Published in J Proteome Res on December 21, 2012
Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins. J Proteome Res (2013) 1.76
Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins. Nat Methods (2013) 1.54
State of the human proteome in 2013 as viewed through PeptideAtlas: comparing the kidney, urine, and plasma proteomes for the biology- and disease-driven Human Proteome Project. J Proteome Res (2013) 1.52
A repository of assays to quantify 10,000 human proteins by SWATH-MS. Sci Data (2014) 1.32
The Human Eye Proteome Project: perspectives on an emerging proteome. Proteomics (2013) 1.23
Direct detection of alternative open reading frames translation products in human significantly expands the proteome. PLoS One (2013) 1.14
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Exploring the potential of public proteomics data. Proteomics (2015) 0.90
Distinct splice variants and pathway enrichment in the cell-line models of aggressive human breast cancer subtypes. J Proteome Res (2013) 0.90
MOPED enables discoveries through consistently processed proteomics data. J Proteome Res (2013) 0.89
Developing top down proteomics to maximize proteome and sequence coverage from cells and tissues. Curr Opin Chem Biol (2013) 0.85
Identifying novel biomarkers through data mining-a realistic scenario? Proteomics Clin Appl (2015) 0.84
The strategy, organization, and progress of the HUPO Human Proteome Project. J Proteomics (2013) 0.82
Novel bioinformatics method for identification of genome-wide non-canonical spliced regions using RNA-Seq data. PLoS One (2014) 0.82
The human eye proteome project. Proteomics (2013) 0.82
Structural Bioinformatics Inspection of neXtProt PE5 Proteins in the Human Proteome. J Proteome Res (2015) 0.80
Plasma proteomics, the Human Proteome Project, and cancer-associated alternative splice variant proteins. Biochim Biophys Acta (2013) 0.80
Identification of multiple metabolic enzymes from mice cochleae tissue using a novel functional proteomics technology. PLoS One (2015) 0.80
Identification of functional metabolic biomarkers from lung cancer patient serum using PEP technology. Biomark Res (2016) 0.78
Priorities and trends in the study of proteins in eye research, 1924-2014. Proteomics Clin Appl (2015) 0.78
2017 update on the relationship between diabetes and colorectal cancer: epidemiology, potential molecular mechanisms and therapeutic implications. Oncotarget (2017) 0.77
Detection of Missing Proteins Using the PRIDE Database as a Source of Mass Spectrometry Evidence. J Proteome Res (2016) 0.77
The Human Skeletal Muscle Proteome Project: a reappraisal of the current literature. J Cachexia Sarcopenia Muscle (2016) 0.75
The potential clinical impact of the release of two drafts of the human proteome. Expert Rev Proteomics (2015) 0.75
Systematic identification of single amino acid variants in glioma stem-cell-derived chromosome 19 proteins. J Proteome Res (2014) 0.75
Identifying the missing proteins in human proteome by biological language model. BMC Syst Biol (2016) 0.75
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature (2002) 37.66
Integration of biological networks and gene expression data using Cytoscape. Nat Protoc (2007) 27.10
Global mapping of the yeast genetic interaction network. Science (2004) 21.34
International network of cancer genome projects. Nature (2010) 20.35
The genetic landscape of a cell. Science (2010) 16.52
Functional impact of global rare copy number variation in autism spectrum disorders. Nature (2010) 14.66
Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature (2009) 12.58
The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res (2010) 10.97
SIN1/MIP1 maintains rictor-mTOR complex integrity and regulates Akt phosphorylation and substrate specificity. Cell (2006) 10.50
MeCP2, a key contributor to neurological disease, activates and represses transcription. Science (2008) 10.11
Cytoscape Web: an interactive web-based network browser. Bioinformatics (2010) 10.03
The BioPAX community standard for pathway data sharing. Nat Biotechnol (2010) 9.19
Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res (2010) 9.18
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
Deubiquitination of p53 by HAUSP is an important pathway for p53 stabilization. Nature (2002) 7.71
A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science (2001) 7.08
Enrichment map: a network-based method for gene-set enrichment visualization and interpretation. PLoS One (2010) 6.61
