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United States Department of Agriculture

Agricultural Research Service

Gregory P Harhay
Computational Biologist


Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)
Comparative methylome analysis of the occasional ruminant respiratory pathogen Bibersteinia trehalosi -
Anton, B.P., Harhay, G.P., Smith, T.P.L., Blom, J., Roberts, R.J. 2016. Comparative methylome analysis of the occasional ruminant respiratory pathogen Bibersteinia trehalosi. PLoS One. 11(8): e0161499.
Observations on macrolide resistance and susceptibility testing performance in field isolates collected from clinical bovine respiratory disease cases -
DeDonder, K.D., Harhay, D.M., Apley, M.D., Lubbers, B.V., Clawson, M.L., Schuller, G., Harhay, G.P., White, B.J., Larson, R.L., Capik, S.F., Riviere, J.E., Kalbfleisch, T., Tessman, R.K. 2016. Observations on macrolide resistance and susceptibility testing performance in field isolates collected from clinical bovine respiratory disease cases. Veterinary Microbiology. 192:186-193.
Haptoglobin concentrations from shipping through sickness and recovery in cattle either mass-medicated with gamithromycin or sham-treated -
Complete and closed genome sequences of 10 Salmonella enterica subsp. enterica serovar Anatum isolated from human and bovine sources Reprint Icon -
Nguyen, S.V., Harhay, D.M., Bono, J.L., Smith, T.P.L., Fields, P.I., Dinsmore, B.A., Santovenia, M., Kelley, C.M., Wang, R., Bosilevac, J.M., Harhay, G.P. 2016. Complete and closed genome sequences of 10 Salmonella enterica subsp. enterica serovar Anatum isolated from human and bovine sources. Genome Announcements. Vol. 4(3): e00447-16. doi: 10.1128/genomeA.00447-16.
Resolving bovine viral diarrhea virus subtypes from persistently infected US beef calves with complete genome sequence -
Workman, A.M., Heaton, M.P., Harhay, G.P., Smith, T.P.L., Grotelueschen, D.M., Sjeklocha, D.B., Brodersen, B.W., Petersen, J.L., Chitko-McKown, C.G. 2016. Resolving bovine viral diarrhea virus subtypes from persistently infected U.S. beef calves with complete genome sequence. Journal of Veterinary Diagnostic Investigation. 28(5):519-528.
Mobilome differences between Salmonella enterica serovars Anatum and Typhimurium isolated from cattle and humans and potential impact on virulence -
Nguyen, S.V., Bono, J.L., Smith, T.P.L., Kelley, C.M., Wang, R., Harhay, G.P., Harhay, D.M. 2016. Mobilome differences between Salmonella enterica serovars Anatum and Typhimurium isolated from cattle and humans and potential impact on virulence. [Abstract] In proceedings: 60th Wind River Conference on Procaryotic Biology, 2016 June 1-5. Estes Park, Colorado. p. 67.
Complete closed genome sequences of Salmonella enterica subsp. enterica serotypes Anatum, Montevideo, Typhimurium and Newport, isolated from beef, cattle, and humans Reprint Icon -
Harhay, D.M., Bono, J.L., Smith, T.P., Fields, P.I., Dinsmore, B.A., Santovenia, M., Kelley, C.M., Wang, R., Harhay, G.P. 2016. Complete closed genome sequences of Salmonella enterica subsp. enterica serotypes Anatum, Montevideo, Typhimurium and Newport, isolated from beef, cattle, and humans. Genome Announcements. 4(1):e01683-15. doi:10.1128/genomeA.01683-15.
A searchable, whole genome resource designed for protein variant analysis in diverse lineages of U.S. beef cattle -
Heaton, M.P., Kalbfleisch, T.S., Carnahan, J.K., Smith, T.P.L., Harhay, G.P., Simpson, B., Qiu, J. 2015. A searchable, whole genome resource designed for protein variant analysis in diverse lineages of U.S. beef cattle [abstract]. International Plant and Animal Genome XXIV Conference Proceedings, January 9-13, 2016, San Diego, CA. Poster #P0506.
Effects of pseudorabies virus infection on the tracheobronchial lymph node transcriptome -
Miller, L.C., Bayles, D.O., Zanella, E.L., Lager, K.M., 2016. Effects of pseudorabies virus infection on the tracheobronchial lymph node transcriptome. Bioinformatics and Biology Insights. 9(Suppl 2):25-36.
Full-length coding sequence for 12 bovine viral diarrhea virus isolates from persistently infected cattle in a feedyard in Kansas -
Workman, A.M., Harhay, G.P., Heaton, M.P., Grotelueschen, D.M., Sjeklocha, D.B., Smith, T.P.L. 2015. Full-length coding sequence for 12 bovine viral diarrhea virus isolates from persistently infected cattle in a feedyard in Kansas. Genome Announcements. 3(3):e00487-15. doi:10.1128/genomeA.00487-15.
Comparative analysis of twenty-four complete aenome aequences of Salmonella enterica Serotypes Anatum, Montevideo, Typhimurium and Newport isolated from ground beef or asymptomatic cattle on farm or at harvest -
Harhay, D.M., Bono, J.L., Smith, T.P., Kalbfleisch, T., Kelley, C., Wang, R., Harhay, G.P. 2015. Comparative analysis of twenty-four complete aenome aequences of Salmonella enterica Serotypes Anatum, Montevideo, Typhimurium and Newport isolated from ground beef or asymptomatic cattle on farm or at harvest [abstract]. American Society for Microbiology 115th General Meeting. Poster No. 397, Session 029.
