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                    U.S. DEPARTMENT OF AGRICULTURE
 Nutrition, Growth and Physiology: Clay Center, NE
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ARS Home Plains Area Clay Center, Nebraska U.S. Meat Animal Research Center Nutrition, Growth and Physiology People & Locations







Amanda Kay Lindholm-Perry
                        Nutrition, Growth and Physiology

                        




                        
                        Research Geneticist
                        Phone: (402) 762-4189
                        
                        
                        Fax: (402) 762-4209(Employee information on this page comes from the REE Directory. Please contact your front office staff to update the REE Directory.)
                            ProjectsMethyl Donor Availability in Utero and Programming of Postnatal Performance in Beef Cattle
                                                    Cooperative Agreement
                                                                    (A)Accession Number: 442168Optimizing Nutrient Management and Efficiency of Beef Cattle and Swine
                                                    In-House Appropriated
                                                                    (D)Accession Number: 442588Identification of Genetic Predictors and Molecular Indicators of Liver Abscesses in Beef Cattle
                                                    Interagency Reimbursable Agreement
                                                                    (I)Accession Number: 444393**Publications**
                                                (Clicking on the reprint icon
                                                    Reprint Icon
                                                    will take you to the publication reprint.)Why are some cows skinny? An evaluation of stress and immune factors

- (Abstract Only)Utilization of rumen protected lysine and methionine in beef feedlot diets: impacts on steer performance

- (Abstract Only)Effects of protein concentration and beta-adrenergic agonists on ruminal bacterial communities in finishing beef heifers
                                                        

- (Peer Reviewed Journal)Pfau, A.P., Henniger, M.T., Samuelson, K.L., Hales, K.E., Loest, C.A., Hubbert, M.E., Lindholm-Perry, A.K., Egert-McLean, A.M., Mason, K., Shepherd, E.A., Voy, B.H., Myer, P.R. 2024. Effects of protein concentration and beta-adrenergic agonists on ruminal bacterial communities in finishing beef heifers. PLOS ONE. 19(2). Article e0296407. https://doi.org/10.1371/journal.pone.0296407.Maternal amino acid supplementation from pre-breeding through early gestation alters fetal muscle development

- (Other)Hauxwell, K.M., Cushman, R.A., Caton, J.S., Ward, A.K., Lindholm-Perry, A.K., Snider, A.P., Freetly, H.C., Dahlen, C.R., Amat, S., Neville, B.W., Thorson, J.F., Oliver, W.T., Miles, J.R., Crouse, M.S. 2023. Maternal amino acid supplementation from pre-breeding through early gestation alters fetal muscle development. North Dakota Livestock Research Report. 18-21. Available: https://www.ndsu.edu/agriculture/extension/publications/2023-north-dakota-livestock-research-reportEstimation of cell type proportions from bulk RNA-Seq of porcine whole blood samples using partial reference-free deconvolution
                                                        

- (Peer Reviewed Journal)Keel-Mercer, B.N., Lindholm-Perry, A.K., Rohrer, G.A., Oliver, W.T. 2023. Estimation of cell type proportions from bulk RNA-Seq of porcine whole blood samples using partial reference-free deconvolution. Animal Gene. 30. Article 200159. https://doi.org/10.1016/j.angen.2023.200159.Rumen and cecum bacteria of beef cattle that differ in feed efficiency fed a forage diet
                                                        

- (Peer Reviewed Journal)Freetly, H.C., Lindholm-Perry, A.K. 2023. Rumen and cecum bacteria of beef cattle that differ in feed efficiency fed a forage diet. Journal of Animal Science. 101. Article skad292. https://doi.org/10.1093/jas/skad292.Leveraging the potential of molecular and genetic markers to improve feed efficiency in beef cattle
                                                        

- (Abstract Only)Lindholm-Perry, A.K. 2023. Leveraging the potential of molecular and genetic markers to improve feed efficiency in beef cattle. Journal of Animal Science. 101(Supplement 3):94. https://doi.org/10.1093/jas/skad281.115.Methionine and guanidinoacetic acid supplementation throughout the periconceptual period of gestation alters metabolite concentrations and fetal development
                                                        

- (Abstract Only)Hauxwell, K.M., Cushman, R.A., Caton, J.S., Ward, A.K., Lindholm-Perry, A.K., Snider, A.P., Freetly, H.C., Dahlen, C.R., Amat, S., Oliver, W.T., Miles, J.R., Crouse, M.S. 2023. Methionine and guanidinoacetic acid supplementation throughout the periconceptual period of gestation alters metabolite concentrations and fetal development. Journal of Animal Science. 101(Supplement 3):329-330. https://doi.org/10.1093/jas/skad281.395.Methionine and guanidinoacetic acid supplementation during the periconceptual period of gestation shifts methionine metabolism of fetal bull calves at d 63 of gestation
                                                        

- (Abstract Only)Crouse, M.S., Hauxwell, K., Caton, J.S., Ward, A., Dahlen, C.R., Amat, S., Freetly, H.C., Lindholm-Perry, A., Neville, B.W., Oliver, W.T., Thorson, J., Snider, A.P., Miles, J.R., Cushman, R.A. 2023. Methionine and guanidinoacetic acid supplementation during the periconceptual period of gestation shifts methionine metabolism of fetal bull calves at d 63 of gestation. Journal of Animal Science. 101(Supplement 3):172. https://doi.org/10.1093/jas/skad281.208.Influence of dietary methionine and guanidinoacetic acid on estrous cycles and early pregnancy in beef heifers
                                                        

- (Abstract Only)Cushman, R., Hauxwell, K., Snider, A.P., Freetly, H., Oliver, W.T., Amat, S., Neville, B.W., Thorson, J., Lindholm-Perry, A., Miles, J.R., Dahlen, C.R., Ward, A., Perry, G.A., Caton, J.S., Crouse, M.S. 2023. Influence of dietary methionine and guanidinoacetic acid on estrous cycles and early pregnancy in beef heifers. Journal of Animal Science. 101(Supplement 3):580-581. https://doi.org/10.1093/jas/skad281.678.Effects of adding ruminal propionate on dry matter intake and glucose metabolism in steers fed a finishing ration
                                                        

- (Peer Reviewed Journal)Rathert-Williams, A.R., McConnell, H.L., Salisbury, C.M., Lindholm-Perry, A.K., Lalman, D.L., Pezeshki, A., Foote, A.P. 2023. Effects of adding ruminal propionate on dry matter intake and glucose metabolism in steers fed a finishing ration. Journal of Animal Science. 101. Article skad072. https://doi.org/10.1093/jas/skad072.One-carbon metabolite supplementation to heifers for the first 14 d of the...alters the plasma and hepatic one-carbon metabolite pool and methionine-folate cycle enzyme transcript abundance in a dose-dependent manner
                                                        

