Professor Ben Hayes

Featured projects	Duration
Multi-contact Pore-C Genome Innovation Hub Collaborative Project (UQ infrastructure)	2022
Identification and exploitation of genome landing pads for cattle. Genome Innovation Hub Collaborative Project (UQ infrastructure)	2022

Chen, Chunpeng James, Rutkoski, Jessica, Schnable, James C., Murray, Seth C., Wang, Lizhi, Jin, Xiuliang, Stich, Benjamin, Crossa, Jose, Hayes, Ben J. and Zhang, Zhiwu (2023). Role of the genomics-phenomics-agronomy paradigm in plant breeding. Plant breeding reviews. (pp. 627-673) edited by Irwin Goldman. Hoboken, NJ United States: John Wiley and Sons. doi: 10.1002/9781119874157.ch10

Hayes, B. J. and Cocks, B. (2021). Cattle genomics. Encyclopedia of dairy sciences. (pp. 620-625) edited by John W. Fuquay. Amsterdam, Netherlands: Elsevier. doi: 10.1016/B978-0-12-818766-1.00338-X

Voss-Fels, Kai P., Herzog, Eva, Dreisigacker, Susanne, Sukumaran, Sivakumar, Watson, Amy, Frisch, Matthias, Hayes, Ben and Hickey, Lee T. (2019). “SpeedGS” to accelerate genetic gain in spring wheat. Applications of genetic and genomic research in cereals. (pp. 303-327) edited by Thomas Miedaner and Viktor Korzun. Amsterdam, Netherlands: Elsevier. doi: 10.1016/b978-0-08-102163-7.00014-4

Hayes, Ben (2013). Overview of statistical methods for genome-wide association studies (GWAS). Genome-wide association studies and genomic prediction. (pp. 149-169) New York, NY, United States: Humana Press. doi: 10.1007/978-1-62703-447-0_6

Goddard, M. E. and Hayes, B. J. (2012). Genome-wide association studies and linkage disequilibrium in cattle. Bovine genomics. (pp. 192-210) edited by James E. Womack. Oxford, United Kingdom: John Wiley & Sons. doi: 10.1002/9781118301739.ch13

Hayes, B. J., Cocks, B. and Goddard, M. E. (2011). Genetics: cattle genomics. Encyclopedia of dairy sciences. (pp. 663-668) edited by John W. Fuquay. Kidlington, Oxford, United Kingdom: Elsevier. doi: 10.1016/B978-0-12-374407-4.00211-9

Andersen, Oivind and Hayes, Ben (2005). Population genetics. Selection and Breeding Programs in Aquaculture. (pp. 23-33) Berlin/Heidelberg: Springer Netherlands. doi: 10.1007/1-4020-3342-7_3

Hayes, Ben and Andersen, Oivind (2005). Modern biotechnology and aquaculture. Selection and Breeding Programs in Aquaculture. (pp. 301-317) Springer Netherlands. doi: 10.1007/1-4020-3342-7_19

Hayes B.J., Kinghorn B.P. and Ruvinsky A. (2004). Genome scanning for quantitative trait loci. Mammalian Genomics. (pp. 507-539) CABI Publishing.

Mantilla Valdivieso, Emily F., Ross, Elizabeth M., Raza, Ali, Nguyen, Loan, Hayes, Ben J., Jonsson, Nicholas N., James, Peter and Tabor, Ala E. (2024). Expression network analysis of bovine skin infested with Rhipicephalus australis identifies pro-inflammatory genes contributing to tick susceptibility. Scientific Reports, 14 (1) 4419, 1-14. doi: 10.1038/s41598-024-54577-w

Tong, Jingyang, Tarekegn, Zerihun T., Jambuthenne, Dilani, Alahmad, Samir, Periyannan, Sambasivam, Hickey, Lee, Dinglasan, Eric and Hayes, Ben (2024). Stacking beneficial haplotypes from the Vavilov wheat collection to accelerate breeding for multiple disease resistance. Theoretical and Applied Genetics, 137 (12) 274. doi: 10.1007/s00122-024-04784-w

Copley, James P., Hayes, Benjamin J., Ross, Elizabeth M., Speight, Shannon, Fordyce, Geoffry, Wood, Benjamin J. and Engle, Bailey N. (2024). Investigating genotype by environment interaction for beef cattle fertility traits in commercial herds in northern Australia with multi-trait analysis. Genetics Selection Evolution, 56 (1) 70. doi: 10.1186/s12711-024-00936-0

Bang, Nguyen N., Hayes, Ben J., Lyons, Russell E., Randhawa, Imtiaz A. S., Gaughan, John B., Trach, Nguyen X. and McNeill, David M. (2024). Genomic Prediction and Genome‐Wide Association Studies for Productivity, Conformation and Heat Tolerance Traits in Tropical Smallholder Dairy Cows. Journal of Animal Breeding and Genetics. doi: 10.1111/jbg.12907

Hayes, Ben J., Mahony, Timothy J., Villiers, Kira, Warburton, Christie, Kemper, Kathryn E., Dinglasan, Eric, Robinson, Hannah, Powell, Owen, Voss-Fels, Kai, Godwin, Ian D. and Hickey, Lee T. (2024). Potential approaches to create ultimate genotypes in crops and livestock. Nature Genetics, 56 (11), 2310-2317. doi: 10.1038/s41588-024-01942-0

Ong, Chian Teng, Blackall, Patrick. J., Boe-Hansen, Gry B., deWet, Sharon, Hayes, Ben J., Indjein, Lea, Korolik, Victoria, Minchin, Catherine, Nguyen, Loan To, Nordin, Yusralimuna, Siddle, Hannah, Turni, Conny, Venus, Bronwyn, Westman, Mark E., Zhang, Zhetao and Tabor, Ala E. (2024). Whole-genome comparison using complete genomes from Campylobacter fetus strains revealed single nucleotide polymorphisms on non-genomic islands for subspecies differentiation. Frontiers in Microbiology, 15 1452564. doi: 10.3389/fmicb.2024.1452564

Tong, Jingyang, Zhao, Cong, Liu, Dan, Jambuthenne, Dilani T., Sun, Mengjing, Dinglasan, Eric, Periyannan, Sambasivam K., Hickey, Lee T. and Hayes, Ben J. (2024). Genome-wide atlas of rust resistance loci in wheat. Theoretical and Applied Genetics, 137 (8) 179, 1-16. doi: 10.1007/s00122-024-04689-8

Olasege, Babatunde S., van den Berg, Irene, Haile‐Mariam, Mekonnen, Ho, Phuong N., Yin Oh, Zhen, Porto‐Neto, Laercio R., Hayes, Ben J., Pryce, Jennie E. and Fortes, Marina R. S. (2024). Dissecting loci that underpin the genetic correlations between production, fertility, and urea traits in Australian Holstein cattle. Animal Genetics, 55 (4), 540-558. doi: 10.1111/age.13455

Forutan, Mehrnush, Engle, Bailey N., Chamberlain, Amanda J., Ross, Elizabeth M., Nguyen, Loan T., D’Occhio, Michael J., Snr, Alf Collins, Kho, Elise A., Fordyce, Geoffry, Speight, Shannon, Goddard, Michael E. and Hayes, Ben J. (2024). Genome-wide association and expression quantitative trait loci in cattle reveals common genes regulating mammalian fertility. Communications Biology, 7 (1) 724, 724. doi: 10.1038/s42003-024-06403-2

Hayes, Ben and Elayavalli, Srivatsav Kunnawalkam (2024). On sofic approximations of non amenable groups. Mathematische Zeitschrift, 307 (2) ARTN 38. doi: 10.1007/s00209-024-03509-5

Villiers, Kira, Voss‐Fels, Kai P., Dinglasan, Eric, Jacobs, Bertus, Hickey, Lee and Hayes, Ben J. (2024). Evolutionary computing to assemble standing genetic diversity and achieve long‐term genetic gain. The Plant Genome, 17 (2) e20467, e20467. doi: 10.1002/tpg2.20467

Kemper, Kathryn E., Sidorenko, Julia, Wang, Huanwei, Hayes, Ben J., Wray, Naomi R., Yengo, Loic, Keller, Matthew C., Goddard, Michael and Visscher, Peter M. (2024). Genetic influence on within-person longitudinal change in anthropometric traits in the UK Biobank. Nature Communications, 15 (1) 3776, 3776. doi: 10.1038/s41467-024-47802-7

Owada, Kei, Mahony, Timothy J., Ambrose, Rebecca K., Hayes, Ben J. and Soares Magalhães, Ricardo J. (2024). Epidemiological Risk Factors and Modelling Approaches for Risk Assessment of Lumpy Skin Disease Virus Introduction and Spread: Methodological Review and Implications for Risk-Based Surveillance in Australia. Transboundary and Emerging Diseases, 2024 ARTN 3090226, 1-16. doi: 10.1155/2024/3090226

Chen, Chensong, Bhuiyan, Shamsul A., Ross, Elizabeth, Powell, Owen, Dinglasan, Eric, Wei, Xianming, Atkin, Felicity, Deomano, Emily and Hayes, Ben (2024). Genomic prediction for sugarcane diseases including hybrid Bayesian-machine learning approaches. Frontiers in Plant Science, 15 1398903. doi: 10.3389/fpls.2024.1398903

Hayes, B J, Duff, C J, Hine, B C and Mahony, T J (2024). Short Communication: Genomic estimated breeding values for bovine respiratory disease resistance in Angus feedlot cattle. Journal of Animal Science, 102 skae113. doi: 10.1093/jas/skae113

D’Occhio, Michael J, Campanile, Giuseppe, Baruselli, Pietro S, Porto Neto, Laercio R, Hayes, Ben J, Collins, Alf and Fortes, Marina R S (2024). Pleomorphic adenoma gene (PLAG1) in reproduction and implication for embryonic survival in cattle: A review. Journal of Animal Science, 102 ARTN skae103. doi: 10.1093/jas/skae103

Olasege, Babatunde S, Oh, Zhen Yin, Tahir, Muhammad S, Porto-Neto, Laercio R, Hayes, Ben J and Fortes, Marina R S (2024). Genomic regions and biological pathways associated with sex-limited reproductive traits in bovine species. Journal of Animal Science, 102 ARTN skae085. doi: 10.1093/jas/skae085

Hayes, Ben and Kunnawalkam Elayavalli, Srivatsav (2024). Approximate homomorphisms and sofic approximations of orbit equivalence relations. Ergodic Theory and Dynamical Systems, 44 (12), 3455-3480. doi: 10.1017/etds.2024.22

Hayes, Ben, Jekel, David and Elayavalli, Srivatsav Kunnawalkam (2024). Vanishing first cohomology and strong 1-boundedness for von Neumann algebras. Journal of Noncommutative Geometry, 18 (1), 383-409. doi: 10.4171/JNCG/530

Yadav, Seema, Ross, Elizabeth M., Wei, Xianming, Liu, Shouye, Nguyen, Loan To, Powell, Owen, Hickey, Lee T., Deomano, Emily, Atkin, Felicity, Voss‐Fels, Kai P. and Hayes, Ben J. (2023). Use of continuous genotypes for genomic prediction in sugarcane. The Plant Genome, 17 (1) e20417, e20417. doi: 10.1002/tpg2.20417

Lamb, H. J., Nguyen, L. T., Copley, J. P., Engle, B. N., Hayes, B. J. and Ross, E. M. (2023). Imputation strategies for genomic prediction using nanopore sequencing. BMC Biology, 21 (1) 286, 1-18. doi: 10.1186/s12915-023-01782-0

Costilla, R., Zeng, J., Al Kalaldeh, M., Swaminathan, M., Gibson, J.P., Ducrocq, V. and Hayes, B.J. (2023). Developing flexible models for genetic evaluations in smallholder crossbred dairy farms. Journal of Dairy Science, 106 (12), 9125-9135. doi: 10.3168/jds.2022-23135

Yadav, Seema, Ross, Elizabeth M., Wei, Xianming, Powell, Owen, Hivert, Valentin, Hickey, Lee T., Atkin, Felicity, Deomano, Emily, Aitken, Karen S., Voss-Fels, Kai P. and Hayes, Ben J. (2023). Optimising clonal performance in sugarcane: leveraging non-additive effects via mate-allocation strategies. Frontiers in Plant Science, 14 1260517, 1260517. doi: 10.3389/fpls.2023.1260517

Hayes, Ben J., Copley, James, Dodd, Elsie, Ross, Elizabeth M., Speight, Shannon and Fordyce, Geoffry (2023). Multi-breed genomic evaluation for tropical beef cattle when no pedigree information is available. Genetics Selection Evolution, 55 (1) 71, 1-13. doi: 10.1186/s12711-023-00847-6

Warburton, Christie L., Costilla, Roy, Engle, Bailey N., Moore, Stephen S., Corbet, Nicholas J., Fordyce, Geoffry, McGowan, Michael R., Burns, Brian M. and Hayes, Ben J. (2023). Concurrently mapping quantitative trait loci associations from multiple subspecies within hybrid populations. Heredity, 131 (5-6), 350-360. doi: 10.1038/s41437-023-00651-4

Chen, Chensong, Powell, Owen, Dinglasan, Eric, Ross, Elizabeth M., Yadav, Seema, Wei, Xianming, Atkin, Felicity, Deomano, Emily and Hayes, Ben J. (2023). Genomic prediction with machine learning in sugarcane, a complex highly polyploid clonally propagated crop with substantial non‐additive variation for key traits. The Plant Genome, 16 (4) e20390, 1-13. doi: 10.1002/tpg2.20390

Hayes, Ben J., Chen, Chensong, Powell, Owen, Dinglasan, Eric, Villiers, Kira, Kemper, Kathryn E. and Hickey, Lee T. (2023). Advancing artificial intelligence to help feed the world. Nature Biotechnology, 41 (9), 1-2. doi: 10.1038/s41587-023-01898-2

Lamb, H. J., Nguyen, L. T., Briody, T. E., Ambrose, R. K., Hayes, B. J., Mahony, T. J. and Ross, E. M. (2023). Skim-Nanopore sequencing for routine genomic evaluation and bacterial pathogen detection in cattle. Animal Production Science, 63 (11), 1074-1085. doi: 10.1071/an22451

Forutan, Mehrnush, Lynn, Andrew, Aliloo, Hassan, Clark, Samuel A., McGilchrist, Peter, Polkinghorne, Rod and Hayes, Ben J. (2023). Predicting phenotypes of beef eating quality traits. Frontiers in Genetics, 14 1089490, 1089490. doi: 10.3389/fgene.2023.1089490

Nguyen, Tuan V., Vander Jagt, Christy J., Wang, Jianghui, Daetwyler, Hans D., Xiang, Ruidong, Goddard, Michael E., Nguyen, Loan T., Ross, Elizabeth M, Hayes, Ben J., Chamberlain, Amanda J. and MacLeod, Iona M. (2023). In it for the long run: perspectives on exploiting long-read sequencing in livestock for population scale studies of structural variants. Genetics Selection Evolution, 55 (1) 9, 1-15. doi: 10.1186/s12711-023-00783-5

Porto-Neto, Laercio R., Alexandre, Pamela A., Hudson, Nicholas J., Bertram, John, McWilliam, Sean M., Tan, Andre W. L., Fortes, Marina R. S., McGowan, Michael R., Hayes, Ben J. and Reverter, Antonio (2023). Multi-breed genomic predictions and functional variants for fertility of tropical bulls. PLoS One, 18 (1) e0279398, 1-19. doi: 10.1371/journal.pone.0279398

Cameron, Kenneth N., Mombouli, Jean-Vivien, Niama, Fabien R., Hayes, Ben, Olson, Sarah H., Smith, Brett R., Pante, Jasmine, Roy, Sanjit, Laudisoit, Anne, Goldstein, Tracey, Joly, Damien O., Bagamboula MPassi, Romain and Lange, Christian E. (2023). Orbivirus RNA in a banana serotine (Afronycteris nanus) bat in the Republic of the Congo. Ecohealth, 19 (4), 443-449. doi: 10.1007/s10393-022-01619-2

Meuwissen, Theo, Hayes, Ben, MacLeod, Iona and Goddard, Michael (2022). Identification of genomic variants causing variation in quantitative traits: a review. Agriculture, 12 (10) 1713, 1-11. doi: 10.3390/agriculture12101713

Olasege, Babatunde S., Porto-Neto, Laercio R., Tahir, Muhammad S., Gouveia, Gabriela C., Cánovas, Angela, Hayes, Ben J. and Fortes, Marina R. S. (2022). Correlation scan: identifying genomic regions that affect genetic correlations applied to fertility traits. BMC Genomics, 23 (1) 684, 1-20. doi: 10.1186/s12864-022-08898-7

Bang, Nguyen N., Gaughan, John B., Hayes, Ben J., Lyons, Russell E. and McNeill, David M. (2022). Application of infrared thermal technology to assess the level of heat stress and milk yield reduction of cows in tropical smallholder dairy farms. Journal of Dairy Science, 105 (10), 8454-8469. doi: 10.3168/jds.2021-21343

Villiers, Kira, Dinglasan, Eric, Hayes, Ben J and Voss-Fels, Kai P (2022). genomicSimulation: fast R functions for stochastic simulation of breeding programs. G3 Genes|Genomes|Genetics, 12 (10) jkac216, 1-6. doi: 10.1093/g3journal/jkac216

Bang, Nguyen N., Chanh, Nguyen V., Trach, Nguyen X., Khang, Duong N., Hayes, Ben J., Gaughan, John B., Lyons, Russell E. and McNeill, David M. (2022). Multivariate analysis identifying the main factors associated with cow productivity and welfare in tropical smallholder dairy farms in Vietnam. Tropical Animal Health and Production, 54 (5) 313, 313. doi: 10.1007/s11250-022-03303-7

