메뉴 건너뛰기




Volumn 194, Issue 3, 2013, Pages 573-596

Priors in whole-genome regression: The Bayesian alphabet returns

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BAYESIAN LEARNING; BREEDING; DROSOPHILA; GENE STRUCTURE; GENOME; GENOTYPE; INSECT GENETICS; INSECT GENOME; NONHUMAN; PHENOTYPE; PLANT BREEDING; PRIORITY JOURNAL; QUANTITATIVE TRAIT;

EID: 84879743015     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.113.151753     Document Type: Article
Times cited : (319)

References (69)
  • 6
    • 2242491935 scopus 로고    scopus 로고
    • Computational and in-ferential difficulties with mixture posterior distributions
    • Celeux, G., M. Hurn, and C. Robert, 2000 Computational and in-ferential difficulties with mixture posterior distributions. J. Am. Stat. Assoc. 95: 957-979.
    • (2000) J. Am. Stat. Assoc , vol.95 , pp. 957-979
    • Celeux, G.1    Hurn, M.2    Robert, C.3
  • 7
    • 78649325488 scopus 로고    scopus 로고
    • Prediction of genetic value of quantitative traits in plant breeding using pedigree and molecular markers
    • Crossa, J., G. de los Campos, P. Pérez, D. Gianola, J. Burgueño et al., 2010 Prediction of genetic value of quantitative traits in plant breeding using pedigree and molecular markers. Genet-ics 186: 713-724.
    • (2010) Genet-ics , vol.186 , pp. 713-724
    • Crossa, J.1    de los Campos, G.2    Pérez, P.3    Gianola, D.4    Burgueño, J.5
  • 8
    • 0002384709 scopus 로고
    • Conditional independence in statistical theory (with discussion)
    • Dawid, A. P., 1979 Conditional independence in statistical theory (with discussion). J. R. Stat. Soc. B 41: 1-31.
    • (1979) J. R. Stat. Soc. B , vol.41 , pp. 1-31
    • Dawid, A.P.1
  • 10
    • 69149088569 scopus 로고    scopus 로고
    • Reproducing kernel Hilbert spaces regression: A general framework for genetic evaluation
    • de los Campos, G., D. Gianola, and G. J. M. Rosa, 2009a Reproducing kernel Hilbert spaces regression: a general framework for genetic evaluation. J. Anim. Sci. 87: 1883-1887.
    • (2009) J. Anim. Sci , vol.87 , pp. 1883-1887
    • de los Campos, G.1    Gianola, D.2    Rosa, G.J.M.3
  • 11
    • 67849130524 scopus 로고    scopus 로고
    • Predicting quantitative traits with regression models for dense molecular markers and pedigrees
    • de los Campos, G., H. Naya, D. Gianola, J. Crossa, A. Legarra et al., 2009b Predicting quantitative traits with regression models for dense molecular markers and pedigrees. Genetics 182: 375-385.
    • (2009) Genetics , vol.182 , pp. 375-385
    • de los Campos, G.1    Naya, H.2    Gianola, D.3    Crossa, J.4    Legarra, A.5
  • 12
    • 78649317608 scopus 로고    scopus 로고
    • Predicting genetic predisposition in humans: The promise of whole-genome markers
    • de los Campos, G., D. Gianola, and D. B. Allison, 2010 Predicting genetic predisposition in humans: the promise of whole-genome markers. Nat. Rev. Genet. 11: 880-886.
    • (2010) Nat. Rev. Genet , vol.11 , pp. 880-886
    • de los Campos, G.1    Gianola, D.2    Allison, D.B.3
  • 13
    • 84876390765 scopus 로고    scopus 로고
    • Whole genome regression and pre-diction methods applied to plant an animal breeding
    • de los Campos, G., J. M. Hickey, R. Pong-Wong, H. D. Daetwyler, and M. P. L. Calus, 2012a Whole genome regression and pre-diction methods applied to plant an animal breeding. Genetics 193: 327-345.
    • (2012) Genetics , vol.193 , pp. 327-345
    • de los Campos, G.1    Hickey, J.M.2    Pong-Wong, R.3    Daetwyler, H.D.4    Calus, M.P.L.5
  • 16
    • 84862511727 scopus 로고    scopus 로고
    • Improving accuracy of genomic predictions within and between dairy cattle breeds with imputed high-density sin-gle nucleotide polymorphism panels
    • Erbe, M., B. J. Hayes, L. K. Matukumali, S. Goswami, P. J. Bowman et al., 2012 Improving accuracy of genomic predictions within and between dairy cattle breeds with imputed high-density sin-gle nucleotide polymorphism panels. J. Dairy Sci. 95: 4114-4129.