- (Peer Reviewed Journal)Crouse, M.S., Freetly, H.C., Lindholm-Perry, A.K., Neville, B.W., Oliver, W.T., Lee, R.T., Syring, J.G., King, L.E., Reynolds, L.P., Dahlen, C.R., Caton, J.S., Ward, A.K., Cushman, R.A. 2023. One-carbon metabolite supplementation to heifers for the first 14 d of the estrous cycle alters the plasma and hepatic one-carbon metabolite pool and methionine-folate cycle enzyme transcript abundance in a dose-dependent manner. Journal of Animal Science. 101. Article skac419. https://doi.org/10.1093/jas/skac419.First description of LPS-treated, pen-housed feeder cattle as a model of bacterial infection

- (Abstract Only)Recent developments and future directions in meta-analysis of differential gene expression in livestock RNA-Seq
                                                        

- (Review Article)Keel, B.N., Lindholm-Perry, A.K. 2022. Recent developments and future directions in meta-analysis of differential gene expression in livestock RNA-Seq. Frontiers in Genetics. 13. Article 983043. https://doi.org/10.3389/fgene.2022.983043.Influence of cow’s perinatal diet on calf microbiota

- (Abstract Only)Genes involved in feed efficiency identified in a meta-analysis of rumen tissue from two populations of beef steers
                                                        

- (Peer Reviewed Journal)Lindholm-Perry, A.K., Meyer, A.M., Kern-Lunbery, R.J., Cunningham-Hollinger, H.C., Funk, T.H., Keel, B.N. 2022. Genes involved in feed efficiency identified in a meta-analysis of rumen tissue from two populations of beef steers. Animals. 12(12). Article 1514. https://doi.org/10.3390/ani12121514.One-carbon metabolite supplementation influences pancreatic a-amylase activity and protein concentration in a dose-dependent manner in beef heifers
                                                        

- (Abstract Only)Trotta, R.J., Freetly, H., Cushman, R.A., Oliver, W., Lindholm-Perry, A., Caton, J.S., Ward, A.K., Crouse, M.S. 2022. One-carbon metabolite supplementation influences pancreatic a-amylase activity and protein concentration in a dose-dependent manner in beef heifers [abstract]. Journal of Animal Science. 100(Supplement 3):259. https://doi.org/10.1093/jas/skac247.469.Effects of a moderate or aggressive implant strategy on the rumen microbiome and metabolome in steers
                                                        

- (Peer Reviewed Journal)Henniger, M.T., Wells, J.E., Hales, K.E., Lindholm-Perry, A.K., Freetly, H.C., Kuehn, L.A., Schneider, L.G., McLean, K.J., Campagna, S.R., Christopher, C.J., Myer, P.R. 2022. Effects of a moderate or aggressive implant strategy on the rumen microbiome and metabolome in steers. Frontiers in Animal Science.  3. Article 889817. https://doi.org/10.3389/fanim.2022.889817.DNA methylation dataset of bovine embryonic fibroblast cells treated with epigenetic modifiers and divergent energy supply
                                                        

- (Database / Dataset)Diniz, W.J., Crouse, M.S., Caton, J.S., Claycombe-Larson, K.J., Lindholm-Perry, A.K., Reynolds, L.P., Dahlen, C.R., Borowicz, P.P., Ward, A.K. 2022. DNA methylation dataset of bovine embryonic fibroblast cells treated with epigenetic modifiers and divergent energy supply. Data in Brief. 42. Article 108074. https://doi.org/10.1016/j.dib.2022.108074.Epigenetic modifier supplementation improves mitochondrial respiration growth rates and alters DNA methylation of bovine embryonic fibroblast cells cultured in divergent energy supply
                                                        

- (Peer Reviewed Journal)Crouse, M.S., Caton, J.S., Claycombe-Larson, K.J., Diniz, W.J., Lindholm-Perry, A.K., Reynolds, L.P., Dahlen, C.R., Borowicz, P.P., Ward, A.K. 2022. Epigenetic modifier supplementation improves mitochondrial respiration growth rates and alters DNA methylation of bovine embryonic fibroblast cells cultured in divergent energy supply. Frontiers in Genetics. 13. Article 812764. https://doi.org/10.3389/fgene.2022.812764.Global analysis of differential gene expression within the porcine conceptus transcriptome as it transitions through spherical, ovoid, and tubular morphologies during the initiation of elongation
                                                        

- (Peer Reviewed Journal)Walsh, S.C., Miles, J.R., Keel, B.N., Rempel, L.A., Wright-Johnson, E.C., Lindholm-Perry, A.K., Oliver, W.T., Pannier, A.K. 2022. Global analysis of differential gene expression within the porcine conceptus transcriptome as it transitions through spherical, ovoid, and tubular morphologies during the initiation of elongation. Molecular Reproduction and Development. Article 23553. https://doi.org/10.1002/mrd.23553.Hematology parameters as potential indicators of feed efficiency in pigs
                                                        

- (Peer Reviewed Journal)Lindholm-Perry, A.K., Kuehn, L.A., Wells, J., Rempel, L.A., Chitko-McKown, C.G., Keel, B.N., Oliver, W.T. 2021. Hematology parameters as potential indicators of feed efficiency in pigs. Translational Animal Science. 5(4). Article txab219. https://doi.org/10.1093/tas/txab219.Transcriptomic analysis for pork color – The ham halo effect in biceps femoris
                                                        

- (Peer Reviewed Journal)Nonneman, D.J., Keel-Mercer, B.N., Lindholm-Perry, A.K., Rohrer, G.A., Wheeler, T.L., Shackelford, S.D., King, D.A. 2022. Transcriptomic analysis for pork color – The ham halo effect in biceps femoris. Meat and Muscle Biology. 6(1):1-8. Article 13050. https://doi.org/10.22175/mmb.13050.Effects of increasing calcium propionate in a finishing diet on dry matter intake and glucose metabolism in steers
                                                        

- (Peer Reviewed Journal)Rathert-Williams, A.R., Salisbury, C.M., Lindholm-Perry, A.K., Pezeshki, A., Lalman, D.L., Foote, A.P. 2021. Effects of increasing calcium propionate in a finishing diet on dry matter intake and glucose metabolism in steers. Journal of Animal Science. 99(12). Article skab314. https://doi.org/10.1093/jas/skab314.Testicular transcriptomics in GnRHR-II knockdown boars

- (Abstract Only)Transcriptome profiles of the skeletal muscle of mature cows during feed restriction and realimentation
                                                        

- (Peer Reviewed Journal)Cunningham-Hollinger, H.C., Kuehn, L.A., Cammack, K.M., Hales, K.E., Oliver, W.T., Crouse, M.S., Chen, C.T., Freetly, H.C., Lindholm-Perry, A.K. 2021. Transcriptome profiles of the skeletal muscle of mature cows during feed restriction and realimentation. BMC Research Notes. 14. Article 361. https://doi.org/10.1186/s13104-021-05757-8.Characterization and comparative analysis of transcriptional profiles of porcine colostrum and mature milk at different parities
                                                        

