2009","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","8","Y","Y","N","N","N","48.77516","10","25","1321-1328","PMC2677739",NA,NA,"code.google.com"
"1224","20569493","MED","20569493","10.1186/1756-0500-3-175","OntoFox: web-based support for ontology reuse.","Xiang Z, Courtot M, Brinkman RR, Ruttenberg A, He Y.","BMC Res Notes","2010","1756-0500","journal article; research-article","Y","Y","Y","22","Y","Y","N","N","N","48.77516",NA,"3","175","PMC2911465",NA,NA,"code.google.com"
"1225","19390155","MED","19390155","10.1107/s0907444909009500","The role of entropy and polarity in intermolecular contacts in protein crystals.","CieÅlik M, Derewenda ZS.","Acta Crystallogr D Biol Crystallogr","2009","0907-4449","journal article; research support, n.i.h., extramural; research-article","N","Y","Y","7","N","Y","N","N","N","48.77516","pt 5","65","500-509","PMC2672819",NA,NA,"code.google.com"
"1226","20871783","MED","20871783","10.1177/1947601909359929","Molecular Stratification of Clear Cell Renal Cell Carcinoma by Consensus Clustering Reveals Distinct Subtypes and Survival Patterns.","Brannon AR, Reddy A, Seiler M, Arreola A, Moore DT, Pruthi RS, Wallen EM, Nielsen ME, Liu H, Nathanson KL, Ljungberg B, Zhao H, Brooks JD, Ganesan S, Bhanot G, Rathmell WK.","Genes Cancer","2010","1947-6019","journal article; research-article","N","Y","Y","37","Y","Y","N","N","N","48.77516","2","1","152-163","PMC2943630",NA,NA,"code.google.com"
"1227","19251739","MED","19251739","10.1101/gr.089532.108","ABySS: a parallel assembler for short read sequence data.","Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I.","Genome Res","2009","1088-9051","journal article; research support, non-u.s. gov't; research-article","N","Y","Y","640","Y","Y","N","Y","N","48.77516","6","19","1117-1123","PMC2694472",NA,NA,"code.google.com"
"1228","20971988","MED","20971988","10.1093/bioinformatics/btq599","The GMOD Drupal bioinformatic server framework.","Papanicolaou A, Heckel DG.","Bioinformatics","2010","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","5","Y","Y","N","N","N","48.77516","24","26","3119-3124","PMC2995126",NA,NA,"code.google.com"
"1229","20171285","MED","20171285","10.1016/j.neuroimage.2010.02.036","Quantifying the effects of normal ageing on white matter structure using unsupervised tract shape modelling.","Bastin ME, MuÃ±oz Maniega S, Ferguson KJ, Brown LJ, Wardlaw JM, MacLullich AM, Clayden JD.","Neuroimage","2010","1053-8119","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","15","Y","Y","N","N","N","48.77516","1","51","1-10","PMC3763188",NA,NA,"code.google.com"
"1230","19451168","MED","19451168","10.1093/bioinformatics/btp324","Fast and accurate short read alignment with Burrows-Wheeler transform.","Li H, Durbin R.","Bioinformatics","2009","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","3070","Y","Y","N","Y","N","48.77516","14","25","1754-1760","PMC2705234",NA,NA,"code.google.com"
"1231","19836008","MED","19836008","10.1016/j.ajhg.2009.09.012","A genome-wide association study of lung cancer identifies a region of chromosome 5p15 associated with risk for adenocarcinoma.","Landi MT, Chatterjee N, Yu K, Goldin LR, Goldstein AM, Rotunno M, Mirabello L, Jacobs K, Wheeler W, Yeager M, Bergen AW, Li Q, Consonni D, Pesatori AC, Wacholder S, Thun M, Diver R, Oken M, Virtamo J, Albanes D, Wang Z, Burdette L, Doheny KF, Pugh EW, Laurie C, Brennan P, Hung R, Gaborieau V, McKay JD, Lathrop M, McLaughlin J, Wang Y, Tsao MS, Spitz MR, Wang Y, Krokan H, Vatten L, Skorpen F, Arnesen E, Benhamou S, Bouchard C, Metspalu A, Vooder T, Nelis M, VÃ¤lk K, Field JK, Chen C, Goodman G, Sulem P, Thorleifsson G, Rafnar T, Eisen T, Sauter W, Rosenberger A, BickebÃ¶ller H, Risch A, Chang-Claude J, Wichmann HE, Stefansson K, Houlston R, Amos CI, Fraumeni JF Jr, Savage SA, Bertazzi PA, Tucker MA, Chanock S, Caporaso NE.","Am J Hum Genet","2009","0002-9297","journal article; research support, non-u.s. gov't; brief-report","N","Y","Y","171","Y","Y","Y","Y","Y","48.77516","5","85","679-691","PMC2775843","refsnp","OMIMUNIPROT","code.google.com"
"1232","20362542","MED","20362542","10.1016/j.stem.2010.03.004","An expanded Oct4 interaction network: implications for stem cell biology, development, and disease.","Pardo M, Lang B, Yu L, Prosser H, Bradley A, Babu MM, Choudhary J.","Cell Stem Cell","2010","1934-5909","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","141","Y","Y","Y","N","N","48.77516","4","6","382-395","PMC2860244",NA,"INTACTUNIPROT","code.google.com"
"1233","19158238","MED","19158238","10.1128/jvi.01556-08","Demonstration of sustained drug-resistant human immunodeficiency virus type 1 lineages circulating among treatment-naÃ¯ve individuals.","HuÃ© S, Gifford RJ, Dunn D, Fernhill E, Pillay D, UK Collaborative Group on HIV Drug Resistance.","J Virol","2009","0022-538x","journal article; research support, non-u.s. gov't; research-article","N","Y","Y","44","Y","Y","Y","N","Y","48.77516","6","83","2645-2654","PMC2648277","gen","EMBLUNIPROT","code.google.com"
"1234","19435614","MED","19435614","10.1016/j.jbi.2009.05.002","ConText: an algorithm for determining negation, experiencer, and temporal status from clinical reports.","Harkema H, Dowling JN, Thornblade T, Chapman WW.","J Biomed Inform","2009","1532-0464","journal article; research support, n.i.h., extramural; research-article","N","Y","Y","34","Y","Y","N","N","N","48.665234","5","42","839-851","PMC2757457",NA,NA,"code.google.com"
"1235","20540779","MED","20540779","10.1186/1471-2105-11-317","Introducing W.A.T.E.R.S.: a workflow for the alignment, taxonomy, and ecology of ribosomal sequences.","Hartman AL, Riddle S, McPhillips T, LudÃ¤scher B, Eisen JA.","BMC Bioinformatics","2010","1471-2105","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; product-review","Y","Y","Y","9","Y","Y","N","N","N","48.4548",NA,"11","317","PMC2898799",NA,NA,"code.google.com"
"1236","19367702","MED","19367702","10.1021/pr8004887","Characterization and comprehensive proteome profiling of exosomes secreted by hepatocytes.","Conde-Vancells J, Rodriguez-Suarez E, Embade N, Gil D, Matthiesen R, Valle M, Elortza F, Lu SC, Mato JM, Falcon-Perez JM.","J Proteome Res","2008","1535-3893","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","64","Y","Y","N","N","N","48.4548","12","7","5157-5166","PMC2696236",NA,NA,"code.google.com"
"1237","23504193","MED","23504193","10.1559/152304010792194930","Bicomponent Trend Maps: A Multivariate Approach to Visualizing Geographic Time Series.","Schroeder JP.","Cartogr Geogr Inf Sci","2010","1523-0406","journal article; research-article","N","Y","Y","0","Y","Y","N","N","N","48.4548","3","37","169-187","PMC3595555",NA,NA,"code.google.com"
"1238","20501635","MED","20501635","10.1124/jpet.110.167304","Simultaneous pharmacokinetics/pharmacodynamics modeling of recombinant human erythropoietin upon multiple intravenous dosing in rats.","Ait-Oudhia S, Scherrmann JM, Krzyzanski W.","J Pharmacol Exp Ther","2010","0022-3565","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","6","Y","Y","N","N","N","48.4548","3","334","897-910","PMC2939674",NA,NA,"code.google.com"
"1239","20584339","MED","20584339","10.1186/1471-2164-11-408","Small RNAs, DNA methylation and transposable elements in wheat.","Cantu D, Vanzetti LS, Sumner A, Dubcovsky M, Matvienko M, Distelfeld A, Michelmore RW, Dubcovsky J.","BMC Genomics","2010","1471-2164","journal article; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","25","Y","Y","Y","N","N","48.4548",NA,"11","408","PMC2996936",NA,"ARXPR","code.google.com"
"1240","18487092","MED","18487092","10.1016/j.jbi.2008.04.001","HCLS 2.0/3.0: health care and life sciences data mashup using Web 2.0/3.0.","Cheung KH, Yip KY, Townsend JP, Scotch M.","J Biomed Inform","2008","1532-0464","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","Y","10","Y","Y","N","N","N","48.4548","5","41","694-705","PMC2933816",NA,NA,"code.google.com"
"1241","19162232","MED","19162232","10.1016/j.jbi.2008.12.006","Improving accuracy for identifying related PubMed queries by an integrated approach.","Lu Z, Wilbur WJ.","J Biomed Inform","2009","1532-0464","journal article; research support, n.i.h., intramural; research-article","N","Y","Y","4","Y","Y","N","N","N","48.4548","5","42","831-838","PMC2764279",NA,NA,"code.google.com"
"1242","18586841","MED","18586841","10.1529/biophysj.108.134049","Double bilayers and transmembrane gradients: a molecular dynamics study of a highly charged peptide.","Denning EJ, Woolf TB.","Biophys J","2008","0006-3495","journal article; research support, n.i.h., extramural; research-article","N","Y","Y","4","Y","Y","N","N","Y","48.4548","7","95","3161-3173","PMC2547445","pdb",NA,"code.google.com"
"1243","19714205","MED","19714205","10.1371/journal.pgen.1000623","Genome-wide association study implicates chromosome 9q21.31 as a susceptibility locus for asthma in mexican children.","Hancock DB, Romieu I, Shi M, Sienra-Monge JJ, Wu H, Chiu GY, Li H, del Rio-Navarro BE, Willis-Owen SA, Weiss ST, Raby BA, Gao H, Eng C, Chapela R, Burchard EG, Tang H, Sullivan PF, London SJ.","PLoS Genet","2009","1553-7390","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","71","Y","Y","Y","Y","Y","48.4548","8","5","e1000623","PMC2722731","refsnp; omim","UNIPROT","code.google.com"
"1244","20019791","MED","20019791","10.1371/journal.pcbi.1000608","Predicting functional alternative splicing by measuring RNA selection pressure from multigenome alignments.","Lu H, Lin L, Sato S, Xing Y, Lee CJ.","PLoS Comput Biol","2009","1553-734x","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","10","Y","Y","N","N","N","48.4548","12","5","e1000608","PMC2784930",NA,NA,"code.google.com"
"1245","20034392","MED","20034392","10.1186/1471-2105-10-447","Next generation transcriptomes for next generation genomes using est2assembly.","Papanicolaou A, Stierli R, Ffrench-Constant RH, Heckel DG.","BMC Bioinformatics","2009","1471-2105","journal article; research support, non-u.s. gov't; product-review","Y","Y","Y","29","Y","Y","N","Y","N","48.4548",NA,"10","447","PMC3087352",NA,NA,"code.google.com"
"1246","21203427","MED","21203427","10.1371/journal.pone.0014448","Mitochondrial cox1 sequence data reliably uncover patterns of insect diversity but suffer from high lineage-idiosyncratic error rates.","Hendrich L, Pons J, Ribera I, Balke M.","PLoS One","2010","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","18","Y","Y","N","N","N","48.4548","12","5","e14448","PMC3010977",NA,NA,"code.google.com"
"1247","20675161","MED","20675161","10.1016/j.jmgm.2010.06.010","GPU-accelerated molecular modeling coming of age.","Stone JE, Hardy DJ, Ufimtsev IS, Schulten K.","J Mol Graph Model","2010","1093-3263","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","Y","32","Y","Y","N","N","N","48.4548","2","29","116-125","PMC2934899",NA,NA,"code.google.com"
"1248","19622144","MED","19622144","10.1186/1471-2105-10-226","Information management for high content live cell imaging.","Jameson D, Turner DA, Ankers J, Kennedy S, Ryan S, Swainston N, Griffiths T, Spiller DG, Oliver SG, White MR, Kell DB, Paton NW.","BMC Bioinformatics","2009","1471-2105","journal article; research support, non-u.s. gov't; product-review","Y","Y","Y","2","Y","Y","N","N","N","48.4548",NA,"10","226","PMC2723092",NA,NA,"code.google.com"
"1249","21152420","MED","21152420","10.1371/journal.pone.0013876","Predicting DNA-binding specificities of eukaryotic transcription factors.","SchrÃ¶der A, Eichner J, Supper J, Eichner J, Wanke D, Henneges C, Zell A.","PLoS One","2010","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","N","N","N","48.4548","11","5","e13876","PMC2994704",NA,NA,"code.google.com"
"1250","20017957","MED","20017957","10.1186/1471-2164-10-618","A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments.","Laajala TD, Raghav S, Tuomela S, Lahesmaa R, Aittokallio T, Elo LL.","BMC Genomics","2009","1471-2164","journal article; research support, non-u.s. gov't; comparative study; research-article","Y","Y","Y","49","Y","Y","N","N","N","48.4548",NA,"10","618","PMC2804666",NA,NA,"code.google.com"
"1251","20077162","MED","20077162","10.1007/s12021-009-9061-2","The Java Image Science Toolkit (JIST) for rapid prototyping and publishing of neuroimaging software.","Lucas BC, Bogovic JA, Carass A, Bazin PL, Prince JL, Pham DL, Landman BA.","Neuroinformatics","2010","1539-2791","journal article; research support, n.i.h., extramural; research support, n.i.h., intramural; research-article","N","Y","Y","38","Y","Y","N","Y","N","48.4548","1","8","5-17","PMC2860951",NA,NA,"code.google.com"
"1252","21122111","MED","21122111","10.1186/1752-0509-4-166","Systems biology approach reveals that overflow metabolism of acetate in Escherichia coli is triggered by carbon catabolite repression of acetyl-CoA synthetase.","Valgepea K, Adamberg K, Nahku R, Lahtvee PJ, Arike L, Vilu R.","BMC Syst Biol","2010","1752-0509","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","32","Y","Y","N","N","N","48.4548",NA,"4","166","PMC3014970",NA,NA,"code.google.com"
"1253","19881494","MED","19881494","10.1038/nbt.1583","Microdroplet-based PCR enrichment for large-scale targeted sequencing.","Tewhey R, Warner JB, Nakano M, Libby B, Medkova M, David PH, Kotsopoulos SK, Samuels ML, Hutchison JB, Larson JW, Topol EJ, Weiner MP, Harismendy O, Olson J, Link DR, Frazer KA.","Nat Biotechnol","2009","1087-0156","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","131","Y","Y","N","N","N","48.4548","11","27","1025-1031","PMC2779736",NA,NA,"code.google.com"
"1254","20064465","MED","20064465","10.1016/j.molcel.2009.12.003","Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping.","Xue Y, Zhou Y, Wu T, Zhu T, Ji X, Kwon YS, Zhang C, Yeo G, Black DL, Sun H, Fu XD, Zhang Y.","Mol Cell","2009","1097-2765","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","137","Y","Y","Y","N","N","48.4548","6","36","996-1006","PMC2807993",NA,"ARXPR","code.google.com"
"1255","21194449","MED","21194449","10.1186/1471-2148-10-395","454 sequencing reveals extreme complexity of the class II Major Histocompatibility Complex in the collared flycatcher.","Zagalska-Neubauer M, Babik W, Stuglik M, Gustafsson L, CichoÅ M, Radwan J.","BMC Evol Biol","2010","1471-2148","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","32","Y","Y","Y","N","Y","48.4548",NA,"10","395","PMC3024992","gen","EMBLUNIPROT","code.google.com"
"1256","21073723","MED","21073723","10.1186/1471-2229-10-246","Sequencing of 6.7 Mb of the melon genome using a BAC pooling strategy.","GonzÃ¡lez VM, Benjak A, HÃ©naff EM, Mir G, Casacuberta JM, Garcia-Mas J, PuigdomÃ¨nech P.","BMC Plant Biol","2010","1471-2229","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","13","Y","Y","Y","N","Y","48.4548",NA,"10","246","PMC3095328","gen","EMBLUNIPROT","code.google.com"
"1257","19381256","MED","19381256","10.1371/journal.pcbi.1000361","Adventures in semantic publishing: exemplar semantic enhancements of a research article.","Shotton D, Portwin K, Klyne G, Miles A.","PLoS Comput Biol","2009","1553-734x","journal article; review-article","Y","Y","Y","17","Y","Y","N","N","N","48.13443","4","5","e1000361","PMC2663789",NA,NA,"code.google.com"
"1258","20482806","MED","20482806","10.1186/1476-072x-9-23","HEALTH GeoJunction: place-time-concept browsing of health publications.","MacEachren AM, Stryker MS, Turton IJ, Pezanowski S.","Int J Health Geogr","2010","1476-072x","journal article; review; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","1","Y","Y","N","N","N","48.13443",NA,"9","23","PMC2889882",NA,NA,"code.google.com"
"1259","19085989","MED","19085989","10.1002/0471143030.cb0421s41","Photoactivated localization microscopy (PALM) of adhesion complexes.","Shroff H, White H, Betzig E.","Curr Protoc Cell Biol","2008","1934-2500","journal article; research support, non-u.s. gov't; research-article","N","Y","Y","3","Y","Y","N","N","N","48.13443",NA,"Chapter 4","unit 4.21","PMC3640801",NA,NA,"code.google.com"
"1260","19662154","MED","19662154","10.1371/journal.pcbi.1000438","The logic of EGFR/ErbB signaling: theoretical properties and analysis of high-throughput data.","Samaga R, Saez-Rodriguez J, Alexopoulos LG, Sorger PK, Klamt S.","PLoS Comput Biol","2009","1553-734x","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","53","Y","Y","N","N","N","48.13443","8","5","e1000438","PMC2710522",NA,NA,"code.google.com"
"1261","20613864","MED","20613864","10.1371/journal.pbio.1000409","Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homologs.","Woodhouse MR, Schnable JC, Pedersen BS, Lyons E, Lisch D, Subramaniam S, Freeling M.","PLoS Biol","2010","1544-9173","journal article; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","53","Y","Y","N","N","N","48.13443","6","8","e1000409","PMC2893956",NA,NA,"code.google.com"
"1262","20975932","MED","20975932","10.1371/journal.pcbi.1000967","Non-centered spike-triggered covariance analysis reveals neurotrophin-3 as a developmental regulator of receptive field properties of ON-OFF retinal ganglion cells.","Cantrell DR, Cang J, Troy JB, Liu X.","PLoS Comput Biol","2010","1553-734x","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","10","Y","Y","Y","N","N","48.13443","10","6","e1000967","PMC2958799",NA,"UNIPROT","code.google.com"
"1263","19885390","MED","19885390","10.1371/journal.pbio.1000236","Identification and functional characterization of N-terminally acetylated proteins in Drosophila melanogaster.","Goetze S, Qeli E, Mosimann C, Staes A, Gerrits B, Roschitzki B, Mohanty S, Niederer EM, Laczko E, Timmerman E, Lange V, Hafen E, Aebersold R, Vandekerckhove J, Basler K, Ahrens CH, Gevaert K, Brunner E.","PLoS Biol","2009","1544-9173","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","41","Y","Y","Y","Y","N","48.13443","11","7","e1000236","PMC2762599",NA,"UNIPROT","code.google.com"
"1264","20937096","MED","20937096","10.1186/1471-2148-10-302","A maximum pseudo-likelihood approach for estimating species trees under the coalescent model.","Liu L, Yu L, Edwards SV.","BMC Evol Biol","2010","1471-2148","journal article; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","43","Y","Y","N","N","N","48.13443",NA,"10","302","PMC2976751",NA,NA,"code.google.com"
"1265","21637730","MED","21637730","10.3233/ao-2010-0079","Ontological realism: A methodology for coordinated evolution of scientific ontologies.","Smith B, Ceusters W.","Appl Ontol","2010","1570-5838","journal article; research-article","N","Y","Y","18","Y","Y","N","N","N","47.814068","3-4","5","139-188","PMC3104413",NA,NA,"code.google.com"
"1266","IND43986588","AGR",NA,"10.1111/j.1471-8286.2007.01884.x","msatcommander: detection of microsatellite repeat arrays and automated, locus-specific primer design","FAIRCLOTH BRANTC.","Mol Ecol Notes","2008","1471-8278","journal article","N","N","N","31","N","N","N","N","N","10.987897","1","8","92-94",NA,NA,NA,"code.google.com"
"1267","25322836","MED","25322836","10.1093/bioinformatics/btu680","Rcount: simple and flexible RNA-Seq read counting.","Schmid MW, Grossniklaus U.","Bioinformatics","2015","1367-4803","journal article","N","N","N","0","N","N","N","N","N","724.49384","3","31","436-437",NA,NA,NA,"github.com"
"1268","25573920","MED","25573920","10.1093/bioinformatics/btv012","Acquire: An Open-Source Comprehensive Cancer Biobanking System.","Dowst H, Pew B, Watkins C, McOwiti A, Barney J, Qu S, Becnel LB.","Bioinformatics","2015","1367-4803","journal article","N","N","N","0","N","N","N","N","N","719.9546",NA,NA,NA,NA,NA,NA,"github.com"
"1269","25600946","MED","25600946","10.1093/bioinformatics/btv028","drexplorer: A tool to explore dose-response relationships and drug-drug interactions.","Tong P, Coombes KR, Johnson FM, Byers LA, Diao L, Liu DD, Lee JJ, Heymach JV, Wang J.","Bioinformatics","2015","1367-4803","journal article","N","N","N","0","N","N","N","N","N","719.17584",NA,NA,NA,NA,NA,NA,"github.com"
"1270","25649617","MED","25649617",NA,"Analysis of Nanopore Data using Hidden Markov Models.","Schreiber J, Karplus K.","Bioinformatics","2015","1367-4803","journal article","N","N","N","0","N","N","N","N","N","719.17584",NA,NA,NA,NA,NA,NA,"github.com"
"1271","25573116","MED","25573116","10.1002/cyto.a.22625","FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data.","Van Gassen S, Callebaut B, Van Helden MJ, Lambrecht BN, Demeester P, Dhaene T, Saeys Y.","Cytometry A","2015","1552-4922","journal article","N","N","N","0","N","N","N","N","N","719.1758",NA,NA,NA,NA,NA,NA,"github.com"
"1272","25192740","MED","25192740","10.1093/bioinformatics/btu593","Genomon ITDetector: a tool for somatic internal tandem duplication detection from cancer genome sequencing data.","Chiba K, Shiraishi Y, Nagata Y, Yoshida K, Imoto S, Ogawa S, Miyano S.","Bioinformatics","2015","1367-4803","journal article","N","N","N","0","N","N","N","N","N","719.1758","1","31","116-118",NA,NA,NA,"github.com"
"1273","25212755","MED","25212755","10.1093/bioinformatics/btu605","cddApp: a Cytoscape app for accessing the NCBI conserved domain database.","Morris JH, Wu A, Yamashita RA, Marchler-Bauer A, Ferrin TE.","Bioinformatics","2015","1367-4803","journal article","N","N","N","0","N","N","N","N","N","719.1758","1","31","134-136",NA,NA,NA,"github.com"
"1274","25273112","MED","25273112","10.1093/bioinformatics/btu648","MulRF: a software package for phylogenetic analysis using multi-copy gene trees.","Chaudhary R, FernÃ¡ndez-Baca D, Burleigh JG.","Bioinformatics","2015","1367-4803","journal article","N","N","N","0","N","N","N","N","N","719.1758","3","31","432-433",NA,NA,NA,"github.com"
"1275","25626454","MED","25626454","10.1186/s12859-014-0428-5","Quantitative analysis of differences in copy numbers using read depth obtained from PCR-enriched samples and controls.","Reinecke F, Satya R, DiCarlo J.","BMC Bioinformatics","2015","1471-2105","journal article","N","N","N","0","N","N","N","N","N","719.1758","1","16","17",NA,NA,NA,"github.com"
"1276","25637556","MED","25637556",NA,"RAMPART: a workflow management system for de novo genome assembly.","Mapleson D, Drou N, Swarbreck D.","Bioinformatics","2015","1367-4803","journal article","N","N","N","0","N","N","N","N","N","719.1758",NA,NA,NA,NA,NA,NA,"github.com"
"1277","25638815","MED","25638815",NA,"Starcode: sequence clustering based on all-pairs search.","Zorita EV, CuscÃ³ P, Filion G.","Bioinformatics","2015","1367-4803","journal article","N","N","N","0","N","N","N","N","N","719.1758",NA,NA,NA,NA,NA,NA,"github.com"
"1278","25648531","MED","25648531",NA,"xiNET: cross-link network maps with residue resolution.","Combe CW, Fischer L, Rappsilber J.","Mol Cell Proteomics","2015","1535-9476","journal article","N","N","N","0","N","N","N","N","N","719.1758",NA,NA,NA,NA,NA,NA,"github.com"
"1279","25586514","MED","25586514","10.1093/bioinformatics/btv005","NLR-parser: Rapid annotation of plant NLR complements.","Steuernagel B, Jupe F, Witek K, Jones JD, Wulff BB.","Bioinformatics","2015","1367-4803","journal article","N","N","N","0","N","N","N","N","N","717.571",NA,NA,NA,NA,NA,NA,"github.com"
"1280","25609795","MED","25609795","10.1093/bioinformatics/btv025","Large-scale extraction of brain connectivity from the neuroscientific literature.","Richardet R, Chappelier JC, Telefont M, Hill S.","Bioinformatics","2015","1367-4803","journal article","N","N","N","0","N","N","N","N","N","717.571",NA,NA,NA,NA,NA,NA,"github.com"
"1281","25649621","MED","25649621",NA,"Incorporating peak grouping information for alignment of multiple liquid chromatography-mass spectrometry datasets.","Wandy J, Daly R, Breitling R, Rogers S.","Bioinformatics","2015","1367-4803","journal article","N","N","N","0","N","N","N","N","N","717.571",NA,NA,NA,NA,NA,NA,"github.com"
"1282","25192739","MED","25192739","10.1093/bioinformatics/btu547","mod_bio: Apache modules for Next-Generation sequencing data.","Lindenbaum P, Redon R.","Bioinformatics","2015","1367-4803","journal article","N","N","N","0","N","N","N","N","N","717.5709","1","31","112-113",NA,NA,NA,"github.com"
"1283","25178461","MED","25178461","10.1093/bioinformatics/btu588","GenPlay Multi-Genome, a tool to compare and analyze multiple human genomes in a graphical interface.","Lajugie J, Fourel N, Bouhassira EE.","Bioinformatics","2015","1367-4803","journal article","N","N","N","0","N","N","N","N","N","717.5709","1","31","109-111",NA,NA,NA,"github.com"
"1284","25520192","MED","25520192","10.1093/nar/gku1327","Annotating RNA motifs in sequences and alignments.","Gardner PP, Eldai H.","Nucleic Acids Res","2015","0305-1048","journal article","N","N","N","0","N","N","N","N","N","717.5709","2","43","691-698",NA,NA,NA,"github.com"
"1285","25609793","MED","25609793","10.1093/bioinformatics/btv033","MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.","Li D, Liu CM, Luo R, Sadakane K, Lam TW.","Bioinformatics","2015","1367-4803","journal article","N","N","N","0","N","N","N","N","N","717.5709",NA,NA,NA,NA,NA,NA,"github.com"
"1286","24890372","MED","24890372","10.1111/1755-0998.12286","Pipeliner: software to evaluate the performance of bioinformatics pipelines for next-generation resequencing.","Nevado B, Perez-Enciso M.","Mol Ecol Resour","2015","1755-098x","journal article; research support, non-u.s. gov't","N","N","N","1","Y","N","N","N","N","717.5709","1","15","99-106",NA,NA,NA,"github.com"
"1287","25645318","MED","25645318","10.1002/jssc.201401235","Robust alignment of chromatograms by statistically analyzing the shift matrix generated by moving window fast Fourier transform cross-correlation.","Zhang M, Wen M, Zhang ZM, Lu H, Liang Y, Zhan D.","J Sep Sci","2015","1615-9306","journal article","N","N","N","0","N","N","N","N","N","717.5709",NA,NA,NA,NA,NA,NA,"github.com"
"1288","25183485","MED","25183485","10.1093/bioinformatics/btu589","Over-representation of correlation analysis (ORCA): a method for identifying associations between variable sets.","Pomyen Y, Segura M, Ebbels TM, Keun HC.","Bioinformatics","2015","1367-4803","journal article","N","N","N","0","N","N","N","N","N","715.96606","1","31","102-108",NA,NA,NA,"github.com"
"1289","25573919","MED","25573919","10.1093/bioinformatics/btv002","RNA-Rocket: An RNA-Seq Analysis Resource for Infectious Disease Research.","Warren AS, Aurrecoechea C, Brunk B, Desai P, Emrich S, Giraldo-CalderÃ³n GI, Harb O, Hix D, Lawson D, Machi D, Mao C, McClelland M, Nordberg E, Shukla M, Vosshall LB, Wattam AR, Will R, Yoo HS, Sobral B.","Bioinformatics","2015","1367-4803","journal article","N","N","N","0","N","N","N","N","N","715.96606",NA,NA,NA,NA,NA,NA,"github.com"
"1290","25577434","MED","25577434","10.1093/bioinformatics/btu856","Shifted Hamming Distance: A Fast and Accurate SIMD-Friendly Filter to Accelerate Alignment Verification in Read Mapping.","Xin H, Greth J, Emmons J, Pekhimenko G, Kingsford C, Alkan C, Mutlu O.","Bioinformatics","2015","1367-4803","journal article","N","N","N","0","N","N","N","N","N","715.96606",NA,NA,NA,NA,NA,NA,"github.com"
"1291","25614471","MED","25614471","10.1093/bioinformatics/btv014","Gaussian process test for high-throughput sequencing time series: application to experimental evolution.","Topa H, JÃ³nÃ¡s Ã, Kofler R, Kosiol C, Honkela A.","Bioinformatics","2015","1367-4803","journal article","N","N","N","0","N","N","N","N","N","715.96606",NA,NA,NA,NA,NA,NA,"github.com"
"1292","25352552","MED","25352552","10.1093/nar/gku1010","Ensembl 2015.","Cunningham F, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, Gil L, GirÃ³n CG, Gordon L, Hourlier T, Hunt SE, Janacek SH, Johnson N, Juettemann T, KÃ¤hÃ¤ri AK, Keenan S, Martin FJ, Maurel T, McLaren W, Murphy DN, Nag R, Overduin B, Parker A, Patricio M, Perry E, Pignatelli M, Riat HS, Sheppard D, Taylor K, Thormann A, Vullo A, Wilder SP, Zadissa A, Aken BL, Birney E, Harrow J, Kinsella R, Muffato M, Ruffier M, Searle SM, Spudich G, Trevanion SJ, Yates A, Zerbino DR, Flicek P.","Nucleic Acids Res","2015","0305-1048","journal article","N","N","N","0","N","N","N","N","N","715.96606","database issue","43","d662-9",NA,NA,NA,"github.com"
"1293","25617415","MED","25617415","10.1093/bioinformatics/btv031","ASSIGN: Context-specific Genomic Profiling of Multiple Heterogeneous Biological Pathways.","Shen Y, Rahman M, Piccolo SR, Gusenleitner D, Ei-Chaar NN, Cheng L, Monti S, Bild AH, Johnson WE.","Bioinformatics","2015","1367-4803","journal article","N","N","N","0","N","N","N","N","N","715.96606",NA,NA,NA,NA,NA,NA,"github.com"
"1294","25435543","MED","25435543","10.1074/mcp.o114.041376","Preprocessing Significantly Improves the Peptide/Protein Identification Sensitivity of High-resolution Isobarically Labeled Tandem Mass Spectrometry Data.","Sheng Q, Li R, Dai J, Li Q, Su Z, Guo Y, Li C, Shyr Y, Zeng R.","Mol Cell Proteomics","2015","1535-9476","journal article","N","N","N","0","N","N","N","N","N","715.96606","2","14","405-417",NA,NA,NA,"github.com"
"1295","25406361","MED","25406361","10.1261/rna.046037.114","IsoSCM: improved and alternative 3' UTR annotation using multiple change-point inference.","Shenker S, Miura P, Sanfilippo P, Lai EC.","RNA","2015","1355-8382","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural","N","N","N","0","N","N","N","N","N","715.96606","1","21","14-27",NA,NA,NA,"github.com"
"1296","25236461","MED","25236461","10.1093/bioinformatics/btu613","The Ensembl REST API: Ensembl Data for Any Language.","Yates A, Beal K, Keenan S, McLaren W, Pignatelli M, Ritchie GR, Ruffier M, Taylor K, Vullo A, Flicek P.","Bioinformatics","2015","1367-4803","journal article; research-article","Y","Y","N","0","Y","Y","N","N","Y","714.67596","1","31","143-145","PMC4271150","ensembl",NA,"github.com"
"1297","25569221","MED","25569221","10.1371/journal.pcbi.1004008","A RESTful API for Accessing Microbial Community Data for MG-RAST.","Wilke A, Bischof J, Harrison T, Brettin T, D'Souza M, Gerlach W, Matthews H, Paczian T, Wilkening J, Glass EM, Desai N, Meyer F.","PLoS Comput Biol","2015","1553-734x","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","712.6169","1","11","e1004008","PMC4287624",NA,NA,"github.com"
"1298","25621171","MED","25621171","10.1186/s40168-014-0066-1","VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data.","Laczny CC, Sternal T, Plugaru V, Gawron P, Atashpendar A, Margossian HH, Coronado S, der Maaten Lv, Vlassis N, Wilmes P.","Microbiome","2015","2049-2618","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","711.89624","1","3","1","PMC4305225",NA,NA,"github.com"
"1299","25628874","MED","25628874","10.1002/ece3.1261","4P: fast computing of population genetics statistics from large DNA polymorphism panels.","Benazzo A, Panziera A, Bertorelle G.","Ecol Evol","2015","2045-7758","journal article; research-article","Y","Y","N","0","N","Y","N","N","N","710.3489","1","5","172-175","PMC4298444",NA,NA,"github.com"
"1300","25273102","MED","25273102","10.1093/bioinformatics/btu630","A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature.","Hart RK, Rico R, Hare E, Garcia J, Westbrook J, Fusaro VA.","Bioinformatics","2015","1367-4803","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","710.3489","2","31","268-270","PMC4287946",NA,NA,"github.com"
"1301","25651527","MED","25651527","10.1186/s13059-015-0587-3","Extending reference assembly models.","Church DM, Schneider VA, Steinberg KM, Schatz MC, Quinlan AR, Chin CS, Kitts PA, Aken B, Marth GT, Hoffman MM, Herrero J, Mendoza ML, Durbin R, Flicek P.","Genome Biol","2015","1465-6906","journal article; research-article","Y","Y","N","0","N","Y","N","N","N","710.3489","1","16","13","PMC4305238",NA,NA,"github.com"
"1302","25012901","MED","25012901","10.1038/ismej.2014.114","The subgingival microbiome of clinically healthy current and never smokers.","Mason MR, Preshaw PM, Nagaraja HN, Dabdoub SM, Rahman A, Kumar PS.","ISME J","2015","1751-7362","journal article; letter","Y","Y","N","0","Y","Y","N","N","N","710.3489","1","9","268-272","PMC4274424",NA,NA,"github.com"
"1303","25293804","MED","25293804","10.1093/sysbio/syu081","Cancer evolution: mathematical models and computational inference.","Beerenwinkel N, Schwarz RF, Gerstung M, Markowetz F.","Syst Biol","2015","1063-5157","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","709.9254","1","64","e1-25","PMC4265145",NA,NA,"github.com"
"1304","25323575","MED","25323575","10.1093/molbev/msu287","Reassortment between Influenza B Lineages and the Emergence of a Coadapted PB1-PB2-HA Gene Complex.","Dudas G, Bedford T, Lycett S, Rambaut A.","Mol Biol Evol","2015","0737-4038","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","709.7412","1","32","162-172","PMC4271528",NA,NA,"github.com"
"1305","25548154","MED","25548154","10.1073/pnas.1322632112","Directional selection can drive the evolution of modularity in complex traits.","Melo D, Marroig G.","Proc Natl Acad Sci U S A","2015","0027-8424","journal article; research-article","N","Y","N","0","Y","Y","N","N","Y","709.74115","2","112","470-475","PMC4299217","doi",NA,"github.com"
"1306","25544043","MED","25544043","10.1016/j.chembiol.2014.11.010","Topological Models of Heteromeric Protein Assemblies from Mass Spectrometry: Application to the Yeast eIF3:eIF5 Complex.","Politis A, Schmidt C, Tjioe E, Sandercock AM, Lasker K, Gordiyenko Y, Russel D, Sali A, Robinson CV.","Chem Biol","2015","1074-5521","journal article; research-article","Y","Y","N","0","Y","Y","N","N","Y","709.74115","1","22","117-128","PMC4306531","pdb",NA,"github.com"
"1307","25650807","MED","25650807","10.1186/s13059-014-0558-0","Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data.","Fernandez-Cuesta L, Sun R, Menon R, George J, Lorenz S, Meza-Zepeda LA, Peifer M, Plenker D, Heuckmann JM, Leenders F, Zander T, Dahmen I, Koker M, SchÃ¶ttle J, Ullrich RT, AltmÃ¼ller J, Becker C, NÃ¼rnberg P, Seidel H, BÃ¶hm D, GÃ¶ke F, AnsÃ©n S, Russell PA, Wright GM, Wainer Z, Solomon B, Petersen I, Clement JH, SÃ¤nger J, Brustugun OT, Helland Ã, Solberg S, Lund-Iversen M, Buettner R, Wolf J, Brambilla E, Vingron M, Perner S, Haas SA, Thomas RK.","Genome Biol","2015","1465-6906","journal article; research-article","Y","Y","N","0","N","Y","N","N","N","709.74115","1","16","7","PMC4300615",NA,NA,"github.com"
"1308","25608737","MED","25608737","10.1038/srep07918","Cloud computing approaches for prediction of ligand binding poses and pathways.","Lawrenz M, Shukla D, Pande VS.","Sci Rep","2015","2045-2322","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","709.54645",NA,"5","7918","PMC4302315",NA,NA,"github.com"
"1309","25650158","MED","25650158","10.7717/peerj.740","First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking.","Sekiguchi Y, Ohashi A, Parks DH, Yamauchi T, Tyson GW, Hugenholtz P.","PeerJ","2015","2167-8359","journal article; research-article","Y","Y","N","0","N","Y","N","N","Y","709.1738",NA,"3","e740","PMC4312070","gen; doi",NA,"github.com"
"1310","25252269","MED","25252269","10.1111/nph.13027","The genetics of divergence and reproductive isolation between ecotypes of Panicum hallii.","Lowry DB, Hernandez K, Taylor SH, Meyer E, Logan TL, Barry KW, Chapman JA, Rokhsar DS, Schmutz J, Juenger TE.","New Phytol","2015","0028-646x","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","N","0","Y","Y","N","N","N","709.1738","1","205","402-414","PMC4265272",NA,NA,"github.com"
"1311","25583564","MED","25583564","10.1186/preaccept-3491466321328530","ALLMAPS: robust scaffold ordering based on multiple maps.","Tang H, Zhang X, Miao C, Zhang J, Ming R, Schnable JC, Schnable PS, Lyons E, Lu J.","Genome Biol","2015","1465-6906","journal article; research-article","Y","Y","N","0","N","Y","N","N","Y","709.1738","1","16","3","PMC4305236","doi",NA,"github.com"
"1312","25587016","MED","25587016","10.1128/mbio.02400-14","The Ordospora colligata Genome: Evolution of Extreme Reduction in Microsporidia and Host-To-Parasite Horizontal Gene Transfer.","Pombert JF, Haag KL, Beidas S, Ebert D, Keeling PJ.","MBio","2015","2150-7511","journal article; research-article","Y","Y","N","0","N","Y","N","N","N","709.1738","1","6",NA,"PMC4313915",NA,NA,"github.com"
"1313","25653903","MED","25653903","10.7717/peerj.718","Intragenomic polymorphisms among high-copy loci: a genus-wide study of nuclear ribosomal DNA in Asclepias (Apocynaceae).","Weitemier K, Straub SC, Fishbein M, Liston A.","PeerJ","2015","2167-8359","journal article; research-article","Y","Y","N","0","N","Y","N","N","Y","709.1738",NA,"3","e718","PMC4304868","gen",NA,"github.com"
"1314","25411411","MED","25411411","10.1098/rsif.2014.1125","Predictability in a highly stochastic system: final size of measles epidemics in small populations.","Caudron Q, Mahmud AS, Metcalf CJ, GottfreÃ°sson M, Viboud C, Cliff AD, Grenfell BT.","J R Soc Interface","2015","1742-5689","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","N","0","Y","Y","N","N","N","709.1453","102","12","20141125","PMC4277111",NA,NA,"github.com"
"1315","25615858","MED","25615858","10.1107/s1399004714016617","Protein-ligand interactions investigated by thermal shift assays (TSA) and dual polarization interferometry (DPI).","GrÃ¸ftehauge MK, Hajizadeh NR, Swann MJ, Pohl E.","Acta Crystallogr D Biol Crystallogr","2015","0907-4449","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","709.1453","pt 1","71","36-44","PMC4304684",NA,NA,"github.com"
"1316","24797101","MED","24797101","10.1002/hep.27192","Next-generation sequencing sheds light on the natural history of hepatitis C infection in patients who fail treatment.","Abdelrahman T, Hughes J, Main J, McLauchlan J, Thursz M, Thomson E.","Hepatology","2015","0270-9139","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","709.1453","1","61","88-97","PMC4303934",NA,NA,"github.com"
"1317","25602758","MED","25602758","10.1371/journal.pone.0116776","FastGCN: A GPU Accelerated Tool for Fast Gene Co-Expression Networks.","Liang M, Zhang F, Jin G, Zhu J.","PLoS One","2015","1932-6203","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","709.1453","1","10","e0116776","PMC4300192",NA,NA,"github.com"
"1318","25398865","MED","25398865","10.1128/aem.03117-14","Ecological succession and viability of human-associated microbiota on restroom surfaces.","Gibbons SM, Schwartz T, Fouquier J, Mitchell M, Sangwan N, Gilbert JA, Kelley ST.","Appl Environ Microbiol","2015","0099-2240","journal article; research-article","N","Y","N","0","Y","Y","N","N","Y","708.744","2","81","765-773","PMC4277569","doi",NA,"github.com"
"1319","25189778","MED","25189778","10.1093/bioinformatics/btu595","BigDataScript: a scripting language for data pipelines.","Cingolani P, Sladek R, Blanchette M.","Bioinformatics","2015","1367-4803","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","708.744","1","31","10-16","PMC4271142",NA,NA,"github.com"
"1320","25610775","MED","25610775","10.1016/j.nicl.2014.11.014","Capturing the dynamics of response variability in the brain in ADHD.","van Belle J, van Raalten T, Bos DJ, Zandbelt BB, Oranje B, Durston S.","Neuroimage Clin","2015","2213-1582","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","708.744",NA,"7","132-141","PMC4299975",NA,NA,"github.com"
"1321","24936765","MED","24936765","10.1038/ismej.2014.97","A single genus in the gut microbiome reflects host preference and specificity.","Eren AM, Sogin ML, Morrison HG, Vineis JH, Fisher JC, Newton RJ, McLellan SL.","ISME J","2015","1751-7362","journal article; research support, n.i.h., extramural; research-article","Y","Y","N","2","Y","Y","N","N","Y","708.744","1","9","90-100","PMC4274434","gen",NA,"github.com"
"1322","25411354","MED","25411354","10.1261/rna.047803.114","Dissecting noncoding and pathogen RNA-protein interactomes.","Flynn RA, Martin L, Spitale RC, Do BT, Sagan SM, Zarnegar B, Qu K, Khavari PA, Quake SR, Sarnow P, Chang HY.","RNA","2015","1355-8382","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","N","0","Y","Y","N","N","N","708.744","1","21","135-143","PMC4274633",NA,NA,"github.com"
"1323","25587012","MED","25587012","10.1128/mbio.02250-14","Comparative genomics suggests primary homothallism of pneumocystis species.","Almeida JM, CissÃ© OH, Fonseca Ã, Pagni M, Hauser PM.","MBio","2015","2150-7511","journal article; research-article","Y","Y","N","0","N","Y","N","N","N","708.744","1","6",NA,"PMC4313921",NA,NA,"github.com"
"1324","25266224","MED","25266224","10.1093/bioinformatics/btu641","Sigma: Strain-level inference of genomes from metagenomic analysis for biosurveillance.","Ahn TH, Chai J, Pan C.","Bioinformatics","2015","1367-4803","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","708.744","2","31","170-177","PMC4287953",NA,NA,"github.com"
"1325","25625594","MED","25625594","10.1371/journal.pone.0114911","Dynamic Epistasis under Varying Environmental Perturbations.","Barker B, Xu L, Gu Z.","PLoS One","2015","1932-6203","journal article; research-article","Y","Y","N","0","N","Y","N","N","N","708.744","1","10","e0114911","PMC4308068",NA,NA,"github.com"
"1326","25569531","MED","25569531","10.1371/journal.pgen.1004912","A regulatory hierarchy controls the dynamic transcriptional response to extreme oxidative stress in archaea.","Tonner PD, Pittman AM, Gulli JG, Sharma K, Schmid AK.","PLoS Genet","2015","1553-7390","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","708.34283","1","11","e1004912","PMC4287449",NA,NA,"github.com"
