Published in Bioinformatics on February 05, 2007
GPS 2.0, a tool to predict kinase-specific phosphorylation sites in hierarchy. Mol Cell Proteomics (2008) 4.33
PhosphoGRID: a database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae. Database (Oxford) (2010) 1.78
Predicting protein post-translational modifications using meta-analysis of proteome scale data sets. Mol Cell Proteomics (2008) 1.76
The sphingolipid long-chain base-Pkh1/2-Ypk1/2 signaling pathway regulates eisosome assembly and turnover. J Biol Chem (2008) 1.45
Prediction of kinase-specific phosphorylation sites using conditional random fields. Bioinformatics (2008) 1.38
The PhosphoGRID Saccharomyces cerevisiae protein phosphorylation site database: version 2.0 update. Database (Oxford) (2013) 1.20
Prediction of ubiquitination sites by using the composition of k-spaced amino acid pairs. PLoS One (2011) 1.18
Posttranslational regulation impacts the fate of duplicated genes. Proc Natl Acad Sci U S A (2009) 1.16
Toward a complete in silico, multi-layered embryonic stem cell regulatory network. Wiley Interdiscip Rev Syst Biol Med (2010) 1.06
Phosphorylation of the yeast nitrate transporter Ynt1 is essential for delivery to the plasma membrane during nitrogen limitation. J Biol Chem (2008) 0.99
Evaluation and properties of the budding yeast phosphoproteome. Mol Cell Proteomics (2012) 0.96
Genome and proteome annotation: organization, interpretation and integration. J R Soc Interface (2009) 0.95
PostMod: sequence based prediction of kinase-specific phosphorylation sites with indirect relationship. BMC Bioinformatics (2010) 0.94
Reconstruction and logical modeling of glucose repression signaling pathways in Saccharomyces cerevisiae. BMC Syst Biol (2009) 0.93
Identifying protein phosphorylation sites with kinase substrate specificity on human viruses. PLoS One (2012) 0.93
Charge environments around phosphorylation sites in proteins. BMC Struct Biol (2008) 0.91
Prediction of phosphothreonine sites in human proteins by fusing different features. Sci Rep (2016) 0.86
Alterations in the Ure2 αCap domain elicit different GATA factor responses to rapamycin treatment and nitrogen limitation. J Biol Chem (2012) 0.86
PhosTryp: a phosphorylation site predictor specific for parasitic protozoa of the family trypanosomatidae. BMC Genomics (2011) 0.84
A phosphodegron controls nutrient-induced proteasomal activation of the signaling protease Ssy5. Mol Biol Cell (2011) 0.83
Bioinformatics and evolutionary insight on the spike glycoprotein gene of QX-like and Massachusetts strains of infectious bronchitis virus. Virol J (2012) 0.82
Phosphorylation provides a negative mode of regulation for the yeast Rab GTPase Sec4p. PLoS One (2011) 0.82
Exploiting holistic approaches to model specificity in protein phosphorylation. Front Genet (2014) 0.81
Rice_Phospho 1.0: a new rice-specific SVM predictor for protein phosphorylation sites. Sci Rep (2015) 0.81
The regulation of coenzyme q biosynthesis in eukaryotic cells: all that yeast can tell us. Mol Syndromol (2014) 0.81
GB Virus C/Hepatitis G Virus Envelope Glycoprotein E2: Computational Molecular Features and Immunoinformatics Study. Hepat Mon (2013) 0.79
The Aquaporin Splice Variant NbXIP1;1α Is Permeable to Boric Acid and Is Phosphorylated in the N-terminal Domain. Front Plant Sci (2016) 0.78
PhosphoRice: a meta-predictor of rice-specific phosphorylation sites. Plant Methods (2012) 0.78
FUN26 (function unknown now 26) protein from saccharomyces cerevisiae is a broad selectivity, high affinity, nucleoside and nucleobase transporter. J Biol Chem (2014) 0.77
Characterization of PROPPIN-Phosphoinositide Binding and Role of Loop 6CD in PROPPIN-Membrane Binding. Biophys J (2015) 0.77
PhosphoChain: a novel algorithm to predict kinase and phosphatase networks from high-throughput expression data. Bioinformatics (2013) 0.77
δ-COP contains a helix C-terminal to its longin domain key to COPI dynamics and function. Proc Natl Acad Sci U S A (2016) 0.76
Assigning quantitative function to post-translational modifications reveals multiple sites of phosphorylation that tune yeast pheromone signaling output. PLoS One (2013) 0.75