- (Peer Reviewed Journal)Keel, B.N., Lindholm-Perry, A.K., Oliver, W.T., Wells, J.E., Jones, S.A., Rempel, L.A. 2021. Characterization and comparative analysis of transcriptional profiles of porcine colostrum and mature milk at different parities. BMC Genomic Data. 22. Article 25. https://doi.org/10.1186/s12863-021-00980-5.Parity and lactation stage affect the sow milk microbiome
                                                        

- (Abstract Only)Henniger, M.T., Rempel, L.A., Oliver, W.T., Miles, J.R., Lindholm-Perry, A.K., Myer, P.R. 2021. Parity and lactation stage affect the sow milk microbiome. Journal of Animal Science. 99(Supplement 3):498. https://doi.org/10.1093/jas/skab235.878.Epimural microbiota and rumen epithelial gene expression in healthy and liver-abscessed  animals
                                                        

- (Abstract Only)Abbas, W., Lindholm-Perry, A.K., Keel, B.N., Wells, J., Hales, K., Knoell, A., Paz, H.A., Fernando, S. 2020. Epimural microbiota and rumen epithelial gene expression in healthy and liver-abscessed  animals [abstract]. Journal of Animal Science. 98(Supplement 3):135. https://doi.org/10.1093/jas/skaa054.234.Rumen epithelial transcriptome and microbiome profiles of rumen epithelium and contents of beef cattle with and without liver abscesses
                                                        

- (Peer Reviewed Journal)Abbas, W., Keel, B.N., Kachman, S.D., Fernando, S.C., Wells, J.E., Hales, K.E., Lindholm-Perry, A.K. 2020. Rumen epithelial transcriptome and microbiome profiles of rumen epithelium and contents of beef cattle with and without liver abscesses. Journal of Animal Science. 98(12):1-13. https://doi.org/10.1093/jas/skaa359.Assessment of imputation from low-pass sequencing to predict merit of beef steers
                                                        

- (Peer Reviewed Journal)Snelling, W.M., Hoff, J.L., Li, J.H., Kuehn, L.A., Keel, B.N., Lindholm-Perry, A.K., Pickrell, J.K. 2020. Assessment of imputation from low-pass sequencing to predict merit of beef steers. Genes. 11(11). Article 1312. https://doi.org/10.3390/genes11111312.The effects of feeding ferric citrate on ruminal bacteria, methanogenic archaea, and methane production in growing beef steers
                                                        

- (Peer Reviewed Journal)Clemmons, B.A., Schneider, L.G., Melchior, E.A., Lindholm-Perry, A.K., Hales, K.E., Wells, J., Freetly, H.C., Hansen, S.L., Drewnowski, M.E., Hartman, S.J., Myer, P.R. 2021. The effects of feeding ferric citrate on ruminal bacteria, methanogenic archaea, and methane production in growing beef steers. Access Microbiology. 3(1). Article 000180. https://doi.org/10.1099/acmi.0.000180.Effects of the F94L Limousin associated myostatin gene marker on metabolic index in growing beef heifers
                                                        

- (Peer Reviewed Journal)Hales, K.E., Tait Jr, R.G., Lindholm-Perry, A.K., Cushman, R.A., Freetly, H.C., Brown-Brandl, T.M., Bennett, G.L. 2020. Effects of the F94L Limousin associated myostatin gene marker on metabolic index in growing beef heifers. Applied Animal Science. 36(6):851-856. https://doi.org/10.15232/aas.2020-02046.Associations of mucosal disaccharidase kinetics and expression in the jejunum of steers with divergent average daily gain
                                                        

- (Peer Reviewed Journal)Smith, W.N., Brake, D.W., Lindholm-Perry, A.K., Oliver, W.T., Freetly, H.C., Foote, A.P. 2020. Associations of mucosal disaccharidase kinetics and expression in the jejunum of steers with divergent average daily gain. Journal of Animal Science. 98(9):1-6. https://doi.org/10.1093/jas/skaa285.Evaluation of transcript assembly in multiple porcine tissues suggests optimal sequencing depth for RNA-Seq using total RNA library
                                                        

- (Peer Reviewed Journal)Keel, B.N., Oliver, W.T., Keele, J.W., Lindholm-Perry, A.K. 2020. Evaluation of transcript assembly in multiple porcine tissues suggests optimal sequencing depth for RNA-Seq using total RNA library. Animal Gene. 17-18. Article 200105. https://doi.org/10.1016/j.angen.2020.200105.Effects of a moderate and aggressive implant strategy on the rumen microbial community in steers
                                                        

- (Abstract Only)Henniger, M.T., Wells, J.E., Hales, K.E., Lindholm-Perry, A.K., Freetly, H.C., Kuehn, L.A., Schneider, L.G., McLean, K.J., Clemmons, B.A., Myer, P.R. 2020. Effects of a moderate and aggressive implant strategy on the rumen microbial community in steers. Journal of Animal Science. 98(Supplement 4):269. https://doi.org/10.1093/jas/skaa278.484.Abundance of rumen methanogens did not differ in cattle that differed in residual feed intake
                                                        

- (Abstract Only)Freetly, H.C., Lindholm-Perry, A.K., Foote, A.P., Bennett, S., Wells, J. 2020. Abundance of rumen methanogens did not differ in cattle that differed in residual feed intake [abstract]. Journal of Animal Science. 98(Supplement 4):150. https://doi.org/10.1093/jas/skaa278.274.Methods of determining the presence or absence of a plurality of target polynucleotides in a sample

- (Pct (patent Cooperation Treaty))Curry, J.D., Koshinsky, H., Lindholm-Perry, A.K., Thallman, R.M. 2020. Methods of determining the presence or absence of a plurality of target polynucleotides in a sample. U.S. Patent and Trademark Office. Patenet #10/648,030 B2.Ruminal transcript abundance of the centromere-associated protein E gene may influence residual feed intake in beef steers
                                                        

- (Peer Reviewed Journal)Rathert, A.R., Meyer, A.M., Foote, A.P., Kern, R.J., Cunningham-Hollinger, H.C., Kuehn, L.A., Lindholm-Perry, A.K. 2020. Ruminal transcript abundance of the centromere-associated protein E gene may influence residual feed intake in beef steers. Animal Genetics. 51(3):453-456. https://doi.org/10.1111/age.12926.Digestive tract microbiota of beef cattle that differed in feed efficiency
                                                        

- (Peer Reviewed Journal)Freetly, H.C., Dickey, A., Lindholm-Perry, A.K., Thallman, R.M., Keele, J.W., Foote, A.P., Wells, J.E. 2020. Digestive tract microbiota of beef cattle that differed in feed efficiency. Journal of Animal Science. 98(2):1-16. https://doi.org/10.1093/jas/skaa008.Using SNP weights derived from gene expression modules to improve GWAS power for feed efficiency in pigs

