Derek M. Bickhart

Office Phone: (301) 504-8679
Fax: (301) 504-8092

1925 Linden Dr. W
Bldg 005 BARC-WEST Room 215
Madison, WI 53706

Personal Background 

Meet the Scientist

• Publications

  • (Clicking on the reprint icon will take you to the publication reprint.)
  • Expression and variation of the genes involved in rhizobium nodulation in red clover -(Peer Reviewed Journal)
    Dinkins, R.D., Hancock, J.A., Bickhart, D.M., Sullivan, M.L., Zhu, H. 2022. Expression and variation of the genes involved in rhizobium nodulation in red clover. Plants. Article 11:2888. https://doi.org/10.3390/plants11212888.
    
  • Assembly of a pan-genome for global cattle reveals missing sequence and novel structural variation, providing new insights into their diversity and evolution history -(Peer Reviewed Journal)
    Zhou, Y., Yang, L., Han, X., Hu, Y., Li, F., Xia, H., Han, J., Peng, L., Boschiero, C., Rosen, B.D., Bickhart, D.M., Zhang, S., Guo, A., Van Tassell, C.P., Smith, T.P., Yang, L., Liu, G. 2022. Assembly of a pan-genome for global cattle reveals missing sequence and novel structural variation, providing new insights into their diversity and evolution history. Genome Research. 32(8):1585-1601. https://doi.org/10.1101/gr.276550.122.
    
  • Truncation of IFT80 causes early embryonic loss in Holstein cattle associated with Holstein haplotype 2 -(Peer Reviewed Journal)
    Ortega, M.S., Bickhart, D.M., Clark, K.N., Null, D.J., Hutchison, J.L., Mcclure, J.C., Cole, J.B. 2022. Truncation of IFT80 causes early embryonic loss in Holstein cattle associated with Holstein haplotype 2. Journal of Dairy Science. 105(11):9001-9011. https://doi.org/10.3168/jds.2022-21853.
    
  • Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies -(Peer Reviewed Journal)
    Leonard, A.S., Crysnanto, D., Fang, Z., Heaton, M.P., Vander Ley, B.L., Herrera, C., Bollwein, H., Bickhart, D.M., Kuhn, K.L., Smith, T.P.L., Rosen, B.D., Pausch, H. 2022. Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies. Nature Communications. 13. Article 3012. https://doi.org/10.1038/s41467-022-30680-2.
    
  • Gaur genome reveals expansion of sperm odorant receptors in domesticated cattle -(Peer Reviewed Journal)
    Low, W.Y., Rosen, B.D., Ren, Y., Bickhart, D.M., To, T., Martin, F.J., Billis, K., Sonstegard, T.S., Sullivan, S.T., Hiendleder, S., Williams, J.L., Heaton, M.P., Smith, T.P. 2022. Gaur genome reveals expansion of sperm odorant receptors in domesticated cattle. BMC Genomics. 23(1):344. https://doi.org/10.1186/s12864-022-08561-1.
    
  • Chromosome-scale assembly of the highly heterozygous genome of red clover (Trifolium pratense L.), an allogamous forage crop species -(Peer Reviewed Journal)
    Bickhart, D.M., Koch, L.M., Smith, T.P., Riday, H., Sullivan, M.L. 2022. Chromosome-scale assembly of the highly heterozygous genome of red clover (Trifolium pratense L.), an allogamous forage crop species. GigaByte. 42:1-13. https://doi.org/10.46471/gigabyte.42.
    
  • Defining the caprine ¿d T cell WC1 multigenic array and evaluation of its expressed sequences and gene structure conservation among goat breeds and relative to cattle-(Peer Reviewed Journal)
    
    
  • Supporting data for "Chromosome-scale assembly of the highly heterozygous genome of red clover (Trifolium pratense L.), an allogamous forage crop species"-(Database / Dataset)
    
    
  • Chromosome-scale assembly of the highly heterozygous genome of red clover (Trifolium pratense L.), an allogamous forage crop species -(Pre-print Publication)
    Bickhart, D.M., Koch, L.M., Smith, T.P., Riday, H., Sullivan, M.L. 2022. Chromosome-scale assembly of the highly heterozygous genome of red clover (Trifolium pratense L.), an allogamous forage crop species. bioRxiv. https://doi.org/10.1101/2022.01.06.475143.
    
