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United States Department of Agriculture

Agricultural Research Service

Related Topics

John B Cole
Animal Genomics and Improvement Laboratory
Genetics

Phone: (301) 504-8665
Fax: (301) 504-8092
Room 320

10300 BALTIMORE AVENUE
BLDG 005 BARC-WEST
BELTSVILLE , MD 207052350

Projects
Improving Genetic Predictions in Dairy Animals Using Phenotypic and Genomic Information
In-House Appropriated (D)
  Accession Number: 423282
National Dairy Genetic Evaluation Program
Non-Funded Cooperative Agreement (N)
  Accession Number: 424155
1000 Bull Genomes Project
Non-Funded Cooperative Agreement (N)
  Accession Number: 426790
Sequence-Based Big Data Genomic Discovery and Application to Improve Dairy Fertility
Reimbursable Cooperative Agreement (R)
  Accession Number: 430498
Systems Biology Analyses Comparison of Gene and Protein Expression from Slick and Normal Haired Cattle
Non-Assistance Cooperative Agreement (S)
  Accession Number: 427589

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)
Genetics, genomics and fertility -
Dalton, J., Moore, D., Spencer, T.E., Hansen, P.J., Cole, J.B., Neibergs, H. 2016. Genetics, genomics and fertility. Society of Theriogenology Annual Conference Proceedings. Clinical Theriogenology 8(3):165-170.
Stochastic dynamic simulation modeling including multitrait genetics to estimate genetic, technical, and financial consequences of dairy farm reproduction and selection strategies -
Kaniyamattam, K., Elzo, M.A., Cole, J.B., De Vries, A. 2016. Stochastic dynamic simulation modeling including multitrait genetics to estimate genetic, technical, and financial consequences of dairy farm reproduction and selection strategies. Journal of Dairy Science. 99(10):8187-8202.
Phenotypic and genetic effects of recessive haplotypes on yield, longevity, and fertility -
Cole, J.B., Null, D.J., Van Raden, P.M. 2016. Phenotypic and genetic effects of recessive haplotypes on yield, longevity, and fertility. Journal of Dairy Science. 99(9):7274-7288.
Opportunities for genetic improvement of metabolic diseases -
Pryce, J., Parker Gaddis, K.L., Koeck, A., Bastin, C., Abdelsayed, M., Gengler, N., Miglior, F., Heringstad, B., Egger-Danner, C., Stock, K., Bradley, A., Cole, J.B. 2016. Invited review: Opportunities for genetic improvement of metabolic diseases. Journal of Dairy Science. 99(9):6855-6873.
Changes in genetic selection differentials and generation intervals in US dairy cattle as a result of genomic selection -
Garcia, A., Cole, J.B., Van Raden, P.M., Wiggans, G.R., Ruiz, F., Van Tassell, C.P. 2016. Changes in genetic selection differentials and generation intervals in US dairy cattle as a result of genomic selection. Proceedings of the National Academy of Sciences. 113:E3995–E4004.
Use of a threshold animal model to estimate calving ease and stillbirth (co)variance components for US Holsteins -
Cole, J.B., Null, D.J., Tsuruta, S. 2016. Use of a threshold animal model to estimate calving ease and stillbirth (co)variance components for US Holsteins. Journal of Dairy Science. 99(E-Suppl. 1)/Journal of Animal Science. 94(E-Suppl. 5):182-183(abstr. 0385).
Genomic analysis of lactation persistency in four breeds of dairy cattle -
Cole, J.B., Null, D.J., Parker Gaddis, K.L. 2016. Genomic analysis of lactation persistency in four breeds of dairy cattle. Journal of Dairy Science. 99(E-Suppl. 1)/Journal of Animal Science. 94(E-Suppl. 5):156(abstr. 0333).
Genetic analysis of superovulation and embryo transfer traits in Holstein cattle -
Parker Gaddis, K.L., Dikmen, S., Cole, J.B., Hansen, P.J. 2016. Genetic analysis of superovulation and embryo transfer traits in Holstein cattle. Journal of Dairy Science. 99(E-Suppl. 1)/Journal of Animal Science. 94(E-Suppl. 5):179(abstr. 0379).
Genetic solutions to infertility caused by heat stress -
Hansen, P.J., Dikmen, S., Cole, J.B., Ortega, M.S., Dahl, G.E. 2016. Genetic solutions to infertility caused by heat stress. Journal of Dairy Science. 99(E-Suppl. 1)/Journal of Animal Science. 94(E-Suppl. 5):192(abstr. 0405).
Improving fertility of dairy cattle using translational genomics -
Spencer, T.E., Neibergs, H., Hansen, P.J., Cole, J.B., Dalton, J.C., Moore, D.A., Chahine, M., De Vries, A. 2016. Improving fertility of dairy cattle using translational genomics. Journal of Dairy Science. 99(E-Suppl. 1)/Journal of Animal Science. 94(E-Suppl. 5):325-326(abstr. 0694).
Exploring the feasibility of using copy number variants as genetic markers through large-scale whole genome sequencing experiments -
Bickhart, D.M., Xu, L., Hutchison, J.L., Cole, J.B., Null, D.J., Schroeder, S.G., Song, J., Garcia, J.F., Sonstegardq, T.S., Van Tassell, C.P., Schnabel, R.D., Taylor, J.F., Lewin, H.A., Liu, G. 2016. Exploring the feasibility of using copy number variants as genetic markers through large-scale whole genome sequencing experiments. Journal of Dairy Science. 99(E-Suppl. 1)/Journal of Animal Science. 94(E-Suppl. 5):142(abstr. 0306).
Calculation of genomic predicted transmitting abilities for bovine respiratory disease complex in Holsteins -
Van Tassell, C.P., Spangler, G.L., Bickhart, D.M., Wiggans, G.R., Cole, J.B., Taylor, J.F., Neibergs, H.L., Seabury, C., Van Eenennaam, A.L., Womack, J.E., Brd Consortium 2016. Calculation of genomic predicted transmitting abilities for bovine respiratory disease complex in Holsteins. Journal of Dairy Science. 99(E-Suppl. 1)/Journal of Animal Science. 94(E-Suppl. 5):133(abstr. 0288).
Explorations in genome-wide association studies and network analyses with dairy cattle fertility traits -
Parker Gaddis, K.L., Null, D.J., Cole, J.B. 2016. Explorations in genome-wide association studies and network analyses with dairy cattle fertility traits. Journal of Dairy Science. 99(8):6420-6435.
Whole-genome sequencing reveals the diversity of cattle copy number variations and multicopy genes -
Bickhart, D.M., Xu, L., Hutchison, J.L., Cole, J.B., Schroeder, S.G., Song, J., Garcia, J., Van Tassell, C.P., Sonstegard, T.S., Schnabel, R.D., Taylor, J.F., Lewin, H.A., Liu, G. 2016. Whole-genome sequencing reveals the diversity of cattle copy number variations and multicopy genes. DNA Research. 23(3):253-62.
Diversity and population-genetic properties of copy number variations and multicopy genes in cattle -
Bickhart, D.M., Xu, L., Hutchison, J.L., Cole, J.B., Null, D.J., Schroeder, S.G., Song, J., Garcia, J., Van Tassell, C.P., Sonstegard, T.S., Schnabel, R.D., Taylor, J.F., Lewin, H.A., Liu, G. 2016. Diversity and population-genetic properties of copy number variations and multicopy genes in cattle [abstract]. USDA NIFA Animal Genome Program PD Meeting, January 8, 2016, San Diego, California.
Effect of sex, age, and breed on genetic recombination features in cattle -
Shen, B., Wang, Z., Jiang, J., Cole, J.B., Bickhart, D.M., Wiggans, G.R., Liu, G., Ma, L. 2016. Effect of sex, age, and breed on genetic recombination features in cattle. Plant and Animal Genome Conference Proceedings. San Diego, CA, Jan. 9–13, P0522.
