Published in Nat Methods on June 29, 2011
ChEMBL: a large-scale bioactivity database for drug discovery. Nucleic Acids Res (2011) 14.51
The Reactome pathway knowledgebase. Nucleic Acids Res (2013) 8.56
PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res (2013) 7.63
The IntAct molecular interaction database in 2012. Nucleic Acids Res (2011) 7.49
A travel guide to Cytoscape plugins. Nat Methods (2012) 6.53
MINT, the molecular interaction database: 2012 update. Nucleic Acids Res (2011) 5.25
The BioGRID interaction database: 2015 update. Nucleic Acids Res (2014) 4.06
Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nat Methods (2012) 3.17
The ConsensusPathDB interaction database: 2013 update. Nucleic Acids Res (2012) 2.94
GeneMANIA prediction server 2013 update. Nucleic Acids Res (2013) 2.74
InnateDB: systems biology of innate immunity and beyond--recent updates and continuing curation. Nucleic Acids Res (2012) 2.66
HIPPIE: Integrating protein interaction networks with experiment based quality scores. PLoS One (2012) 2.17
mentha: a resource for browsing integrated protein-interaction networks. Nat Methods (2013) 1.60
Minimum information about a bioactive entity (MIABE). Nat Rev Drug Discov (2011) 1.44
The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies. J Biomed Semantics (2013) 1.44
canSAR: an integrated cancer public translational research and drug discovery resource. Nucleic Acids Res (2011) 1.41
Public domain databases for medicinal chemistry. J Med Chem (2012) 1.23
Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments. Proteomics (2012) 1.21
Analyzing protein-protein interactions from affinity purification-mass spectrometry data with SAINT. Curr Protoc Bioinformatics (2012) 1.20
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. J Biomed Semantics (2014) 1.12
A new reference implementation of the PSICQUIC web service. Nucleic Acids Res (2013) 1.11
The Disease and Gene Annotations (DGA): an annotation resource for human disease. Nucleic Acids Res (2012) 1.11
Adding protein context to the human protein-protein interaction network to reveal meaningful interactions. PLoS Comput Biol (2013) 1.10
Harnessing the heart of big data. Circ Res (2015) 1.10
BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology. Nucleic Acids Res (2015) 1.07
t4 workshop report: Pathways of Toxicity. ALTEX (2013) 1.06
Linking proteomic and transcriptional data through the interactome and epigenome reveals a map of oncogene-induced signaling. PLoS Comput Biol (2013) 1.06
TopFIND 2.0--linking protein termini with proteolytic processing and modifications altering protein function. Nucleic Acids Res (2011) 1.03
Extreme multifunctional proteins identified from a human protein interaction network. Nat Commun (2015) 1.02
R-based software for the integration of pathway data into bioinformatic algorithms. Biology (Basel) (2014) 1.01
iRefR: an R package to manipulate the iRefIndex consolidated protein interaction database. BMC Bioinformatics (2011) 0.99
VirusMentha: a new resource for virus-host protein interactions. Nucleic Acids Res (2014) 0.99
A Pan-Cancer Catalogue of Cancer Driver Protein Interaction Interfaces. PLoS Comput Biol (2015) 0.98
SAMNet: a network-based approach to integrate multi-dimensional high throughput datasets. Integr Biol (Camb) (2012) 0.98
The BioJS article collection of open source components for biological data visualisation. F1000Res (2014) 0.97
Using biological networks to integrate, visualize and analyze genomics data. Genet Sel Evol (2016) 0.96
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. Database (Oxford) (2016) 0.95
Fundamentals of protein interaction network mapping. Mol Syst Biol (2015) 0.93
Affinity purification-mass spectrometry and network analysis to understand protein-protein interactions. Nat Protoc (2014) 0.92
Popular computational methods to assess multiprotein complexes derived from label-free affinity purification and mass spectrometry (AP-MS) experiments. Mol Cell Proteomics (2012) 0.92
The MI bundle: enabling network and structural biology in genome visualization tools. Bioinformatics (2015) 0.91