    • (2012) J. Dairy Sci , vol.95 , pp. 4114-4129
    • Erbe, M.1    Hayes, B.J.2    Matukumali, L.K.3    Goswami, S.4    Bowman, P.J.5
  • 18
    • 1542784498 scopus 로고    scopus 로고
    • Variable selection via nonconcave penal-ized likelihood and its oracle properties
    • Fan, J., and R. Li, 2001 Variable selection via nonconcave penal-ized likelihood and its oracle properties. J. Am. Stat. Assoc. 96: 1348-1360.
    • (2001) J. Am. Stat. Assoc , vol.96 , pp. 1348-1360
    • Fan, J.1    Li, R.2
  • 20
    • 0442309445 scopus 로고    scopus 로고
    • Identifiability, improper pri-ors, and Gibbs sampling for generalized linear models
    • Gelfand, A. E., and S. K. Sahu, 1999 Identifiability, improper pri-ors, and Gibbs sampling for generalized linear models. J. Am. Stat. Assoc. 94: 247-253.
    • (1999) J. Am. Stat. Assoc , vol.94 , pp. 247-253
    • Gelfand, A.E.1    Sahu, S.K.2
  • 21
    • 0000849009 scopus 로고
    • Bayesian methods in ani-mal breeding theory
    • Gianola, D., and R. L. Fernando, 1986 Bayesian methods in ani-mal breeding theory. J. Anim. Sci. 63: 217-244.
    • (1986) J. Anim. Sci , vol.63 , pp. 217-244
    • Gianola, D.1    Fernando, R.L.2
  • 22
    • 33747870143 scopus 로고    scopus 로고
    • On the quanti-tative genetics of mixture characters
    • Gianola, D., B. Heringstad, and J. Ødegård, 2006 On the quanti-tative genetics of mixture characters. Genetics 173: 2247-2255.
    • (2006) Genetics , vol.173 , pp. 2247-2255
    • Gianola, D.1    Heringstad, B.2    ødegård, J.3
  • 25
    • 79956199958 scopus 로고    scopus 로고
    • Extension of the Bayesian alphabet for genomic selection
    • Available at
    • Habier, D., R. L. Fernando, K. Kizilkaya, and D. J. Garrick, 2011 Extension of the Bayesian alphabet for genomic selection. BMC Bioinformatics. Available at: http://www.biomedcentral.com/1471-2105/12/186
    • (2011) BMC Bioinformatics
    • Habier, D.1    Fernando, R.L.2    Kizilkaya, K.3    Garrick, D.J.4
  • 27
    • 59249106951 scopus 로고    scopus 로고
    • Genomic selection for crop improvement
    • Heffner, E. L., M. E. Sorrells, and J. L. Jannink, 2009 Genomic selection for crop improvement. Crop Sci. 49: 1-12.
    • (2009) Crop Sci , vol.49 , pp. 1-12
    • Heffner, E.L.1    Sorrells, M.E.2    Jannink, J.L.3
  • 28
    • 0001358661 scopus 로고
    • Best linear unbiased prediction of breed-ing values not in the model for records
    • Henderson, C. R., 1977 Best linear unbiased prediction of breed-ing values not in the model for records. J. Dairy Sci. 60: 783-787.
    • (1977) J. Dairy Sci , vol.60 , pp. 783-787
    • Henderson, C.R.1
  • 30
    • 82955176938 scopus 로고    scopus 로고
    • Genomic selection in plant breeding: A comparison of models
    • Heslot, N., M. E. Sorrells, J. L. Jannink, and H. P. Yang, 2012 Genomic selection in plant breeding: a comparison of models. Crop Sci. 52: 146-160.
    • (2012) Crop Sci , vol.52 , pp. 146-160
    • Heslot, N.1    Sorrells, M.E.2    Jannink, J.L.3    Yang, H.P.4
  • 31
    • 84860525343 scopus 로고    scopus 로고
    • Quantitative genetics in the genomics era
    • Hill, W. G., 2012 Quantitative genetics in the genomics era. Curr. Genomics 13: 196-206.
