Published in BMC Bioinformatics on December 18, 2006
Human Protein Reference Database--2009 update. Nucleic Acids Res (2008) 21.25
Overview of the protein-protein interaction annotation extraction task of BioCreative II. Genome Biol (2008) 6.38
Protein networks in disease. Genome Res (2008) 5.65
Visualization of omics data for systems biology. Nat Methods (2010) 4.59
Literature-curated protein interaction datasets. Nat Methods (2009) 4.21
Network-based elucidation of human disease similarities reveals common functional modules enriched for pluripotent drug targets. PLoS Comput Biol (2010) 3.23
Positive selection at the protein network periphery: evaluation in terms of structural constraints and cellular context. Proc Natl Acad Sci U S A (2007) 2.55
Network-based analysis of affected biological processes in type 2 diabetes models. PLoS Genet (2007) 2.54
eQED: an efficient method for interpreting eQTL associations using protein networks. Mol Syst Biol (2008) 2.45
PDZ domains and their binding partners: structure, specificity, and modification. Cell Commun Signal (2010) 2.07
DroID: the Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions. BMC Genomics (2008) 1.89
Proteomic profiling of Myc-associated proteins. Cell Cycle (2010) 1.80
Neuroscience in the era of functional genomics and systems biology. Nature (2009) 1.80
Exploiting the proteome to improve the genome-wide genetic analysis of epistasis in common human diseases. Hum Genet (2008) 1.72
DASMI: exchanging, annotating and assessing molecular interaction data. Bioinformatics (2009) 1.64
Network properties of complex human disease genes identified through genome-wide association studies. PLoS One (2009) 1.42
Literature curation of protein interactions: measuring agreement across major public databases. Database (Oxford) (2010) 1.33
Identification of candidate disease genes by integrating Gene Ontologies and protein-interaction networks: case study of primary immunodeficiencies. Nucleic Acids Res (2008) 1.23
Oncofinder, a new method for the analysis of intracellular signaling pathway activation using transcriptomic data. Front Genet (2014) 1.22
Role for protein-protein interaction databases in human genetics. Expert Rev Proteomics (2009) 1.20
Integrating siRNA and protein-protein interaction data to identify an expanded insulin signaling network. Genome Res (2009) 1.17
Adding protein context to the human protein-protein interaction network to reveal meaningful interactions. PLoS Comput Biol (2013) 1.10
Network-based pipeline for analyzing MS data: an application toward liver cancer. J Proteome Res (2011) 1.07
Signaling pathways activation profiles make better markers of cancer than expression of individual genes. Oncotarget (2014) 1.05
TcoF-DB: dragon database for human transcription co-factors and transcription factor interacting proteins. Nucleic Acids Res (2010) 1.05
The OncoFinder algorithm for minimizing the errors introduced by the high-throughput methods of transcriptome analysis. Front Mol Biosci (2014) 1.04
Network integration and graph analysis in mammalian molecular systems biology. IET Syst Biol (2008) 1.03
Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention. Genome Res (2009) 1.02
Protein-protein interaction as a predictor of subcellular location. BMC Syst Biol (2009) 1.01
Walking the interactome to identify human miRNA-disease associations through the functional link between miRNA targets and disease genes. BMC Syst Biol (2013) 1.01
A network-based biomarker approach for molecular investigation and diagnosis of lung cancer. BMC Med Genomics (2011) 1.01
Evidence for systems-level molecular mechanisms of tumorigenesis. BMC Genomics (2007) 1.00
Linking gene expression and functional network data in human heart failure. PLoS One (2007) 0.96
Looking at cerebellar malformations through text-mined interactomes of mice and humans. PLoS Comput Biol (2009) 0.95
A protein interaction atlas for the nuclear receptors: properties and quality of a hub-based dimerisation network. BMC Syst Biol (2007) 0.94
