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csiu/ismb-round1-accepted-abstracts.tsv

Created May 6, 2016 16:18
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List of ISMB 2016 accepted abstracts (as of Fri, May 6, 2016)
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ismb-round1-accepted-abstracts.tsv
category title
A Petabyte cancer genomics analysis in the cloud
A RNA-seq based Absolute Subtyping of Breast Cancer
A Neopepsee: machine learning-based prediction of neoantigen using next-generation sequencing data
A Prediction of compound-target interactions by using deep-learning networks
A A bioinformatics tool to improve the efficacy of exon skipping therapy for Duchenne muscular dystrophy
A Significant Random Signatures Have Information
A Pinpointing HLHS-related genes by integrating RNA-seq and whole genome sequencing in Trio analysis
A Meta-analysis of human host gene expression response to Mycobacterium tuberculosis infection
A Using Latent Semantic Analysis for automated keyword extraction from PubChem BioAssay
A Putative effectors for prognosis in lung adenocarcinoma are ethnic and gender specific
A Understanding Escherichia coli’s multiple drug resistance (MDR) through QSPR modeling– Is it really possible???
A Species-independent identification of known and novel recurrent genomic entities in multiple cancer patients
A An in silico approach for targeting the cell wall proteins of Mycobacterium tuberculosis by novel anti-tubercular inhibitors
A Accelerated NGS Interpretation via the GeneCards Suite
A A Bayesian Tensor Factorization Method to Predict Drug Response Curves in Cancer Cell Lines
A BRIDGES – BIOMARKERS REUSE IN DIFFERENT GENE EXPRESSION SYSTEMS
A HUeMR: Intuitive Mining of Electronic Medical Records for Disease Informatics
A VARIFI - Automatic Variant Identification, Filtering and Annotation of Amplicon Sequencing Data
A Therapeutic target prediction exploiting gene regulatory network
A Accurately and efficiently identify differentially expressed genes or epigenetic changes with a novel balanced permutation method in parallel computing from next-generation sequencing data
A OpenGeneMed: a portable, flexible and customizable informatics hub for the coordination of next-generation sequencing studies in support of precision medicine trials.
A An ensemble feature selection using L1-norm support vector machine for high-dimensional gene expression data
A An R Package for Discovering Disease Subtypes within Complex Heterogeneous Human Datasets
A Survival time prediction by integrating RNA-sequencing and RPPA data
A A Novel Method for Bolstering Prediction of Therapeutically Similar Drugs using Text Mining.
A The Knowledge Hub: A Graph-based Approach to Big Data Analysis for Cancer Research and Therapy
A Whole exome and transcriptome sequencing of type I and type II enteropathy-associated T cell lymphoma reveals genetic basis of EATL oncogenesis
A Defining the microbiome of lymphomas
A Defining the genetic overlap of patient tumors and patient derived xenograft models in colorectal cancer
A Frequent Item-set Mining for Detecting Building Blocks of Lymphoma
A Applications of machine learning for explaining systematic sources of variability in neuroscience data produced by large-scale literature text-mining
A TCGA2BED: extracting, extending, integrating, and querying The Cancer Genome Atlas
A From 3D Visualization of Molecules to Annotation and Visualization of Molecular Information in Genome Browsers
A Drug synergy prediction on cancer cell lines based on genomic features
A A gene-signature progression approach to identifying candidate small-molecule cancer therapeutics with connectivity mapping
A Epigenetic age predicted from H3K9ac ChIP-seq data is associated with Alzheimer's disease pathologies in the human prefrontal cortex
A OncoTope: A platform to data mine T-cell neo-epitopes from cancer-causing genes in 28 different cancer type
A Topic Modeling for Mining Tobacco Use Related Themes from Textual Documents
A Development of a new Pharmacogenomics database combining genetic variants, DNA methylation, and exon expression data
A Human MHC-I Presentation Shapes Somatic Mutational Landscape in Cancer
A Epigenetic and genomic landscape in cancer
A A knowledgebase for identifying relationships between plant pathways and affects on human nutrition
A CAMUR: Knowledge extraction from RNA-seq cancer data through equivalent classification rules
