Publications

Automated inference of Boolean models from molecular interaction maps using CaSQ. Bioinformatics, 2020.

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Setting the basis of best practices and standards for curation and annotation of logical models in biology—highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop. Briefings in Bioinformatics, 2020.

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On Inferring Reactions from Data Time Series by a Statistical Learning Greedy Heuristics. In Luca Bortolussi, Guido Sanguinetti, editor, CMSB 2019 - 17th Computational Methods in Systems Biology, LNCS, Springer-Verlag, 2019.

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A Statistical Unsupervised Learning Algorithm for Inferring Reaction Networks from Time Series Data. In ICML 2019 - Workshop on Computational Biology, 2019.

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Influence Networks compared with Reaction Networks: Semantics, Expressivity and Attractors. IEEE/ACM Transactions on Computational Biology and Bioinformatics, PP (99):1-14, 2018.

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Graphical Requirements for Multistationarity in Reaction Networks and their Verification in BioModels. Journal of Theoretical Biology, 459:79–89, 2018.

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On Robustness Computation and Optimization in BIOCHAM-4. In 16th Int. Conf. on Computational Methods in Systems Biology, 2018.

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Executable Disease Networks: Adding dynamics to molecular maps. ECCB 2018 - 17th European Conference on Computational Biology, 2018.

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Probably Approximately Correct Learning of Regulatory Networks from Time-Series Data. In J. Feret, H. Koeppl, editor, CMSB'17 - 15th International Conference on Computational Methods for Systems Biology, pages 74-90, 2017.

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Model-based Investigation of the Circadian Clock and Cell Cycle Coupling in Mouse Embryonic Fibroblasts: Prediction of RevErb-α Up-regulation During Mitosis. In Dynamics Days 2017 - XXXVII Dynamics Days Europe International Conference, 2017.

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A structural perspective on the dynamics of biochemical systems. Habilitation à diriger des recherches, Université Paris Sud - Orsay, 2016.

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Model-based investigation of the circadian clock and cell cycle coupling in mouse embryonic fibroblasts: Prediction of RevErb-α up-regulation during mitosis. BioSystems, 149:59–69, 2016.

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Influence Systems vs Reaction Systems. In Ezio Bartocci, Pietro Lio, Nicola Paoletti, editor, CMSB'16: Proceedings of the fourteenth international conference on Computational Methods in Systems Biology, volume 9859 of Lecture Notes in Computer Science, pages 98-115, Springer-Verlag, 2016.

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On Enumerating Minimal Siphons in Petri nets using CLP and SAT solvers: Theoretical and Practical Complexity. Constraints, 21 (2):251–276, 2016.

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Model-based Investigation of the Effect of the Cell Cycle on the Circadian Clock through Transcription Inhibition during Mitosis. In Olivier Roux, Jérémie Bourdon, editor, CMSB'15 - Proceedings of the thirteenth international conference on Computational Methods in Systems Biology, volume 9308 of Lecture Notes in BioInformatics, pages 208–221, Springer-Verlag, 2015.

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Inferring reaction systems from ordinary differential equations. Theoretical Computer Science, 599:64–78, 2015.

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Search by Constraint Propagation. In ACM, editor, PPDP ‘15- 17th International Symposium on Principles and Practice of Declarative Programming, pages 173–183, 2015.

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Hybrid Simulations of Heterogeneous Biochemical Models in SBML. ACM Transactions on Modeling and Computer Simulation, 25 (2):14:1-14:22, 2015.

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A constraint solving approach to model reduction by tropical equilibration. Algorithms for Molecular Biology, 9 (1):24, 2014.

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Trace Simplifications preserving Temporal Logic Formulae with Case Study in a Coupled Model of the Cell Cycle and the Circadian Clock (Best Student Paper Prize). In CMSB'14: Proceedings of the twelth international conference on Computational Methods for Systems Biology, LNBI, pages 114–128, Springer Verlag, 2014.

