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Staff at EMBL

Thomas Zichner

Postdoctoral Fellow
Korbel Group

EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

E-mail: send a mail

Publications

Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma. Northcott, P.A., Lee, C., Zichner, T., Stutz, A.M., Erkek, S., Kawauchi, D., Shih, D.J., Hovestadt, V., Zapatka, M., Sturm, D., Jones, D.T., Kool, M., Remke, M., Cavalli, F.M., Zuyderduyn, S., Bader, G.D., VandenBerg, S., Esparza, L.A., Ryzhova, M., Wang, W., Wittmann, A., Stark, S., Sieber, L., Seker-Cin, H., Linke, L., Kratochwil, F., Jager, N., Buchhalter, I., Imbusch, C.D., Zipprich, G., Raeder, B., Schmidt, S., Diessl, N., Wolf, S., Wiemann, S., Brors, B., Lawerenz, C., Eils, J., Warnatz, H.J., Risch, T., Yaspo, M.L., Weber, U.D., Bartholomae, C.C., von Kalle, C., Turanyi, E., Hauser, P., Sanden, E., Darabi, A., Siesjo, P., Sterba, J., Zitterbart, K., Sumerauer, D., van Sluis, P., Versteeg, R., Volckmann, R., Koster, J., Schuhmann, M.U., Ebinger, M., Grimes, H.L., Robinson, G.W., Gajjar, A., Mynarek, M., von Hoff, K., Rutkowski, S., Pietsch, T., Scheurlen, W., Felsberg, J., Reifenberger, G., Kulozik, A.E., von Deimling, A., Witt, O., Eils, R., Gilbertson, R.J., Korshunov, A., Taylor, M.D., Lichter, P., Korbel, J.O., Wechsler-Reya, R.J. & Pfister, S.M. Nature. 2014 Jun 22. doi: 10.1038/nature13379. Europe PMC

Epigenomic alterations define lethal CIMP-positive ependymomas of infancy. Mack, S.C., Witt, H., Piro, R.M., Gu, L., Zuyderduyn, S., Stutz, A.M., Wang, X., Gallo, M., Garzia, L., Zayne, K., Zhang, X., Ramaswamy, V., Jager, N., Jones, D.T., Sill, M., Pugh, T.J., Ryzhova, M., Wani, K.M., Shih, D.J., Head, R., Remke, M., Bailey, S.D., Zichner, T., Faria, C.C., Barszczyk, M., Stark, S., Seker-Cin, H., Hutter, S., Johann, P., Bender, S., Hovestadt, V., Tzaridis, T., Dubuc, A.M., Northcott, P.A., Peacock, J., Bertrand, K.C., Agnihotri, S., Cavalli, F.M., Clarke, I., Nethery-Brokx, K., Creasy, C.L., Verma, S.K., Koster, J., Wu, X., Yao, Y., Milde, T., Sin-Chan, P., Zuccaro, J., Lau, L., Pereira, S., Castelo-Branco, P., Hirst, M., Marra, M.A., Roberts, S.S., Fults, D., Massimi, L., Cho, Y.J., Van Meter, T., Grajkowska, W., Lach, B., Kulozik, A.E., von Deimling, A., Witt, O., Scherer, S.W., Fan, X., Muraszko, K.M., Kool, M., Pomeroy, S.L., Gupta, N., Phillips, J., Huang, A., Tabori, U., Hawkins, C., Malkin, D., Kongkham, P.N., Weiss, W.A., Jabado, N., Rutka, J.T., Bouffet, E., Korbel, J.O., Lupien, M., Aldape, K.D., Bader, G.D., Eils, R., Lichter, P., Dirks, P.B., Pfister, S.M., Korshunov, A. & Taylor, M.D. Nature. 2014 Feb 27;506(7489):445-50. doi: 10.1038/nature13108. Epub 2014 Feb 19. Europe PMC

SPAG7 is a candidate gene for the periodic fever, aphthous stomatitis, pharyngitis and adenopathy (PFAPA) syndrome. Bens, S., Zichner, T., Stutz, A.M., Caliebe, A., Wagener, R., Hoff, K., Korbel, J.O., von Bismarck, P. & Siebert, R. Genes Immun. 2014 Jan 23. doi: 10.1038/gene.2013.73. Europe PMC

The genomic and transcriptomic landscape of a HeLa cell line. Landry, J.J., Pyl, P.T., Rausch, T., Zichner, T., Tekkedil, M.M., Stutz, A.M., Jauch, A., Aiyar, R.S., Pau, G., Delhomme, N., Gagneur, J., Korbel, J.O., Huber, W. & Steinmetz, L.M. G3 (Bethesda). 2013 Aug 7;3(8):1213-24. doi: 10.1534/g3.113.005777. Europe PMC

