A. Zanzoni, L. Montecchi-palazzi, M. Quondam, G. Ausiello, and M. Helmer-citterich, MINT: a Molecular INTeraction database, FEBS Letters, vol.28, issue.1, pp.135-175, 2002.
DOI : 10.1016/S0014-5793(01)03293-8

H. Hermjakob, L. Montecchi-palazzi, C. Lewington, S. Mudali, and S. Kerrien, IntAct: an open source molecular interaction database, Nucleic Acids Research, vol.32, issue.90001, pp.452-457, 2004.
DOI : 10.1093/nar/gkh052

URL : https://hal.archives-ouvertes.fr/hal-00306577

S. Peri, J. Navarro, T. Kristiansen, R. Amanchy, and V. Surendranath, Human protein reference database as a discovery resource for proteomics, Nucleic Acids Research, vol.32, issue.90001, pp.497-501, 2004.
DOI : 10.1093/nar/gkh070

M. Kanehisa, S. Goto, S. Kawashima, Y. Okuno, and M. Hattori, The KEGG resource for deciphering the genome, Nucleic Acids Research, vol.32, issue.90001, pp.277-80, 2004.
DOI : 10.1093/nar/gkh063

. Ingenuity-systems, Ingenuity pathways knowledge base, Avalaible, 1998.

H. Salgado, S. Gama-castro, M. Peralta-gil, E. Diaz-peredo, and F. Sanchez-solano, RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions, Nucleic Acids Research, vol.34, issue.90001, pp.394-401, 2006.
DOI : 10.1093/nar/gkj156

T. Reguly, A. Breitkreutz, L. Boucher, B. Breitkreutz, and G. Hon, Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae, Journal of Biology, vol.5, issue.4, p.11, 2006.
DOI : 10.1186/jbiol36

A. Joyce and B. Palsson, The model organism as a system: integrating 'omics' data sets, Nature Reviews Molecular Cell Biology, vol.103, issue.3, pp.198-210, 2006.
DOI : 10.1038/nrm1857

J. Faith, B. Hayete, J. Thaden, I. Mogno, and J. Wierzbowski, Largescale mapping and validation of escherichia coli transcriptional regulation from a compendium of expression profiles, PLoS Biology, vol.5, 2007.

M. Bansal, V. Belcastro, A. Ambesi-impiombato, and D. Di-bernardo, How to infer gene networks from expression profiles, Mol Syst Biol, vol.3, 2007.

T. Lee, N. Rinaldi, F. Robert, D. Odom, and Z. Bar-joseph, Transcriptional Regulatory Networks in Saccharomyces cerevisiae, Transcriptional regulatory networks in Saccharomyces cerevisiae, pp.799-804, 2002.
DOI : 10.1126/science.1075090

C. Harbison, D. Gordon, T. Lee, N. Rinaldi, and K. Macisaac, Transcriptional regulatory code of a eukaryotic genome, Nature, vol.18, issue.7004, pp.99-104, 2004.
DOI : 10.1093/bioinformatics/15.7.607

K. Macisaac, T. Wang, D. Gordon, D. Gifford, and G. Stormo, An improved map of conserved regulatory sites for Saccharomyces cerevisiae, BMC Bioinformatics, vol.7, issue.1, p.113, 2006.
DOI : 10.1186/1471-2105-7-113

B. Xing and M. Van-der-laan, A causal inference approach for constructing transcriptional regulatory networks, Bioinformatics, vol.21, issue.21, pp.4007-4020, 2005.
DOI : 10.1093/bioinformatics/bti648

E. Segal, M. Shapira, A. Regev, D. Pe-'er, and D. Botstein, Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data, Nature Genetics, vol.291, issue.2, pp.166-76, 2003.
DOI : 10.1038/35057062

N. Nariai, Y. Tamada, S. Imoto, and S. Miyano, Estimating gene regulatory networks and protein-protein interactions of Saccharomyces cerevisiae from multiple genome-wide data, Bioinformatics, vol.21, issue.Suppl 2, pp.206-212, 2005.
DOI : 10.1093/bioinformatics/bti1133

F. Ferrazzi, P. Magni, L. Sacchi, A. Nuzzo, and U. Petrovic, Inferring gene regulatory networks by integrating static and dynamic data, International Journal of Medical Informatics, vol.76, 2007.
DOI : 10.1016/j.ijmedinf.2007.07.005

S. B. Eils and R. , Inferring genetic regulatory logic from expression data, Bioinformatics, vol.21, pp.2706-2719, 2005.

T. Ideker, A Systems Approach to Discovering Signaling and Regulatory Pathways ???or, how to digest large interaction networks into relevant pieces, Adv Exp Med Biol, vol.547, pp.21-30, 2004.
DOI : 10.1007/978-1-4419-8861-4_3

C. Yeang, H. Mak, S. Mccuine, C. Workman, and T. Jaakkola, Validation and refinement of gene-regulatory pathways on a network of physical interactions, 2005.

