06/10/2019

03/16/2020

29. 
    
    
    
    1. Liu R, Low WY, Tearle R, Koren S, Ghurye J, Rhie A, Phillippy AM, Rosen BD, Bickhart DM, Smith TPL, Hiendleder S, Williams JL. New insights into mammalian sex chromosome structure and evolution using high-quality sequences from bovine X
    
    
    
    

    and Y chromosomes. BMC Genomics. 2019 Dec 19;20(1):1000

    
    
    
    
    2. Fang L, Zhou Y, Liu S, Jiang J, Bickhart DM, Null DJ, Li B, Schroeder SG,
    
    
    
    

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

    
    

    DNA methylomes among human, mouse and cattle provide insights into epigenomic

    
    

    evolution and complex traits. Epigenetics. 2019 Mar;14(3):260-276.

    
    
    
    
    3. Liu S, Kang X, Catacchio CR, Liu M, Fang L, Schroeder SG, Li W, Rosen BD,
    
    
    
    

    Iamartino D, Iannuzzi L, Sonstegard TS, Van Tassell CP, Ventura M, Low WY,

    
    

    Williams JL, Bickhart DM, Liu GE. Computational detection and experimental

    
    

    validation of segmental duplications and associated copy number variations in

    
    

    water buffalo ( Bubalus bubalis ). Funct Integr Genomics. 2019 May;19(3):409-419.

    
    
    
    
    4. Johnson T, Keehan M, Harland C, Lopdell T, Spelman RJ, Davis SR, Rosen BD,
    
    
    
    

    Smith TPL, Couldrey C. Short communication: Identification of the pseudoautosomal

    
    

    region in the Hereford bovine reference genome assembly ARS-UCD1.2. J Dairy Sci.

    
    
    
    
    • ;102(4):3254-3258.
    
    
    
    
    
    
    5. Rowan TN, Hoff JL, Crum TE, Taylor JF, Schnabel RD, Decker JE. A multi-breed reference panel and additional rare variants maximize imputation accuracy in cattle. Genet Sel Evol. 2019 Dec 26;51(1):77.
    
    
    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.
    
    
    22. Van Eenennaam, A.L. 2019. Application of genome editing in farm animals: cattle. Transgenic Research. 28(Suppl 2):93-100.
    
    
    23. Young, A.E., T.A. Mansour, B.R. McNabb, J.R. Owen, J.F.Trott, C.T. Brown, and A.L. Van Eenennaam, 2020. Comparative evaluation of the phenotype and genome from offspring of a genome edited, hornless bull and controls. Nature Biotechology. 38:225–232.
    
    
    24. Kirkpatrick, B.W., R.M. Thallman and L.A. Kuehn. Validation of SNP associations with bovine ovulation and twinning rate.  Animal Genetics 50(3):259-261. doi: 10.1111/age.12793. Epub 2019 Apr 12.
    
    
    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.
    
    
    
    1. Greene E., J Flees, A Dhamad, A Alrubaye, S Hennigan, J Pleimann, M Smeltzer, S Murray, J Kugel, J Goodrich, A Robertson, R Wideman, D Rhoads, S Dridi. (2019). Double-stranded RNA is a novel molecular target in osteomyelitis pathogenesis: A translational avian model for human bacterial chondronecrosis with osteomyelitis', The American Journal of Pathology 189(10): 2077-2089. doi.org/10.1016/j.ajpath.2019.06.013
    
    
    2. Al-Zahrani K, T Licknack, DL Watson, NB Anthony, DD Rhoads. (2019) Further Investigation of Mitochondrial Biogenesis and Gene Expression of Key Regulators in Ascites- Susceptible and Ascites-Resistant Broiler Research Lines. PLOS One 14: e0205480 doi.org/10.1371/journal.pone.0205480
    
    
    3. Tarrant K, JE Fulton, A Lund, DD Rhoads, NB Anthony. 2018. Predicting ascites incidence in a simulated altitude-challenge using single nucleotide polymorphisms identified in multi-generational genome wide association studies. Poultry Science 97(11):3801-3806. org/10.3382/ps/pey273.
    
    
    4. Dey S., A. Parveen, K.J. Tarrant, T. Licknack, B.C. Kong, N.B. Anthony, D.D. Rhoads. 2018. Whole Genome Resequencing Identifies the CPQ Gene as a Determinant of Ascites Syndrome in Broilers. PLOS One 13(1): e0189544. doi.org/10.1371/journal.pone.0189544.
    
    
    5. Lassiter K, Kong B, Piekarski-Welsher A, Dridi S, and Bottje WG. 2019. Gene expression essential for myostatin signaling and skeletal muscle development is associated with divergent feed efficiency in pedigree male broilers. Frontiers in Physiology. 10:126.
    
    
    6. Khatri, B., S. Kang, S. Shouse, N. Anthony, W. Kuenzel and B.C. Kong. 2019. Copy number variation study in Japanese quail associated with stress related traits using whole genome re-sequencing data. PLoS ONE 14(3): e0214543. doi.org/10.1371/journal.pone.0214543.
    
    
    7. Kang, S.W., K.D. Christensen, D. Aldridge and W.J. Kuenzel. 2019. Effects of light intensity and dual light intensity choice on plasma corticosterone, central serotonergic and dopaminergic activities in birds, Gallus gallus. Gen. Comp. Endocrinol. doi.org/10.1016/j.ygcen.2019.113289.
    
    
    8. Kadhim, H.K., M. Kidd Jr., S.W. Kang and W.J. Kuenzel. 2019. Differential delayed responses of arginine vasotocin and its receptors in septo-hypothalamic brain structures and anterior pituitary that sustain hypothalamic-pituitary-adrenal (HPA) axis functions during acute stress. Gen. Comp. Endocrinol. doi.org/10.1016/j.ygcen.2019.113302.
    
    
    9. Kadhim, H.K., S.W. Kang and W.J. Kuenzel. 2019. Differential and temporal expression of corticotropin releasing hormone and its receptors in the nucleus of the hippocampal commissure and paraventricular nucleus during the stress response in chickens (Gallus gallus). Brain Res. 1714:1-7. doi.org/10.1016/j.brainres.2019.02.018.
    
    
    10. Saelao, P., Y. Wang, G. Chanthavixay, V. Yu, J. Dekkers, R. Gallardo, T.R. Kelly, S.J. Lamont. Zhou, H. 2018. Integrated proteomic and transcriptomic analysis of differential expression of chicken lung tissue in response to NDV infection during heat stress. Genes 9, 579; doi:10.3390/genes9120579.
    
    
    11. Silva APD, Hauck R, Kern C, Wang Y, Zhou H, Gallardo RA. 2019 Effects of Chicken MHC Haplotype on Resistance to Distantly Related Infectious Bronchitis Viruses. Avian Dis. 63(2):310-317. doi: 10.1637/11989-103118-Reg.1
    
    
    12. Litvak Y., K.K.Z. Mon, H. Nguyen, G. Chanthavixay, M. Liou, E. M. Velazquez, L. Kutter, M. A. Alcantara, M. X. Byndloss, C.R. Tiffany, G. T. Walker, F. Faber, Y. Zhu, D. N. Bronner, A. J. Byndloss, R. M. Tsolis, H. Zhou. A. J. Baumler. 2019. Commensal Enterobacteriaceae protect against Salmonella colonization by competing for oxygen. Cell Host & Microbe 25, 1-12https://doi.org/10.1016/j.chom.2018.12.003.
    
