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Timothy P Smith (Tim)
Research Chemist


Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)
QTL mapping to identify loci and candidate genes associated with freezing tolerance trait in camelina sativa. - (Peer Reviewed Journal)
Shaikh, T., Rahman, M., Anderson, J.V., Sthapit Kandel, J., Vaughn, J.N., Smith, T.P., Abernathy, B., Ontano, A., Dobrin, B.H., Horvath, D.P., Dorn, K.M. 2024. QTL mapping to identify loci and candidate genes associated with freezing tolerance trait in camelina sativa.. Industrial Crops and Products. 222:119562. https://doi.org/10.1016/j.indcrop.2024.119562.
Assembly and analysis of sequence from a spring and winter type Camelina sativa by whole genome PacBio Hifi technologies - (Peer Reviewed Journal)
Ontano, A., Dobrin, B.H., Smith, T.P., Abernathy, B., Sthapit Kandel, J., Shaikh, T., Rahman, M., Anderson, J.V., Vaughn, J.N., Horvath, D.P. 2024. Assembly and analysis of sequence from a spring and winter type Camelina sativa by whole genome PacBio Hifi technologies. Industrial Crops and Products. 221:119346. https://doi.org/10.1016/j.indcrop.2024.119346.
Disentangling river and swamp buffalo genetic diversity: initial insights from the 1000 buffalo genomes project - (Peer Reviewed Journal)
Pineda, P.S., Flores, E.B., Villamor, L.P., Parac, C.J.M., Khatkar, M.S., Thu, H.T., Smith, T.P.L., Rosen, B.D., Ajmone-Marsan, P., Colli, L., Williams, J.L., Low, W. et al. 2024. Disentangling river and swamp buffalo genetic diversity: initial insights from the 1000 buffalo genomes project. Gigascience. 13. Article giae053. https://doi.org/10.1093/gigascience/giae053.
Ultra-long sequencing experiences with a variety of mammalian sample types - ()
Enhanced bovine genome annotation through integration of transcriptomics and epi-transcriptomics datasets facilitates genomic biology - (Peer Reviewed Journal)
Beiki, H., Murdoch, B.M., Park, C.A., Kern, C., Kontechy, D., Becker, G., Rincon, G., Jiang, H., Zhou, H., Thorne, J., Koltes, J.E., Michal, J.J., Davenport, K.G., Rijnkels, M., Ross, P.J., Hu, R., Corum, S., McKay, S., Smith, T.P.L., Liu, W., Ma, W., Zhang, X., Xu, X., Han, X., Jiang, Z., Hu, Z., Reecy, J.M. 2024. Enhanced bovine genome annotation through integration of transcriptomics and epi-transcriptomics datasets facilitates genomic biology. Gigascience. 13. Article giae019. https://doi.org/10.1093/gigascience/giae019.
In search of a better way: Exploring the impact of enrichment and DNA extraction on long-read sequencing of rumen protozoa. - (Abstract Only)
McClure, J., Panke-Buisse, K. Lai, E., deHegedus, R.A., Zanton, G., French, E., Smith, T., Suen, G., Bickhart, D. 2024. In search of a better way: Exploring the effects of enrichment and DNA extraction on long-read sequencing of rumen protozoa [abstract]. Journal of Dairy Science. 107 (Supplement 1):268
Introgression and disruption of migration routes have shaped the genetic integrity of wildebeest populations - (Peer Reviewed Journal)
Liu, X., Lin, L., Sinding, M.S., Bertola, L.D., Hanghoj, K., Quinn, L., Garcia-Erill, G., Rasmussen, M.S., Schubert, M., Pecnerova, P., Balboa, R.F., Li, Z., Heaton, M.P., Smith, T.P.L., Pinto, R., Wang, X., Kuja, J., Bruniche-Olsen, A., Meisner, J., Santander, C.G., Ogutu, J.O., Masembe, C., da Fonseca, R.R., Muwanika, V., Siegismund, H.R., Albrechtsen, A., Moltke, I., Heller, R. 2024. Introgression and disruption of migration routes have shaped the genetic integrity of wildebeest populations. Nature Communications. 15. Article 2921. https://doi.org/10.1038/s41467-024-47015-y.
The genome of the yellow mealworm, Tenebrio molitor: It’s bigger than you think - (Peer Reviewed Journal)
Oppert, B.S., Dossey, A.T., Chu, F., Satovic-Vuksi, E., Plohl, M., Koren, S., Olmstead, M.L., Leierer, D., Ragan, G.C., Smith, T.P., Johnston, J. 2023. The genome of the yellow mealworm, Tenebrio molitor: It’s bigger than you think. Genes. 14(12). Article 2209. https://doi.org/10.3390/genes14122209.
African bush pigs exhibit porous species boundaries and appeared in Madagascar concurrently with human arrival - (Peer Reviewed Journal)
Balboa, R.F., Bertola, L., Bruniche-Olsen, A., Rasmussen, M., Liu, X., Besnard, G., Salmona, J., Santander, C.G., He, S., Zinner, D., Heaton, M.P., Smith, T.P., Moltke, I., Albrechtsen, A., Heller, R. et al. 2024. African bush pigs exhibit porous species boundaries and appeared in Madagascar concurrently with human arrival. Nature Communications. 15. Article 172. https://doi.org/10.1038/s41467-023-44105-1.
Escherichia coli O157:H7 tir 255 T > A allele strains differ in chromosomal and plasmid composition - (Peer Reviewed Journal)
Weinroth, M.D., Clawson, M.L., Harhay, G.P., Eppinger, M., Harhay, D.M., Smith, T.P.L., Bono, J.L. 2023. Escherichia coli O157:H7 tir 255 T > A allele strains differ in chromosomal and plasmid composition. Frontiers in Microbiology. 14. Article 1303387. https://doi.org/10.3389/fmicb.2023.1303387.
A reference assembly for the legume cover crop hairy vetch (Vicia villosa) - (Peer Reviewed Journal)
Fuller, T.D., Bickhart, D.M., Koch, L.M., Kucek, L.K., Ali, S., Mangelson, H., Monteros, M.J., Hernandez, T., Smith, T.P., Riday, H., Sullivan, M.L. 2023. A reference assembly for the legume cover crop hairy vetch (Vicia villosa). GigaByte. https://doi.org/10.46471/gigabyte.98.
Supporting data for "A reference assembly for the legume cover crop hairy vetch, Vicia villosa" - ()
Fuller, T.D., Bickhart, D.M., Koch, L.M., Kucek, L.K., Ali, S., Mangelson, H., Monteros, M.J., Hernandez, T., Smith, T.P., Riday, H., Sullivan, M.L. 2023. Supporting data for "A reference assembly for the legume cover crop hairy vetch, Vicia villosa". GigaByte. http://dx.doi.org/10.5524/102446.
African bush pigs exhibit porous species boundaries and appeared in Madagascar concurrently with human arrival - ()
Balboa, R.F., Bertola, L., Bruniche-Olsen, A., Rasmussen, M., Liu, X., Santander, C.G., He, S., Zinner, D., Heaton, M.P., Smith, T.P.L., Muwanika, V., Masembe, C., Schubert, M., Kuja, J., Quinn, L., Garcia-Erill, G., Lin, L., Wang, X., Moltke, I., Albrechtsen, A., Heller, R., et. al. 2023. African bush pigs exhibit porous species boundaries and appeared in Madagascar concurrently with human arrival. bioRxiv. https://doi.org/10.1101/2023.08.23.553838.
The bovine pangenome consortium: Democratizing production and accessibility of genome assemblies for global cattle breeds and other bovine species - (Peer Reviewed Journal)
Smith, T.P.L., Bickhart, D.M., Boichard, D., Chamberlain, A.J., Djikeng, A., Jiang, Y., Low, W., Pausch, H., Demyda-Peyras, S., Prendergast, J., Schnabel, R.D., Rosen, B.D. 2023. The bovine pangenome consortium: Democratizing production and accessibility of genome assemblies for global cattle breeds and other bovine species. Genome Biology. 24. Article 139. https://doi.org/10.1186/s13059-023-02975-0.
A reference assembly for the legume cover crop hairy vetch, Vicia villosa - ()
Fuller, T.D., Koch, L.M., Kucek, L.K., Ali, S., Haley, M., Hernandez, T., Smith, T.P., Bickhart, D.M., Riday, H., Sullivan, M.L. 2023. A reference assembly for the legume cover crop hairy vetch, Vicia villosa. bioRxiv. https://doi.org/10.1101/2023.03.28.534423.
Long read isoform sequencing reveals hidden transcriptional complexity between cattle subspecies - (Peer Reviewed Journal)
Ren, Y., Tseng, E., Smith, T.P.L., Hiendleder, S., Williams, J.L., Low, W. 2023. Long read isoform sequencing reveals hidden transcriptional complexity between cattle subspecies. BMC Genomics. 24. Article 108. https://doi.org/10.1186/s12864-023-09212-9.
Homozygosity mapping identified loci and candidate genes responsible for freezing tolerance in Camelina sativa - (Peer Reviewed Journal)
Shaikh, T., Rahman, M., Horvath, D.P., Smith, T.P., Anderson, J.V., Chao, W.S. 2023. Homozygosity mapping identified loci and candidate genes responsible for freezing tolerance in Camelina sativa. The Plant Genome. 16(2). Article e20318. https://doi.org/10.1002/tpg2.20318.
Improving blood phenomics: ISU station report - (Abstract Only)
Colonialism in Southern Africa leaves a lasting legacy of reduced genetic diversity in Cape buffalo - (Peer Reviewed Journal)
Quinn, L., Garcia-Erill, G., Santander, C., Bruniche-Olsen, A., Liu, X., Sinding, M.S., Heaton, M.P., Smith, T.P.L., Pecnerova, P., Bertola, L.D., Hanghoj, K., Rasmussen, M.S., De Jager, D., Siegismund, H.R., Albrechtsen, A., Heller, R., Moltke, I. 2023. Colonialism in Southern Africa leaves a lasting legacy of reduced genetic diversity in Cape buffalo. Molecular Ecology. Article 16851. https://doi.org/10.1111/mec.16851.
Genetic diversity and connectivity of moose (Alces americanus americanus) in eastern North America - (Peer Reviewed Journal)
Rosenblatt, E., Gieder, K., Donovan, T., Murdoch, J., Smith, T.P.L., Heaton, M.P., Kalbfleisch, T.S., Murdoch, B.M., Bhattarai, S., Pacht, E., Verbist, E., Basnayake, V., McKay, S. 2023. Genetic diversity and connectivity of moose (Alces americanus americanus) in eastern North America. Conservation Genetics. 24:235-248. https://doi.org/10.1007/s10592-022-01496-w.
Insight into weevil biology from a reference quality genome of the boll weevil, Anthonomus grandis grandis Boheman (Coleoptera: Curculionidae) - (Peer Reviewed Journal)
Cohen, Z.P., Perkin, L.C., Sim, S.B., Stahlke, A.R., Geib, S.M., Childers, A.K., Smith, T.P., Suh, C.P. 2022. Insight into weevil biology from a reference quality genome of the boll weevil, Anthonomus grandis grandis Boheman (Coleoptera: Curculionidae). G3, Genes/Genomes/Genetics. Article jkac309. https://doi.org/10.1093/g3journal/jkac309.
Assembly of a pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history - (Peer Reviewed Journal)
Zhou, Y., Yang, L., Han, X., Han, J., Hu, Y., Li, F., Xia, H., Peng, L., Boschiero, C., Rosen, B.D., Bickhart, D.M., Zhang, S., Guo, A., Van Tassell, C.P., Smith, T.P., Yang, L., Liu, G. 2022. Assembly of a pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history. Genome Research. 32(8):1585-1601. https://doi.org/10.1101/gr.276550.122.
Diversity of Alternative Splicing in Porcine Peripheral Blood Immune Cells - (Abstract Only)
Bacterial communities of the uterus and rumen during heifer development with protein supplementation - (Peer Reviewed Journal)
Ault-Seay, T.B., Brandt, K.J., Henniger, M.T., Payton, R.R., Mathew, D.J., Moorey, S.E., Schrick, F.N., Pohler, K.G., Smith, T.P.L., Rhinehart, J.D., Schneider, L.G., McLean, K.J., Myer, P.R. 2022. Bacterial communities of the uterus and rumen during heifer development with protein supplementation. Frontiers in Animal Science. 3. Article 903909. https://doi.org/10.3389/fanim.2022.903909.
Table 1. Genome sequence context for JMJD1C SNPs associated with bovine congestive heart failure (BCHF) - ()
Heaton, M., Harhay, G., Smith, T.P.L., Kuhn, K., Kalbfleisch, T.S., Jobman, E., Vander Ley, B. 2022. Table 1. Genome sequence context for JMJD1C SNPs associated with bovine congestive heart failure (BCHF). Figshare. Dataset. https://doi.org/10.6084/m9.figshare.19780558.v1.
Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies - (Peer Reviewed Journal)
Leonard, A.S., Crysnanto, D., Fang, Z., Heaton, M.P., Vander Ley, B.L., Herrera, C., Bollwein, H., Bickhart, D.M., Kuhn, K.L., Smith, T.P.L., Rosen, B.D., Pausch, H. 2022. Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies. Nature Communications. 13. Article 3012. https://doi.org/10.1038/s41467-022-30680-2.
Gaur genome reveals expansion of sperm odorant receptors in domesticated cattle - (Peer Reviewed Journal)
Low, W.Y., Rosen, B.D., Ren, Y., Bickhart, D.M., To, T., Martin, F.J., Billis, K., Sonstegard, T.S., Sullivan, S.T., Hiendleder, S., Williams, J.L., Heaton, M.P., Smith, T.P. 2022. Gaur genome reveals expansion of sperm odorant receptors in domesticated cattle. BMC Genomics. 23. Article 344. https://doi.org/10.1186/s12864-022-08561-1.
Discrete distributions of simple sequence repeat lengths in DNA template vary at individual loci in Mannheimia haemolytica isolates - (Proceedings)
The Australian dingo is an early offshoot of modern breed dogs - (Peer Reviewed Journal)
Field, M.A., Yadav, S., Dudchenko, O., Esvaran, M., Rosen, B.D., Skvortsova, K., Edwards, R.J., Keilwagen, J., Cochran, B.J., Manandhar, B., Bustamante, S., Rasmussen, J.A., Melvin, R.G., Chernoff, B., Omer, A., Colaric, Z., Chan, E.K., Minoche, A.E., Smith, T.P., Gilbert, T.P., Bogdanovic, O., Zammit, R.A., Thomas, T., Aien, E.L., Ballard, J.W. 2022. The Australian dingo is an early offshoot of modern breed dogs. Science Advances. 8(16):eabm5944. https://doi.org/10.1126/sciadv.abm5944.
Variations in antibody repertoires correlate with vaccine responses - (Peer Reviewed Journal)
Safonova, Y., Shin, S.B., Kramer, L., Reecy, J., Watson, C.T., Smith, T.P.L., Pevzner, P.A. 2022. Variations in antibody repertoires correlate with vaccine responses. Genome Research. 32:791-804. https://doi.org/10.1101/gr.276027.121.
The genome of Rhyzopertha dominica (Fab.) (Coleoptera: Bostrichidae): Adaptation for success - (Peer Reviewed Journal)
Oppert, B.S., Muszewska, A., Steczkiewicz, K., Šatovic-Vukšic, E., Plohl, M., Fabrick, J.A., Vinokurov, K.S., Koloniuk, I., Johnston, J., Smith, T.P., Guedes, R.C., Terra, W.R., Ferreira, C., Dias, R.O., Chaply, K.A., Elpidina, E.N., Tereshchenkova, V., Mitchell, M.F., Jenson, A.J., Mckay, R., Shan, T., Cao, X., Xiong, C., Jiang, H., Morrison III, W.R., Koren, S., Schlipalius, D., Lorenzen, M.D., Bansal, R., Wang, Y., Perkin, L.C., Poelcheau, M., Friesen, K.S., Olmstead, M.L., Scully, E.D., Campbell, J.F., et al. 2022. The genome of Rhyzopertha dominica (Fab.) (Coleoptera: Bostrichidae): Adaptation for success. Genes. 13(3). Article 446. https://doi.org/10.3390/genes13030446.
Chromosome-scale assembly of the highly heterozygous genome of red clover (Trifolium pratense L.), an allogamous forage crop species - (Peer Reviewed Journal)
Bickhart, D.M., Koch, L.M., Smith, T.P., Riday, H., Sullivan, M.L. 2022. Chromosome-scale assembly of the highly heterozygous genome of red clover (Trifolium pratense L.), an allogamous forage crop species. GigaByte. 42:1-13. https://doi.org/10.46471/gigabyte.42.
Defining the caprine ¿d T cell WC1 multigenic array and evaluation of its expressed sequences and gene structure conservation among goat breeds and relative to cattle - (Peer Reviewed Journal)
Supporting data for "Chromosome-scale assembly of the highly heterozygous genome of red clover (Trifolium pratense L.), an allogamous forage crop species" - ()
Chromosome-scale assembly of the highly heterozygous genome of red clover (Trifolium pratense L.), an allogamous forage crop species - ()
Bickhart, D.M., Koch, L.M., Smith, T.P., Riday, H., Sullivan, M.L. 2022. Chromosome-scale assembly of the highly heterozygous genome of red clover (Trifolium pratense L.), an allogamous forage crop species. bioRxiv. https://doi.org/10.1101/2022.01.06.475143.
An improved ovine reference genome assembly to facilitate in depth functional annotation of the sheep genome - (Peer Reviewed Journal)
Davenport, K.M., Bickhart, D.M., Worley, K.C., Murali, S.C., Salavati, M., Clark, E.L., Cockett, N., Heaton, M.P., Smith, T.P., Murdoch, B.M., Rosen, B.D. 2022. An improved ovine reference genome assembly to facilitate in depth functional annotation of the sheep genome. Gigascience. 11. Article giab096. https://doi.org/10.1093/gigascience/giab096.
FLC MidWest Regional Technology Transfer Award - (Abstract Only)
Evaluating large spontaneous deletions in a bovine cell line selected for bovine viral diarrhea virus resistance - (Peer Reviewed Journal)
Workman, A.M., Heaton, M.P., Webster, D.A., Harhay, G.P., Kalbfleisch, T.S., Smith, T.P.L., Falkenberg, S.M., Carlson, D.F., Sonstegard, T.S. 2021. Evaluating large spontaneous deletions in a bovine cell line selected for bovine viral diarrhea virus resistance. Viruses. 13(11). Article 2147. https://doi.org/10.3390/v13112147.
Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities - (Peer Reviewed Journal)
Bickhart, D.M., Kolmogorov, M., Tseng, E., Portik, D., Korobeynikov, A., Tolstoganov, I., Uritskiy, G., Liachko, I., Sullivan, S.T., Shin, S.B., Zorea, A., Andreu, V., Panke-Buisse, K., Medema, M., Mizrahi, I., Pevzner, P., Smith, T.P. 2022. Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities. Nature Biotechnology. 40:711-719. https://doi.org/10.1038/s41587-021-01130-z.
A conserved Histophilus somni 23S intervening sequence yields functional, fragmented 23S rRNA - (Peer Reviewed Journal)
Harhay, G.P., Harhay, D.M., Brader, K.D., Smith, T.P.L. 2021. A conserved Histophilus somni 23S intervening sequence yields functional, fragmented 23S rRNA. Microbiology Spectrum. 9(3). Article e0143121. https://doi.org/10.1128/Spectrum.01431-21.
Characterization of the respiratory microbiome and virome associated with bovine respiratory disease - (Abstract Only)
McDaneld, T., Earley, B., Cosby, L., McGee, M., Duffy, K., Cuevas-Gomez, I., Kuehn, L., Workman, A., Conant, G., Cormican, P., McCabe, M., Duffy, C., Lemon, K., McMenamy, M., Smyth, V., Smith, T. 2021. Characterization of the respiratory microbiome and virome associated with bovine respiratory disease [abstract]. In proceedings: Conference of Research Workers in Animal Diseases, December 4-7, 2021, Chicago, Illinois. V-P048. Available: https://crwad.org/wp-content/uploads/CRWAD-2021/
Adaptive selection signatures in river buffalo with emphasis on immune and major histocompatibility complex genes - (Peer Reviewed Journal)
Ren, Y., MacPhillamy, C., To, T., Smith, T.P.L., Williams, J.L., Low, W.Y. 2021. Adaptive selection signatures in river buffalo with emphasis on immune and major histocompatibility complex genes. Genomics. 113(6):3599-3609. https://doi.org/10.1016/j.ygeno.2021.08.021.
Revealing how variations in antibody repertoires correlate with vaccine responses - ()
Safonova, Y., Shin, S.B., Kramer, L., Reecy, J., Watson, C.T., Smith, T.P.L., Pevzner, P.A. 2021. Revealing how variations in antibody repertoires correlate with vaccine responses. bioRxiv. Article 454618. https://doi.org/10.1101/2021.08.06.454618.
Relationship of molecular breeding value for beef tenderness with heifer traits through weaning of their first calf - (Peer Reviewed Journal)
Cushman, R.A., Bennett, G.L., Tait, R.G., McNeel, A.K., Casas, E., Smith, T.P.L., Freetly, H.C. 2021. Relationship of molecular breeding value for beef tenderness with heifer traits through weaning of their first calf. Theriogenology. 173:128-132. https://doi.org/10.1016/j.theriogenology.2021.07.020.
Classification of small ruminant lentivirus subtype A2, subgroups 1 and 2 based on whole genome comparisons and complex recombination patterns [version 2; revised] - (Peer Reviewed Journal)
The USDA-ARS Ag100Pest Initiative: High-quality genome assemblies for agricultural pest Arthropod research - (Peer Reviewed Journal)
Childers, A.K., Geib, S.M., Sim, S.B., Poelchau, M.F., Coates, B.S., Simmonds, T.J., Scully, E.D., Smith, T.P.L., Childers, C., Corpuz, R.L., Hackett, K.J., Scheffler, B.E. 2021. The USDA-ARS Ag100Pest Initiative: High-quality genome assemblies for agricultural pest insect research. Insects. 12(7):626. https://doi.org/10.3390/insects12070626.
Ruminal protozoal populations of Angus steers differing in feed efficiency - (Peer Reviewed Journal)
Clemmons, B.A., Shin, S.B., Smith, T.P.L., Embree, M.M., Voy, B.H., Schneider, L.G., Donohoe, D.R., McLean, K.J., Myer, P. 2021. Ruminal protozoal populations of Angus steers differing in feed efficiency. Animals. 11(6). Article 1561. https://doi.org/10.3390/ani11061561.
Reference transcriptomes of porcine peripheral immune cells created through bulk and single-cell RNA sequencing - (Peer Reviewed Journal)
Herrera-Uribe, J., Wiarda, J., Sivasankaran, S.K., Daharsh, L., Liu, H., Byrne, K.A., Smith, T.P., Lunney, J.K., Loving, C.L., Tuggle, C.K. 2021. Reference transcriptomes of porcine peripheral immune cells created through bulk and single-cell RNA sequencing. Frontiers in Genetics. 12. Article 689406. https://doi.org/10.3389/fgene.2021.689406.
Generation of lineage-resolved complete metagenome-assembled genomes by precision phasing - ()
Bickhart, D.M., Kolmogorov, M., Tseng, E., Portik, D., Korobeynikov, A., Tolstoganov, I., Uritskiy, G., Liachko, I., Sullivan, S.T., Shin, S.B., Zorea, A., Andreu, V., Panke-Buisse, K., Medema, M., Mizrahi, I., Pevzner, P., Smith, T.P. 2021. Generation of lineage-resolved complete metagenome-assembled genomes by precision phasing. bioRxiv. https://doi.org/10.1101/2021.05.04.442591.
Variants in the mitochondrial genome sequence of Rhyzopertha dominica (Fabricius)(Coleoptera: Bostrycidae) - (Peer Reviewed Journal)
Perkin, L.C., Smith, T.P., Oppert, B.S., Poelchau, M. 2021. Variants in the mitochondrial genome sequence of Rhyzopertha dominica (Fabricius)(Coleoptera: Bostrycidae). Insects. 12(5). Article 387. https://doi.org/10.3390/insects12050387. LOG NO. 378692
Distinctive gene expression patterns and imprinting signatures revealed in reciprocal crosses between cattle sub-species - (Peer Reviewed Journal)
Liu, R., Tearle, R., Low, W., Chen, T., Thomsen, D., Smith, T.P.L., Hiendleder, S., Williams, J.L. 2021. Distinctive gene expression patterns and imprinting signatures revealed in reciprocal crosses between cattle sub-species. Biomed Central (BMC) Genomics. 22. Article 410. https://doi.org/10.1186/s12864-021-07667-2.
