John B. Cole's Publications

Updated July 23, 2024

Refereed Journal Articles | Book Chapters and Technical Reports | POPULAR PRESS ARTICLES | PROCEEDINGS | SOFTWARE


Refereed Journal Articles

2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 1999 )


Note: Titles link to local copies of articles and DOI link to journal websites

2024

  1. Cai, Wentao, John B. Cole, Iona M. MacLeod, Hans D. Daetwyler, Michael E. Goddard, Shuisheng Hou, Junya Li, Shengli Zhang, and Jiuzhou Song. 2024. Deciphering genetic architecture of milk production traits and genomic predictions using mammary multi-omics data in Holstein dairy cattle. Journal of Advanced Research (Submitted 05/15/2024.)
  2. Cole, J.B. 2024. Are there too many traits in selection indices? Journal of Dairy Science. (In preparation.)
  3. Cole, J.B. 2024. Perspective: Can we actually do anything about inbreeding? Journal of Dairy Science. 107:643–648. https://doi.org/10.3168/jds.2023-23958.
  4. Cole, John B., Christine F. Baes, Sophie A.E. Eaglen, Thomas J. Lawlor, Jr., Christian Maltecca, M. Sofía Ortega, and Paul M. VanRaden. 2024. Invited Review: Management of genetic defects in dairy cattle populations. Journal of Dairy Science (In preparation.)
  5. Fang, Lingzhao, Jinyan Teng, Qing Lin, Zhonghao Bai, Shuli Liu, Dailu Guan, Bingjie Li, Yahui Gao, Yali Hou, Mian Gong, the FarmGTEx Consortium, Emily Clark, Konrad Rawlik, Ruidong Xiang, Amanda J. Chamberlain, Mathew Littlejohn, Greger Larson, David Machugh, John Ogrady, Peter Sørensen, Goutam Sahana, Mogens Sandø Lund, Zhihua Jiang, Jacqueline Smith, Xiangchun Pan, Wentao Gong, Guoqiang Yi, Haihan Zhang, Pengju Zhao, Yang Zhou, Yuwen Liu, Xiao Wang, Xiang Zhou, Wei Li, Robert Young, Xia Shen, Charley Xia, Hao Cheng, Li Ma, John B. Cole, Randy Baldwin, Congjun Li, Joan Lunney, Wansheng Liu, Leluo Guan, Xin Zhao, Eveline Ibeagha-Awemu, Yonglun Luo, Lin Lin, Oriol Canela Xandri, Marta Godia Perello, Ole Madsen, Martien Groenen, James E. Koltes, Christopher K. Tuggle, Fiona M. McCarthy, Dominique Rocha, Marcelo Amills Eras, Alex Clop, Gwenola Tosser, Jing Li, Ming Fang, Qishan Wang, Qin Wang, Fuping Zhao, Lin Jiang, Guiping Zhao, Zhuocheng Hou, Zhengkui Zhou, Hehe Liu, Xi He, Yuebo Zhang, Ning Gao, Jun He, Rong Zhou, Delin Mo, Mingzhou Li, Xiangdong Ding, Dongxiao Sun, Huizeng Sun, Ying Yu, Dongdong Wu, Cong Li, Yu Jiang, Zhangyuan Pan, Qin Zhang, Kui Li, Ning Yang, Xiaoxiang Hu, Michael Schatz, Jingyi Jessica Li, Abraham Palmer, Laurent Frantz, Huaijun Zhou, Zhe Zhang, and George E. Liu. 2024. The Farm Animal Genotype-Tissue Expression (FarmGTEx) Project for advancing agriculture and biomedicine. Nature Genetics (Submitted 05/20/2024.)
  6. Gao, Yahui, Liu Yang, Kristen Kuhn, Wenli Li, Mary Bowman, Lingzhao Fang, John B. Cole, Benjamin D. Rosen, Li Ma, Congjun Li, Ransom L. Baldwin, VI, Curtis P. Van Tassell, Zhe Zhang, Timothy P.L. Smith, and George E. Liu. 2024. Long read and pangenome analyses reveal breed-specific structural variations and novel sequences in Holstein and Jersey cattle. Nature Communications (Submitted 07/12/2024.)
  7. Hoorn, Quinn A., Maria B. Rabaglino, Thiago F. Amaral, Tatiane Silva Maia, Fahong Yu, John B. Cole, and Peter J. Hansen. 2024. Machine learning to identify endometrial biomarkers predictive of pregnancy success following artificial insemination in dairy cows. Biology of Reproduction. 111:54–62. https://doi.org/10.1093/biolre/ioae052.
  8. Lozada-Soto, Emmanuel, Christian Maltecca, Jicai Jiang, John Cole, Paul VanRaden, and Francesco Tiezzi. 2024. Effect of germplasm exchange strategies on genetic gain, homozygosity, and genetic diversity in dairy stud populations: A simulation study. Journal of Dairy Science. (Submitted 04/01/2024.)
  9. Miles, Asha M., Kristen L. Parker Gaddis, John B. Cole, and Robert H. Fourdraine. 2024. Symposium Review: The value of a national evaluation system in promoting dairy sustainability. Journal of Dairy Science (In preparation.)
  10. Wu, Xiao-Lin, Paul M. VanRaden, John B. Cole, and H. Duane Norman. 2024. Variance reduction and measurement errors in estimating lactation milk yields using Best Prediction: An analytical review. JDS Communications (Submitted 06/20/2024.)

2023

  1. Brink, Amber A., Wanda J. Weber, John D. Lippolis, John B. Cole, A.K. Rendahl, Luciano Caixeta, Sandra M. Godden, Anthony Seykora, and Brian A. Crooker. 2023. Short communication: Effect of Holstein genotype on ex-vivo innate immune response to lipopolysaccharide (LPS), lipoteichoic acid (LTA), and killed Gram-negative and Gram-positive bacteria. Veterinary Immunology and Immunopathology. 258:110573. https://doi.org/10.1016/j.vetimm.2023.110573.
  2. Cole, John B., Bayode O. Makanjuola, Christina M. Rochus, Nienke van Staaveren, and Christine Baes. 2023. The effects of breeding and selection on lactation in dairy cattle. Animal Frontiers. 13:55–63. https://doi.org/10.1093/af/vfad044.
  3. Guinan, Fiona Louise, George Wiggans, Duane Norman, João Dürr, John Cole, Curtis Van Tassell, Ignacy Misztal, and Daniela Lourenco. 2023. Changes in genetic trends in US dairy cattle since the implementation of genomic selection. Journal of Dairy Science. 106:1110-1129. https://doi.org/10.3168/jds.2022-22205.
  4. Neupane, M., J.L. Hutchison, J.B. Cole, C.P. Van Tassell, and P.M. VanRaden. 2023. Genomic evaluation of late term abortion recorded through Dairy Herd Improvement test plans. JDS Communications. (In press.) https://doi.org/10.3168/jdsc.2022-0341.
  5. Schmidt, Patrícia Iana, Lucio Flavio Macedo Mota, Larissa Fernanda Simielli Fonseca, Danielly Beraldo dos Santos Silva, Gabriela Bonfá Frezzarim, Leonardo Machestropa Arikawa, Daniel Jordan de Abreu Santos, Ana Fabrícia Braga Magalhães, John Bruce Cole, Roberto Carvalheiro, Henrique Nunes de Oliveira, Daniel Joshua Null, Paul VanRaden, Li Ma, and Lucia Galvão de Albuquerque. 2023. Identification of candidate lethal haplotypes and genomic association with post-natal mortality and reproductive traits in Nellore cattle. Scientific Reports. 13:10399. https://doi.org/10.1038/s41598-023-37586-z.

2022

  1. Al-Khudhair, A.S., D.J. Null, J.B. Cole, C.W. Wolfe, D.J. Steffen, and P.M. VanRaden. 2022. Inheritance of a mutation causing neuropathy with splayed forelimbs in Jersey cattle. Journal of Dairy Science. 105:1338–1345. https://doi.org/10.3168/jds.2021-20600.
  2. Brink, Amber A., Wanda J. Weber, John D. Lippolis, John B. Cole, Sandra M. Godden, Anthony Seykora, and Brian A. Crooker. 2022. Effect of Holstein genotype on ex-vivo cytokine response to lipopolysaccharide (LPS) and lipoteichoic acid (LTA) during the periparturient period. Veterinary Immunology and Immunopathology. 251:110463. https://doi.org/10.1016/j.vetimm.2022.110463.
  3. Gao, Y., S. Liu, R.L. Baldwin, VI, E.E. Connor, J.B. Cole, L. Ma, C.-J. Li, L. Fang, and G.E. Liu. 2022. Functional annotation of regulatory elements in cattle genome reveals the roles of extracellular interaction and dynamic change of chromatin states in rumen development during weaning. Genomics. 114:110296. https://doi.org/10.1016/j.ygeno.2022.110296.
  4. Liu, Shuli, Yahui Gao, Oriol Canela-Xandri, Sheng Wang, Ying Yu, Wentao Cai, Bingjie Li, Ruidong Xiang, Amanda J. Chamberlain, Erola Pairo-Castineira, Kenton D'Mellow, Konrad Rawlik, Charley Xia, Yuelin Yao, Paul Navarro, Dominique Rocha, Xiujin Li, Ze Yan, Congjun Li, Benjamin D. Rosen, Curtis P. Van Tassell, Paul M. VanRaden, Shengli Zhang, Li Ma, John B. Cole, George E. Liu, Albert Tenesa, and Lingzhao Fang. 2022. A multi-tissue atlas of regulatory variants in cattle. Nature Genetics. 54:1438–1447. https://doi.org/10.1038/s41588-022-01153-5.
  5. Lozada-Soto, Emmanuel A., Christian Maltecca, Jicai Jiang, John B. Cole, Paul VanRaden, and Francesco Tiezzi. 2022. Genomic characterization of autozygosity and recent inbreeding trends in all major breeds of US dairy cattle. Journal of Dairy Science. 105:8956-8971. https://doi.org/10.3168/jds.2022-22116. (November 2022 Editor’s Choice Paper for Production: Genetics and Genomics)
  6. Ortega, M. Sofía, Derek M. Bickhart, Kelsey N. Clark, Daniel J. Null, Jana L. Hutchison, Jennifer C. McClure, and John B. Cole. 2022. Truncation of IFT80 causes early embryonic loss in Holstein cattle associated with Holstein haplotype 2. Journal of Dairy Science. 105:9001-9011. https://doi.org/10.3168/jds.2022-21853. (Preprint on bioRxiv: https://doi.org/10.1101/2021.07.02.450952)
  7. Yang, Liu, Yahui Gao, Mingxun Li, Ki-Eun Park, Shuli Liu, Xiaolong Kang, Mei Liu, Adam Oswalt, Bhanu P. Telugu, Charles G. Sattler, Cong-jun Li, John B. Cole, Eyal Seroussi, Lingyang Xu, Lv Yang, Yang Zhou, Li Li, Hongping Zhang, Benjamin D. Rosen, Curtis P. Van Tassell, Li Ma, and George E. Liu. 2022. Genome-wide recombination map construction from single sperm sequencing in cattle. BMC Genomics. 23:181. https://doi.org/10.1186/s12864-022-08415-w.
  8. Yao, Yuelin, Shuli Liu, Charley Xia, Yahui Gao, Zhangyuan Pan, Oriol Canela-Xandri, Ava Khamseh, Sheng Wang, Bingjie Li, Jianbin Li, Gaozhan Cai, Yi Zhang, Erola Pairo-Castineira, Kenton D'Mellow, Konrad Rawlik, Xiujin Li, Ze Yan, Congjun Li, Ying Yu, Shengli Zhang, Li Ma, Paul M. Vanraden, John B. Cole, Pablo J. Ross, Huaijun Zhou, Chris Haley, George E. Liu, Lingzhao Fang, and Albert Tenesa. 2022. Comparative transcriptome in large-scale human and cattle populations. Genome Biology. 23:176. https://doi.org/10.1186/s13059-022-02745-4.

2021

  1. Bakshy, K., D. Heimeier, J.C. Schwartz, E.J. Glass, S. Wilkinson, R.A. Skuce, A.R. Allen, J. Young, J.C. McClure, J.B. Cole, D.J. Null, J.A. Hammond, T.P.L. Smith, and D.M. Bickhart. 2021. Development of polymorphic markers in the immune gene complex loci of cattle. Journal of Dairy Science. 104:6897-6908. https://doi.org/10.3168/jds.2020-19809.
  2. Cole, J.B., J.W. Dürr, and E.L. Nicolazzi. 2021. Invited Review: The future of selection decisions and breeding programs: What are we breeding for, and who decides? Journal of Dairy Science. 104:5111-5124. https://doi.org/10.3168/jds.2020-19777.
  3. Cole, J.B., and P.J. Hansen. 2021. Dairy cattle fertility after 12 years of genomic selection: Lessons learned, current applications, and future development. Proceedings of the Dairy Cattle Reproduction Council Annual Meeting (Submitted 09/10/2020.) Authors' submitted draft (unedited and not typeset).
  4. Gao, Y., L. Fang, R.L. Baldwin, E.E. Connor, J.B. Cole, L. Ma, C.J. Li, and G.E. Liu. 2021. Single-cell transcriptomic analyses of cattle ruminal epithelial cells during weaning. Genomics. https://doi.org/10.1016/j.ygeno.2021.04.039.
  5. Houlahan, Kerry, Flavio S. Schenkel, Dagnachew Hailemariam, Jan Lassen, Morten Kargo, John B. Cole, Erin E. Connor, Silvia Wegmann, Gerson A. Oliveira, Filippo Miglior, Allison Fleming, Tatiane C.S. Chud, Christine F. Baes. 2021. Effects of incorporating dry matter intake and residual feed intake into a selection index for dairy cattle using deterministic modeling. MDPI Animals. 11:1157. https://www.mdpi.com/2076-2615/11/4/1157.
  6. Li, B., P.M. VanRaden, D.J. Null, J.R. O’Connell, and J.B. Cole. 2021. Major quantitative trait loci influencing milk production and conformation traits in Guernsey dairy cattle detected on BTA19. Journal of Dairy Science. 104:550-560. https://doi.org/10.3168/jds.2020-18766.
  7. Lozada-Soto, E.A., C. Maltecca, D. Lu, S. Miller, J.B. Cole, and F. Tiezzi. 2021. Trends in genetic diversity and the effect of inbreeding in American Angus cattle under genomic selection. Genetics, Selection, Evolution. 53:50. https://doi.org/10.1186/s12711-021-00644-z.
  8. Mueller, M.L., J.B. Cole, N.K. Connors, D.J. Johnston, I.A.S. Randhawa, and A.L. Van Eenennaam. 2021. Comparison of gene editing versus conventional breeding to introgress the POLLED allele into the tropically adapted Australian beef cattle population. Frontiers in Genetics. https://doi.org/10.3389/fgene.2021.593154.
  9. Shen, Botong, Ellen Freebern, Jicai Jiang, Christian Maltecca, John B. Cole, George E. Liu and Li Ma. 2021. Effect of temperature and maternal age on recombination rate in cattle. Front. Genetics. 12:682718. https://doi.org/10.3389/fgene.2021.682718.
  10. Wu, Xiao-Lin, Kristen L. Parker Gaddis, Javier Burchard, H. Duane Norman, Ezequiel Nicolazzi, Erin E. Connor, John B. Cole, and João Dürr. 2021. An alternative Interpretation of residual feed intake by phenotypic recursive relationships in dairy cattle. JDS Communications. https://doi.org/10.3168/jdsc.2021-0080.