R. Gutierrez-rios, D. Rosenblueth, J. Loza, A. Huerta, and J. Glasner, Regulatory Network of Escherichia coli: Consistency Between Literature Knowledge and Microarray Profiles, Genome Research, vol.13, issue.11, pp.2435-2443, 2003.
DOI : 10.1101/gr.1387003

C. Yeang, T. Ideker, and T. Jaakkola, Physical Network Models, Journal of Computational Biology, vol.11, issue.2-3, pp.243-62, 2004.
DOI : 10.1089/1066527041410382

O. Radulescu, S. Lagarrigue, A. Siegel, P. Veber, and M. Borgne, Topology and static response of interaction networks in molecular biology, Journal of The Royal Society Interface, vol.84, issue.5, pp.185-96, 2006.
DOI : 10.1002/sim.1237

URL : https://hal.archives-ouvertes.fr/inria-00178842

A. Siegel, O. Radulescu, M. Borgne, P. Veber, and J. Ouy, Qualitative analysis of the relation between DNA microarray data and behavioral models of regulation networks, Biosystems, vol.84, issue.2, pp.153-74, 2006.
DOI : 10.1016/j.biosystems.2005.10.006

URL : https://hal.archives-ouvertes.fr/inria-00178809

P. Veber, M. Borgne, A. Siegel, S. Lagarrique, and O. Radulescu, Complex Qualitative Models in Biology: A New Approach, Complexus, vol.2, issue.3-4, pp.140-151, 2004.
DOI : 10.1159/000093686

URL : https://hal.archives-ouvertes.fr/inria-00178819

C. Guziolowski, P. Veber, M. Borgne, O. Radulescu, and A. Siegel, Checking consistency between expression data and large scale regulatory networks: a case study, Journal of Biological Physics and Chemistry, vol.7, issue.2, 2007.
DOI : 10.4024/20701.jbpc.07.02

URL : https://hal.archives-ouvertes.fr/inria-00145537

A. Gasch, P. Spellman, C. Kao, O. Eisen, and M. , Genomic Expression Programs in the Response of Yeast Cells to Environmental Changes, Molecular Biology of the Cell, vol.11, issue.12, pp.4241-57, 2000.
DOI : 10.1091/mbc.11.12.4241

G. Roberts and A. Hudson, Transcriptome profiling of Saccharomyces cerevisiae during a transition from fermentative to glycerol-based respiratory growth reveals extensive metabolic and structural remodeling, Molecular Genetics and Genomics, vol.4, issue.2, pp.170-86, 2006.
DOI : 10.1007/s00438-006-0133-9

J. Derisi, V. Iyer, and P. Brown, Exploring the Metabolic and Genetic Control of Gene Expression on a Genomic Scale, Science, vol.278, issue.5338, pp.680-686, 1997.
DOI : 10.1126/science.278.5338.680

S. Kauffman, C. Peterson, B. Samuelsson, and C. Troein, Random Boolean network models and the yeast transcriptional network, Proceedings of the National Academy of Sciences, vol.100, issue.25, pp.14796-14805, 2003.
DOI : 10.1073/pnas.2036429100

H. De-jong, Modeling and Simulation of Genetic Regulatory Systems: A Literature Review, Journal of Computational Biology, vol.9, issue.1, pp.67-103, 2002.
DOI : 10.1089/10665270252833208

S. Chu, J. Derisi, M. Eisen, J. Mulholland, and D. Botstein, The Transcriptional Program of Sporulation in Budding Yeast, Science, vol.282, issue.5389, pp.699-705, 1998.
DOI : 10.1126/science.282.5389.699

P. Sudarsanam, V. Iyer, P. Brown, and F. Winston, Whole-genome expression analysis of snf/swi mutants of Saccharomyces cerevisiae, Proceedings of the National Academy of Sciences, vol.97, issue.7, pp.3364-3373, 2000.
DOI : 10.1073/pnas.97.7.3364

N. Ogawa, J. Derisi, and P. Brown, New Components of a System for Phosphate Accumulation and Polyphosphate Metabolism in Saccharomyces cerevisiae Revealed by Genomic Expression Analysis, Molecular Biology of the Cell, vol.11, issue.12, pp.4309-4330, 2000.
DOI : 10.1091/mbc.11.12.4309

A. Gasch, M. Huang, S. Metzner, D. Botstein, and S. Elledge, Genomic Expression Responses to DNA-damaging Agents and the Regulatory Role of the Yeast ATR Homolog Mec1p, Molecular Biology of the Cell, vol.12, issue.10, pp.2987-3003, 2001.
DOI : 10.1091/mbc.12.10.2987

P. Cullen, W. Sabbagh, E. Graham, M. Irick, and E. Van-olden, A signaling mucin at the head of the Cdc42- and MAPK-dependent filamentous growth pathway in yeast, Genes & Development, vol.18, issue.14, pp.1695-708, 2004.
DOI : 10.1101/gad.1178604