A Unraveling Lentiviral Vector Integration Machinery through the Analysis of Integration Sites Landing in Repetitive Elements from Gene Therapy Patients
A Candidate gene prioritization with Endeavour
A Sample alignment: A critical QC step for integrative analysis using multi-omics data
A In Silico Analysis from Protein Structures Reveals Loss and Gain of Functional Sites as Active Mechanism of Disease
A Single-cell RNA-seq reveals lineage and X-chromosome dynamics in human preimplantation embryos
A An Integrated Gene Expression and Radiomics Database System to Support Precision Medicine
A Computational analysis of alternative splicing abnormalities in Spinal Muscular Atrophy using RNA-Sequencing technology
A AML-Varan – a web-based platform to display and analyze genomic variants from targeted Next-generation sequencing data in clinical practice
A Maximizing the power of cell-type specific differential expression analysis in heterogeneous gene expression data
A Multi ‘omics integration in Leishmania donovani
A Data fusion in drug target interaction prediction and drug repositionig
A Genomicper: discovering variants through genomic permutations
A Host-microbiome interaction: exploring blood-microbiome crosstalk
A A new method to predict the anti-cancer activity of pairs of compounds
A Prediction of Advanced Liver Fibrosis using Machine Learning Approaches in Chronic Hepatitis C Patients
A Supervised ensembles to boost the predictive power of DREAM challenges
A Predicting polypharmacology of kinase-targeted inhibitors by combining function-site interaction fingerprints and a support vector machine
A Bayesian approach for modelling condition-specific signal rewiring reveals possible mechanism of gene dysregulation in acquired resistance in breast cancer cell-lines
A MOVD: A model validation database for human inflammatory diseases
A Urothelial cancer cell line models of tumor biology and drug response
A Massively Parallel Phenotypic Screening for Faster Drug Discovery
A Diagnostic Role of Exome Sequencing in Immune Deficiency Disorders
A Data Mining Diverse Compendia of Triple Negative Breast Cancer Samples for Improved Tumor Subtyping
A Virtual Screening of PfM-18 Aminopeptidases from a natural product library
A Gene-Level Phenotype and Disease Model Representation at MGI
A Data-driven analysis of lymphocyte infiltration in breast cancer development and progression
A Widespread misannotation of samples in genomics studies
A Single-cell RNA-Seq Portal for Brain Research Collaboration and Dissemination
A ZIKV-CDB: A collaborative database to help understanding symptoms induced by ZIKA virus infection mediated by small noncoding RNAs
A Identification of novel markers for mammalian brain cell types
A Biological validation of computationally derived candidate regulatory modules for PDGFRβ
A RNA sequencing-based cell proliferation analysis across 19 cancers identifies a subset of proliferation-informative cancers with a common survival signature
B Comparative genomics and evolution of transcriptional regulons in Proteobacteria
B AODP: An improved method for signature oligonucleotide design
B Comparative Genomics Reveals Genetic Relationships between Filoviruses: Ebola, Lloviu and Marburg
B Comparative genomics study of the core components of the Exon Junction Complex in eukaryotes
B Deciphering evolutionary strata on plant and algal sex chromosomes and fungal mating-type chromosomes through compositional segmentation
B Comparative study of de novo genome assemblies for highly heterozygous seedless grape
B Identification of anthocyanin-related genes for black rice plants using microarray-based transcriptome data
B The RadioP1 – An Integrative Web Resource for Radioresistant Prokaryotes
B 'What does this gene do': Strategies for Summary Data Presentation in MODs
B LinkedOmics : A web-based platform for analyzing multi-omics data
B The evolutionary origin of orphan genes
B Novel meta-analysis of RNA-seq data across tissues and species reveal evolutionarily conserved gene expression and splicing patterns implicated in pain states in sensory tissues
C TeSS: ELIXIR Training Portal for Life Sciences
C Centralizing Bioinformatics via High-Performance Computing: Applications, Opportunities, and Challenges in the Era of Large-scale -Omics Data
C Modified Moore Method for an Undergraduate Introduction to Bioinformatics Course
C GOBLET’s Bioinformatics Learning, Education and Training Activities
C Assessing bioinformatics training impact – what, why, when and how?