"1327","25588043","MED","25588043","10.1371/journal.pone.0116656","Ontology-Based Data Integration between Clinical and Research Systems.","Mate S, KÃ¶pcke F, Toddenroth D, Martin M, Prokosch HU, BÃ¼rkle T, Ganslandt T.","PLoS One","2015","1932-6203","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","708.34283","1","10","e0116656","PMC4294641",NA,NA,"github.com"
"1328","25592313","MED","25592313",NA,"Pollux: platform independent error correction of single and mixed genomes.","Marinier E, Brown DG, McConkey BJ.","BMC Bioinformatics","2015","1471-2105","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","708.34283","1","16","10","PMC4307147",NA,NA,"github.com"
"1329","25613955","MED","25613955","10.1186/s12864-014-1191-8","Overlapping mouse subcongenic strains successfully separate two linked body fat QTL on distal MMU 2.","Gularte-MÃ©rida R, Farber CR, Verdugo RA, Islas Trejo A, Famula TR, Warden CH, Medrano JF.","BMC Genomics","2015","1471-2164","journal article; research-article","Y","Y","N","0","Y","Y","N","N","Y","708.34283","1","16","16","PMC4308015","refsnp; doi",NA,"github.com"
"1330","25394363","MED","25394363","10.1101/gr.177840.114","Decoupling of evolutionary changes in transcription factor binding and gene expression in mammals.","Wong ES, Thybert D, Schmitt BM, Stefflova K, Odom DT, Flicek P.","Genome Res","2015","1088-9051","journal article; research-article","N","Y","N","0","N","Y","N","N","Y","708.34283","2","25","167-178","PMC4315291","arrayexpress",NA,"github.com"
"1331","25648772","MED","25648772","10.7717/peerj.705","Lung cancer incidence decreases with elevation: evidence for oxygen as an inhaled carcinogen.","Simeonov KP, Himmelstein DS.","PeerJ","2015","2167-8359","journal article; research-article","Y","Y","N","0","N","Y","N","N","N","708.34283",NA,"3","e705","PMC4304851",NA,NA,"github.com"
"1332","25615592","MED","25615592","10.1371/journal.pcbi.1004032","Laminar and Dorsoventral Molecular Organization of the Medial Entorhinal Cortex Revealed by Large-scale Anatomical Analysis of Gene Expression.","Ramsden HL, SÃ¼rmeli G, McDonagh SG, Nolan MF.","PLoS Comput Biol","2015","1553-734x","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","708.32263","1","11","e1004032","PMC4304787",NA,NA,"github.com"
"1333","25451469","MED","25451469","10.1016/j.neuroimage.2014.10.001","Automated segmentation of multifocal basal ganglia T2*-weighted MRI hypointensities.","Glatz A, Bastin ME, Kiker AJ, Deary IJ, Wardlaw JM, ValdÃ©s HernÃ¡ndez MC.","Neuroimage","2015","1053-8119","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","707.94165",NA,"105","332-346","PMC4275576",NA,NA,"github.com"
"1334","25234705","MED","25234705","10.1093/molbev/msu266","Dynamics of copy number variation in host races of the pea aphid.","Duvaux L, Geissmann Q, Gharbi K, Zhou JJ, Ferrari J, Smadja CM, Butlin RK.","Mol Biol Evol","2015","0737-4038","journal article; research-article","Y","Y","N","0","Y","Y","N","Y","N","707.9416","1","32","63-80","PMC4271520",NA,NA,"github.com"
"1335","25649125","MED","25649125","10.1186/s13073-014-0120-4","Bayesian models for syndrome- and gene-specific probabilities of novel variant pathogenicity.","Ruklisa D, Ware JS, Walsh R, Balding DJ, Cook SA.","Genome Med","2015","1756-994x","journal article; research-article","Y","Y","N","0","N","Y","N","N","Y","707.9416","1","7","5","PMC4308924","omim",NA,"github.com"
"1336","PMC4318444","PMC",NA,NA,"âRhizoponicsâ: a novel hydroponic rhizotron for root system analyses on mature Arabidopsis thaliana plants.","Mathieu L, Lobet G, Tocquin P, PÃ©rilleux C.","Plant Methods","2015","1746-4811","journal article; research-article","Y","Y","Y","0","N","Y","N","N","N","491.52673",NA,"11",NA,"PMC4318444",NA,NA,"github.com"
"1337","24470571","MED","24470571","10.1093/bioinformatics/btu050","Bio Simulators: a web UI for biological simulation.","Pedersen M, Oury N, Gravill C, Phillips A.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","0","N","N","N","N","N","340.36902","10","30","1491-1492",NA,NA,NA,"github.com"
"1338","25348214","MED","25348214","10.1093/bioinformatics/btu711","PPDMs-a resource for mapping small molecule bioactivities from ChEMBL to Pfam-A protein domains.","Kruger FA, Gaulton A, Nowotka M, Overington JP.","Bioinformatics","2014","1367-4803","journal article","N","N","N","0","N","N","N","N","N","340.36902",NA,NA,NA,NA,NA,NA,"github.com"
"1339","24078712","MED","24078712","10.1093/bioinformatics/btt568","BooleSim: an interactive Boolean network simulator.","Bock M, Scharp T, Talnikar C, Klipp E.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","1","Y","N","N","N","N","338.26065","1","30","131-132",NA,NA,NA,"github.com"
"1340","24130307","MED","24130307","10.1093/bioinformatics/btt588","Comment on 'Bayesian parentage analysis with systematic accountability of genotyping error, missing data and false matching'.","Anderson EC, Ng TC.","Bioinformatics","2014","1367-4803","comment; letter; research support, non-u.s. gov't","N","N","N","0","Y","N","N","N","N","338.26065","5","30","743-745",NA,NA,NA,"github.com"
"1341","25367074","MED","25367074","10.1186/preaccept-1252669119119544","Bayesian transcriptome assembly.","Maretty L, Sibbesen J, Krogh A.","Genome Biol","2014","1465-6906","journal article","N","N","N","0","N","N","N","N","N","338.26065","10","15","501",NA,NA,NA,"github.com"
"1342","25332377","MED","25332377","10.1093/bioinformatics/btu693","Seed: a user-friendly tool for exploring and visualizing microbial community data.","Beck D, Dennis C, Foster JA.","Bioinformatics","2014","1367-4803","journal article","N","N","N","0","N","N","N","N","N","338.26065",NA,NA,NA,NA,NA,NA,"github.com"
"1343","25107872","MED","25107872","10.1093/bioinformatics/btu541","Fast construction of FM-index for long sequence reads.","Li H.","Bioinformatics","2014","1367-4803","journal article; research support, n.i.h., extramural","N","N","N","0","N","N","N","N","N","338.26065","22","30","3274-3275",NA,NA,NA,"github.com"
"1344","25540185","MED","25540185","10.1093/bioinformatics/btu843","UProC: tools for ultra-fast protein domain classification.","Meinicke P.","Bioinformatics","2014","1367-4803","journal article","N","N","N","0","N","N","N","N","N","338.26065",NA,NA,NA,NA,NA,NA,"github.com"
"1345","25481007","MED","25481007","10.1093/bioinformatics/btu808","Kablammo: an interactive, web-based BLAST results visualizer.","Wintersinger JA, Wasmuth JD.","Bioinformatics","2014","1367-4803","journal article","N","N","N","0","N","N","N","N","N","338.26065",NA,NA,NA,NA,NA,NA,"github.com"
"1346","25147357","MED","25147357","10.1093/bioinformatics/btu561","SecureMA: protecting participant privacy in genetic association meta-analysis.","Xie W, Kantarcioglu M, Bush WS, Crawford D, Denny JC, Heatherly R, Malin BA.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural","N","N","N","0","N","N","N","N","N","335.8297","23","30","3334-3341",NA,NA,NA,"github.com"
"1347","24743991","MED","24743991","10.1007/978-1-4939-0512-6_4","Use model-based Analysis of ChIP-Seq (MACS) to analyze short reads generated by sequencing protein-DNA interactions in embryonic stem cells.","Liu T.","Methods Mol Biol","2014","1064-3745","journal article; research support, non-u.s. gov't","N","N","N","1","N","N","N","N","N","335.0509",NA,"1150","81-95",NA,NA,NA,"github.com"
"1348","24123672","MED","24123672","10.1093/bioinformatics/btt584","Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets.","Rodriguez-R LM, Konstantinidis KT.","Bioinformatics","2014","1367-4803","journal article; research support, u.s. gov't, non-p.h.s.","N","N","N","3","Y","N","N","Y","N","335.0509","5","30","629-635",NA,NA,NA,"github.com"
"1349","25504847","MED","25504847",NA,"andi: Fast and accurate estimation of evolutionary distances between closely related genomes.","Haubold B, KlÃ¶tzl F, Pfaffelhuber P.","Bioinformatics","2014","1367-4803","journal article","N","N","N","0","N","N","N","N","N","335.0509",NA,NA,NA,NA,NA,NA,"github.com"
"1350","25505087","MED","25505087",NA,"Sputnik: Ad hoc distributed computation.","VÃ¶lkel G, Lausser L, Schmid F, Kraus JM, Kestler HA.","Bioinformatics","2014","1367-4803","journal article","N","N","N","0","N","N","N","N","N","335.0509",NA,NA,NA,NA,NA,NA,"github.com"
"1351","25336502","MED","25336502","10.1093/bioinformatics/btu691","Simple, rapid and accurate genotyping-by-sequencing from aligned whole genomes with ArrayMaker.","Willet CE, Haase B, Charleston MA, Wade CM.","Bioinformatics","2014","1367-4803","journal article","N","N","N","0","N","N","N","N","N","335.0509",NA,NA,NA,NA,NA,NA,"github.com"
"1352","25371478","MED","25371478","10.1093/bioinformatics/btu729","JAMSS: proteomics mass spectrometry simulation in Java.","Smith R, Prince JT.","Bioinformatics","2014","1367-4803","journal article","N","N","N","0","N","N","N","N","N","335.0509",NA,NA,NA,NA,NA,NA,"github.com"
"1353","25322835","MED","25322835","10.1093/bioinformatics/btu676","miRseqViewer: multi-panel visualization of sequence, structure and expression for analysis of microRNA sequencing data.","Jang I, Chang H, Jun Y, Park S, Yang JO, Lee B, Kim W, Kim VN, Lee S.","Bioinformatics","2014","1367-4803","journal article","N","N","N","0","N","N","N","N","N","335.0509",NA,NA,NA,NA,NA,NA,"github.com"
"1354","25028724","MED","25028724","10.1093/bioinformatics/btu486","AffyPipe: an open-source pipeline for Affymetrix Axiom genotyping workflow.","Nicolazzi EL, Iamartino D, Williams JL.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","0","Y","N","N","N","N","335.0509","21","30","3118-3119",NA,NA,NA,"github.com"
"1355","24489371","MED","24489371","10.1093/bioinformatics/btu057","StochHMM: a flexible hidden Markov model tool and C++ library.","Lott PC, Korf I.","Bioinformatics","2014","1367-4803","journal article; research support, n.i.h., extramural","N","N","N","0","Y","N","N","N","N","335.0509","11","30","1625-1626",NA,NA,NA,"github.com"
"1356","24511145","MED","24511145","10.1167/14.2.6","RenderToolbox3: MATLAB tools that facilitate physically based stimulus rendering for vision research.","Heasly BS, Cottaris NP, Lichtman DP, Xiao B, Brainard DH.","J Vis","2014","1534-7362","journal article; research support, n.i.h., extramural","N","N","N","0","N","N","N","N","N","335.0509","2","14",NA,NA,NA,NA,"github.com"
"1357","24588150","MED","24588150","10.1063/1.4866448","Recovering position-dependent diffusion from biased molecular dynamics simulations.","LjubetiÄ A, UrbanÄiÄ I, Å trancar J.","J Chem Phys","2014","0021-9606","journal article; research support, non-u.s. gov't","N","N","N","0","Y","N","N","N","N","335.0509","8","140","084109",NA,NA,NA,"github.com"
"1358","24939150","MED","24939150","10.1093/bioinformatics/btu394","DAFGA: diversity analysis of functional gene amplicons.","Kim Y, Liesack W.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","0","Y","N","N","N","N","335.0509","19","30","2820-2821",NA,NA,NA,"github.com"
"1359","24930140","MED","24930140","10.1093/bioinformatics/btu380","miR-PREFeR: an accurate, fast and easy-to-use plant miRNA prediction tool using small RNA-Seq data.","Lei J, Sun Y.","Bioinformatics","2014","1367-4803","journal article; research support, u.s. gov't, non-p.h.s.","N","N","N","0","Y","N","N","N","N","335.0509","19","30","2837-2839",NA,NA,NA,"github.com"
"1360","24371154","MED","24371154","10.1093/bioinformatics/btt755","MSIsensor: microsatellite instability detection using paired tumor-normal sequence data.","Niu B, Ye K, Zhang Q, Lu C, Xie M, McLellan MD, Wendl MC, Ding L.","Bioinformatics","2014","1367-4803","journal article; research support, n.i.h., extramural","N","N","N","0","Y","N","N","Y","N","335.0509","7","30","1015-1016",NA,NA,NA,"github.com"
"1361","25165093","MED","25165093","10.1093/bioinformatics/btu564","MR_predictor: a simulation engine for Mendelian Randomization studies.","Voight BF.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","0","N","N","N","N","N","335.0509","23","30","3432-3434",NA,NA,NA,"github.com"
"1362","25075120","MED","25075120","10.1093/bioinformatics/btu501","NetPathMiner: R/Bioconductor package for network path mining through gene expression.","Mohamed A, Hancock T, Nguyen CH, Mamitsuka H.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","0","Y","N","N","N","N","335.0509","21","30","3139-3141",NA,NA,NA,"github.com"
"1363","24990608","MED","24990608","10.1093/bioinformatics/btu424","PyWATER: a PyMOL plug-in to find conserved water molecules in proteins by clustering.","Patel H, GrÃ¼ning BA, GÃ¼nther S, Merfort I.","Bioinformatics","2014","1367-4803","journal article","N","N","N","0","Y","N","N","N","N","335.0509","20","30","2978-2980",NA,NA,NA,"github.com"
"1364","24700534","MED","24700534","10.1002/pmic.201400036","GradientOptimizer: an open-source graphical environment for calculating optimized gradients in reversed-phase liquid chromatography.","Moruz L, KÃ¤ll L.","Proteomics","2014","1615-9853","journal article; research support, non-u.s. gov't","N","N","N","0","Y","N","N","N","N","335.0509","12","14","1464-1466",NA,NA,NA,"github.com"
"1365","25399553","MED","25399553","10.1017/s1431927614013506","Atom column indexing: atomic resolution image analysis through a matrix representation.","Sang X, Oni AA, LeBeau JM.","Microsc Microanal","2014","1431-9276","journal article","N","N","N","0","N","N","N","N","N","335.0509","6","20","1764-1771",NA,NA,NA,"github.com"
"1366","24152167","MED","24152167","10.1021/pr400820p","Tools to covisualize and coanalyze proteomic data with genomes and transcriptomes: validation of genes and alternative mRNA splicing.","Pang CN, Tay AP, Aya C, Twine NA, Harkness L, Hart-Smith G, Chia SZ, Chen Z, Deshpande NP, Kaakoush NO, Mitchell HM, Kassem M, Wilkins MR.","J Proteome Res","2014","1535-3893","journal article; validation studies; research support, non-u.s. gov't","N","N","N","2","N","N","N","N","N","333.44598","1","13","84-98",NA,NA,NA,"github.com"
"1367","24319000","MED","24319000","10.1093/bioinformatics/btt708","Chemical structure informing statistical hypothesis testing in metabolomics.","Zhu H, Luo M.","Bioinformatics","2014","1367-4803","journal article; comparative study","N","N","N","0","Y","N","N","N","N","333.44598","4","30","514-522",NA,NA,NA,"github.com"
"1368","25344497","MED","25344497","10.1093/bioinformatics/btu707","Semantic Body Browser: graphical exploration of an organism and spatially resolved expression data visualization.","Lekschas F, Stachelscheid H, Seltmann S, Kurtz A.","Bioinformatics","2014","1367-4803","journal article","N","N","N","0","N","N","N","N","N","333.44598",NA,NA,NA,NA,NA,NA,"github.com"
"1369","25338717","MED","25338717","10.1093/bioinformatics/btu696","FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data.","Hoogstrate Y, Jenster G, Martens-Uzunova ES.","Bioinformatics","2014","1367-4803","journal article","N","N","N","0","N","N","N","N","N","333.44598",NA,NA,NA,NA,NA,NA,"github.com"
"1370","25388149","MED","25388149","10.1093/bioinformatics/btu742","MeRP: a high-throughput pipeline for Mendelian randomization analysis.","Yin P, Voight BF.","Bioinformatics","2014","1367-4803","journal article","N","N","N","0","N","N","N","N","N","333.44598",NA,NA,NA,NA,NA,NA,"github.com"
"1371","25338721","MED","25338721","10.1093/bioinformatics/btu695","A model for the expression of gap genes based on the Jeffreys-type equation.","Gula IA, Samsonov AM.","Bioinformatics","2014","1367-4803","journal article","N","N","N","0","N","N","N","N","N","333.44598",NA,NA,NA,NA,NA,NA,"github.com"
"1372","25115706","MED","25115706","10.1093/bioinformatics/btu544","Figmop: a profile HMM to identify genes and bypass troublesome gene models in draft genomes.","Curran DM, Gilleard JS, Wasmuth JD.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","0","N","N","N","N","N","333.44598","22","30","3266-3267",NA,NA,NA,"github.com"
"1373","24336412","MED","24336412","10.1093/bioinformatics/btt706","slaMEM: efficient retrieval of maximal exact matches using a sampled LCP array.","Fernandes F, Freitas AT.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","0","Y","N","N","Y","N","333.44598","4","30","464-471",NA,NA,NA,"github.com"
"1374","24363381","MED","24363381","10.1093/bioinformatics/btt741","SurpriseMe: an integrated tool for network community structure characterization using Surprise maximization.","Aldecoa R, MarÃn I.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","0","Y","N","N","N","N","333.44598","7","30","1041-1042",NA,NA,NA,"github.com"
"1375","24458950","MED","24458950","10.1093/bioinformatics/btu041","ngsTools: methods for population genetics analyses from next-generation sequencing data.","Fumagalli M, Vieira FG, Linderoth T, Nielsen R.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural","N","N","N","1","Y","N","N","Y","N","333.44598","10","30","1486-1487",NA,NA,NA,"github.com"
"1376","25553811","MED","25553811","10.1142/s0219720014420050","AKSmooth: Enhancing low-coverage bisulfite sequencing data via kernel-based smoothing.","Chen J, Lutsik P, Akulenko R, Walter J, Helms V.","J Bioinform Comput Biol","2014","0219-7200","journal article","N","N","N","0","N","N","N","N","N","333.44598","6","12","1442005",NA,NA,NA,"github.com"
"1377","24574113","MED","24574113","10.1093/bioinformatics/btu113","CanSNPer: a hierarchical genotype classifier of clonal pathogens.","LÃ¤rkeryd A, MyrtennÃ¤s K, Karlsson E, Dwibedi CK, Forsman M, Larsson P, Johansson A, SjÃ¶din A.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","0","Y","N","N","N","N","333.44598","12","30","1762-1764",NA,NA,NA,"github.com"
"1378","25147360","MED","25147360","10.1093/bioinformatics/btu567","Visualization of protein sequence features using JavaScript and SVG with pViz.js.","Mukhyala K, Masselot A.","Bioinformatics","2014","1367-4803","journal article","N","N","N","0","N","N","N","N","N","333.44598","23","30","3408-3409",NA,NA,NA,"github.com"
"1379","24728856","MED","24728856","10.1093/bioinformatics/btu183","Lossy compression of quality scores in genomic data.","CÃ¡novas R, Moffat A, Turpin A.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","0","Y","N","N","N","N","333.44598","15","30","2130-2136",NA,NA,NA,"github.com"
"1380","24974202","MED","24974202","10.1093/bioinformatics/btu356","Toward better understanding of artifacts in variant calling from high-coverage samples.","Li H.","Bioinformatics","2014","1367-4803","journal article; review; research support, n.i.h., extramural","N","N","N","4","Y","N","N","N","N","333.44598","20","30","2843-2851",NA,NA,NA,"github.com"
"1381","24677618","MED","24677618","10.1002/humu.22531","Jannovar: a java library for exome annotation.","JÃ¤ger M, Wang K, Bauer S, Smedley D, Krawitz P, Robinson PN.","Hum Mutat","2014","1059-7794","journal article","N","N","N","2","Y","N","N","N","N","333.44598","5","35","548-555",NA,NA,NA,"github.com"
"1382","24567544","MED","24567544","10.1093/bioinformatics/btu094","jHeatmap: an interactive heatmap viewer for the web.","Deu-Pons J, Schroeder MP, Lopez-Bigas N.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","2","Y","N","N","N","N","333.44598","12","30","1757-1758",NA,NA,NA,"github.com"
"1383","25294822","MED","25294822","10.1093/nar/gku864","svaseq: removing batch effects and other unwanted noise from sequencing data.","Leek JT.","Nucleic Acids Res","2014","0305-1048","journal article; research support, n.i.h., extramural","N","N","N","0","N","N","N","N","N","333.44598","21","42",NA,NA,NA,NA,"github.com"
"1384","25480375","MED","25480375","10.1093/bioinformatics/btu802","QuASAR: Quantitative Allele Specific Analysis of Reads.","Harvey CT, Moyerbrailean GA, Davis GO, Wen X, Luca F, Pique-Regi R.","Bioinformatics","2014","1367-4803","journal article","N","N","N","0","N","N","N","N","N","333.44598",NA,NA,NA,NA,NA,NA,"github.com"
"1385","25481009","MED","25481009","10.1093/bioinformatics/btu809","ICMA: An integrated Cardiac modeling and Analysis platform.","Hussan JR, Hunter PJ, Gladding PA, Greenberg N, Christie R, Wu A, Sorby H, Thomas JD.","Bioinformatics","2014","1367-4803","journal article","N","N","N","0","N","N","N","N","N","333.44598",NA,NA,NA,NA,NA,NA,"github.com"
"1386","25543048","MED","25543048","10.1093/bioinformatics/btu849","An automatic tool to analyze and cluster macromolecular conformations based on Self-Organizing Maps.","Bouvier G, Desdouits N, Ferber M, Blondel A, Nilges M.","Bioinformatics","2014","1367-4803","journal article","N","N","N","0","N","N","N","N","N","333.44598",NA,NA,NA,NA,NA,NA,"github.com"
"1387","24830957","MED","24830957","10.1021/ci500173w","iBIOMES Lite: summarizing biomolecular simulation data in limited settings.","Thibault JC, Cheatham TE 3rd, Facelli JC.","J Chem Inf Model","2014","1549-9596","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural","N","N","N","0","N","N","N","N","N","333.44598","6","54","1810-1819",NA,NA,NA,"github.com"
"1388","25202595","MED","25202595","10.3732/apps.1300083","2matrix: A utility for indel coding and phylogenetic matrix concatenation(1.).","Salinas NR, Little DP.","Appl Plant Sci","2014","2168-0450","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","332.97772","1","2",NA,"PMC4123383",NA,NA,"github.com"
"1389","25520778","MED","25520778","10.12688/f1000research.4510.2","Cytoscape tools for the web age: D3.js and Cytoscape.js exporters.","Ono K, Demchak B, Ideker T.","F1000Res","2014","2046-1402","journal article; research-article","Y","Y","N","0","Y","Y","N","N","Y","332.82715",NA,"3","143","PMC4264639","doi",NA,"github.com"
"1390","25075287","MED","25075287","10.12688/f1000research.3-44.v1","PsicquicGraph, a BioJS component to visualize molecularÂ interactions from PSICQUIC servers.","Villaveces JM, Jimenez RC, Habermann BH.","F1000Res","2014","2046-1402","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","Y","331.94092",NA,"3","44","PMC4097353","doi",NA,"github.com"
"1391","24715980","MED","24715980","10.12688/f1000research.3-43.v1","KEGGViewer, a BioJS component to visualize KEGGÂ Pathways.","Villaveces JM, Jimenez RC, Habermann BH.","F1000Res","2014","2046-1402","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","Y","331.94092",NA,"3","43","PMC3954160","doi",NA,"github.com"
"1392","24794932","MED","24794932","10.1093/bioinformatics/btu311","Bioclojure: a functional library for the manipulation of biological sequences.","Plieskatt J, Rinaldi G, Brindley PJ, Jia X, Potriquet J, Bethony J, Mulvenna J.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","331.84116","17","30","2537-2539","PMC4147884",NA,NA,"github.com"
"1393","25524895","MED","25524895",NA,"VarSim: A high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications.","Mu JC, Mohiyuddin M, Li J, Asadi NB, Gerstein MB, Abyzov A, Wong WH, Lam HY.","Bioinformatics","2014","1367-4803","journal article","N","N","N","0","N","N","N","N","N","331.84116",NA,NA,NA,NA,NA,NA,"github.com"
"1394","24191071","MED","24191071","10.1093/bioinformatics/btt635","Phylowood: interactive web-based animations of biogeographic and phylogeographic histories.","Landis MJ, Bedford T.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","331.84116","1","30","123-124","PMC3866560",NA,NA,"github.com"
"1395","25414349","MED","25414349","10.1093/nar/gku1196","Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.","Croucher NJ, Page AJ, Connor TR, Delaney AJ, Keane JA, Bentley SD, Parkhill J, Harris SR.","Nucleic Acids Res","2014","0305-1048","journal article","N","N","N","0","N","N","N","N","N","331.84116",NA,NA,NA,NA,NA,NA,"github.com"
"1396","25344498","MED","25344498","10.1093/bioinformatics/btu706","Using 2kâ+â2 bubble searches to find single nucleotide polymorphisms in k-mer graphs.","Younsi R, MacLean D.","Bioinformatics","2014","1367-4803","journal article","N","N","N","0","N","N","N","N","N","331.84116",NA,NA,NA,NA,NA,NA,"github.com"
"1397","24994890","MED","24994890","10.1093/bioinformatics/btu407","Inter-species prediction of protein phosphorylation in the sbv IMPROVER species translation challenge.","Biehl M, Sadowski P, Bhanot G, Bilal E, Dayarian A, Meyer P, Norel R, Rhrissorrakrai K, Zeller MD, Hormoz S.","Bioinformatics","2014","1367-4803","journal article","N","N","N","0","Y","N","N","N","N","331.84116",NA,NA,NA,NA,NA,NA,"github.com"
"1398","25428347","MED","25428347","10.1093/nar/gku1197","HiTSelect: a comprehensive tool for high-complexity-pooled screen analysis.","Diaz AA, Qin H, Ramalho-Santos M, Song JS.","Nucleic Acids Res","2014","0305-1048","journal article","N","N","N","0","N","N","N","N","N","331.84116",NA,NA,NA,NA,NA,NA,"github.com"
"1399","25406329","MED","25406329","10.1093/bioinformatics/btu762","EPGA: de novo assembly using the distributions of reads and insert size.","Luo J, Wang J, Zhang Z, Wu FX, Li M, Pan Y.","Bioinformatics","2014","1367-4803","journal article","N","N","N","0","N","N","N","N","N","331.84116",NA,NA,NA,NA,NA,NA,"github.com"
"1400","25408304","MED","25408304","10.1007/s11548-014-1124-7","The NifTK software platform for image-guided interventions: platform overview and NiftyLink messaging.","Clarkson MJ, Zombori G, Thompson S, Totz J, Song Y, Espak M, Johnsen S, Hawkes D, Ourselin S.","Int J Comput Assist Radiol Surg","2014","1861-6410","journal article","N","N","N","0","N","N","N","N","N","331.84116",NA,NA,NA,NA,NA,NA,"github.com"
"1401","25129695","MED","25129695","10.1074/mcp.o113.030932","Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements.","Webb-Robertson BJ, Matzke MM, Datta S, Payne SH, Kang J, Bramer LM, Nicora CD, Shukla AK, Metz TO, Rodland KD, Smith RD, Tardiff MF, McDermott JE, Pounds JG, Waters KM.","Mol Cell Proteomics","2014","1535-9476","journal article","N","N","N","0","N","N","N","N","N","331.84116",NA,NA,NA,NA,NA,NA,"github.com"
"1402","24950811","MED","24950811","10.1093/bioinformatics/btu387","BEETL-fastq: a searchable compressed archive for DNA reads.","Janin L, Schulz-Trieglaff O, Cox AJ.","Bioinformatics","2014","1367-4803","journal article","N","N","N","0","Y","N","N","N","N","331.84116","19","30","2796-2801",NA,NA,NA,"github.com"
"1403","24658388","MED","24658388","10.1088/1741-2560/11/2/026017","A fast, robust algorithm for power line interference cancellation in neural recording.","Keshtkaran MR, Yang Z.","J Neural Eng","2014","1741-2560","journal article","N","N","N","0","N","N","N","N","N","331.84116","2","11","026017",NA,NA,NA,"github.com"
"1404","24281695","MED","24281695","10.1093/bioinformatics/btt624","Flexible analysis of RNA-seq data using mixed effects models.","Turro E, Astle WJ, TavarÃ© S.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","1","Y","N","N","Y","N","331.84116","2","30","180-188",NA,NA,NA,"github.com"
"1405","24532725","MED","24532725","10.1093/bioinformatics/btu093","EXTREME: an online EM algorithm for motif discovery.","Quang D, Xie X.","Bioinformatics","2014","1367-4803","journal article; research support, n.i.h., extramural","N","N","N","0","Y","N","N","N","N","331.84116","12","30","1667-1673",NA,NA,NA,"github.com"
"1406","24128146","MED","24128146","10.1111/1755-0998.12187","StreamingTrim 1.0: a Java software for dynamic trimming of 16S rRNA sequence data from metagenetic studies.","Bacci G, Bazzicalupo M, Benedetti A, Mengoni A.","Mol Ecol Resour","2014","1755-098x","journal article; research support, non-u.s. gov't","N","N","N","0","Y","N","N","N","N","331.84116","2","14","426-434",NA,NA,NA,"github.com"
"1407","25123903","MED","25123903","10.1093/bioinformatics/btu537","HapMuC: somatic mutation calling using heterozygous germ line variants near candidate mutations.","Usuyama N, Shiraishi Y, Sato Y, Kume H, Homma Y, Ogawa S, Miyano S, Imoto S.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","0","N","N","N","N","N","331.84116","23","30","3302-3309",NA,NA,NA,"github.com"
"1408","25064568","MED","25064568","10.1093/bioinformatics/btu499","e-Driver: a novel method to identify protein regions driving cancer.","Porta-Pardo E, Godzik A.","Bioinformatics","2014","1367-4803","journal article; research support, u.s. gov't, non-p.h.s.","N","N","N","0","Y","N","N","N","N","331.84116","21","30","3109-3114",NA,NA,NA,"github.com"
"1409","24695406","MED","24695406","10.1093/bioinformatics/btu174","Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity.","Li Y, Xie X.","Bioinformatics","2014","1367-4803","journal article; research support, n.i.h., extramural","N","N","N","0","Y","N","N","N","N","331.84116","15","30","2121-2129",NA,NA,NA,"github.com"
"1410","24728855","MED","24728855","10.1093/bioinformatics/btu181","geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees.","Pennell MW, Eastman JM, Slater GJ, Brown JW, Uyeda JC, FitzJohn RG, Alfaro ME, Harmon LJ.","Bioinformatics","2014","1367-4803","journal article; research support, u.s. gov't, non-p.h.s.","N","N","N","0","Y","N","N","N","N","331.84116","15","30","2216-2218",NA,NA,NA,"github.com"
"1411","24845654","MED","24845654","10.1093/bioinformatics/btu342","Estimates of allele-specific expression in Drosophila with a single genome sequence and RNA-seq data.","Quinn A, Juneja P, Jiggins FM.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","0","N","N","N","N","N","331.84116","18","30","2603-2610",NA,NA,NA,"github.com"
"1412","24034598","MED","24034598","10.1111/1755-0998.12160","HeFPipe: a complete analytical pipeline for heterozygosity-fitness correlation studies.","Fisher MA.","Mol Ecol Resour","2014","1755-098x","journal article; research support, non-u.s. gov't","N","N","N","0","Y","N","N","N","N","331.84116","1","14","215-217",NA,NA,NA,"github.com"
"1413","25505094","MED","25505094",NA,"Detection of Circular Permutations within Protein Structures using CE-CP.","Bliven SE, Bourne PE, PrliÄ A.","Bioinformatics","2014","1367-4803","journal article","N","N","N","0","N","N","N","N","N","331.84116",NA,NA,NA,NA,NA,NA,"github.com"
"1414","25138168","MED","25138168","10.1093/bioinformatics/btu534","Comparative assembly hubs: web-accessible browsers for comparative genomics.","Nguyen N, Hickey G, Raney BJ, Armstrong J, Clawson H, Zweig A, Karolchik D, Kent WJ, Haussler D, Paten B.","Bioinformatics","2014","1367-4803","journal article; research support, n.i.h., extramural","N","N","N","0","N","N","N","N","N","331.84116","23","30","3293-3301",NA,NA,NA,"github.com"
"1415","24703969","MED","24703969","10.1016/j.ygeno.2014.03.006","Multi-perspective quality control of Illumina exome sequencing data using QC3.","Guo Y, Zhao S, Sheng Q, Ye F, Li J, Lehmann B, Pietenpol J, Samuels DC, Shyr Y.","Genomics","2014","0888-7543","journal article; research support, n.i.h., extramural","N","N","N","1","Y","N","N","N","N","331.84116","5-6","103","323-328",NA,NA,NA,"github.com"
"1416","25372312","MED","25372312","10.1021/jp504942t","Implementation of the forward-reverse method for calculating the potential of mean force using a dynamic restraining protocol.","Nategholeslam M, Gray CG, Tomberli B.","J Phys Chem B","2014","1520-6106","journal article","N","N","N","0","N","N","N","N","N","331.84116","49","118","14203-14214",NA,NA,NA,"github.com"
"1417","25035321","MED","25035321","10.1128/genomea.00592-14","Curtobacterium sp. Genome Sequencing Underlines Plant Growth Promotion-Related Traits.","Bulgari D, Minio A, Casati P, Quaglino F, Delledonne M, Bianco PA.","Genome Announc","2014","2169-8287","journal article; brief-report","Y","Y","Y","0","Y","Y","N","N","N","331.2904","4","2",NA,"PMC4102858",NA,NA,"github.com"
"1418","25035325","MED","25035325","10.1128/genomea.00628-14","Strain Kaplan of Pseudorabies Virus Genome Sequenced by PacBio Single-Molecule Real-Time Sequencing Technology.","TombÃ¡cz D, Sharon D, OlÃ¡h P, Csabai Z, Snyder M, BoldogkÅi Z.","Genome Announc","2014","2169-8287","journal article; brief-report","Y","Y","Y","0","Y","Y","Y","N","Y","331.2904","4","2",NA,"PMC4102862","gen","EMBLUNIPROT","github.com"
"1419","25057255","MED","25057255","10.3897/bdj.2.e1125","Enriched biodiversity data as a resource and service.","Vos RA, Biserkov JV, Balech B, Beard N, Blissett M, Brenninkmeijer C, van Dooren T, Eades D, Gosline G, Groom QJ, Hamann TD, Hettling H, Hoehndorf R, Holleman A, Hovenkamp P, Kelbert P, King D, Kirkup D, Lammers Y, DeMeulemeester T, Mietchen D, Miller JA, Mounce R, Nicolson N, Page R, Pawlik A, Pereira S, Penev L, Richards K, Sautter G, Shorthouse DP, TÃ¤htinen M, Weiland C, Williams AR, Sierra S.","Biodivers Data J","2014","1314-2828","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","330.63745","2",NA,"e1125","PMC4092319",NA,NA,"github.com"
"1420","24470576","MED","24470576","10.1093/bioinformatics/btu036","NGSANE: a lightweight production informatics framework for high-throughput data analysis.","Buske FA, French HJ, Smith MA, Clark SJ, Bauer DC.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","Y","N","330.55106","10","30","1471-1472","PMC4016703",NA,NA,"github.com"
"1421","24790156","MED","24790156","10.1093/bioinformatics/btu300","Vacceed: a high-throughput in silico vaccine candidate discovery pipeline for eukaryotic pathogens based on reverse vaccinology.","Goodswen SJ, Kennedy PJ, Ellis JT.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","330.23627","16","30","2381-2383","PMC4207429",NA,NA,"github.com"
"1422","25505086","MED","25505086",NA,"Phy-Mer: a novel alignment-free and reference-independent mitochondrial haplogroup classifier.","Navarro-Gomez D, Leipzig J, Shen L, Lott M, Stassen AP, Wallace DC, Wiggs JL, Falk MJ, van Oven M, Gai X.","Bioinformatics","2014","1367-4803","journal article","N","N","N","0","N","N","N","N","N","330.23627",NA,NA,NA,NA,NA,NA,"github.com"
"1423","24657354","MED","24657354","10.1016/j.neuroimage.2014.03.037","Derivation of high-resolution MRI atlases of the human cerebellum at 3T and segmentation using multiple automatically generated templates.","Park MT, Pipitone J, Baer LH, Winterburn JL, Shah Y, Chavez S, Schira MM, Lobaugh NJ, Lerch JP, Voineskos AN, Chakravarty MM.","Neuroimage","2014","1053-8119","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural","N","N","N","2","Y","N","N","N","N","330.23627",NA,"95","217-231",NA,NA,NA,"github.com"
"1424","24493035","MED","24493035","10.1093/bioinformatics/btu075","ARTS: automated randomization of multiple traits for study design.","Maienschein-Cline M, Lei Z, Gardeux V, Abbasi T, Machado RF, Gordeuk V, Desai AA, Saraf S, Bahroos N, Lussier Y.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural","N","N","N","0","Y","N","N","N","N","330.23627","11","30","1637-1639",NA,NA,NA,"github.com"
"1425","24947752","MED","24947752","10.1093/bioinformatics/btu396","PGS: a tool for association study of high-dimensional microRNA expression data with repeated measures.","Zheng Y, Fei Z, Zhang W, Starren JB, Liu L, Baccarelli AA, Li Y, Hou L.","Bioinformatics","2014","1367-4803","journal article; research support, n.i.h., extramural","N","N","N","0","Y","N","N","N","N","330.23627","19","30","2802-2807",NA,NA,NA,"github.com"
"1426","25527832","MED","25527832",NA,"Population-based structural variation discovery with Hydra-Multi.","Lindberg MR, Hall IM, Quinlan AR.","Bioinformatics","2014","1367-4803","journal article","N","N","N","0","N","N","N","N","N","330.23627",NA,NA,NA,NA,NA,NA,"github.com"
"1427","25135945","MED","25135945","10.1093/molbev/msu244","Detecting recent positive selection with high accuracy and reliability by conditional coalescent tree.","Wang M, Huang X, Li R, Xu H, Jin L, He Y.","Mol Biol Evol","2014","0737-4038","journal article; research support, non-u.s. gov't","N","N","N","0","N","N","N","N","N","330.23627","11","31","3068-3080",NA,NA,NA,"github.com"
"1428","24860160","MED","24860160","10.1093/bioinformatics/btu351","Identification of chromosomal translocation hotspots via scan statistics.","Silva IT, Rosales RA, Holanda AJ, Nussenzweig MC, Jankovic M.","Bioinformatics","2014","1367-4803","journal article; research support, n.i.h., extramural","N","N","N","0","Y","N","N","N","N","330.23627","18","30","2551-2558",NA,NA,NA,"github.com"
"1429","24872423","MED","24872423","10.1093/bioinformatics/btu359","Massifquant: open-source Kalman filter-based XC-MS isotope trace feature detection.","Conley CJ, Smith R, Torgrip RJ, Taylor RM, Tautenhahn R, Prince JT.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.","N","N","N","0","Y","N","N","N","N","330.23627","18","30","2636-2643",NA,NA,NA,"github.com"
"1430","24681267","MED","24681267","10.1016/j.jmb.2014.03.010","Systematic detection of internal symmetry in proteins using CE-Symm.","Myers-Turnbull D, Bliven SE, Rose PW, Aziz ZK, Youkharibache P, Bourne PE, PrliÄ A.","J Mol Biol","2014","0022-2836","evaluation studies; journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural","N","N","N","0","Y","N","N","N","N","330.23627","11","426","2255-2268",NA,NA,NA,"github.com"
"1431","25165537","MED","25165537","10.12688/f1000research.4492.1","Cytoscape: the network visualization tool for GenomeSpace workflows.","Demchak B, Hull T, Reich M, Liefeld T, Smoot M, Ideker T, Mesirov JP.","F1000Res","2014","2046-1402","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","Y","330.23627",NA,"3","151","PMC4133763","doi",NA,"github.com"
"1432","25123904","MED","25123904","10.1093/bioinformatics/btu539","Cordova: web-based management of genetic variation data.","Ephraim SS, Anand N, DeLuca AP, Taylor KR, Kolbe DL, Simpson AC, Azaiez H, Sloan CM, Shearer AE, Hallier AR, Casavant TL, Scheetz TE, Smith RJ, Braun TA.","Bioinformatics","2014","1367-4803","journal article; research support, n.i.h., extramural","N","N","N","0","N","N","N","N","N","330.23627","23","30","3438-3439",NA,NA,NA,"github.com"
"1433","24860644","MED","24860644","10.12688/f1000research.3-48.v1","HeatMapViewer: interactive display of 2D data in biology.","Yachdav G, Hecht M, Pasmanik-Chor M, Yeheskel A, Rost B.","F1000Res","2014","2046-1402","journal article; research-article","Y","Y","Y","2","Y","Y","N","N","Y","330.23627",NA,"3","48","PMC4023661","doi; refseq; sprot; pfam",NA,"github.com"
"1434","24733292","MED","24733292","10.1093/bioinformatics/btu196","Association analysis using next-generation sequence data from publicly available control groups: the robust variance score statistic.","Derkach A, Chiang T, Gong J, Addis L, Dobbins S, Tomlinson I, Houlston R, Pal DK, Strug LJ.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","0","Y","N","N","N","N","330.23627","15","30","2179-2188",NA,NA,NA,"github.com"
"1435","24825614","MED","24825614","10.1093/bioinformatics/btu310","PLAAC: a web and command-line application to identify proteins with prion-like amino acid composition.","Lancaster AK, Nutter-Upham A, Lindquist S, King OD.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural","N","N","N","0","Y","N","Y","N","N","330.23627","17","30","2501-2502",NA,NA,"UNIPROT","github.com"
"1436","24903420","MED","24903420","10.1093/bioinformatics/btu379","Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures.","Phanstiel DH, Boyle AP, Araya CL, Snyder MP.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","N","0","Y","Y","N","N","N","330.15558","19","30","2808-2810","PMC4173017",NA,NA,"github.com"
"1437","24634654","MED","24634654","10.3389/fninf.2014.00015","Data management routines for reproducible research using the G-Node Python Client library.","Sobolev A, Stoewer A, Pereira M, Kellner CJ, Garbers C, Rautenberg PL, Wachtler T.","Front Neuroinform","2014","1662-5196","journal article; research-article","Y","Y","Y","2","Y","Y","N","N","N","330.15558",NA,"8","15","PMC3942789",NA,NA,"github.com"
"1438","25352981","MED","25352981",NA,"PAGAL - Properties and corresponding graphics of alpha helical structures in proteins.","Chakraborty S, Rao B, Dandekar A.","F1000Res","2014","2046-1402","journal article; research-article","Y","Y","N","0","Y","Y","N","N","Y","330.07413",NA,"3","206","PMC4207245","doi; pdb",NA,"github.com"
"1439","25056180","MED","25056180","10.1186/1756-0500-7-468","SnipViz: a compact and lightweight web site widget for display and dissemination of multiple versions of gene and protein sequences.","Jaschob D, Davis TN, Riffle M.","BMC Res Notes","2014","1756-0500","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","330.07413",NA,"7","468","PMC4118779",NA,NA,"github.com"
"1440","24855438","MED","24855438","10.3897/bdj.2.e1041","Morphological and geographical traits of the british odonata.","Powney GD, Brooks SJ, Barwell LJ, Bowles P, Fitt RN, Pavitt A, Spriggs RA, Isaac NJ.","Biodivers Data J","2014","1314-2828","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","330.07413","2",NA,"e1041","PMC4030211",NA,NA,"github.com"
"1441","25202639","MED","25202639","10.3732/apps.1400033","Easy Leaf Area: Automated digital image analysis for rapid and accurate measurement of leaf area.","Easlon HM, Bloom AJ.","Appl Plant Sci","2014","2168-0450","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","330.07413","7","2",NA,"PMC4103476",NA,NA,"github.com"
"1442","25079944","MED","25079944","10.1371/journal.pcbi.1003750","A real-time all-atom structural search engine for proteins.","Gonzalez G, Hannigan B, DeGrado WF.","PLoS Comput Biol","2014","1553-734x","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","Y","329.82446","7","10","e1003750","PMC4117414","pdb",NA,"github.com"
"1443","25324962","MED","25324962",NA,"mfSBA: Multifractal analysis of spatial patterns in ecological communities.","Saravia LA.","F1000Res","2014","2046-1402","journal article; research-article","Y","Y","N","0","Y","Y","N","N","Y","329.38907",NA,"3","14","PMC4197745","doi",NA,"github.com"