- (Abstract Only)Keel, B.N., Snelling, W.M., Lindholm-Perry, A.K., Oliver, W.T., Kuehn, L.A., Rohrer, G.A. 2020. Using SNP weights derived from gene expression modules to improve GWAS power for feed efficiency in pigs [abstract]. In proceedings: Plant and Animal Genome Conference Proceedings, San Diego, CA, 11-15 Jan 2020. W222. Available: https://plan.core-apps.com/pag_2020/abstractGenes associated with body weight gain and feed intake identified by meta-analysis of the mesenteric fat from crossbred beef steers
                                                        

- (Peer Reviewed Journal)Lindholm-Perry, A.K., Freetly, H.C., Oliver, W.T., Rempel, L.A., Keel, B.N. 2020. Genes associated with body weight gain and feed intake identified by meta-analysis of the mesenteric fat from crossbred beef steers. PLoS One. 15(1):e0227154. https://doi.org/10.1371/journal.pone.0227154.Using SNP weights derived from gene expression modules to improve GWAS power for feed efficiency in pigs
                                                        

- (Peer Reviewed Journal)Keel, B.N., Snelling, W.M., Lindholm-Perry, A.K., Oliver, W.T., Kuehn, L.A., Rohrer, G.A. 2020. Using SNP weights derived from gene expression modules to improve GWAS power for feed efficiency in pigs. Frontiers in Genetics. 10:1339. https://doi.org/10.3389/fgene.2019.01339.Influence of age of dam on daughter reproductive performance and follicle numbers in beef heifers
                                                        

- (Abstract Only)Cushman, R., Spuri-Gomes, R., Tenley, S., Rosasco, S., Rich, J., Northrop, E., Miles, J., Lindholm-Perry, A., Keel, B., Perry, G., Summers, A., Cupp, A. 2020. Influence of age of dam on daughter reproductive performance and follicle numbers in beef heifers [abstract]. Journal of Animal Science. 98(Supplement 3):115. https://doi.org/10.1093/jas/skaa054.195.Rumen epithelial transcriptome and microbiome profiles of beef cattle with liver abscesses

- (Abstract Only)Lindholm-Perry, A.K., Abbas, W., Keel, B.N., Fernando, S., Wells, J., Hales, K.E. 2020. Rumen epithelial transcriptome and microbiome profiles of beef cattle with liver abscesses [abstract]. International Plant & Animal Genome XXVIII Conference, January 11-15, 2020, San Diego, California. Poster Number PO0325. Available at: https://plan.core-apps.com/pag_2020/abstract/720aec4f687fb81a6ae44784bf04eela.Evaluation of transcript assembly in multiple porcine tissues suggests optimal sequencing depth for RNA-Seq using total RNA library

- (Abstract Only)Keel, B.N., Oliver, W.T., Keele, J.W., Lindholm-Perry, A.K. 2020. Evaluation of transcript assembly in multiple porcine tissues suggests optimal sequencing depth for RNA-Seq using total RNA library. In: Proceedings of Plant and Animal Genome XXVIII Conference, January 11-15, 2020, San Diego, California. Poster No. PE0128. Available: https://plan.core-apps.com/pag_2020/abstractA survey of copy number variation in the porcine genome detected from whole-genome sequence
                                                        

- (Peer Reviewed Journal)Keel, B.N., Nonneman, D.J., Lindholm-Perry, A.K., Oliver, W.T., Rohrer, G.A. 2019. A survey of copy number variation in the porcine genome detected from whole-genome sequence. Frontiers in Genetics. 10:737. https://doi.org/10.3389/fgene.2019.00737.A survey of genomic variants in commercial swine germplasm identified from whole-genome sequence

- (Abstract Only)Rumen epithelial transcriptome profile of beef cattle with liver abscesses

- (Abstract Only)The influence of preovulatory estradiol on trophectoderm and uterine gene transcript abundance around maternal recognition of pregnancy in beef cattle

- (Abstract Only)Northrop, E.J., Rich, J.J., Cushman, R.A., Miles, J.R., Lindholm-Perry, A.K., Keel, B.N., Yao, R., Ge, X., Perry, G.A. 2019. The influence of preovulatory estradiol on trophectoderm and uterine gene transcript abundance around maternal recognition of pregnancy in beef cattle [abstract]. Society for the Study of Reproduction Annual Meeting. Abstract Program, p. 317.  Available: https://community.ssr.org/news-events/past-meetings/annual-meeting575Digestive tract microbiota of beef cattle that differed in feed efficiency

- (Abstract Only)Freetly, H.C., Wells, J., Dickey, A., Lindholm-Perry, A., Keele, J., Foote, A. 2019. Digestive tract microbiota of beef cattle that differed in feed efficiency [abstract]. 2019 Congress on Gastrointestinal Function, April 15-17, 2019, Chicago, IL. p. 41-42.Porcine single nucleotide polymorphisms and their functional effect: an update
                                                        

- (Peer Reviewed Journal)Keel, B.N., Nonneman, D.J., Lindholm-Perry, A.K., Oliver, W.T., Rohrer, G.A. 2018. Porcine single nucleotide polymorphisms and their functional effect: an update. BMC Research Notes. 11:860. https://doi.org/10.1186/s13104-018-3973-6.Complete blood count data and leukocyte expression of cytokine genes and cytokine receptor genes associated with bovine respiratory disease in calves
                                                        

- (Peer Reviewed Journal)Lindholm-Perry, A.K., Kuehn, L.A., McDaneld, T.G., Miles, J.R., Workman, A.M., Chitko-McKown, C.G., Keele, J.W. 2018. Complete blood count data and leukocyte expression of cytokine genes and cytokine receptor genes associated with bovine respiratory disease in calves. BMC Research Notes. 11:786. https://doi.org/10.1186/s13104-018-3900-x.Multi-cohort study of the mesenteric fat from crossbred beef steers identifies genes associated with body weight gain
                                                        

- (Abstract Only)Lindholm-Perry, A.K., Freetly, H.C., Keel, B.N. 2018. Multi-cohort study of the mesenteric fat from crossbred beef steers identifies genes associated with body weight gain [abstract]. Journal of Animal Science. 96(Supplement S3):232-233. https://doi.org/10.1093/jas/sky404.506.The effects of Capn1 gene inactivation on the differential expression of genes in skeletal muscle
                                                        

- (Peer Reviewed Journal)Oliver, W.T., Keel, B.N., Lindholm-Perry, A.K., Horodyska, J., Foote, A.P. 2018. The effects of Capn1 gene inactivation on the differential expression of genes in skeletal muscle. Gene. 668:54-58. https://doi.org/10.1016/j.gene.2018.05.040.RNA-seq meta-analysis identifies genes in skeletal muscle associated with gain and intake across a multi-season study of crossbred beef steers
                                                        

- (Peer Reviewed Journal)Keel, B.N., Zarek, C.M., Keele, J.W., Kuehn, L.A., Snelling, W.M., Oliver, W.T., Freetly, H.C., Lindholm-Perry, A.K. 2018. RNA-seq meta-analysis identifies genes in skeletal muscle associated with gain and intake across a multi-season study of crossbred beef steers. BMC Genomics. 19:430. https://doi.org/10.1186/s12864-018-4769-8.Succession of ruminal bacterial species and fermentation characteristics in preweaned Brangus calves
                                                        