D Comprehensive analysis of chromatin landscape in filamentous fungus Aspergillus nidulans
D BioWardrobe: an integrated platform for analysis of epigenomics and transcriptomics data.
D Disturbances of transcriptional networks in congenital heart disease
D Mutation in TET genes induce microsatellite instability by epigenetic silencing of MLH1
D Contribution of developmental stage and genetic variation to methylome dynamics during myeloid differentiation
D miRNome Analysis in Patients with Tetralogy of Fallot
D DEScan: A novel strategy for the analysis of epigenomic data with multiple biological replicates
D Detection of Wide Amplification Regions in ChIP-seq analysis
D skewr: Visualizing 450k Methylation Data for Quality Control
D Sex-mutual and sexually-dimorphic alterations in hippocampal DNA methylation with aging
E GeneiASE: Detection of condition-dependent and static allele-specific expression from RNA-seq data without haplotype information
E Expression Atlas and ArrayExpress: Functional Genomics Resources at EMBL-EBI
E Genome-wide discovery of active enhancers from eRNAs
E Deep sequencing of whole transcriptomes across the Drosophila Genetic Reference Panel
E Reliable differential expression calls across labs, by use of a simple reference sample
E GenomeSpace: Interoperable bioinformatics tools with crowd-sourced analysis recipes
E Integrated bioinformatics analysis identifies major pathways and target genes specific to biodiesel exposure.
E Identification of key mutation signatures from conservation analysis of gene-pseudogene families in primates
E From genomes to phenotypes: Traitar, the microbial trait analyzer
E Transcriptomic and proteomic changes during photoperiod induced growth cessation and dormancy induction in Vitis riparia
E Enhancers reprogramming in mammalian genomes
E A survey of Trypanosoma cruzi putative non-coding RNAs and their expression after irradiation
E Elaborating deconvolution of immune cell sub-populations from PBMC transcriptomic data of a Singaporean cohort
E Cross-platform normalization of microarray and RNA-seq data for machine learning applications
E Through a glass darkly: Single-cell co-expression as seen through the Gene Ontology
E Cap-seq Reveals Complicated miRNA Transcriptional Mechanisms in C. elegans and Mouse
E Quantification of SR-BI Deficiency on Lipoprotein and Biliary small RNAs using TIGER
E Complementary Post Transcriptional Regulatory Information is Detected by PUNCH-P and Ribosome Profiling
E HUNTING PHENOTYPE-ASSOCIATED GENES USING KERNEL DATA FUSION BASED ON ORDERED WEIGHTING AVERAGING
E Predictive modelling framework for splice factor knockdown experiments
E Evaluating Differential Ribosome Occupancy with Mixture Models in a Bio-remediation Candidate Strain of Pseudomonas aeruginosa
E Clustering Gene Ontology terms using different similarity measures – comparison of the measures performance and visualization of the dependences among Gene Ontology terms.
