Published in Genome Biol on August 13, 2004
Large-scale mapping of human protein-protein interactions by mass spectrometry. Mol Syst Biol (2007) 8.16
An empirical framework for binary interactome mapping. Nat Methods (2008) 6.59
g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments. Nucleic Acids Res (2007) 6.44
Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes. Am J Hum Genet (2006) 6.10
FlyMine: an integrated database for Drosophila and Anopheles genomics. Genome Biol (2007) 5.23
Global topological features of cancer proteins in the human interactome. Bioinformatics (2006) 4.17
Protein interaction mapping: a Drosophila case study. Genome Res (2005) 4.15
Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome. Genome Biol (2005) 3.79
HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms. BMC Bioinformatics (2005) 3.75
How complete are current yeast and human protein-interaction networks? Genome Biol (2006) 3.50
T1DBase: integration and presentation of complex data for type 1 diabetes research. Nucleic Acids Res (2006) 3.25
Tissue specificity and the human protein interaction network. Mol Syst Biol (2009) 3.20
Comprehensive interaction map of the Arabidopsis MADS Box transcription factors. Plant Cell (2005) 3.12
Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissues. Bioinformatics (2005) 2.82
Construction, visualisation, and clustering of transcription networks from microarray expression data. PLoS Comput Biol (2007) 2.73
UniHI: an entry gate to the human protein interactome. Nucleic Acids Res (2006) 2.45
Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network. Genome Biol (2009) 2.43
A predicted interactome for Arabidopsis. Plant Physiol (2007) 2.41
HIPPIE: Integrating protein interaction networks with experiment based quality scores. PLoS One (2012) 2.17
Filtering high-throughput protein-protein interaction data using a combination of genomic features. BMC Bioinformatics (2005) 1.96
Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes. Genome Biol (2007) 1.73
Analysis of the human E2 ubiquitin conjugating enzyme protein interaction network. Genome Res (2009) 1.68
DASMI: exchanging, annotating and assessing molecular interaction data. Bioinformatics (2009) 1.64
Protein-protein interactions more conserved within species than across species. PLoS Comput Biol (2006) 1.61
Ontological visualization of protein-protein interactions. BMC Bioinformatics (2005) 1.56
A map of human protein interactions derived from co-expression of human mRNAs and their orthologs. Mol Syst Biol (2008) 1.53
An integrated approach to the prediction of domain-domain interactions. BMC Bioinformatics (2006) 1.52
Analysis of intraviral protein-protein interactions of the SARS coronavirus ORFeome. PLoS One (2007) 1.42
Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression. BMC Genomics (2009) 1.34
Controllability in protein interaction networks. Proc Natl Acad Sci U S A (2014) 1.34
Probabilistic prediction and ranking of human protein-protein interactions. BMC Bioinformatics (2007) 1.31
Cardiovascular networks: systems-based approaches to cardiovascular disease. Circulation (2010) 1.30
UniHI 4: new tools for query, analysis and visualization of the human protein-protein interactome. Nucleic Acids Res (2008) 1.28
Integrative analysis for finding genes and networks involved in diabetes and other complex diseases. Genome Biol (2007) 1.27
Building and analyzing protein interactome networks by cross-species comparisons. BMC Syst Biol (2010) 1.27
ppiPre: predicting protein-protein interactions by combining heterogeneous features. BMC Syst Biol (2013) 1.12
Ulysses - an application for the projection of molecular interactions across species. Genome Biol (2005) 1.12
Network-based Identification of novel cancer genes. Mol Cell Proteomics (2009) 1.12
A simple principle concerning the robustness of protein complex activity to changes in gene expression. BMC Syst Biol (2008) 1.09
The proteins of human chromosome 21. Am J Med Genet C Semin Med Genet (2006) 1.07
Genomes, phylogeny, and evolutionary systems biology. Proc Natl Acad Sci U S A (2005) 1.07
Protein-protein interaction detection: methods and analysis. Int J Proteomics (2014) 1.03
Response of the mosquito protein interaction network to dengue infection. BMC Genomics (2010) 1.02
UniHI 7: an enhanced database for retrieval and interactive analysis of human molecular interaction networks. Nucleic Acids Res (2013) 1.02
Protein-protein interaction as a predictor of subcellular location. BMC Syst Biol (2009) 1.01
Evidence for systems-level molecular mechanisms of tumorigenesis. BMC Genomics (2007) 1.00
Viral organization of human proteins. PLoS One (2010) 1.00
InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes. BMC Bioinformatics (2007) 0.95
Tools enabling the elucidation of molecular pathways active in human disease: application to Hepatitis C virus infection. BMC Bioinformatics (2005) 0.95
Small molecules, big targets: drug discovery faces the protein-protein interaction challenge. Nat Rev Drug Discov (2016) 0.93
Predicting combinatorial binding of transcription factors to regulatory elements in the human genome by association rule mining. BMC Bioinformatics (2007) 0.93
The prediction of protein-protein interaction networks in rice blast fungus. BMC Genomics (2008) 0.93
Reconstruction of human protein interolog network using evolutionary conserved network. BMC Bioinformatics (2007) 0.92
Systematic prediction of human membrane receptor interactions. Proteomics (2009) 0.90
Topology and weights in a protein domain interaction network--a novel way to predict protein interactions. BMC Genomics (2006) 0.88
Predicting protein phenotypes based on protein-protein interaction network. PLoS One (2011) 0.87
Prediction of body fluids where proteins are secreted into based on protein interaction network. PLoS One (2011) 0.87
Global protein interactome exploration through mining genome-scale data in Arabidopsis thaliana. BMC Genomics (2010) 0.86
iWRAP: An interface threading approach with application to prediction of cancer-related protein-protein interactions. J Mol Biol (2010) 0.86
Bio::Homology::InterologWalk--a Perl module to build putative protein-protein interaction networks through interolog mapping. BMC Bioinformatics (2011) 0.86
Local network topology in human protein interaction data predicts functional association. PLoS One (2009) 0.85
Interspecies data mining to predict novel ING-protein interactions in human. BMC Genomics (2008) 0.84
Co-expression among constituents of a motif in the protein-protein interaction network. J Bioinform Comput Biol (2009) 0.84
Reconstruction of gene regulatory modules in cancer cell cycle by multi-source data integration. PLoS One (2010) 0.83
Shared molecular strategies of the malaria parasite P. falciparum and the human virus HIV-1. Mol Cell Proteomics (2011) 0.83
Genome-wide identification of heat shock proteins (Hsps) and Hsp interactors in rice: Hsp70s as a case study. BMC Genomics (2014) 0.82
Connectedness of PPI network neighborhoods identifies regulatory hub proteins. Bioinformatics (2011) 0.81
Inferring modules from human protein interactome classes. BMC Syst Biol (2010) 0.79
Reversal of mitochondrial defects with CSB-dependent serine protease inhibitors in patient cells of the progeroid Cockayne syndrome. Proc Natl Acad Sci U S A (2015) 0.79
Perturbation of interaction networks for application to cancer therapy. Cancer Inform (2007) 0.77
Protein-protein interaction map is a key gateway into liver regeneration. World J Gastroenterol (2010) 0.77
FragViz: visualization of fragmented networks. BMC Bioinformatics (2010) 0.76
Empirical multiscale networks of cellular regulation. PLoS Comput Biol (2007) 0.76
DASMIweb: online integration, analysis and assessment of distributed protein interaction data. Nucleic Acids Res (2009) 0.75
Sensitive detection of pathway perturbations in cancers. BMC Bioinformatics (2012) 0.75
Deducing topology of protein-protein interaction networks from experimentally measured sub-networks. BMC Bioinformatics (2008) 0.75
Prediction and characterization of protein-protein interaction network in Bacillus licheniformis WX-02. Sci Rep (2016) 0.75
Network Modules of the Cross-Species Genotype-Phenotype Map Reflect the Clinical Severity of Human Diseases. PLoS One (2015) 0.75
HAPPI-2: a Comprehensive and High-quality Map of Human Annotated and Predicted Protein Interactions. BMC Genomics (2017) 0.75
Evaluation of the collaborative network of highly correlating skin proteins and its change following treatment with glucocorticoids. Theor Biol Med Model (2010) 0.75
Complementary Post Transcriptional Regulatory Information is Detected by PUNCH-P and Ribosome Profiling. Sci Rep (2016) 0.75
The genetic regulatory network centered on Pto-Wuschela and its targets involved in wood formation revealed by association studies. Sci Rep (2015) 0.75
High-throughput discovery and characterization of fetal protein trafficking in the blood of pregnant women. Proteomics Clin Appl (2009) 0.75
HDNetDB: A Molecular Interaction Database for Network-Oriented Investigations into Huntington's Disease. Sci Rep (2017) 0.75
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res (2003) 52.80
A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature (2000) 47.15
Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature (2002) 45.19
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature (2002) 37.66
