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Staff at EMBL

Dr. Jan Korbel

Group Leader
Korbel Group Joint appointment: EMBL-EBI Hinxton

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

E-mail: send a mail

Biography

PhD 2005, EMBL Heidelberg/Humboldt University, Berlin.
Postdoctoral research at Yale University, New Haven, Connecticut, USA.
Group leader at EMBL since October 2008.
Joint appointment with EMBL-EBI.
ERC Investigator.

Publications

TMPRSS2-ERG Fusions Are Strongly Linked to Young Patient Age in Low-grade Prostate Cancer. Steurer, S., Mayer, P.S., Adam, M., Krohn, A., Koop, C., Ospina-Klinck, D., Tehrani, A.A., Simon, R., Tennstedt, P., Graefen, M., Wittmer, C., Brors, B., Plass, C., Korbel, J., Weischenfeldt, J., Sauter, G., Huland, H., Tsourlakis, M.C., Minner, S. & Schlomm, T. Eur Urol. 2014 Jul 8. pii: S0302-2838(14)00601-0. doi:10.1016/j.eururo.2014.06.027. Europe PMC

The activating STAT5B N642H mutation is a common abnormality in pediatric T-cell acute lymphoblastic leukemia and confers a higher risk of relapse. Bandapalli, O.R., Schuessele, S., Kunz, J.B., Rausch, T., Stutz, A.M., Tal, N., Geron, I., Gershman, N., Izraeli, S., Eilers, J., Vaezipour, N., Kirschner-Schwabe, R., Hof, J., von Stackelberg, A., Schrappe, M., Stanulla, M., Zimmermann, M., Koehler, R., Avigad, S., Handgretinger, R., Frismantas, V., Bourquin, J.P., Bornhauser, B., Korbel, J.O., Muckenthaler, M.U. & Kulozik, A.E. Haematologica. 2014 Jun 27. pii: haematol.2014.104992. Europe PMC

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

Genome sequencing of SHH medulloblastoma predicts genotype-related response to smoothened inhibition. Kool, M., Jones, D.T., Jager, N., Northcott, P.A., Pugh, T.J., Hovestadt, V., Piro, R.M., Esparza, L.A., Markant, S.L., Remke, M., Milde, T., Bourdeaut, F., Ryzhova, M., Sturm, D., Pfaff, E., Stark, S., Hutter, S., Seker-Cin, H., Johann, P., Bender, S., Schmidt, C., Rausch, T., Shih, D., Reimand, J., Sieber, L., Wittmann, A., Linke, L., Witt, H., Weber, U.D., Zapatka, M., Konig, R., Beroukhim, R., Bergthold, G., van Sluis, P., Volckmann, R., Koster, J., Versteeg, R., Schmidt, S., Wolf, S., Lawerenz, C., Bartholomae, C.C., von Kalle, C., Unterberg, A., Herold-Mende, C., Hofer, S., Kulozik, A.E., von Deimling, A., Scheurlen, W., Felsberg, J., Reifenberger, G., Hasselblatt, M., Crawford, J.R., Grant, G.A., Jabado, N., Perry, A., Cowdrey, C., Croul, S., Zadeh, G., Korbel, J.O., Doz, F., Delattre, O., Bader, G.D., McCabe, M.G., Collins, V.P., Kieran, M.W., Cho, Y.J., Pomeroy, S.L., Witt, O., Brors, B., Taylor, M.D., Schuller, U., Korshunov, A., Eils, R., Wechsler-Reya, R.J., Lichter, P. & Pfister, S.M. Cancer Cell. 2014 Mar 17;25(3):393-405. doi: 10.1016/j.ccr.2014.02.004. 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

Primate genome architecture influences structural variation mechanisms and functional consequences. Gokcumen, O., Tischler, V., Tica, J., Zhu, Q., Iskow, R.C., Lee, E., Fritz, M.H., Langdon, A., Stutz, A.M., Pavlidis, P., Benes, V., Mills, R.E., Park, P.J., Lee, C. & Korbel, J.O. Proc Natl Acad Sci U S A. 2013 Sep 24;110(39):15764-9. doi:10.1073/pnas.1305904110. Epub 2013 Sep 6. 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