Widyas, Nuzul, Widi, Tri Satya Mastuti, Prastowo, Sigit, Sumantri, Ika, Hayes, Ben J. and Burrow, Heather M. (2022). Promoting sustainable utilization and genetic improvement of Indonesian local beef cattle breeds: a review. Agriculture, 12 (10) 1566, 1566. doi: 10.3390/agriculture12101566

Ong, Chian Teng, Ross, Elizabeth M., Boe-Hansen, Gry, Turni, Conny, Hayes, Ben J., Fordyce, Geoffry and Tabor, Ala E. (2022). Adaptive sampling during sequencing reveals the origins of the bovine reproductive tract microbiome across reproductive stages and sexes. Scientific reports, 12 (1) 15075, 1-12. doi: 10.1038/s41598-022-19022-w

Fang, Lingzhao and Hayes, Ben (2022). The CattleGTEx atlas reveals regulatory mechanisms underlying complex traits. Nature Genetics, 54 (9), 1273-1274. doi: 10.1038/s41588-022-01155-3

Ross, Elizabeth M. and Hayes, Ben J. (2022). Metagenomic predictions: a review 10 years on. Frontiers in Genetics, 13 865765, 1-9. doi: 10.3389/fgene.2022.865765

Mantilla Valdivieso, Emily F., Ross, Elizabeth M., Raza, Ali, Naseem, Muhammad Noman, Kamran, Muhammad, Hayes, Ben J., Jonsson, Nicholas N., James, Peter and Tabor, Ala E. (2022). Transcriptional changes in the peripheral blood leukocytes from Brangus cattle before and after tick challenge with Rhipicephalus australis. BMC Genomics, 23 (1) 454, 1-20. doi: 10.1186/s12864-022-08686-3

Yáñez, José M., Xu, Peng, Carvalheiro, Roberto and Hayes, Ben (2022). Genomics applied to livestock and aquaculture breeding. Evolutionary Applications, 15 (4), 517-522. doi: 10.1111/eva.13378

Ong, Chian Teng, Boe-Hansen, Gry, Ross, Elizabeth M., Blackall, Patrick J., Turni, Conny, Hayes, Ben J. and Tabor, Ala E. (2022). Evaluation of host depletion and extraction methods for shotgun metagenomic analysis of bovine vaginal samples. Microbiology Spectrum, 10 (2), e0041221. doi: 10.1128/spectrum.00412-21

Copley, James P., Engle, Bailey N., Ross, Elizabeth M., Speight, Shannon, Fordyce, Geoffry, Wood, Benjamin J., Voss-Fels, Kai P. and Hayes, Benjamin J. (2022). Environmental variation effects fertility in tropical beef cattle. Translational Animal Science, 6 (2) txac035, 1-10. doi: 10.1093/tas/txac035

Ross, Elizabeth M., Sanjana, Hari, Nguyen, Loan T., Cheng, YuanYuan, Moore, Stephen S. and Hayes, Ben J. (2022). Extensive variation in gene expression is revealed in 13 fertility-related genes using RNA-Seq, ISO-Seq, and CAGE-Seq from Brahman cattle. Frontiers in Genetics, 13 784663, 784663. doi: 10.3389/fgene.2022.784663

Engle, Bailey N and Hayes, Ben J (2022). Genetic variation in PLAG1 is associated with early fertility in Australian Brahman cattle. Journal of Animal Science, 100 (4) skac084. doi: 10.1093/jas/skac084

Ong, Chian Teng, Ross, Elizabeth M., Boe-Hansen, Gry B., Turni, Conny, Hayes, Ben J. and Tabor, Ala E. (2022). Technical note: overcoming host contamination in bovine vaginal metagenomic samples with nanopore adaptive sequencing. Journal of Animal Science, 100 (1) skab344. doi: 10.1093/jas/skab344

Lamb, Harrison J., Hayes, Ben J., Randhawa, Imtiaz A. S., Nguyen, Loan T. and Ross, Elizabeth M. (2021). Genomic prediction using low-coverage portable Nanopore sequencing. PLoS One, 16 (12) e0261274, e0261274. doi: 10.1371/journal.pone.0261274

Hayes, Ben J., Nguyen, Loan T., Forutan, Mehrnush, Engle, Bailey N., Lamb, Harrison J., Copley, James P., Randhawa, Imtiaz A. S. and Ross, Elizabeth M. (2021). An Epigenetic Aging Clock for Cattle Using Portable Sequencing Technology. Frontiers in Genetics, 12 760450, 760450. doi: 10.3389/fgene.2021.760450

Burrow, Heather M., Mrode, Raphael, Mwai, Ally Okeyo, Coffey, Mike P. and Hayes, Ben J. (2021). Challenges and opportunities in applying genomic selection to ruminants owned by smallholder farmers. Agriculture, 11 (11) 1172, 1172. doi: 10.3390/AGRICULTURE11111172

Yadav, Seema, Ross, Elizabeth M., Aitken, Karen S., Hickey, Lee T., Powell, Owen, Wei, Xianming, Voss-Fels, Kai P. and Hayes, Ben J. (2021). A linkage disequilibrium-based approach to position unmapped SNPs in crop species. BMC Genomics, 22 (1) 773, 1-9. doi: 10.1186/s12864-021-08116-w

Bang, Nguyen N., Hayes, Ben J., Lyons, Russell E., Randhawa, Imtiaz A. S., Gaughan, John B. and McNeill, David M. (2021). Genomic diversity and breed composition of Vietnamese smallholder dairy cows. Journal of Animal Breeding and Genetics, 139 (2), 1-16. doi: 10.1111/jbg.12651

Lee, Simon, Nguyen, Loan T., Hayes, Ben J. and Ross, Elizabeth (2021). Prowler: a novel trimming algorithm for Oxford Nanopore sequence data. Bioinformatics, 37 (21), 3936-3937. doi: 10.1093/bioinformatics/btab630

Olasege, Babatunde S., Tahir, Muhammad S., Gouveia, Gabriela C., Kour, Jagish, Porto-Neto, Laercio R., Hayes, Ben J. and Fortes, Marina R. S. (2021). Genetic parameter estimates for male and female fertility traits using genomic data to improve fertility in Australian beef cattle. Animal Production Science, 61 (18), 1863-1872. doi: 10.1071/an21097

Forutan, Mehrnush, Ross, Elizabeth, Chamberlain, Amanda J., Nguyen, Loan, Mason, Brett, Moore, Stephen, Garner, Josie B., Xiang, Ruidong and Hayes, Ben J. (2021). Evolution of tissue and developmental specificity of transcription start sites in Bos taurus indicus. Communications Biology, 4 (1) 829, 1-14. doi: 10.1038/s42003-021-02340-6

Cardoso, Fernando Flores, Matika, Oswald, Djikeng, Appolinaire, Mapholi, Ntanganedzeni, Burrow, Heather M., Yokoo, Marcos Jun Iti, Campos, Gabriel Soares, Gulias-Gomes, Claudia Cristina, Riggio, Valentina, Pong-Wong, Ricardo, Engle, Bailey, Porto-Neto, Laercio, Maiwashe, Azwihangwisi and Hayes, Ben J. (2021). Multiple country and breed genomic prediction of tick resistance in beef cattle. Frontiers in Immunology, 12 620847, 1-11. doi: 10.3389/fimmu.2021.620847

Ong, Chian Teng, Turni, Conny, Blackall, Patrick J., Boe-Hansen, Gry, Hayes, Ben J. and Tabor, Ala E. (2021). Interrogating the bovine reproductive tract metagenomes using culture-independent approaches: a systematic review. Animal Microbiome, 3 (1) 41, 41. doi: 10.1186/s42523-021-00106-3

O’Connor, Katie M., Hayes, Ben J., Hardner, Craig M., Alam, Mobashwer, Henry, Robert J. and Topp, Bruce L. (2021). Genomic selection and genetic gain for nut yield in an Australian macadamia breeding population. BMC Genomics, 22 (1) 370, 1-12. doi: 10.1186/s12864-021-07694-z

Allais-Bonnet, Aurélie, Hintermann, Aurélie, Deloche, Marie-Christine, Cornette, Raphaël, Bardou, Philippe, Naval-Sanchez, Marina, Pinton, Alain, Haruda, Ashleigh, Grohs, Cécile, Zakany, Jozsef, Bigi, Daniele, Medugorac, Ivica, Putelat, Olivier, Greyvenstein, Ockert, Hadfield, Tracy, Jemaa, Slim Ben, Bunevski, Gjoko, Menzi, Fiona, Hirter, Nathalie, Paris, Julia M., Hedges, John, Palhiere, Isabelle, Rupp, Rachel, Lenstra, Johannes A., Gidney, Louisa, Lesur, Joséphine, Schafberg, Renate, Stache, Michael, Wandhammer, Marie-Dominique ... Capitan, Aurélien (2021). Analysis of polycerate mutants reveals the evolutionary co-option of HOXD1 for horn patterning in Bovidae. Molecular Biology and Evolution, 38 (6), 2260-2272. doi: 10.1093/molbev/msab021

Trigo, Beatriz B., Utsunomiya, Adam T. H., Fortunato, Alvaro A. A. D., Milanesi, Marco, Torrecilha, Rafaela B. P., Lamb, Harrison, Nguyen, Loan, Ross, Elizabeth M., Hayes, Ben, Padula, Romulo C. M., Sussai, Thayla S., Zavarez, Ludmilla B., Cipriano, Rafael S., Caminhas, Maria M. T., Lopes, Flavia L., Pelle, Cassiano, Leeb, Tosso, Bannasch, Danika, Bickhart, Derek, Smith, Timothy P. L., Sonstegard, Tad S., Garcia, Jose F. and Utsunomiya, Yuri T. (2021). Variants at the ASIP locus contribute to coat color darkening in Nellore cattle. Genetics Selection Evolution, 53 (1) 40, 40. doi: 10.1186/s12711-021-00633-2

Yadav, Seema, Wei, Xianming, Joyce, Priya, Atkin, Felicity, Deomano, Emily, Sun, Yue, Nguyen, Loan T., Ross, Elizabeth M., Cavallaro, Tony, Aitken, Karen S., Hayes, Ben J. and Voss-Fels, Kai P. (2021). Improved genomic prediction of clonal performance in sugarcane by exploiting non-additive genetic effects. Theoretical and Applied Genetics, 134 (7), 2235-2252. doi: 10.1007/s00122-021-03822-1

Randhawa, Imtiaz A. S., McGowan, Michael R., Porto-Neto, Laercio R., Hayes, Ben J. and Lyons, Russell E. (2021). Comparison of genetic merit for weight and meat traits between the polled and horned cattle in multiple beef breeds. Animals, 11 (3) 870, 1-21. doi: 10.3390/ani11030870

Fernandes Junior, Gerardo A., Carvalheiro, Roberto, de Oliveira, Henrique N., Sargolzaei, Mehdi, Costilla, Roy, Ventura, Ricardo V., Fonseca, Larissa F. S., Neves, Haroldo H. R., Hayes, Ben J. and de Albuquerque, Lucia G. (2021). Imputation accuracy to whole-genome sequence in Nellore cattle. Genetics Selection Evolution, 53 (1) 27. doi: 10.1186/s12711-021-00622-5

Bang, Nguyen N., Chanh, Nguyen V., Trach, Nguyen X., Khang, Duong N., Hayes, Ben J., Gaughan, John B., Lyons, Russell E., Hai, Nguyen T. and McNeill, David M. (2021). Issues of feeding strategy for lactating cows in Vietnamese smallholder dairy farms. Animals, 11 (3) 729, 1-25. doi: 10.3390/ani11030729

Bang, Nguyen N., Chanh, Nguyen V., Trach, Nguyen X., Khang, Duong N., Hayes, Ben J., Gaughan, John B., Lyons, Russell E., Hai, Nguyen T. and McNeill, David M. (2021). Assessment of performance and some welfare indicators of cows in Vietnamese smallholder dairy farms. Animals, 11 (3) 674, 1-22. doi: 10.3390/ani11030674

Chen, Long, Pryce, Jennie E., Hayes, Ben J. and Daetwyler, Hans D. (2021). Investigating the effect of imputed structural variants from whole‐genome sequence on genome‐wide association and genomic prediction in dairy cattle. Animals, 11 (2) 541, 1-16. doi: 10.3390/ani11020541

Voss-Fels, Kai P., Wei, Xianming, Ross, Elizabeth M., Frisch, Matthias, Aitken, Karen S., Cooper, Mark and Hayes, Ben J. (2021). Strategies and considerations for implementing genomic selection to improve traits with additive and non-additive genetic architectures in sugarcane breeding. Theoretical and Applied Genetics, 134 (5), 1493-1511. doi: 10.1007/s00122-021-03785-3

Hayes, Ben J., Wei, Xianming, Joyce, Priya, Atkin, Felicity, Deomano, Emily, Yue, Jenny, Nguyen, Loan, Ross, Elizabeth M., Cavallaro, Tony, Aitken, Karen S. and Voss-Fels, Kai P. (2021). Accuracy of genomic prediction of complex traits in sugarcane. Theoretical and Applied Genetics, 134 (5), 1455-1462. doi: 10.1007/s00122-021-03782-6

Bang, Nguyen N., Gaughan, John B., Hayes, Ben J., Lyons, Russell E., Chanh, Nguyen V., Trach, Nguyen X., Khang, Duong N. and McNeill, David M. (2021). Characteristics of cowsheds in Vietnamese smallholder dairy farms and their associations with microclimate—a preliminary study. Animals, 11 (2) 351, 1-21. doi: 10.3390/ani11020351

Warburton, Christie L., Costilla, Roy, Engle, Bailey N., Corbet, Nicholas J., Allen, Jack M., Fordyce, Geoffry, McGowan, Michael R., Burns, Brian M. and Hayes, Ben J. (2021). Breed-adjusted genomic relationship matrices as a method to account for population stratification in multibreed populations of tropically adapted beef heifers. Animal Production Science, 61 (18), 1788-1795. doi: 10.1071/an21057

Ngo, Thi Thuy, Bang, Nguyen N., Dart, Peter, Callaghan, Matthew, Klieve, Athol, Hayes, Ben and McNeill, David (2020). Feed preference response of weaner bull calves to Bacillus amyloliquefaciens H57 probiotic and associated volatile organic compounds in high concentrate feed pellets. Animals, 11 (1) 51, 51-15. doi: 10.3390/ani11010051

Lamb, Harrison J., Hayes, Ben J., Nguyen, Loan T. and Ross, Elizabeth M. (2020). The future of livestock management: a review of real-time portable sequencing applied to livestock. Genes, 11 (12) 1478, 1-27. doi: 10.3390/genes11121478

Garner, J. B., Chamberlain, A. J., Vander Jagt, C., Nguyen, T. T.T., Mason, B. A., Marett, L. C., Leury, B. J., Wales, W. J. and Hayes, B. J. (2020). Gene expression of the heat stress response in bovine peripheral white blood cells and milk somatic cells in vivo. Scientific Reports, 10 (1) 19181, 19181. doi: 10.1038/s41598-020-75438-2

Ross, Elizabeth M., Hayes, Ben J., Tucker, David, Bond, Jude, Denman, Stuart E. and Oddy, Victor Hutton (2020). Genomic predictions for enteric methane production are improved by metabolome and microbiome data in sheep (Ovis aries). Journal of Animal Science, 98 (10) skaa262. doi: 10.1093/jas/skaa262

Raymond, Biaty, Yengo, Loic, Costilla, Roy, Schrooten, Chris, Bouwman, Aniek C., Hayes, Ben J., Veerkamp, Roel F. and Visscher, Peter M. (2020). Using prior information from humans to prioritize genes and gene-associated variants for complex traits in livestock. PLoS Genetics , 16 (9) e1008780, 1-20. doi: 10.1371/journal.pgen.1008780

Costilla, Roy, Kemper, Kathryn E., Byrne, Enda M., Porto-Neto, Laercio R., Carvalheiro, Roberto, Purfield, Deirdre C., Doyle, Jennifer L., Berry, Donagh P., Moore, Stephen S., Wray, Naomi R. and Hayes, Ben J. (2020). Genetic control of temperament traits across species: association of autism spectrum disorder risk genes with cattle temperament. Genetics Selection Evolution, 52 (1) 51, 51. doi: 10.1186/s12711-020-00569-z

Fortes, Marina R. S., Porto-Neto, Laercio R., Satake, Nana, Nguyen, Loan T., Freitas, Ana Claudia, Melo, Thaise P., Scalez, Daiane Cristina Becker, Hayes, Ben, Raidan, Fernanda S. S., Reverter, Antonio and Boe-Hansen, Gry B. (2020). X chromosome variants are associated with male fertility traits in two bovine populations. Genetics Selection Evolution, 52 (1) 46, 46. doi: 10.1186/s12711-020-00563-5

Naval-Sánchez, Marina, Porto-Neto, Laercio R., Cardoso, Diercles F., Hayes, Ben J., Daetwyler, Hans D., Kijas, James and Reverter, Antonio (2020). Selection signatures in tropical cattle are enriched for promoter and coding regions and reveal missense mutations in the damage response gene HELB. Genetics Selection Evolution, 52 (1) 27, 27. doi: 10.1186/s12711-020-00546-6

Warburton, Christie L., Engle, Bailey N., Ross, Elizabeth M., Costilla, Roy, Moore, Stephen S., Corbet, Nicholas J., Allen, Jack M., Laing, Alan R., Fordyce, Geoffry, Lyons, Russell E., McGowan, Michael R., Burns, Brian M. and Hayes, Ben J. (2020). Use of whole-genome sequence data and novel genomic selection strategies to improve selection for age at puberty in tropically-adapted beef heifers. Genetics Selection Evolution, 52 (1) 28, 28. doi: 10.1186/s12711-020-00547-5

Lamb, Harrison J., Ross, Elizabeth M., Nguyen, Loan T., Lyons, Russell E., Moore, Stephen S. and Hayes, Ben J. (2020). Characterization of the poll allele in Brahman cattle using long-read Oxford Nanopore sequencing. Journal of Animal Science, 98 (5) skaa127, skaa127. doi: 10.1093/jas/skaa127