Genomic selection in multi-breed dairy cattle populations -
Cole, J.B., Da Silva, M.V. 2016. Genomic selection in multi-breed dairy cattle populations. Brazilian Animal Science Society. 45(4):195–202.
Invited review: genomic selection in multi-breed dairy cattle populations -
Cole, J.B., Da Silva, M. 2016. Invited review: genomic selection in multi-breed dairy cattle populations. Revista Brasileira de Zootecnia. 45(4):195-202.
Use of single nucleotide polymorphisms in candidate genes associated with daughter pregnancy rate for prediction of genetic merit for reproduction in Holstein cows -
Ortega, M., Denicol, A.C., Cole, J.B., Null, D.J., Hansen, P.J. 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(3):288–297.
Reducing animal sequencing redundancy by preferentially selecting animals with low-frequency haplotypes -
Bickhart, D.M., Hutchison, J.L., Null, D.J., Van Raden, P.M., Cole, J.B. 2016. Reducing animal sequencing redundancy by preferentially selecting animals with low-frequency haplotypes. Journal of Dairy Science. 99(7):5526-5534.
A simple strategy for managing many recessive disorders in a dairy cattle breeding program -
Cole, J.B. 2015. A simple strategy for managing many recessive disorders in a dairy cattle breeding program. Genetic Selection Evolution. 47:94.
Benchmarking dairy herd health status using routinely recorded herd summary data -
Parker Gaddis, K., Cole, J.B., Clay, J.S., Maltecca, C. 2016. Benchmarking dairy herd health status using routinely recorded herd summary data. Journal of Dairy Science. 99(2):1298-1314.
Cattle sex-specific recombination and genetic control from a very large pedigree -
Ma, L., O'Connell, J.R., Van Raden, P.M., Shen, B., Padhi, A., Sun, C., Bickhart, D.M., Cole, J.B., Null, D.J., Liu, G., Da, Y., Wiggans, G.R. 2015. Cattle sex-specific recombination and genetic control from a very large pedigree. PLoS Genetics. 11(11):e1005387.
Single nucleotide polymorphisms associated with thermoregulation in lactating dairy cows exposed to heat stress -
Dikmen, S., Wang, X., Ortega, M., Null, D.J., Cole, J.B., Hansen, P.J. 2015. Single nucleotide polymorphisms associated with thermoregulation in lactating dairy cows exposed to heat stress. Journal of Animal Breeding and Genetics. 132(6):409-419.
Animal selection for whole genome sequencing by quantifying the unique contribution of homozygous haplotypes sequenced -
Bickhart, D.M., Cole, J.B., Hutchison, J.L. 2015. Animal selection for whole genome sequencing by quantifying the unique contribution of homozygous haplotypes sequenced. Journal of Dairy Science. 98(Suppl. 2)/Journal of Animal Science 93(Suppl. 3):649(abstr. W86).
Genome-wide association study of fertility traits in dairy cattle using high-density single nucleotide polymorphism marker panels -
Parker Gaddis, K.L., Cole, J.B. 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)/Journal of Animal Science 93(Suppl. 3):578(abstr. 538).
Using routinely recorded herd data to predict and benchmark herd and cow health status -
Parker Gaddis, K.L., Cole, J.B., Clay, J.S., Maltecca, C. 2015. Using routinely recorded herd data to predict and benchmark herd and cow health status. Journal of Dairy Science. 98(Suppl. 2)/Journal of Animal Science 93(Suppl. 3):815(abstr. 687).
Assignment of polled status using single nucleotide polymorphism genotypes and predicted gene content -
Null, D.J., Cole, J.B., Sun, C., Van Raden, P.M. 2015. Assignment of polled status using single nucleotide polymorphism genotypes and predicted gene content. Journal of Dairy Science. 98(Suppl. 2)/Journal of Animal Science 93(Suppl. 3):800(abstr. 647).
Identification of gene networks underlying dystocia in dairy cattle -
Arceo, M.E., Tiezzi, F., Cole, J.B., Maltecca, C. 2015. Identification of gene networks underlying dystocia in dairy cattle. Journal of Dairy Science. 98(Suppl. 2)/Journal of Animal Science 93(Suppl. 3):840(abstr. 749).
Single nucleotide polymorphisms in specific candidate genes are associated with phenotypic differences in days open for first lactation in Holstein cows -
Ortega, M., Denicol, A., Null, D.J., Cole, J.B., Hansen, P.J. 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)/Journal of Animal Science 93(Suppl. 3):648–649(abstr. W85).
Selection signature analysis in Holstein cattle identified genes known to affect reproduction -
Ma, L., Sonstegard, T.S., Van Tassell, C.P., Cole, J.B., Wiggans, G.R., Crooker, B., Ponce De Leon, F., Yang, D. 2015. Selection signature analysis in Holstein cattle identified genes known to affect reproduction. Journal of Dairy Science. 98(Suppl. 2)/Journal of Animal Science 93(Suppl. 3):350(abstr. T102).
Genomic prediction of disease occurrence using producer-recorded health data: A comparison of methods Reprint Icon -
Parker Gaddis, K.L., Tiezzi, F., Cole, J.B., Clay, J.S., Maltecca, C. 2015. Genomic prediction of disease occurrence using producer-recorded health data: A comparison of methods. Genetic Selection Evolution. 47:41.
Assessment of autozygosity in Nellore cows (Bos indicus) through high-density SNP genotypes Reprint Icon -
Zavarez, L.B., Utsunomiya, Y.T., Carmo, A.S., Neves, H.H., Carvalheiro, R., Ferencakovic, M., Pérez O’Brien, A.M., Curik, I., Cole, J.B., Van Tassell, C.P., Silva, M.V., Sonstegard, T.S., Sölkner, J., Garcia, J.F. 2015. Assessment of autozygosity in Nellore cows (Bos indicus) through high-density SNP genotypes. Frontiers in Genetics. 6:5.
Genome changes due to forty years of artificial selection associated with divergent dairy production and reproduction -
Sonstegard, T.S., Ma, L., Kim, E., Van Tassell, C.P., Wiggans, G.R., Crooker, B.A., Cole, J.B., Liu, G., Garbe, J.R., Fahrenkug, S.C., Ponce De Leon, F., Da, Y. 2015. Genome changes due to forty years of artificial selection associated with divergent dairy production and reproduction. Plant and Animal Genome Conference. San Diego, CA, January 10–14, W150.
Genomic signatures reveal geographic adaption and human selection in cattle -
Xu, L., Bickhart, D.M., Cole, J.B., Schroeder, S.G., Song, J., Van Tassell, C.P., Sonstegard, T.S., Liu, G. 2014. Genomic signatures reveal geographic adaption and human selection in cattle. Molecular Biology and Evolution. 32(3):711-25.
A genome-wide association study for clinical mastitis in first parity US Holstein cows using a single-step approach and a genomic matrix re-weighting procedure Reprint Icon -
Tiezzi, F., Parker Gaddis, K.L., Cole, J.B., Clay, J.S., Maltecca, C. 2015. A genome-wide association study for clinical mastitis in first parity US Holstein cows using a single-step approach and genomic matrix re-weighting procedure. PLoS One. 10(2):e0114919.
Genetic base changes for December 2014 -
Van Raden, P.M., Tooker, M.E., Wright, J.R., Cole, J.B., Null, D.J., Lawlor, T.J. 2014. Genetic base changes for December 2014. AIP Research Report BASE3(10-14).
Net merit as a measure of lifetime profit: 2014 revision -
Van Raden, P.M., Cole, J.B. 2014. Net merit as a measure of lifetime profit: 2014 revision. AIP Research Report NM$5 (10-14).
Invited review: overview of new traits and phenotyping strategies in dairy cattle with a focus on functional traits Reprint Icon -
Egger-Danner, C., Cole, J.B., Pryce, J., Gengler, N., Heringstad, B., Stock, K., Bradley, A., Andrews, L. 2015. Invited review: overview of new traits and phenotyping strategies in dairy cattle with a focus on functional traits. Animal. 9(2):191-207.
