The BioGRID Interaction Database: 2011 update.

STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res (2012) 18.26

Architecture of the human regulatory network derived from ENCODE data. Nature (2012) 10.28

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res (2011) 8.18

A travel guide to Cytoscape plugins. Nat Methods (2012) 6.53

The BioGRID interaction database: 2013 update. Nucleic Acids Res (2012) 6.09

g:Profiler--a web server for functional interpretation of gene lists (2011 update). Nucleic Acids Res (2011) 3.94

WormBase 2012: more genomes, more data, new website. Nucleic Acids Res (2011) 3.87

Differential network biology. Mol Syst Biol (2012) 3.74

Global identification of modular cullin-RING ligase substrates. Cell (2011) 3.13

Combinatorial drug therapy for cancer in the post-genomic era. Nat Biotechnol (2012) 3.10

The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. BMC Bioinformatics (2011) 3.03

A gene ontology inferred from molecular networks. Nat Biotechnol (2013) 2.95

The ConsensusPathDB interaction database: 2013 update. Nucleic Acids Res (2012) 2.94

PomBase: a comprehensive online resource for fission yeast. Nucleic Acids Res (2011) 2.84

Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. Pharmacol Ther (2013) 2.64

The BioPlex Network: A Systematic Exploration of the Human Interactome. Cell (2015) 2.41

Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies. PLoS Biol (2012) 2.37

PINA v2.0: mining interactome modules. Nucleic Acids Res (2011) 2.23

modMine: flexible access to modENCODE data. Nucleic Acids Res (2011) 2.18

HIPPIE: Integrating protein interaction networks with experiment based quality scores. PLoS One (2012) 2.17

AnimalTFDB: a comprehensive animal transcription factor database. Nucleic Acids Res (2011) 2.15

IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. Nucleic Acids Res (2012) 2.01

Interactome3D: adding structural details to protein networks. Nat Methods (2012) 1.89

Systematic exploration of synergistic drug pairs. Mol Syst Biol (2011) 1.89

Hierarchical modularity and the evolution of genetic interactomes across species. Mol Cell (2012) 1.88

HINT: High-quality protein interactomes and their applications in understanding human disease. BMC Syst Biol (2012) 1.73

ExoCarta as a resource for exosomal research. J Extracell Vesicles (2012) 1.69

Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community. BMC Bioinformatics (2011) 1.69

AutismKB: an evidence-based knowledgebase of autism genetics. Nucleic Acids Res (2011) 1.59

Tissue-specific functional networks for prioritizing phenotype and disease genes. PLoS Comput Biol (2012) 1.54

Preferential duplication of intermodular hub genes: an evolutionary signature in eukaryotes genome networks. PLoS One (2013) 1.45

The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies. J Biomed Semantics (2013) 1.44

Systems pharmacology: network analysis to identify multiscale mechanisms of drug action. Annu Rev Pharmacol Toxicol (2012) 1.41

INDI: a computational framework for inferring drug interactions and their associated recommendations. Mol Syst Biol (2012) 1.40

Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder. Am J Hum Genet (2013) 1.39

A SPARSE CONDITIONAL GAUSSIAN GRAPHICAL MODEL FOR ANALYSIS OF GENETICAL GENOMICS DATA. Ann Appl Stat (2011) 1.39

Evolution and function of CAG/polyglutamine repeats in protein-protein interaction networks. Nucleic Acids Res (2012) 1.38

The protein expression landscape of the Arabidopsis root. Proc Natl Acad Sci U S A (2012) 1.36

An Interspecies Regulatory Network Inferred from Simultaneous RNA-seq of Candida albicans Invading Innate Immune Cells. Front Microbiol (2012) 1.35

Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types. Genome Res (2013) 1.33

A genome-wide resource of cell cycle and cell shape genes of fission yeast. Open Biol (2013) 1.32

Large-scale event extraction from literature with multi-level gene normalization. PLoS One (2013) 1.30

SignaLink 2 - a signaling pathway resource with multi-layered regulatory networks. BMC Syst Biol (2013) 1.30

Protein misinteraction avoidance causes highly expressed proteins to evolve slowly. Proc Natl Acad Sci U S A (2012) 1.29

Retracted Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK. Nature (2012) 1.29

SLiMSearch 2.0: biological context for short linear motifs in proteins. Nucleic Acids Res (2011) 1.23

How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience. Database (Oxford) (2012) 1.23

Distinct transcriptional regulatory modules underlie STAT3's cell type-independent and cell type-specific functions. Nucleic Acids Res (2013) 1.21

The PhosphoGRID Saccharomyces cerevisiae protein phosphorylation site database: version 2.0 update. Database (Oxford) (2013) 1.20