- (Proceedings)Smith, K.E., Garza, A.L., Butterfield, K.M., Dickey, A.M., Lindholm-Perry, A.K., Wells, J. E., Freetly, H.C., Lodge-Ivey, S.L. 2018. Succession of ruminal bacterial species and fermentation characteristics in preweaned Brangus calves. Translational Animal Science. 2(Supplement 1):S48-S52. https://doi.org/10.1093/tas/txy043.The effects of feeding monensin on rumen microbial communities and methanogenesis in bred heifers fed in a drylot
                                                        

- (Peer Reviewed Journal)Melchior, E.A., Hales, K.E., Lindholm-Perry, A.K., Freetly, H.C., Wells, J.E, Hemphill, C.A., Wickersham, T.A., Sawyer, J.E., Myer, P.R. 2018. The effects of feeding monensin on rumen microbial communities and methanogenesis in bred heifers fed in a drylot. Livestock Science. 212:131-136. https://doi.org/10.1016/j.livsci.2018.03.019.Differential transcript abundance in adipose tissue of mature beef cows during feed restriction and realimentation
                                                        

- (Peer Reviewed Journal)Cunningham, H.C., Cammack, K.M., Hales, K.E., Freetly, H.C., Lindholm-Perry, A.K. 2018. Differential transcript abundance in the adipose tissue of mature beef cows during feed restriction and realimentation. PLoS One. 13(3):e0194104. https://doi.org/10.1371/journal.pone.0194104.Microarray analysis of subcutaneous adipose tissue from mature cows with divergent body weight gain after feed restriction and realimentation
                                                        

- (Peer Reviewed Journal)Cunningham, H.C., Cammack, K.M., Hales Paxton, K.E., Freetly, H.C., Lindholm-Perry, A.K. 2017. Microarray analysis of subcutaneous adipose tissue from mature cows with divergent body weight gain after feed restriction and realimentation. Data in Brief. 16:303-311. https://doi.org/10.1016/j.dib.2017.10.016.Microarray analysis of subcutaneous adipose tissue from mature cows with divergent body weight gain after feed restriction and realimentation
                                                        

- (Peer Reviewed Journal)Cunningham, H.C., Cammack, K.M., Hales, K.E., Freetly, H.C., Lindholm-Perry, A.K. 2018. Microarray analysis of subcutaneous adipose tissue from mature cows with divergent body weight gain after feed restriction and realimentation. Data in Brief. 16:303-311. https://doi.org/10.1016/j.dib.2017.10.016.Expression of cytokine genes and receptors in white blood cells associated with divergent body weight gain in beef steers
                                                        

- (Peer Reviewed Journal)Lindholm-Perry, A.K., Artegoitia, V.M., Miles, J.R., Foote, A.P. 2017. Expression of cytokine genes and receptors in white blood cells associated with divergent body weight gain in beef steers. AGRI GENE. 6:37-39.. https://doi.org/10.1016/j.aggene.2017.09.005.Beef steers with average dry matter intake and divergent average daily gain have altered gene expression in the jejunum
                                                        

- (Peer Reviewed Journal)Foote, A.P., Keel, B.N., Zarek, C.M., Lindholm-Perry, A.K. 2017. Beef steers with average dry matter intake and divergent average daily gain have altered gene expression in the jejunum. Journal of Animal Science. 95(10):4430-4439. https://doi.org/10.2527/jas2017.1804.Lipid metabolism and mitochondrial energy production are key pathways involved in adipose tissue of cows transitioning from feed restriction to ad libitum diets

- (Abstract Only)Cunningham, H.C., Cammack, K.M., Hales, K.E., Freetly, H.C., Lindholm-Perry, A.K. 2017. Lipid metabolism and mitochondrial energy production are key pathways involved in adipose tissue of cows transitioning from feed restriction to ad libitum diets [abstract]. Journal of Animal Science. 95(Supplement 4):373.Meta-analysis of RNA-Seq data across cohorts in a multi-season feed efficiency study of crossbred beef steers accounts for biological and technical variability within season

- (Abstract Only)Keel, B.N., Zarek, C.M., Keele, J.W., Kuehn, L.A., Snelling, W.M., Oliver, W.T., Freetly, H.C., Lindholm-Perry, A.K. 2017. Meta-analysis of RNA-Seq data across cohorts in a multi-season feed efficiency study of crossbred beef steers accounts for biological and technical variability within season [abstract]. Journal of Animal Science Supplement. 95(Suppl4):98. doi:10.2527/asasann.2017/198.Genes in skeletal muscle associated with gain and intake identified in a multi-season study of crossbred beef steers

- (Abstract Only)Lindholm-Perry, A.K., Keel, B.N., Zarek, C.M., Keele, J.W., Kuehn, L.A., Snelling, W.M., Oliver, W.T., Freetly, H.C. 2017. Genes in skeletal muscle associated with gain and intake identified in a multi-season study of crossbred beef steers [abstract]. Journal of Animal Science. 95(Supplement 4):161.Alteration in gene expression in the jejunum mucosa of Angus steers with divergent ADG

- (Abstract Only)Foote, A.P., Keel, B.N., Lindholm-Perry, A.K. 2017. Alteration in gene expression in the jejunum mucosa of Angus steers with divergent ADG [abstract]. Journal of Animal Science Supplement. 95(Supplement 4):64.Relationships between the genes expressed in the mesenteric adipose tissue of beef cattle and feed intake and gain
                                                        

- (Peer Reviewed Journal)Lindholm-Perry, A.K., Cunningham, H.C., Kuehn, L.A., Vallet, J.L., Keele, J.W., Foote, A.P., Cammack, K.M., Freetly, H.C. 2017. Relationships between the genes expressed in the mesenteric adipose tissue of beef cattle and feed intake and gain. Animal Genetics. 48(4):386-394. https://doi.org/10.1111/age.12565.Determination of succession of rumen bacterial species in nursing beef calves

- (Abstract Only)Smith, K.E., Garza, A.L., Butterfield, K.M., Dickey, A.M., Lindholm-Perry, A.K., Wells, J., Freetly, H.C., Lodge-Ivey, S.L. 2017. Determination of succession of rumen bacterial species in nursing beef calves [abstract]. 2017 Congress on Gastrointestinal Function, April 10-12, 2017, Chicago, IL. p. 40-41.Effect of abomasal butyrate infusion on gene expression in the duodenum of lambs

- (Peer Reviewed Journal)Foote, A.P., Zarek, C.M., Kuehn, L.A., Cunningham, H.C., Cammack, K.M., Freetly, H.C., Lindholm-Perry, A.K. 2017. Effect of abomasal butyrate infusion on gene expression in the duodenum of lambs. Journal of Animal Science. 95(3):1191-1196. https://doi.org/10.2527/jas2016.1022.Relationships between inflammation- and immunity-related transcript abundance in the rumen and jejunum of beef steers with divergent average daily gain
                                                        

