Published in Mol Cell Proteomics on November 08, 2011
The DegraBase: a database of proteolysis in healthy and apoptotic human cells. Mol Cell Proteomics (2012) 1.34
Functional interplay between caspase cleavage and phosphorylation sculpts the apoptotic proteome. Cell (2012) 1.23
The Online Protein Processing Resource (TOPPR): a database and analysis platform for protein processing events. Nucleic Acids Res (2012) 0.95
High resolution quantitative proteomics of HeLa cells protein species using stable isotope labeling with amino acids in cell culture(SILAC), two-dimensional gel electrophoresis(2DE) and nano-liquid chromatograpohy coupled to an LTQ-OrbitrapMass spectrometer. Mol Cell Proteomics (2012) 0.84
Identification of factors that function in Drosophila salivary gland cell death during development using proteomics. Cell Death Differ (2012) 0.80
Integration of proteomics into systems biology of cancer. Wiley Interdiscip Rev Syst Biol Med (2012) 0.76
Caspase-dependent Proteolysis of Human Ribonucleotide Reductase Small Subunits R2 and p53R2 during Apoptosis. J Biol Chem (2015) 0.76
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc (2009) 137.99
KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res (2000) 117.00
Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res (2003) 103.76
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res (2008) 54.83
Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics (2002) 30.58
BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics (2005) 24.04
Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics (2004) 19.05
Two CD95 (APO-1/Fas) signaling pathways. EMBO J (1998) 10.42
Programmed cell death in animal development. Cell (1997) 8.95
Molecular mechanisms of caspase regulation during apoptosis. Nat Rev Mol Cell Biol (2004) 6.76
Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal Chem (2003) 6.63
iRefIndex: a consolidated protein interaction database with provenance. BMC Bioinformatics (2008) 5.77
Promoting apoptosis as a strategy for cancer drug discovery. Nat Rev Cancer (2005) 5.65
Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis (1997) 5.06
Ubiquitin and ubiquitin-like proteins as multifunctional signals. Nat Rev Mol Cell Biol (2005) 4.88
Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini. Cell (2008) 4.00
Global mapping of the topography and magnitude of proteolytic events in apoptosis. Cell (2008) 3.64
Apoptosis and caspases in neurodegenerative diseases. N Engl J Med (2003) 3.40
Posttranslational N-myristoylation of BID as a molecular switch for targeting mitochondria and apoptosis. Science (2000) 3.06
Apoptosis in the development and maintenance of the immune system. Nat Immunol (2003) 3.02
Common and distinct elements in cellular signaling via EGF and FGF receptors. Science (2004) 2.99
The CASBAH: a searchable database of caspase substrates. Cell Death Differ (2007) 2.89
Caspase-specific and nonspecific in vivo protein processing during Fas-induced apoptosis. Nat Methods (2005) 2.33
Functional diversity of the hnRNPs: past, present and perspectives. Biochem J (2010) 2.29
Regulation of the Apaf-1-caspase-9 apoptosome. J Cell Sci (2010) 1.91
Caspase cleavage of vimentin disrupts intermediate filaments and promotes apoptosis. Cell Death Differ (2001) 1.87
Caspase activation inhibits proteasome function during apoptosis. Mol Cell (2004) 1.78
Role of apoptosis in cardiovascular disease. Apoptosis (2009) 1.74
Insulin protects islets from apoptosis via Pdx1 and specific changes in the human islet proteome. Proc Natl Acad Sci U S A (2006) 1.63
RVB1/RVB2: running rings around molecular biology. Mol Cell (2009) 1.62
Cytosolic accumulation of HSP60 during apoptosis with or without apparent mitochondrial release: evidence that its pro-apoptotic or pro-survival functions involve differential interactions with caspase-3. J Biol Chem (2007) 1.57
GraBCas: a bioinformatics tool for score-based prediction of Caspase- and Granzyme B-cleavage sites in protein sequences. Nucleic Acids Res (2005) 1.57
Bis, a Bcl-2-binding protein that synergizes with Bcl-2 in preventing cell death. Oncogene (1999) 1.54
Mechanisms of renal apoptosis in health and disease. J Am Soc Nephrol (2008) 1.50
Regulation of apoptosis proteins in cancer cells by ubiquitin. Oncogene (2004) 1.46
Protein-protein interaction databases: keeping up with growing interactomes. Hum Genomics (2009) 1.32
Global profiling of protease cleavage sites by chemoselective labeling of protein N-termini. Proc Natl Acad Sci U S A (2009) 1.32
Toward computer-based cleavage site prediction of cysteine endopeptidases. Biol Chem (2003) 1.27
Apoptosis as a mechanism for liver disease progression. Semin Liver Dis (2010) 1.21
Multiple mechanisms promote the inhibition of classical nuclear import upon exposure to severe oxidative stress. Cell Death Differ (2004) 1.17
