David James Sherman


Bâtiment A30

Domaine Universitaire

351 cours de la Libération

F-33405 Talence cedex



+33 540-00-6922


+33 540-00-6669





44°48'30" -00°35'49.3" +52m


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.


I am a Directeur de recherche (Senior Research Scientist) at the INRIA, the French National Institute for Computer Science and Control, in the Bordeaux – Sud-Ouest research center.


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. 1.Canelas A, et al. Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains. Nature Comm. 2010 1(9):45 doi:10.1038/ncomms1150.

  2. 2.Bourbeillon J, et al. Minimum information about a protein affinity reagent (MIAPAR). Nature Biotechnol. 2010 Jul;28(7):650-3.

  3. 3.Gloriam DA. et al. A community standard format for the representation of protein affinity reagents. Mol Cell Proteomics. 2010 9(1):1-10

  4. 4.Souciet C, et al. (Génolevures Consortium) Comparative genomics of protoploid Saccharomycetaceae. Genome Research 2009 19(10):1696-709.

  5. 5.Payen C, et al. Unusual composition of a yeast chromosome arm is associated with its delayed replication. Genome Research 2009 19(10):1710-21.

  6. 6.Jean G, Sherman DJ, Nikolski M. Mining the semantics of genome super-blocks to infer ancestral architectures. J. Computational Biology 16(9) (2009) pp. 1267-84.

  7. 7.Vyahhi N, Goëffon A, Sherman DJ, Nikolski M. Swarming Along the Evolutionary Branches Sheds Light on Genome Rearrangement Scenarios - ACM SIGEVO Conference on Genetic and evolutionary computation (GECCO’09) 2009.

  8. 8.Durrens D, Nikolski M, Sherman DJ. Fusion and Fission of Genes Define a Metric between Fungal Genomes. PLoS Comput. Biol. 2008 4(10):e1000200.

  9. 9.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 37:D550-D554.

  10. 10.Iragne F, Nikolski M, Sherman DJ. Extrapolation of metabolic pathways as an aid to modelling completely sequenced nonSaccharomyces yeasts. FEMS Yeast Res. 2008 Feb;8(1):132-9.

  11. 11.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.

  12. 12.Nikolski M, Sherman DJ. Family relationships: should consensus reign?--consensus clustering for protein families. Bioinformatics. 2007 Jan 15;23(2):e71-6.

  13. 13.Sherman DJ, 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.

  14. 14.Durrens P, Sherman DJ. A systematic nomenclature of chromosomal elements for hemiascomycete yeasts. Yeast. 2005 Apr 15;22(5):337-42.

  15. 15.Dujon B, Sherman DJ, 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.

  16. 16.Barriot R, Poix J, Groppi A, Barré A, Goffard N, Sherman DJ, 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.

  17. 17.De Hertogh B, Talla E, Tekaia F, Beyne E, Sherman DJ, Baret PV, Dujon B, Goffeau A. Novel transporters from hemiascomycete yeasts. J Mol Microbiol Biotechnol. 2003;6(1):19-28.


Razanne Issa
Natalia Golenetskaya
Rodrigo Assar
Nicolás Loira
Hayssam Soueidan PhD 2009
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
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