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For: Su SY, Balding DJ, Coin LJM. Disease association tests by inferring ancestral haplotypes using a hidden markov model. ACTA ACUST UNITED AC 2008;24:972-8. [PMID: 18296746 DOI: 10.1093/bioinformatics/btn071] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Number Cited by Other Article(s)
1
Benchmarking phasing software with a whole-genome sequenced cattle pedigree. BMC Genomics 2022;23:130. [PMID: 35164677 PMCID: PMC8845340 DOI: 10.1186/s12864-022-08354-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/24/2022] [Indexed: 12/30/2022]  Open
2
Faux P, Druet T. A strategy to improve phasing of whole-genome sequenced individuals through integration of familial information from dense genotype panels. Genet Sel Evol 2017;49:46. [PMID: 28511677 PMCID: PMC5434521 DOI: 10.1186/s12711-017-0321-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 05/05/2017] [Indexed: 11/21/2022]  Open
3
New Genetic Approaches to AD: Lessons from APOE-TOMM40 Phylogenetics. Curr Neurol Neurosci Rep 2016;16:48. [DOI: 10.1007/s11910-016-0643-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
4
Efficiency of haplotype-based methods to fine-map QTLs and embryonic lethal variants affecting fertility: Illustration with a deletion segregating in Nordic Red cattle. Livest Sci 2014. [DOI: 10.1016/j.livsci.2014.04.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
5
Yau C, Holmes CC. A decision-theoretic approach for segmental classification. Ann Appl Stat 2013. [DOI: 10.1214/13-aoas657] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
6
Druet T, Farnir F. Use of ancestral haplotypes in genome-wide association studies. Methods Mol Biol 2013;1019:347-380. [PMID: 23756899 DOI: 10.1007/978-1-62703-447-0_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
7
Fine-scale mapping of disease susceptibility locus with Bayesian partition model. Genes Genomics 2012. [DOI: 10.1007/s13258-011-0220-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
8
Zhang Z, Guillaume F, Sartelet A, Charlier C, Georges M, Farnir F, Druet T. Ancestral haplotype-based association mapping with generalized linear mixed models accounting for stratification. ACTA ACUST UNITED AC 2012;28:2467-73. [PMID: 22711794 DOI: 10.1093/bioinformatics/bts348] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
9
de Roos APW, Schrooten C, Druet T. Genomic breeding value estimation using genetic markers, inferred ancestral haplotypes, and the genomic relationship matrix. J Dairy Sci 2011;94:4708-14. [PMID: 21854945 DOI: 10.3168/jds.2010-3905] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Accepted: 05/10/2011] [Indexed: 11/19/2022]
10
He Y, Li C, Amos CI, Xiong M, Ling H, Jin L. Accelerating haplotype-based genome-wide association study using perfect phylogeny and phase-known reference data. PLoS One 2011;6:e22097. [PMID: 21789217 PMCID: PMC3137625 DOI: 10.1371/journal.pone.0022097] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Accepted: 06/17/2011] [Indexed: 11/18/2022]  Open
11
Lam TY, Meyer IM. Efficient algorithms for training the parameters of hidden Markov models using stochastic expectation maximization (EM) training and Viterbi training. Algorithms Mol Biol 2010;5:38. [PMID: 21143925 PMCID: PMC3019189 DOI: 10.1186/1748-7188-5-38] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Accepted: 12/09/2010] [Indexed: 11/10/2022]  Open
12
Coin LJM, Asher JE, Walters RG, El-Sayed Moustafa JS, de Smith AJ, Sladek R, Balding DJ, Froguel P, Blakemore AIF. cnvHap: an integrative population and haplotype–based multiplatform model of SNPs and CNVs. Nat Methods 2010;7:541-6. [DOI: 10.1038/nmeth.1466] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Accepted: 05/05/2010] [Indexed: 11/09/2022]
13
Su SY, Asher JE, Jarvelin MR, Froguel P, Blakemore AIF, Balding DJ, Coin LJM. Inferring combined CNV/SNP haplotypes from genotype data. ACTA ACUST UNITED AC 2010;26:1437-45. [PMID: 20406911 DOI: 10.1093/bioinformatics/btq157] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
14
Teo YY, Small KS. A novel method for haplotype clustering and visualization. Genet Epidemiol 2010;34:34-41. [PMID: 19479748 DOI: 10.1002/gepi.20432] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
15
Buil A, Martinez-Perez A, Perera-Lluna A, Rib L, Caminal P, Soria JM. A new gene-based association test for genome-wide association studies. BMC Proc 2009;3 Suppl 7:S130. [PMID: 20017997 PMCID: PMC2795904 DOI: 10.1186/1753-6561-3-s7-s130] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]  Open
16
Liu Y, Li YJ, Satten GA, Allen AS, Tzeng JY. A regression-based association test for case-control studies that uses inferred ancestral haplotype similarity. Ann Hum Genet 2009;73:520-6. [PMID: 19622101 PMCID: PMC2747372 DOI: 10.1111/j.1469-1809.2009.00536.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
17
Li M, Wang K, Grant SFA, Hakonarson H, Li C. ATOM: a powerful gene-based association test by combining optimally weighted markers. ACTA ACUST UNITED AC 2008;25:497-503. [PMID: 19074959 DOI: 10.1093/bioinformatics/btn641] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
18
Su SY, White J, Balding DJ, Coin LJM. Inference of haplotypic phase and missing genotypes in polyploid organisms and variable copy number genomic regions. BMC Bioinformatics 2008;9:513. [PMID: 19046436 PMCID: PMC2647950 DOI: 10.1186/1471-2105-9-513] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2008] [Accepted: 12/01/2008] [Indexed: 12/18/2022]  Open
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