Genome wide CNV analysis reveals additional variants associated with milk production traits in Holsteins -
Xu, L., Cole, J.B., Bickhart, D.M., Hou, Y., Song, J., Van Raden, P.M., Sonstegard, T.S., Van Tassell, C.P., Liu, G. 2014. Genome wide CNV analysis reveals additional variants associated with milk production traits in Holsteins. Biomed Central (BMC) Genomics. 15:683.
Systems biology approaches to understanding conceptus elongation and early pregnancy loss -
Spencer, T.E., Geary, T.W., Hansen, P.J., Neibergs, H., Dalton, J., Cole, J.B. 2014. Systems biology approaches to understanding conceptus elongation and early pregnancy loss. Society for the Study of Reproduction Annual Meeting. Grand Rapids, MI, July 19-23, abstr. 64. 2014.
Improvement of prediction ability for genomic selection of dairy cattle by including dominance effects Reprint Icon -
Sun, C., Van Raden, P.M., Cole, J.B., O'Connell, J.R. 2014. Improvement of prediction ability for genomic selection of dairy cattle by including dominance effects. PLoS One. 9(8):e103934.
Dissection of genomic correlation matrices of US Holsteins using multivariate factor analysis Reprint Icon -
Macciotta, N., Dimauro, C., Null, D.J., Gaspa, G., Castellini, M., Cole, J.B. 2015. Dissection of genomic correlation matrices of US Holsteins using multivariate factor analysis. Journal of Animal Breeding and Genetics. 132(1):9-20.
ICAR guidelines for recording, evaluation and genetic improvement of female fertility in dairy cattle -
Andrews, L., Bradley, A.J., Cole, J.B., Egger-Danner, C., Gengler, N., Heringstad, B., Pryce, J., Stock, K., Strandberg, E. 2014. ICAR guidelines for recording, evaluation and genetic improvement of female fertility in dairy cattle. International Committee for Animal Recording Guidelines. Rome, Italy: International Committee for Animal Recording. 262–278 p.
The development of genomics applied to dairy breeding Reprint Icon -
Da Silva, M., Dos Santos, D.J., Boison, S.A., Utsunomiya, A.T., Do Carmo, A.S., Sonstegard, T.S., Cole, J.B., Van Tassell, C.P. 2014. The development of genomics applied to dairy breeding. Livestock Science. 166:66-75.
The hunt for a functional mutation affecting conformation and calving traits on chromosome 18 in Holstein cattle -
Cole, J.B., Hutchison, J.L., Null, D.J., Van Raden, P.M., Liu, G., Schroeder, S.G., Smith, T.P., Sonstegard, T.S., Van Tassell, C.P., Bickhart, D.M. 2014. The hunt for a functional mutation affecting conformation and calving traits on chromosome 18 in Holstein cattle. World Congress of Genetics Applied in Livestock Production. Vancouver, Canada, Aug. 17–22. 3 pp.
Using the whole read: structural variant detection using NGS data -
Bickhart, D.M., Cole, J.B., Hutchison, J.L., Xu, L., Liu, G. 2014. Using the whole read: structural variant detection using NGS data. World Congress of Genetics Applied in Livestock Production. Vancouver, Canada, Aug. 17–22. 5 pp.
Increasing predictive ability using dominance in genomic selection -
Sun, C., Van Raden, P.M., Cole, J.B., O'Connell, J.R. 2014. Increasing predictive ability using dominance in genomic selection. World Congress of Genetics Applied in Livestock Production. Vancouver, Canada, Aug. 17–22. 3 pp.
Single nucleotide polymorphisms in candidate genes related to daughter pregnancy rate in Holstein cows -
Ortega, M.S., Denicol, A.C., Null, D.J., Cole, J.B., Hansen, P.J. 2014. Single nucleotide polymorphisms in candidate genes related to daughter pregnancy rate in Holstein cows. World Congress of Genetics Applied in Livestock Production. Vancouver, Canada, Aug. 17–22. 2 pp.
Genome wide CNV analysis reveals additional variants associated with milk production traits in Holsteins -
Xu, L., Cole, J.B., Bickhart, D.M., Hou, Y., Song, J., Van Raden, P.M., Sonstegard, T.S., Van Tassell, C.P., Liu, G. 2014. Genome wide CNV analysis reveals additional variants associated with milk production traits in Holsteins. BARC Poster Day. BARC Poster Day.p.67, abstract 54.
Genotypes are useful for more than genomic evaluation -
Van Raden, P.M., Sun, C., Cooper, T.A., Null, D.J., Cole, J.B. 2014. Genotypes are useful for more than genomic evaluation. International Committee on Animal Recording(ICAR). Proc. 39th Int. Comm. Anim. Recording Sess., Berlin, Germany, May 19–23, 4 pp.
An updated version of lifetime net merit incorporating additional fertility traits and new economic values -
Cole, J.B., Van Raden, P.M. 2014. An updated version of lifetime net merit incorporating additional fertility traits and new economic values. Journal of Dairy Science. 97(E-Suppl. 1):78 (abstr. 0153).
Development of a lifetime merit-based selection index for US dairy grazing systems Reprint Icon -
Gay, K.D., Widmar, N.J., Nennich, T.D., Schinckel, A.P., Cole, J.B., Schutz, M.M. 2014. Development of a lifetime merit-based selection index for US dairy grazing systems. Journal of Dairy Science. 97(7):4568-4578.
Genomewide association study of reproductive efficiency in female cattle Reprint Icon -
McDaneld, T.G., Kuehn, L.A., Thomas, M.G., Snelling, W.M., Smith, T.P.L., Pollak, E.J., Cole, J.B., Keele, J.W. 2014. Genomewide association study of reproductive efficiency in female cattle. Journal of Animal Science. 92(5):1945-1957.
Bovine exome sequence analysis and targeted SNP genotyping of recessive fertility defects HH2, HH3, and BH1 reveals causative mutation in SMC2 for HH3 Reprint Icon -
Mc Clure, M., Bickhart, D.M., Null, D.J., Van Raden, P.M., Xu, L., Wiggans, G.R., Liu, G., Schroeder, S.G., Glasscock, J., Armstrong, J., Cole, J.B., Sonstegard, T.S., Van Tassell, C.P. 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.
Accuracy of genomic predictions in Bos indicus (Nellore) cattle Reprint Icon -
Neves, H.H., Carvalheiro, R., Perez O'Brien, A.M., Utsunomiya, Y.T., Do Carmo, A.S., Schenkel, F.S., Solkner, J., Ncewab, J.C., Van Tassell, C.P., Sonstegard, T.S., Cole, J.B., Da Silva, M.V., Queiroz, S.A., Garcia, J.F. 2014. Accuracy of genomic predictions in Bos indicus (Nellore) cattle. Genetic Selection Evolution. 46:17.
Genomic selection for producer-recorded health event data in US dairy cattle Reprint Icon -
Gaddis Parker, K., Cole, J.B., Clay, J., Maltecca, C. 2014. Genomic selection for producer-recorded health event data in US dairy cattle. Journal of Dairy Science. 97(5):3190-3199.
Genomic evaluation, breed identification, and discovery of a haplotype affecting fertility for Ayrshire dairy cattle Reprint Icon -
Cooper, T.A., Wiggans, G.R., Null, D.J., Hutchison, J.L., Cole, J.B. 2014. Genomic evaluation, breed identification, and discovery of a haplotype affecting fertility for Ayrshire dairy cattle. Journal of Dairy Science. 97(6):3878-3882.
Genotypes are useful for more than genomic evaluation -
Van Raden, P.M., Sun, C., Cooper, T.A., Cole, J.B. 2014. Genotypes are useful for more than genomic evaluation. International Committee on Animal Recording(ICAR). Proc. 39th Int. Comm. Anim. Recording Sess., Berlin, Germany, May 19–23, 4 pp.
