AIP scientific journal articles

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2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 | 1999 | 1998 | 1997 | 1996 | 1995 | 1994 | 1993 | 1992 | 1991 | 1990 | selected earlier articles

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2022 

• Al-Khudhair, A., Null, D.J., Wolfe, C.W., Cole, J.B., Steffen, D.J., and VanRaden, P.M. Inheritance of a mutation causing neuropathy with splayed forelimbs in Jersey cattle. J. Dairy Sci. 105(2):1338-1345. 2022. 

• Khanal, P., Parker Gaddis, K.L., Vandehaar, M., Weigel, K., White, H., Penagaricano, F., Koltes, J., Santos, J., Baldwin, R.L., Buchard, J., Durr, J., and Templeton, R. Inheritance of a mutation causing neuropathy with splayed forelimbs in Jersey cattle. J. Dairy Sci. 105(2):1338-1345. 2022. 

• Masuda, Y., VanRaden, P.M., Tsuruta, S., Lourenco, D.A.L., and Misztal, I. Invited review: Unknown-parent groups and metafounders in single-step genomic BLUP. J. Dairy Sci. 105(2):923-929. 2022. 

• Wu, X.-L., Wiggans, G.R., Norman, H.D., Miles, A.M., Van Tassell, C.P., Baldwin, R.L., VanRaden, P.M., Burchard, J., and Durr, J. Statistical methods revisited for estimating daily milk yields: how well do they work? Front. Genet. 13:943705. 2022. 

2021

• Al-Khudhair, A., VanRaden, P.M., Null, D.J., and Li, B. Marker selection and genomic prediction of economically important traits using imputed high-density genotypes for 5 breeds of dairy cattle. J. Dairy Sci. 104(4):4478–4485. 2021. 

• Cesarani, A., Masuda, Y., Tsuruta, S., Nicolazzi, E.L., VanRaden, P.M., Lourenco, D., and Misztal, I. Genomic predictions for yield traits in US Holsteins with unknown parent groups. J. Dairy Sci. 104(5):5843–5853. 2021. 

• Cole, J.B., Dürr, J.W., and Nicolazzi, E.L. Invited review: The future of selection decisions and breeding programs: What are we breeding for, and who decides? J. Dairy Sci. 104(5):5111–5124. 2021. 

• Houlahan, K., Schenkel, F.S., Hailemariam, D., Lassen, J., Kargo, M., Cole, J.B., Connor, E.E., Wegmann, S., Junior, O., Miglior, F., Fleming, A., Chud, T.C.S., and Baes, C.F. Effects of incorporating dry matter intake and residual feed intake into a selection index for dairy cattle using deterministic modeling. Animals 11(4):1157. 2021. 

• Li, B., VanRaden, P.M., Null, D.J., O'Connell, J.R., and Cole, J.B. Major quantitative trait loci influencing milk production and conformation traits in Guernsey dairy cattle detected on Bos taurus autosome 19. J. Dairy Sci. 104(1):550–560. 2021. 

• Lozada-Soto, E.A., Maltecca, C., Lu, D., Miller, S., Cole, J.B., and Tiezzi, F. Trends in genetic diversity and the effect of inbreeding in American Angus cattle under genomic selection. Genet. Sel. Evol. 53:50. 2021. 

• Miles, A.M., Posbergh, C.J., and Huson, H.J. Direct phenotyping and principal component analysis of type traits implicate novel QTL in bovine mastitis through genome-wide association. Animals 11(4):1147. 2021. 

• Mueller, M.L., Cole, J.B., Connors, N.K., Johnston, D.J., Randhawa, I.A.S., and Van Eenennaam, A.L. Comparison of gene editing versus conventional breeding to introgress the POLLED allele into the tropically adapted Australian beef cattle population. Front. Genet. 12:593154. 2021. 

• Neupane, M., Hutchison, J.L., Van Tassell, C.P., and VanRaden, P.M. Genomic evaluation of dairy heifer livability. J. Dairy Sci. 104(8):8959–8965. 2021. 

• Sumreddee, P., Hay, E.H., Toghiani, S., Roberts, A., Aggrey, S.E., and Rekaya, R. Grid search approach to discriminate between old and recent inbreeding using phenotypic, pedigree and genomic information. BMC Genomics 22:538. 2021. 

• Wu, X.-L., Parker Gaddis, K.L., Burchard, J., Norman, H.D., Nicolazzi, E., Connor, E.E., Cole, J.B., and Durr, J. An alternative interpretation of residual feed intake by phenotypic recursive relationships in dairy cattle. JDS Commun. 2(6):371-375. 2021.

2020

• Cole, J.B., Eaglen, A.E., Maltecca, C., Mulder, H.A., and Pryce, J.E. The future of phenomics in dairy cattle breeding. Anim. Front. 10(2):37–44. 2020.

• Freebern, E., Santos, D.J.A., Fang, L., Jiang, J., Parker Gaddis, K.L., Liu, G.E., VanRaden, P.M., Maltecca, C., Cole, J.B., and Ma, L. GWAS and fine-mapping of livability and six diseases traits in Holstein cattle. BMC Genomics 21:41. 2020. 

• Li, B., VanRaden, P.M., Guduk, E., O'Connell, J.R., Null, D.J., Connor, E.E., VandeHaar, M.J., Tempelman, R.J., Weigel, K.A., and Cole, J.B. Genomic prediction of residual feed intake in US Holstein dairy cattle. J. Dairy Sci. 103(3):2477–2486. 2020. 

• Maltecca, C., Tiezzi, F., Cole, J.B., and Baes, C. Symposium review: Exploiting homozygosity in the era of genomics— Selection, inbreeding, and mating programs. J. Dairy Sci. 103(6):5302–5313. 2020. 

• McWhorter, T.M., Hutchison, J.L., Norman, H.D., Cole, J.B., Fok, G.C., Lourenco, D.A.L., and VanRaden, P.M. Investigating conception rate for beef service sires bred to dairy cows and heifers. J. Dairy Sci. 103(11):10374–10382. 2020.

• Nani, J.P., Bacheller, L.R., Cole, J.B., and VanRaden, P.M. Discovering ancestors and connecting relatives in large genomic databases. J. Dairy Sci. 103(2):1729–1734. 2020.

• Parker Gaddis, K.L., VanRaden, P.M., Cole, J.B., Norman, H.D., Nicolazzi, E., and Dürr, J.W. Symposium review: Development, implementation, and perspectives of health evaluations in the United States J. Dairy Sci. 103(6):5354–5365. 2020.

• Rosen, B.D., Bickhart, D.M., Schnabel, R.D., Koren, S., Elsik, C.G., Tseng, E., Rowan, T.N., Low, W.Y., Zimin, A., Couldrey, C., Hall, R., Li, W., Rhie, A., Ghurye, J., McKay, S.D., Thibaud-Nissen, F., Hoffman, J., Murdoch, B.M., Snelling, W.M., McDaneld, T.G., Hammond, J.A., Schwartz, J.C., Nandolo, W., Hagen, D.E., Dreischer, C., Schultheiss, S.J., Schroeder, S.G., Cole, J.B., Van Tassell, C.P., Liu, G., Smith, T.P.L., Medrano, J.F. De novo assembly of the cattle reference genome with single-molecule sequencing. GigaScience 9(3):1–9. 2020. 

• Santos, D.J., Cole, J.B., Liu, G.E., VanRaden, P.M., and Ma, L. Gamevar.f90: a software package for calculating individual gametic diversity. BMC Bioinformatics 21:100. 2020.

• Sumreddee, P., Toghiani, S., Hay, E.H., Roberts, A., Aggrey, S.E., and Rekaya, R. Runs of homozygosity and analysis of inbreeding depression. J. Anim. Sci. 98(12):1–11. 2020. 

• VanRaden, P.M., Tooker, M.E., Chud, T.C.S., Norman, H.D., Megonigal, Jr., J.H., Haagen, I.W., and Wiggans, G.R. Genomic predictions for crossbred dairy cattle. J. Dairy Sci. 103(2):1620–1631. 2020. 

• VanRaden, P.M. Symposium review: How to implement genomic selection. J. Dairy Sci. 103(6):5291–5301. 2020. 

2019

• Bradford, H.L., Masuda, Y., Cole, J.B., Misztal, I., and VanRaden, P.M. Modeling pedigree accuracy and uncertain parentage in single-step genomic evaluations of simulated and US Holstein datasets. J. Dairy Sci. 102(3):2308–2318. 2019. 

• Bradford, H.L., Masuda, Y., VanRaden, P.M., Legarra, A., and Misztal, I. Modeling missing pedigree in single-step genomic BLUP. J. Dairy Sci. 102(3):2336–2346. 2019.

• Cole, J.B. and Null, D.J. Short communication: Phenotypic and genetic effects of the polled haplotype on yield, longevity, and fertility in US Brown Swiss, Holstein, and Jersey cattle. J. Dairy Sci. 102 (9):8247–8250. 2019.

• Connor, E.E., Hutchison, J.L., Van Tassell, C.P., and Cole, J.B. Defining the optimal period length and stage of growth or lactation to estimate residual feed intake in dairy cows. J. Dairy Sci. 102(7):6131–6143. 2019. 

• Fang, L., Cai, W., Liu, S., Canela-Xandri, O., Gao, Y., Jiang, J., Rawlik, K., Li, B., Schroeder, S.G., Rosen, B.D., Li, C.-J., Sonstegard, T.S., Alexander, L.J., Van Tassell, C.P., VanRaden, P.M., Cole, J.B., Yu, Y., Zhang, S., Tenesa, A., Ma, L., Liu, G.E. Comprehensive analyses of 723 transcriptomes enhance biological interpretation and genomic prediction for complex traits in cattle. Genome Research. 30(5):790–801. 2019. 

• Fang, L., Jiang, J., Li, B., Zhou, Y., Freebern, E., VanRaden, P.M., Cole, J.B., Liu, G.E., and Li, M. Genetic and epigenetic architecture of paternal origin contribute to gestation length in cattle. Communications Biol. 2:100. 2019. 

• Fang, L., Zhou, Y., Liu, S., Jiang, J., Bickhart, D.M., Null, D.J., Li, B., Schroeder, S.G., Rosen, B.D., Cole, J.B., Van Tassell, C.P., Ma, L., and Liu, G. Comparative analyses of sperm DNA methylomes among human, mouse and cattle provide insights into epigenomic evolution and complex traits. Epigenetics. 14(3):260–276. 2019. 

• Fang, L., Zhou, Y., Liu, S., Jiang, J., Bickhart, D.M., Null, D.J., Li, B., Schroeder, S.G., Rosen, B.D., Cole, J.B., Van Tassell, C.P., Ma, L., and Liu, G. Integrating signals from sperm methylome analysis and genome-wide association study for a better understanding of male fertility in cattle. Epigenomes. 3(2):10. 2019. 

• Fragomeni, B.O., Lourenco, D.A.L., Legarra, A., VanRaden, P.M., and Misztal, I. Alternative SNP weighting for single-step genomic best linear unbiased predictor evaluation of stature in US Holsteins in the presence of selected sequence variants. J. Dairy Sci. 102(11):10012–10019. 2019. 

• García-Ruiz, A., Wiggans, G.R., and Ruiz-López, F.J. Pedigree verification and parentage assignment using genomic information in the Mexican Holstein population. J. Dairy Sci. 102(2):1806–1810. 2019. 

• Guarini, A., Sargolzaei, M., Brito, L., Kroezen, V., Lourenco, D., Baes, C., Miglior, F., Cole, J.B., and Schenkel, F. Estimating the effect of the deleterious recessive haplotypes AH1 and AH2 on reproduction performance of Ayrshire cattle. J. Dairy Sci. 102(6):5315–5322. 2019. 

• Jiang, J., Cole, J.B., Freebern, E., Da, Y., VanRaden, P.M., and Ma, L. Functional annotation and Bayesian fine-mapping reveals candidate genes for important agronomic traits in Holstein bulls. Comms. Bio. 2:212. 2019. 

• Jiang, J., Ma, L., Prakapenka, D., VanRaden, P.M., Cole, J.B., and Da, Y. A large-scale genome-wide association study in U.S. Holstein cattle. Front. Genet. 10:412. 2019.