"1444","25452688","MED","25452688","10.4137/cin.s13979","Toolbox for mobile-element insertion detection on cancer genomes.","Lee WP, Wu J, Marth GT.","Cancer Inform","2014","1176-9351","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","329.38907","suppl 4","13","45-52","PMC4218655",NA,NA,"github.com"
"1445","25135245","MED","25135245","10.1016/j.jclinepi.2014.06.012","Open-source electronic data capture system offered increased accuracy and cost-effectiveness compared with paper methods in Africa.","Dillon DG, Pirie F, Rice S, Pomilla C, Sandhu MS, Motala AA, Young EH, African Partnership for Chronic Disease Research (APCDR).","J Clin Epidemiol","2014","0895-4356","journal article; research support, non-u.s. gov't; comparative study; brief-report","Y","Y","N","0","Y","Y","N","N","N","329.38907","12","67","1358-1363","PMC4271740",NA,NA,"github.com"
"1446","24627804","MED","24627804","10.12688/f1000research.3-51.v1","BioJS DAGViewer: A reusable JavaScript component forÂ displaying directed graphs.","Kalderimis A, Stepan R, Sullivan J, Lyne R, Lyne M, Micklem G.","F1000Res","2014","2046-1402","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","Y","329.38907",NA,"3","51","PMC3945768","doi",NA,"github.com"
"1447","24812344","MED","24812344","10.1093/bioinformatics/btu314","SAMBLASTER: fast duplicate marking and structural variant read extraction.","Faust GG, Hall IM.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","329.16116","17","30","2503-2505","PMC4147885",NA,NA,"github.com"
"1448","24478338","MED","24478338","10.1093/bioinformatics/btu053","PUmPER: phylogenies updated perpetually.","Izquierdo-Carrasco F, Cazes J, Smith SA, Stamatakis A.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","1","Y","Y","N","N","N","329.16116","10","30","1476-1477","PMC4016711",NA,NA,"github.com"
"1449","25165519","MED","25165519","10.1068/i004ir","Sharing code.","Kubilius J.","Iperception","2014","2041-6695","journal article; review; review-article","Y","Y","Y","0","N","Y","N","N","N","329.16116","1","5","75-78","PMC4130510",NA,NA,"github.com"
"1450","25075288","MED","25075288","10.12688/f1000research.3-50.v1","PPI layouts: BioJS components for the display ofÂ Protein-Protein Interactions.","Salazar GA, Meintjes A, Mulder N.","F1000Res","2014","2046-1402","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","Y","329.16116",NA,"3","50","PMC4103490","doi; sprot",NA,"github.com"
"1451","25285208","MED","25285208","10.12688/f1000research.4680.1","shinyMethyl: interactive quality control of Illumina 450k DNA methylation arrays in R.","Fortin JP, Fertig E, Hansen K.","F1000Res","2014","2046-1402","journal article; research-article","Y","Y","N","1","Y","Y","N","N","Y","329.16116",NA,"3","175","PMC4176427","doi",NA,"github.com"
"1452","24741440","MED","24741440","10.12688/f1000research.3-47.v2","FeatureViewer, a BioJS component for visualization ofÂ position-based annotations in protein sequences.","Garcia L, Yachdav G, Martin MJ.","F1000Res","2014","2046-1402","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","Y","329.16116",NA,"3","47","PMC3983936","doi; sprot; pdb",NA,"github.com"
"1453","25374784","MED","25374784","10.7717/peerj.642","Characterization of the transcriptome, nucleotide sequence polymorphism, and natural selection in the desert adapted mouse Peromyscus eremicus.","MacManes MD, Eisen MB.","PeerJ","2014","2167-8359","journal article; research-article","Y","Y","N","0","Y","Y","N","Y","Y","329.09134",NA,"2","e642","PMC4217191","doi; gen",NA,"github.com"
"1454","25254104","MED","25254104","10.12688/f1000research.4572.1","GeneMANIA: Fast gene network construction and function prediction for Cytoscape.","Montojo J, Zuberi K, Rodriguez H, Bader GD, Morris Q.","F1000Res","2014","2046-1402","journal article; research-article","Y","Y","N","1","Y","Y","N","N","Y","329.02078",NA,"3","153","PMC4168749","doi",NA,"github.com"
"1455","24930138","MED","24930138","10.1093/bioinformatics/btu390","The Scramble conversion tool.","Bonfield JK.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","329.02078","19","30","2818-2819","PMC4173023",NA,NA,"github.com"
"1456","24262214","MED","24262214","10.1093/bioinformatics/btt666","myChEMBL: a virtual machine implementation of open data and cheminformatics tools.","Ochoa R, Davies M, Papadatos G, Atkinson F, Overington JP.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","329.02078","2","30","298-300","PMC3892694",NA,NA,"github.com"
"1457","25189781","MED","25189781","10.1093/bioinformatics/btu552","subSeq: determining appropriate sequencing depth through efficient read subsampling.","Robinson DG, Storey JD.","Bioinformatics","2014","1367-4803","journal article; research support, n.i.h., extramural; research-article","Y","Y","N","0","Y","Y","N","N","N","329.02078","23","30","3424-3426","PMC4296149",NA,NA,"github.com"
"1458","25110584","MED","25110584","10.12688/f1000research.4521.1","BridgeDb app: unifying identifier mapping services for Cytoscape.","Gao J, Zhang C, van Iersel M, Zhang L, Xu D, Schultz N, R Pico A.","F1000Res","2014","2046-1402","journal article; research-article","Y","Y","Y","2","Y","Y","N","N","Y","329.02078",NA,"3","148","PMC4111116","doi",NA,"github.com"
"1459","24928211","MED","24928211","10.1093/bioinformatics/btu386","BioBlend.objects: metacomputing with Galaxy.","Leo S, Pireddu L, Cuccuru G, Lianas L, Soranzo N, Afgan E, Zanetti G.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","329.02078","19","30","2816-2817","PMC4173020",NA,NA,"github.com"
"1460","24812214","MED","24812214","10.1128/genomea.00331-14","Draft Genome Sequence of Stenotrophomonas maltophilia SeITE02, a Gammaproteobacterium Isolated from Selenite-Contaminated Mining Soil.","Bertolini C, van Aerle R, Lampis S, Moore KA, Paszkiewicz K, Butler CS, Vallini G, van der Giezen M.","Genome Announc","2014","2169-8287","journal article; brief-report","Y","Y","Y","0","Y","Y","N","N","N","328.63135","3","2",NA,"PMC4014682",NA,NA,"github.com"
"1461","24874669","MED","24874669","10.1128/genomea.00381-14","Draft Genome Sequence of Enterobacter cloacae Strain JD6301.","Wilson JG, French WT, Lipzen A, Martin J, Schackwitz W, Woyke T, Shapiro N, Bullard JW, Champlin FR, Donaldson JR.","Genome Announc","2014","2169-8287","journal article; brief-report","Y","Y","Y","0","Y","Y","N","N","N","328.63135","3","2",NA,"PMC4038874",NA,NA,"github.com"
"1462","24948758","MED","24948758","10.1128/genomea.00556-14","Whole-Genome Sequence of Burkholderia sp. Strain RPE67, a Bacterial Gut Symbiont of the Bean Bug Riptortus pedestris.","Takeshita K, Shibata TF, Nikoh N, Nishiyama T, Hasebe M, Fukatsu T, Shigenobu S, Kikuchi Y.","Genome Announc","2014","2169-8287","journal article; brief-report","Y","Y","Y","0","Y","Y","N","N","N","328.63135","3","2",NA,"PMC4064023",NA,NA,"github.com"
"1463","24961236","MED","24961236","10.1093/database/bau059","BioC implementations in Go, Perl, Python and Ruby.","Liu W, Islamaj DoÄan R, Kwon D, Marques H, Rinaldi F, Wilbur WJ, Comeau DC.","Database (Oxford)","2014","1758-0463","journal article; research support, n.i.h., intramural; research-article","Y","Y","Y","1","Y","Y","N","N","N","328.63135",NA,"2014",NA,"PMC4067548",NA,NA,"github.com"
"1464","25080132","MED","25080132","10.1186/1471-2105-15-s7-s12","Variant Tool Chest: an improved tool to analyze and manipulate variant call format (VCF) files.","Ebbert MT, Wadsworth ME, Boehme KL, Hoyt KL, Sharp AR, O'Fallon BD, Kauwe JS, Ridge PG.","BMC Bioinformatics","2014","1471-2105","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","328.63135","Suppl 7","15 Suppl 7","s12","PMC4110736",NA,NA,"github.com"
"1465","25237028","MED","25237028","10.1128/genomea.00935-14","Genome Sequence of Pectobacterium atrosepticum Strain 21A.","Nikolaichik Y, Gorshkov V, Gogolev Y, Valentovich L, Evtushenkov A.","Genome Announc","2014","2169-8287","journal article; brief-report","Y","Y","N","0","Y","Y","N","N","Y","328.63135","5","2",NA,"PMC4172277","gen",NA,"github.com"
"1466","25477405","MED","25477405","10.1128/genomea.01245-14","Complete Genome Sequence of Haemophilus influenzae Strain 375 from the Middle Ear of a Pediatric Patient with Otitis Media.","Mell JC, Sinha S, Balashov S, Viadas C, Grassa CJ, Ehrlich GD, Nislow C, Redfield RJ, Garmendia J.","Genome Announc","2014","2169-8287","journal article; brief-report","Y","Y","N","0","Y","Y","N","N","N","328.63135","6","2",NA,"PMC4256186",NA,NA,"github.com"
"1467","25143289","MED","25143289","10.1093/bioinformatics/btu553","Acceleration of short and long DNA read mapping without loss of accuracy using suffix array.","TÃ¡rraga J, Arnau V, MartÃnez H, Moreno R, Cazorla D, Salavert-Torres J, Blanquer-Espert I, Dopazo J, Medina I.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't","N","N","N","0","N","N","N","N","N","328.63135","23","30","3396-3398",NA,NA,NA,"github.com"
"1468","24723709","MED","24723709","10.1128/genomea.00247-14","Genome Sequence of Enterotoxigenic Escherichia coli Strain B2C.","Madhavan TP, Steen JA, Hugenholtz P, Sakellaris H.","Genome Announc","2014","2169-8287","journal article; brief-report","Y","Y","Y","3","Y","Y","Y","N","N","328.63135","2","2",NA,"PMC3983298",NA,"EMBLUNIPROT","github.com"
"1469","24692635","MED","24692635","10.1128/mbio.01012-14","Metatranscriptomics of the human oral microbiome during health and disease.","Jorth P, Turner KH, Gumus P, Nizam N, Buduneli N, Whiteley M.","MBio","2014","2150-7511","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","4","Y","Y","N","Y","Y","328.5557","2","5","e01012-14","PMC3977359","doi",NA,"github.com"
"1470","24790816","MED","24790816","10.1186/2193-1801-3-167","Development of an open source software module for enhanced visualization during MR-guided interstitial gynecologic brachytherapy.","Chen X, Egger J.","Springerplus","2014","2193-1801","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","328.4919",NA,"3","167","PMC4004789",NA,NA,"github.com"
"1471","24949246","MED","24949246","10.7717/peerj.431","dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms.","Puritz JB, Hollenbeck CM, Gold JR.","PeerJ","2014","2167-8359","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","328.4919",NA,"2","e431","PMC4060032",NA,NA,"github.com"
"1472","25289188","MED","25289188","10.7717/peerj.603","GroopM: an automated tool for the recovery of population genomes from related metagenomes.","Imelfort M, Parks D, Woodcroft BJ, Dennis P, Hugenholtz P, Tyson GW.","PeerJ","2014","2167-8359","journal article; research-article","Y","Y","N","2","Y","Y","N","N","N","328.4919",NA,"2","e603","PMC4183954",NA,NA,"github.com"
"1473","24795618","MED","24795618","10.3389/fninf.2014.00038","libNeuroML and PyLEMS: using Python to combine procedural and declarative modeling approaches in computational neuroscience.","Vella M, Cannon RC, Crook S, Davison AP, Ganapathy G, Robinson HP, Silver RA, Gleeson P.","Front Neuroinform","2014","1662-5196","journal article; research-article","Y","Y","Y","2","Y","Y","N","N","N","328.23013",NA,"8","38","PMC4005938",NA,NA,"github.com"
"1474","24708850","MED","24708850","10.1186/2049-2618-2-11","CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction.","Angly FE, Dennis PG, Skarshewski A, Vanwonterghem I, Hugenholtz P, Tyson GW.","Microbiome","2014","2049-2618","journal article; research-article","Y","Y","Y","3","Y","Y","N","N","N","328.10855",NA,"2","11","PMC4021573",NA,NA,"github.com"
"1475","24403392","MED","24403392","10.1167/14.1.6","Extrafoveal preview benefit during free-viewing visual search in the monkey.","Krishna BS, Ipata AE, Bisley JW, Gottlieb J, Goldberg ME.","J Vis","2014","1534-7362","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","0","Y","Y","N","N","N","327.99832","1","14",NA,"PMC3919102",NA,NA,"github.com"
"1476","25254103","MED","25254103",NA,"WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization.","Kutmon M, Lotia S, Evelo CT, Pico AR.","F1000Res","2014","2046-1402","journal article; research-article","Y","Y","N","1","Y","Y","N","N","Y","327.88596",NA,"3","152","PMC4168754","doi",NA,"github.com"
"1477","25177485","MED","25177485","10.12688/f1000research.4524.1","KEGGscape: a Cytoscape app for pathway data integration.","Nishida K, Ono K, Kanaya S, Takahashi K.","F1000Res","2014","2046-1402","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","Y","327.88596",NA,"3","144","PMC4141640","doi",NA,"github.com"
"1478","25285206","MED","25285206","10.12688/f1000research.4460.1","enhancedGraphics: a Cytoscape app for enhanced node graphics.","Morris JH, Kuchinsky A, Ferrin TE, Pico AR.","F1000Res","2014","2046-1402","journal article; research-article","Y","Y","N","0","Y","Y","N","N","Y","327.88596",NA,"3","147","PMC4176421","doi",NA,"github.com"
"1479","25352980","MED","25352980","10.12688/f1000research.4392.1","setsApp: Set operations for Cytoscape Nodes and Edges.","Morris JH, Wu A, Doncheva NT, Albrecht M, Ferrin TE.","F1000Res","2014","2046-1402","journal article; research-article","Y","Y","N","0","Y","Y","N","N","Y","327.88596",NA,"3","149","PMC4207244","doi",NA,"github.com"
"1480","25075306","MED","25075306","10.12688/f1000research.4536.1","Enrichment Map - a Cytoscape app to visualize and explore OMICs pathway enrichment results.","Isserlin R, Merico D, Voisin V, Bader GD.","F1000Res","2014","2046-1402","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","Y","327.88596",NA,"3","141","PMC4103489","doi",NA,"github.com"
"1481","24907369","MED","24907369","10.1093/bioinformatics/btu376","ABRA: improved coding indel detection via assembly-based realignment.","Mose LE, Wilkerson MD, Hayes DN, Perou CM, Parker JS.","Bioinformatics","2014","1367-4803","journal article; research support, n.i.h., extramural; research-article","Y","Y","N","0","Y","Y","N","N","N","327.88596","19","30","2813-2815","PMC4173014",NA,NA,"github.com"
"1482","24974206","MED","24974206","10.1093/bioinformatics/btu410","bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS).","Malaspinas AS, Tange O, Moreno-Mayar JV, Rasmussen M, DeGiorgio M, Wang Y, Valdiosera CE, Politis G, Willerslev E, Nielsen R.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","327.88596","20","30","2962-2964","PMC4184259",NA,NA,"github.com"
"1483","24876377","MED","24876377","10.1093/bioinformatics/btu363","PatternCNV: a versatile tool for detecting copy number changes from exome sequencing data.","Wang C, Evans JM, Bhagwate AV, Prodduturi N, Sarangi V, Middha M, Sicotte H, Vedell PT, Hart SN, Oliver GR, Kocher JP, Maurer MJ, Novak AJ, Slager SL, Cerhan JR, Asmann YW.","Bioinformatics","2014","1367-4803","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","327.88596","18","30","2678-2680","PMC4155258",NA,NA,"github.com"
"1484","25127889","MED","25127889","10.1186/1471-2105-15-279","SPARQLGraph: a web-based platform for graphically querying biological Semantic Web databases.","Schweiger D, Trajanoski Z, Pabinger S.","BMC Bioinformatics","2014","1471-2105","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","327.88596","1","15","279","PMC4148538",NA,NA,"github.com"
"1485","24609383","MED","24609383","10.1093/nar/gku181","Estimating telomere length from whole genome sequence data.","Ding Z, Mangino M, Aviv A, Spector T, Durbin R, UK10K Consortium.","Nucleic Acids Res","2014","0305-1048","journal article; twin study; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","327.88596","9","42","e75","PMC4027178",NA,NA,"github.com"
"1486","24297520","MED","24297520","10.1093/bioinformatics/btt702","NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries.","Leggett RM, Clavijo BJ, Clissold L, Clark MD, Caccamo M.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","5","Y","Y","N","Y","N","327.88596","4","30","566-568","PMC3928519",NA,NA,"github.com"
"1487","24618462","MED","24618462","10.1093/bioinformatics/btu130","The Bio-Community Perl toolkit for microbial ecology.","Angly FE, Fields CJ, Tyson GW.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","327.82892","13","30","1926-1927","PMC4071200",NA,NA,"github.com"
"1488","25024916","MED","25024916","10.7717/peerj.447","Mobile phones carry the personal microbiome of their owners.","Meadow JF, Altrichter AE, Green JL.","PeerJ","2014","2167-8359","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","Y","327.82892",NA,"2","e447","PMC4081285","doi",NA,"github.com"
"1489","25170024","MED","25170024","10.1093/bioinformatics/btu571","VSEAMS: a pipeline for variant set enrichment analysis using summary GWAS data identifies IKZF3, BATF and ESRRA as key transcription factors in type 1 diabetes.","Burren OS, Guo H, Wallace C.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","N","0","Y","Y","N","N","Y","327.82892","23","30","3342-3348","PMC4296156","ensembl",NA,"github.com"
"1490","25075307","MED","25075307","10.12688/f1000research.4546.1","Porting and using PanGIA for Cytoscape 3: challenges and solutions.","Welker D, Demchak B.","F1000Res","2014","2046-1402","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","327.7713",NA,"3","150","PMC4103495",NA,NA,"github.com"
"1491","25329171","MED","25329171","10.1371/journal.pone.0111090","COPASutils: an R package for reading, processing, and visualizing data from COPAS large-particle flow cytometers.","Shimko TC, Andersen EC.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","N","Y","N","N","N","327.7713","10","9","e111090","PMC4203834",NA,NA,"github.com"
"1492","25403086","MED","25403086","10.1186/1756-0500-7-806","DivA: detection of non-homologous and very divergent regions in protein sequence alignments.","Zepeda Mendoza ML, Nygaard S, da Fonseca RR.","BMC Res Notes","2014","1756-0500","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","327.7713","1","7","806","PMC4240845",NA,NA,"github.com"
"1493","25231498","MED","25231498","10.1093/database/bau095","WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions.","Karr JR, Phillips NC, Covert MW.","Database (Oxford)","2014","1758-0463","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","N","0","Y","Y","N","N","N","327.7713",NA,"2014",NA,"PMC4165886",NA,NA,"github.com"
"1494","25015648","MED","25015648","10.1093/molbev/msu211","selscan: an efficient multithreaded program to perform EHH-based scans for positive selection.","Szpiech ZA, Hernandez RD.","Mol Biol Evol","2014","0737-4038","letter; research support, non-u.s. gov't; research support, n.i.h., extramural","Y","Y","N","0","Y","Y","N","N","N","327.7713","10","31","2824-2827","PMC4166924",NA,NA,"github.com"
"1495","24688855","MED","24688855","10.7717/peerj.277","FragBuilder: an efficient Python library to setup quantum chemistry calculations on peptides models.","Christensen AS, Hamelryck T, Jensen JH.","PeerJ","2014","2167-8359","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","Y","327.7713",NA,"2","e277","PMC3961104","pdb",NA,"github.com"
"1496","24976859","MED","24976859","10.1186/1751-0473-9-12","Modular and configurable optimal sequence alignment software: Cola.","Zamani N, SundstrÃ¶m G, HÃ¶ppner MP, Grabherr MG.","Source Code Biol Med","2014","1751-0473","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","327.7713",NA,"9","12","PMC4064277",NA,NA,"github.com"
"1497","25521444","MED","25521444","10.1186/1471-2164-15-s9-s19","The bacterial proteogenomic pipeline.","Uszkoreit J, Plohnke N, Rexroth S, Marcus K, Eisenacher M.","BMC Genomics","2014","1471-2164","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","327.7713","Suppl 9","15 Suppl 9","s19","PMC4290607",NA,NA,"github.com"
"1498","25322818","MED","25322818","10.1186/1471-2105-15-332","Detection of internal exon deletion with exon Del.","Guo Y, Zhao S, Lehmann BD, Sheng Q, Shaver TM, Stricker TP, Pietenpol JA, Shyr Y.","BMC Bioinformatics","2014","1471-2105","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","N","0","Y","Y","N","N","N","327.7713","1","15","332","PMC4288651",NA,NA,"github.com"
"1499","25128435","MED","25128435","10.1534/g3.114.012468","Resolution of genetic map expansion caused by excess heterozygosity in plant recombinant inbred populations.","Truong SK, McCormick RF, Morishige DT, Mullet JE.","G3 (Bethesda)","2014","2160-1836","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","327.59476","10","4","1963-1969","PMC4199702",NA,NA,"github.com"
"1500","24913605","MED","24913605","10.1186/1471-2105-15-176","QMachine: commodity supercomputing in web browsers.","Wilkinson SR, Almeida JS.","BMC Bioinformatics","2014","1471-2105","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","327.59476",NA,"15","176","PMC4063228",NA,NA,"github.com"
"1501","25628562","MED","25628562","10.3389/fninf.2014.00089","BrainBrowser: distributed, web-based neurological data visualization.","Sherif T, Kassis N, Rousseau MÃ, Adalat R, Evans AC.","Front Neuroinform","2014","1662-5196","journal article; research-article","Y","Y","N","0","N","Y","N","N","N","327.59476",NA,"8","89","PMC4292582",NA,NA,"github.com"
"1502","25254639","MED","25254639","10.1371/journal.pcbi.1003842","IDEPI: rapid prediction of HIV-1 antibody epitopes and other phenotypic features from sequence data using a flexible machine learning platform.","Hepler NL, Scheffler K, Weaver S, Murrell B, Richman DD, Burton DR, Poignard P, Smith DM, Kosakovsky Pond SL.","PLoS Comput Biol","2014","1553-734x","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","N","0","Y","Y","N","N","Y","327.51947","9","10","e1003842","PMC4177671","gen",NA,"github.com"
"1503","25062443","MED","25062443","10.1371/journal.pone.0101271","These are not the k-mers you are looking for: efficient online k-mer counting using a probabilistic data structure.","Zhang Q, Pell J, Canino-Koning R, Howe AC, Brown CT.","PLoS One","2014","1932-6203","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","Y","327.12576","7","9","e101271","PMC4111482","doi",NA,"github.com"
"1504","25228379","MED","25228379","10.1186/1471-2164-15-795","Tangram: a comprehensive toolbox for mobile element insertion detection.","Wu J, Lee WP, Ward A, Walker JA, Konkel MK, Batzer MA, Marth GT.","BMC Genomics","2014","1471-2164","journal article; research support, n.i.h., extramural; research-article","Y","Y","N","1","Y","Y","N","N","N","327.12576","1","15","795","PMC4180832",NA,NA,"github.com"
"1505","25063299","MED","25063299","10.1093/nar/gku644","metaseq: a Python package for integrative genome-wide analysis reveals relationships between chromatin insulators and associated nuclear mRNA.","Dale RK, Matzat LH, Lei EP.","Nucleic Acids Res","2014","0305-1048","journal article; research support, n.i.h., intramural; research-article","Y","Y","N","0","Y","Y","Y","N","N","327.12576","14","42","9158-9170","PMC4132753",NA,"ARXPR","github.com"
"1506","24465499","MED","24465499","10.1371/journal.pone.0085177","Development of ultra-high-density screening tools for microbial ""omics"".","Bean GJ, Jaeger PA, Bahr S, Ideker T.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","327.07635","1","9","e85177","PMC3897414",NA,NA,"github.com"
"1507","24475057","MED","24475057","10.1371/journal.pone.0085879","HTSstation: a web application and open-access libraries for high-throughput sequencing data analysis.","David FP, Delafontaine J, Carat S, Ross FJ, Lefebvre G, Jarosz Y, Sinclair L, Noordermeer D, Rougemont J, Leleu M.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","N","N","Y","327.07635","1","9","e85879","PMC3903476","refseq",NA,"github.com"
"1508","24526831","MED","24526831","10.4137/ebo.s13121","RapidMic: Rapid Computation of the Maximal Information Coefficient.","Tang D, Wang M, Zheng W, Wang H.","Evol Bioinform Online","2014","1176-9343","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","327.07635",NA,"10","11-16","PMC3921152",NA,NA,"github.com"
"1509","24648555","MED","24648555","10.1128/jcm.00029-14","Deriving group A Streptococcus typing information from short-read whole-genome sequencing data.","Athey TB, Teatero S, Li A, Marchand-Austin A, Beall BW, Fittipaldi N.","J Clin Microbiol","2014","0095-1137","evaluation studies; journal article; research support, non-u.s. gov't; research-article","N","Y","N","1","Y","Y","N","N","N","327.07635","6","52","1871-1876","PMC4042799",NA,NA,"github.com"
"1510","24828207","MED","24828207","10.3390/ijms15058491","DEFLATE compression algorithm corrects for overestimation of phylogenetic diversity by Grantham approach to single-nucleotide polymorphism classification.","Schlosberg A, Lam BY, Yeo GS, Clifton-Bligh RJ.","Int J Mol Sci","2014","1422-0067","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","327.07635","5","15","8491-8508","PMC4057744",NA,NA,"github.com"
"1511","24885165","MED","24885165","10.1186/1471-2105-15-129","A web-based protein interaction network visualizer.","Salazar GA, Meintjes A, Mazandu GK, RapanoÃ«l HA, Akinola RO, Mulder NJ.","BMC Bioinformatics","2014","1471-2105","journal article; product-review","Y","Y","Y","0","Y","Y","N","N","Y","327.07635",NA,"15","129","PMC4029974","sprot",NA,"github.com"
"1512","25206364","MED","25206364","10.3389/fgene.2014.00293","A bioinformatics workflow for detecting signatures of selection in genomic data.","Cadzow M, Boocock J, Nguyen HT, Wilcox P, Merriman TR, Black MA.","Front Genet","2014","1664-8021","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","327.07635",NA,"5","293","PMC4144660",NA,NA,"github.com"
"1513","25309716","MED","25309716","10.1186/2041-1480-5-42","Executing SADI services in Galaxy.","Aranguren ME, GonzÃ¡lez AR, Wilkinson MD.","J Biomed Semantics","2014","2041-1480","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","327.07635","1","5","42","PMC4193140",NA,NA,"github.com"
"1514","25545863","MED","25545863","10.1371/journal.pone.0116103","Implementation of a phase detection algorithm for dynamic cardiac computed tomography analysis based on time dependent contrast agent distribution.","Kendziorra C, Meyer H, Dewey M.","PLoS One","2014","1932-6203","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","327.07635","12","9","e116103","PMC4278835",NA,NA,"github.com"
"1515","24688859","MED","24688859","10.7717/peerj.281","Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction.","Kamvar ZN, Tabima JF, GrÃ¼nwald NJ.","PeerJ","2014","2167-8359","journal article; research-article","Y","Y","Y","4","Y","Y","N","N","Y","327.07635",NA,"2","e281","PMC3961149","doi",NA,"github.com"
"1516","24629057","MED","24629057","10.1186/1471-2105-15-71","Transposon Insertion Finder (TIF): a novel program for detection of de novo transpositions of transposable elements.","Nakagome M, Solovieva E, Takahashi A, Yasue H, Hirochika H, Miyao A.","BMC Bioinformatics","2014","1471-2105","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","Y","Y","327.07635",NA,"15","71","PMC4004357","doi",NA,"github.com"
"1517","24151309","MED","24151309","10.1093/infdis/jit524","The global transmission network of HIV-1.","Wertheim JO, Leigh Brown AJ, Hepler NL, Mehta SR, Richman DD, Smith DM, Kosakovsky Pond SL.","J Infect Dis","2014","0022-1899","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","N","4","Y","Y","N","N","N","327.07635","2","209","304-313","PMC3873788",NA,NA,"github.com"
"1518","25161244","MED","25161244","10.1093/bioinformatics/btu461","Point estimates in phylogenetic reconstructions.","Benner P, BaÄÃ¡k M, Bourguignon PY.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","327.0265","17","30","i534-40","PMC4147914",NA,NA,"github.com"
"1519","24265224","MED","24265224","10.1093/nar/gkt1081","Updates to BioSamples database at European Bioinformatics Institute.","Faulconbridge A, Burdett T, Brandizi M, Gostev M, Pereira R, Vasant D, Sarkans U, Brazma A, Parkinson H.","Nucleic Acids Res","2014","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","Y","N","327.0265","database issue","42","d50-2","PMC3965081",NA,NA,"github.com"
"1520","25343723","MED","25343723","10.1371/journal.pone.0109356","An online database for informing ecological network models: http://kelpforest.ucsc.edu.","Beas-Luna R, Novak M, Carr MH, Tinker MT, Black A, Caselle JE, Hoban M, Malone D, Iles A.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","N","0","Y","Y","N","N","N","327.0265","10","9","e109356","PMC4208745",NA,NA,"github.com"
"1521","25330359","MED","25330359","10.1371/journal.pone.0110726","MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems.","Abby SS, NÃ©ron B, MÃ©nager H, Touchon M, Rocha EP.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","1","Y","Y","N","N","N","327.0265","10","9","e110726","PMC4201578",NA,NA,"github.com"
"1522","24659104","MED","24659104","10.1093/bioinformatics/btu144","GOssTo: a stand-alone application and a web tool for calculating semantic similarities on the Gene Ontology.","Caniza H, Romero AE, Heron S, Yang H, Devoto A, Frasca M, Mesiti M, Valentini G, Paccanaro A.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","327.0265","15","30","2235-2236","PMC4103586",NA,NA,"github.com"
"1523","24706808","MED","24706808","10.1073/pnas.1322678111","Global dissemination of a multidrug resistant Escherichia coli clone.","Petty NK, Ben Zakour NL, Stanton-Cook M, Skippington E, Totsika M, Forde BM, Phan MD, Gomes Moriel D, Peters KM, Davies M, Rogers BA, Dougan G, Rodriguez-BaÃ±o J, Pascual A, Pitout JD, Upton M, Paterson DL, Walsh TR, Schembri MA, Beatson SA.","Proc Natl Acad Sci U S A","2014","0027-8424","journal article; research support, non-u.s. gov't; research-article","N","Y","Y","2","Y","Y","N","N","N","327.0265","15","111","5694-5699","PMC3992628",NA,NA,"github.com"
"1524","24733943","MED","24733943","10.1073/pnas.1322420111","Stretched cell cycle model for proliferating lymphocytes.","Dowling MR, Kan A, Heinzel S, Zhou JH, Marchingo JM, Wellard CJ, Markham JF, Hodgkin PD.","Proc Natl Acad Sci U S A","2014","0027-8424","journal article; research support, non-u.s. gov't; research-article","N","Y","Y","0","Y","Y","N","N","N","327.0265","17","111","6377-6382","PMC4036001",NA,NA,"github.com"
"1525","24177719","MED","24177719","10.1093/bioinformatics/btt628","The functional therapeutic chemical classification system.","Croset S, Overington JP, Rebholz-Schuhmann D.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","327.0265","6","30","876-883","PMC3957075",NA,NA,"github.com"
"1526","25372389","MED","25372389","10.1371/journal.pone.0110289","SlideToolkit: an assistive toolset for the histological quantification of whole slide images.","Nelissen BG, van Herwaarden JA, Moll FL, van Diest PJ, Pasterkamp G.","PLoS One","2014","1932-6203","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","327.0265","11","9","e110289","PMC4220929",NA,NA,"github.com"
"1527","24395753","MED","24395753","10.1093/bioinformatics/btt756","CGAT: computational genomics analysis toolkit.","Sims D, Ilott NE, Sansom SN, Sudbery IM, Johnson JS, Fawcett KA, Berlanga-Taylor AJ, Luna-Valero S, Ponting CP, Heger A.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","N","Y","N","327.0265","9","30","1290-1291","PMC3998125",NA,NA,"github.com"
"1528","25390635","MED","25390635","10.1371/journal.pone.0106319","Ensemble-based network aggregation improves the accuracy of gene network reconstruction.","Zhong R, Allen JD, Xiao G, Xie Y.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","N","0","Y","Y","N","N","N","327.0265","11","9","e106319","PMC4229114",NA,NA,"github.com"
"1529","24860690","MED","24860690","10.1371/currents.outbreaks.84eefe5ce43ec9dc0bf0670f7b8b417d","Phylogenetic Analysis of Guinea 2014 EBOV Ebolavirus Outbreak.","Dudas G, Rambaut A.","PLoS Curr","2014","2157-3999","journal article; research-article","Y","Y","Y","2","Y","Y","N","N","N","327.0265",NA,"6",NA,"PMC4024086",NA,NA,"github.com"
"1530","25521965","MED","25521965","10.1186/1755-8794-7-s3-s3","Molecular profiling of thyroid cancer subtypes using large-scale text mining.","Wu C, Schwartz JM, Brabant G, Nenadic G.","BMC Med Genomics","2014","1755-8794","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","327.0265","Suppl 3","7 Suppl 3","s3","PMC4290788",NA,NA,"github.com"
"1531","25610492","MED","25610492","10.1186/s13007-014-0041-7","Mapping mutations in plant genomes with the user-friendly web application CandiSNP.","Etherington GJ, Monaghan J, Zipfel C, MacLean D.","Plant Methods","2014","1746-4811","journal article; research-article","Y","Y","N","0","Y","Y","N","N","Y","327.0265","1","10","41","PMC4301057","doi",NA,"github.com"
"1532","24603872","MED","24603872","10.1371/journal.pone.0090485","Comparison of illumina and 454 deep sequencing in participants failing raltegravir-based antiretroviral therapy.","Li JZ, Chapman B, Charlebois P, Hofmann O, Weiner B, Porter AJ, Samuel R, Vardhanabhuti S, Zheng L, Eron J, Taiwo B, Zody MC, Henn MR, Kuritzkes DR, Hide W, ACTG A5262 Study Team, Wilson CC, Berzins BI, Acosta EP, Bastow B, Kim PS, Read SW, Janik J, Meres DS, Lederman MM, Mong-Kryspin L, Shaw KE, Zimmerman LG, Leavitt R, De La Rosa G, Jennings A.","PLoS One","2014","1932-6203","clinical trial; journal article; research support, n.i.h., extramural; comparative study; research-article","Y","Y","Y","2","Y","Y","N","N","N","327.0265","3","9","e90485","PMC3946168",NA,NA,"github.com"
"1533","24860458","MED","24860458","10.3389/fnhum.2014.00195","Dynamic network participation of functional connectivity hubs assessed by resting-state fMRI.","Schaefer A, Margulies DS, Lohmann G, Gorgolewski KJ, Smallwood J, Kiebel SJ, Villringer A.","Front Hum Neurosci","2014","1662-5161","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","327.0265",NA,"8","195","PMC4018560",NA,NA,"github.com"
"1534","24451623","MED","24451623","10.1093/bioinformatics/btu033","RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.","Stamatakis A.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","51","Y","Y","N","Y","N","327.0265","9","30","1312-1313","PMC3998144",NA,NA,"github.com"
"1535","24413672","MED","24413672","10.1093/bioinformatics/btt765","The EBI RDF platform: linked open data for the life sciences.","Jupp S, Malone J, Bolleman J, Brandizi M, Davies M, Garcia L, Gaulton A, Gehant S, Laibe C, Redaschi N, Wimalaratne SM, Martin M, Le NovÃ¨re N, Parkinson H, Birney E, Jenkinson AM.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","7","Y","Y","N","N","N","327.0265","9","30","1338-1339","PMC3998127",NA,NA,"github.com"
"1536","25526884","MED","25526884",NA,"Linear-time computation of minimal absent words using suffix array.","Barton C, Heliou A, Mouchard L, Pissis SP.","BMC Bioinformatics","2014","1471-2105","journal article; research-article","Y","Y","N","0","N","Y","N","N","N","327.0265","1","15","388","PMC4297395",NA,NA,"github.com"
"1537","25520780","MED","25520780","10.12688/f1000research.5263.1","Using Twitter to investigate opinions about multiple sclerosis treatments: a descriptive, exploratory study.","Ramagopalan S, Wasiak R, Cox AP.","F1000Res","2014","2046-1402","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","326.75113",NA,"3","216","PMC4264640",NA,NA,"github.com"
"1538","25309732","MED","25309732","10.12688/f1000research.4431.1","ReactomeFIViz: the Reactome FI Cytoscape app for pathway and network-based data analysis.","Wu G, Dawson E, Duong A, Haw R, Stein L.","F1000Res","2014","2046-1402","journal article; research-article","Y","Y","N","0","Y","Y","N","N","Y","326.75113",NA,"3","146","PMC4184317","doi",NA,"github.com"
"1539","25324964","MED","25324964",NA,"GASOLINE: a Cytoscape app for multiple local alignment of PPI networks.","Micale G, Continella A, Ferro A, Giugno R, Pulvirenti A.","F1000Res","2014","2046-1402","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","326.75113",NA,"3","140","PMC4197741",NA,NA,"github.com"
"1540","25400907","MED","25400907","10.12688/f1000research.4573.1","Development and use of the Cytoscape app GFD-Net for measuring semantic dissimilarity of gene networks.","Diaz-Montana JJ, Diaz-Diaz N.","F1000Res","2014","2046-1402","journal article; research-article","Y","Y","N","0","Y","Y","N","N","Y","326.75113",NA,"3","142","PMC4224201","doi",NA,"github.com"
"1541","25309419","MED","25309419","10.3389/fninf.2014.00079","LEMS: a language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2.","Cannon RC, Gleeson P, Crook S, Ganapathy G, Marin B, Piasini E, Silver RA.","Front Neuroinform","2014","1662-5196","journal article; research-article","Y","Y","N","2","Y","Y","N","N","N","326.75113",NA,"8","79","PMC4174883",NA,NA,"github.com"
"1542","24271392","MED","24271392","10.1093/nar/gkt1190","Network portal: a database for storage, analysis and visualization of biological networks.","Turkarslan S, Wurtmann EJ, Wu WJ, Jiang N, Bare JC, Foley K, Reiss DJ, Novichkov P, Baliga NS.","Nucleic Acids Res","2014","0305-1048","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","0","Y","Y","N","N","N","326.75113","database issue","42","d184-90","PMC3964938",NA,NA,"github.com"
"1543","24626233","MED","24626233","10.1371/journal.pone.0091650","rAvis: an R-package for downloading information stored in Proyecto AVIS, a citizen science bird project.","Varela S, GonzÃ¡lez-HernÃ¡ndez J, Casabella E, Barrientos R.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","326.75113","3","9","e91650","PMC3953487",NA,NA,"github.com"
"1544","24586241","MED","24586241","10.1371/journal.pone.0085437","Accurate and robust prediction of genetic relationship from whole-genome sequences.","Li H, Glusman G, Huff C, Caballero J, Roach JC.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","1","Y","Y","N","N","N","326.75113","2","9","e85437","PMC3938395",NA,NA,"github.com"
"1545","24589879","MED","24589879","10.1038/srep04278","Efficient sample tracking with OpenLabFramework.","List M, Schmidt S, Trojnar J, Thomas J, Thomassen M, Kruse TA, Tan Q, Baumbach J, Mollenhauer J.","Sci Rep","2014","2045-2322","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","326.75113",NA,"4","4278","PMC3940979",NA,NA,"github.com"
"1546","25181461","MED","25181461","10.1371/journal.pone.0106035","esyN: network building, sharing and publishing.","Bean DM, Heimbach J, Ficorella L, Micklem G, Oliver SG, Favrin G.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","326.75113","9","9","e106035","PMC4152123",NA,NA,"github.com"
"1547","25177537","MED","25177537","10.7717/peerj.542","Women are underrepresented on the editorial boards of journals in environmental biology and natural resource management.","Cho AH, Johnson SA, Schuman CE, Adler JM, Gonzalez O, Graves SJ, Huebner JR, Marchant DB, Rifai SW, Skinner I, Bruna EM.","PeerJ","2014","2167-8359","journal article; research-article","Y","Y","Y","0","Y","Y","N","Y","Y","326.75113",NA,"2","e542","PMC4145067","doi",NA,"github.com"
"1548","25525323","MED","25525323","10.4137/ebo.s18193","SWAMP: Sliding Window Alignment Masker for PAML.","Harrison PW, Jordan GE, Montgomery SH.","Evol Bioinform Online","2014","1176-9343","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","326.75113",NA,"10","197-204","PMC4251194",NA,NA,"github.com"
"1549","25212860","MED","25212860","10.1093/gbe/evu202","First ancient mitochondrial human genome from a prepastoralist southern African.","Morris AG, Heinze A, Chan EK, Smith AB, Hayes VM.","Genome Biol Evol","2014","1759-6653","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","Y","N","Y","326.75113","10","6","2647-2653","PMC4224329","gen","EMBLUNIPROT","github.com"
"1550","24165880","MED","24165880","10.1093/nar/gkt961","EBI metagenomics--a new resource for the analysis and archiving of metagenomic data.","Hunter S, Corbett M, Denise H, Fraser M, Gonzalez-Beltran A, Hunter C, Jones P, Leinonen R, McAnulla C, Maguire E, Maslen J, Mitchell A, Nuka G, Oisel A, Pesseat S, Radhakrishnan R, Rocca-Serra P, Scheremetjew M, Sterk P, Vaughan D, Cochrane G, Field D, Sansone SA.","Nucleic Acids Res","2014","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","N","N","N","326.75113","database issue","42","d600-6","PMC3965009",NA,NA,"github.com"
"1551","25528455","MED","25528455",NA,"BitTorious: global controlled genomics data publication, research and archiving via BitTorrent extensions.","Lee PV, Dinu V.","BMC Bioinformatics","2014","1471-2105","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","326.75113","1","15","424","PMC4280033",NA,NA,"github.com"
"1552","24901003","MED","24901003","10.1155/2014/971857","O18Quant: a semiautomatic strategy for quantitative analysis of high-resolution 16O/18O labeled data.","Guo Y, Miyagi M, Zeng R, Sheng Q.","Biomed Res Int","2014","2314-6133","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","326.75113",NA,"2014","971857","PMC4037588",NA,NA,"github.com"
"1553","25642358","MED","25642358","10.1371/currents.outbreaks.89c0d3783f36958d96ebbae97348d571","Early epidemic dynamics of the west african 2014 ebola outbreak: estimates derived with a simple two-parameter model.","Fisman D, Khoo E, Tuite A.","PLoS Curr","2014","2157-3999","journal article; research-article","Y","Y","N","0","N","Y","N","N","N","326.75113",NA,"6",NA,"PMC4169344",NA,NA,"github.com"
"1554","25183856","MED","25183856","10.1093/database/bau087","Integrating information retrieval with distant supervision for gene ontology annotation.","Zhu D, Li D, Carterette B, Liu H.","Database (Oxford)","2014","1758-0463","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","326.75113",NA,"2014",NA,"PMC4150992",NA,NA,"github.com"