Variants at the ASIP locus contribute to coat color darkening in Nellore cattle - (Peer Reviewed Journal)
Trigo, B.B., Utsunomiya, A.T., Fortunato, A., Milanesi, M., Torrecilha, R.B., Lamb, H., Hayes, B., Nguyen, L., Ross, E., Padula, R.C., Sussai, T.S., Zavarez, L.B., Cipriano, R.S., Caminhas, M.M., Lopes, F.L., Lung, L.H., Pelle, C., Leeb, T., Bannasch, D., Bickhart, D.M., Smith, T.P.L, Garcia, J.F., Utsunomiya, Y.T. 2021. Variants at the ASIP locus contribute to coat color darkening in Nellore cattle. Genetics Selection Evolution. 53. Article 40. https://doi.org/10.1186/s12711-021-00633-2.
Characterizing genetic regulatory elements in ovine tissues - (Peer Reviewed Journal)
Davenport, K.M., Massa, A.T., Bhattarai, S., McKay, S.D., Mousel, M.R., Herndon, M.K., White, S.N., Cockett, N.E., Smith, T.P., Murdoch, B.M. 2021. Characterizing genetic regulatory elements in ovine tissues. Frontiers in Genetics. 12. Article 628849. https://doi.org/10.3389/fgene.2021.628849.
De novo assembly and annotation of the North American bison (Bison bison) reference genome and subsequent variant identification - (Peer Reviewed Journal)
Dobson, L.K., Zimin, A., Bayles, D., Fritz-Waters, E., Alt, D., Olsen, S., Blanchong, J., Reecy, J., Smith, T.P.L., Derr, J.N. 2021. De novo assembly and annotation of the North American bison (Bison bison) reference genome and subsequent variant identification. Animal Genetics. 52(3):263-274. https://doi.org/10.1111/age.13060.
DeNovo assembly and annotation of the North American Bison (bison bison)reference genome and subsequent variant identification - (Peer Reviewed Journal)
Dobson, L., Derr, J., Reecy, J., Zimin, A., Balnchong, J., Olsen, S.C., Alt, D.P., Bayles, D.O., Smith, T.P., Fritz-Waters, E., Konganti, K. 2022. DeNovo assembly and annotation of the North American Bison (bison bison)reference genome and subsequent variant identification. Animal Genetics. Animal Genetics Vol.52, Issue 3, pgs. 263-274. https://doi.org/10.1111/age.13060.
Development of polymorphic markers in the immune gene complex loci of cattle - (Peer Reviewed Journal)
Bakshy, K., Heimeier, D., Schwartz, J.C., Glass, E.J., Wilkinson, S., Skuce, R.A., Allen, A.R., Young, J., McClure, J.C., Cole, J.B., Null, D.J., Hammond, J.A., Smith, T.P.L., Bickhart, D.M. 2021. Development of polymorphic markers in the immune gene complex loci of cattle. Journal of Dairy Science. 104(6):6897-6908. https://doi.org/10.3168/jds.2020-19809.
Characterization of the domestic goat yd T cell receptor gene loci and gene usage - (Peer Reviewed Journal)
Gillespi, A., Yirsaw, A., Gunasekaran, K.P., Smith, T.P., Bickhart, D.M., Turley, M., Connelley, T., Telfer, J.C., Baldwin, C.L. 2021. Characterization of the domestic goat yd T cell receptor gene loci and gene usage. Immunogenetics. 73:187-201. https://doi.org/10.1007/s00251-021-01203-y.
A reference genome assembly of American bison, Bison bison bison - (Peer Reviewed Journal)
Oppenheimer, J., Rosen, B.D., Heaton, M.P., Vander Ley, B.L., Shafer, W.R., Schuetze, F.T., Stroud, B., Kuehn, L.A., McClure, J.C., Barfield, J.P., Blackburn, H.D., Kalbfleisch, T.S., Bickhart, D.M., Davenport, K.M., Kuhn, K.L., Green, R.E., Shapiro, B., Smith, T.P.L. 2021. A reference genome assembly of American bison, Bison bison bison. Journal of Heredity. 112(2):174-183. https://doi.org/10.1093/jhered/esab003.
A reference genome assembly of Simmental cattle, Bos taurus taurus - (Peer Reviewed Journal)
Heaton, M.P., Smith, T.P.L., Bickhart, D.M., Vander Ley, B.L., Kuehn, L.A., Oppenheimer, J., Shafer, W.R., Schuetze, F.T., Stroud, B., McClure, J.C., Barfield, J.P., Blackburn, H.D., Kalbfleisch, T.S., Davenport, K.M., Kuhn, K.L., Green, R.E., Shapiro, B., Rosen, B.D. 2021. A reference genome assembly of Simmental cattle, Bos taurus taurus. Journal of Heredity. 112(2):184-191. https://doi.org/10.1093/jhered/esab002.
Classification of small ruminant lentivirus subtype A2, subgroups 1 and 2 based on whole genome comparisons and complex recombination patterns - ()
Dickey, A.M., Smith, T.P.L., Clawson, M.L., Heaton, M.P., Workman, A.M. 2020. Classification of small ruminant lentivirus subtype A2, subgroups 1 and 2 based on whole genome comparisons and complex recombination patterns. F1000Research. 9:1449. https://doi.org/10.12688/f1000research.27898.1.
Complete genome sequence of Serratia sp. strain CC119 associated with inner cotton boll rot via insect vector transmission - (Peer Reviewed Journal)
Medrano, E.G., Smith, T.P., Bell, A.A., Brewer, M.J., Glover, J.P. 2020. Complete genome sequence of Serratia sp. strain CC119 associated with inner cotton boll rot via insect vector transmission. Microbiology Resource Announcements. 9(50). https://doi.org/10.1128/MRA.01077-20.
Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C - (Peer Reviewed Journal)
Kronenberg, Z.N., Rhie, A., Koren, S., Concepcion, G., Peluso, P., Munson, K.M., Porubsky, D., Kuhn, K.L., Mueller, K.A., Low, W., Hiendleder, S., Fedrigo, O., Liachko, I., Hall, R.J., Phillippy, A.M., Eichler, E.E., Williams, J.L., Smith, T.P.L., Jarvis, E.D., Sullivan, S.T., Kingan, S.B. 2021. Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C. Nature Communications. 12. Article 1935. https://doi.org/10.1038/s41467-020-20536-y.
Improving metagenome assemblies with long read sequence data - (Abstract Only)
Bickhart, D.M., Koren, S., Kolmogorov, M., Watson, M., Pevzner, P., Phillippy, A.M., Smith, T.P. 2020. Improving metagenome assemblies with long read sequence data. Cold Spring Harbor Meeting. October 20-24, 2020. Virtual Meeting.
Global analysis of transcription start sites in the new ovine reference genome (Oar rambouillet v1.0) - (Peer Reviewed Journal)
Salavati, M., Caulton, A., Clark, R., Gazova, I., Smith, T.P.L., Worley, K.C., Cockett, N.E., Archibald, A.L., Clarke, S., Murdoch, B.M., Clark, E.L. 2020. Global analysis of transcription start sites in the new ovine reference genome (Oar rambouillet v1.0). Frontiers in Genetics. Article e580580. https://doi.org/10.3389/fgene.2020.580580.
The Bovine Pangenome Consortium - (Abstract Only)
Bickhart, D.M., Rosen, B.D., Smith, T.P. 2020. The Bovine Pangenome Consortium. Meeting Abstract. Biodiversity Genomics Conference October 5-9, 2020, Virtual Meeting.
metaFlye: scalable long-read metagenome assembly using repeat graphs - (Peer Reviewed Journal)
Kolmogorov, M., Bickhart, D.M., Behsaz, B., Gurevich, A., Rayko, M., Shin, S.B., Kuhn, K.L., Yuan, J., Polevikov, E., Smith, T.P.L., Pevzner, P.A. 2020. metaFlye: scalable long-read metagenome assembly using repeat graphs. Nature Methods. 17:1103-1110. https://doi.org/10.1038/s41592-020-00971-x.
Circular closed contigs in a sheep fecal metagenome using metaFlye and high-fidelity long-reads - (Abstract Only)
Bickhart, D.M., Kolmogorov, M., Medema, M.H., Korobeynikov, A., Mizrahi, I., Pevzner, P., Smith, T.P. 2020. Circular closed contigs in a sheep fecal metagenome using metaFlye and high-fidelity long-reads. Cold Spring Harbor Laboratory's Microbiome Conference. October 20-23, 2020. Virtual Meeting.
Reassembly of cattle immune gene clusters for quantitative analysis - (Abstract Only)
Differences between predicted outer membrane proteins of genotype 1 and 2 Mannheimia haemolytica - (Peer Reviewed Journal)
Clawson, M.L., Schuller, G., Dickey, A.M., Bono, J.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., Blom, J., Chitko-McKown, C.G., Brichta-Harhay, D.M., Smith, T.P.L. 2020. Differences between predicted outer membrane proteins of genotype 1 and 2 Mannheimia haemolytica. BMC Microbiology. 20:250. https://doi.org/10.1186/s12866-020-01932-2.
Classification of 16S rRNA reads is improved using a niche-specific database constructed by near-full length sequencing - (Peer Reviewed Journal)
Myer, P.R., McDaneld, T.G., Kuehn, L.A., Dedonder, K.D., Apley, M.D., Capik, S.F., Lubbers, B.V., Harhay, G.P., Harhay, D.M., Keele, J.W., Henniger, M.T., Clemmons, B.A., Smith, T.P.L. 2020. Classification of 16S rRNA reads is improved using a niche-specific database constructed by near-full length sequencing. PLoS One. 15(7):e0235498. https://doi.org/10.1371/journal.pone.0235498.
Improving metagenome assemblies with long read sequence data - (Abstract Only)
An improved pig reference genome sequence to enable pig genetics and genomics research - (Peer Reviewed Journal)
Warr, A., Affara, N., Aken, B., Beiki, H., Bickhart, D.M., Billis, K., Chow, W., Eory, L., Finlayson, H.A., Flicek, P., Giron, C.G., Griffin, D.K., Hall, R., Hannum, G., Hourlier, T., Howe, K., Hume, D.A., Izuogu, O., Kim, K., Koren, S., Liu, H., Manchanda, N., Martin, F.J., Nonneman, D.J., O'Connor, R.E., Phillippy, A.M., Rohrer, G.A., Rosen, B.D., Rund, L.A., Sargent, C.A., Schook, L.B., Schroeder, S.G., Shwartz, A.S., Skinner, B.M., Talbot, R., Tseng, E., Tuggle, C.K., Watson, M., Smith, T.P., Archibald, A.L. 2020. An improved pig reference genome sequence to enable pig genetics and genomics research. GigaScience. 9(6):giaa051. https://doi.org/10.1093/gigascience/giaa051.
Resistance to bovine viral diarrhea virus (BVDV) infection in the bovine kidney CRIB cell line is not due to PTPN12, GRID2, or RABGAP1L mutations - (Abstract Only)
Workman, A.M., Heaton, M.P., Webster, D.A., Kalbfleisch, T.S., Smith, T.P., Carlson, D.F., Sonstegard, T.S. 2020. Resistance to bovine viral diarrhea virus (BVDV) infection in the bovine kidney CRIB cell line is not due to PTPN12, GRID2, or RABGAP1L mutations [abstract]. In: Proceedings of American Society for Virology Meeting, June 13-17, 2020, Fort Collins, Colorado. Poster No. P37-1.
Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle - (Peer Reviewed Journal)
Low, W., Tearle, R., Liu, C., Koren, S., Rhie, A., Bickhart, D.M., Rosen, B.D., Kronenberg, Z.N., Kingan, S.B., Tseng, E., Thibaud-Nissen, F., Martin, F., Billis, K., Ghurye, J., Hastie, A.R., Lee, J., Pang, A., Heaton, M.P., Phillippy, A.M., Hiendleder, S., Smith, T.P., Williams, J.L. 2020. Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle. Nature Communications. 11:2071. https://doi.org/10.1038/s41467-020-15848-y.
Continuous chromosome-scale haplotypes assembled from a single interspecies F1 hybrid of yak and cattle - (Peer Reviewed Journal)
Rice, E.S., Koren, S., Rhie, A., Heaton, M.P., Kalbfleisch, T., Hardy, T., Hackett, P., Bickhart, D.M., Rosen, B.D., Vander Ley, B., Maurer, N.W., Green, R.E., Phillippy, A.M., Petersen, J.L., Smith, T.P. 2020. Continuous chromosome-scale haplotypes assembled from a single interspecies F1 hybrid of yak and cattle. GigaScience. 9(4):1-9. https://doi.org/10.1093/gigascience/giaa029.
Canfam_GSD: Denovochromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C - (Peer Reviewed Journal)
Field, M.A., Rosen, B.D., Dudchenko, O., Chan, E.K.F., Minoche, A.E., Edwards, R.J., Barton, K., Lyons, R.J., Enosi Tuipulotu, D., Hayes, V.M., Omer, A.D., Colaric, Z., Keilwagen, J., Skvortsova, K., Bogdanovic, O., Smith, M.A., Aiden, E.L., Smith, T.P., Zammit, R.A., Ballard, J.O. 2020. Canfam_GSD: Denovochromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C. GigaScience. 9(4):1-12. https://doi.org/10.1093/gigascience/giaa027.
De novo assembly of the cattle reference genome with single-molecule sequencing - (Peer Reviewed Journal)
Rosen, B.D., Bickhart, D.M., Schnabel, R.D., Koren, S., Elsik, C.G., Tseng, E., Rowan, T.N., Low, W.Y., Zimin, A., Couldrey, C., Hall, R., Li, W., Rhie, A., Ghurye, J., McKay, S.D., Thibaud-Nissen, F., Hoffman, J., Murdoch, B.M., Snelling, W.M., McDaneld, T.G., Hammond, J.A., Schwartz, J.C., Nandolo, W., Hagen, D.E., Dreischer, C., Schultheiss, S.J., Schroeder, S.G., Phillippy, A.M.,Cole, J.B., Van Tassell, C.P., Liu, G., Smith, T.P.L., Medrano, J.F. 2020. De novo assembly of the cattle reference genome with single-molecule sequencing. GigaScience. 9(3):1-9. https://doi.org/10.1093/gigascience/giaa021.
Next-generation sequencing identifies polyunsaturated fatty acid responsive genes in the juvenile rat cerebellum - (Peer Reviewed Journal)
Mehus, A.A., Dickey, A.M., Smith, T.P., Yeater, K.M., Picklo, M.J. 2019. Next-generation sequencing identifies polyunsaturated fatty acid responsive genes in the juvenile rat cerebellum. Nutrients. https://doi.org/10.3390/nu11020407.
Developmental and allele-specific methylation patterns in fetal liver of pigs derived from White Composite x Meishan reciprocal crosses - (Abstract Only)
Corbett, R.J., Liu, H., Nonneman, D., Smith, T.P.L., Raney, N.E., Tuggle, C.K., Ernst, C.W. 2020. Developmental and allele-specific methylation patterns in fetal liver of pigs derived from White Composite x Meishan reciprocal crosses [abstract]. In proceedings: Plant and Animal Genome Conference, San Diego, CA, 11-15 Jan 2020. W034. Available: https://plan.core-apps.com/pag_2020/abstract/b96984cc-5afc-4dce-b908-9c79e4ac4e85.
Advances in sequencing technology herald a new frontier in cattle genomics and genome-enabled selection - ()
Bickhart, D.M., McClure, J.C., Schnabel, R.D., Rosen, B.D., Medrano, J.F., Smith, T.P.L. 2020. Advances in sequencing technology herald a new frontier in cattle genomics and genome-enabled selection. Journal of Dairy Science. 103(6):5278-5290. https://doi.org/10.3168/jds.2019-17693.
New insights into mammalian sex chromosome structure and evolution using high-quality sequences from bovine X and Y chromosomes - (Peer Reviewed Journal)
Liu, R., Yee Low, W., Tearle, R., Koren, S., Ghurye, J., Rhie, A., Phillippy, A.M., Rosen, B.D., Bickhart, D.M., Smith, T.P., Hiendleder, S., Williams, J.L. 2019. New insights into mammalian sex chromosome structure and evolution using high-quality sequences from bovine X and Y chromosomes. BMC Genomics. 20:1000. https://doi.org/10.1186/s12864-019-6364-z.
Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation - (Abstract Only)
Optimized extraction of insect genomic DNA for long-read sequencing - (Peer Reviewed Journal)
Oppert, B.S., Stoss, S.P., Monk, A.L., Smith, T.P. 2019. Optimized extraction of insect genomic DNA for long-read sequencing. Methods and Protocols. 2(4):89. https://doi.org/10.3390/mps2040089.
Genome assemblies of global cattle breeds to create a cattle Pangenome - (Abstract Only)
Smith, T.P.L, Bickhart, D.M., Rosen, B.D. 2020. Genome assemblies of global cattle breeds to create a cattle Pangenome [abstract]. International Plant & Animal Genome XXVIII Conference, January 11-15, 2020, San Diego, California. Poster Number PE0318. Available at: https://plan.core-apps.com/pag_2020/abstracts
The structure, evolution, and gene expression within the caprine leukocyte receptor complex - (Peer Reviewed Journal)
Schwartz, J.C., Sanderson, N.D., Bickhart, D.M., Smith, T.P., Hammond, J.A. 2019. The structure, evolution, and gene expression within the caprine leukocyte receptor complex. Frontiers in Immunology. 10:2302. https://doi.org/10.3389/fimmu.2019.02302.
Progress report on a plains bison-Simmental interspecies cross for genome assembly by trio binning - ()
Heaton, M.P., Kuehn, L.A., Vander Ley, B.L., Clark, H.J., Shafer, W., Schuetze, F., Stroud, B., Barfield, J.P., Blackburn, H.D., Kalbfleisch, T.S., Rosen, B.D., Bickhart, D.M., Oppenheimer, J., Shapiro, B., Green, R.E., Smith, T.P. 2019. Progress report on a plains bison-Simmental interspecies cross for genome assembly by trio binning [abstract]. Fall Focus 2019, Manhattan, Kansas, August 25-27, 2019. Available: https://simmental.org.
Chromosome-length haplotigs for yak and cattle from trio binning assembly of an F1 hybrid - ()
Rice, E.S., Koren, S., Rhie, A., Heaton, M.P., Kalbfleisch, T.S., Hardy, T., Hackett, P.H., Bickhart, D.M., Rosen, B.D., Vander Ley, B., Maurer, N.W., Green, R.E., Phillippy, A.M., Petersen, J.L., Smith, T.P.L. 2019. Chromosome-length haplotigs for yak and cattle from trio binning assembly of an F1 hybrid. bioRxiv. 737171. https://doi.org/10.1101/737171.
Characterization of the respiratory microbiome and virome associated with bovine respiratory disease complex - (Abstract Only)
McDaneld, T.G., Earley, B., McGee, M., Kuehn, L.A., Workman, A.M., Conant, G., Cormican, P., McCabe, M., Duffy, C., Lemon, K., McMenamy, M., Smyth, V., Smith, T.P., Cosby, L. 2019. Characterization of the respiratory microbiome and virome associated with bovine respiratory disease complex [abstract]. Conference of Research Workers in Animal Diseases Conference, November 2-5, 2019, Chicago, Illinois. P213. Available: https://crwad.org/crwad-2019/
Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation - (Peer Reviewed Journal)
Bickhart, D.M., Watson, M., Koren, S., Panke-Buisse, K., Cersosimo, L.M., Press, M.O., Van Tassell, C.P., Van Kessel, J.S., Haley, B.J., Kim, S., Heiner, C., Suen, G., Bakshy, K., Liachko, I., Sullivan, S.T., Myer, P.R., Ghurye, J., Pop, M., Weimer, P., Phillippy, A., Smith, T.P. 2019. Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation. Genome Biology. 20:153. https://doi.org/10.1186/s13059-019-1760-x.
Uterine and vaginal bacterial community diversity prior to artificial insemination between pregnant and nonpregnant postpartum cows - (Peer Reviewed Journal)
Ault, T.B., Clemmons, B.A., Reese, S.T., Dantas, F.G., Franco, G.A., Smith, T.P.L., Edwards, J.L., Myer, P.R., Pohler, K.G. 2019. Uterine and vaginal bacterial community diversity prior to artificial insemination between pregnant and nonpregnant postpartum cows. Journal of Animal Science. 97(10):4298-4304. https://doi.org/10.1093/jas/skz210.
Bacterial taxonomic composition of the postpartum cow uterus and vagina prior to artificial insemination - (Peer Reviewed Journal)
Ault, T.B., Clemmons, B.A., Reese, S.T., Dantas, F.G., Franco, G.A., Smith, T.P.L., Edwards, J.L., Myer, P.R., Pohler, K.G. 2019. Bacterial taxonomic composition of the postpartum cow uterus and vagina prior to artificial insemination. Journal of Animal Science. 97(10):4305-4313. https://doi.org/10.1093/jas/skz212.
Relationship of molecular breeding value for beef tenderness on heifer traits through weaning their first calf - (Abstract Only)
Bennett, G.L., Cushman, R.A., McNeel, A.K., Casas, E., Smith, T.P.L. 2019. Relationship of molecular breeding value for beef tenderness on heifer traits through weaning their first calf [abstract]. Journal of Animal Science. 97(Suppl3):266-267. https://doi.org/10.1093/jas/skz258.542.
Genomics in animal agriculture: current technologies and applications - (Abstract Only)
Smith, T.P.L. 2019. Genomics in animal agriculture: current technologies and applications [abstract}. Journal of Animal Science. 97(Supplement 3):55-56. https://doi.org/10.1093/jas/skz258.113.
Improved annotation of the domestic pig genome through integration of Iso-Seq and RNA-seq data - (Peer Reviewed Journal)
Beiki, H., Liu, H., Manchanda, N., Nonneman, D.J., Smith, T.P.L., Reecy, J., Tuggle, C. 2019. Improved annotation of the domestic pig genome through integration of Iso-Seq and RNA-seq data. BMC Genomics. 20:344-362. https://doi.org/10.1186/s12864-019-5709-y.
Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation - (Abstract Only)
From phenotype to gene discovery: A case study of host genetics influencing porcine circovirus 2 susceptibility - (Abstract Only)
Walker, L., Wijesena, H., Sutton, K., Vu, H., Nonneman, D., Smith, T., Plastow, G., Kachman, S., Ciobanu, D. 2019. From phenotype to gene discovery: A case study of host genetics influencing porcine circovirus 2 susceptibility [abstract]. In proceedings: 37th International Society for Animal Genetics (ISAG). 7-12 July 2019, Lleida, Spain. p. 7. Abstract OP25.
Genome to Phenome: Improving animal health, production, and well-being: A new USDA blueprint for animal genome research 2018–2027 - (Peer Reviewed Journal)
Rexroad III, C.E., Vallet, J.L., Matukumalli, L.K., Ernst, C., Van Tassell, C.P., Cheng, H.H., Reecy, J., Fulton, J., Taylor, J., Lunney, J.K., Liu, J., Cockett, N., Smith, T.P., Van Eenennaam, A., Clutter, A., Telugu, B., Purcell, C., Bickhart, D.M., Blackburn, H.D., Neibergs, H., Wells, K., Boggess, M.V., Sonstegard, T. 2019. Genome to phenome: improving animal health, production, and well-being: a new USDA blueprint for animal genome research 2018–2027. Frontiers in Genetics. 10:327. https://doi.org/10.3389/fgene.2019.00327.
Linking the Resistome to the Microbiome: A Culture-Free Method Links Plasmid, Virus, and Antimicrobial Resistance Genes to their Hosts in Complex Microbial Populations - (Abstract Only)
Characterization of A-to-I editing events in fetal pig tissues - (Abstract Only)
Corbett, R.J., Funkhouser, S.A., Nonneman, D.J., Smith, T.P.L., Ernst, C.W. 2019. Characterization of A-to-I editing events in fetal pig tissues [abstract]. In Proceedings: 37th International Society for Animal Genetics (ISAG). 7-12 July 2019, Lleida, Spain. pg. 24. Abstract OP86.
Structural diversity of ultralong CDRH3s in seven bovine antibody heavy chains - (Peer Reviewed Journal)
Dong, J., Finn, J.A., Larsen, P.A., Smith, T.P.L., Crowe, J.E. 2019. Structural diversity of ultralong CDRH3s in seven bovine antibody heavy chains. Frontiers in Immunology. 10:558. https://doi.org/10.3389/fimmu.2019.00558.
Host synaptogyrin-2 facilitates replication of PCV2b - (Abstract Only)
Walker, L., Engle, T., Vu, H., Tosky, E., Nonneman, D., Smith, T., Borza, T., Burkey, T., Plastow, G., Kachman, S., Ciobanu, D. 2019. Host synaptogyrin-2 facilitates replication of PCV2b [abstract]. In proceedings: 37th International Society for Animal Genetics (ISAG). 7-12 July 2019, Lleida, Spain. pg. 119. Abstract P208.
A computational method to quantify the effects of slipped strand mispairing on bacterial tetranucleotide repeats - (Peer Reviewed Journal)
Harhay, G.P., Harhay, D.M., Bono, J.L., Capik, S.F., DeDonder, K.D., Apley, M.D., Lubbers, B.V., White, B.J., Larson, R.L., Smith, T.P.L. 2019. A computational method to quantify the effects of slipped strand mispairing on bacterial tetranucleotide repeats. Nature Scientific Reports. 9:18087. https://doi.org/10.1038/s41598-019-53866-z.
