S. A. Kauffman, Metabolic stability and epigenesis in randomly constructed genetic nets, Journal of Theoretical Biology, vol.22, issue.3, pp.437-467, 1969.
DOI : 10.1016/0022-5193(69)90015-0

S. A. Kauffman, The origins of order, 1993.

M. Delbrück, Discussion: Unités biologiques douées de continuité génétique, Actes du colloque international du CNRS, pp.33-35, 1949.

R. Thomas, On the Relation Between the Logical Structure of Systems and Their Ability to Generate Multiple Steady States or Sustained Oscillations, pp.180-193, 1981.
DOI : 10.1007/978-3-642-81703-8_24

B. Bollobás, Random graphs, 1985.

F. Robert, Discrete iterations: a metric study, of Springer Series in Computational Mathematics, 1986.
DOI : 10.1007/978-3-642-61607-5

J. Mazoyer, An overview of the firing squad synchronization problem, Automata Networks Lecture Notes in Computer Science, vol.316, pp.82-94, 1988.
DOI : 10.1007/3-540-19444-4_16

G. B. Ermentrout and L. , Cellular Automata Approaches to Biological Modeling, Journal of Theoretical Biology, vol.160, issue.1, pp.97-133, 1993.
DOI : 10.1006/jtbi.1993.1007

M. Cosnard and J. Demongeot, On the definitions of attractors, Lectures Notes in Mathematics, vol.43, issue.6, pp.23-31, 1985.
DOI : 10.1007/BF02684369

M. Cosnard, J. Demongeot, K. Lausberg, and K. Lott, Attractors, confiners and fractal dimensions, Proceedings of the European conference on mathematics in biology and medicine, pp.69-94, 1993.

J. Demongeot, E. Goles, M. Morvan, M. Noual, and S. Sené, Attraction Basins as Gauges of Robustness against Boundary Conditions in Biological Complex Systems, PLoS ONE, vol.98, issue.8, p.11793, 2010.
DOI : 10.1371/journal.pone.0011793.t007

J. Demongeot, M. Noual, and S. Sené, On the Number of Attractors of Positive and Negative Boolean Automata Circuits, 2010 IEEE 24th International Conference on Advanced Information Networking and Applications Workshops, pp.782-789, 2010.
DOI : 10.1109/WAINA.2010.141

URL : https://hal.archives-ouvertes.fr/hal-00647877

A. Elena, H. Ben-amor, N. Glade, and J. Demongeot, Motifs in regulatory networks and their structural robustness, 2008 8th IEEE International Conference on BioInformatics and BioEngineering, pp.234-242, 2008.
DOI : 10.1109/BIBE.2008.4696699

URL : https://hal.archives-ouvertes.fr/hal-00345993

A. Elena and J. Demongeot, Interaction Motifs in Regulatory Networks and Structural Robustness, 2008 International Conference on Complex, Intelligent and Software Intensive Systems, pp.682-686, 2008.
DOI : 10.1109/CISIS.2008.31

A. Elena, Robustesse des réseaux d'automates booléensbooléensà seuil aux modes d'itération. ApplicationàApplicationà la modélisation des réseaux de régulation génétique, 2009.

E. Goles and M. , Block-sequential update schedules and Boolean automata circuits, Discrete Mathematics and Theoretical Computer Science ? Proceedings of Automata, pp.41-50, 2010.

E. Plathe, T. Mestl, and S. W. Omholt, Feedback loops, stability and multistationarity in dynamical systems, Journal of Biological Systems, vol.3, issue.2, pp.569-577, 1995.

J. Gouzé, Positive and Negative Circuits in Dynamical Systems, Journal of Biological Systems, vol.06, issue.01, pp.11-15, 1998.
DOI : 10.1142/S0218339098000054

E. H. Snoussi, Necessary Conditions for Multistationarity and Stable Periodicity, Journal of Biological Systems, vol.06, issue.01, pp.3-10, 1998.
DOI : 10.1142/S0218339098000042

O. Cinquin and J. Demongeot, Positive and Negative Feedback: Striking a Balance Between Necessary Antagonists, Journal of Theoretical Biology, vol.216, issue.2, pp.229-241, 2002.
DOI : 10.1006/jtbi.2002.2544

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

M. Kaufman, C. Soulé, 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

J. Demongeot, J. Aracena, F. Thuderoz, T. P. Baum, and O. Cohen, Genetic regulation networks: circuits, regulons and attractors, Comptes Rendus Biologies, vol.326, issue.2, pp.171-188, 2003.
DOI : 10.1016/S1631-0691(03)00069-6