Yadav, Seema, Jackson, Phillip, Wei, Xianming, Ross, Elizabeth M., Aitken, Karen, Deomano, Emily, Atkin, Felicity, Hayes, Ben J. and Voss-Fels, Kai P. (2020). Accelerating genetic gain in sugarcane breeding using genomic selection. Agronomy, 10 (4) 585, 1-21. doi: 10.3390/agronomy10040585

O’Connor, Katie, Hayes, Ben, Hardner, Craig, Nock, Catherine, Baten, Abdul, Alam, Mobashwer, Henry, Robert and Topp, Bruce (2020). Genome-wide association studies for yield component traits in a macadamia breeding population. BMC Genomics, 21 (1) 199, 199. doi: 10.1186/s12864-020-6575-3

Hunt, Colleen H., Hayes, Ben J., van Eeuwijk, Fred A., Mace, Emma S. and Jordan, David R. (2020). Multi-environment analysis of sorghum breeding trials using additive and dominance genomic relationships. Theoretical and Applied Genetics, 133 (3), 1009-1018. doi: 10.1007/s00122-019-03526-7

Randhawa, Imtiaz A. S., Burns, Brian M., McGowan, Michael R., Porto-Neto, Laercio R., Hayes, Ben J., Ferretti, Ryan, Schutt, Karen M. and Lyons, Russell E. (2019). Optimized genetic testing for polledness in multiple breeds of cattle. G3: Genes, Genomes, Genetics, 10 (2), g3.400866.2019-544. doi: 10.1534/g3.119.400866

Jighly, Abdulqader, Lin, Zibei, Pembleton, Luke W., Cogan, Noel O. I., Spangenberg, German C., Hayes, Ben J. and Daetwyler, Hans D. (2019). Boosting genetic gain in allogamous crops via speed breeding and genomic selection. Frontiers in Plant Science, 10 1364, 1364. doi: 10.3389/fpls.2019.01364

Mulder, Herman A., Lee, Sang Hong, Clark, Sam, Hayes, Ben J. and van der Werf, Julius H. J. (2019). The impact of genomic and traditional selection on the contribution of mutational variance to long-term selection response and genetic variance. Genetics, 213 (2), 361-378. doi: 10.1534/genetics.119.302336

Xiang, Ruidong, Van Den Berg, Irene, MacLeod, Iona M., Hayes, Benjamin J., Prowse-Wilkins, Claire P., Wang, Min, Bolormaa, Sunduimijid, Liu, Zhiqian, Rochfort, Simone J., Reich, Coralie M., Mason, Brett A., Vander Jagt, Christy J., Daetwyler, Hans D., Lund, Mogens S., Chamberlain, Amanda J. and Goddard, Michael E. (2019). Quantifying the contribution of sequence variants with regulatory and evolutionary significance to 34 bovine complex traits. Proceedings of the National Academy of Sciences of the United States of America, 116 (39), 19398-19408. doi: 10.1073/pnas.1904159116

Watson, Amy, Hickey, Lee T., Christopher, Jack, Rutkoski, Jessica, Poland, Jesse and Hayes, Ben J. (2019). Multivariate genomic selection and potential of rapid indirect selection with speed breeding in spring wheat. Crop Science, 59 (5), 1945-1959. doi: 10.2135/cropsci2018.12.0757

Melo, Thaise Pinto, Salinas Fortes, Marina Rufino, Hayes, Ben, Albuquerque, Lucia Galvão and Carvalheiro, Roberto (2019). Across‐breed validation study confirms and identifies new loci associated with sexual precocity in Brahman and Nellore cattle. Journal of Animal Breeding and Genetics, 137 (2) jbg.12429, 139-154. doi: 10.1111/jbg.12429

Carvalheiro, Roberto, Costilla, Roy, Neves, Haroldo H. R., Albuquerque, Lucia G., Moore, Stephen and Hayes, Ben J. (2019). Unraveling genetic sensitivity of beef cattle to environmental variation under tropical conditions. Genetics Selection Evolution, 51 (1) 29, 29. doi: 10.1186/s12711-019-0470-x

Voss-Fels, Kai P., Stahl, Andreas, Wittkop, Benjamin, Lichthardt, Carolin, Nagler, Sabrina, Rose, Till, Chen, Tsu-Wei, Zetzsche, Holger, Seddig, Sylvia, Majid Baig, Mirza, Ballvora, Agim, Frisch, Matthias, Ross, Elizabeth, Hayes, Ben J., Hayden, Matthew J., Ordon, Frank, Leon, Jens, Kage, Henning, Friedt, Wolfgang, Stützel, Hartmut and Snowdon, Rod J. (2019). Breeding improves wheat productivity under contrasting agrochemical input levels. Nature Plants, 5 (7), 706-714. doi: 10.1038/s41477-019-0445-5

Hickey, Lee T., N. Hafeez, Amber, Robinson, Hannah, Jackson, Scott A., Leal-Bertioli, Soraya C. M., Tester, Mark, Gao, Caixia, Godwin, Ian D., Hayes, Ben J. and Wulff, Brande B. H. (2019). Breeding crops to feed 10 billion. Nature Biotechnology, 37 (7), 744-754. doi: 10.1038/s41587-019-0152-9

He, Fei, Pasam, Raj, Shi, Fan, Kant, Surya, Keeble-Gagnere, Gabriel, Kay, Pippa, Forrest, Kerrie, Fritz, Allan, Hucl, Pierre, Wiebe, Krystalee, Knox, Ron, Cuthbert, Richard, Pozniak, Curtis, Akhunova, Alina, Morrell, Peter L., Davies, John P., Webb, Steve R., Spangenberg, German, Hayes, Ben, Daetwyler, Hans, Tibbits, Josquin, Hayden, Matthew and Akhunov, Eduard (2019). Publisher correction: Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome. Nature Genetics, 51 (7), 1194-1194. doi: 10.1038/s41588-019-0463-2

He, Fei, Pasam, Raj, Shi, Fan, Kant, Surya, Keeble-Gagnere, Gabriel, Kay, Pippa, Forrest, Kerrie, Fritz, Allan, Hucl, Pierre, Wiebe, Krystalee, Knox, Ron, Cuthbert, Richard, Pozniak, Curtis, Akhunova, Alina, Morrell, Peter L., Davies, John P., Webb, Steve R., Spangenberg, German, Hayes, Ben, Daetwyler, Hans, Tibbits, Josquin, Hayden, Matthew and Akhunov, Eduard (2019). Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome. Nature Genetics, 51 (5), 896-904. doi: 10.1038/s41588-019-0382-2

Van Den Berg, I., Hayes, B. J., Chamberlain, A. J. and Goddard, M. E. (2019). Overlap between eQTL and QTL associated with production traits and fertility in dairy cattle. BMC Genomics, 20 (1) 291, 291. doi: 10.1186/s12864-019-5656-7

O’Connor, Katie, Kilian, Andrzej, Hayes, Ben, Hardner, Craig, Nock, Catherine, Baten, Abdul, Alam, Mobashwer and Topp, Bruce (2019). Population structure, genetic diversity and linkage disequilibrium in a macadamia breeding population using SNP and silicoDArT markers. Tree Genetics & Genomes, 15 (2) 24, 24. doi: 10.1007/s11295-019-1331-z

Wray, Naomi R., Kemper, Kathryn E., Hayes, Benjamin J., Goddard, Michael E. and Visscher, Peter M. (2019). Complex trait prediction from genome data: contrasting EBV in livestock to PRS in humans: genomic prediction. Genetics, 211 (4), 1131-1141. doi: 10.1534/genetics.119.301859

O’Connor, Katie, Hayes, Ben, Hardner, Craig, Alam, Mobashwer and Topp, Bruce (2019). Selecting for nut characteristics in macadamia using a genome-wide association study. HortScience, 54 (4), 629-632. doi: 10.21273/hortsci13297-18

Hayes, Ben J. and Daetwyler, Hans D. (2019). 1000 Bull Genomes Project to map simple and complex genetic traits in cattle: applications and outcomes. Annual Review of Animal Biosciences, 7 (1), 89-102. doi: 10.1146/annurev-animal-020518-115024

Liu, Zhiqian, Wang, Tingting, Pryce, Jennie E., MacLeod, Iona M., Hayes, Ben J., Chamberlain, Amanda J., Jagt, Christy Vander, Reich, Coralie M., Mason, Brett A., Rochfort, Simone and Cocks, Benjamin G. (2019). Fine-mapping sequence mutations with a major effect on oligosaccharide content in bovine milk. Scientific Reports, 9 (1) 2137, 2137. doi: 10.1038/s41598-019-38488-9

Hardner, Craig M., Hayes, Ben J., Kumar, Satish, Vanderzande, Stijn, Cai, Lichun, Piaskowski, Julia, Quero-Garcia, José, Campoy, José Antonio, Barreneche, Teresa, Giovannini, Daniela, Liverani, Alessandro, Charlot, Gérard, Villamil-Castro, Miguel, Oraguzie, Nnadozie and Peace, Cameron P. (2019). Prediction of genetic value for sweet cherry fruit maturity among environments using a 6K SNP array. Horticulture Research, 6 (1) 6, 6. doi: 10.1038/s41438-018-0081-7

Engle, Bailey N., Corbet, Nicholas J., Allen, Jamie M., Laing, Alan R., Fordyce, Geoffry, McGowan, Michael R., Burns, Brian M., Burns, Brian M. and Hayes, Ben J. (2019). Multivariate genomic predictions for age at puberty in tropically adapted beef heifers. Journal of Animal Science, 97 (1), 90-100. doi: 10.1093/jas/sky428

Hayes, Ben J., Corbet, Nicholas J., Allen, Jack M., Laing, Alan R., Fordyce, Geoffry, Lyons, Russel, McGowan, Michael R. and Burns, Brian M. (2019). Towards multi-breed genomic evaluations for female fertility of tropical beef cattle. Journal of Animal Science, 97 (1), 55-62. doi: 10.1093/jas/sky417

Giuffra, Elisabetta, Tuggle, Christopher K., and the FAANG Consortium, Archibald, Alan L., Acloque, Herve, Chamberlain, Amanda J., Cochrane, Guy, Daetwyler, Hans D., Djebali, Sarah, Eory, Lel, Foissac, Sylvain, Goddard, Michael E., Groenen, Martien A. M., Halstead, Michelle, Harrison, Peter W., Hayes, Benjamin J., Kern, Colin, Khatib, Hasan, Kuo, Richard I., MacHugh, David E., Macleod, Iona M., Madsen, Ole, Reecy, James M., Ross, Pablo J., Watson, Mick, Wells, Jerry M. and Zhou, Huaijun (2019). Functional Annotation of Animal Genomes (FAANG): Current Achievements and Roadmap. Annual Review of Animal Biosciences, Vol 7, 7 (1), 65-88. doi: 10.1146/annurev-animal-020518-114913

Burrow, Heather M., Mans, Ben J., Cardoso, Fernando F., Birkett, Michael A., Kotze, Andrew C., Hayes, Ben J., Mapholi, Ntanganedzeni, Dzama, Kennedy, Marufu, Munyaradzi C., Githaka, Naftaly W. and Djikeng, Appolinaire (2019). Towards a new phenotype for tick resistance in beef and dairy cattle: a review. Animal Production Science, 59 (8), 1401-1427. doi: 10.1071/AN18487

Voss-Fels, Kai Peter, Cooper, Mark and Hayes, Ben John (2018). Accelerating crop genetic gains with genomic selection. Theoretical and Applied Genetics, 132 (3), 669-686. doi: 10.1007/s00122-018-3270-8

Koufariotis, L., Hayes, B. J., Kelly, M., Burns, B. M., Lyons, R., Stothard, P., Chamberlain, A. J. and Moore, S. (2018). Sequencing the mosaic genome of Brahman cattle identifies historic and recent introgression including polled. Scientific Reports, 8 (1) 17761, 17761. doi: 10.1038/s41598-018-35698-5

Georges, Michel, Charlier, Carole and Hayes, Ben (2018). Harnessing genomic information for livestock improvement. Nature Reviews Genetics, 20 (3), 135-156. doi: 10.1038/s41576-018-0082-2

Fortes, Marina Rufino Salinas, Enculescu, Charmaine, Porto Neto, Laercio R., Lehnert, Sigrid A., McCulloch, Russell and Hayes, Ben (2018). Candidate mutations used to aid the prediction of genetic merit for female reproductive traits in tropical beef cattle. Revista Brasileira de Zootecnia, 47 e20170226. doi: 10.1590/rbz4720170226

Xiang, Ruidong, Hayes, Ben J., Vander Jagt, Christy J., MacLeod, Iona M., Khansefid, Majid, Bowman, Phil J., Yuan, Zehu, Prowse-Wilkins, Claire P., Reich, Coralie M., Mason, Brett A., Garner, Josie B., Marett, Leah C., Chen, Yizhou, Bolormaa, Sunduimijid, Daetwyler, Hans D., Chamberlain, Amanda J. and Goddard, Michael E. (2018). Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues. BMC Genomics, 19 (1) 521, 521. doi: 10.1186/s12864-018-4902-8

Wang, Min, Hancock, Timothy P., Chamberlain, Amanda J., Vander Jagt, Christy J., Pryce, Jennie E., Cocks, Benjamin G., Goddard, Mike E. and Hayes, Benjamin J. (2018). Putative bovine topological association domains and CTCF binding motifs can reduce the search space for causative regulatory variants of complex traits. BMC Genomics, 19 (1) 395, 395. doi: 10.1186/s12864-018-4800-0

Mota, Rodrigo Reis, Silva, Fabyano Fonseca e, Guimarães, Simone Eliza Facioni, Hayes, Ben, Fortes, Marina Rufino Salinas, Kelly, Matthew John, Guimarães, José Domingos, Penitente-Filho, Jurandy Mauro, Ventura, Henrique Torres and Moore, Stephen (2018). Benchmarking Bayesian genome enabled-prediction models for age at first calving in Nellore cows. Livestock Science, 211, 75-79. doi: 10.1016/j.livsci.2018.03.009

Newton, J. E., Hayes, B. J. and Pryce, J. E. (2018). The cost-benefit of genomic testing of heifers and using sexed semen in pasture-based dairy herds. Journal of Dairy Science, 101 (7), 6159-6173. doi: 10.3168/jds.2017-13476

Jighly, Abdulqader, Lin, Zibei, Forster, John W., Spangenberg, German C., Hayes, Ben J. and Daetwyler, Hans D. (2018). Insights into population genetics and evolution of polyploids and their ancestors. Molecular Ecology Resources, 18 (5), 1157-1172. doi: 10.1111/1755-0998.12896

Fritz, Sébastien, Hoze, Chris, Rebours, Emmanuelle, Barbat, Anne, Bizard, Méline, Chamberlain, Amanda, Escouflaire, Clémentine, Vander Jagt, Christy, Boussaha, Mekki, Grohs, Cécile, Allais-Bonnet, Aurélie, Philippe, Maëlle, Vallée, Amélie, Amigues, Yves, Hayes, Benjamin J., Boichard, Didier and Capitan, Aurélien (2018). An initiator codon mutation in SDE2 causes recessive embryonic lethality in Holstein cattle. Journal of Dairy Science, 101 (7), 6220-6231. doi: 10.3168/jds.2017-14119

Koufariotis, Lambros T., Chen, Yi-Ping Phoebe, Stothard, Paul and Hayes, Ben J. (2018). Variance explained by whole genome sequence variants in coding and regulatory genome annotations for six dairy traits. BMC Genomics, 19 (237) 237, 237. doi: 10.1186/s12864-018-4617-x

DiGiacomo, K., Norris, E., Dunshea, F. R., Hayes, B. J., Marett, L. C., Wales, W. J. and Leury, B. J. (2018). Responses of dairy cows with divergent residual feed intake as calves to metabolic challenges during midlactation and the nonlactating period. Journal of Dairy Science, 101 (7), 6474-6485. doi: 10.3168/jds.2017-12569

Kemper, Kathryn E., Bowman, Philip J., Hayes, Benjamin J., Visscher, Peter M. and Goddard, Michael E. (2018). A multi-trait Bayesian method for mapping QTL and genomic prediction. Genetics Selection Evolution, 50 (1) 10, 10. doi: 10.1186/s12711-018-0377-y

Calus, M. P. L., Goddard, M. E., Wientjes, Y. C. J., Bowman, P. J. and Hayes, B. J. (2018). Multibreed genomic prediction using multitrait genomic residual maximum likelihood and multitask Bayesian variable selection. Journal of Dairy Science, 101 (5), 4279-4294. doi: 10.3168/jds.2017-13366

Hunt, Colleen H., van Eeuwijk, Fred A., Mace, Emma S., Hayes, Ben J. and Jordan, David R. (2018). Development of genomic prediction in sorghum. Crop Science, 58 (2), 690-700. doi: 10.2135/cropsci2017.08.0469

Nguyen, Quan H., Tellam, Ross L., Naval-Sanchez, Marina, Porto-Neto, Laercio R., Barendse, William, Reverter, Antonio, Hayes, Benjamin, Kijas, James and Dalrymple, Brian P. (2018). Mammalian genomic regulatory regions predicted by utilizing human genomics, transcriptomics, and epigenetics data. Gigascience, 7 (3), 1-17. doi: 10.1093/gigascience/gix136

O'Connor, Katie, Hayes, Ben and Topp, Bruce (2018). Prospects for increasing yield in macadamia using component traits and genomics. Tree Genetics & Genomes, 14 (1) 7. doi: 10.1007/s11295-017-1221-1

