Published in Nat Biotechnol on March 01, 2007
Human Protein Reference Database--2009 update. Nucleic Acids Res (2008) 21.25
TFEB links autophagy to lysosomal biogenesis. Science (2011) 8.87
Discovering sequence motifs with arbitrary insertions and deletions. PLoS Comput Biol (2008) 4.10
Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry. Proc Natl Acad Sci U S A (2007) 4.01
Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs. Sci Signal (2010) 2.95
Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis. Sci Signal (2010) 2.79
Large-scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis. Mol Syst Biol (2008) 2.49
A cannabinoid link between mitochondria and memory. Nature (2016) 2.04
Phosphoproteomics for the masses. ACS Chem Biol (2010) 1.83
Identifying protein kinase target preferences using mass spectrometry. Am J Physiol Cell Physiol (2012) 1.70
Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis. Mol Biosyst (2011) 1.62
ATM regulates 3-methylpurine-DNA glycosylase and promotes therapeutic resistance to alkylating agents. Cancer Discov (2014) 1.52
Phosphoproteomics Identifies CK2 as a Negative Regulator of Beige Adipocyte Thermogenesis and Energy Expenditure. Cell Metab (2015) 1.49
Comparative phosphoproteomics reveals evolutionary and functional conservation of phosphorylation across eukaryotes. Genome Biol (2008) 1.40
Oncogene-specific activation of tyrosine kinase networks during prostate cancer progression. Proc Natl Acad Sci U S A (2012) 1.32
Modification site localization scoring integrated into a search engine. Mol Cell Proteomics (2011) 1.29
In-depth qualitative and quantitative profiling of tyrosine phosphorylation using a combination of phosphopeptide immunoaffinity purification and stable isotope dimethyl labeling. Mol Cell Proteomics (2009) 1.27
Two-site phosphorylation of EPRS coordinates multimodal regulation of noncanonical translational control activity. Mol Cell (2009) 1.27
Attention deficit/hyperactivity disorder-derived coding variation in the dopamine transporter disrupts microdomain targeting and trafficking regulation. J Neurosci (2012) 1.14
Investigation of receptor interacting protein (RIP3)-dependent protein phosphorylation by quantitative phosphoproteomics. Mol Cell Proteomics (2012) 1.13
Proteomic and phospho-proteomic profile of human platelets in basal, resting state: insights into integrin signaling. PLoS One (2009) 1.12
Resequencing and association analysis of the KALRN and EPHB1 genes and their contribution to schizophrenia susceptibility. Schizophr Bull (2010) 1.07
An extensive survey of tyrosine phosphorylation revealing new sites in human mammary epithelial cells. J Proteome Res (2009) 1.07
Toward a complete in silico, multi-layered embryonic stem cell regulatory network. Wiley Interdiscip Rev Syst Biol Med (2010) 1.06
Genome-wide analysis to predict protein sequence variations that change phosphorylation sites or their corresponding kinases. Nucleic Acids Res (2009) 1.05
Systems biology in physiology: the vasopressin signaling network in kidney. Am J Physiol Cell Physiol (2012) 1.04
Phosphorylation by casein kinase 1 regulates tonicity-induced osmotic response element-binding protein/tonicity enhancer-binding protein nucleocytoplasmic trafficking. J Biol Chem (2008) 1.02
Deep proteome profiling of Trichoplax adhaerens reveals remarkable features at the origin of metazoan multicellularity. Nat Commun (2013) 1.01
Tyrosine phosphorylation profiling in FGF-2 stimulated human embryonic stem cells. PLoS One (2011) 0.99
Structurally distinct Ca(2+) signaling domains of sperm flagella orchestrate tyrosine phosphorylation and motility. Cell (2014) 0.98
Phosphorylation directly regulates the intrinsic DNA cytidine deaminase activity of activation-induced deaminase and APOBEC3G protein. J Biol Chem (2011) 0.98
Genetic Analysis Reveals a Longevity-Associated Protein Modulating Endothelial Function and Angiogenesis. Circ Res (2015) 0.97
Proteome and phosphoproteome characterization reveals new response and defense mechanisms of Brachypodium distachyon leaves under salt stress. Mol Cell Proteomics (2013) 0.97
Modulation of GSK-3β activity in Venezuelan equine encephalitis virus infection. PLoS One (2012) 0.95
Discovery of phosphorylation motif mixtures in phosphoproteomics data. Bioinformatics (2008) 0.95
Differential proteomic analysis of mammalian tissues using SILAM. PLoS One (2011) 0.94
