David James Sherman
David James Sherman
OFFICE
Bâtiment A30
Université Bordeaux 1
351 cours de la Libération
F-33405 Talence cedex
France
Phone
+33 540-00-6922
Fax
+33 540-00-6669
Email
Web
Research
My research develops computer science techniques for large-scale comparative genomics and hierarchical modeling of biological systems to better understand the mechanisms of eukaryote genome evolution and the ways that genes and proteins cooperate to realize cellular functions. In my research team we develop tools and algorithms for comparative genomics of eukaryotic microorganisms, inference of interaction and metabolic networks, and construction of hierarchical stochastic models of cell behavior, using techniques from data-mining, modeling, combinatorial analysis and formal methods.
Teaching
I am an Associate Professor in the Computer Science Department of the ENSEIRB, Bordeaux (Talence), France, currently seconded to the INRIA.
Education
SB’86 Mathematics, SM.89, Ph.D’94 Computer Science, University of Chicago, Chicago, USA
(Habilitation) HDR’04 Computer Science, Université Bordeaux 1, Bordeaux (Talence), France
Selected Papers
1.Durrens D, Nikolski M, Sherman DJ. Fusion and Fission of Genes Define a Metric between Fungal Genomes. PLoS Comput. Biol. 2008 In press.
2.Sherman DJ, Martin T, Nikolski M, Cayla C, Souciet JL, Durrens P. Génolevures: protein families and synteny among complete hemiascomycetous yeast proteomes and genomes. Nucleic Acids Res. 2009 In press.
3.Iragne F, Nikolski M, Sherman D. Extrapolation of metabolic pathways as an aid to modelling completely sequenced nonSaccharomyces yeasts. FEMS Yeast Res. 2008 Feb;8(1):132-9.
4.Barriot R, Sherman DJ, Dutour I.. How to decide which are the most pertinent overly-represented features during gene set enrichment analysis. BMC Bioinformatics. 2007 Sep 11;8:332.
5.Nikolski M, Sherman DJ. Family relationships: should consensus reign?--consensus clustering for protein families. Bioinformatics. 2007 Jan 15;23(2):e71-6.
6.Sherman D, Durrens P, Iragne F, Beyne E, Nikolski M, Souciet JL.. Genolevures complete genomes provide data and tools for comparative genomics of hemiascomycetous yeasts. Nucleic Acids Res. 2006 Jan 1;34:D432-5.
7.Durrens P, Sherman DJ. A systematic nomenclature of chromosomal elements for hemiascomycete yeasts. Yeast. 2005 Apr 15;22(5):337-42.
8.Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, Lafontaine I, De Montigny J, Marck C, Neuvéglise C, Talla E, et al. Genome evolution in yeasts. Nature. 2004 Jul 1;430(6995):35-44.
9.Barriot R, Poix J, Groppi A, Barré A, Goffard N, Sherman D, Dutour I, de Daruvar A. New strategy for the representation and the integration of biomolecular knowledge at a cellular scale. Nucleic Acids Res. 2004 Jul 7;32(12):3581-9.
10.De Hertogh B, Talla E, Tekaia F, Beyne E, Sherman D, Baret PV, Dujon B, Goffeau A. Novel transporters from hemiascomycete yeasts. J Mol Microbiol Biotechnol. 2003;6(1):19-28.
Students
Rodrigo Assar
Nicolás Loira
Hayssam Soueidan
Adrien Goëffon Post-doc 2007-9
Emmanuelle Beyne Ph.D 2008
Julie Bourbeillon Post-doc 2007-8
Florian Iragne Ph.D 2007
Hélène Ferry-Dumazet Post-doc 2006
Isabelle Lesur-Kupin Ph.D 2005
Projects, Contracts, Other Links
MAGNOME team INRIA Bordeaux Sud-Ouest
Génolevures GDR 2354 CNRS
GENARISE ANR-05-BLAN-0331 ANR
ProteomeBinders 26008 EU FP6
Yeast Systems Biology Network LSHG-CT-2005-018942 EU FP6
Glendower: I can call spirits from the vasty deep!
Hotspur: Why, so can I, or so can any man; But will they come when you do call for them?
Shakespeare, Henry IV Part I act 3, scene 1