Prediction of kinase-specific phosphorylation sites through an integrative model of protein context and sequence

[1]  K. Hagino-Yamagishi,et al.  [Oncogene]. , 2019, Gan to kagaku ryoho. Cancer & chemotherapy.

[2]  Benjamin Moore,et al.  Biochemical Journal , 2018, Nature.

[3]  Chiung-wen Chang,et al.  Structural Biology and Regulation of Protein Import into the Nucleus. , 2016, Journal of molecular biology.

[4]  Mikael Bodén,et al.  PhosphoPICK: modelling cellular context to map kinase-substrate phosphorylation events , 2015, Bioinform..

[5]  G. von Heijne,et al.  Tissue-based map of the human proteome , 2015, Science.

[6]  Alexandre Masselot,et al.  Visualization of protein sequence features using JavaScript and SVG with pViz.js , 2014, Bioinform..

[7]  Ahmed M. Mehdi,et al.  Dynamics of re-constitution of the human nuclear proteome after cell division is regulated by NLS-adjacent phosphorylation , 2014, Cell cycle.

[8]  L. Jensen,et al.  KinomeXplorer: an integrated platform for kinome biology studies , 2014, Nature Methods.

[9]  G. Chenevix-Trench,et al.  A fine-scale dissection of the DNA double-strand break repair machinery and its implications for breast cancer therapy , 2014, Nucleic acids research.

[10]  Cesare Furlanello,et al.  A promoter-level mammalian expression atlas , 2015 .

[11]  J. Crispino,et al.  The Aurora Kinases in Cell Cycle and Leukemia , 2014, Oncogene.

[12]  A. Magyar,et al.  Phosphorylation adjacent to the nuclear localization signal of human dUTPase abolishes nuclear import: structural and mechanistic insights. , 2013, Acta crystallographica. Section D, Biological crystallography.

[13]  Maria Jesus Martin,et al.  BioJS: an open source JavaScript framework for biological data visualization , 2013, Bioinform..

[14]  Christie S. Chang,et al.  The BioGRID interaction database: 2013 update , 2012, Nucleic Acids Res..

[15]  Damian Szklarczyk,et al.  STRING v9.1: protein-protein interaction networks, with increased coverage and integration , 2012, Nucleic Acids Res..

[16]  Amanda J. Guise,et al.  Aurora B-dependent Regulation of Class IIa Histone Deacetylases by Mitotic Nuclear Localization Signal Phosphorylation* , 2012, Molecular & Cellular Proteomics.

[17]  Bin Zhang,et al.  PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse , 2011, Nucleic Acids Res..

[18]  Mikael Bodén,et al.  Molecular basis for specificity of nuclear import and prediction of nuclear localization. , 2011, Biochimica et biophysica acta.

[19]  Jonathan J. Ellis,et al.  Predicting Protein Kinase Specificity: Predikin Update and Performance in the DREAM4 Challenge , 2011, PloS one.

[20]  Wendell A. Lim,et al.  Scaffold Proteins: Hubs for Controlling the Flow of Cellular Information , 2011, Science.

[21]  Mikael Bodén,et al.  A probabilistic model of nuclear import of proteins , 2011, Bioinform..

[22]  Yu Xue,et al.  GPS 2.1: enhanced prediction of kinase-specific phosphorylation sites with an algorithm of motif length selection. , 2011, Protein engineering, design & selection : PEDS.

[23]  G. Cingolani,et al.  Phosphorylation meets nuclear import: a review , 2010, Cell Communication and Signaling.

[24]  Mike Tyers,et al.  PhosphoGRID: a database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae , 2010, Database J. Biol. Databases Curation.

[25]  S. Brunak,et al.  Quantitative Phosphoproteomics Reveals Widespread Full Phosphorylation Site Occupancy During Mitosis , 2010, Science Signaling.

[26]  Ning Ma,et al.  BLAST+: architecture and applications , 2009, BMC Bioinformatics.

[27]  A. Giordano,et al.  Cell cycle kinases as therapeutic targets for cancer , 2009, Nature Reviews Drug Discovery.

[28]  M. Tomita,et al.  Six Classes of Nuclear Localization Signals Specific to Different Binding Grooves of Importin α* , 2009, Journal of Biological Chemistry.

[29]  M. Tomita,et al.  Design of peptide inhibitors for the importin alpha/beta nuclear import pathway by activity-based profiling. , 2008, Chemistry & biology.