Recurrent somatic alterations of FGFR1 and NTRK2 in pilocytic astrocytoma. Jones, D.T., Hutter, B., Jager, N., Korshunov, A., Kool, M., Warnatz, H.J., Zichner, T., Lambert, S.R., Ryzhova, M., Quang, D.A., Fontebasso, A.M., Stutz, A.M., Hutter, S., Zuckermann, M., Sturm, D., Gronych, J., Lasitschka, B., Schmidt, S., Seker-Cin, H., Witt, H., Sultan, M., Ralser, M., Northcott, P.A., Hovestadt, V., Bender, S., Pfaff, E., Stark, S., Faury, D., Schwartzentruber, J., Majewski, J., Weber, U.D., Zapatka, M., Raeder, B., Schlesner, M., Worth, C.L., Bartholomae, C.C., von Kalle, C., Imbusch, C.D., Radomski, S., Lawerenz, C., van Sluis, P., Koster, J., Volckmann, R., Versteeg, R., Lehrach, H., Monoranu, C., Winkler, B., Unterberg, A., Herold-Mende, C., Milde, T., Kulozik, A.E., Ebinger, M., Schuhmann, M.U., Cho, Y.J., Pomeroy, S.L., von Deimling, A., Witt, O., Taylor, M.D., Wolf, S., Karajannis, M.A., Eberhart, C.G., Scheurlen, W., Hasselblatt, M., Ligon, K.L., Kieran, M.W., Korbel, J.O., Yaspo, M.L., Brors, B., Felsberg, J., Reifenberger, G., Collins, V.P., Jabado, N., Eils, R., Lichter, P. & Pfister, S.M. Nat Genet. 2013 Aug;45(8):927-32. doi: 10.1038/ng.2682. Epub 2013 Jun 30. Europe PMC

Impact of genomic structural variation in Drosophila melanogaster based on population-scale sequencing. Zichner, T., Garfield, D.A., Rausch, T., Stutz, A.M., Cannavo, E., Braun, M., Furlong, E.E. & Korbel, J.O. Genome Res. 2013 Mar;23(3):568-79. doi: 10.1101/gr.142646.112. Epub 2012 Dec 6. Europe PMC

Integrative genomic analyses reveal an androgen-driven somatic alteration landscape in early-onset prostate cancer. Weischenfeldt, J., Simon, R., Feuerbach, L., Schlangen, K., Weichenhan, D., Minner, S., Wuttig, D., Warnatz, H.J., Stehr, H., Rausch, T., Jager, N., Gu, L., Bogatyrova, O., Stutz, A.M., Claus, R., Eils, J., Eils, R., Gerhauser, C., Huang, P.H., Hutter, B., Kabbe, R., Lawerenz, C., Radomski, S., Bartholomae, C.C., Falth, M., Gade, S., Schmidt, M., Amschler, N., Hass, T., Galal, R., Gjoni, J., Kuner, R., Baer, C., Masser, S., von Kalle, C., Zichner, T., Benes, V., Raeder, B., Mader, M., Amstislavskiy, V., Avci, M., Lehrach, H., Parkhomchuk, D., Sultan, M., Burkhardt, L., Graefen, M., Huland, H., Kluth, M., Krohn, A., Sirma, H., Stumm, L., Steurer, S., Grupp, K., Sultmann, H., Sauter, G., Plass, C., Brors, B., Yaspo, M.L., Korbel, J.O. & Schlomm, T. Cancer Cell. 2013 Feb 11;23(2):159-70. doi: 10.1016/j.ccr.2013.01.002. Europe PMC

DELLY: structural variant discovery by integrated paired-end and split-read analysis. Rausch, T., Zichner, T., Schlattl, A., Stutz, A.M., Benes, V. & Korbel, J.O. Bioinformatics. 2012 Sep 15;28(18):i333-i339. Europe PMC

Subgroup-specific structural variation across 1,000 medulloblastoma genomes. Northcott, P.A., Shih, D.J., Peacock, J., Garzia, L., Morrissy, A.S., Zichner, T., Stutz, A.M., Korshunov, A., Reimand, J., Schumacher, S.E., Beroukhim, R., Ellison, D.W., Marshall, C.R., Lionel, A.C., Mack, S., Dubuc, A., Yao, Y., Ramaswamy, V., Luu, B., Rolider, A., Cavalli, F.M., Wang, X., Remke, M., Wu, X., Chiu, R.Y., Chu, A., Chuah, E., Corbett, R.D., Hoad, G.R., Jackman, S.D., Li, Y., Lo, A., Mungall, K.L., Nip, K.M., Qian, J.Q., Raymond, A.G., Thiessen, N.T., Varhol, R.J., Birol, I., Moore, R.A., Mungall, A.J., Holt, R., Kawauchi, D., Roussel, M.F., Kool, M., Jones, D.T., Witt, H., Fernandez-L, A., Kenney, A.M., Wechsler-Reya, R.J., Dirks, P., Aviv, T., Grajkowska, W.A., Perek-Polnik, M., Haberler, C.C., Delattre, O., Reynaud, S.S., Doz, F.F., Pernet-Fattet, S.S., Cho, B.K., Kim, S.K., Wang, K.C., Scheurlen, W., Eberhart, C.G., Fevre-Montange, M., Jouvet, A., Pollack, I.F., Fan, X., Muraszko, K.M., Gillespie, G.Y., Di Rocco, C., Massimi, L., Michiels, E.M., Kloosterhof, N.K., French, P.J., Kros, J.M., Olson, J.M., Ellenbogen, R.G., Zitterbart, K., Kren, L., Thompson, R.C., Cooper, M.K., Lach, B., McLendon, R.E., Bigner, D.D., Fontebasso, A., Albrecht, S., Jabado, N., Lindsey, J.C., Bailey, S., Gupta, N., Weiss, W.A., Bognar, L., Klekner, A., Van Meter, T.E., Kumabe, T., Tominaga, T., Elbabaa, S.K., Leonard, J.R., Rubin, J.B., Liau, L.M., Van Meir, E.G., Fouladi, M., Nakamura, H., Cinalli, G., Garami, M., Hauser, P., Saad, A.G., Iolascon, A., Jung, S., Carlotti, C.G., Vibhakar, R., Ra, Y.S., Robinson, S., Zollo, M., Faria, C.C., Chan, J.A., Levy, M.L., Sorensen, P.H., Meyerson, M., Pomeroy, S.L., Cho, Y.J., Bader, G.D., Tabori, U., Hawkins, C.E., Bouffet, E., Scherer, S.W., Rutka, J.T., Malkin, D., Clifford, S.C., Jones, S.J., Korbel, J.O., Pfister, S.M., Marra, M.A. & Taylor, M.D. Nature. 2012 Aug 2;488(7409):49-56. Europe PMC

