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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.)
Genomic signatures of Mannheimia haemolytica that associate with the lungs of cattle with respiratory disease, an integrative conjugative element, and antibiotic resistance genes -
Clawson, M.L., Murray, R.W., Sweeney, M.T., Apley, M.D., DeDonder, K.D., Capik, S.F., Larson, R.L., Lubbers, B.V., White, B.J., Kalbfleisch, T.S., Schuller, G., Dickey, A.M., Harhay, G.P., Heaton, M.P., Chitko-McKown, C.G., Brichta-Harhay, D.M., Bono, J.L., Smith, T.P.L. 2016. Genomic signatures of Mannheimia haemolytica that associate with the lungs of cattle with respiratory disease, an integrative conjugative element, and antibiotic resistance genes. BMC Genomics. 17:982. doi: 10.1186/s12864-016-3316-8.
Complete, closed genome sequences of 10 Salmonella enterica subsp. enterica serovar Typhimurium strains isolated from human and bovine sources -
Nguyen, S.V., Harhay, D.M., Bono, J.L., Smith, T.P.L., Fields, P.I., Dinsmore, B.A., Santovenia, M., Kelley, C.M., Wang, R., Bosilevac, J.M., Harhay, G.P. 2016. Complete, closed genome sequences of 10 Salmonella enterica subsp. enterica serovar Typhimurium strains isolated from human and bovine sources. Genome Announcements. 4(6):e01212-16. doi:10.1128/genomeA.01212-16.
Comparative methylome analysis of the occasional ruminant respiratory pathogen Bibersteinia trehalosi -
Anton, B.P., Harhay, G.P., Smith, T.P.L., Blom, J., Roberts, R.J. 2016. Comparative methylome analysis of the occasional ruminant respiratory pathogen Bibersteinia trehalosi. PLoS One. 11(8): e0161499.
Using diverse U.S. beef cattle genomes to identify missense mutations in EPAS1, a gene associated with pulmonary hypertension -
Heaton, M.P., Smith, T.P.L., Carnahan, J.K., Basnayake, V., Qiu, J., Simpson, B., Kalbfleisch, T.S. 2016. Using diverse U.S. beef cattle genomes to identify missense mutations in EPAS1, a gene associated with pulmonary hypertension. F1000Research. 5:2003. doi:10.12688/f1000research.9254.2.
Metagenomic and near full-length 16S rRNA sequence data in support of the phylogenetic analysis of the rumen bacterial community in steers -
Myer, P.R., Kim, M.S., Freetly, H.C., Smith, T.P. 2016. Metagenomic and near full-length 16S rRNA sequence data in support of the phylogenetic analysis of the rumen bacterial community in steers. Data in Brief. 8:1048-1053. doi: 10.1016/j.dib.2016.07.027.
Complete genome sequence of highly virulent Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) variants that recently emerged in the United States -
Workman, A.M., Smith, T.P., Osorio, F.A., Vu, H.L. 2016. Complete genome sequence of highly virulent porcine reproductive and respiratory syndrome virus variants that recently emerged in the United States. Genome Announcements. 4(4):e00772-16.
Evaluation of 16S rRNA amplicon sequencing using two next-generation sequencing technologies for phylogenetic analysis of the rumen bacterial community in steers -
Myer, P.R., Kim, M.S., Freetly, H.C., Smith, T.P. 2016. Evaluation of 16S rRNA amplicon sequencing using two next-generation sequencing technologies for phylogenetic analysis of the rumen bacterial community in steers. Journal of Microbiological Methods. 127:132-140. doi: 10.1016/j.mimet.2016.06.004.
Selection enhanced estimates of marker effects on means and variances of beef tenderness -
Tait Jr, R.G., Shackelford, S.D., Wheeler, T.L., King, D.A., Keele, J.W., Casas, E., Thallman, R.M., Smith, T.P., Bennett, G.L. 2016. Selection enhanced estimates of marker effects on means and variances of beef tenderness. In proceedings: 2016 Beef Improvement Federation Annual Meeting & Symposium. Manhattan, KS, Jun 14-17, 2016. pp. 115-121. www.beefimprovement.org/library-2/convention-proceedings.
Complete and closed genome sequences of 10 Salmonella enterica subsp. enterica serovar Anatum isolated from human and bovine sources Reprint Icon -
Nguyen, S.V., Harhay, D.M., Bono, J.L., Smith, T.P.L., Fields, P.I., Dinsmore, B.A., Santovenia, M., Kelley, C.M., Wang, R., Bosilevac, J.M., Harhay, G.P. 2016. Complete and closed genome sequences of 10 Salmonella enterica subsp. enterica serovar Anatum isolated from human and bovine sources. Genome Announcements. Vol. 4(3): e00447-16. doi: 10.1128/genomeA.00447-16.
