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ARS Home Plains Area Clay Center, Nebraska U.S. Meat Animal Research Center Genetics and Animal Breeding People





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Aaron  Dickey    Biologist (Computational/Bioinformatics) Dr. Dickey serves the principal investigators from all research units at the US Meat Animal Research Center as a Biologist (Computational) focusing on big ‘omics’ data access and use. Example data types include mass spectra, nucleic acid sequence and genetic markers. Dr. Dickey develops computational tools to efficiently analyze these data and trains scientists in big data analysis methods. **Post-Training Feedback** Rocky 2019 Poster
 Publications(Clicking on the reprint iconReprint Icon  will take you to the publication reprint.)Comparative genomics of extra intestinal pathogenic E. coli from human clinical and food samples-(Abstract Only)Identification of dominant factors contributing to persistence of third-generation cephalosporin-resistant Salmonella at a beef cattle feedyard-(Abstract Only) Schmidt, J.W., Murray, S.A., Dickey, A.M., Wheeler, T.L., Harhay, D.M., Arthur, T.M. 2023. Identification of dominant factors contributing to persistence of third-generation cephalosporin-resistant Salmonella at a beef cattle feedyard. [Abstract]. International Association for Food Protection Proceedings. T4-10.Distribution of extremely heat-resistant Escherichia coli in the beef production and processing continuum-(Peer Reviewed Journal) Guragain, M., Schmidt, J.W., Dickey, A.M., Bosilevac, J.M. 2023. Distribution of extremely heat-resistant Escherichia coli in the beef production and processing continuum. Journal of Food Protection. 86(1). Article 100031. https://doi.org/10.1016/j.jfp.2022.100031.Detection of Mycoplasma bovirhinis and bovine coronavirus in an outbreak of bovine respiratory disease in nursing beef calves-(Peer Reviewed Journal) McDaneld, T.G., Workman, A.M., Chitko-McKown, C.G., Kuehn, L.A., Dickey, A.M., Bennett, G.L. 2022. Detection of Mycoplasma bovirhinis and bovine coronavirus in an outbreak of bovine respiratory disease in nursing beef calves. Frontiers in Microbiomes. 1. Article 1051241. https://doi.org/10.3389/frmbi.2022.1051241.Whole genome sequencing of Moraxella bovis strains from North America reveals two genotypes with different genetic determinants-(Peer Reviewed Journal) Wynn, E.L., Hille, M.M., Loy, J.D., Schuller, G., Kuhn, K.L., Dickey, A.M., Bono, J.L., Clawson, M.L. 2022. Whole genome sequencing of Moraxella bovis strains from North America reveals two genotypes with different genetic determinants. BMC Microbiology. 22(1). Article 258. https://doi.org/10.1186/s12866-022-02670-3.Characterization of Escherichia coli harboring colibactin genes (clb) isolated from beef production and processing systems-(Peer Reviewed Journal) Guragain, M., Schmidt, J.W., Kalchayanand, N., Dickey, A.M., Bosilevac, J.M. 2022. Characterization of Escherichia coli harboring colibactin genes (clb) isolated from beef production and processing systems. Nature Scientific Reports. 12. Article 5305. https://doi.org/10.1038/s41598-022-09274-x.Twenty-four-month longitudinal study suggests little to no horizontal gene transfer in situ between third-generation cephalosporin-resistant Salmonella and third-generation cephalosporin-resistant Escherichia coli-(Peer Reviewed Journal) Schmidt, J.W., Murray, S.A., Dickey, A.M., Wheeler, T.L., Harhay, D.M., Arthur, T.M. 2022. Twenty-four-month longitudinal study suggests little to no horizontal gene transfer in situ between third-generation cephalosporin-resistant Salmonella and third-generation cephalosporin-resistant Escherichia coli in a beef cattle feedyard. Journal of Food Protection. 