I’m a computational biologist passionate about understanding how biological systems function at the molecular level. Making sense of our necessarily fragmented observations of the extremely complex systems that cells are is one of the most challenging and important current scientific problems.
We employ a multidisciplinary approach and combine mathematical, computational and biological methods to develop predictive models of cellular processes.
We notably focus on two problems:
- analysis and control of natural biological systems (systems biology) and
- design and optimization of novel, useful biological systems (synthetic biology).
I’m currently a senior scientist (Directeur de Recherche) at Inria, the French national institute for computer science and applied mathematics, and the head of Inbio, a research group hosted at Institut Pasteur and affiliated to the Inria Paris Research Center.
See here for a detailed CV [pdf].
Publications
2023
- S. Sosa-Carrillo, H. Galez, S. Napolitano, F. Bertaux* and G. Batt* (2023)
Maximizing protein production by keeping cells at optimal secretory stress levels using real-time control approaches
in Nature Communications, 14: 3028
2022
- F. Bertaux*, S. Sosa-Carrillo*, V. Gross, A. Fraisse, C. Aditya, M. Furstenheim, and G. Batt (2022)
Enhancing bioreactor arrays for automated measurements and reactive control with ReacSight
in Nature Communications, 13: 3363 - Z.R. Fox*, S. Fletcher*, A. Fraisse, C. Aditya, S. Sosa-Carrillo, J. Petit, S. Gilles, F. Bertaux, J. Ruess, and G. Batt (2022),
Enabling reactive microscopy with MicroMator
in Nature Communications, 13: 2199. - A. Davidović, R. Chait, G. Batt, J. Ruess (2022),
Parameter inference for stochastic biochemical models from perturbation experiments parallelised at the single cell level
in PLoS Computational Biology, 18(3): e1009950. - C. Aditya, F. Bertaux, G. Batt, and J. Ruess (2022)
Using single-cell models to predict the functionality of synthetic circuits at the population scale
in Proceedings of the National Academy of Sciences of the U.S.A, 119(11): e2114438119.
2021
- F. Bertaux, J. Ruess, and G. Batt (2021),
External control of microbial populations for bioproduction: A modeling and optimization viewpoint
Current Opinion in Systems Biology, 28:100394. - C. Aditya, F. Bertaux, G. Batt*, and J. Ruess* (2021),
A light tunable differentiation system for the creation and control of consortia in yeast
in Nature Communications, 12(1): 5829. - V. Andreani, L. You, P. Glaser, and G. Batt (2021),
A model-based approach to characterize enzyme-mediated response to antibiotic treatments: going beyond the SIR classification
in bioRxiv. 2021.07.16.452741. - D. Lunz, G. Batt, J. Ruess*, and J. F. Bonnans* (2021),
Beyond the chemical master equation: Stochastic chemical kinetics coupled with auxiliary processes
in PLoS Computational Biology, 17(7): e1009214. - D. Lunz, G. Batt, and J. Ruess (2021),
To quarantine, or not to quarantine: A theoretical framework for disease control via contact tracing
in Epidemics, 34:100428.
2019
- M. Kryukov*, A. Carcano*, G. Batt, and J. Ruess (2019),
Can optimal experimental design serve as a tool to characterize highly non-linear synthetic circuits?
in IEEE European Control Conference (ECC’19), pp. 1176-81, Naples, Italy [pdf] - E. Weill, V. Andréani, C. Aditya, P. Martinon, J. Ruess, G. Batt*, and J.F. Bonnans* (2019),
Optimal control of an artificial microbial differentiation system for protein bioproduction
in IEEE European Control Conference (ECC’19), pp. 2663-8, Naples, Italy [pdf]
2018
- H.R. Meredith, V. Andreani, H.R. Ma, A.J. Lopatkin, A.J. Lee, D.J. Anderson, G. Batt and L. You (2018),
Applying ecological resistance and resilience to dissect bacterial antibiotic responses
in Science Advances, 4(12):eaau1873 [pdf] - J.-B. Lugagne, S. Jain, P. Ivanovitch, Z. Ben Meriem, C. Vulin, C. Fracassi, G. Batt, and P. Hersen (2018)
Identification of individual cells from z-stacks of bright-field microscopy images
in Scientific Reports, 8:11455 [pdf]
2017
- J.-B. Lugagne, S. Sosa Carrillo, M. Kirch, A. Köhler, G. Batt* & P. Hersen* (2017)
Balancing a genetic toggle switch by real-time feedback control and periodic forcing
in Nature Communications, 8:1671 [pdf] - C. Versari, S. Stoma, K. Batmanov, A. Llamosi, F. Mroz, A. Kaczmarek, M. Deyell, C. Lhoussaine*, P. Hersen*, and G. Batt* (2017)
Long-term tracking of budding yeast cells in brightfield microscopy: CellStar and the Evaluation Platform
in Interface, 12(2):e1004706 [pdf] - S. Palaniappan, F. Bertaux, M. Pichené, E. Fabre, G. Batt*, and B. Genest* (2017)
Discrete stochastic abstraction of biological pathway dynamics: A case study of the apoptosis pathway
in Bioinformatics, 33(13):1980–1986 [pdf]. - F. Bertaux, D. Drasdo and G. Batt (2017)
System modeling of receptor-induced apoptosis
in TRAIL, Fas Ligand, TNF and TLR3 in Cancer, O. Micheau Ed., Springer [pdf].
