BOURDON Jérémie
- Professor,
- Head of the ComBi group at LS2N (Laboratoire des Sciences du Numérique de Nantes)
- University of Nantes
- Phone: (+33)2-51-12-58-25
- Mail: Jeremie.Bourdon@univ-nantes.fr
- Web: http://jeremiebourdon.free.fr
Research activities
J. Bourdon develops methods both algorithmic and probabilistic aim at studying biological networks. He also works in dynamical system analysis.
More precisely, his researches span from Number Theory to Systems Biology with a common guideline, the use and the development of probabilistic tools.
Main research activity 1: Dynamical analysis of algorithms. The aim of dynamical analysis of algorithms is to develop and study realistic probabilistic models to perform some average-case studies of algorithms. His main contribution in this field is the definition of dynamical sources, inspired from dynamical systems in Number Theory, allowing to derive precise results in several area of information theory (statistics of pattern-matching, indexing,..)
Main research activity 2: Systems Biology. One of the main issues of systems biology consists in the definition of mathematical models that permits to analyze an/or simulate a living system in a realistic way. In this field, J. Bourdon works in the frontier of qualitative and quantitative descriptions of living systems, applying probabilistic tools that come from ergodic theory to give access to the “normal” behavior of the system.
Education and positions held
- 2015-present Full professor Université de Nantes, LS2N UMR 6004 Université de Nantes, EMN, CNRS France
- 2003-2015 Assistant professor Université de Nantes, LINA UMR 6241 Université de Nantes, EMN, CNRS France
- 2008-2010 Temporal researcher position (Délégation) in the bioinformatic INRIA/IRISA research team SYMBIOSE.
- 2002 PhD, University of Caen, Greyc (Mathematics and Computer Science), France
Responsibilities (selected)
- Nominated member of biogenouest scientific council (2005-2017)
- (Co)-supervision of 6 PhD students: Solenne Carat (defended in october 2010), automatic reconstruction of transcriptomic networks; Vincent Picard (defended in december 2015), Average-case analysis of Biological Systems; Marko Budinich-Abarca *(2012-2017), Constraint-based metabolic methods applied to communities; Hanen Mhamdi (2014-), Integration of regulation knowledge in the analysis of metabolic networks, Victor Gaborit (2016-), Multi-omics data integration for studying Multiple Myeloma; Dimitri Meistermann (2016-), Application of single-cell expression analysis to understand the basic metabolic functions of embryonic cells.
- Participation in more than 6 French National (ANR/CNRS) projects in both Mathematics, informatics and computational biology fields : Biotempo (Partner Leader, Temporal analysis of biological networks), Lareda (study of Lattice reduction algorithms), Guepard (study of multi-objective optimization algorithms), IDEALG (Analysis of the brown algae metabolism), SADA (Development of probabilistic methods for studying algorithms and data structures), Quantoursin (CNRS PEPS, Analysis of the sea urchin traduction initiation)
- Leader of the GRIOTE project (2013-2017), a 1.4M€ project funded by the Region Pays de la Loire.
- Academic Editor for PLOS One
- co-chair of the CMSB 2015 conference.
Selected publications (complete list here):
- Kilens S, Meistermann D, Moreno D, Chariau C, Gaignerie A, Reignier A, Lelièvre Y, Casanova M, Vallot C, Nedellec S, Flippe L, Firmin J, Song J, Charpentier E, Lammers J, Donnart A, Marec N, Deb W, Bihouée A, Le Caignec C, Pecqueur C, Redon R, Barrière P, Bourdon J, Pasque V, Soumillon M, Mikkelsen TS, Rougeulle C, Fréour T, David L; Milieu Intérieur Consortium. Nat Commun. 2018 Jan 24;9(1):360.
- Picard V, Siegel A, Bourdon J. A Logic for Checking the Probabilistic Steady-State Properties of Reaction Networks. J Comput Biol. 2017 Aug;24(8):734-745.
- Budinich M, Bourdon J, Larhlimi A, Eveillard D. A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems. PLoS One. 2017 Feb 10;12(2)
- Prigent S, Frioux C, Dittami SM, Thiele S, Larhlimi A, Collet G, Gutknecht F, Got J, Eveillard D, Bourdon J, Plewniak F, Tonon T, Siegel A. Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks. PLoS Comput Biol. 2017 Jan 27;13(1)
- Picard V, Mulner-Lorillon O, Bourdon J, Morales J, Cormier P, Siegel A, Bellé R. Model of the delayed translation of cyclin B maternal mRNA after sea urchin fertilization. Mol Reprod Dev. 2016 Dec;83(12)
- Abdou-Arbi O, Lemosquet S, Van Milgen J, Siegel A, Bourdon J. Exploring metabolism flexibility in complex organisms through quantitative study of precursor sets for system outputs. BMC Syst Biol. 2014 Jan 23;8:8.
- Bourdon J, Eveillard D, Siegel A. Integrating quantitative knowledge into a qualitative gene regulatory network. PLoS Comput Biol. 2011 Sep;7(9).