  • An improved ovine reference genome assembly to facilitate in depth functional annotation of the sheep genome -(Peer Reviewed Journal)
    Davenport, K.M., Bickhart, D.M., Worley, K.C., Murali, S.C., Salavati, M., Clark, E.L., Cockett, N., Heaton, M.P., Smith, T.P., Murdoch, B.M., Rosen, B.D. 2022. An improved ovine reference genome assembly to facilitate in depth functional annotation of the sheep genome. Gigascience. 11. Article giab096. https://doi.org/10.1093/gigascience/giab096.
    
  • FLC MidWest Regional Technology Transfer Award-(Abstract Only)
    
    
  • Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities -(Peer Reviewed Journal)
    Bickhart, D.M., Kolmogorov, M., Tseng, E., Portik, D., Korobeynikov, A., Tolstoganov, I., Uritskiy, G., Liachko, I., Sullivan, S.T., Shin, S.B., Zorea, A., Andreu, V., Panke-Buisse, K., Medema, M., Mizrahi, I., Pevzner, P., Smith, T.P. 2022. Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities. Nature Biotechnology. 40:711-719. https://doi.org/10.1038/s41587-021-01130-z.
    
  • Generation of lineage-resolved complete metagenome-assembled genomes by precision phasing -(Pre-print Publication)
    Bickhart, D.M., Kolmogorov, M., Tseng, E., Portik, D., Korobeynikov, A., Tolstoganov, I., Uritskiy, G., Liachko, I., Sullivan, S.T., Shin, S.B., Zorea, A., Andreu, V., Panke-Buisse, K., Medema, M., Mizrahi, I., Pevzner, P., Smith, T.P. 2021. Generation of lineage-resolved complete metagenome-assembled genomes by precision phasing. bioRxiv. https://doi.org/10.1101/2021.05.04.442591.
    
  • Variants at the ASIP locus contribute to coat color darkening in Nellore cattle -(Peer Reviewed Journal)
    Trigo, B.B., Utsunomiya, A.T., Fortunato, A., Milanesi, M., Torrecilha, R.B., Lamb, H., Hayes, B., Nguyen, L., Ross, E., Padula, R.C., Sussai, T.S., Zavarez, L.B., Cipriano, R.S., Caminhas, M.M., Lopes, F.L., Lung, L.H., Pelle, C., Leeb, T., Bannasch, D., Bickhart, D.M., Smith, T.P.L, Garcia, J.F., Utsunomiya, Y.T. 2021. Variants at the ASIP locus contribute to coat color darkening in Nellore cattle. Genetics Selection Evolution. 53. Article 40. https://doi.org/10.1186/s12711-021-00633-2.
    
  • Development of polymorphic markers in the immune gene complex loci of cattle -(Peer Reviewed Journal)
    Bakshy, K., Heimeier, D., Schwartz, J.C., Glass, E.J., Wilkinson, S., Skuce, R.A., Allen, A.R., Young, J., McClure, J.C., Cole, J.B., Null, D.J., Hammond, J.A., Smith, T.P.L., Bickhart, D.M. 2021. Development of polymorphic markers in the immune gene complex loci of cattle. Journal of Dairy Science. 104(6):6897-6908. https://doi.org/10.3168/jds.2020-19809.
    
  • Characterization of the domestic goat yd T cell receptor gene loci and gene usage -(Peer Reviewed Journal)
    Gillespi, A., Yirsaw, A., Gunasekaran, K.P., Smith, T.P., Bickhart, D.M., Turley, M., Connelley, T., Telfer, J.C., Baldwin, C.L. 2021. Characterization of the domestic goat yd T cell receptor gene loci and gene usage. Immunogenetics. 73:187-201. https://doi.org/10.1007/s00251-021-01203-y.
    
  • A reference genome assembly of American bison, Bison bison bison -(Peer Reviewed Journal)
    Oppenheimer, J., Rosen, B.D., Heaton, M.P., Vander Ley, B.L., Shafer, W.R., Schuetze, F.T., Stroud, B., Kuehn, L.A., McClure, J.C., Barfield, J.P., Blackburn, H.D., Kalbfleisch, T.S., Bickhart, D.M., Davenport, K.M., Kuhn, K.L., Green, R.E., Shapiro, B., Smith, T.P.L. 2021. A reference genome assembly of American bison, Bison bison bison. Journal of Heredity. 112(2):174-183. https://doi.org/10.1093/jhered/esab003.
    
