Published in J Proteome Res on April 28, 2003
A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. J Proteomics (2010) 3.78
Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation. Proc Natl Acad Sci U S A (2004) 3.43
Accurate and sensitive peptide identification with Mascot Percolator. J Proteome Res (2009) 2.25
Advances and challenges in liquid chromatography-mass spectrometry-based proteomics profiling for clinical applications. Mol Cell Proteomics (2006) 2.14
Rapid and accurate peptide identification from tandem mass spectra. J Proteome Res (2008) 2.13
Identification and characterization of the human ARD1-NATH protein acetyltransferase complex. Biochem J (2005) 1.96
Improvements to the percolator algorithm for Peptide identification from shotgun proteomics data sets. J Proteome Res (2009) 1.80
Automatic validation of phosphopeptide identifications from tandem mass spectra. Anal Chem (2007) 1.70
Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry. Bioinformatics (2008) 1.47
Aquaporin 4 molecular mimicry and implications for neuromyelitis optica. J Neuroimmunol (2013) 1.42
Accurate mass measurements in proteomics. Chem Rev (2007) 1.36
Faster SEQUEST searching for peptide identification from tandem mass spectra. J Proteome Res (2011) 1.33
From bytes to bedside: data integration and computational biology for translational cancer research. PLoS Comput Biol (2007) 1.27
TLR8-dependent TNF-(alpha) overexpression in Fanconi anemia group C cells. Blood (2009) 1.26
Adaptive discriminant function analysis and reranking of MS/MS database search results for improved peptide identification in shotgun proteomics. J Proteome Res (2008) 1.17
DtaRefinery, a software tool for elimination of systematic errors from parent ion mass measurements in tandem mass spectra data sets. Mol Cell Proteomics (2009) 1.17
De novo peptide identification via tandem mass spectrometry and integer linear optimization. Anal Chem (2007) 1.12
Comparison of Mascot and X!Tandem performance for low and high accuracy mass spectrometry and the development of an adjusted Mascot threshold. Mol Cell Proteomics (2008) 1.10
Computational and statistical analysis of protein mass spectrometry data. PLoS Comput Biol (2012) 1.07
The chaperone-like protein HYPK acts together with NatA in cotranslational N-terminal acetylation and prevention of Huntingtin aggregation. Mol Cell Biol (2010) 1.07
Integrated platform for manual and high-throughput statistical validation of tandem mass spectra. Proteomics (2009) 1.03
Transformation and other factors of the peptide mass spectrometry pairwise peak-list comparison process. BMC Bioinformatics (2005) 1.01
K-OPLS package: kernel-based orthogonal projections to latent structures for prediction and interpretation in feature space. BMC Bioinformatics (2008) 1.00
Direct maximization of protein identifications from tandem mass spectra. Mol Cell Proteomics (2011) 0.98
A critical assessment of feature selection methods for biomarker discovery in clinical proteomics. Mol Cell Proteomics (2012) 0.94
A novel human NatA Nalpha-terminal acetyltransferase complex: hNaa16p-hNaa10p (hNat2-hArd1). BMC Biochem (2009) 0.91
Verification of single-peptide protein identifications by the application of complementary database search algorithms. J Biomol Tech (2006) 0.91
Assigning spectrum-specific P-values to protein identifications by mass spectrometry. Bioinformatics (2011) 0.90
Bayesian nonparametric model for the validation of peptide identification in shotgun proteomics. Mol Cell Proteomics (2008) 0.89
The Helicobacter pylori cag pathogenicity island protein CagN is a bacterial membrane-associated protein that is processed at its C terminus. Infect Immun (2006) 0.89
A Mixed-Integer Optimization Framework for De Novo Peptide Identification. AIChE J (2007) 0.88
On the importance of well-calibrated scores for identifying shotgun proteomics spectra. J Proteome Res (2014) 0.88
Extensive and varied modifications in histone H2B of wild-type and histone deacetylase 1 mutant Neurospora crassa. Biochemistry (2010) 0.85
A nonparametric model for quality control of database search results in shotgun proteomics. BMC Bioinformatics (2008) 0.84
