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

https://doi.org/10.1086/428594
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1038/ng1001-229openalex-snapshot
High-resolution haplotype structure in the human genome
inferredcites →https://doi.org/10.1038/ng1001-233openalex-snapshot
Haplotype tagging for the identification of common disease genes
inferredcites →https://doi.org/10.1038/ng1128openalex-snapshot
Additional SNPs and linkage-disequilibrium analyses are necessary for whole-genome association studies in humans
inferredcites →https://doi.org/10.1038/ng1376openalex-snapshot
Evidence for substantial fine-scale variation in recombination rates across the human genome
inferredcites →https://doi.org/10.1038/nrg1247openalex-snapshot
The X chromosome in population genetics
inferredcites →https://doi.org/10.1086/303069openalex-snapshot
Accuracy of Haplotype Frequency Estimation for Biallelic Loci, via the Expectation-Maximization Algorithm for Unphased Diploid Genotype Data
inferredcites →https://doi.org/10.1086/319501openalex-snapshot
A New Statistical Method for Haplotype Reconstruction from Population Data
inferredcites →https://doi.org/10.1086/338446openalex-snapshot
Bayesian Haplotype Inference for Multiple Linked Single-Nucleotide Polymorphisms
inferredcites →https://doi.org/10.1086/344207openalex-snapshot
Partition-Ligation–Expectation-Maximization Algorithm for Haplotype Inference with Single-Nucleotide Polymorphisms
inferredcites →https://doi.org/10.1086/344347openalex-snapshot
Haplotype Inference in Random Population Samples
inferredcites →https://doi.org/10.1086/379378openalex-snapshot
A Comparison of Bayesian Methods for Haplotype Reconstruction from Population Genotype Data
inferredcites →https://doi.org/10.1089/1066527041410300openalex-snapshot
Model-Based Inference of Haplotype Block Variation
inferredcites →https://doi.org/10.1093/bioinformatics/bth149openalex-snapshot
Haplotype reconstruction from genotype data using Imperfect Phylogeny
inferredcites →https://doi.org/10.1093/genetics/159.3.1299openalex-snapshot
Estimating Recombination Rates From Population Genetic Data
inferredcites →https://doi.org/10.1093/genetics/165.4.2213openalex-snapshot
Modeling Linkage Disequilibrium and Identifying Recombination Hotspots Using Single-Nucleotide Polymorphism Data
inferredcites →https://doi.org/10.1093/oxfordjournals.jhered.a111613openalex-snapshot
HAPLO: A Program Using the EM Algorithm to Estimate the Frequencies of Multi-site Haplotypes
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040269openalex-snapshot
Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040591openalex-snapshot
Inference of haplotypes from PCR-amplified samples of diploid populations.
inferredcites →https://doi.org/10.1101/gr.2204604openalex-snapshot
Haplotype and Missing Data Inference in Nuclear Families
inferredcites →https://doi.org/10.1109/5.18626openalex-snapshot
A tutorial on hidden Markov models and selected applications in speech recognition
inferredcites →https://doi.org/10.1111/1467-9868.00254openalex-snapshot
Inference in Molecular Population Genetics
inferredcites →https://doi.org/10.1111/j.2517-6161.1994.tb02001.xopenalex-snapshot
Discussion of the Paper by Grenander and Miller
inferredcites →https://doi.org/10.1126/science.1092500openalex-snapshot
The Fine-Scale Structure of Recombination Rate Variation in the Human Genome
inferredcites →https://doi.org/10.1142/s0219720003000174openalex-snapshot
EFFICIENT RECONSTRUCTION OF HAPLOTYPE STRUCTURE VIA PERFECT PHYLOGENY
inferredcites →https://doi.org/10.1145/640075.640088openalex-snapshot
Large scale reconstruction of haplotypes from genotype data
inferredcites →https://doi.org/10.1145/974614.974616openalex-snapshot
Maximum likelihood resolution of multi-block genotypes
inferredcites →https://doi.org/10.1159/000073729openalex-snapshot
Detecting Disease Associations due to Linkage Disequilibrium Using Haplotype Tags: A Class of Tests and the Determinants of Statistical Power
