Published in FEBS Lett on February 20, 2002
Integration of biological networks and gene expression data using Cytoscape. Nat Protoc (2007) 27.10
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
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Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res (2003) 15.74
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IntAct--open source resource for molecular interaction data. Nucleic Acids Res (2006) 13.82
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The Biomolecular Interaction Network Database and related tools 2005 update. Nucleic Acids Res (2005) 12.94
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Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins. BMC Bioinformatics (2004) 4.44
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Literature-curated protein interaction datasets. Nat Methods (2009) 4.21
HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms. BMC Bioinformatics (2005) 3.75
Epstein-Barr virus and virus human protein interaction maps. Proc Natl Acad Sci U S A (2007) 3.50
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Stratus not altocumulus: a new view of the yeast protein interaction network. PLoS Biol (2006) 3.44
Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases. BMC Bioinformatics (2007) 3.44
The aMAZE LightBench: a web interface to a relational database of cellular processes. Nucleic Acids Res (2004) 3.39
An evaluation of human protein-protein interaction data in the public domain. BMC Bioinformatics (2006) 3.33
T1DBase: integration and presentation of complex data for type 1 diabetes research. Nucleic Acids Res (2006) 3.25
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TRANSPATH: an integrated database on signal transduction and a tool for array analysis. Nucleic Acids Res (2003) 3.17
The landscape of human proteins interacting with viruses and other pathogens. PLoS Pathog (2008) 3.11
Snap: an integrated SNP annotation platform. Nucleic Acids Res (2006) 2.99
APID: Agile Protein Interaction DataAnalyzer. Nucleic Acids Res (2006) 2.91
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BNDB - the Biochemical Network Database. BMC Bioinformatics (2007) 2.75
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MPIDB: the microbial protein interaction database. Bioinformatics (2008) 2.42
PASBio: predicate-argument structures for event extraction in molecular biology. BMC Bioinformatics (2004) 2.41
NAViGaTOR: Network Analysis, Visualization and Graphing Toronto. Bioinformatics (2009) 2.34
Identifying gene-disease associations using centrality on a literature mined gene-interaction network. Bioinformatics (2008) 2.32
Analysis of protein sequence and interaction data for candidate disease gene prediction. Nucleic Acids Res (2006) 2.30
Gene3D: modelling protein structure, function and evolution. Nucleic Acids Res (2006) 2.30
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Building disease-specific drug-protein connectivity maps from molecular interaction networks and PubMed abstracts. PLoS Comput Biol (2009) 1.90
From gene networks to gene function. Genome Res (2003) 1.80
Large scale genotype comparison of human papillomavirus E2-host interaction networks provides new insights for e2 molecular functions. PLoS Pathog (2012) 1.79
High-confidence prediction of global interactomes based on genome-wide coevolutionary networks. Proc Natl Acad Sci U S A (2008) 1.72
VirHostNet: a knowledge base for the management and the analysis of proteome-wide virus-host interaction networks. Nucleic Acids Res (2008) 1.71
BisoGenet: a new tool for gene network building, visualization and analysis. BMC Bioinformatics (2010) 1.69
OntoGene in BioCreative II. Genome Biol (2008) 1.65
DOMINO: a database of domain-peptide interactions. Nucleic Acids Res (2006) 1.63
Protein-protein interactions more conserved within species than across species. PLoS Comput Biol (2006) 1.61
Yeast two-hybrid, a powerful tool for systems biology. Int J Mol Sci (2009) 1.59
Targeting the human cancer pathway protein interaction network by structural genomics. Mol Cell Proteomics (2008) 1.54