Bourneuf, E., Otz, P., Pausch, H., Jagannathan, V., Michot, P., Grohs, C., Piton, G., Ammermüller, S., Deloche, M. C., 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, M. A., Klopp, C., Esquerré, D. ... Capitan, A. (2017). Rapid Discovery of de Novo Deleterious Mutations in Cattle Enhances the Value of Livestock as Model Species. Scientific Reports, 7 (1) 11466, 11466. doi: 10.1038/s41598-017-11523-3

Hayes, B. J., Panozzo, J., Walker, C. K., Choy, A. L., Kant, S., Wong, D., Tibbits, J., Daetwyler, H. D., Rochfort, S., Hayden, M. J. and Spangenberg, G. C. (2017). Accelerating wheat breeding for end-use quality with multi-trait genomic predictions incorporating near infrared and nuclear magnetic resonance-derived phenotypes. Theoretical and Applied Genetics, 130 (12), 2505-2519. doi: 10.1007/s00122-017-2972-7

Slater, Anthony T., Cogan, Noel O. I., Rodoni, Brendan C., Daetwyler, Hans D., Hayes, Benjamin J., Caruana, Brittney, Badenhorst, Pieter E., Spangenberg, German C. and Forster, John W. (2017). Breeding Differently—the Digital Revolution: High-Throughput Phenotyping and Genotyping. Potato Research, 60 (3-4), 337-352. doi: 10.1007/s11540-018-9388-x

Mota, R. R., Guimarães, S. E. F., Fortes, M. R. S., Hayes, B., Silva, F. F., Verardo, L. L., Kelly, M. J., de Campos, C. F., Guimarães, J. D., Wenceslau, R. R., Penitente-Filho, J. M., Garcia, J. F. and Moore, S. (2017). Genome-wide association study and annotating candidate gene networks affecting age at first calving in Nellore cattle. Journal of Animal Breeding and Genetics, 134 (6), 484-492. doi: 10.1111/jbg.12299

Bouwman, Aniek C., Hayes, Ben J. and Calus, Mario P. L. (2017). Estimated allele substitution effects underlying genomic evaluation models depend on the scaling of allele counts. Genetics, Selection, Evolution, 49 (1) 79, 79. doi: 10.1186/s12711-017-0355-9

Van Den Berg, Irene , Bowman, Phil J, MacLeod, Iona M., Hayes, Ben J., Wang, Tingting, Bolormaa, Sunduimijid and Goddard, Mike E. (2017). Multi-breed genomic prediction using Bayes R with sequence data and dropping variants with a small effect. Genetics Selection Evolution, 49 (1) 70, 70. doi: 10.1186/s12711-017-0347-9

Nguyen, Thuy T. T., Bowman, Phil J., Haile-Mariam, Mekonnen, Nieuwhof, Gert J., Hayes, Benjamin J. and Pryce, Jennie E. (2017). Short communication: implementation of a breeding value for heat tolerance in Australian dairy cattle. Journal of Dairy Science, 100 (9), 7362-7367. doi: 10.3168/jds.2017-12898

Qian, Lunwen, Hickey, Lee T., Stahl, Andreas, Werner, Christian R., Hayes, Ben, Snowdon, Rod J. and Voss-Fels, Kai P. (2017). Exploring and Harnessing Haplotype Diversity to Improve Yield Stability in Crops. Frontiers in Plant Science, 8 1534, 1534. doi: 10.3389/fpls.2017.01534

Wang, Tingting, Chen, Yi-Ping Phoebe, MacLeod, Iona M., Pryce, Jennie E., Goddard, Michael E. and Hayes, Ben J. (2017). Application of a Bayesian non-linear model hybrid scheme to sequence data for genomic prediction and QTL mapping. BMC Genomics, 18 (1) 618, 618. doi: 10.1186/s12864-017-4030-x

Wang, Min, Hancock, Timothy P., MacLeod, Iona M., Pryce, Jennie E., Cocks, Benjamin G. and Hayes, Benjamin J. (2017). Putative enhancer sites in the bovine genome are enriched with variants affecting complex traits. Genetics Selection Evolution, 49 (1) 56. doi: 10.1186/s12711-017-0331-4

Couldrey, C., Keehan, M., Johnson, T., Tiplady, K., Winkelman, A., Littlejohn, M. D., Scott, A., Kemper, K. E., Hayes, B., Davis, S. R. and Spelman, R. J. (2017). Detection and assessment of copy number variation using PacBio long-read and Illumina sequencing in New Zealand dairy cattle. Journal of Dairy Science, 100 (7), 5472-5478. doi: 10.3168/jds.2016-12199

Shi, Fan, Tibbits, Josquin, Pasam, Raj K., Kay, Pippa, Wong, Debbie, Petkowski, Joanna, Forrest, Kerrie L., Hayes, Ben J., Akhunova, Alina, Davies, John, Webb, Steven, Spangenberg, German C., Akhunov, Eduard, Hayden, Matthew J. and Daetwyler, Hans D. (2017). Exome sequence genotype imputation in globally diverse hexaploid wheat accessions. Theoretical and Applied Genetics, 130 (7), 1393-1404. doi: 10.1007/s00122-017-2895-3

Bolormaa, S., Brown, D. J., Swan, A. A., van der Werf, J. H. J., Hayes, B. J. and Daetwyler, H. D. (2017). Genomic prediction of reproduction traits for Merino sheep. Animal Genetics, 48 (3), 338-348. doi: 10.1111/age.12541

Phuong, H. N., Friggens, N. C., Martin, O., Blavy, P., Hayes, B. J., Wales, W. J. and Pryce, J. E. (2017). Evaluating the ability of a lifetime nutrient-partitioning model for simulating the performance of Australian Holstein dairy cows. Animal Production Science, 57 (7), 1563-1568. doi: 10.1071/AN16452

Lin, Zibei, Shi, Fan, Hayes, Ben J. and Daetwyler, Hans D. (2017). Mitigation of inbreeding while preserving genetic gain in genomic breeding programs for outbred plants. Theoretical and Applied Genetics, 130 (5), 969-980. doi: 10.1007/s00122-017-2863-y

Marett, L. C., Williams, S. R. O., Hayes, B. J., Pryce, J. E. and Wales, W. J. (2017). Partitioning of energy and nitrogen in lactating primiparous and multiparous Holstein-Friesian cows with divergent residual feed intake. Animal Production Science, 57 (7), 1499-1506. doi: 10.1071/AN16476

Aliloo, H., Pryce, J. E., Gonzalez-Recio, O., Cocks, B. G., Goddard, M. E. and Hayes, B. J. (2017). Including nonadditive genetic effects in mating programs to maximize dairy farm profitability. Journal of Dairy Science, 100 (2), 1203-1222. doi: 10.3168/jds.2016-11261

Chen, Long, Chamberlain, Amanda J., Reich, Coralie M., Daetwyler, Hans D. and Hayes, Ben J. (2017). Detection and validation of structural variations in bovine whole-genome sequence data. Genetics Selection Evolution, 49 (1) 13. doi: 10.1186/s12711-017-0286-5

Garner, J. B., Douglas, M. L., Williams, S. R. O., Wales, W. J., Marett, L. C., Nguyen, T. T. T., Reich, C. M. and Hayes, B. J. (2017). Corrigendum: Genomic selection improves heat tolerance in dairy cattle. Scientific Reports, 7 (1) 39896, 39896. doi: 10.1038/srep39896

Nguyen, Thuy T. T., Hayes, Ben J. and Pryce, Jennie E. (2017). A practical future-scenarios selection tool to breed for heat tolerance in Australian dairy cattle. Animal Production Science, 57 (7), 1488-1493. doi: 10.1071/AN16449

Garner, J. B., Douglas, M., Williams, S. R. O., Wales, W. J., Marett, L. C., DiGiacomo, K., Leury, B. J. and Hayes, B. J. (2017). Responses of dairy cows to short-term heat stress in controlled-climate chambers. Animal Production Science, 57 (7), 1233-1241. doi: 10.1071/AN16472

Lin, Zibei, Wang, Junping, Cogan, Noel O. I., Pembleton, Luke W., Badenhorst, Pieter, Forster, John W., Spangenberg, German C., Hayes, Ben J. and Daetwyler, Hans D. (2017). Optimizing resource allocation in a genomic breeding program for perennial ryegrass to balance genetic gain, cost, and inbreeding. Crop Science, 57 (1), 243-252. doi: 10.2135/cropsci2016.07.0577

Kemper, K. E., Littlejohn, M. D., Lopdell, T., Hayes, B. J., Bennett, L. E., Williams, R. P., Xu, X. Q., Visscher, P. M., Carrick, M. J. and Goddard, M. E. (2016). Leveraging genetically simple traits to identify small-effect variants for complex phenotypes. BMC Genomics, 17 (1) 858, 858. doi: 10.1186/s12864-016-3175-3

Slater, Anthony T., Cogan, Noel O. I., Forster, John W., Hayes, Benjamin J. and Daetwyler, Hans D. (2016). Improving genetic gain with genomic selection in autotetraploid potato. Plant Genome, 9 (3), plantgenome2016.02.0021-15. doi: 10.3835/plantgenome2016.02.0021

Tuggle, Christopher K., Giuffra, Elisabetta, White, Stephen N., Clarke, Laura, Zhou, Huaijun, Ross, Pablo J., Acloque, Herve, Reecy, James M., Archibald, Alan, Bellone, Rebecca R., Boichard, Michele, Chamberlain, Amanda, Cheng, Hans, Crooijmans, Richard P. M. A., Delany, Mary E., Finno, Carrie J., Groenen, Martien A. M., Hayes, Ben, Lunney, Joan K., Petersen, Jessica L., Plastow, Graham S., Schmidt, Carl J., Song, Jiuzhou and Watson, Mick (2016). GO-FAANG meeting: a gathering on functional annotation of animal genomes. Animal Genetics, 47 (5), 528-533. doi: 10.1111/age.12466

Manzanilla-Pech, C. I. V., De Haas, Y., Hayes, B. J., Veerkamp, R. F., Khansefid, M., Donoghue, K. A., Arthur, P. F. and Pryce, J. E. (2016). Genomewide association study of methane emissions in Angus beef cattle with validation in dairy cattle. Journal of Animal Science, 94 (10), 4151-4166. doi: 10.2527/jas.2016-0431

Wang, Tingting, Chen, Yi-Ping Phoebe, Bowman, Phil J., Goddard, Michael E. and Hayes, Ben J. (2016). A hybrid expectation maximisation and MCMC sampling algorithm to implement Bayesian mixture model based genomic prediction and QTL mapping. BMC Genomics, 17 (1) 744, 744. doi: 10.1186/s12864-016-3082-7

Garner, J. B., Douglas, M. L., Williams, S. R. O., Wales, W. J., Marett, L. C., Nguyen, T. T. T., Reich, C. M. and Hayes, B. J. (2016). Genomic selection improves heat tolerance in dairy cattle. Scientific Reports, 6 (1) 34114, 34114. doi: 10.1038/srep34114

Hayes, Ben J., Daetwyler, Hans D. and Goddard, Mike E. (2016). Models for genome x environment interaction: examples in livestock. Crop Science, 56 (5), 2251-2259. doi: 10.2135/cropsci2015.07.0451

Goddard, M. E., Kemper, K. E., MacLeod, I. M., Chamberlain, A. J. and Hayes, B. J. (2016). Genetics of complex traits: prediction of phenotype, identification of causal polymorphisms and genetic architecture. Proceedings of the Royal Society B: Biological Sciences, 283 (1835) 20160569, 20160569. doi: 10.1098/rspb.2016.0569

Greyvenstein, O. F. C., Reich, C. M., van Marle-Koster, E., Riley, D. G. and Hayes, B. J. (2016). Polyceraty (multi-horns) in Damara sheep maps to ovine chromosome 2. Animal Genetics, 47 (2), 263-266. doi: 10.1111/age.12411

Nguyen, Thuy T. T., Bowman, Phil J., Haile-Mariam, Mekonnen, Pryce, Jennie E. and Hayes, Benjamin J. (2016). Genomic selection for tolerance to heat stress in Australian dairy cattle. Journal of Dairy Science, 99 (4), 2849-2862. doi: 10.3168/jds.2015-9685

Bolormaa, Sunduimijid, Hayes, Ben J., van der Werf, Julius H. J., Pethick, David, Goddard, Michael E. and Daetwyler, Hans D. (2016). Detailed phenotyping identifies genes with pleiotropic effects on body composition. BMC Genomics, 17 (224) 224, 1-21. doi: 10.1186/s12864-016-2538-0

Lin, Zibei, Cogan, Noel O. I., Pembleton, Luke W., Spangenberg, German C., Forster, John W., Hayes, Ben J. and Daetwyler, Hans D. (2016). Genetic gain and inbreeding from genomic selection in a simulated commercial breeding program for perennial ryegrass. Plant Genome, 9 (1), 876-883. doi: 10.3835/plantgenome2015.06.0046

Hayes, B. J., Donoghue, K. A., Reich, C. M., Mason, B. A., Bird-Gardiner, T., Herd, R. M. and Arthur, P. F. (2016). Genomic heritabilities and genomic estimated breeding values for methane traits in Angus cattle. Journal of Animal Science, 94 (3), 902-908. doi: 10.2527/jas2015-0078

Liu, Z., Goddard, M. E., Hayes, B. J., Reinhardt, F. and Reents, R. (2016). Technical note: equivalent genomic models with a residual polygenic effect. Journal of Dairy Science, 99 (3), 2016-2025. doi: 10.3168/jds.2015-10394

Raven, Lesley-Ann, Cocks, Benjamin G., Kemper, Kathryn E., Chamberlain, Amanda J., Vander Jagt, Christy J., Goddard, Michael E. and Hayes, Ben J. (2016). Targeted imputation of sequence variants and gene expression profiling identifies twelve candidate genes associated with lactation volume, composition and calving interval in dairy cattle. Mammalian Genome, 27 (1-2), 81-97. doi: 10.1007/s00335-015-9613-8

Aliloo, Hassan, Pryce, Jennie E., Gonzalez-Recio, Oscar, Cocks, Benjamin G. and Hayes, Ben J. (2016). Accounting for dominance to improve genomic evaluations of dairy cows for fertility and milk production traits. Genetics Selection Evolution, 48 (1) 186, 8.1-8.11. doi: 10.1186/s12711-016-0186-0

MacLeod, I. M., Bowman, P. J., Vander Jagt, C. J., Haile-Mariam, M., Kemper, K. E., Chamberlain, A. J., Schrooten, C., Hayes, B. J. and Goddard, M. E. (2016). Exploiting biological priors and sequence variants enhances QTL discovery and genomic prediction of complex traits. BMC Genomics, 17 (1) 144. doi: 10.1186/s12864-016-2443-6

Moore, Stephen G., Pryce, Jennie E., Hayes, Ben J., Chamberlain, Amanda J., Kemper, Kathryn E., Berry, Donagh P., McCabe, Matt, Cormican, Paul, Lonergan, Pat, Fair, Trudee and Butler, Stephen T. (2016). 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. Biology of Reproduction, 94 (1) 19. doi: 10.1095/biolreprod.115.132951

Moate, Peter J., Deighton, Matthew H., Williams, S. Richard O., Pryce, Jennie E., Hayes, Ben J., Jacobs, Joe L., Eckard, Richard J., Hannah, Murray C. and Wales, William J. (2016). Reducing the carbon footprint of Australian milk production by mitigation of enteric methane emissions. Animal Production Science, 56 (7), 1017-1034. doi: 10.1071/AN15222

Meuwissen, Theo, Hayes, Ben and Goddard, Mike (2016). Genomic selection: a paradigm shift in animal breeding. Animal Frontiers, 6 (1), 6-14. doi: 10.2527/af.2016-0002

Wang, Tingting, Chen, Yi-Ping Phoebe and Hayes, Ben (2016). Accuracy and computational efficiency of genomic selection with high-density SNP and whole-genome sequence data. CAB Reviews: Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources, 11 (034) 034, 1-18. doi: 10.1079/PAVSNNR201611034

Moghaddar, Nasir, Gore, Klint P., Daetwyler, Hans D., Hayes, Ben J. and van der Werf, Julius H. J. (2015). 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. Genetics Selection Evolution, 47 (1) 175. doi: 10.1186/s12711-015-0175-8

Gonzalez-Recio, Oscar, Daetwyler, Hans D., MacLeod, Iona M., Pryce, Jennie E., Bowman, Phil J., Hayes, Ben J. and Goddard, Michael E. (2015). Rare variants in transcript and potential regulatory regions explain a small percentage of the missing heritability of complex traits in cattle. PLoS One, 10 (12) e0143945, e0143945. doi: 10.1371/journal.pone.0143945

Chamberlain, Amanda J., Vander Jagt, Christy J., Hayes, Benjamin J., Khansefid, Majid, Marett, Leah C., Millen, Catriona A., Nguyen, Thuy T. T. and Goddard, Michael E. (2015). Extensive variation between tissues in allele specific expression in an outbred mammal. BMC Genomics, 16 (1) 993. doi: 10.1186/s12864-015-2174-0

Tucker, George, Loh, Po-Ru, MacLeod, Iona M., Hayes, Ben J., Goddard, Michael E., Berger, Bonnie and Price, Alkes L. (2015). Two-variance-component model improves genetic prediction in family datasets. American Journal of Human Genetics, 97 (5), 677-690. doi: 10.1016/j.ajhg.2015.10.002

Koufariotis, Lambros T., Chen, Yi-Ping Phoebe, Chamberlain, Amanda, Jagt, Christy Vander and Hayes, Ben J. (2015). A catalogue of novel bovine long noncoding RNA across 18 tissues. PLoS One, 10 (10) e0141225, e0141225. doi: 10.1371/journal.pone.0141225

Bolormaa, S., Gore, K., van der Werf, J. H. J., Hayes, B. J. and Daetwyler, H. D. (2015). Design of a low-density SNP chip for the main Australian sheep breeds and its effect on imputation and genomic prediction accuracy. Animal Genetics, 46 (5), 544-556. doi: 10.1111/age.12340