The enigmatic role of host genetics in disease susceptibility: a case study of Porcine circovirus 2 - (Abstract Only)
Walker, L.R., Engle, T.B., Vu, H., Tosky, E.R., Nonneman, D.J., Smith, T.P.L., Borza, T., Burkey, T.E., Plastow, G.S., Kachman, S.D., Ciobanu, D.C. 2019. The enigmatic role of host genetics in disease susceptibility: a case study of Porcine circovirus 2 [abstract]. In: Plant and Animal Genome Conference Proceedings XXVII, 12-16 January 2019, San Diego, CA. pg. 232. W1128. Available: https://www.intlpag.org/2019/images/pdf/2019/PAGXXVII-abstracts-workshops.pdf
Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity - (Peer Reviewed Journal)
Yee Low, W., Tearle, R., Bickhart, D.M., Rosen, B.D., Kingan, S.B., Swale, T., Thibaud-Nissen, F., Murphy, T., Young, R., Lefevre, L., Hume, D., Collins, A., Ajmone-Marsan, P., Smith, T.P., Williams, J. 2019. Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity. Nature Communications. 10:260. https://doi.org/10.1038/s41467-018-08260-0.
A bovine CD18 signal peptide variant with increased binding activity to Mannheimia hemolytica leukotoxin - (Peer Reviewed Journal)
Workman, A.M., Chitko-McKown, C.G., Smith, T.P.L., Bennett, G.L., Kalbfleisch, T.S., Basnayake, V., Heaton, M.P. 2018. A bovine CD18 signal peptide variant with increased binding activity to Mannheimia hemolytica leukotoxin. F1000Research. 7:1985. https://doi.org/10.12688/f1000research.17187.1.
Complete genome sequence of a Salmonella enterica subsp. enterica serovar Fresno isolate recovered from beef cattle lymph nodes - (Peer Reviewed Journal)
Haley, B.J., Smith, T.P., Harhay, G.P., Loneragan, G.H., Webb, H.E., Bugarel, M., Kim, S., Van Kessel, J.S., Harhay, D.M. 2019. Complete genome sequence of a Salmonella enterica subsp. enterica serovar Fresno isolate recovered from beef cattle lymph nodes. Microbiology Resource Announcements. 8(2):e01338-18. https://doi.org/10.1128/MRA.01338-18.
Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation - (Abstract Only)
Short communication: Identification of the pseudoautosomal region in the Hereford bovine reference genome assembly ARS-UCD1.2 - (Peer Reviewed Journal)
Johnson, T., Keehan, M., Harland, C., Lopdell, T., Spelman, R.J., Davis, S.R., Rosen, B.D., Smith, T.P., Couldrey, C. 2019. Short communication: Identification of the pseudoautosomal region in the Hereford bovine reference genome assembly ARS-UCD1.2. Journal of Dairy Science. 102(4):3254-3258. https://doi.org/10.3168/jds.2018-15638.
Functional annotation of the porcine genome and ISAFG update - (Abstract Only)
Tuggle, C.K., Zhou, H., Ernst, C.W., Loving, C.L., Koltes, J.E., Reecy, J.M., Ross, P.J., Nonneman, D.J., Smith, T.P.L., Steibel, J.P., Huang, W. 2019. Functional annotation of the porcine genome and ISAFG update [abstract]. In: Plant and Animal Genome Conference XXVII Proceedings, 12-16 Jan 2019, San Diego, CA. pg. 96. W448. Available: https://www.intlpag.org/2019/images/pdf/2019/PAGXXVII-abstracts-workshops.pdf
Host genetics influences replication of porcine circovirus 2b - (Abstract Only)
Walker, L.R., Engle, T.B., Vu, H., Tosky, E.R., Nonneman, D.J., Smith, T.P.L., Borza, T., Burkey, T.E., Plastow, G.S., Kachman, S.D., Ciobanu, D.C. 2019. Host genetics influences replication of porcine circovirus 2b [abstract]. In: Plant and Animal Genome Conference XXVII Proceedings, 12-16 January 2019, San Diego, CA. pg. 233. W1136. Available: https://www.intlpag.org/2019/images/pdf/2019/PAGXXVII-abstracts-workshops.pdf
Deciphering the dynamics of porcine circovirus associated diseases using gene silencing and editing - (Abstract Only)
Walker, L., Engle, T., Vu, H., Tosky, E., Nonneman, D.J., Smith, T.P.L., Borza, T., Burkey, T., Plastow, G.S., Kachman, S.D., Ciobanu, D.C. 2019. Deciphering the dynamics of porcine circovirus associated diseases using gene silencing and editing [abstract]. In: Plant and Animal Genome Conference Proceedings XXVII, 12-16 Jan. 2019, San Diego, CA. pg. 216, W1045. Available: https://www.intlpag.org/2019/images/pdf/2019/PAGXXVII-abstracts-workshops.pdf
Enhanced estimates of carcass and meat quality effects for polymorphisms in myostatin and mu-calpain genes - (Peer Reviewed Journal)
Bennett, G.L., Tait, R.G., Shackelford, S.D., Wheeler, T.L., King, D.A., Casas, E., Smith, T.P.L. 2019. Enhanced estimates of carcass and meat quality effects for polymorphisms in myostatin and mu-calpain genes. Journal of Animal Science. 97(2):569-577. https://doi.org/10.1093/jas/sky451.
Complete closed genome sequences of three Salmonella enterica subsp. enterica Serovar Dublin strains isolated from cattle at harvest - (Peer Reviewed Journal)
Harhay, D.M., Smith, T.P.L., Harhay, G.P., Loneragan, G.H., Webb, H.E., Bugarel, M., Haley, B.J., Kim, S.W., Van Kessel, J.S. 2018. Complete closed genome sequences of three Salmonella enterica subsp. enterica Serovar Dublin strains isolated from cattle at harvest. Microbiology Resource Announcements. 7:e01334-18. https://doi.org/10.1128/MRA.01334-18.
Synaptogyrin-2 influences replication of porcine circovirus 2 - (Peer Reviewed Journal)
Walker, L.R., Engle, T.B., Vu, H., Tosky, E.R., Nonneman, D.J., Smith, T.P.L., Borza, T., Burkey, T.E., Plastow, G.S., Kachman, S.D., Ciobanu, D.C. 2018. Synaptogyrin-2 influences replication of porcine circovirus 2. PLoS Genetics. 14(10):e1007750. https://doi.org/10.1371/journal.pgen.1007750.
Contiguity of the goat genome assembly enables comparative analyses and gene discovery within the repetitive immune-related regions - (Abstract Only)
Goat and sheep KIR have independently expanded compared to cattle and a unique subtype is unusually expressed - (Abstract Only)
Closed genome sequences and antibiograms of 16 pasteurella multocida isolates from bovine respiratory disease complex cases and apparently healthy controls - (Peer Reviewed Journal)
Harhay, G.P., Harhay, D.M., Bono, J.L., Smith, T.P.L., Capik, S.F., DeDonder, K.D., Apley, M.D., Lubbers, B.V., White, B.J., Larson, R.L. 2018. Closed genome sequences and antibiograms of 16 pasteurella multocida isolates from bovine respiratory disease complex cases and apparently healthy controls. Microbiology Resource Announcements. 7(11):e00976-18. https://doi.org/10.1128/MRA.00976-18.
Comparative genomics of Salmonella enterica serovar Montevideo reveals lineage-specific gene differences that may influence ecological niche association - (Peer Reviewed Journal)
Nguyen, S.V., Harhay, D.M., Bono, J.L., Smith, T.P.L., Fields, P.I., Dinsmore, B.A., Santovina, M., Wang, R., Bosilevac, J.M., Harhay, G.P. 2018. Comparative genomics of Salmonella enterica serovar Montevideo reveals lineage-specific gene differences that may influence ecological niche association. Microbial Genomics. 4:1-17. https://doi.org/10.1099/mgen.0.000202.
Genome sequences of eight Shiga toxin-producing Escherichia coli strains isolated from a produce-growing region in California - (Peer Reviewed Journal)
Parker, C., Cooper, K.K., Huynh, S., Smith, T.P., Bono, J.L., Cooley, M.B. 2018. Genome sequences of eight Shiga toxin-producing Escherichia coli strains isolated from a produce-growing region in California. Genome Announcements. 7(1):1-3. https://doi.org/10.1128/MRA.00807-18.
Extended haplotype phasing of de novo genome assemblies with FALCON-Phase - ()
Kronenberg, Z.N., Rhie, A., Koren, S., Concepcion, G.T., Peluso, P., Munson, K.M., Hiendleder, S., Fedrigo, O., Jarvis, E.D., Phillippy, A.M., Eichler, E.E., Williams, J.L., Smith, T.P.L, Hall, R.J., Sullivan, S.T., Kingan, S.B. 2019. Extended haplotype phasing of de novo genome assemblies with FALCON-Phase. bioRxiv. 327064. https://doi.org/10.1101/327064.
Haplotype resolution of MHC in cattle through targeted enrichment and SMRT sequencing - (Abstract Only)
Comparison of genomic relationship matrices using differing number of SNP in pooled DNA analyses - (Abstract Only)
Boldt, R.J., Keele, J.W., Kuehn, L.A., McDaneld, T.G., Smith, T.P.L., Enns, R.M. 2018. Comparison of genomic relationship matrices using differing number of SNP in pooled DNA analyses. Journal of Animal Science. 96(Supplement 3):124. https://doi.org/10.1093/jas/sky404.273.
Genomic signatures of a Mannheimia haemolytica lineage associated with bovine respiratory disease - (Abstract Only)
Clawson, M.L., Schuller, G., Dickey, A.M., Murray, R.W., Sweeney, M.T., Apley, M.D., DeDonder, K.D., Capik, S.F., Larson, R.L., Lubbers, B.V., White, B.J., Blom, J., Brichta-Harhay, D.M., Smith, T.P. 2018. Genomic signatures of a Mannheimia haemolytica lineage associated with bovine respiratory disease [abstract]. Society for Molecular Biology & Evolution General Meeting. Abstract POA-070:44. Available: http://evolgen.biol.se.tmu.ac.jp/SMBE2018/POA.pdf
µ-Calpain (CAPN1), calpastatin (CAST), and growth hormone receptor (GHR) genetic effects on Angus beef heifer performance traits and reproduction Reprint Icon - (Peer Reviewed Journal)
Tait Jr, R.G., Cushman, R.A., McNeel, A.K., Casas, E., Smith, T.P.L., Freetly, H.C., Bennett, G.L. 2018. µ-Calpain (CAPN1), calpastatin (CAST), and growth hormone receptor (GHR) genetic effects on Angus beef heifer performance traits and reproduction. Theriogenology. 113:1-7. https://doi.org/10.1016/j.theriogenology.2018.02.002.
Chromosome-level assembly of the water buffalo genome - (Abstract Only)
Long-read sequencing enables the accurate annotation of immune gene clusters in goat - (Abstract Only)
A SNP resource for studying North American moose - (Peer Reviewed Journal)
Kalbfleisch, T.S., Murdoch, B.M., Smith, T.P.L., Murdoch, J.D., Heaton, M.P., Mckay, S.D. 2018. A SNP resource for studying North American moose. F1000Research. 7(40):1-17. https://doi.org/10.12688/f1000research.13501.1.
The Wnt signaling pathway is differentially expressed during the bovine herpesvirus 1 latency-reactivation cycle: evidence that two protein kinases associated with neuronal survival (Akt3 and bone morphogenetic protein.... - (Peer Reviewed Journal)
Workman, A.M., Zhu, L., Keel, B.N., Smith, T.P.L., Jones, C. 2018. The Wnt signaling pathway is differentially expressed during the bovine herpesvirus 1 latency-reactivation cycle: evidence that two protein kinases associated with neuronal survival (Akt3 and bone morphogenetic protein receptor 2) are expressed at higher levels during latency. Journal of Virology. 92:e01937-17. https//doi.org/10.1128/JVI.01937-17.
Third time’s a charm: Into “the Genomics Era” once more - (Abstract Only)
Smith, T.P.L. 2018. Third time’s a charm: Into “the Genomics Era” once more [abstract]. International Plant & Animal Genome XXVI Conference, January 13-17, 2018, San Diego, California. Abstract W169. Available: https://plan.core-apps.com/pag_2018/abstract
Effects and interactions of myostatin and callipyge mutations: I. Growth and carcass traits Reprint Icon - (Peer Reviewed Journal)
Freking, B.A., King, D.A., Shackelford, S.D., Wheeler, T.L., Smith, T.P.L. 2018. Effects and interactions of myostatin and callipyge mutations: I. Growth and carcass traits. Journal of Animal Science. 96:454–461. https://doi.org/10.1093/jas/skx055.
Reassembly of cattle immune gene clusters for quantitative analysis - (Abstract Only)
Additional annotation of the pig transcriptome using integrated Iso-seq and Illumina RNA-seq analysis - (Abstract Only)
Beiki, H., Liu, H., Huang, J., Manchanda, N., Nonneman, D.J., Smith, T.P.L., Tuggle, C.K. 2018. Additional annotation of the pig transcriptome using integrated Iso-seq and Illumina RNA-seq analysis. [abstract] In proceedings: Plant and Animal Genome Conference XXVI, San Diego, CA, 13-17 Jan 2018. Poster abstract P0439. Available: pag.confex.com/pag/xxvi/meetingapp.cgi/paper/30999.
The antibody loci of the domestic goat (Capra hircus) - (Peer Reviewed Journal)
Schwartz, J.C., Philp, R.L., Bickhart, D.M., Smith, T.P., Hammond, J.A. 2018. The antibody loci of the domestic goat (Capra hircus). Immunogenetics. 70: 317-326. doi: https://doi.org/10.1007/s00251-017-1033-3).
Closed genome sequences of seven histophilus somni isolates from beef calves with bovine respiratory disease complex Reprint Icon - (Peer Reviewed Journal)
Harhay, G.P., Harhay, D.M., Bono, J.L., Smith, T.P.L., Capik, S.F., DeDonder, K.D., Apley, M.D., Lubbers, B.V., White, B.J., Larson, R.L. 2017. Closed genome sequences of seven histophilus somni isolates from beef calves with bovine respiratory disease complex. Genome Announcements. 5(40):e01099-17. https://doi.org/10.1128/genomeA.01099-17.
Using sheep genomes from diverse U.S. breeds to identify missense variants in genes affecting fecundity Reprint Icon - (Peer Reviewed Journal)
Heaton, M.P., Smith, T.P.L., Freking, B.A., Workman, A.M., Bennett, G.L., Carnahan, J.K., Kalbfleisch, T.S. 2017. Using sheep genomes from diverse U.S. breeds to identify missense variants in genes affecting fecundity. F1000Research. 6:1303. https://doi.org/10.12688/f1000research.12216.1.
A high-quality annotated transcriptome of swine peripheral blood Reprint Icon - (Peer Reviewed Journal)
Liu, H., Smith, T.P., Nonneman, D.J., Dekkers, J.C., Tuggle, C.K. 2017. A high-quality annotated transcriptome of swine peripheral blood. BMC Genomics. 18:479.. https://doi.org/10.1186/s12864-017-3863-7.
Vaginal and uterine bacterial communities in postpartum lactating cows - (Peer Reviewed Journal)
Clemmons, B.A., Reese, S.T., Dantas, F.G., Franco, G.A., Smith, T.P., Adeyosoye, O.I., Pohler, K.G., Myer, P.R. 2017. Vaginal and uterine bacterial communities in postpartum lactating cows. Frontiers in Microbiology. 8:1047. https://doi.org/10.3389/fmicb.2017.01047.
The evolution of the natural killer complex; a comparison between mammals using new high-quality genome assemblies and targeted annotation - (Peer Reviewed Journal)
Schwartz, J.C., Gibson, M.S., Heimeier, D., Koren, S., Phillippy, A.M., Bickhart, D.M., Smith, T.P., Medrano, J.F., Hammond, J.A. 2017. The evolution of the natural killer complex; a comparison between mammals using new high-quality genome assemblies and targeted annotation. Immunogenetics. 69(2):255-269.
Genetic markers associated with susceptibility to bovine respiratory disease - (Abstract Only)
Enns, R.M., McDaneld, T.G., Keele, J.W., Boldt, R.J., Smith, T.P., Kuehn, L.A. 2017. Genetic markers associated with susceptibility to bovine respiratory disease [abstract]. Journal of Animal Science. 95(Supplement 4):90. https://doi.org/10.2527/asasann.2017.182.
Whole genome sequencing may not be adequate to determine genome relatedness for surveillance and outbreak investigation of foodborne pathogens - (Abstract Only)
Bono, J.L., Arthur, T.M., Harhay, G.P., Smith, T.P. 2017. Whole genome sequencing may not be adequate to determine genome relatedness for surveillance and outbreak investigation of foodborne pathogens. [Abstract]. 12th Annual Sequencing, Finish, and Analysis in the Future Meeting, PS-2.32. Available: http://www.lanl.gov/conferences/sequencing-finishing-analysis-future/index.php.
Haplotype resolution of leukocyte receptor complex in cattle through targeted enrichment and SMRT sequencing - (Abstract Only)
Comparison of the cattle leukocyte receptor complex with related livestock species - (Abstract Only)
Complete genome sequence of the thermotolerant foodborne pathogen Salmonella enterica serovar Senftenberg ATCC 43845 and phylogenetic analysis of loci encoding thermotolerance - (Abstract Only)
Nguyen, S.V., Bono, J.L., Smith, T.P., Harhay, G.P., Harhay, D.M. 2017. Complete genome sequence of the thermotolerant foodborne pathogen Salmonella enterica Serovar Senftenberg ATCC 43845 and phylogenetic analysis of Loci encoding thermotolerance . [Abstract] International Association for Food Protection Proceedings. Session T2-09. Available at: https://iafp.confex.com/iafp/2017/webprogram/authork.html.
Closed genomes and phenotypes of seven Histophilus somni isolates from beef calves with bovine respiratory disease complex - (Abstract Only)
Harhay, G.P., Harhay, D.M., Bono, J.L., Smith, T.P., Heaton, M.P., Clawson, M.L., Chitko-McKown, C.G., Capik, S.F., DeDonder, K.D., Apley, M.D., Lubbers, B.V., White, B.J., Larson, R.L. 2017. Closed genomes and phenotypes of seven Histophilus somni isolates from beef calves with bovine respiratory disease complex [Abstract]. American Society for Microbiology Microbe Meeting, June 1-5, 2017, New Orleans, LA. Poster #Sunday-869.
Complete genome sequences of two genotype A2 small ruminant lentiviruses isolated from infected U.S. sheep - (Peer Reviewed Journal)
Workman, A.M., Dickey, A.M., Heaton, M.P., Clawson, M.L., Smith, T.P.L. 2017. Complete genome sequences of two genotype A2 small ruminant lentiviruses isolated from infected U.S. sheep. Genome Announcements. 5(13):e00109-17.
Single-molecule sequencing and conformational capture enable de novo mammalian reference genomes - (Peer Reviewed Journal)
Bickhart, D.M., Rosen, B.D., Koren, S., Sayre, B.L., Hastie, A.R., Chan, S., Lee, J., Lam, E.T., Liachko, I., Sullivan, S.T., Burton, J., Huson, H.J., Kelley, C.M., Hutchison, J.L., Zhou, Y., Sun, J., Crisa, A., Ponce De Leon, F.A., Schwartz, J.C., Hammond, J.A., Waldbieser, G.C., Schroeder, S.G., Liu, G., Dunham, M., Shendure, J., Sonstegard, T.S., Phillippy, A.M., Van Tassell, C.P., Smith, T.P. 2017. Single-molecule sequencing and conformational capture enable de novo mammalian reference genomes. Nature Genetics. 49(4):643-650.
Genome sequence of the thermotolerant foodborne pathogen Salmonella enterica serovar Senftenberg ATCC 43845 and phylogenetic analysis of Loci encoding increased protein quality control mechanisms - (Peer Reviewed Journal)
Nguyen, S.V., Harhay, G.P., Bono, J.L., Smith, T.P., Harhay, D.M. 2017. Genome sequence of the thermotolerant foodborne pathogen Salmonella enterica serovar Senftenberg ATCC 43845 and phylogenetic analysis of Loci encoding increased protein quality control mechanisms. mSystems. 2:e00190-16. https://doi.org/10.1128/mSystems.00190-16.
Analysis of the gut bacterial communities in beef cattle and their association with feed intake, growth, and efficiency Reprint Icon - ()
Myer, P.R., Freetly, H.C., Wells, J.E., Smith, T.P., Kuehn, L.A. 2017. Analysis of the gut bacterial communities in beef cattle and their association with feed intake, growth, and efficiency. Journal of Animal Science. 95(7):3215-3224. doi: 10.2527/jas2016.1059.
Using an online genome resource to identify myostatin variation in U.S. sheep - (Abstract Only)
Heaton, M.P., Smith, T.P., Kalbfleisch, T.S. 2017. Using an online genome resource to identify myostatin variation in U.S. sheep [abstract]. International Plant & Animal Genome XXV Conference, January 14-18, 2017, San Diego, CA. Poster #P1147.
Swine transcriptome characterization by combined Iso-Seq and RNA-seq for annotating the emerging long read-based reference genome - (Abstract Only)
Liu, H., Manchanda, N., Nonneman, D.J., Smith, T.P., Tuggle, C. 2017. Swine transcriptome characterization by combined Iso-Seq and RNA-seq for annotating the emerging long read-based reference genome [abstract]. In proceedings: Plant and Animal Genome Conference, Jan. 14-18, 2017, San Diego, CA. P1162.
Vaginal and uterine bacterial communities in postpartum lactating cows - (Abstract Only)
Clemmons, B.A., Dantas, F.G., Franco, G.A., Reese, S.T., Adeyosoye, O.I., Smith, T.P., Myer, P.R., Pohler, K.G. 2017. Vaginal and uterine bacterial communities in postpartum lactating cows [abstract]. Journal of Animal Science. 95(Suppl. 2):112. doi:10.2527/asasmw.2017.112.
Genomic signatures of Mannheimia haemolytica that associate with the lungs of cattle with respiratory disease, an integrative conjugative element, and antibiotic resistance genes - (Peer Reviewed Journal)
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.
Exploiting long read sequencing technologies to establish high quality highly contiguous pig reference genome assemblies - (Abstract Only)
Warr, A., Hall, R., Kim, K., Tseng, E., Koren, S., Phillippy, A.M., Bickhart, D.M., Rosen, B.D., Schroeder, S.G., Hume, D.A., Talbot, R., Rund, L., Schook, L.B., Chow, W., Howe, K., Nonneman, D.J., Rohrer, G.A., Putnam, N., Green, E., Watson, M., Smith, T.P., Archibald, A.L. 2017. Exploiting long read sequencing technologies to establish high quality highly contiguous pig reference genome assemblies [abstract]. Plant and Animal Genome Conference XX, January 14-18, 2017, San Diego, California. Paper No. 25025.
Complete, closed genome sequences of 10 Salmonella enterica subsp. enterica serovar Typhimurium strains isolated from human and bovine sources Reprint Icon - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
Myer, P.R., Kim, M.S., Freetly, H.C., Smith, T.P. 2016. Metagenomic and near full-length 16S rRNA sequence data in support of the phylogenetic analysis of the rumen bacterial community in steers. Data in Brief. 8:1048-1053. doi: 10.1016/j.dib.2016.07.027.
Complete genome sequence of highly virulent Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) variants that recently emerged in the United States - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
Myer, P.R., Kim, M.S., Freetly, H.C., Smith, T.P. 2016. Evaluation of 16S rRNA amplicon sequencing using two next-generation sequencing technologies for phylogenetic analysis of the rumen bacterial community in steers. Journal of Microbiological Methods. 127:132-140. doi: 10.1016/j.mimet.2016.06.004.
Selection enhanced estimates of marker effects on means and variances of beef tenderness - (Proceedings)
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 - (Peer Reviewed Journal)
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.
Identification and expression analysis of bovine X degenerate YcChromosome genes - (Abstract Only)
Ponce De Leon, F.A., Guo, Y., Crooker, B.A., McDaneld, T.G., Smith, T.P.L. 2016. Identification and expression analysis of bovine X degenerate YcChromosome genes [abstract]. International Society for Animal Genetics (35th ISAG). Abstract Book. p. 75 (Abstract #P3045). Available: https://www.isag.us.Docs/Proceedings/ISAG_Proceedings_2016.pdf
Using diverse U.S. beef cattle genomes to identify missense mutations in EPAS1, a gene associated with high-altitude pulmonary hypertension - (Abstract Only)
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 - (Abstract Only)
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 - (Abstract Only)
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 - (Peer Reviewed Journal)
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.