Complete closed genome sequences of a Mannheimia haemolytica serotype A1 leukotoxin deletion mutant and its wild type parent strain -
Heaton, M.P., Harhay, G.P., Smith, T.P.L., Bono, J.L., Chitko-McKown, C.G. 2015. Complete closed genome sequences of a Mannheimia haemolytica serotype A1 leukotoxin deletion mutant and its wild-type parent strain. Genome Announcements. 3(3):e00417-15. DOI: 10.1128/genomeA.00417-15.
Joint analysis of bacterial DNA methylation, predicted promoter and regulation motifs for biological significance -
Harhay, G.P., Anton, B.P., Smith, T.P.L. [abstract]. 2015. Joint analysis of bacterial DNA methylation, predicted promoter and regulation motifs for biological significance. American Society for Microbiology 2015, 115th General Meeting, May 30-June 2, 2015, New Orleans, LA. Poster #3468.
Identification of a mannheimia haemolytica genetic subtype that causes bovine respiratory disease -
Clawson, M.L., Murray, R.W., Sweeney, M.T., Apley, M.D., DeDonder, K.D., Capik, S., Larson, R., Lubbers, B.V., Kalbfleisch, T.S., Schuller, G., Harhay, G.P., Heaton, M.P., Chitko-McKown, C.G., Workman, A.M., Harhay, D.M., Bono, J.L., Smith, T.P.L. [abstract]. 2015. Identification of a mannheimia haemolytica genetic subtype that causes bovine respiratory disease. American Society for Microbiology 2015, 115th General Meeting, May 30-June 2, 2015, New Orleans, LA. Poster #1410.
Genomic comparison of Salmonella enterica serotypes commonly associated with cattle and beef – Analysis of variation in virulence potential -
Harhay, D.M., Bono, J.L., Wang, R., Smith, T.P., Harhay, G.P., Kalbfleisch, T., Wheeler, T.L. 2015. Genomic comparison of Salmonella enterica serotypes commonly associated with cattle and beef – Analysis of variation in virulence potential. [Abstract]. Beef Industry Safety Summit. http://www.bifsco.org/2015researchsessionabstracts.aspx.
Cytokine profiles from shipping through sickness and recovery in cattle either mass-medicated with gamithromycin or sham-treated -
Chitko-McKown, C.G., DeDonder, K.D., Bennett, G.L., Apley, M.D., Harhay, G.P., Kuehn, L.A., White, B.J., Larson, R.L., Capik, S.F., Lubbers, B.V., Workman, A.M. 2014. Cytokine profiles from shipping through sickness and recovery in cattle either mass-medicated with gamithromycin or sham-treated [abstract]. Conference on Research Workers in Animal Disease, December 7-9, 2014, Chicago, Illinois. Paper No. 148.
Evolutionary characterization of pig interferon-inducible transmembrane gene family and member expression dynamics in tracheobronchial lymph nodes of pigs infected with swine respiratory disease viruses -
Miller, L.C., Jiang, Z., Sang, Y., Harhay, G.P., Lager, K.M. 2014. Evolutionary characterization of pig interferon-inducible transmembrane gene family and member expression dynamics in tracheobronchial lymph nodes of pigs infected with swine respiratory disease viruses. Veterinary Immunology and Immunopathology. 159(3-4):180-191.
Complete closed genome sequences of four Mannheimia varigena isolates from cattle with shipping fever -
Harhay, G.P., Murray, R.W., Lubbers, B., Griffin, D., Koren, S., Phillippy, A.M., Harhay, D.M., Bono, J.L., Clawson, M.L., Heaton, M.P., Chitko-McKown, C.G., Smith, T.P. 2014. Complete closed genome sequences of four Mannheimia varigena isolates from cattle with shipping fever. Genome Announcements. 2(1):e00088-14.
Complete closed genome sequences of three Bibersteinia trehalosi nasopharyngeal isolates from cattle with shipping fever -
Harhay, G.P., McVey, D.S., Koren, S., Phillippy, A.M., Bono, J.L., Harhay, D.M., Clawson, M.L., Heaton, M.P., Chitko-McKown, C.G., Korlach, J., Smith, T.P. 2014. Complete closed genome sequences of three Bibersteinia trehalosi nasopharyngeal isolates from cattle with shipping fever. Genome Announcements. 2(1):e00084-14.
Characterization of microbiomes related to respiratory disease in cattle -
Smith, T.P., Kim, M.S., Myer, P.R., McDaneld, T.G., Kuehn, L.A., Clawson, M.L., Harhay, D.M., Harhay, G.P. 2014. Characterization of microbiomes related to respiratory disease in cattle [Abstract]. Proceedings of the Plant and Animal Genome XXII Conference, January 11-15, 2014, San Diego, CA. Poster W759.
Evolutionary characterization of pig interferon-inducible transmembrane gene family and member expression dynamics in tracheobronchial lymph nodes of pigs infected with swine respiratory disease viruses -
Miller, L.C., Jiang, Z., Sang, Y., Harhay, G.P., Lager, K.M. 2014.Evolutionary characterization of pig interferon-inducible transmembrane gene family and member expression dynamics in tracheobronchial lymph nodes of pigs infected with swine respiratory disease viruses. International Plant & Animal Genome XXII. P595.
