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For: Shen X, Alam M, Fikse F, Rönnegård L. A novel generalized ridge regression method for quantitative genetics. Genetics 2013;193:1255-68. [PMID: 23335338 DOI: 10.1534/genetics.112.146720] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]  Open
Number Cited by Other Article(s)
1
St-Pierre J, Oualkacha K, Rai Bhatnagar S. Hierarchical selection of genetic and gene by environment interaction effects in high-dimensional mixed models. Stat Methods Med Res 2025;34:180-198. [PMID: 39659138 PMCID: PMC11800719 DOI: 10.1177/09622802241293768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2024]
2
Xiao H, Hu L, Tan Q, Jia J, Xie P, Li J, Wang M. Transcriptional profiles reveal histologic origin and prognosis across 33 The Cancer Genome Atlas tumor types. Transl Cancer Res 2023;12:2764-2780. [PMID: 37969389 PMCID: PMC10643977 DOI: 10.21037/tcr-23-234] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 08/18/2023] [Indexed: 11/17/2023]
3
Wang Q, Jiang S, Li T, Qiu Z, Yan J, Fu R, Ma C, Wang X, Jiang S, Cheng Q. G2P Provides an Integrative Environment for Multi-model genomic selection analysis to improve genotype-to-phenotype prediction. FRONTIERS IN PLANT SCIENCE 2023;14:1207139. [PMID: 37600179 PMCID: PMC10437076 DOI: 10.3389/fpls.2023.1207139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/21/2023] [Indexed: 08/22/2023]
4
Difabachew YF, Frisch M, Langstroff AL, Stahl A, Wittkop B, Snowdon RJ, Koch M, Kirchhoff M, Cselényi L, Wolf M, Förster J, Weber S, Okoye UJ, Zenke-Philippi C. Genomic prediction with haplotype blocks in wheat. FRONTIERS IN PLANT SCIENCE 2023;14:1168547. [PMID: 37229104 PMCID: PMC10203549 DOI: 10.3389/fpls.2023.1168547] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/17/2023] [Indexed: 05/27/2023]
5
Wei C, Zeng H, Zhong Z, Cai X, Teng J, Liu Y, Zhao Y, Wu X, Li J, Zhang Z. Integration of non-additive genome-wide association study with a multi-tissue transcriptome analysis of growth and carcass traits in Duroc pigs. Animal 2023;17:100817. [PMID: 37196577 DOI: 10.1016/j.animal.2023.100817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 04/03/2023] [Accepted: 04/06/2023] [Indexed: 05/19/2023]  Open
6
Lai X, Cao J, Lin Z. An Accelerated Maximally Split ADMM for a Class of Generalized Ridge Regression. IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS 2023;34:958-972. [PMID: 34437070 DOI: 10.1109/tnnls.2021.3104840] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
7
Nantongo JS, Potts BM, Klápště J, Graham NJ, Dungey HS, Fitzgerald H, O'Reilly-Wapstra JM. Genomic selection for resistance to mammalian bark stripping and associated chemical compounds in radiata pine. G3 (BETHESDA, MD.) 2022;12:jkac245. [PMID: 36218439 PMCID: PMC9635650 DOI: 10.1093/g3journal/jkac245] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 08/29/2022] [Indexed: 07/28/2023]
8
Gu B, Xu A, Huo Z, Deng C, Huang H. Privacy-Preserving Asynchronous Vertical Federated Learning Algorithms for Multiparty Collaborative Learning. IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS 2022;33:6103-6115. [PMID: 34161243 DOI: 10.1109/tnnls.2021.3072238] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
9
Danilevicz MF, Gill M, Anderson R, Batley J, Bennamoun M, Bayer PE, Edwards D. Plant Genotype to Phenotype Prediction Using Machine Learning. Front Genet 2022;13:822173. [PMID: 35664329 PMCID: PMC9159391 DOI: 10.3389/fgene.2022.822173] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 03/07/2022] [Indexed: 12/13/2022]  Open