S. Mnaimneh, A. Davierwala, J. Haynes, J. Moffat, and W. Peng, Exploration of Essential Gene Functions via Titratable Promoter Alleles, Cell, vol.118, issue.1, pp.31-44, 2004.
DOI : 10.1016/j.cell.2004.06.013

E. Hong, R. Balakrishnan, K. Christie, M. Costanzo, and S. Dwight, Saccharomyces genome database, Avalaible, 2001.

T. Hughes, M. Marton, A. Jones, C. Roberts, and R. Stoughton, Functional Discovery via a Compendium of Expression Profiles, Cell, vol.102, issue.1, pp.109-126, 2000.
DOI : 10.1016/S0092-8674(00)00015-5

N. Guelzim, N. Bottani, S. Bourgine, and P. , Topological and causal structure of the yeast transcriptional regulatory network, Nature Genetics, vol.31, issue.1, pp.60-63, 2002.
DOI : 10.1038/ng873

P. Shannon, A. Markiel, O. Ozier, N. Baliga, and J. Wang, Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks, Genome Research, vol.13, issue.11, 2003.
DOI : 10.1101/gr.1239303

A. Margolin, I. Nemenman, K. Basso, C. Wiggins, and G. Stolovitzky, ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context, BMC Bioinformatics, vol.7, issue.Suppl 1, p.7, 2006.
DOI : 10.1186/1471-2105-7-S1-S7

N. Friedman, M. Linial, I. Nachman, and D. Pe-'er, Using Bayesian Networks to Analyze Expression Data, Journal of Computational Biology, vol.7, issue.3-4, pp.601-621, 2000.
DOI : 10.1089/106652700750050961

D. Bernardo, D. Thomson, M. Gardner, T. Chobot, S. Eastwood et al., Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks, Nature Biotechnology, vol.176, issue.3, pp.377-383, 2005.
DOI : 10.1126/science.1088697

M. Bansal, D. Gatta, G. Di-bernardo, and D. , Inference of gene regulatory networks and compound mode of action from time course gene expression profiles, Bioinformatics, vol.22, issue.7, pp.815-822, 2006.
DOI : 10.1093/bioinformatics/btl003

R. Bryan, Graph-based algorithm for boolean function manipulation, IEEE Transactions on Computers, vol.8, pp.677-691, 1986.

M. Gebser, B. Kaufmann, A. Neumann, and T. Schaub, clasp: A Conflict-Driven Answer Set Solver, Ninth International Conference on Logic Programming and Nonmonotonic Reasoning, p.17, 2007.
DOI : 10.1007/978-3-540-72200-7_23

M. Giraud, D. Veber, and . Lavenier, Inferring the role of transcription factors in regulatory networks, Path-Equivalent Developments in Acyclic Weighted Automata, 2007.

?. Yanev, . Veber, S. Andonov, and . Balev, Lagrangian approaches for a class of matching problems in computational biology, Computers & Mathematics with Applications, vol.55, issue.5, pp.1054-1067, 2006.
DOI : 10.1016/j.camwa.2006.12.103

URL : https://hal.archives-ouvertes.fr/inria-00335126

O. Siegel, . Radulescu, . Le-borgne, . Veber, S. Ouy et al., Qualitative analysis of the relation between DNA microarray data and behavioral models of regulation networks, Biosystems, vol.84, issue.2, pp.153-174, 2006.
DOI : 10.1016/j.biosystems.2005.10.006

URL : https://hal.archives-ouvertes.fr/inria-00178809

?. O-radulescu, . Laguarrigue, . Siegel, P. Le-borgne, and . Veber, Topology and static response of interaction networks in molecular biology, Journal of The Royal Society Interface, vol.84, issue.5, pp.185-196, 2006.
DOI : 10.1002/sim.1237

?. Andonov, . Lavenier, N. Veber, and . Yanev, Dynamic programming for LR-PCR segmentation of bacterium genomes Concurrency and Computations : Practice and Experience, pp.1657-1668, 2005.

?. N. Zakour, M. Gautier, R. Andonov, D. Lavenier, M. Cochet et al., GenoFrag: software to design primers optimized for whole genome scanning by long-range PCR amplification, Nucleic Acids Research, vol.32, issue.1, pp.17-24, 2004.
DOI : 10.1093/nar/gkg928

URL : https://hal.archives-ouvertes.fr/hal-01454461

?. Veber, . Yanev, V. Andonov, and . Poirriez, Optimal Protein Threading by Cost-Splitting, 5th Workshop on Algorithms in Bioinformatics -WABI, 2005.
DOI : 10.1007/11557067_30

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.503.295

?. Veber, L. Borgne, O. Siegel, and . Radulescu, Complex Qualitative Models in Biology: A New Approach, European Conference on Complex Systems - ECCS'05, 2005.
DOI : 10.1159/000093686

URL : https://hal.archives-ouvertes.fr/inria-00178819

?. Conférences-nationales, . Veber, . Tempel, . Lavenier, . Andonov et al., Détection de domaines dans des séquences génomiques : unprobì eme de couverture optimale ROADEF'07, 2007.

