"Immunetworks", intersecting circuits and dynamics

Journal of Theoretical Biology

Volumn 280, Issue 1, 2011, Pages 19-33

  Demongeot, Jacques ^a,d   Elena, Adrien ^a   Noual, Mathilde ^b,d   Sené, Sylvain ^c,d   Thuderoz, Florence ^a  

^a UNIV GRENOBLE ALPES   (France)

^b UNIVERSITÉ DE LYON   (France)

^c UNIVERSITY OF EVRY   (France)

^d ENS Lyon   (France)

Author keywords

Asymptotic behaviour; Biological regulation networks; Discrete dynamical systems; Immune system networks; Random networks

Indexed keywords

MICRORNA;

GENETIC ANALYSIS; IMMUNE SYSTEM; NETWORK ANALYSIS;

AGING; ARTICLE; AUTOMATION; B LYMPHOCYTE DIFFERENTIATION; CHROMATIN; GENE EXPRESSION; GENE INTERACTION; GENE REGULATORY NETWORK; HUMAN; IMMUNE RESPONSE; IMMUNE SYSTEM; IMMUNE SYSTEM NETWORK; INNATE IMMUNITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SIGNAL TRANSDUCTION;

EID: 79953864701     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2011.03.023     Document Type: Article

References (82)

1. Aldana M., Cluzel P. A natural class of robust networks. Proceedings of the National Academy of Sciences of the USA 2003, 100(15):8710-8714.
2. Anderson M.K., Hernandez-Hoyos G., Dionne C.J., Arias A.M., Chen D., Rothenberg E.V. Definition of regulatory network elements for T cell development by perturbation analysis with PU.1 and GATA-3. Developmental Biology 2002, 246(1):103-121.
3. Anderson M.K., Weiss A.H., Hernandez-Hoyos G., Dionne C.J., Rothenberg E.V. Constitutive expression of PU.1 in fetal hematopoietic progenitors blocks T cell development at the Pro-T cell stage. Immunity 2002, 16(2):285-296.
4. Aracena J., Ben Lamine S., Mermet M.A., Cohen O., Demongeot J. Mathematical modelling in genetic networks: relationships between the genetic expression and both chromosomic breakage and positive circuits. IEEE Transactions Systems Man Cybernetics 2003, 33(5):825-834.
5. Aracena J., Demongeot J. Mathematical methods for inferring regulatory networks interactions: application to genetic regulation. Acta Biotheoretica 2004, 52(4):391-400.
6. Aracena J., Demongeot J., Goles E. Positive and negative circuits in discrete neural networks. IEEE Transactions on Neural Networks 2004, 15(1):77-83.
7. Aracena J., Demongeot J., Goles E. On limit cycles of monotone functions with symmetric connection graphs. Theoretical Computer Science 2004, 322(2):237-244.
8. Álvarez-Buylla E.R., Chaos A., Aldana M., Benítez M., Cortes-Poza Y., Espinosa-Soto C., Hartasánchez D.A., Lotto R.B., Malkin D., Escalera Santos G.J., Padilla-Longoria P. Floral morphogenesis: stochastic explorations of a gene network epigenetic landscape. PLoS One 2008, 3(11):e3626.
9. Barrio R.A., Hernández-Machado A., Varea C., Romero-Arias J.R., Álvarez-Buylla E.R. Flower development as an interplay between dynamical physical fields and genetic networks. PLoS One 2010, 5(10):e13523.
10. Ben Amor H., Demongeot J., Sené S. Structural sensitivity of neural and genetic networks. Proceedings of MICAI'08, Lecture Notes in Computer Science 2008, vol. 5317:973-986. Springer.
11. Benecke A. Chromatin code, local non-equilibrium dynamics, and the emergence of transcription regulatory programs. The European Physical Journal E: Soft Matter and Biological Physics 2006, 19(3):353-366.
12. Berge C. Graphes et hypergraphes 1974, Dunod.
13. Bollobás B. Random Graphs 1985, Academic Press.
14. Braeckman B.P., Demetrius L., Vanfleteren J.R. The dietary restriction effect in C. elegans and humans: is the worm a one-millimeter human?. Biogerontology 2006, 7(3):127-133.
15. Brink T.C., Regenbrecht C., Demetrius L., Lehrach H., Adjaye J. Activation of the immune response is a key feature of aging in mice. Biogerontology 2009, 10(6):721-734.
