EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

Biography

  • PhD 2005, EMBL Heidelberg/Humboldt University, Berlin.
    Postdoctoral research at Yale University, New Haven, Connecticut, USA.
    Group leader at EMBL since October 2008. Senior scientist since 2016.
    Joint appointment with EMBL-EBI.
    Group leader in the Molecular Medicine Partnership Unit.
    ERC Investigator.

Publications

Total: 124 publication(s)

2008

Hasin Y, Olender T, Khen M, Gonzaga-Jauregui C, Kim PM, Urban AE, Snyder M, Gerstein MB, Lancet D, Korbel JO. (2008)

High-resolution copy-number variation map reflects human olfactory receptor diversity and evolution

PLoS Genet. 4(11):e1000249. doi: 10.1371/journal.pgen.1000249
Europe PMC | doi

Korbel JO, Kim PM, Chen X, Urban AE, Weissman S, Snyder M, Gerstein MB. (2008)

The current excitement about copy-number variation: how it relates to gene duplications and protein families

Curr. Opin. Struct. Biol. 18(3):366-374. doi: 10.1016/j.sbi.2008.02.005
Europe PMC | doi

Lee AS, Gutiérrez-Arcelus M, Perry GH, Vallender EJ, Johnson WE, Miller GM, Korbel JO, Lee C. (2008)

Analysis of copy number variation in the rhesus macaque genome identifies candidate loci for evolutionary and human disease studies

Hum. Mol. Genet. 17(8):1127-1136. doi: 10.1093/hmg/ddn002
Europe PMC | doi


2007

Kim PM, Korbel JO, Gerstein MB. (2007)

Positive selection at the protein network periphery: evaluation in terms of structural constraints and cellular context

Proc. Natl. Acad. Sci. U.S.A. 104(51):20274-20279. doi: 10.1073/pnas.0710183104
Europe PMC | doi

Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, Simons JF, Kim PM, Palejev D, Carriero NJ, Du L, Taillon BE, Chen Z, Tanzer A, Saunders AC, Chi J, Yang F, Carter NP, Hurles ME, Weissman SM, Harkins TT, Gerstein MB, Egholm M, Snyder M. (2007)

Paired-end mapping reveals extensive structural variation in the human genome

Science 318(5849):420-426. doi: 10.1126/science.1149504
Europe PMC | doi

Pachkov M, Dandekar T, Korbel J, Bork P, Schuster S. (2007)

Use of pathway analysis and genome context methods for functional genomics of Mycoplasma pneumoniae nucleotide metabolism

Gene 396(2):215-225. doi: 10.1016/j.gene.2007.02.033
Europe PMC | doi

ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA, NISC Comparative Sequencing Program, Baylor College of Medicine Human Genome Sequencing Center, Washington University Genome Sequencing Center, Broad Institute, Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ. (2007)

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

Nature 447(7146):799-816. doi: 10.1038/nature05874
Europe PMC | doi

Gerstein MB, Bruce C, Rozowsky JS, Zheng D, Du J, Korbel JO, Emanuelsson O, Zhang ZD, Weissman S, Snyder M. (2007)

What is a gene, post-ENCODE? History and updated definition

Genome Res. 17(6):669-681. doi: 10.1101/gr.6339607
Europe PMC | doi

Korbel JO, Urban AE, Grubert F, Du J, Royce TE, Starr P, Zhong G, Emanuel BS, Weissman SM, Snyder M, Gerstein MB. (2007)

Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome

Proc. Natl. Acad. Sci. U.S.A. 104(24):10110-10115. doi: 10.1073/pnas.0703834104
Europe PMC | doi

Rozowsky JS, Newburger D, Sayward F, Wu J, Jordan G, Korbel JO, Nagalakshmi U, Yang J, Zheng D, Guigó R, Gingeras TR, Weissman S, Miller P, Snyder M, Gerstein MB. (2007)

The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci

Genome Res. 17(6):732-745. doi: 10.1101/gr.5696007
Europe PMC | doi

Washietl S, Pedersen JS, Korbel JO, Stocsits C, Gruber AR, Hackermüller J, Hertel J, Lindemeyer M, Reiche K, Tanzer A, Ucla C, Wyss C, Antonarakis SE, Denoeud F, Lagarde J, Drenkow J, Kapranov P, Gingeras TR, Guigó R, Snyder M, Gerstein MB, Reymond A, Hofacker IL, Stadler PF. (2007)