A genome-wide association study of calf birth weight in Holstein cattle using single nucleotide polymorphisms and phenotypes predicted from auxiliary traits Reprint Icon -
Cole, J.B., Waurich, B., Wensch-Dorendorf, M., Bickhart, D.M., Swalve, H.H. 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(5):3156-3172.
Candidate causative mutation on BTA18 associated with calving and conformation traits in Holstein bulls -
Cole, J.B., Hutchison, J.L., Null, D.J., Van Raden, P.M., Liu, G., Schroeder, S.G., Sonstegard, T.S., Van Tassell, C.P., Bickhart, D.M. 2014. Candidate causative mutation on BTA18 associated with calving and conformation traits in Holstein bulls. Plant and Animal Genome Conference Proceedings. Plant Animal Genome XXII, San Diego, CA, Jan. 11–15, P1097.
Short communication: Use of young bulls in the United States Reprint Icon -
Hutchison, J.L., Cole, J.B., Bickhart, D.M. 2014. Short communication: Use of young bulls in the United States. Journal of Dairy Science. 97(5):3213-3220.
Genome-wide mapping of loci explaining variance in scrotal circumference in Nellore cattle Reprint Icon -
Utsunomiya, Y.T., Do Carmo, A.S., Neves, H.H., Carvalheiro, R., Matos, M.C., Zavarez, L.B., Rauschkolb Katsuda I, P., Perez Obrien, A.M., Solkner, J., Porto Neto, L.R., Schenkel, F.S., Mcewan, J., Cole, J.B., Da Silva, M., Van Tassell, C.P., Sonstegard, T.S., Garcia, J. 2014. Genome-wide mapping of loci explaining variance in scrotal circumference in Nellore cattle. PLoS One. 9(2):e88561.
Application of the a posteriori granddaughter design to the Holstein genome Reprint Icon -
Weller, J.I., Cole, J.B., Van Raden, P.M., Wiggans, G.R. 2014. Application of the a posteriori granddaughter design to the Holstein genome. Animal. 8(4):511-519.
Genetic evaluation of stillbirth in US Brown Swiss and Jersey cattle Reprint Icon -
Yao, C., Weigel, K.A., Cole, J.B. 2014. Genetic evaluation of stillbirth in US Brown Swiss and Jersey cattle. Journal of Dairy Science. 97(4):2474-2480.
Effect of artificial selection on runs of Homozygosity in U.S. Holstein cattle Reprint Icon -
Kim, E., Cole, J.B., Huson, H.J., Wiggans, G.R., Van Tassell, C.P., Crooker, B.A., Liu, G., Da, Y., Sonstegard, T.S. 2013. Effect of artificial selection on runs of Homozygosity in U.S. Holstein cattle. PLoS One. DOI: 10.1371/journal.pone.0080813.
Single nucleotide polymorphisms in candidate genes associated with fertilizing ability of sperm and subsequent embryonic development in cattle Reprint Icon -
Cochran, S.D., Cole, J.B., Null, D.J., Hansen, P.J. 2013. Single nucleotide polymorphisms in candidate genes associated with fertilizing ability of sperm and subsequent embryonic development in cattle. Biology of Reproduction. 89(3):69.
Genome-wide association mapping for identification of quantitative trait loci for rectal temperature during heat stress in Holstein cattle Reprint Icon -
Dikmen, S., Cole, J.B., Null, D.J., Hansen, P.J. 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.
Genome-wide association study for birth weight Brazilian Nellore cattle (Bos primigenuis indicus) points to previously described orthologous genes affecting human and bovine height Reprint Icon -
Utsunomiya, Y.T., Carmo, A.S., Carvalheiro, R., Neves, H.H., Matos, M.C., Zavarez, L.B., O'Brien, A.M., Solkner, J., Mcewan, J., Cole, J.B., Van Tassell, C.P., Schenkel, F.S., Silva, M.V., Porto Neto, L., Sonstegard, T.S., Garcia, J.F. 2013. Genome-wide association study for birth weight Brazilian Nellore cattle (Bos primigenuis indicus) points to previously described orthologous genes affecting human and bovine height. BioMed Central (BMC) Genetics. 13:14-52.
We are making inroads on health and fitness traits -
Parker Gaddis, K.L., Maltecca, C., Cole, J.B. 2013. We are making inroads on health and fitness traits. Hoard's Dairyman. 158(12):455.
Discovery of single nucleotide polymorphisms in candidate genes associated with fertility and production traits in Holstein cattle Reprint Icon -
Cochran, S.D., Cole, J.B., Null, D.J., Hansen, P.J. 2013. Discovery of single nucleotide polymorphisms in candidate genes associated with fertility and production traits in Holstein cattle. BioMed Central (BMC) Genetics. 14:49.
Standardization of health data – ICAR guidelines including health key -
Stock, K., Cole, J.B., Pryce, J., Gengler, N., Bradley, A., Andrews, L., Heringstad, B., Egger-Danner, C. 2013. Standardization of health data. ICAR guidelines including health key. International Committee on Animal Recording(ICAR). Technical Series 17:75–81. 2013.
Challenges and opportunities for farmer-recorded data in health and welfare selection -
Maltecca, C., Parker Gaddis, K.L., Clay, J., Cole, J.B. 2013. Challenges and opportunities for farmer-recorded data in health and welfare selection. International Committee on Animal Recording(ICAR). Technical Series 17:87–96. 2013.
Genomic evaluation of health traits in dairy cattle -
Cole, J.B., Parker Gaddis, K.L., Clay, J.S., Maltecca, C. 2013. Genomic evaluation of health traits in dairy cattle. International Committee on Animal Recording(ICAR). Technical Series 17:167-175.
Changes in expression of CWC15 during preimplantation development in the bovine embryo -
Ortega, M.S., Cole, J.B., Hansen, P.J. 2013. Changes in expression of CWC15 during preimplantation development in the bovine embryo. Animal Molecular and Cellular Biolology Research Symposium, Fernandina Beach, FL, Apr. 5-6, p. 25.
Optimal age at first calving for U.S. dairy cattle -
Cole, J.B., Hutchison, J.L., Bickhart, D.M., Null, D.J. 2013. Optimal age at first calving for U.S. dairy cattle. Journal of Dairy Science. 96(E-Suppl. 1):289–290 (abstr. W188).
Regression metamodels of an optimal genomic testing strategy in dairy cattle when selection intensity is low -
De Vries, A., Cole, J.B., Galligan, D.T. 2013. Regression metamodels of an optimal genomic testing strategy in dairy cattle when selection intensity is low. Journal of Dairy Science. 96(E-Suppl. 1):74 (abstr. T207).
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 -
Parker Gaddis, K.L., Cole, J.B., Clay, J.S., Maltecca, C. 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(E-Suppl. 1):444 (abstr. 447).
Analysis of health trait data from on-farm computer systems in the U.S. I: Pedigree and genomic variance components estimation -
Parker Gaddis, K.L., Cole, J.B., Clay, J.H., Maltecca, C. 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(E-Suppl. 1):443–444 (abstr. 446).
Breeding for polled dairy cows versus dehorning: Preliminary cost assessments & discussion -
Widmar, N.O., Schutz, M.M., Cole, J.B. 2013. Breeding for polled dairy cows versus dehorning: Preliminary cost assessments & discussion. Journal of Dairy Science. 96(E-Suppl. 1):602 (abstr. TH373).
Dissection of genomic correlation matrices using multivariate factor analysis in dairy and dual-purpose cattle breeds -
Macciotta, N.P., Dimauro, C., Vicario, D., Cole, J.B., Null, D.J. 2013. Dissection of genomic correlation matrices using multivariate factor analysis in dairy and dual-purpose cattle breeds. Journal of Dairy Science. 96(E-Suppl. 1):618 (abstr. 541).
Heritability estimates of performance and health traits of Holstein calves -
Mousa, M.S., Seykora, A.J., Chester-Jones, H., Ziegler, D.M., Cole, J.B. 2013. Heritability estimates of performance and health traits of Holstein calves. Journal of Dairy Science. 96(E-Suppl. 1):291 (abstr. W194).