    • (2012) Curr. Genomics , vol.13 , pp. 196-206
    • Hill, W.G.1
  • 32
    • 84867188975 scopus 로고    scopus 로고
    • Inferences from genomic models in stratified popula-tions
    • Janss, L., G. de los Campos, N. Sheehan, and D. Sorensen, 2012 Inferences from genomic models in stratified popula-tions. Genetics 92: 693-704.
    • (2012) Genetics , vol.92 , pp. 693-704
    • Janss, L.1    de los Campos, G.2    Sheehan, N.3    Sorensen, D.4
  • 33
    • 84870707772 scopus 로고    scopus 로고
    • Multiple trait genomic selection methods increase genetic value prediction accuracy
    • Jia, Y., and J.-L. Jannink, 2012 Multiple trait genomic selection methods increase genetic value prediction accuracy. Genetics 192: 1513-1522.
    • (2012) Genetics , vol.192 , pp. 1513-1522
    • Jia, Y.1    Jannink, J.-L.2
  • 34
    • 84863862138 scopus 로고    scopus 로고
    • Back to basis for Bayesian model building in genomic selection
    • Kärkkäinen, H. P., and M. K. Sillanpää, 2012 Back to basis for Bayesian model building in genomic selection. Genetics 191: 969-987.
    • (2012) Genetics , vol.191 , pp. 969-987
    • Kärkkäinen, H.P.1    Sillanpää, M.K.2
  • 36
    • 84879746501 scopus 로고    scopus 로고
    • Sensitivity to prior specification in Bayesian ge-nome-based prediction models
    • DOI: 10.1515/sagmb-2012-0042
    • Lehermeier, C., V. Wimmer, T. Albrecht, H. Auinger, D. Gianola et al., 2013 Sensitivity to prior specification in Bayesian ge-nome-based prediction models. Stat. Appl. Genet. Mol. Biol. DOI: 10.1515/sagmb-2012-0042.
    • (2013) Stat. Appl. Genet. Mol. Biol
    • Lehermeier, C.1    Wimmer, V.2    Albrecht, T.3    Auinger, H.4    Gianola, D.5
  • 37
    • 78651492289 scopus 로고    scopus 로고
    • Genomic selection in plant breeding: Knowledge and prospects
    • Lorenz, A. J., S. Chao, F. G. Asoro, E. L. Heffner, T. Hayashi et al., 2011 Genomic selection in plant breeding: knowledge and prospects. Adv. Agron. 110: 77-123.
    • (2011) Adv. Agron , vol.110 , pp. 77-123
    • Lorenz, A.J.1    Chao, S.2    Asoro, F.G.3    Heffner, E.L.4    Hayashi, T.5
  • 38
    • 79955643147 scopus 로고    scopus 로고
    • Beyond missing heritability: Predic-tion of complex traits
    • 10.1371/journal. pgen.100205
    • Makowsky, R., N. M. Pajewski, Y. C. Klimentidis, A. I. Vázquez, C. W. Duarte et al., 2011 Beyond missing heritability: predic-tion of complex traits. PLoS Genet. 7(4): 10.1371/journal. pgen.100205.
    • (2011) PLoS Genet , vol.7 , Issue.4
    • Makowsky, R.1    Pajewski, N.M.2    Klimentidis, Y.C.3    Vázquez, A.I.4    Duarte, C.W.5
  • 41
    • 0035045051 scopus 로고    scopus 로고
    • Prediction of total genetic value using genome-wide dense marker maps
    • Meuwissen, T. H. E., B. J. Hayes, and M. E. Goddard, 2001 Prediction of total genetic value using genome-wide dense marker maps. Ge-netics 157: 1819-1829.
    • (2001) Ge-netics , vol.157 , pp. 1819-1829
    • Meuwissen, T.H.E.1    Hayes, B.J.2    Goddard, M.E.3
  • 42
    • 70449706218 scopus 로고    scopus 로고
    • A fast algorithm for BayesB type of prediction of genome-wide estimates of genetic value
    • Meuwissen, T. H. E., T. R. Solberg, R. Shepherd, and J. A. Woolliams, 2009 A fast algorithm for BayesB type of prediction of genome-wide estimates of genetic value. Genet. Sel. Evol. 41: (2) 1-10.