Posttranslational modifications of the retinoblastoma tumor suppressor protein as determinants of function. Genes Cancer (2012) 0.93
Understanding the role of PknJ in Mycobacterium tuberculosis: biochemical characterization and identification of novel substrate pyruvate kinase A. PLoS One (2010) 0.93
Quantitative phosphoproteomic analysis reveals a role for serine and threonine kinases in the cytoskeletal reorganization in early T cell receptor activation in human primary T cells. Mol Cell Proteomics (2012) 0.92
An integrated comparative phosphoproteomic and bioinformatic approach reveals a novel class of MPM-2 motifs upregulated in EGFRvIII-expressing glioblastoma cells. Mol Biosyst (2008) 0.92
In silico analysis of phosphoproteome data suggests a rich-get-richer process of phosphosite accumulation over evolution. Mol Cell Proteomics (2009) 0.91
Diverse functions for the semaphorin receptor PlexinD1 in development and disease. Dev Biol (2010) 0.91
Talking to chromatin: post-translational modulation of polycomb group function. Epigenetics Chromatin (2009) 0.90
Mining recent brain proteomic databases for ion channel phosphosite nuggets. J Gen Physiol (2010) 0.89
Encephalomyocarditis virus leader is phosphorylated by CK2 and syk as a requirement for subsequent phosphorylation of cellular nucleoporins. J Virol (2013) 0.89
Phosphorylation sites in the cerebral cavernous malformations complex. J Cell Sci (2011) 0.89
Cyclin-dependent kinase 5 activates guanine nucleotide exchange factor GIV/Girdin to orchestrate migration-proliferation dichotomy. Proc Natl Acad Sci U S A (2015) 0.89
Integrated phosphoproteomics analysis of a signaling network governing nutrient response and peroxisome induction. Mol Cell Proteomics (2010) 0.88
γ-Catenin at adherens junctions: mechanism and biologic implications in hepatocellular cancer after β-catenin knockdown. Neoplasia (2013) 0.88
The global phosphoproteome of Chlamydomonas reinhardtii reveals complex organellar phosphorylation in the flagella and thylakoid membrane. Mol Cell Proteomics (2014) 0.88
Bioinformatic analysis of proteomics data. BMC Syst Biol (2014) 0.87
Mutations in PAX2 associate with adult-onset FSGS. J Am Soc Nephrol (2014) 0.87
The Lottia gigantea shell matrix proteome: re-analysis including MaxQuant iBAQ quantitation and phosphoproteome analysis. Proteome Sci (2014) 0.87
Numerous proteins with unique characteristics are degraded by the 26S proteasome following monoubiquitination. Proc Natl Acad Sci U S A (2016) 0.87
Glycoprotein capture and quantitative phosphoproteomics indicate coordinated regulation of cell migration upon lysophosphatidic acid stimulation. Mol Cell Proteomics (2010) 0.86
Serine 111 phosphorylation regulates OCT4A protein subcellular distribution and degradation. J Biol Chem (2012) 0.86
Global Phosphoproteomic Mapping of Early Mitotic Exit in Human Cells Identifies Novel Substrate Dephosphorylation Motifs. Mol Cell Proteomics (2015) 0.85
Novel phosphorylation and ubiquitination sites regulate reactive oxygen species-dependent degradation of anti-apoptotic c-FLIP protein. J Biol Chem (2013) 0.85
Reduced-representation Phosphosignatures Measured by Quantitative Targeted MS Capture Cellular States and Enable Large-scale Comparison of Drug-induced Phenotypes. Mol Cell Proteomics (2016) 0.85
Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms. Bioinformatics (2014) 0.84
Phosphoproteomic analysis of platelets activated by pro-thrombotic oxidized phospholipids and thrombin. PLoS One (2014) 0.84
The induction of serine/threonine protein phosphorylations by a PDGFR/TrkA chimera in stably transfected PC12 cells. Mol Cell Proteomics (2011) 0.83
Discovery of protein phosphorylation motifs through exploratory data analysis. PLoS One (2011) 0.82
Large-scale phosphoproteome analysis in seedling leaves of Brachypodium distachyon L. BMC Genomics (2014) 0.82
JNK Signaling: Regulation and Functions Based on Complex Protein-Protein Partnerships. Microbiol Mol Biol Rev (2016) 0.81
Multiple post-translational modifications affect heterologous protein synthesis. J Biol Chem (2012) 0.81
Drosophila bestrophin-1 currents are regulated by phosphorylation via a CaMKII dependent mechanism. PLoS One (2013) 0.81
Differential Cav2.1 and Cav2.3 channel inhibition by baclofen and α-conotoxin Vc1.1 via GABAB receptor activation. J Gen Physiol (2014) 0.81
