Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles, PLoS Biology, vol.280, issue.1, pp.54-0066, 2007. ,
DOI : 10.1371/journal.pbio.0050008.sd001
Global Expression Profiling of Acetate-grown Escherichia coli, Journal of Biological Chemistry, vol.277, issue.15, pp.13175-13183, 2002. ,
DOI : 10.1074/jbc.M110809200
Precise Temporal Modulation in the Response of the SOS DNA Repair Network in Individual Bacteria, PLoS Biology, vol.85, issue.7, p.238, 2005. ,
DOI : 10.1371/journal.pbio.0030238.t001
Gene networks: how to put the function in genomics, Trends in Biotechnology, vol.20, issue.11, pp.467-472, 2002. ,
DOI : 10.1016/S0167-7799(02)02053-X
Identification of regulatory network topological units coordinating the genome-wide transcriptional response to glucose in Escherichia coli, BMC Microbiology, vol.7, issue.1, p.53, 2007. ,
DOI : 10.1186/1471-2180-7-53
Cyclic AMP-Dependent Catabolite Repression Is the Dominant Control Mechanism of Metabolic Fluxes under Glucose Limitation in Escherichia coli, Journal of Bacteriology, vol.190, issue.7, pp.2323-2330, 2008. ,
DOI : 10.1128/JB.01353-07
Topology of the global regulatory network of carbon limitation in Escherichia coli, Journal of Biotechnology, vol.132, issue.4, pp.359-374, 2007. ,
DOI : 10.1016/j.jbiotec.2007.08.029
In Vitro Reconstitution of Catabolite Repression in Escherichia coli, Journal of Biological Chemistry, vol.281, issue.10, pp.6448-6454, 2006. ,
DOI : 10.1074/jbc.M512672200
Regulation of carbon utilization, Escherichia coli and Salmonella: Cellular and Molecular Biology, pp.1325-1343, 1996. ,
Formulating genome-scale kinetic models in the post-genome era, Molecular Systems Biology, vol.46, p.171, 2008. ,
DOI : 10.1093/nar/gkl923
The Regulation of Cellular Systems, 1996. ,
DOI : 10.1007/978-1-4613-1161-4
Simplification of Mathematical Models of Chemical Reaction Systems, Chemical Reviews, vol.98, issue.2, pp.391-408, 1998. ,
DOI : 10.1021/cr950223l
Control theory of regulatory cascades, Journal of Theoretical Biology, vol.153, issue.2, pp.255-285, 1991. ,
DOI : 10.1016/S0022-5193(05)80426-6
URL : https://hal.archives-ouvertes.fr/hal-00697976
Metabolic control theory: A structural approach, Journal of Theoretical Biology, vol.135, issue.2, pp.175-201, 1988. ,
DOI : 10.1016/S0022-5193(88)80073-0
Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations, Science, vol.316, issue.5824, pp.593-597, 2007. ,
DOI : 10.1126/science.1132067
Inferring Genetic Networks and Identifying Compound Mode of Action via Expression Profiling, Science, vol.301, issue.5629, pp.102-105, 2003. ,
DOI : 10.1126/science.1081900
On the Sign Pattern of Metabolic Control Coefficients, Journal of Theoretical Biology, vol.182, issue.3, pp.269-275, 1996. ,
DOI : 10.1006/jtbi.1996.0164
Introduction to Linear System Theory, 1970. ,
Cloning and nucleotide sequence of the Escherichia coli K-12 ppsA gene, encoding PEP synthase, Mol Gen Genet, vol.231, pp.332-336, 1992. ,
Cloning of the two pyruvate kinase isoenzyme structural genes from Escherichia coli: the relative roles of these enzymes in pyruvate biosynthesis., Journal of Bacteriology, vol.177, issue.19, pp.5719-5722, 1995. ,
DOI : 10.1128/jb.177.19.5719-5722.1995
The global regulatory protein FruR modulates the direction of carbon flow in Escherichia coli, Molecular Microbiology, vol.267, issue.6, pp.1157-1169, 1995. ,
DOI : 10.1016/0923-2508(91)90005-U
URL : https://hal.archives-ouvertes.fr/hal-00725014
Frur mediates catabolite activation of pyruvate kinase (pykF) gene expression in Escherichia coli., Journal of Bacteriology, vol.178, issue.1, pp.280-283, 1996. ,
DOI : 10.1128/jb.178.1.280-283.1996
Transcriptome Analysis of Crp-Dependent Catabolite Control of Gene Expression in Escherichia coli, Journal of Bacteriology, vol.186, issue.11, pp.3516-3524, 2004. ,
DOI : 10.1128/JB.186.11.3516-3524.2004
Identification of the CRP regulon using in vitro and in vivo transcriptional profiling, Nucleic Acids Research, vol.32, issue.19, pp.5874-5893, 2004. ,
DOI : 10.1093/nar/gkh908
A Quantitative Approach to Catabolite Repression in Escherichia coli, Journal of Biological Chemistry, vol.281, issue.5, pp.2578-2584, 2005. ,