Colander: a probability-based support vector machine algorithm for automatic screening for CID spectra of phosphopeptides prior to database search. J Proteome Res (2008) 0.83
Beyond laser microdissection technology: follow the yellow brick road for cancer research. Am J Cancer Res (2014) 0.81
Reducing the haystack to find the needle: improved protein identification after fast elimination of non-interpretable peptide MS/MS spectra and noise reduction. BMC Genomics (2010) 0.81
An improved machine learning protocol for the identification of correct Sequest search results. BMC Bioinformatics (2010) 0.80
A novel algorithm for validating peptide identification from a shotgun proteomics search engine. J Proteome Res (2013) 0.79
Plasmodium vivax trophozoite-stage proteomes. J Proteomics (2014) 0.79
Correctness of protein identifications of Bacillus subtilis proteome with the indication on potential false positive peptides supported by predictions of their retention times. J Biomed Biotechnol (2009) 0.78
Prediction of candidate primary immunodeficiency disease genes using a support vector machine learning approach. DNA Res (2009) 0.78
Quality assessment of tandem mass spectra using support vector machine (SVM). BMC Bioinformatics (2009) 0.78
An adaptive classification model for peptide identification. BMC Genomics (2015) 0.75
Application of the support vector machine to predict subclinical mastitis in dairy cattle. ScientificWorldJournal (2013) 0.75
SVM model for quality assessment of medium resolution mass spectra from 18O-water labeling experiments. J Proteome Res (2011) 0.75
Quantitative LC-MS/MS Analysis of Proteins Involved in Metastasis of Breast Cancer. PLoS One (2015) 0.75
Using SEQUEST with Theoretically Complete Sequence Databases. J Am Soc Mass Spectrom (2015) 0.75
Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol (2005) 14.29
Quantifying similarity between motifs. Genome Biol (2007) 9.27
Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat Methods (2007) 8.94
FIMO: scanning for occurrences of a given motif. Bioinformatics (2011) 8.89
Searching for statistically significant regulatory modules. Bioinformatics (2003) 5.72
Assigning significance to peptides identified by tandem mass spectrometry using decoy databases. J Proteome Res (2007) 5.57
Matrix2png: a utility for visualizing matrix data. Bioinformatics (2003) 5.31
Nucleosome positioning signals in genomic DNA. Genome Res (2007) 4.99
The spectrum kernel: a string kernel for SVM protein classification. Pac Symp Biocomput (2002) 4.90
Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nat Methods (2012) 4.89
Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries. Anal Chem (2006) 4.16
Integrative annotation of chromatin elements from ENCODE data. Nucleic Acids Res (2012) 3.80
A statistical framework for genomic data fusion. Bioinformatics (2004) 3.64
The Forkhead transcription factor Hcm1 regulates chromosome segregation genes and fills the S-phase gap in the transcriptional circuitry of the cell cycle. Genes Dev (2006) 3.58
Transmembrane topology and signal peptide prediction using dynamic bayesian networks. PLoS Comput Biol (2008) 3.56
Kernel methods for predicting protein-protein interactions. Bioinformatics (2005) 3.52
Exploring gene expression data with class scores. Pac Symp Biocomput (2002) 3.51
R406, an orally available spleen tyrosine kinase inhibitor blocks fc receptor signaling and reduces immune complex-mediated inflammation. J Pharmacol Exp Ther (2006) 3.46
Mismatch string kernels for discriminative protein classification. Bioinformatics (2004) 3.27
R428, a selective small molecule inhibitor of Axl kinase, blocks tumor spread and prolongs survival in models of metastatic breast cancer. Cancer Res (2010) 2.87
Learning gene functional classifications from multiple data types. J Comput Biol (2002) 2.65
Posterior error probabilities and false discovery rates: two sides of the same coin. J Proteome Res (2007) 2.61
The effect of replication on gene expression microarray experiments. Bioinformatics (2003) 2.49
Discovering patterns to extract protein-protein interactions from full texts. Bioinformatics (2004) 2.42
