Published in Genome Biol on April 15, 2005
Reactome: a knowledge base of biologic pathways and processes. Genome Biol (2007) 13.36
Network-based classification of breast cancer metastasis. Mol Syst Biol (2007) 12.18
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
Protein networks in disease. Genome Res (2008) 5.65
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. J Biol (2006) 5.57
An experimentally derived confidence score for binary protein-protein interactions. Nat Methods (2008) 5.27
A human functional protein interaction network and its application to cancer data analysis. Genome Biol (2010) 4.73
Literature-curated protein interaction datasets. Nat Methods (2009) 4.21
How complete are current yeast and human protein-interaction networks? Genome Biol (2006) 3.50
Network properties of genes harboring inherited disease mutations. Proc Natl Acad Sci U S A (2008) 3.37
Tissue specificity and the human protein interaction network. Mol Syst Biol (2009) 3.20
An integrated workflow for charting the human interaction proteome: insights into the PP2A system. Mol Syst Biol (2009) 2.92
UniHI: an entry gate to the human protein interactome. Nucleic Acids Res (2006) 2.45
Analysis of protein sequence and interaction data for candidate disease gene prediction. Nucleic Acids Res (2006) 2.30
Proteomic analysis of integrin-associated complexes identifies RCC2 as a dual regulator of Rac1 and Arf6. Sci Signal (2009) 2.26
HIPPIE: Integrating protein interaction networks with experiment based quality scores. PLoS One (2012) 2.17
Extraction of semantic biomedical relations from text using conditional random fields. BMC Bioinformatics (2008) 2.12
A biological interpretation of transient anomalous subdiffusion. I. Qualitative model. Biophys J (2006) 2.05
Display technologies: application for the discovery of drug and gene delivery agents. Adv Drug Deliv Rev (2006) 1.92
Community landscapes: an integrative approach to determine overlapping network module hierarchy, identify key nodes and predict network dynamics. PLoS One (2010) 1.74
Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes. Genome Biol (2007) 1.73
HAPPI: an online database of comprehensive human annotated and predicted protein interactions. BMC Genomics (2009) 1.61
A map of human protein interactions derived from co-expression of human mRNAs and their orthologs. Mol Syst Biol (2008) 1.53
Biomedical discovery acceleration, with applications to craniofacial development. PLoS Comput Biol (2009) 1.49
GraphWeb: mining heterogeneous biological networks for gene modules with functional significance. Nucleic Acids Res (2008) 1.45
BIOSMILE: a semantic role labeling system for biomedical verbs using a maximum-entropy model with automatically generated template features. BMC Bioinformatics (2007) 1.44
IntNetDB v1.0: an integrated protein-protein interaction network database generated by a probabilistic model. BMC Bioinformatics (2006) 1.35
Probabilistic prediction and ranking of human protein-protein interactions. BMC Bioinformatics (2007) 1.31
Pirfenidone is renoprotective in diabetic kidney disease. J Am Soc Nephrol (2009) 1.29
UniHI 4: new tools for query, analysis and visualization of the human protein-protein interactome. Nucleic Acids Res (2008) 1.28
A knowledge-driven conditional approach to extract pharmacogenomics specific drug-gene relationships from free text. J Biomed Inform (2012) 1.19
A systems biology view of cancer. Biochim Biophys Acta (2009) 1.17
Modularity and hormone sensitivity of the Drosophila melanogaster insulin receptor/target of rapamycin interaction proteome. Mol Syst Biol (2011) 1.12
Network-based Identification of novel cancer genes. Mol Cell Proteomics (2009) 1.12
VIRGO: computational prediction of gene functions. Nucleic Acids Res (2006) 1.09
HypertenGene: extracting key hypertension genes from biomedical literature with position and automatically-generated template features. BMC Bioinformatics (2009) 1.05
UniHI 7: an enhanced database for retrieval and interactive analysis of human molecular interaction networks. Nucleic Acids Res (2013) 1.02
Improving protein function prediction methods with integrated literature data. BMC Bioinformatics (2008) 1.02
Network-based model weighting to detect multiple loci influencing complex diseases. Hum Genet (2008) 1.02
In silico models of cancer. Wiley Interdiscip Rev Syst Biol Med (2010) 1.01
Viral organization of human proteins. PLoS One (2010) 1.00
A molecular-properties-based approach to understanding PDZ domain proteins and PDZ ligands. Genome Res (2006) 0.98