?. Guziolowski, . Veber, . Le-borgne, . Radulescu, and . Siegel, Checking consistency between expression data and large scale regulatory networks: a case study, Journal of Biological Physics and Chemistry, vol.7, issue.2, 2006.
DOI : 10.4024/20701.jbpc.07.02

URL : https://hal.archives-ouvertes.fr/inria-00145537

?. Bastide, L. Lagarrigue, . Borgne, . Siegel, . Veber et al., Une méthodologie pour l'analyse qualitative des réseaux biologiques : De la base de donnéesdonnéesà la vérification formelle JOBIM 2005, poster session Bibliographie [1] Konstantin Andreev and Harald Räcke. Balanced graph partitioning, SPAA '04 : Proceedings of the sixteenth annual ACM symposium on Parallelism in algorithms and architectures, pp.120-124, 2004.

D. Angeli and E. D. Sontag, Monotone control systems, IEEE Transactions on Automatic Control, vol.48, issue.10, pp.1684-1698, 2003.
DOI : 10.1109/TAC.2003.817920

URL : http://arxiv.org/abs/math/0206133

M. Aviv, . Giladi, A. Schreiber, G. Oppenheim, and . Glaser, Expression of the genes coding for the Escherichia coli integration host factor are controlled by growth phase, rpoS, ppGpp and by autoregulation, Molecular Microbiology, vol.13, issue.5, pp.1021-1031, 1994.
DOI : 10.1016/0378-1119(92)90026-L

V. Balke and J. Gralla, Changes in the linking number of supercoiled DNA accompany growth transitions in Escherichia coli., Journal of Bacteriology, vol.169, issue.10, pp.4499-4506, 1987.
DOI : 10.1128/jb.169.10.4499-4506.1987

M. Bansal, V. Belcastro, A. Ambesi-impiombato, and D. D. Bernardo, How to infer gene networks from expression profiles, Mol Syst Biol, vol.3, p.78, 2007.

M. Bansal, G. D. Gatta, and D. D. Bernardo, Inference of gene regulatory networks and compound mode of action from time course gene expression profiles, Bioinformatics, vol.22, issue.7, pp.815-822, 2006.
DOI : 10.1093/bioinformatics/btl003

Z. Bar-joseph, S. Farkash, K. David, I. Gifford, R. Simon et al., Deconvolving cell cycle expression data with complementary information, Bioinformatics, vol.20, issue.Suppl 1, pp.23-30, 2004.
DOI : 10.1093/bioinformatics/bth915

URL : http://repository.cmu.edu/cgi/viewcontent.cgi?article=2311&context=compsci

T. Barrett, B. Dennis, . Troup, E. Stephen, P. Wilhite et al., NCBI GEO: mining tens of millions of expression profiles--database and tools update, Nucleic Acids Research, vol.35, issue.Database, pp.760-765, 2007.
DOI : 10.1093/nar/gkl887

A. Barrier, A. Lemoine, P. Boelle, C. Tse, D. Brault et al., Colon cancer prognosis prediction by gene expression profiling, Oncogene, vol.9, issue.40, pp.246155-6164, 2005.
DOI : 10.1038/sj.onc.1205613

G. Batt, D. Ropers, J. Hidde-de-jong, R. Geiselmann, P. 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

R. Bonneau, J. David, P. Reiss, M. Shannon, L. Facciotti et al., The Inferelator : an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo

P. Brazhnik, Inferring gene networks from steady-state response to single-gene perturbations, Journal of Theoretical Biology, vol.237, issue.4, pp.427-440, 2005.
DOI : 10.1016/j.jtbi.2005.04.027

R. Bryan, Graph-based algorithm for boolean function manipulation, IEEE Transactions on Computers, vol.8, pp.677-691, 1986.

S. Bulashevska and R. Eils, Inferring genetic regulatory logic from expression data, Bioinformatics, vol.21, issue.11, pp.2706-2713, 2005.
DOI : 10.1093/bioinformatics/bti388

URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/21/11/2706

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

M. Chaves, R. Albert, and E. D. Sontag, Robustness and fragility of Boolean models for genetic regulatory networks, Journal of Theoretical Biology, vol.235, issue.3, pp.431-449, 2005.
DOI : 10.1016/j.jtbi.2005.01.023

M. Chaves, T. Eissing, and F. Allgöwer, Identifying mechanisms for bistability in an apoptosis network. In Réseaux d'interaction : analyse, modélisation et simulation, RIAMS'06, 2006.