10
Mathew B, Hauptmann A, Léon J, Sillanpää MJ. NeuralLasso: Neural Networks Meet Lasso in Genomic Prediction. FRONTIERS IN PLANT SCIENCE 2022;13:800161. [PMID: 35574107 PMCID: PMC9100816 DOI: 10.3389/fpls.2022.800161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 03/18/2022] [Indexed: 06/15/2023]
11
Estimating genetic variance contributed by a quantitative trait locus: A random model approach. PLoS Comput Biol 2022;18:e1009923. [PMID: 35275920 PMCID: PMC8942241 DOI: 10.1371/journal.pcbi.1009923] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 03/23/2022] [Accepted: 02/13/2022] [Indexed: 11/20/2022]  Open
12
Shook JM, Lourenco D, Singh AK. PATRIOT: A Pipeline for Tracing Identity-by-Descent for Chromosome Segments to Improve Genomic Prediction in Self-Pollinating Crop Species. FRONTIERS IN PLANT SCIENCE 2021;12:676269. [PMID: 34737757 PMCID: PMC8562157 DOI: 10.3389/fpls.2021.676269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 09/01/2021] [Indexed: 06/13/2023]
13
Zhang J, Liu F, Reif JC, Jiang Y. On the use of GBLUP and its extension for GWAS with additive and epistatic effects. G3-GENES GENOMES GENETICS 2021;11:6237487. [PMID: 33871030 PMCID: PMC8495923 DOI: 10.1093/g3journal/jkab122] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/04/2021] [Indexed: 11/29/2022]
14
Wang D, Tang H, Liu JF, Xu S, Zhang Q, Ning C. Rapid epistatic mixed-model association studies by controlling multiple polygenic effects. Bioinformatics 2021;36:4833-4837. [PMID: 32614415 DOI: 10.1093/bioinformatics/btaa610] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/21/2020] [Accepted: 06/24/2020] [Indexed: 12/19/2022]  Open
15
Moretti R, Soglia D, Chessa S, Sartore S, Finocchiaro R, Rasero R, Sacchi P. Identification of SNPs Associated with Somatic Cell Score in Candidate Genes in Italian Holstein Friesian Bulls. Animals (Basel) 2021;11:366. [PMID: 33535694 PMCID: PMC7912858 DOI: 10.3390/ani11020366] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 01/01/2023]  Open
16
Wang M, Li R, Xu S. Deshrinking ridge regression for genome-wide association studies. Bioinformatics 2021;36:4154-4162. [PMID: 32379866 DOI: 10.1093/bioinformatics/btaa345] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 04/21/2020] [Accepted: 04/29/2020] [Indexed: 11/15/2022]  Open
17
George AW, Verbyla A, Bowden J. Eagle: multi-locus association mapping on a genome-wide scale made routine. Bioinformatics 2020;36:1509-1516. [PMID: 31596455 DOI: 10.1093/bioinformatics/btz759] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 08/19/2019] [Accepted: 10/02/2019] [Indexed: 12/24/2022]  Open
18
Ohishi M, Yanagihara H, Fujikoshi Y. A fast algorithm for optimizing ridge parameters in a generalized ridge regression by minimizing a model selection criterion. J Stat Plan Inference 2020. [DOI: 10.1016/j.jspi.2019.04.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
19
An B, Gao X, Chang T, Xia J, Wang X, Miao J, Xu L, Zhang L, Chen Y, Li J, Xu S, Gao H. Genome-wide association studies using binned genotypes. Heredity (Edinb) 2019;124:288-298. [PMID: 31641238 DOI: 10.1038/s41437-019-0279-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 09/25/2019] [Accepted: 09/26/2019] [Indexed: 01/23/2023]  Open
20
Genomic Prediction Including SNP-Specific Variance Predictors. G3-GENES GENOMES GENETICS 2019;9:3333-3343. [PMID: 31467030 PMCID: PMC6778789 DOI: 10.1534/g3.119.400381] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
21
