Grégory Batt
PhD student 
INRIA Rhône-Alpes
655 avenue de l'Europe, Montbonnot
38334 Saint Ismier CEDEX
France
Tel. +33 (0)4 76 61 53 72
Fax. +33 (0)4 76 61 54 08
Secretary (Françoise de Coninck)
Tel. +33 (0)4 76 61 53 63
Gregory.Batt@inrialpes.fr
http://www-helix.inrialpes.fr/
I have moved to Boston University: my new web page
 Curriculum vitae
Research
Courses
Publications
Thesis
Talks
References
Curriculum vitae
I was born in Maubeuge (France) on the 23th of February 1977. After secondary school, I attended a general scientific preparation (biology, earth science, mathematics, physics and chemistry) at Lycée Pierre de Fermat in Toulouse.
Then, I had the opportunity to enter the Ecole Normale Supérieure, a 4-year research-oriented school in Lyon. During the first two years, I studied molecular and cellular biology. In the meantime, I joined the european exchange program ERASMUS, and spent a semester at the Uppsala University (Sweden). During the last two years, I studied computer science partly in Lyon and partly at the Université Joseph Fourier in Grenoble.
I started my PhD in computer science in 2002, at the Institut National de Recherche en Informatique et en Automatique, in the Helix research group in bioinformatics, headed by Alain Viari.
Research
My main research interest is in the development of mathematical methods and computer tools for the analysis of complex biological systems.
More specifically, I am involved in a project which focuses on the development of a method for the qualitative modeling and simulation of genetic regulatory networks, and of a computer tool supporting this method, called Genetic Network Analyzer (GNA). This interdisciplinary project involves mathematicians, control theorists, computer scientists and experimentalists.
My PhD thesis consists in extending the existing method and tool towards the automatic analysis and verification of the dynamical properties of genetic regulatory network models. This facilitates the analysis of simulation results obtained for large and complex models. The major application of this extension is the validation of network models, by comparing the predictions with experimentally-measured expression profiles.
From a methodological point of view, three directions for improvement are proposed:
Reformulation: the method is presented using a combination of the formalisms used in qualitative reasoning and in hybrid systems theory. This allows one to take advantage from the specific strengths of each of these. For example, qualitative reasoning offers an intuitive terminology, while the hybrid system framework, by means of the notion of discrete abstraction, makes it possible to establish a clear connection between the continuous and the discrete representations of the system.
Refinement: the use of a finer-grained discrete representation of the system is proposed. This provides a better characterization of the dynamics, especially well adapted to the comparison of predictions with experimentally-measured expression profiles in model validation.
Extension towards model checking: model-checking tools are used for efficiently and automatically testing properties of the dynamics of genetic regulatory network models. Dynamical properties are expressed as temporal logic formulae. Simulation results are exported as text files in the format accepted by standard model checkers, such as NuSMV and CADP.
These extensions have been implemented in a new version of GNA and applied to the initiation of the sporulation in Bacillus subtilis and to the nutritional stress response in Escherichia coli
My PhD advisor is Hidde de Jong. I am also working in collaboration with Michel Page (INRIA Rhône-Alpes), Delphine Ropers (INRIA Rhône-Alpes), Radu Mateescu (INRIA Rhône-Alpes), Hans Geiselmann (UJF, Grenoble), Dominique Schneider (UJF, Grenoble), Jean-Luc Gouzé (INRIA Sophia Antipolis) and Tewfik Sari (Université de Haute Alsace).
Courses
I am currently a teaching assistant (Moniteur) in basic computer science and programming courses in `Licence Sciences et Technologies' at the Université Joseph Fourier. I also gave courses on modeling and simulation of genetic regulatory networks in `Master Sciences, Technologies et Santé' at the Université Joseph Fourier.
Publications
G. Batt, D. Ropers, H. de Jong, J. Geiselmann, R. Mateescu, M. Page and D. Schneider (2005), Analysis and verification of qualitative models of genetic regulatory networks: A model-checking approach, in L. P. Kaelbling and A. Saffiotti, eds., Proceedings of the Nineteenth International Joint Conference on Artificial Intelligence (IJCAI'05), 370-375.
G. Batt, D. Ropers, H. de Jong, J. Geiselmann, R. Mateescu, M. Page and D. Schneider (2005), Validation of qualitative models of genetic regulatory networks by model checking: Analysis of the nutritional stress response in Escherichia coli, Bioinformatics, 21(Suppl 1):i19-i28. Also in G. Perrière, A. Guénoche and C. Geourjon, eds., Working Notes of the Journées Ouvertes Biologie, Informatique et Mathématiques (JOBIM'05) , 471-482, Lyon, France.