- (Peer Reviewed Journal)Reynolds, J.G., Foote, A.P., Freetly, H.C., Oliver, W.T., Lindholm-Perry, A.K. 2017. Relationships between inflammation- and immunity-related transcript abundance in the rumen and jejunum of beef steers with divergent average daily gain. Animal Genetics. 48(4):447-449. doi:10.1111/age.12546.Differential expression of genes related to gain and intake in the liver of beef cattle
                                                        

- (Peer Reviewed Journal)Zarek, C.M., Lindholm-Perry, A.K., Kuehn, L.A., Freetly, H.C. 2017. Differential expression of genes related to gain and intake in the liver of beef cattle. BMC Research Notes. 10:1. doi:10.1186/s13104-016-2345-3.Evolutionary and functional features of copy number variation in the cattle genome

- (Peer Reviewed Journal)Keel, B.N., Lindholm-Perry, A.K., Snelling, W.M. 2016. Evolutionary and functional features of copy number variation in the cattle genome. Frontiers in Genetics. 7:207. doi:10.3389/fgene.2016.00207.Profile of the spleen transcriptome in beef steers with variation in gain and feed intake
                                                        

- (Peer Reviewed Journal)Lindholm-Perry, A.K., Kern, R.J., Keel, B.N., Snelling, W.M., Kuehn, L.A., Freetly, H.C. 2016. Profile of the spleen transcriptome in beef steers with variation in gain and feed intake. Frontiers in Genetics. 7:127. doi:10.3389/fgene.2016.00127.Ruminal expression of the NQO1, RGS5, and ACAT1 genes may be indicators of feed efficiency in beef steers

- (Peer Reviewed Journal)Kern, R.J., Zarek, C.M., Lindholm-Perry, A.K., Kuehn, L.A., Snelling, W.M., Freetly, H.C., Cunningham, H.C., Meyer, A.M. 2017. Ruminal expression of the NQO1, RGS5, and ACAT1 genes may be indicators of feed efficiency in beef steers. Animal Genetics. 48:90-92. doi: 10.1111/age.12490.Transcriptome profile of genes differentially expressed in the mesenteric adipose tissue of beef cattle with variation in feed intake and gain

- (Abstract Only)Lindholm-Perry, A.K., Cunningham, H.C., Kuehn, L.A., Keele, J.W., Cammack, K., Freetly, H.C. 2016. Transcriptome profile of genes differentially expressed in the mesenteric adipose tissue of beef cattle with variation in feed intake and gain. International Society for Animal Genetics (35th ISAG). Abstract Book. p. 73-74 (Abstract #P3042).Key metabolic pathways associated with differences in weight maintenance and gain in mature cow skeletal and adipose tissue

- (Proceedings)Cunningham, H.C., Austin, K.J., Cammack, K.M., Freetly, H.C., Lindholm-Perry, A.K. 2016. Key metabolic pathways associated with differences in weight maintenance and gain in mature cow skeletal and adipose tissue. Proceedings, Western Section, American Society of Animal Science 67:48-51.A reduced panel to determine beef cattle breed composition

- (Abstract Only)Kuehn, L.A., Snelling, W.M., Lindholm-Perry, A.K. 2016. A reduced panel to determine beef cattle breed composition [abstract]. International Society for Animal Genetics (ISAG). Abstract Book. p. 32 (Abstract #P1036). Available: https://www.isag.us/Docs/Proceedings/ISAG_proceedings_2016.pdf.Inferring genotypes of functional variants in crossbred beef cattle

- (Abstract Only)Snelling, W.M., Kuehn, L.A., Lindholm-Perry, A.K. 2016. Inferring genotypes of functional variants in crossbred beef cattle [abstract]. International Society for Animal Genetics (35th ISAG). Abstract Book. p. 26 (Abstract #P1024). Available: https://www.isag.us.Docs/Proceedings/ISAG_Proceedings_2016.pdfTranscriptome differences in the rumen of beef steers with variation in feed intake and gain
                                                        

- (Peer Reviewed Journal)Kern, R.J., Lindholm-Perry, A.K., Freetly, H.C., Snelling, W.M., Kern, J.W., Keele, J.W., Miles, J.R., Foote, A.P., Oliver, W.T., Kuehn, L.A., Ludden, P.A. 2016. Transcriptome differences in the rumen of beef steers with variation in feed intake and gain. Gene. 586:12-26.Rumen papillae morphology of beef steers relative to gain and feed intake and the association of volatile fatty acids with kallikrein gene expression
                                                        

- (Peer Reviewed Journal)Kern, R.J., Lindholm-Perry, A.K., Freetly, H.C., Kuehn, L.A., Rule, D.C., Ludden, P.A. 2016. Rumen papillae morphology of beef steers relative to gain and feed intake and the association of volatile fatty acids with kallikrein gene expression. Livestock Science. 187:24-30.Differential gene expression in the duodenum, jejunum and ileum among crossbred beef steers with divergent gain and feed intake phenotypes
                                                        

- (Peer Reviewed Journal)Lindholm-Perry, A.K., Butler, A.R., Kern, R.J., Hill, R., Kuehn, L.A., Wells, J., Oliver, W.T., Hales, K.E., Foote, A.P., Freetly, H.C. 2016. Differential gene expression in the duodenum, jejunum and ileum among crossbred beef steers with divergent gain and feed intake phenotypes. Animal Genetics. 47(4):408-427. doi: 10.1111/age.12440.Differential expression of genes in the liver associated with gain and intake in beef steers

- (Abstract Only)Zarek, C.M., Lindholm-Perry, A.K., Freetly, H.C. 2016. Differential expression of genes in the liver associated with gain and intake in beef steers [abstract]. Journal of Animal Science. 94(Supplement 2):185.Potential metabolic pathways associated with differences in weight maintenance and gain in mature cow skeletal and adipose tissue

- (Abstract Only)Cunningham, H.C., Cammack, K.M., Austin, K.J., Freetly, H.C., Lindholm-Perry, A.K. 2015. Potential metabolic pathways associated with differences in weight maintenance and gain in mature cow skeletal and adipose tissue. Plant & Animal Genome XXIV Conference, January 9-13, 2016, San Diego, CA. Poster P0270.Relationship of glucocorticoids and hematological measures with feed intake, growth, and efficiency of finishing beef cattle
                                                        

- (Peer Reviewed Journal)Foote, A.P., Hales, K.E., Tait Jr, R.G., Berry, E.D., Lents, C.A., Wells, J. E., Lindholm-Perry, A.K., Freetly, H.C. 2016. Relationship of glucocorticoids and hematological measures with feed intake, growth, and efficiency of finishing beef cattle. Journal of Animal Science. 94(1):275-283. doi: 10.2527/jas2015-9407Differences in transcript abundance of genes on BTA15 located within a region associated with gain in beef steers
                                                        

