Short CV/Education and training

Education

  • 1986 – 1992
    M.D., University of Medicine and Pharmacy, Timisoara, Romania

  • 1994 – 1996
    M.Sc. Computer Science, University of New Mexico, Albuquerque, USA

  • 1996 – 1999
    PhD Computer Science, University of New Mexico, Albuquerque, USA

Employment

  • 1993 – 1994
    Research Associate, The Santa Fe Institute, Santa Fe. Theoretical Immunology

  • 1994 – 1996
    Research Associate, Los Alamos National Laboratory, Los Alamos. Theoretical Biology and Biophysics

  • 1994 – 1996
    Teaching Assistant, University of New Mexico, Albuquerque. Computer Science

  • 1996 – 1999
    Research Assistant, University of New Mexico, Albuquerque. Computer Science

  • 1999 – 2000
    Postdoctoral Fellow, Los Alamos National Laboratory, Los Alamos. Theoretical Biology and Biophysics

  • 2000 – 2003
    Postdoctoral Fellow, The Rockefeller University, New York. Computational Biology

  • 2003 – 2008
    Assistant Professor, Biozentrum, University of Basel, Basel. Bioinformatics and Computational Biology

  • Since 2004
    Group Leader, Swiss Institute of Bioinformatics, Basel. RNA regulatory networks

  • 2008 – 2014
    Associate Professor, Biozentrum, University of Basel, Basel. Computational and Systems Biology

  • Since 2014
    Professor, Biozentrum, University of Basel, Basel. Computational and Systems Biology

Selected publications

  • Gruber AJ, Schmidt R, Gruber AR, Martin G, Ghosh S, Belmadani M, Keller W, Zavolan M. A comprehensive analysis of 3’ end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogeneous ribonucleoprotein C on cleavage and polyadenylation.

    Genome Res. 26:1145-1159 (2016).

  • Breda J, Rzepiela AJ, Gumienny R, van Nimwegen E, Zavolan M. Quantifying the strength of miRNA-target interactions. Methods 85:90-99 (2015).

  • Balwierz PJ, Pachkov M, Arnold P, Gruber AJ, Zavolan M, van Nimwegen E. ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs. Genome Res. 24:869-884 (2014).

  • Hausser J, Syed AP, Selevsek N, van Nimwegen E, Jaskiewicz L, Aebersold R, Zavolan M. Timescales and bottlenecks in miRNA-dependent gene regulation. Mol Syst Biol. 9:711 (2013).

  • Martin G, Gruber AR, Keller W, Zavolan M. Genome-wide analysis of pre-mRNA 3’ end processing reveals a decisive role of human cleavage factor I in the regulation of 3’ UTR length. Cell Rep. 1:753-763 (2012).

  • Kishore S, Jaskiewicz L, Burger L, Hausser J, Khorshid M, Zavolan M. A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins. Nat. Methods 8:559-564 (2011).

  • Gaidatzis D, van Nimwegen E, Hausser J, Zavolan M. Inference of miRNA targets using evolutionary conservation and pathway analysis. BMC Bioinformatics 8:69 (2007).

  • Chern TM, van Nimwegen E, Kai C, Kawai J, Carninci P, Hayashizaki Y, Zavolan M. A simple physical model predicts small exon length variations. PLoS Genet. 2:e45 (2006).

  • Pfeffer S, Sewer A, Lagos-Quintana M, Sheridan R, Sander C, Grässer FA, van Dyk LF, Ho CK, Shuman S, Chien M, Russo JJ, Ju J, Randall G, Lindenbach BD, Rice CM, Simon V, Ho DD, Zavolan M, Tuschl T. Identification of microRNAs of the herpesvirus family. Nat Methods 2:269-276 (2005).



Complete list of publications

Membership in scientific bodies/juries

  • Member Editorial Board: PLoS Genetics, Genome Biology, Bioinformatics, BMC Molecular Biology, Cells.

  • Member of the European Molecular Biology Organization, since 2015

  • Member of Academia Europea, Molecular Biology Section, since 2014

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