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On the subgraph Epimorphism Problem. Discrete Applied Mathematics, 162:214–228, 2014.

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A stronger necessary condition for the multistationarity of chemical reaction networks. Bulletin of Mathematical Biology, 75 (11):2289-2303, 2013.

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Solving Subgraph Epimorphism Problems using CLP and SAT. In WCB - ninth Workshop on Constraint Based Methods for Bioinformatics, colocated with CP 2013 (2013), pages 67–74, 2013.

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On the Hybrid Composition and Simulation of Heterogeneous Biochemical Models. In Gupta, Ashutosh, Henzinger, Thomas A., editor, CMSB - 11th International Conference on Computational Methods for Systems Biology - 2013, volume 8130 of Lecture Notes in Computer Science, pages 192–205, Springer, 2013.

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A Constraint Solving Approach to Tropical Equilibration and Model Reduction. In WCB - ninth Workshop on Constraint Based Methods for Bioinformatics, colocated with CP 2013, pages 27–36, 2013.

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Reifying Global Constraints. Research Report RR-8084, 2012.

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Inferring Reaction Models from ODEs. In CMSB 2012: Computational Methods in Systems Biology, pages 370-373, 2012.

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A Boolean Model for Enumerating Minimal Siphons and Traps in Petri Nets. In CP 2012: Principles and Practice of Constraint Programming, pages 798-814, 2012.

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Automatic Curation of SBML Models based on their ODE Semantics. Research Report RR-8014, 2012.

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Un modèle booléen pour l'énumération des siphons et des pièges minimaux dans les réseaux de Petri. In JFPC 2012 - Huitièmes Journées Francophones de Programmation par Contraintes, 2012.

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Design, optimization and predictions of a coupled model of the cell cycle, circadian clock, DNA repair system, irinotecan metabolism and exposure control under temporal logic constraints.. Theoretical Computer Science, 412 (21):2108-2127, 2011.

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Continuous valuations of temporal logic specifications with applications to parameter optimization and robustness measures. Theoretical Computer Science, 412 (26):2827 - 2839, 2011.

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Steady-state Solution of Biochemical Systems, Beyond S-systems via T-invariants. In Proceedings of the 8th International Conference on Computational Methods in Systems Biology, CMSB ‘10, pages 14–22, ACM, 2010.

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SBGN support in BIOCHAM. Nature Precedings, 2010.

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A graphical method for reducing and relating models in systems biology. Bioinformatics, 26 (18):i575–i581, 2010.

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Modelling molecular networks: relationships between different formalisms and levels of details. Research Report RR-7221, 2010.

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On Coupling Models Using Model-Checking: Effects of Irinotecan Injections on the Mammalian Cell Cycle. In Degano, Pierpaoloand Gorrieri, Roberto, editor, Computational Methods in Systems Biology, pages 142–157, Springer Berlin Heidelberg, 2009.

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Model-based Predictions of the Influence of Circadian Clock Genes Knock-Outs on the Cell Cycle. Research Report RR-7064, 2009.

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Dynamics of the interlocked positive feedback loops explaining the robust epigenetic switching in Candida albicans. Journal of Theoretical Biology, 258 (1):71–88, 2009.

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On Coupling Models Using Model-Checking: Effects of Irinotecan Injections on the Mammalian Cell Cycle. In CMSB 2009: Computational Methods in Systems Biology, pages 142-157, 2009.

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A general computational method for robustness analysis with applications to synthetic gene networks. Bioinformatics, 25 (12):il69–il78, 2009.

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Modelling Biochemical Reaction Networks with BIOCHAM Extracting Qualitative and Quantitative Information from the Structure. In Proceedings of the 6th Vienna Conference on Mathematical Modelling MATHMOD'09, pages 2304–2312, ARGESIM, 2009.