Soltis NE, Atwell S, Shi G, Fordyce R, Gwinner R, Gao D, Shafi A, Kliebenstein DJ. Interactions of Tomato and Botrytis cinerea Genetic Diversity: Parsing the Contributions of Host Differentiation, Domestication, and Pathogen Variation. THE PLANT CELL 2019;31:502-519. [PMID: 30647076 PMCID: PMC6447006 DOI: 10.1105/tpc.18.00857] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 12/18/2018] [Accepted: 01/08/2019] [Indexed: 05/26/2023]
22
Fordyce RF, Soltis NE, Caseys C, Gwinner R, Corwin JA, Atwell S, Copeland D, Feusier J, Subedy A, Eshbaugh R, Kliebenstein DJ. Digital Imaging Combined with Genome-Wide Association Mapping Links Loci to Plant-Pathogen Interaction Traits. PLANT PHYSIOLOGY 2018;178:1406-1422. [PMID: 30266748 PMCID: PMC6236616 DOI: 10.1104/pp.18.00851] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 09/18/2018] [Indexed: 05/04/2023]
23
Coombes BJ, Basu S, McGue M. A linear mixed model framework for gene-based gene-environment interaction tests in twin studies. Genet Epidemiol 2018;42:648-663. [PMID: 30203856 DOI: 10.1002/gepi.22150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 04/25/2018] [Accepted: 04/30/2018] [Indexed: 02/03/2023]
24
Ning C, Wang D, Kang H, Mrode R, Zhou L, Xu S, Liu JF. A rapid epistatic mixed-model association analysis by linear retransformations of genomic estimated values. Bioinformatics 2018;34:1817-1825. [PMID: 29342229 PMCID: PMC5972602 DOI: 10.1093/bioinformatics/bty017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 01/07/2018] [Accepted: 01/10/2018] [Indexed: 12/16/2022]  Open
25
Jonas E, Fikse F, Rönnegård L, Mouresan EF. Genomic Selection. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
26
A novel linkage-disequilibrium corrected genomic relationship matrix for SNP-heritability estimation and genomic prediction. Heredity (Edinb) 2017;120:356-368. [PMID: 29238077 PMCID: PMC5842222 DOI: 10.1038/s41437-017-0023-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 10/13/2017] [Accepted: 10/23/2017] [Indexed: 12/15/2022]  Open
27
Thistlethwaite FR, Ratcliffe B, Klápště J, Porth I, Chen C, Stoehr MU, El-Kassaby YA. Genomic prediction accuracies in space and time for height and wood density of Douglas-fir using exome capture as the genotyping platform. BMC Genomics 2017;18:930. [PMID: 29197325 PMCID: PMC5712148 DOI: 10.1186/s12864-017-4258-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 11/01/2017] [Indexed: 11/11/2022]  Open
28
Mazo Lopera MA, Coombes BJ, de Andrade M. An Efficient Test for Gene-Environment Interaction in Generalized Linear Mixed Models with Family Data. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2017;14:ijerph14101134. [PMID: 28953253 PMCID: PMC5664635 DOI: 10.3390/ijerph14101134] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Revised: 09/20/2017] [Accepted: 09/25/2017] [Indexed: 02/07/2023]
29
An exact approach to ridge regression for big data. Comput Stat 2017. [DOI: 10.1007/s00180-017-0731-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
30
An efficient method to handle the 'large p, small n' problem for genomewide association studies using Haseman-Elston regression. J Genet 2017;95:847-852. [PMID: 27994183 DOI: 10.1007/s12041-016-0705-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
31
Angelovici R, Batushansky A, Deason N, Gonzalez-Jorge S, Gore MA, Fait A, DellaPenna D. Network-Guided GWAS Improves Identification of Genes Affecting Free Amino Acids. PLANT PHYSIOLOGY 2017;173:872-886. [PMID: 27872244 PMCID: PMC5210728 DOI: 10.1104/pp.16.01287] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 11/16/2016] [Indexed: 05/18/2023]