Integrative analysis of congenital muscular torticollis: from gene expression to clinical significance. BMC Med Genomics (2013) 0.95
An integrated systems analysis implicates EGR1 downregulation in simian immunodeficiency virus encephalitis-induced neural dysfunction. J Neurosci (2009) 0.93
Predicting combinatorial binding of transcription factors to regulatory elements in the human genome by association rule mining. BMC Bioinformatics (2007) 0.93
Reconstruction of human protein interolog network using evolutionary conserved network. BMC Bioinformatics (2007) 0.92
Differential C3NET reveals disease networks of direct physical interactions. BMC Bioinformatics (2011) 0.92
The orphan disease networks. Am J Hum Genet (2011) 0.92
Combing the hairball with BioFabric: a new approach for visualization of large networks. BMC Bioinformatics (2012) 0.91
Comparison of automated candidate gene prediction systems using genes implicated in type 2 diabetes by genome-wide association studies. BMC Bioinformatics (2009) 0.89
Topology and weights in a protein domain interaction network--a novel way to predict protein interactions. BMC Genomics (2006) 0.88
Antibody-enabled small-molecule drug discovery. Nat Rev Drug Discov (2012) 0.86
Proteomic approaches and identification of novel therapeutic targets for alcoholism. Neuropsychopharmacology (2013) 0.85
Local network topology in human protein interaction data predicts functional association. PLoS One (2009) 0.85
Proteome-wide discovery of mislocated proteins in cancer. Genome Res (2013) 0.83
Reconstruction of gene regulatory modules in cancer cell cycle by multi-source data integration. PLoS One (2010) 0.83
Inferring potential microRNA-microRNA associations based on targeting propensity and connectivity in the context of protein interaction network. PLoS One (2013) 0.83
Shared molecular strategies of the malaria parasite P. falciparum and the human virus HIV-1. Mol Cell Proteomics (2011) 0.83
Molecular targets of alcohol action: Translational research for pharmacotherapy development and screening. Prog Mol Biol Transl Sci (2011) 0.83
Integration of miRNA and protein profiling reveals coordinated neuroadaptations in the alcohol-dependent mouse brain. PLoS One (2013) 0.81
A vertex similarity-based framework to discover and rank orphan disease-related genes. BMC Syst Biol (2012) 0.81
Investigating the validity of current network analysis on static conglomerate networks by protein network stratification. BMC Bioinformatics (2010) 0.81
Identification of mitochondrial disease genes through integrative analysis of multiple datasets. Methods (2008) 0.80
Pathway mapping and development of disease-specific biomarkers: protein-based network biomarkers. J Cell Mol Med (2015) 0.80
Attenuated monocyte apoptosis, a new mechanism for osteoporosis suggested by a transcriptome-wide expression study of monocytes. PLoS One (2015) 0.79
Inferring modules from human protein interactome classes. BMC Syst Biol (2010) 0.79
Similarity searches in genome-wide numerical data sets. Biol Direct (2006) 0.79
Differentially co-expressed interacting protein pairs discriminate samples under distinct stages of HIV type 1 infection. BMC Syst Biol (2011) 0.78
The Text-mining based PubChem Bioassay neighboring analysis. BMC Bioinformatics (2010) 0.78
Dynamic programming re-ranking for PPI interactor and pair extraction in full-text articles. BMC Bioinformatics (2011) 0.77
Celecoxib exhibits an anti-gastric cancer effect by targeting focal adhesion and leukocyte transendothelial migration-associated genes. Oncol Lett (2016) 0.76
Small-angle X-ray scattering method to characterize molecular interactions: Proof of concept. Sci Rep (2015) 0.75
Complementary Post Transcriptional Regulatory Information is Detected by PUNCH-P and Ribosome Profiling. Sci Rep (2016) 0.75
Computational framework for analysis of prey-prey associations in interaction proteomics identifies novel human protein-protein interactions and networks. J Proteome Res (2012) 0.75
Sensitive detection of pathway perturbations in cancers. BMC Bioinformatics (2012) 0.75
In Vitro Identification of Histatin 5 Salivary Complexes. PLoS One (2015) 0.75
Protein-Protein Interactions: Gene Acronym Redundancies and Current Limitations Precluding Automated Data Integration. Proteomes (2013) 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 KEGG resource for deciphering the genome. Nucleic Acids Res (2004) 53.05
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
Finishing the euchromatic sequence of the human genome. Nature (2004) 41.40
