Published in J Proteome Res on January 01, 2006
ProteoWizard: open source software for rapid proteomics tools development. Bioinformatics (2008) 9.47
A guided tour of the Trans-Proteomic Pipeline. Proteomics (2010) 5.09
Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ. Mol Cell Proteomics (2014) 5.09
A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. J Proteomics (2010) 3.78
Proteomics: a pragmatic perspective. Nat Biotechnol (2010) 2.81
A mouse to human search for plasma proteome changes associated with pancreatic tumor development. PLoS Med (2008) 2.31
Elafin is a biomarker of graft-versus-host disease of the skin. Sci Transl Med (2010) 2.08
LabKey Server: an open source platform for scientific data integration, analysis and collaboration. BMC Bioinformatics (2011) 1.94
openBIS: a flexible framework for managing and analyzing complex data in biology research. BMC Bioinformatics (2011) 1.91
Dynamic changes in histone acetylation regulate origins of DNA replication. Nat Struct Mol Biol (2010) 1.82
Proteomic analysis of ovarian cancer cells reveals dynamic processes of protein secretion and shedding of extra-cellular domains. PLoS One (2008) 1.72
Discovery and validation of graft-versus-host disease biomarkers. Blood (2012) 1.67
Precursor-ion mass re-estimation improves peptide identification on hybrid instruments. J Proteome Res (2008) 1.53
MASPECTRAS: a platform for management and analysis of proteomics LC-MS/MS data. BMC Bioinformatics (2007) 1.34
YPED: a web-accessible database system for protein expression analysis. J Proteome Res (2007) 1.28
Comprehensive proteome analysis of an Apc mouse model uncovers proteins associated with intestinal tumorigenesis. Cancer Prev Res (Phila) (2009) 1.27
Application of serum proteomics to the Women's Health Initiative conjugated equine estrogens trial reveals a multitude of effects relevant to clinical findings. Genome Med (2009) 1.21
Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics. Proteomics Clin Appl (2015) 1.19
Integrated proteomic analysis of human cancer cells and plasma from tumor bearing mice for ovarian cancer biomarker discovery. PLoS One (2009) 1.17
iLAP: a workflow-driven software for experimental protocol development, data acquisition and analysis. BMC Bioinformatics (2009) 1.14
Tumor microenvironment-derived proteins dominate the plasma proteome response during breast cancer induction and progression. Cancer Res (2011) 1.14
A proteomic investigation of ligand-dependent HSP90 complexes reveals CHORDC1 as a novel ADP-dependent HSP90-interacting protein. Mol Cell Proteomics (2009) 1.11
Architecture of the trypanosome RNA editing accessory complex, MRB1. Nucleic Acids Res (2012) 1.10
Postmenopausal estrogen and progestin effects on the serum proteome. Genome Med (2009) 1.07
The development of an integrated platform to identify breast cancer glycoproteome changes in human serum. J Chromatogr A (2009) 1.06
AKAP2 anchors PKA with aquaporin-0 to support ocular lens transparency. EMBO Mol Med (2011) 1.05
Genomic and proteomic biomarkers for cancer: a multitude of opportunities. Biochim Biophys Acta (2009) 1.03
In situ proteomic analysis of human breast cancer epithelial cells using laser capture microdissection: annotation by protein set enrichment analysis and gene ontology. Mol Cell Proteomics (2010) 1.03
The plasma proteome, adductome and idiosyncratic toxicity in toxicoproteomics research. Brief Funct Genomic Proteomic (2008) 1.01
Increased plasma levels of the APC-interacting protein MAPRE1, LRG1, and IGFBP2 preceding a diagnosis of colorectal cancer in women. Cancer Prev Res (Phila) (2012) 0.99
Autoantibody signatures involving glycolysis and splicesome proteins precede a diagnosis of breast cancer among postmenopausal women. Cancer Res (2012) 0.98
HLA-F complex without peptide binds to MHC class I protein in the open conformer form. J Immunol (2010) 0.98
The Zinc-Finger Antiviral Protein ZAP Inhibits LINE and Alu Retrotransposition. PLoS Genet (2015) 0.97