Protein kinase C and rho activated coiled coil protein kinase 2 (ROCK2) modulate Alzheimer's APP metabolism and phosphorylation of the Vps10-domain protein, SorL1. Mol Neurodegener (2010) 0.81
AMP-activated protein kinase phosphorylates EMCV, TMEV and SafV leader proteins at different sites. Virology (2014) 0.81
Motif-All: discovering all phosphorylation motifs. BMC Bioinformatics (2011) 0.80
Temporal profiling of lapatinib-suppressed phosphorylation signals in EGFR/HER2 pathways. Mol Cell Proteomics (2012) 0.80
Bioinformatics analysis reveals biophysical and evolutionary insights into the 3-nitrotyrosine post-translational modification in the human proteome. Open Biol (2013) 0.80
Protein kinases display minimal interpositional dependence on substrate sequence: potential implications for the evolution of signalling networks. Philos Trans R Soc Lond B Biol Sci (2012) 0.80
Increased activity of the vesicular soluble N-ethylmaleimide-sensitive factor attachment protein receptor TI-VAMP/VAMP7 by tyrosine phosphorylation in the Longin domain. J Biol Chem (2013) 0.80
Positive-unlabeled ensemble learning for kinase substrate prediction from dynamic phosphoproteomics data. Bioinformatics (2015) 0.80
The interactome of a PTB domain-containing adapter protein, Odin, revealed by SILAC. J Proteomics (2010) 0.80
A comparative study of ATP analogs for phosphorylation-dependent kinase-substrate crosslinking. Bioorg Med Chem (2014) 0.79
Akt-induced phosphorylation of N-CoR at serine 1450 contributes to its misfolded conformational dependent loss (MCDL) in acute myeloid leukemia of the M5 subtype. PLoS One (2013) 0.79
Proteomics and the analysis of proteomic data: 2013 overview of current protein-profiling technologies. Curr Protoc Bioinformatics (2013) 0.79
Protein Kinase CK2: Intricate Relationships within Regulatory Cellular Networks. Pharmaceuticals (Basel) (2017) 0.79
Methionine residues around phosphorylation sites are preferentially oxidized in vivo under stress conditions. Sci Rep (2017) 0.78
Regulation of lamin properties and functions: does phosphorylation do it all? Open Biol (2015) 0.78
Role of Novel Serine 316 Phosphorylation of the p65 Subunit of NF-κB in Differential Gene Regulation. J Biol Chem (2015) 0.78
Automatic annotation of experimentally derived, evolutionarily conserved post-translational modifications onto multiple genomes. Database (Oxford) (2011) 0.78
Interleukin-2 Receptor β Thr-450 Phosphorylation Is a Positive Regulator for Receptor Complex Stability and Activation of Signaling Molecules. J Biol Chem (2015) 0.78
Comparison of phosphorylation patterns across eukaryotes by discriminative N-gram analysis. BMC Bioinformatics (2015) 0.77
Novel function of the chromosome 7 open reading frame 41 gene to promote leukemic megakaryocyte differentiation by modulating TPA-induced signaling. Blood Cancer J (2014) 0.77
Phosphorylation within the cysteine-rich region of dystrophin enhances its association with β-dystroglycan and identifies a potential novel therapeutic target for skeletal muscle wasting. Hum Mol Genet (2014) 0.77
Integrating Phosphoproteomics and Bioinformatics to Study Brassinosteroid-Regulated Phosphorylation Dynamics in Arabidopsis. BMC Genomics (2015) 0.77
Dissecting the roles of tyrosines 490 and 785 of TrkA protein in the induction of downstream protein phosphorylation using chimeric receptors. J Biol Chem (2013) 0.77
Mapping the stabilome: a novel computational method for classifying metabolic protein stability. BMC Syst Biol (2012) 0.76
Hypofunctional TrkA Accounts for the Absence of Pain Sensitization in the African Naked Mole-Rat. Cell Rep (2016) 0.76
SCP1 regulates c-Myc stability and functions through dephosphorylating c-Myc Ser62. Oncogene (2015) 0.76
Identification of S-phase DNA damage-response targets in fission yeast reveals conservation of damage-response networks. Proc Natl Acad Sci U S A (2016) 0.76
A molecular basis for the presentation of phosphorylated peptides by HLA-B antigens. Mol Cell Proteomics (2016) 0.76
Orthogonal lipid sensors identify transbilayer asymmetry of plasma membrane cholesterol. Nat Chem Biol (2016) 0.76
Identification of a functional nuclear translocation sequence in hPPIP5K2. BMC Cell Biol (2015) 0.76
A phosphotyrosine switch for cargo sequestration at clathrin-coated buds. J Biol Chem (2014) 0.75
Exploiting publicly available biological and biochemical information for the discovery of novel short linear motifs. PLoS One (2011) 0.75
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