V. Chickarmane, C. Troein, A. Ulrike, . Nuber, M. Herbert et al., Transcriptional Dynamics of the Embryonic Stem Cell Switch, PLoS Computational Biology, vol.30, issue.9, p.123, 2006.
DOI : 10.1371/journal.pcbi.0020123.sd001

G. Ontology and C. , The Gene Ontology (GO) project in 2006, Nucleic Acids Res, vol.34, pp.322-326, 2006.

G. A. Bhaskar-dasgupta, E. D. Enciso, Y. Sontag, and . Zhang, Algorithmic and Complexity Results for Decompositions of Biological Networks into Monotone Subsystems, Lecture Notes in Computer Science, vol.4007, pp.253-264, 2006.
DOI : 10.1007/11764298_23

J. Hidde-de-jong, G. Geiselmann, C. Batt, M. Hernandez, and . Page, Qualitative simulation of the initiation of sporulation in bacillus subtilis, Bulletin of Mathematical Biology, vol.66, issue.2, pp.261-300, 2004.

J. Hidde-de-jong, C. Gouze, M. Hernandez, T. Page, J. Sari et al., Qualitative simulation of genetic regulatory networks using piecewise-linear models, Bull Math Biol, vol.66, issue.2, pp.301-340, 2004.

J. Hidde-de-jong, C. Gouzé, M. Hernandez, T. Page, J. Sari et al., Qualitative simulation of genetic regulatory networks using piecewise-linear models, Bulletin of Mathematical Biology, vol.66, pp.301-340, 2004.

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, Consistency of clark's completion and existence of stable models, 1992.

J. J. Faith, B. Hayete, J. T. Thaden, I. Mogno, J. Wierzbowski et al., Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles, PLoS Biology, vol.280, issue.1, 2007.
DOI : 10.1371/journal.pbio.0050008.sd001

D. Fell, Understanding the Control of Metabolism, 1997.

N. Friedman, . Linial, D. Nachman, and . Pe-'er, Using Bayesian Networks to Analyze Expression Data, Journal of Computational Biology, vol.7, issue.3-4, pp.601-621, 2000.
DOI : 10.1089/106652700750050961

S. Timothy, D. Gardner, D. Di-bernardo, J. J. Lorenz, and . Collins, Inferring genetic networks and identifying compound mode of action via expression profiling, Science, vol.301, issue.5629, pp.102-105, 2003.

M. Gebser and B. Kaufmann, André Neumann, and Torsten Schaub. clasp : A conflict-driven answer set solver, LPNMR, pp.260-265, 2007.

M. Gelfond and V. Lifschitz, The stable model semantics for logic programming, Proceedings of the Fifth International Conference on Logic Programming, pp.1070-1080, 1988.

M. Gelfond and V. Lifschitz, Classical negation in logic programs and disjunctive databases, New Generation Computing, vol.38, issue.No. 3, pp.365-386, 1991.
DOI : 10.1007/BF03037169

N. Guelzim, S. Bottani, P. Bourgine, and F. Képès, Topological and causal structure of the yeast transcriptional regulatory network, Nature Genetics, vol.31, issue.1, pp.60-63, 2002.
DOI : 10.1038/ng873

R. Maria-gutierrez-rios, A. David, J. A. Rosenblueth, A. M. Loza, J. D. Huerta et al., Regulatory Network of Escherichia coli: Consistency Between Literature Knowledge and Microarray Profiles, Genome Research, vol.13, issue.11, pp.2435-2443, 2003.
DOI : 10.1101/gr.1387003

H. Salgado, A. Santos-zavaleta, S. Gama-castro, M. Peralta-gil, M. Penaloza-spinola et al., The comprehensive updated regulatory network of Escherichia coli K-12, BMC Bioinformatics, vol.7, issue.1, p.5, 2006.
DOI : 10.1186/1471-2105-7-5

K. Heidtke and S. Schulze-kremer, Design and implementation of a qualitative simulation model of lambda phage infection, Bioinformatics, vol.14, issue.1, pp.81-91, 1998.
DOI : 10.1093/bioinformatics/14.1.81

R. Heinrich and S. Schuster, The Regulation of Cellular Systems, 1996.
DOI : 10.1007/978-1-4613-1161-4

H. Hermjakob, L. Montecchi-palazzi, C. Lewington, S. Mudali, S. Kerrien et al., IntAct: an open source molecular interaction database, Nucleic Acids Research, vol.32, issue.90001, pp.32-452, 2004.
DOI : 10.1093/nar/gkh052

URL : https://hal.archives-ouvertes.fr/hal-00306577

A. Hinkkanen, K. R. Lang, and A. B. Whinston, A Set-Theoretical Foundation of Qualitative Reasoning and its Application to the Modeling of Economics and Business Management Problems, Information Systems Frontiers, vol.5, issue.4, pp.379-399, 2003.
DOI : 10.1023/B:ISFI.0000005652.72048.4d

B. Holst, L. Sogaard-andersen, H. Pedersen, and P. Valentin-hansen, The cAMP- CRP/CytR nucleoprotein complex in Escherichia coli : two pairs of closely linked binding sites for the cAMP-CRP activator complex are involved in combinatorial regulation of the cdd promoter, EMBO J, issue.10, pp.113635-3643, 1992.