Using diverse U.S. beef cattle genomes to identify missense mutations in EPAS1, a gene associated with high-altitude pulmonary hypertension -
Heaton, M.P., Smith, T.P.L., Carnahan, J.K., Basnayake, V., Qiu, J., Simpson, B., Kalbfleisch, T.S. 2016. Using diverse U.S. beef cattle genomes to identify missense mutations in EPAS1, a gene associated with high-altitude pulmonary hypertension [abstract]. 35th International Society for Animal Genetics (ISAG), July 23-27, 2016, Salt Lake City, UT. Poster #P6026.
Analysis of the gut microbiome in beef cattle and its association with feed intake, growth, and efficiency -
Myer, P.R., Wells, J., Smith, T.P., Kuehn, L.A., Freetly, H.C. 2016. Analysis of the gut microbiome in beef cattle and its association with feed intake, growth, and efficiency [abstract]. Journal of Animal Science. 94 (E-Supplement 5):211-212.
Resolving misassembled cattle immune gene clusters with hierarchical, long read sequencing -
Bickhart, D.M., Hammond, J.A., Schwartz, J.C., Heimeier, D., Smith, T.P. 2016. Resolving misassembled cattle immune gene clusters with hierarchical, long read sequencing. International Society for Animal Genetics (ISAG). Salt Lake City, UT, July 23-27. p. 105–106 (P4054).
Molecular evolution of epizootic hemorrhagic disease viruses in North America based on historical isolates -
Wilson, W.C., Ruder, M.G., Jasperson, D.C., Smith, T.P., Naraghi Arani, P., Lenhoff, R., Stallknecht, D.E., Valdivia-Granda, W.A., Sheron, D. 2016. Molecular evolution of epizootic hemorrhagic disease viruses in North America based on historical isolates. Virus Genes. 52:495-508.
Evaluation of 16S Rrna amplicon sequencing using two next-generation sequencing technologies for phylogenetic analysis of the rumen bacterial community in steers -
Myer, P.R., Kim, M.S., Freetly, H.C., Smith, T.P. 2016. Evaluation of 16S Rrna amplicon sequencing using two next-generation sequencing technologies for phylogenetic analysis of the rumen bacterial community in steers [abstract]. American Society for Microbiology. Poster No. SUNDAY-584.
Resolving bovine viral diarrhea virus subtypes from persistently infected US beef calves with complete genome sequence -
Workman, A.M., Heaton, M.P., Harhay, G.P., Smith, T.P.L., Grotelueschen, D.M., Sjeklocha, D.B., Brodersen, B.W., Petersen, J.L., Chitko-McKown, C.G. 2016. Resolving bovine viral diarrhea virus subtypes from persistently infected U.S. beef calves with complete genome sequence. Journal of Veterinary Diagnostic Investigation. 28(5):519-528.
Whole genome sequences of the USMARC sheep diversity panel v 2.4 aligned to the ovine reference genome assembly -
Heaton, M.P., Smith, T.P., Kalbfleisch, T.S. 2016. Whole genome sequences of the USMARC sheep diversity panel v 2.4 aligned to the ovine reference genome assembly. Internet Web Page. www.ars.usda.gov/Services/Docs.htm?docid=25585 and www.ars.usda.gov/Research/docs.htm?docid=25589.
Mobilome differences between Salmonella enterica serovars Anatum and Typhimurium isolated from cattle and humans and potential impact on virulence -
Nguyen, S.V., Bono, J.L., Smith, T.P.L., Kelley, C.M., Wang, R., Harhay, G.P., Harhay, D.M. 2016. Mobilome differences between Salmonella enterica serovars Anatum and Typhimurium isolated from cattle and humans and potential impact on virulence. [Abstract] In proceedings: 60th Wind River Conference on Procaryotic Biology, 2016 June 1-5. Estes Park, Colorado. p. 67.
Large genomic differences between Moraxella bovoculi isolates acquired from the eyes of cattle with conjunctivitis versus the deep nasopharynx of asymptomatic cattle Reprint Icon -
Dickey, A.M., Loy, J.D., Bono, J.L., Smith, T.P.L., Apley, M.D., Lubbers, B.V., DeDonder, K.D., Capik, S.F., Larson, R.L., White, B.J., Blom, J., Chitko-McKown, C.G., Clawson, M.L. 2016. Large genomic differences between Moraxella bovoculi isolates acquired from the eyes of cattle with conjunctivitis versus the deep nasopharynx of asymptomatic cattle. Veterinary Research. 47:31.
Improving the goat long-read assembly with optical mapping -
Bickhart, D.M., Smith, T.P., Rosen, B.D., Koren , S., Phillippy, A., Hastie, A.R., Sullivan, S.T., Liachko, I., Burton, J.N., Sayre, B.L., Liu, G., Schroeder, S.G., Sonstegard, T.S., Van Tassell, C.P. 2016. Improving the goat long-read assembly with optical mapping. Plant and Animal Genome Conference Proceedings. San Diego, CA, Jan. 9–13.
