New Software and Platforms
New Software and Platforms


Publications of the year

Doctoral Dissertations and Habilitation Theses

  • 1K. Chiang.

    Biomolecular System Design: Architecture, Synthesis, and Simulation, National Taiwan University, June 2015.

  • 2S. Gay.

    Subgraph Epimorphisms: Theory and Application to Model Reductions in Systems Biology, Université Paris Diderot, May 2015.

  • 3A. Llamosi.

    Effects of repeated osmotic stress on gene expression and growth: from cell-to-cell variability to cellular individuality in the budding yeast Saccharomyces cerevisiae, Université Paris Diderot, December 2015.

  • 4T. Martinez.

    Execution models for Constraint Programming: kernel language design through semantics equivalence. , Paris Diderot, December 2015.


Articles in International Peer-Reviewed Journals

  • 5H.-J. Chiang, F. Fages, J.-H. Jiang, S. Soliman.

    Hybrid Simulations of Heterogeneous Biochemical Models in SBML, in: ACM Transactions on Modeling and Computer Simulation, April 2015, vol. 25, no 2, pp. 14:1-14:22. [ DOI : 10.1145/2742545 ]

  • 6T.-Y. Chiu, H.-J. Chiang, R.-Y. Huang, J.-H. Jiang, F. Fages.

    Synthesizing Configurable Biochemical Implementation of Linear Systems from Their Transfer Function Specifications, in: PLoS ONE, 2015, vol. 10, no 9. [ DOI : 10.1371/journal.pone.0137442 ]

  • 7F. Fages, S. Gay, S. Soliman.

    Inferring reaction systems from ordinary differential equations, in: Journal of Theoretical Computer Science (TCS), September 2015, vol. 599, pp. 64–78. [ DOI : 10.1016/j.tcs.2014.07.032 ]

  • 8A. Llamosi, A. Gonzalez, C. Versari, E. Cinquemani, G. Ferrari-Trecate, P. Hersen, G. Batt.

    What population reveals about individual cell identity: Single-cell parameter estimation of models of gene expression in yeast, in: PLoS Computational Biology, 2015, forthcoming.

  • 9F. Nabli, T. Martinez, F. Fages, S. Soliman.

    On Enumerating Minimal Siphons in Petri nets using CLP and SAT solvers: Theoretical and Practical Complexity, in: Constraints, 2015, pp. 1–26. [ DOI : 10.1007/s10601-015-9190-1 ]


International Conferences with Proceedings

  • 10S. Bogomolov, C. Schilling, E. Bartocci, G. Batt, H. Kong, R. Grosu.

    Abstraction-Based Parameter Synthesis for Multiaffine Systems, in: 11th International Haifa Verification Conference, HVC 2015, Haifa, Israel, November 17-19, 2015, Proceedings, Haifa, Israel, Springer International Publishing, November 2015, vol. 11, pp. 19-35. [ DOI : 10.1007/978-3-319-26287-1_2 ]

  • 11H.-J. Chiang, J.-H. Jiang, F. Fages.

    Reconfigurable Neuromorphic Computation in Biochemical Systems, in: EMBC 2015 - 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Milano, Italy, August 2015, pp. 937 - 940. [ DOI : 10.1109/EMBC.2015.7318517 ]

  • 12T. Martinez, F. Fages.

    On Translating MiniZinc Constraint Models into Fitness Function for Evolutionary Algorithms: Application to Continuous Placement Problems, in: Proceedings of the sixth Workshop on Bin Packing and Placement Constraints BPPC'15, associated to CP'15, Cork, Ireland, 2015.

  • 13T. Martinez, F. Fages, S. Soliman.

    Search by Constraint Propagation, in: PPDP '15- 17th International Symposium on Principles and Practice of Declarative Programming, Siena, Italy, ACM (editor), July 2015. [ DOI : 10.1145/2790449.2790527 ]

  • 14P. Traynard, F. Fages, S. Soliman.

    Model-based Investigation of the Effect of the Cell Cycle on the Circadian Clock through Transcription Inhibition during Mitosis, in: CMSB'15 - Proceedings of the thirteenth international conference on Computational Methods in Systems Biology, Nantes, France, O. Roux, J. Bourdon (editors), Lecture Notes in BioInformatics, Springer-Verlag, 2015, vol. 9308, pp. 208–221. [ DOI : 10.1007/978-3-319-23401-4_18 ]


Other Publications

  • 15S. K. Palaniappan, F. Bertaux, M. Pichene, E. Fabre, G. Batt, B. Genest.

    Approximating the dynamics of the Hybrid Stochastic-Deterministic Apoptosis pathway, CMSB 2015, 2015, CMSB 2015, Poster.

  • 16P. Traynard, A. Fauré, F. Fages, D. Thieffry.

    Logical modeling of the mammalian cell cycle, October 2015, working paper or preprint.

  • 17P. Traynard, C. Feillet, S. Soliman, F. Delaunay, F. Fages.

    Model-based Investigation of the Coupling between the Cell Cycle and the Circadian Clock in Mouse Embryonic Fibroblasts, December 2015, working paper or preprint.