2016
- A. Llamosi, A.M. Gonzalez-Vargas, C. Versari, E. Cinquemani, G. Ferrari-Trecate*, P. Hersen*, and G. Batt* (2016)
What population reveals about individual cell identity: estimation of single-cell models of gene expression in yeast
in PLoS Computational Biology, 12(2):e1004706 [pdf] - S.K Palaniappan, M. Pichené, G. Batt, E. Fabre, and B. Genest (2016)
A Look-Ahead Simulation Algorithm for DBN Models of Biochemical Pathways
in International Workshop on Hybrid Systems Biology, HSB 2016, p. 3-19. Springer [pdf].
2015
- S. Bogomolov, C. Schilling, E. Bartocci, G. Batt, H. Kong, and R. Grosu (2015)
Abstraction-based parameter synthesis for multiaffine systems
in 11th International Haifa Verification Conference, HVC 2015, p.19-35. Springer - J. Uhlendorf, A. Miermont, T. Delaveau, G. Charvin, F. Fages, S. Bottani, P. Hersen*, and G. Batt* (2015)
In silico control of biomolecular processes
in Computational Methods in Synthetic Biology, M. Marchisio (Ed.), Humana Press, Springer
2014
- X. Duportet, L. Wroblewska, P. Guye, Y. Li, J. Eyquem, J. Rieders, G. Batt* and R. Weiss* (2014)
A platform for rapid prototyping of synthetic gene networks in mammalian cells
Nucleic Acids Research, 42(21):13440–51 - F. Bertaux, S. Stoma, D. Drasdo, and G. Batt (2014)
Modeling dynamics of cell-to-cell variability in TRAIL-induced apoptosis explains fractional killing and predicts reversible resistance
PLoS Computational Biology, 10(10):e1003893 [pdf] - L. Maruthi, I. Tkachev, A. Carta, E. Cinquemani, P. Hersen, G. Batt*, A. Abate* (2014)
Towards real-time control of gene expression at the single cell level: a stochastic control approach
Computational Methods in Systems Biology, CMSB’14, LNCS/LNBI, Springer, 155-172 - G. Batt (2014)
Design, optimization and control in systems and synthetic biology
Habilitation à Diriger des Recherches in Systems Biology, Paris Diderot University, Paris, France [manuscript]
2013
- S. Stoma, A. Donzé, F. Bertaux, O. Maler, G. Batt (2013)
STL-based analysis of TRAIL-induced apoptosis challenges the notion of type I/type II cell line classification
PLoS Computational Biology, 9(5):e1003056 [pdf] - A.M. Gonzalez, J. Uhlendorf, J. Schaul, E. Cinquemani, G. Batt, G. Ferrari-Trecate (2013)
Identification of biological models from single-cell data: a comparison between mixed-effects and moment-based inference
European Control Conterence, ECC’13, pp 3652-57 - N.D. Mendes, F. Lang, Y.S. Le Cornec, R. Mateescu, G. Batt, and C. Chaouiya (2013)
Composition and abstraction of logical regulatory modules: application to multicellular systems
Bioinformatics, 29(6):749-757
2012
- J. Uhlendorf, A. Miermont, T. Delaveau, G. Charvin, F. Fages, S. Bottani, G. Batt* and P. Hersen* (2012)
Long-term model predictive control of gene expression at the population and single-cell levels
PNAS, 109(35):14271-14276 - G. Batt, B. Besson, P.-E. Ciron, H. de Jong, E. Dumas, J. Geiselmann, R. Monte, P.T. Monteiro, M. Page, F. Rechenmann, and D. Ropers (2012)
Genetic Network Analyzer: a tool for the qualitative modeling and simulation of bacterial regulatory networks
J. van Helden, A. Toussaint, D. Thieffry (eds), Bacterial Molecular Networks, Humana Press, Springer, pp. 439-462
2011
- 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, pp 14844-50 - J. Uhlendorf, S. Bottani, F. Fages, P. Hersen*, and G. Batt* (2011)
Towards real-time control of gene expression: controlling the HOG signaling cascade
16th Pacific Symposium of Biocomputing, PSB’2011, 16:338-349 - A. Rizk, G. Batt, F. Fages and S. Soliman (2011)
Continuous valuations of temporal logic specifications with applications to parameter optimization and robustness measures
Theoretical Computer Science, 412(26):2827-2839 - 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 International Conference on Computer Aided Verification, CAV’11, pp 396-411
2010
- 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
Bioinformatics, ECCB10 Special Issue, 26(18):i603-i610 [pdf] and model files [zip]
Note: two typos are present in the original article. A corrigendum is provided [here].