Analyzing protein-protein interactions from affinity purification-mass spectrometry data with SAINT. Curr Protoc Bioinformatics (2012) 1.20

Integrating protein-protein interaction networks with phenotypes reveals signs of interactions. Nat Methods (2013) 1.19

Gadd45 proteins: relevance to aging, longevity and age-related pathologies. Ageing Res Rev (2011) 1.19

Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE. BMC Genomics (2013) 1.18

Molecular links between cellular senescence, longevity and age-related diseases - a systems biology perspective. Aging (Albany NY) (2011) 1.12

Low frequency variants, collapsed based on biological knowledge, uncover complexity of population stratification in 1000 genomes project data. PLoS Genet (2013) 1.12

LC-MS/MS-based serum proteomics for identification of candidate biomarkers for hepatocellular carcinoma. Proteomics (2015) 1.11

A genomic toolkit to investigate kinesin and myosin motor function in cells. Nat Cell Biol (2013) 1.11

The Disease and Gene Annotations (DGA): an annotation resource for human disease. Nucleic Acids Res (2012) 1.11

Genome-wide association study of sleep in Drosophila melanogaster. BMC Genomics (2013) 1.11

Mitotic exit and separation of mother and daughter cells. Genetics (2012) 1.10

Adding protein context to the human protein-protein interaction network to reveal meaningful interactions. PLoS Comput Biol (2013) 1.10

Discovering disease-disease associations by fusing systems-level molecular data. Sci Rep (2013) 1.10

Infection Strategies of Bacterial and Viral Pathogens through Pathogen-Human Protein-Protein Interactions. Front Microbiol (2012) 1.09

Functional knowledge transfer for high-accuracy prediction of under-studied biological processes. PLoS Comput Biol (2013) 1.09

Benchmarking of the 2010 BioCreative Challenge III text-mining competition by the BioGRID and MINT interaction databases. BMC Bioinformatics (2011) 1.09

Stringent homology-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions. Biol Direct (2014) 1.08

INstruct: a database of high-quality 3D structurally resolved protein interactome networks. Bioinformatics (2013) 1.08

Endosomal crosstalk: meeting points for signaling pathways. Trends Cell Biol (2012) 1.08

A systematic analysis of cell cycle regulators in yeast reveals that most factors act independently of cell size to control initiation of division. PLoS Genet (2012) 1.07

IODNE: An integrated optimization method for identifying the deregulated subnetwork for precision medicine in cancer. CPT Pharmacometrics Syst Pharmacol (2017) 1.07

The TissueNet database of human tissue protein-protein interactions. Nucleic Acids Res (2012) 1.07

Linking proteomic and transcriptional data through the interactome and epigenome reveals a map of oncogene-induced signaling. PLoS Comput Biol (2013) 1.06

SpliceAid-F: a database of human splicing factors and their RNA-binding sites. Nucleic Acids Res (2012) 1.06

Building an efficient curation workflow for the Arabidopsis literature corpus. Database (Oxford) (2012) 1.05

Chapter 15: disease gene prioritization. PLoS Comput Biol (2013) 1.05

MDM2 turnover and expression of ATRX determine the choice between quiescence and senescence in response to CDK4 inhibition. Oncotarget (2015) 1.05

Exploring the yeast acetylome using functional genomics. Cell (2012) 1.05

A novel link prediction algorithm for reconstructing protein-protein interaction networks by topological similarity. Bioinformatics (2012) 1.05

A topology-based metric for measuring term similarity in the gene ontology. Adv Bioinformatics (2012) 1.04

Aminopropyltransferases involved in polyamine biosynthesis localize preferentially in the nucleus of plant cells. PLoS One (2012) 1.03

NDEx, the Network Data Exchange. Cell Syst (2015) 1.03

Identifying functional modules in interaction networks through overlapping Markov clustering. Bioinformatics (2012) 1.03

Rewiring of PDZ domain-ligand interaction network contributed to eukaryotic evolution. PLoS Genet (2012) 1.02

Next-generation analysis of cataracts: determining knowledge driven gene-gene interactions using Biofilter, and gene-environment interactions using the PhenX Toolkit. Pac Symp Biocomput (2013) 1.02

Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development. Nucleic Acids Res (2013) 1.02

IMID: integrated molecular interaction database. Bioinformatics (2012) 1.02

RhesusBase: a knowledgebase for the monkey research community. Nucleic Acids Res (2012) 1.02

Spliceosome database: a tool for tracking components of the spliceosome. Nucleic Acids Res (2012) 1.01

Identification of new protein interactions between dengue fever virus and its hosts, human and mosquito. PLoS One (2013) 1.01

A comprehensive performance evaluation on the prediction results of existing cooperative transcription factors identification algorithms. BMC Syst Biol (2014) 1.00