2020

  1. Cole, J.B., S.A.E. Eaglen, C. Maltecca, H.A. Mulder, and J.E. Pryce. 2020. The future of phenomics in dairy cattle breeding. Animal Frontiers 10:37–44. https://doi.org/10.1093/af/vfaa007.
  2. Fang, L., W. Cai, S. Liu, J. Jiang, B. Li, S.G. Schroder, B.D. Rosen, C. Li, T.S. Sonstegard, L.J. Alexander, C.P. Van Tassell, P.M. Vanraden, J.B. Cole, Y. Yu, S. Zhang, L. Ma, and G.E. Liu. 2020. Comprehensive analyses of 723 transcriptomes enhance GWAS biological interpretation and genomic prediction for complex traits in cattle. Genome Research 30:790-801. doi:10.1101/gr.250704.119.
  3. Freebern, E., D.J.A. Santos, L. Fang, J. Jiang, K.L. Parker Gaddis, C. Maltecca, J.B. Cole, and L. Ma. 2020. GWAS and fine-mapping of livability and six health traits in Holstein cattle. BMC Genomics. 21:4. https://doi.org/10.1186/s12864-020-6461-z. Preprint on bioRxiv: https://doi.org/10.1101/775098.
  4. Li, B., P.M. VanRaden, E. Gunal, D.J. Null, E.E. Connor, M.J. VandeHaar, R.J. Tempelman, K.A. Weigel, and J.B. Cole. 2019. Genomic prediction of residual feed intake in US Holstein dairy cattle. Journal of Dairy Science. 103:2477-2486. https://doi.org/10.3168/jds.2019-17332.
  5. Liu, S., Y. Yu, S. Zhang, J.B. Cole, A. Tenesa, T. Wang, T.G. McDaneld, L. Ma, G.E. Liu, and L. Fang. 2020. Epigenomics and genotype-phenotype association analyses reveal conserved genetic architecture of complex traits in cattle and human. BMC Biology. 18:80. https://doi.org/10.1186/s12915-020-00792-6.
  6. Maltecca, C., F. Tiezzi, J. Cole, and C. Baes. 2020. Symposium review: Exploiting homozygosity in the era of genomics—ROH, inbreeding and genomic mating programs. Journal of Dairy Science. 103:5302-5313. https://doi.org/10.3168/jds.2019-17846.
  7. McWhorter, T.M., J.L. Hutchison, H.D. Norman, J.B. Cole, G.C. Fok, D.A.L. Lourenço, and P.M. VanRaden. 2020. Investigating conception rate for beef service sires bred to dairy cows. Journal of Dairy Science. 103:10374-10382. https://doi.org/10.3168/jds.2020-18399. (November 2020 Editor’s Choice Paper for Production: Genetics and Genomics)
  8. Parker Gaddis, K.L., P.M. VanRaden, J.B. Cole, H.D. Norman, E. Nicolazzi, and J.W. Dürr. 2020. Symposium review: Development, implementation and future perspectives of health evaluations in the U.S. Journal of Dairy Science. 103:5354-5365. https://doi.org/10.3168/jds.2019-17687.
  9. Rosen, B.D., D.M. Bickhart, R.D. Schnabel, S. Koren, C.G. Elsik, E. Tseng, T.N. Rowan, P.M. VanRaden, D.J. Null, W.Y. Low, A. Zimin, C. Couldrey, R. Hall, W. Li, A. Rhie, J. Ghurye, S.D. McKay, F. Thibaud-Nissen, J. Hoffman, W.M. Snelling, W. Warren, T.G. McDaneld, J.A. Hammond, J.C. Schwartz, W. Nandolo, S.G. Schroeder, A.M. Phillippy, J.B. Cole, C.P. Van Tassell, G. Liu, T.P.L. Smith, and J.F. Medrano. 2020. De novo assembly of the cattle reference genome with single-molecule sequencing. GigaScience. 3:giaa021. https://doi.org/10.1093/gigascience/giaa021.
  10. Santos, D.J.A., J.B. Cole, G.E. Liu, P.M. VanRaden, and L. Ma. 2020. gamevar.f90: A software package for calculating individual gametic diversity. BMC Bioinformatics. 21:100. https://doi.org/10.1186/s12859-020-3417-x.
  11. Young, J., J.H. Skarlupka, M. Cox, R.T. Resende, A. Fischer, K.F. Kalscheur, J.C. McClure, J.B. Cole, G. Suen, and D.M. Bickhart. 2020. Validating the use of bovine buccal sampling as a proxy for the rumen microbiota using a time course and random forest classification approach. Applied and Environmental Microbiology. 86:e00861-20. https://doi.org/10.1128/AEM.00861-20. (Preprint on bioRxiv: https://doi.org/10.1101/2020.04.10.036665.)
  12. Zhou, Y., S. Liu, Y. Hu, L. Fang, Y. Gao, H. Xia, S.G. Schroeder, B.D. Rosen, E.E. Connor, C. Li, R.L. Baldwin, J.B. Cole, C.P. Van Tassell, L. Yang, L. Ma, and G.E. Liu. 2020. Comparative whole genome DNA methylation profiling of cattle tissues reveals global and tissue-specific methylation patterns. BMC Biology. 18:85. https://doi.org/10.1186/s12915-020-00793-5.

2019

  1. Bradford, H.L., Y.M. Masuda, J.B. Cole, I. Misztal, and P.M. VanRaden. 2019. Modeling pedigree accuracy and uncertain parentage in single-step genomic evaluations of simulated and US Holstein datasets. J. Dairy Sci. 102:2308–2318. https://doi.org/10.3168/jds.2018-15419.
  2. Cole, J.B. 2019. Promotion of alleles by genome engineering. CAB Reviews: Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources. 14:1-15. doi:10.1079/PAVSNNR201914015. (Author's draft accepted for publication.)
  3. Cole, J.B., and D.J. Null. 2019. Short communication: Phenotypic and genetic effects of the polled haplotype on yield, longevity, and fertility in U.S. Brown Swiss, Holstein, and Jersey cattle. J. Dairy Sci. 102:8247–8250. https://doi.org/10.3168/jds.2019-16530.
  4. Connor, E.E., J.L. Hutchison, C.P. Van Tassell, and J.B. Cole. 2019. Determining the optimal period length and stage of growth or lactation to estimate residual feed intake in dairy cows. J. Dairy Sci. 102:6131–6143. https://doi.org/10.3168/jds.2018-15407.
  5. Fang, L., J. Jiang, B. Li, Y. Zhou, E. Freebern, P. VanRaden, J. Cole, and L. Ma. 2019. Genetic and epigenetic architecture of paternal origin contribute to gestation length in cattle. Comm. Biol. 2(100). https://doi.org/10.1038/s42003-019-0341-6.
  6. Fang, L., Y. Zhou, S. Liu, J. Jiang, D.M. Bickhart, D.J. Null, B. Li, S.G. Schroeder, B.D. Rosen, J.B. Cole, C.P. Van Tassell, L. Ma, and G.E. Liu. 2019. Comparative analyses of sperm DNA methylomes among human, mouse and cattle provide insights into epigenomic evolution and complex traits. Epigenetics. 3:260-276. https://doi.org/10.1080/15592294.2019.1582217.
  7. Fang, L., Y. Zhou, S. Liu, J. Jiang, D.M. Bickhart, D.J. Null, B. Li, S.G. Schroeder, B.D. Rosen, J.B. Cole, C.P. Van Tassell, L. Ma, and G.E. Liu. 2019. Integrating signals from sperm methylome analysis and genome-wide association study for a better understanding of male fertility in cattle. Epigenomes. 3(2):10. https://doi.org/10.3390/epigenomes3020010.
  8. Guarini, A., M. Sargolzaei, L. Brito, V. Kroezen, D. Lourenço, C. Baes, F. Miglior, J.B. Cole, and F. Schenkel. 2019. Estimating the impact of the deleterious recessive haplotypes AH1 and AH2 on reproduction performance of Ayrshire cattle. J. Dairy Sci. 102:5315–5322. https://doi.org/10.3168/jds.2018-15366.
  9. Jiang, J., L. Ma, D. Prakapenka, P.M. VanRaden, J.B. Cole, and Y. Da. 2019. A large-scale genome-wide association study in U.S. Holstein cattle. Front. Genet. 10:412. doi:10.3389/fgene.2019.00412.
  10. Jiang, J., P.M. VanRaden, J.B. Cole, and L. Ma. 2019. Functional annotation and Bayesian fine-mapping reveals candidate genes for important agronomic traits in Holstein bulls. Comm. Biol. 2:212. https://doi.org/10.1038/s42003-019-0454-y.
  11. Koltes, J.E., J.B. Cole, N.V.L. Serão, M. McCue, J. Woodward, H. Zhang, S. McKay, J. Lunney, L. Kramer, M. Schroeder, R. Clemmens, B. Murdoch, C. Rexroad, III, G.J.M. Rosa, R. Mateescu, S. White, M. Worku, and J.M. Reecy. 2019. A vision for development and utilization of high-throughput phenotyping and big data analytics in livestock. Front. Genet. doi:10.3389/fgene.2019.01197.
  12. Li, B., L. Fang, D.J. Null, J.L. Hutchison, E.E. Connor, P.M. VanRaden, M.J. VandeHaar, R.J. Tempelman, K.A. Weigel, and J.B. Cole. 2019. High-density genome-wide association study for residual feed intake in Holstein dairy cattle. J. Dairy Sci. 102:11067–11080. https://doi.org/10.3168/jds.2019-16645. (December 2019 Editor’s Choice Paper for Production: Genetics and Genomics)
  13. Liu, M., L. Fang, S. Liu, M.G. Pan, E. Seroussi, J.B. Cole, L. Ma, H. Chen, and G. Liu. 2019. Array CGH-based detection of CNV regions and their potential association with reproduction and other economic traits in Holsteins. BMC Genomics. 20:181. https://doi.org/10.1186/s12864-019-5552-1.
  14. Liu, S., L. Fang, Y. Zhou, D. Santos, R. Xiang, H.D. Daetwyler, A.J. Chamberlain, J.B. Cole, Y. Yu, L. Ma, S. Zhang, G.E. Liu. 2019. Analyses of inter-individual variations in sperm DNA methylation reveal their regulatory role in gene expression and association with reproduction traits in cattle. BMC Genomics. 20:888. https://doi.org/10.1186/s12864-019-6228-6.
  15. Ma, L., J.B. Cole, Y. Da, and P.M. VanRaden. 2019. Symposium review: Genetics, genome-wide association study, and genetic improvement of dairy fertility traits. J. Dairy Sci. 102:3735-3743. https://doi.org/10.3168/jds.2018-15269.
  16. Ma, L., T.S. Sonstegard, J.B. Cole, C.P. Van Tassell, G.R. Wiggans, B.A. Crooker, C. Tan, D. Prakapenka, G. Liu, and Y. Da. 2019. Genome changes due to artificial selection in U.S. Holstein cattle. BMC Genomics. 20:128. https://doi.org/10.1186/s12864-019-5459-x.
  17. Mueller, M., J. Cole, T. Sonstegard, and A. Van Eenennaam. 2019. Comparison of gene editing vs. conventional breeding to introgress the POLLED allele into the U.S. dairy cattle population. J. Dairy Sci. 102:4215-4226. https://doi.org/10.3168/jds.2018-15892. (May 2019 Editor’s Choice Paper for Production: Genetics and Genomics)
  18. Nani, J.P., L.R. Bacheller, J.B. Cole, and P.M. VanRaden. 2019. Discovering ancestors and connecting relatives in large genomic databases. J. Dairy Sci. 103:1729-1734. https://doi.org/10.3168/jds.2019-17580.
  19. Santos, D.J.A., J.B. Cole, T.J. Lawlor, P.M. VanRaden, H. Tonhati, and L. Ma. 2019. Variance of gametic diversity and its application in selection programs. J. Dairy Sci. 102:5279–5294. https://doi.org/10.3168/jds.2018-15971. (June 2019 Editor’s Choice Paper for Production: Genetics and Genomics)

2018

  1. Heringstad, B., C. Egger-Danner, N. Charfeddine, J. Pryce, K. Stock, J. Kofler, Å.M. Sogstad, M. Holzhauer, A. Fiedler, K.E. Müller, P. Nielsen, G. Thomas, N. Gengler, G. Jong, C. Ødegård, F. Malchiodi, F. Miglior, M. Alsaaod, and J. Cole. 2018. Invited review: Genetics and claw health: Opportunities to enhance claw health by genetic selection. Journal of Dairy Science. 101:4801–4821. doi:https://doi.org/10.3168/jds.2017-13531.
  2. Santos, D.J.A., J.B. Cole, D.J. Null, T.M. Byrem, and L. Ma. 2018. Genetic and nongenetic profiling of milk pregnancy-associated glycoproteins in Holstein cattle. J. Dairy Sci. 101:9987-10000. https://doi.org/10.3168/jds.2018-14682.
  3. Tiezzi, F., M.E. Arceo, J.B. Cole, and C. Maltecca. 2018. Including gene networks to predict calving ease in Holstein, Brown Swiss and Jersey cattle. BMC Genetics. 19:20. https://doi.org/10.1186/s12863-018-0606-y.

