E. Emerson, Temporal and modal logic Handbook of Theoretical Computer Science. Volume B: Formal Models and Sematics, pp.995-1072, 1990.

S. Eker, M. Knapp, K. Laderoute, P. Lincoln, J. Meseguer et al., PATHWAY LOGIC: SYMBOLIC ANALYSIS OF BIOLOGICAL SIGNALING, Biocomputing 2002, pp.400-412, 2002.
DOI : 10.1142/9789812799623_0038

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

G. Bernot, J. P. 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

M. Calder, V. Vyshemirsky, D. Gilbert, and R. Orton, Analysis of Signalling Pathways Using Continuous Time Markov Chains, CMSB'05 Special Issue, pp.44-67, 2006.
DOI : 10.1007/11880646_3

J. Heath, M. Kwiatkowska, G. Norman, D. Parker, and O. Tymchyshyn, Probabilistic Model Checking of Complex Biological Pathways, Proc. Computational Methods in Systems Biology (CMSB'06, pp.32-47, 2006.
DOI : 10.1007/11885191_3

URL : http://doi.org/10.1016/j.tcs.2007.11.013

L. Calzone, N. Chabrier-rivier, F. Fages, and S. Soliman, Machine Learning Biochemical Networks from Temporal Logic Properties, CMSB'05 Special Issue, pp.68-94, 2006.
DOI : 10.1007/11880646_4

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=

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

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=

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

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

K. W. Kohn, Molecular Interaction Map of the Mammalian Cell Cycle Control and DNA Repair Systems, Molecular Biology of the Cell, vol.10, issue.8, pp.2703-2734, 1999.
DOI : 10.1091/mbc.10.8.2703

F. Fages and A. Rizk, On temporal logic constraint solving for analyzing numerical data time series, Theoretical Computer Science, vol.408, issue.1, pp.55-65, 2008.
DOI : 10.1016/j.tcs.2008.07.004

G. Batt, B. Yordanov, R. Weiss, and C. Belta, Robustness analysis and tuning of synthetic gene networks, Bioinformatics, vol.23, issue.18, pp.2415-2422, 2007.
DOI : 10.1093/bioinformatics/btm362

L. A. Segel, Modeling dynamic phenomena in molecular and cellular biology, 1984.

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

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

D. Gilbert, M. Heiner, and S. Lehrack, A Unifying Framework for Modelling and Analysing Biochemical Pathways Using Petri Nets, CMSB'07: Proceedings of the fifth international conference on Computational Methods in Systems Biology, 2007.
DOI : 10.1007/978-3-540-75140-3_14

H. Matsuno, A. Doi, M. Nagasaki, and S. Miyano, HYBRID PETRI NET REPRESENTATION OF GENE REGULATORY NETWORK, Biocomputing 2000, pp.338-349, 2000.
DOI : 10.1142/9789814447331_0032

C. Priami, A. Regev, W. Silverman, and E. Shapiro, Application of a stochastic name-passing calculus to representation and simulation of molecular processes, Information Processing Letters, vol.80, issue.1, pp.25-31, 2001.
DOI : 10.1016/S0020-0190(01)00214-9

A. Phillips and L. Cardelli, A correct abstract machine for the stochastic pi-calculus, Transactions on Computational Systems Biology, 2004.

D. Nickovic and O. Maler, AMT: A Property-Based Monitoring Tool for Analog Systems, Proceedings of 5th International Conference on Formal Modelling and Analysis of Times Systems, FORMATS'07, 2007.
DOI : 10.1007/978-3-540-75454-1_22

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=

H. Kitano, Towards a theory of biological robustness, Molecular Systems Biology, vol.406, p.137, 2007.
DOI : 10.1038/msb4100179

N. Hansen and A. Ostermeier, Completely Derandomized Self-Adaptation in Evolution Strategies, Evolutionary Computation, vol.9, issue.2, pp.159-195, 2001.
DOI : 10.1016/0004-3702(95)00124-7

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, 2009.
DOI : 10.1093/bioinformatics/btp200

