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Guillaume COLLET Print
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gcollet Title PhD Student
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Address Symbiose Projet - Room D 151
  INRIA/Irisa - Campus de Beaulieu
  35042 RENNES Cedex - France
Tel +33 2 99 84 71 22
   
   
   


Current Position Post-doc at CEA (Saclay)
Phd Thesis Local Alignments for Protein Threading by a Mixed Integer Programming Approach.
Scientific Advisors : Rumen Andonov and Jean-François Gibrat.
 My new page  http://gcollet.ouvaton.org




Education



 2006-2010
 
PhD student in Bioinformatics (Université de Rennes 1).

Thesis Title : Local Alignments for Protein Threading, a by Mixed Integer Programming Approach.

Brief Synopsis of Research: Detecting similarities and homologies between proteins is a key step during the annotation process. To find such homologies, multiple sequence alignments are widely used. These methods provide global to local alignment features. Nevertheless, in the so called "Twilight Zone", one must relies on fold recognition methods to find homologous proteins. In this field, the Protein Threading Problem (PTP) uses pairwise parameters to globaly align a protein sequence with a protein structure. As far as we know, no local alignment  method using pairwise parameters exists. Based on the PTP, we proposed 5 mathematical formulations of such local alignments. Then, we developed an efficient edicated algorithm to solve these problems. Our algorithm uses well-known techniques from Operational Research : Branch \& Bound, Subgradient Descent and Lagrangian Relaxation. We show that, despite greater complexity, local alignments using pairwise parameters are feasible
2006
  Master degree in Bioinformatic (Université Rennes 1). Ranked first
2005   Master degree in Computer Science (Université Rennes 1).
2003   Bachelor degree in Computer Science (Université Rennes 1).

Publications


 

2009    G. Collet, R. Andonov, N. Yanev and J-F. Gibrat.
     Local Protein Threading by Mixed Integer Programming.
    Discrete Applied Mathematics, Special issue on "Graphs and Combinatorial Optimization". In Press.
     
     G. Collet, R. Andonov, N. Yanev and J-F. Gibrat.
    ProteinThreading.
     Proceedings and oral presentation. 8th Cologne-Twente Workshop on Graphs and Combinatorial Optimization, June 2-4, pp. 341-344 (Paris)
     
2007
 
R. Andonov, G. Collet, J-F. Gibrat, A. Marin, V. Poirriez and N. Yanev.
    Recent Advances in Solving the Protein Threading Problem.
    Chapter in "Parallel Computing for Bioinformatics and Computational Biology", pp. 325-356, E-G Talbi and A Zomaya (editors), Wiley-Interscience.
     
2006
  G. Collet, N. Yanev, A. marin, R. Andonov, J-F. Gibrat.
    A flexible model for protein fold recognition.
    Poster and Oral presentation. JOBIM 2006, bordeaux.
     
    G. Collet, A. marin, N. Yanev, R. Andonov, J-F. Gibrat.
    Implémentation d'un algorithme d'alignement semi-global utilisant des paramètres non locaux pour la reconnaissance de repliements.
    Proceedings and oral presentation. ROADEF 2006, Lilles.
     

Employment



2009-2010   ATER Position. Université de Rennes 1 (Rennes)
    Teaching : Logic, Graph theory and Office Suite.
     
 2007-2009   Part-time Teacher. Lycée Chateaubriand (Rennes)
    Teaching : Algorithms and Math Programming.
     
 2007   Internship in Parallel Computing. IPP-BAS laboratory (Sofia, Bulgaria)
 

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