Hidden Markov Dirichlet process: Modeling genetic recombination in open ancestral space

Advances in Neural Information Processing Systems

Volumn , Issue , 2007, Pages 1305-1312

  Sohn, Kyung Ah ^a   Xing, Eric P ^a  

^a Carnegie Mellon University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DIRICHLET PROCESS; EFFICIENT SAMPLING; GENETIC MARKERS; GENETIC PATTERNS; GENETIC RECOMBINATIONS; HAPLOTYPES; HOTSPOTS; INFINITE NUMBERS; MARKOV TRANSITION PROCESS; POPULATION STRUCTURES; RECOMBINATION EVENTS; SEQUENCE VARIATIONS; STATISTICAL FRAMEWORK;

CHROMOSOMES; COALESCENCE;

POPULATION STATISTICS;

EID: 66349129465     PISSN: 10495258     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (15)

1. E. C. Anderson and J. Novembre. Finding haplotype block boundaries by using the minimum-descriptionlength principle. Am J Hum Genet, 73:336-354, 2003.
2. M. J. Beal, Z. Ghahramani, and C. E. Rasmussen. The infinite hidden Markov model. In Advances in Neural Information Processing Systems 13, 2001.
3. D. Blackwell and J. B. MacQueen. Ferguson distributions via polya urn schemes. Annals of Statistics, 1:353-355, 1973.
4. M. J. Daly, J. D. Rioux, S. F. Schaffner, T. J. Hudson, and E. S. Lander. High-resolution haplotype structure in the human genome. Nature Genetics, 29(2):229-232, 2001.
5. D. Greenspan and D. Geiger. Model-based inference of haplotype block variation. In Proceedings of RECOMB 2003, 2003.
6. J. S. Liu, C. Sabatti, J. Teng, B.J.B. Keats, and N. Risch. Bayesian analysis of haplotypes for linkage disequilibrium mapping. Genome Res., 11:1716-1724, 2001.
7. T. Niu, S. Qin, X. Xu, and J. Liu. Bayesian haplotype inference for multiple linked single nucleotide polymorphisms. American Journal of Human Genetics, 70:157-169, 2002.
8. N. Patil, A. J. Berno, D. A. Hinds, et al. Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science, 294:1719-1723, 2001.
9. N. A. Rosenberg, J. K. Pritchard, J. L. Weber, H. M. Cann, K. K. Kidd, L. A. Zhivotovsky, and M. W. Feldman. Genetic structure of human populations. Science, 298:2381-2385, 2002.
10. Y. Teh, M. I. Jordan, M. Beal, and D. Blei. Hierarchical Dirichlet processes. Technical Report 653, Department of Statistics, University of California, Berkeley, 2004.
11. G.A. Thorisson, A.V. Smith, L. Krishnan, and L.D. Stein. The international hapmap project web site. Genome Research, 15:1591-1593, 2005.
12. E.P. Xing, R. Sharan, and M.I Jordan. Bayesian haplotype inference via the Dirichlet process. In Proceedings of the 21st International Conference on Machine Learning, 2004.
13. E.P. Xing, K.-A. Sohn, M.I Jordan, and Y. W. Teh. Bayesian multi-population haplotype inference via a hierarchical dirichlet process mixture. In Proceedings of the 23st International Conference on Machine Learning, 2006.
14. E.P. Xing and K.-A. Sohn. Hidden Markov Dirichlet Process: Modeling Genetic Recombination in Open Ancestral Space. In Bayesian Analysis, to appear, 2007.
15. K. Zhang, M. Deng, T. Chen, M. Waterman, and F. Sun. A dynamic programming algorithm for haplotype block partitioning. Proc. Natl. Acad. Sci. USA, 99(11):7335-39, 2002.