32
Li W, Liu H, Yang P, Xie W. Supporting Regularized Logistic Regression Privately and Efficiently. PLoS One 2016;11:e0156479. [PMID: 27271738 PMCID: PMC4894560 DOI: 10.1371/journal.pone.0156479] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 04/18/2016] [Indexed: 12/03/2022]  Open
33
Accuracy of Genomic Prediction in Switchgrass (Panicum virgatum L.) Improved by Accounting for Linkage Disequilibrium. G3-GENES GENOMES GENETICS 2016;6:1049-62. [PMID: 26869619 PMCID: PMC4825640 DOI: 10.1534/g3.115.024950] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
34
Kooke R, Kruijer W, Bours R, Becker F, Kuhn A, van de Geest H, Buntjer J, Doeswijk T, Guerra J, Bouwmeester H, Vreugdenhil D, Keurentjes JJB. Genome-Wide Association Mapping and Genomic Prediction Elucidate the Genetic Architecture of Morphological Traits in Arabidopsis. PLANT PHYSIOLOGY 2016;170:2187-203. [PMID: 26869705 PMCID: PMC4825126 DOI: 10.1104/pp.15.00997] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 02/11/2016] [Indexed: 05/05/2023]
35
Corwin JA, Copeland D, Feusier J, Subedy A, Eshbaugh R, Palmer C, Maloof J, Kliebenstein DJ. The Quantitative Basis of the Arabidopsis Innate Immune System to Endemic Pathogens Depends on Pathogen Genetics. PLoS Genet 2016;12:e1005789. [PMID: 26866607 PMCID: PMC4750985 DOI: 10.1371/journal.pgen.1005789] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 12/16/2015] [Indexed: 01/19/2023]  Open
36
Francisco M, Joseph B, Caligagan H, Li B, Corwin JA, Lin C, Kerwin RE, Burow M, Kliebenstein DJ. Genome Wide Association Mapping in Arabidopsis thaliana Identifies Novel Genes Involved in Linking Allyl Glucosinolate to Altered Biomass and Defense. FRONTIERS IN PLANT SCIENCE 2016;7:1010. [PMID: 27462337 PMCID: PMC4940622 DOI: 10.3389/fpls.2016.01010] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 06/27/2016] [Indexed: 05/17/2023]
37
Exploiting Linkage Disequilibrium for Ultrahigh-Dimensional Genome-Wide Data with an Integrated Statistical Approach. Genetics 2015;202:411-26. [PMID: 26661113 DOI: 10.1534/genetics.115.179507] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 11/19/2015] [Indexed: 01/08/2023]  Open
38
Dumancas GG, Ramasahayam S, Bello G, Hughes J, Kramer R. Chemometric regression techniques as emerging, powerful tools in genetic association studies. Trends Analyt Chem 2015. [DOI: 10.1016/j.trac.2015.05.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
39
Lachowiec J, Shen X, Queitsch C, Carlborg Ö. A Genome-Wide Association Analysis Reveals Epistatic Cancellation of Additive Genetic Variance for Root Length in Arabidopsis thaliana. PLoS Genet 2015;11:e1005541. [PMID: 26397943 PMCID: PMC4580642 DOI: 10.1371/journal.pgen.1005541] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 08/27/2015] [Indexed: 12/19/2022]  Open
40
Kierczak M, Jabłońska J, Forsberg SKG, Bianchi M, Tengvall K, Pettersson M, Scholz V, Meadows JRS, Jern P, Carlborg Ö, Lindblad-Toh K. cgmisc: enhanced genome-wide association analyses and visualization. Bioinformatics 2015;31:3830-1. [PMID: 26249815 PMCID: PMC4653382 DOI: 10.1093/bioinformatics/btv426] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 07/17/2015] [Indexed: 12/20/2022]  Open
41
The Current and Future Use of Ridge Regression for Prediction in Quantitative Genetics. BIOMED RESEARCH INTERNATIONAL 2015;2015:143712. [PMID: 26273586 PMCID: PMC4529984 DOI: 10.1155/2015/143712] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 12/24/2014] [Indexed: 01/05/2023]
