메뉴 건너뛰기




Volumn 9, Issue , 2008, Pages

Shape-IT: New rapid and accurate algorithm for haplotype inference

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL ALGORITHM; HAPLOTYPE INFERENCE; HIGH-THROUGHPUT; INFERENCE PROBLEM; LARGE DATASETS; ORDERS OF MAGNITUDE; POSTERIOR PROBABILITY; TREE REPRESENTATION;

EID: 61449086542     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-540     Document Type: Article
Times cited : (138)

References (43)
  • 2
    • 0034791035 scopus 로고    scopus 로고
    • High-resolution haplotype structure in the human genome
    • 10.1038/ng1001-229 11586305
    • Daly MJ Rioux JD Schaffner SF Hudson TJ Lander ES High-resolution haplotype structure in the human genome Nature genetics 2001, 29(2):229-232 10.1038/ng1001-229 11586305
    • (2001) Nature Genetics , vol.29 , Issue.2 , pp. 229-232
    • Daly, M.J.1    Rioux, J.D.2    Schaffner, S.F.3    Hudson, T.J.4    Lander, E.S.5
  • 7
    • 79959503826 scopus 로고    scopus 로고
    • The International HapMap Project
    • 10.1038/nature02168 14685227
    • The International HapMap Project Nature 2003, 426(6968):789-796 10.1038/ nature02168 14685227
    • (2003) Nature , vol.426 , Issue.6968 , pp. 789-796
  • 8
    • 79959524146 scopus 로고    scopus 로고
    • A haplotype map of the human genome
    • 1880871 16255080 10.1038/nature04226
    • A haplotype map of the human genome Nature 2005, 437(7063):1299-1320 1880871 16255080 10.1038/nature04226
    • (2005) Nature , vol.437 , Issue.7063 , pp. 1299-1320
  • 10
    • 0348013052 scopus 로고    scopus 로고
    • Clone-based systematic haplotyping (CSH): A procedure for physical haplotyping of whole genomes
    • 403814 14656974 10.1101/gr.1442303
    • Burgtorf C Kepper P Hoehe M Schmitt C Reinhardt R Lehrach H Sauer S Clone-based systematic haplotyping (CSH): A procedure for physical haplotyping of whole genomes Genome research 2003, 13(12):2717-2724 403814 14656974 10.1101/gr.1442303
    • (2003) Genome Research , vol.13 , Issue.12 , pp. 2717-2724
    • Burgtorf, C.1    Kepper, P.2    Hoehe, M.3    Schmitt, C.4    Reinhardt, R.5    Lehrach, H.6    Sauer, S.7
  • 12
    • 0025269067 scopus 로고
    • Inference of haplotypes from PCR-amplified samples of diploid populations
    • 2108305
    • Clark AG Inference of haplotypes from PCR-amplified samples of diploid populations Mol Biol Evol 1990, 7(2):111-122 2108305
    • (1990) Mol Biol Evol , vol.7 , Issue.2 , pp. 111-122
    • Clark, A.G.1
  • 13
    • 0029130796 scopus 로고
    • Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population
    • 7476138
    • Excoffier L Slatkin M Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population Mol Biol Evol 1995, 12(5):921-927 7476138
    • (1995) Mol Biol Evol , vol.12 , Issue.5 , pp. 921-927
    • Excoffier, L.1    Slatkin, M.2
  • 14
    • 0036844521 scopus 로고    scopus 로고
    • Partition-ligation-expectation-maximization algorithm for haplotype inference with single-nucleotide polymorphisms
    • 385113 12452179 10.1086/344207
    • Qin ZS Niu T Liu JS Partition-ligation-expectation-maximization algorithm for haplotype inference with single-nucleotide polymorphisms American journal of human genetics 2002, 71(5):1242-1247 385113 12452179 10.1086/344207
    • (2002) American Journal of Human Genetics , vol.71 , Issue.5 , pp. 1242-1247
    • Qin, Z.S.1    Niu, T.2    Liu, J.S.3