J. Aracena, S. Ben-lamine, M. A. Mermet, O. Cohen, and J. Demongeot, Mathematical modelling in genetic networks: relationships between the genetic expression and both chromosomic breakage and positive circuits, Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering, pp.825-834, 2003.
DOI : 10.1109/BIBE.2000.889601

A. Richard and J. Comet, Necessary conditions for multistationarity in discrete dynamical systems, Discrete Applied Mathematics, vol.155, issue.18, pp.2403-2413, 2007.
DOI : 10.1016/j.dam.2007.04.019

URL : https://hal.archives-ouvertes.fr/hal-00342169

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, pp.335-350, 2008.
DOI : 10.1016/j.aam.2007.11.003

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

C. Georgescu, W. J. Longabaugh, D. D. Scripture-adams, E. S. David-fung, M. A. Yui et al., A gene regulatory network armature for T lymphocyte specification, Proceedings of the National Academy of Sciences of the USA 105, pp.20100-20105, 2008.
DOI : 10.1073/pnas.0806501105

M. K. Anderson, G. Hernandez-hoyos, C. J. Dionne, A. M. Arias, D. Chen et al., Definition of Regulatory Network Elements for T Cell Development by Perturbation Analysis with PU.1 and GATA-3, Developmental Biology, vol.246, issue.1, pp.103-121, 2002.
DOI : 10.1006/dbio.2002.0674

M. K. Anderson, A. H. Weiss, G. Hernandez-hoyos, C. J. Dionne, and E. V. Rothenberg, Constitutive Expression of PU.1 in Fetal Hematopoietic Progenitors Blocks T Cell Development at the Pro-T Cell Stage, Immunity, vol.16, issue.2, pp.285-296, 2002.
DOI : 10.1016/S1074-7613(02)00277-7

C. B. Franco, D. D. Scripture-adams, I. Proekt, T. Taghon, A. H. Weiss et al., Notch/Delta signaling constrains reengineering of pro-T cells by PU.1, Proceedings of the National Academy of Sciences, pp.11993-11998, 2006.
DOI : 10.1073/pnas.0601188103

X. Wang and I. , Prediction of both conserved and nonconserved microRNA targets in animals, Bioinformatics, vol.24, issue.3, pp.325-332, 2008.
DOI : 10.1093/bioinformatics/btm595

X. Wang, miRDB: A microRNA target prediction and functional annotation database with a wiki interface, RNA, vol.14, issue.6, pp.1012-1017, 2008.
DOI : 10.1261/rna.965408

H. Singh and R. Grossched, Molecular analysis of B lymphocyte development and activation, 2005.
DOI : 10.1007/b137478

J. Li, B. H. Wang, W. X. Wang, and T. Zhou, Network entropy based on topology configuration and its computation to random networks, Chinese Physics Letters, vol.25, issue.11, pp.4177-4180, 2008.

H. Ben-amor, J. Demongeot, and S. Sené, Structural Sensitivity of Neural and Genetic Networks, Proceedings of MICAI'08, pp.973-986, 2008.
DOI : 10.1016/j.jtbi.2007.07.010

URL : https://hal.archives-ouvertes.fr/hal-00346566

DOI : 10.1142/9789812704856_0045

R. Thomas, S. Mehrotra, E. T. Papoutsakis, and V. Hatzimanikatis, A model-based optimization framework for the inference on gene regulatory networks from DNA array data, Bioinformatics, vol.20, issue.17, pp.3221-3235, 2004.
DOI : 10.1093/bioinformatics/bth389

F. Corblin, S. Tripodi, E. Fanchon, D. Ropers, and L. Trilling, A declarative constraint-based method for analyzing discrete genetic regulatory networks, Biosystems, vol.98, issue.2, pp.91-104, 2009.
DOI : 10.1016/j.biosystems.2009.07.007

URL : https://hal.archives-ouvertes.fr/hal-00793012

F. Delaplace, H. Klaudel, and A. Cartier-michaud, Discrete causal model view of biological networks, Proceedings of the 8th International Conference on Computational Methods in Systems Biology, CMSB '10, pp.4-13, 2010.
DOI : 10.1145/1839764.1839767

URL : https://hal.archives-ouvertes.fr/hal-00654465

J. Saez-rodriguez, L. Simeoni, J. A. Lindquist, R. Hemenway, U. Bommhardt et al., A Logical Model Provides Insights into T Cell Receptor Signaling, PLoS Computational Biology, vol.284, issue.8, p.163, 2007.
DOI : 10.1371/journal.pcbi.0030163.st002

T. C. Brink, C. Regenbrecht, L. Demetrius, H. Lehrach, and J. Adjaye, Activation of the immune response is a key feature of aging in mice, Biogerontology, vol.75, issue.23, pp.721-734, 2009.
DOI : 10.1007/s10522-009-9219-1