2017

  1. Cole, J.B., J.M. Bormann, C.A. Gill, H. Khatib, J.E. Koltes, C. Maltecca, and F. Miglior. 2017. Breeding and Genetics Symposium: Resilience of livestock to changing environments. J. Animal Sci. 95:1777-1779. doi:10.2527/jas.2017.1402.
  2. Cole, J.B., and P.M. VanRaden. 2017. Possibilities in an age of genomics: The future of selection indices. Journal of Dairy Science. 101:3686-3701. doi:https://doi.org/10.3168/jds.2017-13335.
  3. Dikmen, S., G.E. Dahl, J.B. Cole, D.J. Null, and P.J. Hansen. 2017. The Larson Blue coat color phenotype in Holsteins: characteristics and effects on body temperature regulation and production in lactating cows in a hot climate. Journal of Animal Science. 95:1164-1169. doi:10.2527/jas.2016.1148.
  4. Hutchison, J.L., P.M. VanRaden, D.J. Null, J.B. Cole, and D.M. Bickhart. 2017. Genomic evaluation of age at first calving. Journal of Dairy Science. 100:6853–6861. doi:http://dx.doi.org/10.3168/jds.2016-12060.
  5. Jiang, J., B. Shen, J.R. O'Connell, P.M. VanRaden, J.B. Cole, and L. Ma. 2017. Dissection of additive, dominance, and imprinting effects for production and reproduction traits in Holstein cattle. BMC Genomics. 18:425. doi:10.1186/s12864-017-3821-4.
  6. McClure, M.C., T.S. Sonstegard, C.W. Wolfe, D.J. Null, D.M. Bickhart, L. Xu, H.J. Huson, H.D. Blackburn, G.R. Wiggans, G.E. Liu, J.B. Cole, and C.P. Van Tassell. 2017. A rectovaginal constriction defect of Jersey cattle maps to the location of the Early B-Cell 1 Factor (EBF1) gene on chromosome 7. Genetics, Selection, Evolution. (Submitted.)
  7. Oliveira, Jr., G.A., T.C.S. Chud, R.V. Ventura, D.J. Garrick, J.B. Cole, D.P. Munari, J.B.S. Ferraz, E. Mullart, S. DeNise, S. Smith, and M.V.G.B. da Silva. 2017. Genotype imputation in a tropical crossbred dairy cattle population. Journal of Dairy Science. 100:9623–9634.  doi:http://dx.doi.org/10.3168/jds.2017-12732.
  8. Oliveira, Jr., G.A., B.C. Perez, J.B. Cole, M.H.A. Santana, J. Silveira, G. Mazzoni, R.V. Ventura, M.L. Santana, Jr., H.N. Kadarmideen, D.J. Garrick, and J.B.S. Ferraz. 2017. Genomic study and MeSH enrichment analysis of early pregnancy rate and antral follicle numbers in Nelore heifers. Journal of Animal Science. 95:4796-4812. doi:10.2527/jas2017.1752.
  9. Ortega, M.S., A.C. Denicol, J.B. Cole, D.J. Null, J.F. Taylor, R.D. Schnabel, and P.J. Hansen. 2017. Association of single nucleotide polymorphisms in candidate genes previously related to genetic variation in fertility with phenotypic measurements of reproductive function in Holstein cows. Journal of Dairy Science. 100:3725–3734. doi:http://dx.doi.org/10.3168/jds.2016-12260. (May 2017 Editor’s Choice Paper for Production: Breeding, Genetics, and Genomics)
  10. Ortega, M.S., S. Wohlgemuth, P. Tribulo, L.G. Siqueira, D.J. Null, J.B. Cole, M.V.G.B. Da Silva, and P.J. Hansen. 2017. A single nucleotide polymorphism in COQ9 affects mitochondrial and ovarian function, body weight change after calving, and fertility in Holstein cows. Biology of Reproduction. 96:652–663. https://doi.org/10.1093/biolre/iox004.
  11. Parker Gaddis, K.L., S. Dikmen, D.J. Null, J.B. Cole, and P.J. Hansen. 2017. Evidence of a genetic component in traits related to superovulation, in vitro fertilization, and embryo transfer in Holstein cattle. Journal of Dairy Science. 100:2877–2891. doi:http://dx.doi.org/10.3168/jds.2016-11907. (April 2017 Editor’s Choice Paper for Production: Breeding, Genetics, and Genomics)
  12. Porto-Neto, L.R., D.M. Bickhart, A.J. Landaeta-Hernandez, Y.T. Utsunomiya, M. Pagan, E. Jimenez, P.J. Hansen, S. Dikmen, S.G. Schroeder, E.-S. Kim, J. Sun, E. Crespo, N. Amati, J.B. Cole, D.J. Null, J.F. Garcia, A. Reverter, W. Barendse, and T.S. Sonstegard. 2017. Convergent evolution of slick coat in cattle through truncation mutations in the prolactin receptor. Frontiers in Genetics. 9:57. https://doi.org/10.3389/fgene.2018.00057.
  13. Stafuzza, N.B., A. Zerlotini, F.P. Lobo, M.E.B. Yamagishi, T.C.S. Chud, A.R. Caetano, D.P. Munari, D.J. Garrick, M.A. Machado, M.F. Martins, M.R. Carvalho, J.B. Cole, M.V.G.B. da Silva. 2017. Single nucleotide variants and indels identified from whole-genome re-sequencing of Guzerat, Gyr, Girolando and Holstein cattle breeds. PLOS ONE 12(3): e0173954. http://dx.doi.org/10.1371/journal.pone.0173954.
  14. Stafuzza, N.B., A. Zerlotini, M.E.B. Yamagishi, M.E. Buzanskas, T.C.S. Chud, A.R. Caetano, D.P. Munari, D.J. Garrick, M.A. Machado, M.F. Martins, M.R. Carvalho, J.B. Cole, and M.V.G.B. da Silva. 2017. Next generation sequence variants with potential loss of function in influential sires of the Gyr, Girolando, and Guzerat cattle breeds. BMC Genomics. (Submitted.)
  15. Thompson, N.M., N.O. Widmar, M.M. Schutz, J.B. Cole, and C.A. Wolf. 2017. Economic and social considerations of breeding for polled dairy cows versus dehorning. Journal of Dairy Science. 100:4941–4952. doi:http://dx.doi.org/10.3168/jds.2016-12099. (June 2017 Editor’s Choice Paper for Production: Management and Economics)
  16. VanRaden, P.M., M.E. Tooker, J.R. O'Connell, J.B. Cole, and D.M. Bickhart. 2017. Selecting sequence variants to improve genomic predictions for dairy cattle. Genetics, Selection, Evolution. 49:32. doi:10.1186/s12711-017-0307-4.
  17. Wiggans, G.R., J.B. Cole, S.M. Hubbard, and T.S. Sonstegard. 2017. Genomic selection in dairy cattle: the USDA experience. Annual Review of Animal Biosciences. 5:309-327. doi:10.1146/annurev-animal-021815-111422.
  18. Zhou, Y., B. Shen, J. Jiang, A. Padhi, K.-E. Park, A. Oswalt, C.G. Sattler, B.P. Telugu, H. Chen, J.B. Cole, G.E. Liu, and L. Ma. 2017. Construction of PRDM9 allele-specific recombination maps in cattle using large-scale pedigree analysis and genome-wide single sperm genomics. DNA Research. doi:https://doi.org/10.1093/dnares/dsx048.

2016

  1. Bickhart, D.M., J.L. Hutchison, D.J. Null, P.M. VanRaden, and J.B. Cole. 2016. Reducing animal sequencing redundancy by preferentially selecting animals with low-frequency haplotypes. Journal of Dairy Science. 99:5526-5534. doi:10.3168/jds.2015-10347.
  2. Bickhart, D.M., L. Xu, J.L. Hutchison, J.B. Cole, D.J. Null, S.G. Schroeder, J. Song, J.F. Garcia, T.S. Sonstegard, C.P. Van Tassell, R.D. Schnabel, J.F. Taylor, H.A. Lewin, and G.E. Liu. 2016. Diversity and population-genetic properties of copy number variations and multicopy genes in cattle. DNA Research. doi:10.1093/dnares/dsw013.
  3. Cole, J.B., D.J. Null, and P.M. VanRaden. 2016. Phenotypic and genetic effects of recessive haplotypes on yield, longevity, and fertility. Journal of Dairy Science. 99:7274-7288. http://dx.doi.org/10.3168/jds.2015-10777. (September 2016 Editor’s Choice Paper for Production: Breeding, Genetics, and Genomics)
  4. Cole, J.B., and M.V.G.B. da Silva. 2016. Invited Review: Genomic selection in multi-breed dairy cattle populations. Revista Brasileira de Zootecnia. 45:195-202. http://dx.doi.org/10.1590/S1806-92902016000400008.
  5. García-Ruiz, A., J.B. Cole, P.M. VanRaden, G.R. Wiggans, F.J. Ruiz-López, and C.P. Van Tassell. 2016. Changes in genetic selection differentials and generation intervals in US Holstein dairy cattle as a result of genomic selection. Proceedings of the National Academy of Sciences of the USA. 113:E3995-4004. doi:10.1073/pnas.1519061113.
  6. Kaniyamattam, K., M.A. Elzo, J.B. Cole, and A. De Vries. 2016. A stochastic dynamic simulation model including multi-trait genetics to estimate genetic, technical and financial consequences of dairy farm reproduction and selection strategies. Journal of Dairy Science. 99:8187–8202. http://dx.doi.org/10.3168/jds.2016-11136. (October 2016 Editor’s Choice Paper for Production: Breeding, Genetics, and Genomics)
  7. Ortega, M.S., A.C. Denicol, J.B. Cole, D.J. Null, and P.J. Hansen. 2016. Use of single nucleotide polymorphisms in candidate genes associated with daughter pregnancy rate for prediction of genetic merit for reproduction in Holstein cows. Animal Genetics. 47:288-297. doi: 10.1111/age.12420.
  8. Parker Gaddis, K.L., J.B. Cole, J.S. Clay, and C. Maltecca. 2016. Benchmarking dairy herd health status using routinely recorded herd summary data. Journal of Dairy Science. 99:1298-1314.
  9. Parker Gaddis, K.L., D.J. Null, and J.B. Cole. 2016. Explorations in genome-wide association studies and network analyses with dairy cattle fertility traits. Journal of Dairy Science. 99:6420-6435. doi:10.3168/jds.2015-10444.
  10. Pryce, J., K. Parker Gaddis, A. Koeck, C. Bastin, M. Abdelsayed, N. Gengler, F. Miglior, B. Heringstad, C. Egger-Danner, K. Stock, A. Bradley, and J. Cole. 2016. Invited Review: Opportunities for genetic improvement of metabolic diseases. Journal of Dairy Science. 99:6856-6873. doi:http://dx.doi.org/10.3168/jds.2016-10854.

2015

  1. Cole, J.B. 2015. A simple strategy for managing many recessive disorders in a dairy cattle breeding program (revised manuscript). Genetics Selection Evolution. 47:94. doi:10.1186/s12711-015-0174-9. (original submission) (first revision) (second revision) (third revision)
  2. Dikmen, S., X. Wang, M.S. Ortega, J.B. Cole, D.J. Null, and P.J. Hansen. 2015. Single nucleotide polymorphisms associated with thermoregulation in lactating dairy cows exposed to heat stress. Journal of Animal Breeding and Genetics. Published online: 21 July 2015. doi:10.1111/jbg.12176.
  3. Ma, L., J.R. O'Connell, P.M. VanRaden, B. Shen, A, Padhi, C. Sun, D.M. Bickhart, J.B. Cole, D.J. Null, G. Liu, Y. Da, and G.R. Wiggans. 2015. Cattle sex-specific recombination and genetic control from a large pedigree analysis. PLoS Genetics. doi:10.1371/journal.pgen.1005387.
  4. Parker Gaddis, K.L., F. Tiezzi, J.B. Cole, J.S. Clay, and C. Maltecca. 2015. Genomic prediction of disease occurrence using producer-recorded health data: A comparison of methods. Genetics Selection Evolution. 47:41. doi:10.1186/s12711-015-0093-9.
  5. Tiezzi, F., K.L. Parker Gaddis, J.B. Cole, J.S. Clay, and C. Maltecca. 2015. A genome-wide association study for clinical mastitis in first parity US Holstein cows using single-step approach and genomic matrix re-weighting procedure. PLoS ONE. 10(2): e0114919. doi: 10.1371/journal.pone.0114919.
  6. Zavarez, L.B., Y.T. Utsunomiya, A.S. Carmo, H.H.R. Neves, R. Carvalheiro, M. Feren?akovi?, A.M. Pérez O’Brien, I. Curik, J.B. Cole, C.P. Van Tassell, M.V.G.B. da Silva, T.S. Sonstegard, J. Sölkner, and J.F. Garcia. 2015. Assessment of autozygosity in Nellore cows (Bos indicus) through high-density SNP genotypes. Frontiers in Genetics. doi: 10.3389/fgene.2015.00005.

