R. Alur, C. Courcoubetis, T. A. Henzinger, and P. Ho, Hybrid Automata: An Algorithmic Approach to the Specification and Verification of Hybrid Systems, in 'Hybrid Systems, pp.209-229, 1992.

R. Alur and D. L. Dill, A theory of timed automata, Theoretical Computer Science, vol.126, issue.2, pp.183-235, 1994.
DOI : 10.1016/0304-3975(94)90010-8

C. Areces and B. Ten-cate, Hybrid Logics, in 'Handbook of Modal Logics, 2006.

G. Batt, D. Ropers, H. De-jong, J. Geiselmann, R. Mateescu et al., Analysis and Verification of Qualitative Models of Genetic Regulatory Networks: A Model-Checking Approach, 'International Joint Conferences on Artificial Intelligence, pp.370-375, 2005.

J. Bengtsson and W. Yi, Timed Automata: Semantics, Algorithms and Tools, in 'Lectures on Concurrency and Petri Nets, LNCS, vol.3098, pp.87-124, 2003.

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. Cardelli and A. D. Gordon, Mobile Ambients, Foundations of Software Science and Computation Structures, pp.140-155, 1998.

F. Ciocchetta and J. Hillston, Bio-PEPA: An Extension of the Process Algebra PEPA for Biochemical Networks, Electronic Notes in Theoretical Computer Science, vol.194, issue.3, pp.103-117, 2008.
DOI : 10.1016/j.entcs.2007.12.008

M. Dam, On the decidability of process equivalences for the ??-calculus, Theoretical Computer Science, vol.183, issue.2, pp.215-228, 1997.
DOI : 10.1016/S0304-3975(96)00325-8

J. Elf and M. Ehrenberg, Spontaneous separation of bi-stable biochemical systems into spatial domains of opposite phases, Systems Biology, vol.1, issue.2, pp.230-236, 2004.
DOI : 10.1049/sb:20045021

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

M. Fränzle, C. Herde, T. Teige, S. Ratschan, and T. Schubert, Efficient Solving of Large Non-linear Arithmetic Constraint Systems with Complex Boolean Structure, J. on Satisfiability, Boolean Modeling and Computation, vol.1, pp.209-236, 2007.

J. Heath, M. Kwiatkowska, G. Norman, D. Parker, and O. Tymchyshyn, Probabilistic Model Checking of Complex Biological Pathways, TCS, vol.319, issue.3, pp.239-257, 2008.

T. A. Henzinger, P. W. Kopke, A. Puri, and P. Varaiya, What's Decidable about Hybrid Automata?, Journal of Computer and System Sciences, vol.57, issue.1, pp.94-124, 1998.
DOI : 10.1006/jcss.1998.1581

T. A. Henzinger, J. Preussig, and H. Wong-toi, Some Lessons from the HyTech Experience, in 'Conference on Decision and Control, pp.2887-2892, 2001.

M. John, R. Ewald, and A. M. Uhrmacher, A Spatial Extension to the Pi Calculus, ENTCS, vol.194, issue.3, pp.133-148, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00656206

M. John, C. Lhoussaine, J. Niehren, and A. M. Uhrmacher, The Attributed Pi Calculus, in 'Computational Methods in Systems Biology, pp.83-102, 2008.

B. N. Kholodenko, Cell-signalling dynamics in time and space, Nature Reviews Molecular Cell Biology, vol.20, issue.3, pp.165-176, 2006.
DOI : 10.1038/nrm1838

I. Letunic, R. R. Copley, B. Pils, S. Pinkert, J. Schultz et al., SMART 5: domains in the context of genomes and networks, Nucleic Acids Research, vol.34, issue.90001, pp.257-260, 2006.
DOI : 10.1093/nar/gkj079

R. Meyer, V. Khomenko, and T. Strazny, A Practical Approach to Verification of Mobile Systems Using Net Unfoldings, in 'Applications and Theory of Petri Nets, LNCS, vol.5062, pp.327-347, 2008.

T. Meyvis, S. De-smedt, P. Van-oostveldt, and J. Demeester, Fluorescence Recovery After Photobleaching: A Versatile Tool for Mobility and Interaction Measurements in Pharmaceutical Research, Pharmaceutical Research, issue.8, pp.16-1153, 1999.

R. Milner, Communicating and Mobile Systems: the Pi-Calculus, 1999.

P. Polakis, The Many Ways of Wnt in Cancer' , Current Opinion in, Genetics & Development, vol.17, issue.1, pp.45-51, 2007.

J. Quesel and A. Schäfer, Spatio-Temporal Model Checking for Mobile Real-Time Systems, in 'Theoretical Aspects of Computing, LNCS, vol.4281, pp.347-361, 2006.

A. Regev, E. M. Panina, W. Silverman, L. Cardelli, and E. Shapiro, BioAmbients: an abstraction for biological compartments, Theoretical Computer Science, vol.325, issue.1, pp.141-167, 2004.
DOI : 10.1016/j.tcs.2004.03.061

E. Rivas and S. R. Eddy, A dynamic programming algorithm for RNA structure prediction including pseudoknots11Edited by I. Tinoco, Journal of Molecular Biology, vol.285, issue.5, pp.2053-2068, 1999.
DOI : 10.1006/jmbi.1998.2436

W. C. Rounds and H. Song, The Phi-Calculus: A Language for Distributed Control of Reconfigurable Embedded Systems, in 'Hybrid Systems: Computation and Control, pp.435-449, 2003.

A. Schäfer, Axiomatisation and Decidability of Multi-dimensional Duration Calculus, 12th International Symposium on Temporal Representation and Reasoning (TIME'05), pp.25-64, 2007.
DOI : 10.1109/TIME.2005.15

K. Takahashi, N. Ishikawa, Y. Sadamoto, H. Sasamoto, S. Ohta et al., Multi-Platform E-Cell Simulation System, Cell Bioinformatics, vol.2, issue.1913, pp.1727-1729, 2003.

K. Takahashi, S. Nanda, V. Arjunan, and M. Tomita, Space in systems biology of signaling pathways - towards intracellular molecular crowding in silico, FEBS Letters, vol.20, issue.8, pp.579-1783, 2005.
DOI : 10.1016/j.febslet.2005.01.072

C. B. Thompson, Apoptosis in the pathogenesis and treatment of disease, Science, vol.267, issue.5203, pp.1456-1462, 1995.
DOI : 10.1126/science.7878464

H. Vieira, L. Caires, and R. Viegas, The Spatial Logic Model Checker User's Manual v1, 2005.

T. Zhao and R. F. Murphy, Automated learning of generative models for subcellular location: Building blocks for systems biology, Cytometry Part A, vol.85, issue.12, pp.71-978, 2007.
DOI : 10.1002/cyto.a.20487

M. Zuker, Mfold web server for nucleic acid folding and hybridization prediction, Nucleic Acids Research, vol.31, issue.13, pp.3406-3415, 2003.
DOI : 10.1093/nar/gkg595
URL : http://doi.org/10.1093/nar/gkg595