G. Batt, R. Casey, H. de Jong, J. Geiselmann, J.-L. Gouzé, M. Page, D. Ropers, T. Sari and D. Schneider (2005), Qualitative analysis of the dynamics of genetic regulatory networks using piewise-linear models. In E. Pecou, S. Martinez and A. Maass, eds., Mathematical and Computational Methods in Biology, Nonlinear Phenomena and Complex Systems. Editions Hermann, Paris. In press.
G. Batt, D. Ropers, H. de Jong, J. Geiselmann, M. Page and D. Schneider (2004), Qualitative analysis and verification of hybrid models of genetic regulatory networks : Nutritional stress response in Escherichia coli, In M. Morari and L. Thiele, eds., Eighth International Workshop on Hybrid Systems : Computation and Control (HSCC'05), Lecture Notes in Computer Science 3414, Springer-Verlag, 134-150.
G. Batt, H. de Jong, J. Geiselmann, M. Page, D. Ropers and D. Schneider (2004), Symbolic reachability analysis of genetic regulatory networks using qualitative abstraction, Technical Report RR-5362, INRIA Rhône-Alpes.
G. Batt, D. Bergamini, H. de Jong, H. Gavarel and R. Mateescu (2004), Model checking genetic regulatory networks using GNA and CADP, In S. Graf and L. Mounier, eds., Eleventh International SPIN Workshop on Model Checking Software (SPIN'04), Lecture Notes in Computer Science 2989, Springer-Verlag, 158-163. See also Vasy team.
H. de Jong, J. Geiselmann, G. Batt, C. Hernandez and M. Page (2003), Qualitative simulation of the initiation of sporulation in Bacillus subtilis, Bulletin of Mathematical Biology, 66(2):261-300.
G. Batt, H. de Jong, J. Geiselmann and M. Page (2003), Analysis of genetic regulatory networks : A model-checking approach, In B. Bredeweg and P. Salles, eds., Working Notes of the Seventeenth International Workshop on Qualitative Reasoning (QR'03), 31-38, Brasilia, Brazil. Also in M. Benerecetti and C. Pecheur, eds., Working Notes of the Second International Workshop on Model Checking and Artificial Intelligence (MoChArt'03), 51-58, Acapulco, Mexico.
G. Batt (2002). Representation of protein/protein interactions in the framework of a method for modeling genetic networks, Technical Report RR-4382, INRIA Rhône-Alpes (In french).
Thesis
Validation de modèles qualitatifs de réseaux de régulation génique : une méthode basée sur des techniques de vérification formelle
Talks
Validation of qualitative models of genetic regulatory networks by model checking: Analysis of the nutritional stress response in Escherichia coli, in Workshop on Computation of Biochemical Pathways and Genetic Networks , September 2005, Heidelberg, Germany. Invited.
Analysis and verification of qualitative models of genetic regulatory networks: A model-checking approach, in Nineteenth International Joint Conference on Artificial Intelligence (IJCAI'05), August 2005, Edinburgh, UK.
Validation of qualitative models of genetic regulatory networks by model checking: Analysis of the nutritional stress response in Escherichia coli, in Journées Ouvertes Biologie, Informatique et Mathématiques (JOBIM'05) , July 2005, Lyon, France.
Validation of qualitative models of genetic regulatory networks by model checking: Analysis of the nutritional stress response in Escherichia coli, in Thirteenth International Conference on Intelligent Systems for Molecular Biology (ISMB'05) , June 2005, Detroit, USA.
Validation of qualitative models of genetic regulatory networks by model checking: Analysis of the nutritional stress response in Escherichia coli, in Workshop on Dynamical Modeling and Analysis of Biological Regulatory Networks , May 2005, Marseille, France. Invited.
Qualitative analysis and verification of hybrid models of genetic regulatory networks : Nutritional stress response in Escherichia coli, in Eighth International Workshop on Hybrid Systems : Computation and Control (HSCC'05), March 2005, Zurich, Switzerland.
Qualitative modeling and simulation of genetic regulatory networks, in Minisymposium on Cell Biology with Control and System Theory of Mathematical Theory of Networks and Systems Conference, July 2004, Leuven, Belgium. Invited.
Model checking genetic regulatory networks using GNA and CADP, in International SPIN Workshop on Model Checking of Software (SPIN'04), a satellite workshop of European joint conferences on Theory And Practice of Software, April 2004, Barcelona, Spain.
Formal validation of models of genetic regulatory networks, in Modeling and Simulation of Biological Regulatory Processes, a satellite meeting of European Conference on Computational Biology, October 2003, Paris, France.
Analysis of genetic regulatory networks: a model-checking approach, in International Workshop on Qualitative Reasoning (QR'03), August 2003, Brasilia, Brazil.
Analysis of genetic regulatory networks: a model-checking approach, in Model Checking and Artificial Intelligence (MoChArt'03), a satellite workshop of International Joint Conference on Artificial Intelligence, August 2003, Acapulco, Mexico.
References
Bibtex references
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