E Postmortem transcriptomic profiling of three psychiatric disorders reveals widespread dysregulation of cell-type associated transcripts and novel disease-related transcription changes
E Human VEGF-A121 Dimerization by SUMO Fusion Technology in Prokaryotic System
F Analysis of high-dimensional image-based cell morphology and gene expression profiles to investigate compounds mechanism of action
F Disclosing microorganisms, enzymes and pathways from a specialized lignin-degrading microbial community
F An integrated pipeline and monitoring system for de novo genome analysis
F The Role of Genome Accessibility in Transcription Factor Binding in Bacteria
F GMAP: Identifying Topologically Associating Domains by Gaussian Mixture model And Proportion tests
F Identification of Potential Interaction-Controls from Whole-Genome Contact Maps
F annTrans, a Functional Annotation Transfer Tool for de novo Transcriptome Assemblies
F Comprehensive profiling of somatic mosaicism in the human brain
G Conserved differences in protein sequence determine the human pathogenicity of Ebolaviruses
G Detection and genotyping of short indels using sequence data from multiple samples
G The assessment of small deletions impact within human exons in protein domains of 66 genomes in the 1000genomes project using transcriptome data.
G The SNPs associated with protein-drug binding sites
G Improved VCF Normalization for Evaluation of DNA Variant Calling Algorithms
G Identification of molecular subtypes, somatic and metastasis-associated driver genes in Triple-Negative Breast cancers and association to clinical prognosis
G KAMP: a structure-based computational approach for the prediction of activating missense mutations in kinases
G Learning Quantitative Trait Locus Models and Detecting Associations between HSV-1 Genotypes and Ocular Disease Phenotypes
G MyGene.info, MyVariant.info: Providing Gene and Genetic Variant Annotations as a Service
G Integrated database of insect genomes and ortholog genes, chemical interaction networks between insects and plants, and prediction of plant metabolic pathways.
G A Genomic Negative Storage Model enables precise, rapid queries with reduced storage needs
G Joint Sparse Canonical Correlation Analysis for Detecting Multivariate Differential Imaging Genetics Associations
G Using the Neandertal genome to study the evolution of small insertions and deletions in modern humans
G Mononucleotide repeats are enriched in differentially expressed genes among latitudinal populations of common sunflower
H Novel thermophilic antibiotic resistance enzymes from Atlantis II Deep Red Sea brine pool
H MetaCRAST: Reference-guided metagenomic CRISPR detection to map virus-host interactions
H Microbial diversity in a copper mine tailings dam
H Proxy regression: A novel regression method for deciphering environmental gradients
H Towards more robust metagenome profiling
I Lightweight Sample Labeling, Barcoding and Tracking Systems for the Academic Laboratory
I BioStudies – a database of biological studies
I RImmPort: enabling ready-for-analysis immunology research data
I Linuxbrew and Homebrew-Science to Navigate the Software Dependency Labyrinth
I Many hands make light work.
J CRISPR-Cas Systems Impact Pseudomonas aeruginosa Genome Structure
J Integration of data from immunoinformatics and protein disorder prediction for discovery of diagnostic targets for Schistosoma mansoni
J Identification of novel genomic islands in Liverpool epidemic strain of Pseudomonas aeruginosa using segmentation and clustering
J Enhancing geospatial metadata for GenBank records from contextual information
J Targeted sequencing for molecular detection and identification of foodborne pathogens in mixed samples.
J Differential expression of Blumeria effector repertoires on barley loss-of-function mutant hosts
K Ancestral Gene Blocks Reconstruction Using an Event-based Method
L Force Field Comparison: Protein-lipid interactions
L Tech Startups of the Genome: De novo genes arise frequently, try to be useful, and occasionally succeed and survive
L CoDNaS 2.0: A comprehensive database of protein conformational diversity in the native state
L Molecular Docking Studies for The Odorant Binding Protein of Aedes Aegypti Using Virtual Screening Approach
L In Silico Screening of Maytenus Chemical Compounds as New Proton Pump H+/K+-ATPase Inhibitors
L VarQ: Predicting the effects of SNPs based on protein structure
L Cholesterol-conditioned dynamic CXCR4 dimerization
L iCn3D, a Web-based 3D Viewer for Biomolecular Structures
L AraPPISite: a database of fine-grained protein-protein interaction site annotations for Arabidopsis thaliana
L Protein Classification using Specific Domain Architectures
L Natural language processing in text mining for protein docking
L An EM Algorithm for Binding Energy Estimation Using HT-SELEX Data
L Conserved Domain Database (CDD): Improving Functional Annotation of Protein Sequences, using SPARCLE, the SPecific ARChitecture Labeling Engine
L Assessing Impact of Taxonomic Diversity and Sequence Conservation-based Filters on Mirrortree Method
L Capturing and modeling structural flexibility
L Utilizing computational chemistry to characterize the functions of Structural Genomics proteins
L Accurate Prediction of Metal Binding Sites in Proteins
L A structural view of signaling through the Toll-like receptor pathway and its implications to inflammation and cancer crosstalk
L The Protein Topology Graph Library web server
L Modelling conformational entropy in the scoring function of the molecular docking software FlexAID
L Understanding Sequence-Structure-Function Relationships of Orphan GPCRs through NCBI’s Conserved Domain Database (CDD).