2014

  1. Cole, J.B., B. Waurich, M. Wensch-Dorendorf, D.M. Bickhart, and H.H. Swalve. 2014. A genome-wide association study of calf birth weight in Holstein cattle using single nucleotide polymorphisms and phenotypes predicted from auxiliary traits. Journal of Dairy Science. 97:3156-3172. doi:10.3168/jds.2013-7409.
  2. Cooper, T.A., G.R. Wiggans, D.J. Null, J.L. Hutchison, and J.B. Cole. 2014. Genomic evaluation, breed identification, and discovery of a haplotype affecting fertility for Ayrshire dairy cattle. Journal of Dairy Science. 97:3878–3882. doi:10.3168/jds.2013-7427.
  3. da Silva, M.V.B., D.J.A. dos Santos, S.A. Boison, A.T.H. Utsunomiya, A.S. do Carmo, T.S. Sonstegard, J.B. Cole, and C.P. Van Tassell. 2014. The development of genomics applied to dairy breeding. Livestock Science. Published online before print May 24, 2014. doi:10.1016/j.livsci.2014.05.017.
  4. Egger-Danner, C., J.B. Cole, J. Pryce, N. Gengler, B. Heringstad, A. Bradley, L. Andrews, and K.F. Stock. 2014. Invited review: overview of new traits and phenotyping strategies in dairy cattle with a focus on functional traits. Animal. Published online: 12 November 2014. doi:10.1017/S1751731114002614.
  5. Gay, K.D., N.J. Widmar, T.D. Nennich, A.P. Schinckel, J.B. Cole, and M.M. Schutz. 2014. Development of a Lifetime Merit-based selection index for US dairy grazing systems. Journal of Dairy Science. 97:4568–4578. doi:10.3168/jds.2013-7474.
  6. Hutchison, J.L., J.B. Cole, and D.M. Bickhart. 2014. Short Communication: Use of young bulls in the United States. Journal of Dairy Science. 97:3213-3220. doi:10.3168/jds.2013-7525.
  7. Macciotta, N.P.P., C. Dimauro, D.J. Null, G. Gaspa, M. Cellesi, and J.B. Cole. 2014. Dissection of genomic correlation matrices of US Holsteins using multivariate factor analysis. Journal of Animal Breeding and Genetics. Published online before print August 6, 2014. doi:10.1111/jbg.12113.
  8. McClure, M.C., D.M. Bickhart, D.J. Null, P.M. VanRaden, L. Xu, G.R. Wiggans, G. Liu, S.G. Schroeder, J. Glasscock, J. Armstrong, J.B. Cole, T.S. Sonstegard, and C.P. Van Tassell. 2014. Bovine exome sequence analysis and targeted SNP genotyping of recessive fertility defects HH2, HH3, and BH1 reveals causative mutation in SMC2 for HH3. PLoS ONE. 9(3):e92769. doi:10.1371/journal.pone.0092769.
  9. McDaneld, T.G., L.A. Kuehn, M.G. Thomas, W.M. Snelling, T.P.L. Smith, E.J. Pollak, J.B. Cole, and J.W. Keele. 2014. Genomewide association study of reproductive efficiency in female cattle. Journal of Animal Science. 92:1945-1957. doi:10.2527/jas.2012-6807.
  10. Neves, H.H.R., R. Carvalheiro, A. M. Pérez O’Brien, Y.T. Utsunomiya, A.S. do Carmo, F.S. Schenkel, J. Sölkner, J.C. McEwan, C.P. Van Tassell, T.S. Sonstegard, J.B. Cole, M.V.G.B. da Silva, S.A. Queiroz, and J.F. Garcia. 2014. Accuracy of genomic predictions in Bos indicus (Nellore) cattle. Genetics, Selection, Evolution. 46:17. doi:10.1186/1297-9686-46-17.
  11. Parker Gaddis, K.L., J.B. Cole, J.S. Clay, and C. Maltecca. 2014. Genomic selection for producer-recorded health event data in U.S. dairy cattle. Journal of Dairy Science. 97:3190-3199. doi:10.3168/jds.2013-7543.
  12. Sun, C., P.M. VanRaden, J.B. Cole, and J.R. O'Connell. 2014. Improvement of prediction ability for genomic selection of dairy cattle by including dominance effects. PLoS ONE. 9(8):e103934. doi:10.1371/journal.pone.0103934.
  13. Utsunomiya, Y.T., A.S. do Carmo, H.H.R. Neves, R. Carvalheiro, L.B. Zavarez, P.K.R.K. Ito, A.M. Pérez O’Brien, J. Sölkner, L.R. Porto Neto, F.S. Schenkel, J. McEwan, J.B. Cole, M.V.G.B. da Silva, C.P. Van Tassell, T.S. Sonstegard, and J.F. Garcia. 2014. Genome-wide scan identifies putative genetic variants and genes associated with scrotal circumference in Nellore cattle. PLoS ONE. doi:10.1371/journal.pone.0088561.
  14. Weller, J.I., J.B. Cole, P.M. VanRaden, and G.R. Wiggans. 2014. Application of the a posteriori granddaughter design to the Holstein genome. Animal. 8:511-519. http://dx.doi.org/10.1017/S1751731114000111.
  15. Xu, L., D.M. Bickhart, J.B. Cole, P.M. VanRaden, J. Song, T.S. Sonstegard, C.P. Van Tassell, and G.E. Liu. 2014. Genomic signatures reveal new evidences for selection of important traits in domestic cattle. Molecular Biology and Evolution. First published online November 26, 2014. doi:10.1093/molbev/msu333.
  16. Xu, L., J.B. Cole, Y. Hou, D.M. Bickhart, J. Song, P.M. VanRaden, T.S. Sonstegard, C.P. Van Tassell, and G.E. Liu. 2014. Genome wide CNV analysis reveals additional variants associated with milk production traits in Holsteins. BMC Genomics. 15:683. doi:10.1186/1471-2164-15-683.
  17. Yao, C., K.A. Weigel, and J.B. Cole. 2014. Short Communication: Genetic evaluation of stillbirth in US Brown Swiss and Jersey cattle. Journal of Dairy Science. 97:2474-2480. doi:10.3168/jds.2013-7320.

2013

  1. Cochran, S.D., J.B. Cole, D.J. Null, and P.J. Hansen. 2013. Discovery of single nucleotide polymorphisms in candidate genes associated with fertility and production traits in Holstein cattle. BMC Genetics. 14:49. doi:10.1186/1471-2156-14-49.
  2. Cochran, S.D., J.B. Cole, D.J. Null, and P.J. Hansen. 2013. Single nucleotide polymorphisms in candidate genes associated with fertilizing ability of sperm and subsequent embryonic development in cattle. Biology of Reproduction. Published online before print July 31, 2013. doi:10.1095/?biolreprod.113.111260.
  3. Cole, J.B., R.M. Lewis, C. Maltecca, S. Newman, K.M. Olson, and R.G. Tait, Jr. 2013. Systems Biology in Animal Breeding: Identifying relationships among markers, genes, and phenotypes. Journal of Animal Science. 91:521-522. doi:10.2527/jas.2012-6166.
  4. Cole, J.B., and D.J. Null. 2013. Visualization of the transmission of direct genomic values for paternal and maternal chromosomes for fifteen traits in U.S. Brown Swiss, Holstein, and Jersey cattle. Journal of Dairy Science 96:2713-2726. doi:10.3168/jds.2012-6008.
  5. Dikmen, S., J.B. Cole, D.J. Null, and P.J. Hansen. 2013. Genome-wide association mapping for identification of quantitative trait loci for rectal temperature during heat stress in Holstein cattle. PLoS ONE. 8(7):e69202. doi:10.1371/journal.pone.0069202.
  6. Hutchison, J.L., P.M. VanRaden, H.D. Norman, and J.B. Cole. 2013. Technical Note: Changes to herd cutoff date in conception rate evaluations. Journal of Dairy Science 96:1264-1268. doi:10.3168/jds.2012-6203.
  7. Kim, E.-S., J.B. Cole, H. Huson, G.R. Wiggans, C.P. Van Tassell, B.A. Crooker, Y. Da, and T.S. Sonstegard. 2013. Effect of artificial selection on runs of homozygosity in U.S. Holstein cattle. PLoS ONE. 8(11):e80813. doi:10.1371/journal.pone.0080813.
  8. McClure, M.C., E.-S. Kim, D. Bickhart, D.J. Null, T.A. Cooper, J.B. Cole, G.R. Wiggans, P.A. Marsan, L. Colli, E. Santus, G. Liu, S.G. Schroeder, L.K. Matukumalli, C.P. Van Tassell, and T.S. Sonstegard. 2013. Fine mapping for Weaver Syndrome in the Brown Swiss breed with the identification of possible causal mutations across NRCAM, PNPLA8 and CTTNBP2 and development of a diagnostic SNP haplotype. PLoS ONE. doi:10.1371/journal.pone.0059251.
  9. Sonstegard, T.S., J.B. Cole, P.M. VanRaden, C.P. Van Tassell, D.J. Null, S.G. Schroeder, D. Bickhart, and M.C. McClure. 2013. Identification of a nonsense mutation in CWC15 associated with decreased reproductive efficiency in Jersey cattle. PLoS ONE. doi:10.1371/journal.pone.0054872.
  10. Utsunomiya, Y.T., A.S. do Carmo, R. Carvalheiro, H.H.R. Neves, M.C. Matos, L.B. Zavarez, A.M. Pérez O’Brien, J. Sölkner, J. McEwan, J.B. Cole, C.P. Van Tassell, F.S. Schenkel, M.V.G.B. da Silva, L.R. Porto Neto, T.S. Sonstegard, and J.F. Garcia. 2013. Genome-wide association study for birth weight in Brazilian Nellore cattle (Bos taurus indicus) points to previously described orthologous genes affecting human and bovine height. BMC Genetics. 14:52. doi:10.1186/1471-2156-14-52.
  11. VanRaden, P.M., D.J. Null, M. Sargolzaei, G.R. Wiggans, M.E. Tooker, J.B. Cole, T.S. Sonstegard, E.E. Connor, M. Winters, J.B.C.H.M. van Kaam, B.J. Van Doormaal, M.A. Faust, and G.A. Doak. 2013. Genomic imputation and evaluation using high density Holstein genotypes. Journal of Dairy Science 96:668-678. doi:10.3168/jds.2012-5702.

2012

  1. Cole, J.B., J.L. Ehrlich, and D.J. Null. 2012. Short communication: Projecting milk yield using best prediction and the MilkBot lactation model. Journal of Dairy Science 95:4041-4044.
  2. Cole, J.B., S. Newman, F. Foertter, I. Aguilar, and M. Coffey. 2012. Really big data: processing and analysis of large datasets. Journal of Animal Science 90:723-733.
  3. Dikmen, S., J.B. Cole, D.J. Null, and P.J. Hansen. 2012. Heritability of rectal temperature and genetic correlations with production and reproduction traits in dairy cattle. Journal of Dairy Science 95:3401-3405.
  4. Ma, L., G.R. Wiggans, S. Wang, T.S. Sonstegard, J. Yang, B.A. Crooker, J.B. Cole, C.P. Van Tassell, and Y. Da. 2012. Effect of sample stratification on dairy GWAS results. BMC Genomics 13:536. doi: 10.1186/1471-2164-13-536.
  5. Parker Gaddis, K.L., J.B. Cole, J.S. Clay, and C. Maltecca. 2012. Incidence validation and causal relationship analysis of producer-recorded health event data from on-farm computer systems in the U.S. Journal of Dairy Science 95:5422-5435.

2011

  1. Cole, J.B., D.J. Null, and A. De Vries. 2011. Short communication: Best prediction of 305-day lactation yields with regional and seasonal effects. Journal of Dairy Science. 94:1601-1604.
  2. Cole, J.B., and P.M. VanRaden. 2011. Use of haplotypes to estimate Mendelian sampling effects and selection limits. Journal of Animal Breeding and Genetics. doi:10.1111/j.1439-0388.2011.00922.x
  3. Cole, J.B., G.R. Wiggans, L. Ma, T.S. Sonstegard, T.J. Lawlor, Jr., B.A. Crooker, C.P. Van Tassell, J. Yang, S. Wang, L.K. Matukumalli, and Y. Da. 2011. Genome-wide association analysis of thirty one production, health, reproduction and body conformation traits in contemporary U.S. Holstein cows. BMC Genomics 12:408.
  4. VanRaden, P.M., K.M. Olson, G.R. Wiggans, J.B. Cole, and M.E. Tooker. 2011. Genomic inbreeding and relationships among Holsteins, Jerseys, and Brown Swiss. Journal of Dairy Science 94:6153-6161.
  5. Wiggans, G.R., T.A. Cooper, P.M. VanRaden, and J.B. Cole. 2011. Adjustment of traditional cow evaluations to improve accuracy of genomic predictions. Journal of Dairy Science 94:6188-6193.

2010

  1. Attalla, S.A., A.J. Seykora, J.B. Cole, and B.J. Heins. 2010. Genetic parameters of milk ELISA scores for Johne's disease. Journal of Dairy Science 93:1729-1735.
  2. Cole, J.B., and P.M. VanRaden. 2010. Visualization of results from genomic evaluations. Journal of Dairy Science 93:2727-2740.

2009

  1. Appuhamy, J.A.D.R.N., B.G. Cassell, and J.B. Cole. 2009. Phenotypic and genetic relationships between common health disorders and milk and fat yield persistencies from producer recorded health data and test day yields. Journal of Dairy Science 92:1785-1795
  2. Cole, J.B., D.J. Null, and P.M. VanRaden. 2009. Best prediction of yields for long lactations. Journal of Dairy Science 92:1796-1810.
  3. Cole, J.B., and D.J. Null. 2009. Genetic evaluation of lactation persistency for five breeds of dairy cattle. Journal of Dairy Science 92:2248-2258.
  4. Cole, J.B., P.M. VanRaden, J.R. O'Connell, C.P. Van Tassell, T.S. Sonstegard, R.D. Schnabel, J.F. Taylor, and G.R. Wiggans. 2009. Distribution and location of genetic effects for dairy traits. Journal of Dairy Science 92:2931-2946.
  5. Miller, R.H., H.D. Norman, J.R. Wright, and J.B. Cole. 2008. Relationship of productive life of daughters to predicted transmitting ability milk somatic cell score of their sires and maternal grandsires. Journal of Dairy Science 92:2224-2228.
  6. Norman, H.D., J.R. Wright, M.T. Kuhn, S.M. Hubbard, J.B. Cole, and P.M. VanRaden. 2009. Genetic and environmental factors that impact gestation length. Journal of Dairy Science 92:2259-2269.