Evolutionary characterization of pig interferon-inducible transmembrane gene family and member expression dynamics in tracheobronchial lymph nodes of pigs infected with swine respiratory disease viruses -
Reducing assembly complexity of microbial genomes with single-molecule sequencing -
Koren, S., Harhay, G.P., Smith, T.P.L., Bono, J.L., Harhay, D.M., McVey, D.S., Radune, D., Bergman, N.H., Phillippy, A.M. 2013. Reducing assembly complexity of microbial genomes with single-molecule sequencing. Genome Biology. 14:R101. DOI: 10.1186/GB-2013-14-9-R101.
Effects of TMEM154 haplotypes 1 and 3 on susceptibility to ovine progressive pneumonia virus following natural exposure in sheep -
Leymaster, K.A., Chitko-McKown, C.G., Clawson, M.L., Harhay, G.P., Heaton, M.P. 2013. Effects of TMEM154 haplotypes 1 and 3 on susceptibility to ovine progressive pneumonia virus following natural exposure in sheep. Journal of Animal Science. 91(11):5114-5121.
Small ruminant lentivirus genetic subgroups associate with sheep TMEM154 genotypes -
Sider, L.H., Heaton, M.P., Chitko-Mckown, C.G., Harhay, G.P., Smith, T.P.L., Leymaster, K.A., Laegreid, W.W., and Clawson, M.L. 2013. Small ruminant lentivirus genetic subgroups associate with sheep TMEM154 genotypes. Veterinary Research. 44:64. DOI: 10.1186/1297-9716-44-64.
The methylome and virulence of bovine respiratory disease bacterial pathogens -
Harhay, G.P. 2013. The methylome and virulence of bovine respiratory disease bacterial pathogens. American Society for Microbiology. Presentation in WS-24, Studying Whole-Genome Microbial Epigenetics.
Complete closed genome sequences of Mannheimia haemolytica serotypes A1 and A6 isolated from cattle -
Harhay, G.P., Koren, S., Phillippy, A.M., McVey, D.S., Kuszak, J., Clawson, M.L., Harhay, D.M., Heaton, M.P., Chitko-McKown, C.G., Smith, T.P.L. 2013. Complete closed genome sequences of Mannheimia haemolytica serotypes A1 and A6 isolated from cattle. Genome Announcements. 1(3):e00188-13. DOI: 10.1128/GENOMEA.00188-13.
Evolutionary characterization of pig interferon-inducible transmembrane gene family and member expression dynamics in tracheobronchial lymph nodes of pigs infected with influenza A virus -
Miller, L.C., Jiang, Z., Sang, Y., Harhay, G.P., Lager, K.M. 2013. Evolutionary characterization of pig interferon-inducible transmembrane gene family and member expression dynamics in tracheobronchial lymph nodes of pigs infected with influenza A virus. Second Annual Great Plains Emerging Infectious Diseases Conference. p. 23.
Evolutionary characterization of pig interferon-inducible transmembrane gene family and member expression dynamics in tracheobronchial lymph nodes of pigs infected with swine respiratory disease viruses -
Reactomes of porcine alveolar macrophages infected with porcine reproductive and respiratory syndrome virus Reprint Icon -
Jiang, Z., Zhou, X., Michal, J.J., Wu, X.-L., Zhang, L., Zhang, M., Ding, B., Liu, B., Manoranjan, V.S., Neill, J.D., Harhay, G.P., Kehrli, Jr., M.E., Miller, L.C. 2013. Reactomes of porcine alveolar macrophages infected with porcine reproductive and respiratory syndrome virus. PLoS One. 8(3):e59229.
Salmonella virulence, genomics and interactions with the immune system -
Harhay, D.M., Smith, T.P., Harhay, G.P., Bono, J.L., Bosilevac, J.M. 2013. Salmonella virulence, genomics and interactions with the immune system. Meeting Abstract. The Beef Industry Safety Summit, March 13-15, 2013, Dallas Texas, FLASHDRIVE.
Genetic testing for TMEM154 mutations associated with lentivirus susceptibility in sheep -
Heaton, M.P., Kalbfleisch, T.S., Petrik, D.T., Simpson, B., Kijas, J.W., Clawson, M.L., Chitko MckKown, C.G., Harhay, G.P., Leymaster, K.A. 2013. Genetic testing for TMEM154 mutations associated with lentivirus susceptibility in sheep. PLoS One. 8(2):e55490. doi:10.1371/journal.pone.0055490.
Application of SMRT genome sequencing to reveal the methylomes of bacteria associated with respiratory disease outbreaks in beef cattle -
Harhay, G.P., McVey, D.S., Korlach, J., Roberts, R., Chitko-McKown, C.G., Clawson, M.L., Heaton, M.P., Harhay, D.M., Smith, T.P.L., Anton, B.P. 2013. Application of SMRT genome sequencing to reveal the methylomes of bacteria associated with respiratory disease outbreaks in beef cattle [Abstract]. Advances in Genome Biology and Technology Conference, February 20-23, 2013, Marco Island, FL. Page 99.
Genetic testing for TMEM154 mutations associated with lentivirus susceptibility in sheep -
Heaton, M.P., Kalbfleisch, T., Petrik, D.T., Simpson, B., Kijas, J., Clawson, M.L., Chitko-McKown, C.G., Leymaster, K.A., Harhay, G.P. 2013. Genetic testing for TMEM154 mutations associated with lentivirus susceptibility in sheep [abstract]. International Plant & Animal Genome XXI Conference. No. P0625.
