A population genetic hidden Markov model for detecting genomic regions under selection.
暂无分享,去创建一个
[1] David Haussler,et al. Combining phylogenetic and hidden Markov models in biosequence analysis , 2003, RECOMB '03.
[2] A. Hobolth,et al. Genomic Relationships and Speciation Times of Human, Chimpanzee, and Gorilla Inferred from a Coalescent Hidden Markov Model , 2006, PLoS genetics.
[3] J. Gillespie. Genetic drift in an infinite population. The pseudohitchhiking model. , 2000, Genetics.
[4] N. Risch,et al. Estimation of individual admixture: Analytical and study design considerations , 2005, Genetic epidemiology.
[5] Gabor T. Marth,et al. The Allele Frequency Spectrum in Genome-Wide Human Variation Data Reveals Signals of Differential Demographic History in Three Large World Populations , 2004, Genetics.
[6] J. Pritchard,et al. A Map of Recent Positive Selection in the Human Genome , 2006, PLoS biology.
[7] J. Gillespie. Substitution processes in molecular evolution. III. Deleterious alleles. , 1994, Genetics.
[8] M. Stephens,et al. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. , 2003, Genetics.
[9] Colin N. Dewey,et al. Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans , 2007, PLoS biology.
[10] D. Hartl,et al. Population genetics of polymorphism and divergence. , 1992, Genetics.
[11] M. Kimura,et al. Theoretical foundation of population genetics at the molecular level. , 1971, Theoretical population biology.
[12] M. Shriver,et al. Interrogating a high-density SNP map for signatures of natural selection. , 2002, Genome research.
[13] M. A. McClure,et al. Hidden Markov models of biological primary sequence information. , 1994, Proceedings of the National Academy of Sciences of the United States of America.
[14] J. Gillespie. Substitution processes in molecular evolution. I. Uniform and clustered substitutions in a haploid model. , 1993, Genetics.
[15] G. Coop,et al. THE SIGNATURE OF POSITIVE SELECTION ON STANDING GENETIC VARIATION , 2005, Evolution; international journal of organic evolution.
[16] N. Barton,et al. Genetic hitchhiking. , 2000, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.
[17] J. Gillespie. SUBSTITUTION PROCESSES IN MOLECULAR EVOLUTION. II. EXCHANGEABLE MODELS FROM POPULATION GENETICS , 1994, Evolution; international journal of organic evolution.
[18] L. Baum,et al. Statistical Inference for Probabilistic Functions of Finite State Markov Chains , 1966 .
[19] P. Andolfatto. Adaptive evolution of non-coding DNA in Drosophila , 2005, Nature.
[20] A. Clark,et al. Recent and ongoing selection in the human genome , 2007, Nature Reviews Genetics.
[21] N. Risch,et al. Reconstructing genetic ancestry blocks in admixed individuals. , 2006, American journal of human genetics.
[22] Michael I. Jordan,et al. On the Inference of Ancestries in Admixed Populations , 2008, RECOMB.
[23] A. Kern,et al. Molecular Population Genetics of Male Accessory Gland Proteins in the Drosophila simulans Complex , 2004, Genetics.
[24] Obi L. Griffith,et al. ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation , 2006, Bioinform..
[25] F. Tajima. Evolutionary relationship of DNA sequences in finite populations. , 1983, Genetics.
[26] D. Haussler,et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. , 2005, Genome research.
[27] J. Gillespie. Junk ain't what junk does: neutral alleles in a selected context. , 1997, Gene.
[28] S. Wright. Evolution and the Genetics of Populations, Volume 3: Experimental Results and Evolutionary Deductions , 1977 .
[29] D. Haussler,et al. Protein modeling using hidden Markov models: analysis of globins , 1993, [1993] Proceedings of the Twenty-sixth Hawaii International Conference on System Sciences.
[30] R. Lewontin,et al. The Genetic Basis of Evolutionary Change , 2022 .
[31] D. Rubin,et al. Maximum likelihood from incomplete data via the EM - algorithm plus discussions on the paper , 1977 .
[32] Richard R. Hudson,et al. Generating samples under a Wright-Fisher neutral model of genetic variation , 2002, Bioinform..
[33] C. Bustamante,et al. Population Genetics of Polymorphism and Divergence for Diploid Selection Models With Arbitrary Dominance , 2004, Genetics.
[34] W. Li,et al. Statistical tests of neutrality of mutations. , 1993, Genetics.