  • 16
    • 33644974019 scopus 로고    scopus 로고
    • A fast and flexible statistical model for large-scale population genotype data: Applications to inferring missing genotypes and haplotypic phase
    • 1424677 16532393 10.1086/502802
    • Scheet P Stephens M A fast and flexible statistical model for large-scale population genotype data: Applications to inferring missing genotypes and haplotypic phase American journal of human genetics 2006, 78(4):629-644 1424677 16532393 10.1086/502802
    • (2006) American Journal of Human Genetics , vol.78 , Issue.4 , pp. 629-644
    • Scheet, P.1    Stephens, M.2
  • 18
    • 33645015512 scopus 로고    scopus 로고
    • A block-free hidden Markov model for genotypes and its application to disease association
    • 10.1089/cmb.2005.12.1243 16379532
    • Kimmel G Shamir R A block-free hidden Markov model for genotypes and its application to disease association J Comput Biol 2005, 12(10):1243-1260 10.1089/cmb.2005.12.1243 16379532
    • (2005) J Comput Biol , vol.12 , Issue.10 , pp. 1243-1260
    • Kimmel, G.1    Shamir, R.2
  • 19
    • 0036138183 scopus 로고    scopus 로고
    • Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms
    • 448439 11741196 10.1086/338446
    • Niu T Qin ZS Xu X Liu JS Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms American journal of human genetics 2002, 70(1):157-169 448439 11741196 10.1086/338446
    • (2002) American Journal of Human Genetics , vol.70 , Issue.1 , pp. 157-169
    • Niu, T.1    Qin, Z.S.2    Xu, X.3    Liu, J.S.4
  • 20
    • 0035071957 scopus 로고    scopus 로고
    • A new statistical method for haplotype reconstruction from population data
    • 1275651 11254454 10.1086/319501
    • Stephens M Smith NJ Donnelly P A new statistical method for haplotype reconstruction from population data American journal of human genetics 2001, 68(4):978-989 1275651 11254454 10.1086/319501
    • (2001) American Journal of Human Genetics , vol.68 , Issue.4 , pp. 978-989
    • Stephens, M.1    Smith, N.J.2    Donnelly, P.3
  • 21
    • 0242691208 scopus 로고    scopus 로고
    • A comparison of bayesian methods for haplotype reconstruction from population genotype data
    • 1180495 14574645 10.1086/379378
    • Stephens M Donnelly P A comparison of bayesian methods for haplotype reconstruction from population genotype data American journal of human genetics 2003, 73(5):1162-1169 1180495 14574645 10.1086/379378
    • (2003) American Journal of Human Genetics , vol.73 , Issue.5 , pp. 1162-1169
    • Stephens, M.1    Donnelly, P.2
  • 22
    • 13844270527 scopus 로고    scopus 로고
    • Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation
    • 1196397 15700229 10.1086/428594
    • Stephens M Scheet P Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation American journal of human genetics 2005, 76(3):449-462 1196397 15700229 10.1086/428594
    • (2005) American Journal of Human Genetics , vol.76 , Issue.3 , pp. 449-462
    • Stephens, M.1    Scheet, P.2
  • 23
    • 32144441985 scopus 로고    scopus 로고
    • 2SNP: Scalable phasing based on 2-SNP haplotypes
    • 10.1093/bioinformatics/bti785 16287933
    • Brinza D Zelikovsky A 2SNP: Scalable phasing based on 2-SNP haplotypes Bioinformatics (Oxford, England) 2006, 22(3):371-373 10.1093/ bioinformatics/bti785 16287933