  • A reference genome assembly of Simmental cattle, Bos taurus taurus -(Peer Reviewed Journal)
    Heaton, M.P., Smith, T.P.L., Bickhart, D.M., Vander Ley, B.L., Kuehn, L.A., Oppenheimer, J., Shafer, W.R., Schuetze, F.T., Stroud, B., McClure, J.C., Barfield, J.P., Blackburn, H.D., Kalbfleisch, T.S., Davenport, K.M., Kuhn, K.L., Green, R.E., Shapiro, B., Rosen, B.D. 2021. A reference genome assembly of Simmental cattle, Bos taurus taurus. Journal of Heredity. 112(2):184-191. https://doi.org/10.1093/jhered/esab002.
    
  • Big data from small cells: Metagenome assembly of ruminant microbial communities-(Abstract Only)
    Bickhart, D.M. 2020. Big data from small cells: Metagenome assembly of ruminant microbial communities. Meeting Abstract. US Dairy Forage Research Center Webinar Series. November 18, 2020. Virtual.
    
  • Improving metagenome assemblies with long read sequence data-(Abstract Only)
    Bickhart, D.M., Koren, S., Kolmogorov, M., Watson, M., Pevzner, P., Phillippy, A.M., Smith, T.P. 2020. Improving metagenome assemblies with long read sequence data. Cold Spring Harbor Meeting. October 20-24, 2020. Virtual Meeting.
    
  • The Bovine Pangenome Consortium-(Abstract Only)
    Bickhart, D.M., Rosen, B.D., Smith, T.P. 2020. The Bovine Pangenome Consortium. Meeting Abstract. Biodiversity Genomics Conference October 5-9, 2020, Virtual Meeting.
    
  • metaFlye: scalable long-read metagenome assembly using repeat graphs -(Peer Reviewed Journal)
    Kolmogorov, M., Bickhart, D.M., Behsaz, B., Gurevich, A., Rayko, M., Shin, S.B., Kuhn, K.L., Yuan, J., Polevikov, E., Smith, T.P.L., Pevzner, P.A. 2020. metaFlye: scalable long-read metagenome assembly using repeat graphs. Nature Methods. 17:1103-1110. https://doi.org/10.1038/s41592-020-00971-x.
    
  • Reassembly of cattle immune gene clusters for quantitative analysis-(Abstract Only)
    
    
  • Circular closed contigs in a sheep fecal metagenome using metaFlye and high-fidelity long-reads-(Abstract Only)
    Bickhart, D.M., Kolmogorov, M., Medema, M.H., Korobeynikov, A., Mizrahi, I., Pevzner, P., Smith, T.P. 2020. Circular closed contigs in a sheep fecal metagenome using metaFlye and high-fidelity long-reads. Cold Spring Harbor Laboratory's Microbiome Conference. October 20-23, 2020. Virtual Meeting.
    
  • Identifying and linking antimicrobial resistance genes in metagenomes with new DNA sequencing technologies-(Abstract Only)
    Bickhart, D.M. 2020. Identifying and linking antimicrobial resistance genes in metagenomes with new DNA sequencing technologies. Meeting Abstract. LabRoots Microbiology Virtual Week, September 8-10, 2020. Virtual Meeting.
    
  • Machine learning validation of Buccal swabs as a proxy for rumen microbial contents-(Abstract Only)
    
    
  • Validating the use of bovine buccal sampling as a proxy for the rumen microbiota using a time course and random forest classification approach -(Peer Reviewed Journal)
    Young, J.N., Skarlupka, J.H., Resende, R.T., Fischer, A., Kalscheur, K., Mcclure, J.C., Cole, J.B., Suen, G., Bickhart, D.M. 2020. Validating the use of bovine buccal sampling as a proxy for the rumen microbiota using a time course and random forest classification approach. Applied and Environmental Microbiology. 86(17). Article e00861-20.. https://doi.org/10.1128/AEM.00861-20 .
    