Whole genomic sequence analysis of Bacillus infantis: defining the genetic blueprint of strain NRRL B-14911, an emerging cardiopathogenic microbe -
Massilamany, C., Mohammed, A., Loy, J.D., Purvis, T., Krishnan, B., Basavalingappa, R.H., Kelley, C.M., Guda, C., Barletta, R.G., Moriyama, E.N., Smith, T.P.L., Reddy, J. 2016. Whole genomic sequence analysis of Bacillus infantis: defining the genetic blueprint of strain NRRL B-14911, an emerging cardiopathogenic microbe. Biomed Central (BMC) Genomics. 17(Suppl. 7):511. doi: 10.1186/s12864-016-2900-2.
Investigation and validation of the role of a QTL on SSC12 in PCV2b viremia -
Tosky, E., Smith, T.P.L., Engle, T., Davis, E., Moural, T., Nonneman, D., Chin, J., Burkey, T., Plastow, G.S., Kachman, S.D., Ciobanu, D.C. 2016. Investigation and validation of the role of a QTL on SSC12 in PCV2b viremia [abstract]. Plant and Animal Genome XXIV Conference Proceedings. Abstract #P0638.
Development of resources and tools for mapping genetic sources of phenotypic variation -
Ciobanu, D.C., Tosky, E., Olson, S., Trenhaile, M., Lents, C.A., Smith, T.P.L., Nonneman, D., Rohrer, G.A., Chin, J., Miller, P.S., Burkey, T., Spangler, M.L., Riethoven, J.-J., Plastow, G.S., Kachman, S.D. 2016. Development of resources and tools for mapping genetic sources of phenotypic variation [abstract]. Plant and Animal Genome XXIV Conference Proceedings. Abstract #W914.
Do you really know where this SNP goes? -
Rohrer, G.A., Nonneman, D., Schroeder, S.G., Chin, J., Koren, S., Phillippy, A., Green, R., Putnam, N., Smith, T.P.L. 2016. Do you really know where this SNP goes? [abstract] Plant and Animal Genome XXIV Conference Proceedings. Abstract #W909.
Progress toward a low budget reference grade genome assembly Reprint Icon -
Rosen, B.D., Bickhart, D.M., Koren, S., Hastie, A.R., Schroeder, S.G., Smith, T.P., Sullivan, S.T., Liachko, I., Burton, J.N., Dunham, M.J., Sendure, J., Sayre, B.L., Huson, H.J., Liu, G., Connor, E.E., Sonstegard, T.S., Phillippy, A., Van Tassell, C.P. 2016. Progress toward a low budget reference grade genome assembly. Plant and Animal Genome Conference Proceedings. San Diego, CA, Jan. 9–13, P0612.
Estimates of epistatic and pleiotropic effects of casein alpha s1 (CSN1S1) and thyroglobulin (TG) genetic markers on beef heifer performance traits enhanced by selection Reprint Icon -
Tait Jr, R.G., Cushman, R.A., McNeel, A.K., Casas, E., Smith, T.P., Freetly, H.C., Bennett, G.L. 2016. Estimates of epistatic and pleiotropic effects of casein alpha s1 (CSN1S1) and thyroglobulin (TG) genetic markers on beef heifer performance traits enhanced by selection. Journal of Animal Science. 94(3):920-926. doi:10.2527/jas2015-9860.
Gut bacterial communities and their association with production parameters in beef cattle -
Myer, P.R., Wells, J., Smith, T.P., Kuehn, L.A., Freetly, H.C. 2016. Gut bacterial communities and their association with production parameters in beef cattle [abstract]. Journal of Animal Science. 94(Supplement 2):179.
Complete closed genome sequences of Salmonella enterica subsp. enterica serotypes Anatum, Montevideo, Typhimurium and Newport, isolated from beef, cattle, and humans Reprint Icon -
Harhay, D.M., Bono, J.L., Smith, T.P., Fields, P.I., Dinsmore, B.A., Santovenia, M., Kelley, C.M., Wang, R., Harhay, G.P. 2016. Complete closed genome sequences of Salmonella enterica subsp. enterica serotypes Anatum, Montevideo, Typhimurium and Newport, isolated from beef, cattle, and humans. Genome Announcements. 4(1):e01683-15. doi:10.1128/genomeA.01683-15.
A searchable, whole genome resource designed for protein variant analysis in diverse lineages of U.S. beef cattle -
Heaton, M.P., Kalbfleisch, T.S., Carnahan, J.K., Smith, T.P.L., Harhay, G.P., Simpson, B., Qiu, J. 2015. A searchable, whole genome resource designed for protein variant analysis in diverse lineages of U.S. beef cattle [abstract]. International Plant and Animal Genome XXIV Conference Proceedings, January 9-13, 2016, San Diego, CA. Poster #P0506.
