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Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues.

Xiang R, Hayes BJ, Vander Jagt CJ, MacLeod IM, Khansefid M, Bowman PJ, Yuan Z, Prowse-Wilkins CP, Reich CM, Mason BA, Garner JB, Marett LC, Chen Y, Bolormaa S, Daetwyler HD, Chamberlain AJ, Goddard ME.

BMC Genomics. 2018 Jul 4;19(1):521. doi: 10.1186/s12864-018-4902-8.


Putative bovine topological association domains and CTCF binding motifs can reduce the search space for causative regulatory variants of complex traits.

Wang M, Hancock TP, Chamberlain AJ, Vander Jagt CJ, Pryce JE, Cocks BG, Goddard ME, Hayes BJ.

BMC Genomics. 2018 May 24;19(1):395. doi: 10.1186/s12864-018-4800-0.


The cost-benefit of genomic testing of heifers and using sexed semen in pasture-based dairy herds.

Newton JE, Hayes BJ, Pryce JE.

J Dairy Sci. 2018 Jul;101(7):6159-6173. doi: 10.3168/jds.2017-13476. Epub 2018 Apr 26.


Insights into population genetics and evolution of polyploids and their ancestors.

Jighly A, Lin Z, Forster JW, Spangenberg GC, Hayes BJ, Daetwyler HD.

Mol Ecol Resour. 2018 Apr 26. doi: 10.1111/1755-0998.12896. [Epub ahead of print]


An initiator codon mutation in SDE2 causes recessive embryonic lethality in Holstein cattle.

Fritz S, Hoze C, Rebours E, Barbat A, Bizard M, Chamberlain A, Escouflaire C, Vander Jagt C, Boussaha M, Grohs C, Allais-Bonnet A, Philippe M, Vallée A, Amigues Y, Hayes BJ, Boichard D, Capitan A.

J Dairy Sci. 2018 Jul;101(7):6220-6231. doi: 10.3168/jds.2017-14119. Epub 2018 Apr 19.


Variance explained by whole genome sequence variants in coding and regulatory genome annotations for six dairy traits.

Koufariotis LT, Chen YP, Stothard P, Hayes BJ.

BMC Genomics. 2018 Apr 5;19(1):237. doi: 10.1186/s12864-018-4617-x.


Responses of dairy cows with divergent residual feed intake as calves to metabolic challenges during midlactation and the nonlactating period.

DiGiacomo K, Norris E, Dunshea FR, Hayes BJ, Marett LC, Wales WJ, Leury BJ.

J Dairy Sci. 2018 Jul;101(7):6474-6485. doi: 10.3168/jds.2017-12569. Epub 2018 Mar 28.


A multi-trait Bayesian method for mapping QTL and genomic prediction.

Kemper KE, Bowman PJ, Hayes BJ, Visscher PM, Goddard ME.

Genet Sel Evol. 2018 Mar 24;50(1):10. doi: 10.1186/s12711-018-0377-y.


Engineering a multicellular vascular niche to model hematopoietic cell trafficking.

Kotha SS, Hayes BJ, Phong KT, Redd MA, Bomsztyk K, Ramakrishnan A, Torok-Storb B, Zheng Y.

Stem Cell Res Ther. 2018 Mar 23;9(1):77. doi: 10.1186/s13287-018-0808-2.


Multibreed genomic prediction using multitrait genomic residual maximum likelihood and multitask Bayesian variable selection.

Calus MPL, Goddard ME, Wientjes YCJ, Bowman PJ, Hayes BJ.

J Dairy Sci. 2018 May;101(5):4279-4294. doi: 10.3168/jds.2017-13366. Epub 2018 Mar 15.


Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals.

Bouwman AC, Daetwyler HD, Chamberlain AJ, Ponce CH, Sargolzaei M, Schenkel FS, Sahana G, Govignon-Gion A, Boitard S, Dolezal M, Pausch H, Brøndum RF, Bowman PJ, Thomsen B, Guldbrandtsen B, Lund MS, Servin B, Garrick DJ, Reecy J, Vilkki J, Bagnato A, Wang M, Hoff JL, Schnabel RD, Taylor JF, Vinkhuyzen AAE, Panitz F, Bendixen C, Holm LE, Gredler B, Hozé C, Boussaha M, Sanchez MP, Rocha D, Capitan A, Tribout T, Barbat A, Croiseau P, Drögemüller C, Jagannathan V, Vander Jagt C, Crowley JJ, Bieber A, Purfield DC, Berry DP, Emmerling R, Götz KU, Frischknecht M, Russ I, Sölkner J, Van Tassell CP, Fries R, Stothard P, Veerkamp RF, Boichard D, Goddard ME, Hayes BJ.