"1555","25075290","MED","25075290","10.12688/f1000research.3-55.v1","BioJS: an open source standard for biological visualisation - its status in 2014.","Corpas M, Jimenez R, Carbon SJ, GarcÃa A, Garcia L, Goldberg T, Gomez J, Kalderimis A, Lewis SE, Mulvany I, Pawlik A, Rowland F, Salazar G, Schreiber F, Sillitoe I, Spooner WH, Thanki AS, Villaveces JM, Yachdav G, Hermjakob H.","F1000Res","2014","2046-1402","journal article; discussion","Y","Y","Y","1","Y","Y","N","N","N","326.75113",NA,"3","55","PMC4103492",NA,NA,"github.com"
"1556","25329319","MED","25329319","10.1371/journal.pone.0109656","De novo transcriptome sequencing analysis and comparison of differentially expressed genes (DEGs) in Macrobrachium rosenbergii in China.","Nguyen Thanh H, Zhao L, Liu Q.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","326.69763","10","9","e109656","PMC4203760",NA,NA,"github.com"
"1557","24914678","MED","24914678","10.1371/journal.pone.0098679","ForceAtlas2, a continuous graph layout algorithm for handy network visualization designed for the Gephi software.","Jacomy M, Venturini T, Heymann S, Bastian M.","PLoS One","2014","1932-6203","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","326.69763","6","9","e98679","PMC4051631",NA,NA,"github.com"
"1558","24753423","MED","24753423","10.1093/nar/gku323","TEMP: a computational method for analyzing transposable element polymorphism in populations.","Zhuang J, Wang J, Theurkauf W, Weng Z.","Nucleic Acids Res","2014","0305-1048","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","2","Y","Y","N","Y","N","326.69763","11","42","6826-6838","PMC4066757",NA,NA,"github.com"
"1559","24808906","MED","24808906","10.3389/fgene.2014.00098","categoryCompare, an analytical tool based on feature annotations.","Flight RM, Harrison BJ, Mohammad F, Bunge MB, Moon LD, Petruska JC, Rouchka EC.","Front Genet","2014","1664-8021","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","326.69763",NA,"5","98","PMC4010757",NA,NA,"github.com"
"1560","24824880","MED","24824880","10.1371/journal.pone.0097176","A correspondence between individual differences in the brain's intrinsic functional architecture and the content and form of self-generated thoughts.","Gorgolewski KJ, Lurie D, Urchs S, Kipping JA, Craddock RC, Milham MP, Margulies DS, Smallwood J.","PLoS One","2014","1932-6203","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","326.69763","5","9","e97176","PMC4019564",NA,NA,"github.com"
"1561","25048512","MED","25048512","10.1371/journal.pone.0102541","A kernel-based multivariate feature selection method for microarray data classification.","Sun S, Peng Q, Shakoor A.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","326.38144","7","9","e102541","PMC4105478",NA,NA,"github.com"
"1562","25252881","MED","25252881","10.1186/1471-2105-15-s9-s12","ARYANA: Aligning Reads by Yet Another Approach.","Gholami M, Arbabi A, Sharifi-Zarchi A, Chitsaz H, Sadeghi M.","BMC Bioinformatics","2014","1471-2105","journal article; research support, u.s. gov't, non-p.h.s.; abstract","Y","Y","N","0","Y","Y","N","N","N","326.38144","Suppl 9","15 Suppl 9","s12","PMC4168712",NA,NA,"github.com"
"1563","25407910","MED","25407910","10.1186/s12859-014-0357-3","NeatFreq: reference-free data reduction and coverage normalization for De Novo sequence assembly.","McCorrison JM, Venepally P, Singh I, Fouts DE, Lasken RS, MethÃ© BA.","BMC Bioinformatics","2014","1471-2105","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","326.38144","1","15","357","PMC4245761",NA,NA,"github.com"
"1564","25281234","MED","25281234","10.1093/database/bau098","CanvasDB: a local database infrastructure for analysis of targeted- and whole genome re-sequencing projects.","Ameur A, Bunikis I, Enroth S, Gyllensten U.","Database (Oxford)","2014","1758-0463","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","Y","326.38144",NA,"2014",NA,"PMC4184106","refsnp",NA,"github.com"
"1565","24502833","MED","24502833","10.1186/1471-2105-15-44","The HTS barcode checker pipeline, a tool for automated detection of illegally traded species from high-throughput sequencing data.","Lammers Y, Peelen T, Vos RA, Gravendeel B.","BMC Bioinformatics","2014","1471-2105","journal article; product-review","Y","Y","Y","0","Y","Y","N","N","N","326.38144",NA,"15","44","PMC3922334",NA,NA,"github.com"
"1566","24653694","MED","24653694","10.3389/fninf.2014.00022","SCoT: a Python toolbox for EEG source connectivity.","Billinger M, Brunner C, MÃ¼ller-Putz GR.","Front Neuroinform","2014","1662-5196","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","326.38144",NA,"8","22","PMC3949292",NA,NA,"github.com"
"1567","24715856","MED","24715856","10.3389/fncir.2014.00028","Simultaneous optogenetic manipulation and calcium imaging in freely moving C. elegans.","Shipley FB, Clark CM, Alkema MJ, Leifer AM.","Front Neural Circuits","2014","1662-5110","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","1","Y","Y","N","N","N","326.38144",NA,"8","28","PMC3970007",NA,NA,"github.com"
"1568","24795616","MED","24795616","10.3389/fninf.2014.00032","Integrated platform and API for electrophysiological data.","Sobolev A, Stoewer A, Leonhardt A, Rautenberg PL, Kellner CJ, Garbers C, Wachtler T.","Front Neuroinform","2014","1662-5196","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","326.38144",NA,"8","32","PMC4005939",NA,NA,"github.com"
"1569","24847245","MED","24847245","10.3389/fninf.2014.00046","Reproducibility of graph metrics of human brain structural networks.","Duda JT, Cook PA, Gee JC.","Front Neuroinform","2014","1662-5196","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","326.38144",NA,"8","46","PMC4019854",NA,NA,"github.com"
"1570","24904399","MED","24904399","10.3389/fninf.2014.00053","Web based tools for visualizing imaging data and development of XNATView, a zero footprint image viewer.","Gutman DA, Dunn WD Jr, Cobb J, Stoner RM, Kalpathy-Cramer J, Erickson B.","Front Neuroinform","2014","1662-5196","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","326.38144",NA,"8","53","PMC4034701",NA,NA,"github.com"
"1571","24925680","MED","24925680","10.1186/1471-2105-15-182","Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads.","Jiang H, Lei R, Ding SW, Zhu S.","BMC Bioinformatics","2014","1471-2105","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","326.38144",NA,"15","182","PMC4074385",NA,NA,"github.com"
"1572","24976580","MED","24976580","10.1186/1471-2105-15-227","A universal genomic coordinate translator for comparative genomics.","Zamani N, SundstrÃ¶m G, Meadows JR, HÃ¶ppner MP, Dainat J, Lantz H, Haas BJ, Grabherr MG.","BMC Bioinformatics","2014","1471-2105","journal article; research support, non-u.s. gov't; product-review","Y","Y","Y","0","Y","Y","N","Y","N","326.38144",NA,"15","227","PMC4086997",NA,NA,"github.com"
"1573","25024921","MED","25024921","10.7717/peerj.453","scikit-image: image processing in Python.","van der Walt S, SchÃ¶nberger JL, Nunez-Iglesias J, Boulogne F, Warner JD, Yager N, Gouillart E, Yu T, scikit-image contributors.","PeerJ","2014","2167-8359","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","326.38144",NA,"2","e453","PMC4081273",NA,NA,"github.com"
"1574","25071988","MED","25071988","10.7717/peerj.462","Automated analysis of invadopodia dynamics in live cells.","Berginski ME, Creed SJ, Cochran S, Roadcap DW, Bear JE, Gomez SM.","PeerJ","2014","2167-8359","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","326.38144",NA,"2","e462","PMC4103095",NA,NA,"github.com"
"1575","25077016","MED","25077016","10.1002/ece3.1107","An Illumina metabarcoding pipeline for fungi.","BÃ¡lint M, Schmidt PA, Sharma R, Thines M, Schmitt I.","Ecol Evol","2014","2045-7758","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","Y","326.38144","13","4","2642-2653","PMC4113289","doi",NA,"github.com"
"1576","24647222","MED","24647222","10.1371/journal.pone.0089204","openSNP--a crowdsourced web resource for personal genomics.","Greshake B, Bayer PE, Rausch H, Reda J.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","326.38144","3","9","e89204","PMC3960092",NA,NA,"github.com"
"1577","24755918","MED","24755918","10.1371/journal.pone.0095567","Systematic design of 18S rRNA gene primers for determining eukaryotic diversity in microbial consortia.","Hugerth LW, Muller EE, Hu YO, Lebrun LA, Roume H, Lundin D, Wilmes P, Andersson AF.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","N","Y","N","N","Y","326.38144","4","9","e95567","PMC3995771","gen",NA,"github.com"
"1578","25558360","MED","25558360","10.1002/ece3.1273","MODISTools - downloading and processing MODIS remotely sensed data in R.","Tuck SL, Phillips HR, Hintzen RE, Scharlemann JP, Purvis A, Hudson LN.","Ecol Evol","2014","2045-7758","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","326.38144","24","4","4658-4668","PMC4278818",NA,NA,"github.com"
"1579","24667828","MED","24667828","10.1371/journal.pone.0092108","Open source software to control Bioflo bioreactors.","Burdge DA, Libourel IG.","PLoS One","2014","1932-6203","journal article; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","0","Y","Y","N","N","N","326.38144","3","9","e92108","PMC3965399",NA,NA,"github.com"
"1580","24931998","MED","24931998","10.1093/bioinformatics/btu280","Ragout-a reference-assisted assembly tool for bacterial genomes.","Kolmogorov M, Raney B, Paten B, Pham S.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","1","Y","Y","N","N","N","326.38144","12","30","i302-9","PMC4058940",NA,NA,"github.com"
"1581","25485095","MED","25485095","10.12688/f1000research.4831.1","FALCON: a software package for analysis of nestedness in bipartite networks.","Beckett SJ, Boulton CA, Williams HT.","F1000Res","2014","2046-1402","journal article; research-article","Y","Y","N","0","Y","Y","N","N","Y","326.38144",NA,"3","185","PMC4244763","doi",NA,"github.com"
"1582","24443382","MED","24443382","10.1093/bioinformatics/btu023","Exploring genome characteristics and sequence quality without a reference.","Simpson JT.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","N","N","N","326.38144","9","30","1228-1235","PMC3998141",NA,NA,"github.com"
"1583","24936976","MED","24936976","10.1371/journal.pone.0099979","Standardized metadata for human pathogen/vector genomic sequences.","Dugan VG, Emrich SJ, Giraldo-CalderÃ³n GI, Harb OS, Newman RM, Pickett BE, Schriml LM, Stockwell TB, Stoeckert CJ Jr, Sullivan DE, Singh I, Ward DV, Yao A, Zheng J, Barrett T, Birren B, Brinkac L, Bruno VM, Caler E, Chapman S, Collins FH, Cuomo CA, Di Francesco V, Durkin S, Eppinger M, Feldgarden M, Fraser C, Fricke WF, Giovanni M, Henn MR, Hine E, Hotopp JD, Karsch-Mizrachi I, Kissinger JC, Lee EM, Mathur P, Mongodin EF, Murphy CI, Myers G, Neafsey DE, Nelson KE, Nierman WC, Puzak J, Rasko D, Roos DS, Sadzewicz L, Silva JC, Sobral B, Squires RB, Stevens RL, Tallon L, Tettelin H, Wentworth D, White O, Will R, Wortman J, Zhang Y, Scheuermann RH.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research support, n.i.h., intramural; research support, u.s. gov't, p.h.s.; research-article","Y","Y","Y","3","Y","Y","N","N","N","326.38144","6","9","e99979","PMC4061050",NA,NA,"github.com"
"1584","25174814","MED","25174814","10.1038/srep06240","Effective connectivity during animacy perception--dynamic causal modelling of Human Connectome Project data.","Hillebrandt H, Friston KJ, Blakemore SJ.","Sci Rep","2014","2045-2322","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","326.38144",NA,"4","6240","PMC4150124",NA,NA,"github.com"
"1585","24928874","MED","24928874","10.1128/aem.01403-14","DegePrime, a program for degenerate primer design for broad-taxonomic-range PCR in microbial ecology studies.","Hugerth LW, Wefer HA, Lundin S, Jakobsson HE, Lindberg M, Rodin S, Engstrand L, Andersson AF.","Appl Environ Microbiol","2014","0099-2240","journal article; research support, non-u.s. gov't; research-article","N","Y","N","0","N","Y","N","N","N","326.38144","16","80","5116-5123","PMC4135748",NA,NA,"github.com"
"1586","24845653","MED","24845653","10.1093/bioinformatics/btu340","Exploration and retrieval of whole-metagenome sequencing samples.","Seth S, VÃ¤limÃ¤ki N, Kaski S, Honkela A.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","326.22403","17","30","2471-2479","PMC4230234",NA,NA,"github.com"
"1587","24271393","MED","24271393","10.1093/nar/gkt1164","ExoLocator--an online view into genetic makeup of vertebrate proteins.","Khoo AA, Ogrizek-Tomas M, Bulovic A, Korpar M, GÃ¼rler E, Slijepcevic I, Å ikic M, Mihalek I.","Nucleic Acids Res","2014","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","326.22403","database issue","42","d879-81","PMC3965120",NA,NA,"github.com"
"1588","25506197","MED","25506197","10.4137/cin.s19519","FocalCall: An R Package for the Annotation of Focal Copy Number Aberrations.","Krijgsman O, Benner C, Meijer GA, van de Wiel MA, Ylstra B.","Cancer Inform","2014","1176-9351","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","326.22403",NA,"13","153-156","PMC4251178",NA,NA,"github.com"
"1589","24929426","MED","24929426","10.1186/1756-0500-7-365","FastaValidator: an open-source Java library to parse and validate FASTA formatted sequences.","Waldmann J, Gerken J, Hankeln W, Schweer T, GlÃ¶ckner FO.","BMC Res Notes","2014","1756-0500","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","326.22403",NA,"7","365","PMC4094456",NA,NA,"github.com"
"1590","25404939","MED","25404939","10.3389/fgene.2014.00378","Replicon: a software to accurately predict DNA replication timing in metazoan cells.","Gindin Y, Meltzer PS, Bilke S.","Front Genet","2014","1664-8021","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","326.22403",NA,"5","378","PMC4217517",NA,NA,"github.com"
"1591","25229481","MED","25229481","10.1371/journal.pone.0107468","pRRophetic: an R package for prediction of clinical chemotherapeutic response from tumor gene expression levels.","Geeleher P, Cox N, Huang RS.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","N","0","Y","Y","N","N","N","326.22403","9","9","e107468","PMC4167990",NA,NA,"github.com"
"1592","25135957","MED","25135957","10.1101/gr.177774.114","The landscape of human STR variation.","Willems T, Gymrek M, Highnam G, 1000 Genomes Project Consortium, Mittelman D, Erlich Y.","Genome Res","2014","1088-9051","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","N","Y","N","0","Y","Y","N","N","N","326.22403","11","24","1894-1904","PMC4216929",NA,NA,"github.com"
"1593","24382166","MED","24382166","10.1186/1471-2164-15-2","Structure and expression of GSL1 and GSL2 genes encoding gibberellin stimulated-like proteins in diploid and highly heterozygous tetraploid potato reveals their highly conserved and essential status.","Meiyalaghan S, Thomson SJ, Fiers MW, Barrell PJ, Latimer JM, Mohan S, Jones EE, Conner AJ, Jacobs JM.","BMC Genomics","2014","1471-2164","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","Y","326.22403",NA,"15","2","PMC3890649","gen; pfam",NA,"github.com"
"1594","25402475","MED","25402475","10.1371/journal.pone.0110263","Exome-wide somatic microsatellite variation is altered in cells with DNA repair deficiencies.","Vaksman Z, Fonville NC, Tae H, Garner HR.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","N","0","Y","Y","N","N","N","326.22403","11","9","e110263","PMC4234249",NA,NA,"github.com"
"1595","25405470","MED","25405470","10.1371/journal.pone.0111516","RADIA: RNA and DNA integrated analysis for somatic mutation detection.","Radenbaugh AJ, Ma S, Ewing A, Stuart JM, Collisson EA, Zhu J, Haussler D.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","N","0","Y","Y","N","N","N","326.22403","11","9","e111516","PMC4236012",NA,NA,"github.com"
"1596","24817849","MED","24817849","10.3389/fninf.2014.00044","The Insight ToolKit image registration framework.","Avants BB, Tustison NJ, Stauffer M, Song G, Wu B, Gee JC.","Front Neuroinform","2014","1662-5196","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","326.22403",NA,"8","44","PMC4009425",NA,NA,"github.com"
"1597","24987574","MED","24987574","10.1371/currents.outbreaks.c0e035c86d721668a6ad7353f7f6fe86","Clock Rooting Further Demonstrates that Guinea 2014 EBOV is a Member of the ZaÃ¯re Lineage.","Calvignac-Spencer S, Schulze JM, Zickmann F, Renard BY.","PLoS Curr","2014","2157-3999","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","326.22403",NA,"6",NA,"PMC4073806",NA,NA,"github.com"
"1598","25093067","MED","25093067","10.1186/2041-1480-5-26","Generalising semantic category disambiguation with large lexical resources for fun and profit.","Stenetorp P, Pyysalo S, Ananiadou S, Tsujii J.","J Biomed Semantics","2014","2041-1480","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","326.22403",NA,"5","26","PMC4107982",NA,NA,"github.com"
"1599","25210596","MED","25210596","10.1016/j.csbj.2014.05.004","Simple Ligand-Receptor Interaction Descriptor (SILIRID) for alignment-free binding site comparison.","Chupakhin V, Marcou G, Gaspar H, Varnek A.","Comput Struct Biotechnol J","2014","2001-0370","journal article; research-article","Y","Y","N","0","Y","Y","N","N","Y","326.22403","16","10","33-37","PMC4151984","pdb",NA,"github.com"
"1600","25172923","MED","25172923","10.1093/bioinformatics/btu579","The Naked Mole Rat Genome Resource: facilitating analyses of cancer and longevity-related adaptations.","Keane M, Craig T, AlfÃ¶ldi J, Berlin AM, Johnson J, Seluanov A, Gorbunova V, Di Palma F, Lindblad-Toh K, Church GM, de MagalhÃ£es JP.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","N","1","Y","Y","N","N","N","326.22403","24","30","3558-3560","PMC4253829",NA,NA,"github.com"
"1601","24586045","MED","24586045","10.1093/molbev/msu082","Efficient inference of recombination hot regions in bacterial genomes.","Yahara K, Didelot X, Ansari MA, Sheppard SK, Falush D.","Mol Biol Evol","2014","0737-4038","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","3","Y","Y","N","Y","N","326.22403","6","31","1593-1605","PMC4032127",NA,NA,"github.com"
"1602","25410596","MED","25410596","10.1186/preaccept-2573980311437212","The Harvest suite for rapid core-genome  alignment and visualization of thousands of  intraspecific microbial genomes.","Treangen TJ, Ondov BD, Koren S, Phillippy AM.","Genome Biol","2014","1465-6906","journal article; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","N","1","Y","Y","N","N","Y","326.22403","11","15","524","PMC4262987","refseq",NA,"github.com"
"1603","24637747","MED","24637747","10.1107/s2053230x13034262","Structure determination of BA0150, a putative polysaccharide deacetylase from Bacillus anthracis.","Strunk RJ, Piemonte KM, Petersen NM, Koutsioulis D, Bouriotis V, Perry K, Cole KE.","Acta Crystallogr F Struct Biol Commun","2014","2053-230x","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","N","0","Y","Y","Y","N","Y","326.22403","pt 2","70","156-159","PMC3936449","pdb","PDBUNIPROT","github.com"
"1604","25288879","MED","25288879","10.4137/cin.s13783","Integrated analysis of whole-genome paired-end and mate-pair sequencing data for identifying genomic structural variations in multiple myeloma.","Yang R, Chen L, Newman S, Gandhi K, Doho G, Moreno CS, Vertino PM, Bernal-Mizarchi L, Lonial S, Boise LH, Rossi M, Kowalski J, Qin ZS.","Cancer Inform","2014","1176-9351","journal article; review; review-article","Y","Y","N","0","Y","Y","N","N","N","326.22403","suppl 2","13","49-53","PMC4179644",NA,NA,"github.com"
"1605","25273068","MED","25273068","10.1101/gr.174920.114","Alignathon: a competitive assessment of whole-genome alignment methods.","Earl D, Nguyen N, Hickey G, Harris RS, Fitzgerald S, Beal K, Seledtsov I, Molodtsov V, Raney BJ, Clawson H, Kim J, Kemena C, Chang JM, Erb I, Poliakov A, Hou M, Herrero J, Kent WJ, Solovyev V, Darling AE, Ma J, Notredame C, Brudno M, Dubchak I, Haussler D, Paten B.","Genome Res","2014","1088-9051","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","N","0","Y","Y","N","N","N","326.22403","12","24","2077-2089","PMC4248324",NA,NA,"github.com"
"1606","25202630","MED","25202630","10.3732/apps.1400015","Development of phylogenetic markers for Sebacina (Sebacinaceae) mycorrhizal fungi associated with Australian orchids.","Ruibal MP, Peakall R, Foret S, Linde CC.","Appl Plant Sci","2014","2168-0450","journal article; research-article","Y","Y","Y","0","Y","Y","Y","N","N","326.22403","6","2",NA,"PMC4103437",NA,"EMBL","github.com"
"1607","25364504","MED","25364504","10.5334/jors.at","Fourteen Years of R/qtl: Just Barely Sustainable.","Broman KW.","J Open Res Softw","2014","2049-9647","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","326.22403","1","2",NA,"PMC4212690",NA,NA,"github.com"
"1608","24297534","MED","24297534",NA,"Systematic assessment of analytical methods for drug sensitivity prediction from cancer cell line data.","Jang IS, Neto EC, Guinney J, Friend SH, Margolin AA.","Pac Symp Biocomput","2014","2335-6936","journal article; research support, n.i.h., extramural; research-article","N","Y","N","2","Y","Y","N","N","N","326.18372",NA,NA,"63-74","PMC3995541",NA,NA,"github.com"
"1609","25503996","MED","25503996","10.1371/journal.pone.0113119","Calculation and visualization of atomistic mechanical stresses in nanomaterials and biomolecules.","Fenley AT, Muddana HS, Gilson MK.","PLoS One","2014","1932-6203","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","326.18372","12","9","e113119","PMC4263534",NA,NA,"github.com"
"1610","25000497","MED","25000497","10.1371/journal.pone.0101357","DyCoNet: a Gephi plugin for community detection in dynamic complex networks.","Kauffman J, Kittas A, Bennett L, Tsoka S.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","326.18372","7","9","e101357","PMC4084810",NA,NA,"github.com"
"1611","25056481","MED","25056481","10.1186/1471-2164-15-s4-s10","Reference-free SNP detection: dealing with the data deluge.","Leggett RM, MacLean D.","BMC Genomics","2014","1471-2164","journal article; review-article","Y","Y","Y","0","Y","Y","N","N","N","326.18372","Suppl 4","15 Suppl 4","s10","PMC4083407",NA,NA,"github.com"
"1612","24982883","MED","24982883","10.1155/2014/493825","Comprehensive transcriptome study to develop molecular resources of the copepod Calanus sinicus for their potential ecological applications.","Yang Q, Sun F, Yang Z, Li H.","Biomed Res Int","2014","2314-6133","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","326.18372",NA,"2014","493825","PMC4055022",NA,NA,"github.com"
"1613","24499370","MED","24499370","10.1186/1471-2105-15-43","Mining locus tags in PubMed Central to improve microbial gene annotation.","Stubben CJ, Challacombe JF.","BMC Bioinformatics","2014","1471-2105","journal article; research support, non-u.s. gov't; product-review","Y","Y","Y","0","Y","Y","N","N","N","326.18372",NA,"15","43","PMC3937057",NA,NA,"github.com"
"1614","24555450","MED","24555450","10.1186/1759-8753-5-6","Whole genome sequencing in Drosophila virilis identifies Polyphemus, a recently activated Tc1-like transposon with a possible role in hybrid dysgenesis.","Blumenstiel JP.","Mob DNA","2014","1759-8753","journal article; research-article","Y","Y","Y","0","Y","Y","N","Y","N","326.18372","1","5","6","PMC3941972",NA,NA,"github.com"
"1615","24685258","MED","24685258","10.1186/1471-2105-15-93","SPiCE: a web-based tool for sequence-based protein classification and exploration.","van den Berg BA, Reinders MJ, Roubos JA, de Ridder D.","BMC Bioinformatics","2014","1471-2105","journal article; research support, non-u.s. gov't; product-review","Y","Y","Y","0","Y","Y","N","N","N","326.18372",NA,"15","93","PMC4021553",NA,NA,"github.com"
"1616","24855446","MED","24855446","10.3897/bdj.2.e1059","Open source data logger for low-cost environmental monitoring.","Baker E.","Biodivers Data J","2014","1314-2828","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","326.18372","2",NA,"e1059","PMC4030251",NA,NA,"github.com"
"1617","24904398","MED","24904398","10.3389/fninf.2014.00052","A simple tool for neuroimaging data sharing.","Haselgrove C, Poline JB, Kennedy DN.","Front Neuroinform","2014","1662-5196","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","326.18372",NA,"8","52","PMC4033259",NA,NA,"github.com"
"1618","25202605","MED","25202605","10.3732/apps.1300085","A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae.","Mandel JR, Dikow RB, Funk VA, Masalia RR, Staton SE, Kozik A, Michelmore RW, Rieseberg LH, Burke JM.","Appl Plant Sci","2014","2168-0450","journal article; research-article","Y","Y","Y","0","Y","Y","N","Y","Y","326.18372","2","2",NA,"PMC4103609","doi",NA,"github.com"
"1619","25202470","MED","25202470","10.1155/2014/379010","Detection of rift valley Fever virus interepidemic activity in some hotspot areas of kenya by sentinel animal surveillance, 2009-2012.","Lichoti JK, Kihara A, Oriko AA, Okutoyi LA, Wauna JO, Tchouassi DP, Tigoi CC, Kemp S, Sang R, Mbabu RM.","Vet Med Int","2014","2090-8113","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","326.18372",NA,"2014","379010","PMC4147350",NA,NA,"github.com"
"1620","25276334","MED","25276334","10.1186/2041-1480-5-39","The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology.","Thacker RW, DÃaz MC, Kerner A, Vignes-Lebbe R, Segerdell E, Haendel MA, Mungall CJ.","J Biomed Semantics","2014","2041-1480","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","326.18372","1","5","39","PMC4177528",NA,NA,"github.com"
"1621","25276506","MED","25276506","10.7717/peerj.593","Swarm: robust and fast clustering method for amplicon-based studies.","MahÃ© F, Rognes T, Quince C, de Vargas C, Dunthorn M.","PeerJ","2014","2167-8359","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","326.18372",NA,"2","e593","PMC4178461",NA,NA,"github.com"
"1622","25332844","MED","25332844","10.7717/peerj.561","Removing batch effects for prediction problems with frozen surrogate variable analysis.","Parker HS, Corrada Bravo H, Leek JT.","PeerJ","2014","2167-8359","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","326.18372",NA,"2","e561","PMC4179553",NA,NA,"github.com"
"1623","25494900","MED","25494900",NA,"COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project.","Bergmann FT, Adams R, Moodie S, Cooper J, Glont M, Golebiewski M, Hucka M, Laibe C, Miller AK, Nickerson DP, Olivier BG, Rodriguez N, Sauro HM, Scharm M, Soiland-Reyes S, Waltemath D, Yvon F, Le NovÃ¨re N.","BMC Bioinformatics","2014","1471-2105","journal article; research-article","Y","Y","N","0","Y","Y","N","N","Y","326.18372","1","15","369","PMC4272562","doi",NA,"github.com"
"1624","25354213","MED","25354213","10.1089/jmf.2014.0061","TRAMP prostate tumor growth is slowed by walnut diets through altered IGF-1 levels, energy pathways, and cholesterol metabolism.","Kim H, Yokoyama W, Davis PA.","J Med Food","2014","1096-620x","journal article; research support, non-u.s. gov't; research-article","N","Y","N","0","Y","Y","N","N","N","326.18372","12","17","1281-1286","PMC4259176",NA,NA,"github.com"
"1625","25149694","MED","25149694","10.1162/neco_a_00661","High-dimensional cluster analysis with the masked EM algorithm.","Kadir SN, Goodman DF, Harris KD.","Neural Comput","2014","0899-7667","journal article; research-article","N","Y","N","0","Y","Y","N","N","N","326.18372","11","26","2379-2394","PMC4298163",NA,NA,"github.com"
"1626","24194600","MED","24194600","10.1093/nar/gkt977","The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data.","Koscielny G, Yaikhom G, Iyer V, Meehan TF, Morgan H, Atienza-Herrero J, Blake A, Chen CK, Easty R, Di Fenza A, Fiegel T, Grifiths M, Horne A, Karp NA, Kurbatova N, Mason JC, Matthews P, Oakley DJ, Qazi A, Regnart J, Retha A, Santos LA, Sneddon DJ, Warren J, Westerberg H, Wilson RJ, Melvin DG, Smedley D, Brown SD, Flicek P, Skarnes WC, Mallon AM, Parkinson H.","Nucleic Acids Res","2014","0305-1048","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","3","Y","Y","N","N","N","326.18372","database issue","42","d802-9","PMC3964955",NA,NA,"github.com"
"1627","25273863","MED","25273863","10.1534/g3.114.013532","Revised annotations, sex-biased expression, and lineage-specific genes in the Drosophila melanogaster group.","Rogers RL, Shao L, Sanjak JS, Andolfatto P, Thornton KR.","G3 (Bethesda)","2014","2160-1836","journal article; research support, n.i.h., extramural; research-article","Y","Y","N","0","Y","Y","N","N","N","326.18372","12","4","2345-2351","PMC4267930",NA,NA,"github.com"
"1628","24931408","MED","24931408","10.1534/genetics.114.166306","A simple regression-based method to map quantitative trait loci underlying function-valued phenotypes.","Kwak IY, Moore CR, Spalding EP, Broman KW.","Genetics","2014","0016-6731","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","326.18372","4","197","1409-1416","PMC4125409",NA,NA,"github.com"
"1629","25029912","MED","25029912","10.1186/1472-6750-14-66","Screening and genetic characterization of thermo-tolerant Synechocystis sp. PCC6803 strains created by adaptive evolution.","Tillich UM, Wolter N, Franke P, DÃ¼hring U, Frohme M.","BMC Biotechnol","2014","1472-6750","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","Y","325.80045",NA,"14","66","PMC4110520","gen",NA,"github.com"
"1630","25485311","MED","25485311",NA,"Breaking and Fixing Origin-Based Access Control in Hybrid Web/Mobile Application Frameworks.","Georgiev M, Jana S, Shmatikov V.","NDSS symposium","2014",NA,"journal article; research-article","N","Y","N","0","N","Y","N","N","N","325.80045",NA,"2014","1-15","PMC4254737",NA,NA,"github.com"
"1631","24672471","MED","24672471","10.3389/fninf.2014.00024","BROCCOLI: Software for fast fMRI analysis on many-core CPUs and GPUs.","Eklund A, Dufort P, Villani M, Laconte S.","Front Neuroinform","2014","1662-5196","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.80045",NA,"8","24","PMC3953750",NA,NA,"github.com"
"1632","24675810","MED","24675810","10.1371/journal.pcbi.1003515","Viral quasispecies assembly via maximal clique enumeration.","TÃ¶pfer A, Marschall T, Bull RA, Luciani F, SchÃ¶nhuth A, Beerenwinkel N.","PLoS Comput Biol","2014","1553-734x","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","325.68652","3","10","e1003515","PMC3967922",NA,NA,"github.com"
"1633","25161891","MED","25161891","10.1016/j.nicl.2014.07.002","Optimizing real time fMRI neurofeedback for therapeutic discovery and development.","Stoeckel LE, Garrison KA, Ghosh S, Wighton P, Hanlon CA, Gilman JM, Greer S, Turk-Browne NB, deBettencourt MT, Scheinost D, Craddock C, Thompson T, Calderon V, Bauer CC, George M, Breiter HC, Whitfield-Gabrieli S, Gabrieli JD, LaConte SM, Hirshberg L, Brewer JA, Hampson M, Van Der Kouwe A, Mackey S, Evins AE.","Neuroimage Clin","2014","2213-1582","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; review-article","Y","Y","Y","0","Y","Y","N","N","N","325.68652",NA,"5","245-255","PMC4141981",NA,NA,"github.com"
"1634","25004097","MED","25004097","10.1371/journal.pone.0101704","Contextual cross-referencing of species names for fiddler crabs (genus Uca): an experiment in cyber-taxonomy.","Rosenberg MS.","PLoS One","2014","1932-6203","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.68652","7","9","e101704","PMC4086947",NA,NA,"github.com"
"1635","24398039","MED","24398039","10.1093/biostatistics/kxt053","Differential expression analysis of RNA-seq data at single-base resolution.","Frazee AC, Sabunciyan S, Hansen KD, Irizarry RA, Leek JT.","Biostatistics","2014","1465-4644","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","Y","Y","325.68652","3","15","413-426","PMC4059460","gen",NA,"github.com"
"1636","25473421","MED","25473421","10.1186/1756-8935-7-33","Chromatin accessibility: a window into the genome.","Tsompana M, Buck MJ.","Epigenetics Chromatin","2014","1756-8935","journal article; review; review-article","Y","Y","N","0","Y","Y","N","N","N","325.68652","1","7","33","PMC4253006",NA,NA,"github.com"
"1637","25104606","MED","25104606","10.1186/1471-2164-15-657","Discovery and validation of novel and distinct RNA regulators for ribosomal protein S15 in diverse bacterial phyla.","Slinger BL, Deiorio-Haggar K, Anthony JS, Gilligan MM, Meyer MM.","BMC Genomics","2014","1471-2164","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.68652","1","15","657","PMC4137082",NA,NA,"github.com"
"1638","24823361","MED","24823361","10.1371/journal.pbio.1001858","The evolutionary origin of somatic cells under the dirty work hypothesis.","Goldsby HJ, Knoester DB, Ofria C, Kerr B.","PLoS Biol","2014","1544-9173","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","N","Y","Y","325.68652","5","12","e1001858","PMC4019463","doi",NA,"github.com"
"1639","24639646","MED","24639646","10.3389/fninf.2014.00020","Software and hardware infrastructure for research in electrophysiology.","MouÄek R, JeÅ¾ek P, VaÅeka L, RondÃk T, BrÅ¯ha P, PapeÅ¾ V, Mautner P, NovotnÃ½ J, Prokop T, StÄbetÃ¡k J.","Front Neuroinform","2014","1662-5196","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","325.68652",NA,"8","20","PMC3945519",NA,NA,"github.com"
"1640","25122667","MED","25122667","10.1534/g3.114.012526","Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing.","Devisetty UK, Covington MF, Tat AV, Lekkala S, Maloof JN.","G3 (Bethesda)","2014","2160-1836","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","325.68652","11","4","2065-2078","PMC4232532",NA,NA,"github.com"
"1641","24624315","MED","24624315","10.7717/peerj.266","Analyzing machupo virus-receptor binding by molecular dynamics simulations.","Meyer AG, Sawyer SL, Ellington AD, Wilke CO.","PeerJ","2014","2167-8359","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","Y","325.68652",NA,"2","e266","PMC3940602","pdb",NA,"github.com"
"1642","24709563","MED","24709563","10.1093/gbe/evu073","An expanded genomic representation of the phylum cyanobacteria.","Soo RM, Skennerton CT, Sekiguchi Y, Imelfort M, Paech SJ, Dennis PG, Steen JA, Parks DH, Tyson GW, Hugenholtz P.","Genome Biol Evol","2014","1759-6653","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","325.68652","5","6","1031-1045","PMC4040986",NA,NA,"github.com"
"1643","24742000","MED","24742000","10.1186/1471-2148-14-82","Selecting optimal partitioning schemes for phylogenomic datasets.","Lanfear R, Calcott B, Kainer D, Mayer C, Stamatakis A.","BMC Evol Biol","2014","1471-2148","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","N","N","Y","325.68652",NA,"14","82","PMC4012149","doi",NA,"github.com"
"1644","25232357","MED","25232357","10.3389/fpls.2014.00435","Genome-wide transcriptional profiling of Botrytis cinerea genes targeting plant cell walls during infections of different hosts.","Blanco-Ulate B, Morales-Cruz A, Amrine KC, Labavitch JM, Powell AL, Cantu D.","Front Plant Sci","2014","1664-462x","journal article; research-article","Y","Y","N","1","Y","Y","N","N","N","325.68652",NA,"5","435","PMC4153048",NA,NA,"github.com"
"1645","25566535","MED","25566535","10.3389/fbioe.2014.00072","MetaDB a Data Processing Workflow in Untargeted MS-Based Metabolomics Experiments.","Franceschi P, Mylonas R, Shahaf N, Scholz M, Arapitsas P, Masuero D, Weingart G, Carlin S, Vrhovsek U, Mattivi F, Wehrens R.","Front Bioeng Biotechnol","2014","2296-4185","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","325.68652",NA,"2","72","PMC4267269",NA,NA,"github.com"
"1646","24570371","MED","24570371","10.1128/mbio.01064-13","Single clinical isolates from acute uncomplicated urinary tract infections are representative of dominant in situ populations.","Willner D, Low S, Steen JA, George N, Nimmo GR, Schembri MA, Hugenholtz P.","MBio","2014","2150-7511","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","325.68652","2","5","e01064-13","PMC3940035",NA,NA,"github.com"
"1647","25184442","MED","25184442","10.1371/journal.pone.0104087","Biological time series analysis using a context free language: applicability to pulsatile hormone data.","Dean DA 2nd, Adler GK, Nguyen DP, Klerman EB.","PLoS One","2014","1932-6203","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.68652","9","9","e104087","PMC4153563",NA,NA,"github.com"
"1648","25403317","MED","25403317","10.1186/s12870-014-0307-2","RNA-sequencing reveals early, dynamic transcriptome changes in the corollas of pollinated petunias.","Broderick SR, Wijeratne S, Wijeratn AJ, Chapin LJ, Meulia T, Jones ML.","BMC Plant Biol","2014","1471-2229","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","325.68652","1","14","307","PMC4245787",NA,NA,"github.com"
"1649","25348801","MED","25348801","10.1186/s12870-014-0287-2","Analysis of wild-species introgressions in tomato inbreds uncovers ancestral origins.","Menda N, Strickler SR, Edwards JD, Bombarely A, Dunham DM, Martin GB, Mejia L, Hutton SF, Havey MJ, Maxwell DP, Mueller LA.","BMC Plant Biol","2014","1471-2229","journal article; research-article","Y","Y","N","0","Y","Y","Y","N","Y","325.68652","1","14","287","PMC4219026","gen","EMBL","github.com"
"1650","25161247","MED","25161247","10.1093/bioinformatics/btu464","Drug susceptibility prediction against a panel of drugs using kernelized Bayesian multitask learning.","GÃ¶nen M, Margolin AA.","Bioinformatics","2014","1367-4803","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.6163","17","30","i556-63","PMC4147917",NA,NA,"github.com"
"1651","25161257","MED","25161257","10.1093/bioinformatics/btu473","Microarray R-based analysis of complex lysate experiments with MIRACLE.","List M, Block I, Pedersen ML, Christiansen H, Schmidt S, Thomassen M, Tan Q, Baumbach J, Mollenhauer J.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.6163","17","30","i631-8","PMC4147925",NA,NA,"github.com"
"1652","25161223","MED","25161223","10.1093/bioinformatics/btu484","Probabilistic single-individual haplotyping.","Kuleshov V.","Bioinformatics","2014","1367-4803","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.6163","17","30","i379-85","PMC4147930",NA,NA,"github.com"
"1653","24192544","MED","24192544","10.1093/bioinformatics/btt611","WaveCNV: allele-specific copy number alterations in primary tumors and xenograft models from next-generation sequencing.","Holt C, Losic B, Pai D, Zhao Z, Trinh Q, Syam S, Arshadi N, Jang GH, Ali J, Beck T, McPherson J, Muthuswamy LB.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","Y","N","325.6163","6","30","768-774","PMC3957071",NA,NA,"github.com"
"1654","25202745","MED","25202745","10.1155/2014/967294","Database constraints applied to metabolic pathway reconstruction tools.","Vilaplana J, Solsona F, Teixido I, UsiÃ© A, Karathia H, Alves R, Mateo J.","ScientificWorldJournal","2014","2356-6140","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.6163",NA,"2014","967294","PMC4151372",NA,NA,"github.com"
"1655","25253358","MED","25253358","10.1186/1471-2105-15-s9-s16","Detecting epigenetic motifs in low coverage and metagenomics settings.","Beckmann ND, Karri S, Fang G, Bashir A.","BMC Bioinformatics","2014","1471-2105","journal article; research support, non-u.s. gov't; abstract","Y","Y","N","0","Y","Y","N","N","N","325.6163","Suppl 9","15 Suppl 9","s16","PMC4168715",NA,NA,"github.com"
"1656","25233860","MED","25233860","10.1186/1471-2164-15-803","Unlocking the mystery of the hard-to-sequence phage genome: PaP1 methylome and bacterial immunity.","Lu S, Le S, Tan Y, Li M, Liu C, Zhang K, Huang J, Chen H, Rao X, Zhu J, Zou L, Ni Q, Li S, Wang J, Jin X, Hu Q, Yao X, Zhao X, Zhang L, Huang G, Hu F.","BMC Genomics","2014","1471-2164","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","Y","325.6163","1","15","803","PMC4177049","gen",NA,"github.com"
"1657","25081493","MED","25081493","10.1186/1471-2164-15-s5-s2","RandAL: a randomized approach to aligning DNA sequences to reference genomes.","Vo NS, Tran Q, Niraula N, Phan V.","BMC Genomics","2014","1471-2164","journal article; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.6163","Suppl 5","15 Suppl 5","s2","PMC4120144",NA,NA,"github.com"
"1658","25058488","MED","25058488","10.1371/journal.pone.0101756","Large carbon dioxide fluxes from headwater boreal and sub-boreal streams.","Venkiteswaran JJ, Schiff SL, Wallin MB.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","Y","325.6163","7","9","e101756","PMC4109928","doi",NA,"github.com"
"1659","25408143","MED","25408143","10.1186/s12859-014-0366-2","Rapid evaluation and quality control of next generation sequencing data with FaQCs.","Lo CC, Chain PS.","BMC Bioinformatics","2014","1471-2105","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","325.6163","1","15","366","PMC4246454",NA,NA,"github.com"
"1660","24501098","MED","24501098","10.1093/bioinformatics/btu054","Visualization and probability-based scoring of structural variants within repetitive sequences.","Halper-Stromberg E, Steranka J, Burns KH, Sabunciyan S, Irizarry RA.","Bioinformatics","2014","1367-4803","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.6163","11","30","1514-1521","PMC4029030",NA,NA,"github.com"
"1661","24505263","MED","24505263","10.1371/journal.pone.0086733","The smartphone brain scanner: a portable real-time neuroimaging system.","Stopczynski A, Stahlhut C, Larsen JE, Petersen MK, Hansen LK.","PLoS One","2014","1932-6203","clinical trial; journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","325.6163","2","9","e86733","PMC3914802",NA,NA,"github.com"
