Team Contraintes

Members
Overall Objectives
Scientific Foundations
Application Domains
Software
New Results
Other Grants and Activities
Dissemination
Bibliography

Bibliography

Publications of the year

Articles in International Peer-Reviewed Journal

[1]
G. Batt, C. Belta, R. Weiss.
Temporal logic analysis of gene networks under parameter uncertainty, in: IEEE Transactions on Circuits and Systems and IEEE Transactions on Automatic Control, 2008, vol. 58, no Joint Special Issue on Systems Biology, p. 215–229.
[2]
C. Chaouiya, E. Remy, D. Thieffry.
Petri net modelling of biological regulatory networks, in: Journal of Discrete Algorithms, June 2008, vol. 6, no 2, p. 165–177.
[3]
F. Fages, A. Rizk.
On Temporal Logic Constraint Solving for the Analysis of Numerical Data Time series, in: Theoretical Computer Science, November 2008, vol. 408, no 1, p. 55–65.
[4]
F. Fages, S. Soliman.
Abstract Interpretation and Types for Systems Biology, in: Theoretical Computer Science, 2008, vol. 403, no 1, p. 52–70.
[5]
A.-G. González, C. Chaouiya, D. Thieffry.
Qualitative dynamical modelling of the formation of the anterior-posterior compartment boundary in the Drosophila wing imaginal disc, in: Bioinformatics, 2008, vol. 24, p. 234–240.
[6]
S. Krishnamachari, F. Fages, S. Soliman.
Dynamics of the interlocked positive feedback loops explaining the robust epigenetic switching in Candida albicans, in: Journal of Theoretical Biology, submitted 2008.
[7]
A. Martínez-Antonio, S. C. Janga, D. Thieffry.
Functional organisation of Escherichia coli transcriptional regulatory network, in: Journal of Molecular Biology, 2008, vol. 381, no 1, p. 238–247.
[8]
E. Remy, P. Ruet, D. Thieffry.
Graphic requirements for multistability and attractive cycles in a Boolean dynamical framework, in: Advances in Applied Mathematics, 2008, vol. 41, no 3, p. 335–350.
[9]
L. Sánchez, C. Chaouiya, D. Thieffry.
Segmenting the fly embryo: logical analysis of the role of the Segment Polarity cross-regulatory module, in: International Journal of Developmental Biology, 2008, vol. 52, p. 1059–1075.