2008

  1. Wiggans, G.R., J.B. Cole, and L.L.M.Thornton. 2008. Multiparity evaluation of calving ease and stillbirth with separate genetic effects by parity. Journal of Dairy Science 91:3173-3178.

2007

  1. Appuhamy, J.A.D.R.N., B.G. Cassell, C.D. Dechow, and J.B. Cole. 2007. Phenotypic relationships of common health disorders in dairy cows to lactation persistency estimated from daily milk weights. Journal of Dairy Science 90:4424-4434.
  2. Bohmanova, J., I. Misztal, and J.B. Cole. 2007. Comparison of seven temperature humidity indices as indicators of milk production losses due to heat stress in semi-arid and humid climates. Journal of Dairy Science 90:1947-1956.
  3. Cole, J.B. 2007. PyPedal: A package for pedigree analysis using the Python programming language. Computers and Electronics in Agriculture 57:107-113.
  4. Cole, J.B., G.R. Wiggans, and P.M. VanRaden. 2007. Genetic evaluation of stillbirth in United States Holsteins using a sire-maternal grandsire threshold model. Journal of Dairy Science 90:2480-2488.
  5. Cole, J.B., G.R. Wiggans, P.M. VanRaden, and R.H. Miller. 2007. Stillbirth (co)variance components for a sire-maternal grandsire threshold model and development of a calving ability index for sire selection. Journal of Dairy Science 90:2489-2496.
  6. VanRaden, P.M., M.E. Tooker, J.B. Cole, G.R. Wiggans, and J.H. Megonigal, Jr. 2007. Genetic evaluations for mixed breed populations. Journal of Dairy Science 90:2434-2441.

2006

  1. Cole, J.B., and P.M. VanRaden. 2006. Genetic evaluation and best prediction of lactation persistency. Journal of Dairy Science 89:2722-2728.

2005

  1. Cole, J.B., R.C. Goodling, Jr., G.R. Wiggans, and P.M. VanRaden. 2005. Genetic evaluation of calving ease for Brown Swiss and Jersey bulls from purebred and crossbred calvings. Journal of Dairy Science 88:1529-1539.

2004

  1. Cole, J.B., D.E. Franke, and E.A. Leighton. 2004. Population genetic structure of a colony of dog guides. Journal of Animal Science 82:2906-2912. https://doi.org/10.2527/2004.82102906x.
  2. Rohli, R.V., M.M. Russo, A.J. Vega, and J.B. Cole. 2004. Atmospheric and statewide anomalously-high tropospheric ozone concentrations in Louisiana. Journal of Applied Meteorology 43:1438-1451.

1999

  1. Hansen, L.B., J.B. Cole, G.D. Marx, and A.J. Seykora. 1999. Productive life and reasons for disposal of Holstein cows selected for large versus small body size. Journal of Dairy Science 82:795-801. https://doi.org/10.3168/jds.S0022-0302(99)75298-7.

Book Chapters and Technical Reports


2019

Cole, J.B. 2019. Chapter 13 - Advances in Dairy Cattle Breeding to Improve Resistance to Mastitis. In Advances in Breeding of Dairy Cattle. J. van der Werf and J. Pryce, ed. Burleigh Dodds Science Publishing Limited, Cambridge, UK.


2018

Cole, J.B., P.M. VanRaden, D.J. Null, J.L. Hutchison, and S.M. Hubbard. 2018. AIP Research Report NM$8: Haplotype tests for economically important traits of dairy cattle.
VanRaden, P.M., J.B. Cole, and K.L. Parker Gaddis. 2018. AIP Research Report NM$7: Net merit as a measure of lifetime profit: 2018 revision.


2016

Cole, J.B., and D.M. Spurlock. 2016. Improving Production Efficiency through Genetic Selection. In Large Dairy Herd Management, 3rd Edition. D. Beede et al., ed. American Dairy Science Association, Champaign, IL.


2014

Cole, J.B. 2014. Use of Gene Markers for Genetic Selection of Dairy Cattle. Encyclopedia of Biotechnology in Agriculture and Food, Taylor & Francis, Florence, KY. Published online May 7, 2014. doi:10.1081/E-EBAF-120045389. (Author's draft, neither typeset nor edited.)

ICAR Functional Traits Working Group (Andrews, L., Bradley, A.J., Cole, J.B., Egger-Danner, C., Gengler, N., Heringstad, B., Pryce, J., Stock, K., and Strandberg, E.). 2014. Section 7.1 – Guidelines for recording, evaluation and genetic improvement of health traits. ICAR Recording Guidelines. pp. 235–261. Int. Comm. Anim. Recording, Rome, Italy.

ICAR Functional Traits Working Group (Andrews, L., Bradley, A.J., Cole, J.B., Egger-Danner, C., Gengler, N., Heringstad, B., Pryce, J., Stock, K., and Strandberg, E.). 2014. Section 7.2 – Guidelines for recording, evaluation and genetic improvement of female fertility in dairy cattle. ICAR Recording Guidelines. pp. 262–278. Int. Comm. Anim. Recording, Rome, Italy.

VanRaden, P.M., M.E. Tooker, J.R. Wright, J.B. Cole, D.J. Null, and T.J. Lawlor. 2014. AIP Research Report BASE3: Genetic base changes for December 2014.

VanRaden, P.M., and J.B. Cole. 2014. AIP Research Report NM$5: Net merit as a measure of lifetime profit: 2014 revision.


2013

Cole, J.B., P.M. VanRaden, D.J. Null, J.L. Hutchison, and T.A. Cooper. 2013. AIPL Research Report GENOMIC3: Haplotype tests for recessive disorders that affect fertility and other traits.

Egger-Danner, C., O.K. Hansen, K. Stock, J. Pryce, J. Cole, N. Gengler, and B. Heringstad (ed.). 2013. ICAR Technical Series no. 17: Challenges and benefits of health data recording in the context of food chain quality, management and breeding. ICAR Tech. Ser. No. 17. ICAR, Rome, Italy.

2012

Cole, J.B., and D.J. Null. 2012. AIPL Research Report GENOMIC2: Use of chromosomal predicted transmitting abilities.

2010

Cooper, T.A., M.E. Tooker, P.M. VanRaden, G.R. Wiggans, and J.B. Cole. 2010. AIPL Research Report GENOMIC1: Imputation of Cow Genotypes and Adjustment of PTAs.

VanRaden, P.M., J.B. Cole, M.E. Tooker, and T.A. Cooper. 2010. AIPL Research Report BASE2: Genetic base changes for January 2010.

2009

Cole, J.B., P.M. VanRaden, and Multi-State Project S-1040. 2009. AIPL Research Report NM$4: Net merit as a measure of lifetime profit: 2010 revision.

2008

De Vries, A., and J.B. Cole. 2008. Profitable dairy cow traits for hot climatic conditions in Breeding for robustness in cattle -- EAAP 126 (M. Klopcic, R. Reents, J. Philipsson, and A. Kuipers, Eds.) Wageningen Academic Publishers, Waginengen, The Netherlands.

2007

Cole, J.B. 2007. AIPL Research Report SB1: Genetic evaluation of stillbirth.

VanRaden, P.M., M.E. Tooker, G.R. Wiggans, J.B. Cole, and J.H. Megonigal, Jr. 2007. AIPL Research Report AB1: All-breed evaluation.

2005

Cole, J.B. 2005. AIPL Research Report CE1: Brown Swiss and Holstein calving ease.

2004

Lanting, F.L., and J.B. Cole. 2004. Chapter 13: Basics of Genetics. Pages 256-290 in The Total German Shepherd Dog, 2nd ed. Hoflin Publishing, Wheat Ridge, CO.

Popular Press Articles


2020

Cole, J.B., S.A.E. Eaglen, T.J. Lawlor, and E.L. Nicolazzi. 2020. August 2020 calving traits will reflect lower breed averages. CDCB Connection. June 5, 2020. (Article on CDCB website.)

Eaglen, S.A.E., and J.B. Cole. 2020. What's going on with calving ease? CDCB Connection. May 7, 2020. (Article on CDCB website.)

2015

Cole, J.B. 2015. Calving outcomes on dairy farms: We've been collecting data for decades. Dairy Herd Management. January 21, 2015.


2014

Cole, J.B. 2014. We need your help to breed healthier dairy cows! DairyBusiness/HolsteinWorld. (Submitted.)

2013

Parker Gaddis, K.L., C. Maltecca, and J.B. Cole. 2013. We are making inroads on health and fitness traits. Hoard's Dairyman 158(12):455.

Parker Gaddis, K.L., C. Maltecca, and J.B. Cole. 2013. Verso il successo nella selezione per la salute della vacca [In Italian]. Bianconero (Accepted.)

2011

De Vries, A., D.T. Galligan, and J.B. Cole. 2011. The use and economic value of the 3K SNP genomic test for calves on dairy farms. EDIS Publ. AN270. Department of Animal Sciences, Florida Cooperative Extension Service, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL.

De Vries, A., D.T. Galligan, and J.B. Cole. 2011. Some ideas on the use and economic value of the 3K SNP genomic test for calves on dairy farms. Dairy Update 11(3):5-9.

2008

Cole, J.B. 2008. Using Python to study pedigrees with PyPedal. Python Magazine 3:12-20.

2006

Cole, J.B., R.C. Goodling, Jr., G.R. Wiggans, and P.M. VanRaden. 2006. Genetic calving ease study on crossbreeds. Jersey Journal 53(5):83-84.

Seykora, A.J., P.M. VanRaden, and J.B. Cole. 2006. Net Merit receives face-lift. Hoard's Dairyman 151(14):557.

2005

Cole, J.B. 2005. How can we genetically improve dairy cattle health? The Dairy Focus 6(4):3.

Proceedings


2022

J.B. Cole, R.A. Mrode, K.M. Olson, and P. Knap. A panel discussion: broadening learning by incorporating industry professionals in education. Proc. 12th World Congr. Genet. Appl. Livest. Prod., Rotterdam, The Netherlands, Jul. 3–8. (Submitted.)

Guinan, F.L., G.R. Wiggans, J.W. Dürr, H.D. Norman, J.B. Cole, C.P. Van Tassell, I. Misztal, and D. Lourenco. 2022. Changes in genetic trends for dairy cattle in the U.S. since the implementation of genomic selection. Proc. 12th World Congr. Genet. Appl. Livest. Prod., Rotterdam, The Netherlands, Jul. 3–8. (Submitted.)

Lozada-Soto, E.A., F. Tiezzi, J.B. Cole, P.M. VanRaden, and C. Maltecca. Patterns of inbreeding and selection using runs of homozygosity in North American dairy cattle. Proc. 12th World Congr. Genet. Appl. Livest. Prod., Rotterdam, The Netherlands, Jul. 3–8. (Submitted.)

2020

Bickhart, D.M., Cole, J.B., Hutchison,J.L., Null, D.J., and Ortega, M.S. Haplotype- and sequence-based identification of a deletion associated with early embryonic loss in Holstein cattle and functional validation using CRISPR-Cas9 knockouts. J. Dairy Sci. 103(Suppl. 1):(abstr.). 2020.

Cole, J.B. The future of selection decisions and breeding programs. J. Dairy Sci. 103(Suppl. 1):(abstr.). 2020.

Freebern, E., Jiang, J., Cole, J.B., VanRaden, P.M., and Ma, L. Genome changes due to selection in U.S. dairy cattle. J. Dairy Sci. 103(Suppl. 1):(abstr.). 2020.

Nani, J.P., Cole, J.B., and VanRaden, P.M. Methods to implement ancestor discovery in the US dairy cattle database. J. Dairy Sci. 103(Suppl. 1):(abstr.). 2020.

Null, D.J., Cole, J.B., Al-Khudhair, A., and VanRaden, P.M. Quality control to improve properties of sequence genotypes from different sources. J. Dairy Sci. 103(Suppl. 1):(abstr.). 2020.

VanRaden, P.M., Cole, J.B., VandeHaar, M.J., Neupane, M., and Hutchison, J.L. New traits and economic updates for the net merit index. J. Dairy Sci. 103(Suppl. 1):(abstr.). 2020.

2019

Freeman, E., Santos, D.J.A, Cole, J.B., Fang, L., Jiang, J., and Ma, L. GWAS and fine-mapping of livability and six health traits in Holstein cattle. Plant Anim. Genome XXVII Conf., San Diego, CA, Jan. 12–16, PO0363. 2019.

Houdek, E.S., Heins, B.M., Hazel, A.R., Hansen, L.B., and Cole, J.B. Alternative input parameters for Wood’s curve within Best Prediction used by USDA-AGIL for genetic evaluation of production traits in the United States. J. Dairy Sci. 102(Suppl. 1):399(abstr. 468). 2019.

Ma, L., Jiang, J., Prakapenka, D., Cole, J.B., and Da, Y. Approximate generalized least squares method for large-scale genome-wide association study. J. Dairy Sci. 102(Suppl. 1):30(abstr. M64). 2019.

Nicolazzi, E.L., Bacheller, L.R., Fok, G.C., Parker Gaddis, K.L., Jensen, L., Megonigal, Jr., J.H., Norman, H.D., Null, D.J., Walton, L.M., Wiggans, G.R., Cole, J.B., Durr, J.W., and VanRaden, P.M. Enhancements to U.S. genetic and genomic evaluations in 2018 and 2019. Interbull Bull. 55:26–29. 2019.

Parker Gaddis, K.L., VanRaden, P.M., Cole, J.B., Niccolazi, E., and Durr, J.W. Development, implementation, and future perspectives of health evaluations in the United States. J. Dairy Sci. 102(Suppl. 1):141(abstr. 175). 2019.