"1662","24970839","MED","24970839","10.1136/amiajnl-2014-002883","Are Meaningful Use Stage 2 certified EHRs ready for interoperability? Findings from the SMART C-CDA Collaborative.","D'Amore JD, Mandel JC, Kreda DA, Swain A, Koromia GA, Sundareswaran S, Alschuler L, Dolin RH, Mandl KD, Kohane IS, Ramoni RB.","J Am Med Inform Assoc","2014","1067-5027","journal article; research support, u.s. gov't, p.h.s.; research-article","Y","Y","N","0","Y","Y","N","N","N","325.6163","6","21","1060-1068","PMC4215060",NA,NA,"github.com"
"1663","24811236","MED","24811236","10.1371/journal.pgen.1004328","Epistatically interacting substitutions are enriched during adaptive protein evolution.","Gong LI, Bloom JD.","PLoS Genet","2014","1553-7390","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","2","Y","Y","N","N","N","325.6163","5","10","e1004328","PMC4014419",NA,NA,"github.com"
"1664","24626287","MED","24626287","10.1534/g3.113.010124","A high-resolution genetic map of yellow monkeyflower identifies chemical defense QTLs and recombination rate variation.","Holeski LM, Monnahan P, Koseva B, McCool N, Lindroth RL, Kelly JK.","G3 (Bethesda)","2014","2160-1836","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.6163","5","4","813-821","PMC4025480",NA,NA,"github.com"
"1665","24162466","MED","24162466","10.1093/bioinformatics/btt610","A pathway-based data integration framework for prediction of disease progression.","Seoane JA, Day IN, Gaunt TR, Campbell C.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","325.6163","6","30","838-845","PMC3957070",NA,NA,"github.com"
"1666","24808858","MED","24808858","10.3389/fninf.2014.00040","NeuroElectro: a window to the world's neuron electrophysiology data.","Tripathy SJ, Savitskaya J, Burton SD, Urban NN, Gerkin RC.","Front Neuroinform","2014","1662-5196","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.6163",NA,"8","40","PMC4010726",NA,NA,"github.com"
"1667","24904397","MED","24904397","10.3389/fninf.2014.00051","Allen Brain Atlas-Driven Visualizations: a web-based gene expression energy visualization tool.","Zaldivar A, Krichmar JL.","Front Neuroinform","2014","1662-5196","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.6163",NA,"8","51","PMC4033128",NA,NA,"github.com"
"1668","24931983","MED","24931983","10.1093/bioinformatics/btu261","EPIQ-efficient detection of SNP-SNP epistatic interactions for quantitative traits.","Arkin Y, Rahmani E, Kleber ME, Laaksonen R, MÃ¤rz W, Halperin E.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","Y","325.6163","12","30","i19-25","PMC4229902","refsnp",NA,"github.com"
"1669","24931986","MED","24931986","10.1093/bioinformatics/btu292","Probabilistic method for detecting copy number variation in a fetal genome using maternal plasma sequencing.","RampÃ¡Å¡ek L, Arbabi A, Brudno M.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.6163","12","30","i212-8","PMC4058944",NA,NA,"github.com"
"1670","25024918","MED","25024918","10.7717/peerj.449","A third-generation dispersion and third-generation hydrogen bonding corrected PM6 method: PM6-D3H+.","Kromann JC, Christensen AS, Steinmann C, Korth M, Jensen JH.","PeerJ","2014","2167-8359","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","Y","325.6163",NA,"2","e449","PMC4081274","pdb",NA,"github.com"
"1671","25278960","MED","25278960","10.3389/fgene.2014.00325","DaVIE: Database for the Visualization and Integration of Epigenetic data.","Fejes AP, Jones MJ, Kobor MS.","Front Genet","2014","1664-8021","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","325.6163",NA,"5","325","PMC4166999",NA,NA,"github.com"
"1672","24464852","MED","24464852","10.1136/amiajnl-2013-002155","Bionimbus: a cloud for managing, analyzing and sharing large genomics datasets.","Heath AP, Greenway M, Powell R, Spring J, Suarez R, Hanley D, Bandlamudi C, McNerney ME, White KP, Grossman RL.","J Am Med Inform Assoc","2014","1067-5027","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","N","0","Y","Y","N","N","N","325.6163","6","21","969-975","PMC4215034",NA,NA,"github.com"
"1673","25548736","MED","25548736","10.7717/peerj.703","A statistical assessment of population trends for data deficient Mexican amphibians.","Quintero E, Thessen AE, Arias-Caballero P, Ayala-Orozco B.","PeerJ","2014","2167-8359","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","325.6163",NA,"2","e703","PMC4273930",NA,NA,"github.com"
"1674","25066046","MED","25066046","10.1186/1471-2105-15-253","Hamiltonian Monte Carlo methods for efficient parameter estimation in steady state dynamical systems.","Kramer A, Calderhead B, Radde N.","BMC Bioinformatics","2014","1471-2105","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","325.6163","1","15","253","PMC4262080",NA,NA,"github.com"
"1675","24828244","MED","24828244","10.1371/journal.pone.0096793","Sequencing degraded DNA from non-destructively sampled museum specimens for RAD-tagging and low-coverage shotgun phylogenetics.","Tin MM, Economo EP, Mikheyev AS.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.6163","5","9","e96793","PMC4020769",NA,NA,"github.com"
"1676","25295002","MED","25295002","10.3389/fninf.2014.00080","SIMA: Python software for analysis of dynamic fluorescence imaging data.","Kaifosh P, Zaremba JD, Danielson NB, Losonczy A.","Front Neuroinform","2014","1662-5196","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","325.6163",NA,"8","80","PMC4172099",NA,NA,"github.com"
"1677","23985301","MED","23985301","10.1017/s0031182013001121","Open source drug discovery - a limited tutorial.","Robertson MN, Ylioja PM, Williamson AE, Woelfle M, Robins M, Badiola KA, Willis P, Olliaro P, Wells TN, Todd MH.","Parasitology","2014","0031-1820","journal article; review; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","Y","325.6163","1","141","148-157","PMC3884843","doi",NA,"github.com"
"1678","24594988","MED","24594988","10.1371/journal.pone.0089550","Knowledge extraction and semantic annotation of text from the encyclopedia of life.","Thessen AE, Parr CS.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","N","N","N","325.6163","3","9","e89550","PMC3940440",NA,NA,"github.com"
"1679","25472428","MED","25472428","10.1186/1471-2105-15-s14-s4","linkedISA: semantic representation of ISA-Tab experimental metadata.","GonzÃ¡lez-BeltrÃ¡n A, Maguire E, Sansone SA, Rocca-Serra P.","BMC Bioinformatics","2014","1471-2105","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","325.6163","Suppl 14","15 Suppl 14","s4","PMC4255742",NA,NA,"github.com"
"1680","24564732","MED","24564732","10.1186/1471-2105-15-s1-s11","The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again.","GonzÃ¡lez-BeltrÃ¡n A, Neumann S, Maguire E, Sansone SA, Rocca-Serra P.","BMC Bioinformatics","2014","1471-2105","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","N","N","N","325.6163","Suppl 1","15 Suppl 1","s11","PMC4015122",NA,NA,"github.com"
"1681","25161245","MED","25161245","10.1093/bioinformatics/btu462","ASTRAL: genome-scale coalescent-based species tree estimation.","Mirarab S, Reaz R, Bayzid MS, Zimmermann T, Swenson MS, Warnow T.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","3","Y","Y","N","N","N","325.6163","17","30","i541-8","PMC4147915",NA,NA,"github.com"
"1682","25253180","MED","25253180","10.1186/1471-2105-15-s9-s9","ILP-based maximum likelihood genome scaffolding.","Lindsay J, Salooti H, MÄndoiu I, Zelikovsky A.","BMC Bioinformatics","2014","1471-2105","journal article; research support, u.s. gov't, non-p.h.s.; abstract","Y","Y","N","0","Y","Y","N","N","N","325.6163","Suppl 9","15 Suppl 9","s9","PMC4168704",NA,NA,"github.com"
"1683","25601911","MED","25601911","10.3389/fbioe.2014.00079","Using CellML with OpenCMISS to Simulate Multi-Scale Physiology.","Nickerson DP, Ladd D, Hussan JR, Safaei S, Suresh V, Hunter PJ, Bradley CP.","Front Bioeng Biotechnol","2014","2296-4185","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","325.6163",NA,"2","79","PMC4283644",NA,NA,"github.com"
"1684","24281424","MED","24281424","10.1534/g3.113.008326","Diversity, differentiation, and linkage disequilibrium: prospects for association mapping in the malaria vector Anopheles arabiensis.","Marsden CD, Lee Y, Kreppel K, Weakley A, Cornel A, Ferguson HM, Eskin E, Lanzaro GC.","G3 (Bethesda)","2014","2160-1836","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","1","Y","Y","N","N","N","325.6163","1","4","121-131","PMC3887528",NA,NA,"github.com"
"1685","24211736","MED","24211736","10.1016/j.ymeth.2013.10.015","Hyb: a bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data.","Travis AJ, Moody J, Helwak A, Tollervey D, Kudla G.","Methods","2014","1046-2023","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","325.6163","3","65","263-273","PMC3969109",NA,NA,"github.com"
"1686","25628587","MED","25628587","10.3389/fpsyg.2014.01565","Constrained statistical inference: sample-size tables for ANOVA and regression.","Vanbrabant L, Van De Schoot R, Rosseel Y.","Front Psychol","2014","1664-1078","journal article; research-article","Y","Y","N","0","N","Y","N","N","N","325.6163",NA,"5","1565","PMC4292225",NA,NA,"github.com"
"1687","25334030","MED","25334030","10.1038/ncomms6257","Genome flux and stasis in a five millennium transect of European prehistory.","Gamba C, Jones ER, Teasdale MD, McLaughlin RL, Gonzalez-Fortes G, Mattiangeli V, DomborÃ³czki L, KÅvÃ¡ri I, Pap I, Anders A, Whittle A, Dani J, Raczky P, Higham TF, Hofreiter M, Bradley DG, Pinhasi R.","Nat Commun","2014","2041-1723","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","Y","325.6163",NA,"5","5257","PMC4218962","refsnp",NA,"github.com"
"1688","25159659","MED","25159659","10.1186/1471-2164-15-720","The utility of PacBio circular consensus sequencing for characterizing complex gene families in non-model organisms.","Larsen PA, Heilman AM, Yoder AD.","BMC Genomics","2014","1471-2164","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","Y","N","Y","325.6163","1","15","720","PMC4152597","gen; doi","EMBLUNIPROT","github.com"
"1689","24030600","MED","24030600","10.1038/ismej.2013.152","Genomic properties of Marine Group A bacteria indicate a role in the marine sulfur cycle.","Wright JJ, Mewis K, Hanson NW, Konwar KM, Maas KR, Hallam SJ.","ISME J","2014","1751-7362","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","0","Y","Y","Y","N","Y","325.6163","2","8","455-468","PMC3906813","gen","EMBLUNIPROT","github.com"
"1690","24901437","MED","24901437","10.1371/journal.pone.0098443","Using HIV networks to inform real time prevention interventions.","Little SJ, Kosakovsky Pond SL, Anderson CM, Young JA, Wertheim JO, Mehta SR, May S, Smith DM.","PLoS One","2014","1932-6203","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","Y","N","N","325.6163","6","9","e98443","PMC4047027",NA,"EMBLUNIPROT","github.com"
"1691","25350584","MED","25350584","10.1186/1471-2105-15-s11-s15","LacSubPred: predicting subtypes of Laccases, an important lignin metabolism-related enzyme class, using in silico approaches.","Weirick T, Sahu SS, Mahalingam R, Kaundal R.","BMC Bioinformatics","2014","1471-2105","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; abstract","Y","Y","N","1","Y","Y","N","N","N","325.4216","Suppl 11","15 Suppl 11","s15","PMC4251044",NA,NA,"github.com"
"1692","24879305","MED","24879305","10.1371/journal.pone.0097896","The Index-based Subgraph Matching Algorithm with General Symmetries (ISMAGS): exploiting symmetry for faster subgraph enumeration.","Houbraken M, Demeyer S, Michoel T, Audenaert P, Colle D, Pickavet M.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.4216","5","9","e97896","PMC4039476",NA,NA,"github.com"
"1693","24297257","MED","24297257","10.1093/nar/gkt1245","NECTAR: a database of codon-centric missense variant annotations.","Gong S, Ware JS, Walsh R, Cook SA.","Nucleic Acids Res","2014","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","Y","N","325.4216","database issue","42","d1013-9","PMC3965063",NA,NA,"github.com"
"1694","24982878","MED","24982878","10.1155/2014/404578","Gleditsia sinensis: transcriptome sequencing, construction, and application of its protein-protein interaction network.","Zhu L, Zhang Y, Guo W, Wang Q.","Biomed Res Int","2014","2314-6133","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.4216",NA,"2014","404578","PMC4058233",NA,NA,"github.com"
"1695","25473253","MED","25473253","10.1109/cvpr.2014.355","Deformable Registration of Feature-Endowed Point Sets Based on Tensor Fields.","Wassermann D, Ross J, Washko G, Wells WM 3rd, San Jose-Estepar R.","Proc IEEE Comput Soc Conf Comput Vis Pattern Recognit","2014","1063-6919","journal article; research-article","N","Y","N","0","Y","Y","N","N","N","325.4216",NA,"2014","2729-2735","PMC4248604",NA,NA,"github.com"
"1696","25104065","MED","25104065","10.1038/srep05994","Genetic evidence of African slavery at the beginning of the trans-Atlantic slave trade.","Martiniano R, Coelho C, Ferreira MT, Neves MJ, Pinhasi R, Bradley DG.","Sci Rep","2014","2045-2322","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.4216",NA,"4","5994","PMC4125989",NA,NA,"github.com"
"1697","24824529","MED","24824529","10.1371/journal.pone.0097507","OTG-snpcaller: an optimized pipeline based on TMAP and GATK for SNP calling from ion torrent data.","Zhu P, He L, Li Y, Huang W, Xi F, Lin L, Zhi Q, Zhang W, Tang YT, Geng C, Lu Z, Xu X.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.4216","5","9","e97507","PMC4019570",NA,NA,"github.com"
"1698","25414846","MED","25414846","10.3389/fbioe.2014.00049","The Essential Component in DNA-Based Information Storage System: Robust Error-Tolerating Module.","Yim AK, Yu AC, Li JW, Wong AI, Loo JF, Chan KM, Kong SK, Yip KY, Chan TF.","Front Bioeng Biotechnol","2014","2296-4185","journal article; review; review-article","Y","Y","N","0","Y","Y","N","N","N","325.4216",NA,"2","49","PMC4222239",NA,NA,"github.com"
"1699","25103311","MED","25103311","10.1186/1471-2164-15-664","SUGAR: graphical user interface-based data refiner for high-throughput DNA sequencing.","Sato Y, Kojima K, Nariai N, Yamaguchi-Kabata Y, Kawai Y, Takahashi M, Mimori T, Nagasaki M.","BMC Genomics","2014","1471-2164","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.4216","1","15","664","PMC4133631",NA,NA,"github.com"
"1700","25143956","MED","25143956","10.1155/2014/986048","Advanced heat map and clustering analysis using heatmap3.","Zhao S, Guo Y, Sheng Q, Shyr Y.","Biomed Res Int","2014","2314-6133","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.4216",NA,"2014","986048","PMC4124803",NA,NA,"github.com"
"1701","24968249","MED","24968249","10.1371/journal.pone.0099497","Bayesian genome assembly and assessment by markov chain monte carlo sampling.","Howison M, Zapata F, Edwards EJ, Dunn CW.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.4216","6","9","e99497","PMC4072599",NA,NA,"github.com"
"1702","24733403","MED","24733403","10.1371/journal.pone.0095027","The gut microbial community of Midas cichlid fish in repeatedly evolved limnetic-benthic species pairs.","Franchini P, Fruciano C, Frickey T, Jones JC, Meyer A.","PLoS One","2014","1932-6203","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.4216","4","9","e95027","PMC3986361",NA,NA,"github.com"
"1703","25136672","MED","25136672","10.1155/2014/591478","An evaluation and implementation of rule-based Home Energy Management System using the Rete algorithm.","Kawakami T, Fujita N, Yoshihisa T, Tsukamoto M.","ScientificWorldJournal","2014","2356-6140","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","N","Y","N","N","N","325.4216",NA,"2014","591478","PMC4127203",NA,NA,"github.com"
"1704","24753429","MED","24753429","10.1093/nar/gku301","InterMine: extensive web services for modern biology.","Kalderimis A, Lyne R, Butano D, Contrino S, Lyne M, Heimbach J, Hu F, Smith R, StÄpÃ¡n R, Sullivan J, Micklem G.","Nucleic Acids Res","2014","0305-1048","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","N","0","Y","Y","N","N","N","325.4216","web server issue","42","w468-72","PMC4086141",NA,NA,"github.com"
"1705","25081207","MED","25081207","10.1093/nar/gku672","MixMir: microRNA motif discovery from gene expression data using mixed linear models.","Diao L, Marcais A, Norton S, Chen KC.","Nucleic Acids Res","2014","0305-1048","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","N","0","Y","Y","N","N","N","325.4216","17","42","e135","PMC4176157",NA,NA,"github.com"
"1706","24433564","MED","24433564","10.1186/1756-0500-7-40","XS: a FASTQ read simulator.","Pratas D, Pinho AJ, Rodrigues JM.","BMC Res Notes","2014","1756-0500","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.4216",NA,"7","40","PMC3927261",NA,NA,"github.com"
"1707","24461215","MED","24461215","10.1186/1751-0473-9-3","ROVER variant caller: read-pair overlap considerate variant-calling software applied to PCR-based massively parallel sequencing datasets.","Pope BJ, Nguyen-Dumont T, Hammet F, Park DJ.","Source Code Biol Med","2014","1751-0473","journal article; product-review","Y","Y","Y","0","Y","Y","N","N","N","325.4216","1","9","3","PMC3904415",NA,NA,"github.com"
"1708","24472558","MED","24472558","10.1186/1471-2164-15-76","Combinatorial epigenetic patterns as quantitative predictors of chromatin biology.","CieÅlik M, Bekiranov S.","BMC Genomics","2014","1471-2164","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.4216",NA,"15","76","PMC3922690",NA,NA,"github.com"
"1709","24551058","MED","24551058","10.1371/journal.pone.0087446","Inferring nonlinear gene regulatory networks from gene expression data based on distance correlation.","Guo X, Zhang Y, Hu W, Tan H, Wang X.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.4216","2","9","e87446","PMC3925093",NA,NA,"github.com"
"1710","24600470","MED","24600470","10.3389/fgene.2014.00031","Multi-genome alignment for quality control and contamination screening of next-generation sequencing data.","Hadfield J, Eldridge MD.","Front Genet","2014","1664-8021","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","325.4216",NA,"5","31","PMC3930033",NA,NA,"github.com"
"1711","24602274","MED","24602274","10.1186/2049-2618-2-7","Bacterial communities on classroom surfaces vary with human contact.","Meadow JF, Altrichter AE, Kembel SW, Moriyama M, O'Connor TK, Womack AM, Brown GZ, Green JL, Bohannan BJ.","Microbiome","2014","2049-2618","journal article; research-article","Y","Y","Y","3","Y","Y","N","N","Y","325.4216","1","2","7","PMC3945812","doi",NA,"github.com"
"1712","25356683","MED","25356683","10.1371/journal.pcbi.1003929","dcGOR: an R package for analysing ontologies and protein domain annotations.","Fang H.","PLoS Comput Biol","2014","1553-734x","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","325.4216","10","10","e1003929","PMC4214615",NA,NA,"github.com"
"1713","25247298","MED","25247298","10.1371/journal.pone.0108490","Benchmarking undedicated cloud computing providers for analysis of genomic datasets.","Yazar S, Gooden GE, Mackey DA, Hewitt AW.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","325.4216","9","9","e108490","PMC4172764",NA,NA,"github.com"
"1714","24558430","MED","24558430","10.1371/journal.pone.0088800","Hybrid RHF/MP2 geometry optimizations with the effective fragment molecular orbital method.","Christensen AS, Steinmann C, Fedorov DG, Jensen JH.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","Y","325.4216","2","9","e88800","PMC3928295","pdb",NA,"github.com"
"1715","24622612","MED","24622612","10.1093/database/bau018","GigaDB: promoting data dissemination and reproducibility.","Sneddon TP, Zhe XS, Edmunds SC, Li P, Goodman L, Hunter CI.","Database (Oxford)","2014","1758-0463","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","Y","325.4216",NA,"2014","bau018","PMC3950661","doi",NA,"github.com"
"1716","24718290","MED","24718290","10.1371/journal.pone.0093766","Fast principal component analysis of large-scale genome-wide data.","Abraham G, Inouye M.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.4216","4","9","e93766","PMC3981753",NA,NA,"github.com"
"1717","24927817","MED","24927817","10.1186/1471-2164-15-472","Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment.","Worsley Hunt R, Mathelier A, Del Peso L, Wasserman WW.","BMC Genomics","2014","1471-2164","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","1","Y","Y","N","N","N","325.4216","1","15","472","PMC4082612",NA,NA,"github.com"
"1718","24729964","MED","24729964","10.1155/2014/240403","Evaluating word representation features in biomedical named entity recognition tasks.","Tang B, Cao H, Wang X, Chen Q, Xu H.","Biomed Res Int","2014","2314-6133","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.4216",NA,"2014","240403","PMC3963372",NA,NA,"github.com"
"1719","24829452","MED","24829452","10.1093/nar/gku403","TogoTable: cross-database annotation system using the Resource Description Framework (RDF) data model.","Kawano S, Watanabe T, Mizuguchi S, Araki N, Katayama T, Yamaguchi A.","Nucleic Acids Res","2014","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","325.4216","web server issue","42","w442-8","PMC4086138",NA,NA,"github.com"
"1720","25002812","MED","25002812","10.4137/bbi.s14623","A Protocol for mtGenome Analysis on Large Sample Numbers.","Hamoy IG, Ribeiro-Dos-Santos AM, Alvarez L, Barbosa S, Silva A, Santos S, GusmÃ£o L, Ribeiro-Dos-Santos A.","Bioinform Biol Insights","2014","1177-9322","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.4216",NA,"8","127-134","PMC4069038",NA,NA,"github.com"
"1721","25197440","MED","25197440","10.4056/sigs.5008793","Genome sequence of the acid-tolerant Burkholderia sp. strain WSM2230 from Karijini National Park, Australia.","Walker R, Watkin E, Tian R, BrÃ¤u L, O'Hara G, Goodwin L, Han J, Lobos E, Huntemann M, Pati A, Woyke T, Mavromatis K, Markowitz V, Ivanova N, Kyrpides N, Reeve W.","Stand Genomic Sci","2014","1944-3277","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.4216","3","9","551-561","PMC4148995",NA,NA,"github.com"
"1722","25337457","MED","25337457","10.7717/peerj.589","A randomized trial in a massive online open course shows people don't know what a statistically significant relationship looks like, but they can learn.","Fisher A, Anderson GB, Peng R, Leek J.","PeerJ","2014","2167-8359","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","325.4216",NA,"2","e589","PMC4203023",NA,NA,"github.com"
"1723","25371772","MED","25371772","10.4161/cib.28303","On the computational ability of the RNA polymerase II carboxy terminal domain.","Karagiannis J.","Commun Integr Biol","2014","1942-0889","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","325.4216",NA,"7","e28303","PMC4217226",NA,NA,"github.com"
"1724","25374662","MED","25374662","10.1186/2047-217x-3-19","iReport: a generalised Galaxy solution for integrated experimental reporting.","Hiltemann S, Hoogstrate Y, der Spek Pv, Jenster G, Stubbs A.","Gigascience","2014","2047-217x","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","325.4216",NA,"3","19","PMC4220639",NA,NA,"github.com"
"1725","24404133","MED","24404133","10.1371/journal.pone.0083251","Labour-efficient in vitro lymphocyte population tracking and fate prediction using automation and manual review.","Chakravorty R, Rawlinson D, Zhang A, Markham J, Dowling MR, Wellard C, Zhou JH, Hodgkin PD.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","N","N","N","325.4216","1","9","e83251","PMC3880260",NA,NA,"github.com"
"1726","24885416","MED","24885416","10.1186/1471-2334-14-275","Detection of a divergent Parainfluenza 4 virus in an adult patient with influenza like illness using next-generation sequencing.","Bialasiewicz S, McVernon J, Nolan T, Lambert SB, Zhao G, Wang D, Nissen MD, Sloots TP.","BMC Infect Dis","2014","1471-2334","journal article; case reports; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","Y","N","N","325.4216",NA,"14","275","PMC4038074",NA,"EMBLUNIPROT","github.com"
"1727","24497549","MED","24497549","10.7554/elife.02273","A network approach to mixing delegates at meetings.","Vaggi F, Schiavinotto T, Lawson JL, Chessel A, Dodgson J, Geymonat M, Sato M, Carazo Salas RE, CsikÃ¡sz-Nagy A.","Elife","2014","2050-084x","journal article; discussion","Y","Y","Y","0","Y","Y","N","N","N","325.4216",NA,"3","e02273","PMC3912938",NA,NA,"github.com"
"1728","24722319","MED","24722319","10.1371/journal.pcbi.1003537","BEAST 2: a software platform for Bayesian evolutionary analysis.","Bouckaert R, Heled J, KÃ¼hnert D, Vaughan T, Wu CH, Xie D, Suchard MA, Rambaut A, Drummond AJ.","PLoS Comput Biol","2014","1553-734x","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","8","Y","Y","N","N","N","325.4216","4","10","e1003537","PMC3985171",NA,NA,"github.com"
"1729","24558975","MED","24558975","10.1186/2049-2618-2-6","An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform.","Fadrosh DW, Ma B, Gajer P, Sengamalay N, Ott S, Brotman RM, Ravel J.","Microbiome","2014","2049-2618","journal article; research-article","Y","Y","Y","2","Y","Y","N","N","N","325.4216","1","2","6","PMC3940169",NA,NA,"github.com"
"1730","24749011","MED","24749011","10.7717/peerj.332","The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes.","Sahl JW, Caporaso JG, Rasko DA, Keim P.","PeerJ","2014","2167-8359","journal article; research-article","Y","Y","Y","3","Y","Y","N","N","N","325.4216",NA,"2","e332","PMC3976120",NA,NA,"github.com"
"1731","25210619","MED","25210619","10.12688/f1000research.4263.1","Sub-strains of Drosophila Canton-S differ markedly in their locomotor behavior.","Colomb J, Brembs B.","F1000Res","2014","2046-1402","journal article; research-article","Y","Y","N","0","Y","Y","N","N","Y","325.4216",NA,"3","176","PMC4156027","doi",NA,"github.com"
"1732","25006036","MED","25006036","10.7554/elife.03300","The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin.","Thyagarajan B, Bloom JD.","Elife","2014","2050-084x","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","1","Y","Y","N","N","Y","325.4216",NA,"3",NA,"PMC4109307","pdb",NA,"github.com"
"1733","24586139","MED","24586139","10.1371/journal.pcbi.1003493","A novel bayesian method for detection of APOBEC3-mediated hypermutation and its application to zoonotic transmission of simian foamy viruses.","Matsen FA 4th, Small CT, Soliven K, Engel GA, Feeroz MM, Wang X, Craig KL, Hasan MK, Emerman M, Linial ML, Jones-Engel L.","PLoS Comput Biol","2014","1553-734x","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.4216","2","10","e1003493","PMC3937129",NA,NA,"github.com"
"1734","24977143","MED","24977143","10.1155/2014/248090","MultiRankSeq: multiperspective approach for RNAseq differential expression analysis and quality control.","Guo Y, Zhao S, Ye F, Sheng Q, Shyr Y.","Biomed Res Int","2014","2314-6133","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","325.4216",NA,"2014","248090","PMC4058234",NA,NA,"github.com"
"1735","24194598","MED","24194598","10.1093/nar/gkt997","JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles.","Mathelier A, Zhao X, Zhang AW, Parcy F, Worsley-Hunt R, Arenillas DJ, Buchman S, Chen CY, Chou A, Ienasescu H, Lim J, Shyr C, Tan G, Zhou M, Lenhard B, Sandelin A, Wasserman WW.","Nucleic Acids Res","2014","0305-1048","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","42","Y","Y","N","N","N","325.4216","database issue","42","d142-7","PMC3965086",NA,NA,"github.com"
"1736","24516122","MED","24516122","10.1073/pnas.1318678111","Transoceanic drift and the domestication of African bottle gourds in the Americas.","Kistler L, Montenegro A, Smith BD, Gifford JA, Green RE, Newsom LA, Shapiro B.","Proc Natl Acad Sci U S A","2014","0027-8424","historical article; journal article; research support, non-u.s. gov't; research-article","N","Y","Y","1","Y","Y","Y","N","Y","325.4216","8","111","2937-2941","PMC3939861","gen","EMBLUNIPROT","github.com"
"1737","24304889","MED","24304889","10.1093/nar/gkt1270","Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments.","Petryszak R, Burdett T, Fiorelli B, Fonseca NA, Gonzalez-Porta M, Hastings E, Huber W, Jupp S, Keays M, Kryvych N, McMurry J, Marioni JC, Malone J, Megy K, Rustici G, Tang AY, Taubert J, Williams E, Mannion O, Parkinson HE, Brazma A.","Nucleic Acids Res","2014","0305-1048","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","11","Y","Y","N","N","N","325.4216","database issue","42","d926-32","PMC3964963",NA,NA,"github.com"
"1738","25474327","MED","25474327","10.1371/journal.pcbi.1003953","A reaction-diffusion model of cholinergic retinal waves.","Lansdell B, Ford K, Kutz JN.","PLoS Comput Biol","2014","1553-734x","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","325.04886","12","10","e1003953","PMC4256014",NA,NA,"github.com"
"1739","25474353","MED","25474353","10.1371/journal.pcbi.1003919","Bayesian inference of sampled ancestor trees for epidemiology and fossil calibration.","Gavryushkina A, Welch D, Stadler T, Drummond AJ.","PLoS Comput Biol","2014","1553-734x","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","325.04886","12","10","e1003919","PMC4263412",NA,NA,"github.com"
"1740","24885191","MED","24885191","10.1186/1471-2164-15-347","DNA-encoded nucleosome occupancy is associated with transcription levels in the human malaria parasite Plasmodium falciparum.","Bunnik EM, Polishko A, Prudhomme J, Ponts N, Gill SS, Lonardi S, Le Roch KG.","BMC Genomics","2014","1471-2164","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","1","Y","Y","N","N","N","325.04886","1","15","347","PMC4035074",NA,NA,"github.com"
"1741","24662602","MED","24662602","10.1038/ncomms4512","A genetic and computational approach to structurally classify neuronal types.","SÃ¼mbÃ¼l U, Song S, McCulloch K, Becker M, Lin B, Sanes JR, Masland RH, Seung HS.","Nat Commun","2014","2041-1723","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","4","Y","Y","N","Y","N","325.04886",NA,"5","3512","PMC4164236",NA,NA,"github.com"
"1742","25503791","MED","25503791","10.1371/journal.pone.0113036","Characterization of x chromosome inactivation using integrated analysis of whole-exome and mRNA sequencing.","Szelinger S, Malenica I, Corneveaux JJ, Siniard AL, Kurdoglu AA, Ramsey KM, Schrauwen I, Trent JM, Narayanan V, Huentelman MJ, Craig DW.","PLoS One","2014","1932-6203","journal article; research-article","Y","Y","N","0","Y","Y","N","N","Y","325.04886","12","9","e113036","PMC4264736","omim",NA,"github.com"
"1743","25188499","MED","25188499","10.1371/journal.pone.0106689","Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly-repetitive transposable elements.","McCoy RC, Taylor RW, Blauwkamp TA, Kelley JL, Kertesz M, Pushkarev D, Petrov DA, Fiston-Lavier AS.","PLoS One","2014","1932-6203","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","Y","325.04886","9","9","e106689","PMC4154752","doi",NA,"github.com"
"1744","24484323","MED","24484323","10.1186/1471-2105-15-35","Inferring clonal evolution of tumors from single nucleotide somatic mutations.","Jiao W, Vembu S, Deshwar AG, Stein L, Morris Q.","BMC Bioinformatics","2014","1471-2105","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","6","Y","Y","N","N","N","325.04886",NA,"15","35","PMC3922638",NA,NA,"github.com"
"1745","25344330","MED","25344330","10.1186/preaccept-1016030070136510","mirMark: a site-level and UTR-level classifier for miRNA target prediction.","Menor M, Ching T, Zhu X, Garmire D, Garmire LX.","Genome Biol","2014","1465-6906","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","325.04886","10","15","500","PMC4243195",NA,NA,"github.com"
"1746","25192442","MED","25192442","10.1371/journal.pone.0107238","Beta-galactosidase staining in the nucleus of the solitary tract of Fos-Tau-LacZ mice is unaffected by monosodium glutamate taste stimulation.","Stratford JM, Thompson JA.","PLoS One","2014","1932-6203","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.04886","9","9","e107238","PMC4156431",NA,NA,"github.com"
"1747","25100859","MED","25100859","10.1074/mcp.o114.038877","DeMix workflow for efficient identification of cofragmented peptides in high resolution data-dependent tandem mass spectrometry.","Zhang B, Pirmoradian M, Chernobrovkin A, Zubarev RA.","Mol Cell Proteomics","2014","1535-9476","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","325.04886","11","13","3211-3223","PMC4223503",NA,NA,"github.com"
"1748","24784137","MED","24784137","10.1093/molbev/msu151","Reducing pervasive false-positive identical-by-descent segments detected by large-scale pedigree analysis.","Durand EY, Eriksson N, McLean CY.","Mol Biol Evol","2014","0737-4038","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.04886","8","31","2212-2222","PMC4104314",NA,NA,"github.com"
"1749","25057820","MED","25057820","10.1371/journal.pgen.1004518","Requirements for Pseudomonas aeruginosa acute burn and chronic surgical wound infection.","Turner KH, Everett J, Trivedi U, Rumbaugh KP, Whiteley M.","PLoS Genet","2014","1553-7390","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.04886","7","10","e1004518","PMC4109851",NA,NA,"github.com"
"1750","24501022","MED","24501022","10.1101/gr.159624.113","Centromere reference models for human chromosomes X and Y satellite arrays.","Miga KH, Newton Y, Jain M, Altemose N, Willard HF, Kent WJ.","Genome Res","2014","1088-9051","journal article; research support, n.i.h., extramural; research-article","N","Y","N","2","Y","Y","Y","N","Y","325.04886","4","24","697-707","PMC3975068","gen","EMBL","github.com"
"1751","25183835","MED","25183835","10.1261/rna.044321.114","High-throughput mutate-map-rescue evaluates SHAPE-directed RNA structure and uncovers excited states.","Tian S, Cordero P, Kladwang W, Das R.","RNA","2014","1355-8382","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","N","0","Y","Y","N","N","Y","325.04886","11","20","1815-1826","PMC4201832","pdb",NA,"github.com"
"1752","24727652","MED","24727652","10.1038/nmeth.2924","Multiscale representation of genomic signals.","Knijnenburg TA, Ramsey SA, Berman BP, Kennedy KA, Smit AF, Wessels LF, Laird PW, Aderem A, Shmulevich I.","Nat Methods","2014","1548-7091","journal article; research support, n.i.h., extramural; research-article","Y","Y","N","1","Y","Y","N","N","N","325.04886","6","11","689-694","PMC4040162",NA,NA,"github.com"
"1753","24955847","MED","24955847","10.1371/journal.pone.0100163","The roles of standing genetic variation and evolutionary history in determining the evolvability of anti-predator strategies.","O'Donnell DR, Parigi A, Fish JA, Dworkin I, Wagner AP.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.04886","6","9","e100163","PMC4067307",NA,NA,"github.com"
"1754","25294605","MED","25294605","10.1186/1756-0500-7-698","SNPest: a probabilistic graphical model for estimating genotypes.","Lindgreen S, Krogh A, Pedersen JS.","BMC Res Notes","2014","1756-0500","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","325.04886","1","7","698","PMC4203901",NA,NA,"github.com"
"1755","24475049","MED","24475049","10.1371/journal.pone.0085678","istar: a web platform for large-scale protein-ligand docking.","Li H, Leung KS, Ballester PJ, Wong MH.","PLoS One","2014","1932-6203","journal article; research-article","Y","Y","Y","3","Y","Y","N","N","Y","325.04886","1","9","e85678","PMC3901662","pdb",NA,"github.com"
"1756","24482760","MED","24482760","10.7717/peerj.241","Composable languages for bioinformatics: the NYoSh experiment.","Simi M, Campagne F.","PeerJ","2014","2167-8359","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.04886",NA,"2","e241","PMC3898313",NA,NA,"github.com"
"1757","24600386","MED","24600386","10.3389/fninf.2014.00010","Neo: an object model for handling electrophysiology data in multiple formats.","Garcia S, Guarino D, Jaillet F, Jennings T, PrÃ¶pper R, Rautenberg PL, Rodgers CC, Sobolev A, Wachtler T, Yger P, Davison AP.","Front Neuroinform","2014","1662-5196","journal article; research-article","Y","Y","Y","5","Y","Y","N","Y","N","325.04886",NA,"8","10","PMC3930095",NA,NA,"github.com"
"1758","24602450","MED","24602450","10.1186/1748-7188-9-5","Faster algorithms for RNA-folding using the Four-Russians method.","Venkatachalam B, Gusfield D, Frid Y.","Algorithms Mol Biol","2014","1748-7188","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.04886","1","9","5","PMC3996002",NA,NA,"github.com"
"1759","24972832","MED","24972832","10.1093/nar/gku537","Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations.","Giallonardo FD, TÃ¶pfer A, Rey M, Prabhakaran S, Duport Y, Leemann C, Schmutz S, Campbell NK, Joos B, Lecca MR, Patrignani A, DÃ¤umer M, Beisel C, Rusert P, Trkola A, GÃ¼nthard HF, Roth V, Beerenwinkel N, Metzner KJ.","Nucleic Acids Res","2014","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","Y","325.04886","14","42","e115","PMC4132706","gen",NA,"github.com"
"1760","25160522","MED","25160522","10.1186/s13059-014-0443-x","SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization.","Qiao Y, Quinlan AR, Jazaeri AA, Verhaak RG, Wheeler DA, Marth GT.","Genome Biol","2014","1465-6906","journal article; research support, n.i.h., extramural; research-article","Y","Y","N","0","Y","Y","N","N","N","325.04886","8","15","443","PMC4180956",NA,NA,"github.com"
"1761","24795620","MED","24795620","10.3389/fninf.2014.00043","Efficient generation of connectivity in neuronal networks from simulator-independent descriptions.","Djurfeldt M, Davison AP, Eppler JM.","Front Neuroinform","2014","1662-5196","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.04886",NA,"8","43","PMC4001034",NA,NA,"github.com"
"1762","24808842","MED","24808842","10.3389/fnhum.2014.00222","Sparse distributed memory: understanding the speed and robustness of expert memory.","Brogliato MS, Chada DM, Linhares A.","Front Hum Neurosci","2014","1662-5161","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.04886",NA,"8","222","PMC4009432",NA,NA,"github.com"
"1763","24883252","MED","24883252","10.7717/peerj.391","Mining transcriptomic data to study the origins and evolution of a plant allopolyploid complex.","Bombarely A, Coate JE, Doyle JJ.","PeerJ","2014","2167-8359","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","325.04886",NA,"2","e391","PMC4034613",NA,NA,"github.com"
"1764","24918035","MED","24918035","10.7717/peerj.415","Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products.","Beitel CW, Froenicke L, Lang JM, Korf IF, Michelmore RW, Eisen JA, Darling AE.","PeerJ","2014","2167-8359","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","Y","325.04886",NA,"2","e415","PMC4045339","doi; refseq",NA,"github.com"
"1765","24931990","MED","24931990","10.1093/bioinformatics/btu287","Gene network inference by probabilistic scoring of relationships from a factorized model of interactions.","Zitnik M, Å½upan B.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","N","0","Y","Y","N","N","N","325.04886","12","30","i246-i254","PMC4229904",NA,NA,"github.com"
"1766","24932000","MED","24932000","10.1093/bioinformatics/btu291","AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references.","Bao E, Jiang T, Girke T.","Bioinformatics","2014","1367-4803","journal article; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.04886","12","30","i319-i328","PMC4058956",NA,NA,"github.com"
"1767","24516381","MED","24516381","10.1371/journal.ppat.1003904","The master regulator of the cellular stress response (HSF1) is critical for orthopoxvirus infection.","Filone CM, Caballero IS, Dower K, Mendillo ML, Cowley GS, Santagata S, Rozelle DK, Yen J, Rubins KH, Hacohen N, Root DE, Hensley LE, Connor J.","PLoS Pathog","2014","1553-7366","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","1","Y","Y","Y","N","N","325.04886","2","10","e1003904","PMC3916389",NA,"UNIPROT","github.com"
"1768","25191215","MED","25191215","10.3389/fnins.2014.00229","Deep learning for neuroimaging: a validation study.","Plis SM, Hjelm DR, Salakhutdinov R, Allen EA, Bockholt HJ, Long JD, Johnson HJ, Paulsen JS, Turner JA, Calhoun VD.","Front Neurosci","2014","1662-4548","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.04886",NA,"8","229","PMC4138493",NA,NA,"github.com"
"1769","25324841","MED","25324841","10.3389/fimmu.2014.00422","Key Hub and Bottleneck Genes Differentiate the Macrophage Response to Virulent and Attenuated Mycobacterium bovis.","Killick KE, Magee DA, Park SD, Taraktsoglou M, Browne JA, Conlon KM, Nalpas NC, Gormley E, Gordon SV, MacHugh DE, Hokamp K.","Front Immunol","2014","1664-3224","journal article; research-article","Y","Y","N","1","Y","Y","N","N","N","325.04886",NA,"5","422","PMC4181336",NA,NA,"github.com"
"1770","25332847","MED","25332847","10.7717/peerj.620","An evaluation of alternative methods for constructing phylogenies from whole genome sequence data: a case study with Salmonella.","Pettengill JB, Luo Y, Davis S, Chen Y, Gonzalez-Escalona N, Ottesen A, Rand H, Allard MW, Strain E.","PeerJ","2014","2167-8359","journal article; research-article","Y","Y","N","0","Y","Y","N","N","Y","325.04886",NA,"2","e620","PMC4201946","gen",NA,"github.com"
"1771","25393105","MED","25393105","10.1371/journal.pone.0111153","Clonal architectures and driver mutations in metastatic melanomas.","Ding L, Kim M, Kanchi KL, Dees ND, Lu C, Griffith M, Fenstermacher D, Sung H, Miller CA, Goetz B, Wendl MC, Griffith O, Cornelius LA, Linette GP, McMichael JF, Sondak VK, Fields RC, Ley TJ, MulÃ© JJ, Wilson RK, Weber JS.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","Y","325.04886","11","9","e111153","PMC4230926","doi",NA,"github.com"
