A hierarchical semiparametric regression model for combining HIV-1 phylogenetic analyses using iterative reweighting algorithms

Biometrics

Volumn 63, Issue 3, 2007, Pages 733-741

  Liang, Li Jung ^a   Weiss, Robert E ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Dirichlet process; Importance weighting; Kernel density estimation; MCMC; Molecular phylogeny; Monte Carlo swindle; Subsampling

Indexed keywords

BAYESIAN NETWORKS; COMPUTER SOFTWARE; ITERATIVE METHODS; MARKOV PROCESSES; MONTE CARLO METHODS; REGRESSION ANALYSIS;

DIRICHLET PROCESS; IMPORTANCE WEIGHTING; KERNEL DENSITY ESTIMATION; MARKOV CHAIN MONTE CARLO; MARKOV CHAIN MONTE-CARLO; MOLECULAR PHYLOGENY; MONTE CARLO SWINDLE; PHYLOGENETIC ANALYSIS; SEMIPARAMETRIC REGRESSION MODEL; SUBSAMPLING;

PHYLOGENETIC;

ALGORITHM; BAYESIAN ANALYSIS; GENETIC ANALYSIS; MARKOV CHAIN; MONTE CARLO ANALYSIS; PHYLOGENETICS; PHYLOGENY; REGRESSION ANALYSIS;

ALGORITHM; ARTICLE; BAYES THEOREM; COMPUTER PROGRAM; HUMAN IMMUNODEFICIENCY VIRUS 1; LOGISTIC REGRESSION ANALYSIS; NUCLEOTIDE SEQUENCE; PARAMETRIC TEST; PHYLOGENY; PROBABILITY;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 34548378755     PISSN: 0006341X     EISSN: 15410420     Source Type: Journal    
DOI: 10.1111/j.1541-0420.2007.00753.x     Document Type: Article

References (29)

1. Bradlow, E. and Zaslavsky, A. M. (1997). Case influence analysis in Bayesian inference. Journal of Computational and Graphical Statistics 6, 314 331.
2. Burr, D. and Doss, H. (2005). A Bayesian semiparametric model for random-effects meta-analysis. Journal of American Statistical Association 100, 242 251.
3. Bush, C. A. and MacEachern, S. N. (1996). A semiparametric Bayesian model for randomised block designs. Biometrika 83, 275 285.
4. Carlin, B. (1992). Meta-analysis for 2 × 2 tables: A Bayesian approach. Statistics in Medicine 11, 141 158.
5. Escobar, M. D. and West, M. (1995). Bayesian density estimation and inference using mixtures. Journal of American Statistical Association 90, 577 588.
6. Ferguson, T. S. (1973). A Bayesian analysis of some nonparametric problems. The Annals of Statistics 1, 209 230.
7. Hasegawa, M., Kishino, H., and Yano, T. (1985). Dating the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution 22, 160 174.
8. Huelsenbeck, J. P. and Ronquist, F. (2001). MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics Applications Note 17 (8 754 755.
9. Ishwaran, H. and James, L. (2001). Gibbs sampling methods for stick-breaking priors. Journal of American Statistical Association 96, 161 173.
10. Kleinman, K. and Ibrahim, J. G. (1998). A semiparametric Bayesian approach to random effects model. Biometrics 54, 921 938.
11. Kuiken, C., Foley, B., Freed, E., Hahn, B., Marx, P., McCutchan, F., Mellors, L., Wolinsky, S., and Korber, B. (2002). HIV sequence compendium 2002. Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, LA-UR number 03-3564. Available at http://www.hiv.lanl.gov/content/hiv-db/mainpage. html.
12. Larget, B. and Simon, D. L. (1999). Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Molecular Biology Evolution 16, 750 759.
13. Li, S., Pearl, D. K, and Doss, H. (2000). Phylogenetic tree construction using Markov chain Monte Carlo. Journal of American Statistical Association 95, 493 508.
14. Liu, J. (1996). Nonparametric hierarchical Bayes via sequential imputations. The Annals of Statistics 24, 911 930.
15. MacEachern, S. N. and Müller, P. (1998). Estimating mixture of Dirichlet process models. Journal of Computational and Graphical Statistics 7, 223 238.
16. MacEachern, S. N. and Peruggia, M. (2000). Importance link function estimation for Markov chain Monte Carlo methods. Journal of Computational and Graphical Statistics 9, 99 121.
17. Müller, P. and Rosner, G. (1997). A Bayesian population model with hierarchical mixture priors applied to blood count data. Journal of American Statistical Association 92, 1279 1292.
18. Müller, P., Quintana, F., and Rosner, G. (2004). A method for combining inference across related nonparametric Bayesian models. Journal of the Royal Statistical Society, Ser. B 66, 735 749.
19. Rubin, D. (1988). Using the sir algorithm to simulate posterior distributions. Bayesian Statistics 3. In J. M. Bernardo, M. H. DeGroot, D. V. Lindley, and A. F. M. Smith (eds 395 402. Cambridge, MA : Oxford University Press.
20. Sethurman, J. (1994). A constructive definition of Dirichlet priors. Statistica Sinica 4, 639 650.
21. Sharp, P. M., Bailes, E., Gao, F., Beer, B. E., Hirsch, V. M., and Hahn, B. (2000). Origins and evolution of AIDS viruses: Estimating the time-scale. Biochemical Society Transactions 28, 275 282.
22. Smith, A. F. M. and Gelfand, A. (1992). Bayesian statistics without tears: A sampling-resampling perspective. The American Statistician 46, 84 88.
23. Smith, T., Spiegelhalter, D., and Thomas, A. (1995). Bayesian approaches to random-effects meta-analysis: A comparative study. Statistics in Medicine 14, 2685 2699.
24. Suchard, M. A., Weiss, R. E., Dorman, K. S., and Sinsheimer, J. S. (2002). Oh brother, where are thou? A Bayes factor test for recombination with uncertain heritage. Systematic Biology 51, 715 728.
25. Suchard, M. A., Kitchen, C. M. R., Sinsheimer, J. S., and Weiss, R. E. (2003). Hierarchical phylogenetic models for analyzing multipartite sequence data. Systematic Biology 52, 1649 1664.
26. Tierney, L. (1994). Markov chains for exploring posterior distributions. The Annals of Statistics 22, 1701 1762.
27. Warn, D., Thompson, S., and Spiegelhalter, D. (2002). Bayesian random effects meta-analysis of trials with binary outcomes: Methods for the absolute risk difference and relative risk scales. Statistics in Medicine 21, 1601 1623.
28. Weiss, R. E. (1996). An approach to Bayesian sensitivity analysis. Journal of the Royal Statistical Society, Series B 58, 739 750.
29. Yang, Z. (2001). Maximum likelihood analysis of adaptive evolution in hiv-1 gp120 env gene. Pacific Symposium on BioComputing, January 3-7, Hawaii.