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United States Department of Agriculture

Agricultural Research Service

Timothy P. Smith (Tim)

Research Chemist


Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)
A polymorphism in myostatin influences puberty but not fertility in beef heifers, whereas µ-calpain affects first calf birth weight - (Peer Reviewed Journal) - (07-Nov-14)
Selection enhanced estimates of µ-calpain, calpastatin, and dacylglycerol O-acyltransferase 1 genetic effects on pre-weaning performance, carcass quality traits, and residual variance of tenderness in composite ... cattle - (Proceedings)
Tait Jr, R.G., Shackelford, S.D., Wheeler, T.L., King, D.A., Keele, J.W., Casas, E., Smith, T.P.L., Bennett, G.L. 2014. Selection enhanced estimates of µ-calpain, calpastatin, and dacylglycerol O-acyltransferase 1 genetic effects on pre-weaning performance, carcass quality traits, and residual variance of tenderness in composite MARC III beef cattle. In: Proceedings of the 10th World Congress on Genetics Applied to Livestock Production, August 17-22, 2014, Vancouver, BC, Canada. Paper No. 232. Available: https://asas.org/wcgalp-proceedings.
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.
Calpastatin and µ-calpain differ in their control of genotype specific residual variance of beef tenderness in Angus and MARC III steers - (Abstract Only) - (22-Mar-14)
SNPs for parentage testing and traceability in globally diverse breeds of sheep - (Peer Reviewed Journal)
Heaton, M.P., Leymaster, K.A., Kalbfleisch, T.S., Kijas, J.W., Clarke, S.M., McEwan, J., Maddox, J.F., Basnayake, V., Petrik, D.T., Simpson, B., Smith, T.P., Chitko-McKown, C.G. 2014. SNPs for parentage testing and traceability in globally diverse breeds of sheep. PLoS One. 9(4):e94851. DOI: 10.1371/JOURNAL.PONE.0094851.
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.
Changes in the rumen microbiome from steers differing in feed efficiency - (Abstract Only)
Myer, P.R., Freetly, H.C., Smith, T.P. 2014. Changes in the rumen microbiome from steers differing in feed efficiency [abstract]. American Society for Microbiology 114th General Meeting. Poster No. 1292.
Complete closed genome sequences of three Bibersteinia trehalosi nasopharyngeal isolates from cattle with shipping fever - (Peer Reviewed Journal)
Harhay, G.P., McVey, D.S., Koren, S., Phillippy, A.M., Bono, J.L., Harhay, D.M., Clawson, M.L., Heaton, M.P., Chitko-McKown, C.G., Korlach, J., Smith, T.P. 2014. Complete closed genome sequences of three Bibersteinia trehalosi nasopharyngeal isolates from cattle with shipping fever. Genome Announcements. 2(1):e00084-14.
Complete closed genome sequences of four Mannheimia varigena isolates from cattle with shipping fever - (Peer Reviewed Journal)
Harhay, G.P., Murray, R.W., Lubbers, B., Griffin, D., Koren, S., Phillippy, A.M., Harhay, D.M., Bono, J.L., Clawson, M.L., Heaton, M.P., Chitko-McKown, C.G., Smith, T.P. 2014. Complete closed genome sequences of four Mannheimia varigena isolates from cattle with shipping fever. Genome Announcements. 2(1):e00088-14.
µ-Calpain, calpastatin, and growth hormone receptor genetic effects on preweaning performance, carcass quality traits, and residual variance of tenderness in Angus cattle selected to increase minor haplotype ... frequencies Reprint Icon - (Peer Reviewed Journal)
Tait Jr, R.G., Shackelford, S.D., Wheeler, T.L., King, D.A., Casas, E., Thallman, R.M., Smith, T.P., Bennett, G.L. 2014. µ-Calpain, calpastatin, and growth hormone receptor genetic effects on preweaning performance, carcass quality traits, and residual variance of tenderness in Angus cattle selected to increase minor haplotype and allele frequencies. Journal of Animal Science. 92(2):456-466.
Microbiome characterization using SMRT sequencing on 16S rRNA genes across a range of amplicon sizes and variable region content - (Abstract Only) - (04-Dec-13)
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.
SNPs for parentage testing and traceability in globally diverse breeds of sheep - (Abstract Only)
Heaton, M.P., Leymaster, K.A., Kalbfleisch, T.S., Kijas, J.W., Clarke, S.M., McEwan, J., Maddox, J.F., Basnayake, V., Petrik, D.T., Simpson, B., Smith, T.P., Chitko-McKown, C.G. 2014. SNPs for parentage testing and traceability in globally diverse breeds of sheep [Abstract]. Proceedings Plant and Animal Genome XXII Conference, January 11-15, 2014, San Diego, CA. Poster P614.
Reducing assembly complexity of microbial genomes with single-molecule sequencing - (Peer Reviewed Journal)
Koren, S., Harhay, G.P., Smith, T.P.L., Bono, J.L., Harhay, D.M., McVey, D.S., Radune, D., Bergman, N.H., Phillippy, A.M. 2013. Reducing assembly complexity of microbial genomes with single-molecule sequencing. Genome Biology. 14:R101. DOI: 10.1186/GB-2013-14-9-R101.
Small ruminant lentivirus genetic subgroups associate with sheep TMEM154 genotypes - (Peer Reviewed Journal)
Sider, L.H., Heaton, M.P., Chitko-Mckown, C.G., Harhay, G.P., Smith, T.P.L., Leymaster, K.A., Laegreid, W.W., and Clawson, M.L. 2013. Small ruminant lentivirus genetic subgroups associate with sheep TMEM154 genotypes. Veterinary Research. 44:64. DOI: 10.1186/1297-9716-44-64.
Proposed model for the high rate of rearrangement and rapid migration observed in some IncA/C plasmid lineages - (Peer Reviewed Journal)
Meinersmann, R.J., Lindsey, R., Bono, J.L., Smith, T.P., Oakley, B. 2013. Proposed model for the high rate of rearrangement and rapid migration observed in some IncA/C plasmid lineages. Applied and Environmental Microbiology. 79(16):4806-4814.
Genome-wide association study of reproductive efficiency in female cattle - (Abstract Only)
McDaneld, T.G., Kuehn, L.A., Thomas, M.G., Snelling, W.M., Pollak, E.J., Smith, T.P.L., Keele, J.W. 2013. Genome-wide association study of reproductive efficiency in female cattle [Abstract]. Journal of Animal Science. 91 (E-Supplement 2):392. (Abstract #319).
Complete closed genome sequences of Mannheimia haemolytica serotypes A1 and A6 isolated from cattle - (Peer Reviewed Journal)
Harhay, G.P., Koren, S., Phillippy, A.M., McVey, D.S., Kuszak, J., Clawson, M.L., Harhay, D.M., Heaton, M.P., Chitko-McKown, C.G., Smith, T.P.L. 2013. Complete closed genome sequences of Mannheimia haemolytica serotypes A1 and A6 isolated from cattle. Genome Announcements. 1(3):e00188-13. DOI: 10.1128/GENOMEA.00188-13.
The effects of selecting for the myostatin F94L polymorphism on reproductive traits in pubertal heifers - (Abstract Only)
Forbes, E.D., Swanson, O.L., McNeel, A.K., Tait, Jr., R.G., Smith, T.P.L., Bennett, G.L., Hoagland, T.A., Zinn, S.A., Lents, C.A., Perry, G.A., Cushman, R.A. 2013. The effects of selecting for the myostatin F94L polymorphism on reproductive traits in pubertal heifers. Journal of Animal Science. 91 (E-Supplement 2):287 (Abstract #W181).
Capn1 and Gdf8 Genetic Marker Effects on Heifer Performance, Reproduction, and First Calf Performance Traits in Beef Cattle - (Abstract Only) - (24-Feb-13)
Genetic effects of GDF8 and CAPN1 for carcass and meat traits - (Abstract Only) - (23-Feb-13)
Salmonella virulence, genomics and interactions with the immune system - (Proceedings)
Harhay, D.M., Smith, T.P., Harhay, G.P., Bono, J.L., Bosilevac, J.M. 2013. Salmonella virulence, genomics and interactions with the immune system. Meeting Abstract. The Beef Industry Safety Summit, March 13-15, 2013, Dallas Texas, FLASHDRIVE.
Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution - (Peer Reviewed Journal)
Melters, D.P., Bradnan, K., Young, H., Telis, N., May, M., Ruby, G.J., Sebra, R., Peluso, P., Eid, J., Rank, D., Garcia, J., Derisi, J., Smith, T.P., Tobias, C.M., Ross-Ibarra, J., Korf, I., Chan-Simon, W. 2013. Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution. Genome Biology. doi:10.1186/gb-2013-14-1-r10.
Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution - (Peer Reviewed Journal)
Melters, D.P., Bradnam, K.R., Young, H.P., Telis, N., May, M.R., Ruby, J., Sebra, R., Peluso, P., Eid, J., Rank, D., Garcia, J., Derisi, J.L., Smith, T.P., Tobias, C.M., Ross-Ibarra, J., Korf, I., Chan, S.W. 2013. Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution. Genome Biology. 14(1):R10. doi:10.1186/gb-2013-14-1-r10.
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.
Multi-platform next generation sequencing of a high quality genome assembly for the goat - (Abstract Only)
Sonstegard, T.S., Smith, T.P., Schroeder, S.G., Huson, H.J., Zimin, A., Woodward Greene, M.J., Mujibi, D.F., Mcclure, M.C., Silverstein, J., Van Tassell, C.P., Sayre, B.L. 2013. Multi-platform next generation sequencing of a high quality genome assembly for the goat. Plant Animal Genome XXI, paper W417, pp. 171.
Application of SMRT genome sequencing to reveal the methylomes of bacteria associated with respiratory disease outbreaks in beef cattle - (Abstract Only)
Harhay, G.P., McVey, D.S., Korlach, J., Roberts, R., Chitko-McKown, C.G., Clawson, M.L., Heaton, M.P., Harhay, D.M., Smith, T.P.L., Anton, B.P. 2013. Application of SMRT genome sequencing to reveal the methylomes of bacteria associated with respiratory disease outbreaks in beef cattle [Abstract]. Advances in Genome Biology and Technology Conference, February 20-23, 2013, Marco Island, FL. Page 99.
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.
Estimation of genetic marker effects for CAPN1, CAST, and GHR on carcass quality traits in Angus cattle selected to increase minor marker frequencies - (Abstract Only)
Tait Jr, R.G., Shackelford, S.D., Wheeler, T.L., King, D.A., Casas, E., Thallman, R.M., Smith, T.P., Bennett, G.L. 2013. Estimation of genetic marker effects for CAPN1, CAST, and GHR on carcass quality traits in Angus cattle selected to increase minor marker frequencies [abstract]. Journal of Animal Science. 91(Supplement 2):62-63. Abstract No. O186.
Characterizing changes in the immune repertoire of cattle using next-gen sequencing - (Abstract Only)
Smith, T.P.L., Larsen, P.A. 2013. Characterizing changes in the immune repertoire of cattle using next-gen sequencing [Abstract]. Plant & Animal Genome XXI Conference, January 12-16, 2013, San Diego, CA. Paper No. W147.
Development of low-cost, high-throughput genotyping to complement SNP discovery by individual animal whole-genome sequencing - (Abstract Only)
Thallman, R.M., Snelling, W.M., Curry, J.D., Smith, T.P., Kalbfleisch, T.S., Kuehn, L.A., McDaneld, T.G., Bennett, G.L., Lindholm-Perry, A.K., Fofanov, V.Y., Koshinsky, H., Pollak, E.J. 2013. Development of low-cost, high-throughput genotyping to complement SNP discovery by individual animal whole-genome sequencing [abstract]. Plant and Animal Genome XXI Conference. Workshop Abstract No. W146.
Selection for genetic markers in beef cattle reveals complex associations of thyroglobulin and casein1-S1 with carcass and meat traits - (Peer Reviewed Journal)
Bennett, G.L., Shackelford, S.D., Wheeler, T.L., King, D.A., Casas, E., Smith, T.P. 2013. Selection for genetic markers in beef cattle reveals complex associations of thyroglobulin and casein1-S1 with carcass and meat traits. Journal of Animal Science. 91(2):565-571.
Application of circular consensus sequencing and network analysis to characterize the bovine IgG repertoire - (Peer Reviewed Journal)
Larsen, P.A., Smith, T.P. 2012. Application of circular consensus sequencing and network analysis to characterize the bovine IgG repertoire. BioMed Central (BMC) Immunology. 13:52 doi:10.1186/1471-2172-13-52.
Next-generation sequencing of the porcine skeletal muscle transcriptome for computational prediction of microRNA gene targets - (Peer Reviewed Journal)
McDaneld, T.G., Smith, T.P.L., Harhay, G.P., and Wiedmann, R.T. 2012. Next-generation sequencing of the porcine skeletal muscle transcriptome for computational prediction of microRNA gene targets. PLoS One. 7(7):e42039. doi:10.1371/journal.pone.0042039.
Accuracy of genomic breeding values in multibreed beef cattle populations derived from deregressed breeding values and phenotypes - (Peer Reviewed Journal)
Weber, K.L., Thallman, R.M., Keele, J.W., Snelling, W.M., Bennett, G.L., Smith, T.P., McDaneld, T.G., Allan, M.F., Van Eenennaam, A.L., Kuehn, L.A. 2012. Accuracy of genomic breeding values in multibreed beef cattle populations derived from deregressed breeding values and phenotypes. Journal of Animal Science. 90(12):4177-4190.
Phylogenetic clades of ovine progressive pneumonia virus (OPPV) associate with sheep TMEM154 genotypes - (Abstract Only)
Sider, L.H., Clawson, M.L., Heaton, M.P., Chitko Mckown, C.G., Harhay, G.P., Smith, T.P.L., Leymaster, K.A. 2012. Phylogenetic clades of ovine progressive pneumonia virus (OPPV) associate with sheep TMEM154 genotypes. The 58th Genomic Congress, September 11-14, 2012. Foz de Iguacu, Brazil. Poster No. GM001.