    
    13. Rowland K, Saelao P, Wang Y, Fulton JE, Liebe GN, McCarron AM, Wolc A, Gallardo RA, Kelly T, Zhou H, Dekkers JCM, Lamont SJ. 2018. Association of Candidate Genes with Response to Heat and Newcastle Disease Virus. Genes (Basel). 9(11). pii: E560. doi: 10.3390/genes9110560.
    
    
    14. Cadena M, Froenicke L, Britton M, Settles ML, Durbin-Johnson B, Kumimoto E, Gallardo RA, Ferreiro A, Chylkova T, Zhou H, Pitesky M. 2019. Transcriptome analysis of Salmonella Heidelberg after exposure to cetylpyridinium chloride, acidified calcium hypochlorite, and peroxyacetic acid. Journal of Food Protection, Vol. 82, No. 1, 2019, Pages 109–119 doi:10.4315/0362-028X.JFP-18-235.
    
    
    15. Saelao, P., Y. Wang, G. Chanthavixay, J. Dekkers, R. Gallardo, A. Wolc. T.R. Kelly, S.J. Lamont. Zhou, H. 2019. Genetics and Genomic Regions Affecting Response to Newcastle Disease Virus Infection under Heat Stress in Layer Chickens. Genes (Basel). 2019 Jan 18;10(1). pii: E61. doi: 10.3390/genes10010061.
    
    
    16. Walugembe M, Mushi JR, Amuzu-Aweh EN, Chiwanga GH, Msoffe PL, Wang Y, Saelao P, Kelly T, Gallardo RA, Zhou H, Lamont SJ, Muhairwa AP, Dekkers JCM. 2019. Genetic Analyses of Tanzanian Local Chicken Ecotypes Challenged with Newcastle Disease Virus. Genes (Basel). 2019 Jul 17;10(7). pii: E546. doi: 10.3390/genes10070546.
    
    
    17. Egaña-Labrin, S. R. Hauck, A. Figueroa, S. Stoute, H.L. Shivaprasad, M. Crispo, C. Corsiglia, H. Zhou, C. Kern, B. Crossley, R. Gallardo. 2019. Genotypic Characterization of Emerging Avian Reovirus Molecular Variants in California. Sci Rep (9), Article number: 9351 (2019).
    
    
    18. Adentunji, M., Lamont, S.J., Abasht, B.A., and Schmidt, C. J. 2019. Variant analysis pipeline for accurate detection of genomic variants from transcriptome sequencing data. PLOS ONE 14(9): e0216838.doi.org/10.1371/journal.pone.0216838
    
    
    19. Monson, M.S., Van Goor, A.G., Persia, M.E., Rothschild, M. F., Schmidt, C.J., Lamont, S.J. 2019. Genetic lines respond uniquely within the chicken thymic transcriptome to acute heat stress and low dose lipopolysaccharide. Scientific Reports 9:13649 doi.org/10.1038/s41598-019-50051-0
    
    
    20. Barrett, N.W., Schmidt, C.J., Lamont, S.J., Ashwell, C.M., Persia, M.E. 2019. Effects of acute and chronic heat stress on the performance, egg quality, body temperature and blood gas parameters of laying hens. Poultry Science. http://dx.doi.org/10.3382/ps/pez541
    
    
    21. Schilling, M., Memari, S., Cavanaugh, M., Katani, R., Deist, M.S., Radzio-Basu, J., Lamont. S.J., Buza, J.J., and Kapur, V. 2019. Conserved, breed-dependent, and subline-dependent innate immune responses of Fayoumi and Leghorn chicken embryos to NDV infection. Scientific Reports 9:7209 doi.org/10.1038/s41598-019-43483-1.
    
    
    22. Rowland, K., Ashwell, C.M. Persia, M.P., Rothschild, M.F., Schmidt, C., Lamont, S.J. 2019. Genetic analysis of production, physiologic, and egg quality traits in heat-challenged commercial white egg-laying hens using 600k SNP array data. Genetics Selection Evolution 51:31 doi.org/10.1186/s12711-019-0474-6
    
    
    23. Elbeltagy, A.R., Bertolini, F., Fleming, D.S., Van Goor, A., Ashwell, C.M., Schmidt, C.J., Kugonza, D., Lamont, S.J., Rothschild, M.F. 2019. Natural selection footprints among African chicken breeds and village ecotypes. Front. Genet. 10:376. doi: 10.3389/fgene.2019.00376
    
    
    24. Rowland, K., Persia, M., Rothschild, M., Schmidt, C., Lamont, S. 2019. Blood gas and chemistry components are moderately heritable in commercial white egg-laying hens under acute or chronic heat exposure. Poultry Science 0:1–5 http://dx.doi.org/10.3382/ps/pez204
    
    
    25. Walugembe, M., Bertolini, F., Dematawewa, C.M.B., Reis, M.P., Elbeltagy, A.R., Schmidt, C.J., Lamont, S.J., and Rothschild, M.F. 2019. Detection of selection signatures among Brazilian, Sri Lankan, and Egyptian chicken populations under different environmental conditions. Front. Genet. doi: 10.3389/fgene.2018.00737
    
    
    26. Zhuo, Z., Lamont, S., Abasht, B. 2019. RNA-Seq analyses identify additivity as the predominant gene expression pattern in F1 chicken embryonic brain and liver. Genes 10, 27; doi:10.3390/genes10010027
    
    
    27. Drobik-Czwarno, W., Wolc, A., Kucharska, K.,Martyniuk. E., Genetic basis of resistance to highly pathogenic avian influenza in chicken. Review article in Polish. Scientific Annals of Polish Society of Animal Production.
    
    
    28. Wolc, A., Arango, J., Settar, P., Fulton, J.E., O’Sullivan, N.P. and Dekkers, J.C., 2019. Genetics of male reproductive performance in White Leghorns. Poultry Sci. 98: 2729-2733.
    
    
    29. Weng, Z., Wolc, A., Su, H., Fernando, R.L., Dekkers, J.C., Arango, J., Settar, P., Fulton, J.E., O’Sullivan, N.P. and Garrick, D.J., 2019. Identification of recombination hotspots and quantitative trait loci for recombination rate in layer chickens. J. Anim.Sci Tech. 10(1), p.20.
    
    
    30. Ward TL, Weber BP, Mendoza KM, Danzeisen JI, Llop K, Lang K, Clayton JB, Grace E, Brannon J, Radovic I, Beauclaire M, Heisel TJ, Knights D, Cardona C, Kogut M, Johnson C, Noll SL, Arsenault R, Reed KM, and Johnson T. 2019. Antibiotics and host-tailored probiotics similarly modulate effects on the developing microbiome, mycobiome, and host transcriptome. MBio, DOI: 10.1128/mBio.02171-19.
    
