Published in Mol Cell Proteomics on November 19, 2007
Significance analysis of spectral count data in label-free shotgun proteomics. Mol Cell Proteomics (2008) 3.12
Addressing accuracy and precision issues in iTRAQ quantitation. Mol Cell Proteomics (2010) 3.10
Protein analysis by shotgun/bottom-up proteomics. Chem Rev (2013) 2.13
Delayed correlation of mRNA and protein expression in rapamycin-treated cells and a role for Ggc1 in cellular sensitivity to rapamycin. Mol Cell Proteomics (2009) 1.76
Proteomics analysis of human skeletal muscle reveals novel abnormalities in obesity and type 2 diabetes. Diabetes (2009) 1.52
High-fat diet alters gut microbiota physiology in mice. ISME J (2013) 1.44
Combined statistical analyses of peptide intensities and peptide occurrences improves identification of significant peptides from MS-based proteomics data. J Proteome Res (2010) 1.34
Abacus: a computational tool for extracting and pre-processing spectral count data for label-free quantitative proteomic analysis. Proteomics (2011) 1.24
Shotgun proteomics analysis of hibernating arctic ground squirrels. Mol Cell Proteomics (2009) 1.20
Mitochondrial dysfunction and insulin resistance from the outside in: extracellular matrix, the cytoskeleton, and mitochondria. Am J Physiol Endocrinol Metab (2011) 1.17
System response of metabolic networks in Chlamydomonas reinhardtii to total available ammonium. Mol Cell Proteomics (2012) 1.11
PepC: proteomics software for identifying differentially expressed proteins based on spectral counting. Bioinformatics (2010) 1.10
ClpS1 is a conserved substrate selector for the chloroplast Clp protease system in Arabidopsis. Plant Cell (2013) 1.09
Identification of differentially expressed proteins in direct expressed prostatic secretions of men with organ-confined versus extracapsular prostate cancer. Mol Cell Proteomics (2012) 1.08
Increased power for the analysis of label-free LC-MS/MS proteomics data by combining spectral counts and peptide peak attributes. Mol Cell Proteomics (2010) 1.08
Distinct energy metabolism of auditory and vestibular sensory epithelia revealed by quantitative mass spectrometry using MS2 intensity. Proc Natl Acad Sci U S A (2012) 1.05
Improved LC-MS/MS spectral counting statistics by recovering low-scoring spectra matched to confidently identified peptide sequences. J Proteome Res (2010) 1.02
Protein dynamics in iron-starved Mycobacterium tuberculosis revealed by turnover and abundance measurement using hybrid-linear ion trap-Fourier transform mass spectrometry. Anal Chem (2008) 0.96
A label free quantitative proteomic analysis of the Saccharomyces cerevisiae nucleus. J Proteomics (2008) 0.96
Shaggy/glycogen synthase kinase 3β and phosphorylation of Sarah/regulator of calcineurin are essential for completion of Drosophila female meiosis. Proc Natl Acad Sci U S A (2012) 0.95
Unraveling the ubiquitome of the human malaria parasite. J Biol Chem (2011) 0.95
Loss of plastoglobule kinases ABC1K1 and ABC1K3 causes conditional degreening, modified prenyl-lipids, and recruitment of the jasmonic acid pathway. Plant Cell (2013) 0.94
Liver membrane proteome glycosylation changes in mice bearing an extra-hepatic tumor. Mol Cell Proteomics (2010) 0.93
Glycoprotein profiles of human breast cells demonstrate a clear clustering of normal/benign versus malignant cell lines and basal versus luminal cell lines. J Proteome Res (2011) 0.93
Characterization of the Human Adipocyte Proteome and Reproducibility of Protein Abundance by One-Dimensional Gel Electrophoresis and HPLC-ESI-MS/MS. J Proteome Res (2010) 0.92
Measuring the intra-individual variability of the plasma proteome in the chicken model of spontaneous ovarian adenocarcinoma. Anal Bioanal Chem (2010) 0.91
Cerebrospinal fluid proteomics reveals potential pathogenic changes in the brains of SIV-infected monkeys. J Proteome Res (2009) 0.90
Suberoylanilide hydroxamic acid (SAHA)-induced dynamics of a human histone deacetylase protein interaction network. Mol Cell Proteomics (2014) 0.90
Using ProtMAX to create high-mass-accuracy precursor alignments from label-free quantitative mass spectrometry data generated in shotgun proteomics experiments. Nat Protoc (2013) 0.88
Redox state of pentraxin 3 as a novel biomarker for resolution of inflammation and survival in sepsis. Mol Cell Proteomics (2014) 0.87
The membrane-associated proteins FCHo and SGIP are allosteric activators of the AP2 clathrin adaptor complex. Elife (2014) 0.87
Review, evaluation, and discussion of the challenges of missing value imputation for mass spectrometry-based label-free global proteomics. J Proteome Res (2015) 0.87
An assessment of false discovery rates and statistical significance in label-free quantitative proteomics with combined filters. BMC Bioinformatics (2009) 0.87