Identification of a Ninein (NIN) mutation in a family with spondyloepimetaphyseal dysplasia with joint laxity (leptodactylic type)-like phenotype. Grosch, M., Gruner, B., Spranger, S., Stutz, A.M., Rausch, T., Korbel, J.O., Seelow, D., Nurnberg, P., Sticht, H., Lausch, E., Zabel, B., Winterpacht, A. & Tagariello, A. Matrix Biol. 2013 May 9. pii: S0945-053X(13)00070-X. doi:10.1016/j.matbio.2013.05.001. Europe PMC

Whole-exome sequencing links caspase recruitment domain 11 (CARD11) inactivation to severe combined immunodeficiency. Greil, J., Rausch, T., Giese, T., Bandapalli, O.R., Daniel, V., Bekeredjian-Ding, I., Stutz, A.M., Drees, C., Roth, S., Ruland, J., Korbel, J.O. & Kulozik, A.E. J Allergy Clin Immunol. 2013 May;131(5):1376-83.e3. doi:10.1016/j.jaci.2013.02.012. Epub 2013 Apr 3. 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

Phenotypic impact of genomic structural variation: insights from and for human disease. Weischenfeldt, J., Symmons, O., Spitz, F. & Korbel, J.O. Nat Rev Genet. 2013 Feb;14(2):125-38. doi: 10.1038/nrg3373. Europe PMC

Criteria for inference of chromothripsis in cancer genomes. Korbel, J.O. & Campbell, P.J. Cell. 2013 Mar 14;152(6):1226-36. doi: 10.1016/j.cell.2013.02.023. Europe PMC

Genomic deletion of MAP3K7 at 6q12-22 is associated with early PSA recurrence in prostate cancer and absence of TMPRSS2:ERG fusions. Kluth, M., Hesse, J., Heinl, A., Krohn, A., Steurer, S., Sirma, H., Simon, R., Mayer, P.S., Schumacher, U., Grupp, K., Izbicki, J.R., Pantel, K., Dikomey, E., Korbel, J.O., Plass, C., Sauter, G., Schlomm, T. & Minner, S. Mod Pathol. 2013 Feb 1. doi: 10.1038/modpathol.2012.236. Europe PMC

Genome assembly and haplotyping with Hi-C. Korbel, J.O. & Lee, C. Nat Biotechnol. 2013 Dec;31(12):1099-101. doi: 10.1038/nbt.2764. Europe PMC

Recurrent mutation of the ID3 gene in Burkitt lymphoma identified by integrated genome, exome and transcriptome sequencing. Richter J., Schlesner M., Hoffmann S., Kreuz M., Leich E., Burkhardt B., Rosolowski M., Ammerpohl O., Wagener R., Bernhart S.H., Lenze D., Szczepanowski M., Paulsen M., Lipinski S., Russell R.B., Adam-Klages S., Apic G., Claviez A., Hasenclever D., Hovestadt V., Hornig N., Korbel J.O., Kube D., Langenberger D., Lawerenz C., Lisfeld J., Meyer K., Picelli S., Pischimarov J., Radlwimmer B., Rausch T., Rohde M., Schilhabel M., Scholtysik R., Spang R., Trautmann H., Zenz T., Borkhardt A., Drexler H.G., Moller P., Macleod R.A., Pott C., Schreiber S., Trumper L., Loeffler M., Stadler P.F., Lichter P., Eils R., Kuppers R., Hummel M., Klapper W., Rosenstiel P., Rosenwald A., Brors B., Siebert R. Nat Genet. 2012 Nov 11;44(12):1316-1320. doi: 10.1038/ng.2469. Epub 2012 Nov 11. Europe PMC

An integrated map of genetic variation from 1,092 human genomes. 1000 Genomes Project Consortium Nature. 2012 Nov 1;491(7422):56-65. doi: 10.1038/nature11632. 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

A 15q24 microdeletion in transient myeloproliferative disease (TMD) and acute megakaryoblastic leukaemia (AMKL) implicates PML and SUMO3 in the leukaemogenesis of TMD/AMKL. Haemmerling, S., Behnisch, W., Doerks, T., Korbel, J.O., Bork, P., Moog, U., Hentze, S., Grasshoff, U., Bonin, M., Riess, O., Janssen, J.W., Jauch, A., Bartram, C.R., Reinhardt, D., Koch, K.A., Bandapalli, O.R. & Kulozik, A.E. Br J Haematol. 2012 Apr;157(2):180-7. doi: 10.1111/j.1365-2141.2012.09028.x. Epub2012 Feb 1. Europe PMC

Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma. Schwartzentruber, J., Korshunov, A., Liu, X.Y., Jones, D.T., Pfaff, E., Jacob, K., Sturm, D., Fontebasso, A.M., Quang, D.A., Tonjes, M., Hovestadt, V., Albrecht, S., Kool, M., Nantel, A., Konermann, C., Lindroth, A., Jager, N., Rausch, T., Ryzhova, M., Korbel, J.O., Hielscher, T., Hauser, P., Garami, M., Klekner, A., Bognar, L., Ebinger, M., Schuhmann, M.U., Scheurlen, W., Pekrun, A., Fruhwald, M.C., Roggendorf, W., Kramm, C., Durken, M., Atkinson, J., Lepage, P., Montpetit, A., Zakrzewska, M., Zakrzewski, K., Liberski, P.P., Dong, Z., Siegel, P., Kulozik, A.E., Zapatka, M., Guha, A., Malkin, D., Felsberg, J., Reifenberger, G., von Deimling, A., Ichimura, K., Collins, V.P., Witt, H., Milde, T., Witt, O., Zhang, C., Castelo-Branco, P., Lichter, P., Faury, D., Tabori, U., Plass, C., Majewski, J., Pfister, S.M. & Jabado, N. Nature. 2012 Jan 29;482(7384):226-31. doi: 10.1038/nature10833. 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

High-resolution genomic profiling of chronic lymphocytic leukemia reveals new recurrent genomic alterations. Edelmann, J., Holzmann, K., Miller, F., Winkler, D., Buhler, A., Zenz, T., Bullinger, L., Kuhn, M.W., Gerhardinger, A., Bloehdorn, J., Radtke, I., Su, X., Ma, J., Pounds, S., Hallek, M., Lichter, P., Korbel, J., Busch, R., Mertens, D., Downing, J.R., Stilgenbauer, S. & Dohner, H. Blood. 2012 Dec 6;120(24):4783-94. doi: 10.1182/blood-2012-04-423517. Epub 2012Oct 9. Europe PMC

Relating CNVs to transcriptome data at fine resolution: assessment of the effect of variant size, type, and overlap with functional regions. Schlattl, A., Anders, S., Waszak, S.M., Huber, W. & Korbel, J.O. Genome Res. 2011 Dec;21(12):2004-13. doi: 10.1101/gr.122614.111. Epub 2011 Aug23. Europe PMC

Challenges in studying genomic structural variant formation mechanisms: the short-read dilemma and beyond. Onishi-Seebacher, M. & Korbel, J.O. Bioessays. 2011 Nov;33(11):840-50. doi: 10.1002/bies.201100075. Epub 2011Sep 30. Europe PMC

A comprehensive map of mobile element insertion polymorphisms in humans. Stewart, C., Kural, D., Stromberg, M.P., Walker, J.A., Konkel, M.K., Stutz, A.M., Urban, A.E., Grubert, F., Lam, H.Y., Lee, W.P., Busby, M., Indap, A.R., Garrison, E., Huff, C., Xing, J., Snyder, M.P., Jorde, L.B., Batzer, M.A., Korbel, J.O., Marth, G.T.; 1000 Genomes Project. PLoS Genet. 2011 Aug;7(8):e1002236. Epub 2011 Aug 18. Europe PMC

Mapping copy number variation by population-scale genome sequencing. Mills, R.E., Walter, K., Stewart, C., Handsaker, R.E., Chen, K., Alkan, C., Abyzov, A., Yoon, S.C., Ye, K., Cheetham, R.K., Chinwalla, A., Conrad, D.F., Fu, Y., Grubert, F., Hajirasouliha, I., Hormozdiari, F., Iakoucheva, L.M., Iqbal, Z., Kang, S., Kidd, J.M., Konkel, M.K., Korn, J., Khurana, E., Kural, D., Lam, H.Y., Leng, J., Li, R., Li, Y., Lin, C.Y., Luo, R., Mu, X.J., Nemesh, J., Peckham, H.E., Rausch, T., Scally, A., Shi, X., Stromberg, M.P., Stutz, A.M., Urban, A.E., Walker, J.A., Wu, J., Zhang, Y., Zhang, Z.D., Batzer, M.A., Ding, L., Marth, G.T., McVean, G., Sebat, J., Snyder, M., Wang, J., Ye, K., Eichler, E.E., Gerstein, M.B., Hurles, M.E., Lee, C., McCarroll, S.A., Korbel, J.O.; 1000 Genomes Project. Nature. 2011 Feb 3;470(7332):59-65. 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