ResponseNet2.0: Revealing signaling and regulatory pathways connecting your proteins and genes--now with human data. Nucleic Acids Res (2013) 0.90
'Omics' approaches to understanding interstitial cystitis/painful bladder syndrome/bladder pain syndrome. Int Neurourol J (2012) 0.90
Relationships between predicted moonlighting proteins, human diseases, and comorbidities from a network perspective. Front Physiol (2015) 0.89
Ten years of standardizing proteomic data: a report on the HUPO-PSI Spring Workshop: April 12-14th, 2012, San Diego, USA. Proteomics (2012) 0.89
A review on computational systems biology of pathogen-host interactions. Front Microbiol (2015) 0.88
IntScore: a web tool for confidence scoring of biological interactions. Nucleic Acids Res (2012) 0.88
Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study. Database (Oxford) (2015) 0.88
PrOnto database : GO term functional dissimilarity inferred from biological data. Front Genet (2015) 0.87
Teaching the fundamentals of biological data integration using classroom games. PLoS Comput Biol (2012) 0.87
PsicquicGraph, a BioJS component to visualize molecular interactions from PSICQUIC servers. F1000Res (2014) 0.86
Capturing cooperative interactions with the PSI-MI format. Database (Oxford) (2013) 0.86
MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities. Nucleic Acids Res (2014) 0.85
Drug target prioritization by perturbed gene expression and network information. Sci Rep (2015) 0.85
The human DEPhOsphorylation database DEPOD: a 2015 update. Nucleic Acids Res (2014) 0.85
Novel semantic similarity measure improves an integrative approach to predicting gene functional associations. BMC Syst Biol (2013) 0.84
Profiling of Parkin-binding partners using tandem affinity purification. PLoS One (2013) 0.84
Using in vivo biotinylated ubiquitin to describe a mitotic exit ubiquitome from human cells. Mol Cell Proteomics (2014) 0.83
MyProteinNet: build up-to-date protein interaction networks for organisms, tissues and user-defined contexts. Nucleic Acids Res (2015) 0.83
Revealing disease-associated pathways by network integration of untargeted metabolomics. Nat Methods (2016) 0.83
A visual review of the interactome of LRRK2: Using deep-curated molecular interaction data to represent biology. Proteomics (2015) 0.82
A Comprehensive Inter-Tissue Crosstalk Analysis Underlying Progression and Control of Obesity and Diabetes. Sci Rep (2015) 0.81
TRIP database 2.0: a manually curated information hub for accessing TRP channel interaction network. PLoS One (2012) 0.81
Pogo-like transposases have been repeatedly domesticated into CENP-B-related proteins. Genome Biol Evol (2014) 0.81
Simple topological features reflect dynamics and modularity in protein interaction networks. PLoS Comput Biol (2013) 0.81
Inferring the Brassica rapa Interactome Using Protein-Protein Interaction Data from Arabidopsis thaliana. Front Plant Sci (2013) 0.81
APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks. Nucleic Acids Res (2016) 0.81
Computational Prediction of Protein-Protein Interaction Networks: Algo-rithms and Resources. Curr Genomics (2013) 0.81
Shared resources, shared costs--leveraging biocuration resources. Database (Oxford) (2015) 0.80
A method for predicting protein-protein interaction types. PLoS One (2014) 0.80
Visual data mining of biological networks: one size does not fit all. PLoS Comput Biol (2013) 0.79
Tools for visualization and analysis of molecular networks, pathways, and -omics data. Adv Appl Bioinform Chem (2015) 0.79
Swimming upstream: identifying proteomic signals that drive transcriptional changes using the interactome and multiple "-omics" datasets. Methods Cell Biol (2012) 0.79
yApoptosis: yeast apoptosis database. Database (Oxford) (2013) 0.79
Integrated inference and evaluation of host-fungi interaction networks. Front Microbiol (2015) 0.78
ProteINSIDE to Easily Investigate Proteomics Data from Ruminants: Application to Mine Proteome of Adipose and Muscle Tissues in Bovine Foetuses. PLoS One (2015) 0.78