Biomedical discovery acceleration, with applications to craniofacial development. PLoS Comput Biol (2009) 1.49
Biomedical text mining and its applications. PLoS Comput Biol (2009) 1.46
PIG--the pathogen interaction gateway. Nucleic Acids Res (2008) 1.43
Computation of significance scores of unweighted Gene Set Enrichment Analyses. BMC Bioinformatics (2007) 1.41
Impact of vitamin D on immune function: lessons learned from genome-wide analysis. Front Physiol (2014) 1.40
MitoProteome: mitochondrial protein sequence database and annotation system. Nucleic Acids Res (2004) 1.39
A manually curated network of the PML nuclear body interactome reveals an important role for PML-NBs in SUMOylation dynamics. Int J Biol Sci (2010) 1.38
The human-bacterial pathogen protein interaction networks of Bacillus anthracis, Francisella tularensis, and Yersinia pestis. PLoS One (2010) 1.38
SZGR: a comprehensive schizophrenia gene resource. Mol Psychiatry (2010) 1.36
Controllability in protein interaction networks. Proc Natl Acad Sci U S A (2014) 1.34
Lists2Networks: integrated analysis of gene/protein lists. BMC Bioinformatics (2010) 1.33
Protein-protein interaction databases: keeping up with growing interactomes. Hum Genomics (2009) 1.32
HPIDB--a unified resource for host-pathogen interactions. BMC Bioinformatics (2010) 1.31
Discovery of protein interaction networks shared by diseases. Pac Symp Biocomput (2007) 1.30
Modelling protein-protein interaction networks via a stickiness index. J R Soc Interface (2006) 1.29
Computational analysis and prediction of the binding motif and protein interacting partners of the Abl SH3 domain. PLoS Comput Biol (2006) 1.27
Integrative analysis for finding genes and networks involved in diabetes and other complex diseases. Genome Biol (2007) 1.27
An interaction network predicted from public data as a discovery tool: application to the Hsp90 molecular chaperone machine. PLoS One (2011) 1.27
SURFACE: a database of protein surface regions for functional annotation. Nucleic Acids Res (2004) 1.26
Protein protein interactions, evolutionary rate, abundance and age. BMC Bioinformatics (2006) 1.25
Identifying dysfunctional crosstalk of pathways in various regions of Alzheimer's disease brains. BMC Syst Biol (2010) 1.24
Mining physical protein-protein interactions from the literature. Genome Biol (2008) 1.23
A comparative study of cancer proteins in the human protein-protein interaction network. BMC Genomics (2010) 1.23
Candidate gene prioritization by network analysis of differential expression using machine learning approaches. BMC Bioinformatics (2010) 1.21
Walk-weighted subsequence kernels for protein-protein interaction extraction. BMC Bioinformatics (2010) 1.15
Comparative genomics and disorder prediction identify biologically relevant SH3 protein interactions. PLoS Comput Biol (2005) 1.15
SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein-Protein Interactions. Nucleic Acids Res (2007) 1.15
Not all scale-free networks are born equal: the role of the seed graph in PPI network evolution. PLoS Comput Biol (2007) 1.15
Predicting the interactome of Xanthomonas oryzae pathovar oryzae for target selection and DB service. BMC Bioinformatics (2008) 1.14
Characterization of protein-interaction networks in tumors. BMC Bioinformatics (2007) 1.13
Ortholog-based protein-protein interaction prediction and its application to inter-species interactions. BMC Bioinformatics (2008) 1.12
Ulysses - an application for the projection of molecular interactions across species. Genome Biol (2005) 1.12
Hubs with network motifs organize modularity dynamically in the protein-protein interaction network of yeast. PLoS One (2007) 1.11
VIRGO: computational prediction of gene functions. Nucleic Acids Res (2006) 1.09
CellCircuits: a database of protein network models. Nucleic Acids Res (2006) 1.08
The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol (2004) 16.08
IntAct: an open source molecular interaction database. Nucleic Acids Res (2004) 15.02
MINT: the Molecular INTeraction database. Nucleic Acids Res (2006) 11.90
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
MINT, the molecular interaction database: 2009 update. Nucleic Acids Res (2009) 7.19
