Publications

Sarah Keating Et Al (2020). SBML Level 3: an extensible format for the exchange and reuse of biological models. Molecular Systems Biology, 16 (8):1-21.
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Sara Sadat Aghamiri Et Al (2020). Automated inference of Boolean models from molecular interaction maps using CaSQ. Bioinformatics, 36 (16):4473-4482.
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Julien Martinelli, Jeremy Grignard, Sylvain Soliman, François Fages (2019). 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.
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Julien Martinelli, Jeremy Grignard, Sylvain Soliman, François Fages (2019). A Statistical Unsupervised Learning Algorithm for Inferring Reaction Networks from Time Series Data. In ICML 2019 - Workshop on Computational Biology.
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François Fages, Thierry Martinez, David a Rosenblueth, Sylvain Soliman (2018). Influence Networks compared with Reaction Networks: Semantics, Expressivity and Attractors. IEEE/ACM Transactions on Computational Biology and Bioinformatics, PP (99):1-14.
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Adrien Baudier, François Fages, Sylvain Soliman (2018). Graphical Requirements for Multistationarity in Reaction Networks and their Verification in BioModels. Journal of Theoretical Biology, 459:79–89.
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François Fages, Sylvain Soliman (2018). On Robustness Computation and Optimization in BIOCHAM-4. In 16th Int. Conf. on Computational Methods in Systems Biology.
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Vidisha Singh Et Al (2018). Executable Disease Networks: Adding dynamics to molecular maps. In ECCB 2018 - 17th European Conference on Computational Biology.
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Arthur Carcano, François Fages, Sylvain Soliman (2017). 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.
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Pauline Traynard, Celine Feillet, Sylvain Soliman, Franck Delaunay, François Fages (2017). 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.
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Sylvain Soliman (2016). A structural perspective on the dynamics of biochemical systems. Accreditation to supervise research, Université Paris Sud - Orsay.
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Pauline Traynard, Céline Feillet, Sylvain Soliman, Franck Delaunay, François Fages (2016). 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.
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François Fages, Thierry Martinez, David Rosenblueth, Sylvain Soliman (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.
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Faten Nabli, Thierry Martinez, François Fages, Sylvain Soliman (2016). On Enumerating Minimal Siphons in Petri nets using CLP and SAT solvers: Theoretical and Practical Complexity. Constraints, 21 (2):251–276.
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Pauline Traynard, François Fages, Sylvain Soliman (2015). 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.
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François Fages, Steven Gay, Sylvain Soliman (2015). Inferring reaction systems from ordinary differential equations. Theoretical Computer Science, 599:64–78.
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Thierry Martinez, François Fages, Sylvain Soliman (2015). Search by Constraint Propagation. In ACM, editor, PPDP ‘15- 17th International Symposium on Principles and Practice of Declarative Programming, pages 173–183.
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Hui-Ju Chiang, François Fages, Jie-Hong Jiang, Sylvain Soliman (2015). Hybrid Simulations of Heterogeneous Biochemical Models in SBML. ACM Transactions on Modeling and Computer Simulation, 25 (2):14:1-14:22.
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Sylvain Soliman, François Fages, Ovidiu Radulescu (2014). A constraint solving approach to model reduction by tropical equilibration. Algorithms for Molecular Biology, 9 (1):24.
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Pauline Traynard, François Fages, Sylvain Soliman (2014). 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.
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