Identification of She3 as an SCF(Grr1) substrate in budding yeast. PLoS One (2012) 0.75
Probabilistic Prediction of Protein Phosphorylation Sites Using Classification Relevance Units Machines. ACM SIGAPP Appl Comput Rev (2012) 0.75
The basidiomycete Ustilago maydis has two plasma membrane H⁺-ATPases related to fungi and plants. J Bioenerg Biomembr (2013) 0.75
Ypt4 and lvs1 regulate vacuolar size and function in Schizosaccharomyces pombe. Cell Logist (2017) 0.75
Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res (2003) 14.79
Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. Sci Signal (2010) 8.61
Emerging landscape of oncogenic signatures across human cancers. Nat Genet (2013) 6.48
Highly selective enrichment of phosphorylated peptides from peptide mixtures using titanium dioxide microcolumns. Mol Cell Proteomics (2005) 6.34
Proteomic analysis of post-translational modifications. Nat Biotechnol (2003) 5.87
Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway. Mol Cell Proteomics (2005) 5.07
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
Human Proteinpedia enables sharing of human protein data. Nat Biotechnol (2008) 4.21
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
Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs. Nat Biotechnol (2009) 3.66
Phosphoproteomics of the Arabidopsis plasma membrane and a new phosphorylation site database. Plant Cell (2004) 3.51
Prediction of proprotein convertase cleavage sites. Protein Eng Des Sel (2004) 3.05
Large-scale analysis of in vivo phosphorylated membrane proteins by immobilized metal ion affinity chromatography and mass spectrometry. Mol Cell Proteomics (2003) 2.98
Highly selective enrichment of phosphorylated peptides using titanium dioxide. Nat Protoc (2006) 2.71
The pseudokinase domain of JAK2 is a dual-specificity protein kinase that negatively regulates cytokine signaling. Nat Struct Mol Biol (2011) 2.20
SIMAC (sequential elution from IMAC), a phosphoproteomics strategy for the rapid separation of monophosphorylated from multiply phosphorylated peptides. Mol Cell Proteomics (2007) 1.98
A specific p47phox -serine phosphorylated by convergent MAPKs mediates neutrophil NADPH oxidase priming at inflammatory sites. J Clin Invest (2006) 1.92
Analytical strategies for phosphoproteomics. Proteomics (2009) 1.85
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
Identification of phosphorylation sites in protein kinase A substrates using artificial neural networks and mass spectrometry. J Proteome Res (2004) 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
Electron transfer dissociation facilitates the measurement of deuterium incorporation into selectively labeled peptides with single residue resolution. J Am Chem Soc (2008) 1.47
Cell cycle-specific UNG2 phosphorylations regulate protein turnover, activity and association with RPA. EMBO J (2007) 1.46
The sphingolipid long-chain base-Pkh1/2-Ypk1/2 signaling pathway regulates eisosome assembly and turnover. J Biol Chem (2008) 1.45
Identification of ischemia-regulated phosphorylation sites in connexin43: A possible target for the antiarrhythmic peptide analogue rotigaptide (ZP123). J Mol Cell Cardiol (2006) 1.45
Proteomics in chromatin biology and epigenetics: Elucidation of post-translational modifications of histone proteins by mass spectrometry. J Proteomics (2012) 1.44
NetAcet: prediction of N-terminal acetylation sites. Bioinformatics (2004) 1.42
Stable isotope labeling of Arabidopsis thaliana cells and quantitative proteomics by mass spectrometry. Mol Cell Proteomics (2005) 1.39
Peptide sequencing and characterization of post-translational modifications by enhanced ion-charging and liquid chromatography electron-transfer dissociation tandem mass spectrometry. Anal Chem (2007) 1.35
Identification by a differential proteomic approach of heat shock protein 27 as a potential marker of atherosclerosis. Circulation (2004) 1.33
Transcriptional co-activator protein p100 interacts with snRNP proteins and facilitates the assembly of the spliceosome. Nucleic Acids Res (2007) 1.31