Comparison of bacterial communities in faeces of beef cattle fed diets containing corn and wet distillers grain with solubles Reprint Icon - (Peer Reviewed Journal)
Durso, L.M., Wells, J., Harhay, G.P., Rice, W.C., Kuehn, L.A., Bono, J.L., Shackelford, S.D., Wheeler, T.L., Smith, T.P. 2012. Comparison of bacterial communities in faeces of beef cattle fed diets containing corn and wet distillers grain with solubles. Letters in Applied Microbiology. 55(2):109-14. DOI: 10.1111/J.1472-765X.2012.03265.X.
Smrt Sequencing Provides Insight into the Diversity of the Bovine Immunoglobulin Heavy Chain Repertoire - (Abstract Only) - (02-Apr-12)
Evaluation of bovine chemerin (RARRES2) gene variation on beef cattle production traits - (Peer Reviewed Journal)
Lindholm-Perry, A.K., Kuehn, L.A., Rempel, L.A., Smith, T.P., Cushman, R.A., McDaneld, T.G., Wheeler, T.L., Shackelford, S.D., King, D.A., Freetly, H.C. 2012. Evaluation of bovine chemerin (RARRES2) gene variation on beef cattle production traits. Frontiers in Genetics. 3:39.
Analysis of copy number variations among cattle breeds - (Abstract Only)
Liu, G., Hou, Y., Zhu, B., Cardone, M.F., Jiang, L., Cellamare, A., Mitra, A., Alexander, L.J., Coutinho, L.L., Gasbarre, L.C., Li, R.W., Matukumalli, L.K., Nonneman, D.J., Regitano, L.C., Smith, T.P., Song, J., Sonstegard, T.S., Van Tassell, C.P., Ventura, M., Eichler, E.E., Mcdaneld, T.G., Keele, J.W. 2012. Analysis of copy number variations among cattle breeds. [abstract] CONFERENCE ON THE BIOLOGY OF GENOMES. P. 182.
Phylogeny of Shiga toxin-producing Escherichia coli O157 isolated from cattle and clinically ill humans Reprint Icon - (Peer Reviewed Journal)
Bono, J.L., Smith, T.P., Keen, J.E., Harhay, G.P., McDaneld, T.G., Mandrell, R.E., Jung, W., Besser, T.E., Gerner-Smidt, P., Bielaszewska, M., Karch, H., Clawson, M.L. 2012. Phylogeny of Shiga toxin-producing Escherichia coli O157 isolated from cattle and clinically ill humans. Molecular Biology and Evolution. 29(8):2047-2062. doi: 10.1093/molbev/mss072.
Association of genetic markers in cattle receiving differing implant protocols - (Peer Reviewed Journal)
King, D.A., Shackelford, S.D., McDaneld, T.G., Kuehn, L.A., Kemp, C.M., Smith, T.P., Wheeler, T.L., Koohmaraie, M. 2012. Association of genetic markers in cattle receiving differing implant protocols. Journal of Animal Science. 90:2410-2423.
MicroRNA expression profile in bovine cumulus–oocyte complexes: Possible role of let-7 and miR-106a in the development of bovine oocytes Reprint Icon - (Peer Reviewed Journal)
Miles, J.R., McDaneld, T.G., Wiedmann, R.T., Cushman, R.A., Echternkamp, S.E., Vallet, J.L., Smith, T.P.L. 2012. MicroRNA expression profile in bovine cumulus–oocyte complexes: Possible role of let-7 and miR-106a in the development of bovine oocytes. Animal Reproduction Sciences. 130(1-2):16-26.
Association, effects and validation of polymorphisms within the NCAPG - LCORL locus located on BTA6 with feed intake, gain, meat and carcass traits in beef cattle - (Peer Reviewed Journal)
Lindholm-Perry, A.K., Sexten, A.K., Kuehn, L.A., Smith, T.P., King, D.A., Shackelford, S.D., Wheeler, T.L., Ferrell, C.L., Jenkins, T.G., Snelling, W.M., Freetly, H.C. 2011. Association, effects and validation of polymorphisms within the NCAPG - LCORL locus located on BTA6 with feed intake, gain, meat and carcass traits in beef cattle. BioMed Central (BMC) Genetics. 12:103.
Enabling next-gen sequencing and analysis at the USDA-ARS U.S. Meat Animal Research Center with MiniLIMS - (Abstract Only) - (07-Dec-11)
Application of combined SMRT and long-read pyrosequencing to produce reference genome sequences of bacteria associated with respiratory disease outbreaks in beef cattle - (Abstract Only)
Harhay, G.P., Mcvey, D.S., Kitzmiller, A., Clamp, M., Osborne, B., Dwan, C., Zhang, J., Sisneros, N., Wang, S., Peluso, P., Bono, J.L., Chitko Mckown, C.G., Clawson, M.L., Heaton, M.P., Harhay, D.M., Smith, T.P.L. [abstract]. 2012. Application of combined SMRT and long-read pyrosequencing to produce reference genome sequences of bacteria associated with respiratory disease outbreaks in beef cattle. Advances in Genome Biology and Technology, February 15-18, 2012, Marco Island, Florida. Poster No. 129.
Reduced lentivirus susceptibility in sheep with TMEM154 mutations - (Peer Reviewed Journal)
Heaton, M.P., Clawson, M.L., Chitko-Mckown, C.G., Leymaster, K.A., Smith, T.P.L., Harhay, G.P., White, S.N., Herrmann-Hoesing, L.M., Mousel, M.R., Lewis, G.S., Kalbfleisch, T.S., Keen, J.E., Laegreid, W.W. 2012. Reduced lentivirus susceptibility in sheep with TMEM154 mutations. PLoS Genetics. 8(1): e1002467. DOI: 10.1371/journal.pgen.1002467.
Y are you not pregnant: identification of Y chromosome segments in female cattle with decreased reproductive efficiency - (Peer Reviewed Journal)
McDaneld, T.G., Kuehn, L.A., Thomas, M.G., Snelling, W.M., Sonstegard, T.S., Matukumalli, L.K., Smith, T.P., Pollak, E.J., Keele, J.W. 2012. Y are you not pregnant: identification of Y chromosome segments in female cattle with decreased reproductive efficiency. Journal of Animal Science. 90(7):2142-2151.
Genetic markers on BTA14 predictive for residual feed intake in beef steers and their effects on carcass and meat quality traits - (Peer Reviewed Journal)
Lindholm-Perry, A.K., Kuehn, L.A., Snelling, W.M., Smith, T.P., Ferrell, C.L., Jenkins, T.G., King, D.A., Shackelford, S.D., Wheeler, T.L., Freetly, H.C. 2012. Genetic markers on BTA14 predictive for residual feed intake in beef steers and their effects on carcass and meat quality traits. Animal Genetics. 43:599-603.
Genetic markers in bovine chromosome 14 are significant for residual feed intake in steers - (Abstract Only)
Lindholm-Perry, A.K., Kuehn, L.A., Smith, T.P., Snelling, W.M., Freetly, H.C. 2011. Genetic markers in bovine chromosome 14 are significant for residual feed intake in steers. Journal of Animal Science. 89(E-Suppl. 1):422-423.
A region on BTA14 that includes the positional candidate genes LYPLA1, XKR4 and TMEM68 is associated with feed intake and growth phenotypes in cattle - (Peer Reviewed Journal)
Lindholm-Perry, A.K., Kuehn, L.A., Smith, T.P., Ferrell, C.L., Jenkins, T.G., Freetly, H.C., Snelling, W.M. 2012. A region on BTA14 that includes the positional candidate genes LYPLA1, XKR4 and TMEM68 is associated with feed intake and growth phenotypes in cattle. Animal Genetics. 43(2):216-219.
Use of sample pooling in a genome-wide association study identifies chromosomal regions affecting incidence of bovine respiratory disease - (Abstract Only)
Kuehn, L.A., Keele, J.W., Casas, E., Jones, S., King, D.A., McDaneld, T.G., Smith, T.P.L., Wheeler, T.L. 2011. Use of sample pooling in a genome-wide association study identifies chromosomal regions affecting incidence of bovine respiratory disease [abstract]. Journal of Animal Science. 89 (E-Supplement 1):422 (Abstract #336).
Genomic regions associated with incidence of disease in cattle using DNA pooling and a high density single nucleotide polymorphism array - (Abstract Only)
Casas, E., Kuehn, L.A., McDaneld, T.G., Smith, T.P.L., Keele, J.W. 2011. Genomic regions associated with incidence of disease in cattle using DNA pooling and a high density single nucleotide polymorphism array [abstract]. Journal of Animal Science. 89 (E-Supplement 1):158. (Abstract 18).
Evaluation of polymorphisms within the genes GSHR and SLC2A2 that are within a region on bovine chromosome 1 (BTA1) previously associated with feed intake and weight gain - (Peer Reviewed Journal)
Lindholm-Perry, A.K., Kuehn, L.A., Snelling, W.M., Smith, T.P., Ferrell, C.L., Jenkins, T.G., Freetly, H.C. 2012. Evaluation of polymorphisms within the genes GSHR and SLC2A2 that are within a region on bovine chromosome 1 (BTA1) previously associated with feed intake and weight gain. Animal Genetics. 43(1):112.
Gene expression response of multidrug resistant Salmonella enterica serovar Newport to simulated multiple hurdle beef carcass processing interventions - (Abstract Only)
Harhay, D.M., Smith, T.P., Harhay, G.P. 2011. Gene expression response of multidrug resistant Salmonella enterica serovar Newport to simulated multiple hurdle beef carcass processing interventions. In: Proceedings of the American Society for Microbiology. 111th General Meeting of the American Society for Microbiology, May 21-24, 2011, New Orleans, Louisiana. 2011 CDROM. Meeting Abstract K-2692.
Evaluation of pyrosequencing for assembly of plasmids carrying IS elements - (Abstract Only)
Chen, C., Lindsey, R.L., Strobaugh Jr, T.P., Frye, J.G., Bono, J.L., Smith, T.P., Meinersmann, R.J. 2011. Evaluation of pyrosequencing for assembly of plasmids carrying IS elements [abstract]. 111th ASM General Meeting.
Towards an understanding of how Salmonella potentially evades beef carcass processing interventions - (Abstract Only)
Brichta-Harhay, D.M., Gragg, S.E., Smith, T.P.L., Arthur, T.M., Bosilevac, J.M., Kalchayanand, N., Schmidt, J.W., Wang, R., Shackelford, S.D., Wheeler, T.L., Brashears, M.M., Brooks, J.C., Brown, T.R., Harhay, G.P., Loneragan, G.H. 2011. Towards an understanding of how Salmonella potentially evades beef carcass processing interventions [abstract]. 2011 Beef Industry Safety Summit. Abstract No. 2.
Predicting breed composition using breed frequencies of 50,000 markers from the U.S. Meat Animal Research Center 2,000 bull project - (Peer Reviewed Journal)
Kuehn, L.A., Keele, J.W., Bennett, G.L., Mcdaneld, T.G., Smith, T.P., Snelling, W.M., Sonstegard, T.S., Thallman, R.M. 2011. Predicting breed composition using breed frequencies of 50,000 markers from the U.S. Meat Animal Research Center 2,000 bull project. Journal of Animal Science. 89:1742-1750.
Biosurveillance at the United States Meat Animal Research Center - (Abstract Only)
Harhay, G.P., Harhay, D.M., Chitko Mckown, C.G., Smith, T.P. 2011. Biosurveillance at the United States Meat Animal Research Center [abstract]. Global Biosurveillance: Enabling Science and Technology 2nd Biothreat Nonproliferation Conference. Abstract No. 12.
Virulence-associated and antibiotic resistance genes of microbial populations in cattle feces analyzed using a metagenomic approach Reprint Icon - (Peer Reviewed Journal)
Durso, L.M., Harhay, G.P., Bono, J.L., Smith, T.P. 2011. Virulence-associated and antibiotic resistance genes of microbial populations in cattle feces analyzed using a metagenomic approach. Journal of Microbiological Methods. 84: 278-282.
Bacterial community analysis of beef cattle feedlots reveals that pen surface is distinct from feces - (Peer Reviewed Journal)
Durso, L.M., Harhay, G.P., Smith, T.P., Bono, J.L., Desantis, T.Z., Clawson, M.L. 2011. Bacterial community analysis of beef cattle feedlots reveals that pen surface is distinct from feces. Foodborne Pathogens and Disease. 8(5):647-649. Available: DOI: 10.1089/fpd.2010.0774.
The effects of genetic markers on BTA6 significant for steer feed intake and gain traits on carcass and meat traits - (Abstract Only)
Lindholm-Perry, A.K., Sexten, A.K., Kuehn, L.A., Smith, T.P., King, D.A., Shackelford, S.D., Wheeler, T.L., Snelling, W.M., Freetly, H.C. 2011. The effects of genetic markers on BTA6 significant for steer feed intake and gain traits on carcass and meat traits. Plant & Animal Genome XIX Conference. Poster No. P531. p. 230
Association of single nucleotide polymorphisms in the ANKRA2 and CD180 genes with bovine respiratory disease and presence of Mycobacterium avium subsp. paratuberculosis - (Peer Reviewed Journal)
Casas, E., Garcia, M.D., Wells, J., Smith, T.P.L. 2011. Association of single nucleotide polymorphisms in the ANKRA2 and CD180 genes with bovine respiratory disease and presence of Mycobacterium avium subsp. paratuberculosis. Animal Genetics. 42:571-577.
Association of single nucleotide polymorphisms in the ANKRA2 and CD180 genes with bovine respiratory disease and presence of Mycobacterium avium subsp. paratuberculosis - (Abstract Only)
Casas, E., Garcia, M.D., Wells, J., Smith, T.P. 2011. Association of single nucleotide polymorphisms in the ANKRA2 and CD180 genes with bovine respiratory disease and presence of Mycobacterium avium subsp. paratuberculosis [abstract]. Plant and Animal Genome XIX Conference. Poster No. P193.
An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation - (Peer Reviewed Journal)
Harhay, G.P., Smith, T.P.L., Alexander, L.J., Haudenschild, C.D., Keele, J.W., Matukumalli, L.K., Schroeder, S.G., Van Tassell, C.P., Gresham, C.R., Bridges, S.M., Burgess, S.C., Sonstegard, T.S. 2010. An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation. Genome Biology [online serial]. 11:R102.
Whole genome sequence analysis of field strains of bluetongue virus - (Abstract Only)
Wilson, W.C., Smith, T.P. 2010. Whole genome sequence analysis of field strains of bluetongue virus. Meeting Proceedings. 154.