A comprehensive porcine blood transcriptome - (Abstract Only)
Liu, H., Smith, T.P.L., Nonneman, D.J., Dekkers, J.C.M., Tuggle, C.K. 2016. A comprehensive porcine blood transcriptome [abstract]. In: Proceedings of 35th International Society for Animal Genetics (ISAG) Conference, 23-17 July 2016, Salt Lake City, UT. pg. 69. P3033. Available: https://www.isag.us/docs/Proceedings/ISAG_Proceedings_2016.pdf
Identification of the pan and core genomes for Mannheimia haemolytica genotypes 1 and 2 - (Abstract Only)
Clawson, M.L., Schuller, G., Dickey, A.M., Bono, J.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., Harhay, G.P., Heaton, M.P., Chitko-McKown, C.G., Harhay, D.M., Smith, T.P. 2016. Identification of the pan and core genomes for Mannheimia haemolytica genotypes 1 and 2. American Society for Microbiology 2016 Meeting, July 16-20, 2016, Boston, MA. Poster No. Friday-060.
Genome sequencing, metabolic and antibiotic resistance phenotyping of diverse nasopharyngeal bacteria isolated from cattle in an epidemiological study of bovine respiratory disease - (Abstract Only)
Harhay, G.P., Harhay, D.M., Bono, J.L., Smith, T.P., Heaton, M.P., Clawson, M.L., Chitko-McKown, C.G., Capik, S.F., DeDonder, K.D., Apley, M.D., Lubbers, B.V., White, B.J., Larson, R.L. 2016. Genome sequencing, metabolic and antibiotic resistance phenotyping of diverse nasopharyngeal bacteria isolated from cattle in an epidemiological study of bovine respiratory disease [abstract]. American Society for Microbiology 2016 Meeting, July 16-20, 2016, Boston, MA. Poster No. Friday-057.
Evaluation of 16S Rrna amplicon sequencing using two next-generation sequencing technologies for phylogenetic analysis of the rumen bacterial community in steers - (Abstract Only)
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 - (Peer Reviewed Journal)
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 - (Abstract Only)
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 - (Peer Reviewed Journal)
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 - (Abstract Only)
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 - (Peer Reviewed Journal)
Massilamany, C., Mohammed, A., Loy, J.D., Purvis, T., Krishnan, B., Basavalingappa, R.H., Kelley, C.M., Guda, C., Barletta, R.G., Moriyama, E.N., Smith, T.P.L., Reddy, J. 2016. Whole genomic sequence analysis of Bacillus infantis: defining the genetic blueprint of strain NRRL B-14911, an emerging cardiopathogenic microbe. Biomed Central (BMC) Genomics. 17(Suppl. 7):511. doi: 10.1186/s12864-016-2900-2.
Investigation and validation of the role of a QTL on SSC12 in PCV2b viremia - (Abstract Only)
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 - (Abstract Only)
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? - (Abstract Only)
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 - (Abstract Only)
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 - (Peer Reviewed Journal)
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 - (Abstract Only)
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 - (Peer Reviewed Journal)
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 - (Abstract Only)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
Snelling, W.M., Bennett, G.L., Keele, J.W., Kuehn, L.A., McDaneld, T.G., Smith, T.P., Thallman, R.M., Kalbfleisch, T.S., Pollak, E.J. 2015. A survey of polymorphisms detected from sequences of popular beef breeds. Journal of Animal Science. 93(11):5128-5143. doi:10.2527/jas2015-9356.
Cecum microbial communities from steers differing in feed efficiency Reprint Icon - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Proceedings)
Pollak, E.J., Smith, T.P., Snelling, W.M. 2015. Historical overview and current status of genomic technology and marker assisted selection in beef cattle. In Proceedings of the American Meat Science Association. 68th Annual Reciprocal Meat Conference, June 14 - 17, 2015, Lincoln, NE. pg. 32-36.
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 Only)
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 - (Peer Reviewed Journal)
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 - (Abstract Only)
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 - (Abstract Only)
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 - (Abstract Only)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
Keele, J.W., Kuehn, L.A., McDaneld, T.G., Tait Jr., R.G., Jones, S., Smith, T.P., Shackelford, S.D., King, D.A., Wheeler, T.L., Lindholm-Perry, A.K., McNeel, A.K. 2015. Genomewide association study of lung lesions in cattle using sample pooling. Journal of Animal Science. 93(3):956-964. DOI: 10.2527/jas.2014-8492.
Beef cattle metabiomes and their relationships with economically important phenotypes - (Abstract Only)
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 - (Abstract Only)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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.
The hunt for a functional mutation affecting conformation and calving traits on chromosome 18 in Holstein cattle - (Proceedings)
Cole, J.B., Hutchison, J.L., Null, D.J., Van Raden, P.M., Liu, G., Schroeder, S.G., Smith, T.P., Sonstegard, T.S., Van Tassell, C.P., Bickhart, D.M. 2014. The hunt for a functional mutation affecting conformation and calving traits on chromosome 18 in Holstein cattle. World Congress of Genetics Applied in Livestock Production. Vancouver, Canada, Aug. 17–22. 3 pp.
Selection enhanced estimates of µ-calpain, calpastatin, and dacylglycerol O-acyltransferase 1 genetic effects on pre-weaning performance, carcass quality traits, and residual variance of tenderness in composite ... cattle - (Proceedings)
Tait Jr, R.G., Shackelford, S.D., Wheeler, T.L., King, D.A., Keele, J.W., Casas, E., Smith, T.P.L., Bennett, G.L. 2014. Selection enhanced estimates of µ-calpain, calpastatin, and dacylglycerol O-acyltransferase 1 genetic effects on pre-weaning performance, carcass quality traits, and residual variance of tenderness in composite MARC III beef cattle. In: Proceedings of the 10th World Congress on Genetics Applied to Livestock Production, August 17-22, 2014, Vancouver, BC, Canada. Paper No. 232. Available: https://asas.org/wcgalp-proceedings.
Calpastatin and µ-calpain differ in their control of genotype specific residual variance of beef tenderness in Angus and MARC III steers - (Abstract Only)
SNPs for parentage testing and traceability in globally diverse breeds of sheep - (Peer Reviewed Journal)
Heaton, M.P., Leymaster, K.A., Kalbfleisch, T.S., Kijas, J.W., Clarke, S.M., McEwan, J., Maddox, J.F., Basnayake, V., Petrik, D.T., Simpson, B., Smith, T.P., Chitko-McKown, C.G. 2014. SNPs for parentage testing and traceability in globally diverse breeds of sheep. PLoS One. 9(4):e94851. DOI: 10.1371/JOURNAL.PONE.0094851.
Genomewide association study of reproductive efficiency in female cattle Reprint Icon - (Peer Reviewed Journal)
McDaneld, T.G., Kuehn, L.A., Thomas, M.G., Snelling, W.M., Smith, T.P.L., Pollak, E.J., Cole, J.B., Keele, J.W. 2014. Genomewide association study of reproductive efficiency in female cattle. Journal of Animal Science. 92(5):1945-1957.
Changes in the rumen microbiome from steers differing in feed efficiency - (Abstract Only)
Myer, P.R., Freetly, H.C., Smith, T.P. 2014. Changes in the rumen microbiome from steers differing in feed efficiency [abstract]. American Society for Microbiology 114th General Meeting. Poster No. 1292.
Complete closed genome sequences of four Mannheimia varigena isolates from cattle with shipping fever - (Peer Reviewed Journal)
Harhay, G.P., Murray, R.W., Lubbers, B., Griffin, D., Koren, S., Phillippy, A.M., Harhay, D.M., Bono, J.L., Clawson, M.L., Heaton, M.P., Chitko-McKown, C.G., Smith, T.P. 2014. Complete closed genome sequences of four Mannheimia varigena isolates from cattle with shipping fever. Genome Announcements. 2(1):e00088-14.
Complete closed genome sequences of three Bibersteinia trehalosi nasopharyngeal isolates from cattle with shipping fever - (Peer Reviewed Journal)
Harhay, G.P., McVey, D.S., Koren, S., Phillippy, A.M., Bono, J.L., Harhay, D.M., Clawson, M.L., Heaton, M.P., Chitko-McKown, C.G., Korlach, J., Smith, T.P. 2014. Complete closed genome sequences of three Bibersteinia trehalosi nasopharyngeal isolates from cattle with shipping fever. Genome Announcements. 2(1):e00084-14.
µ-Calpain, calpastatin, and growth hormone receptor genetic effects on preweaning performance, carcass quality traits, and residual variance of tenderness in Angus cattle selected to increase minor haplotype ... frequencies Reprint Icon - (Peer Reviewed Journal)
Tait Jr, R.G., Shackelford, S.D., Wheeler, T.L., King, D.A., Casas, E., Thallman, R.M., Smith, T.P., Bennett, G.L. 2014. µ-Calpain, calpastatin, and growth hormone receptor genetic effects on preweaning performance, carcass quality traits, and residual variance of tenderness in Angus cattle selected to increase minor haplotype and allele frequencies. Journal of Animal Science. 92(2):456-466.
Microbiome characterization using SMRT sequencing on 16S rRNA genes across a range of amplicon sizes and variable region content - (Abstract Only)
Characterization of microbiomes related to respiratory disease in cattle - (Abstract Only)
Smith, T.P., Kim, M.S., Myer, P.R., McDaneld, T.G., Kuehn, L.A., Clawson, M.L., Harhay, D.M., Harhay, G.P. 2014. Characterization of microbiomes related to respiratory disease in cattle [Abstract]. Proceedings of the Plant and Animal Genome XXII Conference, January 11-15, 2014, San Diego, CA. Poster W759.
SNPs for parentage testing and traceability in globally diverse breeds of sheep - (Abstract Only)
Heaton, M.P., Leymaster, K.A., Kalbfleisch, T.S., Kijas, J.W., Clarke, S.M., McEwan, J., Maddox, J.F., Basnayake, V., Petrik, D.T., Simpson, B., Smith, T.P., Chitko-McKown, C.G. 2014. SNPs for parentage testing and traceability in globally diverse breeds of sheep [Abstract]. Proceedings Plant and Animal Genome XXII Conference, January 11-15, 2014, San Diego, CA. Poster P614.
Reducing assembly complexity of microbial genomes with single-molecule sequencing - (Peer Reviewed Journal)
Koren, S., Harhay, G.P., Smith, T.P.L., Bono, J.L., Harhay, D.M., McVey, D.S., Radune, D., Bergman, N.H., Phillippy, A.M. 2013. Reducing assembly complexity of microbial genomes with single-molecule sequencing. Genome Biology. 14:R101. DOI: 10.1186/GB-2013-14-9-R101.
Small ruminant lentivirus genetic subgroups associate with sheep TMEM154 genotypes - (Peer Reviewed Journal)
Sider, L.H., Heaton, M.P., Chitko-Mckown, C.G., Harhay, G.P., Smith, T.P.L., Leymaster, K.A., Laegreid, W.W., and Clawson, M.L. 2013. Small ruminant lentivirus genetic subgroups associate with sheep TMEM154 genotypes. Veterinary Research. 44:64. DOI: 10.1186/1297-9716-44-64.
Proposed model for the high rate of rearrangement and rapid migration observed in some IncA/C plasmid lineages - (Peer Reviewed Journal)
Meinersmann, R.J., Lindsey, R., Bono, J.L., Smith, T.P., Oakley, B. 2013. Proposed model for the high rate of rearrangement and rapid migration observed in some IncA/C plasmid lineages. Applied and Environmental Microbiology. 79(16):4806-4814.
Genome-wide association study of reproductive efficiency in female cattle - (Abstract Only)
McDaneld, T.G., Kuehn, L.A., Thomas, M.G., Snelling, W.M., Pollak, E.J., Smith, T.P.L., Keele, J.W. 2013. Genome-wide association study of reproductive efficiency in female cattle [Abstract]. Journal of Animal Science. 91 (E-Supplement 2):392. (Abstract #319).
Complete closed genome sequences of Mannheimia haemolytica serotypes A1 and A6 isolated from cattle - (Peer Reviewed Journal)
Harhay, G.P., Koren, S., Phillippy, A.M., McVey, D.S., Kuszak, J., Clawson, M.L., Harhay, D.M., Heaton, M.P., Chitko-McKown, C.G., Smith, T.P.L. 2013. Complete closed genome sequences of Mannheimia haemolytica serotypes A1 and A6 isolated from cattle. Genome Announcements. 1(3):e00188-13. DOI: 10.1128/GENOMEA.00188-13.
The effects of selecting for the myostatin F94L polymorphism on reproductive traits in pubertal heifers - (Abstract Only)
Forbes, E.D., Swanson, O.L., McNeel, A.K., Tait, Jr., R.G., Smith, T.P.L., Bennett, G.L., Hoagland, T.A., Zinn, S.A., Lents, C.A., Perry, G.A., Cushman, R.A. 2013. The effects of selecting for the myostatin F94L polymorphism on reproductive traits in pubertal heifers. Journal of Animal Science. 91 (E-Supplement 2):287 (Abstract #W181).
CAPN1 and GDF8 genetic marker effects on heifer performance, reproduction, and first calf performance traits in beef cattle - (Abstract Only)
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 - (Abstract Only)
Salmonella virulence, genomics and interactions with the immune system - (Proceedings)
Harhay, D.M., Smith, T.P., Harhay, G.P., Bono, J.L., Bosilevac, J.M. 2013. Salmonella virulence, genomics and interactions with the immune system. Meeting Abstract. The Beef Industry Safety Summit, March 13-15, 2013, Dallas Texas, FLASHDRIVE.
Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution - (Peer Reviewed Journal)
Melters, D.P., Bradnan, K., Young, H., Telis, N., May, M., Ruby, G.J., Sebra, R., Peluso, P., Eid, J., Rank, D., Garcia, J., Derisi, J., Smith, T.P., Tobias, C.M., Ross-Ibarra, J., Korf, I., Chan-Simon, W. 2013. Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution. Genome Biology. doi:10.1186/gb-2013-14-1-r10.
Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution - (Peer Reviewed Journal)
Melters, D.P., Bradnam, K.R., Young, H.P., Telis, N., May, M.R., Ruby, J., Sebra, R., Peluso, P., Eid, J., Rank, D., Garcia, J., Derisi, J.L., Smith, T.P., Tobias, C.M., Ross-Ibarra, J., Korf, I., Chan, S.W. 2013. Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution. Genome Biology. 14(1):R10. doi:10.1186/gb-2013-14-1-r10.
Deep sequencing of immune repertoires during bovine development and in response to respiratory pathogen challenge - (Abstract Only)
Smith, T.P.L., and Larsen, P.A. 2013. Deep sequencing of immune repertoires during bovine development and in response to respiratory pathogen challenge [Abstract]. Advances in Genome Biology and Technology Conference, February 20-23, 2013, Marco Island, FL. Page 126.
Multi-platform next generation sequencing of a high quality genome assembly for the goat - (Abstract Only)
Sonstegard, T.S., Smith, T.P., Schroeder, S.G., Huson, H.J., Zimin, A., Woodward Greene, M.J., Mujibi, D.F., Mcclure, M.C., Silverstein, J., Van Tassell, C.P., Sayre, B.L. 2013. Multi-platform next generation sequencing of a high quality genome assembly for the goat. Plant Animal Genome XXI, paper W417, pp. 171.
Application of SMRT genome sequencing to reveal the methylomes of bacteria associated with respiratory disease outbreaks in beef cattle - (Abstract Only)
Harhay, G.P., McVey, D.S., Korlach, J., Roberts, R., Chitko-McKown, C.G., Clawson, M.L., Heaton, M.P., Harhay, D.M., Smith, T.P.L., Anton, B.P. 2013. Application of SMRT genome sequencing to reveal the methylomes of bacteria associated with respiratory disease outbreaks in beef cattle [Abstract]. Advances in Genome Biology and Technology Conference, February 20-23, 2013, Marco Island, FL. Page 99.
Complete genome assemblies and methylome characterization in infectious diseases - (Abstract Only)
Smith, T.P. 2013. Complete genome assemblies and methylome characterization in infectious diseases [Abstract]. Plant & Animal Genome XXI Conference, January 12-16, 2013, San Diego, CA. Paper No. W483.
Estimation of genetic marker effects for CAPN1, CAST, and GHR on carcass quality traits in Angus cattle selected to increase minor marker frequencies - (Abstract Only)
Tait Jr, R.G., Shackelford, S.D., Wheeler, T.L., King, D.A., Casas, E., Thallman, R.M., Smith, T.P., Bennett, G.L. 2013. Estimation of genetic marker effects for CAPN1, CAST, and GHR on carcass quality traits in Angus cattle selected to increase minor marker frequencies [abstract]. Journal of Animal Science. 91(Supplement 2):62-63. Abstract No. O186.
Characterizing changes in the immune repertoire of cattle using next-gen sequencing - (Abstract Only)
Smith, T.P.L., Larsen, P.A. 2013. Characterizing changes in the immune repertoire of cattle using next-gen sequencing [Abstract]. Plant & Animal Genome XXI Conference, January 12-16, 2013, San Diego, CA. Paper No. W147.
Development of low-cost, high-throughput genotyping to complement SNP discovery by individual animal whole-genome sequencing - (Abstract Only)
Thallman, R.M., Snelling, W.M., Curry, J.D., Smith, T.P., Kalbfleisch, T.S., Kuehn, L.A., McDaneld, T.G., Bennett, G.L., Lindholm-Perry, A.K., Fofanov, V.Y., Koshinsky, H., Pollak, E.J. 2013. Development of low-cost, high-throughput genotyping to complement SNP discovery by individual animal whole-genome sequencing [abstract]. Plant and Animal Genome XXI Conference. Workshop Abstract No. W146.
Selection for genetic markers in beef cattle reveals complex associations of thyroglobulin and casein1-S1 with carcass and meat traits - (Peer Reviewed Journal)
Bennett, G.L., Shackelford, S.D., Wheeler, T.L., King, D.A., Casas, E., Smith, T.P. 2013. Selection for genetic markers in beef cattle reveals complex associations of thyroglobulin and casein1-S1 with carcass and meat traits. Journal of Animal Science. 91(2):565-571.
Application of circular consensus sequencing and network analysis to characterize the bovine IgG repertoire - (Peer Reviewed Journal)
Larsen, P.A., Smith, T.P. 2012. Application of circular consensus sequencing and network analysis to characterize the bovine IgG repertoire. BioMed Central (BMC) Immunology. 13:52 doi:10.1186/1471-2172-13-52.
Next-generation sequencing of the porcine skeletal muscle transcriptome for computational prediction of microRNA gene targets - (Peer Reviewed Journal)
McDaneld, T.G., Smith, T.P.L., Harhay, G.P., and Wiedmann, R.T. 2012. Next-generation sequencing of the porcine skeletal muscle transcriptome for computational prediction of microRNA gene targets. PLoS One. 7(7):e42039. doi:10.1371/journal.pone.0042039.
Accuracy of genomic breeding values in multibreed beef cattle populations derived from deregressed breeding values and phenotypes - (Peer Reviewed Journal)
Weber, K.L., Thallman, R.M., Keele, J.W., Snelling, W.M., Bennett, G.L., Smith, T.P., McDaneld, T.G., Allan, M.F., Van Eenennaam, A.L., Kuehn, L.A. 2012. Accuracy of genomic breeding values in multibreed beef cattle populations derived from deregressed breeding values and phenotypes. Journal of Animal Science. 90(12):4177-4190.
Phylogenetic clades of ovine progressive pneumonia virus (OPPV) associate with sheep TMEM154 genotypes - (Abstract Only)
Sider, L.H., Clawson, M.L., Heaton, M.P., Chitko Mckown, C.G., Harhay, G.P., Smith, T.P.L., Leymaster, K.A. 2012. Phylogenetic clades of ovine progressive pneumonia virus (OPPV) associate with sheep TMEM154 genotypes. The 58th Genomic Congress, September 11-14, 2012. Foz de Iguacu, Brazil. Poster No. GM001.
Comparison of bacterial communities in faeces of beef cattle fed diets containing corn and wet distillers grain with solubles - (Peer Reviewed Journal)
Durso, L.M., Wells, J., Harhay, G.P., Rice, W.C., Kuehn, L.A., Bono, J.L., Shackelford, S.D., Wheeler, T.L., Smith, T.P. 2012. Comparison of bacterial communities in faeces of beef cattle fed diets containing corn and wet distillers grain with solubles. Letters in Applied Microbiology. 55(2):109-14. DOI: 10.1111/J.1472-765X.2012.03265.X.
SMRT sequencing provides insight into the diversity of the bovine immunoglobulin heavy chain repertoire - (Abstract Only)
Evaluation of bovine chemerin (RARRES2) gene variation on beef cattle production traits - (Peer Reviewed Journal)
Lindholm-Perry, A.K., Kuehn, L.A., Rempel, L.A., Smith, T.P., Cushman, R.A., McDaneld, T.G., Wheeler, T.L., Shackelford, S.D., King, D.A., Freetly, H.C. 2012. Evaluation of bovine chemerin (RARRES2) gene variation on beef cattle production traits. Frontiers in Genetics. 3:39.
Analysis of copy number variations among cattle breeds - (Abstract Only)
Liu, G., Hou, Y., Zhu, B., Cardone, M.F., Jiang, L., Cellamare, A., Mitra, A., Alexander, L.J., Coutinho, L.L., Gasbarre, L.C., Li, R.W., Matukumalli, L.K., Nonneman, D.J., Regitano, L.C., Smith, T.P., Song, J., Sonstegard, T.S., Van Tassell, C.P., Ventura, M., Eichler, E.E., Mcdaneld, T.G., Keele, J.W. 2012. Analysis of copy number variations among cattle breeds. [abstract] CONFERENCE ON THE BIOLOGY OF GENOMES. P. 182.
Phylogeny of Shiga toxin-producing Escherichia coli O157 isolated from cattle and clinically ill humans - (Peer Reviewed Journal)
Bono, J.L., Smith, T.P., Keen, J.E., Harhay, G.P., McDaneld, T.G., Mandrell, R.E., Jung, W., Besser, T.E., Gerner-Smidt, P., Bielaszewska, M., Karch, H., Clawson, M.L. 2012. Phylogeny of Shiga toxin-producing Escherichia coli O157 isolated from cattle and clinically ill humans. Molecular Biology and Evolution. 29(8):2047-2062. doi: 10.1093/molbev/mss072.
Association of genetic markers in cattle receiving differing implant protocols - (Peer Reviewed Journal)
King, D.A., Shackelford, S.D., McDaneld, T.G., Kuehn, L.A., Kemp, C.M., Smith, T.P., Wheeler, T.L., Koohmaraie, M. 2012. Association of genetic markers in cattle receiving differing implant protocols. Journal of Animal Science. 90:2410-2423.
MicroRNA expression profile in bovine cumulus–oocyte complexes: Possible role of let-7 and miR-106a in the development of bovine oocytes - (Peer Reviewed Journal)
Miles, J.R., McDaneld, T.G., Wiedmann, R.T., Cushman, R.A., Echternkamp, S.E., Vallet, J.L., Smith, T.P.L. 2012. MicroRNA expression profile in bovine cumulus–oocyte complexes: Possible role of let-7 and miR-106a in the development of bovine oocytes. Animal Reproduction Sciences. 130(1-2):16-26.
Association, effects and validation of polymorphisms within the NCAPG - LCORL locus located on BTA6 with feed intake, gain, meat and carcass traits in beef cattle - (Peer Reviewed Journal)
Lindholm-Perry, A.K., Sexten, A.K., Kuehn, L.A., Smith, T.P., King, D.A., Shackelford, S.D., Wheeler, T.L., Ferrell, C.L., Jenkins, T.G., Snelling, W.M., Freetly, H.C. 2011. Association, effects and validation of polymorphisms within the NCAPG - LCORL locus located on BTA6 with feed intake, gain, meat and carcass traits in beef cattle. BioMed Central (BMC) Genetics. 12:103.
Application of combined SMRT and long-read pyrosequencing to produce reference genome sequences of bacteria associated with respiratory disease outbreaks in beef cattle - (Abstract Only)
Harhay, G.P., Mcvey, D.S., Kitzmiller, A., Clamp, M., Osborne, B., Dwan, C., Zhang, J., Sisneros, N., Wang, S., Peluso, P., Bono, J.L., Chitko Mckown, C.G., Clawson, M.L., Heaton, M.P., Harhay, D.M., Smith, T.P.L. [abstract]. 2012. Application of combined SMRT and long-read pyrosequencing to produce reference genome sequences of bacteria associated with respiratory disease outbreaks in beef cattle. Advances in Genome Biology and Technology, February 15-18, 2012, Marco Island, Florida. Poster No. 129.
Enabling next-gen sequencing and analysis at the USDA-ARS U.S. Meat Animal Research Center with MiniLIMS - (Abstract Only)
Reduced lentivirus susceptibility in sheep with TMEM154 mutations - (Peer Reviewed Journal)
Heaton, M.P., Clawson, M.L., Chitko-Mckown, C.G., Leymaster, K.A., Smith, T.P.L., Harhay, G.P., White, S.N., Herrmann-Hoesing, L.M., Mousel, M.R., Lewis, G.S., Kalbfleisch, T.S., Keen, J.E., Laegreid, W.W. 2012. Reduced lentivirus susceptibility in sheep with TMEM154 mutations. PLoS Genetics. 8(1): e1002467. DOI: 10.1371/journal.pgen.1002467.