A map of human genome variation from population-scale sequencing. 1000 Genomes Project Consortium. Nature. 2010 Oct 28;467(7319):1061-73 Europe PMC

The baker's yeast diploid genome is remarkably stable in vegetative growth and meiosis. Nishant, K.T., Wei, W., Mancera, E., Argueso, J.L., Schlattl, A., Delhomme, N., Ma, X., Bustamante, C.D., Korbel, J.O., Gu, Z., Steinmetz, L.M. & Alani, E. PLoS Genet. 2010 Sep 9;6(9):e1001109. doi: 10.1371/journal.pgen.1001109. Europe PMC

Potential and challenges of personalized genomics and the 1000 Genome Project. St├╝tz, A.M. & Korbel, J.O. Medizinische Genetik 2010 22(2) 242-247

International network of cancer genome projects. International Cancer Genome Consortium. Nature. 2010 Apr 15;464(7291):993-8. doi: 10.1038/nature08987. Europe PMC

Variation in transcription factor binding among humans. Kasowski, M.*, Grubert, F.*, Heffelfinger, C., Hariharan, M., Asabere, A., Waszak, S.M., Habegger, L., Rozowsky, J., Shi, M., Urban, A.E., Hong, M.Y., Karczewski, K.J., Huber, W., Weissman, S.M., Gerstein, M.B., Korbel, J.O. & Snyder, M. Science. 2010 Apr 9;328(5975):232-5. doi: 10.1126/science.1183621. Epub 2010 Mar18.
(*equal contribution) Europe PMC

Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library. Lam, H.Y., Mu, X.J., Stutz, A.M., Tanzer, A., Cayting, P.D., Snyder, M., Kim, P.M., Korbel, J.O. & Gerstein, M.B. Nat Biotechnol. 2010 Jan;28(1):47-55. Epub 2009 Dec 27. Europe PMC

The genetic architecture of Down syndrome phenotypes revealed by high-resolution analysis of human segmental trisomies. Korbel, J.O., Tirosh-Wagner, T., Urban, A.E., Chen, X.N., Kasowski, M., Dai, L., Grubert, F., Erdman, C., Gao, M.C., Lange, K., Sobel, E.M., Barlow, G.M., Aylsworth, A.S., Carpenter, N.J., Clark, R.D., Cohen, M.Y., Doran, E., Falik-Zaccai, T., Lewin, S.O., Lott, I.T., McGillivray, B.C., Moeschler, J.B., Pettenati, M.J., Pueschel, S.M., Rao, K.W., Shaffer, L.G., Shohat, M., Van Riper, A.J., Warburton, D., Weissman, S., Gerstein, M.B., Snyder, M. & Korenberg, J.R. Proc Natl Acad Sci U S A. 2009 Jul 21;106(29):12031-6. Epub 2009 Jul 13. Europe PMC

Distinct genomic aberrations associated with ERG rearranged prostate cancer. Demichelis, F., Setlur, S.R., Beroukhim, R., Perner, S., Korbel, J.O., Lafargue, C.J., Pflueger, D., Pina, C., Hofer, M.D., Sboner, A., Svensson, M.A., Rickman, D.S., Urban, A., Snyder, M., Meyerson, M., Lee, C., Gerstein, M.B., Kuefer, R. & Rubin, M.A. Genes Chromosomes Cancer. 2009 Apr;48(4):366-80. Europe PMC

Quantifying environmental adaptation of metabolic pathways in metagenomics. Gianoulis, T.A., Raes, J., Patel, P.V., Bjornson, R., Korbel, J.O., Letunic, I., Yamada, T., Paccanaro, A., Jensen, L.J., Snyder, M., Bork, P. & Gerstein, M.B. Proc Natl Acad Sci U S A. 2009 Feb 3;106(5):1374-9. Epub 2009 Jan 22. Europe PMC

PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Korbel, J.O., Abyzov, A., Mu, X.J., Carriero, N., Cayting, P., Zhang, Z., Snyder, M. & Gerstein, M.B. Genome Biol. 2009 Feb 23;10(2):R23. Europe PMC

MSB: a mean-shift-based approach for the analysis of structural variation in the genome. Wang, L.Y., Abyzov, A., Korbel, J.O., Snyder, M. & Gerstein, M. Genome Res. 2009 Jan;19(1):106-17. Epub 2008 Nov 26. Europe PMC