Fine mapping for Weaver Syndrome in the Brown Swiss breed with the identification of possible casual mutations across NRCAM, PNPLA8, and CTTNBP2 and Developement of a diagnostic SNP haplotype Reprint Icon -
Mcclure, M.C., Kim, E., Bickhart, D.M., Null, D.J., Cooper, T.A., Cole, J.B., Wiggans, G.R., Marsan, P.A., Colli, L., Santus, E., Liu, G., Schroeder, S.G., Matukumalli, L., Van Tassell, C.P., Sonstegard, T.S. 2013. Fine mapping for Weaver Syndrome in the Brown Swiss breed with the identification of possible casual mutations across NRCAM, PNPLA8, and CTTNBP2 and Developement of a diagnostic SNP haplotype. PLoS One. 8(3):e59251.
Visualization of the transmission of direct genomic values for paternal and maternal chromosomes for 15 traits in U.S. Brown Swiss, Holstein, and Jersey cattle Reprint Icon -
Cole, J.B., Null, D.J. 2013. Visualization of the transmission of direct genomic values for paternal and maternal chromosomes for 15 traits in US Brown Swiss, Holstein, and Jersey cattle. Journal of Dairy Science. 96(4):2713-2726.
Identification of a nonsense mutation in CWC15 associated with decreased reproductive efficiency in Jersey cattle Reprint Icon -
Sonstegard, T.S., Cole, J.B., Van Raden, P.M., Van Tassell, C.P., Null, D.J., Schroeder, S.G., Bickhart, D.M., Mcclure, M.C. 2013. Identification of a nonsense mutation in CWC15 associated with decreased reproductive efficiency in Jersey cattle. PLoS One. 8(1):e54872.
Systems Biology in Animal Breeding: Identifying relationships among markers, genes, and phenotypes Reprint Icon -
Cole, J.B., Lewis, R.M., Maltecca, C., Newman, S., Olson, K.M., Tait, R. 2013. Systems Biology in Animal Breeding: Identifying relationships among markers, genes, and phenotypes. Journal of Animal Science. 91(2):521-522.
Technical Note: Changes to herd cutoff date in conception rate evaluations Reprint Icon -
Hutchison, J.L., Van Raden, P.M., Norman, H.D., Cole, J.B. 2013. Technical Note: Changes to herd cutoff date in conception rate evaluations. Journal of Dairy Science. 96(2):1264-1268.
Genomic imputation and evaluation using high density Holstein genotypes -
Van Raden, P.M., Null, D.J., Sargolzaei, M., Wiggans, G.R., Tooker, M.E., Cole, J.B., Sonstegard, T.S., Connor, E.E., Winters, M., Van Kaam, J., Van Doormaal, B.J., Faust, M.A., Doak, G.A. 2013. Genomic imputation and evaluation using high density Holstein genotypes. Journal of Dairy Science. 96(1):668-678.
Effect of sample stratification on dairy GWAS results -
Ma, L., Wiggans, G.R., Wang, S., Sonstegard, T.S., Yang, J., Crooker, B.A., Cole, J.B., Van Tassell, C.P., Da, Y. 2012. Effect of sample stratification on dairy GWAS results. Biomed Central (BMC) Genomics. 13:536.
Incidence validation and relationship analysis of producer-recorded health event data from on-farm computer systems in the United States -
Parker Gaddis, K.L., Cole, J.B., Clay, J.S., Maltecca, C. 2012. Incidence validation and relationship analysis of producer-recorded health event data from on-farm computer systems in the United States. Journal of Dairy Science. 95(9):5422-5435.
Signature of forty years of artificial selection in U.S. Holstein cattle identified by long-range frequency analyses -
Sonstegard, T.S., Wang, S., Van Tassell, C.P., Ma, L., Wiggans, G.R., Crooker, B., Cole, J.B., Mariani, B.D., Kim, E., Garbe, J.R., Fahrenkrug, S., Liu, G., Da, Y. 2012. Signature of forty years of artificial selection in U.S. Holstein cattle identified by long-range frequency analyses. International Conference on Quantitative Genetics: Understanding Variation in Complex Traits, Edinburgh, Scotland, June 17–22, Programme & Book of Abstracts, p. 213, abstr. P-314.
Applications of haplotypes in dairy farm management -
Cole, J.B. 2012. Applications of haplotypes in dairy farm management. European Association of Animal Production Proceedings. 18:189.
PyPedal, an open source software package for pedigree analysis -
Cole, J.B. 2012. PyPedal, an open source software package for pedigree analysis. European Association of Animal Production Proceedings. 18:239.
Short communication: Projecting milk yield using best prediction and the MilkBot lactation model -
Cole, J.B., Ehrlich, J.L., Null, D.J. 2012. Short communication: Projecting milk yield using best prediction and the MilkBot lactation model. Journal of Dairy Science. 95(7):4041-4044.
An international overview of the recording and use of functional traits in dairy cattle breeding and management -
Cole, J.B., Stock, K.F., Pryce, J., Bradley, A., Gengler, N., Andrews, L., Egger-Daner, C. 2012. An international overview of the recording and use of functional traits in dairy cattle breeding and management. Journal of Dairy Science. (Suppl. 2):443(abstr. 439). 2012.
Genomic evaluation of rectal temperature in Holstein cattle -
Dikmen, S., Cole, J.B., Null, D.J., Hansen, P.J. 2012. Genomic evaluation of rectal temperature in Holstein cattle. Journal of Dairy Science. 95(Suppl. 2):401(abstr. 327). 2012.
Incidence validation and causal relationship analysis of producer-recorded health event data from on-farm computer systems in the U.S. -
Parker Gaddis, K.L., Cassady, J.P., Cole, J.B., Maltecca, C. 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(Suppl. 2):225–226(abstr. 229). 2012.
Increased use of young bulls in dairy cattle breeding programs -
Norman, H.D., Hutchison, J.L., Cole, J.B. 2012. Increased use of young bulls in dairy cattle breeding programs. Journal of Dairy Science. 95(Suppl. 2):521–522(abstr. W60). 2012.
Heritability of rectal temperature and genetic correlations with production and reproduction traits in dairy cattle -
Dikmen, S., Cole, J.B., Null, D.J., Hansen, P.J. 2012. Heritability of rectal temperature and genetic correlations with production and reproduction traits in dairy cattle. Journal of Dairy Science. 95(6):3401-3405.
Really big data: Processing and analysis of large datasets -
Cole, J.B., Newman, S., Foertter, F., Aguilar, I., Coffey, M. 2012. Really big data: Processing and analysis of large datasets. Journal of Animal Science. 90(3):723-733.
The use and economic value of the 3K SNP genomic test for calves on dairy farms -
De Vries, A., Galligan, D.T., Cole, J.B. 2011. The use and economic value of the 3K SNP genomic test for calves on dairy farms. University of Florida Cooperative Extension Service Institute of Food and Agriculture Science. AN270, 5 pp.
Genome-wide association analysis of thirty one production, health, reproduction and body conformation traits in contemporary U.S. Holstein cows -
Cole, J.B., Wiggans, G.R., Ma, L., Sonstegard, T.S., Lawlor, T.J., Crooker, B.A., Van Tassell, C.P., Yang, J., Wang, S., Matukumalli, L.K., Da, Y. 2011. Genome-wide association analysis of thirty one production, health, reproduction and body conformation traits in contemporary U.S. Holstein cows. Biomed Central (BMC) Genomics. Online, 12:408.
Technical note: Adjustment of traditional cow evaluations to improve accuracy of genomic predictions -
Wiggans, G.R., Cooper, T.A., Van Raden, P.M., Cole, J.B. 2011. Technical note: Adjustment of traditional cow evaluations to improve accuracy of genomic predictions. Journal of Dairy Science. 94(12):6188-6193.