Pryce, J. E., Gonzalez-Recio, O., Nieuwhof, G., Wales, W. J., Coffey, M. P., Hayes, B. J. and Goddard, M. E. (2015). Hot topic: Definition and implementation of a breeding value for feed efficiency in dairy cows. Journal of Dairy Science, 98 (10) 73864, 7340-7350. doi: 10.3168/jds.2015-9621

Daetwyler, Hans D., Hayden, Matthew J., Spangenberg, German C. and Hayes, Ben J. (2015). Selection on optimal haploid value increases genetic gain and preserves more genetic diversity relative to genomic selection. Genetics, 200 (4), 1341-1348. doi: 10.1534/genetics.115.178038

Aliloo, Hassan, Pryce, Jennie E., Gonzalez-Recio, Oscar, Cocks, Benjamin G. and Hayes, Ben J. (2015). Validation of markers with non-additive effects on milk yield and fertility in Holstein and Jersey cows. BMC Genetics, 16 (1) 89. doi: 10.1186/s12863-015-0241-9

Pickering, N. K., Oddy, V. H., Basarab, J., Cammack, K., Hayes, B., Hegarty, R. S., Lassen, J., McEwan, J. C., Miller, S., Pinares-Patino, C. S. and de Haas, Y. (2015). Animal board invited review: Genetic possibilities to reduce enteric methane emissions from ruminants. Animal, 9 (9), 1431-1440. doi: 10.1017/S1751731115000968

Wientjes, Yvonne C. J., Calus, Mario P. L., Goddard, Michael E. and Hayes, Ben J. (2015). Impact of QTL properties on the accuracy of multi-breed genomic prediction. Genetics Selection Evolution, 47 (42) 42, 1-16. doi: 10.1186/s12711-015-0124-6

Haile-Mariam, M., Pryce, J. E., Schrooten, C. and Hayes, B. J. (2015). Including overseas performance information in genomic evaluations of Australian dairy cattle. Journal of Dairy Science, 98 (5), 3443-3459. doi: 10.3168/jds.2014-8785

Wang, Tingting, Chen, Yi-Ping Phoebe, Goddard, Michael E., Meuwissen, Theo H. E., Kemper, Kathryn E. and Hayes, Ben J. (2015). A computationally efficient algorithm for genomic prediction using a Bayesian model. Genetics Selection Evolution, 47 (1) 82. doi: 10.1186/s12711-014-0082-4

Kemper, Kathryn E., Reich, Coralie M., Bowman, Philip J., vander Jagt, Christy J., Chamberlain, Amanda J., Mason, Brett A., Hayes, Benjamin J. and Goddard, Michael E. (2015). Improved precision of QTL mapping using a nonlinear Bayesian method in a multi-breed population leads to greater accuracy of across-breed genomic predictions. Genetics Selection Evolution, 47 (1) 29. doi: 10.1186/s12711-014-0074-4

Moser, Gerhard, Lee, Sang Hong, Hayes, Ben J., Goddard, Michael E., Wray, Naomi R. and Visscher, Peter M. (2015). Simultaneous discovery, estimation and prediction analysis of complex traits using a bayesian mixture model. PLoS Genetics, 11 (4) e1004969, 1-22. doi: 10.1371/journal.pgen.1004969

Bolormaa, Sunduimijid, Pryce, Jennie E., Zhang, Yuandan, Reverter, Antonio, Barendse, William, Hayes, Ben J. and Goddard, Michael E. (2015). Non-additive genetic variation in growth, carcass and fertility traits of beef cattle. Genetics Selection Evolution, 47 (1) 26. doi: 10.1186/s12711-015-0114-8

Kemper, K. E., Hayes, B. J., Daetwyler, H. D. and Goddard, M. E. (2015). How old are quantitative trait loci and how widely do they segregate?. Journal of Animal Breeding and Genetics, 132 (2), 121-134. doi: 10.1111/jbg.12152

Howard, Jeremy T., Maltecca, Christian, Haile-Mariam, Mekonnen, Hayes, Ben J. and Pryce, Jennie E. (2015). Characterizing homozygosity across United States, New Zealand and Australian Jersey cow and bull populations. BMC Genomics, 16 (1) 187. doi: 10.1186/s12864-015-1352-4

Bolormaa, S., Hayes, B. J., Hawken, R. J., Zhang, Y., Reverter, A. and Goddard, M. E. (2014). Detection of chromosome segments of zebu and taurine origin and their effect on beef production and growth. Journal of Animal Science, 89 (7), 2050-2060. doi: 10.2527/jas.2010-3363

Bolormaa, S., Hayes, B. J., Savin, K., Hawken, R., Barendse, W., Arthur, P. F., Herd, R. M. and Goddard, M. E. (2014). Genome-wide association studies for feedlot and growth traits in cattle. Journal of Animal Science, 89 (6), 1684-1697. doi: 10.2527/jas.2010-3079

MacLeod, Iona M., Hayes, Ben J. and Goddard, Michael E. (2014). The effects of demography and long-term selection on the accuracy of genomic prediction with sequence data. Genetics, 198 (4), 1671-1684. doi: 10.1534/genetics.114.168344

Pryce, Jennie E., Haile-Mariam, Mekonnen, Goddard, Michael E. and Hayes, Ben J. (2014). Identification of genomic regions associated with inbreeding depression in Holstein and Jersey dairy cattle. Genetics Selection Evolution, 46 (1) 71. doi: 10.1186/s12711-014-0071-7

Slater, Anthony T., Cogan, Noel O. I., Hayes, Benjamin J., Schultz, Lee, Dale, M. Finlay B., Bryan, Glenn J. and Forster, John W. (2014). Improving breeding efficiency in potato using molecular and quantitative genetics. Theoretical and Applied Genetics, 127 (11), 2279-2292. doi: 10.1007/s00122-014-2386-8

Kijas, James W., Porto-Neto, Laercio, Dominik, Sonja, Reverter, Antonio, Bunch, Rowan, McCulloch, Russell, Hayes, Ben J., Brauning, Rudiger and McEwan, John (2014). Linkage disequilibrium over short physical distances measured in sheep using a high-density SNP chip. Animal Genetics, 45 (5), 754-757. doi: 10.1111/age.12197

Fariello, Maria-Ines, Servin, Bertrand, Tosser-Klopp, Gwenola, Rupp, Rachel, Moreno, Carole, San Cristobal, Magali, Boitard, Simon, International Sheep Genomics Consortium and Hayes, Ben (2014). Selection signatures in worldwide sheep populations. PLoS One, 9 (8) e103813, e103813. doi: 10.1371/journal.pone.0103813

Daetwyler, Hans D., Bansal, Urmil K., Bariana, Harbans S., Hayden, Matthew J. and Hayes, Ben J. (2014). Genomic prediction for rust resistance in diverse wheat landraces. Theoretical and Applied Genetics, 127 (8), 1795-1803. doi: 10.1007/s00122-014-2341-8

Thornhill, J. B., Marett, L. C., Auldist, M. J., Greenwood, J. S., Pryce, J. E., Hayes, B. J. and Wales, W. J. (2014). Whole-tract dry matter and nitrogen digestibility of lactating dairy cows selected for phenotypic divergence in residual feed intake. Animal Production Science, 54 (9), 1460-1464. doi: 10.1071/AN14200

van Binsbergen, Rianne, Bink, Marco C. A. M., Calus, Mario P. L., van Eeuwijk, Fred A., Hayes, Ben J., Hulsegge, Ina and Veerkamp, Roel F. (2014). Accuracy of imputation to whole-genome sequence data in Holstein Friesian cattle. Genetics Selection Evolution, 46 (1) 41, 1-13. doi: 10.1186/1297-9686-46-41

Koufariotis, Lambros, Chen, Yi-Ping Phoebe, Bolormaa, Sunduimijid and Hayes, Ben J. (2014). Regulatory and coding genome regions are enriched for trait associated variants in dairy and beef cattle. BMC Genomics, 15 (1) 436. doi: 10.1186/1471-2164-15-436

Gonzalez-Recio, O., Pryce, J. E., Haile-Mariam, M. and Hayes, B. J. (2014). Incorporating heifer feed efficiency in the Australian selection index using genomic selection. Journal of Dairy Science, 97 (6), 3883-3893. doi: 10.3168/jds.2013-7515

Raven, Lesley-Ann, Cocks, Benjamin G., Goddard, Michael E., Pryce, Jennie E. and Hayes, Ben J. (2014). Genetic variants in mammary development, prolactin signalling and involution pathways explain considerable variation in bovine milk production and milk composition. Genetics Selection Evolution, 46 (1) 29. doi: 10.1186/1297-9686-46-29

Slater, Anthony T., Wilson, Graeme M., Cogan, Noel O. I., Forster, John W. and Hayes, Benjamin J. (2014). Improving the analysis of low heritability complex traits for enhanced genetic gain in potato. Theoretical and Applied Genetics, 127 (4), 809-820. doi: 10.1007/s00122-013-2258-7

Kemper, Kathryn E., Saxton, Sarah J., Bolormaa, Sunduimijid, Hayes, Benjamin J. and Goddard, Michael E. (2014). Selection for complex traits leaves little or no classic signatures of selection. BMC Genomics, 15 (1) 246. doi: 10.1186/1471-2164-15-246

Macdonald, K. A., Pryce, J. E., Spelman, R. J., Davis, S. R., Wales, W. J., Waghorn, G. C., Williams, Y. J., II, Marett, L. C. and Hayes, B. J. (2014). Holstein-Friesian calves selected for divergence in residual feed intake during growth exhibited significant but reduced residual feed intake divergence in their first lactation. Journal of Dairy Science, 97 (3), 1427-1435. doi: 10.3168/jds.2013-7227

Pryce, J. E., Johnston, J., Hayes, B. J., Sahana, G., Weigel, K. A., McParland, S., Spurlock, D., Krattenmacher, N., Spelman, R. J., Wall, E. and Calus, M. P. L. (2014). Imputation of genotypes from low density (50,000 markers) to high density (700,000 markers) of cows from research herds in Europe, North America, and Australasia using 2 reference populations. Journal of Dairy Science, 97 (3), 1799-1811. doi: 10.3168/jds.2013-7368

Bolormaa, Sunduimijid, Pryce, Jennie E., Reverter, Antonio, Zhang, Yuandan, Barendse, William, Kemper, Kathryn, Tier, Bruce, Savin, Keith, Hayes, Ben J. and Goddard, Michael E. (2014). A multi-trait, meta-analysis for detecting pleiotropic polymorphisms for stature, fatness and reproduction in beef cattle. PLoS Genetics, 10 (3) e1004198, e1004198. doi: 10.1371/journal.pgen.1004198

Knight, Matthew I., Daetwyler, Hans D., Hayes, Ben J., Hayden, Matthew J., Ball, Alex J., Pethick, David W. and McDonagh, Matthew B. (2014). An independent validation association study of carcass quality, shear force, intramuscular fat percentage and omega-3 polyunsaturated fatty acid content with gene markers in Australian lamb. Meat Science, 96 (2), 1025-1033. doi: 10.1016/j.meatsci.2013.07.008

Amador, Carmen, Hayes, Ben J. and Daetwyler, Hans D. (2014). Genomic selection for recovery of original genetic background from hybrids of endangered and common breeds. Evolutionary Applications, 7 (2), 227-237. doi: 10.1111/eva.12113

Raven, Lesley-Ann, Cocks, Benjamin G. and Hayes, Ben J. (2014). Multibreed genome wide association can improve precision of mapping causative variants underlying milk production in dairy cattle. BMC Genomics, 15 (1) 62. doi: 10.1186/1471-2164-15-62

Nguyen, Thuy T. T., Hayes, Ben J. and Ingram, Brett A. (2014). Genetic parameters and response to selection in blue mussel (Mytilus galloprovincialis) using a SNP-based pedigree. Aquaculture, 420-421, 295-301. doi: 10.1016/j.aquaculture.2013.11.021

Pryce, J. E., Wales, W. J., de Haas, Y., Veerkamp, R. F. and Hayes, B. J. (2014). Genomic selection for feed efficiency in dairy cattle. Animal, 8 (1), 1-10. doi: 10.1017/S1751731113001687

DiGiacomo, K., Marett, L. C., Wales, W. J., Hayes, B. J., Dunshea, F. R. and Leury, B. J. (2014). Thermoregulatory differences in lactating dairy cattle classed as efficient or inefficient based on residual feed intake. Animal Production Science, 54 (10), 1877-1881. doi: 10.1071/AN14311

Druet, T., Macleod, I. M. and Hayes, B. J. (2014). Toward genomic prediction from whole-genome sequence data: impact of sequencing design on genotype imputation and accuracy of predictions. Heredity, 112 (1), 39-47. doi: 10.1038/hdy.2013.13

Pryce, J. E., Gonzalez-Recio, O., Thornhill, J. B., Marett, L. C., Wales, W. J., Coffey, M. P., de Haas, Y., Veerkamp, R. F. and Hayes, B. J. (2014). Short communication: Validation of genomic breeding value predictions for feed intake and feed efficiency traits. Journal of Dairy Science, 97 (1), 537-542. doi: 10.3168/jds.2013-7376

Erbe, M., Hayes, B. J., Matukumalli, L. K., Goswami, S., Bowman, P. J., Reich, C. M., Mason, B. A. and Goddard, M. E. (2014). Erratum: Improving accuracy of genomic predictions within and between dairy cattle breeds with imputed high-density single nucleotide polymorphism panels (J. Dairy Sci. 95:4114-4129). Journal of Dairy Science, 97 (10), 6622-6622. doi: 10.3168/jds.2014-97-10-6622

Wray, Naomi R., Yang, Jian, Hayes, Ben J., Price, Alkes L., Goddard, Michael E. and Visscher, Peter M. (2013). Author reply to A commentary on Pitfalls of predicting complex traits from SNPs. Nature Reviews Genetics, 14 (12), 894-894. doi: 10.1038/nrg3457-c2

Ross, Elizabeth M., Petrovski, Steve, Moate, Peter J. and Hayes, Ben J. (2013). Metagenomics of rumen bacteriophage from thirteen lactating dairy cattle. BMC Microbiology, 13. doi: 10.1186/1471-2180-13-242

Nicolazzi, Ezequiel L., Negrini, Riccardo, Chamberlain, Amanda J., Goddard, Michael E., Marsan, Paolo Ajmone and Hayes, Ben J. (2013). Effect of prior distributions on accuracy of genomic breeding values for two dairy traits. Italian Journal of Animal Science, 12 (4) e91, 555-561. doi: 10.4081/ijas.2013.e91

Ross, Elizabeth M., Moate, Peter J., Marett, Leah C., Cocks, Ben G. and Hayes, Ben J. (2013). Metagenomic predictions: from microbiome to complex health and environmental phenotypes in humans and cattle. PLoS One, 8 (9) e73056, e73056. doi: 10.1371/journal.pone.0073056

Ross, E. M., Moate, P. J., Marett, L., Cocks, B. G. and Hayes, B. J. (2013). Investigating the effect of two methane-mitigating diets on the rumen microbiome using massively parallel sequencing. Journal of Dairy Science, 96 (9), 6030-6046. doi: 10.3168/jds.2013-6766

MacLeod, Iona M., Larkin, Denis M., Lewin, Harris A., Hayes, Ben J. and Goddard, Mike E. (2013). Inferring demography from runs of homozygosity in whole-genome sequence, with correction for sequence errors. Molecular Biology and Evolution, 30 (9), 2209-2223. doi: 10.1093/molbev/mst125

Raven, Lesley-Ann, Cocks, Benjamin G., Pryce, Jennie E., Cottrell, Jeremy J. and Hayes, Ben J. (2013). Genes of the RNASE5 pathway contain SNP associated with milk production traits in dairy cattle. Genetics Selection Evolution, 45 (1) 25, 391-398. doi: 10.1186/1297-9686-45-25

Wray, Naomi R., Yang, Jian, Hayes, Ben J., Price, Alkes L., Goddard, Michael E. and Visscher, Peter M. (2013). Pitfalls of predicting complex traits from SNPs. Nature Reviews Genetics, 14 (7), 507-515. doi: 10.1038/nrg3457

Hayes, Benjamin J., Cogan, Noel O. I., Pembleton, Luke W., Goddard, Michael E., Wang, Junping, Spangenberg, German C. and Forster, John W. (2013). Prospects for genomic selection in forage plant species. Plant Breeding, 132 (2), 133-143. doi: 10.1111/pbr.12037

Hayes, Ben J., Lewin, Harris A. and Goddard, Michael E. (2013). The future of livestock breeding: genomic selection for efficiency, reduced emissions intensity, and adaptation. Trends in Genetics, 29 (4), 206-214. doi: 10.1016/j.tig.2012.11.009

Maher, Anthony D., Hayes, Benjamin, Cocks, Benjamin, Marett, Leah, Wales, William J. and Rochfort, Simone J. (2013). Latent biochemical relationships in the blood-milk metabolic axis of dairy cows revealed by statistical integration of 1H NMR spectroscopic data. Journal of Proteome Research, 12 (3), 1428-1435. doi: 10.1021/pr301056q

Haile-Mariam, M., Nieuwhof, G. J., Beard, K. T., Konstatinov, K. V. and Hayes, B. J. (2013). Comparison of heritabilities of dairy traits in Australian Holstein-Friesian cattle from genomic and pedigree data and implications for genomic evaluations. Journal of Animal Breeding and Genetics, 130 (1), 20-31. doi: 10.1111/j.1439-0388.2013.01001.x

Meuwissen, Theo, Hayes, Ben and Goddard, Mike (2013). Accelerating improvement of livestock with genomic selection. Annual Review of Animal Biosciences, 1 (1), 221-237. doi: 10.1146/annurev-animal-031412-103705