Microbial community profiles of the jejunum from steers differing in feed efficiency Reprint Icon -
Myer, P.R., Wells, J., Smith, T.P., Kuehn, L.A., Freetly, H.C. 2016. Microbial community profiles of the jejunum from steers differing in feed efficiency. Journal of Animal Science. 94(1):327-338. doi: 10.2527/jas2015-9839.
A survey of polymorphisms detected from sequences of popular beef breeds -
Snelling, W.M., Bennett, G.L., Keele, J.W., Kuehn, L.A., McDaneld, T.G., Smith, T.P., Thallman, R.M., Kalbfleisch, T.S., Pollak, E.J. 2015. A survey of polymorphisms detected from sequences of popular beef breeds. Journal of Animal Science. 93(11):5128-5143. doi:10.2527/jas2015-9356.
Cecum microbial communities from steers differing in feed efficiency Reprint Icon -
Myer, P.R., Wells, J.E., Smith, T.P.L., Kuehn, L.A., Freetly, H.C. 2015. Cecum microbial communities from steers differing in feed efficiency. Journal of Animal Science. 93(11):5327-5340. doi: 10.2527/jas2015-9415
Microbial community profiles of the colon from steers differing in feed efficiency Reprint Icon -
Myer, P.R., Wells, J., Smith, T.P., Kuehn, L.A., Freetly, H.C. 2015. Microbial community profiles of the colon from steers differing in feed efficiency. SpringerPlus. 4:454.
Whole genome sequences of the USMARC beef cattle diversity panel v2.9 aligned to the bovine reference genome assembly -
Heaton, M.P., Smith, T.P., Kalbfleisch, T.S. 2015. Whole genome sequences of the USMARC beef cattle diversity panel v2.9 aligned to the bovine reference genome assembly. Internet Web Page. www.ars.usda.gov/Services/Docs.htm?docid=25585 and www.ars.usda.gov/Research/docs.htm?docid=25586.
Rumen microbiome from steers differing in feed efficiency Reprint Icon -
Myer, P.R., Smith, T.P., Wells, J., Kuehn, L.A., Freetly, H.C. 2015. Rumen microbiome from steers differing in feed efficiency. PLoS One. 10(6):e0129174.
Full-length coding sequence for 12 bovine viral diarrhea virus isolates from persistently infected cattle in a feedyard in Kansas -
Workman, A.M., Harhay, G.P., Heaton, M.P., Grotelueschen, D.M., Sjeklocha, D.B., Smith, T.P.L. 2015. Full-length coding sequence for 12 bovine viral diarrhea virus isolates from persistently infected cattle in a feedyard in Kansas. Genome Announcements. 3(3):e00487-15. doi:10.1128/genomeA.00487-15.
Historical overview and current status of genomic technology and marker assisted selection in beef cattle -
Pollak, E.J., Smith, T.P., Snelling, W.M. 2015. Historical overview and current status of genomic technology and marker assisted selection in beef cattle. In Proceedings of the American Meat Science Association. 68th Annual Reciprocal Meat Conference, June 14 - 17, 2015, Lincoln, NE. pg. 32-36.
Comparative analysis of twenty-four complete aenome aequences of Salmonella enterica Serotypes Anatum, Montevideo, Typhimurium and Newport isolated from ground beef or asymptomatic cattle on farm or at harvest -
Harhay, D.M., Bono, J.L., Smith, T.P., Kalbfleisch, T., Kelley, C., Wang, R., Harhay, G.P. 2015. Comparative analysis of twenty-four complete aenome aequences of Salmonella enterica Serotypes Anatum, Montevideo, Typhimurium and Newport isolated from ground beef or asymptomatic cattle on farm or at harvest [abstract]. American Society for Microbiology 115th General Meeting. Poster No. 397, Session 029.
Complete closed genome sequences of a Mannheimia haemolytica serotype A1 leukotoxin deletion mutant and its wild type parent strain -
Heaton, M.P., Harhay, G.P., Smith, T.P.L., Bono, J.L., Chitko-McKown, C.G. 2015. Complete closed genome sequences of a Mannheimia haemolytica serotype A1 leukotoxin deletion mutant and its wild-type parent strain. Genome Announcements. 3(3):e00417-15. DOI: 10.1128/genomeA.00417-15.
Joint analysis of bacterial DNA methylation, predicted promoter and regulation motifs for biological significance -
Harhay, G.P., Anton, B.P., Smith, T.P.L. [abstract]. 2015. Joint analysis of bacterial DNA methylation, predicted promoter and regulation motifs for biological significance. American Society for Microbiology 2015, 115th General Meeting, May 30-June 2, 2015, New Orleans, LA. Poster #3468.