Functional site plasticity in domain superfamilies. Biochim Biophys Acta (2013) 1.00

High-resolution network biology: connecting sequence with function. Nat Rev Genet (2013) 0.99

SMETANA: accurate and scalable algorithm for probabilistic alignment of large-scale biological networks. PLoS One (2013) 0.99

Genotype to phenotype via network analysis. Curr Opin Genet Dev (2013) 0.99

Viruses are a dominant driver of protein adaptation in mammals. Elife (2016) 0.99

iRefR: an R package to manipulate the iRefIndex consolidated protein interaction database. BMC Bioinformatics (2011) 0.99

Genes2FANs: connecting genes through functional association networks. BMC Bioinformatics (2012) 0.99

Passing messages between biological networks to refine predicted interactions. PLoS One (2013) 0.99

Linking proteins to signaling pathways for experiment design and evaluation. PLoS One (2012) 0.98

Integration of new genes into cellular networks, and their structural maturation. Genetics (2013) 0.98

Integration of biological networks and gene expression data using Cytoscape. Nat Protoc (2007) 27.10

The genetic landscape of a cell. Science (2010) 16.52

Textpresso: an ontology-based information retrieval and extraction system for biological literature. PLoS Biol (2004) 15.72

The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Res (2007) 14.24

FlyBase: enhancing Drosophila Gene Ontology annotations. Nucleic Acids Res (2008) 12.15

MINT: the Molecular INTeraction database. Nucleic Acids Res (2006) 11.90

The BioGRID Interaction Database: 2008 update. Nucleic Acids Res (2007) 11.83

Network organization of the human autophagy system. Nature (2010) 11.38

The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res (2010) 10.97

Big data: The future of biocuration. Nature (2008) 10.81

STRING: a database of predicted functional associations between proteins. Nucleic Acids Res (2003) 9.45

The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol (2007) 8.24

Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol (2007) 8.03

The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species. PLoS Comput Biol (2009) 7.95

GeneDB: a resource for prokaryotic and eukaryotic organisms. Nucleic Acids Res (2004) 6.30

Osprey: a network visualization system. Genome Biol (2003) 6.23

A global protein kinase and phosphatase interaction network in yeast. Science (2010) 5.95

Next-generation genomics: an integrative approach. Nat Rev Genet (2010) 5.88

iRefIndex: a consolidated protein interaction database with provenance. BMC Bioinformatics (2008) 5.77

WormBase: a comprehensive resource for nematode research. Nucleic Acids Res (2009) 5.20

Saccharomyces Genome Database provides mutant phenotype data. Nucleic Acids Res (2009) 3.38

Protein interaction networks from yeast to human. Curr Opin Struct Biol (2004) 3.15

An Overview of BioCreative II.5. IEEE/ACM Trans Comput Biol Bioinform (2010) 3.01

iHOP web services. Nucleic Acids Res (2007) 2.65

ProHits: integrated software for mass spectrometry-based interaction proteomics. Nat Biotechnol (2010) 2.22

GermOnline, a cross-species community knowledgebase on germ cell differentiation. Nucleic Acids Res (2004) 1.90

DroID: the Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions. BMC Genomics (2008) 1.89

PhosphoGRID: a database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae. Database (Oxford) (2010) 1.78

Ontological visualization of protein-protein interactions. BMC Bioinformatics (2005) 1.56

Detailing regulatory networks through large scale data integration. Bioinformatics (2009) 1.38

The publication and database deposition of molecular interaction data. Curr Protoc Protein Sci (2010) 1.09

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature (2008) 38.13

Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature (2002) 37.66

Recurring mutations found by sequencing an acute myeloid leukemia genome. N Engl J Med (2009) 33.09

Somatic mutations affect key pathways in lung adenocarcinoma. Nature (2008) 30.02

BioGRID: a general repository for interaction datasets. Nucleic Acids Res (2006) 22.41

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods (2009) 18.41

The BioGRID Interaction Database: 2008 update. Nucleic Acids Res (2007) 11.83

Receptor interacting protein kinase-3 determines cellular necrotic response to TNF-alpha. Cell (2009) 11.36

Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res (2002) 10.65

Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res (2004) 10.18

R2D2, a bridge between the initiation and effector steps of the Drosophila RNAi pathway. Science (2003) 9.53

Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res (2007) 9.03

The chemical genomic portrait of yeast: uncovering a phenotype for all genes. Science (2008) 8.52

The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol (2007) 8.24

Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol (2007) 8.03

Global analysis of protein phosphorylation in yeast. Nature (2005) 7.46

Systematic identification of pathways that couple cell growth and division in yeast. Science (2002) 6.95