PathwayMatrix: visualizing binary relationships between proteins in biological pathways. BMC Proc (2015) 0.93
Prediction and comparison of Salmonella-human and Salmonella-Arabidopsis interactomes. Chem Biodivers (2012) 0.91
Network inference and network response identification: moving genome-scale data to the next level of biological discovery. Mol Biosyst (2009) 0.91
PPI layouts: BioJS components for the display of Protein-Protein Interactions. F1000Res (2014) 0.90
Systematic prediction of human membrane receptor interactions. Proteomics (2009) 0.90
Human 14-3-3 paralogs differences uncovered by cross-talk of phosphorylation and lysine acetylation. PLoS One (2013) 0.88
BIPS: BIANA Interolog Prediction Server. A tool for protein-protein interaction inference. Nucleic Acids Res (2012) 0.88
Non-thermal plasma treatment altered gene expression profiling in non-small-cell lung cancer A549 cells. BMC Genomics (2015) 0.87
Human Proteinpedia as a resource for clinical proteomics. Mol Cell Proteomics (2008) 0.87
Efficiency of the immunome protein interaction network increases during evolution. Immunome Res (2008) 0.86
MicroRNA-regulated protein-protein interaction networks and their functions in breast cancer. Int J Mol Sci (2013) 0.85
A computational tool for identifying minimotifs in protein-protein interactions and improving the accuracy of minimotif predictions. Proteins (2010) 0.85
Interspecies data mining to predict novel ING-protein interactions in human. BMC Genomics (2008) 0.84
Common dysregulation network in the human prefrontal cortex underlies two neurodegenerative diseases. Mol Syst Biol (2014) 0.84
Identification of biomarkers for hepatocellular carcinoma using network-based bioinformatics methods. Eur J Med Res (2013) 0.84
SIDEKICK: Genomic data driven analysis and decision-making framework. BMC Bioinformatics (2010) 0.84
Network-based biomarkers enhance classical approaches to prognostic gene expression signatures. BMC Syst Biol (2014) 0.83
Approaches to biomarkers in human colorectal cancer: looking back, to go forward. Biomark Med (2009) 0.83
Identification of candidate genes for lung cancer somatic mutation test kits. Genet Mol Biol (2013) 0.82
An approach for the identification of targets specific to bone metastasis using cancer genes interactome and gene ontology analysis. PLoS One (2012) 0.82
A conserved mammalian protein interaction network. PLoS One (2013) 0.81
Discovering functional interaction patterns in protein-protein interaction networks. BMC Bioinformatics (2008) 0.81
Integrated bio-entity network: a system for biological knowledge discovery. PLoS One (2011) 0.80
Computational prediction of protein-protein interactions. Methods Mol Biol (2015) 0.80
Characterization the regulation of herpesvirus miRNAs from the view of human protein interaction network. BMC Syst Biol (2011) 0.80
Reconstruction of the experimentally supported human protein interactome: what can we learn? BMC Syst Biol (2013) 0.79
Protopia: a protein-protein interaction tool. BMC Bioinformatics (2009) 0.79
Network-based analysis of comorbidities risk during an infection: SARS and HIV case studies. BMC Bioinformatics (2014) 0.77
Exploring novel mechanistic insights in Alzheimer's disease by assessing reliability of protein interactions. Sci Rep (2015) 0.77
Revealing the anti-tumor effect of artificial miRNA p-27-5p on human breast carcinoma cell line T-47D. Int J Mol Sci (2012) 0.77
Integrated web visualizations for protein-protein interaction databases. BMC Bioinformatics (2015) 0.76
Epigenetic profiling of human brain differential DNA methylation networks in schizophrenia. BMC Med Genomics (2016) 0.75
VAN: an R package for identifying biologically perturbed networks via differential variability analysis. BMC Res Notes (2013) 0.75
The use of gene interaction networks to improve the identification of cancer driver genes. PeerJ (2017) 0.75
