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bWGR: Bayesian Whole-Genome Regression.

Xavier A, Muir WM, Rainey KM.

Bioinformatics. 2019 Oct 24. pii: btz794. doi: 10.1093/bioinformatics/btz794. [Epub ahead of print]


CIS-Acting Allele-Specific Expression Differences Induced by Alcohol and Impacted by Sex as Well as Parental Genotype of Origin.

Lo CL, Lumeng L, Bell RL, Liang T, Lossie AC, Muir WM, Zhou FC.

Alcohol Clin Exp Res. 2018 Aug;42(8):1444-1453. doi: 10.1111/acer.13776. Epub 2018 Jun 9.


Genome-Wide Analysis of Grain Yield Stability and Environmental Interactions in a Multiparental Soybean Population.

Xavier A, Jarquin D, Howard R, Ramasubramanian V, Specht JE, Graef GL, Beavis WD, Diers BW, Song Q, Cregan PB, Nelson R, Mian R, Shannon JG, McHale L, Wang D, Schapaugh W, Lorenz AJ, Xu S, Muir WM, Rainey KM.

G3 (Bethesda). 2018 Feb 2;8(2):519-529. doi: 10.1534/g3.117.300300.


Genomic prediction of survival time in a population of brown laying hens showing cannibalistic behavior.

Alemu SW, Calus MP, Muir WM, Peeters K, Vereijken A, Bijma P.

Genet Sel Evol. 2016 Sep 13;48(1):68. doi: 10.1186/s12711-016-0247-4.


High Resolution Genomic Scans Reveal Genetic Architecture Controlling Alcohol Preference in Bidirectionally Selected Rat Model.

Lo CL, Lossie AC, Liang T, Liu Y, Xuei X, Lumeng L, Zhou FC, Muir WM.

PLoS Genet. 2016 Aug 4;12(8):e1006178. doi: 10.1371/journal.pgen.1006178. eCollection 2016 Aug.


Walking through the statistical black boxes of plant breeding.

Xavier A, Muir WM, Craig B, Rainey KM.

Theor Appl Genet. 2016 Oct;129(10):1933-49. doi: 10.1007/s00122-016-2750-y. Epub 2016 Jul 19. Review.


Assessing Predictive Properties of Genome-Wide Selection in Soybeans.

Xavier A, Muir WM, Rainey KM.

G3 (Bethesda). 2016 Aug 9;6(8):2611-6. doi: 10.1534/g3.116.032268.


Impact of imputation methods on the amount of genetic variation captured by a single-nucleotide polymorphism panel in soybeans.

Xavier A, Muir WM, Rainey KM.

BMC Bioinformatics. 2016 Feb 2;17:55. doi: 10.1186/s12859-016-0899-7.


NAM: association studies in multiple populations.

Xavier A, Xu S, Muir WM, Rainey KM.

Bioinformatics. 2015 Dec 1;31(23):3862-4. doi: 10.1093/bioinformatics/btv448. Epub 2015 Aug 4.


Mate competition and evolutionary outcomes in genetically modified zebrafish (Danio rerio).

Howard RD, Rohrer K, Liu Y, Muir WM.

Evolution. 2015 May;69(5):1143-57. doi: 10.1111/evo.12662. Epub 2015 May 6.


Selective sweep analysis in the genomes of the 91-R and 91-C Drosophila melanogaster strains reveals few of the 'usual suspects' in dichlorodiphenyltrichloroethane (DDT) resistance.

Steele LD, Coates B, Valero MC, Sun W, Seong KM, Muir WM, Clark JM, Pittendrigh BR.

PLoS One. 2015 Mar 31;10(3):e0123066. doi: 10.1371/journal.pone.0123066. eCollection 2015.


A snapshot of the hepatic transcriptome: ad libitum alcohol intake suppresses expression of cholesterol synthesis genes in alcohol-preferring (P) rats.

Klein JD, Sherrill JB, Morello GM, San Miguel PJ, Ding Z, Liangpunsakul S, Liang T, Muir WM, Lumeng L, Lossie AC.

PLoS One. 2014 Dec 26;9(12):e110501. doi: 10.1371/journal.pone.0110501. eCollection 2014.


Methods to address poultry robustness and welfare issues through breeding and associated ethical considerations.