Sequence analysis for a de novo genome assembly of Bos indicus (Nelore) cattle - (Abstract Only)
Sonstegard, T.S., Schroeder, S.G., Smith, T.P., Zimin, A., Matukumalli, L.K., Ajmone-Marsan, P., Wiedmann, R.T., Negrini, R., Yorke, J., Van Tassell, C.P., Garcia, J.F. 2010. Sequence analysis for a de novo genome assembly of Bos indicus (Nelore) cattle. Animal Genetics International Conference Proceedings.
Molecular analysis of plasmid encoded multi-drug resistance (MDR) in Salmonella enterica animal isolates by PFGE, replicon typing, and DNA microarray screening followed by high-throughput DNA sequencing - (Abstract Only)
Lindsey, R.L., Frye, J.G., Bono, J.L., Smith, T.P., Harhay, D.M., Cray, P.J., Meinersmann, R.J. 2010. Molecular analysis of plasmid encoded multi-drug resistance (MDR) in Salmonella enterica animal isolates by PFGE, replicon typing, and DNA microarray screening followed by high-throughput DNA sequencing. American Society for Microbiology. June 8-11, 2010. Toronto, Canada. B16. p41-42.
Markers on bovine chromosome 20 associated with carcass quality and composition traits and incidence of contracting infectious bovine keratoconjunctivitis - (Peer Reviewed Journal)
Garcia, M.D., Matukumalli, L., Wheeler, T.L., Shackelford, S.D., Smith, T.P., Casas, E. 2010. Markers on bovine chromosome 20 associated with carcass quality and composition traits and incidence of contracting infectious bovine keratoconjunctivitis. Animal Biotechnology. 21(3):188-202.
Polymorphisms in POMC are not associated with dry matter intake and average daily gain phenotypes in beef cattle Reprint Icon - (Peer Reviewed Journal)
Lindholm-Perry, A.K., Kuehn, L.A., Snelling, W.M., Smith, T.P.L., Ferrell, C.L., Jenkins, T.G., Freetly, H.C. 2010. Polymorphisms in POMC are not associated with dry matter intake and average daily gain phenotypes in beef cattle. Animal Genetics. 41(6):669-670.
Predicting Breed Composition Using Breed Frequencies of 50,000 Markers from the U.S. Meat Animal Research Center 2,000 Bull Project - (Proceedings)
Kuehn, L.A., Keele, J.W., Bennett, G.L., McDaneld, T.G., Smith, T.P., Snelling, W.M., Sonstegard, T.S., Thallman, R.M. 2010. Predicting Breed Composition Using Breed Frequencies of 50,000 Markers from the U.S. Meat Animal Research Center 2,000 Bull Project. Proceedings of the 9th World Congress on Genetics Applied to Livestock Production, Leipzig, Germany. August 1-6, 2010. CD-ROM Communication No. 0283.
Application of marker selection to enhance estimation of genetic effects and gene interaction in cattle - (Proceedings)
Bennett, G.L., Shackelford, S.D., Wheeler, T.L., King, D.A., Casas, E., Smith, T.P. 2010. Application of marker selection to enhance estimation of genetic effects and gene interaction in cattle. Proceedings, 9th World Congress on Genetics Applied to Livestock Production, Leipzig, Germany. August 1-6, 2010. CD-ROM Communication No. 0286.
Animal-to-Animal Variation in Fecal Microbial Diversity among Beef Cattle - (Peer Reviewed Journal)
Durso, L.M., Harhay, G.P., Smith, T.P.L., Bono, J.L., Desantis, T.Z., Harhay, D.M., Andersen, G.L., Keen, J.E., Laegreid, W.W., Clawson, M.L. 2010. Animal-to-Animal Variation in Fecal Microbial Diversity among Beef Cattle. Applied and Environmental Microbiology. 76(14):4858-4862.
Comparison of cattle fecal communities from animals fed diets containing corn and distiller's grains - (Abstract Only)
Durso, L.M., Harhay, G.P., Wells, J., Bono, J.L., Riethoven, J.M., Shackelford, S.D., Wheeler, T.L., Smith, T.P. 2010. Comparison of cattle fecal communities from animals fed diets containing corn and distiller's grains. PS.25.018, Abstract #393A. Abstract for Microbial Ecology International Symposium, Seattle, WA, Aug. 22-27, 2010. Abstract Book, Pg. 128
Ovine Reference Materials and Assays for Prion Genetic Testing Reprint Icon - (Peer Reviewed Journal)
Heaton, M.P., Leymaster, K.A., Kalbfleisch, T.S., Freking, B.A., Smith, T.P., Clawson, M.L., Laegreid, W.W. 2010. Ovine Reference Materials and Assays for Prion Genetic Testing. BioMed Central (BMC) Veterinary Research [serial online]. 6:23. Available: http://www.biomedcentral.com/1746-6148/6/23.
A Deletion Mutation in Bovine SLC4A2 is Associated with Osteopetrosis in Red Angus Cattle Reprint Icon - (Peer Reviewed Journal)
Meyers, S.N., McDaneld, T.G., Swist, S.L., Marron, B.M., Steffen, D.J., O'Toole, D., O'Connell, J.R., Beever, J.E., Sonstegard, T.S., Smith, T.P. 2010. A Deletion Mutation in Bovine SLC4A2 is Associated with Osteopetrosis in Red Angus Cattle. Biomed Central (BMC) Genomics. 11:337.
A Region on BTA6 Is Associated with Feed Intake and Gain in Beef Cattle - (Abstract Only)
Sexten, A.K., Kuehn, L.A., Smith, T.P., Freetly, H.C., Snelling, W.M., Lindholm-Perry, A.K. 2010. A Region on BTA6 Is Associated with Feed Intake and Gain in Beef Cattle [abstract]. Journal of Animal Science. 88 (E-Supplement 2):185.
Analysis of copy number variations reveals differences among cattle breeds Reprint Icon - (Peer Reviewed Journal)
Liu, G., Hou, Y., Zhu, B., Cardone, M.F., Jiang, L., Cellamare, A., Mitra, A., Alexander, L.J., Coutinho, L.L., Gasbarre, L.C., Heaton, M.P., Li, R.W., Matukumalli, L.K., Nonneman, D.J., De A Regitano, L.C., Smith, T.P., Song, J., Sonstegard, T.S., Van Tassell, C.P., Eichler, E.E., Mcdaneld, T.G., Keele, J.W. 2010. Analysis of copy number variations among cattle breeds. Genome Research. 20:693-703.
Single nucleotide polymorphism discovery in rainbow trout - (Abstract Only)
Rexroad Iii, C.E., Castano, C., Smith, T.P., Vallejo, R.L., Jianbo, Y., Wiedmann, R.T. 2010. Single nucleotide plymorphism discovery in rainbow trout. Aquaculture America Conference.
A Digital Gene Expression-Based Bovine Gene Atlas Evaluating 92 Adult, Juvenile and Fetal Cattle Tissues - (Abstract Only)
Harhay, G.P., Alexander, L.J., Smith, T.P.L., Matukumalli, L.K., Schroeder, S.G., Sonstegard, T.S. 2010. A Digital Gene Expression-Based Bovine Gene Atlas Evaluating 92 Adult, Juvenile and Fetal Cattle Tissues [abstract]. In: Proceedings of the Advances in Genome Biology & Technology Conference, February 24-27, 2010, Marco Island, Florida. p. 67.
De novo Reconstruction of the Pig Skeletal Muscle Transcriptome for Identification of MicroRNA Gene Targets - (Abstract Only)
McDaneld, T.G., Wiedmann, R.T., Harhay, G.P., Smith, T.P.L. 2010. De novo Reconstruction of the Pig Skeletal Muscle Transcriptome for Identification of MicroRNA Gene Targets (abstract). In: Proceedings of the Advances in Genome Biology & Technology Conference, February 24-27,2010, Marco Island, Florida. p. 114.
Information Theoretical Analysis of a Bovine Gene Atlas Reveals Chromosomal Regions with Tissue Specific Gene Expression. - (Abstract Only)
Sonstegard, T.S., Harhay, G.P., Alexander, L.J., Schroeder, S.G., Keele, J.W., Matukumalli, L., Bridges, S., Burgess, S., Van Tassell, C.P., Smith, T.P. 2010. Information Theoretical Analysis of a Bovine Gene Atlas Reveals Chromosomal Regions with Tissue Specific Gene Expression. Plant and Animal Genome VX Conference Abstracts.
Evaluation of Two Positional Candidate Genes on BTA14 for Association with Dry Matter Intake in Beef Cattle - (Abstract Only)
Lindholm-Perry, A.K., Kuehn, L.A., Smith, T.P., Freetly, H.C., Snelling, W.M. 2010. Evaluation of Two Positional Candidate Genes on BTA14 for Association with Dry Matter Intake in Beef Cattle [abstract]. Plant & Animal Genome XVIII Conference. Poster No. P553. p. 216.
Genome-Wide Association Study of Growth in Crossbred Beef Cattle - (Peer Reviewed Journal)
Snelling, W.M., Allan, M.F., Keele, J.W., Kuehn, L.A., Mcdaneld, T.G., Smith, T.P., Sonstegard, T.S., Thallman, R.M., Bennett, G.L. 2010. Genome-Wide Association Study of Growth in Crossbred Beef Cattle. Journal of Animal Science. 88(3):837-848.
Ovine Reference Materials and Assays for Prion Genetic Testing - (Abstract Only)
Heaton, M.P., Leymaster, K.A., Kalbfleisch, T.S., Freking, B.A., Smith, T.P., Clawson, M.L., Laegreid, W.W. 2009. Ovine Reference Materials and Assays for Prion Genetic Testing [abstract]. Plant and Animal Genomes XVIII Conference. Abstract No. P577. Available: http://www.intl-pag.org/18/abstracts/
Markers on Bovine Chromosome 20 Associated with Carcass Quality and Composition Traits and Incidence of Contracting Infectious Bovine Keratoconjunctivitis Reprint Icon - (Abstract Only)
Garcia, M.D., Matukumalli, L., Wheeler, T.L., Shackelford, S.D., Smith, T.P., Casas, E. 2010. Markers on Bovine Chromosome 20 Associated with Carcass Quality and Composition Traits and Incidence of Contracting Infectious Bovine Keratoconjunctivitis [abstract]. Plant and Animal Genome XVIII Conference. Poster No. P196. Available: http://www.intl-pag.org/18/abstracts/P03e_PAGXVIII_196.html
Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library - (Peer Reviewed Journal)
Sanchez Castano, C., Smith, T.P., Wiedmann, R.T., Vallejo, R.L., Salem, M., Yao, J., Rexroad Iii, C.E. 2009. Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library. Biomed Central (BMC) Genomics. 10:559.
Evaluation of Biochemical Parameters and Genetic Markers for Association with Meat Tenderness in South African Cattle Reprint Icon - (Peer Reviewed Journal)
Frylinck, L., Van Wyk, G.L., Smith, T.P., Strydom, P.E., van Marle-Koster, E., Webb, E.C., Koohmaraie, M., Smith, M.F. 2009. Evaluation of Biochemical Parameters and Genetic Markers for Association with Meat Tenderness in South African Feedlot Cattle. Meat Science. 83:657-665.
Design of a High Density SNP Genotyping Assay in the Pig Using SNPs Identified and Characterized by Next Generation Sequencing Technology Reprint Icon - (Peer Reviewed Journal)
Ramos, A.M., Crooijmans, R.P.M.A., Affara, N.A., Amaral, A.J., Archibald, A.L., Beever, J.E., Bendixen, C., Churcher, C., Clark, R., Dehais, P., Hansen, M.S., Hedegaard, J., Hu, Z.L., Kerstens, H.H., Law, A.S., Megens, H.J., Milan, D., Nonneman, D.J., Rohrer, G.A., Rothschild, M.F., Smith, T.P.L., Schnabel, R.D., Van Tassell, C.P., Taylor, J.F., Wiedmann, R.T., Schook, L.B., Groenen, M.A.M. 2009. Design of a High Density SNP Genotyping Assay in the Pig Using SNPs Identified and Characterized by Next Generation Sequencing Technology. PLoS One 4(8):E6524. p. 1-13.
Phylogenetic Classification of Escherichia coli O157:H7 Strains of Human and Bovine Origin Using a Novel Set of Nucleotide Polymorphisms Reprint Icon - (Peer Reviewed Journal)
Clawson, M.L., Keen, J.E., Smith, T.P., Durso, L.M., Mcdaneld, T.G., Mandrell, R.E., Davis, M.A., Bono, J.L. 2009. Phylogenetic Classification of Escherichia coli O157:H7 Strains of Human and Bovine Origin Using a Novel Set of Nucleotide Polymorphisms. Genome Biology [serial online]. 10:R56. Available: http://genomebiology.com/2009/10/5/R56.
Whole Genome Analysis for Beef Tenderness - (Abstract Only)
Snelling, W.M., Smith, T.P., Shackelford, S.D., King, D.A., Wheeler, T.L., Kuehn, L.A., Thallman, R.M., Keele, J.W., Bennett, G.L. 2009. Whole Genome Analysis for Beef Tenderness [abstract]. Bovine Genome Consortium, Cold Spring Harbor, New York. May 9-11, 2009. Session 5 Poster Session, p. 30.
Development and Characterization of a High Density SNP Genotyping Assay for Cattle Reprint Icon - (Peer Reviewed Journal)
Matukumalli, L.K., Lawley, C.T., Schnabel, R.D., Taylor, J.F., Allan, M.F., Heaton, M.P., O'Connell, J., Moore, S.S., Smith, T.P., Sonstegard, T.S., Van Tassell, C.P. 2009. Development and Characterization of a High Density SNP Genotyping Assay for Cattle. PLoS One. 4(4):e5350. Available: http://dx.doi.org/10.1371/journal.pone.0005350.
The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution Reprint Icon - (Peer Reviewed Journal)
Elsik, C.G., Gibbs, R., Skow, L., Tellam, R., Weinstock, G., Worley, K., Kappes, S.M., Green, R.D., Alexander, L.J., Bennett, G.L., Carroll, J.A., Chitko Mckown, C.G., Hamernik, D.L., Harhay, G.P., Keele, J.W., Liu, G., Macneil, M.D., Matukumalli, L.K., Rijnkels, M., Roberts, A.J., Smith, T.P., Snelling, W.M., Stone, R.T., Waterman, R.C., White, S.N. 2009. The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution. Science. 324:522-528.
