Published in J Proteome Res on July 15, 2004
Systematic discovery of in vivo phosphorylation networks. Cell (2007) 6.94
KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites. Nucleic Acids Res (2005) 3.28
NetworKIN: a resource for exploring cellular phosphorylation networks. Nucleic Acids Res (2007) 2.69
Ubiquitination is involved in glucose-mediated downregulation of GIP receptors in islets. Am J Physiol Endocrinol Metab (2007) 1.22
AMS 4.0: consensus prediction of post-translational modifications in protein sequences. Amino Acids (2012) 0.88
Graphlet kernels for prediction of functional residues in protein structures. J Comput Biol (2010) 0.88
AMS 3.0: prediction of post-translational modifications. BMC Bioinformatics (2010) 0.86
SiteSeek: post-translational modification analysis using adaptive locality-effective kernel methods and new profiles. BMC Bioinformatics (2008) 0.84
Toward a systems-level view of dynamic phosphorylation networks. Front Genet (2014) 0.82
Phosphoproteomic analysis of protein phosphorylation networks in Tetrahymena thermophila, a model single-celled organism. Mol Cell Proteomics (2013) 0.82
Computational methods and opportunities for phosphorylation network medicine. Transl Cancer Res (2014) 0.80
Positive-unlabeled ensemble learning for kinase substrate prediction from dynamic phosphoproteomics data. Bioinformatics (2015) 0.80
A reverse-engineering approach to dissect post-translational modulators of transcription factor's activity from transcriptional data. BMC Bioinformatics (2015) 0.78
Missense variants of uncertain significance (VUS) altering the phosphorylation patterns of BRCA1 and BRCA2. PLoS One (2013) 0.78
The viral transactivator HBx protein exhibits a high potential for regulation via phosphorylation through an evolutionarily conserved mechanism. Infect Agent Cancer (2012) 0.77
Knowledge-Based Analysis for Detecting Key Signaling Events from Time-Series Phosphoproteomics Data. PLoS Comput Biol (2015) 0.77
PhosphoPredict: A bioinformatics tool for prediction of human kinase-specific phosphorylation substrates and sites by integrating heterogeneous feature selection. Sci Rep (2017) 0.75
Improved prediction of signal peptides: SignalP 3.0. J Mol Biol (2004) 48.40
A human gut microbial gene catalogue established by metagenomic sequencing. Nature (2010) 43.63
SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods (2011) 33.90
Enterotypes of the human gut microbiome. Nature (2011) 24.36
Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc (2007) 19.50
Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res (2003) 14.79
A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat Biotechnol (2007) 9.90
Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. Sci Signal (2010) 8.61
Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence. Proteomics (2004) 7.76
Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature (2010) 7.51
A new non-linear normalization method for reducing variability in DNA microarray experiments. Genome Biol (2002) 7.12
Richness of human gut microbiome correlates with metabolic markers. Nature (2013) 6.93
Prediction of lipoprotein signal peptides in Gram-negative bacteria. Protein Sci (2003) 6.85
Highly selective enrichment of phosphorylated peptides from peptide mixtures using titanium dioxide microcolumns. Mol Cell Proteomics (2005) 6.34
Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites. Glycobiology (2004) 6.13
Reliable prediction of T-cell epitopes using neural networks with novel sequence representations. Protein Sci (2003) 5.94
Proteomic analysis of post-translational modifications. Nat Biotechnol (2003) 5.87
The genome of the protist parasite Entamoeba histolytica. Nature (2005) 5.33
Analysis and prediction of leucine-rich nuclear export signals. Protein Eng Des Sel (2004) 5.15
Dynamic complex formation during the yeast cell cycle. Science (2005) 5.11
Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway. Mol Cell Proteomics (2005) 5.07
Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science (2007) 4.89
An Aboriginal Australian genome reveals separate human dispersals into Asia. Science (2011) 4.84
Feature-based prediction of non-classical and leaderless protein secretion. Protein Eng Des Sel (2004) 4.54
Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins. BMC Bioinformatics (2004) 4.44
Mining electronic health records: towards better research applications and clinical care. Nat Rev Genet (2012) 4.42
Human Proteinpedia enables sharing of human protein data. Nat Biotechnol (2008) 4.21
The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A (2007) 3.93
Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome. Trends Biotechnol (2002) 3.85
Linear motif atlas for phosphorylation-dependent signaling. Sci Signal (2008) 3.77
Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach. Bioinformatics (2004) 3.72
A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes. Proc Natl Acad Sci U S A (2008) 3.57
Phosphoproteomics of the Arabidopsis plasma membrane and a new phosphorylation site database. Plant Cell (2004) 3.51
Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature (2013) 3.45
Clustering patterns of cytotoxic T-lymphocyte epitopes in human immunodeficiency virus type 1 (HIV-1) proteins reveal imprints of immune evasion on HIV-1 global variation. J Virol (2002) 3.38
Co-evolution of transcriptional and post-translational cell-cycle regulation. Nature (2006) 3.28
Whole-genome pyrosequencing of an epidemic multidrug-resistant Acinetobacter baumannii strain belonging to the European clone II group. Antimicrob Agents Chemother (2008) 3.24