Structured RNAs in the ENCODE selected regions of the human genome

Genome Res. 17(6):852-864. doi: 10.1101/gr.5650707
Europe PMC | doi

Li L, Wang X, Sasidharan R, Stolc V, Deng W, He H, Korbel J, Chen X, Tongprasit W, Ronald P, Chen R, Gerstein M, Deng XW. (2007)

Global identification and characterization of transcriptionally active regions in the rice genome

PLoS ONE 2(3):e294. doi: 10.1371/journal.pone.0000294
Europe PMC | doi

Raes J, Korbel JO, Lercher MJ, von Mering C, Bork P. (2007)

Prediction of effective genome size in metagenomic samples

Genome Biol. 8(1):R10. doi: 10.1186/gb-2007-8-1-r10
Europe PMC | doi


2006

Du J, Rozowsky JS, Korbel JO, Zhang ZD, Royce TE, Schultz MH, Snyder M, Gerstein M. (2006)

A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge

Bioinformatics 22(24):3016-3024. doi: 10.1093/bioinformatics/btl515
Europe PMC | doi

Urban AE, Korbel JO, Selzer R, Richmond T, Hacker A, Popescu GV, Cubells JF, Green R, Emanuel BS, Gerstein MB, Weissman SM, Snyder M. (2006)

High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays

Proc. Natl. Acad. Sci. U.S.A. 103(12):4534-4539. doi: 10.1073/pnas.0511340103
Europe PMC | doi

Yanai I, Korbel JO, Boue S, McWeeney SK, Bork P, Lercher MJ. (2006)

Similar gene expression profiles do not imply similar tissue functions

Trends Genet. 22(3):132-138. doi: 10.1016/j.tig.2006.01.006
Europe PMC | doi

Rozowsky J, Wu J, Lian Z, Nagalakshmi U, Korbel JO, Kapranov P, Zheng D, Dyke S, Newburger P, Miller P, Gingeras TR, Weissman S, Gerstein M, Snyder M. (2006)

Novel transcribed regions in the human genome

Cold Spring Harb. Symp. Quant. Biol. 71:111-116. doi: 10.1101/sqb.2006.71.054
Europe PMC | doi


2005

Korbel JO, Doerks T, Jensen LJ, Perez-Iratxeta C, Kaczanowski S, Hooper SD, Andrade MA, Bork P. (2005)

Systematic association of genes to phenotypes by genome and literature mining

PLoS Biol. 3(5):e134. doi: 10.1371/journal.pbio.0030134
Europe PMC | doi


2004

Korbel JO, Jensen LJ, von Mering C, Bork P. (2004)

Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs

Nat. Biotechnol. 22(7):911-917. doi: 10.1038/nbt988
Europe PMC | doi

Pena RN, Webster J, Kwan S, Korbel J, Whitelaw BA. (2004)

Transgene methylation in mice reflects copy number but not expression level

Mol. Biotechnol. 26(3):215-220. doi: 10.1385/mb:26:3:215
Europe PMC | doi

Crass T, Antes I, Basekow R, Bork P, Buning C, Christensen M, Claussen H, Ebeling C, Ernst P, Gailus-Durner V, Glatting KH, Gohla R, Gössling F, Grote K, Heidtke K, Herrmann A, O'Keeffe S, Kiesslich O, Kolibal S, Korbel JO, Lengauer T, Liebich I, van der Linden M, Luz H, Meissner K, von Mering C, Mevissen HT, Mewes HW, Michael H, Mokrejs M, Müller T, Pospisil H, Rarey M, Reich JG, 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. (2004)

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources

Bioinformatics 20(2):268-270. doi: 10.1093/bioinformatics/btg398
Europe PMC | doi

Korbel JO, Assmus HE, Kielbasa SM, Herzel H. (2004)

Compositional asymmetries and predicted origins of replication of the Saccharomyces Cerevisiae genome

In: Kolchanov N, Hofestaedt R (eds.), Bioinformatics of Genome Regulation and Structure. Springer US. pp 33-38.doi: 10.1007/978-1-4419-7152-4_4
Europe PMC | doi


2003

Morett E, Korbel JO, Rajan E, Saab-Rincon G, Olvera L, Olvera M, Schmidt S, Snel B, Bork P. (2003)

Systematic discovery of analogous enzymes in thiamin biosynthesis

Nat. Biotechnol. 21(7):790-795. doi: 10.1038/nbt834
Europe PMC | doi


2002

Korbel JO, Snel B, Huynen MA, Bork P. (2002)

SHOT: a web server for the construction of genome phylogenies

Trends Genet. 18(3):158-162. doi: 10.1016/s0168-9525(01)02597-5
Europe PMC | doi