Published in Bioinformatics on January 06, 2009
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Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell (2009) 6.54
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CTCF physically links cohesin to chromatin. Proc Natl Acad Sci U S A (2008) 4.89
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The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nat Methods (2013) 4.34
High-throughput generation of selected reaction-monitoring assays for proteins and proteomes. Nat Methods (2009) 4.17
The need for guidelines in publication of peptide and protein identification data: Working Group on Publication Guidelines for Peptide and Protein Identification Data. Mol Cell Proteomics (2004) 4.15
PTEN-deficient intestinal stem cells initiate intestinal polyposis. Nat Genet (2007) 4.09
Integrated genomic and proteomic analyses of gene expression in Mammalian cells. Mol Cell Proteomics (2004) 4.09
Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans. Nature (2009) 4.07
Rewiring of genetic networks in response to DNA damage. Science (2010) 4.03
Identification of cross-linked peptides from large sequence databases. Nat Methods (2008) 4.03
Proteome organization in a genome-reduced bacterium. Science (2009) 3.97
Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol Cell Proteomics (2002) 3.89
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SuperHirn - a novel tool for high resolution LC-MS-based peptide/protein profiling. Proteomics (2007) 3.60
A systematic approach to modeling, capturing, and disseminating proteomics experimental data. Nat Biotechnol (2003) 3.57
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Mechanistic rationale for inhibition of poly(ADP-ribose) polymerase in ETS gene fusion-positive prostate cancer. Cancer Cell (2011) 3.53
Options and considerations when selecting a quantitative proteomics strategy. Nat Biotechnol (2010) 3.51
Reporting protein identification data: the next generation of guidelines. Mol Cell Proteomics (2006) 3.50
Reproducible isolation of distinct, overlapping segments of the phosphoproteome. Nat Methods (2007) 3.46
Systems biology, proteomics, and the future of health care: toward predictive, preventative, and personalized medicine. J Proteome Res (2004) 3.46
Probing native protein structures by chemical cross-linking, mass spectrometry, and bioinformatics. Mol Cell Proteomics (2010) 3.44
Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach. Proc Natl Acad Sci U S A (2012) 3.42
The long noncoding RNA SChLAP1 promotes aggressive prostate cancer and antagonizes the SWI/SNF complex. Nat Genet (2013) 3.39
A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. Mol Cell Proteomics (2011) 3.37
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A predictive model for transcriptional control of physiology in a free living cell. Cell (2007) 3.35
A high-quality catalog of the Drosophila melanogaster proteome. Nat Biotechnol (2007) 3.34
Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry. Anal Chem (2003) 3.33
Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis. Genes Dev (2009) 3.31
Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring. Mol Cell Proteomics (2008) 3.29
Orm family proteins mediate sphingolipid homeostasis. Nature (2010) 3.29
Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells. Cell (2012) 3.26
Contrasting mechanisms of interferon-α inhibition by intravenous immunoglobulin after induction by immune complexes versus Toll-like receptor agonists. Arthritis Rheum (2013) 3.20
A database of mass spectrometric assays for the yeast proteome. Nat Methods (2008) 3.19
PASSEL: the PeptideAtlas SRMexperiment library. Proteomics (2012) 3.14
mProphet: automated data processing and statistical validation for large-scale SRM experiments. Nat Methods (2011) 3.10
Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes. PLoS Biol (2009) 3.09
ProbID: a probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data. Proteomics (2002) 3.01
Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry. Mol Cell Proteomics (2009) 2.96
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An integrated workflow for charting the human interaction proteome: insights into the PP2A system. Mol Syst Biol (2009) 2.92
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A molecular correlate to the Gleason grading system for prostate adenocarcinoma. Proc Natl Acad Sci U S A (2006) 2.89
iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates. Mol Cell Proteomics (2011) 2.88
Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry. Nat Methods (2005) 2.87
Analysis, statistical validation and dissemination of large-scale proteomics datasets generated by tandem MS. Drug Discov Today (2004) 2.82
The implications of proteolytic background for shotgun proteomics. Mol Cell Proteomics (2007) 2.82
Tissue-dependent paired expression of miRNAs. Nucleic Acids Res (2007) 2.82
A human proteome detection and quantitation project. Mol Cell Proteomics (2009) 2.80
The standard protein mix database: a diverse data set to assist in the production of improved Peptide and protein identification software tools. J Proteome Res (2007) 2.77
Dysregulated gene expression networks in human acute myelogenous leukemia stem cells. Proc Natl Acad Sci U S A (2009) 2.76
Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea. Genome Res (2004) 2.75
Mass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins. Nat Biotechnol (2009) 2.70
Direct transfer of alpha-synuclein from neuron to astroglia causes inflammatory responses in synucleinopathies. J Biol Chem (2010) 2.67
Mutant huntingtin impairs axonal trafficking in mammalian neurons in vivo and in vitro. Mol Cell Biol (2004) 2.65
Trifurcate feed-forward regulation of age-dependent cell death involving miR164 in Arabidopsis. Science (2009) 2.63
A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis. Nature (2013) 2.61