    
    31. Reed KM, Mendoza KM, and Coulombe RA. 2019. Altered gene response to aflatoxin B1 the spleens of susceptible and resistant turkeys. Toxins (Basel) 11(5), 242; doi.org/10.3390/toxins11050242
    
    
    32. Reed KM, Mendoza KM, and Coulombe RA Jr. 2019. Differential transcriptome responses to aflatoxin B1 in the cecal tonsil of susceptible and resistant turkeys. Toxins (Basel) 11(1); 55. doi:10.3390/toxins11010055.
    
    
    33. Barnes NE, Strasburg GM, Velleman SG, and Reed KM. 2019. Thermal challenge alters the transcriptional profile of the breast muscle in turkey poults. Poultry Science, 98:74-91. doi: 10.3382/ps/pey401.
    
    
    34. Kern, C,. Wang, Y., Chitwood, J., Korf, I., Delany, M., Cheng, H., Medrano, J.F., Van Eenennaam, A.L., Ernst, C., Ross, P., and Zhou, H. 2018, Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species. BMC Genomics 19(1):684.
    
    
    35. Dunn, J.R., Black Pyrkosz, A., Steep, A., and Cheng, H.H. 2019. Identification of Marek’s disease virus genes associated with virulence of US strains. J. Gen. Virol. 100:1132-1139.
    
    
    36. Umthomg, S., Dunn, J.R., and Cheng, H.H. 2019. Towards a mechanistic understanding of the synergistic response induced by bivalent Marek’s disease vaccines to prevent lymphomas. Vaccine 37:6397-6404.
    
    
    37. Bai, H., He, Y., Ding, Y., Carrillo, J.A., Selvaraj, R.K., Zhang, H., Chen, J. and Song J. 2019. Allele-specific expression of CD4(+) T cells in response to Marek's disease virus infection. Genes (Basel) 10(9). pii: E718.
    
    
    38. Bai, H., He Y., Ding, Y., Chang, S., Zhang, H., Chen, J. and Song, J. 2019. Parent-of-origin has no detectable effect on survival days of Marek's disease virus infected White Leghorns. Poult. Sci .98:4498-503.
    
    
    39. Chu, Q., Ding, Y., Cai, W., Liu, L., Zhang, H. and Song J. 2019. Marek's disease virus infection induced mitochondria changes in chickens. Int. J. Mol. Sci. 20(13). pii: E3150.
    
    
    40. Deng, C., Tan, H., Zhou, H., Wang, M., Lu, Y., Xu, J., Zhang, H., Han, L. and Ai, Y. 2019. Four cysteine residues contribute to homodimerization of chicken interleukin-2. Int. J. Mol. Sci. 20(22). pii: E5744.
    
    
    41. Dong, K., Chang, S., Xie, Q., Zhao, P. and Zhang, H. 2019. RNA Sequencing revealed differentially expressed genes functionally associated with immunity and tumor suppression during latent phase infection of a vv+ MDV in chickens. Sci. Rep. 9:14182.
    
    
    42. He, Y., Han, B., Ding, Y., Zhang, H., Chang, S., Zhang, L., Zhao, C., Yang, N. and Song J. 2019. Linc-GALMD1 regulates viral gene expression in the chicken. Front. Genet. 10:1122.
    
    
    43. Li, H., Wang, P., Lin, L., Shi, M., Gu, Z., Huang, T., Mo, M.L., Wei, T., Zhang, H. and Wei, P. 2019. The emergence of the infection of subgroup J avian leucosis virus escalated the tumour incidence in commercial Yellow chickens in Southern China in recent years. Transbound. Emerg. Dis. 66:312-6.
    
    
    44. Liao, Z., Dai, Z., Cai ,C., Zhang, X., Li A., Zhang, H., Yan, Y., Lin, W., Wu, Y., Li, H., Li, H. and Xie, Q. 2019. Knockout of Atg5 inhibits proliferation and promotes apoptosis of DF-1 cells. In Vitro Cell. Dev. Biol. Anim. 55:341-8.
    
    
    45. Lu, H., Zhang, L., Xiao, J., Wu, C., Zhang, H., Chen, Y., Hu, Z., Lin, W., Xie, Q. and Li, H. 2019. Effect of feeding Chinese herb medicine ageratum-liquid on intestinal bacterial translocations induced by H9N2 AIV in mice. Virol. J. 16:24.
    
    
    46. Mays, J.K., Black-Pyrkosz, A., Mansour, T., Schutte, B.C., Chang, S., Dong, K., Hunt, H.D., Fadly, A.M., Zhang, L. and Zhang H. 2019. Endogenous avian leukosis virus in combination with serotype 2 Marek's disease virus significantly boosted the incidence of lymphoid leukosis-like bursal lymphomas in susceptible chickens. J. Virol. 93(23). pii: e00861-19.
    
    
    47. Zhang, X., Yan ,Y., Lin, W., Li, A., Zhang, H., Lei, X., Dai, Z., Li, X., Li, H., Chen, W., Chen, F., Ma, J. and Xie, Q. 2019. Circular RNA vav3 sponges gga-miR-375 to promote epithelial-mesenchymal transition. RNA Biol. 16:118-32.
    
    
    48. Kelly, Amy C., et al. "Oxygen perfusion (persufflation) of human pancreata enhances insulin secretion and attenuates islet proinflammatory signaling." Transplantation 103.1 (2019): 160-167.
    
    
    49. Bright, Lauren A., et al. "Modeling the pasture-associated severe equine asthma bronchoalveolar lavage fluid proteome identifies molecular events mediating neutrophilic airway inflammation." Veterinary Medicine: Research and Reports 10 (2019): 43.
    
    
    50. McCarthy, Fiona M., et al. "Chickspress: a resource for chicken gene expression." Database 2019 (2019).
    
    
    51. Neerukonda, Sabari Nath, et al. "Comparison of the transcriptomes and proteomes of serum exosomes from Marek’s disease virus-vaccinated and protected and lymphoma-bearing chickens." Genes 10.2 (2019): 116.
    
    
    52. 
        
        
        
        1. Ablondi M., Summer A., Vasini M., Simoni M., Sabbioni A. Genetic parameters estimation in an Italian horse native breed to support the conversion from agricultural uses to riding purposes. J Anim Breed Genet. 2020;137:200–210. https://doi.org/10.1111/jbg.12425 ​
        
        
        2. Ablondi, M., Viklund, Å., Lindgren, G. et al. Signatures of selection in the genome of Swedish warmblood horses selected for sport performance. BMC Genomics 20, 717 (2019).  https://doi.org/10.1186/s12864-019-6079-1​​
        
        
        3. Ablondi, M.; Eriksson, S.; Tetu, S.; Sabbioni, A.; Viklund, Å.; Mikko, S. Genomic Divergence in Swedish Warmblood Horses Selected for Equestrian  Disciplines. Genes 10, 97 (2019).   https://doi.org/10.3390/genes10120976
        
        
        4. Anas M. Khanshour, Eleanore K. Hempsey, Rytis Juras and E. Gus Cothran. 2019. Genetic Characterization of Cleveland Bay Horse Breed. Diversity 2019, 11, 174; doi:10.3390/d11100174.
        
