Staff at EMBL

Dr. Jan Korbel

Group Leader
Korbel Group Joint appointment: EMBL-EBI Hinxton

EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

Biography

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

Publications

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. PubMed

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

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. 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

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. 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

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. PubMed

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. 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

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. PubMed

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. 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

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. PubMed

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. Epub 2011 Aug 23. PubMed

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. PubMed

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. PubMed

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. PubMed

International network of cancer genome projects. International Cancer Genome Consortium. Nature 2010 464(7291) 993-998 PubMed

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

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). pii: e1001109. PubMed

Potential and challenges of personalized genomics and the 1000 Genomes Project Stütz, A.M. & Korbel, J.O. Medizinische Genetik 2010 Jun; 22(2):242-247

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. Epub 2010 Mar 18. PubMed

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. 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

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. PubMed

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. PubMed

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. PubMed

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. PubMed

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. PubMed

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. PubMed

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 May 27;. PubMed

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. PubMed

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. PubMed

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. PubMed

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. PubMed

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. PubMed

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. PubMed

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. PubMed

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. PubMed

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

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. PubMed

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. PubMed

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. PubMed

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. PubMed

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. PubMed

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. PubMed

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. PubMed

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. PubMed

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. PubMed

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. PubMed

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. PubMed

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. PubMed