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    Rosen BD, Cole JB, Van Tassell CP, Ma L, Liu GE. Comparative analyses of sperm

    
    

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    6. Smith JL, Wilson ML, Nilson SM, Rowan TN, Oldeschulte DL, Schnabel RD, Decker JE, Seabury CM. Genome-wide association and genotype by environment interactions for growth traits in U.S. Gelbvieh cattle. BMC Genomics. 2019 Dec 4;20(1):926.
    
    
    7. Zwane AA, Schnabel RD, Hoff J, Choudhury A, Makgahlela ML, Maiwashe A, Van Marle-Koster E, Taylor JF. Genome-Wide SNP Discovery in Indigenous Cattle Breeds of South Africa. Front Genet. 2019 Mar 29;10:273.
    
    
    8. Hoff JL, Decker JE, Schnabel RD, Seabury CM, Neibergs HL, Taylor JF. QTL-mapping and genomic prediction for bovine respiratory disease in U.S. Holsteins using sequence imputation and feature selection. BMC Genomics. 2019 Jul 5;20(1):555.
    
    
    9. Crum TE, Schnabel RD, Decker JE, Regitano LCA, Taylor JF. CRUMBLER: A tool for the prediction of ancestry in cattle. PLoS One. 2019 Aug 26;14(8):e0221471. =
    
    
    10. Maldonado MBC, de Rezende Neto NB, Nagamatsu ST, Carazzolle MF, Hoff JL, Whitacre LK, Schnabel RD, Behura SK, McKay SD, Taylor JF, Lopes FL. Identification of bovine CpG SNPs as potential targets for epigenetic regulation via DNA methylation. PLoS One. 2019 Sep 12;14(9):e0222329.
    
    
    11. Koltes JE, Cole JB, Serao N, McCue M, Woodward J, Zhang H, McKay S, Lunney J, Kramer L, Schroeder M, Clemmens R, Murdoch B, Rexroad C, Rosa G, Mateescu R, White S, Worku M, Reecy J. A vision for development and utilization of high-throughput phenotyping and big data analytics in livestock. Frontiers in Genetics (2019) Dec 17
    
    
    12. Cantrell B, Lachance H, Murdoch B, Sjoquist J, Funston R, Weaber R, McKay S. Global DNA methylation in the limbic system of cattle. Epigenomes – feature cover (2019) 3(2).
    
    
    13. Kern C, Wang Y, Chitwood J, Korf I, Delany M, Cheng H, Medrano JF, Van Eenennaam AL, Ernst C, Ross P, Zhou H. Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species. BMC Genomics. 2018 19(1):684.
    
    
    14. Mueller, M.L., Cole, J.B., Sonstegard, T.S., Van Eenennaam, A.L. 2019. Comparison of gene editing vs. conventional breeding to introgress the POLLED allele into the U.S. dairy cattle population. Journal of Dairy Science. 102(5): 1-12.
    
    
    15. Mueller, M.L., Cole, J.B., Sonstegard, T.S., Van Eenennaam, A.L. Simulation of introgression of the POLLED allele into the Jersey breed via conventional breeding vs. gene editing, Translational Animal Science, Volume 2, Issue suppl_1, September 2018, Pages S57–S60
    
    
    16. Van Eenennaam, A.L., Wells, K.D. and Murray, J.D. Proposed U.S. regulation of gene-edited food animals is not fit for purpose. npj Science of Food, 3(3).
    
    
    17. Rexroad, C.,Vallet, J., Kumar, L., Reecy, J., Bickhart, D., Blackburn, H., Boggess, M., Cheng, H., Clutter, A., Cockett, N., Ernst, C., Fulton, J., Liu, J., Lunney, J., Neibergs, H., Purcell, C., Smith, T., Sonstegard, T., Taylor, J., Telugu, B., Van Eenennaam, A., Van Tassell, C., and Wells, K. 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.
    
    
    18. Dubrovsky, S., Van Eenennaam, A. L., Karle, B. M., Rossitto, P., Lehenbauer, T. and Aly, S. 2019. Epidemiology of Bovine Respiratory Disease (BRD) in preweaned calves on California dairies: The BRD 10K study. Journal of Dairy Science. 102:7306-7319.
    