Comparative transcriptome response in swine tracheobronchial lymph nodes to viral infection -
Miller, L.C., Harhay, G.P., Kehrli, Jr., M.E., Lager, K.M. 2013. Comparative transcriptome response in swine tracheobronchial lymph nodes to viral infection [abstract]. International Plant & Animal Genome XXI, January 12-16, 2013, San Diego, California. Paper No. W756.
Next-generation sequencing of the porcine skeletal muscle transcriptome for computational prediction of microRNA gene targets -
McDaneld, T.G., Smith, T.P.L., Harhay, G.P., and Wiedmann, R.T. 2012. Next-generation sequencing of the porcine skeletal muscle transcriptome for computational prediction of microRNA gene targets. PLoS One. 7(7):e42039. doi:10.1371/journal.pone.0042039.
Phylogenetic clades of ovine progressive pneumonia virus (OPPV) associate with sheep TMEM154 genotypes -
Sider, L.H., Clawson, M.L., Heaton, M.P., Chitko Mckown, C.G., Harhay, G.P., Smith, T.P.L., Leymaster, K.A. 2012. Phylogenetic clades of ovine progressive pneumonia virus (OPPV) associate with sheep TMEM154 genotypes. The 58th Genomic Congress, September 11-14, 2012. Foz de Iguacu, Brazil. Poster No. GM001.
Comparison of bacterial communities in faeces of beef cattle fed diets containing corn and wet distillers grain with solubles Reprint Icon -
Durso, L.M., Wells, J., Harhay, G.P., Rice, W.C., Kuehn, L.A., Bono, J.L., Shackelford, S.D., Wheeler, T.L., Smith, T.P. 2012. Comparison of bacterial communities in faeces of beef cattle fed diets containing corn and wet distillers grain with solubles. Letters in Applied Microbiology. 55(2):109-14. DOI: 10.1111/J.1472-765X.2012.03265.X.
Reduced OPP susceptibility in naturally exposed lambs with homozygous TMEM154 K35 genotypes -
Chitko Mckown, C.G., Leymaster, K.A., Heaton, M.P., Clawson, M.L., Harhay, G.P. 2012. Reduced OPP susceptibility in naturally exposed lambs with homozygous TMEM154 K35 genotypes [abstract]. Immunology 2012. The 99th Annual Meeting of the American Association for Immunology, May 4-8, 2012, Boston, Massachusetts. Page 275. Abstract No. 170.3. Poster No. P1246.
Phylogeny of Shiga toxin-producing Escherichia coli O157 isolated from cattle and clinically ill humans Reprint Icon -
Bono, J.L., Smith, T.P., Keen, J.E., Harhay, G.P., McDaneld, T.G., Mandrell, R.E., Jung, W., Besser, T.E., Gerner-Smidt, P., Bielaszewska, M., Karch, H., Clawson, M.L. 2012. Phylogeny of Shiga toxin-producing Escherichia coli O157 isolated from cattle and clinically ill humans. Molecular Biology and Evolution. 29(8):2047-2062. doi: 10.1093/molbev/mss072.
Application of combined SMRT and long-read pyrosequencing to produce reference genome sequences of bacteria associated with respiratory disease outbreaks in beef cattle -
Harhay, G.P., Mcvey, D.S., Kitzmiller, A., Clamp, M., Osborne, B., Dwan, C., Zhang, J., Sisneros, N., Wang, S., Peluso, P., Bono, J.L., Chitko Mckown, C.G., Clawson, M.L., Heaton, M.P., Harhay, D.M., Smith, T.P.L. [abstract]. 2012. Application of combined SMRT and long-read pyrosequencing to produce reference genome sequences of bacteria associated with respiratory disease outbreaks in beef cattle. Advances in Genome Biology and Technology, February 15-18, 2012, Marco Island, Florida. Poster No. 129.
Enabling next-gen sequencing and analysis at the USDA-ARS U.S. Meat Animal Research Center with MiniLIMS -
Reduced lentivirus susceptibility in sheep with TMEM154 mutations Reprint Icon -
Heaton, M.P., Clawson, M.L., Chitko-Mckown, C.G., Leymaster, K.A., Smith, T.P.L., Harhay, G.P., White, S.N., Herrmann-Hoesing, L.M., Mousel, M.R., Lewis, G.S., Kalbfleisch, T.S., Keen, J.E., Laegreid, W.W. 2012. Reduced lentivirus susceptibility in sheep with TMEM154 mutations. PLoS Genetics. 8(1): e1002467. DOI: 10.1371/journal.pgen.1002467.
Comparison of immune transcriptome response following infection with PRRSV, PCV2 and SIV -
Miller, L.C., Harhay, G., Kehrli, M., Lager, K. 2011. Comparison of immune transcriptome response following infection with PRRSV, PCV2 and SIV [abstract]. 2011 International PRRS Symposium. Paper No. 51. p. 68.
Immune transcriptome response to PRRSV infection -
Miller, L.C., Harhay, G.P., Lager, K.M., Kehrli, Jr., M.E. 2011. Immune transcriptome response to PRRSV infection [abstract]. XIIth International Nidovirus Symposium. p. 79.
Gene expression response of multidrug resistant Salmonella enterica serovar Newport to simulated multiple hurdle beef carcass processing interventions -
Harhay, D.M., Smith, T.P., Harhay, G.P. 2011. Gene expression response of multidrug resistant Salmonella enterica serovar Newport to simulated multiple hurdle beef carcass processing interventions. In: Proceedings of the American Society for Microbiology. 111th General Meeting of the American Society for Microbiology, May 21-24, 2011, New Orleans, Louisiana. 2011 CDROM. Meeting Abstract K-2692.