Bolormaa, S., Pryce, J. E., Kemper, K., Savin, K., Hayes, B. J., Barendse, W., Zhang, Y., Reich, C. M., Mason, B. A., Bunch, R. J., Harrison, B. E., Reverter, A., Herd, R. M., Tier, B., Graser, H. -U. and Goddard, M. E. (2013). Accuracy of prediction of genomic breeding values for residual feed intake and carcass and meat quality traits in Bos taurus, Bos indicus, and composite beef cattle. Journal of Animal Science, 91 (7), 3088-3104. doi: 10.2527/jas.2012-5827

Bolormaa, Sunduimijid, Pryce, Jennie E., Kemper, Kathryn E., Hayes, Ben J., Zhang, Yuandan, Tier, Bruce, Barendse, William, Reverter, Antonio and Goddard, Mike E. (2013). Detection of quantitative trait loci in Bos indicus and Bos taurus cattle using genome-wide association studies. Genetics Selection Evolution, 45 (1) 43, 43.1-43.12. doi: 10.1186/1297-9686-45-43

Gondro, Cedric, Van Der Werf, Julius and Hayes, Ben (2013). Preface. Methods in Molecular Biology, 1019. doi: 10.1007/978-1-62703-447_0

Daetwyler, Hans D., Swan, Andrew A., van der Werf, Julius H. J. and Hayes, Ben J. (2012). Accuracy of pedigree and genomic predictions of carcass and novel meat quality traits in multi-breed sheep data assessed by cross-validation. Genetics Selection Evolution, 44 (1) 33. doi: 10.1186/1297-9686-44-33

Brondum, Rasmus Froberg, Su, Guosheng, Lund, Mogens Sando, Bowman, Philip J., Goddard, Michael E. and Hayes, Benjamin J. (2012). Genome position specific priors for genomic prediction. BMC Genomics, 13 (1) 543. doi: 10.1186/1471-2164-13-543

Khatkar, Mehar S., Moser, Gerhard, Hayes, Ben J. and Raadsma, Herman W. (2012). Strategies and utility of imputed SNP genotypes for genomic analysis in dairy cattle. BMC Genomics, 13 (1) 538, 1-12. doi: 10.1186/1471-2164-13-538

de Haas, Y., Calus, M. P. L., Veerkamp, R. F., Wall, E., Coffey, M. P., Daetwyler, H. D., Hayes, B. J. and Pryce, J. E. (2012). Improved accuracy of genomic prediction for dry matter intake of dairy cattle from combined European and Australian data sets. Journal of Dairy Science, 95 (10), 6103-6112. doi: 10.3168/jds.2011-5280

Dominik, S., Henshall, J. M. and Hayes, B. J. (2012). A single nucleotide polymorphism on chromosome 10 is highly predictive for the polled phenotype in Australian Merino sheep. Animal Genetics, 43 (4), 468-470. doi: 10.1111/j.1365-2052.2011.02271.x

Kemper, K. E., Bowman, R. J., Pryce, J. E., Hayes, B. J. and Goddard, M. E. (2012). Long-term selection strategies for complex traits using high-density genetic markers. Journal of Dairy Science, 95 (8), 4646-4656. doi: 10.3168/jds.2011-5289

Ross, Elizabeth M., Moate, Peter J., Bath, Carolyn R., Davidson, Sophie E., Sawbridge, Tim I., Guthridge, Kathryn M., Cocks, Ben G. and Hayes, Ben J. (2012). High throughput whole rumen metagenome profiling using untargeted massively parallel sequencing. BMC Genetics, 13 53. doi: 10.1186/1471-2156-13-53

Erbe, M., Hayes, B. J., Matukumalli, L. K., Goswami, S., Bowman, P. J., Reich, C. M., Mason, B. A. and Goddard, M. E. (2012). Improving accuracy of genomic predictions within and between dairy cattle breeds with imputed high-density single nucleotide polymorphism panels. Journal of Dairy Science, 95 (7), 4114-4129. doi: 10.3168/jds.2011-5019

Larkin, Denis M., Daetwyler, Hans D., Hernandez, Alvaro G., Wright, Chris L., Hetrick, Lorie A., Boucek, Lisa, Bachman, Sharon L., Band, Mark R., Akraiko, Tatsiana V., Cohen-Zinder, Miri, Thimmapuram, Jyothi, Macleod, Iona M., Harkins, Timothy T., McCague, Jennifer E., Goddard, Michael E., Hayes, Ben J. and Lewin, Harris A. (2012). Whole-genome resequencing of two elite sires for the detection of haplotypes under selection in dairy cattle. Proceedings of the National Academy of Sciences of the United States of America, 109 (20), 7693-7698. doi: 10.1073/pnas.1114546109

Knight, M. I., Daetwyler, H. D., Hayes, B. J., Hayden, M. J., Ball, A. J., Pethick, D. W. and McDonagh, M. B. (2012). Discovery and trait association of single nucleotide polymorphisms from gene regions of influence on meat tenderness and long-chain omega-3 fatty acid content in Australian lamb. Animal Production Science, 52 (7), 591-600. doi: 10.1071/AN11229

Pryce, J. E., Arias, J., Bowman, P. J., Davis, S. R., Macdonald, K. A., Waghorn, G. C., Wales, W. J., Williams, Y. J., Spelman, R. J. and Hayes, B. J. (2012). Accuracy of genomic predictions of residual feed intake and 250-day body weight in growing heifers using 625,000 single nucleotide polymorphism markers. Journal of Dairy Science, 95 (4), 2108-2119. doi: 10.3168/jds.2011-4628

Boichard, Didier, Chung, Hoyoung, Dassonneville, Romain, David, Xavier, Eggen, Andre, Fritz, Sebastien, Gietzen, Kimberly J., Hayes, Ben J., Lawley, Cynthia T., Sonstegard, Tad S., Van Tassell, Curtis P., VanRaden, Paul M., Viaud-Martinez, Karine A. and Wiggans, George R. (2012). Design of a bovine low-density snp array optimized for imputation. PLoS One, 7 (3) e34130, e34130. doi: 10.1371/journal.pone.0034130

Pryce, Jennie and Hayes, Ben (2012). A review of how dairy farmers can use and profit from genomic technologies. Animal Production Science, 52 (3), 180-184. doi: 10.1071/AN11172

Daetwyler, H. D., Kemper, K. E., van der Werf, J. H. J. and Hayes, B. J. (2012). Components of the accuracy of genomic prediction in a multi-breed sheep population. Journal of Animal Science, 90 (10), 3375-3384. doi: 10.2527/jas.2011-4557

Chamberlain, A. J., Hayes, B. J., Savin, K., Bolormaa, S., McPartlan, H. C., Bowman, P. J., Van der Jagt, C., MacEachern, S. and Goddard, M. E. (2012). Validation of single nucleotide polymorphisms associated with milk production traits in dairy cattle. Journal of Dairy Science, 95 (2), 864-875. doi: 10.3168/jds.2010-3786

Hayes, B. J., Bowman, P. J., Daetwyler, H. D., Kijas, J. W. and van der Werf, J. H. J. (2012). Accuracy of genotype imputation in sheep breeds. Animal Genetics, 43 (1), 72-80. doi: 10.1111/j.1365-2052.2011.02208.x

Kijas, James W., Lenstra, Johannes A., Hayes, Ben, Boitard, Simon, Neto, Laercio R. Porto, San Cristobal, Magali, Servin, Bertrand, McCulloch, Russell, Whan, Vicki, Gietzen, Kimberly, Paiva, Samuel, Barendse, William, Ciani, Elena, Raadsma, Herman, McEwan, John, Dalrymple, Brian and Int Sheep Genomics Consortium (2012). Genome-Wide Analysis of the World's Sheep Breeds Reveals High Levels of Historic Mixture and Strong Recent Selection. PLoS Biology, 10 (2) e1001258, e1001258. doi: 10.1371/journal.pbio.1001258

Pryce, J. E., Hayes, B. J. and Goddard, M. E. (2012). Novel strategies to minimize progeny inbreeding while maximizing genetic gain using genomic information. Journal of Dairy Science, 95 (1), 377-388. doi: 10.3168/jds.2011-4254

Lien, Sigbjorn, Gidskehaug, Lars, Moen, Thomas, Hayes, Ben J., Berg, Paul R., Davidson, William S., Omholt, Stig W. and Kent, Matthew P. (2011). A dense SNP-based linkage map for Atlantic salmon (Salmo salar) reveals extended chromosome homeologies and striking differences in sex-specific recombination patterns. BMC Genomics, 12 (1) 615. doi: 10.1186/1471-2164-12-615

Goddard, M. E., Hayes, B. J. and Meuwissen, T. H. E. (2011). Using the genomic relationship matrix to predict the accuracy of genomic selection. Journal of Animal Breeding and Genetics, 128 (6), 409-421. doi: 10.1111/j.1439-0388.2011.00964.x

Nguyen, T. T. T., Hayes, B. J., Guthridge, K., Ab Rahim, E. S. and Ingram, B. A. (2011). Use of a microsatellite-based pedigree in estimation of heritabilities for economic traits in Australian blue mussel, Mytilus galloprovincialis. Journal of Animal Breeding and Genetics, 128 (6), 482-490. doi: 10.1111/j.1439-0388.2011.00948.x

Ingram, B. A., Hayes, B. and Rourke, M. L. (2011). Impacts of stock enhancement strategies on the effective population size of Murray cod, Maccullochella peelii, a threatened Australian fish. Fisheries Management and Ecology, 18 (6), 467-481. doi: 10.1111/j.1365-2400.2011.00798.x

Sodeland, M., Kent, M. P., Olsen, H. G., Opsal, M. A., Svendsen, M., Sehested, E., Hayes, B. J. and Lien, S. (2011). Quantitative trait loci for clinical mastitis on chromosomes 2, 6, 14 and 20 in Norwegian Red cattle. Animal Genetics, 42 (5), 457-465. doi: 10.1111/j.1365-2052.2010.02165.x

Olsen, H. G., Hayes, B. J., Kent, M. P., Nome, T., Svendsen, M., Larsgard, A. G. and Lien, S. (2011). Genome-wide association mapping in Norwegian Red cattle identifies quantitative trait loci for fertility and milk production on BTA12. Animal Genetics, 42 (5), 466-474. doi: 10.1111/j.1365-2052.2011.02179.x

Williams, Y. J., Pryce, J. E., Grainger, C., Wales, W. J., Linden, N., Porker, M. and Hayes, B. J. (2011). Variation in residual feed intake in Holstein-Friesian dairy heifers in southern Australia. Journal of Dairy Science, 94 (9), 4715-4725. doi: 10.3168/jds.2010-4015

Daetwyler, Hans D., Wiggans, George R., Hayes, Ben J., Woolliams, John A. and Goddard, Mike E. (2011). Imputation of missing genotypes from sparse to high density using long-range phasing. Genetics, 189 (1), 317-327. doi: 10.1534/genetics.111.128082

Sodeland, Marte, Grove, Harald, Kent, Matthew, Taylor, Simon, Svendsen, Morten, Hayes, Ben J. and Lien, Sigbjorn (2011). Molecular characterization of a long range haplotype affecting protein yield and mastitis susceptibility in Norwegian Red cattle. BMC Genetics, 12 70. doi: 10.1186/1471-2156-12-70

Krishna, Gopal, Gopikrishna, Gopalapillay, Gopal, Chavali, Jahageerdar, Shrinivas, Ravichandran, Pitchaiyappan, Kannappan, Sudalyandi, Pillai, Subramaniapillai M., Paulpandi, Sivagnanam, Kiran, Remanibhaskaran P., Saraswati, Ramamoorthy, Venugopal, Gundaboena, Kumar, Dilip, Gitterle, Thomas, Lozano, Carlos, Rye, Morten and Hayes, Ben (2011). Genetic parameters for growth and survival in Penaeus monodon cultured in India. Aquaculture, 318 (1-2), 74-78. doi: 10.1016/j.aquaculture.2011.04.028

Gopikrishna, G., Gopal, C., Krishna, G., Jahageerdar, S., Rye, M., Lozano, C., Gitterle, T., Venugopal, G., Paulpandi, S., Ravichandran, P., Pillai, S. M., Ponniah, A. G. and Hayes, B. (2011). Effect of stocking density, water exchange rate and tank substrate on growth and survival of post-larvae of Penaeus monodon (Fabricius, 1798). Indian Journal of Fisheries, 58 (3), 57-61.

Qanbari, Saber, Gianola, Daniel, Hayes, Ben, Schenkel, Flavio, Miller, Steve, Moore, Stephen, Thaller, Georg and Simianer, Henner (2011). Application of site and haplotype-frequency based approaches for detecting selection signatures in cattle. BMC Genomics, 12 (1) 318. doi: 10.1186/1471-2164-12-318

Pryce, J. E., Gredler, B., Bolormaa, S., Bowman, P. J., Egger-Danner, C., Fuerst, C., Emmerling, R., Soelkner, J., Goddard, M. E. and Hayes, B. J. (2011). Short communication: Genomic selection using a multi-breed, across-country reference population. Journal of Dairy Science, 94 (5), 2625-2630. doi: 10.3168/jds.2010-3719

Hayes, B. J. (2011). Technical note: Efficient parentage assignment and pedigree reconstruction with dense single nucleotide polymorphism data. Journal of Dairy Science, 94 (4), 2114-2117. doi: 10.3168/jds.2010-3896

Pryce, Jennie E., Hayes, Ben J., Bolormaa, Sunduimijid and Goddard, Michael E. (2011). Polymorphic regions affecting human height also control stature in cattle. Genetics, 187 (3), 981-984. doi: 10.1534/genetics.110.123943

Gidskehaug, Lars, Kent, Matthew, Hayes, Ben J. and Lien, Sigbjorn (2011). Genotype calling and mapping of multisite variants using an Atlantic salmon iSelect SNP array. Bioinformatics, 27 (3) btq673, 303-310. doi: 10.1093/bioinformatics/btq673

Sodeland, Marte, Kent, Matthew, Hayes, Ben J., Grove, Harald and Lien, Sigbjorn (2011). Recent and historical recombination in the admixed Norwegian Red cattle breed. BMC Genomics, 12 (1) 33. doi: 10.1186/1471-2164-12-33

Kemper, Kathryn E., Emery, David L., Bishop, Stephen C., Oddy, Hutton, Hayes, Benjamin J., Dominik, Sonja, Henshall, John M. and Goddard, Michael E. (2011). The distribution of SNP marker effects for faecal worm egg count in sheep, and the feasibility of using these markers to predict genetic merit for resistance to worm infections. Genetics Research, 93 (3), 203-219. doi: 10.1017/S0016672311000097

Goddard, Michael E., Hayes, Ben J. and Meuwissen, Theo H. E. (2010). Genomic selection in livestock populations. Genetics Research, 92 (5-6), 413-421. doi: 10.1017/S0016672310000613

Daetwyler, H. D., Hickey, J. M., Henshall, J. M., Dominik, S., Gredler, B., van der Werf, J. H. J. and Hayes, B. J. (2010). Accuracy of estimated genomic breeding values for wool and meat traits in a multi-breed sheep population. Animal Production Science, 50 (12), 1004-1010. doi: 10.1071/AN10096

Pryce, J. E., Goddard, M. E., Raadsma, H. W. and Hayes, B. J. (2010). Deterministic models of breeding scheme designs that incorporate genomic selection. Journal of Dairy Science, 93 (11), 5455-5466. doi: 10.3168/jds.2010-3256

Moser, Gerhard, Khatkar, Mehar S., Hayes, Ben J. and Raadsma, Herman W. (2010). Accuracy of direct genomic values in Holstein bulls and cows using subsets of SNP markers. Genetics Selection Evolution, 42 (1) 37, 37.1-37.15. doi: 10.1186/1297-9686-42-37

Hayes, Ben J., Gitterle, Thomas, Gopikrishna, Gopalapillay, Gopal, Chavali, Krishna, Gopal, Jahageerdar, Shrivinas, Lozano, Carlos, Alavandi, Shankar, Paulpandi, Sivagnanam, Ravichandran, Pitchaiyappan and Rye, Morten (2010). Limited evidence for genetic variation for resistance to the white spot syndrome virus in Indian populations of Penaeus monodon. Aquaculture Research, 41 (11), e872-e877. doi: 10.1111/j.1365-2109.2010.02611.x

Hayes, Ben J., Pryce, Jennie, Chamberlain, Amanda J., Bowman, Phil J. and Goddard, Mike E. (2010). Genetic architecture of complex traits and accuracy of genomic prediction: coat colour, milk-fat percentage, and type in Holstein cattle as contrasting model traits. PLoS Genetics, 6 (9) e1001139, e1001139. doi: 10.1371/journal.pgen.1001139

Robinson, Nick, Li, Xiaoxu and Hayes, Ben (2010). Testing options for the commercialization of abalone selective breeding using bioeconomic simulation modelling. Aquaculture Research, 41 (9), e268-e288. doi: 10.1111/j.1365-2109.2010.02528.x

Bolormaa, S., Pryce, J. E., Hayes, B. J. and Goddard, M. E. (2010). Multivariate analysis of a genome-wide association study in dairy cattle. Journal of Dairy Science, 93 (8), 3818-3833. doi: 10.3168/jds.2009-2980

Pryce, J. E., Bolormaa, S., Chamberlain, A. J., Bowman, P. J., Savin, K., Goddard, M. E. and Hayes, B. J. (2010). A validated genome-wide association study in 2 dairy cattle breeds for milk production and fertility traits using variable length haplotypes. Journal of Dairy Science, 93 (7), 3331-3345. doi: 10.3168/jds.2009-2893

Olsen, H. G., Hayes, B. J., Kent, M. P., Nome, T., Svendsen, M. and Lien, S. (2010). A genome wide association study for QTL affecting direct and maternal effects of stillbirth and dystocia in cattle. Animal Genetics, 41 (3), 273-280. doi: 10.1111/j.1365-2052.2009.01998.x

Pryce, J. E., Haile-Mariam, M., Verbyla, K., Bowman, P. J., Goddard, M. E. and Hayes, B. J. (2010). Genetic markers for lactation persistency in primiparous Australian dairy cows. Journal of Dairy Science, 93 (5), 2202-2214. doi: 10.3168/jds.2009-2666

MacLeod, I. M., Hayes, B. J., Savin, K. W., Chamberlain, A. J., McPartlan, H. C. and Goddard, M. E. (2010). Power of a genome scan to detect and locate quantitative trait loci in cattle using dense single nucleotide polymorphisms. Journal of Animal Breeding and Genetics, 127 (2), 133-142. doi: 10.1111/j.1439-0388.2009.00831.x

Gopal, Chavali, Gopikrishna, Gopalapillay, Krishna, Gopal, Jahageerdar, Shrinivas S., Rye, Morten, Hayes, Ben J., Paulpandi, Sivagnanam, Kiran, Remanibhaskaran P., Pillai, Subramaniapillai M., Ravichandran, Pitchaiyappan, Ponniah, Alphis G. and Kumar, Dilip (2010). Weight and time of onset of female-superior sexual dimorphism in pond reared Penaeus monodon. Aquaculture, 300 (1-4), 237-239. doi: 10.1016/j.aquaculture.2010.01.007

Usai, M. Graziano, Goddard, Mike E. and Hayes, Ben J. (2009). LASSO with cross-validation for genomic selection. Genetics Research, 91 (6), 427-436. doi: 10.1017/S0016672309990334

MacLeod, I. M., Meuwissen, T. H. E., Hayes, B. J. and Goddard, M. E. (2009). A novel predictor of multilocus haplotype homozygosity: comparison with existing predictors. Genetics Research, 91 (6), 413-426. doi: 10.1017/S0016672309990358

Hayes, B. J., MacLeod, I. M. and Baranski, M. (2009). Sampling strategies for whole genome association studies in aquaculture and outcrossing plant species. Genetics Research, 91 (6), 367-371. doi: 10.1017/S0016672309990310

de Roos, A. P. W., Hayes, B. J. and Goddard, M. E. (2009). Reliability of genomic predictions across multiple populations. Genetics, 183 (4), 1545-1553. doi: 10.1534/genetics.109.104935

Usai, Mario Graziano, Goddard, Mike E. and Hayes, Ben J. (2009). Using LASSO to estimate marker effects for Genomic Selection. Italian Journal of Animal Science, 8 (SUPPL. 2), 168-170.