[30]  S. Elledge,et al.  A quantitative atlas of mitotic phosphorylation , 2008, Proceedings of the National Academy of Sciences.

[31]  Hsien-Da Huang,et al.  KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns , 2007, Nucleic Acids Res..

[32]  Nikolaj Blom,et al.  NetPhosYeast: prediction of protein phosphorylation sites in yeast , 2007, Bioinform..

[33]  Frederick R. Cross,et al.  Multiple levels of cyclin specificity in cell-cycle control , 2007, Nature Reviews Molecular Cell Biology.

[34]  S. Gammeltoft,et al.  Phosphoproteomics toolbox: Computational biology, protein chemistry and mass spectrometry , 2006, FEBS letters.

[35]  Bostjan Kobe,et al.  Substrate specificity of protein kinases and computational prediction of substrates. , 2005, Biochimica et biophysica acta.

[36]  刘金明,et al.  IL-13受体α2降低血吸虫病肉芽肿的炎症反应并延长宿主存活时间[英]/Mentink-Kane MM,Cheever AW，Thompson RW，et al//Proc Natl Acad Sci U S A , 2005 .

[37]  Kunio Kondoh,et al.  The duration, magnitude and compartmentalization of ERK MAP kinase activity: mechanisms for providing signaling specificity , 2005, Journal of Cell Science.

[38]  S. Nef,et al.  Prostaglandin D2 induces nuclear import of the sex‐determining factor SOX9 via its cAMP‐PKA phosphorylation , 2005, The EMBO journal.

[39]  Guozhi Zhu,et al.  Protein Kinase Specificity: A Strategic Collaboration between Kinase Peptide Specificity and Substrate Recruitment , 2005, Cell cycle.

[40]  G. Crooks,et al.  WebLogo: a sequence logo generator. , 2004, Genome research.

[41]  N. Blom,et al.  Prediction of post‐translational glycosylation and phosphorylation of proteins from the amino acid sequence , 2004, Proteomics.

[42]  N. Blom,et al.  Identification of phosphorylation sites in protein kinase A substrates using artificial neural networks and mass spectrometry. , 2004, Journal of proteome research.

[43]  B. Kobe,et al.  Role of flanking sequences and phosphorylation in the recognition of the simian-virus-40 large T-antigen nuclear localization sequences by importin-alpha. , 2003, The Biochemical journal.

[44]  B. Kobe,et al.  Structural basis and prediction of substrate specificity in protein serine/threonine kinases , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[45]  T. Hunter,et al.  The Protein Kinase Complement of the Human Genome , 2002, Science.

[46]  J. Blenis,et al.  Identification of the tuberous sclerosis complex-2 tumor suppressor gene product tuberin as a target of the phosphoinositide 3-kinase/akt pathway. , 2002, Molecular cell.

[47]  Marc Montminy,et al.  Transcriptional regulation by the phosphorylation-dependent factor CREB , 2001, Nature Reviews Molecular Cell Biology.

[48]  R. White,et al.  Phosphorylation near nuclear localization signal regulates nuclear import of adenomatous polyposis coli protein. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[49]  Pierre Baldi,et al.  Assessing the accuracy of prediction algorithms for classification: an overview , 2000, Bioinform..

[50]  T. Hunter,et al.  Protein kinase B/Akt-mediated phosphorylation promotes nuclear exclusion of the winged helix transcription factor FKHR1. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[51]  B. Rost.  Twilight zone of protein sequence alignments. , 1999, Protein engineering.

[52]  Jiri Bartek,et al.  Phosphorylation of mammalian CDC6 by Cyclin A/CDK2 regulates its subcellular localization , 1999, The EMBO journal.

[53]  D. Jans,et al.  Regulation of protein transport to the nucleus: central role of phosphorylation. , 1996, Physiological reviews.

[54]  D. Jans.  The regulation of protein transport to the nucleus by phosphorylation. , 1995, The Biochemical journal.

[55]  Lee Kennett,et al.  For the Duration , 1985 .

[56]  Charles Elkan,et al.  Expectation Maximization Algorithm , 2010, Encyclopedia of Machine Learning.

[57]  J. Slingerland,et al.  PKB/Akt phosphorylates p27, impairs nuclear import of p27 and opposes p27-mediated G1 arrest , 2002, Nature Medicine.

[58]  V. Hu.  The Cell Cycle , 1994, GWUMC Department of Biochemistry Annual Spring Symposia.