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\bibitem{Rijswijk2017}
1. van Rijswijk,M., Beirnaert,C., Caron,C., Cascante,M., Dominguez,V., Dunn,W.B., Ebbels,T.M.D., Giacomoni,F., Gonzalez-Beltran,A., Hankemeier,T., {\em et al.,} (2017) The future of metabolomics in ELIXIR. {\em F1000Research,}, {\bf 6}, 1649+. undefined
\bibitem{Diehl2016}
2. Diehl,A.D., Meehan,T.F., Bradford,Y.M., Brush,M.H., Dahdul,W.M., Dougall,D.S., He,Y., Osumi-Sutherland,D., Ruttenberg,A., Sarntivijai,S., {\em et al.,} (2016) The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. {\em J Biomed Semantics,}, {\bf 7}. undefined
\bibitem{Kuhn2017}
3. Kuhn,T., Willighagen,E., Evelo,C., Queralt-Rosinach,N., Centeno,E. and Furlong,L.I. (2017) Reliable Granular References to Changing Linked Data. In {\em The Semantic Web – ISWC 2017,}. undefined
\bibitem{Mons2011}
4. Mons,B., van Haagen,H., Chichester,C., Hoen,P.-B., den Dunnen,J.T., van Ommen,G., van Mulligen,E., Singh,B., Hooft,R., Roos,M., {\em et al.,} (2011) The value of data. {\em Nat. Genet.,}, {\bf 43}, 281–283. undefined
\bibitem{Putman2017}
5. Putman,T.E., Lelong,S., Burgstaller-Muehlbacher,S., Waagmeester,A., Diesh,C., Dunn,N., Munoz-Torres,M., Stupp,G.S., Wu,C., Su,A.I., {\em et al.,} (2017) WikiGenomes: an open web application for community consumption and curation of gene annotation data in Wikidata. {\em Database,}, {\bf 2017}. undefined
\bibitem{Waagmeester2016}
6. Waagmeester,A., Kutmon,M., Riutta,A., Miller,R., Willighagen,E.L., Evelo,C.T. and Pico,A.R. (2016) Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources. {\em PLoS Comput. Biol.,}, {\bf 12}, e1004989+. undefined
\bibitem{Osborne2009}
7. Osborne,J.D., Flatow,J., Holko,M., Lin,S.M., Kibbe,W.A., Zhu,L., Danila,M.I., Feng,G. and Chisholm,R.L. (2009) Annotating the human genome with Disease Ontology. {\em BMC Genomics,}, {\bf 10}, S6+. undefined
\bibitem{Kutmon2014}
8. Kutmon,M., Lotia,S., Evelo,C.T. and Pico,A.R. (2014) WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization. {\em F1000Research,}. undefined
\bibitem{Petri2014}
9. Petri,V., Jayaraman,P., Tutaj,M., Hayman,T.T., Smith,J.R., De Pons,J., Jf,S., Lowry,T.F., Nigam,R., Wang,S.-J.J., {\em et al.,} (2014) The Pathway Ontology - updates and applications. {\em J Biomed Semantics,}, {\bf 5}. undefined
\bibitem{Whetzel2011}
10. Whetzel,P.L., Noy,N.F., Shah,N.H., Alexander,P.R., Nyulas,C., Tudorache,T. and Musen,M.A. (2011) BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. {\em Nucleic Acids Res.,}, {\bf 39}, W541–W545. undefined
\bibitem{Kozhenkov2012}
11. Kozhenkov,S. and Baitaluk,M. (2012) Mining and integration of pathway diagrams from imaging data. {\em Bioinformatics,}, {\bf 28}, 739–742. undefined
\bibitem{Cerami2010}
12. Cerami,E.G., Gross,B.E., Demir,E., Rodchenkov,I., Babur,O., Anwar,N., Schultz,N., Bader,G.D. and Sander,C. (2010) Pathway Commons, a web resource for biological pathway data. {\em Nucleic Acids Res.,}, {\bf 39}, D685–D690. undefined