On-line 1D and 2D porous layer open tubular/LC-ESI-MS using 10-microm-i.d. poly(styrene-divinylbenzene) columns for ultrasensitive proteomic analysis. Anal Chem (2007) 0.97
Voa1p functions in V-ATPase assembly in the yeast endoplasmic reticulum. Mol Biol Cell (2008) 0.96
LabKey Server NAb: a tool for analyzing, visualizing and sharing results from neutralizing antibody assays. BMC Immunol (2011) 0.96
Lapatinib-binding protein kinases in the African trypanosome: identification of cellular targets for kinase-directed chemical scaffolds. PLoS One (2013) 0.96
SeMoP: a new computational strategy for the unrestricted search for modified peptides using LC-MS/MS data. J Proteome Res (2008) 0.96
Staphylococcus aureus elicits marked alterations in the airway proteome during early pneumonia. Infect Immun (2008) 0.93
Plasma proteome profiles associated with inflammation, angiogenesis, and cancer. PLoS One (2011) 0.93
A conserved deubiquitinating enzyme controls cell growth by regulating RNA polymerase I stability. Cell Rep (2012) 0.92
Two-dimensional strong cation exchange/porous layer open tubular/mass spectrometry for ultratrace proteomic analysis using a 10 microm id poly(styrene- divinylbenzene) porous layer open tubular column with an on-line triphasic trapping column. Electrophoresis (2008) 0.92
Novel proteins associated with risk for coronary heart disease or stroke among postmenopausal women identified by in-depth plasma proteome profiling. Genome Med (2010) 0.92
Use of cancer-specific yeast-secreted in vivo biotinylated recombinant antibodies for serum biomarker discovery. J Transl Med (2008) 0.91
FCH domain only-2 organizes clathrin-coated structures and interacts with Disabled-2 for low-density lipoprotein receptor endocytosis. Mol Biol Cell (2012) 0.90
Proteome and transcriptome profiles of a Her2/Neu-driven mouse model of breast cancer. Proteomics Clin Appl (2011) 0.89
Microproteomic analysis of 10,000 laser captured microdissected breast tumor cells using short-range sodium dodecyl sulfate-polyacrylamide gel electrophoresis and porous layer open tubular liquid chromatography tandem mass spectrometry. J Chromatogr A (2011) 0.87
Antagonism of the protein kinase R pathway by the guinea pig cytomegalovirus US22-family gene gp145. Virology (2012) 0.86
Electrospray mass spectrometry for quantitative plasma proteome analysis. Methods Mol Biol (2009) 0.84
A Deeper Look into Comet-Implementation and Features. J Am Soc Mass Spectrom (2015) 0.84
An evolving computational platform for biological mass spectrometry: workflows, statistics and data mining with MASSyPup64. PeerJ (2015) 0.84
Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress. Mol Cell Proteomics (2011) 0.83
Automated platform for fractionation of human plasma glycoproteome in clinical proteomics. Anal Chem (2010) 0.83
Proteomic risk markers for coronary heart disease and stroke: validation and mediation of randomized trial hormone therapy effects on these diseases. Genome Med (2013) 0.82
Linker for activation of T-cell family member2 (LAT2) a lipid raft adaptor protein for AKT signaling, is an early mediator of alkylphospholipid anti-leukemic activity. Mol Cell Proteomics (2012) 0.82
Extensive gene acquisition in the extremely psychrophilic bacterial species Psychroflexus torquis and the link to sea-ice ecosystem specialism. Genome Biol Evol (2014) 0.82
SpyA is a membrane-bound ADP-ribosyltransferase of Streptococcus pyogenes which modifies a streptococcal peptide, SpyB. Mol Microbiol (2012) 0.81
Quantitative serum proteomics using dual stable isotope coding and nano LC-MS/MSMS. J Proteome Res (2009) 0.81
An Autoimmune Response Signature Associated with the Development of Triple-Negative Breast Cancer Reflects Disease Pathogenesis. Cancer Res (2015) 0.80
Impact of protein stability, cellular localization, and abundance on proteomic detection of tumor-derived proteins in plasma. PLoS One (2011) 0.80