CASVM: web server for SVM-based prediction of caspase substrates cleavage sites. Bioinformatics (2007) 1.16
Functional significance of apoptosis in chronic obstructive pulmonary disease. COPD (2007) 1.16
Apoptotic release of histones from nucleosomes. J Biol Chem (2002) 1.14
Use of RNA interference and complementation to study the function of the Drosophila and human 26S proteasome subunit S13. Mol Cell Biol (2003) 1.08
Cytoskeletal reorganization during process of apoptosis induced by cytostatic drugs in K-562 and HL-60 leukemia cell lines. Biochem Pharmacol (2003) 1.00
CaSPredictor: a new computer-based tool for caspase substrate prediction. Bioinformatics (2005) 0.98
Rearrangement of nuclear ribonucleoprotein (RNP)-containing structures during apoptosis and transcriptional arrest. Biol Cell (2004) 0.97
Caspase-dependent inactivation of proteasome function during programmed cell death in Drosophila and man. J Biol Chem (2004) 0.97
Generation of anti-apoptotic presenilin-2 polypeptides by alternative transcription, proteolysis, and caspase-3 cleavage. J Biol Chem (1997) 0.96
Shotgun proteome analysis of protein cleavage in apoptotic cells. Proteomics (2005) 0.96
The oncoprotein SF2/ASF promotes non-small cell lung cancer survival by enhancing survivin expression. Clin Cancer Res (2010) 0.95
14-3-3 proteins in apoptosis. Braz J Med Biol Res (2003) 0.93
Proteome analysis of apoptotic cells. Mass Spectrom Rev (2004) 0.93
Isobaric peptide termini labeling for MS/MS-based quantitative proteomics. J Proteome Res (2009) 0.90
Mitochondrial chloride channels--What are they for? FEBS Lett (2010) 0.89
From proteome lists to biological impact--tools and strategies for the analysis of large MS data sets. Proteomics (2010) 0.88
Actin depolymerization and polymerization are required during apoptosis in endothelial cells. J Cell Physiol (2000) 0.88
Pripper: prediction of caspase cleavage sites from whole proteomes. BMC Bioinformatics (2010) 0.88
The nuclear pore complex, nuclear transport, and apoptosis. Can J Physiol Pharmacol (2006) 0.86
Prediction of translocation and cleavage of heterogeneous ribonuclear proteins and Rho guanine nucleotide dissociation inhibitor 2 during apoptosis by subcellular proteome analysis. Proteomics (2002) 0.86
Taxol induces concomitant hyperphosphorylation and reorganization of vimentin intermediate filaments in 9L rat brain tumor cells. J Cell Biochem (1998) 0.81
Large-scale quantitative proteomic study of PUMA-induced apoptosis using two-dimensional liquid chromatography-mass spectrometry coupled with amino acid-coded mass tagging. J Proteome Res (2004) 0.81
Proteases, proteasomes and apoptosis: breaking Ub is hard to do. Cell Death Differ (2005) 0.80
Structural change of ribosomes during apoptosis: degradation and externalization of ribosomal proteins in doxorubicin-treated Jurkat cells. J Biochem (2002) 0.79
Sam50 functions in mitochondrial intermembrane space bridging and biogenesis of respiratory complexes. Mol Cell Biol (2012) 1.22
Extracellular identification of a processed type II ComR/ComS pheromone of Streptococcus mutans. J Bacteriol (2012) 1.21
A global approach combining proteome analysis and phenotypic screening with RNA interference yields novel apoptosis regulators. Mol Cell Proteomics (2004) 1.21
Proteomic identification of secreted proteins from human skeletal muscle cells and expression in response to strength training. Am J Physiol Endocrinol Metab (2011) 1.21
New chemical tools for investigating human mitotic kinesin Eg5. Bioorg Med Chem (2007) 1.12
Isobaric protein and peptide quantification: perspectives and issues. Expert Rev Proteomics (2010) 1.07
MiR-133b targets antiapoptotic genes and enhances death receptor-induced apoptosis. PLoS One (2012) 1.06
The preferred substrates for transglutaminase 2 in a complex wheat gluten digest are Peptide fragments harboring celiac disease T-cell epitopes. PLoS One (2010) 1.05
Validating divergent ORF annotation of the Mycobacterium leprae genome through a full translation data set and peptide identification by tandem mass spectrometry. Proteomics (2009) 1.04
Proteogenomic analysis of polymorphisms and gene annotation divergences in prokaryotes using a clustered mass spectrometry-friendly database. Mol Cell Proteomics (2010) 1.02
Caspase-2 is an initiator caspase responsible for pore-forming toxin-mediated apoptosis. EMBO J (2012) 1.01
CD147 (Basigin/Emmprin) identifies FoxP3+CD45RO+CTLA4+-activated human regulatory T cells. Blood (2011) 1.00
Using a label-free proteomics method to identify differentially abundant proteins in closely related hypo- and hypervirulent clinical Mycobacterium tuberculosis Beijing isolates. Mol Cell Proteomics (2010) 1.00
Rapid determination of amino acid incorporation by stable isotope labeling with amino acids in cell culture (SILAC). Rapid Commun Mass Spectrom (2007) 0.98