Identification of a mannheimia haemolytica genetic subtype that causes bovine respiratory disease -
Clawson, M.L., Murray, R.W., Sweeney, M.T., Apley, M.D., DeDonder, K.D., Capik, S., Larson, R., Lubbers, B.V., Kalbfleisch, T.S., Schuller, G., Harhay, G.P., Heaton, M.P., Chitko-McKown, C.G., Workman, A.M., Harhay, D.M., Bono, J.L., Smith, T.P.L. [abstract]. 2015. Identification of a mannheimia haemolytica genetic subtype that causes bovine respiratory disease. American Society for Microbiology 2015, 115th General Meeting, May 30-June 2, 2015, New Orleans, LA. Poster #1410.
Genomic comparison of Salmonella enterica serotypes commonly associated with cattle and beef – Analysis of variation in virulence potential -
Harhay, D.M., Bono, J.L., Wang, R., Smith, T.P., Harhay, G.P., Kalbfleisch, T., Wheeler, T.L. 2015. Genomic comparison of Salmonella enterica serotypes commonly associated with cattle and beef – Analysis of variation in virulence potential. [Abstract]. Beef Industry Safety Summit. http://www.bifsco.org/2015researchsessionabstracts.aspx.
Genetic subgroup of small ruminant lentiviruses that infects sheep homozygous for TMEM154 frameshift deletion mutation A4delta53 -
Clawson, M.L., Redden, R., Schuller, G., Heaton, M.P., Workman, A.M., Chitko-McKown, C.G., Smith, T.P.L., Leymaster, K.A. 2015. Genetic subgroup of small ruminant lentiviruses that infects sheep homozygous for TMEM154 frameshift deletion mutation A4delta53. Veterinary Research. 46:22.
Genomewide association study of lung lesions in cattle using sample pooling -
Keele, J.W., Kuehn, L.A., McDaneld, T.G., Tait Jr., R.G., Jones, S., Smith, T.P., Shackelford, S.D., King, D.A., Wheeler, T.L., Lindholm-Perry, A.K., McNeel, A.K. 2015. Genomewide association study of lung lesions in cattle using sample pooling. Journal of Animal Science. 93(3):956-964. DOI: 10.2527/jas.2014-8492.
Beef cattle metabiomes and their relationships with economically important phenotypes -
Myer, P.R., Wells, J., Smith, T.P., Kuehn, L.A., Freetly, H.C. 2015. Beef cattle metabiomes and their relationships with economically important phenotypes [abstract]. Journal of Animal Science. 93(Supplement 2):7.
Characterizing the microbiome across the gastrointestinal tract from steers differing in feed efficiency -
Myer, P.R., Wells, J., Smith, T.P., Kuehn, L.A., Freetly, H.C. 2015. Characterizing the microbiome across the gastrointestinal tract from steers differing in feed efficiency. Plant and Animal Genome XXIII Conference, January 10-14, 2015, San Diego, California. Abstract No. W288.
A polymorphism in myostatin influences puberty but not fertility in beef heifers, whereas µ-calpain affects first calf birth weight Reprint Icon -
Cushman, R.A., Tait Jr, R.G., McNeel, A.K., Forbes, E.D., Amundson, O.L., Lents, C.A., Lindholm-Perry, A.K., Perry, G.A., Wood, J.A., Cupp, A.S., Smith, T.P., Freetly, H.C., Bennett, G.L. 2015. A polymorphism in myostatin influences puberty but not fertility in beef heifers, whereas µ-calpain affects first calf birth weight. Journal of Animal Science. 93(1):117-126.
Comparative genomics of the Campylobacter lari group -
Miller, W.G., Yee, E., Chapman, M.H., Smith, T.P., Bono, J.L., Huynh, S., Parker, C., Vandamme, P., Luong, K., Korlach, J. 2014. Comparative genomics of the Campylobacter lari group. Genome Biology and Evolution. doi: 10.1093/gbe/evu249.
CAPN1, CAST, and DGAT1 genetic effects on preweaning performance, carcass quality traits, and residual variance of tenderness in a beef cattle population selected for haplotype and allele equalization Reprint Icon -
Tait, R.G., Jr., Shackelford, S.D., Wheeler, T.L., King, D.A., Keele, J.W., Casas, E., Smith, T.P., Bennett, G.L. 2014. CAPN1, CAST, and DGAT1 genetic effects on preweaning performance, carcass quality traits, and residual variance of tenderness in a beef cattle population selected for haplotype and allele equalization. Journal of Animal Science. 92(12):5382-5393.
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 -
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 -
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 -
SNPs for parentage testing and traceability in globally diverse breeds of sheep -
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 Reprint Icon -
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 -
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 -
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 -
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 -
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 -
Characterization of microbiomes related to respiratory disease in cattle -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
Tait Jr, R.G., Cushman, R.A., Smith, T.P., Freetly, H.C., Bennett, G.L. 2013. CAPN1 and GDF8 genetic marker effects on heifer performance, reproduction, and first calf performance traits in beef cattle [abstract]. Journal of Animal Science. 91(E-Supplement 2):392.