85(2):323-335. https://doi.org/10.4315/JFP-21-371.Classification of small ruminant lentivirus subtype A2, subgroups 1 and 2 based on whole genome comparisons and complex recombination patterns [version 2; revised]-(Peer Reviewed Journal)Using genomics to measure phenomics: Repeatability of bull prolificacy in multiple-bull pastures-(Peer Reviewed Journal) Bennett, G.L., Keele, J.W., Kuehn, L.A., Snelling, W.M., Dickey, A.M., Light, D.E., Cushman, R.A., McDaneld, T.G. 2021. Using genomics to measure phenomics: Repeatability of bull prolificacy in multiple-bull pastures. Agriculture. 11(7). Article 603. https://doi.org/10.3390/agriculture11070603.Using genomics to measure phenomics: Repeatability of bull prolificacy in multiple-bull pastures-(Pre-print Publication) Bennett, G.L., Keele, J.W., Kuehn, L.A., Snelling, W.M., Dickey, A.M., Light, D.E., Cushman, R.A., McDaneld, T.G. 2021. Using genomics to measure phenomics: Repeatability of bull prolificacy in multiple-bull pastures. Agriculture. 11(7). Article 603. https://doi.org/10.3390/agriculture11070603.MALDI-TOF MS biomarker detection models to distinguish RTX toxin phenotypes of Moraxella bovoculi strains are enhanced using calcium chloride supplemented agar-(Peer Reviewed Journal) Hille, M.M., Clawson, M.L., Dickey, A.M., Lowery, J.H., Loy, J.D. 2021. MALDI-TOF MS biomarker detection models to distinguish RTX toxin phenotypes of Moraxella bovoculi strains are enhanced using calcium chloride supplemented agar. Frontiers in Cellular and Infection Microbiology. 11. Article 632647. https://doi.org/10.3389/fcimb.2021.632647.Classification of small ruminant lentivirus subtype A2, subgroups 1 and 2 based on whole genome comparisons and complex recombination patterns-(Rapid Release Publication) Dickey, A.M., Smith, T.P.L., Clawson, M.L., Heaton, M.P., Workman, A.M. 2020. Classification of small ruminant lentivirus subtype A2, subgroups 1 and 2 based on whole genome comparisons and complex recombination patterns. F1000Research. 9:1449. https://doi.org/10.12688/f1000research.27898.1.Differences between predicted outer membrane proteins of genotype 1 and 2 Mannheimia haemolytica-(Peer Reviewed Journal) Clawson, M.L., Schuller, G., Dickey, A.M., Bono, J.L., Murray, R.W., Sweeney, M.T., Apley, M.D., DeDonder, K.D., Capik, S.F., Larson, R.L., Lubbers, B.V., White, B.J., Blom, J., Chitko-McKown, C.G., Brichta-Harhay, D.M., Smith, T.P.L. 2020. Differences between predicted outer membrane proteins of genotype 1 and 2 Mannheimia haemolytica. BMC Microbiology. 20:250. https://doi.org/10.1186/s12866-020-01932-2.Potential relationship of the porcine muscle thanatotranscriptome to pork quality-(Abstract Only) King, D.A., Dickey, A.M., Shackelford, S.D., Wheeler, T.L., Rohrer, G.A., Nonneman, D.J. 2020. Potential relationship of the porcine muscle thanatotranscriptome to pork quality. [Abstract]. International Congress of Meat Science and Technology Proceedings. Poster No. 206.Rapid differentiation of Moraxella bovoculi genotypes 1 and 2 using MALDI-TOF mass spectrometry profiles-(Peer Reviewed Journal) Hille, M., Dickey, A.M., Robbins, K., Clawson, M.L., Loy, J.D. 2020. Rapid differentiation of Moraxella bovoculi genotypes 1 and 2 using MALDI-TOF mass spectrometry profiles. Journal of Microbiological Methods. 