Frequency domain analysis of noise in simple gene circuits

Chaos

Volumn 16, Issue 2, 2006, Pages

  Cox, Chris D ^a,b   McCollum, James M ^a   Austin, Derek W ^c   Allen, Michael S ^a,b,d   Dar, Roy D ^b,d   Simpson, Michael L ^a,b,d  

^a University of Tennessee Knoxville   (United States)

^b UNIVERSITY OF TENNESSEE   (United States)

^c SIEMENS CORPORATE RESEARCH   (United States)

^d OAK RIDGE NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 33748755369     PISSN: 10541500     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2204354     Document Type: Article

References (51)

1. M. Delbruck, J. Chem. Phys. 8, 120 (1940).
2. M. Delbruck, J. Bacteriol. 50, 131 (1945).
3. A. Novick and M. Weiner, Proc. Natl. Acad. Sci. U.S.A. 43, 553 (1957).
4. M. Ptashne, A Genetic Switch: Gene Control and Phage Lambda (Cell Press, Cambridge, MA, 1986).
5. A. Arkin, J. Ross, and H. H. McAdams, Genetics 149, 1633 (1998).
6. J. L. Spudich and D. E. KoshlandJr., Nature (London) 262, 467 (1976).
7. A. Colman-Lerner, A. Gordon, E. Serra, T. Chin, O. Resnekov, D. Endy, C. G. Pesce, and R. Brent, Nature (London) 437, 699 (2005).
8. P. Simpson, Curr. Opin. Genet. Dev. 7, 537 (1997).
9. M. Thattai and A. van Oudenaarden, Genetics 167, 523 (2004);
10. E. Kussell and S. Leibler, Science 309, 2075 (2005).
11. C. V. Rao, D. M. Wolf, and A. P. Arkin, Nature (London) 420, 231 (2002).
12. M. Kaern, T. C. Elston, W. J. Blake, and J. J. Collins, Nat. Rev. Genet. 6 (6), 451 (2005);
13. J. M. Raser and E. K. O'Shea, Science 309, 2010 (2005).
14. M. B. Elowitz, A. J. Levine, E. D. Siggia, and P. S. Swain, Science 297, 1183 (2002).
15. P. S. Swain, M. B. Elowitz, and E. D. Siggia, Proc. Natl. Acad. Sci. U.S.A. 99, 12795 (2002).
16. J. M. Pedraza and A. van Oudenaarden, Science 307, 1965 (2005).
17. M. A. Gibson and J. Bruck, J. Phys. Chem. A 104, 1876 (2000).
18. D. T. Gillespie, J. Comput. Phys. 22, 403 (1976).
19. D. T. Gillespie, J. Phys. Chem. 81, 2340 (1977).
20. D. T. Gillespie, Physica A 188, 404 (1992).
21. D. T. Gillespie, J. Chem. Phys. 113, 297 (2000).
22. D. T. Gillespie, W. O. Alltop, and J. M. Martin, Chaos 11, 548 (2001);
23. J. Hasty, D. McMillen, F. Isaacs, and J. J. Collins, Nat. Rev. Genet. 2, 268 (2001);
24. H. H. McAdams and A. Arkin, Annu. Rev. Biophys. Biomol. Struct. 27, 199 (1998);
25. C. V. Rao and A. P. Arkin, J. Chem. Phys. 118, 4999 (2003).
26. T. B. Kepler and T. C. Elston, Biophys. J. 81, 3116 (2001).
27. E. M. Ozbudak, M. Thattai, I. Kurtser, A. D. Grossman, and A. van Oudenaarden, Nat. Genet. 31, 69 (2002).
28. M. Thattai and A. van Oudenaarden, Proc. Natl. Acad. Sci. U.S.A. 98, 8614 (2001).
29. M. L. Simpson, C. D. Cox, and G. S. Sayler, Proc. Natl. Acad. Sci. U.S.A. 100, 4551 (2003).
30. M. L. Simpson, C. D. Cox, and G. S. Sayler, J. Theor. Biol. 229, 383 (2004).
31. C. D. Cox, G. D. Peterson, M. S. Allen, J. M. Lancaster, J. M. McCollum, D. Austin, L. Yan, G. S. Sayler, and M. L. Simpson, Omics, a Journal of Integrative Biology 7, 317 (2003).
32. J. Hasty, J. Pradines, M. Dolnik, and J. J. Collins, Proc. Natl. Acad. Sci. U.S.A. 97, 2075 (2000);
33. D. T. Gillespie, J. Phys. Chem. A 106, 5063 (2002).
34. W. J. Blake, M. Kaern, C. R. Cantor, and J. J. Collins, Nature (London) 422, 633 (2003).
35. J. M. Raser and E. K. O'Shea, Science 304, 1811 (2004).
36. A. Becskei and I. W. Mattaj, Curr. Opin. Cell Biol. 17, 27 (2005).
37. N. Rosenfeld, J. W. Young, U. Alon, P. S. Swain, and M. B. Elowitz, Science 307, 1962 (2005).
38. D. W. Austin, M. S. Allen, J. M. McCollum, R. D. Dar, J. W. Wilgus, G. S. Sayler, N. F. Samatova, C. D. Cox, and M. L. Simpson, Nature (London) 439 (7076), 608 (2006).
39. G. Stephanopoulos, A. Aristidou, and J. Nielsen, Metabolic Engineering: Principals and Methodologies (Academic, New York, 1998).
40. T. S. Gardner, C. R. Cantor, and J. J. Collins, Nature (London) 403, 339 (2000).
41. M. B. Elowitz and S. Leibler, Nature (London) 403, 335 (2000).
42. D. Volfson, J. Marciniak, W. J. Blake, N. Ostroff, L. S. Tsimring, and J. Hasty, Nature (London) 439, 861(2006).
43. Y. Cao, H. Li, and L. R. Petzold, J. Chem. Phys. 121, 4059 (2004).
44. J. M. McCollum, G. D. Peterson, C. D. Cox, M. L. Simpson, and N. F. Samatova, Comput. Biol. Chem. 30, 39 (2006).
45. J. S. Bendat and A. B. Piersol, Random Data: Analysis and Measurement Procedures (Wiley, New York, 2000).
46. J. B. Andersen, C. Sternberg, L. K. Poulsen, S. P. Bjørn, M. Givskov, and S. Molin, Appl. Environ. Microbiol. 64, 2240 (1998).
47. R. Lutz and H. Bujard, Nucleic Acids Res. 25, 1203 (1997).
48. I. Chopra and M. Roberts, Microbiol. Mol. Biol. Rev. 65, 232 (2001).
49. C. Petersen, in Control of Messenger RNA Stability, edited by J. G. Belasco and G. Brawerman (Academic, San Diego, 1993), pp. 117-145.
50. P. J. Lopez, I. Marchand, O. Yarchuk, and M. Dreyfus, Proc. Natl. Acad. Sci. U.S.A. 95, 6067 (1998).
51. G. M. Süel, J. Garcia-Ojalvo, L. M. Liberman, and M. B. Elowitz, Nature (London) 440, 545 (2006).