Global histone analysis by mass spectrometry reveals a high content of acetylated lysine residues in the malaria parasite Plasmodium falciparum. J Proteome Res (2009) 1.30
Quantitative mass spectrometry of histones H3.2 and H3.3 in Suz12-deficient mouse embryonic stem cells reveals distinct, dynamic post-translational modifications at Lys-27 and Lys-36. Mol Cell Proteomics (2010) 1.23
VEMS 3.0: algorithms and computational tools for tandem mass spectrometry based identification of post-translational modifications in proteins. J Proteome Res (2005) 1.22
Microbial community structure of Arctic multiyear sea ice and surface seawater by 454 sequencing of the 16S RNA gene. ISME J (2011) 1.22
Metastasis-related plasma membrane proteins of human breast cancer cells identified by comparative quantitative mass spectrometry. Mol Cell Proteomics (2009) 1.21
WAVE regulatory complex activation by cooperating GTPases Arf and Rac1. Proc Natl Acad Sci U S A (2011) 1.20
Autophosphorylation is essential for the in vivo function of the Lotus japonicus Nod factor receptor 1 and receptor-mediated signalling in cooperation with Nod factor receptor 5. Plant J (2010) 1.17
p130Cas mediates the transforming properties of the anaplastic lymphoma kinase. Blood (2005) 1.16
Functional heterogeneity within the CD44 high human breast cancer stem cell-like compartment reveals a gene signature predictive of distant metastasis. Mol Med (2012) 1.15
The SH2 domain interaction landscape. Cell Rep (2013) 1.13
Phosphorylation of JAK2 at serine 523: a negative regulator of JAK2 that is stimulated by growth hormone and epidermal growth factor. Mol Cell Biol (2006) 1.12
Middle-down hybrid chromatography/tandem mass spectrometry workflow for characterization of combinatorial post-translational modifications in histones. Proteomics (2014) 1.11
The tyrosine phosphatase Shp2 interacts with NPM-ALK and regulates anaplastic lymphoma cell growth and migration. Cancer Res (2007) 1.08
Analysis of posttranslational modifications of proteins by tandem mass spectrometry. Biotechniques (2006) 1.08
Analysis of histidine phosphorylation using tandem MS and ion-electron reactions. Anal Chem (2007) 1.07
Assessment of lectin and HILIC based enrichment protocols for characterization of serum glycoproteins by mass spectrometry. J Proteomics (2008) 1.06
BRAG1, a Sec7 domain-containing protein, is a component of the postsynaptic density of excitatory synapses. Brain Res (2006) 1.06
TiO(2)-based phosphoproteomic analysis of the plasma membrane and the effects of phosphatase inhibitor treatment. J Proteome Res (2008) 1.05
Efficient isolation and quantitative proteomic analysis of cancer cell plasma membrane proteins for identification of metastasis-associated cell surface markers. J Proteome Res (2009) 1.05
Feedback inactivation of D-serine synthesis by NMDA receptor-elicited translocation of serine racemase to the membrane. Proc Natl Acad Sci U S A (2009) 1.02
Kinase-specific prediction of protein phosphorylation sites. Methods Mol Biol (2009) 1.02
Phosphosite mapping of P-type plasma membrane H+-ATPase in homologous and heterologous environments. J Biol Chem (2011) 1.02
High-oxygen packaging atmosphere influences protein oxidation and tenderness of porcine longissimus dorsi during chill storage. Meat Sci (2007) 1.00
Quantitative assessment of in-solution digestion efficiency identifies optimal protocols for unbiased protein analysis. Mol Cell Proteomics (2013) 0.99
Quantitative proteomics identifies Gemin5, a scaffolding protein involved in ribonucleoprotein assembly, as a novel partner for eukaryotic initiation factor 4E. J Proteome Res (2006) 0.99
Highly Efficient Phosphopeptide Enrichment by Calcium Phosphate Precipitation Combined with Subsequent IMAC Enrichment. Mol Cell Proteomics (2007) 0.98
Utility of immonium ions for assignment of epsilon-N-acetyllysine-containing peptides by tandem mass spectrometry. Anal Chem (2008) 0.98
Serum protein profiling by solid phase extraction and mass spectrometry: a future diagnostics tool? Proteomics (2009) 0.98
Quantitative phosphoproteomics of tomato mounting a hypersensitive response reveals a swift suppression of photosynthetic activity and a differential role for hsp90 isoforms. J Proteome Res (2009) 0.97