173:105942. https://doi.org/10.1016/j.mimet.2020.105942.Identification of pan and core genomes of Moraxella bovis-(Abstract Only) Clawson, M.L., Schuller, G., Dickey, A.M., Hille, M.M., Wynn, E.L., Loy, J.D. 2020. Identification of pan and core genomes of Moraxella bovis [abstract]. American Society for Microbiology Microbe, June 18-22, 2020, Chicago, Illinois. Poster No. 6697.Digestive tract microbiota of beef cattle that differed in feed efficiency-(Peer Reviewed Journal) Freetly, H.C., Dickey, A., Lindholm-Perry, A.K., Thallman, R.M., Keele, J.W., Foote, A.P., Wells, J.E. 2020. Digestive tract microbiota of beef cattle that differed in feed efficiency. Journal of Animal Science. 98(2):1-16. https://doi.org/10.1093/jas/skaa008.Next-generation sequencing identifies polyunsaturated fatty acid responsive genes in the juvenile rat cerebellum-(Peer Reviewed Journal) Mehus, A.A., Dickey, A.M., Smith, T.P., Yeater, K.M., Picklo, M.J. 2019. Next-generation sequencing identifies polyunsaturated fatty acid responsive genes in the juvenile rat cerebellum. Nutrients. https://doi.org/10.3390/nu11020407.The porcine muscle thanatotranscriptome-(Abstract Only) Nonneman, D.J., Dickey, A.M., King, D.A. 2020. The porcine muscle thanatotranscriptome [abstract]. In: Proceedings of XXVIII Plant and Animal Genome Conference, Swine Workshop. San Diego, CA, 11-15 Jan 2020. W1030.Pipelines, workflows and virtualization to build institutional informatics capacity-(Abstract Only) Dickey, A.M., Nonneman, D.J., Freetly, H.C., Workman, A.M., Kuehn, L.A. 2019. Pipelines, workflows and virtualization to build institutional informatics capacity [abstract]. In: Proceedings of Rocky 2019, December 5-7, 2019, Aspen/Snowmass, Colorado. Paper No. P22.Unexpected high intragenomic variation in two of three major pest thrips species does not affect ribosomal internal transcribed spacer 2 (ITS2) utility for thrips identification-(Abstract Only) Kumar, V., Dickey, A.M., Seal, D., Shatters, R.G., Osborne, L., McKenzie, C.L. 2019. Unexpected high intragenomic variation in two of three major pest thrips species does not affect ribosomal internal transcribed spacer 2 (ITS2) utility for thrips identification [abstract]. Entomological Society of America Annual Meeting. D#3467.Digestive tract microbiota of beef cattle that differed in feed efficiency-(Abstract Only) Freetly, H.C., Wells, J., Dickey, A., Lindholm-Perry, A., Keele, J., Foote, A. 2019. Digestive tract microbiota of beef cattle that differed in feed efficiency [abstract]. 2019 Congress on Gastrointestinal Function, April 15-17, 2019, Chicago, IL. p. 41-42.Whole genome sequencing of Moraxella bovoculi reveals high genetic diversity and evidence for interspecies recombination at multiple loci-(Peer Reviewed Journal) Dickey, A.M., Schuller, G., Loy, J.D., Clawson, M.L. 2018. Whole genome sequencing of Moraxella bovoculi reveals high genetic diversity and evidence for interspecies recombination at multiple loci. PLoS One. 13(12):e0209113. https://doi.org/10.1371/journal.pone.0209113.Transcriptome profiling of olfactory epithelium in normal cycling and acyclic gilts-(Abstract Only) Nonneman, D.J., Dickey, A.M., Lents, C.A. 2019. Transcriptome profiling of olfactory epithelium in normal cycling and acyclic gilts [abstract]. Journal of Animal Science. 97(Supplement 2):125. Abstract 213. https://doi.org/10.1093/jas/skz122.222.First complete genome sequence of a genotype A2, subgroup 4 small ruminant lentivirus-(Peer Reviewed Journal) Workman, A.M., Clawson, M.L., Heaton, M.P., Dickey, A.M. 2018. First complete genome sequence of a genotype A2, subgroup 4 small ruminant lentivirus. MICROBIOLOGY RESOURCE ANNOUNCEMENTS. 7(19):e01337-18. https://doi.org/10.1128/MRA.01337-18.Complete genome sequence of Moraxella bovis strain Epp63, an etiologic agent of infectious bovine keratoconjunctivitis-(Peer Reviewed Journal) Loy, J.D., Dickey, A.M., Clawson, M.L. 2018. Complete genome sequence of Moraxella bovis strain Epp63, an etiologic agent of infectious bovine keratoconjunctivitis. Microbiology Resource Announcements. 