Association of Single Nucleotide Polymorphisms in the CAST Gene Associated with Longissimus Tenderness in Beef Cattle - (Abstract Only)
Casas, E., Wheeler, T.L., Shackelford, S.D., Bennett, G.L., Smith, T.P.L. 2009. Association of Single Nucleotide Polymorphisms in the CAST Gene Associated with Longissimus Tenderness in Beef Cattle [abstract]. Journal of Animal Science Supplement. 87(E-Suppl. 2):533. Abstract #628.
Phylogenetic Classification of Escherichia coli O157:H7 Isolates of Human and Bovine Origin Using a Novel Set of Nucleotide Polymorphisms - (Abstract Only)
Clawson, M.L., Keen, J.E., Smith, T.P., Durso, L.M., McDaneld, T.G., Mandrell, R.E., Davis, M.A., Bono, J.L. 2009. Phylogenetic Classification of Escherichia coli O157:H7 Isolates of Human and Bovine Origin Using a Novel Set of Nucleotide Polymorphisms [abstract]. American Society for Microbiology. Abstract No. Z-006. p. 612. 2009 CDROM.
Bacterial Communities Associated with Shiga-Toxigenic E. coli O157:H7 (STEC O157) in Beef Cattle Feedlot Environments - (Abstract Only)
Durso, L.M., Harhay, G.P., Bono, J.L., Smith, T.P., Laegreid, W.W., Keen, J.E., Clawson, M.L. 2009. Bacterial Communities Associated with Shiga-Toxigenic E. coli O157:H7 (STEC O157) in Beef Cattle Feedlot Environments [abstract]. Microbial Ecology 57(3):569.
MicroRNA Transcriptome Profiles During Swine Skeletal Muscle Development Reprint Icon - (Peer Reviewed Journal)
McDaneld, T.G., Smith, T.P., Doumit, M.E., Miles, J.R., Coutinho, L.L., Sonstegard, T.S., Matukumalli, L.K., Nonneman, D.J., Wiedmann, R.T. 2009. MicroRNA Transcriptome Profiles During Swine Skeletal Muscle Development. Biomed Central (BMC) Genomics. 10:77.
A Limousin specific myostatin allele affects longissimus muscle area and fatty acid profiles in a Wagyu-Limousin F*2* population - (Peer Reviewed Journal)
Alexander, L.J., Kuehn, L.A., Smith, T.P., Matukumalli, L.K., Mote, B., Koltes, J.E., Reecy, J., Geary, T.W., Rule, D.C., Macneil, M.D. 2009. A Limousin specific myostatin allele affects longissimus muscle area and fatty acid profiles in a Wagyu-Limousin F*2* population. Journal of Animal Science 87:1576-1581.
Profiling miRNA Expression in Bovine Tissues by Deep Sequencing - (Abstract Only)
Matukumalli, L.K., Alexander, L.J., Mcdaneld, T.G., Smith, T.P., Schroeder, S.G., Sonstegard, T.S., Van Tassell, C.P. 2009. Profiling miRNA Expression in Bovine Tissues by Deep Sequencing. Plant and Animal Genome Conference.
Snp Discovery in Swine by Reduced Representation and High Throughput Pyrosequencing Reprint Icon - (Abstract Only)
Nonneman, D.J., Wiedmann, R.T., Smith, T.P. 2009. SNP Discovery in Swine by Reduced Representation and High Throughput Pyrosequencing. Plant and Animal Genome Conference XVII Proceedings. 1/10-14/2009, San Diego, CA. Abstract P531.
Design of the Illumina Porcine 50K+ SNP Iselect(TM) Beadchip and Characterization of the Porcine HapMap Population Reprint Icon - (Abstract Only)
Groenen, M.A., Crooijmans, R.P., Ramos, A.M., Amaral, A.J., Kerstens, H., Bendixen, C., Hedegaard, J., Rohrer, G.A., Smith, T.P., Van Tassell, C.P., Taylor, J.F., Rothschild, M., Hu, Z., Nonneman, D.J., Beever, J., Archibald, A., Law, A., Milan, D., Hansen, M., Schook, L. 2009. Design of the Illumina Porcine 50K+ SNP Iselect(TM) Beadchip and Characterization of the Porcine HapMap Population. Plant and Animal Genome Conference Proceedings. 1/10-14/09, San Diego, CA. Abstract W493.
The artiodactyl APOBEC3 innate immune repertoire shows evidence for a multi-functional domain organization that existed in the ancestor of placental mammals Reprint Icon - (Peer Reviewed Journal)
Larue, R.S., Jonsson, S.R., Silverstein, K.A., Lajoie, M., Bertrand, D., El-Mabrouk, N., Hotzel, I., Andresdottir, V., Smith, T.P., Harris, R. 2008. The artiodactyl APOBEC3 innate immune repertoire shows evidence for a multi-functional domain organization that existed in the ancestor of placental mammals. BioMed Central (BMC) Molecular Biology. 9:104.
SNP discovery in swine by reduced representation and high throughput pyrosequencing Reprint Icon - (Peer Reviewed Journal)
Wiedmann, R.T., Smith, T.P., Nonneman, D.J. 2008. SNP discovery in swine by reduced representation and high throughput pyrosequencing. BioMed Central (BMC) Genetics. 9:81.
Association of single nucleotide polymorphisms in candidate genes residing under quantitative trait loci in beef cattle - (Abstract Only)
Casas, E., Wheeler, T.L., Shackelford, S.D., Bennett, G.L., Smith, T.P.L. 2009. Association of single nucleotide polymorphisms in candidate genes residing under quantitative trait loci in beef cattle [abstract]. Plant and Animal Genome XVII Conference Proceedings. Poster No. P477.
Extreme muscle development in sheep heterozygous for both myostatin and callipyge mutations Reprint Icon - (Abstract Only)
Smith, T.P., Freking, B.A., Shackelford, S.D., King, D.A., Wheeler, T.L., Leymaster, K.A. 2009. Extreme muscle development in sheep heterozygous for both myostatin and callipyge mutations. Plant and Animal Genome Conference Proceedings. Jan. 10-14, 2009. San Diego, CA. Abstract W084.
Single nucleotide polymorphism discovery in rainbow trout using reduced representation libraries - (Abstract Only)
Castano, C., Smith, T.P., Wiedmann, R.T., Yao, J., Rexroad III, C.E. 2009. Single nucleotide polymorphism discovery in rainbow trout using reduced representation libraries. Meeting Abstract.
Studies on cattle genomic structural variation provide insights into ruminant speciation and adaptation - (Abstract Only)
Liu, G., Zhu, B., Alexander, L.J., Matukumalli, L.K., Van Tassell, C.P., Sonstegard, T.S., Nonneman, D.J., Keele, J.W. 2009. Studies on cattle genomic structural variation provide insights into ruminant speciation and adaptation. [abstract]. Plant and Animal Genome Conference Proceedings. W093.
MicroRNA expression profile in bovine cumulus-oocyte complexes during late oogenesis - (Abstract Only)
Miles, J.R., McDaneld, T.G., Wiedmann, R.T., Cushman, R.A., Echternkamp, S.E., Vallet, J.L., Smith, T.P.L. 2009. MicroRNA expression profile in bovine cumulus-oocyte complexes during late oogenesis [abstract]. Reproduction, Fertility and Development. 21(1):186 (Abstract #174).
Prevalence of the prion gene E211K variant in U.S. cattle - (Peer Reviewed Journal)
Heaton, M.P., Keele, J.W., Harhay, G.P., Richt, J., Koohmaraie, M., Wheeler, T.L., Shackelford, S.D., Casas, E., King, D.A., Sonstegard, T.S., Van Tassell, C.P., Neibergs, H.L., Chase, C.C., Kalbfleisch, T.S., Smith, T.P., Clawson, M.L., Laegreid, W.W. 2008. Prevalence of the prion gene E211K variant in U.S. cattle. BioMed Central (BMC) Veterinary Research [journal online]. 4:25. Available: (http://www.biomedcentral.com/1746-6148/4/25).
A sequencing strategy for identifying variation throughout the prion gene of BSE-affected cattle - (Peer Reviewed Journal)
Clawson, M.L., Heaton, M.P., Keele, J.W., Smith, T.P., Harhay, G.P., Richt, J., Laegreid, W.W. 2008. A sequencing strategy for identifying variation throughout the prion gene of BSE-affected cattle. BMC Research Notes [journal online]. 1:32. Available: http://www.biomedcentral.com/1756-0500/1/32.
MicroRNA profiles of the fetal pig during skeletal muscle development Reprint Icon - (Abstract Only)
McDaneld, T.G., Wiedmann, R.T., Miles, J.R., Smith, T.P. 2008. MicroRNA profiles in skeletal muscle of fetal pig. XXXI Animal Genetics International Conference Proceedings. Poster #2206.
Present and future applications of DNA technologies to improve beef production - (Literature Review)
Allan, M.F., Smith, T.P. 2008. Present and future applications of DNA technologies to improve beef production. Meat Science. 80(1):79-85.
High throughput SNP discovery and validation in the pig: towards the development of a high density swine SNP chip - (Abstract Only)
Ramos, A.M., Crooijmans, R.P., Fonseca, A., Kerstens, H., Bendixen, C., Hedegaard, J., Rohrer, G.A., Smith, T.P., Van Tassell, C.P., Taylor, J.F., Rothschild, M., Nonneman, D.J., Beever, J., Archibald, A., Schook, L., Groenen, M.A. 2008. High throughput SNP discovery and validation in the pig: towards the development of a high density swine SNP chip. Proc., 2nd European Conference on Pig Genomics, June 4-5, 2008, Ljubljana, Slovenia. Poster #2234.
Markers on bovine chromosome 20 associated with fat related traits and incidence of contracting bovine respiratory disease Reprint Icon - (Abstract Only)
Garcia, M.D., Matukumalli, L., Wheeler, T.L., Shackelford, S.D., Koohmaraie, M., Smith, T.P., Casas, E. 2008. Markers on bovine chromosome 20 associated with fat related traits and incidence of contracting bovine respiratory disease [abstract]. Journal of Animal Science Supplement. 86(E-Suppl. 2):210. Abstract #W54.
Analysis of Cattle Copy Number Variation Reveals Insights into the Evolution of Ruminants - (Abstract Only)
Liu, G., Keele, J.W., Van Tassell, C.P., Sonstegard, T.S., Li, R.W., Alexander, L.J., Matukumalli, L.K., Smith, T.P., Gasbarre, L.C. 2008. Analysis of cattle copy number variation reveals insights into the evolution of ruminants. [abstract]. 2008 meeting on the Biology of Genomes, May 6-10, 2007, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. p197.
Development and Applications of a Bovine 50,000 SNP Chip - (Abstract Only)
Taylor, J.F., Sonstegard, T.S., Van Tassell, C.P., Matukumalli, L., Smith, T.P., Allen, M.L. 2008. Development and Applications of a Bovine 50,000 SNP Chip. International Symposium of Animal Functional Genomics.
Microbial Community Structure of Feedlot Cattle Feces - (Abstract Only)
Durso, L.M., Harhay, G.P., Clawson, M.L., Laegreid, W.W., Bono, J.L., Keen, J.E., Smith, T.P. Microbial community structure of feedlot cattle feces. In: Proceedings of the 108th General Meeting of the American Society for Microbiology, June 1-5, 2008, Boston, Massachusetts. 2008 CDROM.
Effect of porcine reproductive and respiratory syndrome virus on porcine alveolar macrophage function as determined using serial analysis of gene expression (SAGE) - (Peer Reviewed Journal)
Miller, L.C., Harhay, G.P., Lager, K.M., Smith, T.P., Neill, J.D. 2008. Effect of porcine reproductive and respiratory syndrome virus on porcine alveolar macrophage function as determined using serial analysis of gene expression (SAGE). Developments in Biologicals. 132:169-174.
Association of a bovine prion gene haplotype with atypical BSE - (Peer Reviewed Journal)
Clawson, M.L., Richt, J., Baron, T., Biacabe, A., Czub, S., Heaton, M.P., Smith, T.P., Laegreid, W.W. 2008. Association of a bovine prion gene haplotype with atypical BSE. PLoS One [serial online]. 3(3):e1830. Available: http://www.plosone.org.
Application of the BovineSNP50 assay for QTL mapping and prediction of genetic merit in Holstein cattle - (Abstract Only)
Schnabel, R.D., Van Tassell, C.P., Matukumalli, L., Sonstegard, T.S., Smith, T.P., Moore, S.S., Lawley, C.T., Taylor, J.F. 2008. Application of the BovineSNP50 assay for QTL mapping and prediction of genetic merit in Holstein cattle. Plant and Animal Genome Conference Proceedings.
A high-resolution map of copy number variation in the cattle genome - (Abstract Only)
Liu, G., Keele, J.W., Van Tassell, C.P., Sonstegard, T.S., Alexander, L.J., Li, R.W., Matukumalli, L.K., Smith, T.P., Gasbarre, L.C. 2008. A high-resolution map of copy number variation in the cattle genome. Plant and Animal Genome VX Conference Abstracts. The NRI Animal Genome PD Meeting, San Diego, CA. p84.
Analysis of copy number variation in the bovine genome - (Abstract Only)
Liu, G., Van Tassell, C.P., Sonstegard, T.S., Li, R.W., Alexander, L.J., Keele, J.W., Matukumalli, L.K., Brown, T., Smith, T.P., Gasbarre, L.C. 2008. Analysis of copy number variation in the bovine genome. Plant and Animal Genome (PAG) XVI Conference. San Diego, CA. p517.
Characterization of the Cattle HapMap Population using the Illumina Bovine-50K SNP Chip - (Abstract Only)
Matukumalli, L.K., Schnabel, R.D., Lawley, C.T., Sonstegard, T.S., Smith, T.P., Moore, S.S., Taylor, J.F., Van Tassell, C.P. 2008. Characterization of the Cattle HapMap Population using the Illumina Bovine-50K SNP Chip. Plant and Animal Genome Conference.