Towards the collaborative curation of the registry underlying Identifiers.org. Database (Oxford) (2013) 0.78
Reactome from a WikiPathways Perspective. PLoS Comput Biol (2016) 0.78
Exploring novel mechanistic insights in Alzheimer's disease by assessing reliability of protein interactions. Sci Rep (2015) 0.77
Glycosaminoglycanomics: where we are. Glycoconj J (2016) 0.77
MONGKIE: an integrated tool for network analysis and visualization for multi-omics data. Biol Direct (2016) 0.76
Coupling an EML4-ALK-centric interactome with RNA interference identifies sensitizers to ALK inhibitors. Sci Signal (2016) 0.76
Optimization criteria and biological process enrichment in homologous multiprotein modules. Proc Natl Acad Sci U S A (2013) 0.76
Comprehensive data resources and analytical tools for pathological association of aminoacyl tRNA synthetases with cancer. Database (Oxford) (2015) 0.76
HVint: A Strategy for Identifying Novel Protein-Protein Interactions in Herpes Simplex Virus Type 1. Mol Cell Proteomics (2016) 0.76
Path2enet: generation of human pathway-derived networks in an expression specific context. BMC Genomics (2016) 0.75
HIPPIE v2.0: enhancing meaningfulness and reliability of protein-protein interaction networks. Nucleic Acids Res (2016) 0.75
Tyrosine Kinase Signaling in Clear Cell and Papillary Renal Cell Carcinoma Revealed by Mass Spectrometry-Based Phosphotyrosine Proteomics. Clin Cancer Res (2016) 0.75
Inbreeding Affects Gene Expression Differently in Two Self-Incompatible Arabidopsis lyrata Populations with Similar Levels of Inbreeding Depression. Mol Biol Evol (2015) 0.75
Gene regulation knowledge commons: community action takes care of DNA binding transcription factors. Database (Oxford) (2016) 0.75
Contextual Hub Analysis Tool (CHAT): A Cytoscape app for identifying contextually relevant hubs in biological networks. F1000Res (2016) 0.75
HPIDB 2.0: a curated database for host-pathogen interactions. Database (Oxford) (2016) 0.75
Protein-Protein Interactions: Gene Acronym Redundancies and Current Limitations Precluding Automated Data Integration. Proteomes (2013) 0.75
Visualisation of BioPAX Networks using BioLayout Express (3D). F1000Res (2014) 0.75
Exploring the cross talk between ER stress and inflammation in age-related macular degeneration. PLoS One (2017) 0.75
Endothelium-Independent Primitive Myxoid Vascularization Creates Invertebrate-Like Channels to Maintain Blood Supply in Optic Gliomas. Am J Pathol (2017) 0.75
Perturbed human sub-networks by Fusobacterium nucleatum candidate virulence proteins. Microbiome (2017) 0.75
Integration of miRNA and mRNA expression profiles reveals microRNA-regulated networks during muscle wasting in cardiac cachexia. Sci Rep (2017) 0.75
Unraveling a tumor type-specific regulatory core underlying E2F1-mediated epithelial-mesenchymal transition to predict receptor protein signatures. Nat Commun (2017) 0.75
Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res (2003) 103.76
The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol (2004) 16.08
Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol (2007) 8.03
Five years of progress in the Standardization of Proteomics Data 4th Annual Spring Workshop of the HUPO-Proteomics Standards Initiative April 23-25, 2007 Ecole Nationale Supérieure (ENS), Lyon, France. Proteomics (2007) 3.69
DASMI: exchanging, annotating and assessing molecular interaction data. Bioinformatics (2009) 1.64
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature (2002) 37.66
The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol (2008) 31.04
Integration of biological networks and gene expression data using Cytoscape. Nat Protoc (2007) 27.10
Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics (2010) 26.76
The Database of Interacting Proteins: 2004 update. Nucleic Acids Res (2004) 23.67
BioGRID: a general repository for interaction datasets. Nucleic Acids Res (2006) 22.41
Global mapping of the yeast genetic interaction network. Science (2004) 21.34
STRING 8--a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res (2008) 20.62