"1772","24304890","MED","24304890","10.1093/nar/gkt1237","Vespucci: a system for building annotated databases of nascent transcripts.","Allison KA, Kaikkonen MU, Gaasterland T, Glass CK.","Nucleic Acids Res","2014","0305-1048","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.04886","4","42","2433-2447","PMC3936758",NA,NA,"github.com"
"1773","24599324","MED","24599324","10.1371/journal.pone.0090581","MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping.","Lee WP, Stromberg MP, Ward A, Stewart C, Garrison EP, Marth GT.","PLoS One","2014","1932-6203","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","8","Y","Y","N","N","N","325.04886","3","9","e90581","PMC3944147",NA,NA,"github.com"
"1774","24410921","MED","24410921","10.1186/1471-2164-15-17","Comparative genomics of enterohemorrhagic Escherichia coli O145:H28 demonstrates a common evolutionary lineage with Escherichia coli O157:H7.","Cooper KK, Mandrell RE, Louie JW, Korlach J, Clark TA, Parker CT, Huynh S, Chain PS, Ahmed S, Carter MQ.","BMC Genomics","2014","1471-2164","journal article; research support, non-u.s. gov't; comparative study; research-article","Y","Y","Y","4","Y","Y","Y","N","Y","325.04886",NA,"15","17","PMC3893438","gen","EMBLUNIPROT","github.com"
"1775","25375164","MED","25375164","10.1371/journal.pone.0111795","Computational approaches for predicting biomedical research collaborations.","Zhang Q, Yu H.","PLoS One","2014","1932-6203","journal article; research support, n.i.h., extramural; research-article","Y","Y","N","0","Y","Y","N","N","N","325.04886","11","9","e111795","PMC4222920",NA,NA,"github.com"
"1776","25355509","MED","25355509","10.1093/nar/gku972","The role of nucleobase interactions in RNA structure and dynamics.","Bottaro S, Di Palma F, Bussi G.","Nucleic Acids Res","2014","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","Y","325.04886","21","42","13306-13314","PMC4245972","pdb",NA,"github.com"
"1777","24637117","MED","24637117","10.1101/gad.235770.113","Rbfox2 controls autoregulation in RNA-binding protein networks.","Jangi M, Boutz PL, Paul P, Sharp PA.","Genes Dev","2014","0890-9369","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","N","5","Y","Y","Y","N","N","325.04886","6","28","637-651","PMC3967051",NA,"UNIPROT","github.com"
"1778","25485096","MED","25485096","10.12688/f1000research.4702.1","EpiCollect+: linking smartphones to web applications for complex data collection projects.","Aanensen DM, Huntley DM, Menegazzo M, Powell CI, Spratt BG.","F1000Res","2014","2046-1402","journal article; research-article","Y","Y","N","0","Y","Y","N","N","Y","325.04886",NA,"3","199","PMC4244764","doi",NA,"github.com"
"1779","24488179","MED","24488179","10.1002/embj.201386225","The long non-coding RNA Paupar regulates the expression of both local and distal genes.","Vance KW, Sansom SN, Lee S, Chalei V, Kong L, Cooper SE, Oliver PL, Ponting CP.","EMBO J","2014","0261-4189","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","8","Y","Y","Y","N","Y","325.04886","4","33","296-311","PMC3983687","gen","EMBLARXPR","github.com"
"1780","24618470","MED","24618470","10.1093/bioinformatics/btu134","Probabilistic PCA of censored data: accounting for uncertainties in the visualization of high-throughput single-cell qPCR data.","Buettner F, Moignard V, GÃ¶ttgens B, Theis FJ.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.04886","13","30","1867-1875","PMC4071202",NA,NA,"github.com"
"1781","25102416","MED","25102416","10.1371/journal.pcbi.1003665","SciClone: inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution.","Miller CA, White BS, Dees ND, Griffith M, Welch JS, Griffith OL, Vij R, Tomasson MH, Graubert TA, Walter MJ, Ellis MJ, Schierding W, DiPersio JF, Ley TJ, Mardis ER, Wilson RK, Ding L.","PLoS Comput Biol","2014","1553-734x","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","1","Y","Y","N","N","N","325.04886","8","10","e1003665","PMC4125065",NA,NA,"github.com"
"1782","24771338","MED","24771338","10.1093/nar/gku326","Nucleosome regulatory dynamics in response to TGFÎ².","Enroth S, Andersson R, Bysani M, Wallerman O, TermÃ©n S, Tuch BB, De La Vega FM, Heldin CH, Moustakas A, Komorowski J, Wadelius C.","Nucleic Acids Res","2014","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.04886","11","42","6921-6934","PMC4066760",NA,NA,"github.com"
"1783","25514851","MED","25514851",NA,"Determining the quality and complexity of next-generation sequencing data without a reference genome.","Anvar S, Khachatryan L, Vermaat M, van Galen M, Pulyakhina I, Ariyurek Y, Kraaijeveld K, den Dunnen JT, de Knijff P, T Hoen P, Laros J.","Genome Biol","2014","1465-6906","journal article; research-article","Y","Y","N","0","N","Y","N","N","Y","325.04886","12","15","555","PMC4298064","arrayexpress",NA,"github.com"
"1784","25071822","MED","25071822","10.3389/fgene.2014.00192","Identification of structural variation in mouse genomes.","Keane TM, Wong K, Adams DJ, Flint J, Reymond A, Yalcin B.","Front Genet","2014","1664-8021","journal article; review; review-article","Y","Y","Y","1","Y","Y","N","N","N","325.04886",NA,"5","192","PMC4079067",NA,NA,"github.com"
"1785","25177538","MED","25177538","10.7717/peerj.545","Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences.","Rideout JR, He Y, Navas-Molina JA, Walters WA, Ursell LK, Gibbons SM, Chase J, McDonald D, Gonzalez A, Robbins-Pianka A, Clemente JC, Gilbert JA, Huse SM, Zhou HW, Knight R, Caporaso JG.","PeerJ","2014","2167-8359","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","325.04886",NA,"2","e545","PMC4145071",NA,NA,"github.com"
"1786","25642185","MED","25642185","10.3389/fninf.2014.00090","Automatic analysis (aa): efficient neuroimaging workflows and parallel processing using Matlab and XML.","Cusack R, Vicente-Grabovetsky A, Mitchell DJ, Wild CJ, Auer T, Linke AC, Peelle JE.","Front Neuroinform","2014","1662-5196","journal article; research-article","Y","Y","N","0","N","Y","N","N","N","325.04886",NA,"8","90","PMC4295539",NA,NA,"github.com"
"1787","24400075","MED","24400075","10.1371/journal.pone.0083675","Exploring candidate genes for pericarp russet pigmentation of sand pear (Pyrus pyrifolia) via RNA-Seq data in two genotypes contrasting for pericarp color.","Wang YZ, Dai MS, Zhang SJ, Shi ZB.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","Y","N","Y","325.04886","1","9","e83675","PMC3882208","gen","EMBL","github.com"
"1788","24809511","MED","24809511","10.1371/journal.pgen.1004355","A lack of parasitic reduction in the obligate parasitic green alga Helicosporidium.","Pombert JF, Blouin NA, Lane C, Boucias D, Keeling PJ.","PLoS Genet","2014","1553-7390","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","Y","N","N","325.04886","5","10","e1004355","PMC4014436",NA,"EMBLUNIPROT","github.com"
"1789","25122613","MED","25122613","10.1101/gr.176784.114","High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA-tRNA interface.","Schmitt BM, Rudolph KL, Karagianni P, Fonseca NA, White RJ, Talianidis I, Odom DT, Marioni JC, Kutter C.","Genome Res","2014","1088-9051","journal article; research support, non-u.s. gov't; research-article","N","Y","N","0","Y","Y","N","N","Y","325.04886","11","24","1797-1807","PMC4216921","arrayexpress; doi",NA,"github.com"
"1790","24297551","MED","24297551",NA,"Imputation-based assessment of next generation rare exome variant arrays.","Martin AR, Tse G, Bustamante CD, Kenny EE.","Pac Symp Biocomput","2014","2335-6936","journal article; research support, n.i.h., extramural; research-article","N","Y","N","0","Y","Y","N","N","N","325.0204",NA,NA,"241-252","PMC3900244",NA,NA,"github.com"
"1791","25243705","MED","25243705","10.1111/gtc.12178","Quality control method for RNA-seq using single nucleotide polymorphism allele frequency.","Endo TA.","Genes Cells","2014","1356-9597","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","325.0204","11","19","821-829","PMC4231238",NA,NA,"github.com"
"1792","24217915","MED","24217915","10.1093/nar/gkt1044","WormQTLHD--a web database for linking human disease to natural variation data in C. elegans.","van der Velde KJ, de Haan M, Zych K, Arends D, Snoek LB, Kammenga JE, Jansen RC, Swertz MA, Li Y.","Nucleic Acids Res","2014","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","Y","N","325.0204","database issue","42","d794-801","PMC3965109",NA,NA,"github.com"
"1793","24225320","MED","24225320","10.1093/nar/gkt1012","The Genome Database for Rosaceae (GDR): year 10 update.","Jung S, Ficklin SP, Lee T, Cheng CH, Blenda A, Zheng P, Yu J, Bombarely A, Cho I, Ru S, Evans K, Peace C, Abbott AG, Mueller LA, Olmstead MA, Main D.","Nucleic Acids Res","2014","0305-1048","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","2","Y","Y","N","N","N","325.0204","database issue","42","d1237-44","PMC3965003",NA,NA,"github.com"
"1794","25375120","MED","25375120","10.1371/journal.pcbi.1003914","Mouse hair cycle expression dynamics modeled as coupled mesenchymal and epithelial oscillators.","Tasseff R, Bheda-Malge A, DiColandrea T, Bascom CC, Isfort RJ, Gelinas R.","PLoS Comput Biol","2014","1553-734x","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","325.0204","11","10","e1003914","PMC4222602",NA,NA,"github.com"
"1795","24373676","MED","24373676","10.1016/j.neurobiolaging.2013.11.029","Genetic and neuroanatomic associations in sporadic frontotemporal lobar degeneration.","McMillan CT, Toledo JB, Avants BB, Cook PA, Wood EM, Suh E, Irwin DJ, Powers J, Olm C, Elman L, McCluskey L, Schellenberg GD, Lee VM, Trojanowski JQ, Van Deerlin VM, Grossman M.","Neurobiol Aging","2014","0197-4580","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","1","Y","Y","N","N","Y","325.0204","6","35","1473-1482","PMC3961542","refsnp",NA,"github.com"
"1796","25404913","MED","25404913","10.3389/fncom.2014.00137","OpenWorm: an open-science approach to modeling Caenorhabditis elegans.","Szigeti B, Gleeson P, Vella M, Khayrulin S, Palyanov A, Hokanson J, Currie M, Cantarelli M, Idili G, Larson S.","Front Comput Neurosci","2014","1662-5188","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","325.0204",NA,"8","137","PMC4217485",NA,NA,"github.com"
"1797","24941260","MED","24941260","10.1371/journal.pone.0099825","ClinicalCodes: an online clinical codes repository to improve the validity and reproducibility of research using electronic medical records.","Springate DA, Kontopantelis E, Ashcroft DM, Olier I, Parisi R, Chamapiwa E, Reeves D.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","Y","325.0204","6","9","e99825","PMC4062485","doi",NA,"github.com"
"1798","24965213","MED","24965213","10.1186/1471-2105-15-221","Steady state analysis of Boolean molecular network models via model reduction and computational algebra.","Veliz-Cuba A, Aguilar B, Hinkelmann F, Laubenbacher R.","BMC Bioinformatics","2014","1471-2105","journal article; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","N","0","Y","Y","N","N","N","325.0204",NA,"15","221","PMC4230806",NA,NA,"github.com"
"1799","25050811","MED","25050811","10.1371/journal.pone.0102642","Bioinformatics on the cloud computing platform Azure.","Shanahan HP, Owen AM, Harrison AP.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.0204","7","9","e102642","PMC4106841",NA,NA,"github.com"
"1800","25147968","MED","25147968","10.3201/eid2009.131095","Genomic epidemiology of Salmonella enterica serotype Enteritidis based on population structure of prevalent lineages.","Deng X, Desai PT, den Bakker HC, Mikoleit M, Tolar B, Trees E, Hendriksen RS, Frye JG, Porwollik S, Weimer BC, Wiedmann M, Weinstock GM, Fields PI, McClelland M.","Emerg Infect Dis","2014","1080-6040","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research support, u.s. gov't, p.h.s.; research-article","Y","Y","N","0","Y","Y","N","N","N","325.0204","9","20","1481-1489","PMC4178404",NA,NA,"github.com"
"1801","24141493","MED","24141493","10.1038/nmeth.2694","Quantitative assessment of single-cell RNA-sequencing methods.","Wu AR, Neff NF, Kalisky T, Dalerba P, Treutlein B, Rothenberg ME, Mburu FM, Mantalas GL, Sim S, Clarke MF, Quake SR.","Nat Methods","2014","1548-7091","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; comparative study; research-article","N","Y","Y","22","Y","Y","Y","N","N","325.0204","1","11","41-46","PMC4022966",NA,"ARXPR","github.com"
"1802","25253095","MED","25253095","10.1186/1471-2105-15-s9-s14","A better sequence-read simulator program for metagenomics.","Johnson S, Trost B, Long JR, Pittet V, Kusalik A.","BMC Bioinformatics","2014","1471-2105","journal article; research support, non-u.s. gov't; abstract","Y","Y","N","0","Y","Y","N","N","N","325.0204","Suppl 9","15 Suppl 9","s14","PMC4168713",NA,NA,"github.com"
"1803","24614698","MED","24614698","10.1371/journal.pone.0090784","Meconium microbiome analysis identifies bacteria correlated with premature birth.","Ardissone AN, de la Cruz DM, Davis-Richardson AG, Rechcigl KT, Li N, Drew JC, Murgas-Torrazza R, Sharma R, Hudak ML, Triplett EW, Neu J.","PLoS One","2014","1932-6203","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","5","Y","Y","N","N","N","325.0204","3","9","e90784","PMC3948723",NA,NA,"github.com"
"1804","24395971","MED","24395971","10.1098/rstb.2013.0044","Predicting human visuomotor behaviour in a driving task.","Johnson L, Sullivan B, Hayhoe M, Ballard D.","Philos Trans R Soc Lond B Biol Sci","2014","0962-8436","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","325.0204","1636","369","20130044","PMC3886332",NA,NA,"github.com"
"1805","24475107","MED","24475107","10.1371/journal.pone.0086341","Cloud-enabled microscopy and droplet microfluidic platform for specific detection of Escherichia coli in water.","Golberg A, Linshiz G, Kravets I, Stawski N, Hillson NJ, Yarmush ML, Marks RS, Konry T.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.0204","1","9","e86341","PMC3903517",NA,NA,"github.com"
"1806","24478743","MED","24478743","10.3389/fpsyg.2014.00012","Hedonic appreciation and verbal description of pleasant and unpleasant odors in untrained, trainee cooks, flavorists, and perfumers.","Sezille C, Fournel A, Rouby C, Rinck F, Bensafi M.","Front Psychol","2014","1664-1078","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","325.0204",NA,"5","12","PMC3900918",NA,NA,"github.com"
"1807","24498398","MED","24498398","10.1371/journal.pone.0087908","A computational approach to qualitative analysis in large textual datasets.","Evans MS.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.0204","2","9","e87908","PMC3912071",NA,NA,"github.com"
"1808","24495746","MED","24495746","10.1186/1471-2105-15-38","DRUMS: Disk Repository with Update Management and Select option for high throughput sequencing data.","Nettling M, Thieme N, Both A, Grosse I.","BMC Bioinformatics","2014","1471-2105","journal article; product-review","Y","Y","Y","0","Y","Y","N","N","N","325.0204",NA,"15","38","PMC3915617",NA,NA,"github.com"
"1809","24505288","MED","24505288","10.1371/journal.pone.0087418","The fastest saccadic responses escape visual masking.","Crouzet SM, Overgaard M, Busch NA.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.0204","2","9","e87418","PMC3914826",NA,NA,"github.com"
"1810","24549300","MED","24549300","10.1038/mtna.2013.72","A Kinetic Model Explains Why Shorter and Less Affine Enzyme-recruiting Oligonucleotides Can Be More Potent.","Pedersen L, Hagedorn PH, Lindholm MW, Lindow M.","Mol Ther Nucleic Acids","2014","2162-2531","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","325.0204","2","3","e149","PMC3951909",NA,NA,"github.com"
"1811","24567737","MED","24567737","10.3389/fgene.2014.00013","On the optimal trimming of high-throughput mRNA sequence data.","Macmanes MD.","Front Genet","2014","1664-8021","journal article; research-article","Y","Y","Y","5","Y","Y","N","Y","Y","325.0204",NA,"5","13","PMC3908319","doi",NA,"github.com"
"1812","24982954","MED","24982954","10.1155/2014/437684","A meta-analysis of the bacterial and archaeal diversity observed in wetland soils.","Lv X, Yu J, Fu Y, Ma B, Qu F, Ning K, Wu H.","ScientificWorldJournal","2014","2356-6140","journal article; research support, non-u.s. gov't; review-article","Y","Y","Y","0","Y","Y","N","N","Y","325.0204",NA,"2014","437684","PMC4058131","gen",NA,"github.com"
"1813","24696402","MED","24696402","10.1093/gbe/evu070","Transcriptomic analysis of the highly derived radial body plan of a sea urchin.","Wygoda JA, Yang Y, Byrne M, Wray GA.","Genome Biol Evol","2014","1759-6653","letter; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.","Y","Y","Y","0","Y","Y","N","N","N","325.0204","4","6","964-973","PMC4007537",NA,NA,"github.com"
"1814","24554752","MED","24554752","10.1128/jcm.03554-13","Characterization of invasive group B streptococcus strains from the greater Toronto area, Canada.","Teatero S, McGeer A, Low DE, Li A, Demczuk W, Martin I, Fittipaldi N.","J Clin Microbiol","2014","0095-1137","journal article; research support, non-u.s. gov't; research-article","N","Y","N","0","Y","Y","N","N","N","325.0204","5","52","1441-1447","PMC3993709",NA,NA,"github.com"
"1815","24595159","MED","24595159","10.1371/journal.pone.0089323","Parallel-META 2.0: enhanced metagenomic data analysis with functional annotation, high performance computing and advanced visualization.","Su X, Pan W, Song B, Xu J, Ning K.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","325.0204","3","9","e89323","PMC3940597",NA,NA,"github.com"
"1816","25405477","MED","25405477","10.1371/journal.pone.0111928","CollaborationViz: interactive visual exploration of biomedical research collaboration networks.","Bian J, Xie M, Hudson TJ, Eswaran H, Brochhausen M, Hanna J, Hogan WR.","PLoS One","2014","1932-6203","journal article; research support, n.i.h., extramural; research-article","Y","Y","N","0","Y","Y","N","N","N","325.0204","11","9","e111928","PMC4236011",NA,NA,"github.com"
"1817","25406753","MED","25406753","10.1097/qad.0000000000000412","Recent HIV prevalence trends among pregnant women and all women in sub-Saharan Africa: implications for HIV estimates.","Eaton JW, Rehle TM, Jooste S, Nkambule R, Kim AA, Mahy M, Hallett TB.","AIDS","2014","0269-9370","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","2","Y","Y","N","N","N","325.0204","4","28 Suppl 4","s507-14","PMC4247272",NA,NA,"github.com"
"1818","24608104","MED","24608104","10.1371/journal.pone.0089676","Palindromic sequence artifacts generated during next generation sequencing library preparation from historic and ancient DNA.","Star B, Nederbragt AJ, Hansen MH, Skage M, Gilfillan GD, Bradbury IR, Pampoulie C, Stenseth NC, Jakobsen KS, Jentoft S.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.0204","3","9","e89676","PMC3946424",NA,NA,"github.com"
"1819","25420108","MED","25420108","10.1371/journal.pone.0113496","Synergy: a web resource for exploring gene regulation in Synechocystis sp. PCC6803.","MÃ¤hler N, Cheregi O, Funk C, Netotea S, Hvidsten TR.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","325.0204","11","9","e113496","PMC4242644",NA,NA,"github.com"
"1820","24772079","MED","24772079","10.3389/fninf.2014.00034","Graph-based active learning of agglomeration (GALA): a Python library to segment 2D and 3D neuroimages.","Nunez-Iglesias J, Kennedy R, Plaza SM, Chakraborty A, Katz WT.","Front Neuroinform","2014","1662-5196","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.0204",NA,"8","34","PMC3983515",NA,NA,"github.com"
"1821","24857970","MED","24857970","10.1093/database/bau041","PTM-SD: a database of structurally resolved and annotated posttranslational modifications in proteins.","Craveur P, Rebehmed J, de Brevern AG.","Database (Oxford)","2014","1758-0463","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","Y","325.0204",NA,"2014",NA,"PMC4038255","pdb",NA,"github.com"
"1822","25009556","MED","25009556","10.3389/fgene.2014.00190","A consensus approach to vertebrate de novo transcriptome assembly from RNA-seq data: assembly of the duck (Anas platyrhynchos) transcriptome.","Moreton J, Dunham SP, Emes RD.","Front Genet","2014","1664-8021","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","Y","325.0204",NA,"5","190","PMC4070175","doi",NA,"github.com"
"1823","25093072","MED","25093072","10.1186/2041-1480-5-s1-s3","Semantic Web repositories for genomics data using the eXframe platform.","Merrill E, Corlosquet S, Ciccarese P, Clark T, Das S.","J Biomed Semantics","2014","2041-1480","journal article; abstract","Y","Y","Y","0","Y","Y","N","N","N","325.0204","suppl 1 proceedings of the bio-ontologies spec interest","5","s3","PMC4108874",NA,NA,"github.com"
"1824","25197442","MED","25197442","10.4056/sigs.5018795","Genome sequence of the acid-tolerant Burkholderia sp. strain WSM2232 from Karijini National Park, Australia.","Walker R, Watkin E, Tian R, BrÃ¤u L, O'Hara G, Goodwin L, Han J, Reddy T, Huntemann M, Pati A, Woyke T, Mavromatis K, Markowitz V, Ivanova N, Kyrpides N, Reeve W.","Stand Genomic Sci","2014","1944-3277","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.0204","3","9","1168-1180","PMC4148988",NA,NA,"github.com"
"1825","25202645","MED","25202645","10.3732/apps.1400005","A practical introduction to skeletons for the plant sciences.","Bucksch A.","Appl Plant Sci","2014","2168-0450","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.0204","8","2",NA,"PMC4141711",NA,NA,"github.com"
"1826","25202302","MED","25202302","10.3389/fmicb.2014.00431","Hidden state prediction: a modification of classic ancestral state reconstruction algorithms helps unravel complex symbioses.","Zaneveld JR, Thurber RL.","Front Microbiol","2014","1664-302x","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.0204",NA,"5","431","PMC4142861",NA,NA,"github.com"
"1827","25210663","MED","25210663","10.7717/peerj.559","Metagenome fragment classification based on multiple motif-occurrence profiles.","Matsushita N, Seno S, Takenaka Y, Matsuda H.","PeerJ","2014","2167-8359","journal article; research-article","Y","Y","N","0","Y","Y","N","N","Y","325.0204",NA,"2","e559","PMC4157293","gen",NA,"github.com"
"1828","25225629","MED","25225629","10.3732/apps.1400042","Hyb-Seq: Combining target enrichment and genome skimming for plant phylogenomics.","Weitemier K, Straub SC, Cronn RC, Fishbein M, Schmickl R, McDonnell A, Liston A.","Appl Plant Sci","2014","2168-0450","journal article; research-article","Y","Y","N","0","Y","Y","N","N","Y","325.0204","9","2",NA,"PMC4162667","gen; doi",NA,"github.com"
"1829","25392735","MED","25392735","10.1186/2047-217x-3-25","A comprehensive resource of genomic, epigenomic and transcriptomic sequencing data for the black truffle Tuber melanosporum.","Chen PY, Montanini B, Liao WW, Morselli M, Jaroszewicz A, Lopez D, Ottonello S, Pellegrini M.","Gigascience","2014","2047-217x","journal article; research-article","Y","Y","N","0","Y","Y","N","N","Y","325.0204",NA,"3","25","PMC4228822","doi",NA,"github.com"
"1830","25221627","MED","25221627","10.1186/s13321-014-0040-8","A document classifier for medicinal chemistry publications trained on the ChEMBL corpus.","Papadatos G, van Westen GJ, Croset S, Santos R, Trubian S, Overington JP.","J Cheminform","2014","1758-2946","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","325.0204","1","6","40","PMC4158272",NA,NA,"github.com"
"1831","25168168","MED","25168168","10.1111/ele.12345","A general ecophysiological framework for modelling the impact of pests and pathogens on forest ecosystems.","Dietze MC, Matthes JH.","Ecol Lett","2014","1461-023x","journal article; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","N","0","Y","Y","N","N","N","325.0204","11","17","1418-1426","PMC4257091",NA,NA,"github.com"
"1832","24598230","MED","24598230","10.1016/j.jviromet.2014.02.020","Low copy target detection by Droplet Digital PCR through application of a novel open access bioinformatic pipeline, 'definetherain'.","Jones M, Williams J, GÃ¤rtner K, Phillips R, Hurst J, Frater J.","J Virol Methods","2014","0166-0934","journal article; research-article","Y","Y","Y","2","Y","Y","N","N","N","325.0204","100","202","46-53","PMC4003534",NA,NA,"github.com"
"1833","25403617","MED","25403617","10.1186/s12862-014-0228-6","Evolutionary origin of highly repetitive plastid genomes within the clover genus ( Trifolium ).","Sveinsson S, Cronk Q.","BMC Evol Biol","2014","1471-2148","journal article; research-article","Y","Y","N","0","Y","Y","Y","Y","Y","325.0204","1","14","228","PMC4241210","gen","EMBLUNIPROT","github.com"
"1834","25566051","MED","25566051","10.3389/fneng.2014.00043","A low-cost programmable pulse generator for physiology and behavior.","Sanders JI, Kepecs A.","Front Neuroeng","2014","1662-6443","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","325.0204",NA,"7","43","PMC4263096",NA,NA,"github.com"
"1835","25552936","MED","25552936",NA,"Efficient Inference of Gaussian-Process-Modulated Renewal Processes with Application to Medical Event Data.","Lasko TA.","Uncertain Artif Intell","2014","1525-3384","journal article; research-article","N","Y","N","0","Y","Y","N","N","N","325.0204",NA,"2014","469-476","PMC4278374",NA,NA,"github.com"
"1836","25414722","MED","25414722","10.3389/fgene.2014.00352","Controlling for population structure and genotyping platform bias in the eMERGE multi-institutional biobank linked to electronic health records.","Crosslin DR, Tromp G, Burt A, Kim DS, Verma SS, Lucas AM, Bradford Y, Crawford DC, Armasu SM, Heit JA, Hayes MG, Kuivaniemi H, Ritchie MD, Jarvik GP, de Andrade M, electronic Medical Records and Genomics (eMERGE) Network.","Front Genet","2014","1664-8021","journal article; research-article","Y","Y","N","1","Y","Y","N","N","N","325.0204",NA,"5","352","PMC4220165",NA,NA,"github.com"
"1837","24699270","MED","24699270","10.1371/journal.pone.0092725","ss3sim: an R package for fisheries Stock Assessment simulation with stock synthesis.","Anderson SC, Monnahan CC, Johnson KF, Ono K, Valero JL.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","0","Y","Y","N","N","N","325.0204","4","9","e92725","PMC3974719",NA,NA,"github.com"
"1838","24415924","MED","24415924","10.1371/journal.pbio.1001745","Best practices for scientific computing.","Wilson G, Aruliah DA, Brown CT, Chue Hong NP, Davis M, Guy RT, Haddock SH, Huff KD, Mitchell IM, Plumbley MD, Waugh B, White EP, Wilson P.","PLoS Biol","2014","1544-9173","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","5","Y","Y","N","N","N","325.0204","1","12","e1001745","PMC3886731",NA,NA,"github.com"
"1839","25452747","MED","25452747","10.3389/fmicb.2014.00601","The R package otu2ot for implementing the entropy decomposition of nucleotide variation in sequence data.","Ramette A, Buttigieg PL.","Front Microbiol","2014","1664-302x","journal article; research-article","Y","Y","N","1","Y","Y","N","N","N","325.0204",NA,"5","601","PMC4231947",NA,NA,"github.com"
"1840","25530613","MED","25530613","10.3390/ijms151223589","The Sesquiterpene Biosynthesis and Vessel-Occlusion Formation in Stems of Aquilaria sinensis (Lour.) Gilg Trees Induced by Wounding Treatments without Variation of Microbial Communities.","Zhang Z, Wei J, Han X, Liang L, Yang Y, Meng H, Xu Y, Gao Z.","Int J Mol Sci","2014","1422-0067","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","325.0204","12","15","23589-23603","PMC4284782",NA,NA,"github.com"
"1841","24705512","MED","24705512","10.1038/nnano.2014.54","Single-molecule spectroscopy of amino acids and peptides by recognition tunnelling.","Zhao Y, Ashcroft B, Zhang P, Liu H, Sen S, Song W, Im J, Gyarfas B, Manna S, Biswas S, Borges C, Lindsay S.","Nat Nanotechnol","2014","1748-3387","journal article; research support, n.i.h., extramural; research-article","Y","Y","N","1","Y","Y","N","N","N","325.0204","6","9","466-473","PMC4047173",NA,NA,"github.com"
"1842","25614798","MED","25614798","10.1002/ece3.1151","Dispersal and spatial heterogeneity allow coexistence between enemies and protective mutualists.","Poisot T, Bever JD, Thrall PH, Hochberg ME.","Ecol Evol","2014","2045-7758","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","325.0204","19","4","3841-3850","PMC4301050",NA,NA,"github.com"
"1843","24270787","MED","24270787","10.1093/nar/gkt1168","The UCSC Genome Browser database: 2014 update.","Karolchik D, Barber GP, Casper J, Clawson H, Cline MS, Diekhans M, Dreszer TR, Fujita PA, Guruvadoo L, Haeussler M, Harte RA, Heitner S, Hinrichs AS, Learned K, Lee BT, Li CH, Raney BJ, Rhead B, Rosenbloom KR, Sloan CA, Speir ML, Zweig AS, Haussler D, Kuhn RM, Kent WJ.","Nucleic Acids Res","2014","0305-1048","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","57","Y","Y","N","N","N","325.0204","database issue","42","d764-70","PMC3964947",NA,NA,"github.com"
"1844","24773628","MED","24773628","10.1186/1471-2164-15-314","EgoNet: identification of human disease ego-network modules.","Yang R, Bai Y, Qin Z, Yu T.","BMC Genomics","2014","1471-2164","journal article; research support, n.i.h., extramural; research-article","Y","Y","N","0","Y","Y","N","N","N","325.0204",NA,"15","314","PMC4234496",NA,NA,"github.com"
"1845","25234577","MED","25234577","10.1038/ncomms5890","Warped linear mixed models for the genetic analysis of transformed phenotypes.","Fusi N, Lippert C, Lawrence ND, Stegle O.","Nat Commun","2014","2041-1723","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","N","0","Y","Y","N","N","N","325.0204",NA,"5","4890","PMC4199105",NA,NA,"github.com"
"1846","24043593","MED","24043593","10.1007/s10278-013-9633-4","Development of a software for quantitative evaluation radiotherapy target and organ-at-risk segmentation comparison.","Kalpathy-Cramer J, Awan M, Bedrick S, Rasch CR, Rosenthal DI, Fuller CD.","J Digit Imaging","2014","0897-1889","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; brief-report","N","Y","N","0","Y","Y","N","N","N","325.0204","1","27","108-119","PMC3903974",NA,NA,"github.com"
"1847","24344789","MED","24344789","10.1021/pr400937n","Fast and accurate database searches with MS-GF+Percolator.","Granholm V, Kim S, Navarro JC, SjÃ¶lund E, Smith RD, KÃ¤ll L.","J Proteome Res","2014","1535-3893","journal article; research-article","N","Y","N","1","N","Y","N","N","N","325.0204","2","13","890-897","PMC3975676",NA,NA,"github.com"
"1848","24328097","MED","24328097","10.1021/pr400675n","SILAC peptide ratio calculator: a tool for SILAC quantitation of peptides and post-translational modifications.","Guan X, Rastogi N, Parthun MR, Freitas MA.","J Proteome Res","2014","1535-3893","journal article; research support, n.i.h., extramural; research-article","N","Y","N","1","N","Y","N","N","N","325.0204","2","13","506-516","PMC3953147",NA,NA,"github.com"
"1849","24600385","MED","24600385","10.3389/fninf.2014.00008","Dipy, a library for the analysis of diffusion MRI data.","Garyfallidis E, Brett M, Amirbekian B, Rokem A, van der Walt S, Descoteaux M, Nimmo-Smith I, Dipy Contributors.","Front Neuroinform","2014","1662-5196","journal article; research-article","Y","Y","Y","4","Y","Y","N","N","N","324.99158",NA,"8","8","PMC3931231",NA,NA,"github.com"
"1850","25009181","MED","25009181","10.1073/pnas.1319091111","The fossilized birth-death process for coherent calibration of divergence-time estimates.","Heath TA, Huelsenbeck JP, Stadler T.","Proc Natl Acad Sci U S A","2014","0027-8424","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","Y","2","Y","Y","N","N","N","324.99158","29","111","e2957-66","PMC4115571",NA,NA,"github.com"
"1851","24967877","MED","24967877","10.1371/journal.pcbi.1003652","Unsupervised learning of cone spectral classes from natural images.","Benson NC, Manning JR, Brainard DH.","PLoS Comput Biol","2014","1553-734x","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.99158","6","10","e1003652","PMC4072515",NA,NA,"github.com"
"1852","25159222","MED","25159222","10.1186/1471-2164-15-717","HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers.","Zhu Q, Kosoy M, Dittmar K.","BMC Genomics","2014","1471-2164","journal article; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","N","0","Y","Y","N","N","Y","324.99158","1","15","717","PMC4155097","gen",NA,"github.com"
"1853","24586468","MED","24586468","10.1371/journal.pone.0088977","OpenStage: a low-cost motorized microscope stage with sub-micron positioning accuracy.","Campbell RA, Eifert RW, Turner GC.","PLoS One","2014","1932-6203","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.99158","2","9","e88977","PMC3935852",NA,NA,"github.com"
"1854","24572152","MED","24572152","10.1186/1752-0509-8-22","GraTeLPy: graph-theoretic linear stability analysis.","Walther GR, Hartley M, Mincheva M.","BMC Syst Biol","2014","1752-0509","journal article; product-review","Y","Y","Y","0","Y","Y","N","N","N","324.99158",NA,"8","22","PMC4016541",NA,NA,"github.com"
"1855","25232314","MED","25232314","10.3389/fninf.2014.00073","PyNCS: a microkernel for high-level definition and configuration of neuromorphic electronic systems.","Stefanini F, Neftci EO, Sheik S, Indiveri G.","Front Neuroinform","2014","1662-5196","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.99158",NA,"8","73","PMC4152885",NA,NA,"github.com"
"1856","25461763","MED","25461763","10.1371/journal.pone.0114253","PERGA: a paired-end read guided de novo assembler for extending contigs using SVM and look ahead approach.","Zhu X, Leung HC, Chin FY, Yiu SM, Quan G, Liu B, Wang Y.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","Y","324.99158","12","9","e114253","PMC4252104","refseq",NA,"github.com"
"1857","24992937","MED","24992937","10.1186/1471-2148-14-150","An improved approximate-Bayesian model-choice method for estimating shared evolutionary history.","Oaks JR.","BMC Evol Biol","2014","1471-2148","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","N","0","Y","Y","N","N","Y","324.6441",NA,"14","150","PMC4227068","doi",NA,"github.com"
"1858","25520805","MED","25520805","10.1186/s40168-014-0050-9","Microbial shifts in the aging mouse gut.","Langille MG, Meehan CJ, Koenig JE, Dhanani AS, Rose RA, Howlett SE, Beiko RG.","Microbiome","2014","2049-2618","journal article; research-article","Y","Y","N","0","Y","Y","N","N","Y","324.61914","1","2","50","PMC4269096","pfam",NA,"github.com"
"1859","25520738","MED","25520738","10.3389/fgene.2014.00420","On the processes generating latitudinal richness gradients: identifying diagnostic patterns and predictions.","Hurlbert AH, Stegen JC.","Front Genet","2014","1664-8021","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.61914",NA,"5","420","PMC4251432",NA,NA,"github.com"
"1860","25489858","MED","25489858","10.1371/journal.pone.0114577","Dynamic approximate entropy electroanatomic maps detect rotors in a simulated atrial fibrillation model.","Ugarte JP, Orozco-Duque A, TobÃ³n C, Kremen V, Novak D, Saiz J, Oesterlein T, Schmitt C, Luik A, Bustamante J.","PLoS One","2014","1932-6203","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.61914","12","9","e114577","PMC4260907",NA,NA,"github.com"
"1861","25015380","MED","25015380","10.1101/gr.174052.114","High resolution mapping of modified DNA nucleobases using excision repair enzymes.","Bryan DS, Ransom M, Adane B, York K, Hesselberth JR.","Genome Res","2014","1088-9051","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","N","Y","N","0","Y","Y","Y","N","N","324.61914","9","24","1534-1542","PMC4158761",NA,"UNIPROT","github.com"
"1862","24748384","MED","24748384","10.1371/journal.pone.0095292","Genotyping-by-sequencing for Populus population genomics: an assessment of genome sampling patterns and filtering approaches.","Schilling MP, Wolf PG, Duffy AM, Rai HS, Rowe CA, Richardson BA, Mock KE.","PLoS One","2014","1932-6203","journal article; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","0","Y","Y","N","Y","Y","324.61914","4","9","e95292","PMC3991623","doi",NA,"github.com"
"1863","24752080","MED","24752080","10.1038/nbt.2862","Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms.","Patro R, Mount SM, Kingsford C.","Nat Biotechnol","2014","1087-0156","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","N","4","Y","Y","N","N","N","324.61914","5","32","462-464","PMC4077321",NA,NA,"github.com"
"1864","24281428","MED","24281428","10.1534/g3.113.008870","The pattern and distribution of deleterious mutations in maize.","Mezmouk S, Ross-Ibarra J.","G3 (Bethesda)","2014","2160-1836","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.61914","1","4","163-171","PMC3887532",NA,NA,"github.com"
"1865","24291769","MED","24291769","10.1093/bfgp/elt046","Advances in genomics of bony fish.","Spaink HP, Jansen HJ, Dirks RP.","Brief Funct Genomics","2014","2041-2649","journal article; review; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.61914","2","13","144-156","PMC3954040",NA,NA,"github.com"
"1866","25177549","MED","25177549","10.3389/fcimb.2014.00108","Functional expression of dental plaque microbiota.","Peterson SN, Meissner T, Su AI, Snesrud E, Ong AC, Schork NJ, Bretz WA.","Front Cell Infect Microbiol","2014","2235-2988","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.61914",NA,"4","108","PMC4132376",NA,NA,"github.com"
"1867","24636731","MED","24636731","10.1186/1746-6148-10-71","EpiContactTrace: an R-package for contact tracing during livestock disease outbreaks and for risk-based surveillance.","NÃ¶remark M, Widgren S.","BMC Vet Res","2014","1746-6148","journal article; product-review","Y","Y","Y","0","Y","Y","N","N","N","324.61914",NA,"10","71","PMC3974595",NA,NA,"github.com"
"1868","25358459","MED","25358459","10.1186/preaccept-1380752981388541","How much is tuberculosis screening worth? Estimating the value of active case finding for tuberculosis in South Africa, China, and India.","Azman AS, Golub JE, Dowdy DW.","BMC Med","2014","1741-7015","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.61914","1","12","216","PMC4224697",NA,NA,"github.com"
"1869","24772189","MED","24772189","10.1155/2014/957231","BioTCM-SE: a semantic search engine for the information retrieval of modern biology and traditional Chinese medicine.","Chen X, Chen H, Bi X, Gu P, Chen J, Wu Z.","Comput Math Methods Med","2014","1748-670x","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.61914",NA,"2014","957231","PMC3989774",NA,NA,"github.com"
"1870","25502724","MED","25502724","10.1371/journal.pgen.1004801","Large-scale Metabolomic Profiling Identifies Novel Biomarkers for Incident Coronary Heart Disease.","Ganna A, Salihovic S, SundstrÃ¶m J, Broeckling CD, Hedman AK, Magnusson PK, Pedersen NL, Larsson A, Siegbahn A, Zilmer M, Prenni J, ArnlÃ¶v J, Lind L, Fall T, Ingelsson E.","PLoS Genet","2014","1553-7390","journal article; research-article","Y","Y","N","0","Y","Y","N","N","Y","324.61914","12","10","e1004801","PMC4263376","refsnp",NA,"github.com"
"1871","25495537","MED","25495537","10.1186/s12859-014-0398-7","solGS: a web-based tool for genomic selection.","Tecle IY, Edwards JD, Menda N, Egesi C, Rabbi IY, Kulakow P, Kawuki R, Jannink JL, Mueller LA.","BMC Bioinformatics","2014","1471-2105","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","324.61914","1","15","398","PMC4269960",NA,NA,"github.com"
"1872","25538643","MED","25538643","10.3389/fpsyg.2014.01365","Cross-cultural differences in crossmodal correspondences between basic tastes and visual features.","Wan X, Woods AT, van den Bosch JJ, McKenzie KJ, Velasco C, Spence C.","Front Psychol","2014","1664-1078","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.61914",NA,"5","1365","PMC4259000",NA,NA,"github.com"
"1873","24985530","MED","24985530","10.1007/s40264-014-0189-0","Bridging islands of information to establish an integrated knowledge base of drugs and health outcomes of interest.","Boyce RD, Ryan PB, NorÃ©n GN, Schuemie MJ, Reich C, Duke J, Tatonetti NP, TrifirÃ² G, Harpaz R, Overhage JM, Hartzema AG, Khayter M, Voss EA, Lambert CG, Huser V, Dumontier M.","Drug Saf","2014","0114-5916","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research support, n.i.h., intramural; editorial","Y","Y","Y","0","Y","Y","N","N","N","324.61914","8","37","557-567","PMC4134480",NA,NA,"github.com"
"1874","24801682","MED","24801682","10.1371/journal.pone.0096194","Modeling the electric potential across neuronal membranes: the effect of fixed charges on spinal ganglion neurons and neuroblastoma cells.","Pinto TM, Wedemann RS, Cortez CM.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","324.61914","5","9","e96194","PMC4011737",NA,NA,"github.com"
"1875","25358118","MED","25358118","10.7554/elife.04418","Real-time observation of signal recognition particle binding to actively translating ribosomes.","Noriega TR, Chen J, Walter P, Puglisi JD.","Elife","2014","2050-084x","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","N","0","Y","Y","N","N","N","324.61914",NA,"3",NA,"PMC4213662",NA,NA,"github.com"
"1876","25279560","MED","25279560","10.1371/journal.pone.0108496","A dynamic study of protein secretion and aggregation in the secretory pathway.","Mossuto MF, Sannino S, Mazza D, Fagioli C, Vitale M, Yoboue ED, Sitia R, Anelli T.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","324.61914","10","9","e108496","PMC4184786",NA,NA,"github.com"
