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United States Department of Agriculture

Agricultural Research Service

John B Cole
Animal Genomics and Improvement Laboratory
Research Geneticist (Animals)

Phone: (301) 504-8665
Fax: (301) 504-8092
Room 320
10300 BALTIMORE AVENUE
BLDG 005 BARC-WEST
BELTSVILLE, MD, 20705-2350

Projects
Improving Genetic Predictions in Dairy Animals Using Phenotypic and Genomic Information
Appropriated (D)
  Accession Number: 423282
Development of Statistical Methods for the Analysis of Genetic (co)Variance Matrices Calculated Using Single Nucleotide Polymorphisms
Nonfunded Cooperative Agreement (N)
  Accession Number: 423545
National Dairy Genetic Evaluation Program
Nonfunded Cooperative Agreement (N)
  Accession Number: 424155
Identification of Gene Networks Associated with Dystocia in Dairy Cattle
Nonfunded Cooperative Agreement (N)
  Accession Number: 424484
IMPROVING FERTILITY OF DAIRY CATTLE USING TRANSLATIONAL GENOMICS
Reimbursable (R)
  Accession Number: 423517

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)
Genetic base changes for December 2014 - (Government Publication)
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 - (Government Publication)
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).
Overview of new traits and phenotyping strategies in dairy cattle with a focus on functional traits - (Peer Reviewed Journal) - (11-Sep-14)
Improvement of prediction ability for genomic selection of dairy cattle by including dominance effects - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
Macciotta, N., Dimauro, C., Null, D.J., Gaspa, G., Castellini, M., Cole, J.B. 2014. Dissection of genomic correlation matrices of US Holsteins using multivariate factor analysis. Journal of Animal Breeding and Genetics. 131(60):1-12.
The development of genomics applied to dairy breeding - (Peer Reviewed Journal) - (16-May-14)
The hunt for a functional mutation affecting conformation and calving traits on chromosome 18 in Holstein cattle - (Proceedings)
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 - (Proceedings)
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 - (Proceedings)
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 - (Proceedings)
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 - (Abstract Only)
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 - (Proceedings)
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 - (Abstract Only)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Proceedings)
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 - (Peer Reviewed Journal)
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 - (Abstract Only)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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. PLoS One.2013 Nov 14;8(11):e80813.
Single nucleotide polymorphisms in candidate genes associated with fertilizing ability of sperm and subsequent embryonic development in cattle Reprint Icon - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Popular Publication)
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 - (Peer Reviewed Journal)
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.
Optimal age at first calving for U.S. dairy cattle - (Abstract Only)
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).
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 - (Abstract Only)
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 - (Abstract Only)
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).
Regression metamodels of an optimal genomic testing strategy in dairy cattle when selection intensity is low - (Abstract Only)
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).
Breeding for polled dairy cows versus dehorning: Preliminary cost assessments & discussion - (Abstract Only)
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 - (Abstract Only)
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 - (Abstract Only)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Proceedings)
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 - (Abstract Only)
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 - (Abstract Only)
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 - (Peer Reviewed Journal)
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 - (Abstract Only)
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 - (Abstract Only)
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.
Increased use of young bulls in dairy cattle breeding programs - (Abstract Only)
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.
Incidence validation and causal relationship analysis of producer-recorded health event data from on-farm computer systems in the U.S. - (Abstract Only)
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.
Heritability of rectal temperature and genetic correlations with production and reproduction traits in dairy cattle - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Popular Publication)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Abstract Only)
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 - (Abstract Only)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Abstract Only)
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 - (Proceedings)
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 - (Abstract Only)
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 - (Proceedings)
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 - (Proceedings)
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 - (Government Publication)
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 - (Abstract Only)
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 - (Abstract Only)
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 - (Peer Reviewed Journal)
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 - (Abstract Only)
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 - (Abstract Only)
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 - (Abstract Only)
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 - (Government Publication)
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 - (Peer Reviewed Journal)
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 - (Government Publication)
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 - (Popular Publication)
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 - (Abstract Only)
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 - (Abstract Only)
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? - (Abstract Only)
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 - (Abstract Only)
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 - (Peer Reviewed Journal)
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 - (Abstract Only)
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 - (Peer Reviewed Journal)
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 - (Popular Publication)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Book / Chapter)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Abstract Only) - (20-Jun-08)
Distribution and Location of Genetic Effects for Dairy Traits - (Proceedings)
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 - (Proceedings)
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 - (Abstract Only)
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 - (Book / Chapter)
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 - (Peer Reviewed Journal)
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 - (Abstract Only)
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 - (Abstract Only)
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 - (Abstract Only)
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 - (Abstract Only)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Government Publication)
Cole, J.B. 2006. Genetic evaluation of stillbirth. AIPL Research Report. SB1 (8-06).
Genetic Evaluations for Mixed-Breed Populations - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Popular Publication)
Seykora, T., Van Raden, P.M., Cole, J.B. 2006. Net merit receives face-lift. Hoard's Dairyman. 151(14):557.
Genetic Evaluation of Stillbirth in United States Holsteins Using a Sire-Maternal Grandsire Threshold Model - (Proceedings)
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 Correlations Between First and Later Parity Calving Ease in a Sire-Maternal Grandsire Model - (Proceedings)
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 Calving Ease Study on Crossbreds - (Popular Publication)
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.
Use of Producer-Recorded Health Data in Determining Incidence Risks and Relationships Between Health Events and Culling - (Abstract Only)
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 - (Abstract Only)
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 - (Abstract Only)
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).
Effect of Mastitis and Postpartum Metabolic Diseases on Lactation Persistency of Holstein and Jersey Cows - (Abstract Only)
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).
Genetic Evaluation and Best Prediction of Lactation Persistency - (Peer Reviewed Journal)
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 - (Book / Chapter)
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? - (Other)
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 - (Abstract Only)
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 - (Abstract Only)
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 - (Abstract Only)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Abstract Only)
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 - (Abstract Only)
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 - (Peer Reviewed Journal)
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.
Breed Composition Codes for Crossbred Dairy Cattle in the United States - (Abstract Only)
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.
Heterosis and Breed Differences for Daughter Pregnancy Rate in Crossbred Dairy Cows - (Abstract Only)
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.
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Last Modified: 11/27/2014