•  Koltes, J.E., Cole, J.B., Clemmens, R., Dilger, R.N., Kramer, L.M., Lunney, J.K., McCue, M.E., McKay, S., Mateescu, R., Murdoch, B.M., Reuter, R., Rexroad, C., Rosa, G.J., Serao, N.V., White, S.N., Woodward-Greene, M.J., Worku, M., Zhang, H., and Reecy, J. A vision for development and utilization of high-throughput phenotyping and big data analytics in livestock. Front. Genet. 10:1197. 2019. 

• Li, B., Fang, L., Null, D.J., Hutchison, J.L., Connor, E.E., VanRaden, P.M., and Cole, J.B. High-density genome-wide association study for residual feed intake in Holstein dairy cattle. J. Dairy Sci. 102(12):11067–11080. 2019. | AbstractLiu, S., Fang, L., Zhou, Y., Santos, D.J.A., Xiang, R., Daetwyler, H.D., Chamberlain, A.J., Cole, J.B., Li, C.-J., Yu, Y., Ma, L., Zhang, S., Liu, G.E. . BMC Genomics. 20:181. 2019. 

• Liu, M., Fang, L., Liu, S., Pan, M.G., Seroussi, E., Cole, J.B., Ma, L., Chen, H., and Liu, G. Analyses of inter-individual variations in sperm DNA methylation reveal their regulatory role in gene expression and association with reproduction traits in cattle. BMC Genomics. 20:888. 2019. 

• lung, L.H.S., Petrini, J., Ramirez-Diaz, J., Salvian, M., Rovadoscki, G.A., Pilonetto, F., Dauria, D.B., Machado, P.F., Coutinho, L.L., Wiggans, G.R., and Mourao, G.B. Genome-wide association study for milk production traits in a Brazilian Holstein population. J. Dairy Sci. 102(6):5305–5314. 2019. 

• Ma, L., Cole, J.B., Da, Y., and VanRaden, P.M. Symposium review: Genetics, genome-wide association study, and genetic improvement of dairy fertility traits. J. Dairy Sci. 102(4):3735–3743. 2019. 

• Ma, L., Sonstegard, T.S., Cole, J.B., Van Tassell, C.P., Wiggans, G.R., Crooker, B.A., Tan, C., Prakapenka, D., Liu, G.E., and Da, Y. Genome changes due to artificial selection in U.S. Holstein cattle. BMC Genomics 20:128. 2019. 

• Mueller, M.L., Cole, J.B., Sonstegard, T.S., and Van Eenennaamn, A.L. Comparison of gene editing versus conventional breeding to introgress the POLLED allele into the US dairy cattle population. J. Dairy Sci. 102(5):4215–4226. 2019. 

• Santos, D.J., Cole, J.B., Lawlor, T.J., VanRaden, P.V., Tonhati, H., and Ma, L. Variance of gametic diversity and its use in selection programs. J. Dairy Sci. 102(6):5279–5294. 2019. 

• Schmitt, M.R., VanRaden, P.M., and De Vries, A. Ranking sires using genetic selection indices based on financial investment methods versus lifetime net merit. J. Dairy Sci. 102(10):9060–9075. 2019. 

• VanRaden, P.M., Bickhart, D.M., and O'Connell, J.R. Calling known variants and identifying new variants while rapidly aligning sequence data. J. Dairy Sci. 102(4):3216–3229. 2019. 

2018

• Cole. J.B., and VanRaden, P.M. Symposium review: Possibilities in an age of genomics: The future of selection indices. J. Dairy Sci. 101(4):3686–3701. 2018. 

• Heringstad, B., Egger-Danner, C., Charfeddine, N., Pryce, J.E., Stock, K.F., Kofler, J., Sogstad, A.M., Holzhauer, M., Fiedler, A., Müller, K., Nielsen, P., Thomas, G., Gengler, N., de Jong, G., Ødegård, C., Malchiodi, F., Miglior, F., Alsaaod, M., and Cole, J.B. Invited review: Genetics and claw health: Opportunities to enhance claw health by genetic selection. J. Dairy Sci. 101:(6)4801–4821. 2018. 

• Masuda, Y., VanRaden, P.M., Misztal, I., and Lawlor, T.J. Differing genetic trend estimates from traditional and genomic evaluations for genotyped animals as evidence of preselection bias in US Holsteins. J. Dairy Sci. 101(6):5194–5206. 2018. 

• Porto-Neto, L.R., Bickhart, D.M., Landaeta-Hernandez, A.J., Utsunomiya, Y.T., Pagan, M., Jimenez, E., Hansen, P.J., Dikmen, S., Schroeder, S.G., Kim, E.-S., Sun, J., Crespo, E., Amati, N., Cole, J.B., Null, D.J., García, J.F., Reverter, A., Barendse, W., and Sonstegard, T.S. Convergent evolution of slick coat in cattle through truncation mutations in the prolactin receptor. Front. Genet. 9:57. 2018. 

• Santos, D.J.A., Cole, J.B., Null, D.J., Byrem, T.M. and Ma, L. Genetic and nongenetic profiling of milk pregnancy-associated glycoproteins in Holstein cattle. J. Dairy Sci. 101(11):9987–10000. 2018. 

• Tiezzi, F., Arceo, M.E., Cole, J.B., and Maltecca, C. Including gene networks to predict calving difficulty in Holstein, Brown Swiss and Jersey cattle. BMC Genet. 19:20. 2018. 

• Weller, J.I., Bickhart, D.M., Wiggans, G.R., Tooker, M.E., O’Connell, J.R., Jiang, J., Ron, M., and VanRaden, P.M. Determination of quantitative trait nucleotides by concordance analysis between quantitative trait loci and marker genotypes of US Holsteins. J. Dairy Sci. 101(10):9089-9107. 2018.  

• Zhou, Y., Shen, B., Jiang, J., Padhi, A., Park, K.-E., Oswalt, A., Sattler, C.G., Telugu, B.P., Chen, H., Cole, J.B., Liu, G.E., and Ma, L. Construction of PRDM9 allele-specific recombination maps in cattle using large-scale pedigree analysis and genome-wide single sperm genomics. DNA Res. 25(2):183–194. 2018. 

2017

• Dikmen, S., Dahl, G.E., Cole, J.B., Null, D.J., and Hansen, P.J. The Larson Blue coat color phenotype in Holsteins: Characteristics and effects on body temperature regulation and production in lactating cows in a hot climate. J. Anim. Sci. 95(3):1164–1169. 2017. 

• Hutchison, J.L., VanRaden, P.M., Null, D.J., Cole, J.B., and Bickhart, D.M. Genomic evaluation of age at first calving. J. Dairy Sci. 100(8):6853–6861. 2017. 
  Jenko, J., Wiggans, G.R., Cooper, T.A., Eaglen, S.A.E., Luff, W.G. de L., Bichard, M., Pong-Wong, R., and Woolliams, J.A. Cow genotyping strategies for genomic selection in a small dairy cattle population. J. Dairy Sci. 100(1):439–452. 2017. 

• Jiang, J., Shen, B., O’Connell, J.R., VanRaden, P.M., Cole, J.B., and Ma, L. Dissection of additive, dominance, and imprinting effects for production and reproduction traits in Holstein cattle. BMC Genomics 18:425. 2017. 

• Oliveira Júnior, G.A., Chud, T.C.S., Ventura, R.V., Garrick, D.J., Cole, J.B., Munari, D.P., Ferraz, J.B.S., Mullart, E., DeNise, S., Smith, S., and da Silva, M.V.G.B. Genotype imputation in a tropical crossbred dairy cattle population. J. Dairy Sci. 100(12):9623-9634. 2017. 

• Oliveira Júnior, G.A., Perez, B.C., Cole, J.B., Santana, M.H.A., Silveira, J., Mazzoni, G., Ventura, R.V., Santana Júnior, M.L., Kadarmideen, H.N., Garrick, D.J., and Ferraz, J.B.S. Genomic study and Medical Subject Headings enrichment analysis of early pregnancy rate and antral follicle numbers in Nelore heifers. J. Anim. Sci. 95(11):4796–4812. 2017. 

• Ortega, M.S., Denicol, A.C., Cole, J.B., Null, D.J., Taylor, J.F., Schnabel, R.D., and Hansen, P.J. Association of single nucleotide polymorphisms in candidate genes previously related to genetic variation in fertility with phenotypic measurements of reproductive function in Holstein cows. J. Dairy Sci. 100(5):3725–3734. 2017.

• Ortega, M., Wohlgemuth, S., Tribulo, P., Siqueira, L.G.B., Null, D.J., Cole, J.B., Da Silva, M.V., and Hansen, P.J. A single nucleotide polymorphism in COQ9 affects mitochondrial and ovarian function and fertility in Holstein cows. Biol. Reprod. 96(3):652–663. 2017. 

• Parker Gaddis, K.L., Dikmen, S., Null, D.J., Cole, J.B., and Hansen, P.J. Evaluation of genetic components in traits related to superovulation, in vitro fertilization, and embryo transfer in Holstein cattle. J. Dairy Sci. 100(4):2877–2891. 2017. 

• Schwartz, J.C., Gibson, M.S., Heimeier, D., Koren, S., Phillippy, A.M., Bickhart, D.M., Smith, T.P.L., Medrano, J.F., and Hammond, J.A The evolution of the natural killer complex; a comparison between mammals using new high-quality genome assemblies and targeted annotation. Immunogenetics 69:255–269. 2017. 

• Stafuzza, N.B., Zerlotini, A., Lobo, F.P., Yamagishi, M.E.B., Chud, T.C.S., Caetano, A.R., Munari, D.P., Garrick, D.J., Machado, M.A., Martins, M.F., Carvalho, M.R., Cole, J.B., and da Silva, M.V.G.B. Single nucleotide variants and InDels identified from whole-genome re-sequencing of Guzerat, Gyr, Girolando and Holstein cattle breeds. PLoS One 12(3):e0173954. 

• Thompson, N.M., Widmar, N.O., Schutz, M.M., Cole, J.B., and Wolf, C.A. Economic considerations of breeding for polled dairy cows versus dehorning in the United States. J. Dairy Sci. 100(6):4941–4952. 2017. 

• VanRaden, P.M., Tooker, M.E., O’Connell, J.R., Cole, J.B., and Bickhart, D.M. Selecting sequence variants to improve genomic predictions for dairy cattle. Genet. Sel. Evol. 49:32. 2017. 

• Weigel, K.A., VanRaden, P.M., Norman, H.D., and Grosu, H. A 100-year review: Methods and impact of genetic selection in dairy cattle—From daughter–dam comparisons to deep learning algorithms. J. Dairy Sci. 100(12):10234-10250. 2017. 

• Wiggans, G.R., Cole, J.B., Hubbard, S.M., and Sonstegard, T.S. Genomic Selection in Dairy Cattle: The USDA Experience. Annu. Rev. Anim. Biosci. 5:309-327. 2017.

2016

• Adams, H.A., Sonstegard, T.S., VanRaden, P.M., Null, D.J., Van Tassell, C.P., Larkin, D.M., and Lewin, H.A. Identification of a nonsense mutation in APAF1 that is likely causal for a decrease in reproductive efficiency in Holstein dairy cattle. J. Dairy Sci. 99(8):6693–6701. 2016. 

• Bickhart, D.M., Hutchison, J.L., Null, D.J., VanRaden, P.M., and Cole, J.B. Reducing animal sequencing redundancy by preferentially selecting animals with low-frequency haplotypes. J. Dairy Sci. 99(7):5526–5534. 2016.

• Chesnais, J., Cooper, T.A., Wiggans, G.R., Sargolzaei, M., Pryce, J., and Miglior, F. Using genomics to enhance selection of novel traits in North American dairy cattle. J. Dairy Sci. 99(3):2413–2427. 2016.

• Cole, J.B. and da Silva, M.V. Invited review: Genomic selection in multi-breed dairy cattle populations. R. Bras. Zootec. 45(4):195–202. 2016.

• Cole, J.B., Null, D.J., and VanRaden, P.M. Phenotypic and genetic effects of recessive haplotypes on yield, longevity, and fertility. J. Dairy Sci. 99(9):7274–7288. 2016.

• Cooper, T.A., Eaglen, S.A.E., Wiggans, G.R., Jenko, J., Huson, H.J., Morrice, D.M., Bichard, M., de L. Luff, W.G., and Woolliams, J.A. Genomic evaluation, breed identification, and population structure of Guernsey cattle in North America, Great Britain, and the Isle of Guernsey. J. Dairy Sci. 99(7):5508–5515. 2016.