Nat Genet. 2018 Mar;50(3):362-367. doi: 10.1038/s41588-018-0056-5. Epub 2018 Feb 19.


Estimated allele substitution effects underlying genomic evaluation models depend on the scaling of allele counts.

Bouwman AC, Hayes BJ, Calus MPL.

Genet Sel Evol. 2017 Oct 30;49(1):79. doi: 10.1186/s12711-017-0355-9.


Multi-breed genomic prediction using Bayes R with sequence data and dropping variants with a small effect.

van den Berg I, Bowman PJ, MacLeod IM, Hayes BJ, Wang T, Bolormaa S, Goddard ME.

Genet Sel Evol. 2017 Sep 21;49(1):70. doi: 10.1186/s12711-017-0347-9.


Rapid Discovery of De Novo Deleterious Mutations in Cattle Enhances the Value of Livestock as Model Species.

Bourneuf E, Otz P, Pausch H, Jagannathan V, Michot P, Grohs C, Piton G, Ammermüller S, Deloche MC, Fritz S, Leclerc H, Péchoux C, Boukadiri A, Hozé C, Saintilan R, Créchet F, Mosca M, Segelke D, Guillaume F, Bouet S, Baur A, Vasilescu A, Genestout L, Thomas A, Allais-Bonnet A, Rocha D, Colle MA, Klopp C, Esquerré D, Wurmser C, Flisikowski K, Schwarzenbacher H, Burgstaller J, Brügmann M, Dietschi E, Rudolph N, Freick M, Barbey S, Fayolle G, Danchin-Burge C, Schibler L, Bed'Hom B, Hayes BJ, Daetwyler HD, Fries R, Boichard D, Pin D, Drögemüller C, Capitan A.

Sci Rep. 2017 Sep 13;7(1):11466. doi: 10.1038/s41598-017-11523-3.


Accelerating wheat breeding for end-use quality with multi-trait genomic predictions incorporating near infrared and nuclear magnetic resonance-derived phenotypes.

Hayes BJ, Panozzo J, Walker CK, Choy AL, Kant S, Wong D, Tibbits J, Daetwyler HD, Rochfort S, Hayden MJ, Spangenberg GC.

Theor Appl Genet. 2017 Dec;130(12):2505-2519. doi: 10.1007/s00122-017-2972-7. Epub 2017 Aug 24.


Application of a Bayesian non-linear model hybrid scheme to sequence data for genomic prediction and QTL mapping.

Wang T, Chen YP, MacLeod IM, Pryce JE, Goddard ME, Hayes BJ.

BMC Genomics. 2017 Aug 15;18(1):618. doi: 10.1186/s12864-017-4030-x.


Short communication: Implementation of a breeding value for heat tolerance in Australian dairy cattle.

Nguyen TTT, Bowman PJ, Haile-Mariam M, Nieuwhof GJ, Hayes BJ, Pryce JE.

J Dairy Sci. 2017 Sep;100(9):7362-7367. doi: 10.3168/jds.2017-12898. Epub 2017 Jul 12.


Putative enhancer sites in the bovine genome are enriched with variants affecting complex traits.

Wang M, Hancock TP, MacLeod IM, Pryce JE, Cocks BG, Hayes BJ.

Genet Sel Evol. 2017 Jul 6;49(1):56. doi: 10.1186/s12711-017-0331-4.


Exome sequence genotype imputation in globally diverse hexaploid wheat accessions.

Shi F, Tibbits J, Pasam RK, Kay P, Wong D, Petkowski J, Forrest KL, Hayes BJ, Akhunova A, Davies J, Webb S, Spangenberg GC, Akhunov E, Hayden MJ, Daetwyler HD.

Theor Appl Genet. 2017 Jul;130(7):1393-1404. doi: 10.1007/s00122-017-2895-3. Epub 2017 Apr 4.


Mitigation of inbreeding while preserving genetic gain in genomic breeding programs for outbred plants.

Lin Z, Shi F, Hayes BJ, Daetwyler HD.

Theor Appl Genet. 2017 May;130(5):969-980. doi: 10.1007/s00122-017-2863-y. Epub 2017 Mar 31.


Implementation of 'Goals of Patient Care' medical treatment orders in residential aged care facilities: protocol for a randomised controlled trial.

Martin RS, Hayes BJ, Hutchinson A, Yates P, Lim WK.

BMJ Open. 2017 Mar 10;7(3):e013909. doi: 10.1136/bmjopen-2016-013909.


Erratum to: Detection and validation of structural variations in bovine whole-genome sequence data.

Chen L, Chamberlain AJ, Reich CM, Daetwyler HD, Hayes BJ.