C. Huang and J. Ferrell, Ultrasensitivity in the mitogen-activated protein kinase cascade., Proceedings of the National Academy of Sciences, vol.93, issue.19, pp.10078-10083, 1996.
DOI : 10.1073/pnas.93.19.10078

P. John, B. Huelsenbeck, . Larget, E. Michael, and . Alfaro, Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo, Mol Biol Evol, vol.21, issue.6, pp.1123-1133, 2004.

T. Hughes, M. Marton, A. Jones, C. Roberts, R. Stoughton et al., Functional Discovery via a Compendium of Expression Profiles, Cell, vol.102, issue.1, pp.109-126, 2000.
DOI : 10.1016/S0092-8674(00)00015-5

. Ingenuity-systems, Ingenuity pathways knowledge base Avalaible : http :// www.ingenuity.com, 1998.

A. Ishihama, RNA Polymerase, Annual Review of Microbiology, vol.54, issue.1, pp.499-518, 2000.
DOI : 10.1146/annurev.micro.54.1.499

R. Andrew, . Joyce, O. Bernhard, and . Palsson, The model organism as a system : integrating 'omics' data sets, Nat Rev Mol Cell Biol, vol.7, issue.3, pp.198-210, 2006.

N. Kaminski and N. Friedman, Practical Approaches to Analyzing Results of Microarray Experiments, American Journal of Respiratory Cell and Molecular Biology, vol.27, issue.2, pp.125-132, 2002.
DOI : 10.1165/ajrcmb.27.2.f247

M. Kanehisa, S. Goto, S. Kawashima, Y. Okuno, and M. Hattori, The KEGG resource for deciphering the genome, Nucleic Acids Research, vol.32, issue.90001, pp.277-80, 2004.
DOI : 10.1093/nar/gkh063

M. Kaufman, C. Soule, and R. Thomas, A new necessary condition on interaction graphs for multistationarity, Journal of Theoretical Biology, vol.248, issue.4, pp.675-685, 2007.
DOI : 10.1016/j.jtbi.2007.06.016

N. Boris and . Kholodenko, Cell-signalling dynamics in time and space, Nat Rev Mol Cell Biol, vol.7, issue.3, pp.165-176, 2006.

N. Boris, A. Kholodenko, . Kiyatkin, J. Frank, E. D. Bruggeman et al., Untangling the wires : a strategy to trace functional interactions in signaling and gene networks, Proc Natl Acad Sci U S A, issue.20, pp.9912841-12846, 2002.

K. 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

B. J. Kuipers, Qualitative reasoning. Mdeling and simulation with incomplete knowledge, 1994.

A. Kundaje, M. Middendorf, M. Shah, C. H. Wiggins, Y. Freund et al., A classification-based framework for predicting and analyzing gene regulatory response, BMC Bioinformatics, vol.7, issue.Suppl 1, p.5, 2006.
DOI : 10.1186/1471-2105-7-S1-S5

N. Leone, G. Pfeifer, W. Faber, T. Eiter, G. Gottlob et al., The DLV system for knowledge representation and reasoning, ACM Transactions on Computational Logic, vol.7, issue.3, pp.499-562, 2006.
DOI : 10.1145/1149114.1149117

C. James, R. Liao, Y. Boscolo, L. M. Yang, C. Tran et al., Network component analysis : reconstruction of regulatory signals in biological systems, Proc Natl Acad Sci U S A, vol.100, issue.26, pp.15522-15527, 2003.

Y. Lierler, cmodels ??? SAT-Based Disjunctive Answer Set Solver, Lecture Notes in Computer Science, vol.3662, pp.447-451, 2005.
DOI : 10.1007/11546207_44

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.102.6244

K. Liolios, N. Tavernarakis, P. Hugenholtz, and N. C. Kyrpides, The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide, Nucleic Acids Research, vol.34, issue.90001, pp.332-334, 2006.
DOI : 10.1093/nar/gkj145

D. Kenzie, T. Macisaac, . Wang, . Benjamin-gordon, K. David et al., An improved map of conserved regulatory sites for Saccharomyces cerevisiae, BMC Bioinformatics, vol.7, issue.NIL, p.113, 2006.

H. Marchand, P. Bournai, M. L. Borgne, and P. L. Guernic, Synthesis of discreteevent controllers based on the signal environment. Discrete Event Dynamic System : Theory and Applications, pp.325-346, 2000.
URL : https://hal.archives-ouvertes.fr/hal-00546147

A. Adam, I. Margolin, K. Nemenman, C. Basso, G. Wiggins et al., ARACNE : an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context, BMC Bioinformatics, vol.7, issue.1, p.7, 2006.