• Garcia-Ruiz, A., Cole, J.B, VanRaden, P.M., Wiggans, G.R., Ruiz-López, F.J., and Van Tassell, C.P. Changes in genetic selection differentials and generation intervals in US Holstein dairy cattle as a result of genomic selection. Proc. Natl. Acad. Sci. 113(28):E3995–4004. 2016.

• Kaniyamattam, K., Elzo, M.A., Cole, J.B., and De Vries, A. Stochastic dynamic simulation modeling including multitrait genetics to estimate genetic, technical, and financial consequences of dairy farm reproduction and selection strategies. J. Dairy Sci. 99(10):8187–8202. 2016. 

• Ortega, M.S., Denicol, A.C., Cole, J.B., Null, D.J., and Hansen, P.J. Use of single nucleotide polymorphisms in candidate genes associated with daughter pregnancy rate for prediction of genetic merit for reproduction in Holstein cows. Anim. Genet. 47(3):288–297. 2016. 

• Parker Gaddis, K.L., Cole, J.B., Clay, J.S., and Maltecca, C. Benchmarking dairy herd health status using routinely recorded herd summary data. J. Dairy Sci. 99(2):1298–1314. 2016.

• Parker Gaddis, K.L., Null, D.J., and Cole, J.B. Explorations in genome-wide association studies and network analyses with dairy cattle fertility traits. J. Dairy Sci. 99(8):6420–6435. 2016. 

• Petrini, J., Iung, L.H.S., Rodriguez, M.A.P., Salvian, M., Pertille, F., Rovadoscki, G.A., Cassoli, L.D., Coutinho, L.L., Machado, P.F., Wiggans, G.R., and Mourao, G.B. Genetic parameters for milk fatty acids, milk yield and quality traits of a Holstein cattle population reared under tropical conditions. J. Anim. Breeding Genet. 133(5):384–395. 2016.

• Pryce, J.E., Parker Gaddis, K.L., Loeck, A., Bastin, C., Abdelsayed, M., Gengler, N., Miglior, F., Heringstad, B., Egger-Danner, C., Stock, K.F., Bradley, A.J., and Cole, J.B. Invited review: Opportunities for genetic improvement of metabolic diseases. J. Dairy Sci. 99(9):6856–6873. 2016.

• Su, G., Ma, P., Nielsen, U.S., Aamand, G.P., Wiggans, G.R., Guldbrandtsen, B., and Lund, M.S. Sharing reference data and including cows in reference population improve genomic predictions in Danish Jersey. Anim. 10(6):1067–1075. 2016.

• Utsunomiya, A.T.H., Santos, D.J.A., Boison, S.A., Utsunomiya, Y.T., Milanesi, M., Bickhart, D.M., Ajmone-Marsan, P., Solkner, J., Garcia, J.F., da Fonseca, R., and da Silva, M.V.G.B. Revealing misassembled segments in the bovine reference genome by high resolution linkage disequilibrium scan. BMC Genomics 17:705. 2016.

• VanRaden, P.M. Practical implications for genetic modeling in the genomics era. J. Dairy Sci. 99(3):2405–2412. 2016.

• Wiggans, G.R., Cooper, T.A., VanRaden, P.M., Van Tassell, C.P., Bickhart, D.M., and Sonstegard, T.S. Increasing the number of single nucleotide polymorphisms used in genomic evaluation of dairy cattle. J. Dairy Sci. 99(6):4504–4511. 2016.

• Wu, X-L., Xu, J., Feng, G., Wiggans, G.R., Taylor, J.F., He, J., Qian, C., Qiu, J., Simpson, B., Walter, J., and Bauck, S. Optimal design of low-density SNP arrays for genomic prediction: algorithm and applications. PLoS ONE. 11(9):e0161719. 2016.

2015

• Bermejo-Alvarez, P., Ramos-Ibeas, P., Park, K.E., Powell, A.P., Vansandt, L., Bickhart, D.M., Ramirez, M.A., Gutierrez-Adan, A., and Telugu, B.P. Tet-mediated imprinting erasure in H19 locus following reprogramming of spermatogonial stem cells to induced pluripotent stem cells. Sci. Rpt. 5:13691. 2015.

• Bickhart, D.M., Hutchison, J.L., Xu, L., Schnabel, R.D., Taylor, J.F., Reecy, J.M., Schroeder, S.G., Van Tassell, C.P., Sonstegard, T.S., and Liu, G. RAPTR-SV: a hybrid method for the detection of structural variants. Bioinformatics. 31(13):2084–2090. 2015.

• Cole, J.B. A simple strategy for managing many recessive disorders in a dairy cattle breeding program. Genet. Sel. Evol. 47:94. 2015.

• Cooper, T.A., Wiggans, G.R., and VanRaden, P.M. Short communication: Analysis of genomic predictor population for Holstein dairy cattle in the US—Effects of sex and age. J. Dairy Sci. 98(4):2785–2788. 2015.

• Dikmen, S., Wang, X., Ortega, M., Null, D.J., Cole, J.B., Hansen, P.J. Single nucleotide polymorphisms associated with thermoregulation in lactating dairy cows exposed to heat stress. J. Anim. Breed. Genet. 132(6):409–419. 2015.

• Egger-Danner, C., Cole, J.B., Pryce, J., Gengler, N., Heringstad, B., Stock, K., Bradley, A., and Andrews, L. Invited review: Overview of new traits and phenotyping strategies in dairy cattle with a focus on functional traits. Animal 9(2):191–207. 2015.

• García-Ruiz, A., Ruiz-Lopez, F.J., Wiggans, G.R., Van Tassell, C.P., and Montaldo, H.H. Effect of reference population size and available ancestor genotypes on imputation of Mexican Holstein genotypes. J. Dairy Sci. 98(5):3478–3484. 2015.

• Kim, E-S., Sonstegard, T.S., Van Tassell, C.P., Wiggans, G.R., and Rothschild, M.F. The relationship between runs of homozygosity and inbreeding in Jersey cattle under selection. PLoS ONE 10(7):e0129967. 2015.

• Ma, L., O’Connell, J.R., VanRaden, P.M., Shen, B., Padhi, A. Sun, C., Bickhart, D.M., Cole, J.B., Null, D.J., Liu, G.E., Da, Y., and Wiggans, G.R. Cattle sex-specific recombination and genetic control from a large pedigree analysis. PLoS Genet. 11(11):e1005387. 2015.

• Macciotta, N.P.P., Dimauro, C., Null, D.J., Gaspa, G., Cellesi, M., and Cole, J.B. Dissection of genomic correlation matrices of US Holsteins using multivariate factor analysis. J. Anim. Breed. Genet. 132(1):9–20. 2015.

• Parker Gaddis, K.L., Tiezzi, F., Cole, J.B., Clay, J.S., and Maltecca, C. Genomic prediction of disease occurrence using producer-recorded health data: a comparison of methods. Genet. Sel. Evol. 47:41. 2015.

• Tiezzi, F., Parker Gaddis, K.L., Cole, J.B., Clay, J.S., and Maltecca, C. A genome-wide association study for clinical mastitis in first parity US Holsein cows using a single-step approach and genomic matrix re-weighting procedure. PLoS ONE 10(2):e0114919. 2015.

• VanRaden, P.M., Sun, C., and O’Connell, J.R. Fast imputation using medium or low-coverage sequence data. BMC Genetics 16(82). 2015. 

• Wiggans, G.R., Su, G., Cooper, T.A., Nielsen, U.S., Aamand, G.P., Buldgrandtsen, B., Lund, M.S., and VanRaden, P.M. Short communication: Improving accuracy of Jersey genomic evaluations in the United States and Denmark by sharing reference population bulls. J. Dairy Sci. 98(5):3508–3513. 2015.

• Wiggans, G.R., VanRaden, P.M., and Cooper, T.A. Technical note: Rapid calculation of genomic evaluations for new animals. J. Dairy Sci. 98(3):2039–2042. 2015.

• Zavarez, L.B., Utsunomiya, Y.T., Carmo, A.S., Neves, H.H.R., Carvalheiro, R., Ferencakovic, M., Perez O’Brien, A.M., Curik, I., Cole, J.B., Van Tassell, C.P., da Silva, M.V.G.B., Sonstegard, T.S., Sölkner, J., and Garcia, J.F. Assessment of autozygosity in Nellore cows (Bos indicus) through high-density SNP genotypes. Front. Genet. 6:5. 2015.

2014

• Bickhart, D.M. and Liu, G.E. The challenges and importance of structural variation detection in livestock. Front. Genet. 5:37. 2014. 

• Cole, J.B., Waurich, B., Wensch-Dorendorf, M., Bickhart, D.M., and Swalve, H.H. A genome-wide association study of calf birth weight in Holstein cattle using single nucleotide polymorphisms and phenotypes predicted from auxiliary traits. J. Dairy Sci. 97(5):3156–3172. 2014.

• Cooper, T.A., Wiggans, G.R., Null, D.J., Hutchison, J.L., and Cole, J.B. Genomic evaluation, breed identification, and discovery of a haplotype affecting fertility for Ayrshire dairy cattle. J. Dairy Sci. 97(6):3878–3882. 2014. 

• Gay, K.D., Widmar, N.J.O., Nennich. T.D., Schinckel, A.P., Cole, J.B., and Schutz, M.M. Development of a lifetime merit-based selection index for US dairy grazing systems. J. Dairy Sci. 97(7):4568–4578. 2014. 

• Hutchison, J.L., Cole, J.B., and Bickhart, D.M. Short communication: Use of young bulls in the United States. J. Dairy Sci. 97(5):3213–3220. 2014. 

• McClure, M.C., Bickhart, D., Null, D., VanRaden, P., Xu, L., Wiggans, G., Liu, G., Schroeder, S., Glasscock, J., Armstrong, J., Cole, J.B., Van Tassell, C.P., and Sonstegard, T.S. Bovine exome sequence analysis and targeted SNP genotyping of recessive fertility defects BH1, HH2, and HH3 reveal a putative causative mutation in SMC2 for HH3. PLoS ONE 9(3):e92769. 2014.

• McDaneld, T.G., Kuehn, L.A., Thomas, M.G., Snelling, W.M., Smith, T.P.L., Pollak, E.J., Cole, J.B., and Keele, J.W. Genomewide association study of reproductive efficiency in female cattle. J. Anim. Sci. 92(5):1945–1957. 2014.

• Neves, H.H.R., Carvalheiro, R., Perez O’Brien, A.M., Utsunomiya, Y.T., do Carmo, A.S., Schenkel, F.S., Solkner, J., McEwan, J.C., Van Tassell, C.P., Cole, J.B., da Silva, M.V.G.B., Queiroz, S.A., Sonstegard, T.S., and Garcia, J. F. Accuracy of genomic predictions in Bos indicus (Nellore) cattle. Genet. Sel. Evol. 46:17. 2014.

• Parker Gaddis, K.L., Cole, J.B., Clay, J.S., and Maltecca, C. Genomic selection for producer-recorded health event data in US dairy cattle. J. Dairy Sci. 97(5):3190–3199. 2014. 

• Silva, M.V.B., dos Santos, D.J.A., Boison, S.A., Utsunomiya, A.T.H., Carmo, S., Sonstegard, T.S., Cole, J.B., and Van Tassell, C.P. The development of genomics applied to dairy breeding. Livest. Sci. 166:66–75. 2014. 

• Sun, C., VanRaden, P.M., Cole, J.B., and O’Connell, J.R. Improvement of prediction ability for genomic selection of dairy cattle by including dominance effects. PLoS ONE 9(8):e103934. 2014. 

• Sun, C., and VanRaden P.M. Increasing long-term response by selecting for favorable minor alleles. PLoS ONE 9(2):e88510. 2014.

• Utsunomiya, Y.T., Carmo, A.S., Neves, H.H.R., Carvalheiro, R., Matos, M.C., Zavarez, L.B., Ito, P.K.R.K., Perez O’Brien, A.M., Sölkner, J., Porto-Neto, L.R., Schenkel, F.S., McEwan, J., Cole, J.B., da Silva, M.V.G.B., Van Tassell, C.P., Sonstegard, T.S., and Garcia, J.F. Genome-wide mapping of loci explaining variance in scrotal circumference in Nellore cattle. PLoS ONE 9(2):e88561. 2014. 