Y are you not pregnant: identification of Y chromosome segments in female cattle with decreased reproductive efficiency - (Peer Reviewed Journal)
McDaneld, T.G., Kuehn, L.A., Thomas, M.G., Snelling, W.M., Sonstegard, T.S., Matukumalli, L.K., Smith, T.P., Pollak, E.J., Keele, J.W. 2012. Y are you not pregnant: identification of Y chromosome segments in female cattle with decreased reproductive efficiency. Journal of Animal Science. 90(7):2142-2151.
Genetic markers on BTA14 predictive for residual feed intake in beef steers and their effects on carcass and meat quality traits - (Peer Reviewed Journal)
Lindholm-Perry, A.K., Kuehn, L.A., Snelling, W.M., Smith, T.P., Ferrell, C.L., Jenkins, T.G., King, D.A., Shackelford, S.D., Wheeler, T.L., Freetly, H.C. 2012. Genetic markers on BTA14 predictive for residual feed intake in beef steers and their effects on carcass and meat quality traits. Animal Genetics. 43:599-603.
Whole genome sequence analysis of field strains of bluetongue virus: an Update. - (Proceedings)
Genetic markers in bovine chromosome 14 are significant for residual feed intake in steers - (Abstract Only)
Lindholm-Perry, A.K., Kuehn, L.A., Smith, T.P., Snelling, W.M., Freetly, H.C. 2011. Genetic markers in bovine chromosome 14 are significant for residual feed intake in steers. Journal of Animal Science. 89(E-Suppl. 1):422-423.
Use of sample pooling in a genome-wide association study identifies chromosomal regions affecting incidence of bovine respiratory disease - (Abstract Only)
Kuehn, L.A., Keele, J.W., Casas, E., Jones, S., King, D.A., McDaneld, T.G., Smith, T.P.L., Wheeler, T.L. 2011. Use of sample pooling in a genome-wide association study identifies chromosomal regions affecting incidence of bovine respiratory disease [abstract]. Journal of Animal Science. 89 (E-Supplement 1):422 (Abstract #336).
A region on BTA14 that includes the positional candidate genes LYPLA1, XKR4 and TMEM68 is associated with feed intake and growth phenotypes in cattle - (Peer Reviewed Journal)
Lindholm-Perry, A.K., Kuehn, L.A., Smith, T.P., Ferrell, C.L., Jenkins, T.G., Freetly, H.C., Snelling, W.M. 2012. A region on BTA14 that includes the positional candidate genes LYPLA1, XKR4 and TMEM68 is associated with feed intake and growth phenotypes in cattle. Animal Genetics. 43(2):216-219.
Genomic regions associated with incidence of disease in cattle using DNA pooling and a high density single nucleotide polymorphism array - (Abstract Only)
Casas, E., Kuehn, L.A., McDaneld, T.G., Smith, T.P.L., Keele, J.W. 2011. Genomic regions associated with incidence of disease in cattle using DNA pooling and a high density single nucleotide polymorphism array [abstract]. Journal of Animal Science. 89 (E-Supplement 1):158. (Abstract 18).
Evaluation of polymorphisms within the genes GSHR and SLC2A2 that are within a region on bovine chromosome 1 (BTA1) previously associated with feed intake and weight gain - (Peer Reviewed Journal)
Lindholm-Perry, A.K., Kuehn, L.A., Snelling, W.M., Smith, T.P., Ferrell, C.L., Jenkins, T.G., Freetly, H.C. 2012. Evaluation of polymorphisms within the genes GSHR and SLC2A2 that are within a region on bovine chromosome 1 (BTA1) previously associated with feed intake and weight gain. Animal Genetics. 43(1):112.
Gene expression response of multidrug resistant Salmonella enterica serovar Newport to simulated multiple hurdle beef carcass processing interventions - (Abstract Only)
Harhay, D.M., Smith, T.P., Harhay, G.P. 2011. Gene expression response of multidrug resistant Salmonella enterica serovar Newport to simulated multiple hurdle beef carcass processing interventions. In: Proceedings of the American Society for Microbiology. 111th General Meeting of the American Society for Microbiology, May 21-24, 2011, New Orleans, Louisiana. 2011 CDROM. Meeting Abstract K-2692.
Evaluation of pyrosequencing for assembly of plasmids carrying IS elements - (Abstract Only)
Chen, C., Lindsey, R.L., Strobaugh Jr, T.P., Frye, J.G., Bono, J.L., Smith, T.P., Meinersmann, R.J. 2011. Evaluation of pyrosequencing for assembly of plasmids carrying IS elements [abstract]. 111th ASM General Meeting.
Towards an understanding of how Salmonella potentially evades beef carcass processing interventions - (Abstract Only)
Brichta-Harhay, D.M., Gragg, S.E., Smith, T.P.L., Arthur, T.M., Bosilevac, J.M., Kalchayanand, N., Schmidt, J.W., Wang, R., Shackelford, S.D., Wheeler, T.L., Brashears, M.M., Brooks, J.C., Brown, T.R., Harhay, G.P., Loneragan, G.H. 2011. Towards an understanding of how Salmonella potentially evades beef carcass processing interventions [abstract]. 2011 Beef Industry Safety Summit. Abstract No. 2.
Predicting breed composition using breed frequencies of 50,000 markers from the U.S. Meat Animal Research Center 2,000 bull project - (Peer Reviewed Journal)
Kuehn, L.A., Keele, J.W., Bennett, G.L., Mcdaneld, T.G., Smith, T.P., Snelling, W.M., Sonstegard, T.S., Thallman, R.M. 2011. Predicting breed composition using breed frequencies of 50,000 markers from the U.S. Meat Animal Research Center 2,000 bull project. Journal of Animal Science. 89:1742-1750.
Biosurveillance at the United States Meat Animal Research Center - (Abstract Only)
Harhay, G.P., Harhay, D.M., Chitko Mckown, C.G., Smith, T.P. 2011. Biosurveillance at the United States Meat Animal Research Center [abstract]. Global Biosurveillance: Enabling Science and Technology 2nd Biothreat Nonproliferation Conference. Abstract No. 12.
Virulence-associated and antibiotic resistance genes of microbial populations in cattle feces analyzed using a metagenomic approach - (Peer Reviewed Journal)
Durso, L.M., Harhay, G.P., Bono, J.L., Smith, T.P. 2011. Virulence-associated and antibiotic resistance genes of microbial populations in cattle feces analyzed using a metagenomic approach. Journal of Microbiological Methods. 84: 278-282.
Bacterial community analysis of beef cattle feedlots reveals that pen surface is distinct from feces - (Peer Reviewed Journal)
Durso, L.M., Harhay, G.P., Smith, T.P., Bono, J.L., Desantis, T.Z., Clawson, M.L. 2011. Bacterial community analysis of beef cattle feedlots reveals that pen surface is distinct from feces. Foodborne Pathogens and Disease. 8(5):647-649. Available: DOI: 10.1089/fpd.2010.0774.
The effects of genetic markers on BTA6 significant for steer feed intake and gain traits on carcass and meat traits - (Abstract Only)
Lindholm-Perry, A.K., Sexten, A.K., Kuehn, L.A., Smith, T.P., King, D.A., Shackelford, S.D., Wheeler, T.L., Snelling, W.M., Freetly, H.C. 2011. The effects of genetic markers on BTA6 significant for steer feed intake and gain traits on carcass and meat traits. Plant & Animal Genome XIX Conference. Poster No. P531. p. 230
Association of single nucleotide polymorphisms in the ANKRA2 and CD180 genes with bovine respiratory disease and presence of Mycobacterium avium subsp. paratuberculosis - (Peer Reviewed Journal)
Casas, E., Garcia, M.D., Wells, J., Smith, T.P.L. 2011. Association of single nucleotide polymorphisms in the ANKRA2 and CD180 genes with bovine respiratory disease and presence of Mycobacterium avium subsp. paratuberculosis. Animal Genetics. 42:571-577.
Association of single nucleotide polymorphisms in the ANKRA2 and CD180 genes with bovine respiratory disease and presence of Mycobacterium avium subsp. paratuberculosis - (Abstract Only)
Casas, E., Garcia, M.D., Wells, J., Smith, T.P. 2011. Association of single nucleotide polymorphisms in the ANKRA2 and CD180 genes with bovine respiratory disease and presence of Mycobacterium avium subsp. paratuberculosis [abstract]. Plant and Animal Genome XIX Conference. Poster No. P193.
An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation - (Peer Reviewed Journal)
Harhay, G.P., Smith, T.P.L., Alexander, L.J., Haudenschild, C.D., Keele, J.W., Matukumalli, L.K., Schroeder, S.G., Van Tassell, C.P., Gresham, C.R., Bridges, S.M., Burgess, S.C., Sonstegard, T.S. 2010. An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation. Genome Biology [online serial]. 11:R102.
Whole genome sequence analysis of field strains of bluetongue virus - (Abstract Only)
Wilson, W.C., Smith, T.P. 2010. Whole genome sequence analysis of field strains of bluetongue virus. Meeting Proceedings. 154.
Sequence analysis for a de novo genome assembly of Bos indicus (Nelore) cattle - (Abstract Only)
Sonstegard, T.S., Schroeder, S.G., Smith, T.P., Zimin, A., Matukumalli, L.K., Ajmone-Marsan, P., Wiedmann, R.T., Negrini, R., Yorke, J., Van Tassell, C.P., Garcia, J.F. 2010. Sequence analysis for a de novo genome assembly of Bos indicus (Nelore) cattle. Animal Genetics International Conference Proceedings.
Molecular analysis of plasmid encoded multi-drug resistance (MDR) in Salmonella enterica animal isolates by PFGE, replicon typing, and DNA microarray screening followed by high-throughput DNA sequencing - (Abstract Only)
Lindsey, R.L., Frye, J.G., Bono, J.L., Smith, T.P., Harhay, D.M., Cray, P.J., Meinersmann, R.J. 2010. Molecular analysis of plasmid encoded multi-drug resistance (MDR) in Salmonella enterica animal isolates by PFGE, replicon typing, and DNA microarray screening followed by high-throughput DNA sequencing. American Society for Microbiology. June 8-11, 2010. Toronto, Canada. B16. p41-42.
Markers on bovine chromosome 20 associated with carcass quality and composition traits and incidence of contracting infectious bovine keratoconjunctivitis - (Peer Reviewed Journal)
Garcia, M.D., Matukumalli, L., Wheeler, T.L., Shackelford, S.D., Smith, T.P., Casas, E. 2010. Markers on bovine chromosome 20 associated with carcass quality and composition traits and incidence of contracting infectious bovine keratoconjunctivitis. Animal Biotechnology. 21(3):188-202.
Polymorphisms in POMC are not associated with dry matter intake and average daily gain phenotypes in beef cattle - (Peer Reviewed Journal)
Lindholm-Perry, A.K., Kuehn, L.A., Snelling, W.M., Smith, T.P.L., Ferrell, C.L., Jenkins, T.G., Freetly, H.C. 2010. Polymorphisms in POMC are not associated with dry matter intake and average daily gain phenotypes in beef cattle. Animal Genetics. 41(6):669-670.
Predicting Breed Composition Using Breed Frequencies of 50,000 Markers from the U.S. Meat Animal Research Center 2,000 Bull Project - (Proceedings)
Kuehn, L.A., Keele, J.W., Bennett, G.L., McDaneld, T.G., Smith, T.P., Snelling, W.M., Sonstegard, T.S., Thallman, R.M. 2010. Predicting Breed Composition Using Breed Frequencies of 50,000 Markers from the U.S. Meat Animal Research Center 2,000 Bull Project. Proceedings of the 9th World Congress on Genetics Applied to Livestock Production, Leipzig, Germany. August 1-6, 2010. CD-ROM Communication No. 0283.
Application of marker selection to enhance estimation of genetic effects and gene interaction in cattle - (Proceedings)
Bennett, G.L., Shackelford, S.D., Wheeler, T.L., King, D.A., Casas, E., Smith, T.P. 2010. Application of marker selection to enhance estimation of genetic effects and gene interaction in cattle. Proceedings, 9th World Congress on Genetics Applied to Livestock Production, Leipzig, Germany. August 1-6, 2010. CD-ROM Communication No. 0286.
Animal-to-Animal Variation in Fecal Microbial Diversity among Beef Cattle - (Peer Reviewed Journal)
Durso, L.M., Harhay, G.P., Smith, T.P.L., Bono, J.L., Desantis, T.Z., Harhay, D.M., Andersen, G.L., Keen, J.E., Laegreid, W.W., Clawson, M.L. 2010. Animal-to-Animal Variation in Fecal Microbial Diversity among Beef Cattle. Applied and Environmental Microbiology. 76(14):4858-4862.
Comparison of cattle fecal communities from animals fed diets containing corn and distiller's grains - (Abstract Only)
Durso, L.M., Harhay, G.P., Wells, J., Bono, J.L., Riethoven, J.M., Shackelford, S.D., Wheeler, T.L., Smith, T.P. 2010. Comparison of cattle fecal communities from animals fed diets containing corn and distiller's grains. PS.25.018, Abstract #393A. Abstract for Microbial Ecology International Symposium, Seattle, WA, Aug. 22-27, 2010. Abstract Book, Pg. 128
Ovine Reference Materials and Assays for Prion Genetic Testing - (Peer Reviewed Journal)
Heaton, M.P., Leymaster, K.A., Kalbfleisch, T.S., Freking, B.A., Smith, T.P., Clawson, M.L., Laegreid, W.W. 2010. Ovine Reference Materials and Assays for Prion Genetic Testing. BioMed Central (BMC) Veterinary Research [serial online]. 6:23. Available: http://www.biomedcentral.com/1746-6148/6/23.
A Deletion Mutation in Bovine SLC4A2 is Associated with Osteopetrosis in Red Angus Cattle - (Peer Reviewed Journal)
Meyers, S.N., McDaneld, T.G., Swist, S.L., Marron, B.M., Steffen, D.J., O'Toole, D., O'Connell, J.R., Beever, J.E., Sonstegard, T.S., Smith, T.P. 2010. A Deletion Mutation in Bovine SLC4A2 is Associated with Osteopetrosis in Red Angus Cattle. Biomed Central (BMC) Genomics. 11:337.
A Region on BTA6 Is Associated with Feed Intake and Gain in Beef Cattle - (Abstract Only)
Sexten, A.K., Kuehn, L.A., Smith, T.P., Freetly, H.C., Snelling, W.M., Lindholm-Perry, A.K. 2010. A Region on BTA6 Is Associated with Feed Intake and Gain in Beef Cattle [abstract]. Journal of Animal Science. 88 (E-Supplement 2):185.
Analysis of copy number variations reveals differences among cattle breeds - (Peer Reviewed Journal)
Liu, G., Hou, Y., Zhu, B., Cardone, M.F., Jiang, L., Cellamare, A., Mitra, A., Alexander, L.J., Coutinho, L.L., Gasbarre, L.C., Heaton, M.P., Li, R.W., Matukumalli, L.K., Nonneman, D.J., De A Regitano, L.C., Smith, T.P., Song, J., Sonstegard, T.S., Van Tassell, C.P., Eichler, E.E., Mcdaneld, T.G., Keele, J.W. 2010. Analysis of copy number variations among cattle breeds. Genome Research. 20:693-703.
Single nucleotide polymorphism discovery in rainbow trout - (Abstract Only)
Rexroad Iii, C.E., Castano, C., Smith, T.P., Vallejo, R.L., Jianbo, Y., Wiedmann, R.T. 2010. Single nucleotide plymorphism discovery in rainbow trout. Aquaculture America Conference.
De novo Reconstruction of the Pig Skeletal Muscle Transcriptome for Identification of MicroRNA Gene Targets - (Abstract Only)
McDaneld, T.G., Wiedmann, R.T., Harhay, G.P., Smith, T.P.L. 2010. De novo Reconstruction of the Pig Skeletal Muscle Transcriptome for Identification of MicroRNA Gene Targets (abstract). In: Proceedings of the Advances in Genome Biology & Technology Conference, February 24-27,2010, Marco Island, Florida. p. 114.
A Digital Gene Expression-Based Bovine Gene Atlas Evaluating 92 Adult, Juvenile and Fetal Cattle Tissues - (Abstract Only)
Harhay, G.P., Alexander, L.J., Smith, T.P.L., Matukumalli, L.K., Schroeder, S.G., Sonstegard, T.S. 2010. A Digital Gene Expression-Based Bovine Gene Atlas Evaluating 92 Adult, Juvenile and Fetal Cattle Tissues [abstract]. In: Proceedings of the Advances in Genome Biology & Technology Conference, February 24-27, 2010, Marco Island, Florida. p. 67.
Information Theoretical Analysis of a Bovine Gene Atlas Reveals Chromosomal Regions with Tissue Specific Gene Expression. - (Abstract Only)
Sonstegard, T.S., Harhay, G.P., Alexander, L.J., Schroeder, S.G., Keele, J.W., Matukumalli, L., Bridges, S., Burgess, S., Van Tassell, C.P., Smith, T.P. 2010. Information Theoretical Analysis of a Bovine Gene Atlas Reveals Chromosomal Regions with Tissue Specific Gene Expression. Plant and Animal Genome VX Conference Abstracts.
Genome-Wide Association Study of Growth in Crossbred Beef Cattle - (Peer Reviewed Journal)
Snelling, W.M., Allan, M.F., Keele, J.W., Kuehn, L.A., Mcdaneld, T.G., Smith, T.P., Sonstegard, T.S., Thallman, R.M., Bennett, G.L. 2010. Genome-Wide Association Study of Growth in Crossbred Beef Cattle. Journal of Animal Science. 88(3):837-848.
Evaluation of Two Positional Candidate Genes on BTA14 for Association with Dry Matter Intake in Beef Cattle - (Abstract Only)
Lindholm-Perry, A.K., Kuehn, L.A., Smith, T.P., Freetly, H.C., Snelling, W.M. 2010. Evaluation of Two Positional Candidate Genes on BTA14 for Association with Dry Matter Intake in Beef Cattle [abstract]. Plant & Animal Genome XVIII Conference. Poster No. P553. p. 216.
Ovine Reference Materials and Assays for Prion Genetic Testing - (Abstract Only)
Heaton, M.P., Leymaster, K.A., Kalbfleisch, T.S., Freking, B.A., Smith, T.P., Clawson, M.L., Laegreid, W.W. 2009. Ovine Reference Materials and Assays for Prion Genetic Testing [abstract]. Plant and Animal Genomes XVIII Conference. Abstract No. P577. Available: http://www.intl-pag.org/18/abstracts/
Markers on Bovine Chromosome 20 Associated with Carcass Quality and Composition Traits and Incidence of Contracting Infectious Bovine Keratoconjunctivitis - (Abstract Only)
Garcia, M.D., Matukumalli, L., Wheeler, T.L., Shackelford, S.D., Smith, T.P., Casas, E. 2010. Markers on Bovine Chromosome 20 Associated with Carcass Quality and Composition Traits and Incidence of Contracting Infectious Bovine Keratoconjunctivitis [abstract]. Plant and Animal Genome XVIII Conference. Poster No. P196. Available: http://www.intl-pag.org/18/abstracts/P03e_PAGXVIII_196.html
Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library - (Peer Reviewed Journal)
Sanchez Castano, C., Smith, T.P., Wiedmann, R.T., Vallejo, R.L., Salem, M., Yao, J., Rexroad Iii, C.E. 2009. Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library. Biomed Central (BMC) Genomics. 10:559.
Evaluation of Biochemical Parameters and Genetic Markers for Association with Meat Tenderness in South African Cattle - (Peer Reviewed Journal)
Frylinck, L., Van Wyk, G.L., Smith, T.P., Strydom, P.E., van Marle-Koster, E., Webb, E.C., Koohmaraie, M., Smith, M.F. 2009. Evaluation of Biochemical Parameters and Genetic Markers for Association with Meat Tenderness in South African Feedlot Cattle. Meat Science. 83:657-665.
Design of a High Density SNP Genotyping Assay in the Pig Using SNPs Identified and Characterized by Next Generation Sequencing Technology - (Peer Reviewed Journal)
Ramos, A.M., Crooijmans, R.P.M.A., Affara, N.A., Amaral, A.J., Archibald, A.L., Beever, J.E., Bendixen, C., Churcher, C., Clark, R., Dehais, P., Hansen, M.S., Hedegaard, J., Hu, Z.L., Kerstens, H.H., Law, A.S., Megens, H.J., Milan, D., Nonneman, D.J., Rohrer, G.A., Rothschild, M.F., Smith, T.P.L., Schnabel, R.D., Van Tassell, C.P., Taylor, J.F., Wiedmann, R.T., Schook, L.B., Groenen, M.A.M. 2009. Design of a High Density SNP Genotyping Assay in the Pig Using SNPs Identified and Characterized by Next Generation Sequencing Technology. PLoS One 4(8):E6524. p. 1-13.
Phylogenetic Classification of Escherichia coli O157:H7 Strains of Human and Bovine Origin Using a Novel Set of Nucleotide Polymorphisms - (Peer Reviewed Journal)
Clawson, M.L., Keen, J.E., Smith, T.P., Durso, L.M., Mcdaneld, T.G., Mandrell, R.E., Davis, M.A., Bono, J.L. 2009. Phylogenetic Classification of Escherichia coli O157:H7 Strains of Human and Bovine Origin Using a Novel Set of Nucleotide Polymorphisms. Genome Biology [serial online]. 10:R56. Available: http://genomebiology.com/2009/10/5/R56.
Whole Genome Analysis for Beef Tenderness - (Abstract Only)
Snelling, W.M., Smith, T.P., Shackelford, S.D., King, D.A., Wheeler, T.L., Kuehn, L.A., Thallman, R.M., Keele, J.W., Bennett, G.L. 2009. Whole Genome Analysis for Beef Tenderness [abstract]. Bovine Genome Consortium, Cold Spring Harbor, New York. May 9-11, 2009. Session 5 Poster Session, p. 30.
Development and Characterization of a High Density SNP Genotyping Assay for Cattle - (Peer Reviewed Journal)
Matukumalli, L.K., Lawley, C.T., Schnabel, R.D., Taylor, J.F., Allan, M.F., Heaton, M.P., O'Connell, J., Moore, S.S., Smith, T.P., Sonstegard, T.S., Van Tassell, C.P. 2009. Development and Characterization of a High Density SNP Genotyping Assay for Cattle. PLoS One. 4(4):e5350. Available: http://dx.doi.org/10.1371/journal.pone.0005350.
The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution - (Peer Reviewed Journal)
Elsik, C.G., Gibbs, R., Skow, L., Tellam, R., Weinstock, G., Worley, K., Kappes, S.M., Green, R.D., Alexander, L.J., Bennett, G.L., Carroll, J.A., Chitko Mckown, C.G., Hamernik, D.L., Harhay, G.P., Keele, J.W., Liu, G., Macneil, M.D., Matukumalli, L.K., Rijnkels, M., Roberts, A.J., Smith, T.P., Snelling, W.M., Stone, R.T., Waterman, R.C., White, S.N. 2009. The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution. Science. 324:522-528.
Association of Single Nucleotide Polymorphisms in the CAST Gene Associated with Longissimus Tenderness in Beef Cattle - (Abstract Only)
Casas, E., Wheeler, T.L., Shackelford, S.D., Bennett, G.L., Smith, T.P.L. 2009. Association of Single Nucleotide Polymorphisms in the CAST Gene Associated with Longissimus Tenderness in Beef Cattle [abstract]. Journal of Animal Science Supplement. 87(E-Suppl. 2):533. Abstract #628.
Phylogenetic Classification of Escherichia coli O157:H7 Isolates of Human and Bovine Origin Using a Novel Set of Nucleotide Polymorphisms - (Abstract Only)
Clawson, M.L., Keen, J.E., Smith, T.P., Durso, L.M., McDaneld, T.G., Mandrell, R.E., Davis, M.A., Bono, J.L. 2009. Phylogenetic Classification of Escherichia coli O157:H7 Isolates of Human and Bovine Origin Using a Novel Set of Nucleotide Polymorphisms [abstract]. American Society for Microbiology. Abstract No. Z-006. p. 612. 2009 CDROM.
Bacterial Communities Associated with Shiga-Toxigenic E. coli O157:H7 (STEC O157) in Beef Cattle Feedlot Environments - (Abstract Only)
Durso, L.M., Harhay, G.P., Bono, J.L., Smith, T.P., Laegreid, W.W., Keen, J.E., Clawson, M.L. 2009. Bacterial Communities Associated with Shiga-Toxigenic E. coli O157:H7 (STEC O157) in Beef Cattle Feedlot Environments [abstract]. Microbial Ecology 57(3):569.
MicroRNA Transcriptome Profiles During Swine Skeletal Muscle Development - (Peer Reviewed Journal)
McDaneld, T.G., Smith, T.P., Doumit, M.E., Miles, J.R., Coutinho, L.L., Sonstegard, T.S., Matukumalli, L.K., Nonneman, D.J., Wiedmann, R.T. 2009. MicroRNA Transcriptome Profiles During Swine Skeletal Muscle Development. Biomed Central (BMC) Genomics. 10:77.