MicroRNA (MiRNA) technology in livestock: expression profiling of bovine oocyte and developmental stages of porcine skeletal muscle - (Proceedings)
Mcdaneld, T.G., Wiedmann, R.T., Miles, J.R., Cushman, R.A., Vallet, J.L., Smith, T.P. 2007. MicroRNA (MiRNA) technology in livestock: expression profiling of bovine oocyte and developmental stages of porcine skeletal muscle. Conference Proc., National Swine Improvement Federation Conference & Ann. Mtg., Dec. 5-7, 2007. Kansas City, MO, NSIF Volume 32, www.nsif.com.
SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries - (Peer Reviewed Journal)
Van Tassell, C.P., Smith, T.P., Matukumalli, L.K., Taylor, J.F., Schnabel, R.D., Lawley, C.T., Haudenschild, C., Moore, S.S., Warren, W.C., Sonstegard, T.S. 2008. SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nature Methods. 5:247-252.
Gene Expression Profiling of Porcine Reproductive and Respiratory Syndrome Virus Infected Porcine Alveolar Macrophages - (Abstract Only)
Miller, L.C., Harhay, G.P., Lager, K.M., Smith, T.P., Neill, J.D. 2007. Gene expression profiling of PRRSV-infected porcine alveolar macrophages [abstract]. Porcine Reproductive and Respiratory Syndrome International Symposium. Paper No. 47.
Detection of germline and somatic copy number variations in cattle - (Proceedings)
Liu, G., Van Tassell, C.P., Sonstegard, T.S., Li, R.W., Alexander, L.J., Keele, J.W., Matukumalli, L.K., Smith, T.P., Gasbarre, L.C. 2008. Detection of germline and somatic copy number variations in cattle. Developments in Biologicals. 132:231-237.
Prevalence of the prion gene E211K variant in U.S. cattle - (Abstract Only)
Heaton, M.P., Keele, J.W., Harhay, G.P., Richt, J., Koohmaraie, M., Wheeler, T.L., Shackelford, S.D., Casas, E., King, D.A., Sonstegard, T.S., Van Tassell, C.P., Neibergs, H.L., Chase, C.C., Kalbfleisch, T.S., Smith, T.P., Clawson, M.L., Laegreid, W.W. 2008. Prevalence of the prion gene E211K variant in U.S. cattle (abstract). Plant and Animal Genome XVI Conference. Poster No. P538.
Generation of large numbers of SNP in cattle by coupling reduced genome representation with high throughput sequencing - (Abstract Only)
Smith, T.P., Matukumalli, L., Sonstegard, T.S., Schnabel, R., Taylor, J., Haudenschild, C., Lawley, C., Moore, S., Van Tassell, C.P. 2008. Generation of large numbers of SNP in cattle by coupling reduced genome representation with high throughput sequencing (abstract). Plant and Animal Genome XVI Conference Proceedings. Poster No. P90.
Description and analysis of the Bovine Gene Atlas - An extensive compendium of bovine transcript profiles - (Abstract Only)
Harhay, G.P., Keele, J.W., Smith, T.P., Alexander, L.J., Matukumalli, L.K., Schroeder, S.G., Liu, G., Van Tassell, C.P., Sonstegard, T.S. 2008. Description and analysis of the Bovine Gene Atlas - An extensive compendium of bovine transcript profiles (abstract). Plant and Animal Genome XVI Conference. Poster No. P516.
Bovine copy number variation and its implication in animal health - (Abstract Only)
Liu, G., Van Tassell, C.P., Sonstegard, T.S., Alexander, L.J., Keele, J.W., Matukumalli, L.K., Smith, T.P., Gasbarre, L.C. 2007. Bovine copy number variation and its implication in animal health. [ abstract]. International Symposium on Animal Genomics for Animal Health. pp. 32.
A physical map of the bovine genome - (Peer Reviewed Journal)
Snelling, W.M., Chiu, R., Schein, J.E., Hobbs, M., Abbey, C.A., Adelson, D.L., Aerts, J., Bennett, G.L., Bosdet, I.E., Boussaha, M., Brauning, R., Caetano, A.R., Costa, M.M., Crawford, A.M., Dalrymple, B.P., Eggen, A., Everts-Van Der Wind, A., Floriot, S., Gautier, M., Gill, C.A., Green, R.D., Holt, R., Jann, O., Jones, S.J., Kappes, S.M., Keele, J.W., De Jong, P.J., Larkin, D.M., Lewin, H.A., Mcewan, J.C., Mckay, S., Marra, M.A., Mathewson, C.A., Matukumalli, L.K., Moore, S.S., Murdoch, B., Nicholas, F.W., Osoegawa, K., Roy, A., Salih, H., Schibler, L., Schnabel, R.D., Silveri, L., Skow, L.C., Smith, T.P., Sonstegard, T.S., Taylor, J.F., Tellam, R., Van Tassell, C.P., Williams, J.L., Womack, J.E., Wye, N.H., Yang, G., Zhao, S. 2007. A physical map of the bovine genome. Genome Biology. 8:R165 (17 pp).
Assessing the association of single nucleotide polymorphisms at the thyroglobulin gene with carcass traits in beef cattle Reprint Icon - (Peer Reviewed Journal)
Casas, E., White, S.N., Shackelford, S.D., Wheeler, T.L., Koohmaraie, M., Bennett, G.L., Smith, T.P.L. 2007. Assessing the association of single nucleotide polymorphisms at the thyroglobulin gene with carcass traits in beef cattle. Journal of Animal Science. 85:2807-2814.
Initial analysis of copy number variation in the cow genome - (Abstract Only)
Liu, G., Van Tassell, C.P., Sonstegard, T.S., Li, R.W., Alexander, L.J., Keele, J.W., Matukumalli, L.K., Smith, T.P., Gasbarre, L.C. 2007. Initial analysis of copy number variation in the cow genome. [abstract}. Gordon Research Conference Proceedings.
The u-Calpain and Calpastatin Tenderness Markers are Predictive of Tenderness Variation Among Samples Obtained From Commercial U.S. Select Beef Carcasses - (Abstract Only)
Shackelford, S.D., Casas, E., Smith, T.P., Wheeler, T.L., Koohmaraie, M. 2007. The u-calpain and calpastatin tenderness markers are predictive of tenderness variation among samples obtained from commercial U.S. select beef carcasses. Proc. 60th Reciprocal Meat Conference, June 17-20, 2007, Brookings, SD. http://www.meatscience.org/pubs/rmcarchv/2007/presentations/RMC_2007_060_4_073_Shackelford.pdf
The role of microRNAs in muscle development - (Abstract Only)
Smith, T.P.L., McDaneld, T.G., Doumit, M.E., Matukumalli, L.K., Sonstegard, T.S., Coutinho, L.L., Wiedmann, R.T. The role of microRNAs in muscle development. Journal of Animal Science (Suppl. 1):637. 2007
Construction and application of a bovine high-density SNP assay - (Abstract Only)
Van Tassell, C.P., Matukumalli, L.K., Taylor, C., Smith, T.P., Sonstegard, T.S., Schnabel, R., Silva, M.V., Wiggans, G.R., Liu, G., Moore, S., Taylor, J.F. 2007. Construction and application of a bovine high-density SNP assay. Joint Abstracts of the American Dairy Science and Society of Animal Science.
Creation of a Gene Atlas in cattle using sequence-based transcriptional profiling - (Abstract Only)
Sonstegard, T.S., Keele, J.W., Harhay, G.P., Smith, T.P., Matukumalli, L.K., Van Tassell, C.P., Liu, G., Alexander, L.J. 2007. Creation of a Gene Atlas in cattle using sequence-based transcriptional profiling. [abstract] Joint Abstracts of the American Dairy Science and Society of Animal Science.
Discovery and Profiling of Bovine Micrornas from Immune Related and Embryonic Tissues - (Peer Reviewed Journal)
Coutinho, L.L., Matukumalli, L.K., Sonstegard, T.S., Van Tassell, C.P., Gasbarre, L.C., Capuco, A.V., Smith, T.P. 2007. Discovery and profiling of bovine micrornas from immune related and embryonic tissues. Physiological Genomics. 29(1):35-43.
A second generation radiation hybrid map to aid the assembly of the bovine genome sequence - (Peer Reviewed Journal)
Jann, O.C., Aerts, J., Jones, M., Hastings, N., Law, A., Mckay, S., Marques, E., Prasad, A., Yu, J., Moore, S.S., Florita, S., Mahe, M., Eggen, A., Silveri, L., Negrini, R., Milanesi, E., Ajmone-Marsan, P., Vakebtubu, A., Marchitelli, C., Janitz, M., Herwig, R., Hennig, S., Savarese, M., Gorni, C., Connor, E.E., Sonstegard, T.S., Smith, T.P., Drogemuller, C., Williams, J. 2006. A second generation radiation hybrid map to aid the assembly of the bovine genome sequence. BMC Genomics. 7:283-298.
Prion gene haplotypes of U.S. cattle Reprint Icon - (Peer Reviewed Journal)
Clawson, M.L., Heaton, M.P., Keele, J.W., Smith, T.P., Harhay, G.P., Laegreid, W.W. 2006. Prion gene haplotypes of U.S. cattle. BioMed Central (BMC) Genetics. 7:51.
Genome adaptations of a tripartite motif protein for retroviral defense in cattle and sheep - (Abstract Only)
Smith, T.P., Heaton, M.P., Snelling, W.M., Ylinen, L., Keckesova, Z., Webb, B.L., Towers, G.J. 2007. Genome adaptations of a tripartite motif protein for retroviral defense in cattle and sheep [abstract]. Plant and Animal Genome XV Conference. Poster No. P540.
Polymorphisms and haplotype structure of bovine PRND (doppel) and PRNT - (Abstract Only)
Laegreid, W.W., Clawson, M.L., Smith, T.P., Harhay, G.P., Keele, J.W., Heaton, M.P. 2007. Polymorphisms and haplotype structure of bovine PRND (doppel) and PRNT [abstract]. Plant and Animal Genome XV Conference. Poster No. P535.
A marker set for parentage-based DNA traceback in beef and dairy cattle - (Abstract Only)
Heaton, M.P., Snelling, W.M., Smith, T.P., Keele, J.W., Harhay, G.P., Wiedmann, R.T., Bennett, G.L., Freking, B.A., Van Tassell, C.P., Sonstegard, T.S., Gasbarre, L.C., Moore, S.S., Murdoch, B., Mckay, S.D., Kalbfleisch, T., Laegreid, W.W. 2007. A marker set for parentage-based DNA traceback in beef and dairy cattle [abstract]. Plant and Animal Genome XV Conference. Poster No. P516.
A rapid sequence-based method for comprehensive polymorphism identification within a 25.2-kb region of the bovine prion gene in BSE-affected cattle - (Abstract Only)
Clawson, M.L., Heaton, M.P., Keele, J.W., Smith, T.P., Harhay, G.P., Laegreid, W.W. 2007. A rapid sequence-based method for comprehensive polymorphism identification within a 25.2-kb region of the bovine prion gene in BSE-affected cattle [abstract]. Plant and Animal Genome XV Conference. Poster No. P533.
Association of a Single Nucleotide Polymorphism in Spp1 with Growth Traits and Twinning in a Cattle Population Selected for Twinning Rate - (Peer Reviewed Journal)
Allan, M.F., Thallman, R.M., Cushman, R.A., Echternkamp, S.E., White, S.N., Kuehn, L.A., Casas, E., Smith, T.P. 2007. Association of a single nucleotide polymorphism in spp1 with growth traits and twinning in a cattle population selected for twinning rate. Journal of Animal Science. 85(2):341-347.
Evaluation in beef cattle of six deoxyribonucleic acid markers developed for dairy traits reveals an osteopontin polymorphism associated with postweaning growth. Reprint Icon - (Peer Reviewed Journal)
White, S.N., Casas, E., Allan, M.F., Keele, J.W., Snelling, W.M., Wheeler, T.L., Shackelford, S.D., Koohmaraie, M., Smith, T.P. 2007. Evaluation in beef cattle of six deoxyribonucleic acid markers developed for dairy traits reveals an osteopontin polymorphism associated with post-weaning growth. Journal of Animal Science. 85:1-10.
Isolation of An Active Lv1 Gene from Cattle Indicates That Tripartite Motif Protein-Mediated Innate Immunity to Retroviral Infection Is Widespread among Mammals Reprint Icon - (Peer Reviewed Journal)
Ylinen, L.M., Keckesova, Z., Webb, B.L., Gifford, R.J., Smith, T.P., Towers, G.J. 2006. Isolation of an active Lv1 gene from cattle indicates that tripartite motif protein-mediated innate immunity to retroviral infection is widespread among mammals. Journal of Virology. 80(15):7332-7338.
Expression Profiles of Micro-Rnas in Swine Muscle Development Reprint Icon - (Abstract Only)
Wiedmann, R.T., Doumit, M.E., Matukumalli, L.K., Sonstegard, T.S., Coutinho, L.L., Nonneman, D.J., Smith, T.P. 2006. Expression profiles of micro-RNAs in swine muscle development. (Abstract) International Conference on Animal Genetics. p. 70. Abstract #C278.
Isolation of the First Non-Primate Trim5-Alpha from Cattle Indicates That Trim5-Alpha Mediated Innate Immunity to Retroviral Infection May Be Widespread among Mammals - (Abstract Only)
Schaller, T., Ylinen, L.M., Keckesova, Z., Webb, B.L., Smith, T.P., Towers, G.J. 2006. Isolation of the first non-primate trim5-alpha from cattle indicates that trim5-alpha mediated innate immunity to retroviral infection may be widespread among mammals. Proc., 31st Annual Meeting on Retroviruses, Cold Spring Harbor Lab, Cold Spring Harbor, NY, May 23-28, 2006.
Comprehensive Search of Bovine Micrornas Expressed in Immune and Gut Tissues by Deep Sequencing - (Abstract Only)
Sonstegard, T.S., Matukumalli, L.K., Coutinho, L.L., Liu, G., Gasbarre, L.C., Smith, T.P. 2006. Comprehensive search of bovine micrornas expressed in immune and gut tissues by deep sequencing [abstract]. International Conference on Animal Genetics. pp. C354.