Santos, D.J.A., Cole, J.B., VanRaden, P.M., Lawlor, T.J., and Ma, L. Utilizing variance of gametic diversity in dairy cattle improvement. Plant Anim. Genome XXVII Conf., San Diego, CA, Jan. 12–16, PE0340. 2019.

Wiggans, G.R., VanRaden, P.M., Null, D.J., and Cole, J.B. Genomic predictions using more markers and gene test. J. Dairy Sci. 102(Suppl. 1):397(abstr. 462). 2019.

2018

Bradford, H.L., Y. Masuda, J.B. Cole, I. Misztal, and P.M. VanRaden. 2018. Modelling uncertain paternity to address differential pedigree accuracy. J. Dairy Sci. 101 (Suppl. 2):181-182(abstr. 170).

Chud, T.S., D.M. Bickhart, J.B. Cole, F. Baldi Rey, M.V.G.B. da Silva, and D. Munari. 2018. Copy number variation of PRAME gene across dairy breeds. ASAS-CSAS (accepted Mar. 2018)

Cole, J.B., K.L. Parker Gaddis, D.J. Null, C. Maltecca, and J.S. Clay. 2018. Genome-wide association study and gene network analysis of fertility, retained placenta, and metritis in US Holstein cattle. Proc. 11th World Congr. Genet. Appl. Livest. Prod., Auckland, New Zealand, Feb. 11–16, Vol. Biol.–Dis. Resist. 1, p. 171. 2018.

Cole, J.B., K.L. Parker Gaddis, C. Willard, D.J. Null, C. Maltecca, and J.S. Clay. 2018. Identification of genomic regions associated with resistance to clinical mastitis in US Holstein cattle. J. Dairy Sci. 101(Suppl. 2):138(abstr. 58).

Jiang, J., L. Ma, D. Prakapenka, M.E. Tooker, P.M. VanRaden, J.B. Cole, and Y. Da. 2018. Extreme antagonistic pleiotropy effects of DGAT1 on fat, milk and protein yields. Proc. 11th World Congr. Genet. Appl. Livest. Prod., Auckland, New Zealand, Feb. 11–16, Vol. Electron. Poster Sess.–Mol. Genet. 3, p. 142.

Jiang, J., P.M. VanRaden, J.B. Cole, Y. Da, and L. Ma. 2018. Big data genomic investigation of dairy fertility and related traits with imputed sequences of 24K Holstein bulls. J. Dairy Sci. 101 (Suppl. 2):328(abstr. 277).

Mueller, M.L., J.B. Cole, T.S. Sonstegard, and A.L. Van Eenennaam. 2018. Simulation of introgression of the polled allele into the Holstein breed via conventional breeding versus gene editing. Proc. 11th World Congr. Genet. Appl. Livest. Prod., Auckland, New Zealand, Feb. 11–16, Vol. Gene Editing, p. 755.

Mueller, M.L., J.B. Cole, T.S. Sonstegard, and A.L. Van Eenennaam. 2018. Simulation of introgression of the POLLED allele into the Jersey breed via conventional breeding vs. gene editing. Transl. Anim. Sci. 2(Suppl. 1):S57-S60.

Null, D.J., P.M. VanRaden, D.M. Bickhart, J.B. Cole, J.R. O'Connell, and B.D. Rosen. 2018. Potential benefits from using a new reference map in genomic prediction. J. Dairy Sci. 101 (Suppl. 2):181-182(abstr. 168).

Ortega, M.S., J.B. Cole, T.E. Spencer, and P.J. Hansen. 2018. Genetic cues from fertilization to pregnancy establishment. J. Dairy Sci. 101 (Suppl. 2):328(abstr. 278). 2018.

Parker Gaddis, K.L., M.E. Tooker, J.R. Wright, J.H. Megonigal Jr., J.S. Clay, J.B. Cole, and P.M. VanRaden. 2018. Development of national genomic evaluations for health traits in U.S. Holsteins. Proc. 11th World Congr. Genet. Appl. Livest. Prod., Auckland, New Zealand, Feb. 11–16, Vol. Biol. & Species–Bovine (dairy) 1, p. 594.

Ruiz-Lopez, F.J., A. Garcia-Ruiz, J.B. Cole, G.R. Wiggans, and C.P. Van Tassell. 2018. Impact of genomic selection on genetic gain of net merit of US dairy cattle. Proc. 11th World Congr. Genet. Appl. Livest. Prod., Auckland, New Zealand, Feb. 11–16, Vol. Electron. Poster Sess.–Biol. & Species–Bovine (dairy) 2, p. 710.

Santos, D.J.A., J.B. Cole, P.M. VanRaden, T.J. Lawlor, H. Tonhati, and L. Ma. 2018. Obtaining variance of gametic diversity with genomic models. Proc. 11th World Congr. Genet. Appl. Livest. Prod., Auckland, New Zealand, Feb. 11–16, Vol. Methods & Tools–Prediction 2, p. 176.

Verardo, L.L. N.B. Stafuzza, D.P. Munari, A. Zerlotini, T.C.S. Chud, D.J. Garrick, J.B. Cole, J.C.C. Panetto, M.A. Machado, M.F. Martins, and M.V.G.B. Silva. 2018. A gene-transcription factor network associated with residual feed intake based on SNVs/InDels identified in Gir, Girolando and Holstein cattle breeds. Proc. 11th World Congr. Genet. Appl. Livest. Prod., Auckland, New Zealand, Feb. 11–16, Vol. Electron. Poster Sess.– Biol. & Species–Bovine (dairy) 1, p. 193.

2017

Cole, J.B. 2017. A dairy calf DNA biobank for the discovery of new recessive genetic disorders. J. Anim. Sci. 95(Suppl. 4):83(abstr. 169). 2017.

Cole, J.B. 2017. Management of Mendelian Traits in Breeding Programs by Gene Editing. EAAP (accepted Apr. 2017)

Cole, J.B. 2017. Possibilities in an age of genomics: The future of the breeding index. J. Dairy. Sci. 100(Suppl. 2):337(abstr. 274).

Hutchison, J.L., P.M. VanRaden, J.B. Cole, G.C. Fok, and H.D. Norman, H.D. 2017. Bull fertility evaluations for Angus service sires bred to Holstein cows. J. Dairy. Sci. 100(Suppl. 2):242(abstr. T45).

Null, D.J., J.L. Hutchison, D.M. Bickhart, P.M. VanRaden, and J.B. Cole. 2017. Discovery of a Haplotype Affecting Fertility in Ayrshire Dairy Cattle and Identification of a Putative Causal Variant. J. Dairy. Sci. 100(Suppl. 2):199(abstr. 205).
Parker Gaddis, K.L., M.E. Tooker, J.R. Wright, J.H. Megonigal, J.S. Clay, J.B. Cole, and P.M. VanRaden. 2017. Development of genomic evaluations for direct measures of health in U.S. Holsteins and their correlations with fitness traits. J. Dairy. Sci. 100(Suppl. 2):378(abstr. 377).
Stafuzza, N.B., A. Zerlotini, F.P. Lobo, M.E.P. Yamagishi, T.C.S. Chud, A.R. Caetano, D.P. Munari, D.J. Garrick, J.B. Cole, M.A. Machado, M.F. Martins, M.R. Carvalho, and M.V.G.B. da Silva. 2017. Single nucleotide variants and indels identified from whole-genome resequencing of Gyr, Girolando, and Holstein cattle breeds. J. Anim. Sci. 95(Suppl. 4):80–81(abstr. 164).
Stafuzza, N.B., A. Zerlotini, F.P. Lobo, M.E.P. Yamagishi, M.E. Buzanskas, T.C.S. Chud, A.R. Caetano, D.P. Munari, D.J. Garrick, M.A. Machado, M.F. Martins, M.R. Carvalho, J.B. Cole, and M.V.G.B. da Silva. 2017. Genetic variants with potential loss of function in Gyr, Girolando, and Guzerat cattle breeds by resequencing. J. Anim. Sci. 95(Suppl. 4):81(abstr. 165).

2016

Bickhart, D.M., L. Xu, J.L. Hutchison, J.B. Cole, D.J. Null, S.G. Schroeder, J. Song, J.F. Garcia, T.S. Sonstegard, C.P. Van Tassell, R.D. Schnabel, J.F. Taylor, H.A. Lewin, and G.E. Liu. 2016. Exploring the feasibility of using copy number variants as genetic markers through large-scale whole genome sequencing experiments. J. Dairy Sci. 99(E–Suppl. 1)/J. Anim. Sci. 94(E–Suppl. 5):142(abstr. 0306).

Cole, J.B., D.J. Null, and S. Tsuruta. 2016. Use of a threshold animal model to estimate calving ease and stillbirth (co)variance components for US Holsteins. J. Dairy Sci. 99(E–Suppl. 1)/J. Anim. Sci. 94(E–Suppl. 5):182–183(abstr. 0385).

Dalton, J., D. Moore, T.E. Spencer, P.J. Hansen, J.B. Cole, and H. Neibergs. 2016. Genetics, genomics and fertility. Clinical Theriogenology 8(3):165–170.

Hansen, P.J., S. Dikmen, J.B. Cole, M.S. Ortega, and G.E. Dahl. 2016. Genetic solutions to infertility caused by heat stress. J. Dairy Sci. 99(E–Suppl. 1)/J. Anim. Sci. 94(E–Suppl. 5):192(abstr. 0405).

Parker Gaddis, K.L., S. Dikmen, J.B. Cole, and P.J. Hansen. 2016. Genetic analysis of superovulation and embryo transfer traits in Holstein cattle. J. Dairy Sci. 99(E–Suppl. 1)/J. Anim. Sci. 94(E–Suppl. 5):179(abstr. 0379).

Shen, B., Z. Wang, J. Jiang, J.B. Cole, D. Bickhart, G.R. Wiggans, Y. Da, G.E. Liu, and L. Ma. 2016. Effects of sex, age, and breed on genetic recombination features in cattle. Plant Anim. Genome XXIV Conf., San Diego, CA, Jan. 9–13, P0522.
Spencer, T.E., H.L. Neibergs, P.J. Hansen, J.B. Cole, J.C. Dalton, D.A. Moore, M. Chahine, and A. De Vries. 2016. Improving fertility of dairy cattle using translational genomics. J. Dairy Sci. 99(E–Suppl. 1)/J. Anim. Sci. 94(E–Suppl. 5):325–326(abstr. 0694).
Van Tassell, C.P., G. Spangler, D.M. Bickhart, G.R. Wiggans, J.B. Cole, J.F. Taylor, H.L. Neibergs, C.M. Seabury, A.L. Van Eenennaam, and J.E. Womack. 2016. Calculation of genomic predicted transmitting abilities for bovine respiratory disease complex in Holsteins. J. Dairy Sci. 99(E–Suppl. 1)/J. Anim. Sci. 94(E–Suppl. 5):133(abstr. 0288).


2015

Arceo, M., F. Tiezzi, J.B. Cole, and C. Maltecca. 2015. Identification of gene networks underlying dystocia in dairy cattle. J. Dairy Sci. 98(Suppl. 2)/J. Anim. Sci. 93(Suppl. 3):840(abstr. 749).

Bickhart, D.M., L. Xu, J.L. Hutchison, J.B. Cole, S.G. Schroeder, J. Song, J.F. Garcia, C.P. Van Tassell, T.S. Sonstegard, R.D. Schnabel, J.F. Taylor, H.A. Lewin, E.E. Eichler, and G.E. Liu. 2014. Next generation sequencing reveals the diversity and population-genetic properties of cattle CNVs. Proc. Plant Anim. Genome XXIII Conf., San Diego, CA, Jan. 11-15. (Submitted.)

Cole, J.B., D.J. Null, C. Sun, and P.M. VanRaden. 2015. Assignment of polled status using single nucleotide polymorphism genotypes and predicted gene content. J. Dairy Sci. 98(Suppl. 2)/J. Anim. Sci. 93(Suppl. 3):800(abstr. 647).

Cole, J.B., and K.L. Parker Gaddis. 2015. Genome-wide association study of fertility traits in dairy cattle using high-density single nucleotide polymorphism marker panels. Journal of Dairy Science 98(Suppl. 2):(Submitted.)

Hutchison, J.L., J.B. Cole, and D.M. Bickhart. 2015. Animal selection for whole-genome sequencing by quantifying the unique contribution of homozygous haplotypes sequenced. J. Dairy Sci. 98(Suppl. 2)/J. Anim. Sci. 93(Suppl. 3):649(abstr. W86).

Liu, G.E., D. Bickhart, L. Xu, J.L. Hutchison, J.B. Cole, S.G. Schroeder, J. Song, J.F. Garcia, C.P. Van Tassell, T.S. Sonstegard, R.D. Schnabel, J.F. Taylor, and H. Lewin. 2015. Whole-genome sequencing reveals the diversity and population-genetic properties of cattle CNVs. Plant Anim. Genome XXIII Conf., San Diego, CA, Jan. 10–14, W141.

Ma, L., J.R. O'Connell, P.M. VanRaden, B. Shen, C. Sun, D.M. Bickhart, J.B. Cole, D.J. Null, Y. Da, and G.R. Wiggans. 2015. Cattle sex-specific recombinations and their genetic control from a large pedigree analysis. Plant Anim. Genome XXIII Conf., San Diego, CA, Jan. 10–14, P0273.

Ma, L., T.S. Sonstegard, C.P. VanTassell, J.B. Cole, G.R. Wiggans, B.A. Crooker, F. Abel Ponce de Leon, and Y. Da. 2015. Selection signature analysis in Holstein cattle identified genes known to affect reproduction. n. J. Dairy Sci. 98(Suppl. 2)/J. Anim. Sci. 93(Suppl. 3):350(abstr. T102).

Ortega, M.S., S.D. Cochran, D.J. Null, J.B. Cole, A.C. Denicol, and P.J. Hansen. 2015. Identification of candidate genes associated with reproduction in dairy cattle. Plant Anim. Genome XXIII Conf., San Diego, CA, Jan. 10–14, GeneSeek – Next Generation Genomic Solutions for Agri-Research Workshop, 17773.