A Limousin specific myostatin allele affects longissimus muscle area and fatty acid profiles in a Wagyu-Limousin F*2* population - (Peer Reviewed Journal)
Alexander, L.J., Kuehn, L.A., Smith, T.P., Matukumalli, L.K., Mote, B., Koltes, J.E., Reecy, J., Geary, T.W., Rule, D.C., Macneil, M.D. 2009. A Limousin specific myostatin allele affects longissimus muscle area and fatty acid profiles in a Wagyu-Limousin F*2* population. Journal of Animal Science 87:1576-1581.
Profiling miRNA Expression in Bovine Tissues by Deep Sequencing - (Abstract Only)
Matukumalli, L.K., Alexander, L.J., Mcdaneld, T.G., Smith, T.P., Schroeder, S.G., Sonstegard, T.S., Van Tassell, C.P. 2009. Profiling miRNA Expression in Bovine Tissues by Deep Sequencing. Plant and Animal Genome Conference.
SNP Discovery in Swine by Reduced Representation and High Throughput Pyrosequencing - (Abstract Only)
Nonneman, D.J., Wiedmann, R.T., Smith, T.P. 2009. SNP Discovery in Swine by Reduced Representation and High Throughput Pyrosequencing. Plant and Animal Genome Conference XVII Proceedings. 1/10-14/2009, San Diego, CA. Abstract P531.
Design of the Illumina Porcine 50K+ SNP Iselect(TM) Beadchip and Characterization of the Porcine HapMap Population - (Abstract Only)
Groenen, M.A., Crooijmans, R.P., Ramos, A.M., Amaral, A.J., Kerstens, H., Bendixen, C., Hedegaard, J., Rohrer, G.A., Smith, T.P., Van Tassell, C.P., Taylor, J.F., Rothschild, M., Hu, Z., Nonneman, D.J., Beever, J., Archibald, A., Law, A., Milan, D., Hansen, M., Schook, L. 2009. Design of the Illumina Porcine 50K+ SNP Iselect(TM) Beadchip and Characterization of the Porcine HapMap Population. Plant and Animal Genome Conference Proceedings. 1/10-14/09, San Diego, CA. Abstract W493.
The artiodactyl APOBEC3 innate immune repertoire shows evidence for a multi-functional domain organization that existed in the ancestor of placental mammals - (Peer Reviewed Journal)
Larue, R.S., Jonsson, S.R., Silverstein, K.A., Lajoie, M., Bertrand, D., El-Mabrouk, N., Hotzel, I., Andresdottir, V., Smith, T.P., Harris, R. 2008. The artiodactyl APOBEC3 innate immune repertoire shows evidence for a multi-functional domain organization that existed in the ancestor of placental mammals. BioMed Central (BMC) Molecular Biology. 9:104.
SNP discovery in swine by reduced representation and high throughput pyrosequencing - (Peer Reviewed Journal)
Wiedmann, R.T., Smith, T.P., Nonneman, D.J. 2008. SNP discovery in swine by reduced representation and high throughput pyrosequencing. BioMed Central (BMC) Genetics. 9:81.
Association of single nucleotide polymorphisms in candidate genes residing under quantitative trait loci in beef cattle - (Abstract Only)
Casas, E., Wheeler, T.L., Shackelford, S.D., Bennett, G.L., Smith, T.P.L. 2009. Association of single nucleotide polymorphisms in candidate genes residing under quantitative trait loci in beef cattle [abstract]. Plant and Animal Genome XVII Conference Proceedings. Poster No. P477.
Extreme muscle development in sheep heterozygous for both myostatin and callipyge mutations - (Abstract Only)
Smith, T.P., Freking, B.A., Shackelford, S.D., King, D.A., Wheeler, T.L., Leymaster, K.A. 2009. Extreme muscle development in sheep heterozygous for both myostatin and callipyge mutations. Plant and Animal Genome Conference Proceedings. Jan. 10-14, 2009. San Diego, CA. Abstract W084.
Single nucleotide polymorphism discovery in rainbow trout using reduced representation libraries - (Abstract Only)
Castano, C., Smith, T.P., Wiedmann, R.T., Yao, J., Rexroad III, C.E. 2009. Single nucleotide polymorphism discovery in rainbow trout using reduced representation libraries. Meeting Abstract.
Studies on cattle genomic structural variation provide insights into ruminant speciation and adaptation - (Abstract Only)
Liu, G., Zhu, B., Alexander, L.J., Matukumalli, L.K., Van Tassell, C.P., Sonstegard, T.S., Nonneman, D.J., Keele, J.W. 2009. Studies on cattle genomic structural variation provide insights into ruminant speciation and adaptation. [abstract]. Plant and Animal Genome Conference Proceedings. W093.
MicroRNA expression profile in bovine cumulus-oocyte complexes during late oogenesis - (Abstract Only)
Miles, J.R., McDaneld, T.G., Wiedmann, R.T., Cushman, R.A., Echternkamp, S.E., Vallet, J.L., Smith, T.P.L. 2009. MicroRNA expression profile in bovine cumulus-oocyte complexes during late oogenesis [abstract]. Reproduction, Fertility and Development. 21(1):186 (Abstract #174).
Prevalence of the prion gene E211K variant in U.S. cattle - (Peer Reviewed Journal)
Heaton, M.P., Keele, J.W., Harhay, G.P., Richt, J., Koohmaraie, M., Wheeler, T.L., Shackelford, S.D., Casas, E., King, D.A., Sonstegard, T.S., Van Tassell, C.P., Neibergs, H.L., Chase, C.C., Kalbfleisch, T.S., Smith, T.P., Clawson, M.L., Laegreid, W.W. 2008. Prevalence of the prion gene E211K variant in U.S. cattle. BioMed Central (BMC) Veterinary Research [journal online]. 4:25. Available: (http://www.biomedcentral.com/1746-6148/4/25).
A sequencing strategy for identifying variation throughout the prion gene of BSE-affected cattle - (Peer Reviewed Journal)
Clawson, M.L., Heaton, M.P., Keele, J.W., Smith, T.P., Harhay, G.P., Richt, J., Laegreid, W.W. 2008. A sequencing strategy for identifying variation throughout the prion gene of BSE-affected cattle. BMC Research Notes [journal online]. 1:32. Available: http://www.biomedcentral.com/1756-0500/1/32.
MicroRNA profiles of the fetal pig during skeletal muscle development - (Abstract Only)
McDaneld, T.G., Wiedmann, R.T., Miles, J.R., Smith, T.P. 2008. MicroRNA profiles in skeletal muscle of fetal pig. XXXI Animal Genetics International Conference Proceedings. Poster #2206.
Present and future applications of DNA technologies to improve beef production - ()
Allan, M.F., Smith, T.P. 2008. Present and future applications of DNA technologies to improve beef production. Meat Science. 80(1):79-85.
High throughput SNP discovery and validation in the pig: towards the development of a high density swine SNP chip - (Abstract Only)
Ramos, A.M., Crooijmans, R.P., Fonseca, A., Kerstens, H., Bendixen, C., Hedegaard, J., Rohrer, G.A., Smith, T.P., Van Tassell, C.P., Taylor, J.F., Rothschild, M., Nonneman, D.J., Beever, J., Archibald, A., Schook, L., Groenen, M.A. 2008. High throughput SNP discovery and validation in the pig: towards the development of a high density swine SNP chip. Proc., 2nd European Conference on Pig Genomics, June 4-5, 2008, Ljubljana, Slovenia. Poster #2234.
Markers on bovine chromosome 20 associated with fat related traits and incidence of contracting bovine respiratory disease - (Abstract Only)
Garcia, M.D., Matukumalli, L., Wheeler, T.L., Shackelford, S.D., Koohmaraie, M., Smith, T.P., Casas, E. 2008. Markers on bovine chromosome 20 associated with fat related traits and incidence of contracting bovine respiratory disease [abstract]. Journal of Animal Science Supplement. 86(E-Suppl. 2):210. Abstract #W54.
ANALYSIS OF CATTLE COPY NUMBER VARIATION REVEALS INSIGHTS INTO THE EVOLUTION OF RUMINANTS - (Abstract Only)
Liu, G., Keele, J.W., Van Tassell, C.P., Sonstegard, T.S., Li, R.W., Alexander, L.J., Matukumalli, L.K., Smith, T.P., Gasbarre, L.C. 2008. Analysis of cattle copy number variation reveals insights into the evolution of ruminants. [abstract]. 2008 meeting on the Biology of Genomes, May 6-10, 2007, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. p197.
Development and Applications of a Bovine 50,000 SNP Chip - (Abstract Only)
Taylor, J.F., Sonstegard, T.S., Van Tassell, C.P., Matukumalli, L., Smith, T.P., Allen, M.L. 2008. Development and Applications of a Bovine 50,000 SNP Chip. International Symposium of Animal Functional Genomics.
Microbial Community Structure of Feedlot Cattle Feces - (Abstract Only)
Durso, L.M., Harhay, G.P., Clawson, M.L., Laegreid, W.W., Bono, J.L., Keen, J.E., Smith, T.P. Microbial community structure of feedlot cattle feces. In: Proceedings of the 108th General Meeting of the American Society for Microbiology, June 1-5, 2008, Boston, Massachusetts. 2008 CDROM.
Effect of porcine reproductive and respiratory syndrome virus on porcine alveolar macrophage function as determined using serial analysis of gene expression (SAGE) - (Peer Reviewed Journal)
Miller, L.C., Harhay, G.P., Lager, K.M., Smith, T.P., Neill, J.D. 2008. Effect of porcine reproductive and respiratory syndrome virus on porcine alveolar macrophage function as determined using serial analysis of gene expression (SAGE). Developments in Biologicals. 132:169-174.
Association of a bovine prion gene haplotype with atypical BSE - (Peer Reviewed Journal)
Clawson, M.L., Richt, J., Baron, T., Biacabe, A., Czub, S., Heaton, M.P., Smith, T.P., Laegreid, W.W. 2008. Association of a bovine prion gene haplotype with atypical BSE. PLoS One [serial online]. 3(3):e1830. Available: http://www.plosone.org.
Application of the BovineSNP50 assay for QTL mapping and prediction of genetic merit in Holstein cattle - (Abstract Only)
Schnabel, R.D., Van Tassell, C.P., Matukumalli, L., Sonstegard, T.S., Smith, T.P., Moore, S.S., Lawley, C.T., Taylor, J.F. 2008. Application of the BovineSNP50 assay for QTL mapping and prediction of genetic merit in Holstein cattle. Plant and Animal Genome Conference Proceedings.
Analysis of copy number variation in the bovine genome - (Abstract Only)
Liu, G., Van Tassell, C.P., Sonstegard, T.S., Li, R.W., Alexander, L.J., Keele, J.W., Matukumalli, L.K., Brown, T., Smith, T.P., Gasbarre, L.C. 2008. Analysis of copy number variation in the bovine genome. Plant and Animal Genome (PAG) XVI Conference. San Diego, CA. p517.
A high-resolution map of copy number variation in the cattle genome - (Abstract Only)
Liu, G., Keele, J.W., Van Tassell, C.P., Sonstegard, T.S., Alexander, L.J., Li, R.W., Matukumalli, L.K., Smith, T.P., Gasbarre, L.C. 2008. A high-resolution map of copy number variation in the cattle genome. Plant and Animal Genome VX Conference Abstracts. The NRI Animal Genome PD Meeting, San Diego, CA. p84.
Characterization of the Cattle HapMap Population using the Illumina Bovine-50K SNP Chip - (Abstract Only)
Matukumalli, L.K., Schnabel, R.D., Lawley, C.T., Sonstegard, T.S., Smith, T.P., Moore, S.S., Taylor, J.F., Van Tassell, C.P. 2008. Characterization of the Cattle HapMap Population using the Illumina Bovine-50K SNP Chip. Plant and Animal Genome Conference.
MicroRNA (MiRNA) technology in livestock: expression profiling of bovine oocyte and developmental stages of porcine skeletal muscle - (Proceedings)
Mcdaneld, T.G., Wiedmann, R.T., Miles, J.R., Cushman, R.A., Vallet, J.L., Smith, T.P. 2007. MicroRNA (MiRNA) technology in livestock: expression profiling of bovine oocyte and developmental stages of porcine skeletal muscle. Conference Proc., National Swine Improvement Federation Conference & Ann. Mtg., Dec. 5-7, 2007. Kansas City, MO, NSIF Volume 32, www.nsif.com.
SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries - (Peer Reviewed Journal)
Van Tassell, C.P., Smith, T.P., Matukumalli, L.K., Taylor, J.F., Schnabel, R.D., Lawley, C.T., Haudenschild, C., Moore, S.S., Warren, W.C., Sonstegard, T.S. 2008. SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nature Methods. 5:247-252.
Gene Expression Profiling of Porcine Reproductive and Respiratory Syndrome Virus Infected Porcine Alveolar Macrophages - (Abstract Only)
Miller, L.C., Harhay, G.P., Lager, K.M., Smith, T.P., Neill, J.D. 2007. Gene expression profiling of PRRSV-infected porcine alveolar macrophages [abstract]. Porcine Reproductive and Respiratory Syndrome International Symposium. Paper No. 47.
Detection of germline and somatic copy number variations in cattle - (Proceedings)
Liu, G., Van Tassell, C.P., Sonstegard, T.S., Li, R.W., Alexander, L.J., Keele, J.W., Matukumalli, L.K., Smith, T.P., Gasbarre, L.C. 2008. Detection of germline and somatic copy number variations in cattle. Developments in Biologicals. 132:231-237.
Prevalence of the prion gene E211K variant in U.S. cattle - (Abstract Only)
Heaton, M.P., Keele, J.W., Harhay, G.P., Richt, J., Koohmaraie, M., Wheeler, T.L., Shackelford, S.D., Casas, E., King, D.A., Sonstegard, T.S., Van Tassell, C.P., Neibergs, H.L., Chase, C.C., Kalbfleisch, T.S., Smith, T.P., Clawson, M.L., Laegreid, W.W. 2008. Prevalence of the prion gene E211K variant in U.S. cattle (abstract). Plant and Animal Genome XVI Conference. Poster No. P538.
Description and analysis of the Bovine Gene Atlas - An extensive compendium of bovine transcript profiles - (Abstract Only)
Harhay, G.P., Keele, J.W., Smith, T.P., Alexander, L.J., Matukumalli, L.K., Schroeder, S.G., Liu, G., Van Tassell, C.P., Sonstegard, T.S. 2008. Description and analysis of the Bovine Gene Atlas - An extensive compendium of bovine transcript profiles (abstract). Plant and Animal Genome XVI Conference. Poster No. P516.
Generation of large numbers of SNP in cattle by coupling reduced genome representation with high throughput sequencing - (Abstract Only)
Smith, T.P., Matukumalli, L., Sonstegard, T.S., Schnabel, R., Taylor, J., Haudenschild, C., Lawley, C., Moore, S., Van Tassell, C.P. 2008. Generation of large numbers of SNP in cattle by coupling reduced genome representation with high throughput sequencing (abstract). Plant and Animal Genome XVI Conference Proceedings. Poster No. P90.
Bovine copy number variation and its implication in animal health - (Abstract Only)
Liu, G., Van Tassell, C.P., Sonstegard, T.S., Alexander, L.J., Keele, J.W., Matukumalli, L.K., Smith, T.P., Gasbarre, L.C. 2007. Bovine copy number variation and its implication in animal health. [ abstract]. International Symposium on Animal Genomics for Animal Health. pp. 32.
A physical map of the bovine genome - (Peer Reviewed Journal)
Snelling, W.M., Chiu, R., Schein, J.E., Hobbs, M., Abbey, C.A., Adelson, D.L., Aerts, J., Bennett, G.L., Bosdet, I.E., Boussaha, M., Brauning, R., Caetano, A.R., Costa, M.M., Crawford, A.M., Dalrymple, B.P., Eggen, A., Everts-Van Der Wind, A., Floriot, S., Gautier, M., Gill, C.A., Green, R.D., Holt, R., Jann, O., Jones, S.J., Kappes, S.M., Keele, J.W., De Jong, P.J., Larkin, D.M., Lewin, H.A., Mcewan, J.C., Mckay, S., Marra, M.A., Mathewson, C.A., Matukumalli, L.K., Moore, S.S., Murdoch, B., Nicholas, F.W., Osoegawa, K., Roy, A., Salih, H., Schibler, L., Schnabel, R.D., Silveri, L., Skow, L.C., Smith, T.P., Sonstegard, T.S., Taylor, J.F., Tellam, R., Van Tassell, C.P., Williams, J.L., Womack, J.E., Wye, N.H., Yang, G., Zhao, S. 2007. A physical map of the bovine genome. Genome Biology. 8:R165 (17 pp).
Assessing the association of single nucleotide polymorphisms at the thyroglobulin gene with carcass traits in beef cattle - (Peer Reviewed Journal)
Casas, E., White, S.N., Shackelford, S.D., Wheeler, T.L., Koohmaraie, M., Bennett, G.L., Smith, T.P.L. 2007. Assessing the association of single nucleotide polymorphisms at the thyroglobulin gene with carcass traits in beef cattle. Journal of Animal Science. 85:2807-2814.
Initial analysis of copy number variation in the cow genome - (Abstract Only)
Liu, G., Van Tassell, C.P., Sonstegard, T.S., Li, R.W., Alexander, L.J., Keele, J.W., Matukumalli, L.K., Smith, T.P., Gasbarre, L.C. 2007. Initial analysis of copy number variation in the cow genome. [abstract}. Gordon Research Conference Proceedings.
The u-Calpain and Calpastatin Tenderness Markers are Predictive of Tenderness Variation Among Samples Obtained From Commercial U.S. Select Beef Carcasses - (Abstract Only)
Shackelford, S.D., Casas, E., Smith, T.P., Wheeler, T.L., Koohmaraie, M. 2007. The u-calpain and calpastatin tenderness markers are predictive of tenderness variation among samples obtained from commercial U.S. select beef carcasses. Proc. 60th Reciprocal Meat Conference, June 17-20, 2007, Brookings, SD. http://www.meatscience.org/pubs/rmcarchv/2007/presentations/RMC_2007_060_4_073_Shackelford.pdf
Construction and application of a bovine high-density SNP assay - (Abstract Only)
Van Tassell, C.P., Matukumalli, L.K., Taylor, C., Smith, T.P., Sonstegard, T.S., Schnabel, R., Silva, M.V., Wiggans, G.R., Liu, G., Moore, S., Taylor, J.F. 2007. Construction and application of a bovine high-density SNP assay. Joint Abstracts of the American Dairy Science and Society of Animal Science.
The role of microRNAs in muscle development - (Abstract Only)
Smith, T.P.L., McDaneld, T.G., Doumit, M.E., Matukumalli, L.K., Sonstegard, T.S., Coutinho, L.L., Wiedmann, R.T. The role of microRNAs in muscle development. Journal of Animal Science (Suppl. 1):637. 2007
Creation of a Gene Atlas in cattle using sequence-based transcriptional profiling - (Abstract Only)
Sonstegard, T.S., Keele, J.W., Harhay, G.P., Smith, T.P., Matukumalli, L.K., Van Tassell, C.P., Liu, G., Alexander, L.J. 2007. Creation of a Gene Atlas in cattle using sequence-based transcriptional profiling. [abstract] Joint Abstracts of the American Dairy Science and Society of Animal Science.
DISCOVERY AND PROFILING OF BOVINE MICRORNAS FROM IMMUNE RELATED AND EMBRYONIC TISSUES - (Peer Reviewed Journal)
Coutinho, L.L., Matukumalli, L.K., Sonstegard, T.S., Van Tassell, C.P., Gasbarre, L.C., Capuco, A.V., Smith, T.P. 2007. Discovery and profiling of bovine micrornas from immune related and embryonic tissues. Physiological Genomics. 29(1):35-43.
A second generation radiation hybrid map to aid the assembly of the bovine genome sequence - (Peer Reviewed Journal)
Jann, O.C., Aerts, J., Jones, M., Hastings, N., Law, A., Mckay, S., Marques, E., Prasad, A., Yu, J., Moore, S.S., Florita, S., Mahe, M., Eggen, A., Silveri, L., Negrini, R., Milanesi, E., Ajmone-Marsan, P., Vakebtubu, A., Marchitelli, C., Janitz, M., Herwig, R., Hennig, S., Savarese, M., Gorni, C., Connor, E.E., Sonstegard, T.S., Smith, T.P., Drogemuller, C., Williams, J. 2006. A second generation radiation hybrid map to aid the assembly of the bovine genome sequence. BMC Genomics. 7:283-298.
Prion gene haplotypes of U.S. cattle - (Peer Reviewed Journal)
Clawson, M.L., Heaton, M.P., Keele, J.W., Smith, T.P., Harhay, G.P., Laegreid, W.W. 2006. Prion gene haplotypes of U.S. cattle. BioMed Central (BMC) Genetics. 7:51.
Polymorphisms and haplotype structure of bovine PRND (doppel) and PRNT - (Abstract Only)
Laegreid, W.W., Clawson, M.L., Smith, T.P., Harhay, G.P., Keele, J.W., Heaton, M.P. 2007. Polymorphisms and haplotype structure of bovine PRND (doppel) and PRNT [abstract]. Plant and Animal Genome XV Conference. Poster No. P535.
Genome adaptations of a tripartite motif protein for retroviral defense in cattle and sheep - (Abstract Only)
Smith, T.P., Heaton, M.P., Snelling, W.M., Ylinen, L., Keckesova, Z., Webb, B.L., Towers, G.J. 2007. Genome adaptations of a tripartite motif protein for retroviral defense in cattle and sheep [abstract]. Plant and Animal Genome XV Conference. Poster No. P540.
A rapid sequence-based method for comprehensive polymorphism identification within a 25.2-kb region of the bovine prion gene in BSE-affected cattle - (Abstract Only)
Clawson, M.L., Heaton, M.P., Keele, J.W., Smith, T.P., Harhay, G.P., Laegreid, W.W. 2007. A rapid sequence-based method for comprehensive polymorphism identification within a 25.2-kb region of the bovine prion gene in BSE-affected cattle [abstract]. Plant and Animal Genome XV Conference. Poster No. P533.
A marker set for parentage-based DNA traceback in beef and dairy cattle - (Abstract Only)
Heaton, M.P., Snelling, W.M., Smith, T.P., Keele, J.W., Harhay, G.P., Wiedmann, R.T., Bennett, G.L., Freking, B.A., Van Tassell, C.P., Sonstegard, T.S., Gasbarre, L.C., Moore, S.S., Murdoch, B., Mckay, S.D., Kalbfleisch, T., Laegreid, W.W. 2007. A marker set for parentage-based DNA traceback in beef and dairy cattle [abstract]. Plant and Animal Genome XV Conference. Poster No. P516.
ASSOCIATION OF A SINGLE NUCLEOTIDE POLYMORPHISM IN SPP1 WITH GROWTH TRAITS AND TWINNING IN A CATTLE POPULATION SELECTED FOR TWINNING RATE - (Peer Reviewed Journal)
Allan, M.F., Thallman, R.M., Cushman, R.A., Echternkamp, S.E., White, S.N., Kuehn, L.A., Casas, E., Smith, T.P. 2007. Association of a single nucleotide polymorphism in spp1 with growth traits and twinning in a cattle population selected for twinning rate. Journal of Animal Science. 85(2):341-347.
Evaluation in beef cattle of six deoxyribonucleic acid markers developed for dairy traits reveals an osteopontin polymorphism associated with postweaning growth. - (Peer Reviewed Journal)
White, S.N., Casas, E., Allan, M.F., Keele, J.W., Snelling, W.M., Wheeler, T.L., Shackelford, S.D., Koohmaraie, M., Smith, T.P. 2007. Evaluation in beef cattle of six deoxyribonucleic acid markers developed for dairy traits reveals an osteopontin polymorphism associated with post-weaning growth. Journal of Animal Science. 85:1-10.
ISOLATION OF AN ACTIVE LV1 GENE FROM CATTLE INDICATES THAT TRIPARTITE MOTIF PROTEIN-MEDIATED INNATE IMMUNITY TO RETROVIRAL INFECTION IS WIDESPREAD AMONG MAMMALS - (Peer Reviewed Journal)
Ylinen, L.M., Keckesova, Z., Webb, B.L., Gifford, R.J., Smith, T.P., Towers, G.J. 2006. Isolation of an active Lv1 gene from cattle indicates that tripartite motif protein-mediated innate immunity to retroviral infection is widespread among mammals. Journal of Virology. 80(15):7332-7338.
EXPRESSION PROFILES OF MICRO-RNAS IN SWINE MUSCLE DEVELOPMENT - (Abstract Only)
Wiedmann, R.T., Doumit, M.E., Matukumalli, L.K., Sonstegard, T.S., Coutinho, L.L., Nonneman, D.J., Smith, T.P. 2006. Expression profiles of micro-RNAs in swine muscle development. (Abstract) International Conference on Animal Genetics. p. 70. Abstract #C278.