• VanRaden, P.M., Tooker, M.E., Wright, J.R., Sun, C., and Hutchison, J.L. Comparison of single-trait to multi-trait national evaluations for yield, health, and fertility. J. Dairy Sci. 97(12):7952–7962. 2014.

• Weller, J.I., Cole, J.B., VanRaden, P.M., and Wiggans, G.R. Application of the a posteriori granddaughter design to the Holstein genome. Animal 8(4):511–519. 2014.

• Xu, L., Cole, J.B., Bickhart, D.M., Hou, Y., Song, J., VanRaden, P.M., Sonstegard, T.S., Van Tassell, C.P., and Liu, G.E. Genome wide CNV analysis reveals additional variants associated with milk production traits in Holsteins. BMC Genomics 15:683. 2014.

• Yao, C., Weigel, K.A., and Cole, J.B. Short communication: Genetic evaluation of stillbirth in US Brown Swiss and Jersey cattle. J. Dairy Sci. 97(4):2474–2480. 2014.

2013

• Cochran, S.D., Cole, J.B., Null, D.J., and Hansen, P.J. Discovery of single nucleotide polymorphisms in candidate genes associated with fertility and production traits in Holstein cattle. BMC Genet. 14:49. 2013.

• Cochran, S.D., Cole, J.B., Null, D.J., and Hansen, P.J. Single nucleotide polymorphisms in candidate genes associated with fertilizing ability of sperm and subsequent embryonic development in cattle. Biol. Reprod. 89(3):69. 2013.

• Cole, J.B., Lewis, R.M., Maltecca, C., Newman, S., Olson, K.M., and Tait, Jr., R.G. Breeding and Genetics Symposium: Systems biology in animal breeding: Identifying relationships among markers, genes, and phenotypes. J. Anim. Sci. 91(2):521–522. 2013.

• Cole, J.B., and Null, D.J. Visualization of the transmission of direct genomic values for paternal and maternal chromosomes for 15 traits in US Brown Swiss, Holstein, and Jersey cattle. J. Dairy Sci. 96(4):2713–2726. 2013.

• Connor, E.E., Hutchison, J.L., Norman, H.D., Olson, K.M., Van Tassell, C.P., Leith, J.M., and Baldwin VI, R.L. Use of residual feed intake in Holsteins during early lactation shows potential to improve feed efficiency through genetic selection. J. Anim. Sci. 91(8):3978–3988. 2013.

• Cooper, T.A., Wiggans, G.R., and VanRaden, P.M. Short communication: Relationship of call rate and accuracy of single nucleotide polymorphism genotypes in dairy cattle. J. Dairy Sci. 96(5):3336–3339. 2013. 

• Dikmen, S., Cole, J.B., Null, D.J., and Hansen, P.J. Genome-wide association mapping for identification of quantitative trait loci for rectal temperature during heat stress in Holstein cattle. PLoS ONE 8(7):e69202. 2013.

• Hutchison, J.L., VanRaden, P.M., Norman, H.D., and Cole, J.B. Technical note: Changes to herd cutoff date in conception rate evaluations. J. Dairy Sci. 96(2):1264–1268. 2013. 

• McClure, M., Kim, E., Bickhart, D., Null, D., Cooper, T., Cole, J., Wiggans, G., Ajmone-Marsan, P., Colli, L., Santus, E., Liu, G.E., Schroeder, S., Matukumalli, L., Van Tassell, C., and Sonstegard T. Fine mapping for Weaver Syndrome in Brown Swiss cattle and the identification of 41 concordant mutations across NRCAM, PNPLA8 and CTTNBP2. PLoS One 8(3):e59251. 2013.

• McClure, M.C., Sonstegard T.S., Wiggans, G.R., Van Eenennaam, A.L., Weber, K.L., Penedo, C.T., Berry, D.P., Flynn, J., Garcia, J.F., Carmo, A.S., Regitano, L.C.A., Albuquerque, M., Silva, M.V.G.B., Machado, M.A., Coffey, M., Moore, K., Boscher, M-Y., Genestout, L., Mazza, R., Taylor, J.F., Schnabel, R.D., Simpson, B., Marques, E., McEwan, J.C., Cromie, A., Coutinho, L.L., Kuehn, L.A., Keele, J.W., Piper, E.K., Cook, J., Williams, R., Bovine HapMap Consortium, and Van Tassell, C.P. Imputation of microsatellite alleles from dense SNP genotypes for parentage verification across multiple Bos taurus and Bos indicus breeds. Front. Genet. 4:176. 2013. 

• Misztal, I., Tsuruta, S., Aguilar, Legarra, A., VanRaden, P.M., and Lawlor, T.J. Methods to approximate reliabilities in single-step genomic evaluation. J. Dairy Sci. 96(1):647–654. 2013.

• Porto-Neto, L.R., Sonstegard, T.S., Liu, G.E., Bickhart, D.M., da Silva, M.V.B., Machado, M.M., Utsunomiya, Y.T., Garcia, J.F., Gondro, C., and Van Tassell, C.P. Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping. BMC Genomics 14:876. 2013.

• Sonstegard, T.S., Cole, J.B., VanRaden, P.M., Van Tassell, C.P., Null, D.J., Schroeder, S.G., Bickhart, D.M., and McClure, M.C. Identification of a nonsense mutation in CWC15 associated with decreased reproductive efficiency in Jersey cattle. PLoS ONE. 8(1):e54872. 2013.

• Sun, C., VanRaden, P.M., O’Connell, J.R., Weigel, K.A., and Gianola, D. Mating programs including genomic relationships and dominance effects. J. Dairy Sci. 96(12):8014–8023. 2013. 

• Utsunomiya, Y.T., do Carmo, A.S., Carvalheiro, R., Neves, H.H.R., Matos, M.C., Zavarez, L.B., Pérez O’Brien, A.M., Sölkner, J., McEwan, J.C., Cole, J.B., Van Tassell, C.P., Schenkel, F.S., da Silva, M.V.G.B., Porto Neto, L.R., Sonstegard, T.S., and Garcia, J.F. Genome-wide association study for birth weight in Nellore cattle points to previously described orthologous genes affecting human and bovine height. BMC Genet. 14:52. 2013.

• VanRaden, 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.B.C.H.M., Valentini, A., Van Doormaal, B.J., Faust, M.A., and Doak, G.A. Genomic imputation and evaluation using high density Holstein genotypes. J. Dairy Sci. 96(1):668–678. 2013.

• VanRaden, P.M., Cooper, T.A., Wiggans, G.R., O’Connell, J.R., and Bacheller, L.R. Confirmation and discovery of maternal grandsires and great-grandsires in dairy cattle. J. Dairy Sci. 96(3):1874–1879. 2013.

• Weller, J.I., VanRaden,P.M., and Wiggans, G.R. Application of a posteriori granddaughter and modified granddaughter designs to determine Holstein haplotype effects. J. Dairy Sci. 96(8):5376–5387. 2013.

• Wiggans, G.R., Cooper, T.A., Van Tassell, C.P., Sonstegard, T.S., and Simpson, E.B. Technical note: Characteristics and use of the Illumina BovineLD and GeneSeek Genomic Profiler low-density bead chips for genomic evaluation. J. Dairy Sci. 96(2):1258–1263. 2013.

• Wright, J.R., Wiggans, G.R., Muenzenberger, C.J., and Neitzel, R.R. Short communication: Genetic evaluation of mobility for Brown Swiss dairy cattle. J. Dairy Sci. 96(4):2657–2660. 2013.

• Yao, C., Spurlock, D.M., Armentano, L., Page, C.D., VandeHaar, M.J., Bickhart, D.M., and Weigel, K.A. Random Forests approach for identifying additive and epistatic single nucleotide polymorphisms associated with residual feed intake in dairy cattle. J. Dairy Sci. 96(10):6716–6729. 2013.

2012

• Boichard, D., Chung, H., Dassonneville, R., David, X., Eggen, A., Fritz, S., Gietzen, K.J., Hayes, B.J., Lawley, C.T., Sonstegard, T.S., Van Tassell, C.P., VanRaden, P.M., Viaud-Martinez, K.A., and Wiggans, G.R. Design of a bovine low-density SNP array optimized for imputation. PLoS ONE 7(3):e34130. 2012.

• Cole, J.B., Ehrlich, J.L., and Null, D.J. Short communication: Projecting milk yield using best prediction and the MilkBot lactation model. J. Dairy Sci. 95(7):4041–4044. 2012.

• Cole, J.B., Newman, S., Foertter, F., Aguilar, I., and Coffey, M. Really big data: Processing and analysis of large datasets. J. Anim. Sci. 90(3):723–733. 2012.

• Connor, E.E., Hutchison, J.L., Olson, K.M., and Norman, H.D. Triennial Lactation Symposium: Opportunities for improving milk production efficiency in dairy cattle. J. Anim. Sci. 90(5):1687–1694. 2012.

• Dikmen, S., Cole, J.B., Null D.J., and Hansen, P.J. Heritability of rectal temperature and genetic correlations with production and reproduction traits in dairy cattle. J. Dairy Sci. 95(6):3401–3405. 2012.

• García-Peniche, T.B., Montaldo, H.H., Valencia-Posadas, M., Wiggans, G.R., Hubbard, S.M., Torres-Vázquez, J.A., and Shepard, L. Breed differences over time and heritability estimates for production and reproduction traits of dairy goats in the United States. J. Dairy Sci. 95(5):2707–2717. 2012.

• Hou, Y., Bickhart, D.M., Hvinden, M.L., Li, C., Song, J., Boichard, D.A., Fritz, S., Eggen, A., DeNise, S., Wiggans, G.R., Sonstegard, T.S., Van Tassell, C.P., and Liu, G.E. Fine mapping of copy number variations on two cattle genomes assembles using high density SNP array. BMC Genomics 13:376.

• Ma, L., Wiggans, G.R., Wang, S., Sonstegard, T.S., Yang, J., Crooker, B.A., Cole, J.B., Van Tassell, C.P., Lawlor, T.J., and Da, Y. Effect of sample stratification on dairy GWAS results. BMC Genomics 13:536. 2012.

• McClure, M., Sonstegard, T., Wiggans, G.R., and Van Tassell, C.P. Imputation of microsatellite alleles from dense SNP genotypes for parental verification. Frontiers Livest. Genomics 3:140. 

• Norman, H.D, Miller, R.H., Wright, J.R., Hutchison, J.L., and Olson, K.M. Factors associated with frequency of abortions recorded through Dairy Herd Improvement test plans. J. Dairy Sci. 95(7):4074–4084. 2012.

• Olson, K.M., VanRaden, P.M., and Tooker, M.E. Multibreed genomic evaluations using purebred Holsteins, Jerseys, and Brown Swiss . J. Dairy Sci. 95(9):5378–5383. 2012.

• Parker Gaddis, K.L, Cole, J.B., Clay, J.S., and Maltecca, C. Incidence validation and relationship analysis of producer-recorded health event data from on-farm computer systems in the United States J. Dairy Sci. 95(9):5422–5435. 2012.

• Wiggans, G.R., Cooper, T.A., VanRaden, P.M., Olson, K.M., and Tooker, M.E. Use of the Illumina Bovine3K BeadChip in dairy genomic evaluation. J. Dairy Sci. 95(3):1552–1558. 2012.

• Wiggans, G.R., VanRaden, P.M., and Cooper, T.A. Technical note: Adjustment of all cow evaluations for yield traits to be comparable with bull evaluations. J. Dairy Sci. 95(6):3444–3447. 2012. 

2011

• Aguilar, I., Misztal, I., Tsuruta, S., Wiggans, G.R., and Lawlor, T.J. Multiple trait genomic evaluation of conception rate in Holsteins. J. Dairy Sci. 94(5):2621–2624. 2011. 

• Cole, J.B., Null, D.J., and De Vries, A. Short communication: Best prediction of 305-day lactation yields with regional and seasonal effects. J. Dairy Sci. 94(3):1601–1604. 2011.

• Cole, J.B., and VanRaden, P.M. Use of haplotyes to estimate Mendelian sampling effects and selection limits. J. Anim. Breed. Genet. 128(6):448–455. 2011.

• 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., and Da, Y. Genome-wide association analysis of thirty one production, health, reproduction and body conformation traits in contemporary U.S. Holstein cows. BMC Genomics 12:408. 2011.

