Timothy P Smith
(Tim)
Genetics & Breeding Research
Research Chemist
Phone: (402) 762-4366
Fax: (402) 762-4390
U.S. MEAT ANIMAL RESEARCH CENTER
STATE SPUR 18D CLAY CENTER, NE, 68933-0000
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.
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.
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.
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.
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.
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.
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.
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. 2008 meeting on the Biology of Genomes, May 6-10, 2007, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. p197.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.