Dr. Jan O. Korbel

Computational Biology & Genomics, Gerstein lab
Yale University School of Medicine

Curriculum Vitae

EDUCATION AND QUALIFICATIONS

Since May 2005: Yale University Center for Excellence in Genome Science (CEGS) & Molecular Biology and Biophysics Dept., New Haven, CT, USA
EMBO & Marie Curie Fellow at Yale University (postdoctoral fellow/guest researcher), associated with Mark Gerstein's group. Main focus of research: utilizing next generation oligonucleotide tiling arrays to characterize the "dark matter" of the genome, and to study human variation (i.e. structural variants in the genome) and its effect on human diversity and disease.

July 2001 - April 2005: Ph.D./Dr. rer. nat. Molecular Biology/Biology at the European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
The Ph.D. studies were carried out in Peer Bork's group. Title of the dissertation: "Protein function prediction: utilising the genomic context". The Dr. rer. nat. (Ph.D.) in Biology, specialization Molecular Biology, was awarded by the Humboldt-University Berlin; University supervisor: Hanspeter Herzel. Achieved highest possible grade (summa cum laude).

May 2001: University degree Dipl-Ing. Biotechnology, specialization Medical Biotechnology (comparable to M.Sc.) from Technical University of Berlin, Germany
Overall grade 1.0, "mit Auszeichnung" (summa cum laude; highest possible grade).

November 1999 - November 2000: Institute for Theoretical Biology, Humboldt University Berlin, Germany
Research project in Hanspeter Herzel's group; completion of my "Diplomarbeit" (masters thesis): "Computational prediction of DNA regulatory elements", receiving the highest possible grade.

 

ADDITONAL RESEARCH EXPERIENCE (OUTSIDE GERMANY)

October 2002: Institute for Biotechnology, Universidad Nacional Autonoma de Mexico, Cuernavaca, Mexico
Visitor in Enrique Morett's group at the Institute for Biotechnology (collaborators from Mexico): discovery of analogous enzymes in the thiamin biosynthesis pathway.

September - November 1999: Department of Dermatology, Yale School of Medicine, New Haven, Connecticut
Two-month experimental project in the group of Ruth Halaban: study of the role of the protein kinase B (PKB, also known as Akt) within the signal cascade of H-Ras in normal human melanocytes and malignant melanoma cells using western-blotting.

March - April 1999: Department of Gene Expression and Development, Roslin Institute, Edinburgh
Research project in the group of Bruce Whitelaw (2 months): study of methylation-patterns within the genome of transgenic mice applying southern-blotting and methylation-specific restriction enzymes.

AWARDS & FELLOWSHIPS

2006-2008: Marie Curie Fellow (Outgoing International Fellowship).
2007: “EMBO World practical course” Fellowship from EMBO for co-organizing scientific meeting.
2005-2007: EMBO Fellow (EMBO Long Term Fellowship).
2001-2005: Ph.D. student fellowship awarded from the EMBL Heidelberg.
2002-2004:‘e-fellows grant‘ (for outstanding academic achievements).
2002: Katharina-Heinroth-Prize awarded by the "Gesellschaft naturforschender Freunde zu Berlin e.V." (Berlin Society of Researching Friends) for my "Diplomarbeit" (masters thesis).
2002: Erwin-Stephan-Prize awarded by the Technical University Berlin for excellent study results and short duration of study.
1999: DAAD support for research project at Yale University, New Haven, CT, USA.
1998: Erasmus stipend for research project at Napier University, Edinburgh, UK.

MISCELLANEOUS

August 2007: Organizing Committee/Co-Organizer of EMBL world practical course on Computational Biology: "From genomes to cells & ecosystems" in Cuernavaca, Mexico 2007.
November 2002: Co-Organizer of the 3rd EMBL PhD Student International Symposium "Life within Boundaries - Membranes & Compartments in Biology" in Heidelberg, Germany, 2002.
November 2001-November 2002: Representative of the Ph.D. students at the European Molecular Biology Laboratory (EMBL).

