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Staff at EMBL

Dr. Jonathon Blake

Bioinformatician
Genomics Core Facility

EMBL Heidelberg, Meyerhofstra├če 1, 69117 Heidelberg, Germany

E-mail: send a mail

Publications

Sequencing of a patient with balanced chromosome abnormalities and neurodevelopmental disease identifies disruption of multiple high risk Loci by structural variation. Blake, J., Riddell, A., Theiss, S., Gonzalez, A.P., Haase, B., Jauch, A., Janssen, J.W., Ibberson, D., Pavlinic, D., Moog, U., Benes, V. & Runz, H. PLoS One. 2014 Mar 13;9(3):e90894. doi: 10.1371/journal.pone.0090894. eCollection2014. Europe PMC

Disruption of EXOC6B in a patient with developmental delay, epilepsy, and a de novo balanced t(2;8) translocation. Fruhmesser, A., Blake, J., Haberlandt, E., Baying, B., Raeder, B., Runz, H., Spreiz, A., Fauth, C., Benes, V., Utermann, G., Zschocke, J. & Kotzot, D. Eur J Hum Genet. 2013 Feb 20. doi: 10.1038/ejhg.2013.18. Europe PMC

Actin-binding protein regulation by microRNAs as a novel microbial strategy to modulate phagocytosis by host cells: the case of N-Wasp and miR-142-3p. Bettencourt, P., Marion, S., Pires, D., Santos, L.F., Lastrucci, C., Carmo, N., Blake, J., Benes, V., Griffiths, G., Neyrolles, O., Lugo-Villarino, G. & Anes, E. Front Cell Infect Microbiol. 2013;3:19. doi: 10.3389/fcimb.2013.00019. Europe PMC

RNA-sequencing as useful screening tool in the combat against the misuse of anabolic agents. Riedmaier, I., Benes, V., Blake, J., Bretschneider, N., Zinser, C., Becker, C., Meyer, H.H. & Pfaffl, M.W. Anal Chem. 2012 Aug 7;84(15):6863-8. Epub 2012 Jul 13. Europe PMC

Genome-wide RNAi screening identifies human proteins with a regulatory function in the early secretory pathway. Simpson, J.C., Joggerst, B., Laketa, V., Verissimo, F., Cetin, C., Erfle, H., Bexiga, M.G., Singan, V.R., Heriche, J.K., Neumann, B., Mateos, A., Blake, J., Bechtel, S., Benes, V., Wiemann, S., Ellenberg, J. & Pepperkok, R. Nat Cell Biol. 2012 Jun 3;14(7):764-74. doi: 10.1038/ncb2510. Europe PMC

Role of CXCL13 in asthma: novel therapeutic target. Baay-Guzman, G.J., Huerta-Yepez, S., Vega, M.I., Aguilar-Leon, D., Campillos, M., Blake, J., Benes, V., Hernandez-Pando, R. & Teran, L.M. Chest. 2012 Apr;141(4):886-94. doi: 10.1378/chest.11-0633. Epub 2011 Oct 20. Europe PMC

Genome Sequencing of Pediatric Medulloblastoma Links Catastrophic DNA Rearrangements with TP53 Mutations. Rausch, T., Jones, D.T., Zapatka, M., Stutz, A.M., Zichner, T., Weischenfeldt, J., Jager, N., Remke, M., Shih, D., Northcott, P.A., Pfaff, E., Tica, J., Wang, Q., Massimi, L., Witt, H., Bender, S., Pleier, S., Cin, H., Hawkins, C., Beck, C., von Deimling, A., Hans, V., Brors, B., Eils, R., Scheurlen, W., Blake, J., Benes, V., Kulozik, A.E., Witt, O., Martin, D., Zhang, C., Porat, R., Merino, D.M., Wasserman, J., Jabado, N., Fontebasso, A., Bullinger, L., Rucker, F.G., Dohner, K., Dohner, H., Koster, J., Molenaar, J.J., Versteeg, R., Kool, M., Tabori, U., Malkin, D., Korshunov, A., Taylor, M.D., Lichter, P., Pfister, S.M. & Korbel, J.O. Cell. 2012 Jan 20;148(1-2):59-71. Europe PMC