Human Protein Reference Database--2009 update. Nucleic Acids Res (2008) 21.25
ONCOMINE: a cancer microarray database and integrated data-mining platform. Neoplasia (2004) 17.08
The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol (2004) 16.08
Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res (2003) 14.79
Human protein reference database--2006 update. Nucleic Acids Res (2006) 12.16
Human protein reference database as a discovery resource for proteomics. Nucleic Acids Res (2004) 9.99
Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. Proc Natl Acad Sci U S A (2004) 9.42
The BioPAX community standard for pathway data sharing. Nat Biotechnol (2010) 9.19
Pyruvate kinase M2 is a PHD3-stimulated coactivator for hypoxia-inducible factor 1. Cell (2011) 7.33
Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat Genet (2006) 6.74
GCN5 acetyltransferase complex controls glucose metabolism through transcriptional repression of PGC-1alpha. Cell Metab (2006) 4.50
Exosomes: proteomic insights and diagnostic potential. Expert Rev Proteomics (2009) 4.27
Human Proteinpedia enables sharing of human protein data. Nat Biotechnol (2008) 4.21
Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry. Proc Natl Acad Sci U S A (2007) 4.01
Probabilistic model of the human protein-protein interaction network. Nat Biotechnol (2005) 3.99
Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome. Trends Biotechnol (2002) 3.85
p62 is a key regulator of nutrient sensing in the mTORC1 pathway. Mol Cell (2011) 3.46
An evaluation of human protein-protein interaction data in the public domain. BMC Bioinformatics (2006) 3.33
Vesiclepedia: a compendium for extracellular vesicles with continuous community annotation. PLoS Biol (2012) 3.18
A compendium of potential biomarkers of pancreatic cancer. PLoS Med (2009) 3.00
Enhanced CellClassifier: a multi-class classification tool for microscopy images. BMC Bioinformatics (2010) 2.84
A role for thymic stromal lymphopoietin in CD4(+) T cell development. J Exp Med (2004) 2.81
Biomarker discovery from pancreatic cancer secretome using a differential proteomic approach. Mol Cell Proteomics (2005) 2.66
NetPath: a public resource of curated signal transduction pathways. Genome Biol (2010) 2.62
Sequential phosphorylation of CCAAT enhancer-binding protein beta by MAPK and glycogen synthase kinase 3beta is required for adipogenesis. Proc Natl Acad Sci U S A (2005) 2.51
Human Protein Reference Database and Human Proteinpedia as discovery tools for systems biology. Methods Mol Biol (2009) 2.47
Comparison of ultracentrifugation, density gradient separation, and immunoaffinity capture methods for isolating human colon cancer cell line LIM1863-derived exosomes. Methods (2012) 2.46
Insights into the role of histone H3 and histone H4 core modifiable residues in Saccharomyces cerevisiae. Mol Cell Biol (2005) 2.33
Phosphoproteomic analysis of Her2/neu signaling and inhibition. Proc Natl Acad Sci U S A (2006) 2.30
Human Proteinpedia: a unified discovery resource for proteomics research. Nucleic Acids Res (2008) 2.30
From biological databases to platforms for biomedical discovery. Trends Biotechnol (2003) 2.27
K63-specific deubiquitination by two JAMM/MPN+ complexes: BRISC-associated Brcc36 and proteasomal Poh1. EMBO J (2009) 2.17
BioBuilder as a database development and functional annotation platform for proteins. BMC Bioinformatics (2004) 2.13
Quantitative proteomics using stable isotope labeling with amino acids in cell culture. Nat Protoc (2008) 2.07
Protein pyrophosphorylation by inositol pyrophosphates is a posttranslational event. Proc Natl Acad Sci U S A (2007) 2.03
Significant conservation of synthetic lethal genetic interaction networks between distantly related eukaryotes. Proc Natl Acad Sci U S A (2008) 2.01
Hsp70 and CHIP selectively mediate ubiquitination and degradation of hypoxia-inducible factor (HIF)-1alpha but Not HIF-2alpha. J Biol Chem (2009) 1.97
Chemical rescue of a mutant enzyme in living cells. Science (2006) 1.95
Global impact of oncogenic Src on a phosphotyrosine proteome. J Proteome Res (2008) 1.94
Comparative proteomics evaluation of plasma exosome isolation techniques and assessment of the stability of exosomes in normal human blood plasma. Proteomics (2013) 1.93
Comprehensive proteomic analysis of human pancreatic juice. J Proteome Res (2004) 1.93
