A coalescent dual process for a Wright–Fisher diffusion with recombination and its application to haplotype partitioning
Tài liệu tham khảo
Barbour, 2000, A transition function expansion for a diffusion model with selection, Ann. Appl. Probab., 10, 123, 10.1214/aoap/1019737667
Bobrowski, 2010, Asymptotic behavior of a Moran model with mutations, drift and recombination among multiple loci, J. Math. Biol., 61, 455, 10.1007/s00285-009-0308-1
Donnelly, 1999, Genealogical processes for Fleming–Viot models with selection and recombination, Ann. Appl. Probab., 9, 1091, 10.1214/aoap/1029962866
Donnelly, 1987, The population genealogy of the infinitely-many neutral alleles model, J. Math. Biol., 25, 381, 10.1007/BF00277163
Esser, 2016, Partitioning, duality, and linkage disequilibria in the Moran model with recombination, J. Math. Biol., 73, 161, 10.1007/s00285-015-0936-6
Etheridge, 2009, A coalescent dual process in a Moran model with genic selection, Theor. Popul. Biol., 75, 320, 10.1016/j.tpb.2009.03.004
Etheridge, 2010, A coalescent dual process in a Moran model with genic selection, and the lambda coalescent limit, Theor. Popul. Biol., 78, 77, 10.1016/j.tpb.2010.05.004
Ethier, 1987, The infinitely-many-sites model as a measure-valued diffusion, Ann. Probab., 15, 515, 10.1214/aop/1176992157
Ethier, 1990, The neutral two-locus model as a measure-valued diffusion, Adv. Appl. Probab., 22, 773, 10.2307/1427561
Ethier, 1990, On the two-locus sampling distribution, J. Math. Biol., 29, 131, 10.1007/BF00168175
Ethier, 1993, The transition function of a Fleming–Viot process, Ann. Probab., 21, 1571, 10.1214/aop/1176989131
Ethier, 1993, Fleming–Viot processes in population genetics, SIAM J. Control Optim., 31, 345, 10.1137/0331019
Fearnhead, 2002, The common ancestor at a nonneutral locus, J. Appl. Probab., 39, 38, 10.1239/jap/1019737986
Fearnhead, 2003, Haplotypes: the joint distribution of alleles at linked loci, J. Appl. Probab., 40, 505, 10.1239/jap/1053003559
Fearnhead, 2001, Estimating recombination rates from population genetic data, Genetics, 159, 1299, 10.1093/genetics/159.3.1299
Golding, 1984, The sampling distribution of linkage disequilibrium, Genetics, 108, 257, 10.1093/genetics/108.1.257
Griffiths, 1979, A transition density expansion for a multi-allele diffusion model, Adv. Appl. Probab., 11, 310, 10.2307/1426842
Griffiths, 1980, Lines of descent in the diffusion approximation of neutral Wright–Fisher models, Theor. Popul. Biol., 17, 37, 10.1016/0040-5809(80)90013-1
Griffiths, 1981, Neutral two-locus multiple allele models with recombination, Theor. Popul. Biol., 19, 169, 10.1016/0040-5809(81)90016-2
Griffiths, 1991, The two-locus ancestral graph, vol. 18, 100
Griffiths, 2008, Importance sampling and the two-locus model with subdivided population structure, Adv. Appl. Probab., 40, 473, 10.1239/aap/1214950213
Griffiths, 1996, Ancestral inference from samples of DNA sequences with recombination, J. Comput. Biol., 3, 479, 10.1089/cmb.1996.3.479
Griffiths, 1997, An ancestral recombination graph, 257
Handa, 2002, Quasi-invariance and reversibility in the Fleming–Viot process, Probab. Theory Related Fields, 122, 545, 10.1007/s004400100178
Hudson, 1983, Properties of a neutral allele model with intragenic recombination, Theor. Popul. Biol., 23, 183, 10.1016/0040-5809(83)90013-8
Jansen, 2014, On the notion(s) of duality for Markov processes, Probab. Surv., 11, 59, 10.1214/12-PS206
Jenkins, 2011, Inference from samples of DNA sequences using a two-locus model, J. Comput. Biol., 18, 109, 10.1089/cmb.2009.0231
Jenkins, 2009, Closed-form two-locus sampling distributions: accuracy and universality, Genetics, 183, 1087, 10.1534/genetics.109.107995
Kamm, 2016, Two-locus likelihoods under variable population size and fine-scale recombination rate estimation, Genetics, 203, 1381, 10.1534/genetics.115.184820
Kingman, 1982, The coalescent, Stochastic Process. Appl., 13, 235, 10.1016/0304-4149(82)90011-4
Krone, 1997, Ancestral processes with selection, Theor. Popul. Biol., 51, 210, 10.1006/tpbi.1997.1299
Larribe, 2008, A composite-conditional-likelihood approach for gene mapping based on linkage disequilibrium in windows of marker loci, Stat. Appl. Genet. Mol. Biol., 7, 10.2202/1544-6115.1298
Larribe, 2002, Gene mapping via the ancestral recombination graph, Theor. Popul. Biol., 62, 215, 10.1006/tpbi.2002.1601
Lohse, 2016, Efficient strategies for calculating blockwise likelihoods under the coalescent, Genetics, 202, 775, 10.1534/genetics.115.183814
Lohse, 2011, A general method for calculating likelihoods under the coalescent process, Genetics, 189, 977, 10.1534/genetics.111.129569
Mano, 2013, Duality between the two-locus Wright–Fisher diffusion model and the ancestral process with recombination, J. Appl. Probab., 50, 256, 10.1239/jap/1363784437
Neuhauser, 1997, The genealogy of samples in models with selection, Genetics, 145, 519, 10.1093/genetics/145.2.519
OEIS Foundation Inc., 2011. The on-line encyclopedia of integer sequences. URL http://oeis.org.
Simonsen, 1997, A Markov chain model of coalescence with recombination, Theor. Popul. Biol., 52, 43, 10.1006/tpbi.1997.1307
Stephens, 2007, Inference under the coalescent, 878
Stephens, 2003, Ancestral inference in population genetics models with selection, Aust. N. Z. J. Stat., 45, 395, 10.1111/1467-842X.00295
Wiuf, 1997, On the number of ancestors to a DNA sequence, Genetics, 147, 1459, 10.1093/genetics/147.3.1459
Wright, 1949, Adaptation and selection, 365