Members
Overall Objectives
Research Program
Application Domains
Highlights of the Year
New Software and Platforms
New Results
Partnerships and Cooperations
Dissemination
Bibliography
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Bibliography

Publications of the year

Doctoral Dissertations and Habilitation Theses

[1]
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.
https://tel.archives-ouvertes.fr/tel-01405430
[2]
J.-B. Lugagne.
Real-time control of a genetic toggle switch, Université Paris 7, December 2016.
https://tel.archives-ouvertes.fr/tel-01417700
[3]
S. Soliman.
A structural perspective on the dynamics of biochemical systems, Université Paris Sud - Orsay, December 2016, Habilitation à diriger des recherches.
https://tel.archives-ouvertes.fr/tel-01403712
[4]
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.
https://tel.archives-ouvertes.fr/tel-01404060

Articles in International Peer-Reviewed Journals

[5]
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 ]
https://hal.inria.fr/hal-01406082
[6]
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 ]
https://hal.inria.fr/hal-01248298
[7]
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 ]
https://hal.archives-ouvertes.fr/hal-01170962
[8]
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 ]
https://hal.archives-ouvertes.fr/hal-01378465
[9]
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 ]
https://hal.archives-ouvertes.fr/hal-01378466

International Conferences with Proceedings

[10]
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 ]
https://hal.archives-ouvertes.fr/hal-01378469
[11]
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 ]
https://hal.archives-ouvertes.fr/hal-01378470
[12]
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 ]
https://hal.archives-ouvertes.fr/hal-01378468
[13]
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.
https://hal.archives-ouvertes.fr/hal-01378467
[14]
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 ]
https://hal.inria.fr/hal-01406115

Internal Reports

[15]
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.
https://hal.inria.fr/hal-01420311

Scientific Popularization

[16]
A. Aggoun, N. Beldiceanu, G. Chabert, F. Fages.
Packing with Complex Shapes, in: ERCIM News, 2016, no 105, 32 p.
https://hal.archives-ouvertes.fr/hal-01378471

Other Publications

[17]
F. Fages.
AI in Biological Modelling, November 2016, working paper or preprint.
https://hal.inria.fr/hal-01409753
[18]
F. Fages, G. Le Guludec.
Programmes biochimiques et algorithmes mixtes analogiques-digitaux dans la cellule, October 2016, working paper or preprint.
https://hal.inria.fr/hal-01409743
[19]
N. Vasselin, F. Fages.
Mixture Model-CMA-ES , December 2016, internship report.
https://hal.inria.fr/hal-01420342