"1877","25304126","MED","25304126","10.1186/s12918-014-0115-1","A computational platform to maintain and migrate manual functional annotations for BioCyc databases.","Walsh JR, Sen TZ, Dickerson JA.","BMC Syst Biol","2014","1752-0509","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.61914","1","8","115","PMC4203924",NA,NA,"github.com"
"1878","25013771","MED","25013771","10.1155/2014/264519","A bioinformatics pipeline for the analyses of viral escape dynamics and host immune responses during an infection.","Leung P, Bull R, Lloyd A, Luciani F.","Biomed Res Int","2014","2314-6133","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","Y","324.61914",NA,"2014","264519","PMC4072169","gen",NA,"github.com"
"1879","24972019","MED","24972019","10.1371/journal.pone.0101158","Phylogenomic analysis of ""red"" genes from two divergent species of the ""green"" secondary phototrophs, the chlorarachniophytes, suggests multiple horizontal gene transfers from the red lineage before the divergence of extant chlorarachniophytes.","Yang Y, Matsuzaki M, Takahashi F, Qu L, Nozaki H.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.61914","6","9","e101158","PMC4074131",NA,NA,"github.com"
"1880","25289637","MED","25289637","10.1371/journal.pone.0109326","Dynamic epigenetic control of highly conserved noncoding elements.","Seridi L, Ryu T, Ravasi T.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","324.61914","10","9","e109326","PMC4188601",NA,NA,"github.com"
"1881","25437873","MED","25437873","10.1371/journal.pone.0113838","The connectome visualization utility: software for visualization of human brain networks.","LaPlante RA, Douw L, Tang W, Stufflebeam SM.","PLoS One","2014","1932-6203","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.61914","12","9","e113838","PMC4250035",NA,NA,"github.com"
"1882","25006672","MED","25006672","10.1371/journal.pone.0102188","Large-scale structure of a network of co-occurring MeSH terms: statistical analysis of macroscopic properties.","Kastrin A, Rindflesch TC, Hristovski D.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research support, n.i.h., intramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.61914","7","9","e102188","PMC4090190",NA,NA,"github.com"
"1883","25121495","MED","25121495","10.1371/journal.pone.0105043","Phylobetadiversity among forest types in the Brazilian Atlantic Forest complex.","Duarte Lda S, Bergamin RS, Marcilio-Silva V, Seger GD, Marques MC.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.61914","8","9","e105043","PMC4133375",NA,NA,"github.com"
"1884","25331649","MED","25331649","10.1186/1471-2164-15-914","The genomic landscape of the verrucomicrobial methanotroph Methylacidiphilum fumariolicum SolV.","Anvar SY, Frank J, Pol A, Schmitz A, Kraaijeveld K, den Dunnen JT, Op den Camp HJ.","BMC Genomics","2014","1471-2164","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","324.61914","1","15","914","PMC4210602",NA,NA,"github.com"
"1885","25052703","MED","25052703","10.1093/database/bau076","APADB: a database for alternative polyadenylation and microRNA regulation events.","MÃ¼ller S, Rycak L, Afonso-Grunz F, Winter P, Zawada AM, Damrath E, Scheider J, SchmÃ¤h J, Koch I, Kahl G, Rotter B.","Database (Oxford)","2014","1758-0463","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.61914",NA,"2014",NA,"PMC4105710",NA,NA,"github.com"
"1886","25100051","MED","25100051","10.1186/1472-6947-14-66","Casebook: a virtual patient iPad application for teaching decision-making through the use of electronic health records.","Bloice MD, Simonic KM, Holzinger A.","BMC Med Inform Decis Mak","2014","1472-6947","journal article; product-review","Y","Y","Y","0","Y","Y","N","N","N","324.61914",NA,"14","66","PMC4149039",NA,NA,"github.com"
"1887","25062922","MED","25062922","10.1093/gbe/evu155","Comparative genomics suggests that the human pathogenic fungus Pneumocystis jirovecii acquired obligate biotrophy through gene loss.","CissÃ© OH, Pagni M, Hauser PM.","Genome Biol Evol","2014","1759-6653","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","Y","324.61914","8","6","1938-1948","PMC4159005","pfam; interpro; sprot",NA,"github.com"
"1888","25473480","MED","25473480","10.1002/ece3.1182","Visualization of species pairwise associations: a case study of surrogacy in bird assemblages.","Lane PW, Lindenmayer DB, Barton PS, Blanchard W, Westgate MJ.","Ecol Evol","2014","2045-7758","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.61914","16","4","3279-3289","PMC4222214",NA,NA,"github.com"
"1889","24886400","MED","24886400","10.1186/1479-5876-12-124","Modeling the transmission of community-associated methicillin-resistant Staphylococcus aureus: a dynamic agent-based simulation.","Macal CM, North MJ, Collier N, Dukic VM, Wegener DT, David MZ, Daum RS, Schumm P, Evans JA, Wilder JR, Miller LG, Eells SJ, Lauderdale DS.","J Transl Med","2014","1479-5876","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","1","Y","Y","N","N","N","324.61914",NA,"12","124","PMC4049803",NA,NA,"github.com"
"1890","25350546","MED","25350546","10.1371/journal.pone.0109032","The impact of text message reminders on adherence to antimalarial treatment in northern Ghana: a randomized trial.","Raifman JR, Lanthorn HE, Rokicki S, Fink G.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","324.61914","10","9","e109032","PMC4211682",NA,NA,"github.com"
"1891","25270300","MED","25270300","10.1038/srep06480","Improved assemblies using a source-agnostic pipeline for MetaGenomic Assembly by Merging (MeGAMerge) of contigs.","Scholz M, Lo CC, Chain PS.","Sci Rep","2014","2045-2322","journal article; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","N","0","Y","Y","N","N","N","324.61914",NA,"4","6480","PMC4180827",NA,NA,"github.com"
"1892","24586303","MED","24586303","10.1371/journal.pone.0088072","Comprehensive detection of genes causing a phenotype using phenotype sequencing and pathway analysis.","Harper M, Gronenberg L, Liao J, Lee C.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.61914","2","9","e88072","PMC3935835",NA,NA,"github.com"
"1893","24970375","MED","24970375","10.1038/srep05421","Ataxia telangiectasia derived iPS cells show preserved x-ray sensitivity and decreased chromosomal instability.","Fukawatase Y, Toyoda M, Okamura K, Nakamura K, Nakabayashi K, Takada S, Yamazaki-Inoue M, Masuda A, Nasu M, Hata K, Hanaoka K, Higuchi A, Takubo K, Umezawa A.","Sci Rep","2014","2045-2322","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","324.61914",NA,"4","5421","PMC4073166",NA,NA,"github.com"
"1894","25413600","MED","25413600","10.1186/s12859-014-0368-0","Bayesian neural networks for detecting epistasis in genetic association studies.","Beam AL, Motsinger-Reif A, Doyle J.","BMC Bioinformatics","2014","1471-2105","journal article; research-article","Y","Y","N","0","Y","Y","N","N","Y","324.61914","1","15","368","PMC4256933","refsnp",NA,"github.com"
"1895","24366880","MED","24366880","10.1093/nar/gkt1315","TeloTool: a new tool for telomere length measurement from terminal restriction fragment analysis with improved probe intensity correction.","GÃ¶hring J, Fulcher N, Jacak J, Riha K.","Nucleic Acids Res","2014","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","324.61914","3","42","e21","PMC3919618",NA,NA,"github.com"
"1896","24413527","MED","24413527","10.1093/bioinformatics/btu014","Efficient haplotype matching and storage using the positional Burrows-Wheeler transform (PBWT).","Durbin R.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","N","N","N","324.61914","9","30","1266-1272","PMC3998136",NA,NA,"github.com"
"1897","24475911","MED","24475911","10.1186/1471-2105-15-30","Launching genomics into the cloud: deployment of Mercury, a next generation sequence analysis pipeline.","Reid JG, Carroll A, Veeraraghavan N, Dahdouli M, Sundquist A, English A, Bainbridge M, White S, Salerno W, Buhay C, Yu F, Muzny D, Daly R, Duyk G, Gibbs RA, Boerwinkle E.","BMC Bioinformatics","2014","1471-2105","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","5","Y","Y","N","Y","N","324.61914",NA,"15","30","PMC3922167",NA,NA,"github.com"
"1898","24475928","MED","24475928","10.1186/1471-2105-15-31","geneCommittee: a web-based tool for extensively testing the discriminatory power of biologically relevant gene sets in microarray data classification.","Reboiro-Jato M, Arrais JP, Oliveira JL, Fdez-Riverola F.","BMC Bioinformatics","2014","1471-2105","journal article; research support, non-u.s. gov't; product-review","Y","Y","Y","0","Y","Y","N","Y","N","324.61914",NA,"15","31","PMC3909759",NA,NA,"github.com"
"1899","24476915","MED","24476915","10.1093/nar/gku071","A phylogenomics approach for selecting robust sets of phylogenetic markers.","Capella-Gutierrez S, Kauff F, GabaldÃ³n T.","Nucleic Acids Res","2014","0305-1048","journal article; validation studies; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","Y","324.61914","7","42","e54","PMC3985644","sprot",NA,"github.com"
"1900","24529162","MED","24529162","10.1186/2049-2618-2-5","Comparison of brush and biopsy sampling methods of the ileal pouch for assessment of mucosa-associated microbiota of human subjects.","Huse SM, Young VB, Morrison HG, Antonopoulos DA, Kwon J, Dalal S, Arrieta R, Hubert NA, Shen L, Vineis JH, Koval JC, Sogin ML, Chang EB, Raffals LE.","Microbiome","2014","2049-2618","journal article; research-article","Y","Y","Y","2","Y","Y","N","N","N","324.61914","1","2","5","PMC3931571",NA,NA,"github.com"
"1901","24627814","MED","24627814","10.4258/hir.2014.20.1.11","Free/Libre open source software in health care: a review.","Karopka T, Schmuhl H, Demski H.","Healthc Inform Res","2014","2093-3681","journal article; review; review-article","Y","Y","Y","0","Y","Y","N","N","N","324.61914","1","20","11-22","PMC3950260",NA,NA,"github.com"
"1902","24634472","MED","24634472","10.1093/database/bau017","Linking tissues to phenotypes using gene expression profiles.","Oellrich A, Sanger Mouse Genetics Project, Smedley D.","Database (Oxford)","2014","1758-0463","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.61914",NA,"2014","bau017","PMC3982582",NA,NA,"github.com"
"1903","24970883","MED","24970883","10.1534/g3.114.012195","The functional significance of common polymorphisms in zinc finger transcription factors.","Lockwood SH, Guan A, Yu AS, Zhang C, Zykovich A, Korf I, Rannala B, Segal DJ.","G3 (Bethesda)","2014","2160-1836","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","N","0","Y","Y","N","N","Y","324.61914","9","4","1647-1655","PMC4169156","pfam",NA,"github.com"
"1904","24611607","MED","24611607","10.1021/pr401143e","Signatures for mass spectrometry data quality.","Amidan BG, Orton DJ, Lamarche BL, Monroe ME, Moore RJ, Venzin AM, Smith RD, Sego LH, Tardiff MF, Payne SH.","J Proteome Res","2014","1535-3893","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","0","Y","Y","N","N","N","324.61914","4","13","2215-2222","PMC4104976",NA,NA,"github.com"
"1905","24999823","MED","24999823","10.1371/journal.pone.0098986","Some limitations of public sequence data for phylogenetic inference (in plants).","Hinchliff CE, Smith SA.","PLoS One","2014","1932-6203","journal article; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","0","Y","Y","N","Y","N","324.61914","7","9","e98986","PMC4085032",NA,NA,"github.com"
"1906","25275010","MED","25275010","10.1073/pnas.1400374111","Network histograms and universality of blockmodel approximation.","Olhede SC, Wolfe PJ.","Proc Natl Acad Sci U S A","2014","0027-8424","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","N","Y","N","0","Y","Y","N","N","N","324.61914","41","111","14722-14727","PMC4205664",NA,NA,"github.com"
"1907","24465607","MED","24465607","10.1371/journal.pone.0085585","The fiber walk: a model of tip-driven growth with lateral expansion.","Bucksch A, Turk G, Weitz JS.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","1","Y","Y","N","N","N","324.61914","1","9","e85585","PMC3899046",NA,NA,"github.com"
"1908","25426102","MED","25426102","10.3389/fmicb.2014.00505","Bacteria in Ostreococcus tauri cultures - friends, foes or hitchhikers?","Abby SS, Touchon M, De Jode A, Grimsley N, Piganeau G.","Front Microbiol","2014","1664-302x","journal article; research-article","Y","Y","N","0","Y","Y","N","N","Y","324.61914",NA,"5","505","PMC4224133","gen",NA,"github.com"
"1909","25133800","MED","25133800","10.1371/journal.pone.0104417","Evaluation of exome sequencing to estimate tumor burden in plasma.","Klevebring D, Neiman M, Sundling S, Eriksson L, Darai Ramqvist E, Celebioglu F, Czene K, Hall P, Egevad L, GrÃ¶nberg H, Lindberg J.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.61914","8","9","e104417","PMC4136786",NA,NA,"github.com"
"1910","24489671","MED","24489671","10.1371/journal.pone.0085777","Powerlaw: a Python package for analysis of heavy-tailed distributions.","Alstott J, Bullmore E, Plenz D.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research support, n.i.h., intramural; research-article","Y","Y","Y","4","Y","Y","N","N","N","324.61914","1","9","e85777","PMC3906378",NA,NA,"github.com"
"1911","25371418","MED","25371418","10.1136/bmjopen-2014-006278","Seeking the source of Pseudomonas aeruginosa infections in a recently opened hospital: an observational study using whole-genome sequencing.","Quick J, Cumley N, Wearn CM, Niebel M, Constantinidou C, Thomas CM, Pallen MJ, Moiemen NS, Bamford A, Oppenheim B, Loman NJ.","BMJ Open","2014","2044-6055","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","324.61914","11","4","e006278","PMC4225241",NA,NA,"github.com"
"1912","24824441","MED","24824441","10.1371/journal.pone.0096953","Ecotype diversity and conversion in Photobacterium profundum strains.","Lauro FM, Eloe-Fadrosh EA, Richter TK, Vitulo N, Ferriera S, Johnson JH, Bartlett DH.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.61914","5","9","e96953","PMC4019646",NA,NA,"github.com"
"1913","24782521","MED","24782521","10.1093/nar/gku324","Enriched domain detector: a program for detection of wide genomic enrichment domains robust against local variations.","Lund E, Oldenburg AR, Collas P.","Nucleic Acids Res","2014","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","Y","N","N","324.61914","11","42","e92","PMC4066758",NA,"ARXPR","github.com"
"1914","25313068","MED","25313068","10.1073/pnas.1323007111","Why the proportion of transmission during early-stage HIV infection does not predict the long-term impact of treatment on HIV incidence.","Eaton JW, Hallett TB.","Proc Natl Acad Sci U S A","2014","0027-8424","journal article; research support, non-u.s. gov't; research-article","N","Y","N","0","Y","Y","N","N","N","324.61914","45","111","16202-16207","PMC4234601",NA,NA,"github.com"
"1915","24598259","MED","24598259","10.1093/nar/gku178","Impact of sequencing depth in ChIP-seq experiments.","Jung YL, Luquette LJ, Ho JW, Ferrari F, Tolstorukov M, Minoda A, Issner R, Epstein CB, Karpen GH, Kuroda MI, Park PJ.","Nucleic Acids Res","2014","0305-1048","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","Y","N","324.61914","9","42","e74","PMC4027199",NA,NA,"github.com"
"1916","24892086","MED","24892086","10.1155/2014/760301","Unsupervised quality estimation model for English to German translation and its application in extensive supervised evaluation.","Han AL, Wong DF, Chao LS, He L, Lu Y.","ScientificWorldJournal","2014","2356-6140","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","N","Y","N","N","N","324.61914",NA,"2014","760301","PMC4032676",NA,NA,"github.com"
"1917","25083859","MED","25083859","10.1371/journal.pone.0103177","Lack of genomic heterogeneity at high-resolution aCGH between primary breast cancers and their paired lymph node metastases.","Vollebergh MA, Klijn C, Schouten PC, Wesseling J, Israeli D, Ylstra B, Wessels LF, Jonkers J, Linn SC.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.61914","8","9","e103177","PMC4118860",NA,NA,"github.com"
"1918","25376098","MED","25376098","10.1038/srep06957","Assessment of quality control approaches for metagenomic data analysis.","Zhou Q, Su X, Ning K.","Sci Rep","2014","2045-2322","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","324.61914",NA,"4","6957","PMC4223665",NA,NA,"github.com"
"1919","25057252","MED","25057252","10.3897/bdj.2.e1114","Symbiota - A virtual platform for creating voucher-based biodiversity information communities.","Gries C, Gilbert EE, Franz NM.","Biodivers Data J","2014","1314-2828","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","324.61914","2",NA,"e1114","PMC4092327",NA,NA,"github.com"
"1920","24692656","MED","24692656","10.1093/molbev/mst139","The evolution of human cells in terms of protein innovation.","Sardar AJ, Oates ME, Fang H, Forrest AR, Kawaji H, FANTOM Consortium, Gough J, Rackham OJ.","Mol Biol Evol","2014","0737-4038","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.61914","6","31","1364-1374","PMC4032124",NA,NA,"github.com"
"1921","24653693","MED","24653693","10.3389/fninf.2014.00021","Pain Research Forum: application of scientific social media frameworks in neuroscience.","Das S, McCaffrey PG, Talkington MW, Andrews NA, Corlosquet S, Ivinson AJ, Clark T.","Front Neuroinform","2014","1662-5196","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.61914",NA,"8","21","PMC3949323",NA,NA,"github.com"
"1922","24678591","MED","24678591","10.1186/1471-2105-15-90","Consistency of metagenomic assignment programs in simulated and real data.","Garcia-Etxebarria K, Garcia-GarcerÃ  M, Calafell F.","BMC Bioinformatics","2014","1471-2105","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","324.61914",NA,"15","90","PMC3986635",NA,NA,"github.com"
"1923","24757214","MED","24757214","10.1128/mbio.01017-13","Diverse antibiotic resistance genes in dairy cow manure.","Wichmann F, Udikovic-Kolic N, Andrew S, Handelsman J.","MBio","2014","2150-7511","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","Y","N","Y","324.61914","2","5","e01017","PMC3993861","gen","EMBLUNIPROT","github.com"
"1924","24790557","MED","24790557","10.1155/2014/237243","Network-based analysis of software change propagation.","Wang R, Huang R, Qu B.","ScientificWorldJournal","2014","2356-6140","journal article; research-article","Y","Y","Y","0","N","Y","N","N","N","324.61914",NA,"2014","237243","PMC3984771",NA,NA,"github.com"
"1925","24795617","MED","24795617","10.3389/fninf.2014.00036","Integrating neuroinformatics tools in TheVirtualBrain.","Woodman MM, Pezard L, Domide L, Knock SA, Sanz-Leon P, Mersmann J, McIntosh AR, Jirsa V.","Front Neuroinform","2014","1662-5196","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.61914",NA,"8","36","PMC4001068",NA,NA,"github.com"
"1926","24917877","MED","24917877","10.3389/fgene.2014.00153","Copy number variants and selective sweeps in natural populations of the house mouse (Mus musculus domesticus).","Bryk J, Tautz D.","Front Genet","2014","1664-8021","journal article; review; review-article","Y","Y","Y","1","Y","Y","N","N","N","324.61914",NA,"5","153","PMC4042557",NA,NA,"github.com"
"1927","24917883","MED","24917883","10.3389/fgene.2014.00163","Evolution of genomic structural variation and genomic architecture in the adaptive radiations of African cichlid fishes.","Fan S, Meyer A.","Front Genet","2014","1664-8021","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","324.61914",NA,"5","163","PMC4042683",NA,NA,"github.com"
"1928","24368852","MED","24368852","10.1073/pnas.1312213111","Interannual variation in land-use intensity enhances grassland multidiversity.","Allan E, Bossdorf O, Dormann CF, Prati D, Gossner MM, Tscharntke T, BlÃ¼thgen N, Bellach M, Birkhofer K, Boch S, BÃ¶hm S, BÃ¶rschig C, Chatzinotas A, Christ S, Daniel R, DiekÃ¶tter T, Fischer C, Friedl T, Glaser K, Hallmann C, Hodac L, HÃ¶lzel N, Jung K, Klein AM, Klaus VH, Kleinebecker T, Krauss J, Lange M, Morris EK, MÃ¼ller J, Nacke H, Pasalic E, Rillig MC, RothenwÃ¶hrer C, Schall P, Scherber C, Schulze W, Socher SA, Steckel J, Steffan-Dewenter I, TÃ¼rke M, Weiner CN, Werner M, Westphal C, Wolters V, Wubet T, Gockel S, Gorke M, Hemp A, Renner SC, SchÃ¶ning I, Pfeiffer S, KÃ¶nig-Ries B, Buscot F, Linsenmair KE, Schulze ED, Weisser WW, Fischer M.","Proc Natl Acad Sci U S A","2014","0027-8424","journal article; research support, non-u.s. gov't; research-article","N","Y","Y","3","Y","Y","N","N","N","324.61914","1","111","308-313","PMC3890898",NA,NA,"github.com"
"1929","24946774","MED","24946774","10.1186/1475-925x-13-78","Automatic tracking of cells for video microscopy in patch clamp experiments.","Peixoto HM, Munguba H, Cruz RM, Guerreiro AM, Leao RN.","Biomed Eng Online","2014","1475-925x","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.61914",NA,"13","78","PMC4084571",NA,NA,"github.com"
"1930","24982611","MED","24982611","10.3389/fnins.2014.00146","Pre-attentive cortical processing of behaviorally perceptible spatial changes in older adults-a mismatch negativity study.","Freigang C, RÃ¼bsamen R, Richter N.","Front Neurosci","2014","1662-4548","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.61914",NA,"8","146","PMC4059044",NA,NA,"github.com"
"1931","25061514","MED","25061514","10.1186/2049-2618-2-25","The dynamics of a family's gut microbiota reveal variations on a theme.","Schloss PD, Iverson KD, Petrosino JF, Schloss SJ.","Microbiome","2014","2049-2618","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.61914",NA,"2","25","PMC4109379",NA,NA,"github.com"
"1932","25225118","MED","25225118","10.1186/1471-2105-15-302","SAGE: String-overlap Assembly of GEnomes.","Ilie L, Haider B, Molnar M, Solis-Oba R.","BMC Bioinformatics","2014","1471-2105","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","324.61914","1","15","302","PMC4174676",NA,NA,"github.com"
"1933","25285097","MED","25285097","10.3389/fpls.2014.00491","Generalized framework for context-specific metabolic model extraction methods.","Robaina EstÃ©vez S, Nikoloski Z.","Front Plant Sci","2014","1664-462x","journal article; review; review-article","Y","Y","N","0","Y","Y","N","N","N","324.61914",NA,"5","491","PMC4168813",NA,NA,"github.com"
"1934","25374661","MED","25374661","10.1186/2047-217x-3-18","GWATCH: a web platform for automated gene association discovery analysis.","Svitin A, Malov S, Cherkasov N, Geerts P, Rotkevich M, Dobrynin P, Shevchenko A, Guan L, Troyer J, Hendrickson S, Dilks HH, Oleksyk TK, Donfield S, Gomperts E, Jabs DA, Sezgin E, Van Natta M, Harrigan PR, Brumme ZL, O'Brien SJ.","Gigascience","2014","2047-217x","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.61914",NA,"3","18","PMC4220276",NA,NA,"github.com"
"1935","24875832","MED","24875832","10.1371/journal.pone.0098177","Influence of depth of interaction upon the performance of scintillator detectors.","Brown MS, Gundacker S, Taylor A, Tummeltshammer C, Auffray E, Lecoq P, Papakonstantinou I.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.61914","5","9","e98177","PMC4038557",NA,NA,"github.com"
"1936","24038734","MED","24038734","10.1002/stem.1531","Genome-wide analysis of miRNA-mRNA interactions in marrow stromal cells.","Balakrishnan I, Yang X, Brown J, Ramakrishnan A, Torok-Storb B, Kabos P, Hesselberth JR, Pillai MM.","Stem Cells","2014","1066-5099","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","N","Y","Y","0","Y","Y","N","N","N","324.61914","3","32","662-673","PMC4127404",NA,NA,"github.com"
"1937","24841417","MED","24841417","10.1371/journal.pone.0097435","Human and environmental impacts on river sediment microbial communities.","Gibbons SM, Jones E, Bearquiver A, Blackwolf F, Roundstone W, Scott N, Hooker J, Madsen R, Coleman ML, Gilbert JA.","PLoS One","2014","1932-6203","journal article; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","2","Y","Y","N","N","N","324.61914","5","9","e97435","PMC4026135",NA,NA,"github.com"
"1938","24497972","MED","24497972","10.1371/journal.pone.0086707","WBSA: web service for bisulfite sequencing data analysis.","Liang F, Tang B, Wang Y, Wang J, Yu C, Chen X, Zhu J, Yan J, Zhao W, Li R.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.61914","1","9","e86707","PMC3907392",NA,NA,"github.com"
"1939","25566002","MED","25566002","10.3389/fnbeh.2014.00434","Physiological and behavioral patterns of corruption.","Jaber-LÃ³pez T, GarcÃa-Gallego A, Perakakis P, Georgantzis N.","Front Behav Neurosci","2014","1662-5153","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.61914",NA,"8","434","PMC4273640",NA,NA,"github.com"
"1940","25532018","MED","25532018","10.1371/journal.pone.0114979","Spatial complementarity and the coexistence of species.","VelÃ¡zquez J, Garrahan JP, Eichhorn MP.","PLoS One","2014","1932-6203","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.61914","12","9","e114979","PMC4274010",NA,NA,"github.com"
"1941","25545818","MED","25545818","10.1371/journal.pone.0115280","Fear extinction as a model for synaptic plasticity in major depressive disorder.","Kuhn M, HÃ¶ger N, Feige B, Blechert J, Normann C, Nissen C.","PLoS One","2014","1932-6203","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.61914","12","9","e115280","PMC4278908",NA,NA,"github.com"
"1942","25546581","MED","25546581","10.1371/journal.pone.0115700","An Antidote to the Imager's Fallacy, or How to Identify Brain Areas That Are in Limbo.","de Hollander G, Wagenmakers EJ, Waldorp L, Forstmann B.","PLoS One","2014","1932-6203","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.61914","12","9","e115700","PMC4278760",NA,NA,"github.com"
"1943","25241745","MED","25241745","10.1016/j.stemcr.2014.06.019","Transiently active Wnt/Î²-catenin signaling is not required but must be silenced for stem cell function during muscle regeneration.","Murphy MM, Keefe AC, Lawson JA, Flygare SD, Yandell M, Kardon G.","Stem Cell Reports","2014","2213-6711","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","N","0","Y","Y","N","N","N","324.61914","3","3","475-488","PMC4266007",NA,NA,"github.com"
"1944","25404257","MED","25404257","10.1186/1471-2164-15-975","Structure and decay of a proto-Y region in Tilapia, Oreochromis niloticus.","Gammerdinger WJ, Conte MA, Acquah EA, Roberts RB, Kocher TD.","BMC Genomics","2014","1471-2164","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","N","0","Y","Y","N","N","N","324.61914","1","15","975","PMC4251933",NA,NA,"github.com"
"1945","24834435","MED","24834435","10.1155/2014/745298","Using the Sadakane compressed suffix tree to solve the all-pairs suffix-prefix problem.","Rachid MH, Malluhi Q, Abouelhoda M.","Biomed Res Int","2014","2314-6133","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.61914",NA,"2014","745298","PMC4009283",NA,NA,"github.com"
"1946","24586791","MED","24586791","10.1371/journal.pone.0089456","A semi-automated pipeline for the segmentation of rhesus macaque hippocampus: validation across a wide age range.","Hunsaker MR, Amaral DG.","PLoS One","2014","1932-6203","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","0","N","Y","N","N","N","324.61914","2","9","e89456","PMC3933562",NA,NA,"github.com"
"1947","25123659","MED","25123659","10.1093/nar/gku744","A comprehensive survey of non-canonical splice sites in the human transcriptome.","Parada GE, Munita R, Cerda CA, Gysling K.","Nucleic Acids Res","2014","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","324.61914","16","42","10564-10578","PMC4176328",NA,NA,"github.com"
"1948","24353264","MED","24353264","10.1093/dnares/dst054","Summarizing specific profiles in Illumina sequencing from whole-genome amplified DNA.","Tsai IJ, Hunt M, Holroyd N, Huckvale T, Berriman M, Kikuchi T.","DNA Res","2014","1340-2838","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","Y","N","324.61914","3","21","243-254","PMC4060946",NA,NA,"github.com"
"1949","25336405","MED","25336405","10.1002/mbo3.218","Characterization of the bile and gall bladder microbiota of healthy pigs.","JimÃ©nez E, SÃ¡nchez B, Farina A, Margolles A, RodrÃguez JM.","Microbiologyopen","2014","2045-8827","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","324.61914","6","3","937-949","PMC4263516",NA,NA,"github.com"
"1950","25470125","MED","25470125","10.1371/journal.pone.0114069","The trouble with triplets in biodiversity informatics: a data-driven case against current identifier practices.","Guralnick R, Conlin T, Deck J, Stucky BJ, Cellinese N.","PLoS One","2014","1932-6203","journal article; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","N","0","Y","Y","N","Y","Y","324.61914","12","9","e114069","PMC4254916","doi",NA,"github.com"
"1951","24834071","MED","24834071","10.3389/fgene.2014.00111","Quality control of next-generation sequencing data without a reference.","Trivedi UH, CÃ©zard T, Bridgett S, Montazam A, Nichols J, Blaxter M, Gharbi K.","Front Genet","2014","1664-8021","journal article; research-article","Y","Y","Y","2","Y","Y","N","N","N","324.61914",NA,"5","111","PMC4018527",NA,NA,"github.com"
"1952","25473951","MED","25473951","10.1371/journal.pone.0114230","The role of natural enemy foraging guilds in controlling cereal aphids in Michigan wheat.","Safarzoda S, Bahlai CA, Fox AF, Landis DA.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","324.61914","12","9","e114230","PMC4256412",NA,NA,"github.com"
"1953","24479757","MED","24479757","10.1186/1758-2946-6-3","Efficient ring perception for the Chemistry Development Kit.","May JW, Steinbeck C.","J Cheminform","2014","1758-2946","journal article; product-review","Y","Y","Y","0","Y","Y","N","N","N","324.61914","1","6","3","PMC3922685",NA,NA,"github.com"
"1954","25494902","MED","25494902",NA,"Novel RP1 mutations and a recurrent BBS1 variant explain the co-existence of two distinct retinal phenotypes in the same pedigree.","MÃ©ndez-Vidal C, Bravo-Gil N, GonzÃ¡lez-Del Pozo M, Vela-Boza A, Dopazo J, Borrego S, AntiÃ±olo G.","BMC Genet","2014","1471-2156","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.61914","1","15","143","PMC4271491",NA,NA,"github.com"
"1955","25495907","MED","25495907",NA,"CLAST: CUDA implemented large-scale alignment search tool.","Yano M, Mori H, Akiyama Y, Yamada T, Kurokawa K.","BMC Bioinformatics","2014","1471-2105","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.61914","1","15","406","PMC4271471",NA,NA,"github.com"
"1956","25496383","MED","25496383",NA,"CompPhy: a web-based collaborative platform for comparing phylogenies.","Fiorini N, Lefort V, Chevenet F, Berry V, Chifolleau AM.","BMC Evol Biol","2014","1471-2148","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.61914","1","14","253","PMC4271409",NA,NA,"github.com"
"1957","25431162","MED","25431162","10.1186/preaccept-1977987350137477","PyTMs: a useful PyMOL plugin for modeling common post-translational modifications.","Warnecke A, Sandalova T, Achour A, Harris RA.","BMC Bioinformatics","2014","1471-2105","journal article; research-article","Y","Y","N","0","Y","Y","N","N","Y","324.61914","1","15","370","PMC4256751","pdb",NA,"github.com"
"1958","25493625","MED","25493625",NA,"A GPU-Based Implementation of the Firefly Algorithm for Variable Selection in Multivariate Calibration Problems.","de Paula LC, Soares AS, de Lima TW, Delbem AC, Coelho CJ, Filho AR.","PLoS One","2014","1932-6203","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.61914","12","9","e114145","PMC4262411",NA,NA,"github.com"
"1959","25333065","MED","25333065","10.1002/mgg3.81","Identification of three novel FGF16 mutations in X-linked recessive fusion of the fourth and fifth metacarpals and possible correlation with heart disease.","Laurell T, Nilsson D, Hofmeister W, Lindstrand A, Ahituv N, Vandermeer J, Amilon A, AnnerÃ©n G, Arner M, Pettersson M, JÃ¤ntti N, Rosberg HE, Cattini PA, NordenskjÃ¶ld A, MÃ¤kitie O, Grigelioniene G, Nordgren A.","Mol Genet Genomic Med","2014","2324-9269","journal article; research-article","Y","Y","N","0","Y","Y","Y","N","Y","324.61914","5","2","402-411","PMC4190875","refseq","UNIPROT","github.com"
"1960","25551756","MED","25551756","10.1371/journal.pone.0116125","The kidney transcriptome and proteome defined by transcriptomics and antibody-based profiling.","Habuka M, Fagerberg L, HallstrÃ¶m BM, Kampf C, Edlund K, Sivertsson Ã, Yamamoto T, PontÃ©n F, UhlÃ©n M, Odeberg J.","PLoS One","2014","1932-6203","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.61914","12","9","e116125","PMC4281243",NA,NA,"github.com"
"1961","25276498","MED","25276498","10.1089/big.2014.0020","Structured Open Urban Data: Understanding the Landscape.","Barbosa L, Pham K, Silva C, Vieira MR, Freire J.","Big Data","2014","2167-6461","review; review-article","N","Y","N","1","Y","Y","N","N","N","324.61914","3","2","144-154","PMC4174913",NA,NA,"github.com"
"1962","24288368","MED","24288368","10.1093/nar/gkt1244","Ribosomal Database Project: data and tools for high throughput rRNA analysis.","Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, Brown CT, Porras-Alfaro A, Kuske CR, Tiedje JM.","Nucleic Acids Res","2014","0305-1048","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","17","Y","Y","N","Y","Y","324.61914","database issue","42","d633-42","PMC3965039","gen",NA,"github.com"
"1963","24634442","MED","24634442","10.1093/nar/gku210","RepARK--de novo creation of repeat libraries from whole-genome NGS reads.","Koch P, Platzer M, Downie BR.","Nucleic Acids Res","2014","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","3","Y","Y","N","Y","N","324.61914","9","42","e80","PMC4027187",NA,NA,"github.com"
"1964","25580230","MED","25580230","10.12688/f1000research.4709.1","Metabolomics in psoriatic disease: pilot study reveals metabolite differences in psoriasis and psoriatic arthritis.","Armstrong AW, Wu J, Johnson MA, Grapov D, Azizi B, Dhillon J, Fiehn O.","F1000Res","2014","2046-1402","journal article; research-article","Y","Y","N","1","Y","Y","N","N","Y","324.61914",NA,"3","248","PMC4288418","doi",NA,"github.com"
"1965","25472549","MED","25472549","10.1186/1471-2105-15-s14-s5","EXACT2: the semantics of biomedical protocols.","Soldatova LN, Nadis D, King RD, Basu PS, Haddi E, BaumlÃ© V, Saunders NJ, Marwan W, Rudkin BB.","BMC Bioinformatics","2014","1471-2105","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","324.61914","Suppl 14","15 Suppl 14","s5","PMC4255744",NA,NA,"github.com"
"1966","24600389","MED","24600389","10.3389/fninf.2014.00016","Stimfit: quantifying electrophysiological data with Python.","Guzman SJ, SchlÃ¶gl A, Schmidt-Hieber C.","Front Neuroinform","2014","1662-5196","journal article; research-article","Y","Y","Y","1","Y","Y","N","N","N","324.61914",NA,"8","16","PMC3931263",NA,NA,"github.com"
"1967","24498299","MED","24498299","10.1371/journal.pone.0087176","Thresholds of auditory-motor coupling measured with a simple task in musicians and non-musicians: was the sound simultaneous to the key press?","van Vugt FT, Tillmann B.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","Y","324.61914","2","9","e87176","PMC3911931","doi",NA,"github.com"
"1968","24904358","MED","24904358","10.3389/fnhum.2014.00315","Music-supported motor training after stroke reveals no superiority of synchronization in group therapy.","Van Vugt FT, Ritter J, Rollnik JD, AltenmÃ¼ller E.","Front Hum Neurosci","2014","1662-5161","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.61914",NA,"8","315","PMC4033001",NA,NA,"github.com"
"1969","24936420","MED","24936420","10.1016/j.nicl.2014.04.004","Biased binomial assessment of cross-validated estimation of classification accuracies illustrated in diagnosis predictions.","Noirhomme Q, Lesenfants D, Gomez F, Soddu A, Schrouff J, Garraux G, Luxen A, Phillips C, Laureys S.","Neuroimage Clin","2014","2213-1582","journal article; research-article","Y","Y","Y","2","Y","Y","N","N","N","324.61914",NA,"4","687-694","PMC4053638",NA,NA,"github.com"
"1970","24906298","MED","24906298","10.1186/1471-2164-15-439","Efficient de novo assembly of large and complex genomes by massively parallel sequencing of Fosmid pools.","Alexeyenko A, Nystedt B, Vezzi F, Sherwood E, Ye R, Knudsen B, Simonsen M, Turner B, de Jong P, Wu CC, Lundeberg J.","BMC Genomics","2014","1471-2164","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.61914","1","15","439","PMC4070561",NA,NA,"github.com"
"1971","24888378","MED","24888378","10.1186/1471-2164-15-419","Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling.","Zhao W, He X, Hoadley KA, Parker JS, Hayes DN, Perou CM.","BMC Genomics","2014","1471-2164","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","1","Y","Y","Y","N","N","324.61914","1","15","419","PMC4070569",NA,"ARXPR","github.com"
"1972","24945776","MED","24945776","10.1016/j.neuron.2014.04.046","Ongoing network state controls the length of sleep spindles via inhibitory activity.","BarthÃ³ P, SlÃ©zia A, MÃ¡tyÃ¡s F, Faradzs-Zade L, Ulbert I, Harris KD, AcsÃ¡dy L.","Neuron","2014","0896-6273","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.61914","6","82","1367-1379","PMC4064116",NA,NA,"github.com"
"1973","25342980","MED","25342980","10.1186/s13073-014-0067-5","VISPA: a computational pipeline for the identification and analysis of genomic vector integration sites.","Calabria A, Leo S, Benedicenti F, Cesana D, Spinozzi G, Orsini M, Merella S, Stupka E, Zanetti G, Montini E.","Genome Med","2014","1756-994x","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.61914","9","6","67","PMC4169225",NA,NA,"github.com"
"1974","24509631","MED","24509631","10.1038/nmeth.2841","A mass spectrometry-based hybrid method for structural modeling of protein complexes.","Politis A, Stengel F, Hall Z, HernÃ¡ndez H, Leitner A, Walzthoeni T, Robinson CV, Aebersold R.","Nat Methods","2014","1548-7091","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","2","Y","Y","N","N","Y","324.61914","4","11","403-406","PMC3972104","pdb",NA,"github.com"
"1975","24560925","MED","24560925","10.1016/j.molcel.2014.01.017","A splicing-dependent transcriptional checkpoint associated with prespliceosome formation.","Chathoth KT, Barrass JD, Webb S, Beggs JD.","Mol Cell","2014","1097-2765","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","Y","N","N","324.61914","5","53","779-790","PMC3988880",NA,"UNIPROT","github.com"
"1976","24695404","MED","24695404","10.1093/bioinformatics/btu170","Trimmomatic: a flexible trimmer for Illumina sequence data.","Bolger AM, Lohse M, Usadel B.","Bioinformatics","2014","1367-4803","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","35","Y","Y","N","N","N","324.61914","15","30","2114-2120","PMC4103590",NA,NA,"github.com"
"1977","24022847","MED","24022847","10.1111/2049-632x.12086","Plasmid deficiency in urogenital isolates of Chlamydia trachomatis reduces infectivity and virulence in a mouse model.","Sigar IM, Schripsema JH, Wang Y, Clarke IN, Cutcliffe LT, Seth-Smith HM, Thomson NR, Bjartling C, Unemo M, Persson K, Ramsey KH.","Pathog Dis","2014","2049-632x","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","3","Y","Y","Y","N","Y","324.61914","1","70","61-69","PMC4300952","gen","EMBLUNIPROT","github.com"
"1978","25300236","MED","25300236","10.1038/ncomms6110","Cassava genome from a wild ancestor to cultivated varieties.","Wang W, Feng B, Xiao J, Xia Z, Zhou X, Li P, Zhang W, Wang Y, MÃ¸ller BL, Zhang P, Luo MC, Xiao G, Liu J, Yang J, Chen S, Rabinowicz PD, Chen X, Zhang HB, Ceballos H, Lou Q, Zou M, Carvalho LJ, Zeng C, Xia J, Sun S, Fu Y, Wang H, Lu C, Ruan M, Zhou S, Wu Z, Liu H, Kannangara RM, JÃ¸rgensen K, Neale RL, Bonde M, Heinz N, Zhu W, Wang S, Zhang Y, Pan K, Wen M, Ma PA, Li Z, Hu M, Liao W, Hu W, Zhang S, Pei J, Guo A, Guo J, Zhang J, Zhang Z, Ye J, Ou W, Ma Y, Liu X, Tallon LJ, Galens K, Ott S, Huang J, Xue J, An F, Yao Q, Lu X, Fregene M, LÃ³pez-Lavalle LA, Wu J, You FM, Chen M, Hu S, Wu G, Zhong S, Ling P, Chen Y, Wang Q, Liu G, Liu B, Li K, Peng M.","Nat Commun","2014","2041-1723","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","324.61914",NA,"5","5110","PMC4214410",NA,NA,"github.com"
"1979","25389263","MED","25389263","10.1093/nar/gku1096","Massively parallel determination and modeling of endonuclease substrate specificity.","Thyme SB, Song Y, Brunette TJ, Szeto MD, Kusak L, Bradley P, Baker D.","Nucleic Acids Res","2014","0305-1048","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","N","0","Y","Y","N","N","N","324.61914","22","42","13839-13852","PMC4267613",NA,NA,"github.com"
"1980","24213554","MED","24213554","10.4161/epi.27021","Epigenomic elements enriched in the promoters of autoimmunity susceptibility genes.","Dozmorov MG, Wren JD, AlarcÃ³n-Riquelme ME.","Epigenetics","2014","1559-2294","journal article; research support, n.i.h., extramural; research-article","N","Y","N","1","N","Y","N","N","N","324.61914","2","9","276-285","PMC3962538",NA,NA,"github.com"
"1981","24952747","MED","24952747","10.1038/ng.3015","Inferring human population size and separation history from multiple genome sequences.","Schiffels S, Durbin R.","Nat Genet","2014","1061-4036","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","324.61914","8","46","919-925","PMC4116295",NA,NA,"github.com"
"1982","25425670","MED","25425670","10.1073/pnas.1420822111","Dissecting the clonal origins of childhood acute lymphoblastic leukemia by single-cell genomics.","Gawad C, Koh W, Quake SR.","Proc Natl Acad Sci U S A","2014","0027-8424","journal article; research support, non-u.s. gov't; research-article","N","Y","N","0","Y","Y","N","N","N","324.61914","50","111","17947-17952","PMC4273416",NA,NA,"github.com"