A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science (2001) 7.08
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Res (2003) 6.86
MINT, the molecular interaction database: 2012 update. Nucleic Acids Res (2011) 5.25
PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nat Methods (2011) 5.01
mzML--a community standard for mass spectrometry data. Mol Cell Proteomics (2010) 4.81
The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res (2013) 4.39
Linear motif atlas for phosphorylation-dependent signaling. Sci Signal (2008) 3.77
HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms. BMC Bioinformatics (2005) 3.75
The PSI-MOD community standard for representation of protein modification data. Nat Biotechnol (2008) 3.38
Linking entries in protein interaction database to structured text: the FEBS Letters experiment. FEBS Lett (2008) 3.35
Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nat Methods (2012) 3.17
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
An Overview of BioCreative II.5. IEEE/ACM Trans Comput Biol Bioinform (2010) 3.01
ELM: the status of the 2010 eukaryotic linear motif resource. Nucleic Acids Res (2009) 2.59
The ubiquitin-protein ligase Itch regulates p73 stability. EMBO J (2005) 2.38
The Protein Feature Ontology: a tool for the unification of protein feature annotations. Bioinformatics (2008) 2.33
VirusMINT: a viral protein interaction database. Nucleic Acids Res (2008) 2.30
The use of common ontologies and controlled vocabularies to enable data exchange and deposition for complex proteomic experiments. Pac Symp Biocomput (2005) 2.29
The FEBS Letters/BioCreative II.5 experiment: making biological information accessible. Nat Biotechnol (2010) 2.18
BioCreative III interactive task: an overview. BMC Bioinformatics (2011) 2.16
Inhibition of the c-Abl-TAp63 pathway protects mouse oocytes from chemotherapy-induced death. Nat Med (2009) 2.03
Protein interaction networks by proteome peptide scanning. PLoS Biol (2004) 1.92
Protein interactions: integration leads to belief. Trends Biochem Sci (2008) 1.88
Deciphering a global network of functionally associated post-translational modifications. Mol Syst Biol (2012) 1.86
Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins. PLoS Biol (2009) 1.78
MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data. Genome Biol (2008) 1.76
Unusual binding properties of the SH3 domain of the yeast actin-binding protein Abp1: structural and functional analysis. J Biol Chem (2001) 1.69
Tumor suppressor density-enhanced phosphatase-1 (DEP-1) inhibits the RAS pathway by direct dephosphorylation of ERK1/2 kinases. J Biol Chem (2009) 1.66
DOMINO: a database of domain-peptide interactions. Nucleic Acids Res (2006) 1.63
mentha: a resource for browsing integrated protein-interaction networks. Nat Methods (2013) 1.60
WI-PHI: a weighted yeast interactome enriched for direct physical interactions. Proteomics (2007) 1.55
Convergent evolution of enzyme active sites is not a rare phenomenon. J Mol Biol (2007) 1.55
Normalization of nomenclature for peptide motifs as ligands of modular protein domains. FEBS Lett (2002) 1.46
Recurated protein interaction datasets. Nat Methods (2009) 1.43
Conjugation to Nedd8 instigates ubiquitylation and down-regulation of activated receptor tyrosine kinases. J Biol Chem (2006) 1.42
Structure-based function prediction: approaches and applications. Brief Funct Genomic Proteomic (2008) 1.32
The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary. Database (Oxford) (2013) 1.31
SURFACE: a database of protein surface regions for functional annotation. Nucleic Acids Res (2004) 1.26
Mutation of plasma membrane Ca2+ ATPase isoform 3 in a family with X-linked congenital cerebellar ataxia impairs Ca2+ homeostasis. Proc Natl Acad Sci U S A (2012) 1.26
Query3d: a new method for high-throughput analysis of functional residues in protein structures. BMC Bioinformatics (2005) 1.25
FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures. BMC Bioinformatics (2008) 1.23
The E3 ligase Aip4/Itch ubiquitinates and targets ErbB-4 for degradation. FASEB J (2007) 1.19