[35] Ryan D. Hernandez,et al. Simultaneous inference of selection and population growth from patterns of variation in the human genome , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[36] A. Kern. Correcting the Site Frequency Spectrum for Divergence-Based Ascertainment , 2009, PloS one.
[37] R. A. Fisher,et al. The Genetical Theory of Natural Selection , 1931 .
[38] Sewall Wright,et al. The theory of gene frequencies , 1969 .
[39] C. Bustamante,et al. A Composite-Likelihood Approach for Detecting Directional Selection From DNA Sequence Data , 2005, Genetics.
[40] Kevin R. Thornton,et al. Approximate Bayesian Inference Reveals Evidence for a Recent, Severe Bottleneck in a Netherlands Population of Drosophila melanogaster , 2006, Genetics.
[41] G. Schwarz. Estimating the Dimension of a Model , 1978 .
[42] P. Donnelly,et al. Inference of population structure using multilocus genotype data. , 2000, Genetics.
[43] Ryan D. Hernandez,et al. Assessing the Evolutionary Impact of Amino Acid Mutations in the Human Genome , 2008, PLoS genetics.
[44] M. Adams,et al. Inferring Nonneutral Evolution from Human-Chimp-Mouse Orthologous Gene Trios , 2003, Science.
[45] William H. Press,et al. Numerical recipes in C , 2002 .
[46] H. A. Orr,et al. A Pseudohitchhiking Model of X vs. Autosomal Diversity , 2004, Genetics.
[47] Stephen M. Mount,et al. The genome sequence of Drosophila melanogaster. , 2000, Science.
[48] Andrew G. Clark,et al. Reconstituting the Frequency Spectrum of Ascertained Single-Nucleotide Polymorphism Data , 2004, Genetics.
[49] D. Hartl,et al. Directional selection and the site-frequency spectrum. , 2001, Genetics.
[50] H. Gillespie. EXCHANGEABLE MODELS FROM POPULATION GENETICS , 1994 .
[51] W. Stephan,et al. Detecting a local signature of genetic hitchhiking along a recombining chromosome. , 2002, Genetics.
[52] Andrew J. Viterbi,et al. Error bounds for convolutional codes and an asymptotically optimum decoding algorithm , 1967, IEEE Trans. Inf. Theory.
[53] G. Churchill. Stochastic models for heterogeneous DNA sequences. , 1989, Bulletin of mathematical biology.
[54] J. Felsenstein,et al. A Hidden Markov Model approach to variation among sites in rate of evolution. , 1996, Molecular biology and evolution.
[55] W Stephan,et al. The hitchhiking effect on the site frequency spectrum of DNA polymorphisms. , 1995, Genetics.
[56] Jason E Stajich,et al. Disentangling the effects of demography and selection in human history. , 2004, Molecular biology and evolution.
[57] M. Kimura,et al. The neutral theory of molecular evolution. , 1983, Scientific American.
[58] Sean R. Eddy,et al. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids , 1998 .
[59] S. Wright,et al. The Distribution of Gene Frequencies Under Irreversible Mutation. , 1938, Proceedings of the National Academy of Sciences of the United States of America.
[60] Z. Yang,et al. A space-time process model for the evolution of DNA sequences. , 1995, Genetics.
[61] Carlos Bustamante,et al. Genomic scans for selective sweeps using SNP data. , 2005, Genome research.
[62] L. Baum,et al. A Maximization Technique Occurring in the Statistical Analysis of Probabilistic Functions of Markov Chains , 1970 .
[63] M. Ashburner,et al. Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.
[64] Christian Schlötterer,et al. Detecting Selective Sweeps: A New Approach Based on Hidden Markov Models , 2009, Genetics.
[65] R. Punnett,et al. The Genetical Theory of Natural Selection , 1930, Nature.
[66] Justin C. Fay,et al. Hitchhiking under positive Darwinian selection. , 2000, Genetics.
[67] S. Wright,et al. Evolution and the Genetics of Populations: Volume 2, The Theory of Gene Frequencies , 1968 .
[68] J. Gillespie. The causes of molecular evolution , 1991 .
[69] F. Tajima. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. , 1989, Genetics.
[70] C. Bustamante,et al. Distinguishing Between Selective Sweeps and Demography Using DNA Polymorphism Data , 2005, Genetics.
[71] Stephen L. Hauser,et al. Genome-wide patterns of population structure and admixture in West Africans and African Americans , 2009, Proceedings of the National Academy of Sciences.