Genet Sel Evol. 2017 Mar 3;49(1):31. doi: 10.1186/s12711-017-0305-6. No abstract available.


Genomic prediction of reproduction traits for Merino sheep.

Bolormaa S, Brown DJ, Swan AA, van der Werf JHJ, Hayes BJ, Daetwyler HD.

Anim Genet. 2017 Jun;48(3):338-348. doi: 10.1111/age.12541. Epub 2017 Feb 17.


Human Cord Blood and Bone Marrow CD34+ Cells Generate Macrophages That Support Erythroid Islands.

Belay E, Hayes BJ, Blau CA, Torok-Storb B.

PLoS One. 2017 Jan 30;12(1):e0171096. doi: 10.1371/journal.pone.0171096. eCollection 2017.


Detection and validation of structural variations in bovine whole-genome sequence data.

Chen L, Chamberlain AJ, Reich CM, Daetwyler HD, Hayes BJ.

Genet Sel Evol. 2017 Jan 25;49(1):13. doi: 10.1186/s12711-017-0286-5. Erratum in: Genet Sel Evol. 2017 Mar 3;49(1):31.


Corrigendum: Genomic Selection Improves Heat Tolerance in Dairy Cattle.

Garner JB, Douglas ML, Williams SR, Wales WJ, Marett LC, Nguyen TT, Reich CM, Hayes BJ.

Sci Rep. 2017 Jan 19;7:39896. doi: 10.1038/srep39896. No abstract available.


Including nonadditive genetic effects in mating programs to maximize dairy farm profitability.

Aliloo H, Pryce JE, González-Recio O, Cocks BG, Goddard ME, Hayes BJ.

J Dairy Sci. 2017 Feb;100(2):1203-1222. doi: 10.3168/jds.2016-11261. Epub 2016 Dec 9.


Improving Genetic Gain with Genomic Selection in Autotetraploid Potato.

Slater AT, Cogan NO, Forster JW, Hayes BJ, Daetwyler HD.

Plant Genome. 2016 Nov;9(3). doi: 10.3835/plantgenome2016.02.0021. Review.


Genomewide association study of methane emissions in Angus beef cattle with validation in dairy cattle.

Manzanilla-Pech CI, De Haas Y, Hayes BJ, Veerkamp RF, Khansefid M, Donoghue KA, Arthur PF, Pryce JE.

J Anim Sci. 2016 Oct;94(10):4151-4166. doi: 10.2527/jas.2016-0431.


Genetic Gain and Inbreeding from Genomic Selection in a Simulated Commercial Breeding Program for Perennial Ryegrass.

Lin Z, Cogan NO, Pembleton LW, Spangenberg GC, Forster JW, Hayes BJ, Daetwyler HD.

Plant Genome. 2016 Mar;9(1). doi: 10.3835/plantgenome2015.06.0046.


Leveraging genetically simple traits to identify small-effect variants for complex phenotypes.

Kemper KE, Littlejohn MD, Lopdell T, Hayes BJ, Bennett LE, Williams RP, Xu XQ, Visscher PM, Carrick MJ, Goddard ME.

BMC Genomics. 2016 Nov 3;17(1):858.


Genomic Selection Improves Heat Tolerance in Dairy Cattle.

Garner JB, Douglas ML, Williams SR, Wales WJ, Marett LC, Nguyen TT, Reich CM, Hayes BJ.

Sci Rep. 2016 Sep 29;6:34114. doi: 10.1038/srep34114. Erratum in: Sci Rep. 2017 Jan 19;7:39896.


Genetics of complex traits: prediction of phenotype, identification of causal polymorphisms and genetic architecture.

Goddard ME, Kemper KE, MacLeod IM, Chamberlain AJ, Hayes BJ.

Proc Biol Sci. 2016 Jul 27;283(1835). pii: 20160569. doi: 10.1098/rspb.2016.0569. Review.


Genomic heritabilities and genomic estimated breeding values for methane traits in Angus cattle.

Hayes BJ, Donoghue KA, Reich CM, Mason BA, Bird-Gardiner T, Herd RM, Arthur PF.

J Anim Sci. 2016 Mar;94(3):902-8. doi: 10.2527/jas.2015-0078.


Ankle Arthritis: You Can't Always Replace It.

Hayes BJ, Gonzalez TA, Smith JT, Chiodo CP, Bluman EM.

Instr Course Lect. 2016;65:321-30.


Genomic selection for tolerance to heat stress in Australian dairy cattle.

Nguyen TTT, Bowman PJ, Haile-Mariam M, Pryce JE, Hayes BJ.

J Dairy Sci. 2016 Apr;99(4):2849-2862. doi: 10.3168/jds.2015-9685.