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature (2002) 37.66
Network biology: understanding the cell's functional organization. Nat Rev Genet (2004) 36.62
A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci U S A (2001) 33.71
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
Global mapping of the yeast genetic interaction network. Science (2004) 21.34
A protein interaction map of Drosophila melanogaster. Science (2003) 20.06
Reactome: a knowledgebase of biological pathways. Nucleic Acids Res (2005) 20.05
BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res (2003) 18.75
DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res (2002) 15.70
A map of the interactome network of the metazoan C. elegans. Science (2004) 15.60
A literature network of human genes for high-throughput analysis of gene expression. Nat Genet (2001) 13.88
A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science (2003) 12.07
Tagging gene and protein names in biomedical text. Bioinformatics (2002) 10.03
Human protein reference database as a discovery resource for proteomics. Nucleic Acids Res (2004) 9.99
A probabilistic functional network of yeast genes. Science (2004) 8.35
Toward information extraction: identifying protein names from biological papers. Pac Symp Biocomput (1998) 8.17
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
Protein function in the post-genomic era. Nature (2000) 7.00
Comparative experiments on learning information extractors for proteins and their interactions. Artif Intell Med (2005) 5.44
Accomplishments and challenges in literature data mining for biology. Bioinformatics (2002) 5.19
Mining literature for protein-protein interactions. Bioinformatics (2001) 5.18
GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data. J Biomed Inform (2004) 4.57
A first-draft human protein-interaction map. Genome Biol (2004) 3.64
Function prediction and protein networks. Curr Opin Cell Biol (2003) 3.46
Is there a bias in proteome research? Genome Res (2001) 3.41
Biobibliometrics: information retrieval and visualization from co-occurrences of gene names in Medline abstracts. Pac Symp Biocomput (2000) 3.34
Predictome: a database of putative functional links between proteins. Nucleic Acids Res (2002) 3.32
Protein names and how to find them. Int J Med Inform (2002) 3.29
Functional proteomics mapping of a human signaling pathway. Genome Res (2004) 3.04
LGL: creating a map of protein function with an algorithm for visualizing very large biological networks. J Mol Biol (2004) 1.65
Prediction of protein function and pathways in the genome era. Cell Mol Life Sci (2004) 1.49
Data mining tools for biological sequences. J Bioinform Comput Biol (2003) 1.10
Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotechnol (2006) 9.95
Insights into the regulation of protein abundance from proteomic and transcriptomic analyses. Nat Rev Genet (2012) 8.55
A probabilistic functional network of yeast genes. Science (2004) 8.35
Comparative experiments on learning information extractors for proteins and their interactions. Artif Intell Med (2005) 5.44
Characterising and predicting haploinsufficiency in the human genome. PLoS Genet (2010) 4.85
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol (2008) 4.78
The need for a public proteomics repository. Nat Biotechnol (2004) 4.60
Synthetic biology: engineering Escherichia coli to see light. Nature (2005) 4.58
Global signatures of protein and mRNA expression levels. Mol Biosyst (2009) 4.43
Prioritizing candidate disease genes by network-based boosting of genome-wide association data. Genome Res (2011) 4.39
A census of human soluble protein complexes. Cell (2012) 3.90
A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans. Nat Genet (2008) 3.62
Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line. Mol Syst Biol (2010) 3.56
How complete are current yeast and human protein-interaction networks? Genome Biol (2006) 3.50
A synthetic genetic edge detection program. Cell (2009) 3.20
Expression deconvolution: a reinterpretation of DNA microarray data reveals dynamic changes in cell populations. Proc Natl Acad Sci U S A (2003) 3.19
Protein interaction networks from yeast to human. Curr Opin Struct Biol (2004) 3.15
Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana. Nat Biotechnol (2010) 2.90
An improved, bias-reduced probabilistic functional gene network of baker's yeast, Saccharomyces cerevisiae. PLoS One (2007) 2.84
Systematic discovery of nonobvious human disease models through orthologous phenotypes. Proc Natl Acad Sci U S A (2010) 2.61
Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages. Nat Biotechnol (2003) 2.40
Widespread reorganization of metabolic enzymes into reversible assemblies upon nutrient starvation. Proc Natl Acad Sci U S A (2009) 2.39
Exploiting the co-evolution of interacting proteins to discover interaction specificity. J Mol Biol (2003) 2.24
A probabilistic view of gene function. Nat Genet (2004) 1.99
The planar cell polarity effector Fuz is essential for targeted membrane trafficking, ciliogenesis and mouse embryonic development. Nat Cell Biol (2009) 1.90
Chromatographic alignment of ESI-LC-MS proteomics data sets by ordered bijective interpolated warping. Anal Chem (2006) 1.85
Rational extension of the ribosome biogenesis pathway using network-guided genetics. PLoS Biol (2009) 1.81
Defining the pathway of cytoplasmic maturation of the 60S ribosomal subunit. Mol Cell (2010) 1.79
Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes. Genome Biol (2007) 1.73
Protein abundances are more conserved than mRNA abundances across diverse taxa. Proteomics (2010) 1.71
LGL: creating a map of protein function with an algorithm for visualizing very large biological networks. J Mol Biol (2004) 1.65
Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data. Nat Protoc (2008) 1.62
Predicting genetic modifier loci using functional gene networks. Genome Res (2010) 1.59
Evolutionarily repurposed networks reveal the well-known antifungal drug thiabendazole to be a novel vascular disrupting agent. PLoS Biol (2012) 1.58
It's the machine that matters: Predicting gene function and phenotype from protein networks. J Proteomics (2010) 1.57
The APEX Quantitative Proteomics Tool: generating protein quantitation estimates from LC-MS/MS proteomics results. BMC Bioinformatics (2008) 1.54
Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy. Genome Biol (2008) 1.54
A map of human protein interactions derived from co-expression of human mRNAs and their orthologs. Mol Syst Biol (2008) 1.53
Parallel evolution in Pseudomonas aeruginosa over 39,000 generations in vivo. MBio (2010) 1.50
Identification and characterization of the constituent human serum antibodies elicited by vaccination. Proc Natl Acad Sci U S A (2014) 1.50
Predicting functional linkages from gene fusions with confidence. Appl Bioinformatics (2002) 1.46
Mass spectrometry of the M. smegmatis proteome: protein expression levels correlate with function, operons, and codon bias. Genome Res (2005) 1.43
Bud23 methylates G1575 of 18S rRNA and is required for efficient nuclear export of pre-40S subunits. Mol Cell Biol (2008) 1.38
Integrating shotgun proteomics and mRNA expression data to improve protein identification. Bioinformatics (2009) 1.36
Protein expression regulation under oxidative stress. Mol Cell Proteomics (2011) 1.34
Genetic dissection of the biotic stress response using a genome-scale gene network for rice. Proc Natl Acad Sci U S A (2011) 1.27
Molecular deconvolution of the monoclonal antibodies that comprise the polyclonal serum response. Proc Natl Acad Sci U S A (2013) 1.26
Mechanisms of cell cycle control revealed by a systematic and quantitative overexpression screen in S. cerevisiae. PLoS Genet (2008) 1.23
Age-dependent evolution of the yeast protein interaction network suggests a limited role of gene duplication and divergence. PLoS Comput Biol (2008) 1.23
Coordinated genomic control of ciliogenesis and cell movement by RFX2. Elife (2014) 1.20
MSblender: A probabilistic approach for integrating peptide identifications from multiple database search engines. J Proteome Res (2011) 1.19
Ribosome stalk assembly requires the dual-specificity phosphatase Yvh1 for the exchange of Mrt4 with P0. J Cell Biol (2009) 1.17
A Bacteriophage tailspike domain promotes self-cleavage of a human membrane-bound transcription factor, the myelin regulatory factor MYRF. PLoS Biol (2013) 1.16
Systematic profiling of cellular phenotypes with spotted cell microarrays reveals mating-pheromone response genes. Genome Biol (2006) 1.16
Dynamic reorganization of metabolic enzymes into intracellular bodies. Annu Rev Cell Dev Biol (2012) 1.15
Systematic prediction of gene function in Arabidopsis thaliana using a probabilistic functional gene network. Nat Protoc (2011) 1.14
Two-tiered approach identifies a network of cancer and liver disease-related genes regulated by miR-122. J Biol Chem (2011) 1.11
A fast coarse filtering method for peptide identification by mass spectrometry. Bioinformatics (2006) 1.08
mspire: mass spectrometry proteomics in Ruby. Bioinformatics (2008) 1.07
