Overall Objectives
Research Program
Application Domains
New Software and Platforms
New Results
Bilateral Contracts and Grants with Industry
Partnerships and Cooperations
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Publications of the year

Doctoral Dissertations and Habilitation Theses

G. Batt.
Design, optimization and control in systems and synthetic biology, Université Paris-Diderot - Paris VII, March 2014, Habilitation à diriger des recherches.
X. 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.
D. Fournier.
Metro Regenerative Braking Energy Optimization through Rescheduling: Mathematical Model and Greedy Heuristics Compared to MILP and CMA-ES, Paris-VIII, November 2014.

Articles in International Peer-Reviewed Journals

F. 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 ]
D. 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 ]
M. 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 ]
X. 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 ]
F. 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 ]
S. 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 ]
D. 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 ]
S. 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 ]

Invited Conferences

G. 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 ]
F. Fages.
Cells as Machines: Towards Deciphering Biochemical Programs in the Cell (keynote talk), in: 21st European Conference on Artificial Intelligence, Prague, Czech Republic, 2014.
F. 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 ]

International Conferences with Proceedings

H.-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 ]
T.-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.
D. 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 ]
A. 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 ]
P. 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 ]

Scientific Books (or Scientific Book chapters)

F. 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 ]
L. 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 ]
J. 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 ]

Other Publications

F. Fages.
Machinerie cellulaire et programmation biochimique: vers une informatique de la cellule, 2014, Forum des lauréats en informatique et mathématiques appliquées 2014.