\bibitem{CompToxData2016}
13. Williams,A. (2016) Mapping file of InChIStrings, InChIKeys and DTXSIDs for the EPA CompTox Dashboard Figshare. Figshare, 10.6084/m9.figshare.3578313.v1
\bibitem{McEachran2017}
14. McEachran,A., Sobus,J. and Williams,A. (2017) Identifying known unknowns using the US EPA’s CompTox Chemistry Dashboard. {\em Anal. Bioanal. Chem.,}, {\bf 409}, 1729–1735. undefined
\bibitem{Fahy2009}
15. Fahy,E., Subramaniam,S., Murphy,R.C., Nishijima,M., Raetz,C.R.H., Shimizu,T., Spener,F., van Meer,G., Wakelam,M.J.O. and Dennis,E.A. (2009) Update of the LIPID MAPS comprehensive classification system for lipids. {\em J. Lipid Res.,}, {\bf 50}, S9–S14. undefined
\bibitem{uniprot2017}
16. The UniProt Consortium (2017) UniProt: the universal protein knowledgebase. {\em Nucleic Acids Res.,}, {\bf 45}, D158–D169. undefined
\bibitem{Yates2016}
17. Yates,A., Akanni,W., Amode,M.R., Barrell,D., Billis,K., Carvalho-Silva,D., Cummins,C., Clapham,P., Fitzgerald,S., Gil,L., {\em et al.,} (2016) Ensembl 2016. {\em Nucleic Acids Res.,}, {\bf 44}, D710–D716. undefined
\bibitem{HMDB2013}
18. Wishart,D.S., Jewison,T., Chi,A., Wilson,M., Knox,C., Liu,Y., Djoumbou,Y., Mandal,R., Aziat,F., Dong,E., {\em et al.,} (2013) HMDB 3.0 - The Human Metabolome Database in 2013. {\em Nucleic Acids Res.,}, {\bf 41}, D801–D807. undefined
\bibitem{Hastings2015}
19. Hastings,J., Owen,G., Dekker,A., Ennis,M., Kale,N., Muthukrishnan,V., Turner,S., Swainston,N., Mendes,P. and Steinbeck,C. (2016) ChEBI in 2016: Improved services and an expanding collection of metabolites. {\em Nucleic Acids Res.,}, {\bf 44}, D1214–D1219. undefined
\bibitem{Mietchen2015}
20. Mietchen,D., Hagedorn,G., Willighagen,E., Rico,M., Gómez-Pérez,A., Aibar,E., Rafes,K., Germain,C., Dunning,A., Pintscher,L., {\em et al.,} (2015) Enabling Open Science: Wikidata for Research (Wiki4R). {\em RIO Journal,}, {\bf 1}, e7573+. undefined
\bibitem{Haug2013}
21. Haug,K., Salek,R.M., Conesa,P., Hastings,J., de Matos,P., Rijnbeek,M., Mahendraker,T., Williams,M., Neumann,S., Rocca-Serra,P., {\em et al.,} (2013) MetaboLights - an open-access general-purpose repository for metabolomics studies and associated meta-data. {\em Nucleic Acids Res.,}, {\bf 41}, D781–D786. undefined
\bibitem{Kamburov2013}
22. Kamburov,A., Stelzl,U., Lehrach,H. and Herwig,R. (2013) The ConsensusPathDB interaction database: 2013 update. {\em Nucleic Acids Res.,}, {\bf 41}, D793–D800. undefined
\bibitem{Swainston2016}
23. Swainston,N., Smallbone,K., Hefzi,H., Dobson,P., Brewer,J., Hanscho,M., Zielinski,D., Ang,K., Gardiner,N., Gutierrez,J., {\em et al.,} (2016) Recon 2.2: from reconstruction to model of human metabolism. {\em Metabolomics,}, {\bf 12}, 1–7. undefined
\bibitem{Kanehisa2017}
24. Kanehisa,M., Furumichi,M., Tanabe,M., Sato,Y. and Morishima,K. (2017) KEGG: new perspectives on genomes, pathways, diseases and drugs. {\em Nucleic Acids Res.,}, {\bf 45}, D353–D361. undefined
