N. Angelopoulos and S. H. Muggleton, Machine learning metabolic pathway descriptions using a probabilistic relational representation, Proceedings of Machine Intelligence, 2002.

N. Angelopoulos and S. H. Muggleton, Slps for probabilistic pathways : Modeling and parameter estimation, 2002.

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. Bergamini, H. De-jong, H. Garavel, and R. Mateescu, Model Checking Genetic Regulatory Networks Using GNA and CADP, Proceedings of the 11th International SPIN Workshop on Model Checking of Software SPIN, 2004.
DOI : 10.1007/978-3-540-24732-6_12

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. H. Bryant, S. H. Muggleton, S. G. Oliver, D. B. Kell, P. G. Reiser et al., Combining inductive logic programming, active learning and robotics to discover the function of genes, Electronic Transactions in Artificial Intelligence, vol.6, issue.12, 2001.

L. Calzone, N. Chabrier-rivier, F. Fages, L. Gentils, and S. Soliman, Machine learning bio-molecular interactions from temporal logic properties, CMSB'05 : Proceedings of the third Workshop on Computational Methods in Systems Biology, 2005.
DOI : 10.1007/11880646_4
URL : https://hal.archives-ouvertes.fr/inria-00000117

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

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

N. Chabrier-rivier, F. Fages, and S. Soliman, The Biochemical Abstract Machine BIOCHAM, CMSB'04 : Proceedings of the second Workshop on Computational Methods in Systems Biology, pp.172-191, 2004.
DOI : 10.1007/BF03037227
URL : https://hal.archives-ouvertes.fr/inria-00000814

N. Chabrier-rivier, F. Fages, S. Soliman, and L. Calzone, Learning transition rules from temporal logic properties, Research Report, vol.5543, 2005.
URL : https://hal.archives-ouvertes.fr/inria-00070464

A. Cimatti, E. Clarke, F. G. Enrico-giunchiglia, M. Pistore, M. Roveri et al., NuSMV 2: An OpenSource Tool for Symbolic Model Checking, Proceedings of the International Conference on Computer-Aided Verification, CAV'02, 2002.
DOI : 10.1007/3-540-45657-0_29

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

L. De-raedt, Interactive Theory Revision, an inductive Logic Programming Approach. Knowledge-Based Systems. academic press, 1992.

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

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

G. Giaever, Functional profiling of the Saccharomyces cerevisiae genome, Nature, vol.57, issue.6896, pp.387-391, 2002.
DOI : 10.1073/pnas.95.25.14863

M. Kanehisa and S. Goto, KEGG: Kyoto Encyclopedia of Genes and Genomes, Nucleic Acids Research, vol.28, issue.1, pp.27-30, 2000.
DOI : 10.1093/nar/28.1.27

I. M. Keseler, J. Collado-vides, S. Gama-castro, J. Ingraham, S. Paley et al., EcoCyc: a comprehensive database resource for Escherichia coli, Nucleic Acids Research, vol.33, issue.Database issue, pp.334-337, 2005.
DOI : 10.1093/nar/gki108

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.703-2734, 1999.
DOI : 10.1091/mbc.10.8.2703

J. R. Koza, W. Mydlowec, G. Lanza, J. Yu, and M. A. Keane, REVERSE ENGINEERING OF METABOLIC PATHWAYS FROM OBSERVED DATA USING GENETIC PROGRAMMING, Biocomputing 2001, pp.434-445, 2001.
DOI : 10.1142/9789814447362_0043

P. Langley, H. A. Simon, G. L. Bradshaw, and J. M. Zytkow, Scientific Discovery : Computational Explorations of the Creative Processes, 1987.

R. Mardare and C. Priami, Logical analysis of biological systems, Fundamenta Informaticae, vol.64, pp.271-285, 2005.

S. H. Muggleton, Inverse entailment and progol, New Generation Computing, vol.12, issue.1, pp.245-286, 1995.
DOI : 10.1007/BF03037227
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.31.1630

L. Todorovski and S. D?eroski, Theory Revision in Equation Discovery, Proceedings of the 4th International Conference on Discovery Science, pp.389-400, 2001.
DOI : 10.1007/3-540-45650-3_33

M. Tomita, The E-CELL project, Proceedings of the fourth annual international conference on Computational molecular biology , RECOMB '00, pp.1-12, 2000.
DOI : 10.1145/332306.332567

E. Vbi and . Research, COPASI's manual