inferredcites →https://doi.org/10.1186/1479-7364-1-1-7openalex-snapshot
Gametic phase estimation over large genomic regions using an adaptive window approach
inferredcites →https://doi.org/10.1371/journal.pbio.0020155openalex-snapshot
Absence of the TAP2 Human Recombination Hotspot in Chimpanzees
inferredcites →https://doi.org/10.2307/2409372openalex-snapshot
OXFORD SURVEYS IN EVOLUTIONARY BIOLOGY

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inferred← citeshttps://doi.org/10.1002/9781119487845.ch3openalex-snapshot
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European wild boars and domestic pigs display different polymorphic patterns in the Toll-like receptor (TLR) 1, TLR2, and TLR6 genes
inferred← citeshttps://doi.org/10.1007/s00251-011-0516-xopenalex-snapshot
Characterization and locus-specific typing of MHC class I genes in the red-billed gull (Larus scopulinus) provides evidence for major, minor, and nonclassical loci
inferred← citeshttps://doi.org/10.1007/s00251-015-0855-0openalex-snapshot
Contrasted patterns of variation and evolutionary convergence at the antiviral OAS1 gene in old world primates
inferred← citeshttps://doi.org/10.1007/s00251-015-0892-8openalex-snapshot
Evidence for adaptation of porcine Toll-like receptors
inferred← citeshttps://doi.org/10.1007/s00251-017-0980-zopenalex-snapshot
Evolutionary and polymorphism analyses reveal the central role of BTN3A2 in the concerted evolution of the BTN3 gene family
inferred← citeshttps://doi.org/10.1007/s00251-024-01356-6openalex-snapshot
Using bioinformatics to investigate functional diversity: a case study of MHC diversity in koalas
inferred← citeshttps://doi.org/10.1007/s00251-025-01378-8openalex-snapshot
Genome-wide diversity and MHC characterisation in a critically endangered freshwater turtle susceptible to disease
inferred← citeshttps://doi.org/10.1007/s00280-024-04661-9openalex-snapshot
Gene polymorphisms of TACR1 serve as the potential pharmacogenetic predictors of response to the neurokinin-1 receptor antagonist-based antiemetic regimens: a candidate-gene association study in breast cancer patients
inferred← citeshttps://doi.org/10.1007/s00300-015-1859-9openalex-snapshot
Molecular data support the existence of two species of the Antarctic fish genus Cryodraco (Channichthyidae)
inferred← citeshttps://doi.org/10.1007/s00334-016-0597-4openalex-snapshot
Potential of combining morphometry and ancient DNA information to investigate grapevine domestication
inferred← citeshttps://doi.org/10.1007/s00338-011-0721-yopenalex-snapshot
Do fluctuating temperature environments elevate coral thermal tolerance?
inferred← citeshttps://doi.org/10.1007/s00384-011-1382-6openalex-snapshot
The predictive value of single nucleotide polymorphisms in the VEGF system to the efficacy of first-line treatment with bevacizumab plus chemotherapy in patients with metastatic colorectal cancer
inferred← citeshttps://doi.org/10.1007/s00384-020-03743-3openalex-snapshot
IL6 genetic variants haplotype is associated with susceptibility and disease activity but not with therapy response in patients with inflammatory bowel disease
inferred← citeshttps://doi.org/10.1007/s00403-018-1842-8openalex-snapshot
Haplotypes of ABCB1 1236C >T (rs1128503), 2677G >T/A (rs2032582), and 3435C >T (rs1045642) in patients with bullous pemphigoid
inferred← citeshttps://doi.org/10.1007/s00414-017-1748-6openalex-snapshot
Ancestry inference of 96 population samples using microhaplotypes
inferred← citeshttps://doi.org/10.1007/s00414-021-02719-4openalex-snapshot
A novel set of short microhaplotypes based on non-binary SNPs for forensic challenging samples
inferred← citeshttps://doi.org/10.1007/s00414-022-02820-2openalex-snapshot
An overview of SNP-SNP microhaplotypes in the 26 populations of the 1000 Genomes Project
inferred← citeshttps://doi.org/10.1007/s00415-006-0214-zopenalex-snapshot
No association between synapsin III gene promoter polymorphisms and multiple sclerosis in German patients
