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United States Department of Agriculture

Agricultural Research Service

Research Project: Genomic and Metagenomic Approaches to Enhance Efficient and Sustainable Production of Beef Cattle

Location: Genetics, Breeding, and Animal Health Research

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)

Metagenomic and near full-length 16S rRNA sequence data in support of the phylogenetic analysis of the rumen bacterial community in steers - (Peer Reviewed Journal)
Myer, P.R., Kim, M.S., Freetly, H.C., Smith, T.P. 2016. Metagenomic and near full-length 16S rRNA sequence data in support of the phylogenetic analysis of the rumen bacterial community in steers. Data in Brief. 8:1048-1053. doi: 10.1016/j.dib.2016.07.027.

Evaluation of 16S rRNA amplicon sequencing using two next-generation sequencing technologies for phylogenetic analysis of the rumen bacterial community in steers - (Peer Reviewed Journal)
Myer, P.R., Kim, M.S., Freetly, H.C., Smith, T.P. 2016. Evaluation of 16S rRNA amplicon sequencing using two next-generation sequencing technologies for phylogenetic analysis of the rumen bacterial community in steers. Journal of Microbiological Methods. 127:132-140. doi: 10.1016/j.mimet.2016.06.004.

Whole genomic sequence analysis of Bacillus infantis: defining the genetic blueprint of strain NRRL B-14911, an emerging cardiopathogenic microbe - (Peer Reviewed Journal)
Massilamany, C., Mohammed, A., Loy, J.D., Purvis, T., Krishnan, B., Basavalingappa, R.H., Kelley, C.M., Guda, C., Barletta, R.G., Moriyama, E.N., Smith, T.P.L., Reddy, J. 2016. Whole genomic sequence analysis of Bacillus infantis: defining the genetic blueprint of strain NRRL B-14911, an emerging cardiopathogenic microbe. Biomed Central (BMC) Genomics. 17(Suppl. 7):511. doi: 10.1186/s12864-016-2900-2.

Genomewide association study of liver abscess in beef cattle Reprint Icon - (Peer Reviewed Journal)
Keele, J.W., Kuehn, L.A., McDaneld, T.G., Tait Jr, R.G., Jones, S., Keel, B.N., Snelling, W.M. 2016. Genomewide association study of liver abscess in beef cattle. Journal of Animal Science. 94(2):490-499.

A survey of polymorphisms detected from sequences of popular beef breeds - (Peer Reviewed Journal)
Snelling, W.M., Bennett, G.L., Keele, J.W., Kuehn, L.A., McDaneld, T.G., Smith, T.P., Thallman, R.M., Kalbfleisch, T.S., Pollak, E.J. 2015. A survey of polymorphisms detected from sequences of popular beef breeds. Journal of Animal Science. 93(11):5128-5143. doi:10.2527/jas2015-9356.

Historical overview and current status of genomic technology and marker assisted selection in beef cattle - (Proceedings)
Pollak, E.J., Smith, T.P., Snelling, W.M. 2015. Historical overview and current status of genomic technology and marker assisted selection in beef cattle. In Proceedings of the American Meat Science Association. 68th Annual Reciprocal Meat Conference, June 14 - 17, 2015, Lincoln, NE. pg. 32-36.

Comparison of Bayesian models to estimate direct genomic values in multi-breed commercial beef cattle Reprint Icon - (Peer Reviewed Journal)
Rolf, M.M., Garrick, D.J., Fountain, T., Ramey, H.R., Weaber, R.L., Decker, J.E., Pollak, E.J., Schnabel, R.D., Taylor, J.F. 2015. Comparison of Bayesian models to estimate direct genomic values in multi-breed commercial beef cattle. Genetics Selection Evolution. 47:23. DOI 10.1186/s12711-015-0106-8.

Evaluation of single nucleotide polymorphisms in chromosomal regions impacting pregnancy status in cattle Reprint Icon - (Peer Reviewed Journal)
Psaros, K.M., McDaneld, T.G., Kuehn, L.A., Snelling, W.M., Keele, J.W. 2015. Evaluation of single nucleotide polymorphisms in chromosomal regions impacting pregnancy status in cattle. Journal of Animal Science. 93(3):978-987. doi: 10.2527/jas2014-8509.