- (Peer Reviewed Journal)Lindholm-Perry, A.K., Kern, R.J., Kuehn, L.A., Snelling, W.M., Miles, J.R., Oliver, W.T., Freetly, H.C. 2015. Differences in transcript abundance of genes on BTA15 located within a region associated with gain in beef steers. Gene. 572(1):42-48. doi:10.1016/j.gene.2015.06.076.Methane production and methanogen levels in steers that differ in residual gain
                                                        

- (Peer Reviewed Journal)Freetly, H.C., Lindholm-Perry, A.K., Hales, K.E., Brown-Brandl, T.M., Kim, M.S., Myer, P.R., Wells, J. 2015. Methane production and methanogen levels in steers that differ in residual gain. Journal of Animal Science. 93(5):2375-2381.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.Differential expression of genes in the jejunum of steers with feed efficiency phenotypes

- (Abstract Only)Butler, A.R., Lindholm-Perry, A.K., Freetly, H.C. 2015. Differential expression of genes in the jejunum of steers with feed efficiency phenotypes [abstract]. Journal of Animal Science. 93(Supplement 2):179.A polymorphism in myostatin influences puberty but not fertility in beef heifers, whereas μ-calpain affects first calf birth weight
                                                        

- (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.Genetic markers that influence feed efficiency phenotypes also affect cattle temperament as measured by flight speed
                                                        

- (Peer Reviewed Journal)Lindholm-Perry, A.K., Kuehn, L.A., Freetly, H.C., Snelling, W.M. 2015. Genetic markers that influence feed efficiency phenotypes also affect cattle temperament as measured by flight speed. Animal Genetics. 46(1):60-64.RNA-Seq detection of differential gene expression in the rumen of beef steers associated with feed efficiency phenotypes

- (Abstract Only)Kern, R.J., Lindholm-Perry, A.K., Freetly, H.C., Snelling, W.M., Kern, J.W., Miles, J.R., Ludden, P.A. 2014. RNA-Seq detection of differential gene expression in the rumen of beef steers associated with feed efficiency phenotypes [abstract]. Journal of Animal Science. 92(E-Supplement 2):918.Gentic improvement in cattle -- are we sacrificing reproduction in favor of production?

- (Literature Review)Cushman, R.A., McNeel, A.K., Tait Jr, R.G., Lindholm-Perry, A.K., Perry, G.A., Snelling, W.M., Bennett, G.L. 2014. Gentic improvement in cattle -- are we sacrificing reproduction in favor of production?. In:  Juengel, J. L., Miyamoto, A., Price, C., Reynolds, L. P., Smith, W. F., and Webb, R., editors.  Reproduction in Domestic Ruminants VIII.  Leicestershire, England: Context Products Ltd. p. 27-36.DNA polymorphisms and transcript abundance of PRKAG2 and phosphorylated AMP-activated protein kinase in the rumen are associated with gain and feed intake in beef steers
                                                        

- (Peer Reviewed Journal)Lindholm-Perry, A.K., Kuehn, L.A., Oliver, W.T., Kern, R.J., Cushman, R.A., Miles, J.R., McNeel, A.K., Freetly, H.C. 2014. DNA polymorphisms and transcript abundance of PRKAG2 and phosphorylated AMP-activated protein kinase in the rumen are associated with gain and feed intake in beef steers. Animal Genetics. 45(4):461-472.Surface enlargement factor of rumen papillae and expression of genes involved in dermatological diseases and their relationships with feed intake in beef steers

- (Abstract Only)Kern, R.J., Lindholm-Perry, A.K., Freetly, H.C., Snelling, W.M., Miles, J.R., Ludden, P.A. 2014. Surface enlargement factor of rumen papillae and expression of genes involved in dermatological diseases and their relationships with feed intake in beef steers [abstract]. Journal of Animal Science. 92(Supplement 2):32.An evaluation of the differences in the rumen transcriptome among beef steers with extreme feed efficiency phenotypes

- (Abstract Only)Lindholm-Perry, A.K., Kern, R.J., Kuehn, L.A., Miles, J.R., Freetly, H.C., Snelling, W.M., Ludden, P.A. 2014. An evaluation of the differences in the rumen transcriptome among beef steers with extreme feed efficiency phenotypes.  Plant & Animal Genome XXII Conference, January 11-15, 2014, San Diego, CA. Abstract No. W155.Adipose and muscle tissue gene expression of two genes (NCAPG and LCORL) located in a chromosomal region associated with cattle feed intake and gain
                                                        

- (Peer Reviewed Journal)Lindholm-Perry, A.K., Kuehn, L.A., Oliver, W.T., Sexten, A.K., Miles, J.R., Rempel, L.A., Cushman, R.A., Freetly, H.C. 2013. Adipose and muscle tissue gene expression of two genes (NCAPG and LCORL) located in a chromosomal region associated with cattle feed intake and gain. PLoS One. 8(11):e80882.Ruminal and adipose gene expression in beef steers selected for diverse feed intake and gain phenotypes

- (Abstract Only)Lindholm-Perry, A.K., Rempel, L.A., Hales, K.E., Oliver, W.T., Freetly, H.C., Kuehn, L.A. 2013. Ruminal and adipose gene expression in beef steers selected for diverse feed intake and gain phenotypes [abstract]. Journal of Animal Science Supplement. 91(E-Supplement 2):629.Lipogenic-associated gene activity of adipose tissue from beef heifers and relation to production and reproductive traits

- (Abstract Only)Rempel, L.A., Cushman, R.A., McDaneld, T.G., Miles, J.R., Kuehn, L.A., Lindholm-Perry, A.K. 2013. Lipogenic-associated gene activity of adipose tissue from beef heifers and relation to production and reproductive traits. Journal of Animal Science. 91 (E-Supplement 2):466 (Abstract #510).Ruminal methanogens in steers that are negative or positive for residual gain

- (Abstract Only)Freetly, H., Wells, J., Kim, M., Hales, K., Lindholm-Perry, A. 2013. Ruminal methanogens in steers that are negative or positive for residual gain [abstract]. Journal of Animal Science. 91(E-Supplement 2):437.Prioritizing sequence polymorphisms for potential association with phenotype

- (Abstract Only)Snelling, W.M., Bennett, G.L., Thallman, R.M., Lindholm-Perry, A.K., Kuehn, L.A., McDaneld, T.G., Kachman, S.D., Spangler, M.L., Koshinsky, H., Kalbfleisch, T.S., Pollak, E.J. 2013. Prioritizing sequence polymorphisms for potential association with phenotype [abstract]. Journal of Animal Science. 91(E-Supplement 2):74-75.Development and applications of low-cost, high-throughput genotyping

- (Abstract Only)Thallman, R.M., Lindholm-Perry, A.K., Curry, J.D., Fofanov, V.Y., Koshinsky, H. 2013. Development and applications of low-cost, high-throughput genotyping [abstract]. Journal of Animal Science. 91(Supplement 2):20. Abstract No. O063.Low-cost genotyping by next generation sequencing:  Next generation genotyping