Detailed phenotyping identifies genes with pleiotropic effects on body composition.

Bolormaa S, Hayes BJ, van der Werf JH, Pethick D, Goddard ME, Daetwyler HD.

BMC Genomics. 2016 Mar 12;17:224. doi: 10.1186/s12864-016-2538-0.


Exploiting biological priors and sequence variants enhances QTL discovery and genomic prediction of complex traits.

MacLeod IM, Bowman PJ, Vander Jagt CJ, Haile-Mariam M, Kemper KE, Chamberlain AJ, Schrooten C, Hayes BJ, Goddard ME.

BMC Genomics. 2016 Feb 27;17:144. doi: 10.1186/s12864-016-2443-6.


Accounting for dominance to improve genomic evaluations of dairy cows for fertility and milk production traits.

Aliloo H, Pryce JE, González-Recio O, Cocks BG, Hayes BJ.

Genet Sel Evol. 2016 Feb 1;48:8. doi: 10.1186/s12711-016-0186-0.


Polyceraty (multi-horns) in Damara sheep maps to ovine chromosome 2.

Greyvenstein OF, Reich CM, van Marle-Koster E, Riley DG, Hayes BJ.

Anim Genet. 2016 Apr;47(2):263-6. doi: 10.1111/age.12411. Epub 2016 Jan 14.


Technical note: Equivalent genomic models with a residual polygenic effect.

Liu Z, Goddard ME, Hayes BJ, Reinhardt F, Reents R.

J Dairy Sci. 2016 Mar;99(3):2016-2025. doi: 10.3168/jds.2015-10394. Epub 2015 Dec 24.


Accuracy of genotype imputation based on random and selected reference sets in purebred and crossbred sheep populations and its effect on accuracy of genomic prediction.

Moghaddar N, Gore KP, Daetwyler HD, Hayes BJ, van der Werf JH.

Genet Sel Evol. 2015 Dec 22;47:97. doi: 10.1186/s12711-015-0175-8.


Ankle Arthritis: You Can't Always Replace It.

Hayes BJ, Gonzalez T, Smith JT, Chiodo CP, Bluman EM.

J Am Acad Orthop Surg. 2016 Feb;24(2):e29-38. doi: 10.5435/JAAOS-D-15-00354. Review.


Rare Variants in Transcript and Potential Regulatory Regions Explain a Small Percentage of the Missing Heritability of Complex Traits in Cattle.

Gonzalez-Recio O, Daetwyler HD, MacLeod IM, Pryce JE, Bowman PJ, Hayes BJ, Goddard ME.

PLoS One. 2015 Dec 7;10(12):e0143945. doi: 10.1371/journal.pone.0143945. eCollection 2015.


Role of Smad3 in platelet-derived growth factor-C-induced liver fibrosis.

Lee JI, Wright JH, Johnson MM, Bauer RL, Sorg K, Yuen S, Hayes BJ, Nguyen L, Riehle KJ, Campbell JS.

Am J Physiol Cell Physiol. 2016 Mar 15;310(6):C436-45. doi: 10.1152/ajpcell.00423.2014. Epub 2015 Dec 2.


Targeted imputation of sequence variants and gene expression profiling identifies twelve candidate genes associated with lactation volume, composition and calving interval in dairy cattle.

Raven LA, Cocks BG, Kemper KE, Chamberlain AJ, Vander Jagt CJ, Goddard ME, Hayes BJ.

Mamm Genome. 2016 Feb;27(1-2):81-97. doi: 10.1007/s00335-015-9613-8. Epub 2015 Nov 27.


Differentially Expressed Genes in Endometrium and Corpus Luteum of Holstein Cows Selected for High and Low Fertility Are Enriched for Sequence Variants Associated with Fertility.

Moore SG, Pryce JE, Hayes BJ, Chamberlain AJ, Kemper KE, Berry DP, McCabe M, Cormican P, Lonergan P, Fair T, Butler ST.

Biol Reprod. 2016 Jan;94(1):19. doi: 10.1095/biolreprod.115.132951. Epub 2015 Nov 25.


Extensive variation between tissues in allele specific expression in an outbred mammal.

Chamberlain AJ, Vander Jagt CJ, Hayes BJ, Khansefid M, Marett LC, Millen CA, Nguyen TT, Goddard ME.

BMC Genomics. 2015 Nov 23;16:993. doi: 10.1186/s12864-015-2174-0.


Two-Variance-Component Model Improves Genetic Prediction in Family Datasets.

Tucker G, Loh PR, MacLeod IM, Hayes BJ, Goddard ME, Berger B, Price AL.

Am J Hum Genet. 2015 Nov 5;97(5):677-90. doi: 10.1016/j.ajhg.2015.10.002.

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