    • (2006) Bioinformatics (Oxford, England) , vol.22 , Issue.3 , pp. 371-373
    • Brinza, D.1    Zelikovsky, A.2
  • 25
    • 25444442089 scopus 로고    scopus 로고
    • Comparison of the accuracy of methods of computational haplotype inference using a large empirical dataset
    • 512280 15291970 10.1186/1471-2156-5-22
    • Adkins RM Comparison of the accuracy of methods of computational haplotype inference using a large empirical dataset BMC genetics 2004, 5:22 512280 15291970 10.1186/1471-2156-5-22
    • (2004) BMC Genetics , vol.5 , pp. 22
    • Adkins, R.M.1
  • 28
    • 30344485299 scopus 로고    scopus 로고
    • Haplotypic structure of the X chromosome in the COGA population sample and the quality of its reconstruction by extant software packages
    • 1866704 16451691 10.1186/1471-2156-6-S1-S77
    • Marroni F Toni C Pennato B Tsai YY Duggal P Bailey-Wilson JE Presciuttini S Haplotypic structure of the X chromosome in the COGA population sample and the quality of its reconstruction by extant software packages BMC genetics 2005, 6(Suppl 1):S77 1866704 16451691 10.1186/1471-2156-6-S1-S77
    • (2005) BMC Genetics , vol.6 , Issue.SUPPL. 1
    • Marroni, F.1    Toni, C.2    Pennato, B.3    Tsai, Y.Y.4    Duggal, P.5    Bailey-Wilson, J.E.6    Presciuttini, S.7
  • 29
    • 18444418259 scopus 로고    scopus 로고
    • Comparison of haplotype inference methods using genotypic data from unrelated individuals
    • 10.1159/000083026 15711085
    • Xu H Wu X Spitz MR Shete S Comparison of haplotype inference methods using genotypic data from unrelated individuals Human heredity 2004, 58(2):63-68 10.1159/000083026 15711085
    • (2004) Human Heredity , vol.58 , Issue.2 , pp. 63-68
    • Xu, H.1    Wu, X.2    Spitz, M.R.3    Shete, S.4
  • 30
    • 27544516079 scopus 로고    scopus 로고
    • Inference and analysis of haplotypes from combined genotyping studies deposited in dbSNP
    • 1310648 16251470 10.1101/gr.4297805
    • Zaitlen NA Kang HM Feolo ML Sherry ST Halperin E Eskin E Inference and analysis of haplotypes from combined genotyping studies deposited in dbSNP Genome research 2005, 15(11):1594-1600 1310648 16251470 10.1101/ gr.4297805
    • (2005) Genome Research , vol.15 , Issue.1 , pp. 1594-1600
    • Zaitlen, N.A.1    Kang, H.M.2    Feolo, M.L.3    Sherry, S.T.4    Halperin, E.5    Eskin, E.6
  • 32
    • 33645461311 scopus 로고    scopus 로고
    • Associations of the IL2Ralpha, IL4Ralpha, IL10Ralpha, and IFN (gamma) R1 cytokine receptor genes with AIDS progression in a French AIDS cohort
    • 10.1007/s00251-005-0072-3
    • Do H Vasilescu A Diop G Hirtzig T Coulonges C Labib T Heath SC Spadoni JL Therwath A Lathrop M et al Associations of the IL2Ralpha, IL4Ralpha, IL10Ralpha, and IFN (gamma) R1 cytokine receptor genes with AIDS progression in a French AIDS cohort Immunogenetics 2006, 58:2-3 10.1007/ s00251-005-0072-3
    • (2006) Immunogenetics , vol.58 , pp. 2-3
    • Do, H.1    Vasilescu, A.2    Diop, G.3    Hirtzig, T.4    Coulonges, C.5    Labib, T.6    Heath, S.C.7    Spadoni, J.L.8    Therwath, A.9    Lathrop, M.10
  • 34
    • 0035675042 scopus 로고    scopus 로고
    • Estimating recombination rates from population genetic data
    • 1461855 11729171
    • Fearnhead P Donnelly P Estimating recombination rates from population genetic data Genetics 2001, 159(3):1299-1318 1461855 11729171