Vesiclepedia: a compendium for extracellular vesicles with continuous community annotation. PLoS Biol (2012) 3.18
Non-classical protein secretion in bacteria. BMC Microbiol (2005) 3.17
Cdk5 is essential for synaptic vesicle endocytosis. Nat Cell Biol (2003) 3.11
Prediction of proprotein convertase cleavage sites. Protein Eng Des Sel (2004) 3.05
Prediction of twin-arginine signal peptides. BMC Bioinformatics (2005) 3.03
Large-scale analysis of in vivo phosphorylated membrane proteins by immobilized metal ion affinity chromatography and mass spectrometry. Mol Cell Proteomics (2003) 2.98
Comparison of computational methods for the identification of cell cycle-regulated genes. Bioinformatics (2004) 2.83
A phosphoserine/threonine-binding pocket in AGC kinases and PDK1 mediates activation by hydrophobic motif phosphorylation. EMBO J (2002) 2.72
Highly selective enrichment of phosphorylated peptides using titanium dioxide. Nat Protoc (2006) 2.71
Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology. EMBO J (2013) 2.58
Metagenomic species profiling using universal phylogenetic marker genes. Nat Methods (2013) 2.51
Proteomic screen defines the Polo-box domain interactome and identifies Rock2 as a Plk1 substrate. EMBO J (2007) 2.48
Growth-rate regulated genes have profound impact on interpretation of transcriptome profiling in Saccharomyces cerevisiae. Genome Biol (2006) 2.43
Definition of supertypes for HLA molecules using clustering of specificity matrices. Immunogenetics (2004) 2.39
Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing. BMC Genomics (2005) 2.34
Prediction of glycosylation across the human proteome and the correlation to protein function. Pac Symp Biocomput (2002) 2.29
A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk. Cell (2013) 2.28
Alternative splicing in colon, bladder, and prostate cancer identified by exon array analysis. Mol Cell Proteomics (2008) 2.24
NESbase version 1.0: a database of nuclear export signals. Nucleic Acids Res (2003) 2.21
The pseudokinase domain of JAK2 is a dual-specificity protein kinase that negatively regulates cytokine signaling. Nat Struct Mol Biol (2011) 2.20
An integrative approach to CTL epitope prediction: a combined algorithm integrating MHC class I binding, TAP transport efficiency, and proteasomal cleavage predictions. Eur J Immunol (2005) 2.19
Using electronic patient records to discover disease correlations and stratify patient cohorts. PLoS Comput Biol (2011) 2.14
T-13910 DNA variant associated with lactase persistence interacts with Oct-1 and stimulates lactase promoter activity in vitro. Hum Mol Genet (2005) 2.05
SIMAC (sequential elution from IMAC), a phosphoproteomics strategy for the rapid separation of monophosphorylated from multiply phosphorylated peptides. Mol Cell Proteomics (2007) 1.98
Intrauterine exposure to mild analgesics is a risk factor for development of male reproductive disorders in human and rat. Hum Reprod (2010) 1.97
Modeling the adaptive immune system: predictions and simulations. Bioinformatics (2007) 1.95
A specific p47phox -serine phosphorylated by convergent MAPKs mediates neutrophil NADPH oxidase priming at inflammatory sites. J Clin Invest (2006) 1.92
Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples. J Clin Microbiol (2013) 1.86
Human gut microbes impact host serum metabolome and insulin sensitivity. Nature (2016) 1.85
Analytical strategies for phosphoproteomics. Proteomics (2009) 1.85
Prediction of proteasome cleavage motifs by neural networks. Protein Eng (2002) 1.81
A mass spectrometry-based proteomic approach for identification of serine/threonine-phosphorylated proteins by enrichment with phospho-specific antibodies: identification of a novel protein, Frigg, as a protein kinase A substrate. Mol Cell Proteomics (2002) 1.78
Alterations in gamma-actin and tubulin-targeted drug resistance in childhood leukemia. J Natl Cancer Inst (2006) 1.76
Mechanism for activation of the growth factor-activated AGC kinases by turn motif phosphorylation. EMBO J (2007) 1.74
Modification-specific proteomics of plasma membrane proteins: identification and characterization of glycosylphosphatidylinositol-anchored proteins released upon phospholipase D treatment. J Proteome Res (2006) 1.71
Modification-specific proteomics: strategies for characterization of post-translational modifications using enrichment techniques. Proteomics (2009) 1.66
Protein hydrogen exchange measured at single-residue resolution by electron transfer dissociation mass spectrometry. Anal Chem (2009) 1.65
Proteomic analysis of glycosylphosphatidylinositol-anchored membrane proteins. Mol Cell Proteomics (2003) 1.65
Continuum secondary structure captures protein flexibility. Structure (2002) 1.63
Simultaneous glycan-peptide characterization using hydrophilic interaction chromatography and parallel fragmentation by CID, higher energy collisional dissociation, and electron transfer dissociation MS applied to the N-linked glycoproteome of Campylobacter jejuni. Mol Cell Proteomics (2010) 1.63
Evaluation of the impact of some experimental procedures on different phosphopeptide enrichment techniques. Rapid Commun Mass Spectrom (2007) 1.57
Autophosphorylation of JAK2 on tyrosines 221 and 570 regulates its activity. Mol Cell Biol (2004) 1.55
Dynamic histone H3 epigenome marking during the intraerythrocytic cycle of Plasmodium falciparum. Proc Natl Acad Sci U S A (2009) 1.54
Protein interaction-based genome-wide analysis of incident coronary heart disease. Circ Cardiovasc Genet (2011) 1.54
Cyclebase.org--a comprehensive multi-organism online database of cell-cycle experiments. Nucleic Acids Res (2007) 1.50