Genetic effects of GDF8 and CAPN1 for carcass and meat traits -
Salmonella virulence, genomics and interactions with the immune system -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 Reprint Icon -
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 -
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 -
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 -
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 -
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 -
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 -
Evaluation of bovine chemerin (RARRES2) gene variation on beef cattle production traits -
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 -
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 -
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 -
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 -
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 -
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 -
Application of combined SMRT and long-read pyrosequencing to produce reference genome sequences of bacteria associated with respiratory disease outbreaks in beef cattle -
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 Reprint Icon -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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. -
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 -
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 -
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.
Markers on Bovine Chromosome 20 Associated with Carcass Quality and Composition Traits and Incidence of Contracting Infectious Bovine Keratoconjunctivitis Reprint Icon -
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
Ovine Reference Materials and Assays for Prion Genetic Testing -
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/
Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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) -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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.
A rapid sequence-based method for comprehensive polymorphism identification within a 25.2-kb region of the bovine prion gene in BSE-affected cattle -
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.
Polymorphisms and haplotype structure of bovine PRND (doppel) and PRNT -
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 -
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.
ASSOCIATION OF A SINGLE NUCLEOTIDE POLYMORPHISM IN SPP1 WITH GROWTH TRAITS AND TWINNING IN A CATTLE POPULATION SELECTED FOR TWINNING RATE -
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. -
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 -
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 -
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 -
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 -
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. -
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 -
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.
IDENTIFICATION AND PROFILING OF BOVINE MICRORNAS FROM IMMUNE RELATED AND EMBRYONIC TISSUES. -
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 BOIVNE MICRORNAS EXPRESSED IN IMMUNE AND GUT TISSUES BY DEEP SEQUENCING -
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.
CHARACTERIZATION OF 954 BOVINE FULL-CDS CDNA SEQUENCES -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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. -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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. -
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. -
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 -
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.
PORCINE GENE-DISCOVERY BY NORMALIZED CDNA-LIBRARY SEQUENCING AND EST CLUSTER ASSEMBLY -
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 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 -
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.
DIFFERENTIAL EXPRESSION OF CYCLOOXYGENASE-2 AROUND THE TIME OF ELONGATION IN THE PIG CONCEPTUS -
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 -
Mammalian Genome. 2002. v. 13. p. 272-281.
USE OF BOVINE EST DATA AND HUMAN GENOMIC SEQUENCES TO MAP 100 GENE-SPECIFIC BOVINE MARKERS -
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.
SELECTION AND USE OF SINGLE NUCLEOTIDE POLYMORPHISM (SNP) MARKERS FOR ANIMAL IDENTIFICATION AND PATERNITY ANALYSIS IN U.S. BEEF CATTLE -
HAPLOTYPE STRUCTURE OF THE BOVINE NEONATAL FC RECEPTOR (BFCRN) GENE IN U.S.BEEF CATTLE AND ASSOCIATION WITH SERUM IGG CONCENTRATION IN NEWBORN CALVES -
SINGLE NUCLEOTIDE POLYMORPHISM (SNP) DISCOVERY IN PORCINE EXPRESSED GENES -
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 -
COMPARATIVE RADIATION HYBRID MAPPING OF THE MOUSE HIGH GROWTH (HG) REGION IN CATTLE AND PIGS -
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 -
IDENTIFICATION OF PORCINE LHX3 AND SF1 AS CANDIDATE GENES FOR QTL AFFECTING GROWTH AND REPRODUCTION TRAITS IN SWINE -
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 -
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 -
RAPID COMMUNICATION: LINKAGE MAPPING OF SEVEN BOVINE CDNAS -
SEQUENCE EVALUATION OF FOUR POOLED-TISSUE NORMALIZED BOVINE CDNA LIBRARIES AND CONSTRUCTION OF A GENE INDEX FOR CATTLE -
MAPPING EXPRESSED SEQUENCE TAGS (ESTS) IN PIGS USING SINGLE NUCLEOTIDE POLYMORPHISMS (SNPS) -
CONSTRUCTION OF SNP-BASED EST COMPARATIVE MAP OF SWINE, CATTLE, AND HUMAN GENOMES -
RAPID COMMUNICATION: LINKAGE MAPPING OF THE PORCINE MICROMOLAR CALCIUM ACTIVATED NEUTRAL PROTEASE 1 (UCALPAIN) GENE ON SSC2 -
RAPID COMMUNICATION: NUCLEOTIDE SEQUENCES OF TWO ISOFORMS OF PORCINE MICROMOLAR CALCIUM ACTIVATED NEUTRAL PROTEASE 1 CDNA -
PCR-BASED REACTION SETUP FOR HIGH-THROUGHPUT CDNA LIBRARY SEQUENCING ON THE ABI 3700 AUTOMATED DNA SEQUENCER -
DATABASE MANAGEMENT OF HIGH THROUGHPUT EST SEQUENCING AND SNP DISCOVERY -
BOVINE CAPN1 MAPS TO A REGION OF BTA29 CONTAINING A QTL FOR MEAT TENDERNESS -
RAPID COMMUNICATION: MAPPING OF NINE BOVINE MICROSATELLITE MARKERS OBTAINED FROM LARGE INSERT GENOMIC LIBRARIES -
PORCINE ERYTHROPOIETIN RECEPTOR: MOLECULAR CLONING AND EXPRESSION IN EMBRYONIC AND FETAL LIVER -
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 -
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.
