Prof. Dr. Erik van Nimwegen

Born in 1970 Citizenship: the Netherlands Tel: +41 61 267 1576 Email: Erik.Vannimwegen@unibas.ch   Current position Associate Professor for Computational Systems Biology, Biozentrum, University of Basel Group leader, Genome Systems Biology, Swiss Institute of Bioinformatics. June 2008-present Associate Professor for Computational Systems Biology, Biozentrum, University of Basel July 2004-present Group leader, Genome Systems Biology, Swiss Institute of Bioinformatic Sept. 2003-June 2008 Assistant Professor of Systems Biology, Division of Bioinformatics, Biozentrum, University of Basel Oct. 2000-Sept. 2003 Fellow, Center for Studies in Physics and Biology, The Rockefeller University, NYC Oct. 1999-Sept. 2000 Postdoctoral Researcher, The Santa Fe Institute, Santa Fe, New Mexico Sept. 1995-Sept. 1999 Graduate research at the Santa Fe Institute, Santa Fe, New Mexico and at the Theoretical Biology/Bioinformatics group, Faculty of Biology, Utrecht University, the Netherlands September 27, 1999 PhD Diploma, cum laude, theoretical biology/bioinformatics, Faculty of Biology, University of Utrecht. Supervisors: Prof. Dr. P. Hogeweg and Dr. J.P. Crutchfield >August 28, 1995 Doctoral Diploma, theoretical physics, Faculty of physics and astronomy, University of Amsterdam Supervisor: Prof. Dr. R.H. Dijkgraaf

Honors, additional responsibilities and awards

2004-present: Editor, Journal of Statistical Mechanics: Theory and Experiment 2004-present: Edit. Board, Biology Direct 2007:             Organized ESF exploratory workshop on "Computational approaches to the role of                      epigenetics in transcription regulation"

Relevant publications:

Balwierz PJ, Carninci P, Daub CO, Kawai J, Hayashizaki Y, van Belle W, Beisel C, van Nimwegen E (2009) Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data. Genome Biol 10(7):R97 FANTOM Consortium, Suzuki H, Forrest AR, van Nimwegen E, Daub CO, Balwierz PJ et al (2009) The transcriptional network that controls growth arrest and differentiation in a human myeloid cell line Nat Genet 41(5):553-62. van Nimwegen, E. (2007). Finding regulatory elements and regulatory motifs: a general probabilistic framework. BMC Bioinformatics, 8 Suppl 6, S4. Pachkov, M., Erb, I., Molina, N., & van Nimwegen, E. (2007). SwissRegulon: a database of genome-wide annotations of regulatory sites. Nucleic Acids Res, 35(Database issue), D127-31. Siddharthan, R., Siggia, E. D., & van Nimwegen, E. (2005). PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny. PLoS Comput Biol, 1(7), e67.