Ortega, M.S., A.C. Denicol, D.J. Null, J.B. Cole, and P.J. Hansen. 2015. Single nucleotide polymorphisms in specific candidate genes are associated with phenotypic differences in days open for first lactation in Holstein cows. J. Dairy Sci. 98(Suppl. 2)/J. Anim. Sci. 93(Suppl. 3):648–649(abstr. W85).

Parker Gaddis, K.L., and J.B. Cole. 2015. Genome-wide association study of fertility traits in dairy cattle using high-density single nucleotide polymorphism marker panels. J. Dairy Sci. 98(Suppl. 2)/J. Anim. Sci. 93(Suppl. 3):578(abstr. 538).

Parker Gaddis, K.L., J.B. Cole, J.S. Clay, and C. Maltecca. 2015. Using routinely recorded herd data to predict and benchmark herd and cow health status. J. Dairy Sci. 98(Suppl. 2)/J. Anim. Sci. 93(Suppl. 3):815(abstr. 687).

Sonstegard, T.S., D.M. Bickhart, A. Landaeta-Hernandez, Y.T. Utsonomiya, M.P. Morales, E. Jiminez, S.G. Schroeder, J. Sun, W. Barendse, L. Porto Neto, A. Reverter, J.B. Cole, P.J. Hansen, J.F. Garcia, and H.J. Huson. Discovery of convergent adaptations that alleviate heat stress in Taurine cattle. 2014. Proc. Plant Anim. Genome XXIII Conf., San Diego, CA, Jan. 11-15. W155.

Sonstegard, T.S., L. Ma, E.-S. Kim, C.P. Van Tassell, G.R. Wiggans, B.A. Crooker, J.B. Cole, G.E. Liu, J.R. Garbe, S.C. Fahrenkrug, F.A. Ponce de Leon, and Y. Da. 2014. Genome changes due to forty years of artificial selection associated with divergent dairy production and reproduction. Proc. Plant Anim. Genome XXIII Conf., San Diego, CA, Jan. 11-15. W150.

Xu, L., D.M. Bickhart, J.B. Cole, S.G. Schroeder, J. Song, C.P. Van Tassell, T.S. Sonstegard, and G.E. Liu. 2015. Genomic signatures reveal new evidence for selection of important traits in cattle. Proc. Plant Anim. Genome XXIII Conf., San Diego, CA, Jan. 11-15. P0277.

2014

Bickhart, D.M., J.B. Cole, J.L. Hutchison, L. Xu, and G.E. Liu. 2014. Using the Whole Read: Structural Variant Detection Using NGS Data. 10th World Congress on Genetics Applied to Livestock Production, Vancouver, BC, Canada, Aug. 17-22. Comm. 164.

Bickhart, D.M., L. Xu, J.L. Hutchison, J.B. Cole, S.G. Schroeder, J. Song, T.S. Sonstegard, C.P. Van Tassell, J.F. Garcia, and G.E. Liu. 2014. Population sequencing reveals breed and sub-species specific CNVs in cattle. 34th International Society for Animal Genetics Meeting, Xi'an, China, Jul. 27-Aug. 1. (Submitted.)

Cole, J.B. 2014. Phenotypes for novel functional traits of dairy cattle. ICAR Tech Series 18:(Accepted.)

Cole, J.B., J.L. Hutchison, D.J. Null, P.M. VanRaden, G.E. Liu, S.G. Schroeder, T.S. Sonstegard, C.P. Van Tassell, and D.M. Bickhart. 2014. Candidate causative mutation on BTA18 associated with calving and conformation traits in Holstein bulls. Proc. Plant Anim. Genome XXII Conf., San Diego, CA, Jan. 11-15. P1097.

Cole, J.B., J.L. Hutchison, D.J. Null, P.M. VanRaden, G.E. Liu, S.G. Schroeder, T.P. Smith, T.S. Sonstegard, C.P. Van Tassell, and D.M. Bickhart. 2014. The hunt for a functional mutation affecting conformation and calving traits on chromosome 18 in Holstein cattle. Proc. 10th World Congr. Genet. Appl. Livest. Prod., Vancouver, BC, Canada, Aug. 17–22, Commun. 304. 2014.

Cole. J.B., and P.M. VanRaden. 2014. An updated version of lifetime net merit incorporating additional fertility traits and new economic values. J. Dairy Sci. 97(E-Suppl. 1)/J. Anim. Sci. 92(E-Suppl. 2):78(0153).

Dalton, J.C., D.A. Moore, T. Spencer, H. Neibergs, A. DeVries, P. Hansen, and J. Cole. 2014. Survey of genomic management practices of United States’ dairy producers. In: Proc. New Science, New Practices International Cow Fertility Conference, Westport, Ireland, Cambridge University Press, Volume 5, Part 2, p. 260.

Ortega, M.S., A.C. Denicol, D.J. Null, J.B. Cole, and P.J. Hansen. 2014. Single nucleotide polymorphisms in candidate genes related to daughter pregnancy rate in Holstein cows. 10th World Congress on Genetics Applied to Livestock Production, Vancouver, BC, Canada, Aug. 17-22. Comm. 639.

Spencer, T.E., T.W. Geary, P.J. Hansen, H. Neibergs, J. Dalton, and J.B. Cole. 2014. Systems biology approaches to understanding conceptus elongation and early pregnancy loss. Society for the Study of Reproduction, Grand Rapids, MI, Jul. 19-23. (Accepted.)

Stock, K.F., J.B. Cole, J. Pryce, N. Gengler, A. Bradley, B. Heringstad, L. Andrews, and C. Egger-Danner. 2014. Harmonization of recording and use of direct health data as basis of sustainable improvement of dairy health and longevity. ICAR Tech Series 18:(Accepted.)

Sun, C., P.M. VanRaden, J.B. Cole, and J.R. O'Connell. 2014. Increasing predictive ability using dominance in genomic selection. 10th World Congress on Genetics Applied to Livestock Production, Vancouver, BC, Canada, Aug. 17-22. Comm. 291.

VanRaden, P.M., C. Sun, T.A. Cooper, and J.B. Cole. 2014. Genotypes are useful for more than genomic evaluation. Proc. 39th Int. Commun. Anim. Recording Sess., Berlin, Germany, May 19–23, 4 pp.

Xu, L., J.B. Cole, D.M. Bickhart, Y. Hou, J. Song, P.M. VanRaden, T.S. Sonstegard, C.P. Van Tassell, and G. Liu. 2014. Genome wide CNV analysis reveals additional variants associated with milk production traits in Holsteins. Proc. BARC Poster Day 2014, p. 67, abstr. 54.

2013

Cole, J.B., S. Dikmen, D.J. Null, and P.J. Hansen. 2013. Use of genomewide association mapping to identify chromosomal regions associated with rectal temperature during heat stress in Holstein cattle.3rd Annual BA-UMD Fall Symposium “Trends in Agriculture – Climate Change: Food and Environmental Security”, Beltsville, MD. (Accepted.)

Cole, J.B., J.L. Hutchison, D.M. Bickhart, and D.J. Null. 2013. Optimal age at first calving for U.S. dairy cattle. Journal of Dairy Science 96(Suppl. 2):289-290 (abstr. W188).

Cole, J.B., K.L. Parker Gaddis, J.S. Clay, and C. Maltecca. 2013. Genomic evaluation of dairy cattle health. ICAR Tech Series 17:(Accepted.)

Cole, J.B., K.L. Parker Gaddis, J. S. Clay, and C. Maltecca. 2013. Genomic evaluation of low-heritability traits: dairy cattle health as a model. 5th International Symposium on Animal Functional Genomics, Guarujá, SP, Brazil. AB.09, p. 16.

Costa, M.S., Y.T. Utsunomiya, A.S. Carmo, R. Carvalheiro, H.H.R. Neves, M.C. Matos, L.B. Zavarez, A.M. Pe?rez O’Brien, J. So?lkner, J.C. McEwan, J.B. Cole, C.P. Van Tassell, F.S. Schenkel, M.V.G.B. da Silva, L.R. Porto Neto, T.S. Sonstegard, and J.F. Garcia. 2013. Meta-analysis of two genome-wide scans for birth weight in Nellore cattle replicates the PLAG1 region. 5th International Symposium on Animal Functional Genomics, Guarujá, SP, Brazil. (Accepted.)

De Vries, A., J.B. Cole, and D.T. Galligan. 2013. Regression metamodels of an optimal genomic testing strategy in dairy cattle when selection intensity is low. Journal of Dairy Science 96(Suppl. 2):74 (abstr. T207).

Egger-Danner, C., K.F. Stock, J.B. Cole, J. Pryce, N. Gengler, A. Bradley, L. Andrews, and B. Heringstad. 2013. Which new traits are expected to be available in the near future? Interbull Bulletin 47:236-245.

Macciotta, N.P.P., C. Dimauro, D. Vicario, J.B. Cole, and D.J. Null. 2013. Dissection of genomic correlation matrices using multivariate factor analysis in dairy and dual-purpose dairy breeds. Journal of Dairy Science 96(Suppl. 2):618 (abstr. 541).

Maltecca, C., K.L. Parker Gaddis, J.S. Clay, and J.B. Cole. 2013. Challenges and opportunities for farmer-recorded data in health and welfare selection. ICAR Tech Series 17:87-96.

Mousa, M.S., A.J. Seykora, H. Chester-Jones, D.M. Ziegler, and J.B. Cole. 2013. Heritability estimates of performance and health traits of Holstein calves. Journal of Dairy Science 96(Suppl. 2):291 (abstr. W194).

Olynk Widmar, N.J., M.M. Schutz, and J.B. Cole. 2013. Breeding for polled dairy cows versus dehorning: Preliminary cost assessments & discussion. Journal of Dairy Science 96(Suppl. 2):602 (abstr. TH373).

Ortega, M.S., J.B. Cole, and P.J. Hansen. 2013. Changes in expression of CWC15 during preimplantation development in the bovine embryo. Proceedings of the 11th AMCB Research Symposium, University of Florida:25.

Ortega, M.S., J.B. Cole, T.S. Sonstegard, and P.J. Hansen. 2013. Changes in expression of genes associated with genetic variation in preimplantation development of the bovine embryo. Proceedings of the 40th Annual Conference of the International Embryo Transfer Society, Reno, Nevada. (Submitted.)

Parker Gaddis, K.L., J.B. Cole, J.S. Clay, and C. Maltecca. 2013. Analysis of health trait data from on-farm computer systems in the U.S. I: Pedigree and genomic variance components estimation. Journal of Dairy Science 96(Suppl. 2):443-444 (abstr. 446).

Parker Gaddis, K.L., J.B. Cole, J.S. Clay, and C. Maltecca. 2013. Analysis of health trait data from on-farm computer systems in the U.S. II: Comparison of genomic analyses including two-stage and single-step methods. Journal of Dairy Science 96(Suppl. 2):444 (abstr. 447).

Stock, K.F., J.B. Cole, J. Pryce, N. Gengler, A. Bradley, L. Andrews, B. Heringstad, and C. Egger-Danner. 2013. Standardization of health data – ICAR guidelines including health key. ICAR Tech Series 17:75-81.

Xu, L., J.B. Cole, Y. Hou, D.M. Bickhart, J. Song, P.M. VanRaden, T.S. Sonstegard, C.P. Van Tassell, and G.E. Liu. 2013. A genome-wide association study of between copy number variation and milk production traits in Holstein population. 3rd Annual BA-UMD Fall Symposium “Trends in Agriculture – Climate Change: Food and Environmental Security”, Beltsville, MD. (Accepted.)

2012

Cole, J.B. 2012. Fine-mapping of QTL using SNP genotypes. 16th QTL-MAS Workshop, Alghero, Italy, May 24-25.

Cole, J.B. 2012. Applications of haplotypes in dairy farm management. Proc. European Assoc. Anim. Prod., Bratislava, Slovakia, Aug. 27-31.

Cole, J.B. 2012. PyPedal, an open source software package for pedigree analysis. Proc. European Assoc. Anim. Prod., Bratislava, Slovakia, Aug. 27-31.

Cole, J.B., Stock, K.F., Pryce, J., Bradley, A., Gengler, N., Andrews, L., and Egger-Danner, C. 2012. An international overview of the recording and use of functional traits in dairy cattle breeding and management. J. Dairy Sci. 95(Suppl. 2):443(abstr. 439).

DeVries, A., Cole, J.B., and Galligan, D.T. 2012. Economics of getting cows pregnant: the quality of the pregnancy, Proc. Great Lakes Regional Dairy Conf., Mt. Pleasant, MI, Feb. 9–11, pp. 70–78.

Dikmen, S., Cole, J.B., Null, D.J., and Hansen, P.J. 2012. Genomic evaluation of rectal temperature in Holstein cattle. J. Dairy Sci. 95(Suppl. 2):401(abstr. 327).

Ehrlich, J.L., Cole, J.B., and Null, D. 2012. Measuring a milk response – lactation models add power. Proc. Amer. Assoc. Bovine Practitioners, Montreal, Canada, Sept. 20–22.

McClure, M., E.-S. Kim, J. Cole, G.R. Wiggans, L.K. Matukumalli, S. Schroeder, C. Van Tassell, and T. Sonstegard. 2012. Hunting for the weaver causative mutation in Brown Swiss cattle. Proc. Plant Anim. Genome XX Conf., San Diego, CA, Jan. 14-18, abstr. P0561.

Norman, H.D., Hutchison, J.L., and Cole, J.B. 2012. Increased use of young bulls in dairy cattle breeding programs. J. Dairy Sci. 95(Suppl. 2):521-522(abstr. W60).

Parker Gaddis, K.L., Cassady, J.P., Cole, J.B., and Maltecca, C. 2012. Incidence validation and causal relationship analysis of producer-recorded health event data from on-farm computer systems in the U.S. J. Dairy Sci. 95(Suppl. 2):225-226(abstr. 229).