Genomewide association study of lung lesions in cattle using sample pooling - (Peer Reviewed Journal)
Keele, J.W., Kuehn, L.A., McDaneld, T.G., Tait Jr., R.G., Jones, S., Smith, T.P., Shackelford, S.D., King, D.A., Wheeler, T.L., Lindholm-Perry, A.K., McNeel, A.K. 2015. Genomewide association study of lung lesions in cattle using sample pooling. Journal of Animal Science. 93(3):956-964. DOI: 10.2527/jas.2014-8492.

Multi-tissue omics analyses reveal molecular regulatory networks for puberty in composite beef cattle - (Peer Reviewed Journal)
Canovas, A., Reverter, A., DeAtley, K.L., Ashley, R.L., Colgrave, M.L., Fortes, M.R., Islas-Trejo, A., Lehnert, S.A., Porto-Neto, L.R., Rincon, G., Silver, G.A., Snelling, W.M., Medrano, J.F., Thomas, M.G. 2014. Multi-tissue omics analyses reveal molecular regulatory networks for puberty in composite beef cattle. PLoS One. 9(7):e102551. DOI: 10.1371/journal.pone.0102551.

Evaluation of anthelmintic resistance of intestinal parasitic nematodes in heifers in south central Nebraska - (Abstract Only)
Jones, S., Chase, C.C., Cortinas, R., Griffin, D., Kuehn, L.A., Shuck, K., Whitman, K., Tait Jr, R.G., Keele, J.W. 2014. Evaluation of anthelmintic resistance of intestinal parasitic nematodes in heifers in south central Nebraska [abstract]. Journal of Animal Science Supplement. 92(E-Supplement 2):462.

Filling the knowledge gap: Integrating quantitative genetics and genomics in graduate education and outreach - (Proceedings)
Lewis, R.M., Spangler, M.L., Lockee, B.B., Enns, R.M., Enns, K.J., Dekkers, J.C., Maltecca, C., Cassady, J.P., MacNeil, M.D., Gould, C.A., Boggs, D.L., Misztal, I., Pollak, E.J. 2014. Filling the knowledge gap: Integrating quantitative genetics and genomics in graduate education and outreach. In: Proceedings of the 10th World Congress on Genetics Applied to Livestock Production, August 17-22, 2014, Vancouver, BC, Canada. Paper No. 222. Available: https://asas.org/wcgalp-proceedings.

Genomewide association study of reproductive efficiency in female cattle Reprint Icon - (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.

Utilization of sequence on relatives to improve analysis of individuals' low-coverage NGS data - (Abstract Only)

Deletion on chromosome 5 associated with decreased reproductive efficiency in female cattle - (Peer Reviewed Journal)
McDaneld, T.G., Kuehn, L.A., Thomas, M.G., Pollak, E.J., Keele, J.W. 2014. Deletion on chromosome 5 associated with decreased reproductive efficiency in female cattle. Journal of Animal Science. 92:1378-1384.

Microbiome characterization using SMRT sequencing on 16S rRNA genes across a range of amplicon sizes and variable region content - (Abstract Only)

Characterization of microbiomes related to respiratory disease in cattle - (Abstract Only)
Smith, T.P., Kim, M.S., Myer, P.R., McDaneld, T.G., Kuehn, L.A., Clawson, M.L., Harhay, D.M., Harhay, G.P. 2014. Characterization of microbiomes related to respiratory disease in cattle [Abstract]. Proceedings of the Plant and Animal Genome XXII Conference, January 11-15, 2014, San Diego, CA. Poster W759.

Deep sequencing of immune repertoires during bovine development and in response to respiratory pathogen challenge - (Abstract Only)
Smith, T.P.L., and Larsen, P.A. 2013. Deep sequencing of immune repertoires during bovine development and in response to respiratory pathogen challenge [Abstract]. Advances in Genome Biology and Technology Conference, February 20-23, 2013, Marco Island, FL. Page 126.

Complete genome assemblies and methylome characterization in infectious diseases - (Abstract Only)
Smith, T.P. 2013. Complete genome assemblies and methylome characterization in infectious diseases [Abstract]. Plant & Animal Genome XXI Conference, January 12-16, 2013, San Diego, CA. Paper No. W483.

Last Modified: 2/23/2016
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