Iron regulatory protein-1 and -2: transcriptome-wide definition of binding mRNAs and shaping of the cellular proteome by iron regulatory proteins. Sanchez, M., Galy, B., Schwanhaeusser, B., Blake, J., Bahr-Ivacevic, T., Benes, V., Selbach, M., Muckenthaler, M.U. & Hentze, M.W. Blood. 2011 Nov 24;118(22):e168-79. Epub 2011 Sep 22. Europe PMC

Inhibition of aurora kinases for tailored risk-adapted treatment of multiple myeloma. Hose, D., Reme, T., Meissner, T., Moreaux, J., Seckinger, A., Lewis, J.D., Benes, V., Benner, A., Hundemer, M., Hielscher, T., Shaughnessy JD, J.r, Barlogie, B., Neben, K., Kramer, A., Hillengass, J., Bertsch, U., Jauch, A., De Vos, J., Rossi, J.F., Mohler, T., Blake, J., Zimmermann, J., Klein, B. & Goldschmidt, H. Blood. 2009 Apr 30;113(18):4331-40. Epub 2009 Jan 26. Europe PMC

Aging and replicative senescence have related effects on human stem and progenitor cells. Wagner, W., Bork, S., Horn, P., Krunic, D., Walenda, T., Diehlmann, A., Benes, V., Blake, J., Huber, F.X., Eckstein, V., Boukamp, P. & Ho, A.D. PLoS One. 2009 Jun 9;4(6):e5846. Europe PMC

MicroRNA signatures predict oestrogen receptor, progesterone receptor and HER2/neu receptor status in breast cancer. Lowery, A.J., Miller, N., Devaney, A., McNeill, R.E., Davoren, P.A., Lemetre, C., Benes, V., Schmidt, S., Blake, J., Ball, G. & Kerin, M.J. Breast Cancer Res. 2009;11(3):R27. Epub 2009 May 11. Europe PMC

Transcriptome profiling of estrogen-regulated genes in human primary osteoblasts reveals an osteoblast-specific regulation of the insulin-like growth factor binding protein 4 gene. Denger, S., Bahr-Ivacevic, T., Brand, H., Reid, G., Blake, J., Seifert, M., Lin, C.Y., May, K., Benes, V., Liu, E.T. & Gannon, F. Mol Endocrinol. 2008 Feb;22(2):361-79. Epub 2007 Oct 25. Europe PMC

Replicative senescence of mesenchymal stem cells: a continuous and organized process. Wagner, W., Horn, P., Castoldi, M., Diehlmann, A., Bork, S., Saffrich, R., Benes, V., Blake, J., Pfister, S., Eckstein, V. & Ho, A.D. PLoS ONE. 2008 May 21;3(5):e2213. Europe PMC

Text mining for biology--the way forward: opinions from leading scientists. Altman, R.B., Bergman, C.M., Blake, J., Blaschke, C., Cohen, A., Gannon, F., Grivell, L., Hahn, U., Hersh, W., Hirschman, L., Jensen, L.J., Krallinger, M., Mons, B., O'Donoghue, S.I., Peitsch, M.C., Rebholz-Schuhmann, D., Shatkay, H. & Valencia, A. Genome Biol. 2008;9 Suppl 2:S7. Epub 2008 Sep 1. Europe PMC

The heterogeneity of human mesenchymal stem cell preparations--evidence from simultaneous analysis of proteomes and transcriptomes. Wagner, W., Feldmann RE, J.r, Seckinger, A., Maurer, M.H., Wein, F., Blake, J., Krause, U., Kalenka, A., Burgers, H.F., Saffrich, R., Wuchter, P., Kuschinsky, W. & Ho, A.D. Exp Hematol. 2006 Apr;34(4):536-48. Europe PMC

ChroCoLoc: an application for calculating the probability of co-localization of microarray gene expression. Blake, J., Schwager, C., Kapushesky, M. & Brazma, A. Bioinformatics. 2006 Mar 15;22(6):765-7. Epub 2005 Dec 23. Europe PMC