• Daetwyler, H.D., Wiggans, G.R., Hayes, B.J., Woolliams, J.A., and Goddard, M.E. Imputation of missing genotypes from sparse to high density using long-range phasing. Genetics 189(1):317–327. 2011.

• Hou, Y., Liu, G.E., Bickhart, D.M., Cardone, M., Wang, K., Kim, E.-S., Matukumalli, L.K., Ventura, M., Song, J., VanRaden, P.M., Sonstegard, T.S., and Van Tassell, C.P. Genomic characteristics of cattle copy number variations. BMC Genomics 12:127. 2011. 

• Norman, H.D., Hutchison, J.L., and VanRaden, P.M. Evaluations for service-sire conception rate for heifer and cow inseminations with conventional and sexed semen. J. Dairy Sci. 94(12):6135–6142. 2011. 

• Norman, H.D., Lombard, J.E., Wright, J.R., Kopral, C.A., Rodriquez, J.M., and Miller, R.H. Consequence of alternative standards for bulk tank somatic cell count of dairy herds in the United States. J. Dairy Sci. 94(12):6243–6256. 2011. 

• Norman, H.D., Wright, J.R., and Miller, R.H. Potential consequences of selection to change gestation length on performance of Holstein cows. J. Dairy Sci. 94(2):1005–1010. 2011.

• Olson, K.M., VanRaden, P.M., Tooker, M.E., and Cooper, T.A. Differences among methods to validate genomic evaluations for dairy cattle. J. Dairy Sci. 94(5):2613–2620. 2011. 

• VanRaden, P.M., O’Connell, J.R., Wiggans, G.R., and Weigel, K.A. Genomic evaluations with many more genotypes. Genet. Sel. Evol. 43:10. 2011.

• VanRaden, P.M., Olson, K.M., Null, D.J., and Hutchison, J.L. Harmful recessive effects on fertility detected by absence of homozygous haplotypes. J. Dairy Sci. 94(12):6153–6161. 2011.

• VanRaden, P.M., Olson, K.M., Wiggans, G.R., Cole, J.B., and Tooker, M.E. Genomic inbreeding and relationships among Holsteins, Jerseys, and Brown Swiss . J. Dairy Sci. 94(11):5673–5680. 2011.

• Wiggans, G.R., Cooper, T.A., VanRaden, P.M., and Cole, J.B. Technical note: Adjustment of traditional cow evaluations to improve accuracy of genomic predictions. J. Dairy Sci. 94(12):6188–6193. 2011.

• Wiggans, G.R., VanRaden, P.M., and Cooper, T.A. The genomic evaluation system in the United States: Past, present, future. J. Dairy Sci. 94(6):3202–3211. 2011.

2010

• Attalla, S.A., Seykora, A.J., Cole, J.B., and Heins, B.J. Genetic parameters of milk ELISA scores for Johne's disease. J. Dairy Sci. 93(4):1729–1735. 2010.

• Cole, J.B., and VanRaden, P.M. Visualization of results from genomic evaluations. J. Dairy Sci. 93(6):2727–2740. 2010.

• Montaldo, H.H., Valencia-Posadas, M., Wiggans, G.R., Shepard, L., and Torres-Vazquez, J.A. Short communication: Genetic and environmental relationships between milk yield and kidding interval in dairy goats. J. Dairy Sci. 93(1):370–372. 2010.

• Norman, H.D., Hutchison, J.L., and Miller, R.H. Use of sexed semen and its effect on conception rate, calf sex, dystocia, and stillbirth of Holsteins in the United States. J. Dairy Sci. 93(8):3880–3890. 2010. 

• Norman, H.D., Wright, J.R., and Miller, R.H. Response to alternative genetic-economic indices for Holsteins across 2 generations. J. Dairy Sci. 93(6):2695–2702 . 2010.

• VanRaden, P.M., and Sullivan, P. International genomic evaluation methods for dairy cattle. Genet. Sel. Evol. 42:7. 2010. 

• Weigel, K.A., Van Tassell, C.P., O’Connell, J.R., VanRaden, P.M., and Wiggans, G.R. Prediction of unobserved single nucleotide polymorphism genotypes of Jersey cattle using reference panels and population-based imputation algorithms. J. Dairy Sci. 93(5):2229–2238. 2010.

• Wiggans, G.R., VanRaden, P.M., Bacheller, L.R., Tooker, M.E., Hutchison, J.L., Cooper, T.A., and Sonstegard, T.S. Selection and management of DNA markers for use in genomic evaluation. J. Dairy Sci. 93(5):2287–2292. 2010.

2009

• Appuhamy, A.D.R.N, Cassell, B.G., and Cole, J.B. Phenotypic and genetic relationships of common health disorders with milk and fat yield persistencies from producer-recorded health data and test day yields. J. Dairy Sci. 92(4):1785–1795. 2009.

• Cole, J.B., and Null, D.J. Genetic evaluation of lactation persistency for five breeds of dairy cattle. J. Dairy Sci. 92(5):2248–2258. 2009.

• Cole, J.B., Null, D.J., and VanRaden, P.M. Best prediction of yields for long lactations. J. Dairy Sci. 92(4):1796–1810. 2009.

• Cole, J.B., VanRaden, P.M., O’Connell, J.R., Van Tassell, C.P., Sonstegard, T.S., Schnabel, R.D., Taylor, J.F., and Wiggans, G.R. Distribution and location of genetic effects for dairy traits. J. Dairy Sci. 92(6):2931–2946. 2009. 

• Miller, R.H., Norman, H.D., Wright, J.R., and Cole, J.B. Impact of genetic merit for milk somatic cell score of sires and maternal grandsires on herd life of their daughters. J. Dairy Sci. 92(5):2224–2228. 2009.

• Norman, H.D., Wright, J.R., Hubbard, S.M., Miller, R.H., and Hutchison, J.L. Reproductive status of Holstein and Jersey cows in the United States. J. Dairy Sci. 92(7):3517–3528. 2009. 

• Norman, H.D., Wright, J.R., Kuhn, M.T., Hubbard, S.M., Cole, J.B., and VanRaden, P.M. Genetic and environmental factors that affect gestation length in dairy cattle. J. Dairy Sci. 92(5):2259–2269. 2009. 

• Norman, H.D., Wright, J.R., and Weigel, K.A. Alternatives for examining daughter performance of progeny-test bulls between official evaluations. J. Dairy Sci. 92(5):2348–2355. 2009. 

• VanRaden, P.M. Why we don't patent [editorial]. J. Anim. Breeding Genet. 126(2):91. 2009.

• VanRaden, P.M., Van Tassell, C.P., Wiggans, G.R., Sonstegard, T.S., Schnabel, R.D., Taylor, J.F., and Schenkel, F.S. Invited review: Reliability of genomic predictions for North American Holstein bulls. J. Dairy Sci. 92(1):16–24. 2009.

• Wiggans, G.R., Sonstegard, T.S., VanRaden, P.M., Matukumalli, L.K., Schnabel, R.D., Taylor, J.F., Schenkel, F.S., and Van Tassell, C.P. Selection of single-nucleotide polymorphisms and quality of genotypes used in genomic evaluation of dairy cattle in the United States and Canada. J. Dairy Sci. 92(7):3431–3436. 2009. 

2008

• Bohmanova, J., Misztal, I., Tsuruta, S., Norman, H.D., and Lawlor, T.J. Short communication: Genotype by environment interaction due to heat stress. J. Dairy Sci. 91(2):840–846. 2008.

• Dechow, C.D., Norman, H.D., and Pelensky, C.A. Short communication: Variance estimates among herds stratified by individual herd heritability. J. Dairy Sci. 91(4):1648–1651. 2008.

• Dechow, C.D., Norman, H.D., Zwald, N.R., Cowan, C.M., and Meland, O.M. Relationship between individual herd-heritability estimates and sire misidentification rate. J. Dairy Sci. 91(4):1640–1647. 2008.

• Kuhn, M.T., and Hutchison, J.L. Prediction of dairy bull fertility from field data: Use of multiple services and identification and utilization of factors affecting bull fertility. J. Dairy Sci. 91(6):2481–2492. 2008.

• Kuhn, M.T., Hutchison, J.L., and Norman, H.D. Modeling nuisance variables for prediction of service sire fertility. J. Dairy Sci. 91(7):2823–2835. 2008.

• Miller, R.H., Kuhn, M.T., Norman, H.D., and Wright, J.R. Death losses for lactating cows in herds enrolled in Dairy Herd Improvement test plans. J. Dairy Sci. 91(9):3710–3715. 2008.

• Powell, R.L., Sanders, A.H., and Norman, H.D. Investigation of country bias in international genetic evaluations using full-brother information. J. Dairy Sci. 91(7):2885–2892. 2008.

• VanRaden, P.M. Efficient methods to compute genomic predictions. J. Dairy Sci. 91(11):4414–4423. 2008.

• Wiggans, G.R., Cole, J.B., and Thornton, L.L.M. Multiparity evaluation of calving ease and stillbirth with separate genetic effects by parity. J. Dairy Sci. 91(8):3173–3178. 2008.

• Wiggans, G.R., Tsuruta, S., and Misztal, I. Technical note: Adaptation of an animal-model method for approximation of reliabilities to a sire-maternal grandsire model. J. Dairy Sci. 91(10):4058–4061. 2008.

2007

• Appuhamy, J.A.D.R.N., Cassell, B.G., Dechow, C.D., and Cole, J.B. Phenotypic relationships of common health disorders in dairy cows to lactation persistency estimated from daily milk weights. J. Dairy Sci. 90(9):4424–4434. 2007.

• Bohmanova, J., Misztal, I., and Cole, J.B. Temperature-humidity indices as indicators of milk production losses due to heat stress. J. Dairy Sci. 90(4):1947–1956. 2007.

• Cole, J.B. PyPedal: A computer program for pedigree analysis. Comp. Electron. Agric. 57(1):107–113. 2007.

• Cole, J.B., Wiggans, G.R., and VanRaden, P.M. Genetic evaluation of stillbirth in United States Holsteins using a sire-maternal grandsire threshold model. J. Dairy Sci. 90(5):2480–2488. 2007.

• Cole, J.B., Wiggans, G.R., VanRaden, P.M., and Miller, R.H. Stillbirth (co)variance components for a sire-maternal grandsire threshold model and development of a calving ability index for sire selection. J. Dairy Sci. 90(5):2489–2496. 2007.

• Dechow, C.D., and Norman, H.D. Within-herd heritability estimated with daughter-parent regression for yield and somatic cell score. J. Dairy Sci. 90(1):482–492. 2007.

• Dematawewa, C.M.B., Pearson, R.E., and VanRaden, P.M. Modeling extended lactations of Holsteins.J. Dairy Sci. 90(8):3924–3936. 2007.

• Kuhn, M.T., Hutchison, J.L., and Norman, H.D. Dry period length in US Jerseys: Characterization and effects on performance. J. Dairy Sci. 90(4):2069–2081. 2007.

• Mark, T., Fikse, W.F., Sullivan, P.G., and VanRaden, P.M. Prediction of genetic correlations and international breeding values for missing traits. J. Dairy Sci. 90(10):4805–4813. 2007. 

• Miller, R.H., Norman, H.D., Kuhn, M.T., Clay, J.S., and Hutchison, J.L. Voluntary waiting period and adoption of synchronized breeding in Dairy Herd Improvement herds. J. Dairy Sci. 90(3):1594–1606. 2007.

• Norman, H.D., Hutchison, J.L., Wright, J.R., Kuhn, M.T., and Lawlor, T.J. Selection on yield and fitness traits when culling Holsteins during the first three lactations. J. Dairy Sci. 90(2):1008–1020. 2007.

• Norman, H.D., Wright, J.R., Powell, R.L., VanRaden, P.M., Miglior, F., and de Jong, G. Consistency of maturity rate for milk yield across countries and generations. J. Dairy Sci. 90(8):3937–3944. 2007.

• Paape, M.J., Wiggans, G.R., Bannerman, D.D., Thomas, D.L., Sanders, A.H., Contreras, A., Moroni, P., and Miller, R.H. Monitoring goat and sheep milk somatic cell counts. Small Rumin. Res. 68:114–125. 2007. 

