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.271-286, 2003.
DOI : 10.1385/CBB:38:3:271

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.339-347, 2004.
DOI : 10.1016/j.jtbi.2004.04.003

C. Chaouiya, H. Klaudel, and F. Pommereau, A modular, qualitative modelling of regulatory networks using petri nets

L. Calzone, F. Fages, and S. Soliman, BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge, Bioinformatics, vol.22, issue.14, pp.1805-1807, 2006.
DOI : 10.1093/bioinformatics/btl172

URL : https://hal.archives-ouvertes.fr/hal-01431364

L. Calzone, A. Gelay, A. Zinovyev, F. Radvanyi, and E. Barillot, A comprehensive imodular map of molecular interactions in RB/E2F pathway, Molecular Systems Biology, vol.4, issue.173, 2008.

N. Chabrier and F. Fages, Symbolic Model Checking of Biochemical Networks, CMSB'03: Proceedings of the first workshop on Computational Methods in Systems Biology, pp.149-162, 2003.
DOI : 10.1007/3-540-36481-1_13

C. Chaouiya, Petri net modelling of biological networks, Briefings in Bioinformatics, vol.8, issue.4, pp.210-219, 2007.
DOI : 10.1093/bib/bbm029

C. Chaouiya, A. Naldi, E. Remy, and D. Thieffry, Petri net representation of multi-valued logical regulatory graphs, Natural Computing, vol.57, issue.2
DOI : 10.1007/s11047-010-9178-0

C. Chaouiya, E. Remy, B. Mossé, and D. Thieffry, Qualitative Analysis of Regulatory Graphs: A Computational Tool Based on a Discrete Formal Framework, POSTA'03LNCIS), pp.119-126, 2003.
DOI : 10.1007/978-3-540-44928-7_17

M. Chaves, L. Tournier, and J. Gouzé, Comparison between boolean and piecewise affine differential models for genetic networks, 2009.
URL : https://hal.archives-ouvertes.fr/inria-00426414

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

P. Cousot and R. Cousot, Abstract interpretation, Proceedings of the 4th ACM SIGACT-SIGPLAN symposium on Principles of programming languages , POPL '77, pp.238-252, 1977.
DOI : 10.1145/512950.512973

URL : https://hal.archives-ouvertes.fr/inria-00528590

R. Coutinho, B. Fernandez, R. Lima, and A. Meyroneinc, Discrete time piecewise affine models of genetic regulatory networks, Journal of Mathematical Biology, vol.52, issue.4, pp.524-70, 2006.
DOI : 10.1007/s00285-005-0359-x

URL : https://hal.archives-ouvertes.fr/hal-00004809

H. De-jong, J. Gouzé, C. Hernandez, M. Page, T. Sari et al., Qualitative simulation of genetic regulatory networks using piecewise-linear models, Bulletin of Mathematical Biology, vol.66, issue.2, pp.301-341, 2004.
DOI : 10.1016/j.bulm.2003.08.010

URL : https://hal.archives-ouvertes.fr/hal-00173849

G. Didier and E. Remy, Relations between gene regulatory networks and cell dynamics in Boolean models, Discrete Applied Mathematics, vol.160, issue.15
DOI : 10.1016/j.dam.2012.05.010

URL : https://hal.archives-ouvertes.fr/hal-01258494

G. Didier, E. Remy, and C. Chaouiya, Mapping multivalued onto Boolean dynamics, Journal of Theoretical Biology, vol.270, issue.1
DOI : 10.1016/j.jtbi.2010.09.017

URL : https://hal.archives-ouvertes.fr/hal-00656334

A. Doi, S. Fujita, H. Matsuno, M. Nagasaki, and S. Miyano, Constructing biological pathway models with hybrid functional petri nets, In Silico Biology, vol.4, issue.0013, 2004.