        
        5. Bailey E, Finno C. Translation and application of equine genomics: The Havemeyer principles. Equine Vet J 2019 Mar;51(2):273.
        
        
        6. Beeson SK, Mickelson JR, and McCue ME. (2019). Equine recombination map updated to EquCab3.  Animal Genetics, 2019 Dec 30. doi: 10.1111/age.12898.
        
        
        7. Beeson SK, Mickelson JR, McCue ME (2019). Exploration of fine-scale recombination rate variation in the domestic horse.  Genome Research 29: 1744 - 1752.
        
        
        8. Bellone RR, Ocampo NR, Hughes SS, Le V, Arthur R, Finno CJ, Penedo MCT. Warmblood fragile foal syndrome type 1 mutation (PLOD1 c.2032G>A) is not associated with catastrophic breakdown and has a low allele frequency in the Thoroughbred breed. Equine Vet J 2019 Sep 10. doi: 10.1111/evj.13182. [Epub ahead of print]
        
        
        9. Boakari YL, El-Sheikh Ali H, Dini P, Loux SC, Fernandes CB, Scoggin KE, Esteller-Vico A, Lawrence L, Ball BA. A high protein model alters the endometrial transcriptome of mares.   Genes 2019, 10, 576; doi:10.3390/genes10080576.
        
        
        10. Boakari YL, El-Sheikh Ali H, Dini P, Loux SC, Fernandes CB, Scoggin KE, Esteller-Vico A, Lawrence L, Ball BA. A high protein model alters the endometrial transcriptome of mares.   Genes 2019, 10, 576; doi:10.3390/genes10080576.
        
        
        11. Bookbinder L, Finno CJ*, Firshman AM, Katzman SA, Burns E, Peterson J, Dahlgren A, Ming-Whitfield B, Glessner S, Borer-Matsui A, Valberg SJ. Impact of alpha-tocopherol deficiency and supplementation on sacrocaudalis and gluteal muscle fiber histopathology and morphology in horses. J Vet Intern Med. 2019 Nov;33(6):2770-2779. doi: 10.1111/jvim.15643. Epub 2019 Oct 29. PMID: 31660648
        
        
        12. Brandon D Velie, Marina Solé, Kim Jäderkvist Fegraeus, Maria K Rosengren, Knut H Røed, Carl-Fredrik Ihler, Eric Strand, Gabriella Lindgren. Genomic Measures of Inbreeding in the Norwegian-Swedish Coldblooded Trotter and Their Associations With Known QTL for Reproduction and Health Traits. Genet Sel Evol, 51 (1), 22, 2019.
        
        
        13. Brandon D Velie, Mette Lillie, Kim Jäderkvist Fegraeus, Maria K Rosengren, Maja Wiklund, Carl-Fredrik Ihler, Eric Strand & Gabriella Lindgren. Exploring the genetics of trotting racing ability in horses using a unique Nordic horse model. BMC Genomics, 20 (1), 104, 2019.
        
        
        14. Brosnahan MM, Al Abri MA, Brooks SA, Antczak DF, Osterrieder N. Genome-wide association study of equine herpesvirus type 1-induced myeloencephalopathy identifies a significant single nucleotide polymorphism in a platelet-related gene. Vet J. 2019 245:49-54.
        
        
        15. Bryan K, et al. (2019) Effects of equine myostatin (MSTN) genotype variation on transcriptional responses in Thoroughbred skeletal muscle. Comparative Exercise Physiology 2019 Hill EW
        
        
        16. Caitlin Castaneda, Rytis Juras, Anas Khanshour, Ingrid Randlaht, Barbara Wallner , Doris Rigler , Gabriella Lindgren, Terje Raudsepp, E Gus Cothran. Population Genetic Analysis of the Estonian Native Horse Suggests Diverse and Distinct Genetics, Ancient Origin and Contribution From Unique Patrilines. Genes (Basel), 10 (8), 2019.
        
        
        17. Castaneda, C., Juras, R., Khanshour, A., Randlaht, I., Wallner, W., Rigler, D., Lindgren, G. Raudsepp, T., E. Gus Cothran, E.G. 2019. Population genetic analysis of the Estonian Native Horse suggests diverse and distinct genetics, ancient origin and contribution from unique patrilines. Genes, 2019 Aug 20;10(8). pii: E629. doi: 10.3390/genes10080629.
        
        
        18. Castaneda, Caitlin, Rytis Juras, Anas Khanshour, Ingrid Randlaht, Barbara Wallner, Doris Rigler, Gabriella Lindgren, Terje Raudsepp and E. Gus Cothran. 2019. Population Genetic Analysis of the Estonian Native Horse Suggests Diverse and Distinct Genetics, Ancient Origin and Contribution from Unique Patrilines. Genes 10(8), 629; doi:10.3390/genes10080629
        
        
        19. Dini P, El-Sheik Ali H, Carossino M, Loux S, Esteller-Vico A, Scoggin KE, Daels PD, Ball BA. Expression profile of the chromosome 14 microRNA cluster (C14MC) ortholog in equine maternal circulation throughout pregnancy and its potential implications.  J. Mol. Sci. 2019, 20, 6285; doi:10.3390/ijms20246285.
        
        
        20. Dini P, Esteller-Vico A, Scoggin KE, Ball BA. Extraction of RNA from formalin-fixed, paraffin-embedded equine placenta.  Reprod Dom Anim 54:627-634, 2019.
        
        
        21. Dini P, Norris J, El-Sheikh Ali H, Loux SC, Carossino M, Esteller-Vico A, Bailey E, Kalbfleisch T, Daels P, Ball BA. Landscape of overlapping gene expression in the equine chorioallantois. Genes 2019, 10, 503; doi:10.3390/genes10070503.
        
        
        22. Durward-Akhurst SA, Schultz NS, Norton EM, Rendahl AK, Besselink H, Behnisch PA, Brouwer A, Geor RJ, Mickelson JR, and McCue ME. (2019). Associations between persistent organic pollutants and equine metabolic syndrome phenotypes. Chemosphere 2019  Mar;218:652-661. doi: 10.1016/j.chemosphere.2018.11.136.
        
        
        23. El-Sheikh Ali H, Legacki EL, Loux SC, Esteller-Vico A, Dini P, Scoggin KE, Conley AJ, Stanley SD, Ball BA. Equine placentitis is associated with a downregulation in myometrial progestin signaling.  Biol Reprod  101:162-176, 2019.
        
        
        24. El-Sheikh Ali H, Legacki EL, Scoggin KE, Loux SC, Esteller-Vico A, Conley AJ, Stanley SD, Ball BA. Steroid synthesis and metabolism in equine placenta during placentitis. Reproduction 159:289-302, 2020.
        