International network of cancer genome projects. Nature (2010) 20.35
Toll-like receptor triggering of a vitamin D-mediated human antimicrobial response. Science (2006) 18.74
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res (2010) 18.73
STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res (2012) 18.26
InterPro, progress and status in 2005. Nucleic Acids Res (2005) 17.53
MINT: a Molecular INTeraction database. FEBS Lett (2002) 17.21
Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. Nat Genet (2010) 16.96
The genetic landscape of a cell. Science (2010) 16.52
The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol (2004) 16.08
DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res (2002) 15.70
Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res (2008) 15.69
A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1. Nat Genet (2006) 15.14
IntAct: an open source molecular interaction database. Nucleic Acids Res (2004) 15.02
Functional impact of global rare copy number variation in autism spectrum disorders. Nature (2010) 14.66
The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol (2007) 13.99
Reactome: a knowledge base of biologic pathways and processes. Genome Biol (2007) 13.36
The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res (2012) 13.14
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol (2008) 12.96
New developments in the InterPro database. Nucleic Acids Res (2007) 12.49
MINT: the Molecular INTeraction database. Nucleic Acids Res (2006) 11.90
The BioGRID Interaction Database: 2008 update. Nucleic Acids Res (2007) 11.83
Structure of the cross-beta spine of amyloid-like fibrils. Nature (2005) 11.56
A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotechnol (2004) 11.42
Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res (2010) 11.23
The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res (2010) 10.97
The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol (2007) 10.24
Cytoscape Web: an interactive web-based network browser. Bioinformatics (2010) 10.03
Atomic structures of amyloid cross-beta spines reveal varied steric zippers. Nature (2007) 10.02
A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat Biotechnol (2007) 9.90
The BioPAX community standard for pathway data sharing. Nat Biotechnol (2010) 9.19
Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res (2010) 9.18
The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries. BMC Bioinformatics (2006) 8.68
The Reactome pathway knowledgebase. Nucleic Acids Res (2013) 8.56
The Systems Biology Graphical Notation. Nat Biotechnol (2009) 8.53
The chemical genomic portrait of yeast: uncovering a phenotype for all genes. Science (2008) 8.52
The BioGRID Interaction Database: 2011 update. Nucleic Acids Res (2010) 8.46
The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol (2007) 8.24
The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science (2009) 8.23
Protein interactions: two methods for assessment of the reliability of high throughput observations. Mol Cell Proteomics (2002) 8.11
Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol (2007) 8.03
Agar and broth dilution methods to determine the minimal inhibitory concentration (MIC) of antimicrobial substances. Nat Protoc (2008) 7.92
Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science (2009) 7.64
PRIDE: the proteomics identifications database. Proteomics (2005) 7.52
The IntAct molecular interaction database in 2012. Nucleic Acids Res (2011) 7.49
Global analysis of protein phosphorylation in yeast. Nature (2005) 7.46
Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. N Engl J Med (2011) 7.35
Toward the structural genomics of complexes: crystal structure of a PE/PPE protein complex from Mycobacterium tuberculosis. Proc Natl Acad Sci U S A (2006) 7.29
MINT, the molecular interaction database: 2009 update. Nucleic Acids Res (2009) 7.19
Calling on a million minds for community annotation in WikiProteins. Genome Biol (2008) 7.11
A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science (2001) 7.08