inferred← citeshttps://doi.org/10.1007/s00415-009-5380-3openalex-snapshot
The metabotropic glutamate receptor 1, GRM1: evaluation as a candidate gene for inherited forms of cerebellar ataxia
inferred← citeshttps://doi.org/10.1007/s00425-015-2271-yopenalex-snapshot
Populus endo-β-1,4-glucanases gene family: genomic organization, phylogenetic analysis, expression profiles and association mapping
inferred← citeshttps://doi.org/10.1007/s00429-019-01924-7openalex-snapshot
Impact of COMT haplotypes on functional connectivity density and its association with the gene expression of dopamine receptors
inferred← citeshttps://doi.org/10.1007/s00432-009-0575-7openalex-snapshot
Polymorphisms of survivin promoter are associated with risk of esophageal squamous cell carcinoma
inferred← citeshttps://doi.org/10.1007/s00432-018-2585-9openalex-snapshot
Transforming growth factor beta 1 (TGFβ1) polymorphisms and haplotype structures have dual roles in breast cancer pathogenesis
inferred← citeshttps://doi.org/10.1007/s00432-019-02951-xopenalex-snapshot
FOXP3 immunoregulatory gene variants are independent predictors of human papillomavirus infection and cervical cancer precursor lesions
inferred← citeshttps://doi.org/10.1007/s00438-016-1257-1openalex-snapshot
Allelic variation in PtoPsbW associated with photosynthesis, growth, and wood properties in Populus tomentosa
inferred← citeshttps://doi.org/10.1007/s00439-006-0199-9openalex-snapshot
Association analyses of CYP19 gene polymorphisms with height variation in a large sample of Caucasian nuclear families
inferred← citeshttps://doi.org/10.1007/s00439-007-0397-0openalex-snapshot
Sequence variants in the genes for the interleukin-23 receptor (IL23R) and its ligand (IL12B) confer protection against psoriasis
inferred← citeshttps://doi.org/10.1007/s00439-007-0427-yopenalex-snapshot
Methods to impute missing genotypes for population data
inferred← citeshttps://doi.org/10.1007/s00439-008-0530-8openalex-snapshot
Evolutionary dynamics of the human ABO gene
inferred← citeshttps://doi.org/10.1007/s00439-008-0568-7openalex-snapshot
Missing data imputation and haplotype phase inference for genome-wide association studies
inferred← citeshttps://doi.org/10.1007/s00439-010-0884-6openalex-snapshot
Long-term balancing selection maintains trans-specific polymorphisms in the human TRIM5 gene
inferred← citeshttps://doi.org/10.1007/s00439-011-1009-6openalex-snapshot
Two-marker association tests yield new disease associations for coronary artery disease and hypertension
inferred← citeshttps://doi.org/10.1007/s00439-011-1053-2openalex-snapshot
Identification of a new susceptibility variant for multiple sclerosis in OAS1 by population genetics analysis
inferred← citeshttps://doi.org/10.1007/s00439-011-1104-8openalex-snapshot
Recombination networks as genetic markers in a human variation study of the Old World
inferred← citeshttps://doi.org/10.1007/s00439-016-1641-2openalex-snapshot
Wide distribution and altitude correlation of an archaic high-altitude-adaptive EPAS1 haplotype in the Himalayas
inferred← citeshttps://doi.org/10.1007/s00439-021-02382-0openalex-snapshot
The population genetics characteristics of a 90 locus panel of microhaplotypes
inferred← citeshttps://doi.org/10.1007/s00606-014-1181-yopenalex-snapshot
Allelic variation in the VvMYBA1 and VvMYBA2 domestication genes in natural grapevine populations (Vitis vinifera subsp. sylvestris)
inferred← citeshttps://doi.org/10.1007/s00606-016-1324-4openalex-snapshot
Phylogeographic study revealed microrefugia for an endemic species on the Qinghai–Tibetan Plateau: Rhodiola chrysanthemifolia (Crassulaceae)
inferred← citeshttps://doi.org/10.1007/s00774-016-0774-7openalex-snapshot
Association between SNPs and haplotypes in the METTL21C gene and peak bone mineral density and body composition in Chinese male nuclear families
inferred← citeshttps://doi.org/10.1007/s00774-020-01106-0openalex-snapshot
Association between LGR4 polymorphisms and peak bone mineral density and body composition
