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Selected publications

(for a complete list, see my curriculum vitae)

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 [link] [pdf] [research report RR-8121]
• 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. Accepted. [pdf] [research report RR-8288]
• 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 [pdf]

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 [pdf][movies]
• 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
  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 [pdf][slides]
• 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 [pdf]
• 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 [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 International Conference on Computer Aided Verification, CAV'11 [pdf]

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 [abstract and pdf]

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 [pdf]
• 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 [pdf].
  See also CISE research report [pdf]

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. [abstract] and [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. [pdf]
• 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. [pdf]
• 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 [pdf]
• 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 [pdf]

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, 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 [pdf]
• 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. [pdf]
• 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. [pdf]

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. [pdf]
• 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. [pdf]