Publications

* authors contributing equally to the publication

 

 

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 ,104:10110-10115. [PDF]

ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Nepth S, …, Korbel JO, Emanuelsson O et al.. (2007). Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project, Nature 2007, 447:799-816. [Abstract]

 

Washietl S, Pedersen JS, Korbel JO, Gruber AR, Hackermüller J, Hertel J, Lindemeyer M, Reiche K, Stocsits C, Tanzer A, Ucla C, Wyss C, Antonarakis SE, Denoeud F, Lagarde J, Drenkow J, Kapranov P, Gingeras TR, Snyder M, Gerstein MB, Reymond A et al. (2007). Structured RNAs in the ENCODE selected regions of the human genome. Genome Res., 17:852-64. [Abstract]

 

Rozowsky JS, Newburger D, Sayward F, Wu J, Jordan G, Korbel JO, Nagalakshmi U, Ying J, Zheng D, Guigo R, Gingeras T, Weissman SM, 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., 17:732-45. [Abstract]

 

Gerstein M, Bruce M, Rozowsky J, 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., 17:669-81. [Abstract]

 

Raes J*, Korbel JO*, Lercher MJ, von Mering C, Bork P (2007). Prediction of effective genome size in metagenomic samples. Genome Biol., 8: R10. [PDF}

 

Pachkov M, Dandekar T, Korbel JO, Bork P, Schuster S (2007). Use of pathway analysis and genome context methods for functional genomics of Mycoplasma pneumonia nucleotide metabolism. Gene, 396:215-225. [Abstract]

 

Li L, Wang X, Sasidharan R, Stolc V, Deng W, He H, Korbel JO, Chen X, Tongprasit W, Ronald P, Chen R, Gerstein M, Wang Deng X (2007). Global identification and characterization of transcriptionally active regions in the rice genome. PLoS ONE, 2:e294. [PDF]

 

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 ,103:4534-4539. [PDF]

Du J, Rozowsky JS, Korbel JO, Zhang ZD, Royce TE, Schultz MH, Snyder M, Gerstein MB (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, 22:3016-3024. [Abstract]

 

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. [Abstract]

 

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., 22:132-8. [Abstract]

Korbel JO*, Doerks T*, Jensen LJ, Perez-Iratxeta C, Kaczanowski S, Hooper S, Andrade M & Bork P (2005). Systematic association of genes to phenotypes by genome and literature mining. PLoS Biol., 3:e134. [PDF]

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., 22:911-7. [PDF]

Pena RN, Webster J, Kwan S, Korbel JO & Whitelaw BA (2004). Transgene methylation in mice reflects copy number but not expression level. Mol. Biotechnol., 26:215-220. [Abstract]

Korbel JO*, Assmus HE*, Kielbasa SM & Herzel H (2004). Compositional asymmetries and predicted origins of replication of the Saccharomyces cerevisiae genome. In: Bioinformatics of Genome Regulation and Structure (ed. Kolchanov N, Hofestaedt R), pp. 33-38, KLUWER academic publishers, Boston.

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, Gossling F, Grote K, Heidtke K, Herrmann A, O'Keeffe S, Kiesslich O, Kolibal S, Korbel JO, Lengauer T et al. (2004). The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources. Bioinformatics, 20:268-270. [PDF]

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., 21:790-5. [PDF]

Korbel JO*, Snel B*, Huynen MA & Bork P, (2002). SHOT: a web server for the construction of genome phylogenies. Trends Genet., 18:158-62. [Abstract]

Korbel JO (2002). On the regulation of transcription in eukaryotes and methods for finding DNA regulatory elements using bioinformatics. In: Sitzungsberichte der Gesellschaft Naturforschender Freunde zu Berlin, Vol. 41, p. 57-66 (ed. Sudhaus W) Goecke & Evers, Keltern.

Herzel H, Beule D, Kielbasa S, Korbel JO, Sers C, Malik A, Eickhoff H, Lehrach H & Schuchhardt J, (2001). Extracting information from cDNA arrays. Chaos, 11:98-107. [Abstract]

Kielbasa SM*, Korbel JO*, Beule D, Schuchhardt J & Herzel H, (2001). Combining frequency and positional information to predict transcription factor binding sites. Bioinformatics, 17:1019-26. [PDF]

 

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