Flaws in evaluation schemes for pair-input computational predictions. Nat Methods (2012) 1.06
RFX2 is broadly required for ciliogenesis during vertebrate development. Dev Biol (2011) 1.06
ComplexQuant: high-throughput computational pipeline for the global quantitative analysis of endogenous soluble protein complexes using high resolution protein HPLC and precision label-free LC/MS/MS. J Proteomics (2012) 1.05
Prediction and validation of gene-disease associations using methods inspired by social network analyses. PLoS One (2013) 1.05
Diametrical clustering for identifying anti-correlated gene clusters. Bioinformatics (2003) 1.01
Role of Pseudomonas aeruginosa peptidoglycan-associated outer membrane proteins in vesicle formation. J Bacteriol (2012) 0.99
Prediction of gene-phenotype associations in humans, mice, and plants using phenologs. BMC Bioinformatics (2013) 0.99
Quantitative gene expression assessment identifies appropriate cell line models for individual cervical cancer pathways. BMC Genomics (2007) 0.97
Mining gene functional networks to improve mass-spectrometry-based protein identification. Bioinformatics (2009) 0.96
Group II intron protein localization and insertion sites are affected by polyphosphate. PLoS Biol (2008) 0.96
Systematic definition of protein constituents along the major polarization axis reveals an adaptive reuse of the polarization machinery in pheromone-treated budding yeast. J Proteome Res (2009) 0.96
Revisiting the negative example sampling problem for predicting protein-protein interactions. Bioinformatics (2011) 0.96
RIDDLE: reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene network. Genome Biol (2012) 0.95
Protein function prediction using the Protein Link EXplorer (PLEX). Bioinformatics (2005) 0.95
Pseudomonas aeruginosa enhances production of a non-alginate exopolysaccharide during long-term colonization of the cystic fibrosis lung. PLoS One (2013) 0.94
Development through the eyes of functional genomics. Curr Opin Genet Dev (2004) 0.93
Global metabolic changes following loss of a feedback loop reveal dynamic steady states of the yeast metabolome. Metab Eng (2006) 0.91
A role for central spindle proteins in cilia structure and function. Cytoskeleton (Hoboken) (2011) 0.90
Buffering by gene duplicates: an analysis of molecular correlates and evolutionary conservation. BMC Genomics (2008) 0.89
The proteomic response of Mycobacterium smegmatis to anti-tuberculosis drugs suggests targeted pathways. J Proteome Res (2008) 0.88
Human cell chips: adapting DNA microarray spotting technology to cell-based imaging assays. PLoS One (2009) 0.87
Label-free protein quantitation using weighted spectral counting. Methods Mol Biol (2012) 0.86
Statistical approach to protein quantification. Mol Cell Proteomics (2013) 0.86
A consensus perceived glycemic variability metric. J Diabetes Sci Technol (2013) 0.86
Id2a functions to limit Notch pathway activity and thereby influence the transition from proliferation to differentiation of retinoblasts during zebrafish retinogenesis. Dev Biol (2012) 0.84
Integrating functional genomics data. Methods Mol Biol (2008) 0.84
Proteomic identification of monoclonal antibodies from serum. Anal Chem (2014) 0.84
Yeast cells expressing the human mitochondrial DNA polymerase reveal correlations between polymerase fidelity and human disease progression. J Biol Chem (2014) 0.83
Proteomic and protein interaction network analysis of human T lymphocytes during cell-cycle entry. Mol Syst Biol (2012) 0.82
Protein-to-mRNA ratios are conserved between Pseudomonas aeruginosa strains. J Proteome Res (2014) 0.81
Transiently transfected purine biosynthetic enzymes form stress bodies. PLoS One (2013) 0.81
The proteomic response to mutants of the Escherichia coli RNA degradosome. Mol Biosyst (2013) 0.80
Effects of functional bias on supervised learning of a gene network model. Methods Mol Biol (2009) 0.80
Revisiting and revising the purinosome. Mol Biosyst (2014) 0.78
A self-assembling lanthanide molecular nanoparticle for optical imaging. Dalton Trans (2015) 0.77
Efforts to make and apply humanized yeast. Brief Funct Genomics (2015) 0.77
Absolute abundance for the masses. Nat Biotechnol (2009) 0.76
Corrigendum: The ciliopathy-associated CPLANE proteins direct basal body recruitment of intraflagellar transport machinery. Nat Genet (2016) 0.76
High-throughput immunofluorescence microscopy using yeast spheroplast cell-based microarrays. Methods Mol Biol (2011) 0.75
Lanthanide nano-drums: a new class of molecular nanoparticles for potential biomedical applications. Faraday Discuss (2014) 0.75