    • (2009) Genet. Sel. Evol , vol.41 , Issue.2 , pp. 1-10
    • Meuwissen, T.H.E.1    Solberg, T.R.2    Shepherd, R.3    Woolliams, J.A.4
  • 44
    • 78951473497 scopus 로고    scopus 로고
    • Extended Bayesian LASSO for multiple quantitative trait loci mapping and unob-served phenotype prediction
    • Mutshinda, C.M., and M. J. Sillanpää, 2010 Extended Bayesian LASSO for multiple quantitative trait loci mapping and unob-served phenotype prediction. Genetics 86: 1067-1075.
    • (2010) Genetics , vol.86 , pp. 1067-1075
    • Mutshinda, C.M.1    Sillanpää, M.J.2
  • 45
    • 84863652334 scopus 로고    scopus 로고
    • Using whole-genome sequence data to predict quantita-tive trait phenotypes in Drosophila melanogaster
    • 10.1371/journal.pgen.1002685
    • Ober, U., J. F. Ayroles, E. A. Stone, S. Richards, D. Zhu et al., 2012 Using whole-genome sequence data to predict quantita-tive trait phenotypes in Drosophila melanogaster. PLoS Genet. 8 (5): e1002685 10.1371/journal.pgen.1002685.
    • (2012) PLoS Genet , vol.8 , Issue.5
    • Ober, U.1    Ayroles, J.F.2    Stone, E.A.3    Richards, S.4    Zhu, D.5
  • 48
    • 85168500140 scopus 로고    scopus 로고
    • Genomic-enabled prediction based on molecular markers and pedigree using the Bayesian Linear Regression Package in R
    • Pérez, P., G. de los Campos, J. Crossa, and D. Gianola, 2010 Genomic-enabled prediction based on molecular markers and pedigree using the Bayesian Linear Regression Package in R. Plant Genome 3: 106-116.
    • (2010) Plant Genome , vol.3 , pp. 106-116
    • Pérez, P.1    de los Campos, G.2    Crossa, J.3    Gianola, D.4
  • 49
    • 0442279032 scopus 로고
    • Prediction equations in quantitative genetics
    • Robertson, A., 1955 Prediction equations in quantitative genetics. Biometrics 11: 95-98.
    • (1955) Biometrics , vol.11 , pp. 95-98
    • Robertson, A.1
  • 50
    • 84972496336 scopus 로고
    • That BLUP is a good thing: The estimation of random effects
    • Robinson, G. K., 1991 That BLUP is a good thing: the estimation of random effects. Stat. Sci. 6: 15-32.
    • (1991) Stat. Sci , vol.6 , pp. 15-32
    • Robinson, G.K.1
  • 52
    • 79958717589 scopus 로고    scopus 로고
    • Sensitivity analysis in Bayesian gen-eralized linear mixed models for binary data
    • Roos, M., and L. Held, 2011 Sensitivity analysis in Bayesian gen-eralized linear mixed models for binary data. Bayesian Anal. 6: 259-278.
    • (2011) Bayesian Anal , vol.6 , pp. 259-278
    • Roos, M.1    Held, L.2
  • 58
    • 1842434304 scopus 로고    scopus 로고
    • Normal linear models with genetically structured residual variance heterogeneity: A case study
    • Sorensen, D., and R. Waagepetersen, 2003 Normal linear models with genetically structured residual variance heterogeneity: a case study. Genet. Res. 82: 207-222.
    • (2003) Genet. Res , vol.82 , pp. 207-222
    • Sorensen, D.1    Waagepetersen, R.2
  • 59
    • 84869078769 scopus 로고    scopus 로고
    • A fast EM algorithm for Bayes A-like prediction of geno-mic breeding values
    • 10.1371/journal.pone.0049157
    • Sun, X., L. Qu, D. J. Garrick, J. C. M. Dekkers, and R. L. Fernando, 2012 A fast EM algorithm for Bayes A-like prediction of geno-mic breeding values. PLoS ONE 7(11): 1-9. e49157 10.1371/journal.pone.0049157.
    • (2012) PLoS ONE , vol.7 , Issue.11
    • Sun, X.1    Qu, L.2    Garrick, D.J.3    Dekkers, J.C.M.4    Fernando, R.L.5
  • 60
    • 0001287271 scopus 로고    scopus 로고
    • Regression shrinkage and selection via the Lasso
    • Tibshirani, R., 1996 Regression shrinkage and selection via the Lasso. J. R. Stat. Soc. Ser. A Stat. Soc. 58: 267-288.