42
A comparison of genomic selection models across time in interior spruce (Picea engelmannii × glauca) using unordered SNP imputation methods. Heredity (Edinb) 2015. [PMID: 26126540 DOI: 10.1038/hdy.2015.57.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]  Open
43
Ratcliffe B, El-Dien OG, Klápště J, Porth I, Chen C, Jaquish B, El-Kassaby YA. A comparison of genomic selection models across time in interior spruce (Picea engelmannii × glauca) using unordered SNP imputation methods. Heredity (Edinb) 2015;115:547-55. [PMID: 26126540 DOI: 10.1038/hdy.2015.57] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 04/29/2015] [Accepted: 05/26/2015] [Indexed: 11/09/2022]  Open
44
Gamal El-Dien O, Ratcliffe B, Klápště J, Chen C, Porth I, El-Kassaby YA. Prediction accuracies for growth and wood attributes of interior spruce in space using genotyping-by-sequencing. BMC Genomics 2015;16:370. [PMID: 25956247 PMCID: PMC4424896 DOI: 10.1186/s12864-015-1597-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 04/28/2015] [Indexed: 02/02/2024]  Open
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Accounting for genetic architecture improves sequence based genomic prediction for a Drosophila fitness trait. PLoS One 2015;10:e0126880. [PMID: 25950439 PMCID: PMC4423967 DOI: 10.1371/journal.pone.0126880] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 04/08/2015] [Indexed: 12/01/2022]  Open
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Lee YS, Kim HJ, Cho S, Kim H. The Usage of an SNP-SNP Relationship Matrix for Best Linear Unbiased Prediction (BLUP) Analysis Using a Community-Based Cohort Study. Genomics Inform 2015;12:254-60. [PMID: 25705167 PMCID: PMC4330263 DOI: 10.5808/gi.2014.12.4.254] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Revised: 08/18/2014] [Accepted: 09/16/2014] [Indexed: 11/25/2022]  Open
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Pong-Wong R. Estimation of genomic breeding values using the Horseshoe prior. BMC Proc 2014;8:S6. [PMID: 25519520 PMCID: PMC4195408 DOI: 10.1186/1753-6561-8-s5-s6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
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Shen X, De Jonge J, Forsberg SKG, Pettersson ME, Sheng Z, Hennig L, Carlborg Ö. Natural CMT2 variation is associated with genome-wide methylation changes and temperature seasonality. PLoS Genet 2014;10:e1004842. [PMID: 25503602 PMCID: PMC4263395 DOI: 10.1371/journal.pgen.1004842] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 10/21/2014] [Indexed: 12/30/2022]  Open
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Falke KC, Mahone GS, Bauer E, Haseneyer G, Miedaner T, Breuer F, Frisch M. Genome-wide prediction methods for detecting genetic effects of donor chromosome segments in introgression populations. BMC Genomics 2014;15:782. [PMID: 25213628 PMCID: PMC4169839 DOI: 10.1186/1471-2164-15-782] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 08/20/2014] [Indexed: 11/10/2022]  Open
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Fabregat-Traver D, Sharapov SZ, Hayward C, Rudan I, Campbell H, Aulchenko Y, Bientinesi P. High-Performance Mixed Models Based Genome-Wide Association Analysis with omicABEL software. F1000Res 2014;3:200. [PMID: 25717363 PMCID: PMC4329600 DOI: 10.12688/f1000research.4867.1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/07/2014] [Indexed: 01/06/2023]  Open
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