High-resolution copy-number variation map reflects human olfactory receptor diversity and evolution. Hasin, Y., Olender, T., Khen, M., Gonzaga-Jauregui, C., Kim, P.M., Urban, A.E., Snyder, M., Gerstein, M.B., Lancet, D. & Korbel, J.O. PLoS Genet. 2008 Nov;4(11):e1000249. Epub 2008 Nov 7. Europe PMC

The current excitement about copy-number variation: how it relates to gene duplications and protein families. Korbel, J.O., Kim, P.M., Chen, X., Urban, A.E., Weissman, S., Snyder, M. & Gerstein, M.B. Curr Opin Struct Biol. 2008 Jun;18(3):366-74. doi: 10.1016/j.sbi.2008.02.005.Epub 2008 May 27. Europe PMC

Analysis of copy number variation in the rhesus macaque genome identifies candidate loci for evolutionary and human disease studies. Lee, A.S., Gutierrez-Arcelus, M., Perry, G.H., Vallender, E.J., Johnson, W.E., Miller, G.M., Korbel, J.O. & Lee, C. Hum Mol Genet. 2008 Apr 15;17(8):1127-36. Epub 2008 Jan 7. Europe PMC

Positive selection at the protein network periphery: evaluation in terms of structural constraints and cellular context. Kim, P.M., Korbel, J.O. & Gerstein, M.B. Proc Natl Acad Sci U S A. 2007 Dec 18;104(51):20274-9. Epub 2007 Dec 12. Europe PMC

Paired-end mapping reveals extensive structural variation in the human genome. Korbel, J.O., Urban, A.E., Affourtit, J.P., Godwin, B., Grubert, F., Simons, J.F., Kim, P.M., Palejev, D., Carriero, N.J., Du, L., Taillon, B.E., Chen, Z., Tanzer, A., Saunders, A.C., Chi, J., Yang, F., Carter, N.P., Hurles, M.E., Weissman, S.M., Harkins, T.T., Gerstein, M.B., Egholm, M. & Snyder, M. Science. 2007 Oct 19;318(5849):420-6. Epub 2007 Sep 27. Europe PMC

Use of pathway analysis and genome context methods for functional genomics of Mycoplasma pneumoniae nucleotide metabolism. Pachkov, M., Dandekar, T., Korbel, J., Bork, P. & Schuster, S. Gene. 2007 Jul 15;396(2):215-25. Epub 2007 Mar 24. Europe PMC

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. ENCODE Project Consortium. Nature. 2007 Jun 14;447(7146):799-816. Europe PMC

Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome. Korbel, J.O., Urban, A.E., Grubert, F., Du, J., Royce, T.E., Starr, P., Zhong, G., Emanuel, B.S., Weissman, S.M., Snyder, M. & Gerstein, M.B. Proc Natl Acad Sci U S A. 2007 Jun 12;104(24):10110-5. Epub 2007 Jun 5. Europe PMC

Structured RNAs in the ENCODE selected regions of the human genome. Washietl, S., Pedersen, J.S., Korbel, J.O., Stocsits, C., Gruber, A.R., Hackermuller, J., Hertel, J., Lindemeyer, M., Reiche, K., Tanzer, A., Ucla, C., Wyss, C., Antonarakis, S.E., Denoeud, F., Lagarde, J., Drenkow, J., Kapranov, P., Gingeras, T.R., Guigo, R., Snyder, M., Gerstein, M.B., Reymond, A., Hofacker, I.L. & Stadler, P.F. Genome Res. 2007 Jun;17(6):852-64. Europe PMC

The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci. Rozowsky, J.S., Newburger, D., Sayward, F., Wu, J., Jordan, G., Korbel, J.O., Nagalakshmi, U., Yang, J., Zheng, D., Guigo, R., Gingeras, T.R., Weissman, S., Miller, P., Snyder, M. & Gerstein, M.B. Genome Res. 2007 Jun;17(6):732-45. Europe PMC

What is a gene, post-ENCODE? History and updated definition. Gerstein, M.B., Bruce, C., Rozowsky, J.S., Zheng, D., Du, J., Korbel, J.O., Emanuelsson, O., Zhang, Z.D., Weissman, S. & Snyder, M. Genome Res. 2007 Jun;17(6):669-81. Europe PMC

Prediction of effective genome size in metagenomic samples. Raes, J., Korbel, J.O., Lercher, M.J., von Mering, C. & Bork, P. Genome Biol. 2007;8(1):R10. Europe PMC

