Bayesian analysis of isochores

Journal of the American Statistical Association

Volumn 104, Issue 485, 2009, Pages 132-141

  Fearnhead, Paul ^a   Vasileiou, Despina ^a  

^a LANCASTER UNIVERSITY   (United Kingdom)

Author keywords

Changepoint; Direct simulation; GC content; Hidden Markov model; Recombination

Indexed keywords

EID: 70350644850     PISSN: 01621459     EISSN: None     Source Type: Journal    
DOI: 10.1198/jasa.2009.0009     Document Type: Article

References (34)

1. Barry, D., and Hartigan, J. A. (1992), "Product Partition Models for Change Point Problems," The Annals of Statistics, 20, 260-279.
2. -(1993), "A Bayesian Analysis for Change Point Problems," Journal of the American Statistical Society, 88, 309-319.
3. Baum, L. E., Petrie, T., Soules, G., and Weiss, N. (1970), "A Maximisation Technique Occurring in the Statistical Analysis of Probabilistic Functions of Markov Chains," Annals of Mathematical Statistics, 41, 164-171.
4. Bernaola-Galvan, P., Carpena, P., Román-Roldán, R., and Oliver, J. L. (2002), "Study of Statistical Correlations in DNA," Gene, 300, 105-115.
5. Bernaola-Galvan, P., Roman-Roldan, R., and Oliver, J. L. (1996), "Compositional Segmentation and Long-Range Fractal Correlations in DNA Sequences," Physical Review E: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, 53, 5181-5189.
6. Bernardi, G. (2000), "Isochores and Evolutionary Genomics of Vertebrates," Gene, 241, 3-17.
7. Boys, R. J., Henderson, D. A., and Wilkinson, D. J. (2000), "Detecting Homogeneous Segments in DNA Sequences by Using Hidden Markov Models," Journal of the Royal Statistical Society, Series C, 49, 269-285.
8. Braun, J. V., Braun, R. K., and Muller, H. G. (2000), "Multiple Changepoint Fitting via Quasilikelihood, With Application to DNA Sequence Segmentation," Biometrika, 87, 301-314.
9. Braun, J. V., and Muller, H. G. (1998), "Statistical Methods for DNA Sequence Segmentation," Statistical Science, 13, 142-162.
10. Carpena, P., Bernaola-Galvan, P., Roman-Roldan, R., and Oliver, J. L. (2002), "A Simple and Species-Independent Coding Measure," Gene, 300, 97-104.
11. Cohen, N., Dagan, T., Stone, L., and Graur, D. (2005), "GC Composition of the Human Genome: In Search of Isochores," Molecular Biology and Evolution, 22, 1260-1272.
12. Constantini, M., Clay, O., Auletta, F., and Bernardi, G. (2006), "An Isochore Map of Human Chromosomes," Genome Research, 16, 536-541.
13. Eyre-Walker, A., and Hurst, L. D. (2001), "The Evolution of Isochores," Nature Reviews, Genetics, 2, 549-555.
14. Fearnhead, P. (2005), "Exact Bayesian Curve Fitting and Signal Segmentation," IEEE Transactions on Signal Processing, 53, 2160-2166.
15. - (2006), "Exact and Efficient Inference for Multiple Changepoint Problems," Statistics and Computing, 16, 203-213.
16. - (2008), "Computational Methods for Complex Stochastic Systems: A Review of Some Alternatives to MCMC," Statistics and Computing, 18, 151-171.
17. Fearnhead, P., and Liu, Z. (2007), "Online Inference for Multiple Changepoint Problems," Journal of the Royal Statistical Society: Series B, 69, 589-605.
18. Fearnhead, P., and Sherlock, C. (2006), "Bayesian Analysis of Markov Modulated Poisson Processes," Journal of the Royal Statistical Society: Series B, 68, 767-784.
19. Galtier, N., Piganeau, G., Mouchiroud, D., and Duret, L. (2001), "GC-Content Evolution in Mammalian Genomes: The Biased Gene Conversion Hypothesis," Genetics, 159, 907-911.
20. Hardison, R. C., Roskin, K. M., Yang, S., Diekhans, M., Kent,W. J.,Weber, R., Elnitski, L., Li, J., O'Connor, D., Kolbe, D., Schwartz, S., Furey, T. S., Whelan, S., Goldman, N., Smit, A., Miller, W., Chiaromonte, F., and Haussler, D. (2003), "Covariation in Frequencies of Substitution, Deletion, Transposition, and Recombination During Eutherian Evolution," Genome Research, 13, 13-26.
21. IHGSC. (2001), "Initial Sequencing and Analysis of the Human Genome," Nature, 409, 860-921.
22. Kong, A., Gubdjartsson, D. F., Sainz, J., Jonsdottir, G. M., Gudjonson, S. A., Richardsson, B., Sigurdardottir, S., Barnard, J., Hallbeck, B., Masson, G., Shlien, A., Palsson, S. T., Frigge, M. L., Thorgeirsson, T. E., Gulcher, J. R., and Stefansson, K. (2002), "A High-Resolution Recombination Map of the Human Genome," Nature Genetics, 31, 241-247.
23. Lai, T. L., Liu, H., and Xing, H. (2005), "Autoregressive Models With Piecewise Constant Volatility and Regression Parameters," Statistica Sinica, 15, 279-301.
24. Li, W. T., Bernaola-Galvan, P., Haghighi, F., and Grosse, I. (2002), "Applications of Recursive Segmentation to the Analysis of DNA Sequences," Gene, 276, 57-72.
25. Liu, J. S., Chen, R., and Wong, W. H. (1998), "Rejection Control and Sequential Importance Sampling," Journal of the American Statistical Society, 93, 1022-1031.
26. Liu, J. S., and Lawrence, C. E. (1999), "Bayesian Inference on Biopolymer Models," Bioinformatics (Oxford, England), 15, 38-52.
27. Myers, S., Bottolo, L., Freeman, C., McVean, G. A. T., and Donnelly, P. (2005), "A Fine-Scale Map of Recombination Rates and Hotspots Across the Human Genome," Science, 310, 321-324.
28. Nekruteno, A., and Li, W. H. (2000), "Assessment of Compositional Heterogeneity Within and Between Eukaryotic Genomes," Genome Research, 10, 1986-1995.
29. Oliver, J. L., Carpena, P., Hackenberg, M., and Bernaola-Galvan, P. (2004), "IsoFinder: Computational Prediction of Isochores in Genome Sequences," Nucleic Acids Research, 32, W287-W292.
30. Salmenkivi, M., Kere, J., and Mannila, H. (2002), "Genome Segmentation Using Piecewise Constant Intensity Models and Reversible Jump MCMC," Bioinformatics (Oxford, England), 18, S211-S218.
31. Smith, N. G., and Lercher, M. J. (2002), "Regional Similarities in Polymorphism in the Human Genome Extended for Many Megabases," Trends in Genetics, 18, 281-283.
32. Spencer, C., Deloukas, P., Hunt, S., Mullikin, J., Myers, S., Silverman, B., Donnelly, P., Bentley, D., and McVean, G. (2006), "The Influence of Recombination on Human Genetic Diversity," PLOS Genetics, 2, e148.
33. Venter, J. C.,Adams,M.D.,Myers,E.W.,Li, P.W.,Mural,R. J., Sutton,G.G., et al. (2001), "The Sequence of the Human Genome," Science, 291, 1304-1351.
34. Yao, Y. (1984), "Estimation of a Noisy Discrete-Time Step Function: Bayes and Empirical Bayes Approaches," The Annals of Statistics, 12, 1434-1447.