Towards an understanding of how Salmonella potentially evades beef carcass processing interventions -
Brichta-Harhay, D.M., Gragg, S.E., Smith, T.P.L., Arthur, T.M., Bosilevac, J.M., Kalchayanand, N., Schmidt, J.W., Wang, R., Shackelford, S.D., Wheeler, T.L., Brashears, M.M., Brooks, J.C., Brown, T.R., Harhay, G.P., Loneragan, G.H. 2011. Towards an understanding of how Salmonella potentially evades beef carcass processing interventions [abstract]. 2011 Beef Industry Safety Summit. Abstract No. 2.
Biosurveillance at the United States Meat Animal Research Center -
Harhay, G.P., Harhay, D.M., Chitko Mckown, C.G., Smith, T.P. 2011. Biosurveillance at the United States Meat Animal Research Center [abstract]. Global Biosurveillance: Enabling Science and Technology 2nd Biothreat Nonproliferation Conference. Abstract No. 12.
In depth global analysis of transcript abundance levels in porcine alveolar macrophages following infection with porcine reproductive and respiratory syndrome virus -
Miller, L.C., Neill, J.D., Harhay, G.P., Lager, K.M., Laegreid, W.W., Kehrli, Jr., M.E. 2010. In-depth global analysis of transcript abundance levels in porcine alveolar macrophages following infection with porcine reproductive and respiratory syndrome virus. Advances in Virology. 2010:Article 864181. Available: http://downloads.hindawi.com/journals/av/2010/864181.pdf.
Virulence-associated and antibiotic resistance genes of microbial populations in cattle feces analyzed using a metagenomic approach Reprint Icon -
Durso, L.M., Harhay, G.P., Bono, J.L., Smith, T.P. 2011. Virulence-associated and antibiotic resistance genes of microbial populations in cattle feces analyzed using a metagenomic approach. Journal of Microbiological Methods. 84: 278-282.
Bacterial community analysis of beef cattle feedlots reveals that pen surface is distinct from feces -
Durso, L.M., Harhay, G.P., Smith, T.P., Bono, J.L., Desantis, T.Z., Clawson, M.L. 2011. Bacterial community analysis of beef cattle feedlots reveals that pen surface is distinct from feces. Foodborne Pathogens and Disease. 8(5):647-649. Available: DOI: 10.1089/fpd.2010.0774.
An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation -
Harhay, G.P., Smith, T.P.L., Alexander, L.J., Haudenschild, C.D., Keele, J.W., Matukumalli, L.K., Schroeder, S.G., Van Tassell, C.P., Gresham, C.R., Bridges, S.M., Burgess, S.C., Sonstegard, T.S. 2010. An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation. Genome Biology [online serial]. 11:R102.
Transcript Expression Analysis in Tracheobronchial Lymph Nodes of Pseudorabies Virus Infected Pigs -
Miller, L.C., Harhay, G.P., Bayles, D.O., Zanella, E.L., Lager, K.M. 2010. Transcript expression analysis in tracheobronchial lymph nodes of pseudorabies virus infected pigs [abstract]. Conference of Research Workers in Animal Diseases. Paper No. 115P.
Transcript Expression Analysis in Tracheobronchial Lymph Nodes of Pseudorabies Virus Infected Pigs -
Miller, L.C., Harhay, G.P., Bayles, D.O., Zanella, E.L., Lager, K.M. 2010. Transcript expression analysis in tracheobronchial lymph nodes of pseudorabies virus infected pigs [abstract]. 45th Meeting of the United States-Japan Cooperative Program in Natural Resources Panel of Animal and Avian Health. p. 11.
Transcript Expression Analysis in Tracheobronchial Lymph Nodes of Pseudorabies Virus Infected Pigs -
Miller, L.C., Harhay, G.P., Bayles, D.O., Zanella, E.L., Lager, K.M. 2010. Transcript Expression Analysis in Tracheobronchial Lymph Nodes of Pseudorabies Virus Infected Pigs [abstract]. 32nd Conference for the International Society for Animal Genetics. Paper No. P105.
Animal-to-Animal Variation in Fecal Microbial Diversity among Beef Cattle -
Durso, L.M., Harhay, G.P., Smith, T.P.L., Bono, J.L., Desantis, T.Z., Harhay, D.M., Andersen, G.L., Keen, J.E., Laegreid, W.W., Clawson, M.L. 2010. Animal-to-Animal Variation in Fecal Microbial Diversity among Beef Cattle. Applied and Environmental Microbiology. 76(14):4858-4862.
Comparison of cattle fecal communities from animals fed diets containing corn and distiller's grains -
Durso, L.M., Harhay, G.P., Wells, J., Bono, J.L., Riethoven, J.M., Shackelford, S.D., Wheeler, T.L., Smith, T.P. 2010. Comparison of cattle fecal communities from animals fed diets containing corn and distiller's grains. PS.25.018, Abstract #393A. Abstract for Microbial Ecology International Symposium, Seattle, WA, Aug. 22-27, 2010. Abstract Book, Pg. 128
In Depth Global Analysis of Transcript Abundance Levels Following Infection with Porcine Reproductive and Respiratory Syndrome Virus -
Miller, L.C., Harhay, G.P., Lager, K.M., Neill, J.D., Kehrli, Jr., M.E. 2010. In-Depth Global Analysis of Transcript Abundance Levels Following Infection with Porcine Reproductive and Respiratory Syndrome Virus [abstract]. In: Proceedings of the 9th International Positive Strand RNA Virus Symposium, May 17-21, 2010, Atlanta, Georgia. p. 54.
