Overall Objectives
Research Program
Application Domains
Highlights of the Year
New Software and Platforms
New Results
Partnerships and Cooperations
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Publications of the year

Doctoral Dissertations and Habilitation Theses

K. Chiang.
Biomolecular System Design: Architecture, Synthesis, and Simulation, National Taiwan University, June 2015.
S. Gay.
Subgraph Epimorphisms: Theory and Application to Model Reductions in Systems Biology, Université Paris Diderot, May 2015.
A. 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.
T. Martinez.
Execution models for Constraint Programming: kernel language design through semantics equivalence. , Paris Diderot, December 2015.

Articles in International Peer-Reviewed Journals

H.-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 ]
T.-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 ]
F. 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 ]
A. 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.
F. 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

S. 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 ]
H.-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 ]
T. 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.
T. 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 ]
P. 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

S. 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.
P. Traynard, A. Fauré, F. Fages, D. Thieffry.
Logical modeling of the mammalian cell cycle, October 2015, working paper or preprint.
P. 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.