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Bibliography

Publications of the year

Doctoral Dissertations and Habilitation Theses

  • 1D. Heitzler.

    Modélisation dynamique des mécanismes de signalisation cellulaire induits par l'hormone folliculo-stimulante et l'angiotensine, Univ. François Rabelais de Tours, January 2011.
  • 2A. Rizk.

    Résolution de contraintes temporelles pour l'analyse de systèmes biologiques, Université Denis Diderot, Paris, May 2011.

Articles in International Peer-Reviewed Journal

  • 3R. Charney, J. Cohen, A. Rizk.

    Efficient synthesis of a class of Boolean programs from I-O data: Application to genetic networks, in: Discrete Applied Mathematics, March 2011, vol. 159, no 6, p. 410–419.

    http://dx.doi.org/10.1016/j.dam.2010.10.009
  • 4E. De Maria, F. Fages, A. Rizk, S. Soliman.

    Design, Optimization, and Predictions of a Coupled Model of the Cell Cycle, Circadian Clock, DNA Repair System, Irinotecan Metabolism and Exposure Control under Temporal Logic Constraints, in: Theoretical Computer Science, May 2011, vol. 412, no 21, p. 2108–2127.

    http://dx.doi.org/10.1016/j.tcs.2010.10.036
  • 5S. Gay, F. Fages, T. Martinez, S. Soliman, C. Solnon.

    On the subgraph Epimorphism Problem, in: Discrete Applied Mathematics, 2011, submitted.
  • 6D. Heitzler, G. Durand, 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.

    GRKs: molecular switches controlling the balance between G protein and β-arrestin-mediated signaling by 7TMRs, in: Molecular Systems Biology, 2011, submitted.
  • 7A. Miermont, J. Uhlendorf, M. McClean, P. Hersen.

    The dynamical systems properties of the HOG signaling cascade, in: Journal of Signal Transduction, 2011, no 2011, 930940 p.
  • 8A. Rizk, G. Batt, F. Fages, S. Soliman.

    Continuous Valuations of Temporal Logic Specifications with applications to Parameter Optimization and Robustness Measures, in: Theoretical Computer Science, June 2011, vol. 412, no 26, p. 2827–2839.

    http://dx.doi.org/10.1016/j.tcs.2010.05.008
  • 9S. Stoma, M. Frohlich, S. Gerber, E. Klipp.

    STSE: Spatio-temporal simulation environment dedicated to biology, in: BMC Bioinformatics, 2011, no 12, 126 p.

International Conferences with Proceedings

  • 10S. Gay, T. Martinez, S. Soliman, F. Fages.

    A Constraint Program For Subgraph Epimorphisms with Application to Identifying Model Reductions in Systems Biology, in: Proceedings of the seventh Workshop on Constraint Based Methods for Bioinformatics WCB'11, colocated with CP 2011, September 2011, p. 59–66.
  • 11A. Gonçalves, M. A. A. D. Silva, P. Deransart, J. Robin.

    Towards a Generic Trace for Rule Based Constraint Reasoning, in: Eighth International Workshop on Constraint Handling Rules (CHR2011), J. Sneyers (editor), TR, German University in Cairo, Egypt, 2011.
  • 12R. Grosu, G. Batt, F. Fenton, J. Glimm, C. Le Guernic, S. Smolka, E. Bartocci.

    From cardiac cells to genetic regulatory networks, in: 23rd International Conference on Computer Aided Verification, CAV'11, Cliff Lodge, 2011.
  • 13T. Martinez.

    Angelic CHR, in: Proceedings of the Eighth International Workshop on Constraint Handling Rules CHR'11, J. Sneyers (editor), September 2011.

    http://contraintes.inria.fr/tmartine/papers/martinez11chr.pdf
  • 14F. Nabli.

    Finding minimal siphons as a CSP, in: CP'11: The Seventeenth International Conference on Principles and Practice of Constraint Programming, Doctoral Program, September 2011, p. 67–72.
  • 15J. Uhlendorf, S. Bottani, F. Fages, P. Hersen, G. Batt.