A Digital Gene Expression-Based Bovine Gene Atlas Evaluating 92 Adult, Juvenile and Fetal Cattle Tissues -
Harhay, G.P., Alexander, L.J., Smith, T.P.L., Matukumalli, L.K., Schroeder, S.G., Sonstegard, T.S. 2010. A Digital Gene Expression-Based Bovine Gene Atlas Evaluating 92 Adult, Juvenile and Fetal Cattle Tissues [abstract]. In: Proceedings of the Advances in Genome Biology & Technology Conference, February 24-27, 2010, Marco Island, Florida. p. 67.
De novo Reconstruction of the Pig Skeletal Muscle Transcriptome for Identification of MicroRNA Gene Targets -
McDaneld, T.G., Wiedmann, R.T., Harhay, G.P., Smith, T.P.L. 2010. De novo Reconstruction of the Pig Skeletal Muscle Transcriptome for Identification of MicroRNA Gene Targets (abstract). In: Proceedings of the Advances in Genome Biology & Technology Conference, February 24-27,2010, Marco Island, Florida. p. 114.
Information Theoretical Analysis of a Bovine Gene Atlas Reveals Chromosomal Regions with Tissue Specific Gene Expression. -
Sonstegard, T.S., Harhay, G.P., Alexander, L.J., Schroeder, S.G., Keele, J.W., Matukumalli, L., Bridges, S., Burgess, S., Van Tassell, C.P., Smith, T.P. 2010. Information Theoretical Analysis of a Bovine Gene Atlas Reveals Chromosomal Regions with Tissue Specific Gene Expression. Plant and Animal Genome VX Conference Abstracts.
The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution Reprint Icon -
Elsik, C.G., Gibbs, R., Skow, L., Tellam, R., Weinstock, G., Worley, K., Kappes, S.M., Green, R.D., Alexander, L.J., Bennett, G.L., Carroll, J.A., Chitko Mckown, C.G., Hamernik, D.L., Harhay, G.P., Keele, J.W., Liu, G., Macneil, M.D., Matukumalli, L.K., Rijnkels, M., Roberts, A.J., Smith, T.P., Snelling, W.M., Stone, R.T., Waterman, R.C., White, S.N. 2009. The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution. Science. 324:522-528.
Bacterial Communities Associated with Shiga-Toxigenic E. coli O157:H7 (STEC O157) in Beef Cattle Feedlot Environments -
Durso, L.M., Harhay, G.P., Bono, J.L., Smith, T.P., Laegreid, W.W., Keen, J.E., Clawson, M.L. 2009. Bacterial Communities Associated with Shiga-Toxigenic E. coli O157:H7 (STEC O157) in Beef Cattle Feedlot Environments [abstract]. Microbial Ecology 57(3):569.
Prevalence of the prion gene E211K variant in U.S. cattle -
Heaton, M.P., Keele, J.W., Harhay, G.P., Richt, J., Koohmaraie, M., Wheeler, T.L., Shackelford, S.D., Casas, E., King, D.A., Sonstegard, T.S., Van Tassell, C.P., Neibergs, H.L., Chase, C.C., Kalbfleisch, T.S., Smith, T.P., Clawson, M.L., Laegreid, W.W. 2008. Prevalence of the prion gene E211K variant in U.S. cattle. BioMed Central (BMC) Veterinary Research [journal online]. 4:25. Available: (http://www.biomedcentral.com/1746-6148/4/25).
A sequencing strategy for identifying variation throughout the prion gene of BSE-affected cattle -
Clawson, M.L., Heaton, M.P., Keele, J.W., Smith, T.P., Harhay, G.P., Richt, J., Laegreid, W.W. 2008. A sequencing strategy for identifying variation throughout the prion gene of BSE-affected cattle. BMC Research Notes [journal online]. 1:32. Available: http://www.biomedcentral.com/1756-0500/1/32.
In depth global analysis of gene expression levels in porcine alveolar macrophages following infection with porcine reproductive and respiratory syndrome virus -
Miller, L., Harhay, G., Lager, K., Kehrli Jr., M., Laegreid, W., Neill, J. 2008. In depth global analysis of gene expression levels in porcine alveolar macrophages following infection with porcine reproductive and respiratory syndrome virus [abstract]. ARK-Genomics Conference 2008: 3rd International Symposium on Animal Functional Genomics. Paper No. ISAFG-P22. p. 38.
Microbial Community Structure of Feedlot Cattle Feces -
Durso, L.M., Harhay, G.P., Clawson, M.L., Laegreid, W.W., Bono, J.L., Keen, J.E., Smith, T.P. Microbial community structure of feedlot cattle feces. In: Proceedings of the 108th General Meeting of the American Society for Microbiology, June 1-5, 2008, Boston, Massachusetts. 2008 CDROM.
Effect of porcine reproductive and respiratory syndrome virus on porcine alveolar macrophage function as determined using serial analysis of gene expression (SAGE) -
Miller, L.C., Harhay, G.P., Lager, K.M., Smith, T.P., Neill, J.D. 2008. Effect of porcine reproductive and respiratory syndrome virus on porcine alveolar macrophage function as determined using serial analysis of gene expression (SAGE). Developments in Biologicals. 132:169-174.