A travel guide to Cytoscape plugins. Nat Methods (2012) 6.53
PreBIND and Textomy--mining the biomedical literature for protein-protein interactions using a support vector machine. BMC Bioinformatics (2003) 6.31
Hepatic gene expression discriminates responders and nonresponders in treatment of chronic hepatitis C viral infection. Gastroenterology (2005) 5.33
PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nat Methods (2011) 5.01
ARF-BP1/Mule is a critical mediator of the ARF tumor suppressor. Cell (2005) 4.60
A structural mechanism of integrin alpha(IIb)beta(3) "inside-out" activation as regulated by its cytoplasmic face. Cell (2002) 4.57
The mammalian target of rapamycin complex 2 controls folding and stability of Akt and protein kinase C. EMBO J (2008) 4.49
Chemical screening methods to identify ligands that promote protein stability, protein crystallization, and structure determination. Proc Natl Acad Sci U S A (2006) 4.45
Nanog and Oct4 associate with unique transcriptional repression complexes in embryonic stem cells. Nat Cell Biol (2008) 4.30
Negative regulation of the deacetylase SIRT1 by DBC1. Nature (2008) 4.29
Human Proteinpedia enables sharing of human protein data. Nat Biotechnol (2008) 4.21
Subgroup-specific structural variation across 1,000 medulloblastoma genomes. Nature (2012) 4.13
Comprehensive identification of mutational cancer driver genes across 12 tumor types. Sci Rep (2013) 3.92
Erk associates with and primes GSK-3beta for its inactivation resulting in upregulation of beta-catenin. Mol Cell (2005) 3.89
Autophosphorylation of the DNA-dependent protein kinase catalytic subunit is required for rejoining of DNA double-strand breaks. Genes Dev (2002) 3.83
Purification and functional characterization of the human N-CoR complex: the roles of HDAC3, TBL1 and TBLR1. EMBO J (2003) 3.72
The ATRX syndrome protein forms a chromatin-remodeling complex with Daxx and localizes in promyelocytic leukemia nuclear bodies. Proc Natl Acad Sci U S A (2003) 3.52
An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysis. Proteomics (2005) 3.51
SMC1 is a downstream effector in the ATM/NBS1 branch of the human S-phase checkpoint. Genes Dev (2002) 3.49
A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. Mol Cell Proteomics (2011) 3.37
SCFbeta-TRCP links Chk1 signaling to degradation of the Cdc25A protein phosphatase. Genes Dev (2003) 3.35
PTOP interacts with POT1 and regulates its localization to telomeres. Nat Cell Biol (2004) 3.33
cPath: open source software for collecting, storing, and querying biological pathways. BMC Bioinformatics (2006) 3.24
Cell cycle dependence of DNA-dependent protein kinase phosphorylation in response to DNA double strand breaks. J Biol Chem (2005) 3.19
A specificity map for the PDZ domain family. PLoS Biol (2008) 3.16
Delineation of two clinically and molecularly distinct subgroups of posterior fossa ependymoma. Cancer Cell (2011) 3.11
The SRC-3/AIB1 coactivator is degraded in a ubiquitin- and ATP-independent manner by the REGgamma proteasome. Cell (2006) 3.09
Parc: a cytoplasmic anchor for p53. Cell (2003) 3.06
In situ proteolysis for protein crystallization and structure determination. Nat Methods (2007) 3.05
Acetylation of Smc3 by Eco1 is required for S phase sister chromatid cohesion in both human and yeast. Mol Cell (2008) 3.01
DDX1, DDX21, and DHX36 helicases form a complex with the adaptor molecule TRIF to sense dsRNA in dendritic cells. Immunity (2011) 3.01
A novel family of sequence-specific endoribonucleases associated with the clustered regularly interspaced short palindromic repeats. J Biol Chem (2008) 3.00
Pathway information for systems biology. FEBS Lett (2005) 2.97
Analysis of the human endogenous coregulator complexome. Cell (2011) 2.97
Selective phosphorylations of the SRC-3/AIB1 coactivator integrate genomic reponses to multiple cellular signaling pathways. Mol Cell (2004) 2.95
Germ-line DNA copy number variation frequencies in a large North American population. Hum Genet (2007) 2.94
Too many roads not taken. Nature (2011) 2.93
Kindlin-2 (Mig-2): a co-activator of beta3 integrins. J Cell Biol (2008) 2.88
SeqHound: biological sequence and structure database as a platform for bioinformatics research. BMC Bioinformatics (2002) 2.84
Medicine needs evolution. Science (2006) 2.83
Telosome, a mammalian telomere-associated complex formed by multiple telomeric proteins. J Biol Chem (2004) 2.76
GeneMANIA prediction server 2013 update. Nucleic Acids Res (2013) 2.74