J. Aracena and J. Demongeot, Mathematical Methods for Inferring Regulatory Networks Interactions: Application to Genetic Regulation, Acta Biotheoretica, vol.52, issue.4, pp.391-400, 2004.
DOI : 10.1023/B:ACBI.0000046605.48037.7d

B. P. Braeckman, L. Demetrius, and J. R. Vanfleteren, The dietary restriction effect in C. elegans and humans: is the worm a one-millimeter human?, Biogerontology, vol.272, issue.e223, pp.127-133, 2006.
DOI : 10.1007/s10522-006-9003-4

L. Mendoza, A network model for the control of the differentiation process in Th cells, Biosystems, vol.84, issue.2, pp.101-114, 2006.
DOI : 10.1016/j.biosystems.2005.10.004

L. Mendoza and F. Pardo, A robust model to describe the differentiation of T-helper cells, Theory in Biosciences, vol.453, issue.4, pp.283-293, 2010.
DOI : 10.1007/s12064-010-0112-x

J. Su, Q. Xie, I. Wilson, and L. Li, Differential regulation and role of interleukin-1 receptor associated kinase-M in innate immunity signaling, Cellular Signalling, vol.19, issue.7, pp.1596-1601, 2007.
DOI : 10.1016/j.cellsig.2007.02.009

A. Munitz, I. Bachelet, R. Eliashar, M. Khodoun, F. D. Finkelman et al., CD48 Is an Allergen and IL-3-Induced Activation Molecule on Eosinophils, The Journal of Immunology, vol.177, issue.1, pp.77-83, 2006.
DOI : 10.4049/jimmunol.177.1.77

Y. Fukui, O. Hashimoto, T. Sanui, H. Oono, T. Koga et al., Haematopoietic cell-specific CDM family protein DOCK2 is essential for lymphocyte migration, Nature, vol.96, issue.6849, pp.826-831, 2001.
DOI : 10.1038/35090591

D. Kletsas, H. Pratsinis, G. Mariatos, P. Zacharatos, and V. G. Gorgoulis, The Proinflammatory Phenotype of Senescent Cells: The p53-Mediated ICAM-1 Expression, Annals of the New York Academy of Sciences, vol.408, issue.1, pp.330-332, 2004.
DOI : 10.1196/annals.1297.056

I. M. Kuli´ckuli´c and H. Schiessel, Chromatin dynamics: nucleosomes go mobile through twist defects, Physical Review Letters, vol.91, issue.14, 2003.

A. Benecke, Chromatin code, local non-equilibrium dynamics, and the emergence of transcription regulatory programs, The European Physical Journal E, vol.19, issue.3, pp.353-366, 2006.
DOI : 10.1140/epje/i2005-10068-8

A. Lesne and J. Victor, Chromatin fiber functional organization: Some plausible models, The European Physical Journal E, vol.19, issue.3, pp.279-290, 2006.
DOI : 10.1140/epje/i2005-10050-6

A. Fossey, Epigenetics: beyond genes, Southern Forests: a, Journal of Forest Science, vol.71, issue.2, pp.121-124, 2009.

J. Demongeot, H. Ben-amor, E. Elena, P. Gillois, M. Noual et al., Robustness in Regulatory Interaction Networks. A Generic Approach with Applications at Different Levels: Physiologic, Metabolic and Genetic, International Journal of Molecular Sciences, vol.10, issue.10, pp.4437-4473, 2009.
DOI : 10.3390/ijms10104437

URL : https://hal.archives-ouvertes.fr/hal-00644505

S. Sené, Influence des conditions de bords dans les réseaux d'automates booléensbooléensà seuil et applicationàapplicationà la biologie, 2008.

J. J. Fox and C. C. Hill, From topology to dynamics in biochemical networks, Chaos: An Interdisciplinary Journal of Nonlinear Science, vol.11, issue.4, pp.809-815, 2001.
DOI : 10.1063/1.1414882

M. Aldana and P. , A natural class of robust networks, Proceedings of the National Academy of Sciences of the USA, pp.8710-8714, 2003.
DOI : 10.1073/pnas.1536783100

M. Meringer, Fast generation of regular graphs and construction of cages, Journal of Graph Theory, vol.9, issue.2, pp.137-146, 1999.
DOI : 10.1002/(SICI)1097-0118(199902)30:2<137::AID-JGT7>3.0.CO;2-G

N. C. Wormald, The asymptotic distribution of short cycles in random regular graphs, Journal of Combinatorial Theory, Series B, vol.31, issue.2, pp.168-182, 1981.
DOI : 10.1016/S0095-8956(81)80022-6

B. D. Mckay, N. C. Wormald, and B. Wysocka, Short cycles in random regular graphs, Electronic Journal of Combinatorics, vol.11, issue.1, p.66, 2004.