Sonstegard, T., Wang, S., Van Tassell, C., Ma, Li., Wiggans, G., Crooker, B., Cole, J., Mariani, B. Kim, E.-S., Garbe, J., Fahrenkrug, S., Liu, G., and Da, Y. 2012. Signature of forty years of artificial selection in U.S. Holstein cattle identified by long-range frequency analyses. 4th Int. Conf. on Quantitative Genetics: Understanding Variation in Complex Traits, Edinburgh, Scotland, June 17-22, Programme & Book of Abstracts, p. 213, abstr. P-314.

Stock, K.F., Cole, J.B., Pryce, J., Gengler, N., Bradley, A., Andrew, L., and Egger-Danner, C. 2012. Survey on the recording and use of functional traits in dairy management and breeding. Proc. Intl. Committee Anim. Recording, Cork, Ireland, May 28–June 1, 7 pp.

2011

Cole, J.B. 2011. Data structure and visualization. J. Anim. Sci. 89(E-Suppl. 1)/J. Dairy Sci. 94(E-Suppl. 1):226(abstr. 198).

De Vries, A., Cole, J.B., and Galligan, D.T. 2011. Economics of reproduction: the quality of the pregnancy. Dairy Cattle Reprod. Counc. Annu. Mtg., Kansas City, MO, Nov. 10–11, pp. 90–97.

De Vries, A., J. B. Cole, and D. T. Galligan. 2011. Economics of reproduction and genetics: the quality of the pregnancy. Southeast Dairy Herd Management Conference. Nov. 2, 2011, Macon, GA. pp. 45-56.

Dikmen, S., Cole, J.B., Null, D.J., and Hansen, P.J. 2011. Heritability of rectal temperature and genetic correlations with production and reproduction traits in dairy cattle. J. Dairy Sci. 94(E-Suppl. 1):255(abstr. 275).

Macciotta, N.P.P. and Cole, J.B. 2011. Multivariate factor analysis of genomic correlation matrices in three US dairy cattle breeds. J. Dairy Sci. 94(E-Suppl. 1):i-ii(abstr. LB3).

2010

Cole, J. B. 2010. Use of haplotypes to predict selection limits and Mendelian sampling. Journal of Dairy Science 93(E-Suppl. 1):535(abstr. 623).

Cole, J. B., and D. J. Null. 2010. Age at first calving in Holstein cattle in the United States. Journal of Dairy Science 93(E-Suppl. 1):594(abstr. W28).

Cole, J.B. and P. M. VanRaden. 2010. Use of haplotypes to estimate Mendelian sampling effects and selection limits. Proceedings of the 9th World Congress on Genetics Applied to Livestock Production, Aug. 1-6, 2010, Leipzig, Germany.

Cole, J.B., G. R. Wiggans, L. Ma, T. S. Sonstegard, B. A. Crooker, C. P. Van Tassell, J. Yang, L. K. Matukumalli, and Y. Da, Y.. 2010. High resolution QTL maps of 31 traits in contemporary U.S. Holstein cows. Proceedings of the 9th World Congress on Genetics Applied to Livestock Production, Aug. 1-6, 2010, Leipzig, Germany.

Cole, J. B., T. S. Sonstegard, L. Ma, G. R. Wiggans, B. A. Crooker, C. P. Van Tassell, J. Yang, L. Matukumalli, and Y. Da. 2010 High resolution QTL map of net merit component traits and calving traits from genome-wide association analysis in contemporary U.S. Holstein cows. Proc. Plant Anim. Genome XVII Conf., San Diego, CA, Jan. 9-13, abstr. P565.

Ma, L., T. S. Sonstegard, J. B. Cole, G. R. Wiggans, B. A. Crooker, C. P. Van Tassell, J. Yang, L. Matukumalli, and Y. Da. 2010. X chromosome SNPs were heavily involved in epistasis effects of net merit component traits in contemporary U.S. Holstein cows. Proc. Plant Anim. Genome XVII Conf., San Diego, CA, Jan. 9-13, abstr. P542. 2010.

Wiggans, G. R., L. Ma, T. S. Sonstegard, J. B. Cole, B. A. Crooker, C. P. Van Tassell, J. Yang, L. Matukumalli, and Y. Da. 2010. High resolution QTL map of body conformation traits from genome-wide association analysis in contemporary U.S. Holstein cows. Proc. Plant Anim. Genome XVII Conf., San Diego, CA, Jan. 9-13, abstr. P547. 2010.

2009

Attalla, S.A., Seykora, A.J., Cole, J.B., and Heins, B.J. 2009. Estimation of genetic parameters and transmitting ability for Minnesota Johne's milk ELISA test. J. Dairy Sci. 92(E-Suppl. 1):20(abstr. M56).

Cole, J.B. 2009. Data collection ratings and best prediction of lactation yields. ICAR Tech Ser. 13:403–406.

Cole, J.B. 2009. Visualization of results from genomic predictions. J. Dairy Sci. 92(E-Suppl. 1):314(abstr. 281).

Cole, J.B. and Null, D.J. 2009. Best prediction of lactation yields accounting for regional and seasonal differences. J. Dairy Sci. 92(E-Suppl. 1):209(abstr. T38).

Cole, J.B., VanRaden, P.M., O'Connell, J.R., Van Tassell, C.P., Sonstegard, T.S., Schnabel, R.D., Taylor, J.F., and Wiggans, G.R. 2009. Distribution and location of genetic effects for dairy traits. ICAR Tech Ser. 13:355–360.

Sonstegard, T. S., L. Ma, J. B. Cole, G. R. Wiggans, B. A. Crooker, C. P. Van Tassell1, B. D. Mariani, and Y. Da . 2009. Genome signature of artificial selection for high milk yield in Holstein cattle. Plant and Animal Genome XVII Proceedings. (accepted)

VanRaden, P.M., Tooker, M.E., and Cole, J.B. 2009. Can you believe those genomic evaluations for young bulls? J. Dairy Sci. 92(E-Suppl. 1):314(abstr. 279).

2008

Cole, J. B. 2008. Data collection ratings and best prediction of lactation yields. International Committee on Animal Recording Proceedings. ICAR Technical Series. 13:403-406.

Cole, J. B., D. J. Null, and L. R. Bacheller. 2008. A data exchange format and national database for producer-recorded health event data from on-farm management software. Journal of Dairy Science 91(E-Suppl. 1):2-3(abstr. T6)

Cole, J. B., P. M. VanRaden, J. R. O'Connell, C. P. Van Tassell, and R. D. Schnabel. 2008. Distribution and location of genetic effects for dairy traits. International Committee on Animal Recording Proceedings. ICAR Technical Series. 13:355-360.

Sonstegard, T. S., L. Ma, J. B. Cole, G. R. Wiggans, C. P. Van Tassell, G. Liu, B. D. Mariani, B. A. Crooker, P. M. VanRaden, M. V. da Silva, and Y. Da. 2008. Genomic signatures of artificial selection in U.S. Holstein cows. International Society for Animal Genetics Proceedings (Poster 638 2098)

2007

Cole, J.B. and Null, D.J. 2007. Genetic evaluation of lactation persistency estimated by best prediction for Ayrshire, Brown Swiss, Guernsey, and Milking Shorthorn dairy cattle. J. Dairy Sci. 90(Suppl. 1):20(abstr. M52).

Cole, J.B., VanRaden, P.M., and Dematawewa, C.M.B. 2007. Estimation of yields for long lactations using best prediction. J. Dairy Sci. 90(Suppl. 1):421(abstr. 558).

Cole, J. B., B. R. Southey, D. E. Franke, and E. A. Leighton. 2007. Discrete time survival analysis of longevity in a colony of dog guides in Proceedings of 5th International Working Dog Breeding Conference, San Antonio, TX.

Cole, J. B., P. M. VanRaden, and C. M. B. Dematawewa. 2007. Estimation of yields for long lactations using best prediction. Journal of Dairy Science 90(Suppl. 1):421(abstr. 558).

Norman, H. D., J. R. Wright, M. T. Kuhn, S. M. Hubbard, and J. B. Cole. 2007. Genetic and environmental factors that affect gestation length. Journal of Dairy Science 90(Suppl. 1):264 (abstr. T73)

Norman, H. D., J. R. Wright, and J. B. Cole. 2007. Effect of temperature and humidity on gestation length. Journal of Dairy Science 90(Suppl. 1):16(abstr. M38)

Norman, H. D., J. R. Wright, P. M. VanRaden, and J. B. Cole. 2007. Effect of service sire and cow sire on gestation length. Journal of Dairy Science 90(Suppl. 1):194(abstr. 230)

Wiggans, G. R., J. B. Cole, and L. L. M. Thornton. 2007. Multitrait evaluation for calving ease and stillbirth with separate genetic effects by parity. Journal of Dairy Science 90(Suppl. 1):377(abstr. 422).

2006

Appuhamy, J. A. D. R. N., B. G. Cassell, and J. B. Cole. 2006. Effect of mastitis and postpartum metabolic diseases on lactation persistency of Holstein and Jersey cows. Journal of Dairy Science 89(Suppl. 1):398(abstr. 476).

Cole, J. B., A. H. Sanders, and J. S. Clay. 2006. Use of producer-recorded health data in determining incidence risks and relationships between health events and culling. Journal of Dairy Science 89(Suppl. 1):10(abstr. M7).

Cole, J. B., G. R. Wiggans, and P. M. VanRaden. 2006. Genetic evaluation of stillbirth in United States Holsteins using a sire-maternal grandsire threshold model. Comm. 01-28 in Proceedings of the 8th World Congress on Genetics Applied to Livestock Production, Belo Horizonte, Brazil.

Cole, J. B., G. R. Wiggans, P. M. VanRaden, and R. H. Miller. 2006. Stillbirth (co)variance components for a sire-maternal grandsire threshold model. Journal of Dairy Science 89(Suppl. 1):273(abstr. 339).

VanRaden, P. M., M. E. Tooker, J. B. Cole, G. R. Wiggans, and J. H. Megonigal, Jr. 2006. Genetic evaluations for mixed breed populations. Journal of Dairy Science 89(Suppl. 1):98(abstr. 40).

Wiggans, G. R., C. P. Van Tassell, J. B. Cole, and L. L. M. Thornton. 2006. Genetic correlations between first and later parity calving ease in a sire-maternal grandsire model. Comm. 01-92 in Proceedings of the 8th World Congress on Genetics Applied to Livestock Production, Belo Horizonte, Brazil.

2005

Cole, J. B., and A. H. Sanders. 2005. Genetic evaluation of clinical mastitis in U.S. dairy cattle in Lamont, S.J., M. F. Rothschild, and D. L. Harris, editors. Proceedings of the Third International Symposium on Genetics of Animal Health, July 13-15, 2005, Ames, Iowa. p. 112.

Cole, J. B., B. R. Southey, D. E. Franke, and E. A. Leighton. 2005. Discrete time survival analysis of longevity in a colony of dog guides. Journal of Animal Science 83 (Suppl. 1):103(abstr. 136).

Cole, J. B., and P. M. VanRaden. 2005. Genetic evaluation and best prediction of lactation persistency. Journal of Dairy Science 88 (Suppl. 1):379-380(abstr. 651).

2004

Cole, J. B., and E. A. Leighton. 2004. Linear versus threshold model analysis of trainability in a colony of German Shepherd dog guides. Journal of Animal Science 87(Suppl. 1):391(abstr. 648)

Cole, J. B., H. D. Norman, and P. D. Miller. 2004. Genetic improvement of dairy cattle health in Proceedings of the 12th International Conference on Production Diseases in Farm Animals, July 19-22, 2004, East Lansing, MI. p. 78.

Cole, J. B., and D. J. Null. 2007. Genetic evaluation of lactation persistency estimated by best prediction for Ayrshire, Brown Swiss, Guernsey, and Milking Shorthorn dairy cattle. Journal of Dairy Science 90(Suppl. 1):20(abstr. M52)

Cole, J. B., M. E. Tooker, P. M. VanRaden, and J. H. Megonigal. 2004. Breed composition codes for crossbred dairy cattle in the United States. Journal of Dairy Science 87(Suppl. 1):284(abstr. 536).

VanRaden, P. M., M. E. Tooker, and J. B. Cole. 2004. Heterosis and breed differences for daughter pregnancy rate in crossbred dairy cows. Journal of Dairy Science 87(Suppl. 1):284(abstr. 532)

2003

Cole, J. B., D. E. Franke, and E. A. Leighton. 2003. Genetic parameters for longevity in a colony of German Shepherd dog guides. Journal of Animal Science 81 (Suppl. 1):197(abstr. M76)

Cole, J. B., D. E. Franke, and E. A. Leighton. 2003. Population genetic structure of a colony of German Shepherd and Labrador Retriever dog guides. Journal of Animal Science 81 (Suppl. 1):69(abstr. 272)

2002

Cole, J. B., and D. E. Franke. 2002. PyPedal: A package for pedigree analysis using the Python programming language. Journal of Animal Science 80 (Suppl. 1):323(abstr. 1291)

1998

Hansen, L. B., J. B. Cole, and G. D. Marx. 1998. Body size of lactating dairy cows: Results of divergent selection for over 30 years. Proceedings of the 6th World Congress on Genetics Applied to Livestock Production, Armidale, NSW, Australia XXV:35-38.

1997

Cole, J. B., L. B. Hansen, and G. D. Marx. 1997. Productive life, reasons for disposal, and body dimensions and weights of Holsteins selected for large versus small body size. Journal of Dairy Science 80(Suppl. 1): 252(abstr. P423)

Software

2017

Cole, J. B. 2017. gene-editing: Programs for simulation of gene editing applied to a dairy cattle population. Website: https://github.com/wintermind/multiple-recessives.

2014

Cole, J. B. 2014. multiple-recessives: Programs for simulation of strategies for managing multiple recessives in a dairy cattle population. Website: https://github.com/wintermind/multiple-recessives.

2007

Cole, J. B., and P. M. VanRaden. 2007. A Manual for Use of BESTPRED: A Program for Estimation of Lactation Yield and Persistency Using Best Prediction. Website: http://www.aipl.arsusda.gov/software/bestpred/.

2005

Cole, J. B. 2005. PyPedal: A package for pedigree analysis using the Python programming language, v. 2.0.0. Website: http://pypedal.sourceforge.net/.