A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair. Mol Microbiol (2010) 2.70
ICBP90, a novel methyl K9 H3 binding protein linking protein ubiquitination with heterochromatin formation. Mol Cell Biol (2007) 2.69
Quantitative analysis of fitness and genetic interactions in yeast on a genome scale. Nat Methods (2010) 2.67
Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study. Nat Biotechnol (2006) 2.66
Crystal structure of the CorA Mg2+ transporter. Nature (2006) 2.64
NetPath: a public resource of curated signal transduction pathways. Genome Biol (2010) 2.62
The mitotic spindle is required for loading of the DASH complex onto the kinetochore. Genes Dev (2002) 2.60
clusterMaker: a multi-algorithm clustering plugin for Cytoscape. BMC Bioinformatics (2011) 2.56
Structural basis for the autoinhibition of talin in regulating integrin activation. Mol Cell (2008) 2.53
Mechanism of magnesium activation of calcium-activated potassium channels. Nature (2002) 2.50
N-CoR mediates DNA methylation-dependent repression through a methyl CpG binding protein Kaiso. Mol Cell (2003) 2.47
The protein kinase CK2 facilitates repair of chromosomal DNA single-strand breaks. Cell (2004) 2.46
Regulation of SRC-3 (pCIP/ACTR/AIB-1/RAC-3/TRAM-1) Coactivator activity by I kappa B kinase. Mol Cell Biol (2002) 2.45
Differential protein expression profiling by iTRAQ-2DLC-MS/MS of lung cancer cells undergoing epithelial-mesenchymal transition reveals a migratory/invasive phenotype. J Proteome Res (2006) 2.43
Computational prediction of protein-protein interactions. Mol Biotechnol (2007) 2.35
The human proteome project: current state and future direction. Mol Cell Proteomics (2011) 2.34
The lipid whisker model of the structure of oxidized cell membranes. J Biol Chem (2007) 2.31
Positive selection of tyrosine loss in metazoan evolution. Science (2009) 2.28
The Beta-Carotene and Retinol Efficacy Trial: incidence of lung cancer and cardiovascular disease mortality during 6-year follow-up after stopping beta-carotene and retinol supplements. J Natl Cancer Inst (2004) 2.26
Aspartate-glutamate-alanine-histidine box motif (DEAH)/RNA helicase A helicases sense microbial DNA in human plasmacytoid dendritic cells. Proc Natl Acad Sci U S A (2010) 2.25
Cohesin acetylation speeds the replication fork. Nature (2009) 2.23
The MIG-2/integrin interaction strengthens cell-matrix adhesion and modulates cell motility. J Biol Chem (2007) 2.20
Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases. Sci Signal (2009) 2.16
The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome. Nat Biotechnol (2012) 2.14
ConceptGen: a gene set enrichment and gene set relation mapping tool. Bioinformatics (2009) 2.11
Genome-wide analysis of substrate specificities of the Escherichia coli haloacid dehalogenase-like phosphatase family. J Biol Chem (2006) 2.10
A proteomic analysis of ataxia telangiectasia-mutated (ATM)/ATM-Rad3-related (ATR) substrates identifies the ubiquitin-proteasome system as a regulator for DNA damage checkpoints. J Biol Chem (2007) 2.09
Characterization of KRAS rearrangements in metastatic prostate cancer. Cancer Discov (2011) 2.02
Trim24 targets endogenous p53 for degradation. Proc Natl Acad Sci U S A (2009) 2.00
Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics. Genome Biol (2006) 1.98
An NMR approach to structural proteomics. Proc Natl Acad Sci U S A (2002) 1.95
Structure of the p53 binding domain of HAUSP/USP7 bound to Epstein-Barr nuclear antigen 1 implications for EBV-mediated immortalization. Mol Cell (2005) 1.92
Protein folding: defining a "standard" set of experimental conditions and a preliminary kinetic data set of two-state proteins. Protein Sci (2005) 1.91
Guidelines for reporting the use of mass spectrometry in proteomics. Nat Biotechnol (2008) 1.90
MSH2 and ATR form a signaling module and regulate two branches of the damage response to DNA methylation. Proc Natl Acad Sci U S A (2003) 1.90
Structural and chemical profiling of the human cytosolic sulfotransferases. PLoS Biol (2007) 1.90
Irgm1 protects hematopoietic stem cells by negative regulation of IFN signaling. Blood (2011) 1.86
Requirement of TRAP/mediator for both activator-independent and activator-dependent transcription in conjunction with TFIID-associated TAF(II)s. Mol Cell Biol (2002) 1.86
Rapid evolution of functional complexity in a domain family. Sci Signal (2009) 1.85
VEGF-integrin interplay controls tumor growth and vascularization. Proc Natl Acad Sci U S A (2005) 1.84