Dissecting the genomic complexity underlying medulloblastoma. Jones, D.T., Jager, N., Kool, M., Zichner, T., Hutter, B., Sultan, M., Cho, Y.J., Pugh, T.J., Hovestadt, V., Stutz, A.M., Rausch, T., Warnatz, H.J., Ryzhova, M., Bender, S., Sturm, D., Pleier, S., Cin, H., Pfaff, E., Sieber, L., Wittmann, A., Remke, M., Witt, H., Hutter, S., Tzaridis, T., Weischenfeldt, J., Raeder, B., Avci, M., Amstislavskiy, V., Zapatka, M., Weber, U.D., Wang, Q., Lasitschka, B., Bartholomae, C.C., Schmidt, M., von Kalle, C., Ast, V., Lawerenz, C., Eils, J., Kabbe, R., Benes, V., van Sluis, P., Koster, J., Volckmann, R., Shih, D., Betts, M.J., Russell, R.B., Coco, S., Tonini, G.P., Schuller, U., Hans, V., Graf, N., Kim, Y.J., Monoranu, C., Roggendorf, W., Unterberg, A., Herold-Mende, C., Milde, T., Kulozik, A.E., von Deimling, A., Witt, O., Maass, E., Rossler, J., Ebinger, M., Schuhmann, M.U., Fruhwald, M.C., Hasselblatt, M., Jabado, N., Rutkowski, S., von Bueren, A.O., Williamson, D., Clifford, S.C., McCabe, M.G., Collins, V.P., Wolf, S., Wiemann, S., Lehrach, H., Brors, B., Scheurlen, W., Felsberg, J., Reifenberger, G., Northcott, P.A., Taylor, M.D., Meyerson, M., Pomeroy, S.L., Yaspo, M.L., Korbel, J.O., Korshunov, A., Eils, R., Pfister, S.M. & Lichter, P. Nature. 2012 Aug 2;488(7409):100-5. doi: 10.1038/nature11284. Europe PMC

Identifying the unknowns by aligning fragmentation trees. Rasche, F., Scheubert, K., Hufsky, F., Zichner, T., Kai, M., Svatos, A. & Bocker, S. Anal Chem. 2012 Apr 3;84(7):3417-26. Epub 2012 Mar 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

Systematic inference of copy-number genotypes from personal genome sequencing data reveals extensive olfactory receptor gene content diversity. Waszak, S.M., Hasin, Y., Zichner, T., Olender, T., Keydar, I., Khen, M., Stutz, A.M., Schlattl, A., Lancet, D. & Korbel, J.O. PLoS Comput Biol. 2010 Nov 11;6(11):e1000988. doi: 10.1371/journal.pcbi.1000988. Europe PMC

Temporal analysis of oncogenesis using microRNA expression data. Thomas Zichner, Zelmina Lubovac, Björn Olsson. Proceedings of the German Conference on Bioinformatics (GCB 2008). Lecture Notes in Informatics P-136:128-137, 2008.

Algorithm engineering for color-coding with applications to signaling pathway detection. Hüffner, F., Wernicke, S. & Zichner, T. Algorithmica, 52(2):114-132, 2008.

Faspad: fast signaling pathway detection. Huffner, F., Wernicke, S. & Zichner, T. Bioinformatics. 2007 Jul 1;23(13):1708-9. Epub 2007 Apr 26. Europe PMC

Algorithm engineering for color-coding to facilitate signaling pathway detection. Hüffner, F., Wernicke, S. & Zichner, T. Proceedings of the 5th Asia-Pacific Bioinformatics Conference (APBC 2007). Advances in Bioinformatics and Computational Biology 5, 277-286, Imperial College Press, 2007.