7(8):1-2. https://doi.org/10.1128/MRA01004.18.Succession of ruminal bacterial species and fermentation characteristics in preweaned Brangus calves-(Proceedings) Smith, K.E., Garza, A.L., Butterfield, K.M., Dickey, A.M., Lindholm-Perry, A.K., Wells, J. E., Freetly, H.C., Lodge-Ivey, S.L. 2018. Succession of ruminal bacterial species and fermentation characteristics in preweaned Brangus calves. Translational Animal Science. 2(Supplement 1):S48-S52. https://doi.org/10.1093/tas/txy043.Genomic signatures of a Mannheimia haemolytica lineage associated with bovine respiratory disease-(Abstract Only) Clawson, M.L., Schuller, G., Dickey, A.M., Murray, R.W., Sweeney, M.T., Apley, M.D., DeDonder, K.D., Capik, S.F., Larson, R.L., Lubbers, B.V., White, B.J., Blom, J., Brichta-Harhay, D.M., Smith, T.P. 2018. Genomic signatures of a Mannheimia haemolytica lineage associated with bovine respiratory disease [abstract]. Society for Molecular Biology & Evolution General Meeting. Abstract POA-070:44. Available: http://evolgen.biol.se.tmu.ac.jp/SMBE2018/POA.pdfMatrix-assisted laser desorption/ionization time-of-flight mass spectrometry identification of Moraxella bovoculi and Moraxella bovis isolates from cattle-(Peer Reviewed Journal) Robbins, K., Dickey, A.M., Clawson, M.L., Loy, J.D. 2018. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry identification of Moraxella bovoculi and Moraxella bovis isolates from cattle. Journal of Veterinary Diagnostic Investigation. p. 1-4. Available:  jvdi.sagepub.com. https://doi.org/10.1177/1040638718789725.Evaluation of a functional variant assay for selecting beef cattle-(Proceedings) Snelling, W.M., McDaneld, T.G., Kuehn, L.A., Dickey, A.M., Bennett, G.L. 2018. Evaluation of a functional variant assay for selecting beef cattle. In: Proceedings World Congress of Genetics Applied in Livestock Production. 11-16 Feb 2018. Auckland, New Zealand. Volume Technologies - Genotyping p.589. Available: www.wcgalp.org.Unexpected high intragenomic variation in two of three major pest thrips species does not affect ribosomal internal transcribed spacer 2 (ITS2)utility for thrips identification-(Peer Reviewed Journal) Kumar, V., Dickey, A.M., Seal, D.R., Shatters, R.G., Osborne, L.S., McKenzie, C.L. 2017. Unexpected high intragenomic variation in two of three major pest thrips species does not affect ribosomal transcribed spacer 2(ITS2) utility for thrips identification. International Journal of Molecular Sciences. 18(10):2100.Rediscovering digitules in Aphidomorpha and the question of homology among Sternorrhyncha (Insecta: Hemiptera)-(Peer Reviewed Journal) Metz, M., Miller, D.R., Dickey, A.M., Bauchan, G.R., Ochoa, R., Skvarla, M.J., Miller, G.L. 2017. Rediscovering digitules in Aphidomorpha and the question of homology among Sternorrhyncha (Insecta: Hemiptera). ZooKeys. 4276(1):139-144.Determination of succession of rumen bacterial species in nursing beef calves-(Abstract Only) Smith, K.E., Garza, A.L., Butterfield, K.M., Dickey, A.M., Lindholm-Perry, A.K., Wells, J., Freetly, H.C., Lodge-Ivey, S.L. 2017. Determination of succession of rumen bacterial species in nursing beef calves [abstract]. 2017 Congress on Gastrointestinal Function, April 10-12, 2017, Chicago, IL. p. 40-41.Complete genome sequences of two genotype A2 small ruminant lentiviruses isolated from infected U.S. sheep-(Peer Reviewed Journal) Workman, A.M., Dickey, A.M., Heaton, M.P., Clawson, M.L., Smith, T.P.L. 2017. Complete genome sequences of two genotype A2 small ruminant lentiviruses isolated from infected U.S. sheep. Genome Announcements. 