L Comparative computational analysis of phylloplanin proteins present in different plant species
L Are Protein Models Accurate Enough for Identifying Residue Specific Functional Features?
L Camelids nanobodeis binders: VHH sequences analysis and crucial elements involved in Androctonus australis hector (Aah) scorpion toxins binding and neutralisation
L ProQ3: Improved model quality assessments using Rosetta energy terms
L How to more accurately compute protein residue contacts?
L An efficient DFT approach to unravel Enzymatic Reaction Mechanisms: Mycothiol MshA glycosyl-transferase reaction as a case study.
L Tertiary Structural Propensities Reveal Basic Sequence-Structure Relationships in Proteins
L Measuring Distance between Protein Functions on Gene Ontology with a New Metric
L Critical Assessment of Function Annotation: Moving Forward with the “State-of-the-art"
L Structural characterization of antibody Next Generation Sequencing data
L From Sequence to 3D-model: an efficient use of Homology Modeling, Molecular Dynamics and Ligand Docking techniques to predict Protein-Carbohydrate complexes.
L Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics
L Molecular Dynamics Simulations of Glycosylated HIV-1 gp120 Trimers in the Context of Viral Coreceptor Tropism
L Decomposition of protein structures into structural domains based on hydrophobic core detection
L Regularity of repeat proteins
L Integrative mapping of metabolic pathways
L Structure-based prediction of homeodomain binding specificity using homology models and an integrative energy function
L Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomics
M ACTG (Amino aCids To Genome)
N Exploring the world of non-coding RNAs with RNAcentral
N Somatic mutation of Akt/mTOR pathways in cervical small cell neuroendocrine tumors
N The relationship between duplication and essentiality for mammalian genes
N MultiSyn: a webtool for multiple synteny detection and visualization of user’s interesting sequences compared to public plant species
N Simple and efficient indexing and searching with a hardware-acceleration-friendly k-ordered FM-index structure for biological sequences
N NGS-SWIFT: A Cloud-Based Framework for Analyzing Sequencing Data from NCBI
N Primary and secondary sequence structure requirements for recognition and discrimination of target RNAs by Pseudomonas aeruginosa RsmA and RsmF
N UEKO: an UniRef Enriched KEGG Orthology database for functional annotation
N KIXBASE: A KIX domain database and web server for prediction and analysis.
