Publications
Journal Articles
Visscher, Peter M. and Goddard, Michael E. (2019). From R.A. Fisher’s 1918 paper to GWAS a century later. Genetics, 211 (4) 1125-1130. doi:10.1534/genetics.118.301594
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
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, 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, doi:10.1186/s12864-018-4800-0
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, 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
Bouwman, Aniek C., Daetwyler, Hans D., Chamberlain, Amanda J., Ponce, Carla Hurtado, Sargolzaei, Mehdi, Schenkel, Flavio S., Sahana, Goutam, Govignon-Gion, Armelle, Boitard, Simon, Dolezal, Marlies, Pausch, Hubert, Brøndum, Rasmus F., Bowman, Phil J., Thomsen, Bo, Guldbrandtsen, Bernt, Lund, Mogens S., Servin, Bertrand, Garrick, Dorian J., Reecy, James, Vilkki, Johanna, Bagnato, Alessandro, Wang, Min, Hoff, Jesse L., Schnabel, Robert D., Taylor, Jeremy F., Vinkhuyzen, Anna A. E., Panitz, Frank, Bendixen, Christian, Holm, Lars-Erik, Gredler, Birgit and Hozé, Chris (2018). Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals. Nature Genetics, 50 (3) 362-367. doi:10.1038/s41588-018-0056-5
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, doi:10.1186/s12864-017-4030-x
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, doi:10.1186/s12864-016-3082-7
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
Gratten, Jacob, Wray, Naomi R., Peyrot, Wouter J., McGrath, John J., Visscher, Peter M. and Goddard, Michael E. (2016). Risk of psychiatric illness from advanced paternal age is not predominantly from de novo mutations. Nature Genetics, 48 (7) 718-+. doi:10.1038/ng.3577
Zhu, Zhihong, Zhang, Futao, Hu, Han, Bakshi, Andrew, Robinson, Matthew R., Powell, Joseph E., Montgomery,Grant W., Goddard, Michael E., Wray, Naomi R., Visscher, Peter M. and Yang, Jian (2016). Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets. Nature Genetics, 48 (5) 481-487. doi:10.1038/ng.3538
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
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
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
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
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
Robinson, Matthew R., Hemani, Gibran, Medina-Gomez, Carolina, Mezzavilla, Massimo, Esko, Tonu, Shakhbazov, Konstantin, Powell, Joseph E., Vinkhuyzen, Anna, Berndt, Sonja I., Gustafsson, Stefan, Justice, Anne E., Kahali, Bratati, Locke, Adam E., Pers, Tune H., Vedantam, Sailaja, Wood, Andrew R., van Rheenen, Wouter, Andreassen, Ole A., Gasparini, Paolo, Metspalu, Andres, van den Berg, Leonard H., Veldink, Jan H., Rivadeneira, Fernando, Werge, Thomas M., Abecasis, Goncalo R., Boomsma, Dorret I., Chasman, Daniel I., de Geus, Eco J. C., Frayling, Timothy M., Hirschhorn, Joel N. and Hottenga, Jouke Jan (2015). Population genetic differentiation of height and body mass index across Europe. Nature Genetics, 47 (11) 1357-1361. doi:10.1038/ng.3401
Hayeck, Tristan J., Zaitlen, Noah A., Loh, Po-Ru, Vilhjalmsson, Bjarni, Pollack, Samuela, Gusev, Alexander, Yang, Jian, Chen, Guo-Bo, Goddard, Michael E., Visscher, Peter M., Patterson, Nick and Price, Alkes L. (2015). Mixed model with correction for case-control ascertainment increases association power. American Journal of Human Genetics, 96 (5) 720-730. doi:10.1016/j.ajhg.2015.03.004
O'Dushlaine, Colm, Rossin, Lizzy, Lee, Phil H., Duncan, Laramie, Parikshak, Neelroop N., Newhouse, Stephen, Ripke, Stephan, Neale, Benjamin M., Purcell, Shaun M., Posthuma, Danielle, Nurnberger, John I., Lee, S. Hong, Faraone, Stephen V., Perlis, Roy H., Mowry, Bryan J, Thapar, Anita, Goddard, Michael E., Witte, John S., Absher, Devin, Agartz, Ingrid, Akil, Huda, Amin, Farooq, Andreassen, Ole A., Anjorin, Adebayo, Anney, Richard, Anttila, Verneri, Arking, Dan E., Asherson, Philip, Azevedo, Maria H., Backlund, Lena and Badner, Judith A. (2015). Psychiatric genome-wide association study analyses implicate neuronal, immune and histone pathways. Nature Neuroscience, 18 (2) 199-209. doi:10.1038/nn.3922
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