Muir WM, Cheng HW, Croney C.

Front Genet. 2014 Nov 26;5:407. doi: 10.3389/fgene.2014.00407. eCollection 2014. Review.


The prospects of selection for social genetic effects to improve welfare and productivity in livestock.

Ellen ED, Rodenburg TB, Albers GA, Bolhuis JE, Camerlink I, Duijvesteijn N, Knol EF, Muir WM, Peeters K, Reimert I, Sell-Kubiak E, van Arendonk JA, Visscher J, Bijma P.

Front Genet. 2014 Nov 11;5:377. doi: 10.3389/fgene.2014.00377. eCollection 2014. Review.


Response to commentary on "Examples of overlooking common sense solutions: the domestication gene and selection against mortality".

Bijma P, Muir WM, Ellen ED.

Front Genet. 2014 Sep 30;5:343. doi: 10.3389/fgene.2014.00343. eCollection 2014. No abstract available.


Changes in variance explained by top SNP windows over generations for three traits in broiler chicken.

Fragomeni Bde O, Misztal I, Lourenco DL, Aguilar I, Okimoto R, Muir WM.

Front Genet. 2014 Oct 1;5:332. doi: 10.3389/fgene.2014.00332. eCollection 2014.


Systematic differences in the response of genetic variation to pedigree and genome-based selection methods.

Heidaritabar M, Vereijken A, Muir WM, Meuwissen T, Cheng H, Megens HJ, Groenen MA, Bastiaansen JW.

Heredity (Edinb). 2014 Dec;113(6):503-13. doi: 10.1038/hdy.2014.55. Epub 2014 Jul 30.


The cellular and molecular etiology of the craniofacial defects in the avian ciliopathic mutant talpid2.

Chang CF, Schock EN, O'Hare EA, Dodgson J, Cheng HH, Muir WM, Edelmann RE, Delany ME, Brugmann SA.

Development. 2014 Aug;141(15):3003-12. doi: 10.1242/dev.105924.


Mapping and genotypic analysis of the NK-lysin gene in chicken.

Lee MO, Yang E, Morisson M, Vignal A, Huang YZ, Cheng HH, Muir WM, Lamont SJ, Lillehoj HS, Lee SH, Womack JE.

Genet Sel Evol. 2014 Jul 7;46:43. doi: 10.1186/1297-9686-46-43.


Implications of genomic signatures in the differential vulnerability to fetal alcohol exposure in C57BL/6 and DBA/2 mice.

Lossie AC, Muir WM, Lo CL, Timm F, Liu Y, Gray W, Zhou FC.

Front Genet. 2014 Jun 11;5:173. doi: 10.3389/fgene.2014.00173. eCollection 2014.


Genome-wide sequencing and an open reading frame analysis of dichlorodiphenyltrichloroethane (DDT) susceptible (91-C) and resistant (91-R) Drosophila melanogaster laboratory populations.

Steele LD, Muir WM, Seong KM, Valero MC, Rangesa M, Sun W, Clark JM, Coates B, Pittendrigh BR.

PLoS One. 2014 Jun 10;9(6):e98584. doi: 10.1371/journal.pone.0098584. eCollection 2014.


Genome-wide association mapping including phenotypes from relatives without genotypes in a single-step (ssGWAS) for 6-week body weight in broiler chickens.

Wang H, Misztal I, Aguilar I, Legarra A, Fernando RL, Vitezica Z, Okimoto R, Wing T, Hawken R, Muir WM.

Front Genet. 2014 May 20;5:134. doi: 10.3389/fgene.2014.00134. eCollection 2014.


Experiences with a single-step genome evaluation.

Misztal I, Aggrey SE, Muir WM.

Poult Sci. 2013 Sep;92(9):2530-4. doi: 10.3382/ps.2012-02739.


Multilevel selection with kin and non-kin groups, experimental results with Japanese quail (Coturnix japonica).

Muir WM, Bijma P, Schinckel A.

Evolution. 2013 Jun;67(6):1598-606. doi: 10.1111/evo.12062. Epub 2013 Feb 18.


Genome-wide analysis of genes associated with moderate and high DDT resistance in Drosophila melanogaster.