Global genome response of Escherichia coli O157∶H7 Sakai during dynamic changes in growth kinetics induced by an abrupt downshift in water activity. PLoS One (2014) 0.80
The Aspergillus fumigatus sitA Phosphatase Homologue Is Important for Adhesion, Cell Wall Integrity, Biofilm Formation, and Virulence. Eukaryot Cell (2015) 0.79
Comprehensive proteomic profiling of aldehyde dehydrogenases in lung adenocarcinoma cell lines. Int J Proteomics (2011) 0.79
Proteomics for systems toxicology. Comput Struct Biotechnol J (2014) 0.79
Challenges and solutions in proteomics. Curr Genomics (2007) 0.79
Identification of B6T173 (ZmPrx35) as the prevailing peroxidase in highly insect-resistant maize (Zea mays, p84C3) kernels by activity-directed purification. Front Plant Sci (2015) 0.78
Ribosome biogenesis requires a highly diverged XRN family 5'->3' exoribonuclease for rRNA processing in Trypanosoma brucei. RNA (2013) 0.78
A semantic proteomics dashboard (SemPoD) for data management in translational research. BMC Syst Biol (2012) 0.78
A Disintegrin and Metalloproteinase with Thrombospondin Motifs-5 (ADAMTS-5) Forms Catalytically Active Oligomers. J Biol Chem (2015) 0.77
Graft-versus-host disease biomarkers: omics and personalized medicine. Int J Hematol (2013) 0.77
Contextualised urinary biomarker analysis facilitates diagnosis of paediatric obstructive sleep apnoea. Sleep Med (2014) 0.77
Global genome response of Escherichia coli O157∶H7 Sakai during dynamic changes in growth kinetics induced by an abrupt temperature downshift. PLoS One (2014) 0.77
Ancillary study management systems: a review of needs. BMC Med Inform Decis Mak (2013) 0.76
Annotator: postprocessing software for generating function-based signatures from quantitative mass spectrometry. J Proteome Res (2012) 0.76
Quantitative proteomic profiling identifies protein correlates to EGFR kinase inhibition. Mol Cancer Ther (2012) 0.76
An integrated approach for automating validation of extracted ion chromatographic peaks. Bioinformatics (2008) 0.76
Physiological Response of Escherichia coli O157:H7 Sakai to Dynamic Changes in Temperature and Water Activity as Experienced during Carcass Chilling. Mol Cell Proteomics (2016) 0.75
Aberrant glycosylation of plasma proteins in severe preeclampsia promotes monocyte adhesion. Reprod Sci (2013) 0.75
Down regulation of NO signaling in Trypanosoma cruzi upon parasite-extracellular matrix interaction: changes in protein modification by nitrosylation and nitration. PLoS Negl Trop Dis (2015) 0.75
Simulation of the Protein-Shedding Kinetics of a Fully Vascularized Tumor. Cancer Inform (2015) 0.75
Publishing proteomic data. Proteome Sci (2006) 0.75
Quality control, analysis and secure sharing of Luminex® immunoassay data using the open source LabKey Server platform. BMC Bioinformatics (2013) 0.75
DGCR8 Mediates Repair of UV-Induced DNA Damage Independently of RNA Processing. Cell Rep (2017) 0.75
Proteomic Analysis of Epithelial to Mesenchymal Transition (EMT) Reveals Cross-talk between SNAIL and HDAC1 Proteins in Breast Cancer Cells. Mol Cell Proteomics (2016) 0.75
Novel Effects of Lapatinib Revealed in the African Trypanosome using Hypothesis-Generating Proteomics and Chemical Biology Strategies. Antimicrob Agents Chemother (2016) 0.75
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A (2005) 167.46
A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol Syst Biol (2005) 9.81
The PeptideAtlas project. Nucleic Acids Res (2006) 7.87
PRIDE: the proteomics identifications database. Proteomics (2005) 7.52
ENCODE data in the UCSC Genome Browser: year 5 update. Nucleic Acids Res (2012) 6.29
WormBase: a comprehensive resource for nematode research. Nucleic Acids Res (2009) 5.20
A cross-platform toolkit for mass spectrometry and proteomics. Nat Biotechnol (2012) 4.48
Human Proteinpedia enables sharing of human protein data. Nat Biotechnol (2008) 4.21
Integrated genomic and proteomic analyses of gene expression in Mammalian cells. Mol Cell Proteomics (2004) 4.09
Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol Cell Proteomics (2002) 3.89
WormBase 2012: more genomes, more data, new website. Nucleic Acids Res (2011) 3.87
The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics. Nat Biotechnol (2007) 3.55
Integrated pipeline for mass spectrometry-based discovery and confirmation of biomarkers demonstrated in a mouse model of breast cancer. J Proteome Res (2007) 3.48
Expediting the development of targeted SRM assays: using data from shotgun proteomics to automate method development. J Proteome Res (2009) 3.44
UBXD7 binds multiple ubiquitin ligases and implicates p97 in HIF1alpha turnover. Cell (2008) 3.41
Ovarian cancer biomarker performance in prostate, lung, colorectal, and ovarian cancer screening trial specimens. Cancer Prev Res (Phila) (2011) 3.33
A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS. Bioinformatics (2006) 3.32
A multidimensional chromatography technology for in-depth phosphoproteome analysis. Mol Cell Proteomics (2008) 3.13
A framework for evaluating biomarkers for early detection: validation of biomarker panels for ovarian cancer. Cancer Prev Res (Phila) (2011) 3.03
A targeted proteomics-based pipeline for verification of biomarkers in plasma. Nat Biotechnol (2011) 2.91
Selecting for functional alternative splices in ESTs. Genome Res (2002) 2.90
MRMer, an interactive open source and cross-platform system for data extraction and visualization of multiple reaction monitoring experiments. Mol Cell Proteomics (2008) 2.89
Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together. Nucleic Acids Res (2006) 2.77
Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study. Nat Biotechnol (2006) 2.66
Code developments to improve the efficiency of automated MS/MS spectra interpretation. J Proteome Res (2003) 2.53
The study of macromolecular complexes by quantitative proteomics. Nat Genet (2003) 2.44
Analysis of xbx genes in C. elegans. Development (2005) 2.39
A mouse to human search for plasma proteome changes associated with pancreatic tumor development. PLoS Med (2008) 2.31
Global and distinct targets of IRF-5 and IRF-7 during innate response to viral infection. J Biol Chem (2004) 2.26
Pancreatic cancer proteome: the proteins that underlie invasion, metastasis, and immunologic escape. Gastroenterology (2005) 2.21
Mass spectrometry based targeted protein quantification: methods and applications. J Proteome Res (2009) 2.20
Quantitative analysis of acrylamide labeled serum proteins by LC-MS/MS. J Proteome Res (2006) 2.10
Michigan molecular interactions r2: from interacting proteins to pathways. Nucleic Acids Res (2008) 2.09
Elafin is a biomarker of graft-versus-host disease of the skin. Sci Transl Med (2010) 2.08
Detection of hypermethylated genes in women with and without cervical neoplasia. J Natl Cancer Inst (2005) 2.08
Contribution of protein fractionation to depth of analysis of the serum and plasma proteomes. J Proteome Res (2007) 2.04
Ultra-high-efficiency strong cation exchange LC/RPLC/MS/MS for high dynamic range characterization of the human plasma proteome. Anal Chem (2004) 2.00
Identification of TFB5, a new component of general transcription and DNA repair factor IIH. Nat Genet (2004) 1.99
Head-to-head comparison of serum fractionation techniques. J Proteome Res (2007) 1.98
LabKey Server: an open source platform for scientific data integration, analysis and collaboration. BMC Bioinformatics (2011) 1.94
Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations. Proc Natl Acad Sci U S A (2005) 1.93
Systematic evaluation of candidate blood markers for detecting ovarian cancer. PLoS One (2008) 1.93
Cdc48/p97 mediates UV-dependent turnover of RNA Pol II. Mol Cell (2011) 1.91
Normalization regarding non-random missing values in high-throughput mass spectrometry data. Pac Symp Biocomput (2006) 1.86
A tool to visualize and evaluate data obtained by liquid chromatography-electrospray ionization-mass spectrometry. Anal Chem (2004) 1.74