    • (2001) Genetics , vol.159 , Issue.3 , pp. 1299-1318
    • Fearnhead, P.1    Donnelly, P.2
  • 35
    • 0347361674 scopus 로고    scopus 로고
    • Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data
    • 1462870 14704198
    • Li N Stephens M Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data Genetics 2003, 165(4):2213-2233 1462870 14704198
    • (2003) Genetics , vol.165 , Issue.4 , pp. 2213-2233
    • Li, N.1    Stephens, M.2
  • 36
    • 0024610919 scopus 로고
    • A tutorial on hidden Markov models and selected applications in speech recognition
    • 10.1109/5.18626
    • Rabiner LR A tutorial on hidden Markov models and selected applications in speech recognition Proceedings of the IEEE 1989, 77(2):257-286 10.1109/5.18626
    • (1989) Proceedings of the IEEE , vol.77 , Issue.2 , pp. 257-286
    • Rabiner, L.R.1
  • 37
    • 0037240296 scopus 로고    scopus 로고
    • Human growth hormone 1 (GH1) gene expression: Complex haplotype-dependent influence of polymorphic variation in the proximal promoter and locus control region
    • 10.1002/humu.10167 12655556
    • Horan M Millar DS Hedderich J Lewis G Newsway V Mo N Fryklund L Procter AM Krawczak M Cooper DN Human growth hormone 1 (GH1) gene expression: complex haplotype-dependent influence of polymorphic variation in the proximal promoter and locus control region Human mutation 2003, 21(4):408-423 10.1002/humu.10167 12655556
    • (2003) Human Mutation , vol.21 , Issue.4 , pp. 408-423
    • Horan, M.1    Millar, D.S.2    Hedderich, J.3    Lewis, G.4    Newsway, V.5    Mo, N.6    Fryklund, L.7    Procter, A.M.8    Krawczak, M.9    Cooper, D.N.10
  • 38
    • 0242318309 scopus 로고    scopus 로고
    • Analysis and exploration of the use of rule-based algorithms and consensus methods for the inferral of haplotypes
    • 1462785 14573498
    • Orzack SH Gusfield D Olson J Nesbitt S Subrahmanyan L Stanton VP Jr Analysis and exploration of the use of rule-based algorithms and consensus methods for the inferral of haplotypes Genetics 2003, 165(2):915-928 1462785 14573498
    • (2003) Genetics , vol.165 , Issue.2 , pp. 915-928
    • Orzack, S.H.1    Gusfield, D.2    Olson, J.3    Nesbitt, S.4    Subrahmanyan, L.5    Stanton Jr., V.P.6
  • 39
    • 13444269543 scopus 로고    scopus 로고
    • Haploview: Analysis and visualization of LD and haplotype maps
    • 10.1093/bioinformatics/bth457 15297300
    • Barrett JC Fry B Maller J Daly MJ Haploview: Analysis and visualization of LD and haplotype maps Bioinformatics (Oxford, England) 2005, 21(2):263-265 10.1093/bioinformatics/bth457 15297300
    • (2005) Bioinformatics (Oxford, England) , vol.21 , Issue.2 , pp. 263-265
    • Barrett, J.C.1    Fry, B.2    Maller, J.3    Daly, M.J.4
  • 41
    • 0030894132 scopus 로고    scopus 로고
    • 32 bp CCR-5 gene deletion and resistance to fast progression in HIV-1 infected heterozygotes
    • 10.1016/S0140-6736(05)62697-9 9093257
    • Rappaport J Cho YY Hendel H Schwartz EJ Schachter F Zagury JF 32 bp CCR-5 gene deletion and resistance to fast progression in HIV-1 infected heterozygotes Lancet 1997, 349(9056):922-923 10.1016/ S0140-6736(05)62697-9 9093257
    • (1997) Lancet , vol.349 , Issue.9056 , pp. 922-923
    • Rappaport, J.1    Cho, Y.Y.2    Hendel, H.3    Schwartz, E.J.4    Schachter, F.5    Zagury, J.F.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.