  • High-throughput Phenotyping of Rumen Microbial Contents Using Buccal Swabs-(Abstract Only)
    
    
  • Improving metagenome assemblies with long read sequence data-(Abstract Only)
    
    
  • An improved pig reference genome sequence to enable pig genetics and genomics research -(Peer Reviewed Journal)
    Warr, A., Affara, N., Aken, B., Beiki, H., Bickhart, D.M., Billis, K., Chow, W., Eory, L., Finlayson, H.A., Flicek, P., Giron, C.G., Griffin, D.K., Hall, R., Hannum, G., Hourlier, T., Howe, K., Hume, D.A., Izuogu, O., Kim, K., Koren, S., Liu, H., Manchanda, N., Martin, F.J., Nonneman, D.J., O'Connor, R.E., Phillippy, A.M., Rohrer, G.A., Rosen, B.D., Rund, L.A., Sargent, C.A., Schook, L.B., Schroeder, S.G., Shwartz, A.S., Skinner, B.M., Talbot, R., Tseng, E., Tuggle, C.K., Watson, M., Smith, T.P., Archibald, A.L. 2020. An improved pig reference genome sequence to enable pig genetics and genomics research. GigaScience. 9(6):giaa051. https://doi.org/10.1093/gigascience/giaa051.
    
  • Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle -(Peer Reviewed Journal)
    Low, W., Tearle, R., Liu, C., Koren, S., Rhie, A., Bickhart, D.M., Rosen, B.D., Kronenberg, Z.N., Kingan, S.B., Tseng, E., Thibaud-Nissen, F., Martin, F., Billis, K., Ghurye, J., Hastie, A.R., Lee, J., Pang, A., Heaton, M.P., Phillippy, A.M., Hiendleder, S., Smith, T.P., Williams, J.L. 2020. Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle. Nature Communications. 11:2071. https://doi.org/10.1038/s41467-020-15848-y.
    
  • Haplotype- and sequence-based identification of a deletion associated with early embryonic loss in Holstein cattle and functional validation using CRISPR-Cas9 knockouts -(Abstract Only)
    
    
  • Continuous chromosome-scale haplotypes assembled from a single interspecies F1 hybrid of yak and cattle -(Peer Reviewed Journal)
    Rice, E.S., Koren, S., Rhie, A., Heaton, M.P., Kalbfleisch, T., Hardy, T., Hackett, P., Bickhart, D.M., Rosen, B.D., Vander Ley, B., Maurer, N.W., Green, R.E., Phillippy, A.M., Petersen, J.L., Smith, T.P. 2020. Continuous chromosome-scale haplotypes assembled from a single interspecies F1 hybrid of yak and cattle. GigaScience. 9(4):1-9. https://doi.org/10.1093/gigascience/giaa029.
    
  • High-throughput Phenotyping of Rumen Microbial Contents Using Buccal Swabs-(Abstract Only)
    
    
  • De novo assembly of the cattle reference genome with single-molecule sequencing -(Peer Reviewed Journal)
    Rosen, B.D., Bickhart, D.M., Schnabel, R.D., Koren, S., Elsik, C.G., Tseng, E., Rowan, T.N., Low, W.Y., Zimin, A., Couldrey, C., Hall, R., Li, W., Rhie, A., Ghurye, J., McKay, S.D., Thibaud-Nissen, F., Hoffman, J., Murdoch, B.M., Snelling, W.M., McDaneld, T.G., Hammond, J.A., Schwartz, J.C., Nandolo, W., Hagen, D.E., Dreischer, C., Schultheiss, S.J., Schroeder, S.G., Phillippy, A.M.,Cole, J.B., Van Tassell, C.P., Liu, G., Smith, T.P.L., Medrano, J.F. 2020. De novo assembly of the cattle reference genome with single-molecule sequencing. GigaScience. 9(3):1-9. https://doi.org/10.1093/gigascience/giaa021.
    
  • Advances in sequencing technology herald a new frontier in cattle genomics and genome-enabled selection -(Review Article)
    Bickhart, D.M., McClure, J.C., Schnabel, R.D., Rosen, B.D., Medrano, J.F., Smith, T.P.L. 2020. Advances in sequencing technology herald a new frontier in cattle genomics and genome-enabled selection. Journal of Dairy Science. 103(6):5278-5290. https://doi.org/10.3168/jds.2019-17693.
    