16. Chaves M., Albert R., Sontag E.D. Robustness and fragility of Boolean models for genetic regulatory networks. Journal of Theoretical Biology 2005, 235(3):431-449.
17. Cinquin O., Demongeot J. Positive and negative feedback: striking a balance between necessary antagonists. Journal of Theoretical Biology 2002, 216(2):229-241.
18. Cinquin O., Demongeot J. Positive and negative feedback: mending the ways of sloppy systems. Comptes Rendus Biologies 2002, 325:1085-1095.
19. Corblin F., Tripodi S., Fanchon E., Ropers D., Trilling L. A declarative constraint-based method for analyzing discrete genetic regulatory networks. Biosystems 2009, 98(2):91-104.
20. Cosnard M., Demongeot J. On the definitions of attractors. Lectures Notes in Mathematics 1985, 1163:23-31.
21. Cosnard M., Demongeot J., Lausberg K., Lott K. Attractors, confiners and fractal dimensions. Applications in neuromodelling. Proceedings of the European Conference on Mathematics in Biology and Medicine 1993, 69-94. Wuerz Publishing.
22. Dasika M.S., Gupta A., Maranas C.D., Varner J.D. A mixed integer linear programming (MILP) framework for inferring time delay in gene regulatory networks. Proceedings of PSB'2004 2004, 474-485.
23. Delaplace F., Klaudel H., Cartier-Michaud A. Discrete causal model view of biological networks. Proceedings of CMSB'10 2010, 4-13. ACM.
24. Delbrück M. Discussion: Unités biologiques douées de continuité génétique. Actes du colloque international du CNRS 1949, 33-35.
25. Demongeot J. Multi-stationarity and cell differentiation. Journal of Biological Systems 1998, 6(1):1-2.
26. Demongeot J., Aracena J., Thuderoz F., Baum T.P., Cohen O. Genetic regulation networks: circuits, regulons and attractors. Comptes-Rendus Biologies 2003, 326(2):171-188.
27. Demongeot J., Ben Amor H., Elena E., Gillois P., Noual M., Sené S. Robustness of regulatory networks. A generic approach with applications at different levels: physiologic, metabolic and genetic. International Journal of Molecular Sciences 2009, 10(10):4437-4473.
28. Demongeot J., Goles E., Morvan M., Noual M., Sené S. Attraction basins as gauges of environmental robustness in biological complex systems. PloS One 2010, 5(8):e11793.
29. Demongeot J., Noual M., Sené S. On the number of attractors of positive and negative Boolean automata circuits. Proceedings of WAINA'10 2010, 782-789. IEEE Press.
30. Demongeot, J., Noual, M., Sené, S., Combinatorics of Boolean automata circuits dynamics. Discrete Applied Mathematics, under review.
31. Elena, A., 2009. Robustesse des réseaux d'automates booléens à seuil aux modes d'itération. Application à la modélisation des réseaux de régulation génétique, Ph.D. Thesis, Université Joseph Fourier de Grenoble.
32. Elena A., Demongeot J. Interaction motifs in regulatory networks and structural robustness. Proceedings of CISIS'08 2008, 682-686. IEEE Press.
33. Elena A., Ben Amor H., Glade N., Demongeot J. Motifs in regulatory networks and their structural robustness. Proceedings of BIBE'08 2008, 234-242. IEEE Press.
34. Ermentrout G.B., Edelstein-Keshet L. Cellular automata approaches to biological modeling. Journal of Theoretical Biology 1993, 160(1):97-133.
35. Fossey A. Epigenetics: beyond genes. Southern Forests: A Journal of Forest Science 2009, 71(2):121-124.
36. Fox J.J., Hill C.C. From topology to dynamics in biochemical networks. Chaos 2001, 11(4):809-815.
37. Franco C.B., Scripture-Adams D.D., Proekt I., Taghon T., Weiss A.H., Yui M.A., Adams S.L., Diamond R.A., Rothenberg E.V. Notch/Delta signaling constrains reengineering of pro-T cells by PU.1. Proceedings of the National Academy of Sciences 2006, 103(32):11993-11998.