LINKAGE MAPPING OF ESTS IN PIGS USING SINGLE NUCLEOTIDE POLYMORPHISMS (SNPS): II. HIGH-THROUGHPUT GENOTYPING AND MAPPING -
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 -
LINKAGE MAPPING ESTS IN PIGS USING SINGLE NUCLEOTIDE POLYMORPHISMS (SNPS): SNP DISCOVERY -
BOVINE CAPN1 MAPS TO A REGION OF BTA29 CONTAINING A QTL FOR MEAT TENDERNESS -
CHARACTERIZATION OF THE GENE FOR PORCINE ENDOMETRIAL/PLACENTAL MEMBRANE FOLATE BINDING PROTEIN (MFBP) -
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 -
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) -
FINE MAPPING OF A WARNER-BRATZLER SHEAR FORCE QUANTITATIVE TRAIT LOCUS ON BOVINE CHROMOSOME 15 -
THE PROCESS AND USE OF FUNCTIONAL GENOMICS IN BEEF CATTLE: SO YOU HAVE A QTL, NOW WHAT? -
QUANTITATIVE TRAIT LOCI ON BOVINE CHROMOSOMES 15 AND 29 EVIDENCE THAT HUMAN CHROMOSOME 11 HARBORS ORTHOLOGOUS GENES ASSOCIATED WITH LONGISSIMUS TENDERNESS IN BOVINE -
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)
TECHNICAL NOTE: DIRECT GENOTYPING OF THE DOUBLE-MUSCLING LOCUS (MH) IN PIEDMONTESE AND BELGIAN BLUE CATTLE BY FLUORESCENT PCR -
QUANTITATIVE ANALYSIS OF BIRTH, WEANING AND YEARLING WEIGHTS, AND CALVING DIFFICULTY IN PIEDMONTESE CROSSBREDS SEGREGATING AN INACTIVE MYOSTATIN ALLELE -
ISOLATION OF COMPLEMENTARY DEOXYRIBONUCLEIC ACIDS ENCODING PUTATIVE SECRETED AND MEMBRANE-BOUND FOLATE BINDING PROTEINS FROM ENDOMETRIUM OF SWINE -
PHYSICAL MAPPING OF THE BOVINE, CAPRINE AND OVINE HOMOLOGUES OF THE PAIRED BOX GENE PAX8 -
FINE MAPPING OF THE OVINE CALLIPYGE LOCUS -
FINE MAPPING OF A WARNER-BRATZLER SHEAR FORCE QTL ON BTA15 -
IDENTIFICATION AND GENETIC MAPPING OF BOVINE CHEMOKINE GENES EXPRESSED IN EPITHELIAL CELLS -
COMPARATIVE MAPPING: CYTOGENETIC LOCATION OF PROC, EN1, ALPI, TNP1, AND IL1B GENES IN CATTLE AND SHEEP REVEALS A CONSERVED REARRANGEMENT RELATIVE TO HUMAN GENOME. -
MAPPING BOVINE AND OVINE GENES WITH INTRONIC SINGLE NUCLEOTIDE POLYMORPHISMS -
PORCINE ERYTHROPOIETIN RECEPTOR: CLONING OF A PARTIAL CDNA AND EXPRESSION IN EMBRYONIC/FETAL LIVER -
STRUCTURE OF THE GENE FOR PORCINE ENDOMETRIAL FOLATE BINDING PROTEIN -
DISCOVERY OF MYOSTATIN AS THE GENE RESPONSIBLE FOR DOUBLE MUSCLING, AND IMPLICATIONS FOR MEAT PRODUCTION -
REFINEMENT OF BOVINE CHROMOSOME 2 LINKAGE MAP NEAR THE MH LOCUS REVEALS COMPLEX REARRANGEMENTS BETWEEN THE BOVINE AND HUMAN GENOMES. -
EXPRESSION-BASED GENE IDENTIFICATION AND SINGLE NUCLEOTIDE POLYMORPHISM (SNP) MAPPING IN CATTLE -
EVALUATION OF THE OVINE CALLIPYGE LOCUS: I. RELATIVE CHROMOSOMAL POSITION AND GENE ACTION -
EFFECT OF A MUTATION AT THE MYOSTATIN GENE ON EARLY LIFE WEIGHTS AND CALVING EASE IN A POPULATION OF PIEDMONTESE INHERITANCE -
SIMPLE GENETIC TEST THAT SUPPORTS MARKER ASSISTED SELECTION TO INCREASE RETAIL PRODUCT YIELD IN CATTLE -
MYOSTATIN MUTATIONS CAUSE DOUBLE MUSCLING IN CATTLE -