Using contrast patterns between true complexes and random subgraphs in PPI networks to predict unknown protein complexes. Sci Rep (2016) 0.75
Comparison of modules of wild type and mutant Huntingtin and TP53 protein interaction networks: implications in biological processes and functions. PLoS One (2013) 0.75
Protein network study of human AF4 reveals its central role in RNA Pol II-mediated transcription and in phosphorylation-dependent regulatory mechanisms. Biochem J (2011) 0.75
Triangle network motifs predict complexes by complementing high-error interactomes with structural information. BMC Bioinformatics (2009) 0.75
Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res (2003) 103.76
Towards a proteome-scale map of the human protein-protein interaction network. Nature (2005) 24.76
The Database of Interacting Proteins: 2004 update. Nucleic Acids Res (2004) 23.67
Reactome: a knowledgebase of biological pathways. Nucleic Acids Res (2005) 20.05
A human protein-protein interaction network: a resource for annotating the proteome. Cell (2005) 18.97
MINT: a Molecular INTeraction database. FEBS Lett (2002) 17.21
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
Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res (2003) 14.79
The Biomolecular Interaction Network Database and related tools 2005 update. Nucleic Acids Res (2005) 12.94
Protein interactions: two methods for assessment of the reliability of high throughput observations. Mol Cell Proteomics (2002) 8.11
A physical and functional map of the human TNF-alpha/NF-kappa B signal transduction pathway. Nat Cell Biol (2004) 7.23
Analyzing yeast protein-protein interaction data obtained from different sources. Nat Biotechnol (2002) 7.06
Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat Genet (2006) 6.74
Osprey: a network visualization system. Genome Biol (2003) 6.23
Large-scale proteomic analysis of the human spliceosome. Genome Res (2002) 5.75
The MIPS mammalian protein-protein interaction database. Bioinformatics (2004) 4.66
Inferring domain-domain interactions from protein-protein interactions. Genome Res (2002) 4.36
Systematic discovery of new recognition peptides mediating protein interaction networks. PLoS Biol (2005) 3.28
Protein composition of human prespliceosomes isolated by a tobramycin affinity-selection method. Proc Natl Acad Sci U S A (2002) 3.14
Describing biological protein interactions in terms of protein states and state transitions: the LiveDIP database. Mol Cell Proteomics (2002) 2.76
PDZBase: a protein-protein interaction database for PDZ-domains. Bioinformatics (2004) 2.55
Overview of the Alliance for Cellular Signaling. Nature (2002) 2.15
Inferring protein domain interactions from databases of interacting proteins. Genome Biol (2005) 1.97
Bioinformatic identification of potential autocrine signaling loops in cancers from gene expression profiles. Nat Genet (2001) 1.93
The PEDANT genome database in 2005. Nucleic Acids Res (2005) 1.88
Plasma Proteome Database as a resource for proteomics research. Proteomics (2005) 1.76
Ulysses - an application for the projection of molecular interactions across species. Genome Biol (2005) 1.12
Proteomic resources: integrating biomedical information in humans. Gene (2005) 0.85
Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics (2002) 30.58
Human Protein Reference Database--2009 update. Nucleic Acids Res (2008) 21.25
ONCOMINE: a cancer microarray database and integrated data-mining platform. Neoplasia (2004) 17.08
The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol (2004) 16.08
Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res (2003) 14.79
Human protein reference database--2006 update. Nucleic Acids Res (2006) 12.16
Human protein reference database as a discovery resource for proteomics. Nucleic Acids Res (2004) 9.99
Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. Proc Natl Acad Sci U S A (2004) 9.42
The BioPAX community standard for pathway data sharing. Nat Biotechnol (2010) 9.19