A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci U S A (2001) 33.71
The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res (2003) 24.72
Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science (2001) 24.48
Comparative assessment of large-scale data sets of protein-protein interactions. Nature (2002) 24.25
A protein interaction map of Drosophila melanogaster. Science (2003) 20.06
EnsMart: a generic system for fast and flexible access to biological data. Genome Res (2004) 17.64
Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol (2001) 16.47
A map of the interactome network of the metazoan C. elegans. Science (2004) 15.60
Ensembl 2004. Nucleic Acids Res (2004) 11.88
Protein interaction mapping in C. elegans using proteins involved in vulval development. Science (2000) 11.61
Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs". Genome Res (2001) 5.10
A protein interaction framework for human mRNA degradation. Genome Res (2004) 2.25
Protein-protein interaction panel using mouse full-length cDNAs. Genome Res (2001) 1.84
Prediction, assessment and validation of protein interaction maps in bacteria. J Mol Biol (2002) 1.50
Detection and visualization of protein interactions with protein fragment complementation assays. Methods Mol Biol (2002) 1.03
Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature (2003) 26.58
Genome-wide RNAi analysis of Caenorhabditis elegans fat regulatory genes. Nature (2003) 7.80
Rates of behavior and aging specified by mitochondrial function during development. Science (2002) 6.28
A systematic RNAi screen identifies a critical role for mitochondria in C. elegans longevity. Nat Genet (2002) 6.26
Minimizing the risk of reporting false positives in large-scale RNAi screens. Nat Methods (2006) 5.96
Genetic analysis of tissue aging in Caenorhabditis elegans: a role for heat-shock factor and bacterial proliferation. Genetics (2002) 5.52
Systematic mapping of genetic interactions in Caenorhabditis elegans identifies common modifiers of diverse signaling pathways. Nat Genet (2006) 5.36
Genome-wide RNAi of C. elegans using the hypersensitive rrf-3 strain reveals novel gene functions. PLoS Biol (2003) 5.07
A compendium of RNA-binding motifs for decoding gene regulation. Nature (2013) 4.91
A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans. Nat Genet (2008) 3.62
Identification of genes that protect the C. elegans genome against mutations by genome-wide RNAi. Genes Dev (2003) 2.76
Evolutionary plasticity of genetic interaction networks. Nat Genet (2008) 1.97
A genome-wide screen identifies 27 genes involved in transposon silencing in C. elegans. Curr Biol (2003) 1.92
Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation. Genome Res (2010) 1.80
Chromatin regulation and sumoylation in the inhibition of Ras-induced vulval development in Caenorhabditis elegans. EMBO J (2005) 1.69
Predicting genetic modifier loci using functional gene networks. Genome Res (2010) 1.59
Genome-wide analysis of alternative splicing in Caenorhabditis elegans. Genome Res (2010) 1.46
RNAi screens in Caenorhabditis elegans in a 96-well liquid format and their application to the systematic identification of genetic interactions. Nat Protoc (2006) 1.37
High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans. Genome Biol (2009) 1.36
Loss of LIN-35, the Caenorhabditis elegans ortholog of the tumor suppressor p105Rb, results in enhanced RNA interference. Genome Biol (2006) 1.32
Combinatorial RNA interference in Caenorhabditis elegans reveals that redundancy between gene duplicates can be maintained for more than 80 million years of evolution. Genome Biol (2006) 1.30
Protein domains enriched in mammalian tissue-specific or widely expressed genes. Trends Genet (2004) 1.21
Systematic analysis of off-target effects in an RNAi screen reveals microRNAs affecting sensitivity to TRAIL-induced apoptosis. BMC Genomics (2010) 1.20
The majority of animal genes are required for wild-type fitness. Cell (2012) 0.94
Nuclear receptor binding protein 1 regulates intestinal progenitor cell homeostasis and tumour formation. EMBO J (2012) 0.92
Expression of mammalian GPCRs in C. elegans generates novel behavioural responses to human ligands. BMC Biol (2006) 0.89
5,000 RNAi experiments on a chip. Nat Methods (2004) 0.86
Technique review: how to use RNA interference. Brief Funct Genomic Proteomic (2004) 0.84
Uncover genetic interactions in Caenorhabditis elegans by RNA interference. Biosci Rep (2005) 0.81
Control of feeding behavior in C. elegans by human G protein-coupled receptors permits screening for agonist-expressing bacteria. Proc Natl Acad Sci U S A (2008) 0.78
Systems biology: where it's at in 2005. Genome Biol (2005) 0.77