Qiu X, Sun W, McDonnell CM, Li-Byarlay H, Steele LD, Wu J, Xie J, Muir WM, Pittendrigh BR.

Pest Manag Sci. 2013 Aug;69(8):930-7. doi: 10.1002/ps.3454. Epub 2013 Feb 1.


A fast and efficient approach for genomic selection with high-density markers.

Pungpapong V, Muir WM, Li X, Zhang D, Zhang M.

G3 (Bethesda). 2012 Oct;2(10):1179-84. doi: 10.1534/g3.112.003822. Epub 2012 Oct 1.


Transcriptomic analysis of peritoneal cells in a mouse model of sepsis: confirmatory and novel results in early and late sepsis.

Bhatty M, Fan R, Muir WM, Pruett SB, Nanduri B.

BMC Genomics. 2012 Sep 25;13:509. doi: 10.1186/1471-2164-13-509.


Methamphetamine causes anorexia in Drosophila melanogaster, exhausting metabolic reserves and contributing to mortality.

Walters KR Jr, Rupassara SI, Markelz RJ, Leakey AD, Muir WM, Pittendrigh BR.

J Toxicol Sci. 2012;37(4):773-90.


Genome-wide association mapping including phenotypes from relatives without genotypes.

Wang H, Misztal I, Aguilar I, Legarra A, Muir WM.

Genet Res (Camb). 2012 Apr;94(2):73-83. doi: 10.1017/S0016672312000274.


The CHD3 remodeler PICKLE associates with genes enriched for trimethylation of histone H3 lysine 27.

Zhang H, Bishop B, Ringenberg W, Muir WM, Ogas J.

Plant Physiol. 2012 May;159(1):418-32. doi: 10.1104/pp.112.194878. Epub 2012 Mar 27.


Genome-Wide Identification and Quantification of cis- and trans-Regulated Genes Responding to Marek's Disease Virus Infection via Analysis of Allele-Specific Expression.

Maceachern S, Muir WM, Crosby SD, Cheng HH.

Front Genet. 2012 Jan 13;2:113. doi: 10.3389/fgene.2011.00113. eCollection 2011.


Gene Profiling of Aortic Valve Interstitial Cells under Elevated Pressure Conditions: Modulation of Inflammatory Gene Networks.

Warnock JN, Nanduri B, Pregonero Gamez CA, Tang J, Koback D, Muir WM, Burgess SC.

Int J Inflam. 2011;2011:176412. doi: 10.4061/2011/176412. Epub 2011 Aug 18.


Transgenic salmon: a final leap to the grocery shelf?

Van Eenennaam AL, Muir WM.

Nat Biotechnol. 2011 Aug 5;29(8):706-10. doi: 10.1038/nbt.1938. No abstract available.


Genome-wide identification of allele-specific expression (ASE) in response to Marek's disease virus infection using next generation sequencing.

Maceachern S, Muir WM, Crosby S, Cheng HH.

BMC Proc. 2011 Jun 3;5 Suppl 4:S14. doi: 10.1186/1753-6561-5-S4-S14.


The development and characterization of a 60K SNP chip for chicken.

Groenen MA, Megens HJ, Zare Y, Warren WC, Hillier LW, Crooijmans RP, Vereijken A, Okimoto R, Muir WM, Cheng HH.

BMC Genomics. 2011 May 31;12(1):274. doi: 10.1186/1471-2164-12-274.


Systems-scale analysis reveals pathways involved in cellular response to methamphetamine.

Sun L, Li HM, Seufferheld MJ, Walters KR Jr, Margam VM, Jannasch A, Diaz N, Riley CP, Sun W, Li YF, Muir WM, Xie J, Wu J, Zhang F, Chen JY, Barker EL, Adamec J, Pittendrigh BR.

PLoS One. 2011 Apr 20;6(4):e18215. doi: 10.1371/journal.pone.0018215.


Effect of different genomic relationship matrices on accuracy and scale.

Chen CY, Misztal I, Aguilar I, Legarra A, Muir WM.

J Anim Sci. 2011 Sep;89(9):2673-9. doi: 10.2527/jas.2010-3555. Epub 2011 Mar 31.


Genome-wide marker-assisted selection combining all pedigree phenotypic information with genotypic data in one step: An example using broiler chickens.