N cICB: a modular high-throughput computational pipeline for the annotation of proteins of unknown function by Integrative Cell Biology
N Genome comparative analysis to co-regulated genes of myb transcription factor binding sites in phenylpropanoid biosynthesis pathway
N Prometheus : Omics Portal for Comparative Genomics in KOBIC
N Resampling-Based Read-Level Normalization of RNA-Seq for Differential Expression Analysis
N Benchmark Analysis of RNA-Seq Aligners
N Gene model annotation mapping with use of local sequence similarity and advance distance scoring metrics
N The Landscape of Circular RNA in Cancer
N Substitution rate variability causes memory effects on protein sequence evolution and is triggered by sequence coevolution
N Basic4CSim: A benchmarking approach for 4C-seq pipelines on simulated datasets
N To identify and functional validate of novel long intergenic noncoding RNAs in myogenesis using integrated genomic approach
N ScanIndel: a hybrid framework for indel detection via gapped alignment, split reads and de novo assembly
N Predicting Metabolic Networks using Learning Methods with Sequence and Non-Sequence Kernels
N Adaptive local realignment via parameter advising
N Visualization of TCGA RNA-Seq information with an user-friendly mobile application
N Mapping of RNA binding residues in human proteome using global and local protein sequence features
N Fast and Accurate Fusion Transcript Detection Using the Trinity Cancer Transcriptome Analysis Toolkit
N Insights into the Transcriptional Architecture of Behavioral Plasticity in the Honey Bee Apis mellifera
N CSI-UTR: AN ALGORITHM FOR CHARACTERIZING 3’ UNTRANSLATED REGION (3’UTR) DIVERSITY IN RNA-SEQ DATA BY EMPLOYING RNA CLEAVAGE SITE INTERVALS (CSIs)
N Metagenomic proxy assemblies of single cell genomes
N TEpeaks: A tool for uncovering regulatory roles of retrotransposons from ChIP-seq data
N Micronota: Redefining a Consistent Microbial Reference Database
N Application of Machine Learning Algorithms on Next-generation Sequencing Data Analysis
N Next generation genomic computing
N A software environment for the development of high-performance analysis pipelines.
N BayesTyping: a Tool for HLA typing with PacBio CCS Reads
N New Graph-based Algorithm for Comprehensive Identification and Tracking of Retroviral Integration Sites
N Novel method for barcoding large numbers of single cells with targeted multiplex sequencing
N m6aViewer: software for N6-methyl-adenosine sequencing
N TEsmall: A pipeline for profiling TE-associated small RNAs
N k-SLAM: Accurate and ultra-fast taxonomic classification and gene identification for large metagenomic datasets
N BasicSTARRseq: a Bioconductor R-package for analyzing STARR-seq data
N Pattern Similarity Search in Multiple Genome Browser Tracks
N Biochemical Properties of Proteins as a Function of Evolutionary Age
N TEtranscripts: A package for including transposable elements in differential expression analysis of RNA-seq datasets
N Improve homology search sensitivity of PacBio data by correcting frameshifts
N UniProt Feature Viewer: Visualising protein sequence features and variants
N The reference Trypanosoma cruzi transcriptome generated by de novo assembly of RNA-Seq data
N BrCAT: A Catalog of Breast Cancer Stemness genes and their association with Drug Resistance and Tumor Recurrence
N Hidden RNA Codes Revealed from in vivo RNA Structurome
N Sequence-specific Bias Correction for RNA-seq Data using Recurrent Neural Networks
N The Impact of Sequence Ambiguity on Read Mapping Accuracy
N Supervised learning enables detection of duplicates in biological databases
N Comparison of normalization methods for single cell RNA-seq
N Constructing an iterative method for predicting protein O-glycosylation sites glycosylated by different GalNAc-transferase isoforms.
N New tools to analyze overlapping coding regions
N Creation of a Sequence Database of Gram-Positive Bacteria Commonly Found in Dietary Supplements.
N Robust statistical modelling greatly improves sensitivity of high-throughput RNA structure probing experiments
N A comparison of Illumina and Ion Torrent platforms in a study of differential gene expression
N Potential Protein Isoforms Reveal Additional Information on Biomarkers Obtained from RNA-Seq Data
N A phylodynamics pipeline for pathogen sequence data
N Detection of differentially expressed single nucleotide variations in microRNAs and their targets in cancer
N Transcriptome assemblies: A comparison of de novo and genome-guided assemblers using simulated RNASeq data.
N GapBlaster - A graphical gap filler for prokaryote genomes
N BioXSD | BioJSON | BioYAML - Integrated formats for sequence data
N Comparing Variant Concordance in DNA-seq and RNA-seq from Matched Samples
N A high-performance pipeline for differential methylation analysis
N PatternCNV 2.0: An improved method for detecting copy number changes in tumor samples and germline trio exome sequencing data
N RNA folding kinetics
N p53 - Guardian or Gambler of the Genome?
