Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data.

By Na Li, Matthew Stephens. Genetics, 2003

1,053 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/97de476f5d3485f8fe29548ed061355d596f9d81

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Citations in the corpus

Gene-environment interactions in schizophrenia: review of epidemiological findings and future directions. (2008, methodology): “Fortunately, software allowing for modeling complicated interactions is currently being incorporated in several statistical programs.(143,144)”
MaCH: Using Sequence and Genotype Data to Estimate Haplotypes and Unobserved Genotypes (2010, background): “, 1996; Lander and Green, 1987] and shares several features with other HMMs used to describe sampled haplotypes as a mosaic of a set of reference haplotypes [Daly et al., 2001; Li and Stephens, 2003; Mott et al., 2000; Stephens and Scheet, 2005a].”
Inference of Population Structure using Dense Haplotype Data (2012, methodology): “We do not order the haplotypes in the same manner as the 'Product of Approximate Conditionals' likelihood used by Li and Stephens.”
Linkage disequilibrium levels in Bos indicus and Bos taurus cattle using medium and high density SNP chip data and different minor allele frequency distributions (2014, background): “In population genetics studies LD can be used in the estimation of recombination rates (Li and Stephens, 2003; Conrad et al., 2006), estimating effective population size (Tenesa et al.”
Fast and flexible simulation of DNA sequence data. (2008, methodology): “In addition to ms , we also include two other recently released programs: GENOME (Liang et al. 2007), which employs a retrospective approach to simulation similar to the coalescent, and FORWSIM (Padhukasahasram et al. 2008), which uses a forward-in-time simulation approach.”
Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation. (2005, unknown): “It is in the introduction of these T j values that this conditional distribution differs from those of Li and Stephens (2003) and is similar to the one from Fearnhead and Donnelly (2001).”
Computational pan-genomics: status, promises and challenges (2016, methodology): “One of the most widely used haplotype-based models is the Li-Stephens model [77].”
Accurate, scalable and integrative haplotype estimation (2019, methodology): “We run the LSM onto the resulting conditioning set to get new estimates for G .”
A Map of Recent Positive Selection in the Human Genome (2006, methodology): “Third, we did not implement the bias correction suggested by [24] because this depends in part on the spacing of markers, which varies widely in the data, and because the bias cancels out in our test ratio anyway.”