Random shuffling of switching parameters in a model of gene expression regulatory network

Stochastics and Dynamics

Volumn 5, Issue 1, 2005, Pages 75-95

  Volchenkov, D ^a   Lima, R ^a  

^a CNRS   (France)

Author keywords

Feedback circuits; Gene regulatory networks; Topology of network

Indexed keywords

EID: 33746274616     PISSN: 02194937     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219493705001328     Document Type: Article

References (61)

1. M. Ptashne and A. Gann, Genes and Signals (Cold Spring Harbour Laboratory Press, 2002).
2. F. Jacob and J. Monod, J. Mol. Biol. 3 (1961) 318.
3. R. Dickson, J. Ableson, W. Barnes and W. Reznikoff, Science 187 (1975) 27.
4. von Hippel and P. H. Science 281 (1998) 660-665.
5. L. Glass and S. A. Kauffman, J. Theor. Biol. 39 (1973) 103.
6. M. A. Savageau, Nature 252 (1974) 546.
7. S. Kauffman, J. Theor. Biol. 44 (1974) 167.
8. L. Glass, J. Theor. Biol. 54 (1975) 85.
9. L. Glass, J. Chem. Phys. 63 (1975) 1325.
10. M. Savageau, Biochemical System Analysis (Addison-Wesley, 1976).
11. B. C. Goodwin, Analytical Physiology of Cells and Developing Organisms (Academic Press, 1976).
12. J. J. Tyson and H. G. Othmer, Prog. Theor. Biol. 5 (1978) 1.
13. G. K. Ackers, A. D. Johnson and M. A. Shea, Proc. Natl. Acad. Sci. 79 (1982) 1129.
14. B. O. Palsson and E. N. Lightfoot, J. Theor. Biol. 113 (1985) 279.
15. F. Moran and A. Goldbeter, Biophys. Chem. 20 (1984) 149.
16. J. Reinitz and J. R. Vaisnys, J. Theor. Biol. 145 (1990) 295.
17. H. H. McAdams and L. Shapiro, Science 269 (1995) 650-656.
18. A. Keller, J. Theor. Biol. 172 (1995) 169-185.
19. P. Smolen, D. A. Baxter and J. H. Byrne, Am. J. Physiol. - Cell Ph. 43 (1998) C531-C542.
20. D. M. Wolf and F. H. Eeckman, J. Theor. Biol. 195 (1998) 167-186.
21. I. J. Farkas, H. Jeong, T. Vicsek, A.-L. Barabasi and Z. N. Oltvai, The topology of the transcription regulatory network in the yeast, S. cerevisiae, physics/0205181.
22. K. Rho, H. Jeong and B. Kahng, Identification of essential and functionally moduled genes through the microarray assay, cond-mat/ 0301110.
23. R. Lima, B. Fernandez and A. Meyroneinc, Modelling the discrete dynamics of genetic regulation networks via real mappings, (2004), in preparation.
24. E. H. Snoussi and R. Thomas, Bull. Math. Biol. 55 (1993) 973.
25. R. Thomas and M. Kaufman, Chaos 11 (2001) 180.
26. K. Klemm and S. Bornholdt, Robust gene regulation: Deterministic dynamics from asynchronous networks with delay, q-bio.MN/0309013.
27. K. Klemm and S. Bornholdt, Topology of biological networks and reliability of information processing, q-bio.MN/0409022.
28. W. Bialek, Stability and noise in biochemical switches, cond-mat/0005235.
29. J. Hasty, J. Pradines, M. Dolnik and J. J. Collins, Noise-based switches and amplifiers for gene expression, physics/0003105.
30. A. M. Walczaka, M. Sasaic and P. G. Wolynes, Self consistent proteomic field theory of stochastic gene switches, q-bio.MN/0407041.
31. W. W. Chen, J. L. England and E. I. Shakhnovich, An exact model of fluctuations in gene expression, q-bio.MN/0402021.
32. S. Bilke, Shuffling yeast gene expression data, physics/0006050.
33. J. D. Murray, Mathematical Biology (Springer-Verlag, 1993).
34. S. Maslov and K. Sneppen, Specificity and stability in topology of protein networks, cond-mat/0205380.
35. S. Shaw, Evidence of scale-free topology and dynamics in gene regulatory networks, cond-mat/0301041.
36. A. Groenlund, Networking genetic regulation and neural computation: Directed network topology and its effect on the dynamics, cond-mat/ 0406268.
37. K. Kaneko, Theory and Applications of Coupled Map Lattices (John Wiley & Sons, 1993).
38. A. Wagner, Proc. Natl. Acad. Sci. USA 91 (1994) 4387-4391. We profoundly thank our referee for mentioning this article to us.
39. D. Thieffry, Qualitative analysis of gene networks, in Memoire pour l'obtention d'Agrege de l'Eseignement Superieur, Universite Libre de Bruxelles (2000).
40. S. Maslov and K. Sneppen, Specificity and stability in topology of protein networks, cond-mat/0205380.
41. S. Shaw, Evidence of scale-free topology and dynamics in gene regulatory networks, cond-mat/0301041.
42. A. Wagner, Proc. R. Soc. Lond. B270 (2003) 457-466.
43. G. C. Conant and A. Wagner, Nature Genetics 34 (2003) 264-266.
44. P. M. Gleiss, P. F. Stadler, A. Wagner, D. A. Fell, Adv. Comp. Syst. 1 (2001) 1.
45. D. Volchenkov and Ph. Blanchard, Physica A315 (2002) 677.
46. P. Erdös and A. Rényi, Publ. Math. Inst. Hung. Acad. Sci. 5 (1960) 17.
47. H. Chate and P. Manneville, Chaos 2 (1992) 307.
48. H. Chate and P. Manneville, Europhys. Lett. 6 (1988) 591.
49. D. Volchenkov, S. Sequeira, Ph. Blanchard and M. G. Cosenza, Stoch. Dyn. 2 (2002) 203.
50. A. Wagner, Mol. Biol. Evol. 17 (2000) 1985-1987.
51. T. S. Gardner, D. di Bernardo, D. Lorenz and J. J. Collins, Science 301 (2003) 102-105.
52. S. Kauffman, C. Peterson, B. Samuelsson and C. Troein, Proc. Natl. Acad. Sci. 100 (2003) 14796-14799.
53. R. Thomas and M. Kaufman, Chaos 11 (2001) 180.
54. D. Thieffry and D. Romero, BioSyst. 50 (1999) 49.
55. D. Thieffry, E. H. Snoussi, J. Richelle and R. Thomas, J. Biol. Syst. 3 (1995) 457.
56. R. Thomas, On the Relation between the Logical Structure of Systems and their Ability to Generate Multiple Steady States or Sustained Oscillations, Springer Series in Sinergetics, Vol. 9 (1981), p. 180.
57. R. Thomas, Ber. Brunzenges. Phys. Chem. 98 (1994) 1148.
58. D. Volchenkov and Ph. Blanchard, Physica A315 (2002) 677.
59. R. Pastor-Satorras and A. Vespignani, Phys. Rev. Lett. 86 (2001) 3200
60. D. Volchenkov, L. Volchenkova and Ph. Blanchard, Phys. Rev. E66 (2002) 046137
61. D. Volchenkov, L. Volchenkova and Ph. Blanchard, J. Biol. Phys. Res. 4 (2002), available at http://www.vjbio.org.