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Bibliography

Publications of the year

Doctoral Dissertations and Habilitation Theses

  • 1G. Batt.
    Design, optimization and control in systems and synthetic biology, Université Paris-Diderot - Paris VII, March 2014, Habilitation à diriger des recherches.
    https://tel.archives-ouvertes.fr/tel-00958566
  • 2X. Duportet.
    Developing new tools and platforms for mammalian synthetic biology: From the assembly and chromosomal integration of complex DNA circuits to the engineering of artificial intercellular communication systems, Université Paris Diderot (Paris 7), November 2014.
    https://tel.archives-ouvertes.fr/tel-01108520
  • 3D. Fournier.
    Metro Regenerative Braking Energy Optimization through Rescheduling: Mathematical Model and Greedy Heuristics Compared to MILP and CMA-ES, Paris-VIII, November 2014.
    https://tel.archives-ouvertes.fr/tel-01102408

Articles in International Peer-Reviewed Journals

  • 4F. Bertaux, S. Stoma, D. Drasdo, G. Batt.
    Modeling Dynamics of Cell-to-Cell Variability in TRAIL-Induced Apoptosis Explains Fractional Killing and Predicts Reversible Resistance, in: PLoS Computational Biology, 2014, vol. 10, no 10, 14 p. [ DOI : 10.1371/journal.pcbi.1003893.s016 ]
    https://hal.inria.fr/hal-00942885
  • 5D. Bikard, C. Euler, W. Jiang, N. Philip, G. Goldberg, X. Duportet, V. Fischetti, L. Marraffini.
    Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials, in: Nature Biotechnology, 2014, vol. 32, no 11, 5 p. [ DOI : 10.1038/nbt.3043 ]
    https://hal.archives-ouvertes.fr/hal-01103559
  • 6M. Cvijovic, J. Almquist, J. Hagmar, S. Hohmann, H. Kaltenbach, E. Klipp, M. Krantz, P. Mendes, S. Nelander, J. Nielsen, A. Pagnani, N. Przulj, A. Raue, J. Stelling, S. Stoma, F. Tobin, J. Wodke, R. Zecchina, M. Jirstrand.
    Bridging the gaps in systems biology, in: Molecular Genetics and Genomics, 2014, vol. 289, no 5, 8 p. [ DOI : 10.1007/s00438-014-0843-3 ]
    https://hal.archives-ouvertes.fr/hal-01103558
  • 7X. Duportet, L. Wroblewska, P. Guye, Y. Li, J. Eyquem, J. Rieders, T. Rimchala, G. Batt, R. Weiss.
    A platform for rapid prototyping of synthetic gene networks in mammalian cells, in: Nucleic Acids Research, 2014, vol. 42, no 21, 12 p. [ DOI : 10.1093/nar/gku1082 ]
    https://hal.archives-ouvertes.fr/hal-01103532
  • 8F. Fages, S. Gay, S. Soliman.
    Inferring reaction systems from ordinary differential equations, in: Journal of Theoretical Computer Science (TCS), 2014, 23 p. [ DOI : 10.1016/j.tcs.2014.07.032 ]
    https://hal.inria.fr/hal-01103692
  • 9S. Gay, F. Fages, T. Martinez, S. Soliman, C. Solnon.
    On the subgraph Epimorphism Problem, in: Discrete Applied Mathematics, January 2014, vol. 162, pp. 214–228. [ DOI : 10.1016/j.dam.2013.08.008 ]
    https://hal.inria.fr/hal-01098527
  • 10D. Oyarzun, J.-B. Lugagne, G.-B. Stan.
    Noise propagation in synthetic gene circuits for metabolic control, in: ACS Synthetic Biology, 2014, 10 p. [ DOI : 10.1021/sb400126a ]
    https://hal.archives-ouvertes.fr/hal-01103554
  • 11S. Soliman, F. Fages, O. Radulescu.
    A constraint solving approach to model reduction by tropical equilibration, in: Algorithms for Molecular Biology, December 2014, vol. 9, 24 p. [ DOI : 10.1186/s13015-014-0024-2 ]
    https://hal.inria.fr/hal-01098530