Proteomic analysis of ovarian cancer cells reveals dynamic processes of protein secretion and shedding of extra-cellular domains. PLoS One (2008) 1.72
Gene expression profiling of the cellular transcriptional network regulated by alpha/beta interferon and its partial attenuation by the hepatitis C virus nonstructural 5A protein. J Virol (2003) 1.56
Biomedical informatics for proteomics. Nature (2003) 1.54
High throughput proteome screening for biomarker detection. Mol Cell Proteomics (2005) 1.54
Development of an automated analysis system for data from flow cytometric intracellular cytokine staining assays from clinical vaccine trials. Cytometry A (2008) 1.54
Precursor-ion mass re-estimation improves peptide identification on hybrid instruments. J Proteome Res (2008) 1.53
A platform for accurate mass and time analyses of mass spectrometry data. J Proteome Res (2007) 1.52
Systematic comparison of the human saliva and plasma proteomes. Proteomics Clin Appl (2009) 1.51
A quantitative assay for telomere protection in Saccharomyces cerevisiae. Genetics (2002) 1.49
Longitudinal screening algorithm that incorporates change over time in CA125 levels identifies ovarian cancer earlier than a single-threshold rule. J Clin Oncol (2012) 1.48
Signal maps for mass spectrometry-based comparative proteomics. Mol Cell Proteomics (2005) 1.48
Evaluation of the novel serum markers B7-H4, Spondin 2, and DcR3 for diagnosis and early detection of ovarian cancer. Gynecol Oncol (2007) 1.46
Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas. Genome Biol (2006) 1.45
UniPep--a database for human N-linked glycosites: a resource for biomarker discovery. Genome Biol (2006) 1.43
Quantitative proteomics of cerebrospinal fluid from patients with Alzheimer disease. J Alzheimers Dis (2005) 1.39
Quantitative proteomic analysis of age-related changes in human cerebrospinal fluid. Neurobiol Aging (2005) 1.39
Quantitative proteomic analysis indicates increased synthesis of a quinolone by Pseudomonas aeruginosa isolates from cystic fibrosis airways. Proc Natl Acad Sci U S A (2003) 1.39
Potential role of HE4 in multimodal screening for epithelial ovarian cancer. J Natl Cancer Inst (2011) 1.39
Gene expression patterns that correlate with hepatitis C and early progression to fibrosis in liver transplant recipients. Gastroenterology (2006) 1.38
Phosphoproteome profiling of human skin fibroblast cells in response to low- and high-dose irradiation. J Proteome Res (2006) 1.33
Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae. Nucleic Acids Res (2004) 1.31
A combined dataset of human cerebrospinal fluid proteins identified by multi-dimensional chromatography and tandem mass spectrometry. Proteomics (2007) 1.31
Antibody immunity to the p53 oncogenic protein is a prognostic indicator in ovarian cancer. J Clin Oncol (2006) 1.31
Proteome analysis of low-abundance proteins using multidimensional chromatography and isotope-coded affinity tags. J Proteome Res (2003) 1.28
Deconvoluting the intestine: molecular evidence for a major role of the mesenchyme in the modulation of signaling cross talk. Physiol Genomics (2007) 1.27
Comprehensive proteome analysis of an Apc mouse model uncovers proteins associated with intestinal tumorigenesis. Cancer Prev Res (Phila) (2009) 1.27
Modification of host lipid raft proteome upon hepatitis C virus replication. Mol Cell Proteomics (2006) 1.26
Protein alterations associated with pancreatic cancer and chronic pancreatitis found in human plasma using global quantitative proteomics profiling. J Proteome Res (2011) 1.25
Proteomic analysis of synaptosomes using isotope-coded affinity tags and mass spectrometry. Proteomics (2005) 1.24
Cancer biomarkers: a systems approach. Nat Biotechnol (2006) 1.23
Plasma proteome profiling of a mouse model of breast cancer identifies a set of up-regulated proteins in common with human breast cancer cells. J Proteome Res (2008) 1.22