Quantitative proteomics analysis of Streptomyces coelicolor development demonstrates that onset of secondary metabolism coincides with hypha differentiation. Mol Cell Proteomics (2010) 0.96
Precision mapping of coexisting modifications in histone H3 tails from embryonic stem cells by ETD-MS/MS. Anal Chem (2013) 0.96
Structural analysis and tissue localization of human C4.4A: a protein homologue of the urokinase receptor. Biochem J (2004) 0.96
Towards liquid chromatography time-scale peptide sequencing and characterization of post-translational modifications in the negative-ion mode using electron detachment dissociation tandem mass spectrometry. J Am Soc Mass Spectrom (2008) 0.96
Reproducibility of mass spectrometry based protein profiles for diagnosis of breast cancer across clinical studies: a systematic review. J Proteome Res (2008) 0.96
Phosphorylation of formate dehydrogenase in potato tuber mitochondria. J Biol Chem (2003) 0.95
Coronavirus 3CLpro proteinase cleavage sites: possible relevance to SARS virus pathology. BMC Bioinformatics (2004) 0.95
Allosteric activation of coagulation factor VIIa visualized by hydrogen exchange. J Biol Chem (2006) 0.94
Enrichment and separation of mono- and multiply phosphorylated peptides using sequential elution from IMAC prior to mass spectrometric analysis. Methods Mol Biol (2009) 0.94
β2-Syntrophin is a Cdk5 substrate that restrains the motility of insulin secretory granules. PLoS One (2010) 0.93
Cell-selective labeling using amino acid precursors for proteomic studies of multicellular environments. Nat Methods (2013) 0.92
Database-independent, database-dependent, and extended interpretation of peptide mass spectra in VEMS V2.0. Proteomics (2004) 0.92
Distinction between human cytochrome P450 (CYP) isoforms and identification of new phosphorylation sites by mass spectrometry. J Proteome Res (2008) 0.92
Combined experimental and statistical strategy for mass spectrometry based serum protein profiling for diagnosis of breast cancer: a case-control study. J Proteome Res (2008) 0.92
Optimized preparation of urine samples for two-dimensional electrophoresis and initial application to patient samples. Clin Biochem (2002) 0.91
Functional domain analysis of the Remorin protein LjSYMREM1 in Lotus japonicus. PLoS One (2012) 0.91
Quantitation of multisite EGF receptor phosphorylation using mass spectrometry and a novel normalization approach. J Proteome Res (2007) 0.90
Time-resolved quantitative proteome analysis of in vivo intestinal development. Mol Cell Proteomics (2010) 0.90
Genetic and molecular interactions of the Erv41p-Erv46p complex involved in transport between the endoplasmic reticulum and Golgi complex. J Cell Sci (2006) 0.90
Serum protein profiling by miniaturized solid-phase extraction and matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun Mass Spectrom (2005) 0.90
Unraveling the pathogenesis of type 1 diabetes with proteomics: present and future directions. Mol Cell Proteomics (2005) 0.89
Quantitative profiling of PE, MMPE, DMPE, and PC lipid species by multiple precursor ion scanning: a tool for monitoring PE metabolism. Biochim Biophys Acta (2011) 0.89
Proteomics and the dynamic plasma membrane: Quo Vadis? Proteomics (2010) 0.89
Atorvastatin modulates the profile of proteins released by human atherosclerotic plaques. Eur J Pharmacol (2007) 0.88
Identification of novel genes regulated in the developing human ventral mesencephalon. Exp Neurol (2006) 0.88
NetPhosBac - a predictor for Ser/Thr phosphorylation sites in bacterial proteins. Proteomics (2009) 0.88
Midbrain expression of Delta-like 1 homologue is regulated by GDNF and is associated with dopaminergic differentiation. Exp Neurol (2007) 0.88
Modification-specific proteomics in plant biology. J Proteomics (2010) 0.88
The vacuolar V1/V0-ATPase is involved in the release of the HOPS subunit Vps41 from vacuoles, vacuole fragmentation and fusion. FEBS Lett (2008) 0.88
Characterization of the human atheroma plaque secretome by proteomic analysis. Methods Mol Biol (2007) 0.88