Controlling for gene expression changes in transcription factor protein networks. Mol Cell Proteomics (2014) 0.87
Type VI Secretion System Toxins Horizontally Shared between Marine Bacteria. PLoS Pathog (2015) 0.86
Biomarkers for pancreatic cancer: recent achievements in proteomics and genomics through classical and multivariate statistical methods. World J Gastroenterol (2014) 0.86
Proteomics: from single molecules to biological pathways. Cardiovasc Res (2012) 0.86
Science, marketing and wishful thinking in quantitative proteomics. Proteomics (2008) 0.85
Improved detection of quantitative differences using a combination of spectral counting and MS/MS total ion current. J Proteome Res (2013) 0.84
A bayesian mixture model for comparative spectral count data in shotgun proteomics. Mol Cell Proteomics (2011) 0.84
The transcriptional stress response of Candida albicans to weak organic acids. G3 (Bethesda) (2015) 0.82
Proteins interacting with cloning scars: a source of false positive protein-protein interactions. Sci Rep (2015) 0.80
Using a cell line breast cancer progression system to identify biomarker candidates. J Proteomics (2013) 0.79
Generalized Linear and Mixed Models for Label-Free Shotgun Proteomics. Stat Interface (2012) 0.78
Super-SILAC for tumors and tissues. Nat Methods (2010) 0.77
Mass spectrometry-based shotgun proteomic analysis of C. elegans protein complexes. WormBook (2014) 0.77
QPROT: Statistical method for testing differential expression using protein-level intensity data in label-free quantitative proteomics. J Proteomics (2015) 0.77
The human colostrum whey proteome is altered in gestational diabetes mellitus. J Proteome Res (2014) 0.77
On the tear proteome of the house mouse (Mus musculus musculus) in relation to chemical signalling. PeerJ (2017) 0.76
Statistically enhanced spectral counting approach to TCDD cardiac toxicity in the adult zebrafish heart. J Proteome Res (2013) 0.76
Cytoskeleton-centric protein transportation by exosomes transforms tumor-favorable macrophages. Oncotarget (2016) 0.76
Proteomic and Genomic Analyses of the Rvb1 and Rvb2 Interaction Network upon Deletion of R2TP Complex Components. Mol Cell Proteomics (2016) 0.76
MRG15-mediated tethering of PALB2 to unperturbed chromatin protects active genes from genotoxic stress. Proc Natl Acad Sci U S A (2017) 0.76
SWATH-based proteomics identified carbonic anhydrase 2 as a potential diagnosis biomarker for nasopharyngeal carcinoma. Sci Rep (2017) 0.75
Assigning significance in label-free quantitative proteomics to include single-peptide-hit proteins with low replicates. Int J Proteomics (2010) 0.75
TNIP2 is a Hub Protein in the NF-κB Network with Both Protein and RNA Mediated Interactions. Mol Cell Proteomics (2016) 0.75
Covariation of Peptide Abundances Accurately Reflects Protein Concentration Differences. Mol Cell Proteomics (2017) 0.75
Comparative proteomic profiling of pancreatic ductal adenocarcinoma cell lines. Mol Cells (2014) 0.75
Extracellular matrix proteomics identifies molecular signature of symptomatic carotid plaques. J Clin Invest (2017) 0.75
Sex-Specific Biology of the Human Malaria Parasite Revealed from the Proteomes of Mature Male and Female Gametocytes. Mol Cell Proteomics (2017) 0.75
A multi-model statistical approach for proteomic spectral count quantitation. J Proteomics (2016) 0.75
Differential regulation of vaginal lipocalins (OBP, MUP) during the estrous cycle of the house mouse. Sci Rep (2017) 0.75
Magnesium Presence Prevents Removal of Antigenic Nuclear-Associated Proteins from Bovine Pericardium for Heart Valve Engineering. Tissue Eng Part A (2017) 0.75
Human DNA methylomes at base resolution show widespread epigenomic differences. Nature (2009) 34.27
Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature (2011) 13.94
Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell (2005) 10.68
A proteomic view of the Plasmodium falciparum life cycle. Nature (2002) 10.65
Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature (2002) 8.92
Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell (2010) 8.74
Vpx relieves inhibition of HIV-1 infection of macrophages mediated by the SAMHD1 protein. Nature (2011) 7.92
Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol (2010) 7.00
Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae. J Proteome Res (2006) 6.43
A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses. Science (2005) 5.99
Generation of gut-homing IgA-secreting B cells by intestinal dendritic cells. Science (2006) 5.31
AFF4, a component of the ELL/P-TEFb elongation complex and a shared subunit of MLL chimeras, can link transcription elongation to leukemia. Mol Cell (2010) 4.99
Acetylation by Tip60 is required for selective histone variant exchange at DNA lesions. Science (2004) 4.97
Histone crosstalk between H2B monoubiquitination and H3 methylation mediated by COMPASS. Cell (2007) 4.49