Gene Expression Profiling of Porcine Reproductive and Respiratory Syndrome Virus Infected Porcine Alveolar Macrophages -
Miller, L.C., Harhay, G.P., Lager, K.M., Smith, T.P., Neill, J.D. 2007. Gene expression profiling of PRRSV-infected porcine alveolar macrophages [abstract]. Porcine Reproductive and Respiratory Syndrome International Symposium. Paper No. 47.
Prevalence of the prion gene E211K variant in U.S. cattle -
Heaton, M.P., Keele, J.W., Harhay, G.P., Richt, J., Koohmaraie, M., Wheeler, T.L., Shackelford, S.D., Casas, E., King, D.A., Sonstegard, T.S., Van Tassell, C.P., Neibergs, H.L., Chase, C.C., Kalbfleisch, T.S., Smith, T.P., Clawson, M.L., Laegreid, W.W. 2008. Prevalence of the prion gene E211K variant in U.S. cattle (abstract). Plant and Animal Genome XVI Conference. Poster No. P538.
Integrating the USMARC genetic map for the pig with the pig physical map -
Wiedmann, R.T., Freking, B.A., Nonneman, D.J., Snelling, W.M., Keele, J.W., Harhay, G.P., Rohrer, G.A. Integrating the USMARC genetic map for the pig with the pig physical map. 2008. Annual International Plant & Animal Genome Conference. Poster No. P565, pg 259.
Description and analysis of the Bovine Gene Atlas - An extensive compendium of bovine transcript profiles -
Harhay, G.P., Keele, J.W., Smith, T.P., Alexander, L.J., Matukumalli, L.K., Schroeder, S.G., Liu, G., Van Tassell, C.P., Sonstegard, T.S. 2008. Description and analysis of the Bovine Gene Atlas - An extensive compendium of bovine transcript profiles (abstract). Plant and Animal Genome XVI Conference. Poster No. P516.
Effect of porcine reproductive and respiratory syndrome virus on porcine alveolar macrophage function as determined using serial analysis of gene expression (SAGE) -
Neill, J.D., Miller, L.C., Harhay, G.P., Lager, K.M. 2007. Effect of porcine reproductive and respiratory syndrome virus on porcine alveolar macrophage function as determined using serial analysis of gene expression (SAGE) [abstract]. International Symposium on Animal Genomics for Animal Health. Paper No. PA-070. p. 58.
Creation of a Gene Atlas in cattle using sequence-based transcriptional profiling -
Sonstegard, T.S., Keele, J.W., Harhay, G.P., Smith, T.P., Matukumalli, L.K., Van Tassell, C.P., Liu, G., Alexander, L.J. 2007. Creation of a Gene Atlas in cattle using sequence-based transcriptional profiling. [abstract] Joint Abstracts of the American Dairy Science and Society of Animal Science.
Prion gene haplotypes of U.S. cattle -
Clawson, M.L., Heaton, M.P., Keele, J.W., Smith, T.P., Harhay, G.P., Laegreid, W.W. 2006. Prion gene haplotypes of U.S. cattle. BioMed Central (BMC) Genetics. 7:51.
Polymorphisms and haplotype structure of bovine PRND (doppel) and PRNT -
Laegreid, W.W., Clawson, M.L., Smith, T.P., Harhay, G.P., Keele, J.W., Heaton, M.P. 2007. Polymorphisms and haplotype structure of bovine PRND (doppel) and PRNT [abstract]. Plant and Animal Genome XV Conference. Poster No. P535.
An updated USMARC genetic map for the pig integrated with the pig physical map -
Rohrer, G.A., Snelling, W.M., Freking, B.A., Nonneman, D.J., Harhay, G.P., Keele, J.W. 2007. An updated USMARC genetic map for the pig integrated with the pig physical map [abstract]. Plant and Animal Genome XV Conference. Poster No. W421.
A rapid sequence-based method for comprehensive polymorphism identification within a 25.2-kb region of the bovine prion gene in BSE-affected cattle -
Clawson, M.L., Heaton, M.P., Keele, J.W., Smith, T.P., Harhay, G.P., Laegreid, W.W. 2007. A rapid sequence-based method for comprehensive polymorphism identification within a 25.2-kb region of the bovine prion gene in BSE-affected cattle [abstract]. Plant and Animal Genome XV Conference. Poster No. P533.
A marker set for parentage-based DNA traceback in beef and dairy cattle -
Heaton, M.P., Snelling, W.M., Smith, T.P., Keele, J.W., Harhay, G.P., Wiedmann, R.T., Bennett, G.L., Freking, B.A., Van Tassell, C.P., Sonstegard, T.S., Gasbarre, L.C., Moore, S.S., Murdoch, B., Mckay, S.D., Kalbfleisch, T., Laegreid, W.W. 2007. A marker set for parentage-based DNA traceback in beef and dairy cattle [abstract]. Plant and Animal Genome XV Conference. Poster No. P516.
CHARACTERIZATION OF 954 BOVINE FULL-CDS CDNA SEQUENCES -
Harhay, G.P., Sonstegard, T.S., Keele, J.W., Heaton, M.P., Clawson, M.L., Snelling, W.M., Wiedmann, R.T., Van Tassell, C.P., Smith, T.P. 2005. Characterization of 954 bovine full-CDS cDNA sequences. Biomed Central (BMC) Genomics 6:166 (11 pp).