Profiling of Bovine Micrornas from Immune Related and Embryonic Tissues. - (Abstract Only)
Matukumalli, L.K., Coutinho, L.L., Sonstegard, T.S., Van Tassell, C.P., Gasbarre, L.C., Capuco, A.V., Smith, T.P. 2006. Profiling of bovine micrornas from immune related and embryonic tissues [abstract]. International Conference on Animal Genetics. pp. C329.
Identification of Bovine Micrornas - (Abstract Only)
Matukumalli, L.K., Coutinho, L.L., Sonstegard, T.S., Van Tassell, C.P., Gasbarre, L.C., Capuco, A.V., Smith, T.P. 2006. Identification of bovine micrornas [abstract]. Cold Springs Harbor Laboratories 71 Symposium of Regulatoary RNAs. Cold Spring Harbor, NY. Number 214.
Characterization of Boivne Micrornas Expressed in Immune and Gut Tissues by Deep Sequencing - (Abstract Only)
Matukumalli, L.K., Coutinho, L.L., Sonstegard, T.S., Liu, G., Gasbarre, L.C., Smith, T.P. 2006. Characterization of boivne micrornas expressed in immune and gut tissues by deep sequencing [abstract] 17th Annual BARC Poster Day. Beltsville, MD. No 27.
Identification and Profiling of Bovine Micrornas from Immune Related and Embryonic Tissues. - (Abstract Only)
Coutinho, L.L., Matukumalli, L.K., Sonstegard, T.S., Van Tassell, C.P., Gasbarre, L.C., Capuco, A.V., Smith, T.P. 2006. Identification and profiling of bovine micrornas from immune related and embryonic tissues [abstract]. 17th Annual BARC Poster Day, Beltsville, MD. No 6.
Characterization of 954 Bovine Full-Cds Cdna Sequences - (Peer Reviewed Journal)
Harhay, G.P., Sonstegard, T.S., Keele, J.W., Heaton, M.P., Clawson, M.L., Snelling, W.M., Wiedmann, R.T., Van Tassell, C.P., Smith, T.P. 2005. Characterization of 954 bovine full-CDS cDNA sequences. Biomed Central (BMC) Genomics 6:166 (11 pp).
Callipyge Mutation Affects Gene Expression in Cis: a Potential Role for Chromatin Structure - (Peer Reviewed Journal)
Murphy, S.K., Nolan, C.M., Huang, Z., Kucera, K.S., Freking, B.A., Smith, T.P.L., Leymaster, K.A., Weidman, J.R., Jirtle, R.L. 2006. Callipyge mutation affects gene expression in cis: A potential role for chromatin structure. Genome Research. 16:340-346.
High Density Ests Based Bovine Physical Maps and Their Use to Construct Comparative Maps and Inform the Bovine Genome Sequence Assembly - (Abstract Only)
Williams, J.L., Aerts, J., Law, A., Jann, O., Janitz, M., Hennig, S., Eggen, A., Floriot, S., Ajmone-Marsan, P., Milanse, E., Valentini, A., Marchitelli, C., Mckay, S., Prasad, A., Yu, J., Moore, S.S., Drogemuller, C., Connor, E.E., Sonstegard, T.S., Stone, R.T., Smith, T.P. 2006. High density ESTs based bovine physical maps and their use to construct comparative maps and inform the bovine genome sequence assembly[abstracat]. Plant and Animal Genome XIV:55. Number W214.
Linkage Disequilibrium and Haplotype Structure in the Prion Gene of U.S. Beef and Dairy Cattle - (Abstract Only)
Clawson, M.L., Heaton, M.P., Keele, J.W., Smith, T.P., Laegreid, W.W. 2006. Linkage disequilibrium and haplotype structure in the prion gene of U.S. beef and dairy cattle (abstract). Plant and Animal Genome Conference Proceedings. p. 145.
Testing for Interactions Between Calpastatin and U-Calpain Markers in Beef Cattle on Tenderness Traits - (Peer Reviewed Journal)
Casas, E., White, S.N., Wheeler, T.L., Shackelford, S.D., Koohmaraie, M., Riley, D.G., Chase, C.C. Jr., Johnson, D.D., Smith, T.P. 2006. Effects of calpastatin and u-calpain markers in beef cattle on tenderness traits. Journal of Animal Science. 84:520-525.
Testing for Interactions Between Calpastatin and U-Calpain Markers in Beef Cattle on Tenderness Traits Reprint Icon - (Abstract Only)
Casas, E., White, S.N., Wheeler, T.L., Shackelford, S.D., Koohmaraie, M., Riley, D.G., Chase, C.C., Johnson, D.D., Smith, T.P. 2006. Testing for interactions between Calpastatin and u-Calpain markers in beef cattle on tenderness traits [abstract]. Midwestern Section of the American Society of Animal Science. 84(Suppl. 2):135. Paper No. 329.
Two Promoters Coordinate Transcription from the Human Lhx3 Gene: Regulation by Nuclear Factor I and Sp1 - (Peer Reviewed Journal)
Yaden, B.C., Garcia Iii, M., Smith, T.P., Rhodes, S.J. Two Promoters Mediate Transcription from the Human LHX3 gene: Regulation by Nuclear Factor 1 and Specificity Protein 1. Endocrinology 147:324-337. 2006.
Assignment of 12 Genes to Porcine Chromosome 1q by Linkage and Radiation Hybrid Mapping - (Peer Reviewed Journal)
Nonneman, D.J., Smith, T.P., Freking, B.A., Rohrer, G.A. 2005. Assignment of 12 genes to porcine chromosome 1q by linkage and radiation hybrid mapping. Anim. Genet. 36:532-533. 2005.
Identification of Genetic Markers for Fat Deposition and Meat Tenderness on Bovine Chromosome 5: Development of a Low Density Snp Map - (Peer Reviewed Journal)
Stone, R.T., Casas, E., Smith, T.P.L., Keele, J.W., Harhay, G.P., Bennett, G.L., Koohmaraie, M., Wheeler, T.L., Shackelford, S.D., Snelling, W.M. 2005. Identification of genetic markers for fat deposition and meat tenderness on bovine chromosome 5: Development of a low-density single nucleotide polymorphism map. Journal of Animal Science. 83:2280-2288.
A New Snp in Capn1 Extends the Current Tenderness Marker Test to Include Cattle of Bos Indicus, Bos Taurus, and Crossbred Descent - (Peer Reviewed Journal)
White, S.N., Casas, E., Wheeler, T.L., Shackelford, S.D., Koohmaraie, M., Riley, D.G., Chase, C.C., Johnson, D.D., Keele, J.W., Smith, T.P. 2005. A new snp in capn1 extends the current tenderness marker test to include cattle of bos indicus, bos taurus, and crossbred descent. Journal of Animal Science. 83:2001-2008.
Linkage Mapping Bovine Est-Based Snp - (Peer Reviewed Journal)
Snelling, W.M., Casas, E., Stone, R.T., Keele, J.W., Harhay, G.P., Bennett, G.L., Smith, T.P. 2005. Linkage mapping bovine EST-based SNP. Biomed Central (BMC) Genomics 6:74.
Ut-B Is Expressed in Bovine Rumen: Potential Role in Ruminal Urea Transport - (Peer Reviewed Journal)
Stewart, G.S., Grahman, C., Cattell, S., Smith, T.P., Simmons, N.L., Smith, C.P. 2005. UT-B is expressed in bovine rumen: potential role in ruminal urea transport. American Journal of Physiology. 289:605-612.
Immunogenomics and the Transition Dairy Cow: Physiological Insights and Future Possibilities for Improving Animal Health. - (Abstract Only)
Burton, J.L., Madsen, S.A., Chang, L.C., Weber, P.S., Coussens, P.M., Rosa, G., Matukumalli, L.K., Sonstegard, T.S., Smith, T.P. 2005. Immunogenomics and the transition dairy cow: physiological insights and future possibilities for improving animal health. ADSA/ASAS Joint Meeting, Cincinnati, OH, Abstract 17
Abnormal Postnatal Maintenance of Elevated Prenatal Dlk1 Levels in Callipyge Sheep - (Peer Reviewed Journal)
Murphy, S.K., Freking, B.A., Smith, T.P., Nolan, C.M., Wylie, A.A., Evans, H.K., Jirtle, R.L. 2005. Abnormal postnatal maintenance of elevated prenatal DLK1 levels in callipyge sheep. Mammalian Genome. 16:171-183.
Alignment Genomes Across Species - (Abstract Only)
Williams, J.L., Hastings, N., Jann, O., Law, A., Stone, R.T., Snelling, W.M., Connor, E.E., Sonstegard, T.S., Smith, T.P. 2005. Alignment genomes across species [abstract]. Plant and Animal Genome XVII. p. 241.
A New Snp Marker in Capn1 Is Associated with Tenderness in Cattle of Indicine, Taurine, and Admixed Descent - (Abstract Only)
White, S.N., Casas, E., Wheeler, T.L., Shackelford, S.D., Koohmaraie, M., Riley, D.G., Chase, C.C., Johnson, D.D., Keele, J.W., Smith, T.P. 2005. A new snp marker in capn1 is associated with tenderness in cattle of indicine, taurine, and admixed descent. Proc., Plant & Animal Genome XIII, San Diego, CA. P528. p. 203. 2005.
Assessment of Single Nucleotide Polymorphisms in Genes Residing on Chromosomes 14 and 29 for Association with Carcass Composition Traits in Bos Indicus Cattle - (Abstract Only)
Chase, C.C. Jr., Casas, E., White, S.N., Riley, D.G., Smith, T.P., Brenneman, R.A., Olson, T.A., Johnson, D.D., Coleman, S.W., Bennett, G.L. 2005. Assessment of single nucleotide polymorphisms in genes residing on chromosomes 14 and 29 for association with carcass composition traits in Bos indicus cattle [Abstract]. Plant and Animal Genome XIII, January 15-19, 2005, San Diego, CA. p. 203.
Integrating Linkage and Radiation Hybrid Mapping Data for Bovine Chromosome 15 - (Peer Reviewed Journal)
Snelling, W.M., Gautier, M., Keele, J.W., Smith, T.P., Stone, R.T., Harhay, G.P., Bennett, G.L., Ihara, N., Takasuga, A., Takeda, H., Sugimoto, Y., Eggen, A. Integrating linkage and radiation hybrid mapping data for bovine chromosome 15. Biomed Central (BMC) Genomics. 5:77. 2004.
Assessment of Single Nucleotide Polymorphisms in Genes Residing on Chromosomes 14 and 29 for Association with Carcass Composition Traits in Bos Indicus Cattle - (Peer Reviewed Journal)
Casas, E., White, S.N., Riley, D.G., Smith, T.P., Brenneman, R.A., Olson, T.A., Johnson, D.D., Coleman, S.W., Bennett, G.L., Chase, C.C. 2005. Assessment of single nucleotide polymorphisms in genes residing on chromosomes 14 and 29 for association with carcass composition traits in bos indicus cattle. Journal of Animal Science. 83:13-19.
Regulatory and Coding Sequences of the Pituitary-Specific Transcription Factor, Prop1 Are Evolutionarily and Functionally Conserved - (Abstract Only)
Camper, S.A., Ward, R.D., Cho, M., Raetzman, L.T., Esposito, C., Rubin, E.M., Smith, T.P., Rhodes, S.J., Lyons, R.H. Regulatory and coding sequences of the pituitary-specific transcription factor, PROP1 are evolutionarily and functionally conserved. Proc., 18th Int. Mouse Genome Conference, Seattle, WA, 10/18-21/2004. Abstract.
Association of Markers in the Bovine Capn1 Gene with Meat Tenderness in Large Crossbred Populations That Sample Influential Industry Sires - (Peer Reviewed Journal)
Page, B.T., Casas, E., Quaas, R.L., Thallman, R.M., Wheeler, T.L., Shackelford, S.D., Koohmaraie, M., White, S.N., Bennett, G.L., Keele, J.W., Dikeman, M.E., Smith, T.P. Association of markers in the bovine capn1 gene with meat tenderness in large crossbred populations that sample influential industry sires. Journal of Animal Science. 82:3474-3481. 2004.
The Application of Molecular Genetics in a Commercial Environment to Improve Production and Carcass Composition in Cattle - (Proceedings)
Casas, E., Thallman, R.M., Smith, T.P. 2004. The application of molecular genetics in a commercial environment to improve production and carcass composition in cattle. Advances in Animal Biotechnology and Their Applications in the National Livestock Industry, Symposium & Compendium Series Proceedings. October 13-15, 2004, Villarica, Chile. 10:53-70.
Analysis of Linkage Disequilibrium in the Region Surrounding a Quantitative Trait Locus for Growth in Cattle - (Abstract Only)
Smith, T.P., Snelling, W.M., Casas, E. 2004. Analysis of linkage disequilibrium in the region surrounding a quantitative trait locus for growth in cattle. Proc., Genome Sequencing & Analysis Conference XVI, Washington, DC, Sept. 27-30, 2004. Abstract P-56. p. 46.
Database Directed Full-Length Cdna Generation Using Est Data from Normalized Bovine Cdna Libraries - (Abstract Only)
Harhay, G.P., Smith, T.P., Sonstegard, T.S., Clawson, M.L. 2004. Database directed full-length cDNA generation using EST data from normalized bovine cDNA libraries. Proc., 29th International Conference on Animal Genetics (ISAG), Tokyo, Japan. September 11-16, 2004. Abstract A022, p. 37.
Generation of a Bovine Oocyte Cdna Libarary and Microarray: Resources for Identification of Genes Important for Follicular Development and Early Embryogenesis - (Peer Reviewed Journal)
Yao, J., Ren, X., Ireland, J.J., Coussens, P.M., Smith, T.P., Smith, G.W. 2004. Generation of a bovine oocyte cDNA libarary and microarray: resources for identification of genes important for follicular development and early embryogenesis. Physiological Genomics. 19:84-92. 2004.
Database Directed Full-Length Cdna Generation from Normalized Bovine Cdna Libraries - (Abstract Only)
Harhay, G.P., Sonstegard, T.S., Clawson, M.L., Smith, T.P. 2004. Database directed full-length cDNA generation from normalized bovine cDNA libraries. International Genome Sequencing and Analysis Conference XVI, Washington, DC. September 27-30, 2004. Poster Abstract #49.