Hayes, Ben J., Bowman, Phillip J., Chamberlain, Amanda C., Verbyla, Klara and Goddard, Mike E. (2009). Accuracy of genomic breeding values in multi-breed dairy cattle populations. Genetics Selection Evolution, 41 (1) 51, 321-329. doi: 10.1186/1297-9686-41-51

Verbyla, Klara L., Hayes, Ben J., Bowman, Philip. J. and Goddard, Michael E. (2009). Accuracy of genomic selection using stochastic search variable selection in Australian Holstein Friesian dairy cattle. Genetics Research, 91 (5), 307-311. doi: 10.1017/S0016672309990243

Nilsen, H., Olsen, H. G., Hayes, B., Nome, T., Sehested, E., Svendsen, M., Meuwissen, T. H. E. and Lien, S. (2009). Characterization of a QTL region affecting clinical mastitis and protein yield on BTA6. Animal Genetics, 40 (5), 701-712. doi: 10.1111/j.1365-2052.2009.01908.x

Hayes, Ben J., Bowman, Phil J., Chamberlain, Amanda J., Savin, Keith, van Tassell, Curt P., Sonstegard, Tad S. and Goddard, Mike E. (2009). A validated genome wide association study to breed cattle adapted to an environment altered by climate change. PLoS ONE, 4 (8) e6676, e6676. doi: 10.1371/journal.pone.0006676

Lillehammer, M., Hayes, B. J., Meuwissen, T. H. E. and Goddard, M. E. (2009). Gene by environment interactions for production traits in Australian dairy cattle. Journal of Dairy Science, 92 (8), 4008-4017. doi: 10.3168/jds.2008-1484

Goddard, Michael E. and Hayes, Ben J. (2009). Mapping genes for complex traits in domestic animals and their use in breeding programmes. Nature Reviews Genetics, 10 (6), 381-391. doi: 10.1038/nrg2575

MacEachern, Sean, Hayes, Ben, McEwan, John and Goddard, Mike (2009). An examination of positive selection and changing effective population size in Angus and Holstein cattle populations (Bos taurus) using a high density SNP genotyping platform and the contribution of ancient polymorphism to genomic diversity in Domestic ca. BMC Genomics, 10 181. doi: 10.1186/1471-2164-10-181

Hayes, B. J., Chamberlain, A. J., Maceachern, S., Savin, K., McPartlan, H., MacLeod, I., Sethuraman, L. and Goddard, M. E. (2009). A genome map of divergent artificial selection between Bos taurus dairy cattle and Bos taurus beef cattle. Animal Genetics, 40 (2), 176-184. doi: 10.1111/j.1365-2052.2008.01815.x

Hayes, B. J., Visscher, P. M. and Goddard, M. E. (2009). Increased accuracy of artificial selection by using the realized relationship matrix. (vol 91, pg 47, 2009). Genetics Research, 91 (2), 143-143. doi: 10.1017/S0016672309000111

Nilsen, Heidi, Olsen, Hanne Gro, Hayes, Ben, Sehested, Erling, Svendsen, Morten, Nome, Torfinn, Meuwissen, Theo and Lien, Sigbjorn (2009). Casein haplotypes and their association with milk production traits in Norwegian Red cattle. Genetics Selection Evolution, 41 (1) 24. doi: 10.1186/1297-9686-41-24

Hayes, B. J., Bowman, P. J., Chamberlain, A. J. and Goddard, M. E. (2009). Invited review: genomic selection in dairy cattle: progress and challenges. Journal of Dairy Science, 92 (2), 433-443. doi: 10.3168/jds.2008-1646

Hayes, B. J., Visscher, P. M. and Goddard, M. E. (2009). Increased accuracy of artificial selection by using the realized relationship matrix. Genetics Research, 91 (1), 47-60. doi: 10.1017/S0016672308009981

Robinson, Nick and Hayes, Ben (2008). Modelling the use of gene expression profiles with selective breeding for improved disease resistance in Atlantic salmon (Salmo salar). Aquaculture, 285 (1-4), 38-46. doi: 10.1016/j.aquaculture.2008.08.016

Baranski, M., Rourke, M., Loughnan, S., Hayes, B., Austin, C. and Robinson, N. (2008). Detection of QTL for growth rate in the blacklip abalone (Haliotis rubra Leach) using selective DNA pooling. Animal Genetics, 39 (6), 606-614. doi: 10.1111/j.1365-2052.2008.01773.x

Robinson, N., Goddard, M. and Hayes, B. (2008). Use of gene expression data for predicting continuous phenotypes for animal production and breeding. Animal, 2 (10), 1413-1420. doi: 10.1017/S1751731108002632

Lee, Sang Hong, van der Werf, Julius H. J., Hayes, Ben J., Goddard, Michael E. and Visscher, Peter M. (2008). Predicting unobserved phenotypes for complex traits from whole-genome SNP data. PLoS Genetics, 4 (10) e1000231, e1000231. doi: 10.1371/journal.pgen.1000231

de Roos, A. P. W., Hayes, B. J., Spelman, R. J. and Goddard, M. E. (2008). Linkage disequilibrium and persistence of phase in Holstein-Friesian, Jersey and Angus cattle. Genetics, 179 (3), 1503-1512. doi: 10.1534/genetics.107.084301

Moen, Thomas, Hayes, Ben, Baranski, Matthew, Berg, Paul R., Kjoglum, Sissel, Koop, Ben F., Davidson, Willie S., Omholt, Stig W. and Lien, Sigbjorn (2008). A linkage map of the Atlantic salmon (Salmo salar) based on EST-derived SNP markers. BMC Genomics, 9 223. doi: 10.1186/1471-2164-9-223

Nilsen, H., Hayes, B., Berg, P. R., Roseth, A., Sundsaasen, K. K., Nilsen, K. and Lien, S. (2008). Construction of a dense SNP map for bovine chromosome 6 to assist the assembly of the bovine genome sequence. Animal Genetics, 39 (2), 97-104. doi: 10.1111/j.1365-2052.2007.01686.x

Hayes, B. J., Lien, S., Nilsen, H., Olsen, H. G., Berg, P., Maceachern, S., Potter, S. and Meuwissen, T. H. E. (2008). The origin of selection signatures on bovine chromosome 6. Animal Genetics, 39 (2), 105-111. doi: 10.1111/j.1365-2052.2007.01683.x

Moen, Thomas, Hayes, Ben, Nilsen, Frank, Delghandi, Madjid, Fjalestad, Kjersti T., Fevolden, Svein-Erik, Berg, Paul R. and Lien, Sigbjorn (2008). Identification and characterisation of novel SNP markers in Atlantic cod: evidence for directional selection. BMC Genetics, 9 (1) 18. doi: 10.1186/1471-2156-9-18

Finocchiaro, R., Hayes, B. J., Siwek, M., Spelman, R. J., van Kaam, J. B. C. H. M., Adnoy, T. and Portolano, B. (2008). Comparison of casein haplotypes between two geographically distant European dairy goat breeds. Journal of Animal Breeding and Genetics, 125 (1), 68-72. doi: 10.1111/j.1439-0388.2007.00687.x

Hayes, B. J. and Goddard, M. E. (2008). Technical note: prediction of breeding values using marker-derived relationship matrices. Journal of Animal Science, 86 (9), 2089-2092. doi: 10.2527/jas.2007-0733

Goddard, M. E. and Hayes, B. J. (2007). Genomic selection. Journal of Animal Breeding and Genetics, 124 (6), 323-330. doi: 10.1111/j.1439-0388.2007.00702.x

Moen, Thomas, Sonesson, Anna K., Hayes, Ben, Lien, Sigbjorn, Munck, Hege and Meuwissen, Theo H. E. (2007). Mapping of a quantitative trait locus for resistance against infectious salmon anaemia in Atlantic salmon (Salmo Salar): comparing survival analysis with analysis on affected/resistant data. BMC Genetics, 8 (1) 53. doi: 10.1186/1471-2156-8-53

Hayes, B. J., Chamberlain, A. J., McPartlan, H., Macleod, I., Sethuraman, L. and Goddard, M. E. (2007). Accuracy of marker-assisted selection with single markers and marker haplotypes in cattle. Genetical Research, 89 (4), 215-220. doi: 10.1017/S0016672307008865

Gjuvsland, Arne B., Hayes, Ben J., Meuwissen, Theo H. E., Plahte, Erik and Omholt, Stig W. (2007). Nonlinear regulation enhances the phenotypic expression of trans-acting genetic polymorphisms. BMC Systems Biology, 1 (1) 32. doi: 10.1186/1752-0509-1-32

Olsen, Hanne Gro, Nilsen, Heidi, Hayes, Ben, Berg, Paul R., Svendsen, Morten, Lien, Sigbjorn and Meuwissen, Theo (2007). Genetic support for a quantitative trait nucleotide in the ABCG2 gene affecting milk composition of dairy cattle. BMC Genetics, 8 (1) 32. doi: 10.1186/1471-2156-8-32

Hayes, Ben, Baranski, Matt, Goddard, Mike E. and Robinson, Nick (2007). Optimisation of marker assisted selection for abalone breeding programs. Aquaculture, 265 (1-4), 61-69. doi: 10.1016/j.aquaculture.2007.02.016

Hayes, B., Laerdahl, J. K., Lien, S., Moen, T., Berg, P., Hindar, K., Davidson, W. S., Koop, B. F., Adzhubei, A. and Hoyheim, B. (2007). An extensive resource of single nucleotide polymorphism markers associated with Atlantic salmon (Salmo salar) expressed sequences. Aquaculture, 265 (1-4), 82-90. doi: 10.1016/j.aquaculture.2007.01.037

Gjuvsland, Arne B., Hayes, Ben J., Omholt, Stig W. and Carlborg, Orjan (2007). Statistical epistasis is a generic feature of gene regulatory networks. Genetics, 175 (1), 411-420. doi: 10.1534/genetics.106.058859

Tenesa, Albert, Navarro, Pau, Hayes, Ben J., Duffy, David L., Clarke, Geraldine M., Goddard, Mike E. and Visscher, Peter M. (2007). Recent human effective population size estimated from linkage disequilibrium. Genome Research, 17 (4), 520-526. doi: 10.1101/gr.6023607

Opsal, Monica Aa., Vage, Dag Inge, Hayes, Ben, Berget, Ingunn and Lien, Sigbjorn (2006). Genomic organization and transcript profiling of the bovine toll-like receptor gene cluster TLR6-TLR1-TLR10. Gene, 384 (1-2), 45-50. doi: 10.1016/j.gene.2006.06.027

Hayes, Ben, Hagesaether, Nina, Adnoy, Tormod, Pellerud, Grunde, Berg, Paul R. and Lien, Sigbjorn (2006). Effects on production traits of haplotypes among casein genes in Norwegian goats and evidence for a site of preferential recombination. Genetics, 174 (1), 455-464. doi: 10.1534/genetics.106.058966

Hayes, B. J., Gjuvsland, A. and Omholt, S. (2006). Power of QTL mapping experiments in commercial Atlantic salmon populations, exploiting linkage and linkage disequilibrium and effect of limited recombination in males. Heredity, 97 (1), 19-26. doi: 10.1038/sj.hdy.6800827

Hayes, Ben, He, Jie, Moen, Thomas and Bennewitz, Joern (2006). Use of molecular markers to maximise diversity of founder populations for aquaculture breeding programs. Aquaculture, 255 (1-4), 573-578. doi: 10.1016/j.aquaculture.2005.11.038

Hayes, Ben, Sonesson, Anna K. and Gjerde, Bjarne (2005). Evaluation of three strategies using DNA markers for traceability in aquaculture species. Aquaculture, 250 (1-2), 70-81. doi: 10.1016/j.aquaculture.2005.03.008

Hayes, Ben and Goddard, Mike E. (2004). Break-even cost of genotyping genetic mutations affecting economic traits in Australian pig enterprises. Livestock Production Science, 89 (2-3), 235-242. doi: 10.1016/j.livprodsci.2004.01.005

Hayes, B. J., Carrick, M., Bowman, P. and Goddard, M. E. (2003). Genotype x environment interaction for milk production of daughters of Australian dairy sires from test-day records. Journal of Dairy Science, 86 (11), 3736-3744. doi: 10.3168/jds.S0022-0302(03)73980-0

Hayes, Ben and Goddard, Mike E. (2003). Evaluation of marker assisted selection in pig enterprises. Livestock Production Science, 81 (2-3), 197-211. doi: 10.1016/S0301-6226(02)00257-9

Hayes, Ben J., Visscher, Peter M., McPartlan, Helen C. and Goddard, Mike E. (2003). Novel multilocus measure of linkage disequilibrium to estimate past effective population size. Genome Research, 13 (4), 635-643. doi: 10.1101/gr.387103

Hayes, B., Shepherd, R. K. and Newman, S. (2002). Look ahead mate selection schemes for multi-breed beef populations. Animal Science, 74 (1), 13-23. doi: 10.1017/S1357729800052206

Hayes, Ben and Goddard, Mike E. (2001). The distribution of the effects of genes affecting quantitative traits in livestock. Genetics Selection Evolution, 33 (3), 209-229.

Meuwissen, T. H. E., Hayes, B. J. and Goddard, M. E. (2001). Prediction of total genetic value using genome-wide dense marker maps. Genetics, 157 (4), 1819-1829.

Hayes B.J., Newman S. and Shepherd R.K. (2000). Technical note: Constrained optimization of breed composition in composite populations to balance net merit and risk. Journal of Animal Science, 78 (8), 2105-2107.

Hates, B. J. and Miller, S. P. (2000). Mate selection strategies to exploit across- and within-breed dominance variation. Journal of Animal Breeding and Genetics, 117 (5), 347-359. doi: 10.1046/j.1439-0388.2000.00252.x

Engle, Bailey N., Moser, Gerhard, Villiers, Kira, Suarez, Mathias, Grey, Eliza, Hayes, Ben J. and Kelly, Matthew (2023). Using Digital Twin Simulations to Optimize Genetic Selection in an Admixed Beef Herd. 2023 ASAS-CSAS Annual Meeting, Albuquerque, NM United States, 16-20 July 2023. Champaign, IL United States: American Society of Animal Science. doi: 10.1093/jas/skad281.042

Tabor, Ala, Siddle, Hannah, Juli, Sogra Banu, Raza, Ali, Ong, Chian Teng, McCosker, Kieren, Hayes, Ben and Boe-Hansen, Gry (2023). New diagnostic tools for bovine vibriosis. Northern Beef Research Update Conference, Darwin, NT Australia, 22-25 August 2023.