DOI : 10.1074/jbc.M508090200
Dynamic modeling of the central carbon metabolism ofEscherichia coli, Biotechnology and Bioengineering, vol.81, issue.1, pp.53-73, 2002. ,
DOI : 10.1002/bit.10288
Qualitative simulation of the carbon starvation response in Escherichia coli, Biosystems, vol.84, issue.2, pp.124-152, 2006. ,
DOI : 10.1016/j.biosystems.2005.10.005
URL : https://hal.archives-ouvertes.fr/hal-00171698
A feed-forward loop guarantees robust behavior in Escherichia coli carbohydrate uptake, Bioinformatics, vol.24, issue.5, pp.704-710, 2008. ,
DOI : 10.1093/bioinformatics/btn010
The control of pyruvate kinase of Escherichia coli. Binding of substrate and allosteric effectors to the enzyme activated by fructose 1,6-bisphosphate, Biochemistry, vol.15, issue.2, pp.277-282, 1976. ,
DOI : 10.1021/bi00647a006
Glucose metabolism in Escherichia coli and the effect of increased aldolase, Biochemistry, vol.32, issue.17, pp.4685-4692, 1993. ,
DOI : 10.1021/bi00068a029
From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli, BioEssays, vol.389, issue.5, pp.433-440, 1998. ,
DOI : 10.1002/(SICI)1521-1878(199805)20:5<433::AID-BIES10>3.0.CO;2-2
Topological and causal structure of the yeast transcriptional regulatory network, Nature Genetics, vol.31, issue.1, pp.60-63, 2002. ,
DOI : 10.1038/ng873
Network motifs in the transcriptional regulation network of Escherichia coli, Nature Genetics, vol.31, issue.1, pp.64-68, 2002. ,
DOI : 10.1038/ng881
An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs, Nucleic Acids Research, vol.32, issue.22, pp.6643-6649, 2004. ,
DOI : 10.1093/nar/gkh1009
Effect of cra gene knockout together with edd and iclR genes knockout on the metabolism in Escherichia coli, Archives of Microbiology, vol.68, issue.3, pp.558-571, 2008. ,
DOI : 10.1007/s00203-008-0406-2
ENZYME INDUCTION AS AN ALL-OR-NONE PHENOMENON, Proceedings of the National Academy of Sciences, vol.43, issue.7, pp.553-566, 1957. ,
DOI : 10.1073/pnas.43.7.553
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC528498
Biological Feedback, Boca Raton, 1990. ,
URL : https://hal.archives-ouvertes.fr/hal-00087681
Topology and static response of interaction networks in molecular biology, Journal of The Royal Society Interface, vol.84, issue.5, pp.185-196, 2006. ,
DOI : 10.1002/sim.1237
URL : https://hal.archives-ouvertes.fr/inria-00178842
Network-Free Inference of Knockout Effects in Yeast, PLoS Computational Biology, vol.42, issue.1, p.1000635, 2010. ,
DOI : 10.1371/journal.pcbi.1000635.s003
Physical Network Models, Journal of Computational Biology, vol.11, issue.2-3, pp.243-262, 2004. ,
DOI : 10.1089/1066527041410382
Integrating high-throughput and computational data elucidates bacterial networks, Nature, vol.429, issue.6987, pp.92-100, 2004. ,
DOI : 10.1038/nature02456
Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli, Bioinformatics, vol.24, issue.18, pp.2044-2050, 2008. ,
DOI : 10.1093/bioinformatics/btn352
A genome-scale computational study of the interplay between transcriptional regulation and metabolism, Molecular Systems Biology, vol.102, pp.101-101, 2007. ,
DOI : 10.1038/msb4100141
A Global Regulatory Role of Gluconeogenic Genes in Escherichia coli Revealed by Transcriptome Network Analysis, Journal of Biological Chemistry, vol.280, issue.43, pp.36079-36087, 2005. ,
DOI : 10.1074/jbc.M508202200
Qualitative Stability and Ambiguity in Model Ecosystems, The American Naturalist, vol.161, issue.6, pp.876-888, 2003. ,
DOI : 10.1086/367590
Qualitative modeling of complex systems: An introduction to loop analysis and time averaging, 1985. ,
DOI : 10.4159/harvard.9780674435070
Qualitative comparative statics, Journal of Mathematical Economics, vol.28, issue.2, pp.127-154, 1997. ,
DOI : 10.1016/S0304-4068(97)00800-8
Robustness of Cellular Functions, Cell, vol.118, issue.6, pp.675-686, 2004. ,
DOI : 10.1016/j.cell.2004.09.008
Molecular interaction maps as information organizers and simulation guides, Chaos: An Interdisciplinary Journal of Nonlinear Science, vol.11, issue.1, pp.84-97, 2001. ,
DOI : 10.1063/1.1338126