5(13):e00109-17.Host-associated differentiation in a pecan and water hickory Aphidomorpha community-(Peer Reviewed Journal) Medina, R.F., Dickey, A.M., Harrison, K., Miller, G.L. 2017. Host-associated differentiation in a pecan and water hickory Aphidomorpha community. Entomologia Experimentalis et Applicata. 162:366-378.Genomic signatures of Mannheimia haemolytica that associate with the lungs of cattle with respiratory disease, an integrative conjugative element, and antibiotic resistance genes-(Peer Reviewed Journal) Clawson, M.L., Murray, R.W., Sweeney, M.T., Apley, M.D., DeDonder, K.D., Capik, S.F., Larson, R.L., Lubbers, B.V., White, B.J., Kalbfleisch, T.S., Schuller, G., Dickey, A.M., Harhay, G.P., Heaton, M.P., Chitko-McKown, C.G., Brichta-Harhay, D.M., Bono, J.L., Smith, T.P.L. 2016. Genomic signatures of Mannheimia haemolytica that associate with the lungs of cattle with respiratory disease, an integrative conjugative element, and antibiotic resistance genes. BMC Genomics. 17:982. doi: 10.1186/s12864-016-3316-8.Identification of the pan and core genomes for Mannheimia haemolytica genotypes 1 and 2-(Abstract Only) Clawson, M.L., Schuller, G., Dickey, A.M., Bono, J.L., Murray, R.W., Sweeney, M.T., Apley, M.D., DeDonder, K.D., Capik, S.F., Larson, R.L., Lubbers, B.V., White, B.J., Harhay, G.P., Heaton, M.P., Chitko-McKown, C.G., Harhay, D.M., Smith, T.P. 2016. Identification of the pan and core genomes for Mannheimia haemolytica genotypes 1 and 2. American Society for Microbiology 2016 Meeting, July 16-20, 2016, Boston, MA. Poster No. Friday-060.Florida exotic whitefly invaders from the last decade-(Abstract Only) McKenzie, C.L., Dickey, A.M., Stocks, I., Kumar,V., Osborne, L.S. 2016. Florida exotic whitefly invaders from the last decade[abstract]. International Congress of Entomology. September 25-30, 2016, Orlando, Florida. doi:10.1603/ICE.2016.93962Large genomic differences between Moraxella bovoculi isolates acquired from the eyes of cattle with conjunctivitis versus the deep nasopharynx of asymptomatic cattle-(Peer Reviewed Journal) Dickey, A.M., Loy, J.D., Bono, J.L., Smith, T.P.L., Apley, M.D., Lubbers, B.V., DeDonder, K.D., Capik, S.F., Larson, R.L., White, B.J., Blom, J., Chitko-McKown, C.G., Clawson, M.L. 2016. Large genomic differences between Moraxella bovoculi isolates acquired from the eyes of cattle with conjunctivitis versus the deep nasopharynx of asymptomatic cattle. Veterinary Research. 47:31.New species diversity revealed from molecular and morphological characterization of gall-inducting Calophya spp. (Hemiptera: Calophyidae) from Brazilian peppertree-(Peer Reviewed Journal) Diaz, R., Dickey, A.M., Shatters, R.G., Manrique, V., Vitorino, M.D., Overholt, W.A. 2015. New species diversity revealed from molecular and morphological characterization of gall-inducting Calophya spp. (Hemiptera: Calophyidae) from Brazilian peppertree. Molecular and Cellular Probes. 26:90-98 http:dx.doi.org/10.1016/j.mcp.2011.12.001.Identification of the MEAM1 cryptic species of Bemisia tabaci (Hemiptera: Aleyrodidae) by loop-mediated isothermal amplification-(Peer Reviewed Journal) Dickey, A.M., Osborne, L.S., Shatters, Jr., R.G., McKenzie, C.L. 2013. Identification of the MEAM1 cryptic species of Bemisia tabaci (Hemiptera: Aleyrodidae) by loop-mediated isothermal amplification. Florida Entomologist. 96(3):756-764.Evolution and homoplasy at the Bem6 microsatellite locus in three sweetpotato whitefly (Bemisia tabaci) cryptic species-(Peer Reviewed Journal) Dickey, A., Hall, P.M., Shatters, Jr., R.G., McKenzie, C.L. 2013. Evolution and homoplasy at the Bem6 microsatellite locus in three sweetpotato whitefly (Bemisia tabaci) cryptic species. BioMed Central Research Notes. 