V. Matys, O. Kel-margoulis, E. Fricke, . Liebich, . Land et al., TRANSFAC(R) and its module TRANSCompel(R): transcriptional gene regulation in eukaryotes, Nucleic Acids Research, vol.34, issue.90001, pp.34108-110, 2006.
DOI : 10.1093/nar/gkj143

M. Lisa, E. Maurer, . Yohannes, S. Sandra, M. Bondurant et al., pH regulates genes for flagellar motility, catabolism, and oxidative stress in Escherichia coli K-12, J Bacteriol, vol.187, issue.1, pp.304-319, 2005.

I. Nachman, N. Regev, and . Friedman, Inferring quantitative models of regulatory networks from expression data, Bioinformatics, vol.20, issue.Suppl 1, pp.248-256, 2004.
DOI : 10.1093/bioinformatics/bth941

J. Chris, . Needham, R. James, . Bradford, J. Andrew et al., A primer on learning in Bayesian networks for computational biology, PLoS Comput Biol, vol.3, issue.8, p.129, 2007.

B. Novak, J. John, and . Tyson, A model for restriction point control of the mammalian cell cycle, Journal of Theoretical Biology, vol.230, issue.4, pp.563-579, 2004.
DOI : 10.1016/j.jtbi.2004.04.039

M. Opel, S. Arfin, and G. Hatfield, The effects of DNA supercoiling on the expression of operons of the ilv regulon of Escherichia coli suggest a physiological rationale for divergently transcribed operons, Molecular Microbiology, vol.275, issue.5, pp.1109-1115, 2001.
DOI : 10.1111/j.1365-2958.2001.02309.x

A. Jason, . Papin, O. Bernhard, and . Palsson, Topological analysis of mass-balanced signaling networks : a framework to obtain network properties including crosstalk

R. Barriot, D. Sherman, and I. Dutour, How to decide which are the most pertinent overly-represented features during gene set enrichment analysis, BMC Bioinformatics, vol.8, issue.1, p.332, 2007.
DOI : 10.1186/1471-2105-8-332

URL : https://hal.archives-ouvertes.fr/inria-00202721

O. Radulescu, S. Lagarrigue, A. Siegel, P. Veber, and M. L. Borgne, Topology and static response of interaction networks in molecular biology, Journal of The Royal Society Interface, vol.84, issue.5, pp.185-196, 2006.
DOI : 10.1002/sim.1237

URL : https://hal.archives-ouvertes.fr/inria-00178842

O. Radulescu, A. Siegel, S. Lagarrigue, and E. Pécou, A model for regulated fatty acid metabolism in liver ; equilibria and their changes Arxiv q-bio, p.603021

E. Remy, P. Ruet, and D. Thieffry, Graphic requirements for multistability and attractive cycles in a Boolean dynamical framework, Advances in Applied Mathematics, vol.41, issue.3, 2005.
DOI : 10.1016/j.aam.2007.11.003

URL : https://hal.archives-ouvertes.fr/hal-00692086

K. Rhee, . Opel, . Ito, . Hung, G. Arfin et al., Transcriptional coupling between the divergent promoters of a prototypic LysR-type regulatory system, the ilvYC operon of Escherichia coli, Proceedings of the National Academy of Sciences, vol.96, issue.25, pp.9614294-14299, 1999.
DOI : 10.1073/pnas.96.25.14294

A. Richard and J. Comet, Necessary conditions for multistationarity in discrete dynamical systems, Discrete Applied Mathematics, vol.155, issue.18, 2007.
DOI : 10.1016/j.dam.2007.04.019

URL : https://hal.archives-ouvertes.fr/hal-00967300

A. Richard, J. Comet, and G. Bernot, R. thomas' modeling of biological regulatory networks : introduction of singular states in the qualitative dynamics, Fundamenta Informaticae, vol.65, issue.4, pp.373-392, 2005.
URL : https://hal.archives-ouvertes.fr/hal-01306487

D. Ropers, M. Hidde-de-jong, D. Page, J. Schneider, and . Geiselmann, Qualitative simulation of the carbon starvation response in Escherichia coli, Biosystems, vol.84, issue.2, pp.124-152, 2006.
DOI : 10.1016/j.biosystems.2005.10.005

URL : https://hal.archives-ouvertes.fr/hal-00171698

J. Rual, K. Venkatesan, T. Hao, T. Hirozane-kishikawa, A. Dricot et al., Towards a proteome-scale map of the human protein???protein interaction network, Nature, vol.23, issue.7062, pp.4371173-1178, 2005.
DOI : 10.1126/science.1090100

S. Klamt and J. Stelling, System Modeling in Cellular Biology : From Concepts to Nuts and Bolts, chapter Stoichiometric and constraint-based modelling, pp.73-96, 2006.