Genomic inbreeding and relationships among Holsteins, Jerseys, and Brown Swiss -
Van Raden, P.M., Olson, K.M., Wiggans, G.R., Cole, J.B., Tooker, M.E. 2011. Genomic inbreeding and relationships among Holsteins, Jerseys, and Brown Swiss. Journal of Dairy Science. 94(11):5673-5682.
Data structures and visualization -
Cole, J.B. 2011. Data structures and visualization. Journal of Animal Science 89(E-Suppl. 1)/Journal of Dairy Science 94(E-Suppl. 1):226(abstr. 198).
Heritability of rectal temperature and genetic correlations with production and reproduction traits in dairy cattle -
Dikmen, S., Cole, J.B., Null, D.J., Hansen, P.J. 2011. Heritability of rectal temperature and genetic correlations with production and reproduction traits in dairy cattle. Journal of Animal Science 89(E-Suppl. 1)/Journal of Dairy Science 94(E-Suppl. 1):255(abstr. 275).
Use of Haplotypes to Estimate Mendelian Sampling Effects and Selection Limits -
Cole, J.B., Van Raden, P.M. 2011. Use of Haplotypes to Estimate Mendelian Sampling Effects and Selection Limits. Journal of Animal Breeding and Genetics. 128(6):446-455.
Short communication: Best prediction of 305-day lactation yields with regional and seasonal effects -
Cole, J.B., Null, D.J., De Vries, A. 2011. Short communication: Best prediction of 305-day lactation yields with regional and seasonal effects. Journal of Dairy Science. 94(3):1601-1604.
Use of Haplotypes to Estimate Mendelian Sampling Effects and Selection Limits -
Cole, J.B., Van Raden, P.M. 2010. Use of Haplotypes to Estimate Mendelian Sampling Effects and Selection Limits. World Congress of Genetics Applied in Livestock Production. Proc. 9th World Congr. Genet. Appl. Livest. Prod., Leipzig, Germany, Aug. 1–6, abstr. p. 147.
Use of Haplotypes to Estimate Mendelian Sampling Effects and Selection Limits -
Cole, J.B., Van Raden, P.M. 2010. Use of Haplotypes to Estimate Mendelian Sampling Effects and Selection Limits. World Congress of Genetics Applied in Livestock Production. Proc. 9th World Congr. Genet. Appl. Livest. Prod., Leipzig, Germany, Aug. 1–6, 4 pp.
High Resolution QTL Maps Of 31 Traits in Contemporary U.S. Holstein Cows -
Cole, J.B., Wiggans, G.R., Ma, L., Sonstegard, T.S., Crooker, B.A., Van Tassell, C.P., Yang, J., Matukumalli, L.K., Da, Y. 2010. High Resolution QTL Maps Of 31 Traits in Contemporary U.S. Holstein Cows. World Congress of Genetics Applied in Livestock Production. Proc. 9th World Congr. Genet. Appl. Livest. Prod., Leipzig, Germany, Aug. 1–6., abstr. p. 22.
High Resolution QTL Maps Of 31 Traits in Contemporary U.S. Holstein Cows -
Cole, J.B., Wiggans, G.R., Ma, L., Sonstegard, T.S., Crooker, B.A., Van Tassell, C.P., Yang, J., Matukumalli, L.K., Da, Y. 2010. High Resolution QTL Maps Of 31 Traits in Contemporary U.S. Holstein Cows. World Congress of Genetics Applied in Livestock Production. Proc. 9th World Congr. Genet. Appl. Livest. Prod., Leipzig, Germany, Aug. 1–6., 4 pp.
Forty Years Of Artificial Selection In U.S. Holstein Cattle Had Genome-wide Signatures -
Sonstegard, T.S., Ma, L., Van Tassell, C.P., Kim, E., Cole, J.B., Wiggans, G.R., Crooker, B.A., Mariani, B.D., Gerber, J.R., Fahrenkrug, S.C., Liu, G., Da, Y. 2010. Forty Years Of Artificial Selection In U.S. Holstein Cattle Had Genome-wide Signatures. World Congress of Genetics Applied in Livestock Production.
Imputation of Cow Genotypes and Adjustment of PTAs -
Cooper, T.A., Tooker, M.E., Van Raden, P.M., Wiggans, G.R., Cole, J.B. 2010. Imputation of Cow Genotypes and Adjustment of PTAs. AIPL Research Reports. GENOMICS1 (4-10).
Use of haplotypes to predict selection limits and Mendelian sampling -
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).
Age at First Calving in Holstein Cattle in the United States -
Cole, J.B., Null, D.J. 2010. Age at First Calving in Holstein Cattle in the United States. Journal of Dairy Science. 93(E-Suppl. 1):594(abstr. W28).
Visualization of Results from Genomic Evaluations Reprint Icon -
Cole, J.B., Van Raden, P.M. 2010. Visualization of Results from Genomic Evaluations. Journal of Dairy Science. 93(6):2727-2740.
High Resolution QTL Map Of Net Merit Component Traits And Calving Traits From Genome-Wide Association Analysis In Contemporary U.S. Holstein Cows -
Cole, J.B., Sonstegard, T.S., Ma, L., Wiggans, G.R., Crooker, B.A., Van Tassell, C.P., Yang, J., Matukumalli, L., Da, Y. 2010. High Resolution QTL Map Of Net Merit Component Traits And Calving Traits From Genome-Wide Association Analysis In Contemporary U.S. Holstein Cows. Plant and Animal Genome Conference Proceedings. San Diego, Ca, Jan. 9-13, abstr. P565.
X Chromosome SNPs Were Heavily Involved In Epistasis Effects Of Net Merit Component Traits In Contemporary U.S. Holstein Cows -
Ma, L., Sonstegard, T.S., Cole, J.B., Wiggans, G.R., Crooker, B.A., Van Tassell, C.P., Yang, J., Matukumalli, L., Da, Y. 2010. X Chromosome SNPs Were Heavily Involved In Epistasis Effects Of Net Merit Component Traits In Contemporary U.S. Holstein Cows . Plant and Animal Genome Conference Proceedings. San Diego, Ca, Jan. 9-13, abstr. P542.
High Resolution QTL Map Of Body Conformation Traits From Genome-Wide Association Analysis In Contemporary U.S. Holstein Cows -
Wiggans, G.R., Ma, L., Sonstegard, T.S., Cole, J.B., Crooker, B.A., Van Tassell, C.P., Yang, J., Matukumalli, L.K., Da, Y. 2010. High Resolution QTL Map Of Body Conformation Traits From Genome-Wide Association Analysis In Contemporary U.S. Holstein Cows. Plant and Animal Genome Conference Proceedings. San Diego, Ca, Jan. 9-13, abstr. P547.
Net merit as a measure of lifetime profit: 2010 revision -
Cole, J.B., Van Raden, P.M. 2009. Net merit as a measure of lifetime profit: 2010 revision. AIPL Research Reports. NM$4 (12-09).
Genetic Parameters of Milk ELISA scores for Johne's Disease Reprint Icon -
Attalla, S.A., Seykora, A.J., Cole, J.B., Heins, B.J. 2010. Genetic Parameters of Milk ELISA scores for Johne's Disease. Journal of Dairy Science. 93(4):1729-1735.
Genetic Base Changes for January 2010 -
Van Raden, P.M., Cole, J.B., Tooker, M.E., Cooper, T.A. 2009. Genetic Base Changes for January 2010. AIPL Research Reports. BASE2 (8-09).
Genetic Base Changes for January 2010 -
Van Raden, P.M., Cole, J.B., Tooker, M.E., Cooper, T.A. 2009. Genetic Base Changes for January 2010. Genetic Trends. 61(5):11.
Visualization of Results from Genomic Predictions -
Cole, J.B. 2009. Visualization of Results from Genomic Predictions. Journal of Dairy Science. 92(E-Suppl. 1):314(abstr. 281).
