Our work deals primarily with the development and application of computational methods for the understanding of the behavior of biological systems. In particular, we focus on two problems:
- analysis and control of natural biological systems (systems biology) and
- design and optimization of novel, useful biological systems (synthetic biology).
Problem-driven methodological developments. Our methodological is guided by real-life biological problems defined and studied in close collaboration with experimentalists. This approach ensures the biological relevance of the proposed methods and tools.
Formally, this amounts to the analysis of high-dimensional non-linear uncertain dynamical systems. To deal with this problem, we use high-level representations (stochastic automata, timed automata, state transition graph) and develop abstraction methods to relate them. Additionally, we use state-of-the-art numerical simulation, global optimization and sensitivity analysis techniques.
Feb 2017: InBio officially created as joint unit by Pasteur. Moving to the Pasteur Campus.
CellStar has been published in Interface!
Memip and Cogex: two grants from ANR will start in 2017
- Artemis and Andres paper has been accepted in PLoS CB (see publications).
- workshop Design, optimization and control in systems and synthetic biology (DOC'15) at ENS Paris, November 12-13, 2015 (see web site). Advanced Lecture Course on Computational Systems Biology in Aussois ski resort, April 6-11 2015 (see web site)
- Two important papers for Xavier and François PhD work: NAR and PLoS CB (see publications)
- A Postdoctoral position is available: Quantitative analysis of large stochastic systems (formal methods and computational biology, with the Genest group ) [pdf]
- HDR defense. I recently defended my Habilitation à Diriger les Recherches. The manuscript and slides can be found [here] and [here]
- Modeling cell populations: Identification of biological models from single-cell data: a comparison between mixed-effects and moment-based inference [link]
- Stoch-MC ANR Grant: Scalable model checking of stochastic models, with B. Genest (IRISA), G. Batt, W. Zielonka (Liafa), and H. Gimbert (Labri), 2014-2018
- Quantitative formal verification applied to the analysis of large and complex signal trandusction pathways: STL-based analysis of TRAIL-induced apoptosis challenges the notion of type I/type II cell line classification [link]
- PNAS article: Long-term model predictive control of gene expression at the population and single-cell levels [free text]
- Workshop on design, optimization and control in systems and synthetic biology, June 11-12, Paris [link]
- Associated team with the Weiss lab for synthetic biology [link]
- Iceberg Investissement d'Avenir ANR Grant: From population models to model populations, with G. Batt (PI, INRIA), P. Hersen (MSC, CNRS/Paris7), O. Gandrillon (BM2A, CNRS/Lyon1), C. Lhoussaine (LIFL, CNRS/Lille1), R. Veitia (IJM, CNRS/Paris7), and J. Krivine (PPS, CNRS/Paris7), 2011-2016
- J. Uhlendorf, P. Hersen, and G. Batt (2011), Towards real-time control of gene expression: in silico analysis, 18th IFAC World Congress, IFAC WC'11 [pdf]
- R. Grosu, G. Batt, F. Fenton, J. Glimm, C. Le Guernic, S.A. Smolka, and E. Bartocci (2011), From cardiac cells to genetic regulatory networks, 23rd Conference on Computer Aided Verification, CAV'11, 396-411 [pdf]
- J. Uhlendorf, S. Bottani, F. Fages, P. Hersen, and G. Batt (2011), Towards real-time control of gene expression: controlling the HOG signaling cascade, Pacific Symposium of Biocomputing, PSB'2011, 16:338-349 [pdf]
- G. Batt, M. Page, I. Cantone, G. Goessler, P. Monteiro and H. de Jong (2010), Efficient parameter search for qualitative models of regulatory networks using symbolic model checking, ECCB'2010 and Bioinformatics, 26(18)603:610 [pdf]
- Syne2Arti ANR Grant: from synthetic networks to artificial tissues, with G. Batt (PI, INRIA), D. Drasdo (INRIA), O. Maler (Verimag), and R. Weiss (MIT), Oct. 2010 - Sept 2013 [website]
- Workshop on constructing gene networks: observation, analysis and control [website]
- Toward Systems Biology workshops 2007 and 2011