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

F. Bertaux.
Cell-based multi-scale modeling for systems and synthetic biology: from stochastic gene expression in single cells to spatially organized cell populations, Université Pierre & Marie Curie - Paris 6, June 2016.
J.-B. Lugagne.
Real-time control of a genetic toggle switch, Université Paris 7, December 2016.
S. Soliman.
A structural perspective on the dynamics of biochemical systems, Université Paris Sud - Orsay, December 2016, Habilitation à diriger des recherches.
P. Traynard.
Model Building by Temporal Logic Constraint Solving: Investigation of the Coupling between the Cell Cycle and the Circadian Clock, Université Paris Diderot, May 2016.

Articles in International Peer-Reviewed Journals

O. Béthoux, A. Llamosi, S. Toussaint.
Reinvestigation of <i>Protelytron permianum</i> (Insecta; Early Permian; USA) as an example for applying reflectance transformation imaging to insect imprint fossils, in: Fossil Record, 2016, vol. 20, no 1, pp. 1 - 7. [ DOI : 10.5194/fr-20-1-2016 ]
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, February 2016, vol. 12, no 2, e1004706. [ DOI : 10.1371/journal.pcbi.1004706 ]
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, April 2016, vol. 21, no 2, pp. 251–276. [ DOI : 10.1007/s10601-015-9190-1 ]
P. Traynard, A. Fauré, F. Fages, D. Thieffry.
Logical model specification aided by model- checking techniques: application to the mammalian cell cycle regulation, in: Bioinformatics, 2016, vol. 32, no 17, pp. i772-i780. [ DOI : 10.1093/bioinformatics/btw457 ]
P. Traynard, C. Feillet, S. Soliman, F. Delaunay, F. Fages.
Model-based investigation of the circadian clock and cell cycle coupling in mouse embryonic fibroblasts: Prediction of RevErb-α up-regulation during mitosis, in: BioSystems, November 2016, vol. 149, pp. 59–69. [ DOI : 10.1016/j.biosystems.2016.07.003 ]

International Conferences with Proceedings

A. Aggoun, A. Rhiat, F. Fages.
Panorama of real-life applications in logistics embedding bin packing optimization algorithms, robotics and cloud computing technologies, in: GOL'16 - 3rd IEEE International Conference on Logistics Operations Management, Morocco, Morocco, May 2016. [ DOI : 10.1109/GOL.2016.7731693 ]
F. Fages, T. Martinez, D. Rosenblueth, S. Soliman.
Influence Systems vs Reaction Systems, in: CMSB'16: Proceedings of the fourteenth international conference on Computational Methods in Systems Biology, Cambridge, UK, United Kingdom, E. Bartocci, P. Lio, N. Paoletti (editors), Lecture Notes in Computer Science, Springer-Verlag, September 2016, vol. 9859, pp. 98-115. [ DOI : 10.1007/978-3-319-45177-0_7 ]
T. Martinez, F. Fages, A. Aggoun.
A Stochastic Continuous Optimization Backend for MiniZinc with Applications to Geometrical Placement Problems, in: Proceedings of the 13th International Conference on Integration of Artificial Intelligence and Operations Research Techniques in Constraint Programming, CPAIOR'16, Banff, Canada, C.-G. Quimper (editor), Springer, May 2016, vol. 9676, pp. 262-278. [ DOI : 10.1007/978-3-319-33954-2_19 ]
T. Martinez, F. Fages, A. Aggoun.
Un solveur d'optmization stochastique pour MiniZinc avec des applications à des problèmes de placements géométriques, in: Douzièmes Journées Francophones de Programmation par Contraintes JFPC'16, 2016.
S. K. Palaniappan, M. Pichené, G. Batt, E. Fabre, B. Genest.
A Look-Ahead Simulation Algorithm for DBN Models of Biochemical Pathways, in: Hybrid Systems Biology, 5th International Workshop, HSB 2016, Grenoble, France, E. Cinquemani, A. Donzé (editors), Lecture Notes in Computer Science, October 2016, vol. 9957, pp. 3-15. [ DOI : 10.1007/978-3-319-47151-8_1 ]

Internal Reports

D. Fournier, T. Martinez, F. Fages, D. Mulard.
Metro Energy Optimization through Rescheduling: Mathematical Models and Heuristic Algorithm Compared to MILP and CMA-ES , Inria Saclay Ile de France, December 2016.

Scientific Popularization

A. Aggoun, N. Beldiceanu, G. Chabert, F. Fages.
Packing with Complex Shapes, in: ERCIM News, 2016, no 105, 32 p.

Other Publications

F. Fages.
AI in Biological Modelling, November 2016, working paper or preprint.
F. Fages, G. Le Guludec.
Programmes biochimiques et algorithmes mixtes analogiques-digitaux dans la cellule, October 2016, working paper or preprint.
N. Vasselin, F. Fages.
Mixture Model-CMA-ES , December 2016, internship report.