Global identification and characterization of transcriptionally active regions in the rice genome. Li, L., Wang, X., Sasidharan, R., Stolc, V., Deng, W., He, H., Korbel, J., Chen, X., Tongprasit, W., Ronald, P., Chen, R., Gerstein, M. & Wang Deng, X. PLoS ONE. 2007 Mar 14;2(3):e294. Europe PMC

A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge. Du, J., Rozowsky, J.S., Korbel, J.O., Zhang, Z.D., Royce, T.E., Schultz, M.H., Snyder, M. & Gerstein, M. Bioinformatics. 2006 Dec 15;22(24):3016-24. Epub 2006 Oct 12. Europe PMC

High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays. Urban, A.E., Korbel, J.O., Selzer, R., Richmond, T., Hacker, A., Popescu, G.V., Cubells, J.F., Green, R., Emanuel, B.S., Gerstein, M.B., Weissman, S.M. & Snyder, M. Proc Natl Acad Sci U S A. 2006 Mar 21;103(12):4534-9. Epub 2006 Mar 14. Europe PMC

Similar gene expression profiles do not imply similar tissue functions. Yanai, I., Korbel, J.O., Boue, S., McWeeney, S.K., Bork, P. & Lercher, M.J. Trends Genet. 2006 Mar;22(3):132-8. Epub 2006 Feb 9. Europe PMC

Novel transcribed regions in the human genome. Rozowsky, J., Wu, J., Lian, Z., Nagalakshmi, U., Korbel, J.O., Kapranov, P., Zheng, D., Dyke, S., Newburger, P., Miller, P., Gingeras, T.R., Weissman, S., Gerstein, M. & Snyder, M. Cold Spring Harb Symp Quant Biol. 2006;71:111-6. Europe PMC

Systematic association of genes to phenotypes by genome and literature mining. Korbel, J.O., Doerks, T., Jensen, L.J., Perez-Iratxeta, C., Kaczanowski, S., Hooper, S.D., Andrade, M.A. & Bork, P. PLoS Biol 2005 Apr 5;3(5):e134. Europe PMC

Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs. Korbel, J.O., Jensen, L.J., von Mering, C. & Bork, P. Nat Biotechnol 2004 Jul;22(7):911-7. Europe PMC

Transgene methylation in mice reflects copy number but not expression level. Pena, R.N., Webster, J., Kwan, S., Korbel, J. & Whitelaw, B.A. Mol Biotechnol 2004 Mar;26(3):215-20. Europe PMC

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources. Crass, T., Antes, I., Basekow, R., Bork, P., Buning, C., Christensen, M., Claussen, H., Ebeling, C., Ernst, P., Gailus-Durner, V., Glatting, K.H., Gohla, R., Gossling, F., Grote, K., Heidtke, K., Herrmann, A., O'Keeffe, S., Kiesslich, O., Kolibal, S., Korbel, J.O., Lengauer, T., Liebich, I., Van Der Linden, M., Luz, H., Meissner, K., Von Mering, C., Mevissen, H.T., Mewes, H.W., Michael, H., Mokrejs, M., Muller, T., Pospisil, H., Rarey, M., Reich, J.G., Schneider, R., Schomburg, D., Schulze-Kremer, S., Schwarzer, K., Sommer, I., Springstubbe, S., Suhai, S., Thoppae, G., Vingron, M., Warfsmann, J., Werner, T., Wetzler, D., Wingender, E. & Zimmer, R. Bioinformatics 2004 Jan 22;20(2):268-270. Europe PMC

Systematic discovery of analogous enzymes in thiamin biosynthesis. Morett, E., Korbel, J.O., Rajan, E., Saab-Rincon, G., Olvera, L., Olvera, M., Schmidt, S., Snel, B. & Bork, P. Nat Biotechnol 2003 Jul;21(7):790-5. Europe PMC

Compositional asymmetries and predicted origins of replication of the saccharomyces cerevisiae genome. Korbel, J. O., Assmus, H., Kielbasa, S., & Herzel, H. In "Bioinformatics of Genome Regulation and Structure." N. Kolchanov and R. Hofestaedt R. (Eds). Kluwer Academic Publishers

SHOT: a web server for the construction of genome phylogenies. Korbel, J.O., Snel, B., Huynen, M.A. & Bork, P. Trends Genet 2002 Mar;18(3):158-62. Europe PMC