• VanRaden, P.M., Tooker, M.E., Cole, J.B., Wiggans, G.R., and Megonigal Jr., J.H. Genetic evaluations for mixed-breed populations. J. Dairy Sci. 90(5):2434–2441. 2007.

• Wiggans, G.R., Thornton, L.L.M., Neitzel, R.R., and Gengler, N. Short communication: Genetic evaluation of milking speed for Brown Swiss dairy cattle in the United States. J. Dairy Sci. 90(2):1021–1023. 2007.

2006

• Cole, J.B., and VanRaden, P.M. Genetic evaluation and best prediction of lactation persistency. J. Dairy Sci. 89(7):2722–2728. 2006.

• Fetrow, J., Nordlund, K.V., and Norman, H.D. Invited review: Culling: Nomenclature, definitions, and recommendations. J. Dairy Sci. 89(6):1896–1905. 2006.

• Gengler, N., Wiggans, G.R., Thornton, L.L.M., Wright, J.R., and Druet, T. Accounting for heterogeneous variances in multitrait evaluation of Jersey type traits. J. Dairy Sci. 89(8):3143–3151. 2006.

• Hare, E., Norman, H.D., and Wright, J.R. Survival rates and productive herd life of dairy cattle in the United States. J. Dairy Sci. 89(9):3713–3720. 2006.

• Hare, E., Norman, H.D., and Wright, J.R. Trends in calving ages and calving intervals for dairy cattle breeds in the United States. J. Dairy Sci. 89(1):365–370. 2006.

• Kuhn, M.T., Hutchison, J.L., and Norman, H.D. Dry period length to maximize production across adjacent lactations and lifetime production. J. Dairy Sci. 89(5):1713–1722. 2006.

• Kuhn, M.T., Hutchison, J.L., and Norman, H.D. Effects of length of dry period on yields of milk fat and protein, fertility and milk somatic cell score in the subsequent lactation of dairy cows. J. Dairy Res. 73(2):154–162. 2006.

• Kuhn, M.T., Hutchison, J.L., and Wiggans, G.R. Characterization of Holstein heifer fertility in the United States. J. Dairy Sci. 89(12):4907–4920. 2006.

• Powell, R.L., and Norman, H.D. Major advances in genetic evaluation techniques. J. Dairy Sci. 89(4):1337–1348. 2006.

• VanRaden, P.M., Dematawewa, C.M.B., Pearson, R.E., and Tooker, M.E. Productive life including all lactations and longer lactations with diminishing credits. J. Dairy Sci. 89(8):3213–3220. 2006.

• VanRaden, P.M., and Miller, R.H. Effects of nonadditive genetic interactions, inbreeding, and recessive defects on embryo and fetal loss by seventy days. J. Dairy Sci. 89(7):2716–2721. 2006.

• Wiggans, G.R., Thornton, L.L.M., Neitzel, R.R., and Gengler, N. Genetic parameters and evaluation of rear legs (rear view) for Brown Swiss and Guernseys. J. Dairy Sci. 89(12):4895–4900. 2006. 

2005

• Cole, J.B., Goodling, Jr., R.C., Wiggans, G.R., and VanRaden, P.M. Genetic evaluation of calving ease for Brown Swiss, Jersey, and Holstein bulls from purebred and crossbred calvings. J. Dairy Sci. 88(4):1529–1539. 2005.

• Gengler, N., Wiggans, G.R., and Gillon, A. Adjustment for heterogeneous covariance due to herd milk yield by transformation of test-day random regressions. J. Dairy Sci. 88(8):2981–2990. 2005.

• Kuhn, M.T., and Hutchison, J.L. Methodology for estimation of days dry effects. J. Dairy Sci. 88(4):1499–1508. 2005. 

• Kuhn, M.T., Hutchison, J.L., and Norman, H.D. Characterization of days dry for United States Holstein. J. Dairy Sci. 88(3):1147–1155. 2005.

• Kuhn, M.T., Hutchison, J.L., and Norman, H.D. Minimum days dry to maximize milk yield in subsequent lactation. Anim. Res. 54:351–367. 2005.

• Norman, H.D., VanRaden, P.M., Powell, R.L., Wright, J.R., and VerBoort, W.R. Effectiveness of national and regional sire evaluations in predicting future-daughter milk yield. J. Dairy Sci. 88(2):812–826. 2005.

• Norman, H.D., Wright, J.R., Powell, R.L., and VanRaden, P.M. Impact of maturity rate of daughters on genetic ranking of Holstein bulls. J. Dairy Sci. 88(9):3337–3345. 2005.

• Powell, R.L., Sanders, A.H., and Norman, H.D. Accuracy and stability of national and international somatic cell score evaluations. J. Dairy Sci. 88(7):2624–2631. 2005.

• Powell, R.L., Sanders, A.H., and Norman, H.D. Impact of estimated genetic correlations on international evaluations to predict milk traits. J. Dairy Sci.88(10):3679–3687. 2005.

• Wiggans, G.R., and Goodling, R.C. Accounting for pregnancy diagnosis in predicting days open. J. Dairy Sci. 88(5):1873–1877. 2005. 

2004

• Ashwell, M.S., Heyen, D.W., Sonstegard, T.S., Van Tassell, C.P., Da, Y., VanRaden, P.M., Ron, M., Weller, J.I., and Lewin, H.A. Detection of quantitative trait loci affecting milk production, health, and reproductive traits in Holstein cattle. J. Dairy Sci. 87(2):468–475. 2004.

• DeChow, C.D., Rogers, G.W., Klei, L., Lawlor, T.J., and VanRaden, P.M. Body condition scores and dairy form evaluations as indicators of days open in US Holsteins. J. Dairy Sci. 87(10):3534–3541. 2004.

• Edwards, J.L., and Tozer, P.R. Using activity and milk yield as predicators of fresh cow disorders. J. Dairy Sci. 87(2):524–531. 2004.

• Gengler, N., Wiggans, G.R., and Gillon, A. Estimated heterogeneity of phenotypic variance of test-day yield with a structural variance model. J. Dairy Sci. 87(6):1908–1916. 2004. 

• Hare, E., Norman, H.D., and Wright, J.R. Duration of herd participation in Dairy Herd Improvement milk recording in the United States. J. Dairy Sci. 87(8):2743–2747. 2004.

• Kuhn, M.T., VanRaden, P.M., and Hutchison, J.L. Use of early lactation days open records for genetic evaluation of cow fertility. J. Dairy Sci. 87(7):2277–2284. 2004.

• Miller, R.H., Norman, H.D., Wiggans, G.R., and Wright, J.R. Relationship of test-day somatic cell score with test-day and lactation milk yields. J. Dairy Sci. 87(7):2299–2306. 2004.

• Norman, H.D., Lawlor, T.J., Wright, J.R., and Powell, R.L. Performance of Holstein clones in the United States. J. Dairy Sci. 87(3):729–738. 2004.

• Norman, H.D., and Walsh, M.K. Performance of dairy cattle clones and evaluation of their milk composition. Cloning and Stem Cells 6(2):157–164. 2004.

• Powell, R.L., Sanders, A.H., and Norman, H.D. Accuracy of foreign dairy bull evaluations in predicting United States evaluations for yield. J. Dairy Sci. 87(8):2621–2626. 2004. 

• Powell, R.L., Sanders, A.H., and Norman, H.D. Stability of genetic evaluations for active artificial insemination bulls. J. Dairy Sci. 87(8):2614–2620. 2004.

• Rohli, R.V., Russo, M.M., Vega, A.J., and Cole, J.B. Tropospheric ozone in Louisiana and synoptic circulation. J. Appl. Meteor. 43(10):1438–1451. 2004. 

• Salisbury, M.W., Krehbiel, C.R., Ross, T.T., Schultz, C.L., and Melton, L.L. Effects of supplemental protein type on intake, nitrogen balance, and site, and extent of digestion in whiteface wethers consuming low-quality grass hay. J. Anim. Sci. 82:(12):3567–3576. 2004. 

• VanRaden, P.M. Invited review: Selection on net merit to improve lifetime profit. J. Dairy Sci. 87(10):3125–3131. 2004.

• VanRaden, P.M., Sanders, A.H., Tooker, M.E., Miller, R.H., Norman, H.D., Kuhn, M.T., and Wiggans, G.R. Development of a national genetic evaluation for cow fertility. J. Dairy Sci. 87(7):2285–2292. 2004.

• Wiggans, G.R., Gengler, N., and Wright, J.R. Type trait (co)variance components for five dairy breeds. J. Dairy Sci. 87(7):2324–2330. 2004.

2003

• Bormann, J., Wiggans, G.R, Druet, T., and Gengler, N. Within-herd effects of age at test day and lactation stage on test-day yields. J. Dairy Sci. 86(11):3765–3774. 2003. 

• Montaldo, H.H., Keown, J.F., Van Vleck, L.D., and Van Tassell, C.P. Economic evaluation of Holstein sire selection strategies for herd in Italy, Mexico, The Netherlands, and the United States using stochastic simulation [Evaluación económica de estrategias de selección de sementales Holstein para hatos en Italia, México, Holanda y Estados Unidos utilizando simulación estocástica]. Vet. Méx. 34(2):179–201. 2003.

• Norman, H.D., Powell, R.L., Wright, J.R., and Sattler, C.G. Timeliness and effectiveness of progeny testing through artificial insemination. J. Dairy Sci. 86(4):1513–1525. 2003.

• Powell, R.L., Norman, H.D, and Sanders, A.H. Progeny testing and selection intensity for Holstein bulls in different countries. J. Dairy Sci. 86(10):3386–3393. 2003.

• VanRaden, P.M., and Sanders, A.H. Economic merit of crossbred and purebred US dairy cattle. J. Dairy Sci. 86(3):1036–1044. 2003.

• Van Tassell, C.P., Wiggans, G.R., and Misztal, I. Implementation of a sire-maternal grandsire model for evaluation of calving ease in the United States. J. Dairy Sci. 86(10):3366–3373. 2003. 

• Wiggans, G.R., Misztal, I., and Van Tassell, C.P. Calving ease (co)variance components for a sire-maternal grandsire evaluation model. J. Dairy Sci. 86(5):1845–1848. 2003.

• Wiggans, G.R., VanRaden, P.M., and Philpot, J.C. Technical note: Detection and adjustment of abnormal test-day yields. J. Dairy Sci. 86(8):2721–2724. 2003.

• Zhu, J.J., Lillehoj, H.S., Allen, P.C., Van Tassell, C.P., Sonstegard, T.S., Cheng, H.H., Pollock, D., Sadjadi, M., Min, W., and Emara, M.G. Mapping quantitative trait loci associated with resistance to coccidiosis and growth. Poult. Sci. 82(1):9–16. 2003.

• Zhu, Y.L, Song, Q.J., Hyten, D.L., Van Tassell, C.P., Matukumalli, L.K., Grimm, D.R., Hyatt, S.M., Fickus, E.W., Young, N.D., and Cregan, P.B. Single-nucleotide polymorphisms in soybean. Genetics 163(3):1123–1134. 2003. 

2002

• Bormann, J., Wiggans, G.R., Philpot, J.C., Druet, T., and Gengler, N. Estimating effects of permanent environment, lactation stage, age, and pregnancy on test-day yield. J. Dairy Sci. 85(Jan). Online. 2002.

• Powell, R.L., and VanRaden, P.M. International dairy bull evaluations expressed on national, subglobal, and global scales. J. Dairy Sci. 85(7):1863–1868. 2002.

• Sonstegard, T.S., Capuco, A.V., White, J., Van Tassell, C.P., Connor, E.E., Cho, J., Sultana, R., Shade, L., Wray, J.E., Wells, K.D., and Quackenbush, J. Analysis of bovine mammary gland EST and functional annotation of the Bos taurus gene index. Mamm. Genome 13(7):373–379. 2002.

• Wiggans, G.R., VanRaden, P.M., Bormann, J., Philpot, J.C., Druet, T., and Gengler, N. Deriving lactation yields from test-day yields adjusted for lactation stage, age, pregnancy, and herd test date. J. Dairy Sci. 85(Jan). Online. 2002. 

2001

• Ashwell, M.S., Van Tassell, C.P., and Sonstegard, T.S. A genome scan to identify quantitative trait loci affecting economically important traits in a US Holstein population. J. Dairy Sci. 84(11):2535–2542. 2001.