38. Fukui Y., Hashimoto O., Sanui T., Oono H., adn Koga T., Abe M., Inayoshi A., Noda M., Oike M., Shirai T., Sasazuki T. Haematopoietic cell-specific CDM family protein DOCK2 is essential for lymphocyte migration. Nature 2001, 412(6849):826-831.
39. Georgescu C., Longabaugh W.J.R., Scripture-Adams D.D., David-Fung E.S., Yui M.A., Zarnegar M.A., Bolouri H., Rothenberg E.V. A gene regulatory network armature for T lymphocyte specification. Proceedings of the National Academy of Sciences of the USA 2008, 105(51):20100-20105.
40. Gloes, E., Noual, M., Block-sequential update schedules and Boolean automata circuits. In: Discrete Mathematics and Theoretical Computer Science-Proceedings of Automata'2010, 2010, issue 01, pp. 41-50.
41. Gouzé J.-L. Positive and negative circuits in dynamical systems. Journal of Biological Systems 1998, 6(1):11-15.
42. Hopfield J.J. Neural networks and physical systems with emergent collective computational abilities. Proceedings of the National Academy of Sciences of the USA 1982, 79(8):2554-2558.
43. Kauffman S.A. Metabolic stability and epigenesis in randomly constructed genetic nets. Journal of Theoretical Biology 1969, 22(3):437-467.
44. Kauffman S.A. The Origins of Order 1993, Oxford University Press.
45. Kauffman S.A., Peterson C., Samuelsson B., Troein C. Random Boolean network models and the yeast transcriptional network. Proceedings of the National Academy of Sciences of the USA 2003, 100(25):14796-14799.
46. Kaufman M., Soulé C., Thomas R. A new necessary condition on interaction graphs for multistationarity. Journal of Theoretical Biology 2007, 248(4):675-685.
47. Kletsas D., Pratsinis H., Mariatos G., Zacharatos P., Gorgoulis V.G. The proinflammatory phenotype of senescent cells: the p53-mediated ICAM-1 expression. Annals of the New York Academy of Sciences 2004, 1019:330-332.
48. Kulić I.M., Schiessel H. Chromatin dynamics: nucleosomes go mobile through twist defects. Physical Review Letters 2003, 91(14):148103.
49. Lesne A., Victor J.-M. Chromatin fiber functional organization: some plausible models. The European Physical Journal E: Soft Matter and Biological Physics 2006, 19(3):279-290.
50. Li J., Wang B.H., Wang W.X., Zhou T. Network entropy based on topology configuration and its computation to random networks. Chinese Physics Letters 2008, 25(11):4177-4180.
51. Mazoyer J. An overview of the firing squad synchronization problem. Automata Networks, Lecture Notes in Computer Science 1988, vol. 316:82-94. Springer.
52. McCulloch W., Pitts W. A logical calculus of ideas immanent in nervous activity. Bulletin of Mathematical Biophysics 1943, 5:115-133.
53. McKay B.D., Wormald N.C., Wysocka B. Short cycles in random regular graphs. Electronic Journal of Combinatorics 2004, 11(1):R66.
54. Mendoza L. A network model for the control of the differentiation process in Th cells. Biosystems 2006, 84(2):101-114.
55. Mendoza L., Pardo F. A robust model to describe the differentiation of T-helper cells. Theory in Biosciences 2010, 129(4):283-293.
56. Mendoza L., Álvarez-Buylla E.R. Dynamics of the genetic regulatory network for Arabidopsis thaliana flower morphogenesis. Journal of Theoretical Biology 1998, 193(2):307-319.
57. Mendoza L., Thieffry D., Álvarez-Buylla E.R. Genetic control of flower morphogenesis in Arabidopsis thaliana: a logical analysis. Bioinformatics 1999, 15(7):593-606.
58. Meringer M. Fast generation of regular graphs and construction of cages. Journal of Graph Theory 1999, 30(2):137-146.
59. Munitz A., Bachelet I., Eliashar R., Khodoun M., Finkelman F.D., Rothenberg M.E., Levi-Schaffer F. CD48 is an allergen and IL-3-induced activation molecule on eosinophils. Journal of Immunology 2006, 177(1):77-83.