        
        25. Fages A, Hanghøj K, Khan N, Gaunitz C, Seguin-Orlando A, Leonardi M, McCrory Constantz C, Gamba C, Al-Rasheid KAS, Albizuri S, Alfarhan AH, Allentoft M, Alquraishi S, Anthony D, Baimukhanov N, Barrett JH, Bayarsaikhan J, Benecke N, Bernáldez-Sánchez E, Berrocal-Rangel L, Biglari F, Boessenkool S, Boldgiv B, Brem G, Brown D, Burger J, Crubézy E, Daugnora L, Davoudi H, de Barros Damgaard P, de  Los Ángeles de Chorro Y de Villa-Ceballos M, Deschler-Erb S, Detry C, Dill N, do  Mar Oom M, Dohr A, Ellingvåg S, Erdenebaatar D, Fathi H, Felkel S, Fernández-Rodríguez C, García-Viñas E, Germonpré M, Granado JD, Hallsson JH, Hemmer H, Hofreiter M, Kasparov A, Khasanov M, Khazaeli R, Kosintsev P, Kristiansen K, Kubatbek T, Kuderna L, Kuznetsov P, Laleh H, Leonard JA, Lhuillier J, Liesau von Lettow-Vorbeck C, Logvin A, Lõugas L, Ludwig A, Luis C, Arruda AM,  Marques-Bonet T, Matoso Silva R, Merz V, Mijiddorj E, Miller BK, Monchalov O, Mohaseb FA, Morales A, Nieto-Espinet A, Nistelberger H, Onar V, Pálsdóttir AH, Pitulko V, Pitskhelauri K, Pruvost M, Rajic Sikanjic P, Rapan Papeša A, Roslyakova N, Sardari A, Sauer E, Schafberg R, Scheu A, Schibler J, Schlumbaum A, Serrand N, Serres-Armero A, Shapiro B, Sheikhi Seno S, Shevnina I, Shidrang S, Southon J, Star B, Sykes N, Taheri K, Taylor W, Teegen WR, Trbojević Vukičević T, Trixl S, Tumen D, Undrakhbold S, Usmanova E, Vahdati A, Valenzuela-Lamas S, Viegas C, Wallner B, Weinstock J, Zaibert V, Clavel B, Lepetz S, Mashkour M, Helgason A, Stefánsson K, Barrey E, Willerslev E, Outram AK, Librado P, Orlando L. Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series. Cell. 2019 May 2. pii: S0092-8674(19)30384-8. doi: 10.1016/j.cell.2019.03.049. [Epub ahead of print] PubMed PMID: 31056281.
        
        
        26. Farries et al. (2019) Analysis of genetic variation contributing to measured speed in Thoroughbreds identifies genomic regions involved in the transcriptional response to exercise. . Anim Genet 2019.
        
        
        27. Farries G, et al. (2019) Expression Quantitative Trait Loci in Equine Skeletal Muscle Reveals Heritable Variation in Metabolism and the Training Responsive Transcriptome. Front Genet 2019.
        
        
        28. Fawcett JA, Sato F, Sakamoto T, Iwasaki WM, Tozaki T, Innan H. 2019. Genome-wide SNP analysis of Japanese Thoroughbred racehorses. PLoS One. 14:e0218407.
        
        
        29. Fedorka CE, Loux SC, Adams AA, Ball BA. Alterations in helper T cell transcripts at the maternal-fetal interface throughout equine gestation. Placenta 89:78-87, 2020.
        
        
        30. Felkel S, Vogl C, Rigler D, Dobretsberger V, Chowdhary BP, Distl O, Fries R, Jagannathan V, Janečka JE, Leeb T, Lindgren G, McCue M, Metzger J, Neuditschko M, Rattei T, Raudsepp T, Rieder S, Rubin CJ, Schaefer R, Schlötterer C, Thaller G, Tetens J, Velie B, Brem G, Wallner B. The horse Y chromosome as an informative marker for tracing sire lines. Sci Rep. 2019 Apr 15;9(1):6095. doi: 10.1038/s41598-019-42640-w. PubMed PMID: 30988347; PubMed Central PMCID: PMC6465346.
        
        
        31. Felkel S, Wallner B, Chuluunbat B, Yadamsuren A, Faye B, Brem G, Walzer C, Burger PA. A First Y-Chromosomal Haplotype Network to Investigate Male-Driven Population Dynamics in Domestic and Wild Bactrian Camels. Front Genet. 2019 May 21;10:423. doi: 10.3389/fgene.2019.00423. eCollection 2019. PubMed PMID: 31178891; PubMed Central PMCID: PMC6537670.
        
        
        32. Finno CJ, Petersen J, Kang M, Park S, Bordbari MH, Durbin-Johnson B, Settles M, Perez-Flores MC, Lee JH, Yamoah EN. Single-cell RNA-seq reveals profound alternations in mechanosensitive but not proprioceptive dorsal root ganglia neurons with vitamin E deficiency. 2019 Nov 22;21:720-735. doi: 10.1016/j.isci.2019.10.064. Epub 2019 Oct 31. PMID: 31733517
        
        
        33. Francois, L., Hoskens, H., Velie, B.D., Stinckens, A., Tinel, S., Lamberigts, C., Peeters, L., Savelkoul, H.E J., Tijhaar, E., Lindgren, G., Janssens, S., Ducro, B.J., Buys, N., Schurink, A. (2019). Genomic Regions Associated with IgE Levels against Culicoides spp. Antigens in Three Horse Breeds. GENES, 10 (8), Art.No. ARTN 597. doi: 10.3390/genes10080597 Open Access
        
        
        34. Gertrud Grilz-Seger, Markus Neuditschko , Anne Ricard , Brandon Velie, Gabriella Lindgren, Matjaz Mesaric , Marko Cotman, Michaela Horna, Max Dobretsberger, Gottfried Brem, Thomas Druml. Genome-Wide Homozygosity Patterns and Evidence for Selection in a Set of European and Near Eastern Horse Breeds. Genes (Basel), 10 (7), 2019.
        
        
        35. Gianini, GM, Valberg SJ, Perumbakkam S, Henry ML, Gardner KL, Penedo C, Finno CJ. Prevalence of the E321G MYH1 variant for immune-mediated myositis and non-exertional rhabdomyolysis in performance subgroups of American Quarter Horses. J Vet Intern Med. 2019;33(2):897-901
        
        
        36. Han et al., (2019) Refinement of Global Domestic Horse Biogeography Using Historic Landrace Chinese Mongolian Populations. J Hered 2019.
        
        
        37. Han H, Wallner B, Rigler D, MacHugh DE, Manglai D, Hill EW. Chinese Mongolian horses may retain early domestic male genetic lineages yet to be discovered. Anim Genet. 2019 May 9. doi: 10.1111/age.12780. [Epub ahead of print] PubMed PMID: 31073991.
        