E. Segal, . Shapira, D. Regev, . Pe-'er, . Botstein et al., Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data, Nature Genetics, vol.291, issue.2, pp.166-176, 2003.
DOI : 10.1038/35057062

E. Segal, D. Yelensky, and . Koller, Genome-wide discovery of transcriptional modules from DNA sequence and gene expression, Bioinformatics, vol.19, issue.Suppl 1, pp.273-282, 2003.
DOI : 10.1093/bioinformatics/btg1038

A. Siegel, O. Radulescu, M. L. Borgne, P. Veber, J. Ouy et al., Qualitative analysis of the relation between DNA microarray data and behavioral models of regulation networks, Biosystems, vol.84, issue.2, pp.153-174, 2006.
DOI : 10.1016/j.biosystems.2005.10.006

URL : https://hal.archives-ouvertes.fr/inria-00178809

P. Simons, Extending the Stable Model Semantics with More Expressive Rules, Lecture Notes in Computer Science, vol.1730, pp.305-316, 1999.
DOI : 10.1007/3-540-46767-X_22

K. Gordon, Y. H. Smyth, T. Yang, and . Speed, Statistical issues in cDNA microarray data analysis, Methods Mol Biol, vol.224, pp.111-136, 2003.

. El-houssine and . Snoussi, Necessary conditions for multistationarity and stable periodicity, J.Biol.Syst, vol.6, pp.3-9, 1998.

E. Houssine, S. , and R. Thomas, Logical identification of all steady states : The concept of feedback loop characteristic states, Bulletin of Mathematical Biology, vol.55, pp.973-991, 1993.

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

C. Soulé, Mathematical approaches to differentiation and gene regulation, Comptes Rendus Biologies, vol.329, issue.1, pp.13-20, 2006.
DOI : 10.1016/j.crvi.2005.10.002

R. Steuer, T. Gross, J. Selbig, and B. Blasius, Structural kinetic modeling of metabolic networks, Proceedings of the National Academy of Sciences, vol.103, issue.32, pp.11868-11873, 2006.
DOI : 10.1073/pnas.0600013103

T. Syrjänen and I. Niemelä, The Smodels System, Lecture Notes in Computer Science, vol.2173, pp.434-438, 2001.
DOI : 10.1007/3-540-45402-0_38

R. Thomas and M. Kaufman, Multistationarity, the basis of cell differentiation and memory. I. Structural conditions of multistationarity and other nontrivial behavior, Chaos: An Interdisciplinary Journal of Nonlinear Science, vol.11, issue.1, pp.170-179, 2001.
DOI : 10.1063/1.1350439

L. Travé-massuyès, P. Dague, and F. Guerrin, Le raisonnement qualitatif pour les sciences de l'Ingénieur. Hermes sciences, 1997.

J. John, . Tyson, C. Katherine, B. Chen, and . Novak, Sniffers, buzzers, toggles and blinkers : dynamics of regulatory and signaling pathways in the cell, Curr Opin Cell Biol, vol.15, issue.2, pp.221-231, 2003.

E. Van-someren, B. Vaes, W. Steegenga, A. Sijbers, K. J. Dechering et al., Least absolute regression network analysis of the murine osteoblast differentiation network, Bioinformatics, vol.22, issue.4, pp.477-484, 2006.
DOI : 10.1093/bioinformatics/bti816

P. Veber, M. L. Borgne, A. Siegel, S. Lagarrigue, and O. Radulescu, Complex Qualitative Models in Biology: A New Approach, Complexus, vol.2, issue.3-4, pp.3-4140, 2004.
DOI : 10.1159/000093686

URL : https://hal.archives-ouvertes.fr/inria-00178819

J. Vert, Kernel methods in genomics and computational biology, 2005.
URL : https://hal.archives-ouvertes.fr/hal-00012124

D. Weichart, . Lange, R. Henneberg, and . Hengge-aronis, Identification and characterization of stationary phase inducible genes in Escherichia coli, Molecular Microbiology, vol.174, issue.2, pp.405-425, 1993.
DOI : 10.1111/j.1365-2958.1993.tb02672.x

E. Wingender, J. Hogan, F. Schacherer, P. Anatolij, O. Potapov et al., Integrating pathway data for systems pathology, In Silico Biol, vol.7, issue.2, pp.17-25, 2007.

Y. Yamanishi, J. Vert, and M. Kanehisa, Protein network inference from multiple genomic data: a supervised approach, Bioinformatics, vol.20, issue.Suppl 1, pp.363-370, 2004.
DOI : 10.1093/bioinformatics/bth910

URL : https://hal.archives-ouvertes.fr/hal-00433586

C. Yeang, T. Ideker, and T. Jaakkola, Physical Network Models, Journal of Computational Biology, vol.11, issue.2-3, pp.243-262, 2004.
DOI : 10.1089/1066527041410382

C. Yeang, C. Mak, S. Mccuine, C. Workman, T. Jaakkola et al., Validation and refinement of gene-regulatory pathways on a network of physical interactions, R62, 2005. [105] Necmettin Yildirim, Moises Santillan, Daisuke Horike, and Michael C Mackey. Dynamics and bistability in a reduced model of the lac operon, pp.279-292, 2004.