Accounting for Decay of Linkage Disequilibrium in Haplotype Inference and Missing-Data Imputation

Besag, 1994, Discussion on the paper by Grenander and Miller, J R Stat Soc B, 56, 591

Carlson, 2003, Additional SNPs and linkage-disequilibrium analyses are necessary for whole-genome association studies in humans, Nat Genet, 33, 518, 10.1038/ng1128

Chapman, 2003, Detecting disease associations due to linkage disequilibrium using haplotype tags: a class of tests and the determinants of statistical power, Hum Hered, 56, 18, 10.1159/000073729

Clark, 1990, Inference of haplotypes from PCR-amplified samples of diploid populations, Mol Biol Evol, 7, 111

Crawford, 2004, Evidence for substantial fine-scale variation in recombination rates across the human genome, Nat Genet, 36, 700, 10.1038/ng1376

Daly, 2001, High-resolution haplotype structure in the human genome, Nat Genet, 29, 229, 10.1038/ng1001-229

Eskin, 2003, Efficient reconstruction of haplotype structure via perfect phylogeny, J Bioinform Comput Biol, 1, 1, 10.1142/S0219720003000174

Eskin E, Halperin E, Karp R (2003b) Large scale reconstruction of haplotypes from genotype data. In: Proceedings of the seventh annual international conference on research in computational molecular biology (RECOMB 2003) pp 104–113

Evans, 1993

Excoffier, 2003, Gametic phase estimation over large genomic regions using an adaptive window approach, Hum Genomics, 1, 7, 10.1186/1479-7364-1-1-7

Excoffier, 1995, Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population, Mol Biol Evol, 12, 921

Fallin, 2000, Accuracy of haplotype frequency estimation for biallelic loci, via the expectation-maximization algorithm for unphased diploid genotype data, Am J Hum Genet, 67, 947, 10.1086/303069

Fearnhead, 2001, Estimating recombination rates from population genetic data, Genetics, 159, 1299, 10.1093/genetics/159.3.1299

Greenspan, 2004, Model-based inference of haplotype block variation, J Comput Biol, 11, 493, 10.1089/1066527041410300

Halperin, 2004, Haplotype reconstruction from genotype data using imperfect phylogeny, Bioinformatics, 20, 1842, 10.1093/bioinformatics/bth149

Hawley, 1995, HAPLO: a program using the EM algorithm to estimate the frequencies of multi-site haplotypes, J Hered, 86, 409, 10.1093/oxfordjournals.jhered.a111613

Heckerman, 2000, Dependency networks for inference, collaborative filtering, and data visualization, J Machine Learning Res, 1, 49

Hudson, 1991, Gene genealogies and the coalescent process, Vol 7, 1

Johnson, 2001, Haplotype tagging for the identification of common disease genes, Nat Genet, 29, 233, 10.1038/ng1001-233

Kimmel, 2004, Maximum likelihood resolution of multi-block genotypes, 2

Li, 2003, Modelling linkage disequilibrium, and identifying recombination hotspots using SNP data, Genetics, 165, 2213, 10.1093/genetics/165.4.2213

Lin, 2004, Haplotype and missing data inference in nuclear families, Genome Res, 14, 1624, 10.1101/gr.2204604

Lin, 2002, Haplotype inference in random population samples, Am J Hum Genet, 71, 1129, 10.1086/344347

Long, 1995, An E-M algorithm and testing strategy for multiple locus haplotypes, Am J Hum Genet, 56, 799

McVean, 2004, The fine-scale structure of recombination rate variation in the human genome, Science, 304, 581, 10.1126/science.1092500

Niu, 2002, Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms, Am J Hum Genet, 70, 157, 10.1086/338446

Ptak, 2004, Absence of the TAP2 human recombination hotspot in chimpanzees, PLoS Biol, 2, 849, 10.1371/journal.pbio.0020155

Qin, 2002, Partial-ligation-expectation-maximization algorithm for haplotype inference with single-nucleotide polymorphisms, Am J Hum Genet, 71, 1242, 10.1086/344207

Rabiner, 1989, A tutorial on hidden Markov models and selected applications in speech recognition, Proc IEEE, 77, 257, 10.1109/5.18626

Schaffner, 2004, The X chromosome in population genetics, Nat Rev Genet, 5, 43, 10.1038/nrg1247

Stephens, 2000, Inference in molecular population genetics, J R Stat Soc Ser B, 62, 605, 10.1111/1467-9868.00254

Stephens, 2003, A comparison of Bayesian methods for haplotype reconstruction from population genotype data, Am J Hum Genet, 73, 1162, 10.1086/379378

Stephens, 2001, A new statistical method for haplotype reconstruction from population data, Am J Hum Genet, 68, 978, 10.1086/319501