Jacques Nicolas

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Directeur de Recherche (Senior Researcher), INRIA


Dyliss team, Irisa / Inria Rennes-Bretagne Atlantique,
Campus de Beaulieu, 35042 Rennes Cedex, France.
Tel: +33 (0) 2 99 84  73 12
Fax: +33 (0) 2 99 84 71 71
Email: [jacquesDOTnicolasATirisaDOTfr or jacquesDOTnicolasATinriaDOTfr]

 

I am a computer scientist that discovered the world of life sciences and genomics around 1995.

Since then, my passion for this domain remains undimmed and I still marvel for the wealth of structures and mechanisms that occur in living organisms and can now be observed at the intimate level of molecules.

Above all is their capacity for adapting themselves in the most unlikely environments.

Bioinformaticians should remain modest in their possible contribution to the field but I am convinced that they have to be associated very early to the research question to be solved in biology: the future of this science will depend of increased automation, systematic knowledge formalization and careful modeling. This is the only way to get an explicit view of the huge space of alternative hypotheses explaining the observations, to help the scientist to choose among them and to increase their predictive power.

 

Research


 

Sequence Analysis, Machine Learning, Logic programming.

  • Bio-informatics:  Syntactic analysis, Grammatical inference, Answer set Programming.
  • Bio-analysis:  Crispr, Transposons and mobile genetic elements, Enzyme recognition, Protein interaction networks, Sequence-based discrimination of species.

Publications

  • Hal

     
  • Recent papers :
    • Catherine Belleannée, Olivier Sallou, Jacques Nicolas. Expressive Pattern Matching with Logol. Application to the Modelling of -1 Ribosomal Frameshift events. JOBIM 2012

      This paper presents on a detailed example the expressivity of a dedicated language, Logol, for the search of models on genomic sequences. Logol is based on constrained string variables, a generic concept that allows to handle subsequences as abstract mathematical variables on which various string operations or constraints apply.

       
    • François Coste, Gaelle Garet, Jacques Nicolas. Local Substitutability for Sequence Generalization. Jeffrey Heinz and Colin de la Higuera and Tim Oates. ICGI 2012, Sep 2012, Washington, MIT Press, JMLR Workshop and Conference Proceedings vol 21.

      The paper studies criteria to learn a context-free characterization of a protein family  from a set of sequences. It introduces new classes of substitutable languages using local rather than global substitutability, a reasonable assumption with respect to protein structures, and illustrates its interest  on a difficult benchmark learning set.

       
    • Jacques Nicolas. To detect and analyze sequence repeats whatever be their origin. Yves Bigot. Mobile genetic elements : protocols and genomic applications, 859, Springer, pp. 69-90, Feb. 2012, Springer Protocols, 978-1-61779-602-9. <http://dx.doi.org/10.1007/978-1-61779-603-6>

      The book introduces up-to-date methods for the identification and study of transposable elements. I have contributed with a chapter  that provides an oveview of the formal underpinnings of the search for these highly repeated elements in genomic sequences and describes a selection of practical tools for their analysis. It concludes with the interest of syntactic analysis in this domain.

       

 


PhD students

  • Gaëlle Garet  Discovery of enzymatic functions in the framework of formal languages
  • Valentin Wucher  (joint supervision with  D. Tagu, Inra Le Rheu)     Modelling an RNA interaction network for the prediction of gene functions related to the pea aphid reproduction mode.



     
  • Previous PhD students:
    • 2007 Sébastien Tempel, –MC Marseille- Etude de transposons chez A. Thaliana (joint supervision with  I. Couée et A. El Amrani, labo Ecobio, Rennes)
    • 2006 André Floëter (joint supervision with  T. Schaub, Potsdam)  -Conseiller Gouvernement-. Analysing biological expression data based on decision tree induction
    • 2005 Ingrid Jacquemin -Chef de projet ACII Nantes-  Découverte de motifs relationnels en bioinformatique: application à la prédiction de ponts disulfures.
    • 2005 Aurélien Leroux  –ATER-    Inférence grammaticale sur des alphabets ordonnés : Application à la découverte de motifs dans des familles de protéines.
    • 2003 Daniel Fredouille (joint supervision with F. Coste, Rennes) - Software developper ORACLE Montréal- Inférence d'automates finis non déterministes par gestion de l'ambiguïté, en vue d'applications en bioinformatique.
    • 2000 François CosteChercheur INRIA Rennes- Apprentissage d'automates classifieurs en inférence grammaticale
    • 1998 Christine Sinoquet –MC Nantes-    Grammaires à transformations morphiques. Recherche de motifs -exacte ou approchée- adaptée aux séquences génétiques : le système GTM.
    • 1997 Robin GrasProfesseur University of Windsor-, HDR  Un outil interactif de recherche de motifs dans les grandes séquences génétiques fondé sur l’arbre des suffixes.
    • 1995 Jean-Yves Giordano -Ingénieur  Serono Genetics Institute, Evry-. Inférence de grammaires algébriques
    • 1992 Raoul Vorc’h  -MC Rennes- Généralisation et abstraction en démonstration automatique
    • 1992 Francis Courtot –MC Lille- CARLA : acquisition et induction sur le matériau compositionnel
    • 1991 Catherine Belleannée  -MC Rennes - Vers un démonstrateur de théorèmes adaptatif

  • programmes ASP pour cours introductif : france.lp  hamilton.lp domino1.lp  domino2.lp  draft slides.ppt   draft slides.pdf