Association of Myostatin on Early Calf Mortality, Growth, and Carcass Composition Traits in Crossbred Cattle - (Peer Reviewed Journal)
Casas, E., Bennett, G.L., Smith, T.P., Cundiff, L.V. 2004. Association of myostatin on early calf mortality, growth, and carcass composition traits in crossbred cattle. Journal of Animal Science. 82:2913-1918.
Genetics: Molecular - (Other)
Nonneman, D.J., Smith, T.P. 2004. Genetics: Molecular. Encyclopedia of Animal Science. p. 466-468.
Meat Quality and the Callipyge Gene, Consumer Acceptance and Final Product - (Proceedings)
Freking, B.A., Smith, T.P., Leymaster, K.A. 2004. Meat quality and the callipyge gene, consumer acceptance and final product. In: Proceedings of the 7th World Sheep and Wool Congress 2004, July 17-24, 2004, Quebec, Canada. p. 92-102.
Conserved Amino Acid Sequences Confer Nuclear Localization Upon the Prophet of Pit-1 Pituitary Transcription Factor Protein - (Peer Reviewed Journal)
Guy, J.C., Hunter, C.S., Showalter, A.A., Smith, T.P., Charoonpatrapong, K., Sloop, K.W., Bidwell, J.P., Rhodes, S.J. 2004. Conserved amino acid sequences confer nuclear localization upon the prophet of Pit-1 pituitary transcription factor protein. Gene. 336:263-273.
Correlation of Sry and Zfy Alleles of the Y Chromosome in U.S. Beef Cattle - (Abstract Only)
CLAWSON, M.L., HEATON, M.P., FOX, J.M., CHITKO MCKOWN, C.G., SMITH, T.P., LAEGREID, W.W. CORRELATION OF SRY AND ZFY ALLELES OF THE Y CHROMOSOME IN U.S. BEEF CATTLE. PLANT AND ANIMAL GENOME CONFERENCE PROCEEDINGS. 2004. ABSTRACT NO. P310.
Genetic Risk Factors for Failure of Passive Transfer in the Bovine Neonatal Fc Receptor - (Abstract Only)
LAEGREID, W.W., CLAWSON, M.L., HEATON, M.P., KEEN, J.E., CHITKO MCKOWN, C.G., FOX, J.M., SMITH, T.P., SNELLING, W.M., KEELE, J.W. GENETIC RISK FACTORS FOR FAILURE OF PASSIVE TRANSFER IN THE BOVINE NEONATAL FC RECEPTOR. PLANT AND ANIMAL GENOME CONFERENCE PROCEEDINGS. ABSTRACT NO. P642.
Development and Testing of a High-Density Cdna Microarray Resource for Cattle - (Abstract Only)
Suchyta, S.P., Sipkovsky, S., Kruska, R., Jeffers, A., Mcnulty, A., Coussens, M.J., Tempelman, R.J., Halgren, R.A., Saama, P.M., Bauman, D.E., Boisclair, Y.R., Burton, J.L., Collier, R.J., Depeters, E.J., Ferris, T.A., Lucy, M.C., Mcguire, M.A., Medrano, J.F., Overton, T.4., Smith, T.P., Smith, G.W., Sonstegard, T.S., Spain, J.N., Spiers, D.E., Jianbo, Y., Coussens, P.M. 2004. Development and testing of a high-density cDNA microarray resource for cattle. Proc., Plant and Animal Genome Abstracts. P831. p. 278.
Association of Capn1 Markers with Beef Tenderness in Crossbred, Multibreed Populations - (Abstract Only)
White, S.N., Page, B.T., Casas, E., Koohmaraie, M., Wheeler, T.L., Shackelford, S.D., Keele, J.W., Smith, T.P. 2004. Association of CAPN1 markers with beef tenderness in crossbred, multibreed populations. Proc.,Plant and Animal Genome Abstracts. P644. p. 232.
Male-Specific Sry and Zfy Haplotypes in U.S. Beef Cattle - (Peer Reviewed Journal)
Clawson, M.L., Heaton, M.P., Fox, J.M., Chitko Mckown, C.G., Smith, T.P., Laegreid, W.W. 2004. Male-specific SRY and ZFY haplotypes in U.S. beef cattle. Animal Genetics. 35(3):246-249.
Theory and Application of Genome-Based Approaches to Improve Quality and Value of Beef - (Peer Reviewed Journal)
SMITH, T.P., THALLMAN, R.M., CASAS, E., SHACKELFORD, S.D., WHEELER, T.L., KOOHMARAIE, M. 2003. THEORY AND APPLICATION OF GENOME-BASED APPROACHES TO IMPROVE QUALITY AND VALUE OF BEEF. OUTLOOK IN AGRICULTURE. 32(4):253-265. 2003.
Beta-2-Microglobulin Haplotypes in U.S. Beef Cattle and Association with Failure of Passive Transfer in Newborn Calves - (Peer Reviewed Journal)
Clawson, M.L., Heaton, M.P., Chitko Mckown, C.G., Fox, J.M., Smith, T.P., Snelling, W.M., Keele, J.W., Laegreid, W.W. 2004. Beta-2-microglobulin haplotypes in u.s. beef cattle and association with failure of passive transfer in newborn calves. Mammalian Genome. 2004. V. 15. P. 227-236.
The Callipyge Mutation for Sheep Muscular Hypertrophy - Genetics, Physiology and Meat Quality - (Other)
Freking, B.A., Smith, T.P., Leymaster, K.A. 2004. The callipyge mutation for sheep muscular hypertrophy - genetics, physiology and meat quality. In: M.F.W. te Pas, M.E. Everts and H.P. Haagsman, editors. Muscle Development in Livestock. CAB International, United Kingdom. Chapter 15. p. 317-342.
Development of Animal Cell Lines for Use in Genomic Studies - (Abstract Only)
CHITKO MCKOWN, C.G., FREKING, B.A., MACNEIL, M.D., SMITH, T.P. DEVELOPMENT OF ANIMAL CELL LINES FOR USE IN GENOMIC STUDIES. RESEARCH WORKERS IN ANIMAL DISEASES CONFERENCE PROCEEDINGS. 2003. ABSTRACT NO. 90P.
Recent Advances in the Genetics of Meat Tenderness - (Popular Publication)
CASAS, E., SMITH, T.P. RECENT ADVANCES IN THE GENETICS OF MEAT TENDERNESS. FEEDINFO.COM. 2003. Online available: http://www.feedinfo.com. Accessed Sept. 9, 2003.
Detection of Quantitative Trait Loci for Growth and Carcass Composition in Cattle - (Peer Reviewed Journal)
CASAS, E., SHACKELFORD, S.D., KEELE, J.W., KOOHMARAIE, M., SMITH, T.P., STONE, R.T. DETECTION OF QUANTITATIVE TRAIT LOCI FOR GROWTH AND CARCASS COMPOSITION IN CATTLE. 2003. JOURNAL OF ANIMAL SCIENCE. 81:2976-2983.
Characterization of Gene Expression in Double-Muscled and Normal-Muscled Bovine Embryos - (Peer Reviewed Journal)
POTTS, J.K., ECHTERNKAMP, S.E., SMITH, T.P., REECY, J.M. 2003. CHARACTERIZATION OF GENE EXPRESSION IN DOUBLE-MUSCLED AND NORMAL-MUSCLED BOVINE EMBRYOS. ANIMAL GENETICS. v. 34(6). p. 438-444.
Development and Testing of a High-Density Cdna Microarray Resource for Cattle - (Peer Reviewed Journal)
Suchyta, S.P., Sipkovsky, S., Kruska, R., Jeffers, A., Mcnulty, A., Tempelman, R.J., Halgren, R.G., Saama, P.M., Bauman, D.E., Boisclair, Y.R., Burton, J.L., Collier, R.J., Depeters, E.J., Ferris, T.A., Lucy, M.C., Mcguire, M.A., Medrano, J.F., Overton, T.R., Smith, T.P., Smith, G.W., Sonstegard, T.S., Spain, J.N., Spiers, D.E., Yao, J., Coussens, P.M. 2003.Development and testing of a high-density cdna microarray resource for cattle. Physiological Genomics. 15:158-164.
Prion Gene Sequence Variation Within Diverse Groups of U.S. Sheep, Beef Cattle, and Deer - (Peer Reviewed Journal)
HEATON, M.P., LEYMASTER, K.A., FREKING, B.A., HAWK, D.A., SMITH, T.P., KEELE, J.W., SNELLING, W.M., FOX, J.M., CHITKO MCKOWN, C.G., LAEGREID, W.W. PRION GENE SEQUENCE VARIATION WITHIN DIVERSE GROUPS OF U.S. SHEEP, BEEF CATTLE, AND DEER. MAMMALIAN GENOME. 2003. V. 14. P. 765-777.
Brief Note. Linkage Mapping of the Bovine Bone Morphogenetic Protein Receptor-Ib (Bmpr-Ib) to Chromosome 6 - (Peer Reviewed Journal)
KIM, J.G., SMITH, T.P., SNELLING, W.M., VALLET, J.L., CHRISTENSON, R.K. BRIEF NOTE. LINKAGE MAPPING OF THE BOVINE BONE MORPHOGENETIC PROTEIN RECEPTOR-1B (BMPR1B) TO CHROMOSOME 6. ANIMAL GENETICS. 2003. v. 34(4). p. 311.
Association of Bovine Neonatal Fc Receptor Gene (Fcgrt) Haplotypes with Serum Igg Concentration in Newborn Calves - (Peer Reviewed Journal)
LAEGREID, W.W., HEATON, M.P., KEEN, J.E., GROSSE, W.M., CHITKO MCKOWN, C.G., SMITH, T.P., KEELE, J.W., BENNETT, G.L., BESSER, T.E. ASSOCIATION OF BOVINE NEONATAL FC RECEPTOR GENE ALPHA-CHAIN GENE (FCGRT) HAPLOTYPES WITH SERUM IgG CONCENTRATION IN NEWBORN CALVES. MAMMALIAN GENOME. 2002. v. 13. p. 704-710.
Identification of the Single Base Change Causing the Callipyge Muscle Hypertrophy Phenotype, the Only Known Example of Polar Overdominance in Mammals. - (Peer Reviewed Journal)
Freking, B.A., Murphy, S., Wylie, A., Jirtle, R.L., Rhodes, S., Keele, J.W., Leymaster, K.A., Smith, T.P. 2002. Identification of the single base change causing the callipyge muscle hypertrophy phenotype, the only known example of polar overdominance in animals. Genome Research. 12:1496-1506.
Evaluation of Single Nucleotide Polymorphisms in Capn1 for Association with Meat Tenderness in Cattle. - (Peer Reviewed Journal)
Page, B.T., Casas, E., Heation, M.P., Cullen, N.G., Hyndman, D.L., Morris, C.A., Crawford, A.M., Wheeler, T.L., Koohmaraie, M., Keele, J.W., Smith, T.P.L. Journal Animal Science. 2002. v. 80. p. 3077-3085.
Development of 47 New Microsatellite Markers from a Bta6 Library - (Peer Reviewed Journal)
REED, K.M., IHARA, N., PONCE DE LEON, F.A., SONSTEGARD, T.S., SMITH, T.P., BENNETT, G.L., SUGIMOTO, Y., BEATTIE, C.W. DEVELOPMENT OF 47 NEW MICROSATELLITE MARKERS FROM A BTA6 LIBRARY. ANIMAL BIOTECHNOLOGY JOURNAL. 2002, Vol. 13(2), pp. 195-202.
Differential Conservation of Transcriptional Domains of Mammalian Prophet of Pit-1 Proteins Revealed by Structural Studies of the Bovine Gene and Comparative Functional Analysis of the Protein - (Peer Reviewed Journal)
Showalter, A.D., Smith, T.P., Bennett, G.L., Sloop, K.W., Whitsett, J.A., Rhodes, S.J. 2002. Differential conservation of transcriptional domains of mammalian prophet of pit-1 proteins revealed by structural studies of the bovine gene and comparative functional analysis of the protein. Gene. 291:211-221.
Porcine Gene-Discovery by Normalized Cdna-Library Sequencing and Est Cluster Assembly - (Peer Reviewed Journal)
FAHRENKRUG, S.C., SMITH, T.P., FREKING, B.A., CHO, J., WHITE, J., VALLET, J.L., WISE, T.H., ROHRER, G.A., KEELE, J.W. PORCINE GENE-DISCOVERY BY NORMALIZED CDNA-LIBRARY SEQUENCING AND EST CLUSTER ASSEMBLY. MAMMALIAN GENOME. 2002. v. 13. p. 475-478.
Differential Expression of Cyclooxygenase-2 Around the Time of Elongation in the Pig Conceptus - (Peer Reviewed Journal)
Wilson, M.E., Fahrenkrug, S.C., Smith, T.P., Rohrer, G.A., Ford, S.P. 2001. Differential expression of cyclooxygenase-2 around the time of elongation in the pig conceptus. Animal Reproduction Sciences. 71:229-237.
Selection and Use of Snp Markers for Animal Identification and Paternity Analysis in U.S. Beef Cattle - (Peer Reviewed Journal)
Mammalian Genome. 2002. v. 13. p. 272-281.
Use of Bovine Est Data and Human Genomic Sequences to Map 100 Gene-Specific Bovine Markers - (Peer Reviewed Journal)
Stone, R.T., Grosse, W., Casas, E., Smith, T.P., Keele, J.W., Bennett, G.L. 2002. Use of bovine EST data and human genomic sequences to map 100 gene-specific bovine markers. Mammalian Genome. 13:211-215.
Haplotype Structure of the Bovine Neonatal Fc Receptor (Bfcrn) Gene in U.S.BEEF Cattle and Association with Serum Igg Concentration in Newborn Calves - (Abstract Only) - (06-Dec-01)
Selection and Use of Single Nucleotide Polymorphism (Snp) Markers for Animal Identification and Paternity Analysis in U.S. Beef Cattle - (Abstract Only) - (06-Dec-01)
Single Nucleotide Polymorphism (Snp) Discovery in Porcine Expressed Genes - (Peer Reviewed Journal)
Fahrenkrug, S.C., Freking, B.A., Smith, T.P., Rohrer, G.A., Keele, J.W. 2002. Single nucleotide polymorphism (SNP) discovery in porcine expressed genes. Animal Genetics. 33:186-195.