N Whole-genome DNA methylation universally predicts 3D topological domains across cell types
N Automated Fragment Size Analysis of Pathogenic Expansions in Triplet and Hexanucleotide Repeat Disorders
N RNA-Bloom: de novo RNA-seq assembly with Bloom filters
N ntHash algorithm for bioinformatics
N The applications of genome-derived molecular signatures to microbial diagnostics and classification
N Position-dependent mutation distribution and codon usage bias differs between oncogene and tumor-suppressor genes
N Identification of genomic rearrangements with de novo assemblies and read-based pipelines
N Nucleotide Sequence Difference between DNA-RNA and Blood-Tissue Samples
N 1000 Whole Exomes to Paint a Comprehensive Genetic Portrait of Diffuse Large B-Cell Lymphoma
N The subtle interaction of three structural factors driving site-specific protein evolution
N Computational identification of candidate regulatory modules for PDGFRβ
N NanoSim: nanopore sequence read simulator based on statistical characterization
N Landscape of circRNA Candidates Across 11 Organs and 4 Developmental Stages in Fischer 344 Rat
O Linking transcriptional and metabolic regulation in Chlamydominas reinhardtii using a gene-reaction-metabolite association network
O Visualization of Pathway Collages
O ADAGE-Based Extraction of Biological Context from Public Gene Expression Data
O Effects of thresholding on the topology and entropy of gene co-expression networks
O Learning biological networks from gene knockdown data
O Plasma metabolites as proxy markers for inter-organ processes in diabetic mice
O SSBD: an open database of quantitative data of biological dynamics
O Live single cell quantitative analysis reveals bi-stable and pulsatile behaviour in the cell cycle regulator p21
O Identifying target genes for RNA-binding proteins
O Developing quantitative resource for computational analysis from images of C. elegans embryogenesis in public databases
O Jumping across gene-disease contexts using compressive data fusion
O Structure-based Analysis Reveals Cancer Missense Mutations Target Protein Interaction Interfaces
O The use of an adipocyte metabolic network in the study of mechanisms leading to the development of type 2 diabetes
O Design and analysis of compound synergy screens with SynergyScreen
O Anti-aging and aging molecular networks database
O Processing, Metrics and Quality Control Analysis of RNA-SEQ Experiments
O A deep-learning-based cancer subtyping method using functional profiles overcomes the intrinsic limitations of signature-gene-based approach
O GOView: a web tool for visualizing and comparing multiple GO term lists
O Protein-level regulation drives coordinated gene functions
O DECONVOLUTION OF CELL AND ENVIRONMENT SPECIFIC SIGNALS AND THEIR INTERACTIONS FROM COMPLEX MIXTURES IN BIOLOGICAL SAMPLES
O PhenoCurve: Capturing Dynamic Phenotype-Environment Relationships using Phenomics Data
O Topological Analysis of Protein Interaction Networks
O PSAMM: A Portable System for the Analysis of Metabolic Models
O A GENOME SCALE METABOLIC MODEL DRAFT OF THE PLANT PATHOGEN Xanthomonas axonopodis pv. manihotis
O Gene co-expression networks and their application to cancer biology
O Identification of the role of SRSF1 in T cell activation and functions through the analysis of high-throughput sequencing data.