ISOLATION OF THE FIRST NON-PRIMATE TRIM5-ALPHA FROM CATTLE INDICATES THAT TRIM5-ALPHA MEDIATED INNATE IMMUNITY TO RETROVIRAL INFECTION MAY BE WIDESPREAD AMONG MAMMALS - (Abstract Only)
Schaller, T., Ylinen, L.M., Keckesova, Z., Webb, B.L., Smith, T.P., Towers, G.J. 2006. Isolation of the first non-primate trim5-alpha from cattle indicates that trim5-alpha mediated innate immunity to retroviral infection may be widespread among mammals. Proc., 31st Annual Meeting on Retroviruses, Cold Spring Harbor Lab, Cold Spring Harbor, NY, May 23-28, 2006.
COMPREHENSIVE SEARCH OF BOVINE MICRORNAS EXPRESSED IN IMMUNE AND GUT TISSUES BY DEEP SEQUENCING - (Abstract Only)
Sonstegard, T.S., Matukumalli, L.K., Coutinho, L.L., Liu, G., Gasbarre, L.C., Smith, T.P. 2006. Comprehensive search of bovine micrornas expressed in immune and gut tissues by deep sequencing [abstract]. International Conference on Animal Genetics. pp. C354.
PROFILING OF BOVINE MICRORNAS FROM IMMUNE RELATED AND EMBRYONIC TISSUES. - (Abstract Only)
Matukumalli, L.K., Coutinho, L.L., Sonstegard, T.S., Van Tassell, C.P., Gasbarre, L.C., Capuco, A.V., Smith, T.P. 2006. Profiling of bovine micrornas from immune related and embryonic tissues [abstract]. International Conference on Animal Genetics. pp. C329.
IDENTIFICATION OF BOVINE MICRORNAS - (Abstract Only)
Matukumalli, L.K., Coutinho, L.L., Sonstegard, T.S., Van Tassell, C.P., Gasbarre, L.C., Capuco, A.V., Smith, T.P. 2006. Identification of bovine micrornas [abstract]. Cold Springs Harbor Laboratories 71 Symposium of Regulatoary RNAs. Cold Spring Harbor, NY. Number 214.
IDENTIFICATION AND PROFILING OF BOVINE MICRORNAS FROM IMMUNE RELATED AND EMBRYONIC TISSUES. - (Abstract Only)
Coutinho, L.L., Matukumalli, L.K., Sonstegard, T.S., Van Tassell, C.P., Gasbarre, L.C., Capuco, A.V., Smith, T.P. 2006. Identification and profiling of bovine micrornas from immune related and embryonic tissues [abstract]. 17th Annual BARC Poster Day, Beltsville, MD. No 6.
CHARACTERIZATION OF BOIVNE MICRORNAS EXPRESSED IN IMMUNE AND GUT TISSUES BY DEEP SEQUENCING - (Abstract Only)
Matukumalli, L.K., Coutinho, L.L., Sonstegard, T.S., Liu, G., Gasbarre, L.C., Smith, T.P. 2006. Characterization of boivne micrornas expressed in immune and gut tissues by deep sequencing [abstract] 17th Annual BARC Poster Day. Beltsville, MD. No 27.
CHARACTERIZATION OF 954 BOVINE FULL-CDS CDNA SEQUENCES - (Peer Reviewed Journal)
Harhay, G.P., Sonstegard, T.S., Keele, J.W., Heaton, M.P., Clawson, M.L., Snelling, W.M., Wiedmann, R.T., Van Tassell, C.P., Smith, T.P. 2005. Characterization of 954 bovine full-CDS cDNA sequences. Biomed Central (BMC) Genomics 6:166 (11 pp).
CALLIPYGE MUTATION AFFECTS GENE EXPRESSION IN CIS: A POTENTIAL ROLE FOR CHROMATIN STRUCTURE - (Peer Reviewed Journal)
Murphy, S.K., Nolan, C.M., Huang, Z., Kucera, K.S., Freking, B.A., Smith, T.P.L., Leymaster, K.A., Weidman, J.R., Jirtle, R.L. 2006. Callipyge mutation affects gene expression in cis: A potential role for chromatin structure. Genome Research. 16:340-346.
HIGH DENSITY ESTS BASED BOVINE PHYSICAL MAPS AND THEIR USE TO CONSTRUCT COMPARATIVE MAPS AND INFORM THE BOVINE GENOME SEQUENCE ASSEMBLY - (Abstract Only)
Williams, J.L., Aerts, J., Law, A., Jann, O., Janitz, M., Hennig, S., Eggen, A., Floriot, S., Ajmone-Marsan, P., Milanse, E., Valentini, A., Marchitelli, C., Mckay, S., Prasad, A., Yu, J., Moore, S.S., Drogemuller, C., Connor, E.E., Sonstegard, T.S., Stone, R.T., Smith, T.P. 2006. High density ESTs based bovine physical maps and their use to construct comparative maps and inform the bovine genome sequence assembly[abstracat]. Plant and Animal Genome XIV:55. Number W214.
LINKAGE DISEQUILIBRIUM AND HAPLOTYPE STRUCTURE IN THE PRION GENE OF U.S. BEEF AND DAIRY CATTLE - (Abstract Only)
Clawson, M.L., Heaton, M.P., Keele, J.W., Smith, T.P., Laegreid, W.W. 2006. Linkage disequilibrium and haplotype structure in the prion gene of U.S. beef and dairy cattle (abstract). Plant and Animal Genome Conference Proceedings. p. 145.
TESTING FOR INTERACTIONS BETWEEN CALPASTATIN AND U-CALPAIN MARKERS IN BEEF CATTLE ON TENDERNESS TRAITS - (Peer Reviewed Journal)
Casas, E., White, S.N., Wheeler, T.L., Shackelford, S.D., Koohmaraie, M., Riley, D.G., Chase, C.C. Jr., Johnson, D.D., Smith, T.P. 2006. Effects of calpastatin and u-calpain markers in beef cattle on tenderness traits. Journal of Animal Science. 84:520-525.
TESTING FOR INTERACTIONS BETWEEN CALPASTATIN AND U-CALPAIN MARKERS IN BEEF CATTLE ON TENDERNESS TRAITS - (Abstract Only)
Casas, E., White, S.N., Wheeler, T.L., Shackelford, S.D., Koohmaraie, M., Riley, D.G., Chase, C.C., Johnson, D.D., Smith, T.P. 2006. Testing for interactions between Calpastatin and u-Calpain markers in beef cattle on tenderness traits [abstract]. Midwestern Section of the American Society of Animal Science. 84(Suppl. 2):135. Paper No. 329.
TWO PROMOTERS COORDINATE TRANSCRIPTION FROM THE HUMAN LHX3 GENE: REGULATION BY NUCLEAR FACTOR I AND SP1 - (Peer Reviewed Journal)
Yaden, B.C., Garcia Iii, M., Smith, T.P., Rhodes, S.J. Two Promoters Mediate Transcription from the Human LHX3 gene: Regulation by Nuclear Factor 1 and Specificity Protein 1. Endocrinology 147:324-337. 2006.
ASSIGNMENT OF 12 GENES TO PORCINE CHROMOSOME 1Q BY LINKAGE AND RADIATION HYBRID MAPPING - (Peer Reviewed Journal)
Nonneman, D.J., Smith, T.P., Freking, B.A., Rohrer, G.A. 2005. Assignment of 12 genes to porcine chromosome 1q by linkage and radiation hybrid mapping. Anim. Genet. 36:532-533. 2005.
IDENTIFICATION OF GENETIC MARKERS FOR FAT DEPOSITION AND MEAT TENDERNESS ON BOVINE CHROMOSOME 5: DEVELOPMENT OF A LOW DENSITY SNP MAP - (Peer Reviewed Journal)
Stone, R.T., Casas, E., Smith, T.P.L., Keele, J.W., Harhay, G.P., Bennett, G.L., Koohmaraie, M., Wheeler, T.L., Shackelford, S.D., Snelling, W.M. 2005. Identification of genetic markers for fat deposition and meat tenderness on bovine chromosome 5: Development of a low-density single nucleotide polymorphism map. Journal of Animal Science. 83:2280-2288.
A NEW SNP IN CAPN1 EXTENDS THE CURRENT TENDERNESS MARKER TEST TO INCLUDE CATTLE OF BOS INDICUS, BOS TAURUS, AND CROSSBRED DESCENT - (Peer Reviewed Journal)
White, S.N., Casas, E., Wheeler, T.L., Shackelford, S.D., Koohmaraie, M., Riley, D.G., Chase, C.C., Johnson, D.D., Keele, J.W., Smith, T.P. 2005. A new snp in capn1 extends the current tenderness marker test to include cattle of bos indicus, bos taurus, and crossbred descent. Journal of Animal Science. 83:2001-2008.
LINKAGE MAPPING BOVINE EST-BASED SNP - (Peer Reviewed Journal)
Snelling, W.M., Casas, E., Stone, R.T., Keele, J.W., Harhay, G.P., Bennett, G.L., Smith, T.P. 2005. Linkage mapping bovine EST-based SNP. Biomed Central (BMC) Genomics 6:74.
UT-B IS EXPRESSED IN BOVINE RUMEN: POTENTIAL ROLE IN RUMINAL UREA TRANSPORT - (Peer Reviewed Journal)
Stewart, G.S., Grahman, C., Cattell, S., Smith, T.P., Simmons, N.L., Smith, C.P. 2005. UT-B is expressed in bovine rumen: potential role in ruminal urea transport. American Journal of Physiology. 289:605-612.
IMMUNOGENOMICS AND THE TRANSITION DAIRY COW: PHYSIOLOGICAL INSIGHTS AND FUTURE POSSIBILITIES FOR IMPROVING ANIMAL HEALTH. - (Abstract Only)
Burton, J.L., Madsen, S.A., Chang, L.C., Weber, P.S., Coussens, P.M., Rosa, G., Matukumalli, L.K., Sonstegard, T.S., Smith, T.P. 2005. Immunogenomics and the transition dairy cow: physiological insights and future possibilities for improving animal health. ADSA/ASAS Joint Meeting, Cincinnati, OH, Abstract 17
ABNORMAL POSTNATAL MAINTENANCE OF ELEVATED PRENATAL DLK1 LEVELS IN CALLIPYGE SHEEP - (Peer Reviewed Journal)
Murphy, S.K., Freking, B.A., Smith, T.P., Nolan, C.M., Wylie, A.A., Evans, H.K., Jirtle, R.L. 2005. Abnormal postnatal maintenance of elevated prenatal DLK1 levels in callipyge sheep. Mammalian Genome. 16:171-183.
ALIGNMENT GENOMES ACROSS SPECIES - (Abstract Only)
Williams, J.L., Hastings, N., Jann, O., Law, A., Stone, R.T., Snelling, W.M., Connor, E.E., Sonstegard, T.S., Smith, T.P. 2005. Alignment genomes across species [abstract]. Plant and Animal Genome XVII. p. 241.
A NEW SNP MARKER IN CAPN1 IS ASSOCIATED WITH TENDERNESS IN CATTLE OF INDICINE, TAURINE, AND ADMIXED DESCENT - (Abstract Only)
White, S.N., Casas, E., Wheeler, T.L., Shackelford, S.D., Koohmaraie, M., Riley, D.G., Chase, C.C., Johnson, D.D., Keele, J.W., Smith, T.P. 2005. A new snp marker in capn1 is associated with tenderness in cattle of indicine, taurine, and admixed descent. Proc., Plant & Animal Genome XIII, San Diego, CA. P528. p. 203. 2005.
ASSESSMENT OF SINGLE NUCLEOTIDE POLYMORPHISMS IN GENES RESIDING ON CHROMOSOMES 14 AND 29 FOR ASSOCIATION WITH CARCASS COMPOSITION TRAITS IN BOS INDICUS CATTLE - (Abstract Only)
Chase, C.C. Jr., Casas, E., White, S.N., Riley, D.G., Smith, T.P., Brenneman, R.A., Olson, T.A., Johnson, D.D., Coleman, S.W., Bennett, G.L. 2005. Assessment of single nucleotide polymorphisms in genes residing on chromosomes 14 and 29 for association with carcass composition traits in Bos indicus cattle [Abstract]. Plant and Animal Genome XIII, January 15-19, 2005, San Diego, CA. p. 203.
INTEGRATING LINKAGE AND RADIATION HYBRID MAPPING DATA FOR BOVINE CHROMOSOME 15 - (Peer Reviewed Journal)
Snelling, W.M., Gautier, M., Keele, J.W., Smith, T.P., Stone, R.T., Harhay, G.P., Bennett, G.L., Ihara, N., Takasuga, A., Takeda, H., Sugimoto, Y., Eggen, A. Integrating linkage and radiation hybrid mapping data for bovine chromosome 15. Biomed Central (BMC) Genomics. 5:77. 2004.
ASSESSMENT OF SINGLE NUCLEOTIDE POLYMORPHISMS IN GENES RESIDING ON CHROMOSOMES 14 AND 29 FOR ASSOCIATION WITH CARCASS COMPOSITION TRAITS IN BOS INDICUS CATTLE - (Peer Reviewed Journal)
Casas, E., White, S.N., Riley, D.G., Smith, T.P., Brenneman, R.A., Olson, T.A., Johnson, D.D., Coleman, S.W., Bennett, G.L., Chase, C.C. 2005. Assessment of single nucleotide polymorphisms in genes residing on chromosomes 14 and 29 for association with carcass composition traits in bos indicus cattle. Journal of Animal Science. 83:13-19.
REGULATORY AND CODING SEQUENCES OF THE PITUITARY-SPECIFIC TRANSCRIPTION FACTOR, PROP1 ARE EVOLUTIONARILY AND FUNCTIONALLY CONSERVED - (Abstract Only)
Camper, S.A., Ward, R.D., Cho, M., Raetzman, L.T., Esposito, C., Rubin, E.M., Smith, T.P., Rhodes, S.J., Lyons, R.H. Regulatory and coding sequences of the pituitary-specific transcription factor, PROP1 are evolutionarily and functionally conserved. Proc., 18th Int. Mouse Genome Conference, Seattle, WA, 10/18-21/2004. Abstract.
ASSOCIATION OF MARKERS IN THE BOVINE CAPN1 GENE WITH MEAT TENDERNESS IN LARGE CROSSBRED POPULATIONS THAT SAMPLE INFLUENTIAL INDUSTRY SIRES - (Peer Reviewed Journal)
Page, B.T., Casas, E., Quaas, R.L., Thallman, R.M., Wheeler, T.L., Shackelford, S.D., Koohmaraie, M., White, S.N., Bennett, G.L., Keele, J.W., Dikeman, M.E., Smith, T.P. Association of markers in the bovine capn1 gene with meat tenderness in large crossbred populations that sample influential industry sires. Journal of Animal Science. 82:3474-3481. 2004.
THE APPLICATION OF MOLECULAR GENETICS IN A COMMERCIAL ENVIRONMENT TO IMPROVE PRODUCTION AND CARCASS COMPOSITION IN CATTLE - (Proceedings)
Casas, E., Thallman, R.M., Smith, T.P. 2004. The application of molecular genetics in a commercial environment to improve production and carcass composition in cattle. Advances in Animal Biotechnology and Their Applications in the National Livestock Industry, Symposium & Compendium Series Proceedings. October 13-15, 2004, Villarica, Chile. 10:53-70.
ANALYSIS OF LINKAGE DISEQUILIBRIUM IN THE REGION SURROUNDING A QUANTITATIVE TRAIT LOCUS FOR GROWTH IN CATTLE - (Abstract Only)
Smith, T.P., Snelling, W.M., Casas, E. 2004. Analysis of linkage disequilibrium in the region surrounding a quantitative trait locus for growth in cattle. Proc., Genome Sequencing & Analysis Conference XVI, Washington, DC, Sept. 27-30, 2004. Abstract P-56. p. 46.
DATABASE DIRECTED FULL-LENGTH CDNA GENERATION USING EST DATA FROM NORMALIZED BOVINE CDNA LIBRARIES - (Abstract Only)
Harhay, G.P., Smith, T.P., Sonstegard, T.S., Clawson, M.L. 2004. Database directed full-length cDNA generation using EST data from normalized bovine cDNA libraries. Proc., 29th International Conference on Animal Genetics (ISAG), Tokyo, Japan. September 11-16, 2004. Abstract A022, p. 37.
GENERATION OF A BOVINE OOCYTE CDNA LIBARARY AND MICROARRAY: RESOURCES FOR IDENTIFICATION OF GENES IMPORTANT FOR FOLLICULAR DEVELOPMENT AND EARLY EMBRYOGENESIS - (Peer Reviewed Journal)
Yao, J., Ren, X., Ireland, J.J., Coussens, P.M., Smith, T.P., Smith, G.W. 2004. Generation of a bovine oocyte cDNA libarary and microarray: resources for identification of genes important for follicular development and early embryogenesis. Physiological Genomics. 19:84-92. 2004.
DATABASE DIRECTED FULL-LENGTH CDNA GENERATION FROM NORMALIZED BOVINE CDNA LIBRARIES - (Abstract Only)
Harhay, G.P., Sonstegard, T.S., Clawson, M.L., Smith, T.P. 2004. Database directed full-length cDNA generation from normalized bovine cDNA libraries. International Genome Sequencing and Analysis Conference XVI, Washington, DC. September 27-30, 2004. Poster Abstract #49.
ASSOCIATION OF MYOSTATIN ON EARLY CALF MORTALITY, GROWTH, AND CARCASS COMPOSITION TRAITS IN CROSSBRED CATTLE - (Peer Reviewed Journal)
Casas, E., Bennett, G.L., Smith, T.P., Cundiff, L.V. 2004. Association of myostatin on early calf mortality, growth, and carcass composition traits in crossbred cattle. Journal of Animal Science. 82:2913-1918.
GENETICS: MOLECULAR - ()
Nonneman, D.J., Smith, T.P. 2004. Genetics: Molecular. Encyclopedia of Animal Science. p. 466-468.
MEAT QUALITY AND THE CALLIPYGE GENE, CONSUMER ACCEPTANCE AND FINAL PRODUCT - (Proceedings)
Freking, B.A., Smith, T.P., Leymaster, K.A. 2004. Meat quality and the callipyge gene, consumer acceptance and final product. In: Proceedings of the 7th World Sheep and Wool Congress 2004, July 17-24, 2004, Quebec, Canada. p. 92-102.
CONSERVED AMINO ACID SEQUENCES CONFER NUCLEAR LOCALIZATION UPON THE PROPHET OF PIT-1 PITUITARY TRANSCRIPTION FACTOR PROTEIN - (Peer Reviewed Journal)
Guy, J.C., Hunter, C.S., Showalter, A.A., Smith, T.P., Charoonpatrapong, K., Sloop, K.W., Bidwell, J.P., Rhodes, S.J. 2004. Conserved amino acid sequences confer nuclear localization upon the prophet of Pit-1 pituitary transcription factor protein. Gene. 336:263-273.
DEVELOPMENT AND TESTING OF A HIGH-DENSITY CDNA MICROARRAY RESOURCE FOR CATTLE - (Abstract Only)
Suchyta, S.P., Sipkovsky, S., Kruska, R., Jeffers, A., Mcnulty, A., Coussens, M.J., Tempelman, R.J., Halgren, R.A., Saama, P.M., Bauman, D.E., Boisclair, Y.R., Burton, J.L., Collier, R.J., Depeters, E.J., Ferris, T.A., Lucy, M.C., Mcguire, M.A., Medrano, J.F., Overton, T.4., Smith, T.P., Smith, G.W., Sonstegard, T.S., Spain, J.N., Spiers, D.E., Jianbo, Y., Coussens, P.M. 2004. Development and testing of a high-density cDNA microarray resource for cattle. Proc., Plant and Animal Genome Abstracts. P831. p. 278.
CORRELATION OF SRY AND ZFY ALLELES OF THE Y CHROMOSOME IN U.S. BEEF CATTLE - (Abstract Only)
CLAWSON, M.L., HEATON, M.P., FOX, J.M., CHITKO MCKOWN, C.G., SMITH, T.P., LAEGREID, W.W. CORRELATION OF SRY AND ZFY ALLELES OF THE Y CHROMOSOME IN U.S. BEEF CATTLE. PLANT AND ANIMAL GENOME CONFERENCE PROCEEDINGS. 2004. ABSTRACT NO. P310.
GENETIC RISK FACTORS FOR FAILURE OF PASSIVE TRANSFER IN THE BOVINE NEONATAL FC RECEPTOR - (Abstract Only)
LAEGREID, W.W., CLAWSON, M.L., HEATON, M.P., KEEN, J.E., CHITKO MCKOWN, C.G., FOX, J.M., SMITH, T.P., SNELLING, W.M., KEELE, J.W. GENETIC RISK FACTORS FOR FAILURE OF PASSIVE TRANSFER IN THE BOVINE NEONATAL FC RECEPTOR. PLANT AND ANIMAL GENOME CONFERENCE PROCEEDINGS. ABSTRACT NO. P642.
ASSOCIATION OF CAPN1 MARKERS WITH BEEF TENDERNESS IN CROSSBRED, MULTIBREED POPULATIONS - (Abstract Only)
White, S.N., Page, B.T., Casas, E., Koohmaraie, M., Wheeler, T.L., Shackelford, S.D., Keele, J.W., Smith, T.P. 2004. Association of CAPN1 markers with beef tenderness in crossbred, multibreed populations. Proc.,Plant and Animal Genome Abstracts. P644. p. 232.
MALE-SPECIFIC SRY AND ZFY HAPLOTYPES IN U.S. BEEF CATTLE - (Peer Reviewed Journal)
Clawson, M.L., Heaton, M.P., Fox, J.M., Chitko Mckown, C.G., Smith, T.P., Laegreid, W.W. 2004. Male-specific SRY and ZFY haplotypes in U.S. beef cattle. Animal Genetics. 35(3):246-249.
THEORY AND APPLICATION OF GENOME-BASED APPROACHES TO IMPROVE QUALITY AND VALUE OF BEEF - (Peer Reviewed Journal)
SMITH, T.P., THALLMAN, R.M., CASAS, E., SHACKELFORD, S.D., WHEELER, T.L., KOOHMARAIE, M. 2003. THEORY AND APPLICATION OF GENOME-BASED APPROACHES TO IMPROVE QUALITY AND VALUE OF BEEF. OUTLOOK IN AGRICULTURE. 32(4):253-265. 2003.
BETA-2-MICROGLOBULIN HAPLOTYPES IN U.S. BEEF CATTLE AND ASSOCIATION WITH FAILURE OF PASSIVE TRANSFER IN NEWBORN CALVES - (Peer Reviewed Journal)
Clawson, M.L., Heaton, M.P., Chitko Mckown, C.G., Fox, J.M., Smith, T.P., Snelling, W.M., Keele, J.W., Laegreid, W.W. 2004. Beta-2-microglobulin haplotypes in u.s. beef cattle and association with failure of passive transfer in newborn calves. Mammalian Genome. 2004. V. 15. P. 227-236.
THE CALLIPYGE MUTATION FOR SHEEP MUSCULAR HYPERTROPHY - GENETICS, PHYSIOLOGY AND MEAT QUALITY - ()
Freking, B.A., Smith, T.P., Leymaster, K.A. 2004. The callipyge mutation for sheep muscular hypertrophy - genetics, physiology and meat quality. In: M.F.W. te Pas, M.E. Everts and H.P. Haagsman, editors. Muscle Development in Livestock. CAB International, United Kingdom. Chapter 15. p. 317-342.
DEVELOPMENT OF ANIMAL CELL LINES FOR USE IN GENOMIC STUDIES - (Abstract Only)
CHITKO MCKOWN, C.G., FREKING, B.A., MACNEIL, M.D., SMITH, T.P. DEVELOPMENT OF ANIMAL CELL LINES FOR USE IN GENOMIC STUDIES. RESEARCH WORKERS IN ANIMAL DISEASES CONFERENCE PROCEEDINGS. 2003. ABSTRACT NO. 90P.
RECENT ADVANCES IN THE GENETICS OF MEAT TENDERNESS - ()
CASAS, E., SMITH, T.P. RECENT ADVANCES IN THE GENETICS OF MEAT TENDERNESS. FEEDINFO.COM. 2003. Online available: http://www.feedinfo.com. Accessed Sept. 9, 2003.
DETECTION OF QUANTITATIVE TRAIT LOCI FOR GROWTH AND CARCASS COMPOSITION IN CATTLE - (Peer Reviewed Journal)
CASAS, E., SHACKELFORD, S.D., KEELE, J.W., KOOHMARAIE, M., SMITH, T.P., STONE, R.T. DETECTION OF QUANTITATIVE TRAIT LOCI FOR GROWTH AND CARCASS COMPOSITION IN CATTLE. 2003. JOURNAL OF ANIMAL SCIENCE. 81:2976-2983.
