Dynamics of a two-dimensional model of cell tissues with coupled stochastic gene networks

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 76, Issue 5, 2007, Pages

  Ribeiro, Andre S ^a,b  

^a TAMPERE UNIVERSITY OF TECHNOLOGY   (Finland)

^b UNIVERSITY OF COIMBRA   (Portugal)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; CELLS; GENE EXPRESSION; PHASE TRANSITIONS; PROTEINS; RATE CONSTANTS; STOCHASTIC MODELS;

GENE REGULATORY NETWORK (GRN); STABLE STATES; TIME DELAYED REACTIONS; TOGGLE SWITCH;

TISSUE;

EID: 36249008660     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.76.051915     Document Type: Article

References (42)

1. B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts, and P. Walters, Molecular Biology of the Cell, 4th ed. (Garland Science, Taylor and Francis Group, New York, 2004).
2. M. B. Miller and B. L. Bassler, Annu. Rev. Microbiol. ARMIAZ 0066-4227 10.1146/annurev.micro.55.1.165 55, 165 (2001).
3. M. Freeman and J. B. Gurdon, Annu. Rev. Cell Dev. Biol. ARDBF8 1081-0706 10.1146/annurev.cellbio.18.012502.083458 18, 515 (2002).
4. C. Lindon, O. Albagli, C. Pinset, and D. Montarras, Dev. Biol. DEBIAO 0012-1606 10.1006/dbio.2001.0435 240, 574 (2001).
5. J. Collier, N. A. M. Monk, P. Maini, and J. Lewis, J. Theor. Biol. JTBIAP 0022-5193 10.1006/jtbi.1996.0233 183, 429 (1996).
6. P. Richard, B. Teusink, B. B. Hemker, K. van Dam, and H. V. Westerhoff, Yeast YESTE3 0749-503X 10.1002/(SICI)1097-0061(19960630)12:8<731::AID- YEA961>3.3.CO;2-Q 12, 731 (1996).
7. A. Pikovsky, M. Rosenblum, and J. Kurths, Synchronization: A Universal Concept in Nonlinear Sciences (Cambridge University Press, Cambridge, UK, 2001).
8. M. Elowitz, A. Levine, E. Siggia, and P. Swain, Science SCIEAS 0036-8075 10.1126/science.1070919 297, 1183 (2002).
9. E. Ozbudak, M. Thattai, I. Kurtser, A. Grossman, and A. van Oudenaarden, Nat. Genet. NGENEC 1061-4036 10.1038/ng0502-13 31, 13 (2002).
10. A. Arkin, J. Ross, and H. H. McAdams, Genetics GENTAE 0016-6731 149, 1633 (1998).
11. G. M. Suel, J. Garcia-Ojalvo, L. M. Liberman, and M. B. Elowitz, Nature (London) NATUAS 0028-0836 10.1038/nature04588 440, 545 (2006).
12. A. Becskei and L. Serrano, Nature (London) NATUAS 0028-0836 10.1038/35014651 405, 590 (2000).
13. M. Kaern, T. Elston, W. Blake, and J. Collins, Nat. Rev. Genet. NRGAAM 1471-0056 10.1038/nrg1615 6, 451 (2005).
14. N. A. M. Monk, Science SCIEAS 0036-8075 10.1126/science.1105891 309, 2010 (2005).
15. N. A. M. Monk, Curr. Biol. CUBLE2 0960-9822 10.1016/S0960-9822(03)00494-9 13, 1409 (2003).
16. D. T. Gillespie, J. Comput. Phys. JCTPAH 0021-9991 10.1016/0021-9991(76) 90041-3 22, 403 (1976).
17. D. T. Gillespie, J. Phys. Chem. JPCHAX 0022-3654 10.1021/j100540a008 81, 2340 (1977).
18. D. Bratsun, D. Volfson, L. Tsimring, and J. Hasty, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0503858102 102, 14593 (2005).
19. J. Raser and E. O'Shea, Science SCIEAS 0036-8075 10.1126/science.1098641 304, 1811 (2004).
20. H. H. McAdams and A. Arkin, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.94.3.814 94, 814 (1997).
21. M. R. Roussel and R. Zhu, Phys. Biol. PBHIAT 1478-3975 10.1088/1478-3975/3/4/005 3, 274 (2006).
22. M. Roussel, J. Phys. Chem. JPCHAX 0022-3654 10.1021/jp9600672 100, 8323 (1996).
23. R. Zhu, A. S. Ribeiro, D. Salahub, and S. Kauffman, J. Theor. Biol. JTBIAP 0022-5193 10.1016/j.jtbi.2007.01.021 246, 725 (2007).
24. J. Yu, J. Xiao, X. Ren, K. Lao, and S. Xie, Science SCIEAS 0036-8075 10.1126/science.1119623 311, 1600 (2006).
25. S. Busenberg and J. Mahaffy, J. Math. Biol. JMBLAJ 0303-6812 10.1007/BF00276489 22, 313 (1985).
26. J. Mahaffy and C. Pao, J. Math. Biol. JMBLAJ 0303-6812 10.1007/BF00275860 20, 39 (1984).
27. A. S. Ribeiro and J. Lloyd-Price, Bioinformatics BOINFP 1367-4803 26, 777 (2007).
28. A. S. Ribeiro, R. Zhu, and S. A. Kauffman, J. Comput. Biol. JCOBEM 1066-5277 10.1089/cmb.2006.13.1630 13, 1630 (2006).
29. J. Monod and F. Jacob, Cold Spring Harbor Symp. Quant. Biol. CSHSAZ 0091-7451 26, 389 (1961).
30. H. Rubin, Am. J. Physiol. AJPHAP 0002-9513 262, L111 (1992).
31. T. S. Gardner, C. R. Cantor, and J. J. Collins, Nature (London) NATUAS 0028-0836 10.1038/35002131 403, 339 (2000).
32. M. Ptashne, Genetic Switch: Phage λ and Higher Organisms (Cell Press and Blackwell Scientific Publications, Cambridge, MA, 1992).
33. H. Chang, P. Oh, D. Ingber, and S. Huang, BMC Cell Biol 7, 11 (2005).
34. M. F. Wernet, E. O. Mazzoni, C. Celik, D. D. Duncan, I. Duncan, and C. Desplan, Nature (London) NATUAS 0028-0836 10.1038/nature04615 440, 174 (2006).
35. M. Samoilov, G. Price, and A. Arkin, Science SCIEAS 0036-8075 366, 17 (2006).
36. A. S. Ribeiro, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.75.061903 75, 061903 (2007).
37. T. Toulouse, P. Ao, I. Shmulevich, and S. A. Kauffman, Complexity COMPFS 1076-2787 10.1002/cplx.20099 11, 45 (2005).
38. A. Lipshtat, A. Loinger, N. Q. Balaban, and O. Biham, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.96.188101 96, 188101 (2006).
39. W. R. McClure, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.77.10.5634 77, 5634 (1980).
40. T. Kreuz, F. Mormann, R. Andrezejak, A. Kraskov, K. Lehnertz, and P. Grassberger, Physica D PDNPDT 0167-2789 10.1016/j.physd.2006.09.039 225, 29 (2007).
41. C. E. Shannon, Bell Syst. Tech. J. BSTJAN 0005-8580 27, 379 (1948).
42. L. F. Shampine, S. Thompson, Appl. Numer. Math. ANMAEL 0168-9274 10.1016/S0168-9274(00)00055-6 37, 441 (2001).