NARROWING A REGION OF RECOMBINATION RATE VARIATION ON BTA23 TO THE D23S22-D23S23 INTERVAL USING MEIOTIC BREAKPOINT ANALYSIS AND A YAC CONTIG -
MYOSTATIN MUTATIONS CAUSE DOUBLE MUSCLING IN CATTLE -
MYOSTATIN MAPS TO PORCINE CHROMOSOME 15 BY LINKAGE AND PHYSICAL ASSIGNMENT TO SSC15Q2.3 (SHORT COMMUNICATION) -
ASSOCIATION OF THE MUSCLE HYPERTROPHY LOCUS WITH CARCASS TRAITS IN BEEF CATTLE -
MUTATIONS IN MYOSTATIN (GDF8) IN DOUBLE MUSCLED BELGIAN BLUE CATTLE -
MYOSTATIN MAPS TO THE INTERVAL CONTAINING THE BOVINE MH LOCUS -
COMPARATIVE MAPPING OF BOVINE AND HUMAN CHROMOSOME 2 IDENTIFIES SEGMENTS OF CONSERVED SYNTENY CONTAINING THE BOVINE MH LOCUS -
ASSOCIATION OF THE DOUBLE-MUSCLING LOCUS ON BOVINE CHROMOSOME TWO (BTA2) WITH CARCASS TRAITS -
PORCINE UTERINE FOLATE BINDING PROTEING: FOLATE BINDING, CLONING OF A PARTIAL CDNA, AND MRNA EXPRESSION DURING THE ESTROUS CYCLE AND EARLY PREGNANCY -
DIRECTED COSMID ISOLATION FOR PHYSICAL ASSIGNMENT BY FISH: PCR-BASED ITERATIVE SCREENING OF RANDOM GENOMIC LIBRARIES -
HUMAN:BOVINE COMPARATIVE MAPPING TO IDENTIFY THE MH GENE IN CATTLE -
GENETIC ANALYSIS OF MEAT QUALITY IN CATTLE -
SHORT COMMUNICATION: PHYSICAL ASSIGNMENT OF GLUCAGON AND NEBULIN IN CATTLE, SHEEP AND GOAT -
ANCHORING OF BOVINE CHROMOSOMES 4, 6, 7, 10, AND 14 AND LINKAGE GROUP TELOMERIC ENDS VIA FISH ANALYSIS OF LAMBDA CLONES -
A SECOND GENERATION LINKAGE MAP OF THE BOVINE GENOME -
MAPPING OF HPRT GENE IN SWINE PROVIDES A REFERENCE LOCUS FOR SYNTENY COMPARISON -
PORCINE AROMATASES: STUDIES ON TISSUE-SPECIFIC, FUNCTIONALLY DISTINCT ISOZYMES FROM A SINGLE GENE? -
CONSTRUCTION AND CHARACTERIZATION OF A LARGE INSERT PORCINE YAC LIBRARY (SHORT COMMUNICATION) -
A GENETIC AND CYTOGENETIC MAP FOR BOVINE CHROMOSOME 11 -
USE OF LARGE INSERT GENOMIC LIBRARIES IN LIVESTOCK GENE MAPPING -
LINKAGE ASSIGNMENTS FOR HAS 19 CONSERVED REGIONS OF SYNTENY IN CATTLE, SHEEP AND SWINE -
CONSTRUCTION OF A PORCINE YEAST ARTIFICIAL CHROMOSOME (YAC) LIBRARY -
A COMPREHENSIVE MAP OF THE PORCINE GENOME -
SHORT COMMUNICATION: CONSTRUCTION AND CHARACTERIZATION OF A LARGE INSERT BOVINE YAC LIBRARY WITH 5-FOLD GENOMIC COVERAGE -
PHYSICAL ASSIGNMENTS OF 68 PORCINE COSMID AND LAMBDA CLONES CONTAINING POLYMORPHIC MICROSATELLITES -
IDENTIFYING TUMOR INITIATOR/SUPPRESSOR AND PENETRANCE-ASSOCIATED GENES BY GENE MAPPING -
SHORT COMMUNICATION: MAPPING OF A LINKAGE GROUP TO THE LAST BOVINE CHROMOSOME (BTA27) WITHOUT AN ASSIGNMENT -
DIRECTED INTEGRATION OF THE PHYSICAL AND GENETIC LINKAGE MAPS OF SWINE CHROMOSOME 7 REVEALS THAT THE SLA SPANS THE CENTROMERE -
DIRECTED INTEGRATION OF THE PHYSICAL AND GENETIC LINKAGE MAPS -
MOLECULAR CLONING OF PORCINE FAS ANTIGEN AND EXPRESSION IN CELL LINES DERIVED FROM MINIATURE SWINE -
Last Modified: 8/26/2016
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