CHARACTERIZATION OF GENE EXPRESSION IN DOUBLE-MUSCLED AND NORMAL-MUSCLED BOVINE EMBRYOS - (Peer Reviewed Journal)
POTTS, J.K., ECHTERNKAMP, S.E., SMITH, T.P., REECY, J.M. 2003. CHARACTERIZATION OF GENE EXPRESSION IN DOUBLE-MUSCLED AND NORMAL-MUSCLED BOVINE EMBRYOS. ANIMAL GENETICS. v. 34(6). p. 438-444.
DEVELOPMENT AND TESTING OF A HIGH-DENSITY CDNA MICROARRAY RESOURCE FOR CATTLE - (Peer Reviewed Journal)
Suchyta, S.P., Sipkovsky, S., Kruska, R., Jeffers, A., Mcnulty, A., Tempelman, R.J., Halgren, R.G., Saama, P.M., Bauman, D.E., Boisclair, Y.R., Burton, J.L., Collier, R.J., Depeters, E.J., Ferris, T.A., Lucy, M.C., Mcguire, M.A., Medrano, J.F., Overton, T.R., Smith, T.P., Smith, G.W., Sonstegard, T.S., Spain, J.N., Spiers, D.E., Yao, J., Coussens, P.M. 2003.Development and testing of a high-density cdna microarray resource for cattle. Physiological Genomics. 15:158-164.
PRION GENE SEQUENCE VARIATION WITHIN DIVERSE GROUPS OF U.S. SHEEP, BEEF CATTLE, AND DEER - (Peer Reviewed Journal)
HEATON, M.P., LEYMASTER, K.A., FREKING, B.A., HAWK, D.A., SMITH, T.P., KEELE, J.W., SNELLING, W.M., FOX, J.M., CHITKO MCKOWN, C.G., LAEGREID, W.W. PRION GENE SEQUENCE VARIATION WITHIN DIVERSE GROUPS OF U.S. SHEEP, BEEF CATTLE, AND DEER. MAMMALIAN GENOME. 2003. V. 14. P. 765-777.
BRIEF NOTE. LINKAGE MAPPING OF THE BOVINE BONE MORPHOGENETIC PROTEIN RECEPTOR-IB (BMPR-IB) TO CHROMOSOME 6 - (Peer Reviewed Journal)
KIM, J.G., SMITH, T.P., SNELLING, W.M., VALLET, J.L., CHRISTENSON, R.K. BRIEF NOTE. LINKAGE MAPPING OF THE BOVINE BONE MORPHOGENETIC PROTEIN RECEPTOR-1B (BMPR1B) TO CHROMOSOME 6. ANIMAL GENETICS. 2003. v. 34(4). p. 311.
ASSOCIATION OF BOVINE NEONATAL FC RECEPTOR GENE (FCGRT) HAPLOTYPES WITH SERUM IGG CONCENTRATION IN NEWBORN CALVES - (Peer Reviewed Journal)
LAEGREID, W.W., HEATON, M.P., KEEN, J.E., GROSSE, W.M., CHITKO MCKOWN, C.G., SMITH, T.P., KEELE, J.W., BENNETT, G.L., BESSER, T.E. ASSOCIATION OF BOVINE NEONATAL FC RECEPTOR GENE ALPHA-CHAIN GENE (FCGRT) HAPLOTYPES WITH SERUM IgG CONCENTRATION IN NEWBORN CALVES. MAMMALIAN GENOME. 2002. v. 13. p. 704-710.
IDENTIFICATION OF THE SINGLE BASE CHANGE CAUSING THE CALLIPYGE MUSCLE HYPERTROPHY PHENOTYPE, THE ONLY KNOWN EXAMPLE OF POLAR OVERDOMINANCE IN MAMMALS. - (Peer Reviewed Journal)
Freking, B.A., Murphy, S., Wylie, A., Jirtle, R.L., Rhodes, S., Keele, J.W., Leymaster, K.A., Smith, T.P. 2002. Identification of the single base change causing the callipyge muscle hypertrophy phenotype, the only known example of polar overdominance in animals. Genome Research. 12:1496-1506.
EVALUATION OF SINGLE NUCLEOTIDE POLYMORPHISMS IN CAPN1 FOR ASSOCIATION WITH MEAT TENDERNESS IN CATTLE. - (Peer Reviewed Journal)
Page, B.T., Casas, E., Heation, M.P., Cullen, N.G., Hyndman, D.L., Morris, C.A., Crawford, A.M., Wheeler, T.L., Koohmaraie, M., Keele, J.W., Smith, T.P.L. Journal Animal Science. 2002. v. 80. p. 3077-3085.
DEVELOPMENT OF 47 NEW MICROSATELLITE MARKERS FROM A BTA6 LIBRARY - (Peer Reviewed Journal)
REED, K.M., IHARA, N., PONCE DE LEON, F.A., SONSTEGARD, T.S., SMITH, T.P., BENNETT, G.L., SUGIMOTO, Y., BEATTIE, C.W. DEVELOPMENT OF 47 NEW MICROSATELLITE MARKERS FROM A BTA6 LIBRARY. ANIMAL BIOTECHNOLOGY JOURNAL. 2002, Vol. 13(2), pp. 195-202.
DIFFERENTIAL CONSERVATION OF TRANSCRIPTIONAL DOMAINS OF MAMMALIAN PROPHET OF PIT-1 PROTEINS REVEALED BY STRUCTURAL STUDIES OF THE BOVINE GENE AND COMPARATIVE FUNCTIONAL ANALYSIS OF THE PROTEIN - (Peer Reviewed Journal)
Showalter, A.D., Smith, T.P., Bennett, G.L., Sloop, K.W., Whitsett, J.A., Rhodes, S.J. 2002. Differential conservation of transcriptional domains of mammalian prophet of pit-1 proteins revealed by structural studies of the bovine gene and comparative functional analysis of the protein. Gene. 291:211-221.
PORCINE GENE-DISCOVERY BY NORMALIZED CDNA-LIBRARY SEQUENCING AND EST CLUSTER ASSEMBLY - (Peer Reviewed Journal)
FAHRENKRUG, S.C., SMITH, T.P., FREKING, B.A., CHO, J., WHITE, J., VALLET, J.L., WISE, T.H., ROHRER, G.A., KEELE, J.W. PORCINE GENE-DISCOVERY BY NORMALIZED CDNA-LIBRARY SEQUENCING AND EST CLUSTER ASSEMBLY. MAMMALIAN GENOME. 2002. v. 13. p. 475-478.
DIFFERENTIAL EXPRESSION OF CYCLOOXYGENASE-2 AROUND THE TIME OF ELONGATION IN THE PIG CONCEPTUS - (Peer Reviewed Journal)
Wilson, M.E., Fahrenkrug, S.C., Smith, T.P., Rohrer, G.A., Ford, S.P. 2001. Differential expression of cyclooxygenase-2 around the time of elongation in the pig conceptus. Animal Reproduction Sciences. 71:229-237.
SELECTION AND USE OF SNP MARKERS FOR ANIMAL IDENTIFICATION AND PATERNITY ANALYSIS IN U.S. BEEF CATTLE - (Peer Reviewed Journal)
Mammalian Genome. 2002. v. 13. p. 272-281.
USE OF BOVINE EST DATA AND HUMAN GENOMIC SEQUENCES TO MAP 100 GENE-SPECIFIC BOVINE MARKERS - (Peer Reviewed Journal)
Stone, R.T., Grosse, W., Casas, E., Smith, T.P., Keele, J.W., Bennett, G.L. 2002. Use of bovine EST data and human genomic sequences to map 100 gene-specific bovine markers. Mammalian Genome. 13:211-215.
SELECTION AND USE OF SINGLE NUCLEOTIDE POLYMORPHISM (SNP) MARKERS FOR ANIMAL IDENTIFICATION AND PATERNITY ANALYSIS IN U.S. BEEF CATTLE - (Abstract Only)
HAPLOTYPE STRUCTURE OF THE BOVINE NEONATAL FC RECEPTOR (BFCRN) GENE IN U.S.BEEF CATTLE AND ASSOCIATION WITH SERUM IGG CONCENTRATION IN NEWBORN CALVES - (Abstract Only)
SINGLE NUCLEOTIDE POLYMORPHISM (SNP) DISCOVERY IN PORCINE EXPRESSED GENES - (Peer Reviewed Journal)
Fahrenkrug, S.C., Freking, B.A., Smith, T.P., Rohrer, G.A., Keele, J.W. 2002. Single nucleotide polymorphism (SNP) discovery in porcine expressed genes. Animal Genetics. 33:186-195.
COMPARATIVE RADIATION HYBRID MAPPING OF THE MOUSE HIGH GROWTH (HG) REGION IN CATTLE AND PIGS - (Abstract Only)
Farber, C.R., Smith, T.P., Nonneman, D.J., Medrano, J.F. 2002. Comparative Radiation Hybrid Mapping of the Mouse High Growth (HG) Region in Cattle and Pigs. Plant and Animal Genome Conference Proceedings X. San Diego, CA. 1/12-16/2002. Abstract P136. p. 112.
IDENTIFICATION OF AN SNP ASSOCIATED WITH CALLIPYGE IN SHEEP - (Abstract Only)
BEYOND MYOSTATIN, THE SEARCH FOR INTERACTING ALLELES - (Proceedings)
IDENTIFICATION OF PORCINE LHX3 AND SF1 AS CANDIDATE GENES FOR QTL AFFECTING GROWTH AND REPRODUCTION TRAITS IN SWINE - (Peer Reviewed Journal)
Smith, T.P., Showalter, A.D., Sloop, K.W., Rohrer, G.A., Fahrenkrug, S.C., Meier, B.C., Rhodes, S.J. 2001. Identification of porcine lhx3 and sf1 as candidate genes for qtl affectinggrowth and reproduction traits in swine. Animal Genetics. 32:344-350.
SHORT COMMUNICATION: AN UPDATED LINKAGE AND COMPARATIVE MAP OF PORCINE CHROMOSOME 18 - (Peer Reviewed Journal)
CAMPBELL, E.M., FAHRENKRUG, S.C., VALLET, J.L., SMITH, T.P., ROHRER, G.A. SHORT COMMUNICATION: AN UPDATED LINKAGE AND COMPARATIVE MAP OF PORCINE CHROMOSOME 18. ANIMAL GENETICS. 2001. v. 32. p. 375-379.
COMPARATIVE MAPPING OF BTA15 AND HSA11 INCLUDING A REGION CONTAINING A QTL FOR MEAT TENDERNESS - (Peer Reviewed Journal)
RAPID COMMUNICATION: LINKAGE MAPPING OF SEVEN BOVINE CDNAS - (Peer Reviewed Journal)
SEQUENCE EVALUATION OF FOUR POOLED-TISSUE NORMALIZED BOVINE CDNA LIBRARIES AND CONSTRUCTION OF A GENE INDEX FOR CATTLE - (Peer Reviewed Journal)
MAPPING EXPRESSED SEQUENCE TAGS (ESTS) IN PIGS USING SINGLE NUCLEOTIDE POLYMORPHISMS (SNPS) - (Abstract Only)
CONSTRUCTION OF SNP-BASED EST COMPARATIVE MAP OF SWINE, CATTLE, AND HUMAN GENOMES - (Abstract Only)
RAPID COMMUNICATION: LINKAGE MAPPING OF THE PORCINE MICROMOLAR CALCIUM ACTIVATED NEUTRAL PROTEASE 1 (UCALPAIN) GENE ON SSC2 - (Peer Reviewed Journal)
RAPID COMMUNICATION: NUCLEOTIDE SEQUENCES OF TWO ISOFORMS OF PORCINE MICROMOLAR CALCIUM ACTIVATED NEUTRAL PROTEASE 1 CDNA - (Peer Reviewed Journal)
PCR-BASED REACTION SETUP FOR HIGH-THROUGHPUT CDNA LIBRARY SEQUENCING ON THE ABI 3700 AUTOMATED DNA SEQUENCER - (Peer Reviewed Journal)
DATABASE MANAGEMENT OF HIGH THROUGHPUT EST SEQUENCING AND SNP DISCOVERY - (Abstract Only)
BOVINE CAPN1 MAPS TO A REGION OF BTA29 CONTAINING A QTL FOR MEAT TENDERNESS - (Peer Reviewed Journal)
RAPID COMMUNICATION: MAPPING OF NINE BOVINE MICROSATELLITE MARKERS OBTAINED FROM LARGE INSERT GENOMIC LIBRARIES - (Peer Reviewed Journal)
PORCINE ERYTHROPOIETIN RECEPTOR: MOLECULAR CLONING AND EXPRESSION IN EMBRYONIC AND FETAL LIVER - (Peer Reviewed Journal)
Pearson, P.L., Smith, T.P., Sonstegard, T.S., Klemcke, H.G., Christenson, R.K., Vallet, J.L. 2000. Porcine erythropoietin receptor: molecular cloning and expression in embryonic and fetal liver. Domestic Animal Endocrinology. 19(1):25-38.
STRUCTURE OF THE GENES FOR PORCINE ENDOMETRIAL SECRETED AND MEMBRANE FOLATE BINDING PROTEINS - (Peer Reviewed Journal)
Vallet, J.L., Smith, T.P., Sonstegard, T.S., Heaton, M.P., Fahrenkrug, S.C. 2001. Structure of the genes for porcine endometrial secreted and membrane folate binding proteins. Domestic Animal Endocrinology. 21(1):55-72.
LINKAGE MAPPING OF ESTS IN PIGS USING SINGLE NUCLEOTIDE POLYMORPHISMS (SNPS): II. HIGH-THROUGHPUT GENOTYPING AND MAPPING - (Abstract Only)
LINKAGE MAPPING ESTS IN PIGS USING SINGLE NUCLEOTIDE POLYMORPHISMS (SNPS): SNP DISCOVERY - (Abstract Only)
BOVINE CAPN1 MAPS TO A REGION OF BTA29 CONTAINING A QTL FOR MEAT TENDERNESS - (Abstract Only)
DEVELOPMENT AND MAPPING OF TYPE-I (GENE-RELATED) MARKERS IN THE BOVINE GENOME BY LARGE-SCALE EXPRESSED SEQUENCE TAG (EST) SEQUENCING AND SINGLE NUCLEOTIDE POLYMORPHISM (SNP) DETECTION - (Abstract Only)
CHARACTERIZATION OF THE GENE FOR PORCINE ENDOMETRIAL/PLACENTAL MEMBRANE FOLATE BINDING PROTEIN (MFBP) - (Abstract Only)
Vallet, J.L., Smith, T.P., Sonstegard, T.S., Heaton, M.P., Fahrenkrug, S.C. 2000. Characterization of the gene for porcine endometrial/placental membrane folate binding protein (mFBP) [abstract]. Journal of Animal Science. 78(Supplement 2):77. (Abstract No. 231)
DIFFERENTIAL GENE EXPRESSION DURING ELONGATION IN THE PIG EMBRYO - (Peer Reviewed Journal)
Wilson, M.E., Sonstegard, T.S., Smith, T.P., Fahrenkrug, S.C., Ford, S.P. 2000. Differential gene expression during elongation in the pig embryo. Developmental Genetics. 11(8):682-688.
BOVINE UCP2 AND UCP3 MAP TO BTA15 (SHORT COMMUNICATION) - (Peer Reviewed Journal)
QUANTITATIVE TRAIT LOCI ON BOVINE CHROMOSOMES 15 AND 29 EVIDENCE THAT HUMAN CHROMOSOME 11 HARBORS ORTHOLOGOUS GENES ASSOCIATED WITH LONGISSIMUS TENDERNESS IN BOVINE - (Abstract Only)
Casas, E., Keele, J.W., Shackelford, S.D., Smith, T.P., Koohmaraie, M., Kappes, S.M., Stone, R.T. 1999. Quantitative trait loci on bovine chromosomes 15 and 29 evidence that human chromosome 11 harbors orthologous genes associated with longissimus tenderness in bovine. From Jay Lush to Genomics: Visions for Animal Breeding and Genetics., Iowa State University, Ames, IA. p. 153. (Abstract)
FINE MAPPING OF A WARNER-BRATZLER SHEAR FORCE QUANTITATIVE TRAIT LOCUS ON BOVINE CHROMOSOME 15 - (Abstract Only)
THE PROCESS AND USE OF FUNCTIONAL GENOMICS IN BEEF CATTLE: SO YOU HAVE A QTL, NOW WHAT? - (Abstract Only)
TECHNICAL NOTE: DIRECT GENOTYPING OF THE DOUBLE-MUSCLING LOCUS (MH) IN PIEDMONTESE AND BELGIAN BLUE CATTLE BY FLUORESCENT PCR - (Peer Reviewed Journal)
QUANTITATIVE ANALYSIS OF BIRTH, WEANING AND YEARLING WEIGHTS, AND CALVING DIFFICULTY IN PIEDMONTESE CROSSBREDS SEGREGATING AN INACTIVE MYOSTATIN ALLELE - (Peer Reviewed Journal)
ISOLATION OF COMPLEMENTARY DEOXYRIBONUCLEIC ACIDS ENCODING PUTATIVE SECRETED AND MEMBRANE-BOUND FOLATE BINDING PROTEINS FROM ENDOMETRIUM OF SWINE - (Peer Reviewed Journal)
PHYSICAL MAPPING OF THE BOVINE, CAPRINE AND OVINE HOMOLOGUES OF THE PAIRED BOX GENE PAX8 - (Peer Reviewed Journal)
FINE MAPPING OF A WARNER-BRATZLER SHEAR FORCE QTL ON BTA15 - (Abstract Only)
FINE MAPPING OF THE OVINE CALLIPYGE LOCUS - (Abstract Only)
IDENTIFICATION AND GENETIC MAPPING OF BOVINE CHEMOKINE GENES EXPRESSED IN EPITHELIAL CELLS - (Peer Reviewed Journal)
COMPARATIVE MAPPING: CYTOGENETIC LOCATION OF PROC, EN1, ALPI, TNP1, AND IL1B GENES IN CATTLE AND SHEEP REVEALS A CONSERVED REARRANGEMENT RELATIVE TO HUMAN GENOME. - (Peer Reviewed Journal)
MAPPING BOVINE AND OVINE GENES WITH INTRONIC SINGLE NUCLEOTIDE POLYMORPHISMS - (Abstract Only)
PORCINE ERYTHROPOIETIN RECEPTOR: CLONING OF A PARTIAL CDNA AND EXPRESSION IN EMBRYONIC/FETAL LIVER - (Abstract Only)
STRUCTURE OF THE GENE FOR PORCINE ENDOMETRIAL FOLATE BINDING PROTEIN - (Abstract Only)
DISCOVERY OF MYOSTATIN AS THE GENE RESPONSIBLE FOR DOUBLE MUSCLING, AND IMPLICATIONS FOR MEAT PRODUCTION - (Proceedings)
REFINEMENT OF BOVINE CHROMOSOME 2 LINKAGE MAP NEAR THE MH LOCUS REVEALS COMPLEX REARRANGEMENTS BETWEEN THE BOVINE AND HUMAN GENOMES. - (Peer Reviewed Journal)
EXPRESSION-BASED GENE IDENTIFICATION AND SINGLE NUCLEOTIDE POLYMORPHISM (SNP) MAPPING IN CATTLE - (Abstract Only)
EVALUATION OF THE OVINE CALLIPYGE LOCUS: I. RELATIVE CHROMOSOMAL POSITION AND GENE ACTION - (Peer Reviewed Journal)
SIMPLE GENETIC TEST THAT SUPPORTS MARKER ASSISTED SELECTION TO INCREASE RETAIL PRODUCT YIELD IN CATTLE - (Abstract Only)
EFFECT OF A MUTATION AT THE MYOSTATIN GENE ON EARLY LIFE WEIGHTS AND CALVING EASE IN A POPULATION OF PIEDMONTESE INHERITANCE - (Abstract Only)
MYOSTATIN MUTATIONS CAUSE DOUBLE MUSCLING IN CATTLE - (Proceedings)
NARROWING A REGION OF RECOMBINATION RATE VARIATION ON BTA23 TO THE D23S22-D23S23 INTERVAL USING MEIOTIC BREAKPOINT ANALYSIS AND A YAC CONTIG - (Abstract Only)
MYOSTATIN MUTATIONS CAUSE DOUBLE MUSCLING IN CATTLE - (Proceedings)
MYOSTATIN MAPS TO PORCINE CHROMOSOME 15 BY LINKAGE AND PHYSICAL ASSIGNMENT TO SSC15Q2.3 (SHORT COMMUNICATION) - (Abstract Only)
ASSOCIATION OF THE MUSCLE HYPERTROPHY LOCUS WITH CARCASS TRAITS IN BEEF CATTLE - (Peer Reviewed Journal)
MUTATIONS IN MYOSTATIN (GDF8) IN DOUBLE MUSCLED BELGIAN BLUE CATTLE - (Peer Reviewed Journal)
MYOSTATIN MAPS TO THE INTERVAL CONTAINING THE BOVINE MH LOCUS - (Peer Reviewed Journal)
COMPARATIVE MAPPING OF BOVINE AND HUMAN CHROMOSOME 2 IDENTIFIES SEGMENTS OF CONSERVED SYNTENY CONTAINING THE BOVINE MH LOCUS - (Peer Reviewed Journal)
ASSOCIATION OF THE DOUBLE-MUSCLING LOCUS ON BOVINE CHROMOSOME TWO (BTA2) WITH CARCASS TRAITS - (Abstract Only)
PORCINE UTERINE FOLATE BINDING PROTEING: FOLATE BINDING, CLONING OF A PARTIAL CDNA, AND MRNA EXPRESSION DURING THE ESTROUS CYCLE AND EARLY PREGNANCY - (Abstract Only)
DIRECTED COSMID ISOLATION FOR PHYSICAL ASSIGNMENT BY FISH: PCR-BASED ITERATIVE SCREENING OF RANDOM GENOMIC LIBRARIES - (Peer Reviewed Journal)
HUMAN:BOVINE COMPARATIVE MAPPING TO IDENTIFY THE MH GENE IN CATTLE - (Proceedings)
GENETIC ANALYSIS OF MEAT QUALITY IN CATTLE - (Proceedings)
SHORT COMMUNICATION: PHYSICAL ASSIGNMENT OF GLUCAGON AND NEBULIN IN CATTLE, SHEEP AND GOAT - (Abstract Only)
ANCHORING OF BOVINE CHROMOSOMES 4, 6, 7, 10, AND 14 AND LINKAGE GROUP TELOMERIC ENDS VIA FISH ANALYSIS OF LAMBDA CLONES - (Peer Reviewed Journal)
A SECOND GENERATION LINKAGE MAP OF THE BOVINE GENOME - (Peer Reviewed Journal)
PORCINE AROMATASES: STUDIES ON TISSUE-SPECIFIC, FUNCTIONALLY DISTINCT ISOZYMES FROM A SINGLE GENE? - (Peer Reviewed Journal)
MAPPING OF HPRT GENE IN SWINE PROVIDES A REFERENCE LOCUS FOR SYNTENY COMPARISON - (Proceedings)
CONSTRUCTION AND CHARACTERIZATION OF A LARGE INSERT PORCINE YAC LIBRARY (SHORT COMMUNICATION) - (Abstract Only)
A GENETIC AND CYTOGENETIC MAP FOR BOVINE CHROMOSOME 11 - (Abstract Only)
USE OF LARGE INSERT GENOMIC LIBRARIES IN LIVESTOCK GENE MAPPING - (Abstract Only)
LINKAGE ASSIGNMENTS FOR HAS 19 CONSERVED REGIONS OF SYNTENY IN CATTLE, SHEEP AND SWINE - (Proceedings)
CONSTRUCTION OF A PORCINE YEAST ARTIFICIAL CHROMOSOME (YAC) LIBRARY - (Abstract Only)
A COMPREHENSIVE MAP OF THE PORCINE GENOME - (Peer Reviewed Journal)
SHORT COMMUNICATION: CONSTRUCTION AND CHARACTERIZATION OF A LARGE INSERT BOVINE YAC LIBRARY WITH 5-FOLD GENOMIC COVERAGE - (Abstract Only)
PHYSICAL ASSIGNMENTS OF 68 PORCINE COSMID AND LAMBDA CLONES CONTAINING POLYMORPHIC MICROSATELLITES - (Peer Reviewed Journal)
IDENTIFYING TUMOR INITIATOR/SUPPRESSOR AND PENETRANCE-ASSOCIATED GENES BY GENE MAPPING - (Proceedings)
SHORT COMMUNICATION: MAPPING OF A LINKAGE GROUP TO THE LAST BOVINE CHROMOSOME (BTA27) WITHOUT AN ASSIGNMENT - (Abstract Only)
DIRECTED INTEGRATION OF THE PHYSICAL AND GENETIC LINKAGE MAPS OF SWINE CHROMOSOME 7 REVEALS THAT THE SLA SPANS THE CENTROMERE - (Peer Reviewed Journal)
DIRECTED INTEGRATION OF THE PHYSICAL AND GENETIC LINKAGE MAPS - (Proceedings)
MOLECULAR CLONING OF PORCINE FAS ANTIGEN AND EXPRESSION IN CELL LINES DERIVED FROM MINIATURE SWINE - (Proceedings)