Mule/ARF-BP1, a BH3-only E3 ubiquitin ligase, catalyzes the polyubiquitination of Mcl-1 and regulates apoptosis. Cell (2005) 6.86

TNF-alpha induces two distinct caspase-8 activation pathways. Cell (2008) 6.81

WormBase: better software, richer content. Nucleic Acids Res (2006) 6.78

Mixed lineage kinase domain-like protein mediates necrosis signaling downstream of RIP3 kinase. Cell (2012) 6.56

Argonaute2 cleaves the anti-guide strand of siRNA during RISC activation. Cell (2005) 6.47

Osprey: a network visualization system. Genome Biol (2003) 6.23

A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). Proc Natl Acad Sci U S A (2003) 6.19

Elimination of Mcl-1 is required for the initiation of apoptosis following ultraviolet irradiation. Genes Dev (2003) 6.17

The BioGRID interaction database: 2013 update. Nucleic Acids Res (2012) 6.09

A global protein kinase and phosphatase interaction network in yeast. Science (2010) 5.95

Structural basis for phosphodependent substrate selection and orientation by the SCFCdc4 ubiquitin ligase. Cell (2003) 5.72

Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res (2003) 5.69

Cytochrome C-mediated apoptosis. Annu Rev Biochem (2004) 5.38

Specific ablation of the apoptotic functions of cytochrome C reveals a differential requirement for cytochrome C and Apaf-1 in apoptosis. Cell (2005) 5.37

WormBase: a comprehensive resource for nematode research. Nucleic Acids Res (2009) 5.20

Autocrine TNFalpha signaling renders human cancer cells susceptible to Smac-mimetic-induced apoptosis. Cancer Cell (2007) 5.09

A dynamic transcriptional network communicates growth potential to ribosome synthesis and critical cell size. Genes Dev (2004) 5.08

Jaundice Constrain or Indication? Response. Radiology (2017) 5.07

PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nat Methods (2011) 5.01

Use and misuse of the gene ontology annotations. Nat Rev Genet (2008) 5.01

A small molecule Smac mimic potentiates TRAIL- and TNFalpha-mediated cell death. Science (2004) 4.95

How cells coordinate growth and division. Curr Biol (2004) 4.81

A hitchhiker's guide to the cullin ubiquitin ligases: SCF and its kin. Biochim Biophys Acta (2004) 4.53

The mitochondrial phosphatase PGAM5 functions at the convergence point of multiple necrotic death pathways. Cell (2012) 4.37

A mechanism for cell-cycle regulation of MAP kinase signaling in a yeast differentiation pathway. Cell (2007) 4.21

The BTB protein MEL-26 is a substrate-specific adaptor of the CUL-3 ubiquitin-ligase. Nature (2003) 4.18

TargetDB: a target registration database for structural genomics projects. Bioinformatics (2004) 4.17

WormBase: a multi-species resource for nematode biology and genomics. Nucleic Acids Res (2004) 4.14

The GRID: the General Repository for Interaction Datasets. Genome Biol (2003) 4.09

CDK activity antagonizes Whi5, an inhibitor of G1/S transcription in yeast. Cell (2004) 4.04

WormBase: new content and better access. Nucleic Acids Res (2006) 4.01

Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Brief Bioinform (2011) 3.90

WormBase 2012: more genomes, more data, new website. Nucleic Acids Res (2011) 3.87

WormBase: a comprehensive data resource for Caenorhabditis biology and genomics. Nucleic Acids Res (2005) 3.82

Discovery of biological networks from diverse functional genomic data. Genome Biol (2005) 3.73

WormBase 2007. Nucleic Acids Res (2007) 3.69

Molecular profiling of non-small cell lung cancer and correlation with disease-free survival. Cancer Res (2002) 3.68

Biochemical identification of Argonaute 2 as the sole protein required for RNA-induced silencing complex activity. Proc Natl Acad Sci U S A (2004) 3.63

Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome. Nucleic Acids Res (2006) 3.59

Distinctive roles of PHAP proteins and prothymosin-alpha in a death regulatory pathway. Science (2003) 3.59

SAINT: probabilistic scoring of affinity purification-mass spectrometry data. Nat Methods (2010) 3.50

Saccharomyces genome database: underlying principles and organisation. Brief Bioinform (2004) 3.46

Stratus not altocumulus: a new view of the yeast protein interaction network. PLoS Biol (2006) 3.44

Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD). Nucleic Acids Res (2005) 3.43

Saccharomyces Genome Database provides mutant phenotype data. Nucleic Acids Res (2009) 3.38

Linking entries in protein interaction database to structured text: the FEBS Letters experiment. FEBS Lett (2008) 3.35

Expanded protein information at SGD: new pages and proteome browser. Nucleic Acids Res (2006) 3.31