Published in Mol Cell Proteomics on July 18, 2003
Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea. Genome Biol (2009) 1.69
General transcription factor specified global gene regulation in archaea. Proc Natl Acad Sci U S A (2007) 1.42
TFB1 or TFB2 is sufficient for Thermococcus kodakaraensis viability and for basal transcription in vitro. J Mol Biol (2006) 1.36
Meta-analysis of untargeted metabolomic data from multiple profiling experiments. Nat Protoc (2012) 1.29
Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1. Genome Biol (2004) 1.25
Low-pass sequencing for microbial comparative genomics. BMC Genomics (2004) 1.11
metaXCMS: second-order analysis of untargeted metabolomics data. Anal Chem (2010) 1.10
Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage. J Proteome Res (2008) 1.03
Post-genomics of the model haloarchaeon Halobacterium sp. NRC-1. Saline Systems (2006) 1.03
Archaeal RNA polymerase and transcription regulation. Crit Rev Biochem Mol Biol (2011) 0.92
High-throughput database search and large-scale negative polarity liquid chromatography-tandem mass spectrometry with ultraviolet photodissociation for complex proteomic samples. Mol Cell Proteomics (2013) 0.89
Proteomic analysis of acidic chaperones, and stress proteins in extreme halophile Halobacterium NRC-1: a comparative proteomic approach to study heat shock response. Proteome Sci (2006) 0.86
Functional analysis of the three TATA binding protein homologs in Methanosarcina acetivorans. J Bacteriol (2010) 0.85
Identification of secreted glycoproteins of human prostate and bladder stromal cells by comparative quantitative proteomics. Prostate (2009) 0.83
Systematic investigation of lycopene effects in LNCaP cells by use of novel large-scale proteomic analysis software. Proteomics Clin Appl (2007) 0.83
Transcription Regulation in Archaea. J Bacteriol (2016) 0.78
Metabolic capabilities and systems fluctuations in Haloarcula marismortui revealed by integrative genomics and proteomics analyses. J Proteome Res (2011) 0.78
The effects of extremes of pH on the growth and transcriptomic profiles of three haloarchaea. F1000Res (2014) 0.77
Environmental Pressure May Change the Composition Protein Disorder in Prokaryotes. PLoS One (2015) 0.76
Effects of intracellular Mn on the radiation resistance of the halophilic archaeon Halobacterium salinarum. Extremophiles (2013) 0.75
Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res (2003) 103.76
Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem (2002) 35.30
A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem (2003) 29.58
A distinct lineage of CD4 T cells regulates tissue inflammation by producing interleukin 17. Nat Immunol (2005) 27.17
Integration of biological networks and gene expression data using Cytoscape. Nat Protoc (2007) 27.10
Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science (2002) 20.59
Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science (2010) 18.45
Direct multiplexed measurement of gene expression with color-coded probe pairs. Nat Biotechnol (2008) 15.90
A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotechnol (2004) 11.42
The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol (2007) 10.24
A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol Syst Biol (2005) 9.81
A genomic regulatory network for development. Science (2002) 9.67
Mass spectrometry and protein analysis. Science (2006) 8.05
The PeptideAtlas project. Nucleic Acids Res (2006) 7.87
Computational prediction of proteotypic peptides for quantitative proteomics. Nat Biotechnol (2006) 7.56
Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry. Nat Biotechnol (2003) 6.86
Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell (2009) 6.54
Selected reaction monitoring for quantitative proteomics: a tutorial. Mol Syst Biol (2008) 6.38
Interpretation of shotgun proteomic data: the protein inference problem. Mol Cell Proteomics (2005) 6.28
PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO Rep (2008) 6.10
The program of androgen-responsive genes in neoplastic prostate epithelium. Proc Natl Acad Sci U S A (2002) 5.98
Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol Cell Proteomics (2012) 5.95
Crucial step in cholesterol homeostasis: sterols promote binding of SCAP to INSIG-1, a membrane protein that facilitates retention of SREBPs in ER. Cell (2002) 5.70
An essential switch in subunit composition of a chromatin remodeling complex during neural development. Neuron (2007) 5.35
The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Genome Biol (2006) 5.22
Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat Methods (2007) 5.10
A guided tour of the Trans-Proteomic Pipeline. Proteomics (2010) 5.09
A type VI secretion system of Pseudomonas aeruginosa targets a toxin to bacteria. Cell Host Microbe (2010) 4.98
Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach. Proc Natl Acad Sci U S A (2002) 4.96
Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. Nat Methods (2012) 4.93
Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biol (2004) 4.91
CTCF physically links cohesin to chromatin. Proc Natl Acad Sci U S A (2008) 4.89
High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites. Mol Cell Proteomics (2007) 4.72
Analysis of protein complexes using mass spectrometry. Nat Rev Mol Cell Biol (2007) 4.70
Scoring proteomes with proteotypic peptide probes. Nat Rev Mol Cell Biol (2005) 4.63
Visualization of omics data for systems biology. Nat Methods (2010) 4.59
The quantitative proteome of a human cell line. Mol Syst Biol (2011) 4.57
Human Plasma PeptideAtlas. Proteomics (2005) 4.52
Integrated barcode chips for rapid, multiplexed analysis of proteins in microliter quantities of blood. Nat Biotechnol (2008) 4.40
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
The Gaggle: an open-source software system for integrating bioinformatics software and data sources. BMC Bioinformatics (2006) 4.05
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
Systems medicine: the future of medical genomics and healthcare. Genome Med (2009) 3.85
Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics (2007) 3.74
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
The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics. Nat Biotechnol (2007) 3.55
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
A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. Mol Cell Proteomics (2011) 3.37
An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. J Proteome Res (2008) 3.36
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
A database of mass spectrometric assays for the yeast proteome. Nat Methods (2008) 3.19
The B7 family member B7-H6 is a tumor cell ligand for the activating natural killer cell receptor NKp30 in humans. J Exp Med (2009) 3.17
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
Genetic basis of proteome variation in yeast. Nat Genet (2007) 3.04
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
Peroxiredoxins are conserved markers of circadian rhythms. Nature (2012) 2.95
A data integration methodology for systems biology. Proc Natl Acad Sci U S A (2005) 2.93
An integrated workflow for charting the human interaction proteome: insights into the PP2A system. Mol Syst Biol (2009) 2.92
Mass spectrometry in high-throughput proteomics: ready for the big time. Nat Methods (2010) 2.91
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
Growth phenotypes of Pseudomonas aeruginosa lasR mutants adapted to the airways of cystic fibrosis patients. Mol Microbiol (2007) 2.87
Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry. Nat Methods (2005) 2.87