Chen CY, Misztal I, Aguilar I, Tsuruta S, Meuwissen TH, Aggrey SE, Wing T, Muir WM.

J Anim Sci. 2011 Jan;89(1):23-8. doi: 10.2527/jas.2010-3071. Epub 2010 Oct 1.


Precision genetics for complex objectives in animal agriculture.

Fahrenkrug SC, Blake A, Carlson DF, Doran T, Van Eenennaam A, Faber D, Galli C, Gao Q, Hackett PB, Li N, Maga EA, Muir WM, Murray JD, Shi D, Stotish R, Sullivan E, Taylor JF, Walton M, Wheeler M, Whitelaw B, Glenn BP.

J Anim Sci. 2010 Jul;88(7):2530-9. doi: 10.2527/jas.2010-2847. Epub 2010 Mar 12.


A mixture model approach for the analysis of small exploratory microarray experiments.

Muir WM, Rosa GJ, Pittendrigh BR, Xu S, Rider SD, Fountain M, Ogas J.

Comput Stat Data Anal. 2009 Mar 15;53(5):1566-1576.


Bowman-Birk inhibitor affects pathways associated with energy metabolism in Drosophila melanogaster.

Li HM, Sun L, Mittapalli O, Muir WM, Xie J, Wu J, Schemerhorn BJ, Jannasch A, Chen JY, Zhang F, Adamec J, Murdock LL, Pittendrigh BR.

Insect Mol Biol. 2010 Jun 1;19(3):303-13. doi: 10.1111/j.1365-2583.2009.00984.x. Epub 2009 Dec 23.


Comparison of linkage disequilibrium and haplotype diversity on macro- and microchromosomes in chicken.

Megens HJ, Crooijmans RP, Bastiaansen JW, Kerstens HH, Coster A, Jalving R, Vereijken A, Silva P, Muir WM, Cheng HH, Hanotte O, Groenen MA.

BMC Genet. 2009 Dec 20;10:86. doi: 10.1186/1471-2156-10-86.


Transcriptional signatures in response to wheat germ agglutinin and starvation in Drosophila melanogaster larval midgut.

Li HM, Sun L, Mittapalli O, Muir WM, Xie J, Wu J, Schemerhorn BJ, Sun W, Pittendrigh BR, Murdock LL.

Insect Mol Biol. 2009 Feb;18(1):21-31. doi: 10.1111/j.1365-2583.2008.00844.x.


A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate.

Groenen MA, Wahlberg P, Foglio M, Cheng HH, Megens HJ, Crooijmans RP, Besnier F, Lathrop M, Muir WM, Wong GK, Gut I, Andersson L.

Genome Res. 2009 Mar;19(3):510-9. doi: 10.1101/gr.086538.108. Epub 2008 Dec 16.


Genome-wide assessment of worldwide chicken SNP genetic diversity indicates significant absence of rare alleles in commercial breeds.

Muir WM, Wong GK, Zhang Y, Wang J, Groenen MA, Crooijmans RP, Megens HJ, Zhang H, Okimoto R, Vereijken A, Jungerius A, Albers GA, Lawley CT, Delany ME, MacEachern S, Cheng HH.

Proc Natl Acad Sci U S A. 2008 Nov 11;105(45):17312-7. doi: 10.1073/pnas.0806569105. Epub 2008 Nov 3.


Fitness components and ecological risk of transgenic release: a model using Japanese medaka (Oryzias latipes).

Muir WM, Howard RD.

Am Nat. 2001 Jul;158(1):1-16. doi: 10.1086/320860.


The CHD3 remodeler PICKLE promotes trimethylation of histone H3 lysine 27.

Zhang H, Rider SD Jr, Henderson JT, Fountain M, Chuang K, Kandachar V, Simons A, Edenberg HJ, Romero-Severson J, Muir WM, Ogas J.

J Biol Chem. 2008 Aug 15;283(33):22637-48. doi: 10.1074/jbc.M802129200. Epub 2008 Jun 6.


Improved phytate phosphorus utilization by Japanese medaka transgenic for the Aspergillus niger phytase gene.

Hostetler HA, Collodi P, Devlin RH, Muir WM.

Zebrafish. 2005;2(1):19-31. doi: 10.1089/zeb.2005.2.19.


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