Bibliography

Publications of the year

Articles in International Peer-Reviewed Journal

[1]

C. Chaouiya, A. Naldi, E. Remy, D. Thieffry.
Petri net representation of multi-valued logical regulatory graphs, in: Natural Computing, 2009, to appear.

[2]

A. Fauré, A. Naldi, F. Lopez, C. Chaouiya, A. Ciliberto, D. Thieffry.
Modular logical modelling of the budding Yeast cell cycle, in: Molecular Biosystems, 2009, to appear.

[3]

A. Fauré, D. Thieffry.
Logical modelling of cell cycle control in eukaryotes: a comparative study, in: Molecular Biosystems, 2009.

[4]

D. Heitzler, P. Crépieux, A. Poupon, F. Clément, F. Fages, E. Reiter.
Towards a systems biology approach to G protein-coupled receptor signalling: challenges and expectations, in: C.R. Biologies, 2009, n^o 332, p. 947–957.

[5]

S. Krishnamachari, S. Soliman, F. Fages.
Dynamics of the interlocked positive feedback loops explaining the robust epigenetic switching in Candida albicans, in: Journal of Theoretical Biology, 2009, vol. 258, n^o 1, p. 71–88
http://dx.doi.org/10.1016/j.jtbi.2009.01.008.

[6]

A. Naldi, F. Lopez, D. Thieffry, C. Chaouiya.
Qualitative modelling and analysis of biological regulatory networks with GINsim 2.3, in: Biosystems, 2009, vol. 97, p. 134–139.

[7]

A. Rizk, G. Batt, F. Fages, S. Soliman.
A general computational method for robustness analysis with applications to synthetic gene networks, in: Bioinformatics, June 2009, vol. 12, n^o 25, p. il69–il78
http://dx.doi.org/10.1093/bioinformatics/btp200.

[8]

O. Sahin, H. Fröhlich, C. Löbke, U. Korf, S. Burmester, M. Majety, J. Mattern, I. Schupp, C. Chaouiya, D. Thieffry, A. Poustka, S. Wiemann, T. Beissbarth, D. Arlt.
Modeling ERBB receptor-regulated G1/S transition to find targets for de novo trastuzumab resistance, in: BMC Systems Biology, 2009, vol. 3, n^o 1.

Articles in National Peer-Reviewed Journal

[9]

D. Thieffry.
Biologie des systèmes: des réseaux d'interactions moléculaires à la médecine personnalisée, in: Médecine/Sciences, 2009, vol. 25, p. 547–548.

International Peer-Reviewed Conference/Proceedings

[10]

A. Csikász-Nagy, A. Fauré, R. Larcher, P. Lecca, I. Mura, F. Jordan, A. Palmisano, A. Romanel, S. Sedwards, H. Siebert, S. Soliman, D. Thieffry, J. Zámborszky, T. Mazza, P. Ballarini.
Analyzing various models of Circadian Clock and Cell Cycle coupling, in: Formal Methods in Molecular Biology, Dagstuhl, Germany, R. Breitling, D. R. Gilbert, M. Heiner, C. Priami (editors), Dagstuhl Seminar Proceedings, Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, Germany, May 2009, n^o 09091
http://drops.dagstuhl.de/opus/volltexte/2009/1994.

[11]

E. De Maria, F. Fages, S. Soliman.
On Coupling Models using Model-Checking: Effects of Irinotecan Injections on the Mammalian Cell Cycle, in: CMSB'09: Proceedings of the seventh international conference on Computational Methods in Systems Biology, Lecture Notes in BioInformatics, Springer-Verlag, 2009, vol. 5688, p. 142–157.

[12]

P. Deransart, F. Fages, J. Robin.
Components for Rule-Based Constraint Programming in the large, in: Proceedings of French-brasilian conference COLIBRI 2009 (Colloque d'informatique: Brésil/INRIA, Coopérations, Avancées et Défis), Sociedade Brasileira de Computaçao - SBC (editor), UFRGS, 2009, p. 33–37.

[13]

F. Fages.
A computational method based on temporal logic for parameter search and robustness analysis of biological systems (invited talk), in: PASTA'09: Proceedings of the eigth workshop on Process Algebra and Stochastically Times Activities, University of Edinburgh, UK, September 2009.

[14]

F. Fages, J. Martin.
From Rules to Constraint Programs with the Rules2CP Modelling language, in: Recent Advances in Constraints, Revised Selected Papers of the 13th Annual ERCIM International Workshop on Constraint Solving and Constraint Logic Programming, CSCLP'08, Lecture Notes in Artificial Intelligence, Springer-Verlag, 2009, vol. 5655, p. 66–83.

[15]

F. Fages, J. Martin.
Modelling search strategies in Rules2CP, in: Proceedings of CPAIOR'09, Lecture Notes in Computer Science, Springer-Verlag, 2009, vol. 5547, p. 321–322.

[16]

F. Fages, A. Rizk.
From Model-Checking to Temporal Logic Constraint Solving, in: Proceedings of CP'2009, 15th International Conference on Principles and Practice of Constraint Programming, Lecture Notes in Computer Science, Springer-Verlag, September 2009, n^o 5732, p. 319–334.

