Publications

On BIOCHAM Symbolic Computation Pipeline for Compiling Mathematical Functions into Biochemistry. In ISSAC 2024 - 49th International Symposium on Symbolic and Algebraic Computation, 2024.
Scalable Enumeration of Trap Spaces in Boolean Networks via Answer Set Programming. In AAAI 2024 - The 38th Annual Conference on Artificial Intelligence, pages 10714-10722, 2024.
Efficient Enumeration of Fixed Points in Complex Boolean Networks Using Answer Set Programming. In Roland H. C. Yap, editor, 29th International Conference on Principles and Practice of Constraint Programming (CP 2023), pages 35:1–35:19, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.
Minimal trap spaces of Logical models are maximal siphons of their Petri net encoding. In Ion Petre, Andrei Păun, editor, CMSB 2022 - International Conference on Computational Methods in Systems Biology, volume 13447 of Lecture Notes in Computer Science, pages 158–176, Springer, 2022.
On the Complexity of Quadratization for Polynomial Differential Equations. In CMSB 2020 - 18th International Conference on Computational Methods in Systems Biology, 2020.
Graphical Conditions for Rate Independence in Chemical Reaction Networks. In CMSB 2020 - 18th International Conference on Computational Methods in Systems Biology, 2020.
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.
On Robustness Computation and Optimization in BIOCHAM-4. In 16th Int. Conf. on Computational Methods in Systems Biology, 2018.
Executable Disease Networks: Adding dynamics to molecular maps. In ECCB 2018 - 17th European Conference on Computational Biology, 2018.
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.
A structural perspective on the dynamics of biochemical systems. Habilitation à diriger des recherches, Université Paris Sud - Orsay, 2016.
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.
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.
Search by Constraint Propagation. In ACM, editor, PPDP ‘15- 17th International Symposium on Principles and Practice of Declarative Programming, pages 173–183, 2015.
Hybrid Simulations of Heterogeneous Biochemical Models in SBML. ACM Transactions on Modeling and Computer Simulation, 25 (2):14:1-14:22, 2015.
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.
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.
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.
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.
Inferring Reaction Models from ODEs. In CMSB 2012: Computational Methods in Systems Biology, pages 370-373, 2012.
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.
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.
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.
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.
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.
Modelling of FSHR-induced signalling network. In International Conference for Gonadotropins & their Receptors, pages n.p., 2008.
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.
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.
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.
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.
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.
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.
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.
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.
Concurrent constraint programming and linear logic. Theses, Université Paris Diderot - Paris 7, 2001.