    
    19. Dubrovsky, S., Van Eenennaam, A. L., Karle, B. M., Rossitto, P., Lehenbauer, T. and Aly, S. 2019. Bovine Respiratory Disease (BRD) cause-specific and overall Mortality in preweaned calves on California dairies: The BRD 10K study. Journal of Dairy Science. 102:7320-7328.
    
    
    20. Maier GU, Love WJ, Karle BM, Dubrovsky SA, Williams DR, Champagne JD, Anderson, RJ, Rowe JD, Lehenbauer TW, Van Eenennaam AL, Aly SS. 2019. Management factors associated with bovine respiratory disease in preweaned calves on California dairies: The BRD 100 study. Journal of Dairy Science. 102: 7288-7305
    
    
    21. Upperman, L.R., Kinghorn, B.P., MacNeil, M.D., Van Eenennaam, A.L. 2019. Management of lethal recessive alleles in beef cattle through the use of mate allocation software. Genetics, Selection, Evolution. 6;51(1):36.
    
    
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    25. Lam, P.T., S.L. Padula, T.V. Hoang, J.E. Poth, L. Lin, C. Liang, A.S. LeFever, L.M. Wallace, R. Ashery-Padan, P.K. Riggs, J.E. Shields, O. Shaham, S. Rowan, N.L. Brown, T. Glaser, and M.L. Robinson. Considerations for the use of Cre recombinase for conditional gene deletion in the mouse lens. Human Genomics 10:13. https://doi.org/10.1186/s40246-019-0192-8
    
    
    26. Riley, David G., Rhonda K. Miller, K. L. Nicholson, Clare A. Gill, Andy D. Herring, Penny K. Riggs, Jason E. Sawyer, Jeffrey W. Savell, and James O. Sanders. 2019. “Genome Association of Carcass and Palatability Traits from Bos Indicus-Bos Taurus Crossbred Steers within Electrical Stimulation Status and Correspondence with Steer Temperament; 1. Carcass.” Livestock Science 229: 150–58.
    
    
    27. Riggs, Penny K., Michael J. Fields, and H. Russell Cross. 2018. “Food and Nutrient Security for a Growing Population Introduction.” ANIMAL FRONTIERS 8 (3): 3–4.
    
    
    28. Murano, Elsa A., H. Russell Cross, and Penny K. Riggs. 2018. “The Outbreak That Changed Meat and Poultry Inspection Systems Worldwide.” ANIMAL FRONTIERS 8 (4): 4–8.
    
    
    29. Littlejohn, Brittni P., Deborah M. Price, Don A. Neuendorff, Jeffery A. Carroll, Rhonda C. Vann, Penny K. Riggs, David G. Riley, Charles R. Long, Thomas H. Welsh Jr., and Ronald D. Randel. 2018. “Prenatal Transportation Stress Alters Genome-Wide DNA Methylation in Suckling Brahman Bull Calves.”J. Anim. Sci. 96 (12): 5075–99.
    
    
    
    


30. Phillips, C.A., Reading, B.J., Livingston, M., Livingston, K. and Ashwell, C.M. Accepted. Evaluation via Supervised Machine Learning of the Broiler Pectoralis Major and Liver Transcriptome in Association with the Muscle Myopathy Wooden Breast. Frontiers in Physiology, in press.


31. Hornick, K.M. and Plough, L.V., 2019. Tracking genetic diversity in a large-scale oyster restoration program: effects of hatchery propagation and initial characterization of diversity on restored vs. wild reefs. Heredity 123:92-105.


32. Hughes, A.R., Hanley, T.C., Byers, J.E., Grabowski, J.H., McCrudden, T., Piehler, M.F. and Kimbro, D.L. 2019. Genetic diversity and phenotypic variation within hatchery‐produced oyster cohorts predict size and success in the field. Ecological Applications 29(6): e01940.


33. Jaris, H., Brown, D.S. and Proestou, D.A. 2019. Assessing the contribution of aquaculture and restoration to wild oyster populations in a Rhode Island coastal lagoon. Conservation Genetics 20(3):503-516.


34. Proestou, D.A. and Sullivan, M.E. 2020. Variation in global transcriptomic response to Perkinsus marinus infection among eastern oyster families highlights potential mechanisms of disease resistance. Fish and Shellfish Immunology 96:141-151.


