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Bibliography

Publications of the year

Doctoral Dissertations and Habilitation Theses

  • 1F. Nabli.
    Approches de programmation par contraintes pour l'analyse des propriétés structurelles des réseaux de Petri et application aux réseaux biochimiques, Université Paris-Diderot - Paris VII, July 2013.
    http://hal.inria.fr/tel-00924445
  • 2J. Uhlendorf.
    Real-time feedback control of gene expression, Université Paris-Diderot - Paris VII, April 2013.
    http://hal.inria.fr/tel-00850778

Articles in International Peer-Reviewed Journals

  • 3P. Guye, Y. Li, L. Wroblewska, X. Duportet, R. Weiss.
    Rapid, modular and reliable construction of complex mammalian gene circuits, in: Nucleic Acids Research, 2013, vol. 41, no 16. [ DOI : 10.1093/nar/gkt605 ]
    http://hal.inria.fr/hal-00926598
  • 4N. D. Mendes, F. Lang, Y.-S. Le Cornec, R. Mateescu, G. Batt, C. Chaouiya.
    Composition and abstraction of logical regulatory modules: application to multicellular systems, in: Bioinformatics, January 2013, vol. 29, no 6, pp. 749-757. [ DOI : 10.1093/bioinformatics/btt033 ]
    http://hal.inria.fr/hal-00785564
  • 5S. Soliman.
    A stronger necessary condition for the multistationarity of chemical reaction networks, in: Bulletin of Mathematical Biology, November 2013, vol. 75, no 11, pp. 2289-2303. [ DOI : 10.1007/s11538-013-9893-7 ]
    http://hal.inria.fr/hal-00772438
  • 6S. Stoma, A. Donzé, F. Bertaux, O. Maler, G. Batt.
    STL-based Analysis of TRAIL-induced Apoptosis Challenges the Notion of Type I/Type II Cell Line Classification, in: PLoS Computational Biology, 2013, vol. 9, no 5. [ DOI : 10.1371/journal.pcbi.1003056 ]
    http://hal.inria.fr/hal-00926593

International Conferences with Proceedings

  • 7K. Chiang, F. Fages, J.-H. Jiang, S. Soliman.
    On the Hybrid Composition and Simulation of Heterogeneous Biochemical Models, in: CMSB - 11th International Conference on Computational Methods for Systems Biology - 2013, Klosterneuburg, Austria, A. Gupta, T. A. Henzinger (editors), Lecture Notes in Computer Science, Springer, September 2013, vol. 8130, pp. 192–205. [ DOI : 10.1007/978-3-642-40708-6_15 ]
    http://hal.inria.fr/hal-00913292
  • 8S. Gay, F. Fages, F. Santini, S. Soliman.
    Solving Subgraph Epimorphism Problems using CLP and SAT, in: WCB - ninth Workshop on Constraint Based Methods for Bioinformatics, colocated with CP 2013, Uppsala, Sweden, 2013, pp. 67–74.
    http://hal.inria.fr/hal-00908973
  • 9A. Gonzalez, J. Uhlendorf, J. Schaul, E. Cinquemani, G. Batt, G. Ferrari-Trecate.
    Identification of biological models from single-cell data: a comparison between mixed-effects and moment-based inference, in: ECC - 12th European Control Conference - 2013, Zurich, Switzerland, 2013.
    http://hal.inria.fr/hal-00831641
  • 10R.-Y. Huang, D.-A. Huang, H.-J. Katherine, J.-H. Jiang, F. Fages.
    Species Minimization in Computation with Biochemical Reactions, in: IWBDA'13: Proceedings of the fifth International Workshop on Bio-Design Automation, Imperial College, London, United Kingdom, 2013.
    http://hal.inria.fr/hal-00935829
  • 11J.-B. Lugagne, D. A. Oyarzún, G.-B. Stan.
    Stochastic simulation of enzymatic reactions under transcriptional feedback regulation, in: European Control Conference (ECC), Zurich, Switzerland, July 2013, pp. 3646-3651.
    http://hal.inria.fr/hal-00935727
  • 12T. Martinez, L. Vitorino, F. Fages, A. Aggoun.
    On Solving Mixed Shapes Packing Problems by Continuous Optimization with the CMA Evolution Strategy, in: BRICS-CCI 2013 - First BRICS countries congress on Computational Intelligence, Recife, Brazil, 2013.
    http://hal.inria.fr/hal-00934917
  • 13S. Soliman, F. Fages, O. Radulescu.
    A Constraint Solving Approach to Tropical Equilibration and Model Reduction, in: WCB - ninth Workshop on Constraint Based Methods for Bioinformatics, colocated with CP 2013, Uppsala, Sweden, 2013, pp. 27–36.
    http://hal.inria.fr/hal-00906419

Internal Reports

  • 14F. Bertaux, S. Stoma, D. Drasdo, G. Batt.
    Dynamics of cell-to-cell variability in TRAIL-induced apoptosis explains fractional killing and predicts reversible resistance, February 2014.
    http://hal.inria.fr/hal-00942885
  • 15A. Gonzalez, J. Uhlendorf, J. Schaul, E. Cinquemani, G. Batt, G. Ferrari-Trecate.
    Identification of biological models from single-cell data: a comparison between mixed-effects and moment-based inference, Inria, April 2013, no RR-8288.
    http://hal.inria.fr/hal-00817582

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