O Systems-biology guided identification of disease-specific metabolic genes implicated in the activation of T-cells
O A new cellular network model of liver tissue renewal predicts the key feedback interactions required for maintaining robust homeostasis
O Identification of dysregulated genes and pathways in different stages of colorectal cancer using meta-analysis
O Explicit Modeling of Differential RNA Stability Improves Inference of Transcription Regulation Networks
O Data integration of omics data: a network-oriented approach
O Popularity Enriched Dimension Reduction on Gene Expression and Pathway Data Analysis
O An algorithm for biomarker identification using high-influence perturbed disease networks
O Molecular Dynamics Simulation of the Association of the β-Blocker Propranolol with a Chiral Molecular Micelle
O Multiscale, multifactorial response network of immunization in humans
O Graph-based analysis of CD30+ cell distributions in Hodgkin Lymphoma
O Metabolome wide association of DDT exposure in humans and in mice
O Reanalysis of Snyderome with mummichog and blood transcription modules
O Drug discovery pipeline applied to Clostridium difficile.
O Modeling the role of environmental effect in immune homeostasis
O Multiple network alignment via multiMAGNA++
O TRACE: Reconstructing trajectories of cell cycle evolution using single-cell mass cytometry data
O Functional subgraph enrichments for node sets in interaction networks
O SSA-ME Detection of cancer mutual exclusivity patterns by small subnetwork analysis
O The Systems Toxicology Challenge: Marker of Exposure Response Identification in Blood
O Estimation of ribosome profiling performance and reproducibility at various levels of resolution
O Fair Evaluation of Global Network Aligners
O Construction and analysis of active enhancer-target networks in 935 samples of human primary cells, tissues and cell lines
O MOLAS: Multi-Omics onLine Analysis System for Gene Expression Profiling
O Evaluation of data integrative approaches for network inference
O Uncovering the mechanisms of autophagy modulation by Salmonella – a network biology based approach
O Mining host-pathogen protein interactions to characterize Burkholderia mallei infectivity mechanisms
O A systems biology strategy to identify molecular mechanisms of action and protein indicators of traumatic brain injury
O AuPairWise: biologically focused RNA-seq quality control using co-expression
O Robust method for evaluation of molecular subtypes and classifications in cancers
O The ability of different imputation methods to preserve the significant genes and predictive power for pathway enrichment
O Systems Analysis of the Autoimmune Response in Primary Sclerosing Cholangitis
O Tribe: The collaborative platform for reproducible web-based gene set analyses
O Knowledge-guided fuzzy logic network modeling to infer cancer signaling pathways from time-series data
O Title: FAIRDOM: Data and Model Management for all
O Search of quasi-cliques in multigraphs to find candidate regulatory genes in Mycobacterium tuberculosis
O Universal attenuators and their interactions with feedback loops in gene regulatory networks
O Pathview Web: a systematic online solution for pathway analytics and visualization
O Clustering of gene ontology annotation by matrix factorization
O Bioinformatics without databases: liberating neuroscience's data using large-scale literature text-mining
O Identification of Tissue Specific and Common Coexpression Links Amongst Five Human Tissues
O A Conserved Structural Signature of the Homeobox Coding DNA in HOX genes
O SAR- Segmentation, Analysis, and Reintegration: An Algorithm for a Structural Analysis of Protein Interaction Networks
O Differentially expressed genes are not uniformly distributed
O Building, publishing, simulating, and analyzing large-scale computational models with Cell Collective
O Assessing the Differential Significance of Transcription Factors
O Drug Repositioning for Molecular Subsets of Ovarian Cancer
O Systems perturbation analysis of signal transduction to prioritize cancer therapeutic targets
O An enhanced map of the human Methyl Arginine Proteome
O GRNmap and GRNsight: Open Source Software for Dynamical Systems Modeling and Visualization of Medium-Scale Gene Regulatory Networks
O First-Principles Modeling of Metabolism using Statistical Thermodynamics and Maximum Entropy
O HDMOFA: A Tool for High Dimensional Multi-­Objective Flux Analysis in Genome-­Scale Models of Metabolism
O Regulation of Neuropeptides through Mutual Interactions Identified by Systematic Informatics Strategies
O Identifying Novel Functions of PLEKHA7 by Integrated Bioinformatics Strategies
P Association between antidepressants use during pregnancy and Autistic Spectrum Disorders: a meta-analysis.
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