60. Noual, M., 2010. General iteration graphs and Boolean automata circuits, Tech. rep., LIP, École normale supérieure de Lyon, hal: 00452025.
61. Noual, M., 2011. Dynamics in parallel of double Boolean automata circuits. Tech. rep., LIP, École normale supérieure de Lyon, arxiv:1011.3930.
62. Plathe E., Mestl T., Omholt S.W. Feedback loops, stability and multistationarity in dynamical systems. Journal of Biological Systems 1995, 3(2):569-577.
63. Remy E., Ruet P. From minimal signed circuits to the dynamics of Boolean regulatory networks. Bioinformatics 2008, 24(16):220-226.
64. Remy E., Ruet P., Thieffry D. Graphic requirements for multistability and attractive cycles in a Boolean dynamical framework. Advances in Applied Mathematics 2008, 41(3):335-350.
65. Richard A. Positive circuits and maximal number of fixed points in discrete dynamical systems. Discrete Applied Mathematics 2009, 157(15):3281-3288.
66. Richard A., Comet J.-P. Necessary conditions for multistationarity in discrete dynamical systems. Discrete Applied Mathematics 2007, 155(18):2403-2413.
67. Robert F. Discrete Iterations: A Metric Study 1986, vol. 6. Springer Series in Computational Mathematics, Springer.
68. Saez-Rodriguez J., Simeoni L., Lindquist J.A., Hemenway R., Bommhardt U., Arndt B., Haus U.U., Weismantel R., Gilles E.D., Klamt S., Schraven B. A logical model provides insights into T Cell receptor signaling. PLoS Computational Biology 2007, 3(8):e163.
69. Samuelsson B., Troein C. Superpolynomial growth in the number of attractors in Kauffman networks. Physical Review Letters 2003, 90(9):098701.
70. Sené, S., 2008. Influence des conditions de bords dans les réseaux d'automates booléens à seuil et application à la biologie, Ph.D. Thesis, Université Joseph Fourier de Grenoble.
71. Shmulevich I., Kauffman S.A. Activities and sensitivities in Boolean network models. Physical Review Letters 2004, 93(4):048701.
72. Singh H., Grossched R. Molecular Analysis of B Lymphocyte Development and Activation 2005, Springer.
73. Snoussi E.H. Necessary conditions for multistationarity and stable periodicity. Journal of Biological Systems 1998, 6(1):3-10.
74. Soulé C. Mathematical approaches to differentiation and gene regulation. Comptes rendus de l'Académie des sciences, Biologies 2006, 329(1):13-20.
75. Su J., Xie Q., Wilson I., Li L. Differential regulation and role of interleukin-1 receptor associated kinase-M in innate immunity signaling. Cellular Signaling 2007, 19(7):1596-1601.
76. Thomas R. Boolean formalisation of genetic control circuits. Journal of Theoretical Biology 1973, 42(3):563-585.
77. Thomas R. On the relation between the logical structure of systems and their ability to generate multiple steady states or sustained oscillations. Numerical Methods in the Study of Critical Phenomena 1981, vol. 9:180-193. Springer Series in Synergetics, Springer.
78. Thomas R., Mehrotra S., Papoutsakis E.T., Hatzimanikatis V. A model-based optimization framework for the inference on gene regulatory networks from DNA array data. Bioinformatics 2004, 20(17):3221-3235.
79. Wang X. miRDB: a microRNA target prediction and functional annotation database with a wiki interface. RNA 2008, 14(6):1012-1017.
80. Wang X., El Naqa I. Prediction of both conserved and nonconserved microRNA targets in animals. Bioinformatics 2008, 24(3):325-332.
81. Wormald N.C. The asymptotic distribution of short cycles in random regular graphs. Journal of Combinatorial Theory Series B 1981, 31(2):168-182.
82. Zhang S.Q., Hayashida M., Akutsu T., Ching W.K., Ng M.K. Algorithms for finding small attractors in Boolean networks. EURASIP Journal on Bioinformatics and Systems Biology 2007, 2:20180.