\bibitem{Fabregat2016}
25. Fabregat,A., Sidiropoulos,K., Garapati,P., Gillespie,M., Hausmann,K., Haw,R., Jassal,B., Jupe,S., Korninger,F., McKay,S., {\em et al.,} (2016) The Reactome pathway Knowledgebase. {\em Nucleic Acids Res.,}, {\bf 44}, D481–D487. undefined
\bibitem{Hanumappa2013}
26. Hanumappa,M., Preece,J., Elser,J., Nemeth,D., Bono,G., Wu,K. and Jaiswal,P. (2013) WikiPathways for plants: a community pathway curation portal and a case study in rice and arabidopsis seed development networks. {\em Rice,}, {\bf 6}, 14+. undefined
\bibitem{Ratnam2014}
27. Ratnam,J., Zdrazil,B., Digles,D., Cuadrado-Rodriguez,E., Neefs,J.-M., Tipney,H., Siebes,R., Waagmeester,A., Bradley,G., Chau,C.H., {\em et al.,} (2014) The Application of the Open Pharmacological Concepts Triple Store (Open PHACTS) to Support Drug Discovery Research. {\em PLoS ONE,}, {\bf 9}, e115460+. undefined
\bibitem{pico2008wikipathways}
28. Pico,A.R., Kelder,T., Van Iersel,M.P., Hanspers,K., Conklin,B.R. and Evelo,C. (2008) WikiPathways: pathway editing for the people. {\em PLoS Biol.,}, {\bf 6}, e184. undefined
\bibitem{kutmon2015wikipathways}
29. Kutmon,M., Riutta,A., Nunes,N., Hanspers,K., Willighagen,E.L., Bohler,A., Mélius,J., Waagmeester,A., Sinha,S.R., Miller,R., {\em et al.,} (2015) WikiPathways: capturing the full diversity of pathway knowledge. {\em Nucleic Acids Res.,}, {\bf 44}, D488–D494. undefined
\bibitem{jennen2010biotransformation}
30. Jennen,D.G., Gaj,S., Giesbertz,P.J., van Delft,J.H., Evelo,C.T. and Kleinjans,J.C. (2010) Biotransformation pathway maps in WikiPathways enable direct visualization of drug metabolism related expression changes. {\em Drug Discov. Today,}, {\bf 15}, 851–858. undefined
\bibitem{mastrokolias2016integration}
31. Mastrokolias,A., Pool,R., Mina,E., Hettne,K., van Duijn,E., van der Mast,R., van Ommen,G., ’t Hoen,P., Prehn,C., Adamski,J., {\em et al.,} (2016) Integration of targeted metabolomics and transcriptomics identifies deregulation of phosphatidylcholine metabolism in Huntington’s disease peripheral blood samples. {\em Metabolomics,}, {\bf 12}, 137. undefined
\bibitem{kohonen2017transcriptomics}
32. Kohonen,P., Parkkinen,J.A., Willighagen,E.L., Ceder,R., Wennerberg,K., Kaski,S. and Grafström,R.C. (2017) A transcriptomics data-driven gene space accurately predicts liver cytopathology and drug-induced liver injury. {\em Nat. Commun.,}, {\bf 8}. undefined
\bibitem{azad2017bayesian}
33. Azad,A., Lawen,A. and Keith,J.M. (2017) Bayesian model of signal rewiring reveals mechanisms of gene dysregulation in acquired drug resistance in breast cancer. {\em PLoS one,}, {\bf 12}, e0173331. undefined
\bibitem{kutmon2015pathvisio}
34. Kutmon,M., van Iersel,M.P., Bohler,A., Kelder,T., Nunes,N., Pico,A.R. and Evelo,C.T. (2015) PathVisio 3: an extendable pathway analysis toolbox. {\em PLoS Comput. Biol.,}, {\bf 11}, e1004085. undefined