Wood, Andrew R., Esko, Tonu, Yang, Jian, Vedantam, Sailaja, Pers, Tune H., Gustafsson, Stefan, Chu, Audrey Y., Estrada, Karol, Luan, Jian'an, Kutalik, Zoltan, Amin, Najaf, Buchkovich, Martin L., Croteau-Chonka, Damien C., Day, Felix R., Duan, Yanan, Fall, Tove, Fehrmann, Rudolf, Ferreira, Teresa, Jackson, Anne U., Karjalainen, Juha, Lo, Ken Sin, Locke, Adam E., Magi, Reedik, Mihailov, Evelin, Porcu, Evelin, Randall, Joshua C., Scherag, Andre, Vinkhuyzen, Anne A. E., Westra, Harm-Jan, Winkler, Thomas W. and Workalemahu, Tsegaselassie (2014). Defining the role of common variation in the genomic and biological architecture of adult human height. Nature Genetics, 46 (11) 1173-1186. doi:10.1038/ng.3097
Daetwyler, Hans D., Capitan, Aurelien, Pausch, Hubert, Stothard, Paul, Van Binsbergen, Rianne, Brondum, Rasmus F., Liao, Xiaoping, Djari, Anis, Rodriguez, Sabrina C., Grohs, Cecile, Esquerre, Diane, Bouchez, Olivier, Rossignol, Marie-Noelle, Klopp, Christophe, Rocha, Dominique, Fritz, Sebastien, Eggen, Andre, Bowman, Phil J., Coote, David, Chamberlain, Amanda J., Anderson, Charlotte, VanTassell, Curt P., Hulsegge, Ina, Goddard, Mike E., Guldbrandtsen, Bernt, Lund, Mogens S., Veerkamp, Roel F., Boichard, Didier A., Fries, Ruedi and Hayes, Ben J. (2014). Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle. Nature Genetics, 46 (8) 858-865. doi:10.1038/ng.3034
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, doi:10.1371/journal.pgen.1004198
Lee, S. Hong, Ripke, Stephan, Neale, Benjamin M., Faraone, Stephen V., Purcell, Shaun M., Perlis, Roy H., Mowry, Bryan J., Thapar, Anita, Goddard, Michael E., Witte, John S., Absher, Devin, Agartz, Ingrid, Akil, Huda, Amin, Farooq, Andreassen, Ole A., Anjorin, Adebayo, Anney, Richard, Anttila, Verneri, Arking, Dan E., Asherson, Philip, Azevedo, Maria H., Backlund, Lena, Badner, Judith A., Bailey, Anthony J., Banaschewski, Tobias, Barchas, Jack D., Barnes, Michael R., Barrett, Thomas B., Bass, Nicholas, Battaglia, Agatino and Bauer, Michael (2013). Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs. Nature Genetics, 45 (9) 984-995. doi:10.1038/ng.2711
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
White, Jason D., Allingham, Peter G., Gorman, Chris M., Emery, David L., Hynd, Philip, Owens, John, Bell, Amy, Siddell, Jason, Harper, Greg, Hayes, Ben J., Daetwyler, Hans D., Usmar, Jonathan, Goddard, Mike E., Henshall, John M., Dominik, Sonja, Brewer, Heather, van der Werf, Julius H. J., Nicholas, Frank W., Warner, Robyn, Hofmyer, Chris, Longhurst, Terry, Fisher, Troy, Swan, Paul, Forage, Rob and Oddy, V. Hutton (2012). Design and phenotyping procedures for recording wool, skin, parasite resistance, growth, carcass yield and quality traits of the SheepGENOMICS mapping flock. Animal Production Science, 52 (2-3) 157-171. doi:10.1071/AN11085
Deary, Ian J., Yang, Jian, Davies, Gail, Harris, Sarah E., Tenesa, Albert, Liewald, David, Luciano, Michelle, Lopez, Lorna M., Gow, Alan J., Corley, Janie, Redmond, Paul, Fox, Helen C., Rowe, Suzanne J., Haggarty, Paul, McNeill, Gerald, Goddard, Michael E., Porteous, David J., Whalley, Lawrence J., Starr, John M. and Visscher, Peter M. (2012). Genetic contributions to stability and change in intelligence from childhood to old age. Nature, 482 (7384) 212-215. doi:10.1038/nature10781
Heid, Iris M., Jackson, Anne U., Randall, Joshua C., Winkler, Thomas W., Qi, Lu, Steinthorsdottir, Valgerdur, Thorleifsson, Gudmar, Zillikens, M. Carola, Speliotes, Elizabeth K., Maegi, Reedik, Workalemahu, Tsegaselassie, White, Charles C., Bouatia-Naji, Nabila, Harris, Tamara B., Berndt, Sonja I., Ingelsson, Erik, Willer, Cristen J., Weedon, Michael N., Luan, Jian'an, Vedantam, Sailaja, Esko, Tonu, Kilpelaeinen, Tuomas O., Kutalik, Zoltan, Li, Shengxu, Monda, Keri L., Dixon, Anna L., Holmes, Christopher C., Kaplan, Lee M., Liang, Liming, Min, Josine L. and Moffatt, Miriam F. (2011). Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution. Nature Genetics, 43 (11) 1164-1164. doi:10.1038/ng1111-1164a
Elizabeth K Speliotes, Cristen J Willer, Sonja I Berndt, Keri L Monda, Gudmar Thorleifsson, Anne U Jackson, Hana Lango Allen, Cecilia M Lindgren, Jian'an Luan, Reedik Magi, Joshua C Randall, Sailaja Vedantam, Thomas W Winkler, Lu Qi, Tsegaselassie Workalemahu, Iris M Heid, Valgerdur Steinthorsdottir, Heather M Stringham, Michael N Weedon, Eleanor Wheeler, Andrew R Wood, Teresa Ferreira, Robert J Weyant, Ayellet V Segre, Karol Estrada, Liming Liang, James Nemesh, Ju-Hyun Park, Stefan Gustafsson, Tuomas O Kilpelainen and Jian Yang (2010). Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index. Nature Genetics, 42 (11) 937-948. doi:10.1038/ng.686
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, doi:10.1371/journal.pgen.1001139