Best prediction of lactation yields accounting for regional and seasonal differences -
Cole, J.B., Null, D.J. 2009. Best prediction of lactation yields accounting for regional and seasonal differences. Journal of Dairy Science. 92(E-Suppl. 1):209(abstr. T38).
Can you believe those genomic evaluations for young bulls? -
Van Raden, P.M., Tooker, M.E., Cole, J.B. 2009. Can you believe those genomic evaluations for young bulls?. Journal of Dairy Science. 92(E-Suppl. 1):314(abstr. 279).
Estimation of genetic parameters and transmitting ability for Minnesota Johne’s milk ELISA test -
Attalla, S.A., Seykora, A.J., Cole, J.B., Heins, B.J. 2009. Estimation of genetic parameters and transmitting ability for Minnesota Johne’s milk ELISA test. Journal of Dairy Science. 92(E-Suppl. 1):20(abstr. M56).
Impact of Genetic Merit for Milk Somatic Cell Score of Sires and Maternal Grandsires on Herd Life of Their Daughters Reprint Icon -
Miller, R.H., Norman, H.D., Wright, J.R., Cole, J.B. 2008. Impact of Genetic Merit for Milk Somatic Cell Score of Sires and Maternal Grandsires on Herd Life of Their Daughters. Journal of Dairy Science. 92(5):2224-2228.
Genome Signature of Artificial Selection for High Milk Yield in Holstein Cattle -
Sonstegard, T.S., Ma, L., Cole, J.B., Wiggans, G.R., Crooker, B.A., Van Tassell, C.P., Mariani, B.D., Da, Y. 2009. Genome Signature of Artificial Selection for High Milk Yield in Holstein Cattle. Plant and Animal Genome Conference Proceedings.
Distribution and Location of Genetic Effects for Dairy Traits Reprint Icon -
Cole, J.B., Van Raden, P.M., O'Connell, J.R., Van Tassell, C.P., Sonstegard, T.S., Schnabel, R.D., Taylor, J.F., Wiggans, G.R. 2009. Distribution and Location of Genetic Effects for Dairy Traits. Journal of Dairy Science. 92(6):2931-2946.
Using Python for Pedigree Analysis -
Cole, J.B. 2009. Using Python for Pedigree Analysis. Python Magazine. 3(3):12-20.
Genetic Evaluation of Lactation Persistency for Five Breeds of Dairy Cattle Reprint Icon -
Cole, J.B., Null, D.J. 2009. Genetic Evaluation of Lactation Persistency for Five Breeds of Dairy Cattle. Journal of Dairy Science. 92(5):2248-2258.
Genetic and Environmental Factors That Impact Gestation Length in Dairy Cattle Reprint Icon -
Norman, H.D., Wright, J.R., Kuhn, M.T., Hubbard, S.M., Cole, J.B., Van Raden, P.M. 2009. Genetic and Environmental Factors That Impact Gestation Length in Dairy Cattle. Journal of Dairy Science. 92(5):2259-2269.
Profitable Dairy Cow Traits for Hot Climatic Conditions -
De Vries, A., Cole, J.B. 2009. Profitable Dairy Cow Traits for Hot Climatic Conditions. In: Klopcic, M., Reents, R., Philipsson, J., and Kuipers, A., editors. Breeding for Robustness in Cattle. Wageningen, The Netherlands: Wageningen Academic Publishers. p. 227-248.
Phenotypic and Genetic Relationships of Common Health Disorders with Milk and Fat Yield Persistencies from Producer- Recorded Health Data and Test Day Yields Reprint Icon -
Appuhamy, A.D., Cassell, B.G., Cole, J.B. 2009. Phenotypic and Genetic Relationships of Common Health Disorders with Milk and Fat Yield Persistencies from Producer-Recorded Health Data and Test Day Yields. Journal of Dairy Science. 92(4):1785-1795.
Best Prediction of Yields for Long Lactations Reprint Icon -
Cole, J.B., Null, D.J., Van Raden, P.M. 2009. Best Prediction of Yields for Long Lactations. Journal of Dairy Science. 92(4):1796-1810.
Genomic signatures of artificial selection in U.S. Holstein cows -
Distribution and Location of Genetic Effects for Dairy Traits -
Cole, J.B., Van Raden, P.M., O'Connell, J.R., Van Tassell, C.P., Sonstegard, T.S., Schnabel, R.D., Wiggans, G.R. 2009. Distribution and Location of Genetic Effects for Dairy Traits. International Committee on Animal Recording (ICAR). ICAR Tech Ser. 13:355–360. 2009.
Data Collection Ratings and Best Prediction of Lactation Yields -
Cole, J.B. 2009. Data Collection Ratings and Best Prediction of Lactation Yields. International Committee on Animal Recording (ICAR). ICAR Tech Ser. 13:403–406. 2009.
A data exchange format and national database for producer-recorded health event data from on-farm management software -
Cole, J.B., Null, D.J., Bacheller, L.R. 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).
A Manual for Use of BESTPRED: A Program for Estimation of Lactation Yield and Persistency Using Best Prediction -
Cole, J.B., Van Raden, P.M. 2007. A manual for use of BESTPRED: A program for estimation of lactation yield and persistency using best prediction (Release 2.0 beta 6). Software and User Manual Public Release.
Phenotypic Relationships of Common Health Disorders in Dairy Cows to Lactation Persistency Estimated from Daily Milk Weights -
Appuhamy, J., Cassell, B.G., Dechow, C.D., Cole, J.B. 2007. Phenotypic Relationships of Common Health Disorders in Dairy Cows to Lactation Persistency Estimated from Daily Milk Weights. Journal of Dairy Science. 90(9):4424-4434.
Multitrait evaluation for calving ease and stillbirth with separate genetic effects by parity -
Wiggans, G.R., Cole, J.B., Thornton, L.L. 2007. Multitrait evaluation for calving ease and stillbirth with separate genetic effects by parity. Journal of Dairy Science. 90(Suppl. 1):19(abstr. M49).
Effect of temperature and humidity on gestation length -
Norman, H.D., Wright, J.R., Cole, J.B. 2007. Effect of temperature and humidity on gestation length. Journal of Dairy Science. 90(Suppl. 1):16(abstr. M38).
Effect of service sire and cow sire on gestation length -
Norman, H.D., Wright, J.R., Van Raden, P.M., Cole, J.B. 2007. Effect of service sire and cow sire on gestation length. Journal of Dairy Science. 90(Suppl. 1):194(abstr. 230).
Genetic and environmental factors that affect gestation length -
Norman, H.D., Wright, J.R., Kuhn, M.T., Hubbard, S.M., Cole, J.B. 2007. Genetic and environmental factors that affect gestation length. Journal of Dairy Science. 90(Suppl. 1):264(abstr. T73).
PYPEDAL: A COMPUTER PROGRAM FOR PEDIGREE ANALYSIS -
Cole, J.B. 2007. Pypedal: A computer program for pedigree analysis. Computers and Electronics in Agriculture. 57:107-113.
STILLBIRTH (C0)VARIANCE COMPONENTS FOR A SIRE-MATERNAL GRANDSIRE THRESHOLD MODEL AND DEVELOPMENT OF A CALVING ABILITY INDEX FOR SIRE SELECTION -
Cole, J.B., Wiggans, G.R., Van Raden, P.M., Miller, R.H. 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(5):2489-2496.
GENETIC EVALUATION OF STILLBIRTH -
Cole, J.B. 2006. Genetic evaluation of stillbirth. AIPL Research Report. SB1 (8-06).
Genetic Evaluations for Mixed-Breed Populations -
Van Raden, P.M., Tooker, M.E., Cole, J.B., Wiggans, G.R., Megonigal Jr, J.H. 2007. Genetic Evaluations for Mixed-Breed Populations. Journal of Dairy Science. 90(5):2434-2441.
TEMPERATURE-HUMIDITY INDICES AS INDICATORS OF MILK PRODUCTION LOSSES DUE TO HEAT STRESS -
Bohmanova, J., Misztal, I., Cole, J.B. 2007. Temperature-humidity indices as indicators of milk production losses due to heat stress. Journal of Dairy Science. 90(4):1947-1956.