R. Thomas, Boolean formalization of genetic control circuits, Journal of Theoretical Biology, vol.42, issue.3, pp.563-585, 1973.
DOI : 10.1016/0022-5193(73)90247-6

W. Mcculloch and W. Pitts, A logical calculus of the ideas immanent in nervous activity, The Bulletin of Mathematical Biophysics, vol.5, issue.4, pp.115-133, 1943.
DOI : 10.1007/BF02478259

J. J. Hopfield, Neural networks and physical systems with emergent collective computational abilities, Proceedings of the National Academy of Sciences of the USA, pp.2554-2558, 1982.

B. Samuelsson and C. Troein, Superpolynomial Growth in the Number of Attractors in Kauffman Networks, Physical Review Letters, vol.90, issue.9, p.98701, 2003.
DOI : 10.1103/PhysRevLett.90.098701

I. Shmulevich and S. A. Kauffman, Activities and Sensitivities in Boolean Network Models, Physical Review Letters, vol.93, issue.4, p.48701, 2004.
DOI : 10.1103/PhysRevLett.93.048701

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

S. A. Kauffman, C. Peterson, B. Samuelsson, and C. Troein, Random Boolean network models and the yeast transcriptional network, Proceedings of the National Academy of Sciences of the USA, pp.14796-14799, 2003.
DOI : 10.1073/pnas.2036429100

S. Q. Zhang, M. Hayashida, T. Akutsu, W. K. Ching, and M. K. Ng, Algorithms for Finding Small Attractors in Boolean Networks, EURASIP Journal on Bioinformatics and Systems Biology, vol.9, issue.6, 2007.
DOI : 10.1016/j.jtbi.2006.09.023

J. Aracena, J. Demongeot, and E. Goles, Positive and Negative Circuits in Discrete Neural Networks, IEEE Transactions on Neural Networks, vol.15, issue.1, pp.77-83, 2004.
DOI : 10.1109/TNN.2003.821555

J. Aracena, J. Demongeot, and E. Goles, On limit cycles of monotone functions with symmetric connection graph, Theoretical Computer Science, vol.322, issue.2, pp.237-244, 2004.
DOI : 10.1016/j.tcs.2004.03.010

J. Demongeot, Multistationarity and Cell Differentiation, Journal of Biological Systems, vol.06, issue.01, pp.1-2, 1998.
DOI : 10.1142/S0218339098000030

O. Cinquin and J. Demongeot, Roles of positive and negative feedback in biological systems, Comptes Rendus Biologies, vol.325, issue.11, pp.1085-1095, 2002.
DOI : 10.1016/S1631-0691(02)01533-0

E. Remy and P. Ruet, From minimal signed circuits to the dynamics of Boolean regulatory networks, Bioinformatics, vol.24, issue.16, pp.220-226, 2008.
DOI : 10.1093/bioinformatics/btn287

URL : https://hal.archives-ouvertes.fr/hal-01306956

A. Richard, Positive circuits and maximal number of fixed points in discrete dynamical systems, Discrete Applied Mathematics, vol.157, issue.15, pp.3281-3288, 2009.
DOI : 10.1016/j.dam.2009.06.017

]. L. Mendoza and E. R. Alvarez-buylla, Dynamics of the Genetic Regulatory Network forArabidopsis thalianaFlower Morphogenesis, Journal of Theoretical Biology, vol.193, issue.2, pp.307-319, 1998.
DOI : 10.1006/jtbi.1998.0701

L. Mendoza, D. Thieffry, and E. R. Alvarez-buylla, Genetic control of flower morphogenesis in Arabidopsis thaliana: a logical analysis, Bioinformatics, vol.15, issue.7, pp.593-606, 1999.
DOI : 10.1093/bioinformatics/15.7.593

E. R. Alvarez-buylla, A. Chaos, M. Aldana, M. Benítez, Y. Cortes-poza et al., Floral Morphogenesis: Stochastic Explorations of a Gene Network Epigenetic Landscape, PLoS ONE, vol.10, issue.11, p.3626, 2008.
DOI : 10.1371/journal.pone.0003626.t002

R. A. Barrio, A. Hernández-machado, C. Varea, J. R. Romero-arias, and E. R. Alvarez-buylla, Flower Development as an Interplay between Dynamical Physical Fields and Genetic Networks, PLoS ONE, vol.150, issue.10, p.13523, 2010.
DOI : 10.1371/journal.pone.0013523.g009