C. Alexander, S. Ishikawa, and M. Silverstein, A Pattern Language, 1977.

M. Antoniotti, A. Policriti, N. Ugel, and B. Mishra, Model Building and Model Checking for Biochemical Processes, Cell Biochemistry and Biophysics, vol.38, issue.3, pp.271-86, 2003.
DOI : 10.1385/CBB:38:3:271

G. Batt, H. De-jong, M. Page, and J. Geiselmann, Symbolic reachability analysis of genetic regulatory networks using discrete abstractions, Automatica, vol.44, issue.4, 2007.
DOI : 10.1016/j.automatica.2007.08.004

URL : https://hal.archives-ouvertes.fr/hal-00319485

G. Batt, D. Ropers, H. De-jong, J. Geiselmann, R. Mateescu et al., Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in Escherichia coli, Bioinformatics, vol.21, issue.Suppl 1, pp.19-28, 2005.
DOI : 10.1093/bioinformatics/bti1048

URL : https://hal.archives-ouvertes.fr/hal-00171939

G. Bernot, J. Comet, A. Richard, and J. Guespin, Application of formal methods to biological regulatory networks: extending Thomas??? asynchronous logical approach with temporal logic, Journal of Theoretical Biology, vol.229, issue.3, pp.339-387, 2004.
DOI : 10.1016/j.jtbi.2004.04.003

. Gilles, A quantitative approach to catabolite repression in Escherichia coli

M. Calder, V. Vyshemirsky, D. Gilbert, and R. Orton, Analysis of signalling pathways using the PRISM model checker, Proc. of CMSB, pp.179-90, 2005.

N. Chabrier-rivier, M. Chiaverini, V. Danos, F. Fages, and V. Schächter, Modeling and querying biomolecular interaction networks, Theoretical Computer Science, vol.325, issue.1, pp.25-44, 2004.
DOI : 10.1016/j.tcs.2004.03.063

URL : http://doi.org/10.1016/j.tcs.2004.03.063

K. C. Chen, L. Calzone, A. Csikasz-nagy, F. R. Cross, B. Novak et al., Integrative Analysis of Cell Cycle Control in Budding Yeast, Molecular Biology of the Cell, vol.15, issue.8, pp.153841-62, 2004.
DOI : 10.1091/mbc.E03-11-0794

A. Cimatti, E. Clarke, E. Giunchiglia, F. Giunchiglia, M. Pistore et al., NuSMV 2: An OpenSource Tool for Symbolic Model Checking, Proc. 14th CAV, pp.359-64, 2002.
DOI : 10.1007/3-540-45657-0_29

E. M. Clarke, O. Grumberg, and D. A. Peled, Model Checking, 1999.

M. B. Dwyer, G. S. Avrunin, and J. C. Corbett, Patterns in property specifications for finite-state verification, Proc. 21st Intl. Conf. Software Engineering, pp.411-431, 1999.

J. Fisher and T. A. Henzinger, Executable cell biology, Nature Biotechnology, vol.2034, issue.11, pp.1239-50, 2007.
DOI : 10.1038/nbt1356

J. Fisher, N. Piterman, A. Hajnal, and T. A. Henzinger, Predictive Modeling of Signaling Crosstalk during C. elegans Vulval Development, PLoS Computational Biology, vol.77, issue.5, p.92, 2007.
DOI : 0016-6731(1974)077[0071:TGOCE]2.0.CO;2

E. Gamma, R. Helm, R. Johnson, and J. M. Vlissides, Design Patterns: Elements of Reusable Object-Oriented Software, 1994.

H. Garavel, F. Lang, R. Mateescu, and . Cadp, A toolbox for the construction and analysis of distributed processes, Proc. 19th CAV, pp.158-63, 2006.
URL : https://hal.archives-ouvertes.fr/inria-00189021

T. S. Gardner, C. R. Cantor, and J. J. Collins, Construction of a genetic toggle switch in Escherichia coli, Nature, issue.6767, pp.403339-403381, 2000.

L. Glass and S. A. Kauffman, The logical analysis of continuous, non-linear biochemical control networks, Journal of Theoretical Biology, vol.39, issue.1, pp.103-132, 1973.
DOI : 10.1016/0022-5193(73)90208-7

R. M. Gutierrez-r-´-ios, J. A. Freyre-gonzalez, O. Resendis, J. Collado-vides, M. Saier et al., 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

R. Hengge-aronis, Regulation of gene expression during entry into stationary phase, Escherichia coli and Salmonella, pp.1497-512, 1996.

G. W. Huisman, D. A. Siegele, M. M. Zambrano, and R. Kolter, Morphological and physiological changes during stationary phase, Escherichia coli and Salmonella: Cellular and Molecular Biology, pp.1672-82, 1996.

E. Klipp, B. Nordlander, R. Krüger, P. Gennemark, and S. Hohmann, Integrative model of the response of yeast to osmotic shock, Nature Biotechnology, vol.53, issue.8, pp.975-82, 2005.
DOI : 10.1016/0006-3002(58)90330-5

O. Kupferman, M. Y. Vardi, and P. Wolper, An automata-theoretic approach to branching-time model checking, Journal of the ACM, vol.47, issue.2, pp.312-60, 2000.
DOI : 10.1145/333979.333987

Z. Manna and A. Pnueli, Tools and rules for the practicing verifier, pp.125-159, 1991.

T. J. Oh, I. L. Jung, and I. G. Kim, The Escherichia coli SOS Gene sbmC Is Regulated by H-NS and RpoS during the SOS Induction and Stationary Growth Phase, Biochemical and Biophysical Research Communications, vol.288, issue.4, pp.1052-1060, 2001.
DOI : 10.1006/bbrc.2001.5872

H. Qi, R. Menzel, and Y. C. Tse-dinh, Regulation of Escherichia coli topA gene transcription: involvement of a ??s-dependent promoter, Journal of Molecular Biology, vol.267, issue.3, pp.481-490, 1997.
DOI : 10.1006/jmbi.1997.0901

D. Ropers, H. De-jong, M. Page, D. Schneider, and J. Geiselmann, Qualitative simulation of the carbon starvation response in Escherichia coli, Biosystems, vol.84, issue.2, pp.124-52, 2006.
DOI : 10.1016/j.biosystems.2005.10.005

URL : https://hal.archives-ouvertes.fr/hal-00171698

B. Schoeberl, C. Eichler-jonsson, E. Gilles, and G. Müller, Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors, Nature Biotechnology, vol.20, issue.4, pp.370-75, 2002.
DOI : 10.1038/nbt0402-370

Z. Szallazi, V. Periwal, and J. Stelling, System Modeling in Cellular Biology: From Concepts to Nuts and Bolts, 2006.
DOI : 10.7551/mitpress/9780262195485.001.0001