• Banos, G., Wiggans, G.R., and Powell, R.L. Impact of paternity errors in cow identification on genetic evalutions and international comparisons. J. Dairy Sci. 84(11):2523–2529. 2001.

• Boettcher, P.J., Jairath, L.K., and VanRaden, P.M. Evaluation of sire predicted transmitting abilities for evidence of x-chromosomal inheritance in North American sire families. J. Dairy Sci. 84(1):256–265. 2001.

• Capuco, A.V., Wood, D.L., Elsasser, T.H., Kahl, S., Erdman, R.A., Van Tassell, C.P., Lefcourt, A., and Piperova, L.S. Effect of somatotropin on thyroid hormones and cytokines in lactating dairy cows during ad libitum and restricted feed intake. J. Dairy Sci. 84(11):2430–2439. 2001.

• Gengler, N., Dusseldorf, T., Wiggans, G.R., Wright, J.R., and Druet, T. Heterogeneity of (co)variance components for Jersey type traits. J. Dairy Sci. 84:(July). Online. 2001.

• Gengler, N., Tijani, A., Wiggans, G.R., and Philpot, J.C. Indirect estimation of (co)variance functions for test-day yields during first and second lactations in the United States. J. Dairy Sci. 84(Feb). Online. 2001.

• Miller, R.H., Clay, J.S., and Norman, H.D. Relationship of somatic cell score with fertility measures. J. Dairy Sci. 84(11):2543–2548. 2001.

• Norman, H.D., Edwards, J.L., and Wright, J.R. Accuracy of recorded birth and calving dates of dairy cattle in the United States. J. Dairy Sci. 84(9):2089–2096. 2001.

• Norman, H.D., Powell, R.L., Wright, J.R., and Sattler, C.G. Overview of progeny-test programs of artificial-insemination organizations in the United States. J. Dairy Sci. 84(8):1899–1912. 2001.

• Powell, R.L., and Norman, H.D. Stability and bias of yield evaluations for Holstein bulls in artificial insemination service. J. Dairy Sci. 84(Aug). Online. 2001.

• Sonstegard, T.S., Barendse, C., Bennett, G.L., Brockmann, G.A., Davis, S., Droegemuller, C., Kalm, E., Kappes, S.M., Kuehn, C., Li, Y., Schwerin, M., Taylor, J., Thomsen, H., Van Tassell, C.P., and Yeh, C.C. Consensus and comprehensive linkage maps of the bovine sex chromosomes. Anim. Genet. 32(2):115–117. 2001. 

• Sonstegard, T.S., Bendixen, C., Bennett, G.L., Kalm, E., Kappes, S.M., Lewin, H.A., Lien, S., Nielsen, V.H., Olsaker, I., Schmutz, S., Thomsen, H., Van Tassell, C.P., and Xu, N. Consensus and comprehensive linkage maps of bovine chromosome 17. Anim. Genet. 32(2):112–113. 2001. 

• Sonstegard, T.S., Bennett, G.L., Kalm, E., Kappes, S.M., Lewin, H.A., Olsaker, I., Schmutz, S., Thomsen, H., Vage, D.I., Van Tassell, C.P., and Xu, N. Consensus and comprehensive linkage maps of bovine chromosome 25. Anim. Genet. 32(2):114–115. 2001.

• Sonstegard, T.S., Van Tassell, C.P., and Ashwell, M.S. Dairy cattle genomics: Tools to accelerate genetic improvement? J. Anim. Sci. 79:E307–E315. Online. 2001.

• VanRaden, P.M. Methods to combine estimated breeding values obtained from separate sources. J. Dairy Sci. 84(E. Suppl.):E47–E55. 2001.

• Wiggans, G.R., and Hubbard, S.M. Genetic evaluation of yield and type traits of dairy goats in the United States. J. Dairy Sci. 84(E. Suppl.):E69–E73. 2001.

2000

• Da, Y., VanRaden, P.M., and Schook, L.B. Detection and parameter estimation for quantitative trait loci using regresion models and multiple markers. Genet. Sel. Evol. 32(4):357–381. 2000. 

• Gengler, N., Tijani, A., and Wiggans, G.R. Use of sequential estimation of regressions and effects on regressions to solve large multitrait test-day models. J. Dairy Sci. 83(Feb). Online. 2000.

• Norman, H.D., Miller, R.H., Wright, J.R., and Wiggans, G.R. Herd and state means for somatic cell count from Dairy Herd Improvement. J. Dairy Sci. 83 (12):2782–2788. 2000. 

• Powell, R.L., Norman, H.D., and Banos, G. Improving prediction of national evaluations by use of data from other countries. J. Dairy Sci. 83(Feb). Online. 2000.

• Powell, R.L., and Norman, H.D. Impact of genetic correlations on accuracy of predicting future evaluations. J. Dairy Sci. 83(July). Online. 2000.

• Van Tassell, C.P., Misztal, I., and Varona, L. Method R estimates of additive genetic, dominance genetic, and permanent environmental fraction of variance for yield and health traits of Holsteins. J. Dairy Sci. 83(8):1873–1877. 2000.

• Weigel, K.A., and Powell, R.L. Retrospective analysis of the accuracy of conversion equations and multiple-trait, across-country evaluations of Holstein bulls used internationally. J. Dairy Sci. 83(5):1081–1088. 2000.

1999

• Da, Y., VanRaden, P.M., Ron, M., Beever, J.E., Paszek, A.A., Song, J., Wiggans, G.R., Ma, R., Weller, J.I., and Lewin, H.A. Standardization and conversion of marker polymorphism measures. Anim. Biotech. 10(1&2):25–35. 1999.

• Gengler, N., Tijani, A., Wiggans, G.R., and Misztal, I. Estimation of (co)variance function coefficients for test day yield with expectation-maximization restricted maximum likelihood algorithm. J. Dairy Sci. 82(Aug). Online. 1999.

• Gengler, N., Tijani, A., Wiggans, G.R., Van Tassell, C.P., and Philpot, J.C. Estimation of (co)variances of test day yields for first lactation Holsteins in the United States. J. Dairy Sci. 82:(Jan). Online. 1999. 

• Gengler, N., Wiggans, G.R., and Wright, J.R. Animal model genetic evaluation of type traits for five dairy cattle breeds. J. Dairy Sci. 82(June). Online. 1999.

• Heyen, D.W., Weller, J.I., Ron, M., Band, M. Beever, J.E., Feldmesser, E., Da, Y., Wiggans, G.R., VanRaden, P.M., and Lewin, H.A. A genome scan for QTL influencing milk production and health traits in dairy cattle. Physiol. Genomics 1:165–175. 1999.

• Melvin, E.J., Lindsey, B.R., Quintal-Franco, J., Zanella, E., Fike, K.E., Van Tassell, C.P., and Kinder, J.E. Circulating concentrations of estradiol, luteinizing hormone, and follicle-stimulating hormone during waves of ovarian follicular development in prepubertal cattle. Biol. Reprod. 60:405–415. 1999.

• Norman, H.D., and Powell, R.L. Dairy cows of high genetic merit for yields of milk, fat, and protein (a review). Asian-Australasian J. Anim. Sci. 12(8):1316–1323. 1999.

• Norman, H.D., VanRaden, P.M., Wright, J.M., and Clay, J.S. Comparison of test interval and best prediction methods for estimation of lactation yield from monthly, a.m.-p.m., and trimonthly testing. J. Dairy Sci. 82(2):438–444. 1999.

• Norman, H.D., VanRaden, P.M., Wright, J.R., and Smith, L.A. Mathematical representation of correlations among yield traits and somatic cell score on test day. J. Dairy Sci. 82(10):2205–2211. 1999.

• Powell, R.L., and Norman, H.D. Examination of more frequent genetic evaluations for dairy bulls. J. Dairy Sci. 82(12):2766–2770. 1999.

• Tijani, A., Wiggans, G.R., Van Tassell, C.P., Philpot, J.C., and Gengler, N. Use of (co)variance functions to describe(co)variances for test day yield. J. Dairy Sci. 82:(Jan). Online. 1999.

• VanRaden, P.M., and Smith, L.A. Selection and mating considering expected inbreeding of future progeny. J. Dairy Sci. 82(12):2771–2778. 1999.

• Van Tassell, C.P., Wiggans, G.R., and Norman, H.D. Method R estimates of heritability for milk, fat, and protein yields of United States dairy cattle. J. Dairy Sci. 82(10):2231–2237. 1999. 

1998

• Ashwell, M.S., Da, Y., VanRaden, P.M., Rexroad, Jr., C.E., and Miller, R.H. Detection of putative loci affecting conformational type traits in an elite population of United States Holsteins using microsatellite markers. J. Dairy Sci. 81(4):1120–1125. 1998.

• Ashwell, M.S., Da, Y., Van Tassell, C.P., VanRaden, P.M., Miller, R.H., and Rexroad, C.E., Jr. Detection of putative loci affecting milk production and composition, health, and type traits in a United States Holstein population. J. Dairy Sci. 81(12):3309–3314. 1998.

• Da, Y., VanRaden, P.M., Beattie, C.W., Wu, C., and Schook, L.B. Designs of reference families for the construction of genetic linkage maps. Anim. Biotech. 9(3):205–228. 1998.

• Meinert, T.R., and Norman, H.D. Merit of outliers for milk yield as indicators of accuracy of genetic evaluations of sires. J. Dairy Sci. 81(11):2951–2955. 1998.

• Misztal, I., Varona, L., Culbertson, M., Bertrand, J.K., Mabry, J., Lawlor, T.J., Van Tassell, C.P., and Gengler, N. Studies on the value of incorporating the effect of dominance in genetic evaluations of dairy cattle, beef cattle and swine. Biotechnol. Agron. Soc. Environ. 2(4):227–233. 1998.

• Powell, R.L., and Norman, H.D. Use of multinational data to improve national evaluations of Holstein bulls. J. Dairy Sci. 81(8):2257–2263. 1998.

• Powell, R.L, Wiggans, G.R., and Norman, H.D. Equity of elite cow status across states. J. Dairy Sci. 81(9):2518–2523. 1998.

• Weigel, K.A., Lawlor, Jr., T.J., VanRaden, P.M., and Wiggans, G.R. Use of linear type and production data to supplement early predicted transmitting abilities for productive life. J. Dairy Sci. 81(7):2040–2044. 1998.

1997

• Ashwell, M.S., Rexroad, Jr., C.E., Miller, R.H., VanRaden, P.M., and Da, Y. Detection of loci affecting milk production and health traits in an elite US Holstein population using microsatellite markers. Anim. Genet. 28(3):216–222. 1997. 

• Gengler, N., Wiggans, G.R., Wright, J.R., Norman, H.D., and Wolfe, C.W. Application of canonical transformation with missing values to multitrait evaluation of Jersey type. J. Dairy Sci. 80(10):2563–2571. 1997.

• Gengler, N., Wiggans, G.R., Wright, J.R., Norman, H.D., and Wolfe, C.W. Estimation of (co)variance components for Jersey type traits using a repeatability model. J. Dairy Sci. 80(8):1801–1806. 1997.

• Lee, J.K., VanRaden, P.M., Norman, H.D., Wiggans, G.R., and Meinert, T.R. Relationship of yield during early lactation and days open during current lactation with 305-day yield. J. Dairy Sci. 80(4):771–776. 1997.

• Luo, M.F., Wiggans, G.R., and Hubbard, S.M. Variance component estimation and multitrait genetic evaluation for type traits of dairy goats. J. Dairy Sci. 80(3):594–600. 1997.

• Meinert, T.R., Norman, H.D., Mattison, J.M., and Sattler, C.J. Usability for genetic evaluations of records from herds participating in progeny test programs of artificial insemination organizations. J. Dairy Sci. 80(10):2599–2605. 1997.

• Powell, R.L., VanRaden, P.M., and Wiggans, G.R. Relationship between United States and Canadian genetic evaluations of longevity and somatic cell score. J. Dairy Sci. 80(8):1807–1812. 1997.

• Powell, R.L., Wiggans, G.R., and Sieber, M. Consistency of international genetic evaluations of Holstein bulls. J. Dairy Sci. 80(9):2177–2183. 1997. 

• VanRaden, P.M. Lactation yields and accuracies computed from test day yields and (co)variances by best prediction J. Dairy Sci. 80(11):3015–3022. 1997.

• Wiggans, G.R., and Goddard, M.E. A computationally feasible test day model for genetic evaluation of yield traits in the United States. J. Dairy Sci. 80(8):1795–1800. 1997. 