\bibitem{van2010bridgedb}
35. van Iersel,M.P., Pico,A.R., Kelder,T., Gao,J., Ho,I., Hanspers,K., Conklin,B.R. and Evelo,C.T. (2010) The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services. {\em BMC Bioinf.,}, {\bf 11}, 5. undefined
\bibitem{kell2016metabolome}
36. Kell,D.B. and Oliver,S.G. (2016) The metabolome 18 years on: a concept comes of age. {\em Metabolomics,}, {\bf 12}, 148. undefined
\bibitem{bohler2016reactome}
37. Bohler,A., Wu,G., Kutmon,M., Pradhana,L.A., Coort,S.L., Hanspers,K., Haw,R., Pico,A.R. and Evelo,C.T. (2016) Reactome from a WikiPathways perspective. {\em PLoS Comput. Biol.,}, {\bf 12}, e1004941. undefined
\bibitem{afendi2011knapsack}
38. Afendi,F.M., Okada,T., Yamazaki,M., Hirai-Morita,A., Nakamura,Y., Nakamura,K., Ikeda,S., Takahashi,H., Altaf-Ul-Amin,M., Darusman,L.K., {\em et al.,} (2011) KNApSAcK family databases: integrated metabolite–plant species databases for multifaceted plant research. {\em Plant and Cell Physiol.,}, {\bf 53}, e1–e1. undefined
\bibitem{okada2013multivariate}
39. Okada,T., Afendi,F.M., Katoh,A., Hirai,A. and Kanaya,S. (2013) Multivariate Analysis of Analytical Chemistry Data and Utility of the KNApSAcK Family Database to Understand Metabolic Diversity in Medicinal Plants. In {\em Biotechnology for Medicinal Plants,}. Springer, pp. 413–438. undefined
\bibitem{Wilkinson2016}
40. Wilkinson,M.D., Dumontier,M., Aalbersberg,Ij.J., Appleton,G., Axton,M., Baak,A., Blomberg,N., Boiten,J.-W., da Silva Santos,L.B., Bourne,P.E., {\em et al.,} (2016) The FAIR Guiding Principles for scientific data management and stewardship. {\em Sci. Data,}, {\bf 3}, 160018. undefined
\bibitem{G1PmetabolismOld}
41. Heckman,J., Chichester,C. and Willighagen,E. (2016) Glucose-1-phosphate metabolism, version 89691 (Saccharomyces cerevisiae). http://www.wikipathways.org/instance/WP260_r89691
\bibitem{G1PmetabolismNew}
42. Heckman,J., Chichester,C., Willighagen,E., Slenter,D. and Kutmon,M. (2017) Glucose-1-phosphate metabolism, version 94487 (Saccharomyces cerevisiae). http://www.wikipathways.org/instance/WP260_r94487
\bibitem{glycoglucoOld}
43. Username:Kdahlquist, Coort,S., Fidelman,N., van Iersel,M., Hanspers,K., Kelder,T., Bouwman,J., Pico,A., Willighagen,E., Kutmon,M., {\em et al.,} (2016) Glycolysis and Gluconeogenesis, version 90450 (Homo sapiens). http://www.wikipathways.org/instance/WP534_r90450
\bibitem{glycoglucoNew}
44. Username:Kdahlquist, Coort,S., Fidelman,N., van Iersel,M., Hanspers,K., Kelder,T., Bouwman,J., Pico,A., Willighagen,E., Kutmon,M., {\em et al.,} (2017) Glycolysis and Gluconeogenesis, version 93722 (Homo sapiens). http://www.wikipathways.org/instance/WP534_r93722
\bibitem{BiochemPWsPartI}
45. Giesbertz,P. and Willighagen,E. (2017) Biochemical Pathways Part I (Homo sapiens). http://www.wikipathways.org/instance/WP3604
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