    • (1996) J. R. Stat. Soc. Ser. a Stat. Soc , vol.58 , pp. 267-288
    • Tibshirani, R.1
  • 61
    • 55849133422 scopus 로고    scopus 로고
    • Efficient methods to compute genomic predictions
    • Van Raden, P. M., 2008 Efficient methods to compute genomic predictions. J. Dairy Sci. 91: 4414-4423.
    • (2008) J. Dairy Sci , vol.91 , pp. 4414-4423
    • Van Raden, P.M.1
  • 62
    • 78649277825 scopus 로고    scopus 로고
    • Predictive ability of subsets of single nu-cleotide polymorphisms with and without parent average in US Holsteins
    • Vázquez, A. I., G. J. M. Rosa, K. A. Weigel, G. de los Campos, D. Gianola et al., 2010 Predictive ability of subsets of single nu-cleotide polymorphisms with and without parent average in US Holsteins. J. Dairy Sci. 93: 5942-5949.
    • (2010) J. Dairy Sci , vol.93 , pp. 5942-5949
    • Vázquez, A.I.1    Rosa, G.J.M.2    Weigel, K.A.3    de los Campos, G.4    Gianola, D.5
  • 63
    • 84870690746 scopus 로고    scopus 로고
    • A comprehensive genetic approach for improving prediction of skin cancer risk in humans
    • Vázquez, A. I., G. de los Campos, Y. C. Klimentidis, G. J. M. Rosa, D. Gianola et al., 2012 A comprehensive genetic approach for improving prediction of skin cancer risk in humans. Genetics 192: 1493-1502.
    • (2012) Genetics , vol.192 , pp. 1493-1502
    • Vázquez, A.I.1    de los Campos, G.2    Klimentidis, Y.C.3    Rosa, G.J.M.4    Gianola, D.5
  • 64
    • 80052234022 scopus 로고    scopus 로고
    • Sensitivity of genomic selection to using different prior distributions
    • 03/2010, 1-4 (doi: 10.1186/1753-6561-4-S1-S5)
    • Verbyla, K. L., P. J. Bowman, B. J. Hayes, and M. E. Goddard, 2009 Sensitivity of genomic selection to using different prior distributions. BMC Proc. 03/2010; 4 (Suppl) 1:S5. 1-4 (doi: 10.1186/1753-6561-4-S1-S5).
    • (2009) BMC Proc , vol.4 , Issue.SUPPL. 1
    • Verbyla, K.L.1    Bowman, P.J.2    Hayes, B.J.3    Goddard, M.E.4
  • 65
    • 84873991295 scopus 로고    scopus 로고
    • Bayesian methods for estimating GEBVs of threshold traits
    • Wang, C.-L., X.-D. Ding, J.-Y. Wang, J.-F. Liu, W.-X. Fu et al., 2013 Bayesian methods for estimating GEBVs of threshold traits. Heredity 110: 213-219.
    • (2013) Heredity , vol.110 , pp. 213-219
    • Wang, C.-L.1    Ding, X.-D.2    Wang, J.-Y.3    Liu, J.-F.4    Fu, W.-X.5
  • 67
    • 70349897495 scopus 로고    scopus 로고
    • Predictive ability of direct genomic values for lifetime net merit of Holstein sires using selected subsets of single nucleotide polymorphism markers
    • Weigel, K. A., G. de los Campos, O. González-Recio, H. Naya, X. L. Wu et al., 2009 Predictive ability of direct genomic values for lifetime net merit of Holstein sires using selected subsets of single nucleotide polymorphism markers. J. Dairy Sci. 92: 5248-5257.
    • (2009) J. Dairy Sci , vol.92 , pp. 5248-5257
    • Weigel, K.A.1    de los Campos, G.2    González-Recio, O.3    Naya, H.4    Wu, X.L.5
  • 68
    • 84857564737 scopus 로고    scopus 로고
    • Bayesian models with dominance effects for genomic evaluation of quantitative traits
    • Wellmann, R., and J. Bennewitz, 2012 Bayesian models with dominance effects for genomic evaluation of quantitative traits. Genet. Res. 94: 21-37.
    • (2012) Genet. Res , vol.94 , pp. 21-37
    • Wellmann, R.1    Bennewitz, J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.