Dynamic interplay between O-linked N-acetylglucosaminylation and glycogen synthase kinase-3-dependent phosphorylation. Mol Cell Proteomics (2007) 1.92
Disruption of Plasmodium falciparum development by antibodies against a conserved mosquito midgut antigen. Proc Natl Acad Sci U S A (2007) 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
Plasma Proteome Database as a resource for proteomics research. Proteomics (2005) 1.76
Right pulmonary artery-to-left atrium communication: report of 5 cases. Ann Thorac Surg (2005) 1.75
ExoCarta as a resource for exosomal research. J Extracell Vesicles (2012) 1.69
Stable isotope labeling with amino acids in cell culture (SILAC) for studying dynamics of protein abundance and posttranslational modifications. Sci STKE (2005) 1.67
Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis. Mol Biosyst (2011) 1.62
A proteomic approach for identification of secreted proteins during the differentiation of 3T3-L1 preadipocytes to adipocytes. Mol Cell Proteomics (2002) 1.61
A proteomic approach for quantitation of phosphorylation using stable isotope labeling in cell culture. Anal Chem (2003) 1.60
Histone demethylase JMJD2C is a coactivator for hypoxia-inducible factor 1 that is required for breast cancer progression. Proc Natl Acad Sci U S A (2012) 1.60
Construction of human activity-based phosphorylation networks. Mol Syst Biol (2013) 1.59
Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry. Mol Cell Proteomics (2011) 1.58
Context-specific effects of fibulin-5 (DANCE/EVEC) on cell proliferation, motility, and invasion. Fibulin-5 is induced by transforming growth factor-beta and affects protein kinase cascades. J Biol Chem (2002) 1.58
Comprehensive comparison of collision induced dissociation and electron transfer dissociation. Anal Chem (2008) 1.58
Mutant proteins as cancer-specific biomarkers. Proc Natl Acad Sci U S A (2011) 1.56
Comparisons of tyrosine phosphorylated proteins in cells expressing lung cancer-specific alleles of EGFR and KRAS. Proc Natl Acad Sci U S A (2008) 1.51
Genome annotation of Anopheles gambiae using mass spectrometry-derived data. BMC Genomics (2005) 1.51
Heat shock protein 90 as a drug target against protozoan infections: biochemical characterization of HSP90 from Plasmodium falciparum and Trypanosoma evansi and evaluation of its inhibitor as a candidate drug. J Biol Chem (2010) 1.49
Proteogenomics. Proteomics (2011) 1.48
Proteome profiling of exosomes derived from human primary and metastatic colorectal cancer cells reveal differential expression of key metastatic factors and signal transduction components. Proteomics (2013) 1.46
Genomewide mRNA profiling of esophageal squamous cell carcinoma for identification of cancer biomarkers. Cancer Biol Ther (2009) 1.45
Two distinct populations of exosomes are released from LIM1863 colon carcinoma cell-derived organoids. Mol Cell Proteomics (2012) 1.44
Malaria parasite invasion of the mosquito salivary gland requires interaction between the Plasmodium TRAP and the Anopheles saglin proteins. PLoS Pathog (2009) 1.44
Systematic interactome mapping and genetic perturbation analysis of a C. elegans TGF-beta signaling network. Mol Cell (2004) 1.40
New markers of pancreatic cancer identified through differential gene expression analyses: claudin 18 and annexin A8. Am J Surg Pathol (2008) 1.39
Evaluation of several MS/MS search algorithms for analysis of spectra derived from electron transfer dissociation experiments. Anal Chem (2009) 1.38
Utility of bile duct brushings for the early detection of cholangiocarcinoma in patients with primary sclerosing cholangitis. J Clin Gastroenterol (2006) 1.38
Tyrosine phosphorylation mapping of the epidermal growth factor receptor signaling pathway. J Biol Chem (2001) 1.37
A comprehensive map of the human urinary proteome. J Proteome Res (2011) 1.34
Plasma Proteome Database as a resource for proteomics research: 2014 update. Nucleic Acids Res (2013) 1.34
Human protein reference database and human proteinpedia as discovery resources for molecular biotechnology. Mol Biotechnol (2011) 1.31
Phosphoproteome analysis of HeLa cells using stable isotope labeling with amino acids in cell culture (SILAC). J Proteome Res (2005) 1.29
Identification of miR-21 targets in breast cancer cells using a quantitative proteomic approach. Proteomics (2009) 1.28
A quantitative proteomic approach for identification of potential biomarkers in hepatocellular carcinoma. J Proteome Res (2008) 1.27