2009
- A. Rizk, G. Batt*, F. Fages and S. Soliman (2009)
A general computational method for robustness analysis with applications to synthetic gene networks
Bioinformatics, ISMB09/ECCB09 Special Issue, 25(12):i169-i178
2008
- O. Maler and G. Batt (2008)
Approximating continuous systems by timed automata
First International Conference on Formal Methods in Systems Biology (FMSB’08), Lecture Notes in Bioinformatics LNCS 5054, Springer-Verlag, 77-89 [pdf] - A. Rizk, G. Batt, F. Fages and S. Soliman (2008)
On a continuous degree of satisfaction of temporal logic formulae with applications to systems biology
6th International Conference on Comptational Methods in Systems Biology (CMSB’08), Lecture Notes in Computer Science 5307, Springer-Verlag, 251-268 - G. Batt, C. Belta and R. Weiss (2008)
Temporal logic analysis of gene networks under parameter uncertainty
IEEE Transactions on Circuits and Systems and IEEE Transactions on Automatic Control, Joint Special Issue on Systems Biology, pp 215-229
2007
- G. Batt, R. Ben Salah and O. Maler (2007)
On timed models of gene networks
Fifth International Conference on Formal Modelling and Analysis of Timed Systems (FORMATS’07), Lecture Notes in Computer Science 4763, Springer-Verlag, 38-52. [pdf] - G. Batt, B. Yordanov, C. Belta and R. Weiss (2007)
Robustness analysis and tuning of synthetic gene networks
Bioinformatics, 3(18):2415-2422. [pdf] - G. Batt, C. Belta and R. Weiss (2007)
Model checking genetic regulatory networks with parameter uncertainty
Tenth International Workshop on Hybrid Systems: Computation and Control (HSCC’07), Lecture Notes in Computer Science 4416, Springer-Verlag, 61-75. - G. Batt, C. Belta and R. Weiss (2007)
Model checking liveness properties of genetic regulatory networks
Thirteenth International Conference on Tools and Algorithms for the Construction and Analysis of Systems (TACAS’07), Lecture Notes in Computer Science 4424, Springer-Verlag, 323-338. - B. Yordanov, G. Batt and C. Belta (2007)
Model checking discrete-time piecewise affine systems: Application to gene networks
European Control Conference (ECC’07). [pdf] - G.Batt, H. de Jong, M. Page and J. Geiselmann (2007)
Symbolic reachability analysis of genetic regulatory networks using qualitative abstractions
Automatica, 44(4):982-989. - G. Batt, H. de Jong, J. Geiselmann, J.-L. Gouzé, M. Page, D. Ropers, T. Sari, D. Schneider (2007)
Analyse qualitative de la dynamique de réseaux de régulation génique par des modèles linéaires par morceaux
Technique et Science Informatique, 26(1-2):11-45.
2006
- G. Batt, R. Casey, H. de Jong, J. Geiselmann, J.-L. Gouzé, M. Page, D. Ropers, T. Sari and D. Schneider (2006)
Qualitative analysis of the dynamics of genetic regulatory networks using piecewise-linear models
Mathematical and Computational Methods in Biology. Editions Hermann, Paris. 206-239. - G. Batt (2006)
Validation of qualitative models of genetic regulatory networks: A method based on formal verification techniques
PhD Thesis in Computer Science, Université Joseph Fourier, Grenoble, France. [pdf]
2005
- 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, ISMB05 Special Issue, 21(Suppl 1):i19-i28 - 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
Eighth International Workshop on Hybrid Systems : Computation and Control (HSCC’05), Lecture Notes in Computer Science 3414, Springer-Verlag, 134-150. - 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
19th International Joint Conference on Artificial Intelligence (IJCAI’05), 370-375.
2004
- H. de Jong, J. Geiselmann, G. Batt, C. Hernandez and M. Page (2004)
Qualitative simulation of the initiation of sporulation in Bacillus subtilis
Bulletin of Mathematical Biology, 66(2):261-300. - G. Batt, D. Bergamini, H. de Jong, H. Garavel and R. Mateescu (2004)
Model checking genetic regulatory networks using GNA and CADP
Eleventh International SPIN Workshop on Model Checking Software (SPIN’04), Lecture Notes in Computer Science 2989, Springer-Verlag, 158-163.
