The circular topology of rhythm in asynchronous random Boolean networks

BioSystems

Volumn 73, Issue 2, 2004, Pages 141-152

  Rohlfshagen, Philipp ^a   Di Paolo, Ezequiel A ^a  

^a UNIVERSITY OF SUSSEX   (United Kingdom)

Author keywords

Genetic algorithms; Random asynchronous updating; Random Boolean networks; Rhythmic phenomena; Ring topology

Indexed keywords

GENETIC ALGORITHM; TOPOLOGY;

ALGORITHM; ARTICLE; CELL SYNCHRONIZATION; EVOLUTION; INFORMATION SCIENCE; OSCILLATION; RANDOMIZATION; RHYTHM;

EID: 0842285448     PISSN: 03032647     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biosystems.2003.11.003     Document Type: Article

References (28)

1. Aharonov R., Segev L., Meiilijson E., Ruppin E., Localization of function via lesion analysis. Neural Computat. 15:2003;885-914.
2. Bagley R., Glass L., Counting and classifying attractors in high dimensional dynamical systems. J. Theor. Biol. 183:1996;269-284.
3. Becskei A., Serrano L., Engineering stability in gene networks by autoregulation. Nature. 405:2000;590-593.
4. Chay T.R., A model for biological oscillations. Proc. Natl. Acad. Sci. U.S.A. 78:1981;2204-2207.
5. Di Paolo E.A., Rhythmic and non-rhythmic attractors in asynchronous random Boolean networks. Biosystems. 59:2001;185-195.
6. Fox J.J., Hill C.C., From topology to dynamics in biochemical networks. Chaos. 11:2001;800-815.
7. Gunji Y., Pigment color patterns of molluscs as an autonomous process generated by asynchronous automata. Biosystems. 23:1990;317-324.
8. Harvey, I., Bossomaier, T., 1997. Time out of joint: attractors in asynchronous random Boolean networks. In: Husbands, P., Harvey, I. (Eds.), Proceedings of the Fourth European Conference on Artificial Life. MIT Press, Cambridge, MA, pp. 67-75.
9. Huberman B.A., Glance N.S., Evolutionary games and computer simulations. Proc. Natl. Acad. Sci. U.S.A. 90:1993;7715-7718.
10. Ingerson T.E., Buvel R.L., Structure in asynchronous cellular automata. Phys. D. 10:1984;59-68.
11. Kauffman S.A., Metabolic stability and epigenesis in randomly constructed genetic nets. J. Theor. Biol. 22:1969;437-467.
12. Kauffman, S.A., 1993. The Origins of Order. Oxford University Press, Oxford.
13. Kohn K.W., Molecular interaction map of the mammalian cell cycle control and DNA repair system. Mol. Biol. Cell. 10:1999;2703-2734.
14. Kondo, T., Mori, T., Lebedeva, N.V., Aoki, S., Ishiura, M., Golden, S.S., 1997. Circadian rhythms in rapidly dividing cyanobacteria. Science 275, 224-227.
15. McAdams H.H., Arkin A., Stochastic mechanism in gene expression. Proc. Natl. Acad. Sci. U.S.A. 94:1997;814-819.
16. Mitchell, M., 1996. An Introduction to Genetic Algorithms. MIT Press, Cambridge, MA.
17. Nehaniv, C., 2002. Evolution in asynchronous cellular automata. In: Standish, R.K., Bedau, M.A., Abbass, H.A. (Eds.), Proceedings of the Eighth International Conference on Artificial Life. MIT Press, Cambridge, MA, pp. 67-73.
18. Roennenberg T., Merrow M., Circadian systems: different levels of complexity. Phil. Trans. R. Soc. Lond. B. 356:2001;1687-1696.
19. Ruxton G.D., Saravia L.A., The need for biological realism in the updating of cellular automata models. Ecol. Model. 107:1998;105-112.
20. Schönfisch B., de Roos A., Synchronous and asynchronous updating in cellular automata. Biosystems. 51:1999;123-143.
21. Stahl F.W., Circular genetic maps. J. Cell Physiol. 70(Suppl. 1):1967;1-12.
22. Thomas R., Boolean formalization of genetic control circuits. J. Theor. Biol. 42:1973;563-585.
23. Thomas R., Logical analysis of systems comprising feedback loops. J. Theor. Biol. 73:1978;631-656.
24. Thomas R., Regulatory networks seen as asynchronous automata: a logical description. J. Theor. Biol. 153:1991;1-23.
25. Thomas R., Thieffry D., Kaufman M., Dynamical behaviour of biological regulatory networks - I. Biological role of feedback loops and practical use of the concept of the loop-characteristic state. Bull. Math. Biol. 57:1995;247-276.
26. Thomas C.A. Jr., The rule of the ring. J. Cell Physiol. 70(Suppl. 1):1967;13-34.
27. Winfree, A.T., 2001. The Geometry of Biological Time, 2nd ed. Springer, New York.
28. Young M.W., The molecular control of circadian behavioral rhythms and their entrainment in Drosophila. Annu. Rev. Biochem. 67:1998;135-152.