Bibliography

Publications of the year

Articles in International Peer-Reviewed Journals

1S. Bistarelli, F. Santini.

Coalitions of Arguments: An Approach with Constraint Programming, in: Fundamenta Informaticae, IOS Press, 2012, to appear.
2D. Fournier, T. Martinez, F. Fages, D. Mulard.

Energy optimization of metro timetables: a hybrid approach, in: RAIRO operations research, 2012, Submitted.
3S. Gay, F. Fages, T. Martinez, S. Soliman, C. Solnon.

On the subgraph Epimorphism Problem, in: Discrete Applied Mathematics, 2012, submitted.
4D. Heitzler, G. Durand, N. Gallay, A. Rizk, S. Ahn, J. Kim, J. D. Violin, L. Dupuy, C. Gauthier, V. Piketty, P. Crépieux, A. Poupon, F. Clément, F. Fages, R. J. Lefkowitz, E. Reiter.

Competing G protein-coupled receptor kinases balance G protein and $β$ -arrestin signaling, in: Molecular Systems Biology, June 2012, vol. 8, n^o 590.

http://dx.doi.org/10.1038/msb.2012.22
5S. Soliman.

Invariants and Other Structural Properties of Biochemical Models as a Constraint Satisfaction Problem, in: Algorithms for Molecular Biology, May 2012, vol. 7, n^o 15.

http://dx.doi.org/10.1186/1748-7188-7-15
6J. Uhlendorf, A. Miermont, T. Delaveau, G. Charvin, F. Fages, S. Bottani, G. Batt, P. Hersen.

Long-term model predictive control of gene expression at the population and single-cell levels, in: Proceedings of the National Academy of Sciences USA, 2012, vol. 109, n^o 35, p. 14271–14276.

International Conferences with Proceedings

7S. Bistarelli, G. Gosti, F. Santini.

Solving Fuzzy Distributed CSPs: An Approach with Naming Games, in: DALT, M. Baldoni, L. Dennis, V. Mascardi, W. Vasconcelos (editors), Lecture Notes in Computer Science, Springer, 2012.
8F. Fages, S. Gay, S. Soliman.

Inferring Reaction Models from ODEs, in: CMSB'12: Proceedings of the tenth international conference on Computational Methods in Systems Biology, Lecture Notes in BioInformatics, Springer-Verlag, October 2012, vol. 7605, p. 370–373.
9D. Fournier, D. Mulard, F. Fages.

Optimisation énergétique de tables horaires de métros: une approche hybride, in: Actes de Journées Francophones de Programmation par Contraintes JFPC'12, Toulouse, France, 2012, p. 127–130.
10F. Nabli, F. Fages, T. Martinez, S. Soliman.

A Boolean Model for Enumerating Minimal Siphons and Traps in Petri-nets, in: Proceedings of CP'2012, 18th International Conference on Principles and Practice of Constraint Programming, Lecture Notes in Computer Science, Springer-Verlag, October 2012, vol. 7514, p. 798–814.

http://contraintes.inria.fr/~tmartine/papers/NFMS12cp.pdf
11N. Saeedloei, G. Gupta.

An Extension of $π$ -Calculus with Real-Time and its Realization in Logic Programming, in: Proceedings of Logic Based Program Synthesis and Transformation, LOPSTR'12, 2012.
12N. Saeedloei, G. Gupta.

Coinductive Constraint Logic Programming, in: Proceedings of FLOPS'12, Lecture Notes in Computer Science, Springer-Verlag, 2012, vol. 7294, p. 243–259.
13A. J. da C. C. Lins, F. B. de Lima Neto, F. Fages, C. J. A. B. Filho.

A Comparative Analysis of FSS with CMA-ES and S-PSO in Ill-Conditioned Problems, in: Intelligent Data Engineering and Automated Learning - 13th International Conference IDEAL, Lecture Notes in Computer Science, Springer, 2012, vol. 7435, p. 416–422.

http://dx.doi.org/10.1007/978-3-642-32639-4_51

National Conferences with Proceeding

14F. Nabli, F. Fages, T. Martinez, S. Soliman.

Un modèle Booléen pour l'énumération des siphons et des pièges minimaux dans les réseaux de Petri, in: Actes de Journées Francophones de Programmation par Contraintes JFPC'12, Toulouse, France, 2012.

http://contraintes.inria.fr/~tmartine/papers/NFMS12jfpc.pdf

Conferences without Proceedings

15N. Saeedloei, G. Gupta.

Timed $π$ -Calculus and its Realization in Coinductive Constraint Logic Programming, in: Proceedings of the first Coinductive Logic Programming Workshop Co-LP'12, 2012.

Scientific Books (or Scientific Book chapters)

16G. Batt, B. Besson, P. Ciron, H. de Jong, E. Dumas, J. Geiselmann, R. Monte, P. Monteiro, M. Page, F. Rechenmann, D. Ropers.

Genetic network analyzer: a tool for the qualitative modeling and simulation of bacterial regulatory networks, in: Bacterial Molecular Networks, Springer, 2012, p. 439–462.

Books or Proceedings Editing

17F. Fages, S. Soliman (editors)

Special Section on Computational Methods in Systems Biology, Transactions on Computational Biology and Bioinformatics, IEEE/ACM, Sept.-Oct. 2012, vol. 9, n^o 5, p. 1314–1378, extended versions of selected papers presented at CMSB11.

http://dx.doi.org/10.1109/TCBB.2012.97

Internal Reports

18F. Fages, S. Gay, D. Jovanovska, A. Rizk, S. Soliman.

BIOCHAM v3.5 Reference Manual, Inria, 2012.

http://contraintes.inria.fr/BIOCHAM/
19F. Fages, S. Gay, S. Soliman.

Automatic Curation of SBML Models based on their ODE Semantics, Inria, July 2012, n^o RR-8014.

http://hal.inria.fr/hal-00723554
20F. Fages, S. Soliman.

Reifying Global Constraints, Inria, October 2012, n^o RR-8084, 18 p.

http://hal.inria.fr/hal-00737768
21S. Stoma, A. Donzé, F. Bertaux, O. Maler, G. Batt.

STL-based analysis of TRAIL-induced apoptosis challenges the notion of type I/type II cel l line classification, Inria, October 2012, n^o RR-8121, 35 p.

http://hal.inria.fr/hal-00750063

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