Progress in Establishing Common Standards for Exchanging Proteomics Data: The Second Meeting of the HUPO Proteomics Standards Initiative. Comp Funct Genomics (2003) 1.18
pdbFun: mass selection and fast comparison of annotated PDB residues. Nucleic Acids Res (2005) 1.17
Phospho3D: a database of three-dimensional structures of protein phosphorylation sites. Nucleic Acids Res (2006) 1.17
A structure filter for the Eukaryotic Linear Motif Resource. BMC Bioinformatics (2009) 1.16
HuPho: the human phosphatase portal. FEBS J (2012) 1.14
The SH2 domain interaction landscape. Cell Rep (2013) 1.13
InteroPORC: automated inference of highly conserved protein interaction networks. Bioinformatics (2008) 1.13
Selectivity and promiscuity in the interaction network mediated by protein recognition modules. FEBS Lett (2004) 1.12
Functional annotation by identification of local surface similarities: a novel tool for structural genomics. BMC Bioinformatics (2005) 1.11
A community standard format for the representation of protein affinity reagents. Mol Cell Proteomics (2009) 1.11
Benchmarking of the 2010 BioCreative Challenge III text-mining competition by the BioGRID and MINT interaction databases. BMC Bioinformatics (2011) 1.09
AMBRA1 links autophagy to cell proliferation and tumorigenesis by promoting c-Myc dephosphorylation and degradation. Nat Cell Biol (2015) 1.09
Finding and sharing: new approaches to registries of databases and services for the biomedical sciences. Database (Oxford) (2010) 1.08
Identification of new substrates of the protein-tyrosine phosphatase PTP1B by Bayesian integration of proteome evidence. J Biol Chem (2010) 1.07
The protein interaction network mediated by human SH3 domains. Biotechnol Adv (2011) 1.05
In vitro evolution of recognition specificity mediated by SH3 domains reveals target recognition rules. J Biol Chem (2002) 1.05
Probing protein-tyrosine phosphatase substrate specificity using a phosphotyrosine-containing phage library. J Biol Chem (2003) 1.05
Diverse driving forces underlie the invariant occurrence of the T42A, E139D, I282V and T468M SHP2 amino acid substitutions causing Noonan and LEOPARD syndromes. Hum Mol Genet (2008) 1.04
The human phosphatase interactome: An intricate family portrait. FEBS Lett (2012) 1.04
Exploring the diversity of SPRY/B30.2-mediated interactions. Trends Biochem Sci (2012) 1.01
Comparative interactomics: comparing apples and pears? Trends Biotechnol (2007) 1.00
SH3-Hunter: discovery of SH3 domain interaction sites in proteins. Nucleic Acids Res (2007) 0.99
From sequence to structural analysis in protein phosphorylation motifs. Front Biosci (Landmark Ed) (2011) 0.97
Reply to: Cisplatin-induced primordial follicle oocyte killing and loss of fertility are not prevented by imatinib. Nat Med (2012) 0.97
The intracellular antibody capture technology: towards the high-throughput selection of functional intracellular antibodies for target validation. Methods (2004) 0.96
Modular architecture of nucleotide-binding pockets. Nucleic Acids Res (2010) 0.96
Structural and functional protein network analyses predict novel signaling functions for rhodopsin. Mol Syst Biol (2011) 0.95
Structural motifs recurring in different folds recognize the same ligand fragments. BMC Bioinformatics (2009) 0.94
Superpose3D: a local structural comparison program that allows for user-defined structure representations. PLoS One (2010) 0.94
Phospho3D 2.0: an enhanced database of three-dimensional structures of phosphorylation sites. Nucleic Acids Res (2010) 0.93
Phosphoproteomic analysis of differentiating Leishmania parasites reveals a unique stage-specific phosphorylation motif. J Proteome Res (2013) 0.92
Degradation of p63 by Itch. Cell Cycle (2006) 0.92
The FEBS Letters SDA corpus: a collection of protein interaction articles with high quality annotations for the BioCreative II.5 online challenge and the text mining community. FEBS Lett (2010) 0.92
Seq2Struct: a resource for establishing sequence-structure links. Bioinformatics (2004) 0.91
iSPOT: A web tool to infer the interaction specificity of families of protein modules. Nucleic Acids Res (2003) 0.91
Methods to reveal domain networks. Drug Discov Today (2005) 0.90