GENETIC EVALUATION OF STILLBIRTH IN UNITED STATES HOLSTEINS USING A SIRE-MATERNAL GRANDSIRE THRESHOLD MODEL -
Cole, J.B., Wiggans, G.R., Van Raden, P.M. 2007. Genetic evaluation of stillbirth in United States Holsteins using a sire-maternal grandsire threshold model. Journal of Dairy Science. 90(5):2480-2488.
NET MERIT RECEIVES FACE-LIFT -
Seykora, T., Van Raden, P.M., Cole, J.B. 2006. Net merit receives face-lift. Hoard's Dairyman. 151(14):557.
GENETIC CORRELATIONS BETWEEN FIRST AND LATER PARITY CALVING EASE IN A SIRE-MATERNAL GRANDSIRE MODEL -
Wiggans, G.R., Van Tassell, C.P., Cole, J.B., Thornton, L.L. 2006. Genetic correlations between first and later parity calving ease in a sire-maternal grandsire model. 8th World Congress of Genetics Applied in Livestock Production. Communication 01-92.
GENETIC EVALUATION OF STILLBIRTH IN UNITED STATES HOLSTEINS USING A SIRE-MATERNAL GRANDSIRE THRESHOLD MODEL -
Cole, J.B., Wiggans, G.R., Van Raden, P.M. 2006. Genetic evaluation of stillbirth in United States Holsteins using a sire-maternal grandsire threshold model. 8th World Congress of Genetics Applied in Livestock Production. Communication 01-28.
GENETIC CALVING EASE STUDY ON CROSSBREDS -
Cole, J.B., Goodling, R.C., Wiggans, G.R., Van Raden, P.M. 2006. Genetic calving ease study on crossbreds. Jersey Journal. 53(3):83-84.
EFFECT OF MASTITIS AND POSTPARTUM METABOLIC DISEASES ON LACTATION PERSISTENCY OF HOLSTEIN AND JERSEY COWS -
Appuhamy, R., Cassell, B.G., Cole, J.B. 2006. Effect of mastitis and postpartum metabolic diseases on lactation persistency of Holstein and Jersey cows [abstract]. Journal of Dairy Science. 89(Suppl. 1):398(abstr. 476).
USE OF PRODUCER-RECORDED HEALTH DATA IN DETERMINING INCIDENCE RISKS AND RELATIONSHIPS BETWEEN HEALTH EVENTS AND CULLING -
Cole, J.B., Sanders, A.H., Clay, J.S. 2006. Use of producer-recorded health data in determining incidence risks and relationships between health events and culling [abstract]. Journal of Dairy Science. 89(Suppl. 1):10(abstr. M7).
STILLBIRTH (CO)VARIANCE COMPONENTS FOR A SIRE-MATERNAL GRANDSIRE THRESHOLD MODEL -
Cole, J.B., Wiggans, G.R., Van Raden, P.M., Miller, R.H. 2006. Stillbirth (co)variance components for a sire-maternal grandsire threshold model [abstract]. Journal of Dairy Science. 89(Suppl. 1):273(abstr. 339).
GENETIC EVALUATIONS FOR MIXED BREED POPULATIONS -
Van Raden, P.M., Tooker, M.E., Cole, J.B., Wiggans, G.R., Megonigal Jr, J.H. 2006. Genetic evaluations for mixed breed populations [abstract]. Journal of Dairy Science. 89(Suppl. 1):98(abstr. 40).
GENETIC EVALUATION AND BEST PREDICTION OF LACTATION PERSISTENCY -
Cole, J.B., Van Raden, P.M. 2006. Genetic evaluation and best prediction of lactation persistency. Journal of Dairy Science. 89(7):2722-2728.
A MANUAL FOR USE OF PYPEDAL: A SOFTWARE PACKAGE FOR PEDIGREE ANALYSIS -
Cole, J.B. 2005. A Manual for Use of Pypedal: a Software Package for Pedigree Analysis. Software and User Manual Public Release 2.0.0b15.
HOW CAN WE GENETICALLY IMPROVE DAIRY CATTLE HEALTH? -
Cole, J.B. 2005. How can we genetically improve dairy cattle health? The Dairy Focus. 6(4):3.
GENETIC EVALUATION OF CLINICAL MASTITIS IN U.S. DAIRY CATTLE -
Cole, J.B., Sanders, A.H. 2005. Genetic evaluation of clinical mastitis in U.S. dairy cattle [abstract]. In: Lamont, S.J., Rothschild, M.F., Harris, D.L., editors. Proceedings of the Third International Symposium on Genetics of Animal Health, July 13-15, 2005, Ames, Iowa. p. 112.
GENETIC EVALUATION AND BEST PREDICTION OF LACTATION PERSISTENCY -
Cole, J.B., Van Raden, P.M. 2005. Genetic evaluation and best prediction of lactation persistency [abstract]. Journal of Dairy Science. 88(Suppl. 1):379-380.
DISCRETE TIME SURVIVAL ANALYSIS OF LONGEVITY IN A COLONY OF DOG GUIDES -
Cole, J.B., Southey, B.R., Franke, D.E., Leighton, E.A. 2005. Discrete time survival analysis of longevity in a colony of dog guides [abstract]. Journal of Animal Science. 83(Suppl. 1):103.
GENETIC EVALUATION OF CALVING EASE FOR BROWN SWISS AND JERSEY BULLS FROM PUREBRED AND CROSSBRED CALVINGS -
Cole, J.B., Goodling Jr, R.C., Wiggans, G.R., Van Raden, P.M. 2005. Genetic evaluation of calving ease for Brown Swiss and Jersey bulls from purebred and crossbred calvings. Journal of Dairy Science. 88(4):1529-1539.
POPULATION STRUCTURE OF A COLONY OF DOG GUIDES -
Cole, J.B., Franke, D.E., Leighton, E.A. 2004. Population structure of a colony of dog guides. Journal of Animal Science. 82(10):2906-2912.
GENETIC IMPROVEMENT OF DAIRY CATTLE HEALTH -
Cole, J.B., Miller, P.D., Norman, H.D. 2004. Genetic improvement of dairy cattle health [abstract]. In: Proceedings of 12th International Conference on Production Diseases in Farm Animals, July 19-22, 2004, East Lansing, Michigan. p. 78.
BREED COMPOSITION CODES FOR CROSSBRED DAIRY CATTLE IN THE UNITED STATES -
Cole, J.B., Tooker, M.E., VanRaden, P.M., and Megonigal, Jr., J.H. Breed composition codes for crossbred dairy cattle in the United States. [abstract]. In: Proceedings of Beltsville Agricultural Research Center Poster Day 2004, April 29, 2004, Beltsville, Maryland. Abstract 34.
TROPOSPHERIC OZONE IN LOUISIANA AND SYNOPTIC CIRCULATION -
Rohli, R.V., Russo, M.M., Vega, A.J., Cole, J.B. 2004. Tropospheric ozone in Louisiana and synoptic circulation. Journal of Applied Meterology. 43(10):1438-1451.
HETEROSIS AND BREED DIFFERENCES FOR DAUGHTER PREGNANCY RATE IN CROSSBRED DAIRY COWS -
VanRaden, P.M., Tooker, M.E., Cole, J.B. 2004. Heterosis and breed differences for daughter pregnancy rate in crossbred dairy cows [abstract]. Journal of Dairy Science. 87(Suppl. 1):284.
BREED COMPOSITION CODES FOR CROSSBRED DAIRY CATTLE IN THE UNITED STATES -
Cole, J., Tooker, M., VanRaden, P., Megonigal, J., Jr. 2004. Breed composition codes for crossbred dairy cattle in the United States [abstract]. Journal of Dairy Science. 87(Suppl. 1):284-285.
ARS News Articles
Last Modified: 5/2/2016
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