inferred← citeshttps://doi.org/10.1007/s10048-009-0186-0openalex-snapshot
Ashkenazi Parkinson’s disease patients with the LRRK2 G2019S mutation share a common founder dating from the second to fifth centuries
inferred← citeshttps://doi.org/10.1007/s10048-009-0187-zopenalex-snapshot
Lrrk2 R1441G-related Parkinson’s disease: evidence of a common founding event in the seventh century in Northern Spain
inferred← citeshttps://doi.org/10.1007/s10126-007-9080-7openalex-snapshot
Suggestive Association of Major Histocompatibility IB Genetic Markers with Resistance to Bacterial Cold Water Disease in Rainbow Trout (Oncorhynchus mykiss)
inferred← citeshttps://doi.org/10.1007/s10265-009-0275-zopenalex-snapshot
Molecular evidence for natural intergeneric hybridization between Liquidambar and Altingia
inferred← citeshttps://doi.org/10.1007/s10265-021-01301-8openalex-snapshot
Phylogenetic origin of two Japanese Torreya taxa found in two regions with strongly contrasting snow depth
inferred← citeshttps://doi.org/10.1007/s10336-013-0980-1openalex-snapshot
Multilocus test of the absence of mtDNA phylogeographic structure in a widespread wader, the Common Sandpiper (Actitis hypoleucos)
inferred← citeshttps://doi.org/10.1007/s10336-013-0988-6openalex-snapshot
Phylogenetic origin of the endemic pigeons from Madeira (Columba trocaz) and Azores Islands (Columba palumbus azorica)
inferred← citeshttps://doi.org/10.1007/s10336-018-1598-0openalex-snapshot
No genetic differentiation, but less diversity, in the Iberian breeding population of the Eurasian Curlew (Numenius arquata)
inferred← citeshttps://doi.org/10.1007/s10344-010-0430-9openalex-snapshot
Hares in Corsica: high prevalence of Lepus corsicanus and hybridization with introduced L. europaeus and L. granatensis
inferred← citeshttps://doi.org/10.1007/s10519-007-9162-3openalex-snapshot
The Serotonin Transporter: Sequence Variation in Macaca fascicularis and its Relationship to Dominance
inferred← citeshttps://doi.org/10.1007/s10530-022-02784-9openalex-snapshot
Molecular analysis reveals multiple native and alien Phoxinus species (Leusciscidae) in the Netherlands and Belgium
inferred← citeshttps://doi.org/10.1007/s10592-010-0098-4openalex-snapshot
Phylogeography and conservation of the endemic Hispaniolan Palm-Tanagers (Aves: Phaenicophilus)
inferred← citeshttps://doi.org/10.1007/s10592-013-0488-5openalex-snapshot
From widespread to microendemic: molecular and acoustic analyses show that Ischnocnema guentheri (Amphibia: Brachycephalidae) is endemic to Rio de Janeiro, Brazil
inferred← citeshttps://doi.org/10.1007/s10592-022-01464-4openalex-snapshot
A phylogeographic assessment of the greater kudu (Tragelaphus strepsiceros) across South Africa
inferred← citeshttps://doi.org/10.1007/s10654-012-9666-xopenalex-snapshot
A genetic instrument for Mendelian randomization of fibrinogen
inferred← citeshttps://doi.org/10.1007/s10682-010-9460-8openalex-snapshot
Polymorphism in a common Atlantic reef coral (Montastraea cavernosa) and its long-term evolutionary implications
inferred← citeshttps://doi.org/10.1007/s10689-015-9838-4openalex-snapshot
Screening of HELQ in breast and ovarian cancer families
inferred← citeshttps://doi.org/10.1007/s10709-010-9476-6openalex-snapshot
Confounding from cryptic relatedness in haplotype-based association studies
inferred← citeshttps://doi.org/10.1007/s10709-011-9589-6openalex-snapshot
Phylogeography of the red coral (Corallium rubrum): inferences on the evolutionary history of a temperate gorgonian
inferred← citeshttps://doi.org/10.1007/s10709-014-9794-1openalex-snapshot
Introgression of mitochondrial DNA promoted by natural selection in the Japanese pipistrelle bat (Pipistrellus abramus)
inferred← citeshttps://doi.org/10.1007/s10722-012-9910-yopenalex-snapshot
Characterization of single nucleotide polymorphism in Tunisian grapevine genome and their potential for population genetics and evolutionary studies
inferred← citeshttps://doi.org/10.1007/s10750-015-2559-8openalex-snapshot