Correlation of relative abundance ratios derived from peptide ion chromatograms and spectrum counting for quantitative proteomic analysis using stable isotope labeling. Anal Chem (2005) 4.16
The European dimension for the mouse genome mutagenesis program. Nat Genet (2004) 3.84
Aneuploidy confers quantitative proteome changes and phenotypic variation in budding yeast. Nature (2010) 3.72
Quantitative proteomic analysis of distinct mammalian Mediator complexes using normalized spectral abundance factors. Proc Natl Acad Sci U S A (2006) 3.71
A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies. Nat Biotechnol (2006) 3.68
Nuclear membrane proteins with potential disease links found by subtractive proteomics. Science (2003) 3.64
Global analysis of transcript and protein levels across the Plasmodium falciparum life cycle. Genome Res (2004) 3.63
Analyzing chromatin remodeling complexes using shotgun proteomics and normalized spectral abundance factors. Methods (2006) 3.37
Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Res (2011) 3.36
A set of consensus mammalian mediator subunits identified by multidimensional protein identification technology. Mol Cell (2004) 3.34
Lentiviral Vpx accessory factor targets VprBP/DCAF1 substrate adaptor for cullin 4 E3 ubiquitin ligase to enable macrophage infection. PLoS Pathog (2008) 3.27
Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics. Proc Natl Acad Sci U S A (2008) 3.23
Proteasome recruitment and activation of the Uch37 deubiquitinating enzyme by Adrm1. Nat Cell Biol (2006) 3.14
Refinements to label free proteome quantitation: how to deal with peptides shared by multiple proteins. Anal Chem (2010) 3.07
Poly(ADP-ribosyl)ation directs recruitment and activation of an ATP-dependent chromatin remodeler. Proc Natl Acad Sci U S A (2009) 3.02
Widespread dynamic DNA methylation in response to biotic stress. Proc Natl Acad Sci U S A (2012) 2.90
Molecular regulation of histone H3 trimethylation by COMPASS and the regulation of gene expression. Mol Cell (2005) 2.89
Scm3 is essential to recruit the histone h3 variant cse4 to centromeres and to maintain a functional kinetochore. Mol Cell (2007) 2.82
Evolutionarily conserved multisubunit RBL2/p130 and E2F4 protein complex represses human cell cycle-dependent genes in quiescence. Mol Cell (2007) 2.74
Patterns of population epigenomic diversity. Nature (2013) 2.70
IRF4 transcription factor-dependent CD11b+ dendritic cells in human and mouse control mucosal IL-17 cytokine responses. Immunity (2013) 2.69
Proteomic analysis by multidimensional protein identification technology. Methods Mol Biol (2006) 2.69
Lentiviral Vpr usurps Cul4-DDB1[VprBP] E3 ubiquitin ligase to modulate cell cycle. Proc Natl Acad Sci U S A (2007) 2.64
Human mediator subunit MED26 functions as a docking site for transcription elongation factors. Cell (2011) 2.53
Linking H3K79 trimethylation to Wnt signaling through a novel Dot1-containing complex (DotCom). Genes Dev (2010) 2.53
Cytoskeletal components of an invasion machine--the apical complex of Toxoplasma gondii. PLoS Pathog (2006) 2.43
Identification of Plasmodium falciparum antigens by antigenic analysis of genomic and proteomic data. Proc Natl Acad Sci U S A (2003) 2.38
Chromatin remodelers Isw1 and Chd1 maintain chromatin structure during transcription by preventing histone exchange. Nat Struct Mol Biol (2012) 2.37
Molecular regulation of H3K4 trimethylation by Wdr82, a component of human Set1/COMPASS. Mol Cell Biol (2008) 2.34
Proteomic survey of metabolic pathways in rice. Proc Natl Acad Sci U S A (2002) 2.27
Subunit composition and substrate specificity of a MOF-containing histone acetyltransferase distinct from the male-specific lethal (MSL) complex. J Biol Chem (2009) 2.23
SCF(Cyclin F) controls centrosome homeostasis and mitotic fidelity through CP110 degradation. Nature (2010) 2.15
Genome-wide screen of promoter methylation identifies novel markers in melanoma. Genome Res (2009) 2.13
CD14 regulates the dendritic cell life cycle after LPS exposure through NFAT activation. Nature (2009) 2.13
A mammalian chromatin remodeling complex with similarities to the yeast INO80 complex. J Biol Chem (2005) 2.10
Cyclin F-mediated degradation of ribonucleotide reductase M2 controls genome integrity and DNA repair. Cell (2012) 1.98
The deubiquitylation activity of Ubp8 is dependent upon Sgf11 and its association with the SAGA complex. Mol Cell Biol (2005) 1.95
The mammalian YL1 protein is a shared subunit of the TRRAP/TIP60 histone acetyltransferase and SRCAP complexes. J Biol Chem (2005) 1.93
Probing host pathogen cross-talk by transcriptional profiling of both Mycobacterium tuberculosis and infected human dendritic cells and macrophages. PLoS One (2008) 1.91
ATAC is a double histone acetyltransferase complex that stimulates nucleosome sliding. Nat Struct Mol Biol (2008) 1.90