Choosing negative examples for the prediction of protein-protein interactions. BMC Bioinformatics (2006) 2.36
Sequence and chromatin determinants of cell-type-specific transcription factor binding. Genome Res (2012) 2.24
Combining pairwise sequence similarity and support vector machines for detecting remote protein evolutionary and structural relationships. J Comput Biol (2003) 2.04
Large-scale identification of yeast integral membrane protein interactions. Proc Natl Acad Sci U S A (2005) 2.03
Peptide charge state determination for low-resolution tandem mass spectra. Proc IEEE Comput Syst Bioinform Conf (2005) 1.97
Enhanced sensitivity of multiple myeloma cells containing PTEN mutations to CCI-779. Cancer Res (2002) 1.93
Efficient marginalization to compute protein posterior probabilities from shotgun mass spectrometry data. J Proteome Res (2010) 1.91
Inflammation and bone erosion are suppressed in models of rheumatoid arthritis following treatment with a novel Syk inhibitor. Clin Immunol (2007) 1.91
Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations. Genome Res (2008) 1.90
Multiple roles for the receptor tyrosine kinase axl in tumor formation. Cancer Res (2005) 1.87
Learning to predict protein-protein interactions from protein sequences. Bioinformatics (2003) 1.84
Improvements to the percolator algorithm for Peptide identification from shotgun proteomics data sets. J Proteome Res (2009) 1.80
Critical role of the ubiquitin ligase activity of UHRF1, a nuclear RING finger protein, in tumor cell growth. Mol Biol Cell (2005) 1.68
Protein ranking: from local to global structure in the protein similarity network. Proc Natl Acad Sci U S A (2004) 1.67
Predicting human nucleosome occupancy from primary sequence. PLoS Comput Biol (2008) 1.66
Support vector machine classification on the web. Bioinformatics (2004) 1.65
RACK1, an insulin-like growth factor I (IGF-I) receptor-interacting protein, modulates IGF-I-dependent integrin signaling and promotes cell spreading and contact with extracellular matrix. Mol Cell Biol (2002) 1.60
Identification of the Syk kinase inhibitor R112 by a human mast cell screen. J Allergy Clin Immunol (2006) 1.54
High resolution models of transcription factor-DNA affinities improve in vitro and in vivo binding predictions. PLoS Comput Biol (2010) 1.52
Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification. Bioinformatics (2008) 1.48
Epigenetic priors for identifying active transcription factor binding sites. Bioinformatics (2011) 1.47
Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry. Bioinformatics (2008) 1.47
An orally bioavailable spleen tyrosine kinase inhibitor delays disease progression and prolongs survival in murine lupus. Arthritis Rheum (2008) 1.44
Predicting co-complexed protein pairs from heterogeneous data. PLoS Comput Biol (2008) 1.44
Statistical calibration of the SEQUEST XCorr function. J Proteome Res (2009) 1.43
Semi-supervised protein classification using cluster kernels. Bioinformatics (2005) 1.42
Ranking predicted protein structures with support vector regression. Proteins (2008) 1.41
QVALITY: non-parametric estimation of q-values and posterior error probabilities. Bioinformatics (2009) 1.38
Faster SEQUEST searching for peptide identification from tandem mass spectra. J Proteome Res (2011) 1.33
Activation of the PKB/AKT pathway by ICAM-2. Immunity (2002) 1.31
Support vector machine learning from heterogeneous data: an empirical analysis using protein sequence and structure. Bioinformatics (2006) 1.27
Substrate modification with lysine 63-linked ubiquitin chains through the UBC13-UEV1A ubiquitin-conjugating enzyme. J Biol Chem (2007) 1.25
Targeting Syk as a treatment for allergic and autoimmune disorders. Expert Opin Investig Drugs (2004) 1.20
Targeting aurora kinases as therapy in multiple myeloma. Blood (2007) 1.19
Improving tandem mass spectrum identification using peptide retention time prediction across diverse chromatography conditions. Anal Chem (2007) 1.19
Riboproteomics of the hepatitis C virus internal ribosomal entry site. J Proteome Res (2004) 1.19
