Staff at EMBL
Thomas Zichner
Predoctoral Fellow
Korbel Group
EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
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Publications
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 Mar 26. pii: g3.113.005777v6. doi: 10.1534/g3.113.005777. PubMed
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. PubMed
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. 2012 Dec 6. PubMed
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. PubMed
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. PubMed
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. PubMed
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. PubMed
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. PubMed
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., Stütz, A.M., Schlattl, A., Lancet, D. & Korbel, J.O. PLoS Comput Biol. 2010 Nov 11;6(11):e1000988. PubMed
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. Falk Hüffner, Sebastian Wernicke, and Thomas Zichner. Algorithmica, 52(2):114-132, 2008.
FASPAD: Fast signaling pathway detection. Falk Hüffner, Sebastian Wernicke, and Thomas Zichner. Bioinformatics, 23(13):1708-1709, 2007. PubMed
Algorithm engineering for color-coding to facilitate signaling pathway detection. Falk Hüffner, Sebastian Wernicke, and Thomas Zichner. Proceedings of the 5th Asia-Pacific Bioinformatics Conference (APBC 2007). Advances in Bioinformatics and Computational Biology 5, 277-286, Imperial College Press, 2007.