        
        38. Hill et al., (2019) The contribution of myostatin (MSTN) and additional modifying genetic loci to race distance aptitude in Thoroughbred horses racing in different geographic regions. Equine Vet J 2019.
        
        
        39. Hill EW et al (2019) Racetrack opportunity and success – the ‘Speed Gene’ test. Vet J Ireland Jan 2019
        
        
        40. Holmes CM, Violette N, Miller D, Wagner B, Svansson V, Antczak DF. MHC haplotype diversity in Icelandic horses determined by polymorphic microsatellites. Genes Immun. 2019 8:660-670.
        
        
        41. Kemper, A.M., Drnevich, J., McCue, M.E., McCoy, A.M. Differential gene expression in articular cartilage and subchondral bone of neonatal and adult horses. Genes 2019; 10:745.
        
        
        42. Khanshour, Anas M., Eleanore K. Hempsey, Rytis Juras, and E. Gus Cothran. 2019. Genetic characterization of Cleveland Bay horses. Diversity 11(10), 174; https://doi.org/10.3390/d11100174
        
        
        43. Kingsley NB, Kern C, Creppe C, Hales EN, Zhou H, Kalbfleisch TS, MacLeod JN, Petersen JL, Finno CJ, Bellone RR.   Functionally annotating regulatory elements in the equine genome using histone mark ChIP-Seq.  Genes.  11:3. doi.org/10.3390/genes11010003.
        
        
        44. Klohonatz KM, Coleman SJ, Cameron AD,  Hess AM, Reed KJ, Canovas A, Medrano JF, Islas-Trejo AD, Kalbfleisch T, Bouma GJ, Bruemmer JE.  (2019). Non-coding RNA sequencing of equine endometrium during maternal recognition of pregnancy.  Genes 10: pii: E821. 
        
        
        45. Klohonatz KM, Coleman SJ, Islas-Trejo AD, Medrano, Hess AM, JF Kalbfleisch T, Thomas MG, Bouma GJ, Bruemmer JE.  (2019). Coding RNA sequencing of equine endometrium during maternal recognition of pregnancy.  Genes 10: E749. Doi:  10.3390/genes10100749.
        
        
        46. Klohonatz KM, Nulton LC, Hess AM, Bouma GJ, Bruemmer JE (2019) The role of embryo contact and focal adhesions during maternal recognition of pregnancy. PLoS ONE 14(3): e0213322. https://doi.org/10.1371/journal.pone.0213322
        
        
        47. Kobayashi I, Akita M, Takasu M, Tozaki T, Kakoi H, Nakamura K, Senju N, Matsuyama R, Horii Y. 2019. Genetic characteristics of feral Misaki horses based on polymorphisms of microsatellites and mitochondrial DNA. J Vet Med Sci. 81:707-711.
        
        
        48. Liesbeth François, Hanne Hoskens, Brandon D Velie, Anneleen Stinckens, Susanne Tinel, Chris Lamberigts, Liesbet Peeters, Huub F J Savelkoul, Edwin Tijhaar, Gabriella Lindgren, Steven Janssens, Bart J Ducro, Nadine Buys, Anouk Schurink. Genomic Regions Associated With IgE Levels Against Culicoides Spp. Antigens in Three Horse Breeds. Genes (Basel), 10 (8) 2019.
        
        
        49. Loux SC, Dini P, El-Sheikh Ali H, Kalbfleisch T, Ball BA. Characterization of the placental transcriptome through mid-late gestation in the mare. PLOS ONE 14(11): e0224497,
        
        
        50. Loux SC, Fernandes CB, Dini P, Wang K, Wu X, Baxter D, Troedsson MH, Squires EL, Ball BA. Small RNA expression in the chorioallantois, endometrium and serum of mares following experimental induction of placentitis.  Rep Fertil Devel 31:1144-1156, 2019.
        
        
        51. Marina Solé, Michela Ablondi, Amrei Binzer-Panchal, Brandon D Velie, Nina Hollfelder, Nadine Buys, Bart J Ducro, Liesbeth François, Steven Janssens, Anouk Schurink, Åsa Viklund, Susanne Eriksson, Anders Isaksson, Hanna Kultima, Sofia Mikko, Gabriella Lindgren. Inter- And Intra-Breed Genome-Wide Copy Number Diversity in a Large Cohort of European Equine Breeds. BMC Genomics, 20 (1), 759, 2019 (Oct 22).
        
        
        52. Marquardt SA, Wilcox CV, Burns EN, Peterson JA, Finno CJ*. Previously identified genetic variants in ADGRL3 are not associated with risk for equine degenerative myeloencephalopathy across breeds. Genes (Basel) 2019;10(9):
        
        
        53. McClellan, A., Paterson, Y. Z., Paillot, R. & Guest, D. Equine fetal, adult and embryonic stem cell derived tenocytes are all immune privileged but exhibit different immune suppressive properties in vitro. Stem Cells Dev, doi:10.1089/scd.2019.0120 (2019).
        
        
        54. McCoy, A.M., Beeson, S.K., Rubin, C.-J., Andersson, L., Caputo, P., Lykkjen, S., Moore, A., Piercy, R.J., Mickelson, J.R., McCue, M.E. Identification and validation of genetic variants predictive of gait in Standardbred horses. PLoS Genet. 2019; 15(5):e1008146.
        
        
        55. McCoy, A.M., Norton, E.M., Kemper, A.M., Beeson, S.K., Mickelson, J.R., McCue, M.E. SNP-based heritability and genetic architecture of tarsal osteochondrosis in North American Standardbred horses. Anim Genet. 2019; 50(1):78-81.
        
        
        56. McGivney BA, et al. (2019) A genomic prediction model for racecourse starts in the Thoroughbred horse. Anim Genet 2019.
        
        
        57. Merina Shrestha, Marina Solé, Bart J Ducro, Marie Sundquist, Ruth Thomas, Anouk Schurink, Susanne Eriksson, Gabriella Lindgren. Genome-wide Association Study for Insect Bite Hypersensitivity Susceptibility in Horses Revealed Novel Associated Loci on Chromosome 1. J Anim Breed Genet, 2019 Sep 5 [Online ahead of print].
        
        
        58. Michela Ablondi, Åsa Viklund, Gabriella Lindgren, Susanne Eriksson, Sofia Mikko. Signatures of Selection in the Genome of Swedish Warmblood Horses Selected for Sport Performance. BMC Genomics, 20 (1), 717, 2019 (Sep 18).
        
        
        59. Musiał A.D., Ropka-Molik K., Jaworska J., Piórkowska K., Stefaniuk-Szmukier M., ACTN3 genotype distribution across horses representing different utility types and breeds, Molecular Biology Reports. 46 (6), 5795-5803.
        
        
        60. Norton EM, Avila F, Mickelson JR and McCue ME (2019). Evaluation of an HMGA2 variant for pleiotropic effects on height and insulin sensitivity in Welsh ponies. Journal of Veterinary Internal Medicine, 2019, Jan 21. doi: 10.1111/jvim.15403.
        