35. Proestou, D.A., Corbett, R.J., Ben‐Horin, T., Small, J.M. and Allen Jr, S.K., 2019. Defining Dermo resistance phenotypes in an eastern oyster breeding population. Aquaculture Research 50:2142-2154.


36. Ali A., Al-Tobasei R., Lourenco D., Leeds T., Kenney B. & Salem M. (2019) Genome-Wide Association Study Identifies Genomic Loci Affecting Filet Firmness and Protein Content in Rainbow Trout. Frontiers in Genetics 10: 386.


37. Chapagain P., Arivett B., Cleveland B.M., Walker D.M. & Salem M. (2019) Analysis of the fecal microbiota of fast- and slow-growing rainbow trout (Oncorhynchus mykiss). BMC Genomics 20: 788.


38. Grummer, J.A., L.B. Behergaray, L. Bernatchez, B.K. Hand, G. Luikart, S.R. Narum, and E.B. Taylor. 2019. Aquatic landscape genomics and environmental effects on genetic variation. Trends in Ecology and Evolution 34:641-654.


39. Janowitz-Koch, I., C. Rabe, R. Kinzer, D. Nelson, M.A. Hess, and S.R. Narum. 2019. Long-term evaluation of fitness and demographic effects of a Chinook salmon supplementation program. Evolutionary Applications 12:456-469.


40. Pearse, D.E., Barson, N.J., Nome, T., Gao, G., Campbell, M.A., Abadía-Cardoso, A., Anderson, E.C., Rundio, D.E., Williams, T.H., Naish, K.A., Moen, T., Liu, S., Kent, M., Moser, M., Minkley, D.R., Rondeau, E.B., Brieuc, M.S.O., Sandve, S.R., Miller, M.R., Cedillo, L., Baruch, K., Hernandez, A.G., Ben-Zvi, G., Shem-Tov, D., Barad, O., Kuzishchin, K., Garza, J.C., Lindley, S.T., Koop, B.F., Thorgaard, G.H., Palti, Y., Lien, S. 2019. Sex-dependent dominance maintains migration supergene in rainbow trout. Nature Ecology and Evolution 3: 1731-1742.


41. Silva, R.M.O., Evenhuis, J.P., Vallejo, R.L., Gao, G., Martin, K.E., Leeds, T.D., Palti, Y., Lourenco, D.a.L. 2019. Whole-genome mapping of quantitative trait loci and accuracy of genomic predictions for resistance to columnaris disease in two rainbow trout breeding populations. Genetics Selection Evolution 51: 42.


42. Steele, C.A., M.A. Hess, S.R. Narum, M.R. Campbell. 2019. Parentage-based tagging: reviewing the implementation of a new tool for an old problem. Fisheries 44:412-422.


43. Vallejo, R.L., Cheng, H., Fragomeni, B.O., Shewbridge, K.L., Gao, G., Macmillan, J.R., Towner, R. & Palti, Y. (2019). Genome-wide association analysis and accuracy of genome-enabled breeding value predictions for resistance to infectious hematopoietic necrosis virus in a commercial rainbow trout breeding population. Genetics Selection Evolution 51: 47.


44. Weigel, D., F. Monzyk, C. Sharpe, S.R. Narum, C.C. Caudill. 2019. Evaluation of a trap-and-transport program for a threatened population of steelhead (Oncorhynchus mykiss). Conservation Genetics 20:1195-1199.


45. Guillette, T.C., McCord, J., Guillette, M., Polera, M., Rachels, K.T., Morgeson, C., Kotlarz, N., Strynar, M., Knappe, D., Reading, B.J., and Belcher, S.M. 2019. Per and Polyfluoroalkyl Substance Exposure in Striped Bass (Morone saxatilis) of Cape Fear River is Associated with Biomarkers of Altered Immune and Liver Function. Environmental Science and Technology, in press.


46. Abdelhamed, H., Ozdemir, O., Waldbieser, G., Lawrence, M.L., Karsi, A. 2019. Effects of florfenicol feeding on diversity and composition of the intestinal microbiota of channel catfish (Ictalurus punctatus). Aquaculture Research, in press.