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Model Revision from Temporal Logic Properties in Computational Systems Biology. In Luc de Raedt, Paolo Frasconi, Kristian Kersting, Stephen Muggleton, editor, Probabilistic Inductive Logic Programming, pages 287–304, 2008.

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On a Continuous Degree of Satisfaction of Temporal Logic Formulae with Applications to Systems Biology. In Springer-Verlag, editor, CMSB'08: Proceedings of the fourth international conference on Computational Methods in Systems Biology, volume 5307 of Lecture Notes in Computer Science, pages 251–268, 2008.

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Abstract interpretation and types for systems biology. Theoretical Computer Science, 403 (1):52–70, 2008.

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Formal Cell Biology in Biocham. In SFM 2008: Formal Methods for Computational Systems Biology, volume 5016 of Lecture Notes in Computer Science, pages 54-80, Springer Berlin Heidelberg, 2008.

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From reaction models to influence graphs and back: a theorem. In Springer-Verlag, editor, Proceedings of Formal Methods in Systems Biology FMSB'08, volume 5054 of LNCS, 2008.

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Proceedings of CSCLP 2007: Annual ERCIM Workshop on Constraint Solving and Constraint Logic Programming. In Proceedings of CSCLP 2007: Annual ERCIM Workshop on Constraint Solving and Constraint Logic Programming, INRIA, 2007.

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Langages formels dans la machine abstraite biochimique BIOCHAM. Revue des Sciences et Technologies de l’Information - Série TSI : Technique et Science Informatiques, 26 (1-2):47–72, 2007.

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Closures and Modules Within Linear Logic Concurrent Constraint Programming. In Arvind, V. and Prasad, Sanjiva, editor, FSTTCS 2007: Foundations of Software Technology and Theoretical Computer Science, pages 544–556, Springer Berlin Heidelberg, 2007.

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On Internalizing Modules as Agents in Concurrent Constraint Programming. Research Report RR-5981, 2006.

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Machine Learning Biochemical Networks from Temporal Logic Properties. In Priami, Corradoand Plotkin, Gordon, editor, Transactions on Computational Systems Biology VI, pages 68–94, Springer Berlin Heidelberg, 2006.

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Coupling the Cell cycle and the Circadian Cycle. Research Report RR-5835, 2006.

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BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge. Bioinformatics, 22 (14):1805–1807, 2006.

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Learning Transition Rules from Temporal Logic Properties. Research Report RR-5543, 2005.

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A Machine Learning approach to Biochemical Reaction Rules Discovery. In Francis J. Doyle III, editor, Proceedings of Foundations of Systems Biology and Engineering FOSBE'05, pages 375–379, 2005.

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Apprentissage de règles de réactions biochimiques à partir de propriétés en logique temporelle. In Alain Guénoche et Christophe Geourjon Guy Perrière, editor, Actes de JOBIM'05, pages 183–192, 2005.

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Machine Learning Bio-molecular Interactions from Temporal Logic Properties. In Gordon Plotkin, editor, Third Workshop on Computational Methods in Systems Biology, 2005.

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The Biochemical Abstract Machine BIOCHAM. In Vincent Danos, Vincent Schächter, editor, CMSB'04: Proceedings of the second Workshop on Computational Methods in Systems Biology, pages 172–191, Springer-Verlag, 2004.

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Modelling and Querying Interaction Networks in the Biochemical Abstract Machine BIOCHAM. Journal of Biological Physics and Chemistry, 4 (2):64–73, 2004.

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CLPGUI: A Generic Graphical User Interface for Constraint Logic Programming. Constraints, 9 (4):241 - 262, 2004.

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La programmation par contraintes. Interstices, 2004.

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Pi-calculus and LCC, a Space Odyssey. Research Report RR-4855, 2003.

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Concurrent constraint programming and linear logic. Theses, Université Paris Diderot - Paris 7, 2001.

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Linear Concurrent Constraint Programming: Operational and Phase Semantics. Information and Computation, 165 (1):14–41, 2001.

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