"1983","25547313","MED","25547313","10.1186/s12870-014-0383-3","CenH3 evolution in diploids and polyploids of three angiosperm genera.","Masonbrink RE, Gallagher JP, Jareczek JJ, Renny-Byfield S, Grover CE, Gong L, Wendel JF.","BMC Plant Biol","2014","1471-2229","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.61914","1","14","383","PMC4308911",NA,NA,"github.com"
"1984","25420514","MED","25420514","10.1186/s12859-014-0356-4","ANGSD: Analysis of Next Generation Sequencing Data.","Korneliussen T, Albrechtsen A, Nielsen R.","BMC Bioinformatics","2014","1471-2105","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.61914","1","15","356","PMC4248462",NA,NA,"github.com"
"1985","25642370","MED","25642370","10.1371/currents.outbreaks.02bc6d927ecee7bbd33532ec8ba6a25f","Insights into the early epidemic spread of ebola in sierra leone provided by viral sequence data.","Stadler T, KÃ¼hnert D, Rasmussen DA, du Plessis L.","PLoS Curr","2014","2157-3999","journal article; research-article","Y","Y","N","0","N","Y","N","N","N","324.61914",NA,"6",NA,"PMC4205153",NA,NA,"github.com"
"1986","25566218","MED","25566218","10.3389/fmicb.2014.00703","High temporal and spatial diversity in marine RNA viruses implies that they have an important role in mortality and structuring plankton communities.","Gustavsen JA, Winget DM, Tian X, Suttle CA.","Front Microbiol","2014","1664-302x","journal article; research-article","Y","Y","N","0","Y","Y","Y","N","Y","324.61914",NA,"5","703","PMC4266044","doi","EMBL","github.com"
"1987","24788869","MED","24788869","10.1371/journal.pone.0095850","Host control of symbiont natural product chemistry in cryptic populations of the tunicate Lissoclinum patella.","Kwan JC, Tianero MD, Donia MS, Wyche TP, Bugni TS, Schmidt EW.","PLoS One","2014","1932-6203","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","Y","N","N","324.61914","5","9","e95850","PMC4008419",NA,"EMBLUNIPROT","github.com"
"1988","24808136","MED","24808136","10.1073/pnas.1406468111","Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics.","Gibson J, Shokralla S, Porter TM, King I, van Konynenburg S, Janzen DH, Hallwachs W, Hajibabaei M.","Proc Natl Acad Sci U S A","2014","0027-8424","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","N","Y","Y","1","Y","Y","Y","N","N","324.61914","22","111","8007-8012","PMC4050544",NA,"EMBL","github.com"
"1989","24957798","MED","24957798","10.1038/srep05228","CCL2 enhances pluripotency of human induced pluripotent stem cells by activating hypoxia related genes.","Hasegawa Y, Tang D, Takahashi N, Hayashizaki Y, Forrest AR, FANTOM Consortium, Suzuki H.","Sci Rep","2014","2045-2322","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.61914",NA,"4","5228","PMC4067614",NA,NA,"github.com"
"1990","25538865","MED","25538865","10.7717/peerj.659","The microbes we eat: abundance and taxonomy of microbes consumed in a day's worth of meals for three diet types.","Lang JM, Eisen JA, Zivkovic AM.","PeerJ","2014","2167-8359","journal article; research-article","Y","Y","N","0","Y","Y","N","N","Y","324.48145",NA,"2","e659","PMC4266855","doi",NA,"github.com"
"1991","25255098","MED","25255098","10.7554/elife.02950","Fringe proteins modulate Notch-ligand cis and trans interactions to specify signaling states.","LeBon L, Lee TV, Sprinzak D, Jafar-Nejad H, Elowitz MB.","Elife","2014","2050-084x","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","N","0","Y","Y","Y","N","N","324.48145",NA,"3","e02950","PMC4174579",NA,"UNIPROT","github.com"
"1992","24970577","MED","24970577","10.1186/gb-2014-15-6-r84","LUMPY: a probabilistic framework for structural variant discovery.","Layer RM, Chiang C, Quinlan AR, Hall IM.","Genome Biol","2014","1465-6906","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","N","2","Y","Y","N","N","N","324.48145","6","15","r84","PMC4197822",NA,NA,"github.com"
"1993","25188270","MED","25188270","10.1371/journal.pone.0106713","Amplification biases and consistent recovery of loci in a double-digest RAD-seq protocol.","DaCosta JM, Sorenson MD.","PLoS One","2014","1932-6203","journal article; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.48145","9","9","e106713","PMC4154734",NA,NA,"github.com"
"1994","25102226","MED","25102226","10.1371/journal.pcbi.1003756","Blind predictions of DNA and RNA tweezers experiments with force and torque.","Chou FC, Lipfert J, Das R.","PLoS Comput Biol","2014","1553-734x","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.48145","8","10","e1003756","PMC4125081",NA,NA,"github.com"
"1995","24651862","MED","24651862","10.1371/journal.pone.0092556","Characterisation of genetic variation in ST8SIA2 and its interaction region in NCAM1 in patients with bipolar disorder.","Shaw AD, Tiwari Y, Kaplan W, Heath A, Mitchell PB, Schofield PR, Fullerton JM.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","Y","324.48145","3","9","e92556","PMC3961385","refsnp",NA,"github.com"
"1996","24898754","MED","24898754","10.7554/elife.02535","High-resolution mapping reveals hundreds of genetic incompatibilities in hybridizing fish species.","Schumer M, Cui R, Powell DL, Dresner R, Rosenthal GG, Andolfatto P.","Elife","2014","2050-084x","journal article; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","1","Y","Y","N","Y","Y","324.48145",NA,"3",NA,"PMC4080447","doi",NA,"github.com"
"1997","24484917","MED","24484917","10.1186/1758-2946-6-4","Data model, dictionaries, and desiderata for biomolecular simulation data indexing and sharing.","Thibault JC, Roe DR, Facelli JC, Cheatham TE 3rd.","J Cheminform","2014","1758-2946","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.48145","1","6","4","PMC3915074",NA,NA,"github.com"
"1998","24682824","MED","24682824","10.1093/nar/gku209","Imogene: identification of motifs and cis-regulatory modules underlying gene co-regulation.","Rouault H, Santolini M, Schweisguth F, Hakim V.","Nucleic Acids Res","2014","0305-1048","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","Y","N","324.48145","10","42","6128-6145","PMC4041412",NA,NA,"github.com"
"1999","25126069","MED","25126069","10.3389/fninf.2014.00067","Pydpiper: a flexible toolkit for constructing novel registration pipelines.","Friedel M, van Eede MC, Pipitone J, Chakravarty MM, Lerch JP.","Front Neuroinform","2014","1662-5196","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.48145",NA,"8","67","PMC4115634",NA,NA,"github.com"
"2000","25352777","MED","25352777","10.3389/fncel.2014.00304","Model cerebellar granule cells can faithfully transmit modulated firing rate signals.","RÃ¶ssert C, Solinas S, D'Angelo E, Dean P, Porrill J.","Front Cell Neurosci","2014","1662-5102","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.48145",NA,"8","304","PMC4195316",NA,NA,"github.com"
"2001","25392767","MED","25392767","10.1186/2193-1801-3-116","Vertex collocation profiles: theory, computation, and results.","Lichtenwalter RN, Chawla NV.","Springerplus","2014","2193-1801","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.48145",NA,"3","116","PMC4212056",NA,NA,"github.com"
"2002","25411781","MED","25411781","10.1371/journal.pgen.1004798","Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association.","Ding Z, Ni Y, Timmer SW, Lee BK, Battenhouse A, Louzada S, Yang F, Dunham I, Crawford GE, Lieb JD, Durbin R, Iyer VR, Birney E.","PLoS Genet","2014","1553-7390","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","N","0","Y","Y","N","N","Y","324.48145","11","10","e1004798","PMC4238955","refsnp",NA,"github.com"
"2003","24699269","MED","24699269","10.1371/journal.pcbi.1003544","Exact hybrid particle/population simulation of rule-based models of biochemical systems.","Hogg JS, Harris LA, Stover LJ, Nair NS, Faeder JR.","PLoS Comput Biol","2014","1553-734x","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","2","Y","Y","N","N","N","324.48145","4","10","e1003544","PMC3974646",NA,NA,"github.com"
"2004","24302578","MED","24302578","10.1093/nar/gkt1201","The complex methylome of the human gastric pathogen Helicobacter pylori.","Krebes J, Morgan RD, Bunk B, SprÃ¶er C, Luong K, Parusel R, Anton BP, KÃ¶nig C, Josenhans C, Overmann J, Roberts RJ, Korlach J, Suerbaum S.","Nucleic Acids Res","2014","0305-1048","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","6","Y","Y","N","N","Y","324.48145","4","42","2415-2432","PMC3936762","refseq",NA,"github.com"
"2005","25558364","MED","25558364","10.1002/ece3.1303","The PREDICTS database: a global database of how local terrestrial biodiversity responds to human impacts.","Hudson LN, Newbold T, Contu S, Hill SL, Lysenko I, De Palma A, Phillips HR, Senior RA, Bennett DJ, Booth H, Choimes A, Correia DL, Day J, EcheverrÃa-LondoÃ±o S, Garon M, Harrison ML, Ingram DJ, Jung M, Kemp V, Kirkpatrick L, Martin CD, Pan Y, White HJ, Aben J, Abrahamczyk S, Adum GB, Aguilar-Barquero V, Aizen MA, Ancrenaz M, ArbelÃ¡ez-CortÃ©s E, Armbrecht I, Azhar B, Azpiroz AB, Baeten L, BÃ¡ldi A, Banks JE, Barlow J, BatÃ¡ry P, Bates AJ, Bayne EM, Beja P, Berg Ã, Berry NJ, Bicknell JE, Bihn JH, BÃ¶hning-Gaese K, Boekhout T, Boutin C, Bouyer J, Brearley FQ, Brito I, Brunet J, Buczkowski G, Buscardo E, Cabra-GarcÃa J, CalviÃ±o-Cancela M, Cameron SA, Cancello EM, Carrijo TF, Carvalho AL, Castro H, Castro-Luna AA, Cerda R, Cerezo A, Chauvat M, Clarke FM, Cleary DF, Connop SP, D'Aniello B, da Silva PG, Darvill B, Dauber J, Dejean A, DiekÃ¶tter T, Dominguez-Haydar Y, Dormann CF, Dumont B, Dures SG, Dynesius M, Edenius L, Elek Z, Entling MH, Farwig N, Fayle TM, Felicioli A, Felton AM, Ficetola GF, Filgueiras BK, Fonte SJ, Fraser LH, Fukuda D, Furlani D, Ganzhorn JU, Garden JG, Gheler-Costa C, Giordani P, Giordano S, Gottschalk MS, Goulson D, Gove AD, Grogan J, Hanley ME, Hanson T, Hashim NR, Hawes JE, HÃ©bert C, Helden AJ, Henden JA, HernÃ¡ndez L, Herzog F, Higuera-Diaz D, Hilje B, Horgan FG, HorvÃ¡th R, Hylander K, Isaacs-Cubides P, Ishitani M, Jacobs CT, Jaramillo VJ, Jauker B, Jonsell M, Jung TS, Kapoor V, Kati V, Katovai E, Kessler M, Knop E, Kolb A, KÅrÃ¶si Ã, Lachat T, Lantschner V, Le FÃ©on V, LeBuhn G, LÃ©garÃ© JP, Letcher SG, Littlewood NA, LÃ³pez-Quintero CA, Louhaichi M, LÃ¶vei GL, Lucas-Borja ME, Luja VH, Maeto K, Magura T, Mallari NA, Marin-Spiotta E, Marshall EJ, MartÃnez E, Mayfield MM, Mikusinski G, Milder JC, Miller JR, Morales CL, Muchane MN, Muchane M, Naidoo R, Nakamura A, Naoe S, Nates-Parra G, Navarrete Gutierrez DA, Neuschulz EL, Noreika N, Norfolk O, Noriega JA, NÃ¶ske NM, O'Dea N, Oduro W, Ofori-Boateng C, Oke CO, Osgathorpe LM, Paritsis J, Parra-H A, Pelegrin N, Peres CA, Persson AS, Petanidou T, Phalan B, Philips TK, Poveda K, Power EF, Presley SJ, ProenÃ§a V, Quaranta M, Quintero C, Redpath-Downing NA, Reid JL, Reis YT, Ribeiro DB, Richardson BA, Richardson MJ, Robles CA, RÃ¶mbke J, Romero-Duque LP, Rosselli L, Rossiter SJ, Roulston TH, Rousseau L, Sadler JP, SÃ¡fiÃ¡n S, SaldaÃ±a-VÃ¡zquez RA, SamnegÃ¥rd U, SchÃ¼epp C, Schweiger O, Sedlock JL, Shahabuddin G, Sheil D, Silva FA, Slade EM, Smith-Pardo AH, Sodhi NS, Somarriba EJ, Sosa RA, Stout JC, Struebig MJ, Sung YH, Threlfall CG, Tonietto R, TÃ³thmÃ©rÃ©sz B, Tscharntke T, Turner EC, Tylianakis JM, Vanbergen AJ, Vassilev K, Verboven HA, Vergara CH, Vergara PM, Verhulst J, Walker TR, Wang Y, Watling JI, Wells K, Williams CD, Willig MR, Woinarski JC, Wolf JH, Woodcock BA, Yu DW, Zaitsev AS, Collen B, Ewers RM, Mace GM, Purves DW, Scharlemann JP, Purvis A.","Ecol Evol","2014","2045-7758","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.48145","24","4","4701-4735","PMC4278822",NA,NA,"github.com"
"2006","24586449","MED","24586449","10.1371/journal.pone.0088941","An evaluation framework and comparative analysis of the widely used first programming languages.","Farooq MS, Khan SA, Ahmad F, Islam S, Abid A.","PLoS One","2014","1932-6203","journal article; research-article","Y","Y","Y","0","N","Y","N","N","N","324.48145","2","9","e88941","PMC3933420",NA,NA,"github.com"
"2007","24770359","MED","24770359","10.1371/journal.pone.0095978","Measuring large-scale social networks with high resolution.","Stopczynski A, Sekara V, Sapiezynski P, Cuttone A, Madsen MM, Larsen JE, Lehmann S.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","N","N","N","324.48145","4","9","e95978","PMC4000208",NA,NA,"github.com"
"2008","25013937","MED","25013937","10.1371/journal.pone.0102070","Detecting memory and structure in human navigation patterns using Markov chain models of varying order.","Singer P, Helic D, Taraghi B, Strohmaier M.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","Y","324.48145","7","9","e102070","PMC4094564","doi",NA,"github.com"
"2009","25033262","MED","25033262","10.1371/journal.pcbi.1003733","Analysis of the protein domain and domain architecture content in fungi and its application in the search of new antifungal targets.","Barrera A, Alastruey-Izquierdo A, MartÃn MJ, Cuesta I, VizcaÃno JA.","PLoS Comput Biol","2014","1553-734x","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","Y","324.48145","7","10","e1003733","PMC4102429","pfam",NA,"github.com"
"2010","24482762","MED","24482762","10.7717/peerj.243","PhyloSift: phylogenetic analysis of genomes and metagenomes.","Darling AE, Jospin G, Lowe E, Matsen FA 4th, Bik HM, Eisen JA.","PeerJ","2014","2167-8359","journal article; research-article","Y","Y","Y","20","Y","Y","N","N","Y","324.21796",NA,"2","e243","PMC3897386","doi",NA,"github.com"
"2011","24886177","MED","24886177","10.1186/1471-2229-14-144","Overexpression of UCP1 in tobacco induces mitochondrial biogenesis and amplifies a broad stress response.","Barreto P, Okura VK, Neshich IA, Maia Ide G, Arruda P.","BMC Plant Biol","2014","1471-2229","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","Y","324.21796",NA,"14","144","PMC4046140","gen",NA,"github.com"
"2012","24465792","MED","24465792","10.1371/journal.pone.0085925","Confidence intervals for population allele frequencies: the general case of sampling from a finite diploid population of any size.","Fung T, Keenan K.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","324.21796","1","9","e85925","PMC3897575",NA,NA,"github.com"
"2013","25172853","MED","25172853","10.1128/aem.01774-14","Illuminating microbial dark matter in meromictic Sakinaw Lake.","Gies EA, Konwar KM, Beatty JT, Hallam SJ.","Appl Environ Microbiol","2014","0099-2240","journal article; research support, non-u.s. gov't; research-article","N","Y","N","0","Y","Y","N","N","N","324.21796","21","80","6807-6818","PMC4249029",NA,NA,"github.com"
"2014","25538556","MED","25538556","10.3389/fnins.2014.00405","A systematic framework for functional connectivity measures.","Wang HE, BÃ©nar CG, Quilichini PP, Friston KJ, Jirsa VK, Bernard C.","Front Neurosci","2014","1662-4548","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.21796",NA,"8","405","PMC4260483",NA,NA,"github.com"
"2015","24625888","MED","24625888","10.1371/journal.pone.0091196","The role of education and verbal abilities in altering the effect of age-related gray matter differences on cognition.","Steffener J, Barulli D, Habeck C, O'Shea D, Razlighi Q, Stern Y.","PLoS One","2014","1932-6203","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","1","Y","Y","N","N","N","324.21796","3","9","e91196","PMC3953380",NA,NA,"github.com"
"2016","24270794","MED","24270794","10.1093/nar/gkt1212","Reprogramming homing endonuclease specificity through computational design and directed evolution.","Thyme SB, Boissel SJ, Arshiya Quadri S, Nolan T, Baker DA, Park RU, Kusak L, Ashworth J, Baker D.","Nucleic Acids Res","2014","0305-1048","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","3","Y","Y","N","N","Y","324.21796","4","42","2564-2576","PMC3936771","pdb",NA,"github.com"
"2017","25540641","MED","25540641","10.3389/fmicb.2014.00678","Bacteroides dorei dominates gut microbiome prior to autoimmunity in Finnish children at high risk for type 1 diabetes.","Davis-Richardson AG, Ardissone AN, Dias R, Simell V, Leonard MT, Kemppainen KM, Drew JC, Schatz D, Atkinson MA, Kolaczkowski B, Ilonen J, Knip M, Toppari J, Nurminen N, HyÃ¶ty H, Veijola R, Simell T, MykkÃ¤nen J, Simell O, Triplett EW.","Front Microbiol","2014","1664-302x","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.21796",NA,"5","678","PMC4261809",NA,NA,"github.com"
"2018","25502413","MED","25502413","10.1371/journal.pone.0114608","Predicting Growth Conditions from Internal Metabolic Fluxes in an In-Silico Model of E. coli.","Sridhara V, Meyer AG, Rai P, Barrick JE, Ravikumar P, SegrÃ¨ D, Wilke CO.","PLoS One","2014","1932-6203","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.21796","12","9","e114608","PMC4264753",NA,NA,"github.com"
"2019","24071583","MED","24071583","10.1093/nar/gkt865","Long insert whole genome sequencing for copy number variant and translocation detection.","Liang WS, Aldrich J, Tembe W, Kurdoglu A, Cherni I, Phillips L, Reiman R, Baker A, Weiss GJ, Carpten JD, Craig DW.","Nucleic Acids Res","2014","0305-1048","evaluation studies; journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.21796","2","42","e8","PMC3902897",NA,NA,"github.com"
"2020","24131564","MED","24131564","10.1101/gr.159483.113","Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency.","Wu CS, Yu CY, Chuang CY, Hsiao M, Kao CF, Kuo HC, Chuang TJ.","Genome Res","2014","1088-9051","journal article; research support, non-u.s. gov't; research-article","N","Y","Y","1","Y","Y","Y","N","N","324.21796","1","24","25-36","PMC3875859",NA,"ARXPR","github.com"
"2021","24302589","MED","24302589","10.1167/iovs.13-12420","Characterization of field loss based on microperimetry is predictive of face recognition difficulties.","Wallis TS, Taylor CP, Wallis J, Jackson ML, Bex PJ.","Invest Ophthalmol Vis Sci","2014","0146-0404","journal article; research support, non-u.s. gov't; research support, n.i.h., intramural; comparative study; research-article","N","Y","Y","0","Y","Y","N","N","N","324.21796","1","55","142-153","PMC3885139",NA,NA,"github.com"
"2022","24350677","MED","24350677","10.1111/biom.12112","Bayesian model selection in complex linear systems, as illustrated in genetic association studies.","Wen X.","Biometrics","2014","0006-341x","journal article; research support, n.i.h., extramural; research-article","N","Y","Y","0","Y","Y","N","N","Y","324.21796","1","70","73-83","PMC3954315","refsnp",NA,"github.com"
"2023","24830797","MED","24830797","10.1371/journal.pcbi.1003598","Inference of RNA polymerase II transcription dynamics from chromatin immunoprecipitation time course data.","wa Maina C, Honkela A, Matarese F, Grote K, Stunnenberg HG, Reid G, Lawrence ND, Rattray M.","PLoS Comput Biol","2014","1553-734x","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","Y","N","N","324.21796","5","10","e1003598","PMC4022483",NA,"ARXPR","github.com"
"2024","25375183","MED","25375183","10.1371/journal.pcbi.1003922","Herpes simplex virus-2 genital tract shedding is not predictable over months or years in infected persons.","Dhankani V, Kutz JN, Schiffer JT.","PLoS Comput Biol","2014","1553-734x","journal article; research support, n.i.h., extramural; research-article","Y","Y","N","0","Y","Y","N","N","N","324.21796","11","10","e1003922","PMC4222642",NA,NA,"github.com"
"2025","25375262","MED","25375262","10.1371/journal.pcbi.1003925","A comparative study and a phylogenetic exploration of the compositional architectures of mammalian nuclear genomes.","Elhaik E, Graur D.","PLoS Comput Biol","2014","1553-734x","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.21796","11","10","e1003925","PMC4222635",NA,NA,"github.com"
"2026","24661624","MED","24661624","10.1186/1471-2164-15-229","Transcriptome analysis identifies Bacillus anthracis genes that respond to CO2 through an AtxA-dependent mechanism.","McKenzie AT, Pomerantsev AP, Sastalla I, Martens C, Ricklefs SM, Virtaneva K, Anzick S, Porcella SF, Leppla SH.","BMC Genomics","2014","1471-2164","journal article; research support, n.i.h., intramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.21796",NA,"15","229","PMC3987803",NA,NA,"github.com"
"2027","24991969","MED","24991969","10.1371/journal.pcbi.1003684","Modeling higher-order correlations within cortical microcolumns.","KÃ¶ster U, Sohl-Dickstein J, Gray CM, Olshausen BA.","PLoS Comput Biol","2014","1553-734x","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.21796","7","10","e1003684","PMC4081002",NA,NA,"github.com"
"2028","24762745","MED","24762745","10.1371/journal.pcbi.1003580","Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism.","Machado D, HerrgÃ¥rd M.","PLoS Comput Biol","2014","1553-734x","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","7","Y","Y","N","N","N","324.21796","4","10","e1003580","PMC3998872",NA,NA,"github.com"
"2029","25520726","MED","25520726","10.3389/fpls.2014.00658","Elucidation of the molecular responses to waterlogging in Jatropha roots by transcriptome profiling.","Juntawong P, Sirikhachornkit A, Pimjan R, Sonthirod C, Sangsrakru D, Yoocha T, Tangphatsornruang S, Srinives P.","Front Plant Sci","2014","1664-462x","journal article; research-article","Y","Y","N","0","Y","Y","N","N","N","324.21796",NA,"5","658","PMC4251292",NA,NA,"github.com"
"2030","24765065","MED","24765065","10.3389/fnsys.2014.00045","Large-scale resting state network correlates of cognitive impairment in Parkinson's disease and related dopaminergic deficits.","Lebedev AV, Westman E, Simmons A, Lebedeva A, Siepel FJ, Pereira JB, Aarsland D.","Front Syst Neurosci","2014","1662-5137","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.21796",NA,"8","45","PMC3982053",NA,NA,"github.com"
"2031","25103980","MED","25103980","10.1186/1471-2105-15-268","PhylDiag: identifying complex synteny blocks that include tandem duplications using phylogenetic gene trees.","Lucas JM, Muffato M, Roest Crollius H.","BMC Bioinformatics","2014","1471-2105","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.21796","1","15","268","PMC4155083",NA,NA,"github.com"
"2032","25312340","MED","25312340","10.1038/cr.2014.131","Postzygotic single-nucleotide mosaicisms in whole-genome sequences of clinically unremarkable individuals.","Huang AY, Xu X, Ye AY, Wu Q, Yan L, Zhao B, Yang X, He Y, Wang S, Zhang Z, Gu B, Zhao HQ, Wang M, Gao H, Gao G, Zhang Z, Yang X, Wu X, Zhang Y, Wei L.","Cell Res","2014","1001-0602","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","324.21796","11","24","1311-1327","PMC4220156",NA,NA,"github.com"
"2033","25375153","MED","25375153","10.1371/journal.pcbi.1003916","Stability depends on positive autoregulation in Boolean gene regulatory networks.","Pinho R, Garcia V, Irimia M, Feldman MW.","PLoS Comput Biol","2014","1553-734x","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","324.21796","11","10","e1003916","PMC4222607",NA,NA,"github.com"
"2034","25121731","MED","25121731","10.1371/journal.pntd.0003079","Nitric oxide from IFNÎ³-primed macrophages modulates the antimicrobial activity of Î²-lactams against the intracellular pathogens Burkholderia pseudomallei and Nontyphoidal Salmonella.","Jones-Carson J, Zweifel AE, Tapscott T, Austin C, Brown JM, Jones KL, Voskuil MI, VÃ¡zquez-Torres A.","PLoS Negl Trop Dis","2014","1935-2727","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.21796","8","8","e3079","PMC4133387",NA,NA,"github.com"
"2035","24992939","MED","24992939","10.1186/1746-6148-10-146","Effect of photoperiod on the feline adipose transcriptome as assessed by RNA sequencing.","Mori A, Kappen KL, Dilger AC, Swanson KS.","BMC Vet Res","2014","1746-6148","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.21796",NA,"10","146","PMC4092351",NA,NA,"github.com"
"2036","25285990","MED","25285990","10.1371/journal.pone.0108009","Genome-based comparative analyses of Antarctic and temperate species of Paenibacillus.","Dsouza M, Taylor MW, Turner SJ, Aislabie J.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","324.21796","10","9","e108009","PMC4186907",NA,NA,"github.com"
"2037","24791664","MED","24791664","10.1007/s10071-014-0752-1","Predictability and heritability of individual differences in fear learning.","Shumake J, Furgeson-Moreira S, Monfils MH.","Anim Cogn","2014","1435-9448","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.21796","5","17","1207-1221","PMC4138434",NA,NA,"github.com"
"2038","24980129","MED","24980129","10.1093/database/bau053","BioC interoperability track overview.","Comeau DC, Batista-Navarro RT, Dai HJ, DoÄan RI, Yepes AJ, Khare R, Lu Z, Marques H, Mattingly CJ, Neves M, Peng Y, Rak R, Rinaldi F, Tsai RT, Verspoor K, Wiegers TC, Wu CH, Wilbur WJ.","Database (Oxford)","2014","1758-0463","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., intramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.21796",NA,"2014",NA,"PMC4074764",NA,NA,"github.com"
"2039","24676149","MED","24676149","10.1371/journal.pcbi.1003538","Correction of distortion in flattened representations of the cortical surface allows prediction of V1-V3 functional organization from anatomy.","Benson NC, Butt OH, Brainard DH, Aguirre GK.","PLoS Comput Biol","2014","1553-734x","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","2","Y","Y","N","N","N","324.21796","3","10","e1003538","PMC3967932",NA,NA,"github.com"
"2040","25340822","MED","25340822","10.1371/journal.pgen.1004698","Ancient expansion of the hox cluster in lepidoptera generated four homeobox genes implicated in extra-embryonic tissue formation.","Ferguson L, MarlÃ©taz F, Carter JM, Taylor WR, Gibbs M, Breuker CJ, Holland PW.","PLoS Genet","2014","1553-7390","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","Y","324.21796","10","10","e1004698","PMC4207634","doi; pdb",NA,"github.com"
"2041","24971628","MED","24971628","10.1371/journal.pone.0099290","Direct amplification, sequencing and profiling of Chlamydia trachomatis strains in single and mixed infection clinical samples.","Joseph SJ, Li B, Ghonasgi T, Haase CP, Qin ZS, Dean D, Read TD.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","Y","324.21796","6","9","e99290","PMC4074039","gen",NA,"github.com"
"2042","25142523","MED","25142523","10.1098/rsif.2014.0672","Mapping the stereotyped behaviour of freely moving fruit flies.","Berman GJ, Choi DM, Bialek W, Shaevitz JW.","J R Soc Interface","2014","1742-5689","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","N","0","Y","Y","N","N","N","324.21796","99","11",NA,"PMC4233753",NA,NA,"github.com"
"2043","25193308","MED","25193308","10.1093/gbe/evu198","Genome diversity and divergence in Drosophila mauritiana: multiple signatures of faster X evolution.","Garrigan D, Kingan SB, Geneva AJ, Vedanayagam JP, Presgraves DC.","Genome Biol Evol","2014","1759-6653","journal article; research support, n.i.h., extramural; research-article","Y","Y","N","0","Y","Y","N","N","N","324.21796","9","6","2444-2458","PMC4202334",NA,NA,"github.com"
"2044","25165853","MED","25165853","10.1371/journal.pcbi.1003811","Communication through resonance in spiking neuronal networks.","Hahn G, Bujan AF, FrÃ©gnac Y, Aertsen A, Kumar A.","PLoS Comput Biol","2014","1553-734x","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.21796","8","10","e1003811","PMC4148205",NA,NA,"github.com"
"2045","25116890","MED","25116890","10.1371/journal.pbio.1001926","A bioenergetic basis for membrane divergence in archaea and bacteria.","Sojo V, Pomiankowski A, Lane N.","PLoS Biol","2014","1544-9173","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","1","Y","Y","N","N","N","324.21796","8","12","e1001926","PMC4130499",NA,NA,"github.com"
"2046","25010654","MED","25010654","10.1371/journal.pcbi.1003710","Analysis of graph invariants in functional neocortical circuitry reveals generalized features common to three areas of sensory cortex.","Gururangan SS, Sadovsky AJ, MacLean JN.","PLoS Comput Biol","2014","1553-734x","journal article; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.21796","7","10","e1003710","PMC4091703",NA,NA,"github.com"
"2047","24809476","MED","24809476","10.1371/journal.pgen.1004353","Population genomic analysis of ancient and modern genomes yields new insights into the genetic ancestry of the Tyrolean Iceman and the genetic structure of Europe.","Sikora M, Carpenter ML, Moreno-Estrada A, Henn BM, Underhill PA, SÃ¡nchez-Quinto F, Zara I, Pitzalis M, Sidore C, Busonero F, Maschio A, Angius A, Jones C, Mendoza-Revilla J, Nekhrizov G, Dimitrova D, Theodossiev N, Harkins TT, Keller A, Maixner F, Zink A, Abecasis G, Sanna S, Cucca F, Bustamante CD.","PLoS Genet","2014","1553-7390","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","2","Y","Y","N","N","N","324.21796","5","10","e1004353","PMC4014435",NA,NA,"github.com"
"2048","24906175","MED","24906175","10.1016/j.biosystems.2014.05.002","Fast Bayesian parameter estimation for stochastic logistic growth models.","Heydari J, Lawless C, Lydall DA, Wilkinson DJ.","Biosystems","2014","0303-2647","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","324.21796",NA,"122","55-72","PMC4169184",NA,NA,"github.com"
"2049","25062920","MED","25062920","10.1093/gbe/evu157","Highly variable recombinational landscape modulates efficacy of natural selection in birds.","Gossmann TI, Santure AW, Sheldon BC, Slate J, Zeng K.","Genome Biol Evol","2014","1759-6653","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","Y","324.21796","8","6","2061-2075","PMC4231635","doi",NA,"github.com"
"2050","24356988","MED","24356988","10.1101/gr.160465.113","A novel method for detecting uniparental disomy from trio genotypes identifies a significant excess in children with developmental disorders.","King DA, Fitzgerald TW, Miller R, Canham N, Clayton-Smith J, Johnson D, Mansour S, Stewart F, Vasudevan P, Hurles ME, DDD Study.","Genome Res","2014","1088-9051","journal article; research support, non-u.s. gov't; research-article","N","Y","N","0","Y","Y","N","N","N","324.21796","4","24","673-687","PMC3975066",NA,NA,"github.com"
"2051","24647608","MED","24647608","10.1371/journal.pone.0092111","Transcriptome analysis reveals differential splicing events in IPF lung tissue.","Nance T, Smith KS, Anaya V, Richardson R, Ho L, Pala M, Mostafavi S, Battle A, Feghali-Bostwick C, Rosen G, Montgomery SB.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","2","Y","Y","Y","N","N","324.21796","3","9","e92111","PMC3960165",NA,"ARXPR","github.com"
"2052","25167361","MED","25167361","10.1371/journal.pcbi.1003806","OpenCyto: an open source infrastructure for scalable, robust, reproducible, and automated, end-to-end flow cytometry data analysis.","Finak G, Frelinger J, Jiang W, Newell EW, Ramey J, Davis MM, Kalams SA, De Rosa SC, Gottardo R.","PLoS Comput Biol","2014","1553-734x","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.21796","8","10","e1003806","PMC4148203",NA,NA,"github.com"
"2053","25184813","MED","25184813","10.1371/journal.pone.0094454","On the sympatric evolution and evolutionary stability of coexistence by relative nonlinearity of competition.","Hartig F, MÃ¼nkemÃ¼ller T, Johst K, Dieckmann U.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.21796","9","9","e94454","PMC4153539",NA,NA,"github.com"
"2054","24714673","MED","24714673","10.1371/journal.pone.0093344","Mapping topographic structure in white matter pathways with level set trees.","Kent BP, Rinaldo A, Yeh FC, Verstynen T.","PLoS One","2014","1932-6203","journal article; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.21796","4","9","e93344","PMC3979894",NA,NA,"github.com"
"2055","24992200","MED","24992200","10.1371/journal.ppat.1004244","Genetic analysis of Leishmania donovani tropism using a naturally attenuated cutaneous strain.","Zhang WW, Ramasamy G, McCall LI, Haydock A, Ranasinghe S, Abeygunasekara P, Sirimanna G, Wickremasinghe R, Myler P, Matlashewski G.","PLoS Pathog","2014","1553-7366","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.21796","7","10","e1004244","PMC4081786",NA,NA,"github.com"
"2056","24877076","MED","24877076","10.1155/2014/272915","OWL reasoning framework over big biological knowledge network.","Chen H, Chen X, Gu P, Wu Z, Yu T.","Biomed Res Int","2014","2314-6133","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.21796",NA,"2014","272915","PMC4022201",NA,NA,"github.com"
"2057","24932915","MED","24932915","10.1371/journal.pone.0100195","VMSbase: an R-package for VMS and logbook data management and analysis in fisheries ecology.","Russo T, D'Andrea L, Parisi A, Cataudella S.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","N","Y","N","N","N","324.21796","6","9","e100195","PMC4059747",NA,NA,"github.com"
"2058","24793431","MED","24793431","10.1145/2531602.2531607","Inferring the Origin Locations of Tweets with Quantitative Confidence.","Priedhorsky R, Culotta A, Del Valle SY.","CSCW","2014",NA,"journal article; research-article","N","Y","Y","0","N","Y","N","N","N","324.21796",NA,NA,"1523-1536","PMC4008124",NA,NA,"github.com"
"2059","25375897","MED","25375897","10.1371/journal.pcbi.1003889","Improved contact predictions using the recognition of protein like contact patterns.","Skwark MJ, Raimondi D, Michel M, Elofsson A.","PLoS Comput Biol","2014","1553-734x","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","324.21796","11","10","e1003889","PMC4222596",NA,NA,"github.com"
"2060","24925925","MED","24925925","10.1093/molbev/msu187","Detecting concerted demographic response across community assemblages using hierarchical approximate Bayesian computation.","Chan YL, Schanzenbach D, Hickerson MJ.","Mol Biol Evol","2014","0737-4038","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","1","Y","Y","N","N","N","324.21796","9","31","2501-2515","PMC4137712",NA,NA,"github.com"
"2061","24393201","MED","24393201","10.1186/1471-2229-14-3","Polyploidy and the petal transcriptome of Gossypium.","Rambani A, Page JT, Udall JA.","BMC Plant Biol","2014","1471-2229","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","3","Y","Y","N","N","N","324.21796",NA,"14","3","PMC3890615",NA,NA,"github.com"
"2062","24415955","MED","24415955","10.1371/journal.pgen.1004078","Single nucleus genome sequencing reveals high similarity among nuclei of an endomycorrhizal fungus.","Lin K, Limpens E, Zhang Z, Ivanov S, Saunders DG, Mu D, Pang E, Cao H, Cha H, Lin T, Zhou Q, Shang Y, Li Y, Sharma T, van Velzen R, de Ruijter N, Aanen DK, Win J, Kamoun S, Bisseling T, Geurts R, Huang S.","PLoS Genet","2014","1553-7390","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","12","Y","Y","N","N","Y","324.21796","1","10","e1004078","PMC3886924","gen",NA,"github.com"
"2063","24431999","MED","24431999","10.3389/fninf.2013.00048","Nengo: a Python tool for building large-scale functional brain models.","Bekolay T, Bergstra J, Hunsberger E, Dewolf T, Stewart TC, Rasmussen D, Choo X, Voelker AR, Eliasmith C.","Front Neuroinform","2014","1662-5196","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.21796",NA,"7","48","PMC3880998",NA,NA,"github.com"
"2064","24433567","MED","24433567","10.1186/1471-2105-15-19","Automated alignment-based curation of gene models in filamentous fungi.","van der Burgt A, Severing E, Collemare J, de Wit PJ.","BMC Bioinformatics","2014","1471-2105","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","N","N","N","324.21796",NA,"15","19","PMC3898260",NA,NA,"github.com"
"2065","24466165","MED","24466165","10.1371/journal.pone.0086602","Effects of extrinsic mortality on the evolution of aging: a stochastic modeling approach.","Shokhirev MN, Johnson AA.","PLoS One","2014","1932-6203","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.21796","1","9","e86602","PMC3897743",NA,NA,"github.com"
"2066","24505279","MED","24505279","10.1371/journal.pone.0087178","Detecting and quantifying topography in neural maps.","Yarrow S, Razak KA, Seitz AR, SeriÃ¨s P.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.21796","2","9","e87178","PMC3914801",NA,NA,"github.com"
"2067","24513108","MED","24513108","10.1016/j.jmb.2013.10.024","Flexible gates generate occluded intermediates in the transport cycle of LacY.","Stelzl LS, Fowler PW, Sansom MS, Beckstein O.","J Mol Biol","2014","0022-2836","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","2","Y","Y","N","N","Y","324.21796","3","426","735-751","PMC3905165","pdb",NA,"github.com"
"2068","24523352","MED","24523352","10.1093/nar/gku138","Strain/species identification in metagenomes using genome-specific markers.","Tu Q, He Z, Zhou J.","Nucleic Acids Res","2014","0305-1048","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.21796","8","42","e67","PMC4005670",NA,NA,"github.com"
"2069","24558256","MED","24558256","10.1093/gbe/evu037","Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence.","Renny-Byfield S, Gallagher JP, Grover CE, Szadkowski E, Page JT, Udall JA, Wang X, Paterson AH, Wendel JF.","Genome Biol Evol","2014","1759-6653","journal article; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.21796","3","6","559-571","PMC3971588",NA,NA,"github.com"
"2070","24600387","MED","24600387","10.3389/fninf.2014.00013","ITK: enabling reproducible research and open science.","McCormick M, Liu X, Jomier J, Marion C, Ibanez L.","Front Neuroinform","2014","1662-5196","journal article; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.21796",NA,"8","13","PMC3929840",NA,NA,"github.com"
"2071","24598808","MED","24598808","10.1371/journal.pone.0090830","The Li2 mutation results in reduced subgenome expression bias in elongating fibers of allotetraploid cotton (Gossypium hirsutum L.).","Naoumkina M, Thyssen G, Fang DD, Hinchliffe DJ, Florane C, Yeater KM, Page JT, Udall JA.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research-article","Y","Y","Y","2","Y","Y","N","N","N","324.21796","3","9","e90830","PMC3944810",NA,NA,"github.com"
"2072","25356657","MED","25356657","10.1371/journal.ppat.1004452","Detecting differential transmissibilities that affect the size of self-limited outbreaks.","Blumberg S, Funk S, Pulliam JR.","PLoS Pathog","2014","1553-7366","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","N","0","Y","Y","N","N","N","324.21796","10","10","e1004452","PMC4214794",NA,NA,"github.com"
"2073","24926665","MED","24926665","10.1371/journal.pone.0099625","RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells.","Himes BE, Jiang X, Wagner P, Hu R, Wang Q, Klanderman B, Whitaker RM, Duan Q, Lasky-Su J, Nikolos C, Jester W, Johnson M, Panettieri RA Jr, Tantisira KG, Weiss ST, Lu Q.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","Y","324.21796","6","9","e99625","PMC4057123","omim; refsnp; refseq",NA,"github.com"
"2074","25032992","MED","25032992","10.1371/journal.pcbi.1003696","Modeling bi-modality improves characterization of cell cycle on gene expression in single cells.","McDavid A, Dennis L, Danaher P, Finak G, Krouse M, Wang A, Webster P, Beechem J, Gottardo R.","PLoS Comput Biol","2014","1553-734x","journal article; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.21796","7","10","e1003696","PMC4102402",NA,NA,"github.com"
"2075","24959900","MED","24959900","10.1371/journal.pone.0099581","Amount of information needed for model choice in Approximate Bayesian Computation.","Stocks M, Siol M, Lascoux M, De Mita S.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.21796","6","9","e99581","PMC4069000",NA,NA,"github.com"
"2076","25268270","MED","25268270","10.1371/journal.pone.0108600","Collaborative mining and interpretation of large-scale data for biomedical research insights.","Tsiliki G, Karacapilidis N, Christodoulou S, Tzagarakis M.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","324.21796","9","9","e108600","PMC4182494",NA,NA,"github.com"
"2077","24709938","MED","24709938","10.1371/journal.pone.0094229","Mechanical properties of growing melanocytic nevi and the progression to melanoma.","Taloni A, Alemi AA, Ciusani E, Sethna JP, Zapperi S, La Porta CA.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research support, u.s. gov't, non-p.h.s.; research support, n.i.h., extramural; research-article","Y","Y","Y","0","Y","Y","N","N","N","324.21796","4","9","e94229","PMC3978068",NA,NA,"github.com"
"2078","25123114","MED","25123114","10.1093/gbe/evu171","The transcriptome of Nacobbus aberrans reveals insights into the evolution of sedentary endoparasitism in plant-parasitic nematodes.","Eves-van den Akker S, Lilley CJ, Danchin EG, Rancurel C, Cock PJ, Urwin PE, Jones JT.","Genome Biol Evol","2014","1759-6653","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","1","Y","Y","N","N","N","324.21796","9","6","2181-2194","PMC4202313",NA,NA,"github.com"
"2079","25246241","MED","25246241","10.1534/g3.114.013433","The genetic architecture of seed composition in soybean is refined by genome-wide association scans across multiple populations.","Vaughn JN, Nelson RL, Song Q, Cregan PB, Li Z.","G3 (Bethesda)","2014","2160-1836","journal article; research support, non-u.s. gov't; research-article","Y","Y","N","0","Y","Y","N","N","N","324.21796","11","4","2283-2294","PMC4232554",NA,NA,"github.com"
"2080","24625410","MED","24625410","10.1371/journal.pone.0090735","STEME: a robust, accurate motif finder for large data sets.","Reid JE, Wernisch L.","PLoS One","2014","1932-6203","journal article; research support, non-u.s. gov't; research-article","Y","Y","Y",

## functions.R

      
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## script.R

      
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