Identification of An Snp Associated with Callipyge in Sheep - (Abstract Only) - (01-Nov-01)
Comparative Radiation Hybrid Mapping of the Mouse High Growth (Hg) Region in Cattle and Pigs Reprint Icon - (Abstract Only)
Farber, C.R., Smith, T.P., Nonneman, D.J., Medrano, J.F. 2002. Comparative Radiation Hybrid Mapping of the Mouse High Growth (HG) Region in Cattle and Pigs. Plant and Animal Genome Conference Proceedings X. San Diego, CA. 1/12-16/2002. Abstract P136. p. 112.
Beyond Myostatin, the Search for Interacting Alleles - (Proceedings) - (01-Nov-01)
Identification of Porcine Lhx3 and Sf1 As Candidate Genes for Qtl Affecting Growth and Reproduction Traits in Swine - (Peer Reviewed Journal)
Smith, T.P., Showalter, A.D., Sloop, K.W., Rohrer, G.A., Fahrenkrug, S.C., Meier, B.C., Rhodes, S.J. 2001. Identification of porcine lhx3 and sf1 as candidate genes for qtl affectinggrowth and reproduction traits in swine. Animal Genetics. 32:344-350.
Short Communication: An Updated Linkage and Comparative Map of Porcine Chromosome 18 - (Peer Reviewed Journal)
CAMPBELL, E.M., FAHRENKRUG, S.C., VALLET, J.L., SMITH, T.P., ROHRER, G.A. SHORT COMMUNICATION: AN UPDATED LINKAGE AND COMPARATIVE MAP OF PORCINE CHROMOSOME 18. ANIMAL GENETICS. 2001. v. 32. p. 375-379.
Comparative Mapping of Bta15 and Hsa11 Including a Region Containing a Qtl for Meat Tenderness - (Peer Reviewed Journal) - (13-Mar-01)
Rapid Communication: Linkage Mapping of Seven Bovine Cdnas - (Peer Reviewed Journal) - (21-Feb-01)
Sequence Evaluation of Four Pooled-Tissue Normalized Bovine Cdna Libraries and Construction of a Gene Index for Cattle - (Peer Reviewed Journal) - (12-Feb-01)
Mapping Expressed Sequence Tags (Ests) in Pigs Using Single Nucleotide Polymorphisms (Snps) - (Abstract Only) - (05-Feb-01)
Construction of Snp-Based Est Comparative Map of Swine, Cattle, and Human Genomes - (Abstract Only) - (05-Jan-01)
Rapid Communication: Linkage Mapping of the Porcine Micromolar Calcium Activated Neutral Protease 1 (Ucalpain) Gene on Ssc2 - (Peer Reviewed Journal) - (23-Aug-00)
Rapid Communication: Nucleotide Sequences of Two Isoforms of Porcine Micromolar Calcium Activated Neutral Protease 1 Cdna - (Peer Reviewed Journal) - (23-Aug-00)
Pcr-Based Reaction Setup for High-Throughput Cdna Library Sequencing on the Abi 3700 Automated DNA Sequencer - (Peer Reviewed Journal) - (30-Jun-00)
Database Management of High Throughput Est Sequencing and Snp Discovery - (Abstract Only) - (30-May-00)
Bovine Capn1 Maps to a Region of Bta29 Containing a Qtl for Meat Tenderness - (Peer Reviewed Journal) - (04-May-00)
Rapid Communication: Mapping of Nine Bovine Microsatellite Markers Obtained from Large Insert Genomic Libraries - (Peer Reviewed Journal) - (02-May-00)
Porcine Erythropoietin Receptor: Molecular Cloning and Expression in Embryonic and Fetal Liver - (Peer Reviewed Journal)
Pearson, P.L., Smith, T.P., Sonstegard, T.S., Klemcke, H.G., Christenson, R.K., Vallet, J.L. 2000. Porcine erythropoietin receptor: molecular cloning and expression in embryonic and fetal liver. Domestic Animal Endocrinology. 19(1):25-38.
Structure of the Genes for Porcine Endometrial Secreted and Membrane Folate Binding Proteins - (Peer Reviewed Journal)
Vallet, J.L., Smith, T.P., Sonstegard, T.S., Heaton, M.P., Fahrenkrug, S.C. 2001. Structure of the genes for porcine endometrial secreted and membrane folate binding proteins. Domestic Animal Endocrinology. 21(1):55-72.
Bovine Capn1 Maps to a Region of Bta29 Containing a Qtl for Meat Tenderness - (Abstract Only) - (14-Mar-00)
Linkage Mapping Ests in Pigs Using Single Nucleotide Polymorphisms (Snps): Snp Discovery - (Abstract Only) - (14-Mar-00)
Linkage Mapping of Ests in Pigs Using Single Nucleotide Polymorphisms (Snps): Ii. High-Throughput Genotyping and Mapping - (Abstract Only) - (14-Mar-00)
Development and Mapping of Type-I (Gene-Related) Markers in the Bovine Genome by Large-Scale Expressed Sequence Tag (Est) Sequencing and Single Nucleotide Polymorphism (Snp) Detection - (Abstract Only) - (14-Mar-00)
Characterization of the Gene for Porcine Endometrial/placental Membrane Folate Binding Protein (Mfbp) - (Abstract Only)
Vallet, J.L., Smith, T.P., Sonstegard, T.S., Heaton, M.P., Fahrenkrug, S.C. 2000. Characterization of the gene for porcine endometrial/placental membrane folate binding protein (mFBP) [abstract]. Journal of Animal Science. 78(Supplement 2):77. (Abstract No. 231)
Differential Gene Expression During Elongation in the Pig Embryo - (Peer Reviewed Journal)
Wilson, M.E., Sonstegard, T.S., Smith, T.P., Fahrenkrug, S.C., Ford, S.P. 2000. Differential gene expression during elongation in the pig embryo. Developmental Genetics. 11(8):682-688.
Bovine Ucp2 and Ucp3 Map to Bta15 (Short Communication) - (Peer Reviewed Journal) - (29-Jun-99)
The Process and Use of Functional Genomics in Beef Cattle: So You Have a Qtl, Now What? - (Abstract Only) - (16-May-99)
Quantitative Trait Loci on Bovine Chromosomes 15 and 29 Evidence That Human Chromosome 11 Harbors Orthologous Genes Associated with Longissimus Tenderness in Bovine - (Abstract Only)
Casas, E., Keele, J.W., Shackelford, S.D., Smith, T.P., Koohmaraie, M., Kappes, S.M., Stone, R.T. 1999. Quantitative trait loci on bovine chromosomes 15 and 29 evidence that human chromosome 11 harbors orthologous genes associated with longissimus tenderness in bovine. From Jay Lush to Genomics: Visions for Animal Breeding and Genetics., Iowa State University, Ames, IA. p. 153. (Abstract)
Fine Mapping of a Warner-Bratzler Shear Force Quantitative Trait Locus on Bovine Chromosome 15 - (Abstract Only) - (16-May-99)
Technical Note: Direct Genotyping of the Double-Muscling Locus (Mh) in Piedmontese and Belgian Blue Cattle by Fluorescent Pcr - (Peer Reviewed Journal) - (20-Mar-99)
Quantitative Analysis of Birth, Weaning and Yearling Weights, and Calving Difficulty in Piedmontese Crossbreds Segregating An Inactive Myostatin Allele - (Peer Reviewed Journal) - (06-Mar-99)
Isolation of Complementary Deoxyribonucleic Acids Encoding Putative Secreted and Membrane-Bound Folate Binding Proteins from Endometrium of Swine - (Peer Reviewed Journal) - (02-Mar-99)
Physical Mapping of the Bovine, Caprine and Ovine Homologues of the Paired Box Gene Pax8 - (Peer Reviewed Journal) - (05-Feb-99)
Fine Mapping of a Warner-Bratzler Shear Force Qtl on Bta15 - (Abstract Only) - (15-Jan-99)
Fine Mapping of the Ovine Callipyge Locus - (Abstract Only) - (15-Jan-99)
Identification and Genetic Mapping of Bovine Chemokine Genes Expressed in Epithelial Cells - (Peer Reviewed Journal) - (02-Sep-98)
Comparative Mapping: Cytogenetic Location of Proc, En1, Alpi, Tnp1, and Il1b Genes in Cattle and Sheep Reveals a Conserved Rearrangement Relative to Human Genome. - (Peer Reviewed Journal) - (18-Aug-98)
Mapping Bovine and Ovine Genes with Intronic Single Nucleotide Polymorphisms - (Abstract Only) - (01-Jul-98)
Structure of the Gene for Porcine Endometrial Folate Binding Protein - (Abstract Only) - (29-Jun-98)
Porcine Erythropoietin Receptor: Cloning of a Partial Cdna and Expression in Embryonic/fetal Liver - (Abstract Only) - (29-Jun-98)
Discovery of Myostatin As the Gene Responsible for Double Muscling, and Implications for Meat Production - (Proceedings) - (01-Jun-98)
Refinement of Bovine Chromosome 2 Linkage Map Near the Mh Locus Reveals Complex Rearrangements Between the Bovine and Human Genomes. - (Peer Reviewed Journal) - (05-May-98)
Expression-Based Gene Identification and Single Nucleotide Polymorphism (Snp) Mapping in Cattle - (Abstract Only) - (01-May-98)
Evaluation of the Ovine Callipyge Locus: I. Relative Chromosomal Position and Gene Action - (Peer Reviewed Journal) - (08-Apr-98)
Effect of a Mutation at the Myostatin Gene on Early Life Weights and Calving Ease in a Population of Piedmontese Inheritance - (Abstract Only) - (01-Mar-98)
Simple Genetic Test That Supports Marker Assisted Selection to Increase Retail Product Yield in Cattle - (Abstract Only) - (01-Mar-98)
Myostatin Mutations Cause Double Muscling in Cattle - (Proceedings) - (01-Jan-98)
Narrowing a Region of Recombination Rate Variation on Bta23 to the D23s22-D23s23 Interval Using Meiotic Breakpoint Analysis and a Yac Contig - (Abstract Only) - (01-Jan-98)
Myostatin Mutations Cause Double Muscling in Cattle - (Proceedings) - (27-Oct-97)
Myostatin Maps to Porcine Chromosome 15 by Linkage and Physical Assignment to SSC15Q2.3 (Short Communication) - (Abstract Only) - (11-Sep-97)
Association of the Muscle Hypertrophy Locus with Carcass Traits in Beef Cattle - (Peer Reviewed Journal) - (09-Sep-97)
Mutations in Myostatin (Gdf8) in Double Muscled Belgian Blue Cattle - (Peer Reviewed Journal) - (18-Aug-97)
Myostatin Maps to the Interval Containing the Bovine Mh Locus - (Peer Reviewed Journal) - (02-Jul-97)
Comparative Mapping of Bovine and Human Chromosome 2 Identifies Segments of Conserved Synteny Containing the Bovine Mh Locus - (Peer Reviewed Journal) - (12-May-97)
Association of the Double-Muscling Locus on Bovine Chromosome Two (Bta2) with Carcass Traits - (Abstract Only) - (24-Apr-97)
Porcine Uterine Folate Binding Proteing: Folate Binding, Cloning of a Partial Cdna, and Mrna Expression During the Estrous Cycle and Early Pregnancy - (Abstract Only) - (23-Apr-97)
Directed Cosmid Isolation for Physical Assignment by Fish: Pcr-Based Iterative Screening of Random Genomic Libraries - (Peer Reviewed Journal) - (17-Apr-97)
Human:bovine Comparative Mapping to Identify the Mh Gene in Cattle - (Proceedings) - (02-Mar-97)
Genetic Analysis of Meat Quality in Cattle - (Proceedings) - (01-Feb-97)
Short Communication: Physical Assignment of Glucagon and Nebulin in Cattle, Sheep and Goat - (Abstract Only) - (20-Jan-97)
Anchoring of Bovine Chromosomes 4, 6, 7, 10, and 14 and Linkage Group Telomeric Ends Via Fish Analysis of Lambda Clones - (Peer Reviewed Journal) - (28-Dec-96)
A Second Generation Linkage Map of the Bovine Genome - (Peer Reviewed Journal) - (06-Dec-96)
Porcine Aromatases: Studies on Tissue-Specific, Functionally Distinct Isozymes from a Single Gene? - (Peer Reviewed Journal) - (01-Dec-96)
Mapping of Hprt Gene in Swine Provides a Reference Locus for Synteny Comparison - (Proceedings) - (01-Dec-96)
Construction and Characterization of a Large Insert Porcine Yac Library (Short Communication) - (Abstract Only) - (22-Aug-96)
A Genetic and Cytogenetic Map for Bovine Chromosome 11 - (Abstract Only) - (01-Jul-96)
Use of Large Insert Genomic Libraries in Livestock Gene Mapping - (Abstract Only) - (10-Jun-96)
Linkage Assignments for Has 19 Conserved Regions of Synteny in Cattle, Sheep and Swine - (Proceedings) - (01-Jun-96)
Construction of a Porcine Yeast Artificial Chromosome (Yac) Library - (Abstract Only) - (01-May-96)
A Comprehensive Map of the Porcine Genome - (Peer Reviewed Journal) - (29-Mar-96)
Short Communication: Construction and Characterization of a Large Insert Bovine Yac Library with 5-Fold Genomic Coverage - (Abstract Only) - (19-Dec-95)
Physical Assignments of 68 Porcine Cosmid and Lambda Clones Containing Polymorphic Microsatellites - (Peer Reviewed Journal) - (12-Dec-95)
Identifying Tumor Initiator/suppressor and Penetrance-Associated Genes by Gene Mapping - (Proceedings) - (15-Oct-95)
Short Communication: Mapping of a Linkage Group to the Last Bovine Chromosome (Bta27) Without An Assignment - (Abstract Only) - (09-Oct-95)
Directed Integration of the Physical and Genetic Linkage Maps of Swine Chromosome 7 Reveals That the Sla Spans the Centromere - (Peer Reviewed Journal) - (19-Sep-95)
Directed Integration of the Physical and Genetic Linkage Maps - (Proceedings) - (15-Sep-95)
Molecular Cloning of Porcine Fas Antigen and Expression in Cell Lines Derived from Miniature Swine - (Proceedings) - (01-Feb-95)
Last Modified: 4/1/2013
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