Using a phylogeographic approach to investigate the diversity and determine the distributional range of an isopod (Crustacea: Peracarida), Stenosoma nadejda (Rezig, 1989) in the Atlantic-Mediterranean region
inferred← citeshttps://doi.org/10.1007/s10750-017-3209-0openalex-snapshot
A matter of persistence: differential Late Pleistocene survival of two rocky-shore idoteid isopod species in northern Japan
inferred← citeshttps://doi.org/10.1007/s11032-013-9866-4openalex-snapshot
Molecular characterization and evolutionary pattern of the 9- cis -epoxycarotenoid dioxygenase NCED1 gene in grapevine
inferred← citeshttps://doi.org/10.1007/s11033-011-0794-2openalex-snapshot
Study of polymorphisms in the promoter region of ovine β-lactoglobulin gene and phylogenetic analysis among the Valle del Belice breed and other sheep breeds considered as ancestors
inferred← citeshttps://doi.org/10.1007/s11033-011-1087-5openalex-snapshot
Polymorphisms of beta-lactoglobulin promoter region in three Sicilian goat breeds
inferred← citeshttps://doi.org/10.1007/s11033-014-3583-xopenalex-snapshot
Melanocortin-4 receptor (MC4R) polymorphisms are associated with growth and meat quality traits in sheep
inferred← citeshttps://doi.org/10.1007/s11033-014-3677-5openalex-snapshot
Expression of NAT2 in immune system cells and the relation of NAT2 gene polymorphisms in the anti-tuberculosis therapy in Mexican mestizo population
inferred← citeshttps://doi.org/10.1007/s11033-021-06640-2openalex-snapshot
Transforming growth factor beta 1 (TGFβ1) plasmatic levels and haplotype structures in obesity: a role for TGFβ1 in steatosis development
inferred← citeshttps://doi.org/10.1007/s11033-022-07831-1openalex-snapshot
Genetic modulation of anemia severity, hemolysis level, and hospitalization rate in Angolan children with Sickle Cell Anemia
inferred← citeshttps://doi.org/10.1007/s11033-026-12162-6openalex-snapshot
Interplay between CDH1 polymorphisms, haplotypes, and genomic repetitive elements in urothelial bladder cancer prognosis
inferred← citeshttps://doi.org/10.1007/s11295-014-0786-1openalex-snapshot
Identifying signatures of natural selection in cork oak (Quercus suber L.) genes through SNP analysis
inferred← citeshttps://doi.org/10.1007/s11295-015-0839-0openalex-snapshot
Assessing microsatellite linkage disequilibrium in wild, cultivated, and mapping populations of Theobroma cacao L. and its impact on association mapping
inferred← citeshttps://doi.org/10.1007/s11295-016-1049-0openalex-snapshot
Dissection of additive, dominant, epistatic roles of allelic variation within heat shock factor genes in Chinese indigenous poplar (Populus simonii)
inferred← citeshttps://doi.org/10.1007/s11692-017-9417-8openalex-snapshot
Evolutionary History of the Morocco lizard-Fingered Geckos of the Saurodactylus brosseti Complex
inferred← citeshttps://doi.org/10.1007/s11695-010-0144-9openalex-snapshot
Vitamin D Receptor Polymorphisms in Secondary Hyperparathyroidism After Scopinaro's Biliopancreatic Diversion
inferred← citeshttps://doi.org/10.1007/s12031-021-01877-9openalex-snapshot
Variants in Genes of Calpain System as Modifiers of Spinocerebellar Ataxia Type 3 Phenotype
inferred← citeshttps://doi.org/10.1007/s12035-017-0414-9openalex-snapshot
Melanocortin Receptor-4 Gene Polymorphisms in Glioblastoma Patients Treated with Concomitant Radio-Chemotherapy
inferred← citeshttps://doi.org/10.1007/s12041-007-0034-7openalex-snapshot
Association study of the oestrogen signalling pathway genes in relation to age at natural menopause
inferred← citeshttps://doi.org/10.1007/s12041-014-0415-7openalex-snapshot
LIG1 polymorphisms: the Indian scenario
inferred← citeshttps://doi.org/10.1007/s12192-011-0257-7openalex-snapshot
Cellular thermotolerance is associated with heat shock protein 70.1 genetic polymorphisms in Holstein lactating cows
inferred← citeshttps://doi.org/10.1007/s12686-012-9684-8openalex-snapshot
Anonymous nuclear markers for the African adders (Serpentes: Viperidae: Bitis)
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