F. Fages and S. Soliman, 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

F. Fages and S. Soliman, Formal Cell Biology in Biocham, 8th Int. School on Formal Methods for the Design of Computer, Communication and Software Systems: Computational Systems Biology SFM'08, pp.54-80, 2008.
DOI : 10.1007/978-3-540-68894-5_3

F. Fages, S. Soliman, and N. Chabrier-rivier, Modelling and querying interaction networks in the biochemical abstract machine BIOCHAM, Journal of Biological Physics and Chemistry, vol.4, issue.2, pp.64-73, 2004.
DOI : 10.4024/2040402.jbpc.04.02

URL : https://hal.archives-ouvertes.fr/hal-01431345

M. Feinberg, Mathematical aspects of mass action kinetics, Chemical Reactor Theory: A Review, pp.1-78, 1977.

D. T. Gillespie, A general method for numerically simulating the stochastic time evolution of coupled chemical reactions, Journal of Computational Physics, vol.22, issue.4, pp.403-434, 1976.
DOI : 10.1016/0021-9991(76)90041-3

L. Glass and S. Kauffman, The logical analysis of continuous, non-linear biochemical control networks, Journal of Theoretical Biology, vol.39, issue.1, pp.103-129, 1973.
DOI : 10.1016/0022-5193(73)90208-7

J. Gouzé, Positive and Negative Circuits in Dynamical Systems, Journal of Biological Systems, vol.06, issue.01, pp.11-15, 1998.
DOI : 10.1142/S0218339098000054

M. L. Guerriero, D. Prandi, C. Priami, and P. Quaglia, Process Calculi Abstractions for Biology, Algorithmic Bioprocesses, pp.463-486, 2009.
DOI : 10.1007/978-3-540-88869-7_23

P. V. Ham, How to deal with variables with more than two levels Kinetic logic: a Boolean approach to the analysis of complex regulatory systems, Lecture notes in Biomathematics, vol.29, 1979.

S. Hardy and P. Robillard, MODELING AND SIMULATION OF MOLECULAR BIOLOGY SYSTEMS USING PETRI NETS: MODELING GOALS OF VARIOUS APPROACHES, Journal of Bioinformatics and Computational Biology, vol.02, issue.04, pp.619-656, 2004.
DOI : 10.1142/S0219720004000764

M. Heiner, D. Gilbert, and R. Donaldson, Petri Nets for Systems and Synthetic Biology, In SFM, pp.215-264, 2008.
DOI : 10.1007/978-3-540-68894-5_7

W. S. Hlavacek, J. R. Faeder, M. L. Blinov, R. G. Posner, M. Hucka et al., Rules for Modeling Signal-Transduction Systems, Science Signaling, vol.2006, issue.344, p.6, 2006.
DOI : 10.1126/stke.3442006re6

M. Hucka, The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models, Bioinformatics, vol.19, issue.4, pp.524-531, 2003.
DOI : 10.1093/bioinformatics/btg015

S. Kauffman, Metabolic stability and epigenesis in randomly constructed genetic nets, Journal of Theoretical Biology, vol.22, issue.3, pp.437-67, 1969.
DOI : 10.1016/0022-5193(69)90015-0

I. Koch and M. Heiner, Biological Network Analysis, chapter Petri nets, Number 7 in Series on Bioinformatics. Wiley, pp.139-179, 2008.

L. Mendoza and I. Xenarios, A method for the generation of standardized qualitative dynamical systems of regulatory networks, Theoretical Biology and Medical Modelling, vol.3, issue.1, p.13, 2006.
DOI : 10.1186/1742-4682-3-13

A. Naldi, R. Remy, D. Thieffry, and C. Chaouiya, A reduction method for logical regulatory graphs preserving essential dynamical properties, CMSB'09: Proceedings of the seventh international conference on Computational Methods in Systems Biology, pp.266-280, 2009.

A. Naldi, D. Thieffry, and C. Chaouiya, Decision diagrams for the representation of logical models of regulatory networks, CMSB'07, pp.233-247, 2007.

A. Polynikis, S. J. Hogan, and M. Bernardo, Comparing different ODE modelling approaches for gene regulatory networks, Journal of Theoretical Biology, vol.261, issue.4, pp.511-541, 2009.
DOI : 10.1016/j.jtbi.2009.07.040

URL : https://hal.archives-ouvertes.fr/hal-00554639

V. N. Reddy, M. L. Mavrovouniotis, and M. N. Liebman, Petri net representations in metabolic pathways, Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology (ISMB), pp.328-336, 1993.

