A molecular noise generator

Physical Biology

Volumn 5, Issue 3, 2008, Pages

  Lu, Ting ^a   Ferry, Michael ^b   Weiss, Ron ^a   Hasty, Jeff ^b,c  

^a Princeton University   (United States)

^b UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; MESSENGER RNA;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; COMPUTER SIMULATION; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; METHODOLOGY; PHYSIOLOGY; PROTEIN ENGINEERING; PROTEIN SYNTHESIS; SIGNAL TRANSDUCTION; STATISTICS;

ALGORITHMS; COMPUTER SIMULATION; DNA; GENE EXPRESSION REGULATION; MODELS, GENETIC; PROTEIN BIOSYNTHESIS; PROTEIN ENGINEERING; RNA, MESSENGER; SIGNAL TRANSDUCTION; STOCHASTIC PROCESSES;

EID: 55949129320     PISSN: 14783967     EISSN: 14783975     Source Type: Journal    
DOI: 10.1088/1478-3975/5/3/036006     Document Type: Article

References (37)

1. Stuart R N and Branscomb E W 1971 Quantitative theory of in vivo lac regulation: significance of repressor packaging J. Theor. Biol. 31 313-29
2. Elowitz M B, Levine A J, Siggia E D and Swain P S 2002 Stochastic gene expression in a single cell Science 297 1183-6
3. Kepler T B and Elston T C 2001 Stochasticity in transcriptional regulation: origins, consequences and mathematical representations Biophys. J. 81 3116-36
4. Volfson D, Marciniak J, Ostroff N, Blake W J, Tsimring L S and Hasty J 2006 Origins of extrinsic variability in eukaryotic gene expression Nature 439 861-4
5. Raser J M and O'shea E K 2005 Noise in gene expression: origins, consequences and control Science 309 2010-3
6. Rao C V, Wolf D M and Arkin A P 2002 Control, exploitation and tolerance of intracellular noise Nature 420 231-7
7. Kaern M, Elston T C, Blake W J and Collins J J 2005 Stochasticity in gene expression: from theories to phenotypes Nat. Rev. Genet. 6 451-64
8. Barkai N and Leibler S 1999 Biological rhythms: circadian clocks limited by noise Nature 403 267-8
9. Lapidus S, Han B and Wang J 2008 Intrinsic noise, dissipation cost, and robustness of cellular networks: the underlying energy landscape of mapk signal transduction Proc. Natl Acad. Sci. USA 105 6039-44
10. Weinberger L, Burnett J C, Toettcher J E, Arkin A P and Schaffer D V 2005 Stochastic gene expression in a lentiviral positive-feedback loop: Hiv-1 tat fluctuations drive phenotypic diversity Cell 122 169-82
11. Maamar H, Raj A and Dubnau D 2007 Noise in gene expression determines cell fate in Bacillus subtilis Science 317 526-9
12. Lu T, Shen T, Bennett M, Wolynes P G and Hasty J 2007 Phenotypic variability of growing cellular populations Proc. Natl Acad. Sci. USA 104 18982-7
13. Swain P S, Elowitz M B and Siggia E D 2002 Intrinsic and extrinsic contributions to stochasticity in gene expression Proc. Natl Acad. Sci. USA 99 12795-800
14. Paulsson J 2004 Summing up the noise in gene networks Nature 427 415-8
15. Tan C, Reza F and You L 2007 Noise-limited frequency signal transmission in gene circuits Biophys. J. 93 3753-61
16. Lepzelter D, Kim K and Wang J 2007 Dynamics and intrinsic statistical fluctuations of a gene switch J. Chem. Phys. B 111 10239
17. Han B and Wang J 2007 Quantifying robustness and dissipation cost of yeast cell cycle network: the funneled energy landscape perspectives Biophys. J. 92 3755
18. Kim K and Wang J 2007 Potential energy landscape and robustness of a gene regulatory network: toggle switch PLoS Comput. Biol. 3 e60
19. Kim K, Lepzelter D and Wang J 2007 Single molecule dynamics and statistical fluctuations of gene regulatory networks: a repressilator J. Chem. Phys. 126 034702
20. Lu T, Hasty J and Wolynes P 2006 Effective temperature in stochastic kinetics and gene networks Biophys. J. 91 84-94
21. Austin D W, Allen M S, McCollum J M, Dar R D, Wilgus J R, Sayler G S, Samatova N F, Cox C D and Simpson M L 2006 Gene network shaping of inherent noise spectra Nature 439 608-11
22. Becskei A and Serrano L 2000 Engineering stability in gene networks by autoregulation Nature 405 590-3
23. Raser J M and O'Shea E K 2004 Control of stochasticity in eukaryotic gene expression Science 304 1811-4
24. Thattai M and van Oudenaarden A 2002 Attenuation of noise in ultrasensitive signaling cascades Biophys. J. 82 2943-50
25. McNamara B and Wiesenfeld K 1989 Theory of stochastic resonance Phys. Rev. A 39 4854-69
26. Collins J J, Chow C C and Imhoff T T 1995 Stochastic resonance without tuning Nature 376 236-8
27. Gillespie D T 1977 Exact stochastic simulation of coupled chemical reactions J. Phys. Chem. 81 2340-61
28. Ozbudak E M, Thattai M, Kurtser I, Grossman A D and van Oudennarden A 2002 Regulation of noise in the expression of a single gene Nat. Genet. 31 69-73
29. Levine E, Zhang Z, Kuhlman T and Hwa T 2007 Quantitative characteristics of gene regulation by small RNA PLos Biol. 5 e229
30. Bayer T S and Smolke C D 2005 Programable ligand controlled riboregulators of eukaryotic gene expression Nat. Biotechnol. 23 337-43
31. Isaacs F J, Dwyer D J, Ding C, Pervouchine D D, Cantor C R and Collins J J 2004 Engineered riboregulators enable post-transcriptional control of gene expression Nat. Biotechnol. 22 841-7
32. Fano U 1947 Ionization yield of radiations: II. The fluctuations of the number of ions Phys. Rev. 72 26-9
33. Paulsson J and Ehrenberg M 2001 Noise in a minimal regulatory network: plasmid copy number control Q. Rev. Biophys. 34 1-59
34. Choi S and Kim U J 2001 Construction of a bacterial artificial chromosome library Methods Mol. Biol. 175 57-68
35. Shibata T and Fujimoto K 2005 Noisy signal amplification in ultrasensitive signal transduction Proc. Natl Acad. Sci. USA 102 331-6
36. Valencia-Sanchez M A, Liu J, Hannon G J and Parker R 2006 Control of translation and mrna degradation by mirnas and sirnas Genes Dev. 20 515-24
37. Press W H, Teukolsky S A, Vetterling W T and Flannery B P 2007 Numerical Recipes: The Art of Scientific Computing 3rd edn (Oxford: Cambridge University Press)