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Artificial Intelligence in Medicine
Volume 45, Issue 2
, Pages 135-150
, February 2009
Fully non-homogeneous hidden Markov model double net: A generative model for haplotype reconstruction and block discovery
References
- The structure of haplotype blocks in the human genome. Science. 2002;296(5576):2225–2229
- . Haplotype block structure and its application to association studies: power and study designs. American Journal of Human Genetics. 2002;71(6):1386–1394
- . A comparison of Bayesian methods for haplotype reconstruction from population genotype data. American Journal of Human Genetics. 2003;73(5):1162–1169
- . Volume measures for linkage disequilibrium. BMC Genetics. 2006;7(1):54–61
- . A hidden markov technique for haplotype reconstruction. In: Casadio R, Myers G editor. Algorithms in Bioinformatics, vol. 3692 of Lecture Notes in Computer Science. New York, NY, USA: Springer; 2005;p. 140–151
- . Gerbil: Genotype resolution and block identification using likelihood. Proceedings of the National Academy of Science of the United States of America (PNAS). 2005;102:158–162
- . A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. American Journal of Human Genetics. 2006;78(4):629–644
- . Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms. American Journal of Human Genetics. 2002;78(1):157–169
- . Partition–ligation–expectation–maximization algorithm for haplotype inference with single-nucleotide polymorphisms. American Journal of Human Genetics. 2002;71(5):1242–1247
- D. Clayton, Snphap: A program for estimating frequencies of large haplotypes of snps (version 1.0), http://www-gene.cimr.cam.ac.uk/clayton/software/snphap.txt, Accessed: 11 December 2007 (2001).
- . A tutorial on Hidden Markov Models and selected applications in speech recognition. Proceedings of IEEE. 1989;77(2):257–286
- . An introduction to variational methods for graphical models. Machine Learning. 1999;37(2):183–233
- . Joint discovery of haplotype blocks and complex trait associations from snp sequences. In: Chickering DM, Halpern JY editor. Proceedings of the Uncertainty in artificial intelligence 2004, UAI’04. Arlington, Virginia: UAI Press; 2004;p. 286–292
- . Pattern Classification. 2nd Edition. Hoboken, NJ: Wiley–Interscience; 2000;
- . Dna segmentation as a model selection process. In: Lengauer T, Sankoff D, Istrail S, Peuvzner P, Waterman M editor. RECOMB’01: Proceedings of the fifth annual international conference on computational biology. New York, NY, USA: ACM; 2001;p. 204–210
- An mdl method for finding haplotype blocks and for estimating the strength of haplotype block boundaries. In: Altman RB, Dunker AK, Hunter L, Jung TA, Klein TE editor. Proceedings of the Pacific Symposium on Biocomputing (PSB), vol. 8. Singapore: World Scientific; 2003;p. 502–513
- . Modelling by shortest data description. Automatica. 1978;14:465–471
- . Graphical models and variational methods. In: Opper M, Saad D editor. Advanced mean field methods: theory and practice. Cambridge, MA, USA: MIT Press; 2001;p. 161–178Ch. 11
- D. Heckerman, A tutorial on learning with Bayesian networks, Tech. Re MSR-TR-95–06, Microsoft Research, Redmond, WA, USA, revised November, 1996 (1995).
- . Learning dynamic Bayesian networks. In: Giles CL, Gori M editor. Adaptive Processing of Sequences and Data Structures. Berlin: Springer-Verlag; 1998;p. 168–197
- . Tutorial on variational approximation methods. In: Opper M, Saad D editor. Advanced mean field methods: theory and practice. Cambridge, MA, USA: MIT Press; 2001;p. 129–160Ch. 10
- . Escaping local minima through hierarchical model selection: automatic object discovery, segmentation, and tracking in video. In: CVPR’06: Proceedings of the 2006 IEEE Computer Society Conference on Computer Vision and Pattern Recognition. Washington, DC, USA: IEEE Computer Society; 2006;p. 117–124
- . Maximum likelihood from incomplete data via the EM algorithm. Journal of the Royal Statistical Society. 1977;39:1–38
- . Linkage disequilibrium for different scales and applications. Briefings in Bioinformatics. 2004;5(4):355–364
- . The international hapmap project. Nature. 2003;426(6968):789–796
- . Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Molecular Biology and Evolution. 1995;12(5):921–927
- . Comparison of the accuracy of methods of computational haplotype inference using a large empirical dataset. BMC Genetics. 2004;5:22–28
- Human growth hormone 1 (gh1) gene expression: complex haplotype-dependent influence of polymorphic variation in the proximal promoter and locus control region. Human Mutation. 2003;21(4):408–423
- . Robustness of inference of haplotype block structure. Journal of Computational Biology. 2003;10(1):13–19
- . Analysis of concordance of different haplotype block partitioning algorithms. BMC Bioinformatics. 2005;6(1):303–316
- . Snps of the fads gene cluster are associated with polyunsaturated fatty acids in a cohort of patients with cardiovascular disease. Lipids. 2008;5(4):355–364
- . The interaction of selection of linkage. Genetics. 1964;49(1):49–67
- . Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. American Journal of Human Genetics. 2004;74(1):106–120
- Association of the interleukin-1 receptor antagonist gene with asthma. American Journal Respiratory and Critical Care Medicine. 2004;169(11):1217–1223
PII: S0933-3657(08)00127-9
doi: 10.1016/j.artmed.2008.08.015
© 2008 Elsevier B.V. All rights reserved.
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Artificial Intelligence in Medicine
Volume 45, Issue 2
, Pages 135-150
, February 2009