        
        61. Norton EM, Mickelson JR and McCue ME. (2019). Heritability of metabolic traits associated with equine metabolic syndrome in Welsh ponies and Morgan horses. Equine Veterinary Journal 2019 Jul;51(4):475-480. doi: 10.1111/evj.13053. 
        
        
        62. Norton EM, Schultz N, Geor R, McFarlane D, Mickelson JR and McCue ME. (2019).  Genome-wide association analyses of equine metabolic syndrome phenotypes in Welsh pones and Morgan horses. Genes 2019, 10, 893; doi:10.3390/genes10110893
        
        
        63. Raudsepp T, Finno CJ, Bellone RR, Petersen JL. Ten years of the horse reference genome: insights into equine biology, domestication and population dynamics in the post-genome era.  Animal Genetics.  50:569-597. doi.org/10.1111/age.12857.
        
        
        64. Rivas VN, Aleman M, Peterson JA, Dahlgren AR, Hales EN, Finno CJ*. TRIM39-RPP21 Variants (∆19InsCCC) Are Not Associated with Juvenile Idiopathic Epilepsy in Egyptian Arabian Horses. Genes (Basel). 2019 Oct 16;10(10). pii: E816. doi: 10.3390/genes10100816.
        
        
        65. Rockwell, H et al. Genetic investigation of equine recurrent uveitis in Appaloosa horses”, Animal Genetics (2020), 51 (1):111-116.  https://www.ncbi.nlm.nih.gov/pubmed/31793009
        
        
        66. Ropka-Molik K., Musiał A. D., Stefaniuk-Szmukier M., Velie B., 2019, The genetics of racing performance in Arabian horses, Internatioal Journal of Genomics, doi.org/10.1155/2019/9013239
        
        
        67. Ropka-Molik K., Stefaniuk-Szmukier M., Musiał A. D., Piórkowska K., Szmatoła T., 2019, Sequence analysis and expression profiling of the equine ACTN3 gene during exercise in Arabian horses, Gene, 685, 149-155.
        
        
        68. Ropka-Molik K., Stefaniuk-Szmukier M., Szmatoła T., Piórkowska K., Bugno-Poniewierska M., 2019, The use of the SLC16A1 gene as a potential marker to predict race performance in Arabian horses, BMC Genetics, 20,
        
        
        69. Ruiz A, Castaneda C, Raudsepp T, Tibary A. 2019. Azoospermia and Y chromosome-autosome translocation in a Friesian stallion. Journal of Equine Veterinary Science 2019 Nov;82:102781. doi: 10.1016/j.jevs.2019.07.002. Epub 2019 Jul 11..
        
        
        70. Sadeghi R, Moradi-Shahrbabak M, Miraei Ashtiani SR, Schlamp F, Cosgrove EJ, Antczak DF. Genetic Diversity of Persian Arabian Horses and Their Relationship to Other Native Iranian Horse Breeds. J Hered. 2019 110:173-182.
        
        
        71. Singer-Berk, M et al. “Additional evidence for DDB2 T338M as a genetic risk factor for ocular squamous cell carcinoma in horses", International Journal of Genomics, (2019) Article ID 3610965 https://www.hindawi.com/journals/ijg/2019/3610965/
        
        
        72. Singer-Berk, M et al. “Genetic risk for squamous cell carcinoma of the nictitating membrane parallels that of the limbus in Haflinger horses”, Animal Genetics, (2018), 49: 457-460. https://onlinelibrary.wiley.com/doi/abs/10.1111/age.12695
        
        
        73. Solé, M., Ablondi, M., Binzer-Panchal, A. et al. Inter- and intra-breed genome-wide copy number diversity in a large cohort of European equine breeds. BMC Genomics 20, 759 (2019). https://doi.org/10.1186/s12864-019-6141-z
        
        
        74. Stefaniuk-Szmukier M., Ropka-Molik K., Piórkowska K., Bugno-Poniewierska M., 2019. The expression profile of genes involved in osteoclastogenesis detected in whole blood of Arabian horses during 3 years of competing at race track, Research in Veterinary Science, 123, 59-64.
        
        
        75. Stefaniuk-Szmukier M., Szmatoła T., Łątka J., Długosz B., Ropka-Molik K., 2019, The blood and muscle expression pattern of equine TCAP gene during the race track training of Arabian horses, Animals, 9, 574.
        
        
        76. Stejskalova K, Cvanova M, Oppelt J, Janova E, Horecky C, Horecka E, Knoll A, Leblond A, Horin P.Genetic susceptibility to West Nile virus infection in Camargue horses. Res Vet Sci. 2019 Jun;124:284-292. doi: 10.1016/j.rvsc.2019.04.004. Epub 2019 Apr 10.
        
        
        77. Stejskalova K, Janova E, Horecky C, Horecka E, Vaclavek P, Hubalek Z, Relling K, Cvanova M, D'Amico G, Mihalca AD, Modry D, Knoll A, Horin P. Associations between the presence of specific antibodies to the West Nile Virus infection and candidate genes in Romanian horses from the Danube delta. Mol Biol Rep. 2019 Aug;46(4):4453-4461. doi:
        
        
        78. Tezuka A, Takasu M, Tozaki T, Nagano AJ. 2019. Genetic analysis of Taishu horses on and off Tsushima Island: Implications for conservation. J Equine Sci. 30:33-40.
        
        
        79. Todd, K. Jadervkist Fegraeus, P.C. Thomson, C.F. Ihler, E. Strand, G. Lindgren and B.D. Velie. Premie race participation is associated with increased career longevity and prize money earnings in Norwegian-Swedish Coldblooded Trotters. Acta Agri Scand, Section A: Animal Sci, Volume 68 (2), 2019, pages 112-116. doi: 10.1080/09064702.2018.1563211.
        
        
        80. Tozaki T, Kikuchi M, Kakoi H, Hirota K, Nagata S, Yamashita D, Ohnuma T, Takasu M, Kobayashi I, Hobo S, Manglai D, Petersen JL. 2019. Genetic diversity and relationships among native Japanese horse breeds, the Japanese Thoroughbred and horses outside of Japan using genome-wide SNP data. Anim Genet. 2019. 50:449-459.
        
        
        81. Tozaki T, Miyake T, Kikuchi M, Kakoi H, Hirota KI, Kusano K, Ishikawa Y, Nomura M, Kushiro A, Nagata SI. 2019. Heritability estimates of fractures in Japanese Thoroughbred racehorses using a non-linear model. J Anim Breed Genet. 136:199-204.
        
        
        82. Tozaki T, Ohnuma A, Takasu M, Kikuchi M, Kakoi H, Hirota KI, Kusano K, Nagata SI. 2019. Droplet digital PCR detection of the erythropoietin transgene from horse plasma and urine for gene-doping control. Genes (Basel). 10: E243.
        
        
        83. Twenter H, Klohonatz K, Davis K, Bass L, Coleman SJ, Bouma GJ, Bruemmer JE.  (2019) Transfer of microRNAs from epididymal epithelium to equine spermatozoa. J, Equine Vet. Sci. https://doi.org/10.1016./j.jevs.2019.102841.  
        