6:249. Available: http://www.biomedcentral.com/1756-0500/6/249.Characterizing population and genetic structure of Aleurodicus rugioperculatus Martin (Hemiptera: Aleyrodidae) in Florida-(Abstract Only) Wilkerson, M., Hix, R.L., Dickey, A.M., McKenzie, C.L. 2013. Characterizing population and genetic structure of Aleurodicus rugioperculatus Martin (Hemiptera: Aleyrodidae) in Florida [abstract]. Southeastern Branch of Entomological Society of America. Paper No. 032.Population genetics of invasive Bemisia tabaci cryptic species in the United States based on microsatellite markers-(Peer Reviewed Journal) Dickey, A.M., Osborne, L.S., Shatters, Jr., R.G., Hall, P., McKenzie, C.L. 2013. Population genetics of invasive Bemisia tabaci cryptic species in the United States based on microsatellite markers. Journal of Economic Entomology. 106(3):1355-1364. Available: http://dx.doi.org/10/1603/EC12512.Haplotype analysis of global chili thrips (Schirtothrips dorsalis) populations using the metazoan barcode-(Abstract Only) Dickey, A.M., Osborne, L.S., Kumar, V., Shatters, R.G., Mckenzie, C.L. 2012. Haplotype analysis of global chili thrips (Schirtothrips dorsalis) populations using the metazoan barcode [Abstract]. Entomological Society of America Annual Meeting, November 11-14, Knoxville, Tennessee.LAMP (Loop-mediated isothermal amplification of DNA) - A technique for biotype discrimination in Bemisia tabaci-(Abstract Only) Dickey, A.M., Osborne, L.S., Shatters, R.G., McKenzie, C.L. 2012. LAMP - A technique for biotype discrimination in Bemisia tabaci [abstract]. Florida Entomological Society Annual Meeting.A comparison of two methods of eluting insect DNA from Flinders Technology Associates Cards-(Peer Reviewed Journal) Dickey, A., Shatters, Jr., R.G., McKenzie, C.L. 2012. A comparison of two methods of eluting insect DNA from Flinders Technology Associates Cards. Florida Entomologist. 95(3):790-793.Evolution and homoplasy at the bem6 microsatellite locus in three Bemisia tabaci cryptic species-(Abstract Only) Dickey, A.M., Osborne, L.S., Hall, P.M., Shatters, R.G., McKenzie, C.L. 2012. Evolution and homoplasy at the bem6 microsatellite locus in three Bemisia tabaci cryptic species [Abstract]. Entomological Society of America Annual Meeting, November 11-14, 2012, Knoxville, Tennessee.Isothermal Amplification of Insect DNA-(Abstract Only) Dickey, A.M., Osborne, L.S., Shatters, R.G., McKenzie, C.L. 2012. Isothermal Amplification of Insect DNA [Abstract]. 7th International IPM Symposium, March 27-29, Memphis, Tennessee.Distribution of Bemisia tabaci (Hemiptera: Aleyrodidae) biotypes in North America following the Q invasion-(Peer Reviewed Journal) McKenzie, C.L., Bethke, J.A., Byrne, F.J., Chamberlin, J.R., Dennehy, T.J., Dickey, A.M., Gilrein, D., Hall, P.M., Ludwig, S., Oetting, R.D., Osborne, L.S., Schmale, L., Shatters, Jr., R.G. 2012. Distribution of Bemisia tabaci (Hemiptera: Aleyrodidae) biotypes in North America following the Q invasion. Journal of Economic Entomology. 105(3):753-766. Available: http://dx.doi.org/10.1603/EC11337Papaya is not a host for Tomato Yellow Leaf Curl Virus-(Peer Reviewed Journal) Dickey, A.. Osborne, L.S., McKenzie, C. 2012. Papaya is not a host for tomato yellow leaf-curl virus. Florida Entomologist. 95:211-213. Available: http://dx.doi.org/10.1653/024.095.0136Isothermal amplification of insect DNA-(Abstract Only) Dickey, A.M., Osborne, L.S., Shatters, R.G., Mckenzie, C.L. 2011. Isothermal amplification of insect DNA [abstract]. Entomological Society of America Annual Meeting. Paper No. D0542.


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