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Literature

Kinome profiling and signal transduction

  • J. Scholma, G. M. Fuhler, J. Joore, M. Hulsman, S. Schivo, A. F. List, M. J. T. Reinders, M. P. Peppelenbosch & J. N. Post. Improved intra-array and interarray normalization of peptide microarray phosphorylation for phosphorylome and kinome profiling by rational selection of relevant spots. Sci. Rep. 2016
  • Review Article – Kinome Profiling, Scientifica (2012), M. P. Peppelenbosch 
  • Azijli K, Yuvaraj S, Peppelenbosch MP, Würdinger T, Dekker H, Joore J, van Dijk E, Quax WJ, Peters GJ, de Jong S, Kruyt FA. Kinome profiling of non-canonical TRAIL signaling reveals RIP1-Src-STAT3-dependent invasion in resistant non-small cell lung cancer cells. J Cell Sci. 2012 Oct 1;125(Pt 19):4651-61. doi: 10.1242/jcs.109587. Epub 2012 Jul 13. PubMed PMID: 22797920.
  • Snir E, Joore J, Timmerman P, Yitzchaik S. Monitoring selectivity in kinase-promoted phosphorylation of densely packed peptide monolayers using label-free electrochemical detection. Langmuir. 2011 Sep 6;27(17):11212-21. doi: 10.1021/la202247m. Epub 2011 Jul 29. PubMed PMID: 21774536.
  • Berberich N, Uhl B, Joore J, Schmerwitz UK, Mayer BA, Reichel CA, Krombach F, Zahler S, Vollmar AM, Fürst R. Roscovitine blocks leukocyte extravasation by inhibition of cyclin-dependent kinases 5 and 9. Br J Pharmacol. 2011 Jul;163(5):1086-98. doi: 10.1111/j.1476-5381.2011.01309.x. PubMed PMID: 21391976; PubMed Central PMCID: PMC3130954.
  • Schmerwitz UK, Sass G, Khandoga AG, Joore J, Mayer BA, Berberich N, Totzke F, Krombach F, Tiegs G, Zahler S, Vollmar AM, Fürst R. Flavopiridol protects against inflammation by attenuating leukocyte-endothelial interaction via inhibition of cyclin-dependent kinase 9. Arterioscler Thromb Vasc Biol. 2011 Feb;31(2):280-8. doi: 10.1161/ATVBAHA.110.213934. Epub 2010 Nov 18. PubMed PMID: 21088252.
  • Amanchy R, Kandasamy K, Mathivanan S, Periaswamy B, Reddy R, Yoon WH, Joore J, Beer MA, Cope L, Pandey A. Identification of Novel Phosphorylation Motifs Through an Integrative Computational and Experimental Analysis of the Human Phosphoproteome. J Proteomics Bioinform. 2011;4(2):22-35. PubMed PMID: 21720494; PubMed Central PMCID: PMC3124146.
  • Parikh K, Diks SH, Tuynman JH, Verhaar A, Löwenberg M, Hommes DW, Joore J, Pandey A, Peppelenbosch MP. Comparison of peptide array substrate phosphorylation of c-Raf and mitogen activated protein kinase kinase kinase 8. PLoS One. 2009 Jul 30;4(7):e6440. doi: 10.1371/journal.pone.0006440. PubMed PMID: 19649278; PubMed Central PMCID: PMC2713828.
  • Rothmeier AS, Ischenko I, Joore J, Garczarczyk D, Fürst R, Bruns CJ, Vollmar AM, Zahler S. Investigation of the marine compound spongistatin 1 links the inhibition of PKCalpha translocation to nonmitotic effects of tubulin antagonism in angiogenesis. FASEB J. 2009 Apr;23(4):1127-37. doi: 10.1096/fj.08-117127. Epub 2008 Dec 4. PubMed PMID: 19056838.
  • Amanchy R, Zhong J, Molina H, Chaerkady R, Iwahori A, Kalume DE, Grønborg M, Joore J, Cope L, Pandey A. Identification of c-Src tyrosine kinase substrates using mass spectrometry and peptide microarrays. J Proteome Res. 2008 Sep;7(9):3900-10. doi: 10.1021/pr800198w. Epub 2008 Aug 13. PubMed PMID: 18698806; PubMed Central PMCID: PMC2646669.
  • de la Fuente van Bentem S, Anrather D, Dohnal I, Roitinger E, Csaszar E, Joore J, Buijnink J, Carreri A, Forzani C, Lorkovic ZJ, Barta A, Lecourieux D, Verhounig A, Jonak C, Hirt H. Site-specific phosphorylation profiling of Arabidopsis proteins by mass spectrometry and peptide chip analysis. J Proteome Res. 2008 Jun;7(6):2458-70. doi: 10.1021/pr8000173. Epub 2008 Apr 24. PubMed PMID: 18433157.
  • Merckx A, Echalier A, Langford K, Sicard A, Langsley G, Joore J, Doerig C, Noble M, Endicott J. Structures of P. falciparum protein kinase 7 identify an activation motif and leads for inhibitor design. Structure. 2008 Feb;16(2):228-38. doi: 10.1016/j.str.2007.11.014. PubMed PMID: 18275814.
  • Diks SH, Parikh K, van der Sijde M, Joore J, Ritsema T, Peppelenbosch MP. Evidence for a minimal eukaryotic phosphoproteome? PLoS One. 2007 Aug 22;2(8):e777. PubMed PMID: 17712425; PubMed Central PMCID: PMC1945084.
  • Ritsema T, Joore J, van Workum W, Pieterse CM. Kinome profiling of Arabidopsis using arrays of kinase consensus substrates. Plant Methods. 2007 Feb 12;3:3. PubMed PMID: 17295910; PubMed Central PMCID: PMC1803769.
  • van Baal JW, Diks SH, Wanders RJ, Rygiel AM, Milano F, Joore J, Bergman JJ, Peppelenbosch MP, Krishnadath KK. Comparison of kinome profiles of Barrett’s esophagus with normal squamous esophagus and normal gastric cardia. Cancer Res. 2006 Dec 15;66(24):11605-12. PubMed PMID: 17178854.
  • Diks SH, Kok K, O’Toole T, Hommes DW, van Dijken P, Joore J, Peppelenbosch MP. Kinome profiling for studying lipopolysaccharide signal transduction in human peripheral blood mononuclear cells. J Biol Chem. 2004 Nov 19;279(47):49206-13. Epub 2004 Sep 7. PubMed PMID: 15355981.
  • Joore J, van de Water S, Betist M, van den Eijnden-van Raaij A, Zivkovic D. Protein kinase A is involved in the induction of early mesodermal marker genes by activin. Mech Dev. 1998 Dec;79(1-2):5-15. PubMed PMID: 10349616.

Phosphoproteomics

Erasmus MC

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