1996

• Dimov, G., Keown, J.F., Van Vleck, L.D., and Norman, H.D. Effect of variance of interaction effects of sire and herd on selection for milk and fat yield. J. Dairy Sci. 79(1):140–144. 1996.

• Meinert, T.R., Norman, H.D., and Dickinson, F.N. Consideration of percentage of milk shipped for calculation of total lactation yields from various morning and evening plans of milk sampling. J. Dairy Sci. 79(2):291–300. 1996.

• Norman, H.D., Powell, R.L., Wright, J.R., and Pearson, R.E. Phenotypic relationship of yield and type scores from first lactation with herd life and profitability. J. Dairy Sci. 79(4):689–701. 1996.

• Powell, R.L., Norman, H.D., and Cowan, C.M. Relationship of bovine leukocyte adhesion deficiency with genetic merit for performance traits. J. Dairy Sci. 79(5):895–899. 1996.

• Powell, R.L., and VanRaden, P.M. Examination of international genetic evaluations of Holstein bulls. J. Dairy Sci. 79(9):1659–1665. 1996.

1995

• Dimov, G., Albuquerque, L.G., Keown, J.F., Van Vleck, L.D., and Norman, H.D. Variance of interaction effects of sire and herd for yield traits of Holsteins in California, New York, and Pennsylvania with an animal model. J. Dairy Sci. 78(4):939–946. 1995.

• Norman, H.D., Meinert, T.R., Schutz, M.M., and Wright, J.R. Age and seasonal effects on Holstein yield for four regions of the United States over time. J. Dairy Sci. 78(8):1855–1861. 1995.

• Powell, R.L., and Wiggans, G.R. Holstein conversion equations based on population variances and a full-brother model. J. Dairy Sci. 78(6):1362–1368. 1995.

• Schutz, M.M., VanRaden, P.M., Wiggans, G.R., and Norman, H.D. Standardization of lactation means of somatic cell scores for calculation of genetic evaluations. J. Dairy Sci. 78(8):1843–1854. 1995.

• VanRaden, P.M., and Wiggans, G.R. Productive life evaluations: Calculation, accuracy, and economic value. J. Dairy Sci. 78(3):631–638. 1995.

• Van Tassell, C.P., Casella, G., and Pollak, E.J. Effects of selection on estimates of variance components using Gibbs sampling and restricted maximum likelihood. J. Dairy Sci. 78(3):678–692. 1995. 

• Van Tassell, C.P., Jones, L.R, and Eicker, S.W. Production evaluation techniques based on lactation curves. J. Dairy Sci. 78(2):457–465. 1995.

• Wiggans, G.R., VanRaden, P.M., and Zuurbier, J. Calculation and use of inbreeding coefficients for genetic evaluation of United States dairy cattle. J. Dairy Sci. 78(7):1584–1590. 1995.

1994

• Becerril, C.M., Wilcox, C.J., Wiggans, G.R., and Sigmon, K.N. Transformation of measurements percentage of white coat color for Holsteins and estimation of heritability. J. Dairy Sci. 77(9):2651–2657. 1994.

• Meinert, T.R., and Norman, H.D. Records contributing to national genetic evaluations by year, registration status, herd size, and region. J. Dairy Sci. 77(5):1466–1476. 1994.

• Metzger, J.S., Hansen, L.B., Norman, H.D., Wolfe, C.W., and Pedersen, J. Comparison of United States and Danish strains of Jerseys for yield traits. J. Dairy Sci. 77(5):1457–1465. 1994.

• Norman, H.D., Waite, L.G., Wiggans, G.R., and Walton, L.M. Improving accuracy of the United States genetics database with a new editing system for dairy records. J. Dairy Sci. 77(10):3198–3208. 1994.

• Powell, R.L., Wiggans, G.R., and Norman, H.D. Effect of sampling status and adjustment for heterogeneous variance on bias in bull evaluations. J. Dairy Sci. 77(3):883–890. 1994.

• Powell, R.L., Wiggans, G.R., and VanRaden, P.M. Factors affecting calculation and use of conversion equations for genetic merit of dairy bulls. J. Dairy Sci. 77(9):2679–2686. 1994.

• Schutz, M.M. Genetic evaluation of somatic cell scores for United States dairy cattle. J. Dairy Sci. 77(7):2113–2129. 1994.

• Schutz, M.M., VanRaden, P.M., and Wiggans, G.R. Genetic variation in lactation means of somatic cell scores for six breeds of dairy cattle. J. Dairy Sci. 77(1):284–293. 1994.

• Shook, G.E., and Schutz, M.M. Selection on somatic cell score to improve resistance to mastitis in the United States. J. Dairy Sci. 77(2):648–658. 1994.

• Van Tassell, C.P., and Berger, P.J. Consideration of sire relationships for estimation of variance components with interaction of herd and sire. J. Dairy Sci. 77(1):313–324. 1994.

• Wiggans, G.R. Meeting the needs at the national level for genetic evaluation and health monitoring. J. Dairy Sci. 77(7):1976–1983. 1994.

1993

• Becerril, C.M., Wilcox, C.J., Lawlor, T.J., Wiggans, G.R., and Webb, D.W. Effects of percentage of white coat color on Holstein production and reproduction in a subtropical environment. J. Dairy Sci. 76(8):2286–2291. 1993.

• Miller, R.H., Paape, M.J., Fulton, L.A., and Schutz, M.M. The relationship of milk somatic cell count to milk yields for Holstein heifers after first calving. J. Dairy Sci. 76(3):728–733. 1993.

• Powell, R.L., Wiggans, G.R., and Norman, H.D. Utilization of genetically elite Holstein cows. J. Dairy Sci. 76(5):1412–1420. 1993.

• Schutz, M.M., Freeman, A.E., Lindberg, G.L., and Beitz, D.C. Effects of maternal lineages grouped by mitochondrial genotypes on milk yield and composition. J. Dairy Sci. 76(2):621–629. 1993.

• Schutz, M.M., VanRaden, P.M., Boettcher, P.J., and Hansen, L.B. Relationship of somatic cell score and type trait evaluations of Holstein sires. J. Dairy Sci. 76(2):658–663. 1993.

• VanRaden, P.M., and Klaaskate, E.J.H. Genetic evaluation of length of productive life including predicted longevity of live cows. J. Dairy Sci. 76(9):2758–2764. 1993.

• Żarnecki, A., Norman, H.D., Gierdziewicz, M., and Jamrozik, J. Heterosis for growth and yield traits in crosses of Friesian strains. J. Dairy Sci. 76(6):1661–1670. 1993. 

1992

• Banos, G., Wiggans, G.R., and Robinson, J.A.B. Comparison of methods to rank bulls across countries. J. Dairy Sci. 75(9):2560–2568. 1992.

• Boettcher, P.J., Hansen, L.B., VanRaden, P.M., and Ernst, C.A. Genetic evaluation of Holstein bulls for somatic cells in milk of daughters. J. Dairy Sci. 75(4):1127–1137. 1992. 

• Da, Y., Grossman, M., Misztal, I., and Wiggans, G.R. Estimation of genetic parameters for somatic cell score in Holsteins. J. Dairy Sci. 75(8):2265–2271. 1992. 

• Meinert, T.R., Pearson, R.E., and Hoyt, R.S. Estimates of genetic trend in artificial insemination progeny test program and their association with herd characteristics. J. Dairy Sci. 75(8):2254–2264. 1992.

• Misztal, I., Lawlor, T.J., Short, T.H., and VanRaden, P.M. Multiple-trait estimation of variance components of yield and type traits using an animal model. J. Dairy Sci. 75(2):544–551. 1992.

• Powell, R.L., and Sieber, M. Direct and indirect conversion of bull evaluations for yield traits between countries. J. Dairy Sci.75(4):1138–1146. 1992.

• Schutz, M.M., Freeman, A.E., Beitz, D.C., and Mayfield, J.E. The importance of maternal lineage on milk yield traits of dairy cattle. J. Dairy Sci. 75(5):1331–1341. 1992. 

• VanRaden, P.M. Accounting for inbreeding and crossbreeding in genetic evaluation of large populations. J. Dairy Sci. 75(11):3136–3144. 1992.

• VanRaden, P.M., Lawlor, T.J., Short, T.H., and Hoeschele, I. Use of reproductive technology to estimate variances and predict effects of gene interactions. J. Dairy Sci. 75(10):2892–2901. 1992.

• Wiggans, G.R., VanRaden, P.M., and Powell, R.L. A method for combining United States and Canadian bull evaluations. J. Dairy Sci. 75(10):2834–2839. 1992.

1991

• Hoeschele, I., and VanRaden, P.M. Rapid inversion of dominance relationship matrices for noninbred populations by including sire by dam subclass effects. J. Dairy Sci. 74(2):557–569. 1991. 

• Norman, H.D., Powell, R.L., and Wiggans, G.R. Comparison of genetic evaluations from animal model and modified contemporary comparison. J. Dairy Sci. 74(7):2309–2316. 1991.

• Norman, H.D., Wright, J.R., Covington, C.B., Barton, E.P., and Ernstrom, C.A. Potential for segregating milk: herd differences in milk value for fluid and five manufactured products. J. Dairy Sci. 74(7):2353–2361. 1991.

• Powell, R.L. Impact of imported daughters on evaluations of their sires. J. Dairy Sci. 74(2):623–628. 1991.

• Powell, R.L., and Wiggans, G.R. Animal model evaluations for Mexican Holsteins. J. Dairy Sci. 74(4):1420–1427. 1991.

• Rogers, G.W., Hargrove, G.L., Cooper, J.B., and Norman, H.D. Management and genetic influences on survival in Jerseys. J. Dairy Sci. 74(1):279–285. 1991.

• VanRaden, P.M., and Hoeschele, I. Rapid inversion of additive by additive relationship matrices by including sire-dam combination effects. J. Dairy Sci. 74(2):570–579. 1991. 

• VanRaden, P.M., and Wiggans, G.R. Derivation, calculation, and use of national animal model information. J. Dairy Sci. 74(8):2737–2746. 1991.

• VanRaden, P.M., Wiggans, G.R., and Ernst, C.A. Expansion of projected lactation yield to stabilize genetic variance. J. Dairy Sci. 74(12):4344–4349. 1991.

• Van Tassell, C.P., and Van Vleck, L.D. Estimates of genetic selection differentials and generation intervals for four paths of selection. J. Dairy Sci. 74(3):1078–1086. 1991.

• Wiggans, G.R. National genetic improvement programs for dairy cattle in the United States. J. Anim. Sci. 69(9):3853–3860. 1991.

• Wiggans, G.R., and VanRaden, P.M. Method and effect of adjustment for heterogeneous variance. J. Dairy Sci. 74(12):4350–4357. 1991.

• Żarnecki, A., Jamrozik, J., and Norman, H.D. Comparison of ten Friesian strains in Poland for yield traits from first three parities. J. Dairy Sci. 74(7):2303–2308. 1991.

1990

• Powell, R.L., and Norman, H. Impact of changes in genetic improvement programs and annual cycles on Holstein service sire merit. J. Dairy Sci. 73(4):1123–1129. 1990. 

• Powell, R.L., Wiggans, G.R., and Plowman, R.D. Evaluations of Holstein bulls and cows in Ecuador. J. Dairy Sci. 73(11):3330–3335. 1990.

• VanRaden, P.M., Jensen, E.L., Lawlor, T.J., and Funk, D.A. Prediction of transmitting abilities for Holstein type traits. J. Dairy Sci. 73(1):191–197. 1990.

• Wiggans, G.R., and VanRaden, P.M. Animal model evaluation within herd linked to national evaluations. J. Dairy Sci. 73(7):1956–1963. 1990.

• Wiggans, G.R., and VanRaden, P.M. Including information from records in later herds in animal model evaluations. J. Dairy Sci. 73(11):3336–3339. 1990.

Selected earlier articles

• Wiggans, G.R., and Misztal, I. Approximation of prediction error variance in large-scale animal models. J. Dairy Sci. 71(Suppl. 2):27–32. 1988.

• Wiggans, G.R., Misztal, I., and Van Vleck, L.D. Implementation of an animal model for genetic evaluation of dairy cattle in the United States. J. Dairy Sci. 71(Suppl. 2):54–69. 1988.