        
        84. Ueda T, Tozaki T, Nozawa S, Kinoshita K, Gawahara H. 2019. Identification of metabolomic changes in horse plasma after racing by liquid chromatography-high resolution mass spectrometry as a strategy for doping testing. J Equine Sci. 30:55-61.
        
        
        85. Valberg SJ, Soave K, Williams ZJ, Perumbakkam S, Schott M, Finno CJ, Gardner KL, Petersen JL, Fenger F, Autry JM, Thomas DD. Coding sequences of sarcoplasmic reticulum calcium ATPase regulatory peptides and expression of calcium regulatory genes in recurrent exertional rhabdomyolysis. J Vet Intern Med. 2019;33(2): 933-941 doi: 10.1111/jvim.15425.
        
        
        86. Velie BD, Jäderkvist Fegraeus K, Ihler CF, Lindgren G, Strand E. Competition lifespan survival analysis in the Norwegian-Swedish Coldblooded Trotter racehorse. Equine Vet J. 2019: 51 (2), 206-211. doi: 10.1111/evj.12989.
        
        
        87. Velie, P M Smith, C T Fjordbakk, M Solé, K Jäderkvist Fegraeus, M K Rosengren, K H Røed, C F Ihler, G Lindgren, E Strand^. Exploring the Genetics Underpinning Dynamic Laryngeal Collapse Associated With Poll Flexion in Norwegian-Swedish Coldblooded Trotter Racehorses. Equine Vet J. 2019 Aug 28 [Online ahead of print].
        
        
        88. Yokomori T, Tozaki T, Mita H, Miyake T, Kakoi H, Kobayashi Y, Kusano K, Itou T. 2019. Heritability estimates of the position and number of facial hair whorls in Thoroughbred horses. BMC Res Notes. 12:346.
        
        
        89. 
            
            
            
            1. Rexroad C, Vallet J, Matukumalli LK, Reecy J, Bickhart D, Blackburn H, Boggess M, Cheng H, Clutter A, Cockett N, Ernst C, Fulton JE, Liu J, Lunney J, Neibergs H, Purcell C, Smith TPL, Sonstegard T, Taylor J, Telugu B, Eenennaam AV, Tassell CPV, Wells K. Genome to Phenome: Improving Animal Health, Production, and Well-Being - A New USDA Blueprint for Animal Genome Research 2018-2027. Front Genet. 10:327. 2019. doi: 10.3389/fgene.2019.00327.
            
            
            2. Murphy, T. W., Stewart, W. C., Notter, D. R., Mousel, M. R., Lewis, G. S., and Taylor, J. B. Evaluation of Rambouillet, Polypay, and Romanov-White Dorper x Rambouillet ewes mated to terminal sires in an extensive rangeland production system: Body weight and wool characteristics. J. Anim. Sci. 97(4):1568-1577. 2019.
            
            
            3. Silva, M. G., Madsen, S., Dassanayake, R. P., Mousel, M. R., Knowles, D. P. Tissue inhibitor of metalloproteinase-1 and interleukin-10 in serum from naïve and scrapie infected sheep. Vet. Anim. Sci. 7:100056. 2019.
            
            
            4. Koltes, J.E., Cole, J.B., Serão, N.V.L., McCue, M., Woodward, J., Zhang, H., McKay, S., Lunney, J., Kramer, L., Schroeder, M., Clemmens, R., Murdoch, B., Rexroad, C.E., III, Rosa, G.J.M., Mateescu, R., White, S.N., Worku, M., Reecy, J.M. A vision for development and utilization of high-throughput phenotyping and big data analytics in livestock. Frontiers in Genetics. 10:1197. 2019.
            
            
            5. Wise, L.N., Kappmeyer, L.S., Knowles, D.P., White, S.N. Evolution and diversity of the EMA families of the divergent equid parasites, Theileria equi and haneyi. Infect Genet Evol. 68:153-160. 2019.
            
            
            6. Sears, K.P., Kappmeyer, L.S., Wise, L.N., Silva. M., Ueti, M.W., White, S., Reif, K.E., Knowles, D.P. Infection dynamics of Theileria equi and Theileria haneyi, a newly discovered apicomplexan of the horse. Vet Parasitol. 271:68-75. 2019.
            
            
            7. Osei, B., Worku, M., Eluka‐Okoludoh, Adjei‐Fremah, S., Asiamah, E., E., Ekwemalor, K., & Mulakala, B. (2018). Galectin Secretion and Modulation in Sheep Blood. Journal of Molecular Biology Research, 8(1), 183. 2018.
            
            
            8. Estrada-Reyes Z.M., O. Rae, M.B. Jimenez Medrano, J.D. Leal-Gutiérrez, and G. Mateescu. 2019. Association study reveals Th17, Treg and Th2 loci related to resistance to Haemonchus contortus in Florida Native sheep. J. Anim. Sci. 97(11):4428-4444. doi.org/10.1093/jas/skz299
            
            
            9. Estrada-Reyes Z.M., Y. Tsukahara, R.R. Amadeu, A.L. Goetsch, T.A. Gipson, T. Sahlu, R. Puchala, Z. Wang, S.P. Hart, and G. Mateescu. 2019. Signatures of selection for resistance to Haemonchus contortus in sheep and goats. BMC Genomics. (2019) 20:735. doi:10.21203/rs.2.9164/v5
            
            
            10. Estrada-Reyes Z.M., Y. Tsukahara, A.L. Goetsch, T.A. Gipson, T. Sahlu, R. Puchala, and G. Mateescu. 2019. Association analysis of immune response loci related to Haemonchus contortus exposure in sheep and goats using a targeted approach. Livestock Science. 228:109-119 doi.org/10.1016/j.livsci.2019.08.005
            
            
            11. Zhang, Y.Y., Han D.P., Dong, X.G., Wang, J.K., Chen, J.F., Yao, Y.Z., Darwish, H.Y.A., Liu, W.-S., Deng, X.M. (2019) Genome-wide profiling of RNA editing sites in sheep. Journal of Animal Science and Biotechnology 10, 31.Liu, W.-S. (2019) Mammalian sex chromosome structure, gene content and function in male fertility. Annu Rev Anim Biosci.7,103-124.
            
            
            12. Hughes, C. K., Maalouf, S.W., Liu, W.-S., Pate, J.L. (2019) Molecular profiling demonstrates modulation of immune cell function and matrix remodeling during luteal rescue. Biology of Reproduction 100(6), 1581–1596.
            
            
            13. 
                

                Beiki H, Liu H, Huang J, Manchanda N, Nonneman D, Smith TPL, Reecy JM, Tuggle CK.

                
                

                Improved annotation of the domestic pig genome through integration of Iso-Seq and RNA-seq data. BMC Genomics. 2019 May 7;20(1):344. doi: 10.1186/s12864-019-5709-y.

                
                
            
            
            
            
        
        
        
        
    
    
    
    

03/16/2021

04/22/2022

03/17/2023