- (Abstract Only)Curry, J.D., Snelling, W.M., Lindholm-Perry, A.K., Dier, P., Shin, M., Nguyen, J., Bulsara, N., Thallman, R.M., Fofanov, V.Y., Koshinsky, H. 2013. Low-cost genotyping by next generation sequencing:  Next generation genotyping [abstract]. Plant and Animal Genome XXI Conference. Poster Abstract No. P0525.Use of single nucleotide polymorphisms (SNP) to fine-map quantitative trait loci (QTL) in swine

- (Abstract Only)Rohrer, G.A., Lindholm-Perry, A.K., Shackelford, S.D., King, D.A., Wheeler, T.L., Nonneman, D. 2013. Use of single nucleotide polymorphisms (SNP) to fine-map quantitative trait loci (QTL) in swine [abstract]. Plant and Animal Genome XXI Conference Proceedings. Abstract #W047.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.Adipose and muscle tissue expression of two genes (NCAPG and LCORL) located in a chromosomal region associated with cattle feed intake and gain

- (Abstract Only)Lindholm-Perry, A.K., Sexten, A.K., Kuehn, L.A., Rempel, L.A., Miles, J.R., Cushman, R.A., Freetly, H.C. 2012. Adipose and muscle tissue expression of two genes (NCAPG and LCORL) located in a chromosomal region associated with cattle feed intake and gain [abstract]. Journal of Animal Science. 90(Suppl. 3):453.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.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.Mass genotyping by sequencing technology

- (Abstract Only)Curry, J.D., Lindholm-Perry, A.K., Shin, M., Liu, J.T., Bulsara, N., Dier, P., Thallman, R.M., Fofanov, V.Y., Koshinsky, H. 2012. Mass genotyping by sequencing technology. Plant & Animal Genome XX Conference, January 14-18, 2012, San Diego, California. Poster No. P0182.Genetic markers on BTA14 predictive for residual feed intake in beef steers and their effects on carcass and meat quality traits

- (Peer Reviewed Journal)Lindholm-Perry, A.K., Kuehn, L.A., Snelling, W.M., Smith, T.P., Ferrell, C.L., Jenkins, T.G., King, D.A., Shackelford, S.D., Wheeler, T.L., Freetly, H.C. 2012. Genetic markers on BTA14 predictive for residual feed intake in beef steers and their effects on carcass and meat quality traits. Animal Genetics. 43:599-603.Genetic markers in bovine chromosome 14 are significant for residual feed intake in steers

- (Abstract Only)Lindholm-Perry, A.K., Kuehn, L.A., Smith, T.P., Snelling, W.M., Freetly, H.C. 2011. Genetic markers in bovine chromosome 14 are significant for residual feed intake in steers. Journal of Animal Science. 89(E-Suppl. 1):422-423.A region on BTA14 that includes the positional candidate genes LYPLA1, XKR4 and TMEM68 is associated with feed intake and growth phenotypes in cattle

- (Peer Reviewed Journal)Lindholm-Perry, A.K., Kuehn, L.A., Smith, T.P., Ferrell, C.L., Jenkins, T.G., Freetly, H.C., Snelling, W.M. 2012. A region on BTA14 that includes the positional candidate genes LYPLA1, XKR4 and TMEM68 is associated with feed intake and growth phenotypes in cattle. Animal Genetics. 43(2):216-219.Predictive markers in calpastatin for tenderness in commercial pig populations

- (Peer Reviewed Journal)Nonneman, D.J., Lindholm-Perry, A.K., Shackelford, S.D., King, D.A., Wheeler, T.L., Rohrer, G.A., Bierman, C.D., Schneider, J.F., Miller, R.K., Zerby, H., Moeller, S.J. 2011. Predictive markers in calpastatin for tenderness in commercial pig populations. Journal of Animal Science. 89:2663-2672.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.Genomic regions associated with kyphosis in swine

- (Peer Reviewed Journal)Lindholm-Perry, A.K., Rohrer, G.A., Kuehn, L.A., Keele, J.W., Holl, J.W., Shackelford, S.D., Wheeler, T.L., Nonneman, D.J. 2010. Genomic regions associated with kyphosis in swine. BMC Genetics. 11:112.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. 230Polymorphisms 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.Using growth traits and adipose function to identify indicators of heifer fertility

- (Abstract Only)Cushman, R.A., Allan, M.F., Mcdaneld, T.G., Kuehn, L.A., Rempel, L.A., Lindholm-Perry, A.K., Snelling, W.M., Freetly, H.C. 2010. Using growth traits and adipose function to identify indicators of heifer fertility [abstract]. Proceedings of 8th International Ruminant Reproduction Symposium. p. 130 (Abstract # M43).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.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.Association of Functional SNPs in Pig Calpastatin Regulatory Regions with Tenderness

- (Abstract Only)Nonneman, D.J., Lindholm-Perry, A.K., Shackelford, S.D., King, D.A., Wheeler, T.L., Rohrer, G.A., Bierman, C., Miller, R.K., Zerby, H., Moeller, S.J. 2010. Association of Functional SNPs in Pig Calpastatin Regulatory Regions with Tenderness. Proc., Midwestern Section of the American Society of Animal Science Meeting. March 15-17, 2010. Des Moines, IA. Abstract #34. p. 11-12.Allele-Specific Transcription Factor Binding in Pig Calpastatin Promoter Regions

- (Abstract Only)Nonneman, Dan J., Lindholm-Perry, Amanda K., Shackelford, Steven D., King, D.Andy, Wheeler, Tommy L., Rohrer, Gary A. 2010. Allele-Specific Transcription Factor Binding in Pig Calpastatin Promoter Regions. Plant and Animal Genome Conference Proceedings XVIII. 1/9-13/2010. San Diego, CA. Abstract #P607.Relationships among calpastatin single nucleotide polymorphisms, calpastatin expression and tenderness in pork longissimus

- (Peer Reviewed Journal)Lindholm-Perry, A.K., Rohrer, G.A., Holl, J.W., Shackelford, S.D., Wheeler, T.L., Koohmaraie, M., Nonneman, D.J. 2009. Relationships among calpastatin single nucleotide polymorphisms, calpastatin expression and tenderness in pork longissimus. Animal Genetics. 40(5):713-721.Positional candidate genes for kyphosis in commercial swine populations

- (Abstract Only)Lindholm-Perry, A.K., Rohrer, G.A., Keele, J.W., Holl, J.W., Shackelford, S.D., Wheeler, T.L., Koohmaraie, M., Nonneman, D.J. 2009. Positional Candidate Genes for Kyphosis in Commercial Swine Populations. Proc., Plant and Animal Genome Conference XVII. 1/10-14/2009, San Diego, CA. P529.Update on genetic markers for pork quality

- (Proceedings)Rohrer, G.A., Holl, J.W., Lindholm-Perry, A.K., Nonneman, D.J., Shackelford, S.D., Wheeler, T.L., Koohmaraie, M. 2007. Update on genetic markers for pork quality. Conference Proc., National Swine Improvement Federation Conference & Ann. Mtg., Dec. 5-7, 2007. Kansas City, MO, NSIF Volume 32, www.nsif.com


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