Published in Mol Cell Proteomics on August 11, 2011
STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res (2012) 18.26
FunCoup 3.0: database of genome-wide functional coupling networks. Nucleic Acids Res (2013) 1.56
Diversity in genetic in vivo methods for protein-protein interaction studies: from the yeast two-hybrid system to the mammalian split-luciferase system. Microbiol Mol Biol Rev (2012) 1.11
In silico prediction of physical protein interactions and characterization of interactome orphans. Nat Methods (2014) 0.96
Integrated interactions database: tissue-specific view of the human and model organism interactomes. Nucleic Acids Res (2015) 0.95
Fundamentals of protein interaction network mapping. Mol Syst Biol (2015) 0.93
Structural bioinformatics of the interactome. Annu Rev Biophys (2014) 0.93
A computational framework for boosting confidence in high-throughput protein-protein interaction datasets. Genome Biol (2012) 0.92
Genomics meets proteomics: identifying the culprits in disease. Hum Genet (2013) 0.86
Role of the axonal initial segment in psychiatric disorders: function, dysfunction, and intervention. Front Psychiatry (2014) 0.86
Proteomics Analysis with a Nano Random Forest Approach Reveals Novel Functional Interactions Regulated by SMC Complexes on Mitotic Chromosomes. Mol Cell Proteomics (2016) 0.83
Protein-protein interaction networks: probing disease mechanisms using model systems. Genome Med (2013) 0.81
Forward Individualized Medicine from Personal Genomes to Interactomes. Front Physiol (2015) 0.78
Efficient prediction of human protein-protein interactions at a global scale. BMC Bioinformatics (2014) 0.77
Efficient prediction of progesterone receptor interactome using a support vector machine model. Int J Mol Sci (2015) 0.75
Protein-Protein Interactions: Gene Acronym Redundancies and Current Limitations Precluding Automated Data Integration. Proteomes (2013) 0.75
Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci U S A (2009) 54.68
A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A (2004) 44.81
MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol (2008) 38.00
KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res (2009) 28.60
Integration of biological networks and gene expression data using Cytoscape. Nat Protoc (2007) 27.10
Towards a proteome-scale map of the human protein-protein interaction network. Nature (2005) 24.76
Human Protein Reference Database--2009 update. Nucleic Acids Res (2008) 21.25
STRING 8--a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res (2008) 20.62
A human protein-protein interaction network: a resource for annotating the proteome. Cell (2005) 18.97
Systematic meta-analyses of Alzheimer disease genetic association studies: the AlzGene database. Nat Genet (2007) 12.13
Human genetic variation and its contribution to complex traits. Nat Rev Genet (2009) 12.11
Detecting gene-gene interactions that underlie human diseases. Nat Rev Genet (2009) 12.07
The genetic association database. Nat Genet (2004) 11.29
BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources. Genome Biol (2009) 11.17
A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat Biotechnol (2007) 9.90
Large-scale mapping of human protein-protein interactions by mass spectrometry. Mol Syst Biol (2007) 8.16
Online predicted human interaction database. Bioinformatics (2005) 6.83
An empirical framework for binary interactome mapping. Nat Methods (2008) 6.59
BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals. Nat Methods (2008) 6.51
Endocytosis and signalling: intertwining molecular networks. Nat Rev Mol Cell Biol (2009) 5.83
STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. Nucleic Acids Res (2000) 5.68
Network-based global inference of human disease genes. Mol Syst Biol (2008) 5.01
Systematic analysis of human protein complexes identifies chromosome segregation proteins. Science (2010) 4.69
Probabilistic model of the human protein-protein interaction network. Nat Biotechnol (2005) 3.99
Apolipoprotein E and its receptors in Alzheimer's disease: pathways, pathogenesis and therapy. Nat Rev Neurosci (2009) 3.97
Evaluation of different biological data and computational classification methods for use in protein interaction prediction. Proteins (2006) 3.78
Estimating the size of the human interactome. Proc Natl Acad Sci U S A (2008) 3.66
Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis. Nature (2005) 3.62
Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions. J Cell Biol (2010) 3.61
A protein interaction network links GIT1, an enhancer of huntingtin aggregation, to Huntington's disease. Mol Cell (2004) 3.26
CORUM: the comprehensive resource of mammalian protein complexes. Nucleic Acids Res (2007) 3.23
Tissue specificity and the human protein interaction network. Mol Syst Biol (2009) 3.20
Protein interaction networks from yeast to human. Curr Opin Struct Biol (2004) 3.15
Accumulation of amyloid precursor protein in the mitochondrial import channels of human Alzheimer's disease brain is associated with mitochondrial dysfunction. J Neurosci (2006) 3.00
A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers. Mol Syst Biol (2010) 2.92
Integrating physical and genetic maps: from genomes to interaction networks. Nat Rev Genet (2007) 2.77
A TOMM40 variable-length polymorphism predicts the age of late-onset Alzheimer's disease. Pharmacogenomics J (2009) 2.66
Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network. Genome Biol (2009) 2.43
Global networks of functional coupling in eukaryotes from comprehensive data integration. Genome Res (2009) 2.43