IDENTIFICATION OF GENETIC MARKERS FOR FAT DEPOSITION AND MEAT TENDERNESS ON BOVINE CHROMOSOME 5: DEVELOPMENT OF A LOW DENSITY SNP MAP -
Stone, R.T., Casas, E., Smith, T.P.L., Keele, J.W., Harhay, G.P., Bennett, G.L., Koohmaraie, M., Wheeler, T.L., Shackelford, S.D., Snelling, W.M. 2005. Identification of genetic markers for fat deposition and meat tenderness on bovine chromosome 5: Development of a low-density single nucleotide polymorphism map. Journal of Animal Science. 83:2280-2288.
LINKAGE MAPPING BOVINE EST-BASED SNP -
Snelling, W.M., Casas, E., Stone, R.T., Keele, J.W., Harhay, G.P., Bennett, G.L., Smith, T.P. 2005. Linkage mapping bovine EST-based SNP. Biomed Central (BMC) Genomics 6:74.
INTEGRATING LINKAGE AND RADIATION HYBRID MAPPING DATA FOR BOVINE CHROMOSOME 15 -
Snelling, W.M., Gautier, M., Keele, J.W., Smith, T.P., Stone, R.T., Harhay, G.P., Bennett, G.L., Ihara, N., Takasuga, A., Takeda, H., Sugimoto, Y., Eggen, A. Integrating linkage and radiation hybrid mapping data for bovine chromosome 15. Biomed Central (BMC) Genomics. 5:77. 2004.
USE OF BOVINE SNP MARKERS TO VERIFY SAMPLE TRACKING IN BEEF PROCESSING -
Heaton, M.P., Keen, J.E., Clawson, M.L., Harhay, G.P., Bauer, N., Shultz, C., Green, B.T., Durso, L.M., Chitko Mckown, C.G., Laegreid, W.W. Use of bovine SNP markers to verify sample tracking in beef processing [abstract]. Plant and Animal Genome Conference Proceedings. p. 124.
USE OF BOVINE SINGLE NUCLEOTIDE POLYMORPHISM MARKERS TO VERIFY SAMPLE TRACKING IN BEEF PROCESSING -
Heaton, M.P., Keen, J.E., Clawson, M.L., Harhay, G.P., Bauer, N., Schultz, C., Green, B.T., Durso, L.M., Chitko Mckown, C.G., Laegreid, W.W. 2005. Use of bovine single nucleotide polymorphism markers to verify sample tracking in beef processing. Journal of the American Veterinary Medical Association 226(8):1311-1314.
DATABASE DIRECTED FULL-LENGTH CDNA GENERATION USING EST DATA FROM NORMALIZED BOVINE CDNA LIBRARIES -
Harhay, G.P., Smith, T.P., Sonstegard, T.S., Clawson, M.L. 2004. Database directed full-length cDNA generation using EST data from normalized bovine cDNA libraries. Proc., 29th International Conference on Animal Genetics (ISAG), Tokyo, Japan. September 11-16, 2004. Abstract A022, p. 37.
DATABASE DIRECTED FULL-LENGTH CDNA GENERATION FROM NORMALIZED BOVINE CDNA LIBRARIES -
Harhay, G.P., Sonstegard, T.S., Clawson, M.L., Smith, T.P. 2004. Database directed full-length cDNA generation from normalized bovine cDNA libraries. International Genome Sequencing and Analysis Conference XVI, Washington, DC. September 27-30, 2004. Poster Abstract #49.
PRODUCTION OF EST FROM CDNA LIBRARIES DERIVED FROM IMMUNOLOGICALLY ACTIVATED BOVINE ABOMASUM -
Sonstegard, T.S., Van Tassell, C.P., Matukumalli, L.K., Harhay, G.P., Bosak, S., Rubenfield, M., Gasbarre, L.C. 2004. Production of est from cdna libraries derived from immunologically activated bovine abomasum. Germplasm Release.
PRODUCTION OF EST FROM CDNA LIBRARIES DERIVED FROM IMMUNOLOGICALLY ACTIVATED BOVINE SMALL INTESTINE -
Sonstegard, T.S., Van Tassell, C.P., Matukumalli, L.K., Harhay, G.P., Bosak, S., Rubenfield, M., Gasbarre, L.C. 2004. Production of est from cdna libraries derived from immunologically activated bovine small intestine. Germplasm Release.
PRODUCTION OF A PORCINE-HUMAN COMPARATIVE MAP BASED ON THE PORCINE GENETIC MAP AND HUMAN GENOME SEQUENCE -
Rohrer, G.A., Nonneman, D.J., Freking, B.A., Harhay, G.P., Snelling, W.M., Keele, J.W. 2002. Production of a porcine-human comparative map based on the porcine genetic map and human genome sequence. Plant and Animal Genome Conference Proceedings. Abstract P612.
POSITIONAL CANDIDATE GENE SELECTION FROM LIVESTOCK EST DATABASES USING GENE ONTOLOGY -
Harhay, G.P., Keele, J.W. 2003. Positional candidate gene selection from livestock EST databases using Gene Ontology. Bioinformatics. 19:249-255.
SELECTION AND USE OF SNP MARKERS FOR ANIMAL IDENTIFICATION AND PATERNITY ANALYSIS IN U.S. BEEF CATTLE -
Mammalian Genome. 2002. v. 13. p. 272-281.
SELECTION AND USE OF SINGLE NUCLEOTIDE POLYMORPHISM (SNP) MARKERS FOR ANIMAL IDENTIFICATION AND PATERNITY ANALYSIS IN U.S. BEEF CATTLE -
Last Modified: 8/26/2016
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