S. F. Altschul, T. L. Madden, A. A. Schäffer, J. Zhang, Z. Zhang et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.25-3389, 1997.
DOI : 10.1093/nar/25.17.3389

A. Aravena, C. Guziolowski, M. Ostrowski, T. Schaub, D. Eveillard et al., Deciphering regulatory relationships with a logicbased model of causality for gene expression associations, 2013.

T. L. Bailey, M. Boden, F. A. Buske, M. Frith, C. E. Grant et al., MEME SUITE: tools for motif discovery and searching, Nucleic Acids Research, vol.37, issue.Web Server, p.202, 2009.
DOI : 10.1093/nar/gkp335

C. Baral, Knowledge representation, reasoning and declarative problem solving, 2003.
DOI : 10.1017/CBO9780511543357

A. J. Butte and I. S. Kohane, MUTUAL INFORMATION RELEVANCE NETWORKS: FUNCTIONAL GENOMIC CLUSTERING USING PAIRWISE ENTROPY MEASUREMENTS, Biocomputing 2000, pp.418-447, 2000.
DOI : 10.1142/9789814447331_0040

L. Calzone, F. Fages, and S. Soliman, BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge, Bioinformatics, vol.22, issue.14, 2006.
DOI : 10.1093/bioinformatics/btl172
URL : https://hal.archives-ouvertes.fr/hal-01431364

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

G. Csardi and T. Nepusz, The igraph software package for complex network research. InterJournal , Complex Systems, p.1695, 2006.

V. Danos, J. Feret, W. Fontana, R. Harmer, J. Krivine et al., Rule-Based Modelling of Cellular Signalling, Proceedings of the 18 th International Conference on Concurrency Theory (CONCUR'07), Lecture Notes in Computer Science, pp.17-41, 2007.
DOI : 10.1007/978-3-540-74407-8_3
URL : https://hal.archives-ouvertes.fr/hal-00164297

V. Danos, J. Feret, W. Fontana, R. Harmer, J. Hayman et al., Graphs, rewriting and pathway reconstruction for rule-based models, IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science, FSTTCS 2012 Schloss Dagstuhl -Leibniz-Zentrum für Informatik, pp.276-288, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00809065

E. Davidson and M. Levin, Gene regulatory networks, Proceedings of the National Academy of Sciences of the United States of America, p.4935, 2005.

H. De-jong, J. Geiselmann, C. Hernandez, and M. Page, Genetic Network Analyzer: qualitative simulation of genetic regulatory networks, Bioinformatics, vol.19, issue.3, pp.336-344, 2003.
DOI : 10.1093/bioinformatics/btf851
URL : https://hal.archives-ouvertes.fr/inria-00072325

E. Dijkstra, A note on two problems in connexion with graphs, Numerische Mathematik, vol.4, issue.1, pp.269-271, 1959.
DOI : 10.1007/BF01386390

M. R. Garey and D. S. Johnson, Computers and Intractability (A guide to the theory of NP-completeness). W.H. Freeman and Company, 1979.

M. Gebser, R. Kaminski, M. Ostrowski, T. Schaub, and S. Thiele, On the Input Language of ASP Grounder Gringo, Logic Programming and Nonmonotonic Reasoning, pp.502-508, 2009.
DOI : 10.1007/978-3-642-04238-6_49

M. Gebser, B. Kaufmann, R. Kaminski, M. Ostrowski, T. Schaub et al., Potassco: The potsdam answer set solving collection, pp.107-124, 2011.

M. Gelfond and V. Lifschitz, The stable model semantics for logic programming, ICLP/SLP, pp.1070-1080, 1988.

M. J. Herrgård, M. W. Covert, and B. Ø. Palsson, Reconstruction of microbial transcriptional regulatory networks, Current Opinion in Biotechnology, vol.15, issue.1, pp.70-77, 2004.
DOI : 10.1016/j.copbio.2003.11.002

D. Johnson, M. Yannakakis, and C. Papadimitriou, On generating all maximal independent sets, Information Processing Letters, vol.27, issue.3, pp.119-123, 1988.
DOI : 10.1016/0020-0190(88)90065-8

R. M. Karp, Reducibility Among Combinatorial Problems, Complexity of Computer Computations, pp.85-103, 1972.
DOI : 10.1007/978-3-540-68279-0_8

L. Khachiyan, E. Boros, K. Elbassioni, V. Gurvich, and K. Makino, Enumerating disjunctions and conjunctions of paths and cuts in reliability theory, Discrete Applied Mathematics, vol.155, issue.2, pp.137-149, 2007.
DOI : 10.1016/j.dam.2006.04.032

D. Marbach, R. J. Prill, T. Schaffter, C. Mattiussi, D. Floreano et al., Revealing strengths and weaknesses of methods for gene network inference, Proceedings of the National Academy of Sciences, 2010.
DOI : 10.1073/pnas.0913357107

A. Medina-rivera, C. Abreu-goodger, M. Thomas-chollier, H. Salgado, J. Collado-vides et al., Theoretical and empirical quality assessment of transcription factor-binding motifs, Nucleic Acids Research, vol.39, issue.3, pp.808-832, 2011.
DOI : 10.1093/nar/gkq710

P. E. Meyer, K. Kontos, F. Lafitte, and G. Bontempi, Informationtheoretic inference of large transcriptional regulatory networks, EURASIP J Bioinform Syst Biol, p.79879, 2007.

R. Team, R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, 2012.

A. Streit, M. Tambalo, J. Chen, T. Grocott, M. Anwar et al., Experimental approaches for gene regulatory network construction: The chick as a model system, genesis, vol.11, issue.Suppl 10, pp.51-296, 2013.
DOI : 10.1002/dvg.22359

. Proopdb, Prokaryotic operon database, Database issue ), pp.627-658

Y. Xiao, A Tutorial on Analysis and Simulation of Boolean Gene Regulatory Network Models, Current Genomics, vol.10, issue.7, p.511, 2009.
DOI : 10.2174/138920209789208237