47. Bosworth, B., Waldbieser, G., Garcia, A., Tsuruta, S., Lourenco, D. 2019. Heritability and response to selection for carcass yield and growth in the Delta Select strain of channel catfish, Ictalurus punctatus. Aquaculture, in press.


48. Bosworth, B., Waldbieser, G., Garcia, A., Lourenco, D. 2019. Effect of pond- or strip-spawning on growth and carcass yield of channel catfish progeny. Journal of the World Aquaculture Society, in press.


49. Zhang, Y., Liu, Z.J., and Li, H. 2020. Genomic prediction of columnaris disease resistance in catfish. Marine Biotechnology, in press.


50. Tan, S., Wang, W., Tian, C., Niu, D., Zhou, T., Yang, Y., Gao, D., and Liu, Z.J. 2019. Post-transcriptional regulation through alternative splicing after infection with Flavobacterium columnare in channel catfish (Ictalurus punctatus). Fish and Shellfish Immunology 91: 188-193.


51. Rexroad, C., Vallet, J., Matukumalli, L.K., Reecy, J., Bickhart, D., Blackburn, H., Boggess, M., Cheng, H., Clutter, A., Cockett, N., Ernst, C., Fulton, J., Liu, Z.J,, Lunney, J., Neibergs, H., Purcell, C., Smith, T., Sonstegard, T., Taylor, J., Telugu, B., Van Eenennaam, A., Van Tassell, C., and Wells, K. 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.


52. Tan, S., Wang, W., Zhou, T., Yang, Y., Gao, D., and Liu, Z.J. 2019. Polyadenylation sites and their characteristics in the genome of channel catfish (Ictalurus punctatus) as revealed by using RNA-Seq data. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics 30: 248-255.


53. Gao, L., Yuan, Z., Zhou, T., Yang, Y., Gao, D., Dunham, R., and Liu, Z.J. 2019. Foxo genes in channel catfish and their response after bacterial infection. Developmental and Comparative Immunology 97: 38-44.


54. Wang, W., Tan, S., Luo, J., Shi, H., Jin, Y., Zhou, T., Wang, X., Yang, Y., Niu, D., Yuan, Z., Gao, D., Dunham, R., and Liu, Z.J. 2019. GWAS analysis indicated importance of NF- κB signaling pathway in host resistance against motile Aeromonas septicemia disease in catfish. Marine Biotechnology 21: 335-347.


55. Bao, L., Tian, C., Liu, S., Zhang, Y., Elaswad, A., Yuan, Z., Khalil, K., Sun, F., Yang, Y., Zhou, T., Ning, L., Tan, S., Zeng, Q., Liu, Y., Li, Y., Li, Y., Gao, D., Dunham, R., Davis, K., Waldbieser, G., and Liu, Z.J. 2019. The Y chromosome sequence of the channel catfish suggests novel sex determination mechanisms in teleost fish. BMC Biology 17: 6.


56. Tan, S., Wang, W., Tian, C., Niu, D., Zhou, T., Jin, Y., Yang, Y., Gao, D., Dunham, R., and Liu, Z.J. 2019. Heat stress induced alternative splicing in catfish as determined by transcriptome analysis. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics 29: 166-172.


57. Zhang, X., Yuan, J., Sun, Y., Li, S., Gao, Y., Yu, Y., Liu, C., Wang, Q., Lv, X., Zhang, X., Ma, K.Y., Wang, X., Lin, W., Wang, L., Zhu, X., Zhang, C., Zhang, J., Jin, S., Yu, K., Kong, J., Xu, P., Chen, N., Zhang, H.-B., Sorgeloos, P., Sagi, A., Warren, A., Liu, Z.J., Wang, L., Ruan, J., Chu, K., Liu, B., Li, F., and Xiang, J. 2019. Penaeid shrimp genome provides insights into benthic adaptation and frequent molting. Nature Communications 10:356.


58. Li, N., Bao, L., Zhou, T., Yuan, Z., Liu, S., Dunham, R., Li, Y., Wang, K., Xu, X., Jin, Y., Zeng, Q., Gao, S., Fu, Q., Liu, Y., Yang, Y., Li, Q., Meyer, A., Gao, D., and Liu, Z.J. 2019. Genome sequence of walking catfish (Clarias batrachus) provides insight into terrestrial adaptation. BMC Genomics 19: 952.
    
    
    
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