John B. Cole's Publications

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


Refereed Journal Articles

( 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.

2017

Cole, J.B., J.M. Bormann, C.A. Gill, H. Khatib, J.E. Koltes, C. Maltecca, and F. Miglior. 2016. Breeding and Genetics Symposium: Resilience of livestock to changing environments. Journal of Animal Science. (In press.)

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. (Accepted.)

Hutchison, J.L., P.M. VanRaden, D.J. Null, J.B. Cole, and D.M. Bickhart. 2017. Benefits from reducing age at first calving in U.S. dairy breeds by management and selection. Journal of Dairy Science. (Submitted.)

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.)

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. (Accepted.)

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. (Accepted.)

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. Article in press. doi:http://dx.doi.org/10.3168/jds.2016-11907.

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. (Accepted.)

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. (Submitted.)

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. Review in Advance first posted online on November 16, 2016. doi:10.1146/annurev-animal-021815-111422.

2016

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.

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.

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)

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.

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.

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)

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.

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.

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.

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


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)

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.

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.

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.

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.

Zavarez, L.B., Y.T. Utsunomiya, A.S. Carmo, H.H.R. Neves, R. Carvalheiro, M. Ferenčaković, 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

 
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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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

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.

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

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.

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.

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

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.

Cole, J.B., and P.M. VanRaden. 2010. Visualization of results from genomic evaluations. Journal of Dairy Science 93:2727-2740.

2009

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

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.

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.

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.

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.

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

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

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.

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.

Cole, J.B. 2007. PyPedal: A package for pedigree analysis using the Python programming language. Computers and Electronics in Agriculture 57:107-113.

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.

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.

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

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

2005

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

Cole, J.B., D.E. Franke, and E.A. Leighton. 2004. Population genetic structure of a colony of German Shepherd and Labrador Retriever dog guides. Journal of Animal Science 82:2906-2912.

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

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.

Book Chapters and Technical Reports


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. (Submitted.)


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


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


2015

Arceo, M., F. Tiezzi, J.B. Cole, and C. Maltecca. 2015. Identification of gene networks underlying dystocia in dairy cattle. Journal of Dairy Science 98(Suppl. 2):(Submitted.)

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. Journal of Dairy Science 98(Suppl. 2):(Submitted.)

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.)

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. 2014. Power of a very large cattle pedigree: commona nds ex specific recombination and their genetic control. Proc. Plant Anim. Genome XXIII Conf., San Diego, CA, Jan. 11-15. (Submitted.)

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. Journal of Dairy Science 98(Suppl. 2):(Submitted.)

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. Journal of Dairy Science 98(Suppl. 2):(Submitted.)

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. Journal of Dairy Science 98(Suppl. 2):(Submitted.)

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. (Submitted.)

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. (Submitted.)

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. (Submitted.)

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. (Accepted.)

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., et al. 2014. A Needle in a Haystack: The Hunt for a Functional Mutation Affecting Conformation and Calving Traits on Chromosome 18 in Holstein Cattle. 10th World Congress on Genetics Applied to Livestock Production, Vancouver, BC, Canada, Aug. 17-22. (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. (Accepted.)

Cole. J.B., and P.M. VanRaden. 2014. An updated version of lifetime net merit incorporating additional fertility traits and new economic values. Journal of Dairy Science 97(Suppl. 2):(Accepted.)

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. (Accepted.)

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. (Accepted.)

VanRaden, P.M., C. Sun, T.A. Cooper, and J.B. Cole. 2014. Genotypes are useful for more than genomic evaluation. ICAR Tech Series 18:(Accepted.)

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. Pérez O’Brien, J. Sölkner, 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


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/.