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

F. Fages, S. Soliman, and A. Rizk, BIOCHAM v8 user's manual, INRIA, 2009.

R. Bagnara, P. M. Hill, and E. Zaffanella, The Parma Polyhedra Library: Toward a complete set of numerical abstractions for the analysis and verification of hardware and software systems, Science of Computer Programming, vol.72, issue.1-2, pp.3-21, 2008.
DOI : 10.1016/j.scico.2007.08.001

K. C. Chen, A. Csikász-nagy, B. Györffy, J. Val, B. Novàk et al., Kinetic Analysis of a Molecular Model of the Budding Yeast Cell Cycle, Molecular Biology of the Cell, vol.11, issue.1, pp.396-391, 2000.
DOI : 10.1091/mbc.11.1.369

A. Levchenko, J. Bruck, and P. W. Sternberg, Scaffold proteins may biphasically affect the levels of mitogen-activated protein kinase signaling and reduce its threshold properties, Proceedings of the National Academy of Sciences, vol.97, issue.11, pp.5818-5823, 2000.
DOI : 10.1073/pnas.97.11.5818

L. Qiao, R. B. Nachbar, I. G. Kevrekidis, and S. Y. Shvartsman, Bistability and oscillations in the huang-ferrell model of mapk signaling, PLoS Computational Biology, vol.3, pp.1819-1826, 2007.

F. Fages and S. Soliman, From Reaction Models to Influence Graphs and Back: A Theorem, Proceedings of Formal Methods in Systems Biology FMSB'08. Number 5054 in Lecture Notes in Computer Science, 2008.
DOI : 10.1007/978-3-540-68413-8_7

URL : https://hal.archives-ouvertes.fr/inria-00419921

A. C. Ventura, J. A. Sepulchre, and S. D. Merajver, A Hidden Feedback in Signaling Cascades Is Revealed, PLoS Computational Biology, vol.164, issue.3, p.1000041, 2008.
DOI : 10.1371/journal.pcbi.1000041.s007

URL : https://hal.archives-ouvertes.fr/hal-00267106

M. Kwiatkowska, G. Norman, and D. Parker, Using probabilistic model checking in systems biology, ACM SIGMETRICS Performance Evaluation Review, vol.35, issue.4, pp.14-21, 2008.
DOI : 10.1145/1364644.1364651

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=

L. De-alfaro, M. Faella, and M. Stoelinga, Linear and Branching Metrics for Quantitative Transition Systems, Proceedings of the 31st International Colloquium on Automata, Languages and Programming
DOI : 10.1007/978-3-540-27836-8_11

G. Fainekos, G. Pappas, K. Havelund, M. Núñez, G. Rosu et al., Robustness of Temporal Logic Specifications, Proceedings of the International Workshop on Formal Approaches to Software Testing and Runtime Verification, pp.178-192, 2006.
DOI : 10.1007/11940197_12

G. Fainekos and G. Pappas, Robust Sampling for MITL Specifications, Proceedings of the Fifth International Conference on Formal Modeling and Analysis of Timed Systems, FORMATS'07, pp.147-162, 2007.
DOI : 10.1007/978-3-540-75454-1_12

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=

T. Dang, A. Donze, O. Maler, and N. Shalev, Sensitive state-space exploration, 2008 47th IEEE Conference on Decision and Control, pp.4049-4054, 2008.
DOI : 10.1109/CDC.2008.4739371

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=

R. Donaldson and D. Gilbert, A Model Checking Approach to the Parameter Estimation of Biochemical Pathways, CMSB'08: Proceedings of the fourth international conference on Computational Methods in Systems Biology, pp.269-287, 2008.
DOI : 10.1007/978-3-540-88562-7_20

A. Dayarian, M. Chaves, E. Sontag, and A. Sengupta, Shape, Size, and Robustness: Feasible Regions in the Parameter Space of Biochemical Networks, PLoS Computational Biology, vol.110, issue.1, p.1000256, 2009.
DOI : 10.1371/journal.pcbi.1000256.t002