Gregory Batt  --  Publications  

• 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] (doi: 10.1093/bioinformatics/btp200)
• G. Batt, B. Yordanov, C. Belta and R. Weiss (2007)
  Robustness analysis and tuning of synthetic gene networks
  Bioinformatics, 23(18):2415-2422. [abstract], [original pdf], and [pdf] without typos introduced during editing process (doi: 10.1093/bioinformatics/btm362).
  Also in C. Brun and G. Didier, eds., Working Notes of the Journées Ouvertes Biologie, Informatique et Mathématiques (JOBIM'07), Marseille, France.
• 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].
• 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, 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. [abstract and pdf]
  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.
• 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 [abstract and 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] 

• 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
  In E. Pecou, S. Martinez and A. Maass, eds., Mathematical and Computational Methods in Biology. Editions Hermann, Paris. 206-239.

• G. Batt, C. Belta and R. Weiss (2006)
  Robustness analysis and tuning of synthetic gene networks with parameter uncertainties
  in Cold Spring Harbor conference on Engineering Principles in Biological Systems, 62, Cold Spring Harbor, NY, USA. [pdf]
• 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 E. coli
  in Workshop on Computation of Biochemical Pathways and Genetic Networks, Heidelberg, Germany. [pdf]
  
• G. Batt, H. de Jong, J. Geiselmann and M. Page (2004)
  Qualitative modeling and simulation of genetic regulatory networks
  in Minisymposium on Cell Biology with Control and System Theory of Conference on Mathematical Theory of Networks and Systems (MTNS’04), Leuven, Belgium.
• 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. [abstract and pdf]
• G. Batt, H. de Jong, J. Geiselmann and M. Page (2003)
  Analysis of genetic regulatory networks : A model-checking approach
  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. [abstract and pdf]

• 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. [abstract and pdf]

• G. Batt and C. Belta (2006)
  Model checking genetic regulatory networks with applications to synthetic biology
  Technical report 2006-IR-0030, CISE Boston University. [abstract and pdf]
• 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. [abstract and pdf]
• 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). [abstract and pdf]

• RoVerGeNe 3.0
  RoVerGeNe is a tool for the analysis of genetic regulatory networks under parameter uncertainty.
  A description of the tool is available here.
  Work done in collaboration with Calin Belta, at Boston University.

• Genetic Network Analyzer 6.0
  Genetic Network Analyzer (GNA) is a computer tool for the modeling and simulation of genetic regulatory networks. The aim of GNA is to assist biologists and bioinformaticians in constructing a model of a regulatory network using knowledge about regulatory interactions in combination with gene expression data.
  A description of the tool is available here.  Please contact Genostar for using GNA (free for academic research).
  Work done in collaboration with Michel Page and Hidde de Jong, at INRIA.