A global view of protein expression in human cells, tissues, and organs. Mol Syst Biol (2009) 2.41
Strategies for cellular decision-making. Mol Syst Biol (2009) 2.29
Information assessment on predicting protein-protein interactions. BMC Bioinformatics (2004) 2.14
Emergent behavior of growing knowledge about molecular interactions. Nat Biotechnol (2005) 1.95
PIPs: human protein-protein interaction prediction database. Nucleic Acids Res (2008) 1.91
Methods for investigating gene-environment interactions in candidate pathway and genome-wide association studies. Annu Rev Public Health (2010) 1.88
Comprehensive analysis of APOE and selected proximate markers for late-onset Alzheimer's disease: patterns of linkage disequilibrium and disease/marker association. Genomics (2007) 1.78
Predicting genetic modifier loci using functional gene networks. Genome Res (2010) 1.59
Computational analysis of human protein interaction networks. Proteomics (2007) 1.53
The value of high quality protein-protein interaction networks for systems biology. Curr Opin Chem Biol (2006) 1.44
Towards genome-scale signalling network reconstructions. Nat Rev Genet (2010) 1.39
From individual Wnt pathways towards a Wnt signalling network. Philos Trans R Soc Lond B Biol Sci (2008) 1.37
Integrative analysis for finding genes and networks involved in diabetes and other complex diseases. Genome Biol (2007) 1.27
Cost-effective strategies for completing the interactome. Nat Methods (2008) 1.25
GoGene: gene annotation in the fast lane. Nucleic Acids Res (2009) 1.21
Computational methods for predicting protein-protein interactions. Adv Biochem Eng Biotechnol (2008) 1.00
Looking at cerebellar malformations through text-mined interactomes of mice and humans. PLoS Comput Biol (2009) 0.95
Systematic prediction of human membrane receptor interactions. Proteomics (2009) 0.90
Using structural motif descriptors for sequence-based binding site prediction. BMC Bioinformatics (2007) 0.87
BIOVERSE: enhancements to the framework for structural, functional and contextual modeling of proteins and proteomes. Nucleic Acids Res (2005) 0.86
Accounting for redundancy when integrating gene interaction databases. PLoS One (2009) 0.84
Commonalities in the genetics of Alzheimer's disease and Parkinson's disease. Expert Rev Neurother (2008) 0.79
MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol (2008) 38.00
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature (2002) 37.66
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
Mass spectrometry-based proteomics. Nature (2003) 28.94
Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell (2006) 20.92
Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science (2009) 20.49
miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev (2002) 19.24
Universal sample preparation method for proteome analysis. Nat Methods (2009) 16.88
In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat Protoc (2006) 16.56
Andromeda: a peptide search engine integrated into the MaxQuant environment. J Proteome Res (2011) 14.82
Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. Anal Chem (2003) 13.58
Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat Protoc (2007) 10.71
Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol Cell Proteomics (2005) 10.67
Parts per million mass accuracy on an Orbitrap mass spectrometer via lock mass injection into a C-trap. Mol Cell Proteomics (2005) 10.60
Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature (2008) 10.28
The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol (2007) 10.24
Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes. Nature (2010) 9.95
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (2010) 9.78
Proteomic characterization of the human centrosome by protein correlation profiling. Nature (2003) 8.74
Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. Sci Signal (2010) 8.61
Mass spectrometry-based proteomics turns quantitative. Nat Chem Biol (2005) 7.52
Nucleolar proteome dynamics. Nature (2005) 7.32
Directed proteomic analysis of the human nucleolus. Curr Biol (2002) 7.04
GoPubMed: exploring PubMed with the Gene Ontology. Nucleic Acids Res (2005) 6.95
Identification of a gene causing human cytochrome c oxidase deficiency by integrative genomics. Proc Natl Acad Sci U S A (2003) 6.87
Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria. Cell (2003) 6.77
Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4. Cell (2007) 6.62
An empirical framework for binary interactome mapping. Nat Methods (2008) 6.59
BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals. Nat Methods (2008) 6.51
Mechanism of regulation of WAVE1-induced actin nucleation by Rac1 and Nck. Nature (2002) 6.26
Large-scale proteomic analysis of the human spliceosome. Genome Res (2002) 5.75
Specificity in Toll-like receptor signalling through distinct effector functions of TRAF3 and TRAF6. Nature (2005) 5.72
Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry. Nature (2002) 5.48
Deep proteome and transcriptome mapping of a human cancer cell line. Mol Syst Biol (2011) 5.48
Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle. Mol Cell (2008) 5.38
Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Nat Biotechnol (2004) 5.22
A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC). Nat Protoc (2006) 5.21
Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway. Mol Cell Proteomics (2005) 5.07
Higher-energy C-trap dissociation for peptide modification analysis. Nat Methods (2007) 5.04
SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function. Cell (2008) 5.02
Unbiased quantitative proteomics of lipid rafts reveals high specificity for signaling factors. Proc Natl Acad Sci U S A (2003) 4.87
A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics. Nat Protoc (2009) 4.84
Trypsin cleaves exclusively C-terminal to arginine and lysine residues. Mol Cell Proteomics (2004) 4.79
Proteome-wide analysis of chaperonin-dependent protein folding in Escherichia coli. Cell (2005) 4.78
A dual pressure linear ion trap Orbitrap instrument with very high sequencing speed. Mol Cell Proteomics (2009) 4.75
Systematic analysis of human protein complexes identifies chromosome segregation proteins. Science (2010) 4.69
PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites. Genome Biol (2007) 4.66
A mammalian organelle map by protein correlation profiling. Cell (2006) 4.54
A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. Mol Cell Proteomics (2011) 4.40
The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nat Methods (2013) 4.34
Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers. Cell (2010) 4.31
Cortical constriction during abscission involves helices of ESCRT-III-dependent filaments. Science (2011) 4.26
The ABC's (and XYZ's) of peptide sequencing. Nat Rev Mol Cell Biol (2004) 4.24
Human Proteinpedia enables sharing of human protein data. Nat Biotechnol (2008) 4.21
Paraspeckles: a novel nuclear domain. Curr Biol (2002) 4.19
Quantitative proteomics reveals subset-specific viral recognition in dendritic cells. Immunity (2010) 4.03
Genome-scale RNAi profiling of cell division in human tissue culture cells. Nat Cell Biol (2007) 3.91
Axin-mediated CKI phosphorylation of beta-catenin at Ser 45: a molecular switch for the Wnt pathway. Genes Dev (2002) 3.80
The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins. Genome Biol (2006) 3.79
Protein abundance profiling of the Escherichia coli cytosol. BMC Genomics (2008) 3.78
Decoding signalling networks by mass spectrometry-based proteomics. Nat Rev Mol Cell Biol (2010) 3.78
Proteome analysis of separated male and female gametocytes reveals novel sex-specific Plasmodium biology. Cell (2005) 3.77
Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer. Mol Cell Proteomics (2011) 3.75
An endoribonuclease-prepared siRNA screen in human cells identifies genes essential for cell division. Nature (2004) 3.69
Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions. J Cell Biol (2010) 3.61
Precision mapping of an in vivo N-glycoproteome reveals rigid topological and sequence constraints. Cell (2010) 3.60
Stable isotope labeling by amino acids in cell culture (SILAC) and proteome quantitation of mouse embryonic stem cells to a depth of 5,111 proteins. Mol Cell Proteomics (2007) 3.60
Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins. Mol Cell Proteomics (2012) 3.57
Combination of FASP and StageTip-based fractionation allows in-depth analysis of the hippocampal membrane proteome. J Proteome Res (2009) 3.56
A genome-scale RNAi screen for Oct4 modulators defines a role of the Paf1 complex for embryonic stem cell identity. Cell Stem Cell (2009) 3.55
Analysis of nucleolar protein dynamics reveals the nuclear degradation of ribosomal proteins. Curr Biol (2007) 3.55
A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling. Nat Biotechnol (2003) 3.54
LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation. BMC Struct Biol (2006) 3.54
A systematic mammalian genetic interaction map reveals pathways underlying ricin susceptibility. Cell (2013) 3.53
More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS. J Proteome Res (2011) 3.53
System-wide changes to SUMO modifications in response to heat shock. Sci Signal (2009) 3.50
Phosphotyrosine interactome of the ErbB-receptor kinase family. Mol Syst Biol (2005) 3.48
Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation. Proc Natl Acad Sci U S A (2004) 3.43
Mass spectrometric-based approaches in quantitative proteomics. Methods (2003) 3.38
Mechanism of divergent growth factor effects in mesenchymal stem cell differentiation. Science (2005) 3.37
Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system. Genome Biol (2006) 3.34
Arginine methylation at histone H3R2 controls deposition of H3K4 trimethylation. Nature (2007) 3.32
KNL-1 directs assembly of the microtubule-binding interface of the kinetochore in C. elegans. Genes Dev (2003) 3.29
A protein interaction network links GIT1, an enhancer of huntingtin aggregation, to Huntington's disease. Mol Cell (2004) 3.26
Nucleosome-interacting proteins regulated by DNA and histone methylation. Cell (2010) 3.25
Quantitative, high-resolution proteomics for data-driven systems biology. Annu Rev Biochem (2011) 3.19
Chromatin-Remodeling Components of the BAF Complex Facilitate Reprogramming. Cell (2010) 3.08
STITCH 2: an interaction network database for small molecules and proteins. Nucleic Acids Res (2009) 3.06
ERCC1/XPF removes the 3' overhang from uncapped telomeres and represses formation of telomeric DNA-containing double minute chromosomes. Mol Cell (2003) 3.01
Defining the transcriptome and proteome in three functionally different human cell lines. Mol Syst Biol (2010) 3.00
Regulation of ubiquitin-binding proteins by monoubiquitination. Nat Cell Biol (2006) 2.99
Decoding human cytomegalovirus. Science (2012) 2.98
HAUS, the 8-subunit human Augmin complex, regulates centrosome and spindle integrity. Curr Biol (2009) 2.98
Super-SILAC mix for quantitative proteomics of human tumor tissue. Nat Methods (2010) 2.95