International Peer-Reviewed Conference/Proceedings

[10]
M. Amedia, F. Fages, J. Robin.
Default Reasoning in CHR $ \vee$ , in: Proceedings of the fifth Constraint Handling Rules Workshop CHR'08, T. Frühwirth, T. Schrijvers (editors), 2008.
[11]
M. Carlsson, N. Beldiceanu, J. Martin.
A Geometric Constraint over k-Dimensional Objects and Shapes Subject to Business Rules, in: Proceedings of CP'2008, P. J. Stuckey (editor), Lecture Notes in Computer Science, Springer, 2008, vol. 5202, p. 220–234.
[12]
F. Fages, C. M. de Oliveira Rodrigues, T. Martinez.
Modular CHR with ask and tell, in: Proceedings of the fifth Constraint Handling Rules Workshop CHR'08, T. Frühwirth, T. Schrijvers (editors), 2008.
[13]
F. Fages, C. M. de Oliveira Rodrigues, T. Martinez.
Modular CHR with ask and tell, in: Proceedings of the 13th International Workshop on Constraint Solving and Constraint Programming CSCLP'08, Roma, Italy, 2008.
[14]
F. Fages, J. Martin.
Des règles aux contraintes avec le langage de modélisation Rules2CP, in: Actes de Journées Francophones de Programmation par Contraintes JFPC'08, Nantes, France, 2008.
[15]
F. Fages, J. Martin.
From Rules to Constraint Programs with the Rules2CP modeling language, in: Proceedings of the 13th International Workshop on Constraint Solving and Constraint Programming CSCLP'08, Roma, Italy, 2008.
[16]
F. Fages, A. Rizk.
Analyse de Séries Temporelles par Résolution de Contraintes de Logique Temporelle, in: Actes de Journées Francophones de Programmation par Contraintes JFPC'08, Nantes, France, 2008.
[17]
F. Fages, S. Soliman.
Formal Cell Biology in BIOCHAM, in: 8th Int. School on Formal Methods for the Design of Computer, Communication and Software Systems: Computational Systems Biology SFM'08, Bertinoro, Italy, M. Bernardo, P. Degano, G. Zavattaro (editors), Lecture Notes in Computer Science, Springer-Verlag, February 2008, vol. 5016, p. 54–80.
[18]
F. Fages, S. Soliman.
From reaction models to influence graphs and back: a theorem, in: Proceedings of Formal Methods in Systems Biology FMSB'08, Lecture Notes in Computer Science, Springer-Verlag, February 2008, no 5054.
[19]
A. Fauré, A. Naldi, C. Chaouiya, A. Ciliberto, D. Thieffry.
Comparative analysis of logical models of the cell cycle in eucaryotes, in: Proceedings of the International Conference on Systems Biology ICSB'08, 2008.
[20]
A. Fauré, A. Naldi, F. Lopez, C. Chaouiya, A. Ciliberto, D. Thieffry.
Logical modelling of the budding yeast cell cycle: a modular approach., in: Proceedings of European Conference on Computational Biology ECCB'08, 2008.
[21]
O. Maler, G. Batt.
Approximating continuous systems by timed automata, in: First International Workshop on Formal Methods in Systems Biology, FMSB'08, J. Fisher (editor), Lecture Notes in Bioinformatics, Springer, 2008, vol. 5054, p. 77–89.
[22]
A. Rizk, G. Batt, F. Fages, S. Soliman.
On a Continuous Degree of Satisfaction of Temporal Logic Formulae with Applications to Systems Biology, in: CMSB'08: Proceedings of the fourth international conference on Computational Methods in Systems Biology, M. Heiner, A. Uhrmacher (editors), Lecture Notes in Computer Science, Springer-Verlag, October 2008, vol. 5307, p. 251–268
http://contraintes.inria.fr/~fages/Papers/RGFS08cmsb.pdf.
[23]
S. Soliman.
Finding minimal P/T-invariants as a CSP, in: Proceedings of the fourth Workshop on Constraint Based Methods for Bioinformatics WCB'08, associated to CPAIOR'08, May 2008
http://wcb08.dimi.uniud.it/PAPERS/Soliman.pdf.

Workshops without Proceedings

[24]
F. Fages.
A logical paradigm for systems biology applied to modeling tool design, in: European American Innovation Day EAID'08 From Modeling to Engineering Biological Processes, Harvard Medical School, Boston, USA, December 2008.
[25]
D. Heitzler, G. Durand, L. Dupuy, C. Gauthier, V. Piketty, P. Crépieux, A. Rizk, S. Soliman, F. Fages, F. Clément, E. Reiter.
Modelling of FSHR-induced Signalling Network, in: Poster, International Conference on Gonadotropins and Receptors IGCR'08, London, UK, 2008.
[26]
A. Rizk, G. Batt, F. Fages, S. Soliman.
Towards a general computational method for robustness analysis, in: International Conference Frontiers in Synthetic Biology, Boston, 2008.
[27]
A. Rizk, G. Batt, F. Fages, S. Soliman.
Towards a general computational method for robustness analysis, in: Poster, International Conference Synthetic Biology 4.0, Hong Kong, 2008.

Scientific Books (or Scientific Book chapters)

[28]
F. Fages, S. Soliman.
Model Revision from Temporal Logic Properties in Systems Biology, in: Probabilistic Inductive Logic Programming, Lecture Notes in Computer Science, Springer-Verlag, 2008, vol. 4911, p. 287–304.

Books or Proceedings Editing

[29]
F. Fages, S. Soliman, F. Rossi (editors)
Proceedings of the 12th Annual ERCIM International Workshop on Constraint Solving and Constraint Logic Programming CSCLP'07, Lecture Notes in Computer Science, Springer-Verlag , Rocquencourt, France, 2008, vol. 5129.

Internal Reports

[30]
M. Carlsson, N. Beldiceanu, J. Martin.
A Geometric Constraint over k -Dimensional Objects and Shapes Subject to Business Rules, SICS Technical Report, Swedish Institute of Computer Science, 2008, no T2008:04.
[31]
F. Fages, J. Martin.
From Rules to Constraint Programs with the Rules2CP Modelling Language, INRIA Research Report, Institut National de Recherche en Informatique, April 2008, no RR-6495
http://hal.inria.fr/inria-00270326/fr/.

Other Publications

[32]
P. Deransart.
Semantic View of Tracers and their Traces, and Applications, Document interne, August 2008
http://contraintes.inria.fr/~deransar.

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