A. Regev, W. Silverman, and E. Y. Shapiro, Representation and simulation of biochemical processes using the pi-calculus process algebra, Proceedings of the sixth Pacific Symposium of Biocomputing, pp.459-470, 2001.

E. Remy and P. Ruet, From minimal signed circuits to the dynamics of Boolean regulatory networks, Bioinformatics, vol.24, issue.16, pp.220-226, 2008.
DOI : 10.1093/bioinformatics/btn287

URL : https://hal.archives-ouvertes.fr/hal-01306956

A. Rizk, G. Batt, F. Fages, and S. Soliman, A general computational method for robustness analysis with applications to synthetic gene networks, Bioinformatics, vol.25, issue.12, pp.69-78, 2009.
DOI : 10.1093/bioinformatics/btp200

URL : https://hal.archives-ouvertes.fr/inria-00419708

D. Ropers, V. Baldazzi, H. De, and J. , Model reduction using piecewiselinear approximations preserves dynamic properties of the carbon starvation response in escherichia coli, IEEE/ACM Transactions on Computational Biology and Bioinformatics, p.99, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00793034

E. Snoussi, Qualitative dynamis of piecewise-linear differential equations: a discrete mapping approach, Dyn Stab Syst, vol.4, pp.189-207, 1989.

E. Snoussi and R. Thomas, Logical identification of all steady states: The concept of feedback loop characteristic states, Bulletin of Mathematical Biology, vol.55, issue.5, pp.973-91, 1993.
DOI : 10.1016/S0092-8240(05)80199-5

E. Snoussi, R. Thomas, and R. D. Ari, Generalized kinetic logics, chapter 7, 1990.

E. H. Snoussi, Necessary Conditions for Multistationarity and Stable Periodicity, Journal of Biological Systems, vol.06, issue.01, pp.3-9, 1998.
DOI : 10.1142/S0218339098000042

S. Soliman and M. Heiner, A Unique Transformation from Ordinary Differential Equations to Reaction Networks, PLoS ONE, vol.482, issue.12
DOI : 10.1371/journal.pone.0014284.g007

URL : https://hal.archives-ouvertes.fr/hal-01431261

C. Soulé, Graphic Requirements for Multistationarity, Complexus, vol.1, issue.3, pp.123-133, 2003.
DOI : 10.1159/000076100

R. Srivastava, M. S. Peterson, and W. E. Bentley, Stochastic kinetic analysis of theEscherichia coli stress circuit using ?32-targeted antisense, Biotechnology and Bioengineering, vol.47, issue.1, pp.120-129, 2001.
DOI : 10.1002/bit.1171

M. Sugita, Functional analysis of chemical systems in vivo using a logical circuit equivalent, J Theor Biol, vol.1, pp.415-445, 1961.

D. Thieffry, Dynamical roles of biological regulatory circuits, Briefings in Bioinformatics, vol.8, issue.4, pp.220-225, 2007.
DOI : 10.1093/bib/bbm028

D. Thieffry and R. Thomas, Dynamical behaviour of biological regulatory networks, ii. immunity control in bacteriophage lambda, Bul. Math. Biol, vol.57, issue.2, pp.277-297, 1995.

R. Thomas, Boolean formalisation of genetic control circuits, J. Theor. Biol, vol.42, pp.565-583, 1973.

R. Thomas, Regulatory networks seen as asynchronous automata: A logical description, Journal of Theoretical Biology, vol.153, issue.1, pp.1-23, 1991.
DOI : 10.1016/S0022-5193(05)80350-9

R. Thomas and R. D. Ari, Biological Feedback, 1990.
URL : https://hal.archives-ouvertes.fr/hal-00087681

D. M. Wittmann, J. Krumsiek, J. Saez-rodriguez, D. A. Lauffenburger, S. Klamt et al., Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling, BMC Systems Biology, vol.3, issue.1, p.98, 2009.
DOI : 10.1186/1752-0509-3-98