Pyruvate kinase M2 is a PHD3-stimulated coactivator for hypoxia-inducible factor 1. Cell (2011) 7.33
Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat Genet (2006) 6.74
GCN5 acetyltransferase complex controls glucose metabolism through transcriptional repression of PGC-1alpha. Cell Metab (2006) 4.50
Human Proteinpedia enables sharing of human protein data. Nat Biotechnol (2008) 4.21
Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry. Proc Natl Acad Sci U S A (2007) 4.01
Probabilistic model of the human protein-protein interaction network. Nat Biotechnol (2005) 3.99
Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome. Trends Biotechnol (2002) 3.85
A curated compendium of phosphorylation motifs. Nat Biotechnol (2007) 3.79
Vesiclepedia: a compendium for extracellular vesicles with continuous community annotation. PLoS Biol (2012) 3.18
A compendium of potential biomarkers of pancreatic cancer. PLoS Med (2009) 3.00
Enhanced CellClassifier: a multi-class classification tool for microscopy images. BMC Bioinformatics (2010) 2.84
A role for thymic stromal lymphopoietin in CD4(+) T cell development. J Exp Med (2004) 2.81
Biomarker discovery from pancreatic cancer secretome using a differential proteomic approach. Mol Cell Proteomics (2005) 2.66
NetPath: a public resource of curated signal transduction pathways. Genome Biol (2010) 2.62
Sequential phosphorylation of CCAAT enhancer-binding protein beta by MAPK and glycogen synthase kinase 3beta is required for adipogenesis. Proc Natl Acad Sci U S A (2005) 2.51
Human Protein Reference Database and Human Proteinpedia as discovery tools for systems biology. Methods Mol Biol (2009) 2.47
Insights into the role of histone H3 and histone H4 core modifiable residues in Saccharomyces cerevisiae. Mol Cell Biol (2005) 2.33
Phosphoproteomic analysis of Her2/neu signaling and inhibition. Proc Natl Acad Sci U S A (2006) 2.30
Human Proteinpedia: a unified discovery resource for proteomics research. Nucleic Acids Res (2008) 2.30
From biological databases to platforms for biomedical discovery. Trends Biotechnol (2003) 2.27
K63-specific deubiquitination by two JAMM/MPN+ complexes: BRISC-associated Brcc36 and proteasomal Poh1. EMBO J (2009) 2.17
BioBuilder as a database development and functional annotation platform for proteins. BMC Bioinformatics (2004) 2.13
Quantitative proteomics using stable isotope labeling with amino acids in cell culture. Nat Protoc (2008) 2.07
Protein pyrophosphorylation by inositol pyrophosphates is a posttranslational event. Proc Natl Acad Sci U S A (2007) 2.03
Significant conservation of synthetic lethal genetic interaction networks between distantly related eukaryotes. Proc Natl Acad Sci U S A (2008) 2.01
Hsp70 and CHIP selectively mediate ubiquitination and degradation of hypoxia-inducible factor (HIF)-1alpha but Not HIF-2alpha. J Biol Chem (2009) 1.97
Chemical rescue of a mutant enzyme in living cells. Science (2006) 1.95
Global impact of oncogenic Src on a phosphotyrosine proteome. J Proteome Res (2008) 1.94
Comprehensive proteomic analysis of human pancreatic juice. J Proteome Res (2004) 1.93
Dynamic interplay between O-linked N-acetylglucosaminylation and glycogen synthase kinase-3-dependent phosphorylation. Mol Cell Proteomics (2007) 1.92
Viral immune modulators perturb the human molecular network by common and unique strategies. Nature (2012) 1.86
Disruption of Plasmodium falciparum development by antibodies against a conserved mosquito midgut antigen. Proc Natl Acad Sci U S A (2007) 1.81
A mass spectrometry-based proteomic approach for identification of serine/threonine-phosphorylated proteins by enrichment with phospho-specific antibodies: identification of a novel protein, Frigg, as a protein kinase A substrate. Mol Cell Proteomics (2002) 1.78
Plasma Proteome Database as a resource for proteomics research. Proteomics (2005) 1.76
Right pulmonary artery-to-left atrium communication: report of 5 cases. Ann Thorac Surg (2005) 1.75