    Towards real-time control of gene experession: controlling the HOG signaling cascade, in: Proceedings of the 16th Pacific Symposium on Biocomputing (PSB 2011), Hawaii, USA, January 2011, p. 338–349.
  • 16J. Uhlendorf, P. Hersen, G. Batt.

    Towards real-time control of gene expression: in silico analysis, in: 18th IFAC World Congress, WC'11, Milan, 2011.

National Conferences with Proceeding

  • 17P. Deransart.

    Traces génériques et contraintes, GenTra4CP revisité, in: Septièmes Journées Francophones de Programmation par Contraintes (JFPC 2011), 2011, p. 105–114.

Conferences without Proceedings

  • 18G. Batt.

    Towards Real-Time Control of Gene Expression (invited talk), in: International Workshop Towards Systems Biology, Grenoble, France, May 2011.
  • 19F. Fages.

    A graphical method for reducing and relating models in systems biology (invited talk), in: International Workshop Towards Systems Biology, Grenoble, France, May 2011.
  • 20F. Fages.

    Formal cell biology in Biocham (keynote talk), in: International Symposium on Symbolic Systems Biology ISSSB'11, Shonan Village, Japan, November 2011.
  • 21F. Fages.

    Hiérarchie de formalismes et de modèles en biologie systémique (exposé invité), in: Journée ITMO CMN Inria, Paris, France, March 2011.
  • 22F. Fages.

    Une méthode graphique pour réduire et relier les modèles en biologie des systèmes, in: Symposium Biointelligence, Sophia-Antipolis, France, July 2011.

Scientific Books (or Scientific Book chapters)

  • 23J. Martin, T. Martinez, F. Fages.

    Static Expansion vs Procedural Code Generation in Rule-based Modeling Languages, in: Recent Advances in Constraints, J. Larrosa, B. O'Sullivan (editors), LNAI, Springer-Verlag, 2011, no 6384, p. 38–58.
  • 24A. Randall, P. Guye, S. Gupta, X. Duportet, R. Weiss.

    Design and connection of robust genetic circuits, in: Methods in Enzymology, C. Voigt (editor), Elsevier, 2011, no 497, p. 159–186.

Books or Proceedings Editing

  • 25F. Fages (editor)

    Proc. of the 9th International Conference on Computational Methods in Systems Biology CMSB'11, ACM in cooperation Conference Proceedings, ACM Digital Libray, Paris, France, September 2011.

Internal Reports

  • 26L. Calzone, C. Chaouiya, É. Remy, S. Soliman.

    Qualitative Modelling of the RB/E2F network, ANR CALAMAR (ANR-08-SYSC-003), February 2011, no D3.1.

    http://tagc.univ-mrs.fr/welcome/IMG/pdf/livrable-3-1.pdf
  • 27L. Calzone, S. Soliman.

    Quantitative Modelling of the RB/E2F network, ANR CALAMAR (ANR-08-SYSC-003), September 2011, no D3.2.
  • 28P. Deransart.

    Generic Traces and Constraints, GenTra4CP revisited, Inria HAL report, 2011.

    http://hal.inria.fr/hal-00597033/en
  • 29F. Fages, D. Jovanovska, A. Rizk, S. Soliman.

    BIOCHAM v3.3 Reference Manual, INRIA, 2011.

    http://contraintes.inria.fr/BIOCHAM/
  • 30F. Fages, P. Robin, S. Soliman.

    Simulations hybrides, OSEO project BioIntelligence, 2011, no INR-04-L3-D14.
  • 31D. Fournier.

    Constraint Modeling of Trains Supervision and Timetabling, Chalmers University, Sweden, Ecole des Mines d'Ales, INRIA, France, September 2011.
  • 32S. Soliman.

    Constraint Programming for the Dynamical Analysis of Biochemical Systems – A Survey, ANR CALAMAR (ANR-08-SYSC-003), February 2011, no D1.6.

    http://tagc.univ-mrs.fr/welcome/IMG/pdf/Livrable-1-6.pdf
  • 33S. Soliman, A. Zinovyev.

    Reduction of differential models, ANR CALAMAR (ANR-08-SYSC-003), September 2011, no D1.2.

Other Publications