Comparative characteristics of mesenchymal stem cells from human bone marrow, adipose tissue, and umbilical cord blood. Wagner, W., Wein, F., Seckinger, A., Frankhauser, M., Wirkner, U., Krause, U., Blake, J., Schwager, C., Eckstein, V., Ansorge, W. & Ho, A.D. Exp Hematol 2005 Nov;33(11):1402-16. Europe PMC

Hematopoietic progenitor cells and cellular microenvironment: behavioral and molecular changes upon interaction. Wagner, W., Saffrich, R., Wirkner, U., Eckstein, V., Blake, J., Ansorge, A., Schwager, C., Wein, F., Miesala, K., Ansorge, W. & Ho, A.D. Stem Cells 2005 Sep;23(8):1180-91. Epub 2005 Jun 13. Europe PMC

Retroviral integration sites correlate with expressed genes in hematopoietic stem cells. Wagner, W., Laufs, S., Blake, J., Schwager, C., Wu, X., Zeller, J.W., Ho, A.D. & Fruehauf, S. Stem Cells 2005 Sep;23(8):1050-8. Europe PMC

Bloader--a batch loader application for MIAMExpress. Schwager, C. & Blake, J. Bioinformatics 2005 Apr 15;21(8):1727-9. Epub 2004 Dec 21. Europe PMC

Molecular evidence for stem cell function of the slow-dividing fraction among human hematopoietic progenitor cells by genome-wide analysis. Wagner, W., Ansorge, A., Wirkner, U., Eckstein, V., Schwager, C., Blake, J., Miesala, K., Selig, J., Saffrich, R., Ansorge, W. & Ho, A.D. Blood 2004 Aug 1;104(3):675-86. Epub 2004 Apr 13. Europe PMC

Embryonic stem cell-like features of testicular carcinoma in situ revealed by genome-wide gene expression profiling. Almstrup, K., Hoei-Hansen, C.E., Wirkner, U., Blake, J., Schwager, C., Ansorge, W., Nielsen, J.E., Skakkebaek, N.E., Rajpert-De Meyts, E. & Leffers, H. Cancer Res 2004 Jul 15;64(14):4736-43. Europe PMC

Functional annotation of a full-length mouse cDNA collection. Kawai, J., Shinagawa, A., Shibata, K., Yoshino, M., Itoh, M., Ishii, Y., Arakawa, T., Hara, A., Fukunishi, Y., Konno, H., Adachi, J., Fukuda, S., Aizawa, K., Izawa, M., Nishi, K., Kiyosawa, H., Kondo, S., Yamanaka, I., Saito, T., Okazaki, Y., Gojobori, T., Bono, H., Kasukawa, T., Saito, R., Kadota, K., Matsuda, H.A., Ashburner, M., Batalov, S., Casavant, T., Fleischmann, W., Gaasterland, T., Gissi, C., King, B., Kochiwa, H., Kuehl, P., Lewis, S., Matsuo, Y., Nikaido, I., Pesole, G., Quackenbush, J., Schriml, L.M., Staubli, F., Suzuki, R., Tomita, M., Wagner, L., Washio, T., Sakai, K., Okido, T., Furuno, M., Aono, H., Baldarelli, R., Barsh, G., Blake, J., Boffelli, D., Bojunga, N., Carninci, P., de Bonaldo, M.F., Brownstein, M.J., Bult, C., Fletcher, C., Fujita, M., Gariboldi, M., Gustincich, S., Hill, D., Hofmann, M., Hume, D.A., Kamiya, M., Lee, N.H., Lyons, P., Marchionni, L., Mashima, J., Mazzarelli, J., Mombaerts, P., Nordone, P., Ring, B., Ringwald, M., Rodriguez, I., Sakamoto, N., Sasaki, H., Sato, K., Schonbach, C., Seya, T., Shibata, Y., Storch, K.F., Suzuki, H., Toyo-oka, K., Wang, K.H., Weitz, C., Whittaker, C., Wilming, L., Wynshaw-Boris, A., Yoshida, K., Hasegawa, Y., Kawaji, H., Kohtsuki, S. & Hayashizaki, Y. Nature 2001 Feb 8;409(6821):685-90. Europe PMC