Lamb, H.J., Nguyen, L.T., Randhawa, I.A.S., Hayes, B.J. and Ross, E.M. (2022). The long and short of Nanopore genomic prediction: the effect of read length on prediction accuracy. 12th World Congress on Genetics Applied to Livestock Production (WCGALP), Rotterdam, Netherlands, 3-8 July 2022. Wageningen, Netherlands: Wageningen Academic Publishers. doi: 10.3920/978-90-8686-940-4_279

Mantilla Valdivieso, E. , Nguyen, L., Ross, E., Raza, A., James, P., Hayes, B., Jonsson, N. and Tabor, A. (2022). Identification of differentially expressed transcription factors in Brangus skin infested with Rhipicephalus australis. 12th World Congress on Genetics Applied to Livestock Production (WCGALP), Rotterdam, Netherlands, 3-8 July 2022. Wageningen, Netherlands: Wageningen Academic Publishers. doi: 10.3920/978-90-8686-940-4_557

Ross, E.M., Nguyen, L.T., Engle, B.N., Chamberlain, A.J., Kho, E. and Hayes, B.J. (2022). Bos indicus genome percentage effects gene expression profile and differentially expressed genes in Brahman cattle whole blood. 12th World Congress on Genetics Applied to Livestock Production (WCGALP), Rotterdam, The Netherlands, 3-8 July 2022. Wageningen, The Netherlands: Wageningen Academic Publishers. doi: 10.3920/978-90-8686-940-4_628

Copley, J.P., Corbet, N.J., Allen, J.M., Laing, A.R., Fordyce, G., McGowan, M.R., Burns, B.M., Lyons, R.E. and Hayes, B.J. (2022). Understanding the genetics of fertility and temperament in Northern beef cattle using genomic technologies. 12th World Congress on Genetics Applied to Livestock Production (WCGALP), Rotterdam, The Netherlands, 3-8 July 2022. Wageningen, The Netherlands: Wageningen Academic Publishers. doi: 10.3920/978-90-8686-940-4_650

Warburton, C.L., Costilla, R.C., Engle, B.N. and Hayes, B.J. (2022). Simultaneous mapping of quantitative trait loci in multiple subspecies using hybrid populations. 12th World Congress on Genetics Applied to Livestock Production (WCGALP), Rotterdam, The Netherlands, 3-8 July 2022. Wageningen, The Netherlands: Wageningen Academic Publishers. doi: 10.3920/978-90-8686-940-4_179

Nguyen, L.T., Cheng, Y., Kuo, R., Hayes, B.J. and Ross, E.M. (2022). Predicted isoforms of a Brahman cow revealed by full-length transcript sequencing. 12th World Congress on Genetics Applied to Livestock Production (WCGALP), Rotterdam, Netherlands, 3 - 8 July 2022. Wageningen, Netherlands: Wageningen Academic Publishers. doi: 10.3920/978-90-8686-940-4_513

Hayes, B.J., Copley, J., Dodd, E., Ross, E.M. and Fordyce, G. (2022). Multi-breed genomic predictions from commercial crossbred data. 12th World Congress on Genetics Applied to Livestock Production (WCGALP), Rotterdam, Netherlands, 3-8 July 2022. Wageningen, Netherlands: Wageningen Academic Publishers. doi: 10.3920/978-90-8686-940-4_178

Forutan, M., Engle, B., Goddard, M. E. and Hayes, B. J. (2022). A conditional multi‑trait sequence GWAS of heifer fertility in tropically adapted beef cattle. World Congress on Genetics Applied to Livestock Production, Rotterdam, The Netherlands, 3 July-8 July 2022.

Engle, B.N., Collins Snr, A. and Hayes, B.J. (2021). Genomic prediction of lifetime productivity in Brahman cows. 24th Association for the Advancement of Animal Breeding and Genetics Conference, Online, 2-4 November 2021. Armidale, NSW, Australia: Association for the Advancement of Animal Breeding and Genetics.

Copley, J.P., Engle, B.N., Speight, S., Fordyce, G., Ross, E.M., Voss-Fels, K.P. and Hayes, B.J. (2021). Assessing the relationship between beef cattle fertility traits and novel environmental descriptors in northern Australia. 24th Association for the Advancement of Animal Breeding and Genetics Conference, Online, 2-4 November 2021. Armidale, NSW Australia: Association for the Advancement of Animal Breeding and Genetics.

Forutan, M., Vander Jagt, C.J., Ross, E., Chamberlain, A. J., Mason, B., Nguyen, L., Moore, S., Garner, J. B., Xiang, R. and Hayes, B. J. (2021). Genome wide analysis of bovine enhancers and promoters across developmental stages in liver. 24th Association for the Advancement of Animal Breeding and Genetics Conference, On-line with local hubs in Australia, 2-4 November 2021. Armidale, NSW Australia: Association for the Advancement of Animal Breeding and Genetics.

Lamb, H. J. , Nguyen, L. T., Engle, B. N., Hayes, B. J. and Ross, E. M. (2021). Accuracy of genomic prediction in Brahman cattle using simulated genotypes from low-coverage nanopore sequencing. 24th Association for the Advancement of Animal Breeding and Genetics Conference, On-line with local hubs in Australia, 2-4 November 2021. Armidale, NSW Australia: Association for the Advancement of Animal Breeding and Genetics.

Ross, E. M., Lamb, H. J., Engle, B. N. , Nguyen, L. T. and Hayes, B. J. (2021). Assessing the potential of parentage testing using portable long read sequencing technologies. 24th Association for the Advancement of Animal Breeding and Genetics Conference, On-line with local hubs in Australia, 2-4 November 2021. Armidale, NSW Australia: Association for the Advancement of Animal Breeding and Genetics.

Porto-Neto, L. R., Bertram, J., McWilliam, S., Fortes, M. R. S., Alexandre, P., McGowan, M. R., Hayes, B. J. and Reverter, A. (2021). Multibreed genomic prediction for male fertility in tropical beef cattle. Association for the Advancement of Animal Breeding and Genetics, Adelaide, SA, Australia, 2-4 November 2021. Armidale, NSW, Australia: Association for the Advancement of Animal Breeding and Genetics.

Wockner, K. B., Tahir, M. S., Kour, J., Tan, W. L. A., Olasege, B. S., Porto-Neto, L. R., Little, B. A., Wilson, C. R., Dollemore, W., Reverter, A., Hayes, B. and Fortes, M. R. S. (2021). PHENOBANK: A platform to facilitate collaboration and genomic selection for female fertility in beef cattle. Association for the Advancement of Animal Breeding and Genetics, Adelaide, SA, Australia, 2 - 4 November 2021. Armidale, NSW, Australia: Association for the Advancement of Animal Breeding and Genetics.

Forutan, Mehrnush, Ross, Elizabeth, Nguyen, Loan and Hayes, Ben (2021). Genome-wide analysis of transcription start sites across Bos indicus tissues. 38th International Conference on Animal Genetics, Online, 26 - 30 July 2021.

Nguyen, Loan T., Forutan, Mehrnush, Hayes, Ben J. and Ross, Elizabeth M. (2021). A Bos indicus epigenetic clock predicts age from tail hair. 38th International Society of Animal Genetics (ISAG), Virtual, 26 - 30 July 2021.

Lamb, Harrison, Nguyen, Loan T., Hayes, Ben J., Randhawa, Imtiaz A. S. and Ross, Elizabeth M. (2021). Genomic prediction using low-coverage Nanopore sequencing. 38th International Society of Animal Genetics, Virtual, 26 - 30 July 2021.

Randhawa, Imtiaz A. S., Lyons, Russell E., Hayes, Ben J. and McGowan, Michael R. (2021). The genetic complexity of scurs development in cattle. 38th International Society of Animal Genetics (ISAG), Virtual, 26-30 July 2021.

Copley, J., Engle, B., Ross, E., Landmark, S., Fordyce, G., Burns, B. and Hayes, B. (2021). Factors affecting fertility in northern Australian beef herds. 33rd Biennial Conference of the Australian Association of Animal Sciences, Fremantle, WA, Australia and online, 1-3 February 2020. Toowong, QLD, Australia: Australian Association of Animal Sciences.

Mantilla Valdivieso, E., Ross, E., Raza, A., Hayes, B., Jonsson, N., James, P. and Tabor, A. (2021). Effect of bovine reference genome choice in RNA-SEQ alignment and differential gene expression analysis in Brangus cattle. 24th Association for the Advancement of Animal Breeding and Genetics Conference, On-line with local hubs in Australia, 2-4 November 2021. Armidale, NSW, Australia: Association for the Advancement of Animal Breeding and Genetics.

Mantilla Valdivieso, E., Ross, E., Hayes, B., Jonsson, N., James, P. and Tabor, A. (2021). Investigating host biomarkers associated with cattle tick resistance. 33rd Biennial Conference of the Australian Association of Animal Sciences, Fremantle, WA, Australia and online, 1-3 February 2020. Toowong, QLD, Australia: Australian Association of Animal Sciences.

Voss-Fels, Kai, Powell, Owen, Jordan, David, Hammer, Graeme, Barbier, Francois, Werner, Christian, Hayes, Ben, Beveridge, Christine and Cooper, Mark (2020). The impact of physiological non-additivity on variance components for complex traits. The 6th International Conference on Quantitative Genetics, Brisbane, QLD Australia, 3-13 November 2020.

Amin, Asad, Christopher, Jack, Ababaei, Behnam, Cooper, Mark, Hayes, Ben, Voss-Fels, Kai, Hickey, Lee and Chenu, Karine (2019). Environmental characterization facilitate G × E interaction to highlight the role of stay-green traits for genetic gain. Translational Photosynthesis Conference: Innovations in Agriculture for Food Security (ASPS 2019), Brisbane, QLD, Australia, 30 June - 3 July 2019.

Randhawa, Imtiaz A. S. , Porto-Neto, Laercio R. , McGowan, Michael R. , Hayes, Ben J. , Schutt, Karen M. and Lyons, Russell E. (2019). Production and polledness: genetic correlations between target traits in beef cattle. AAABG2019, Armidale, Australia, 27 October - 1 November 2019.

Randhawa, I.A.S., McGowan, M.R., Porto-Neto, L.R., Hayes, B.J., Schutt, K.M. and Lyons, R.E. (2019). Poll testing efficiency, accuracy and trends in Australian cattle. Association for the Advancement in Animal Breeding Genetics, Armidale, Australia, 27 October - 1 November 2019.

Randhawa, I. A. S., Porto-Neto, L., Hayes, B., McGowan, M., Burns, B. and Lyons, R. (2019). Improving poll gene testing in Australian cattle. RSPCA Australian Animal Welfare Seminar, Canberra, ACT Australia, 22 February 2019.

Randhawa, I. A. S, Hayes, B. J., McGowan, M. R., Porto-Neto, L. R. and Lyons, R. E. (2019). DNA testing and genetic evaluation for poll breeding in tropically adapted beef cattle. International Tropical Agriculture Conference (TROPAG2019), Brisbane, QLD Australia, 11-13 November 2019. Basel, Switzerland: MDPI. doi: 10.3390/proceedings2019036098

Randhawa, I. A. S, Hayes, B. J., Porto-Neto, L. R., Schutt, K. M., McGowan, M. R., Burns, B. M. and Lyons, R. E. (2019). New diagnostic tools helping poll breeding for sustainable beef production. Northern Beef Research Update Conference (NBRUC2019), Brisbane, QLD Australia, 19-22 August 2019.

Randhawa, I. A. S., McGowan, M. R., Porto-Neto, L. R., Hayes, B. J. and Lyons, R. E. (2019). Poll diagnostics, scur genetics and production concurrence in naturally hornless cattle. 37th International Society for Animal Genetics (ISAG) Conference, Lleida, Spain, 7-12 July 2019.

Bang, N.N., Hayes, B.J., Randhawa, I.A.S., Lyons, R.E., Gaughan, J.B., Chanh, N.V., Trach, N.X., Khang, N.D. and McNeill, D.M. (2019). Application of genomic selection to Vietnamese household dairy herds. 23rd AABG Conference, Armidale, Australia, 27 October - 1 November 2019.

O’Connor, K.M., Hardner, C.M., Alam, M.M., Hayes, B.J. and Topp, B.L. (2018). Variation in floral and growth traits in a macadamia breeding population. International Symposia on Tropical and Temperate Horticulture (ISTTH), Cairns, QLD, Australia, 20-25 November, 2016. Leuven, Belgium: International Society for Horticultural Science (ISHS). doi: 10.17660/actahortic.2018.1205.77

Goddard, M.E., MacLeod, I.M., Kemper, K.E., Xiang, R., van den Berg, I., Khansefid, M., Daetwyler, H.D. and Hayes, B.J. (2018). The use of multi-breed reference populations and multi-omic data to maximize accuracy of genomic prediction. 11th World Congress of Genetics Applied to Livestock Production, Auckland, New Zealand, 11-16 February 2018. Auckland, New Zealand: WCGALP.

Engle, B., Corbet, N., Allen, J., Laing, A., Fordyce, G., McGowan, M., Burns, B. and Hayes, B. (2018). Accuracy of multi-trait genomic predictions for age at puberty in Northern Australian beef heifers. 2018 ASAS-CSAS Annual Meeting and Trade Show, Vancouver, Canada, 8-12 July 2018. Cary, NC, United States: Oxford University Press (OUP). doi: 10.1093/jas/sky404.231

O'Connor, Katie, Hayes, Ben, Hardner, Craig, Mobashwer Alam and Topp, Bruce (2017). Indirect prediction of macadamia yield through a genome wide association study of component traits. International Macadamia Research Symposium, Hawaii, United States, 13-14 September 2017.

Slater, A. T., Cogan, N. O.I., Rodoni, B. C., Hayes, B. J. and Forster, J. W. (2016). Improving the selection efficiency in potato breeding. 29th International Horticultural Congress on Horticulture - Sustaining Lives, Livelihoods and Landscapes (IHC) / International Symposium on Plant Breeding in Horticulture, Brisbane, QLD, Australia, 17-22 August 2014. LEUVEN 1: International Society for Horticultural Science. doi: 10.17660/ActaHortic.2016.1127.37

Wang, Tingting, Yi-Ping, Phoebe Chen, Kemper, Kathryn E., Godard, Michael E. and Hayes, Ben J. (2015). Optbr: computationally efficient genomic predictions and QTL mapping in multi-bred populations. Association for the Advancement of Animal Breeding and Genetics, Lorne, VIC, Australia, 28-30 September 2015. Lorne, VIC, Australia: Association for the Advancement of Animal Breeding and Genetics.

Lin, Z., Hayes, B. J. and Daetwyler, H. D. (2014). Genomic selection in crops, trees and forages: a review. Clayton, VIC, Australia: C S I R O Publishing. doi: 10.1071/CP13363

Forster, J. W., Hand, M. L., Cogan, N. O. I., Hayes, B. J., Spangenberg, German C. and Smith, K. F. (2014). Resources and strategies for implementation of genomic selection in breeding of forage species. Clayton, VIC, Australia: C S I R O Publishing. doi: 10.1071/CP13361

Kemper, K. E., Vander Jagt, C. J., Bowman, P. J., Reich, C. M., Mason, B. A., Hayes, B. J. and Goddard, M. E. (2014). Mapping QTL in Australian dairy cattle using genomic selection methodologies. World Congress of Geneics Applied to Livestock Production, Vancouver, BC, Canada, 17-22 August 2014. Vancouver, BC, Canada: World Congress on Genetics Applied to Livestock Production.

Swan, A. A, Brown, D. J., Daetwyler, H. D., Hayes, B. J., Kelly, M., Moghaddar, N. and van der Werf, J. H. J. (2014). Genomic evaluations in the Australian sheep industry. 10th World Congress of Genetics Applied to Livestock Production, Vancouver Canada, 2014.

Spelman, Richard J., Hayes, Ben J. and Berry, Donagh P. (2013). Use of molecular technologies for the advancement of animal breeding: genomic selection in dairy cattle populations in Australia, Ireland and New Zealand. Clayton, VIC, Australia: C S I R O Publishing. doi: 10.1071/AN12304

Bath, C., Morrison, M., Ross, E. M., Hayes, B. J. and Cocks, B. G. (2013). The symbiotic rumen microbiome and cattle performance: a brief review. Clayton, VIC, Australia: CSIRO Publishing. doi: 10.1071/AN12369

Kemper, K. E., Hayes, B. J. and Goddard, M. E. (2013). Genomic regions associated with differences in fat percentage in milk between Holstein and Jersery cattle. Association for the Advancement of Animal Breeding and Genetics, Napier, New Zealand, 20-23 October 2013. Red Hook, NY, United States: Curran Associates.

Daetwyler, H. D., Kemper, K. E., van der Werf, J. H. J. and Hayes, B. J. (2011). The importance of population structure on the accuracy of genomic prediction in a multi-breed sheep population. Association for the Advancement of Animal Breeding and Genetics, Perth, Australia, 19-21 July 2011. Perth, Australia: Association for the Advancement of Animal Breeding and Genetics.

Hayes, Ben and Goddard, Mike (2010). Genome-wide association and genomic selection in animal breeding. International Conference on Exploiting Genome-Wide Association in Oilseed Brassicas - A Model for Genetic Improvement of Major OECD Crops for Sustainable Future Farming, Perth Australia, Nov 09-12, 2009. doi: 10.1139/G10-076

Hayes, Ben J., Nilsen, Kjetil, Berg, Paul R., Grindflek, Eli and Lien, Sigbjorn (2007). SNP detection exploiting multiple sources of redundancy in large EST collections improves validation rates. doi: 10.1093/bioinformatics/btm154

Kelly, M.J., Hayes, B.J. and Miller, S.P. (2007). Design of a whole genome scan experiment for a multi-breed beef cattle population with a complex pedigree. 17th Conference: Genetic Improvement - Making it Happen, Armidale, N.S.W., 23-26 September 2007. Armidale NSW: Association for the Advancement of Animal Breeding Genetics.

Yadav, Seema, Ross, Elizabeth, Wei, Xianming, Powell, Owen, Hivert, Valentin, Hickey, Lee T., Atkin, Felicity, Deomano, Emily, Aitken, Karen S., Voss-Fels, Kai P. and Hayes, Ben J. (2022). Genomic mate-allocation strategies exploiting additive and non-additive genetic effects to maximise total clonal performance in sugarcane.

Smyth, Heather Eunice, Godwin, Ian and Hayes, Ben (2020). Innovation through Partnership with QAAFI. Innovation Showcase. Queensland Government, Department of Agriculture and Fisheries.

O'Connor, Katie, Hayes, Ben, Hardner, Craig, Alam, Mobashwer and Topp, Bruce (2019). SNP and phenotype data, and GWAS results for macadamia breeding progeny population. The University of Queensland. (Dataset) doi: 10.14264/uql.2019.808

Professor Ben Hayes

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