Bayesian statistical analysis of circadian oscillations in fibroblasts

Journal of Theoretical Biology

Volumn 314, Issue , 2012, Pages 182-191

  Cohen, Andrew L ^a   Leise, Tanya L ^b   Welsh, David K ^c,d  

^a UNIVERSITY OF MASSACHUSETTS   (United States)

^b AMHERST COLLEGE   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d VA SAN DIEGO HEALTHCARE SYSTEM   (United States)

Author keywords

Circadian clock; Noisy oscillator; Sinusoidal parameter estimation; Stochastic gene expression

Indexed keywords

BAYESIAN ANALYSIS; CELL ORGANELLE; CIRCADIAN RHYTHM; GENE EXPRESSION; RODENT; STOCHASTICITY; UNCERTAINTY ANALYSIS;

ACCURACY; ANIMAL CELL; ARTICLE; BAYES THEOREM; CELL COUNT; CELL POPULATION; CIRCADIAN RHYTHM; FIBROBLAST; GENE EXPRESSION; MOUSE; NONHUMAN; OSCILLATION; PRIORITY JOURNAL; SIMULATION; STATISTICS;

ANIMALS; BAYES THEOREM; BIOLOGICAL CLOCKS; CELL COUNT; CELL CYCLE; CIRCADIAN RHYTHM; FIBROBLASTS; MICE; MODELS, BIOLOGICAL; TIME FACTORS; UNCERTAINTY;

EID: 84866555161     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2012.08.038     Document Type: Article

References (25)

1. Andrieu C., Doucet A. Joint Bayesian model selection and estimation of noisy sinusoids via reversible jump MCMC. IEEE Trans. Signal Process. 1999, 47:2667-2676.
2. Andrieu C., de Freita N., Doucet A., Jordan M.I. An introduction to MCMC for machine learning. Mach. Learn. 2003, 50:5-43.
3. Bell-Pedersen D., Cassone V., Earnest D., Golden S., Hardin P., Thomas T., Zoran M. Circadian rhythms from multiple oscillators: lessons from diverse organisms. Nat. Rev. Genet. 2005, 6:544-556.
4. Bretthorst G.L. Bayesian Spectrum Analysis and Parameter Estimation. Lecture Notes in Statistics, vol. 48 1988, Springer, Berlin.
5. Chib S., Greenberg E. Understanding the Metropolis-Hastings algorithm. The American Statistician 1995, 49:327-335.
6. de la Iglesia H.O., Cambras T., Schwartz W.J., Díez-Noguera A. Forced desynchronization of dual circadian oscillators within the rat suprachiasmatic nucleus. Curr. Biol. 2004, 14:796-800.
7. Dou L., Hodgson R.J.W. Bayesian inference and Gibbs sampling in spectral analysis and parameter estimation: I. Inverse Problems 1995, 11:1069-1085.
8. Dowse H. Analyses for physiological and behavioral rhythmicity. Methods in Enzymology, vol. 454 2009, 141-174. Academic Press, Burlington. M.L. Johnson, L. Brand (Eds.).
9. Chronobiology: Biological Timekeeping 2004, Sinauer Associates, Inc., Sunderland, MA. J.C. Dunlap, J.J. Loros, P.J. DeCoursey (Eds.).
10. Elowitz M.B., Levine A.J., Siggia E.D., Swain P.S. Stochastic gene expression in a single cell. Science 2002, 297:1183-1186.
11. Gamerman D. Markov Chain Monte Carlo. Texts in Statistical Science 1997, Chapman & Hall, New York.
12. Gonze D., Halloy J., Goldbeter A. Robustness of circadian rhythms with respect to molecular noise. Proc. Natl. Acad. Sci. USA 2002, 99:673-678.
13. Hastings W.K. Monte Carlo sampling methods using Markov chains and their applications. Biometrika 1970, 57:97-109.
14. Hoff P.D. A First Course in Bayesian Statistical Methods 2009, Springer, New York.
15. Jaynes E.T. Bayesian spectrum and chirp analysis. Maximum Entropy and Bayesian Analysis and Estimation Problems 1987, 1-37. Reidel, Dordrecht. C.R. Smith, G.J. Erickson (Eds.).
16. Ko C.H., Yamada Y.R., Welsh D.K., Buhr E., Liu A., Zhang E., Ralph M., Kay S., Forger D., Takahashi J. Emergence of noise-induced oscillations in the central circadian pacemaker. PLoS Biol. 2010, 8:e1000513.
17. Kruschke J.K. Doing Bayesian Data Analysis 2011, Academic Press, Burlington, MA.
18. Leise T.L., Harrington M.E. Wavelet-based time series analysis of circadian rhythms. J. Biol. Rhythms 2011, 26:454-463.
19. Leise T.L., Wang C.W., Gitis P.J., Welsh D.K. Persistent cell-autonomous circadian oscillations in fibroblasts revealed by six-week single-cell imaging of PER2:LUC bioluminescence. PLoS ONE 2012, 73:e33334. 10.1371/journal.pone.0033334.
20. Levine J.D., Funes P., Dowse H.B., Hall J.C. Signal analysis of behavioral and molecular cycles. BMC Neurosci. 2002, 3:1.
21. Nielsen J.K. Sinusoidal Parameter Estimation 2009, Aalborg University.
22. Nielsen J.K., Christensen M.G., Cemgil A.T., Godsill S.J., Jensen S.H. Bayesian interpolation and parameter estimation in a dynamic sinusoidal model. IEEE Trans. Audio Speech Lang. Process. 2011, 19:1986-1998.
23. Price T.S., Baggs J.E., Curtis A.M., Fitzgerald G.A., Hogenesch J.B. WAVECLOCK: wavelet analysis of circadian oscillation. Bioinformatics 2008, 24:2794-2795.
24. Turner, R., Sahani, M., 2011. Probabilistic amplitude and frequency demodulation. In: Neural Information Processing Systems Conference and Workshop, pp. 981-989.
25. Welsh D.K., Yoo S.-H., Liu A., Takahashi J., Kay S. Bioluminescence imaging of individual fibroblasts reveals persistent, independently phased circadian rhythms of clock gene expression. Curr. Biol. 2004, 14:2289-2295.