Stable isotope labeling with amino acids in cell culture (SILAC) for studying dynamics of protein abundance and posttranslational modifications. Sci STKE (2005) 1.67
Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis. Mol Biosyst (2011) 1.62
A proteomic approach for identification of secreted proteins during the differentiation of 3T3-L1 preadipocytes to adipocytes. Mol Cell Proteomics (2002) 1.61
A proteomic approach for quantitation of phosphorylation using stable isotope labeling in cell culture. Anal Chem (2003) 1.60
Histone demethylase JMJD2C is a coactivator for hypoxia-inducible factor 1 that is required for breast cancer progression. Proc Natl Acad Sci U S A (2012) 1.60
Construction of human activity-based phosphorylation networks. Mol Syst Biol (2013) 1.59
Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry. Mol Cell Proteomics (2011) 1.58
Comprehensive comparison of collision induced dissociation and electron transfer dissociation. Anal Chem (2008) 1.58
Context-specific effects of fibulin-5 (DANCE/EVEC) on cell proliferation, motility, and invasion. Fibulin-5 is induced by transforming growth factor-beta and affects protein kinase cascades. J Biol Chem (2002) 1.58
Mutant proteins as cancer-specific biomarkers. Proc Natl Acad Sci U S A (2011) 1.56
Comparisons of tyrosine phosphorylated proteins in cells expressing lung cancer-specific alleles of EGFR and KRAS. Proc Natl Acad Sci U S A (2008) 1.51
Genome annotation of Anopheles gambiae using mass spectrometry-derived data. BMC Genomics (2005) 1.51
Proteogenomics. Proteomics (2011) 1.48
Genomewide mRNA profiling of esophageal squamous cell carcinoma for identification of cancer biomarkers. Cancer Biol Ther (2009) 1.45
Malaria parasite invasion of the mosquito salivary gland requires interaction between the Plasmodium TRAP and the Anopheles saglin proteins. PLoS Pathog (2009) 1.44
Systematic interactome mapping and genetic perturbation analysis of a C. elegans TGF-beta signaling network. Mol Cell (2004) 1.40
New markers of pancreatic cancer identified through differential gene expression analyses: claudin 18 and annexin A8. Am J Surg Pathol (2008) 1.39
Immunoassay and antibody microarray analysis of the HUPO Plasma Proteome Project reference specimens: systematic variation between sample types and calibration of mass spectrometry data. Proteomics (2005) 1.38
Evaluation of several MS/MS search algorithms for analysis of spectra derived from electron transfer dissociation experiments. Anal Chem (2009) 1.38
Utility of bile duct brushings for the early detection of cholangiocarcinoma in patients with primary sclerosing cholangitis. J Clin Gastroenterol (2006) 1.38
Tyrosine phosphorylation mapping of the epidermal growth factor receptor signaling pathway. J Biol Chem (2001) 1.37
A comprehensive map of the human urinary proteome. J Proteome Res (2011) 1.34
Plasma Proteome Database as a resource for proteomics research: 2014 update. Nucleic Acids Res (2013) 1.34
Human protein reference database and human proteinpedia as discovery resources for molecular biotechnology. Mol Biotechnol (2011) 1.31
Phosphoproteome analysis of HeLa cells using stable isotope labeling with amino acids in cell culture (SILAC). J Proteome Res (2005) 1.29
Identification of miR-21 targets in breast cancer cells using a quantitative proteomic approach. Proteomics (2009) 1.28
A quantitative proteomic approach for identification of potential biomarkers in hepatocellular carcinoma. J Proteome Res (2008) 1.27
A proteomic analysis of human bile. Mol Cell Proteomics (2004) 1.20
Antitumor activity and molecular effects of the novel heat shock protein 90 inhibitor, IPI-504, in pancreatic cancer. Mol Cancer Ther (2008) 1.18
Cloning of MASK, a novel member of the mammalian germinal center kinase III subfamily, with apoptosis-inducing properties. J Biol Chem (2001) 1.17
Transcriptomic and proteomic profiling of KEAP1 disrupted and sulforaphane-treated human breast epithelial cells reveals common expression profiles. Breast Cancer Res Treat (2011) 1.15