Synthetic biology: new engineering rules for an emerging discipline, Molecular systems biology, pp.4100073-4100074, 2006. ,
DOI : 10.1038/msb4100073
Synthetic biology, Nature Reviews Genetics, vol.6, issue.7, pp.533-543, 2005. ,
Flux analysis of underdetermined metabolic networks: the quest for the missing constraints, Trends in Biotechnology, vol.15, issue.8, pp.308-314, 1997. ,
DOI : 10.1016/S0167-7799(97)01067-6
Regulation of CodY Activity through Modulation of Intracellular Branched-Chain Amino Acid Pools, Journal of Bacteriology, vol.192, issue.24, pp.6357-6368, 2010. ,
DOI : 10.1128/JB.00937-10
Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization, Biotechnology and Bioengineering, vol.18, issue.6, pp.647-657, 2003. ,
DOI : 10.1002/bit.10803
Formal Reduction for Rule-based Models, the 27th Conference on the Mathematical Foundations of Programming Semantics -MFPS 2011, pp.29-59, 2011. ,
DOI : 10.1016/j.entcs.2011.09.014
URL : https://hal.archives-ouvertes.fr/inria-00636850
The calculational design of a generic abstract interpreter, Calculational System Design. NATO ASI Series F. IOS Press, 1999. ,
Systematic design of program analysis frameworks, Proceedings of the 6th ACM SIGACT-SIGPLAN symposium on Principles of programming languages , POPL '79, pp.269-282, 1979. ,
DOI : 10.1145/567752.567778
Regulation of Gene Expression in Flux Balance Models of Metabolism, Journal of Theoretical Biology, vol.213, issue.1, pp.73-88, 2001. ,
DOI : 10.1006/jtbi.2001.2405
Abstracting the Differential Semantics of Rule-Based Models: Exact and Automated Model Reduction, 2010 25th Annual IEEE Symposium on Logic in Computer Science, pp.362-381, 2010. ,
DOI : 10.1109/LICS.2010.44
URL : https://hal.archives-ouvertes.fr/hal-00520112
A synthetic oscillatory network of transcriptional regulators, Nature, vol.403, issue.6767, pp.335-338, 2000. ,
Abstract interpretation and types for systems biology, Theoretical Computer Science, vol.403, issue.1, pp.52-70, 2008. ,
DOI : 10.1016/j.tcs.2008.04.024
URL : https://hal.archives-ouvertes.fr/hal-01431355
Lumpability abstractions of rule-based systems, Theoretical Computer Science, 2012. ,
DOI : 10.4204/eptcs.40.10
URL : https://hal.archives-ouvertes.fr/inria-00527971
Feedback regulation of opposing enzymes generates robust, allor-none bistable responses, Current biology : CB, vol.18, issue.6, 2008. ,
DOI : 10.1016/j.cub.2008.02.035
URL : http://doi.org/10.1016/j.cub.2008.02.035
SPABBATS: A pathway-discovery method based on Boolean satisfiability that facilitates the characterization of suppressor mutants, BMC Systems Biology, vol.5, issue.1, p.5, 2011. ,
DOI : 10.1186/1752-0509-5-5
Genome-Scale Reconstruction of the Saccharomyces cerevisiae Metabolic Network, Genome Research, vol.13, issue.2, pp.244-253, 2003. ,
DOI : 10.1101/gr.234503
Moment-closure approximations for mass-action models, IET Systems Biology, vol.3, issue.1, pp.52-58, 2009. ,
DOI : 10.1049/iet-syb:20070031
Exact stochastic simulation of coupled chemical reactions, Journal of Physical Chemistry, vol.81, pp.2340-2361, 1977. ,
Reconstruction and analysis of the genetic and metabolic regulatory networks of the central metabolism of Bacillus subtilis, BMC Systems Biology, vol.2, issue.1, p.20, 2008. ,
DOI : 10.1186/1752-0509-2-20
URL : https://hal.archives-ouvertes.fr/hal-00315553
iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations, Genome Biology, vol.10, issue.6, p.69, 2009. ,
DOI : 10.1186/gb-2009-10-6-r69
Synthetic Biology for Synthetic Chemistry, ACS Chemical Biology, vol.3, issue.1, pp.64-76, 2008. ,
DOI : 10.1021/cb7002434
Cell-signalling dynamics in time and space, Nature Reviews Molecular Cell Biology, vol.7, pp.165-176, 2006. ,
OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains, BMC Systems Biology, vol.4, issue.1, p.53, 2010. ,
DOI : 10.1186/1752-0509-4-53
The role of predictive modelling in rationally re-engineering biological systems, Nature Reviews Microbiology, vol.7, issue.4, pp.297-305, 2009. ,
DOI : 10.1038/nrmicro2107
Based on High-throughput Phenotyping and Gene Essentiality Data, Journal of Biological Chemistry, vol.282, issue.39, pp.28791-28799, 2007. ,
DOI : 10.1074/jbc.M703759200
Evolutionary programming as a platform for in silico metabolic engineering, BMC bioinformatics, vol.6, issue.1, p.308, 2005. ,
OptStrain: A computational framework for redesign of microbial production systems, Genome Research, vol.14, issue.11, pp.2367-2376, 2004. ,
DOI : 10.1101/gr.2872004
An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems, Metabolic Engineering, vol.8, issue.1, pp.1-13, 2006. ,
DOI : 10.1016/j.ymben.2005.08.003
Genome-scale models of microbial cells: evaluating the consequences of constraints, Nature Reviews Microbiology, vol.83, issue.11, pp.886-897, 2004. ,
DOI : 10.1074/jbc.M403782200
Flux-balance analysis of mitochondrial energy metabolism: consequences of systemic stoichiometric constraints, American journal of physiology. Regulatory, integrative and comparative physiology, vol.280, issue.3, pp.695-704, 2001. ,
OptForce: An Optimization Procedure for Identifying All Genetic Manipulations Leading to Targeted Overproductions, PLoS Computational Biology, vol.68, issue.72, p.1000744, 2010. ,
DOI : 10.1371/journal.pcbi.1000744.s007
Perspectives on the automatic design of regulatory systems for synthetic biology, FEBS Letters, vol.6, issue.15, pp.2037-2042, 2012. ,
DOI : 10.1016/j.febslet.2012.02.031
Handbook of Constraint Programming, 2006. ,
Metabolic networks in motion: 13C-based flux analysis, Molecular systems biology, 2006. ,
DOI : 10.1038/msb4100109
Analysis of optimality in natural and perturbed metabolic networks, Proceedings of the National Academy of Sciences, pp.15112-15117, 2002. ,
DOI : 10.1073/pnas.232349399
Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways, Bioinformatics, vol.26, issue.4, pp.536-543, 2010. ,
DOI : 10.1093/bioinformatics/btp704
Boolean formalization of genetic control circuits, Journal of Theoretical Biology, vol.42, issue.3, pp.563-585, 1973. ,
DOI : 10.1016/0022-5193(73)90247-6
Metabolic Capabilities of Escherichia coli II. Optimal Growth Patterns, Journal of Theoretical Biology, vol.165, issue.4, pp.503-522, 1993. ,
DOI : 10.1006/jtbi.1993.1203
Metabolic Flux Balancing: Basic Concepts, Scientific and Practical Use, Bio/Technology, vol.43, issue.10, pp.994-998, 1994. ,
DOI : 10.1006/jtbi.1993.1203
Modeling and Simulation of Intracellular Dynamics: Choosing an Appropriate Framework, IEEE Transactions on Nanobioscience, vol.3, issue.3, pp.200-207, 2004. ,
DOI : 10.1109/TNB.2004.833694