[17]

J. Martin, T. Martinez, F. Fages.
On the Specification of Search Tree Heuristics by Pattern-matching in a Rule-based Modelling Language, in: Proceedings of the Eighth International Workshop on Constraint Modelling and Reformulation, associated to CP'09, 2009, p. 73–86
http://www-users.cs.york.ac.uk/~frisch/ModRef/09/proceedings.pdf.

[18]

T. Martinez.
On connections between CHR and LCC, in: Proceedings of the Sixth International Workshop on Constraint Handling Rules CHR'09, T. Frühwirth, T. Schrijvers (editors), July 2009
http://contraintes.inria.fr/~tmartine/papers/martinez09chr.pdf.

[19]

A. Naldi, R. Remy, D. Thieffry, C. Chaouiya.
A reduction method for logical regulatory graphs preserving essential dynamical properties, in: CMSB'09: Proceedings of the seventh international conference on Computational Methods in Systems Biology, Lecture Notes in BioInformatics, Springer-Verlag, 2009, vol. 5688, p. 266–280.

[20]

S. Soliman.
Modelling Biochemical Reaction Networks with BIOCHAM Extracting Qualitative and Quantitative Information from the Structure, in: Proceedings of the 6th Vienna Conference on Mathematical Modelling MATHMOD'09, ARGESIM, February 2009, vol. 35, p. 2304–2312
http://contraintes.inria.fr/~soliman/publi/MathMod09.pdf.

National Peer-Reviewed Conference/Proceedings

[21]

F. Fages, T. Martinez, C. M. de Oliveira Rodrigues.
CHR modulaire avec ask et tell, in: Actes de Journées Francophones de Programmation par Contraintes JFPC'09, Y. Deville (editor), June 2009
http://contraintes.inria.fr/~tmartine/papers/fmo09jfpc.pdf.

Books or Proceedings Editing

[22]

A. Oddi, F. Fages, F. Rossi (editors)
Recent Advances in Constraints, 13th Annual ERCIM International Workshop on Constraint Solving and Constraint Logic Programming CSCLP'08, Lecture Notes in Artificial Intelligence, Springer-Verlag, 2009, vol. 5655.

Internal Reports

[23]

A. Aggoun, P. Rohou, M. Collardey, F. Fages, N. Beldiceanu, P. Gravez, F. Carvalho, D. Koséoglu.
Business application prototypes: Packing solver, Palletizer and the Dispatcher solvers in a WMS, FP6 Strep project Net-WMS, April 2009, n^o D7.1, deliverable.

[24]

E. De Maria, F. Fages, S. Soliman.
Model-based Predictions of the Influence of Circadian Clock Genes Knock-Outs on the Cell Cycle, INRIA, June 2009, n^o RR-7064, INRIA Research Report.

[25]

F. Fages.
Course C2-19 on Computational Methods for Systemic and Synthetic Biology. Master Parisien de Recherche en Informatique, 2009
http://contraintes.inria.fr/~fages/BioTeaching.

[26]

F. Fages.
Course C2-4-1 on Constraint Programming. Master Parisien de Recherche en Informatique, 2009
http://contraintes.inria.fr/~fages/Teaching.

[27]

F. Fages, J. Martin, M. Carlsson, N. Beldiceanu, A. Aggoun.
Transformation of knowledge rules into optimisation programs, FP6 Strep project Net-WMS, April 2009, n^o D6.3, deliverable.

[28]

F. Fages, J. Martin.
Prototype software of the knowledge modeler, FP6 Strep project Net-WMS, April 2009, n^o D6.2, deliverable.

[29]

F. Fages, J. Martin.
Rules2CP/PKML user's manual, INRIA, 2009
http://contraintes.inria.fr/rules2cp/.

[30]

F. Fages, S. Soliman, A. Rizk.
BIOCHAM v8 user's manual, INRIA, 2009
http://contraintes.inria.fr/BIOCHAM/.

[31]

R. Ferreira Oliveira.
A Component Based Approach to Specify and Implement Generic Traces in CHROME, INRIA Paris-Rocquencourt, December 2009, Internship report.

[32]

C. Fonger.
A Java-Choco Compiler of the Rules2CP Modeling Language, INRIA, October 2009, Rapport de stage du MIT.

[33]

V. Gatien-Baron.
Détection de Symétries dans les problèmes de satisfaction de contraintes, INRIA, October 2009, Rapport de stage de Master MPRI.

[34]

S. Gay.
Model reduction on reaction graphs, INRIA, October 2009, Rapport de stage de Master MPRI.

[35]

F. Nabli.
Bipartite Graph Properties and Systems Biology, INRIA, October 2009, Mémoire de Master de l'Université de Tunis.

[36]

R. Oliveira Ferreira, P. Deransart.
Towards a Generic Framework to Generate Explanatory Traces of Constraint Solving and Rule-Based Reasoning, INRIA Paris-Rocquencourt, 2009, n^o RR-7165
http://hal.inria.fr/inria-00443635/fr/, Technical report.

[37]

S. Singh.
Solving Open-Shop Problem in Rules2CP, INRIA, October 2009, Internship report IIT.

[38]

H. Waghmare.
Reaction Rules with Antagonists, INRIA, October 2009, Internship report IIT.

Other Publications

[39]

P. Deransart.
Conception de Trace et Applications (vers une méta-théorie des traces), November 2009, Working document.