Metabolism of fostamatinib, the oral methylene phosphate prodrug of the spleen tyrosine kinase inhibitor R406 in humans: contribution of hepatic and gut bacterial processes to the overall biotransformation. Drug Metab Dispos (2010) 1.17
Consistent probabilistic outputs for protein function prediction. Genome Biol (2008) 1.17
Bile acids enhance the activity of the insulin receptor and glycogen synthase in primary rodent hepatocytes. Hepatology (2004) 1.15
The poxvirus p28 virulence factor is an E3 ubiquitin ligase. J Biol Chem (2004) 1.14
On the assessment of statistical significance of three-dimensional colocalization of sets of genomic elements. Nucleic Acids Res (2012) 1.13
Identification and functional characterization of a novel human misshapen/Nck interacting kinase-related kinase, hMINK beta. J Biol Chem (2004) 1.12
Mechanical force modulates global gene expression and beta-catenin signaling in colon cancer cells. J Cell Sci (2007) 1.11
Improved similarity scores for comparing motifs. Bioinformatics (2011) 1.10
Detecting cross-linked peptides by searching against a database of cross-linked peptide pairs. J Proteome Res (2010) 1.09
Crux: rapid open source protein tandem mass spectrometry analysis. J Proteome Res (2014) 1.06
The Genomedata format for storing large-scale functional genomics data. Bioinformatics (2010) 1.05
PTEN, but not SHIP and SHIP2, suppresses the PI3K/Akt pathway and induces growth inhibition and apoptosis of myeloma cells. Oncogene (2002) 1.05
Retrovirally delivered random cyclic Peptide libraries yield inhibitors of interleukin-4 signaling in human B cells. J Biol Chem (2002) 1.04
A novel E3 ubiquitin ligase TRAC-1 positively regulates T cell activation. J Immunol (2005) 1.04
On using samples of known protein content to assess the statistical calibration of scores assigned to peptide-spectrum matches in shotgun proteomics. J Proteome Res (2011) 1.03
Exploratory analysis of genomic segmentations with Segtools. BMC Bioinformatics (2011) 1.02
Learning kernels from biological networks by maximizing entropy. Bioinformatics (2004) 1.01
Automated mapping of large-scale chromatin structure in ENCODE. Bioinformatics (2008) 0.99
Cell cycle regulatory E3 ubiquitin ligases as anticancer targets. Drug Resist Updat (2002) 0.99
Kernel hierarchical gene clustering from microarray expression data. Bioinformatics (2003) 0.98
Estimating relative abundances of proteins from shotgun proteomics data. BMC Bioinformatics (2012) 0.98
Direct maximization of protein identifications from tandem mass spectra. Mol Cell Proteomics (2011) 0.98
A structural alignment kernel for protein structures. Bioinformatics (2007) 0.97
Rapamycin and UCN-01 synergistically induce apoptosis in human leukemia cells through a process that is regulated by the Raf-1/MEK/ERK, Akt, and JNK signal transduction pathways. Mol Cancer Ther (2005) 0.96
Preferential killing of PTEN-null myelomas by PI3K inhibitors through Akt pathway. Oncogene (2003) 0.96
Assessing phylogenetic motif models for predicting transcription factor binding sites. Bioinformatics (2009) 0.95
Protein ranking by semi-supervised network propagation. BMC Bioinformatics (2006) 0.95
A thermodynamic approach to PCR primer design. Nucleic Acids Res (2009) 0.94
AMPK activation through mitochondrial regulation results in increased substrate oxidation and improved metabolic parameters in models of diabetes. PLoS One (2013) 0.94
Drug discovery in the ubiquitin regulatory pathway. Drug Discov Today (2003) 0.94
The farnesyltransferase inhibitor L744832 potentiates UCN-01-induced apoptosis in human multiple myeloma cells. Clin Cancer Res (2005) 0.93
High-throughput screening for inhibitors of the e3 ubiquitin ligase APC. Methods Enzymol (2005) 0.92
RANKPROP: a web server for protein remote homology detection. Bioinformatics (2008) 0.90
Motif-based protein ranking by network propagation. Bioinformatics (2005) 0.90
JAK3 inhibition significantly attenuates psoriasiform skin inflammation in CD18 mutant PL/J mice. J Immunol (2009) 0.88
Improved network-based identification of protein orthologs. Bioinformatics (2008) 0.88
On the importance of well-calibrated scores for identifying shotgun proteomics spectra. J Proteome Res (2014) 0.88