Invited Conferences

  • 12G. Batt.
    Cells driven by computers: long-term model predictive control of gene expression in yeast (keynote talk), in: HSCC - Proceedings of the 17th international conference on Hybrid Systems: Computation and Control, Berlin, Germany, ACM, April 2014, 2 p. [ DOI : 10.1145/2562059.2562144 ]
    https://hal.archives-ouvertes.fr/hal-01104055
  • 13F. Fages.
    Cells as Machines: Towards Deciphering Biochemical Programs in the Cell (keynote talk), in: 21st European Conference on Artificial Intelligence, Prague, Czech Republic, 2014.
    https://hal.inria.fr/hal-01103333
  • 14F. Fages.
    Cells as Machines: Towards Deciphering Biochemical Programs in the Cell, in: ICDCIT 2014 - 10th International Conference Distributed Computing and Internet Technology, Bhubanesvar, India, R. Natarajan (editor), Lecture Notes in Computer Science, Springer-Verlag, February 2014, vol. 8337, pp. 50 - 67. [ DOI : 10.1007/978-3-319-04483-5_6 ]
    https://hal.inria.fr/hal-01103291

International Conferences with Proceedings

  • 15H.-J. Chiang, J.-H. Jiang, F. Fages.
    Building Reconfigurable Circuitry in a Biochemical World, in: IEEE Proceedings BioCAS 2014 - Biomedical Circuits and Systems Conference, Lausanne, Switzerland, IEEE, October 2014, pp. 560 - 563. [ DOI : 10.1109/BioCAS.2014.6981787 ]
    https://hal.inria.fr/hal-01103266
  • 16T.-Y. Chiu, R.-Y. Huang, H.-J. Chiang, J.-H. Jiang, F. Fages.
    Configurable Linear Control of Biochemical Systems, in: IWBDA 2014 - 6th international workshop on bio-design automation, Boston, United States, June 2014.
    https://hal.inria.fr/hal-01103286
  • 17D. Fournier, F. Fages, D. Mulard.
    A Greedy Heuristic for Optimizing Metro Regenerative Energy Usage, in: Railways 2014, Ajaccio, France, J. Pombo (editor), Proceedings of the Second Internaitonal Conference on Railway Technology: Research, Development and Maintenance, April 2014. [ DOI : 10.4203/ccp.104.240 ]
    https://hal.archives-ouvertes.fr/hal-01103710
  • 18A. Llamosi, A. Mezine, F. D'Alché-Buc, V. Letort, M. Sebag.
    Experimental design in dynamical system identification: A bandit-based active learning approach, in: European Conference on Machine Learning and Knowledge Discovery in Databases (ECML PKDD 2014), Nancy, France, September 2014, vol. 8725, PART 2, pp. 306–321. [ DOI : 10.1007/978-3-662-44851-9_20 ]
    https://hal.archives-ouvertes.fr/hal-01068353
  • 19P. Traynard, F. Fages, S. Soliman.
    Trace Simplifications preserving Temporal Logic Formulae with Case Study in a Coupled Model of the Cell Cycle and the Circadian Clock, in: CMSB'14: Proceedings of the twelth international conference on Computational Methods for Systems Biology, Manchester, United Kingdom, LNBI, Springer Verlag, November 2014, no 8859, pp. 114–128, Best student paper award. [ DOI : 10.1007/978-3-319-12982-2 ]
    https://hal.inria.fr/hal-01098529

Scientific Books (or Scientific Book chapters)

  • 20F. Fages, P. Traynard.
    Temporal Logic Modeling of Dynamical Behaviors: First-Order Patterns and Solvers, in: Logical Modeling of Biological Systems, L. F. del Cerro, K. Inoue (editors), Bioengineering and health science series, Wiley, 2014. [ DOI : 10.1002/9781119005223.ch8 ]
    https://hal.inria.fr/hal-01103305
  • 21L. Maruthi, I. Tkachev, A. Carta, E. Cinquemani, P. Hersen, G. Batt, A. Abate.
    Towards Real-Time Control of Gene Expression at the Single Cell Level: A Stochastic Control Approach, in: Computational Methods in Systems Biology, Lecture Notes in Computer Science, Springer International Publishing, 2014, vol. 8859, pp. 155-172. [ DOI : 10.1007/978-3-319-12982-2_12 ]
    https://hal.inria.fr/hal-01096959
  • 22J. Uhlendorf, A. Miermont, T. Delaveau, G. Charvin, F. Fages, S. Bottani, P. Hersen, G. Batt.
    In silico control of biomolecular processes, in: Computational Methods in Synthetic Biology, M. A. Marchisio (editor), Methods in Molecular Biology, Springer New York, November 2014, vol. 1244, 8 p. [ DOI : 10.1007/978-1-4939-1878-2_13 ]
    https://hal.archives-ouvertes.fr/hal-01104057

Other Publications

  • 23F. Fages.
    Machinerie cellulaire et programmation biochimique: vers une informatique de la cellule, 2014, Forum des lauréats en informatique et mathématiques appliquées 2014.
    https://hal.inria.fr/hal-01103343

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