Expansion of multipotent stem cells from the adult human brain. PLoS One (2013) 0.93
Comprehensive quantitative proteome analysis of 20S proteasome subtypes from rat liver by isotope coded affinity tag and 2-D gel-based approaches. Proteomics (2006) 0.93
Proteome analysis of tunicamycin-induced ER stress. Electrophoresis (2012) 0.93
Distinctive mass losses of tryptic peptides generated by matrix-assisted laser desorption/ionization time-of-flight/time-of-flight. Rapid Commun Mass Spectrom (2006) 0.92
IsobariQ: software for isobaric quantitative proteomics using IPTL, iTRAQ, and TMT. J Proteome Res (2010) 0.90
Isobaric peptide termini labeling for MS/MS-based quantitative proteomics. J Proteome Res (2009) 0.90
Quantitative proteome analysis of cisplatin-induced apoptotic Jurkat T cells by stable isotope labeling with amino acids in cell culture, SDS-PAGE, and LC-MALDI-TOF/TOF MS. Electrophoresis (2007) 0.89
Active transcriptomic and proteomic reprogramming in the C. elegans nucleotide excision repair mutant xpa-1. Nucleic Acids Res (2013) 0.89
Sorafenib-induced mitochondrial complex I inactivation and cell death in human neuroblastoma cells. J Proteome Res (2012) 0.87
Identification of interaction partners of the cytosolic polyproline region of CD95 ligand (CD178). FEBS Lett (2002) 0.86
Proteome analysis of apoptosis signaling by S-trityl-L-cysteine, a potent reversible inhibitor of human mitotic kinesin Eg5. Proteomics (2008) 0.86
Shotgun mass mapping of Lactobacillus species and subspecies from caries related isolates by MALDI-MS. Proteomics (2009) 0.86
Correlation of probiotic Lactobacillus salivarius growth phase with its cell wall-associated proteome. FEMS Microbiol Lett (2005) 0.86
Cloning and biochemical characterization of APIT, a new l-amino acid oxidase from Aplysia punctata. Toxicon (2005) 0.83
Isobaric peptide termini labeling utilizing site-specific N-terminal succinylation. Anal Chem (2011) 0.82
Analysis of detergent-insoluble and whole cell lysate fractions of resting neutrophils using high-resolution mass spectrometry. J Proteome Res (2010) 0.82
The proteome of the human parotid gland secretion in elderly with and without root caries. Acta Odontol Scand (2009) 0.82
Quantitative proteome analysis of detergent-resistant membranes identifies the differential regulation of protein kinase C isoforms in apoptotic T cells. Proteomics (2010) 0.81
An approach for triplex-isobaric peptide termini labeling (triplex-IPTL). Anal Chem (2013) 0.81
Temporal proteome profiling of taxol-induced mitotic arrest and apoptosis. Electrophoresis (2010) 0.81
Decimal place slope, a fast and precise method for quantifying 13C incorporation levels for detecting the metabolic activity of microbial species. Mol Cell Proteomics (2010) 0.81
Schizosaccharomyces pombe Ofd2 is a nuclear 2-oxoglutarate and iron dependent dioxygenase interacting with histones. PLoS One (2011) 0.80
Quantitative proteome analysis reveals RNA processing factors as modulators of ionizing radiation-induced apoptosis in the C. elegans germline. J Proteome Res (2012) 0.79
Proteome analysis of microtubule-associated proteins and their interacting partners from mammalian brain. Amino Acids (2010) 0.79
A rapid approach for isobaric peptide termini labeling. Methods Mol Biol (2012) 0.78
Quantitative proteome analysis of the 20S proteasome of apoptotic Jurkat T cells. Amino Acids (2010) 0.78
Deregulation of Fragile X-related protein 1 by the lipodystrophic lamin A p.R482W mutation elicits a myogenic gene expression program in preadipocytes. Hum Mol Genet (2013) 0.77
Proteomic analysis of a multi-resistant clinical Escherichia coli isolate of unknown genomic background. J Proteomics (2011) 0.77
Quantitative profiling of tyrosine phosphorylation revealed changes in the activity of the T cell receptor signaling pathway upon cisplatin-induced apoptosis. J Proteomics (2013) 0.76
Assembling proteomics data as a prerequisite for the analysis of large scale experiments. Chem Cent J (2009) 0.76
Molecular mechanisms of nutlin-3 involve acetylation of p53, histones and heat shock proteins in acute myeloid leukemia. Mol Cancer (2014) 0.76
Cell death proteomics database: consolidating proteomics data on cell death. J Proteome Res (2013) 0.76
Corrigendum: Sumoylation of Rap1 mediates the recruitment of TFIID to promote transcription of ribosomal protein genes. Genome Res (2017) 0.75
Polyreactivity of monoclonal antibodies made against human erythrocyte membranes with various pathogenic bacteria. Hybridoma (Larchmt) (2011) 0.75
Quantitative proteome analysis using isobaric peptide termini labeling (IPTL). Methods Mol Biol (2011) 0.75
Comparison of data analysis parameters and MS/MS fragmentation techniques for quantitative proteome analysis using isobaric peptide termini labeling (IPTL). Anal Bioanal Chem (2012) 0.75