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, n^o 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, n^o 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, n^o 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, n^o 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, n^o 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