  • New insights into mammalian sex chromosome structure and evolution using high-quality sequences from bovine X and Y chromosomes -(Peer Reviewed Journal)
    Liu, R., Yee Low, W., Tearle, R., Koren, S., Ghurye, J., Rhie, A., Phillippy, A.M., Rosen, B.D., Bickhart, D.M., Smith, T.P., Hiendleder, S., Williams, J.L. 2019. New insights into mammalian sex chromosome structure and evolution using high-quality sequences from bovine X and Y chromosomes. BMC Genomics. 20:1000. https://doi.org/10.1186/s12864-019-6364-z.
    
  • Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation-(Abstract Only)
    
    
  • Bioinformatics training workshop: Introduction to Unix and Advanced Command Line tutorial-(Abstract Only)
    
    
  • Using the ARS-UCD1.2 reference genome in U.S. evaluations -(Proceedings)
    Null, D.J., Van Raden, P.M., Rosen, B.D., O'Connell, J.R., Bickhart, D.M. 2019. Using the ARS-UCD1.2 reference genome in U.S. evaluations. Interbull Bulletin. 55:30-34.
    
  • Genome assemblies of global cattle breeds to create a cattle Pangenome-(Abstract Only)
    Smith, T.P.L, Bickhart, D.M., Rosen, B.D. 2020. Genome assemblies of global cattle breeds to create a cattle Pangenome [abstract]. International Plant & Animal Genome XXVIII Conference, January 11-15, 2020, San Diego, California. Poster Number PE0318. Available at: https://plan.core-apps.com/pag_2020/abstracts
    
  • The structure, evolution, and gene expression within the caprine leukocyte receptor complex -(Peer Reviewed Journal)
    Schwartz, J.C., Sanderson, N.D., Bickhart, D.M., Smith, T.P., Hammond, J.A. 2019. The structure, evolution, and gene expression within the caprine leukocyte receptor complex. Frontiers in Immunology. 10:2302. https://doi.org/10.3389/fimmu.2019.02302.
    
  • Progress report on a plains bison-Simmental interspecies cross for genome assembly by trio binning-(Other)
    Heaton, M.P., Kuehn, L.A., Vander Ley, B.L., Clark, H.J., Shafer, W., Schuetze, F., Stroud, B., Barfield, J.P., Blackburn, H.D., Kalbfleisch, T.S., Rosen, B.D., Bickhart, D.M., Oppenheimer, J., Shapiro, B., Green, R.E., Smith, T.P. 2019. Progress report on a plains bison-Simmental interspecies cross for genome assembly by trio binning [abstract]. Fall Focus 2019, Manhattan, Kansas, August 25-27, 2019. Available: https://simmental.org.
    
  • Chromosome-length haplotigs for yak and cattle from trio binning assembly of an F1 hybrid -(Research Notes)
    Rice, E.S., Koren, S., Rhie, A., Heaton, M.P., Kalbfleisch, T.S., Hardy, T., Hackett, P.H., Bickhart, D.M., Rosen, B.D., Vander Ley, B., Maurer, N.W., Green, R.E., Phillippy, A.M., Petersen, J.L., Smith, T.P.L. 2019. Chromosome-length haplotigs for yak and cattle from trio binning assembly of an F1 hybrid. bioRxiv. 737171. https://doi.org/10.1101/737171.
    
  • Breeding for soft seeded non shattering hairy vetch (Vicia villosa L.)-(Abstract Only)
    Riday, H., Kucek, L.K., Douglas, J.L., Carr, B., Young-Mathews, A., Bhamidimarri, S., Hayes, R.J., Azevedo, M.D., Trammell, M., Monteros, M., Mirsky, S.B., Wiering, N.P., Bickhart, D.M., Sullivan, M.L., Ehlke, N., Englert, J.S. 2019. Breeding for soft seeded non shattering hairy vetch (Vicia villosa L.). National Association of Plant Breeders. 25 to 29 August 2019.
    
  • Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation -(Peer Reviewed Journal)
    Bickhart, D.M., Watson, M., Koren, S., Panke-Buisse, K., Cersosimo, L.M., Press, M.O., Van Tassell, C.P., Van Kessel, J.S., Haley, B.J., Kim, S., Heiner, C., Suen, G., Bakshy, K., Liachko, I., Sullivan, S.T., Myer, P.R., Ghurye, J., Pop, M., Weimer, P., Phillippy, A., Smith, T.P. 2019. Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation. Genome Biology. 20:153. https://doi.org/10.1186/s13059-019-1760-x.
    
  • Integrating signals from sperm methylome analysis and genome-wide association study for a better understanding of male fertility in cattle -(Peer Reviewed Journal)
    Fang, L., Zhou, Y., Liu, S., Jiang, J., Bickhart, D.M., Null, D.J., Li, B., Schroeder, S.G., Rosen, B.D., Cole, J.B., Van Tassell, C.P., Ma, L., Liu, G. 2019. Integrating signals from sperm methylome analysis and genome-wide association study for a better understanding of male fertility in cattle. Epigenomes. 3(2):10. https://doi.org/10.3390/epigenomes3020010.
    
  • US-UK collaborative project: Reassembly of cattle immune gene clusters for quantitative analysis-(Abstract Only)
    
    
  • Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation-(Abstract Only)
    
    
  • Genome to Phenome: Improving animal health, production, and well-being: A new USDA blueprint for animal genome research 2018–2027 -(Peer Reviewed Journal)
    Rexroad III, C.E., Vallet, J.L., Matukumalli, L.K., Ernst, C., Van Tassell, C.P., Cheng, H.H., Reecy, J., Fulton, J., Taylor, J., Lunney, J.K., Liu, J., Cockett, N., Smith, T.P., Van Eenennaam, A., Clutter, A., Telugu, B., Purcell, C., Bickhart, D.M., Blackburn, H.D., Neibergs, H., Wells, K., Boggess, M.V., Sonstegard, T. 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. https://doi.org/10.3389/fgene.2019.00327.
    
  • Linking the Resistome to the Microbiome: A Culture-Free Method Links Plasmid, Virus, and Antimicrobial Resistance Genes to their Hosts in Complex Microbial Populations-(Abstract Only)
    
    
  • From sequence of dominette to 10K and 50K SNP chips-(Abstract Only)
    
    
  • Cattle variant-detection modelling using selective-sequencing experimental design and statistical learning-(Abstract Only)
    
    
  • Comparative analyses of sperm DNA methylomes among human, mouse and cattle provide insights into epigenomic evolution and complex traits -(Peer Reviewed Journal)
    Fang, L., Zhou, Y., Liu, S., Jiang, J., Bickhart, D.M., Null, D.J., Li, B., Schroeder, S.G., Rosen, B.D., Cole, J.B., Van Tassell, C.P., Ma, L., Liu, G. 2019. Comparative analyses of sperm DNA methylomes among human, mouse and cattle provide insights into epigenomic evolution and complex traits. Epigenetics. 14(3):260-276. https://doi.org/10.1080/15592294.2019.1582217.
    
  • Computational detection and experimental validation of segmental duplications and associated copy number variations in water buffalo (Bubalus bubalis) -(Peer Reviewed Journal)
    Liu, S., Kang, X., Catacchio, C.R., Liu, M., Fang, L., Schroeder, S.G., Li, W., Rosen, B.D., Iamartino, D., Iannuzzi, L., Sonstegard, T.S., Van Tassell, C.P., Ventura, M., Low, W., Williams, J.L., Bickhart, D.M., Liu, G. 2019. Computational detection and experimental validation of segmental duplications and associated copy number variations in water buffalo (Bubalus bubalis). Functional and Integrative Genomics. 19(3):409–419. https://doi.org/10.1007/s10142-019-00657-4.
    
  • Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity -(Peer Reviewed Journal)
    Yee Low, W., Tearle, R., Bickhart, D.M., Rosen, B.D., Kingan, S.B., Swale, T., Thibaud-Nissen, F., Murphy, T., Young, R., Lefevre, L., Hume, D., Collins, A., Ajmone-Marsan, P., Smith, T.P., Williams, J. 2019. Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity. Nature Communications. 10:260. https://doi.org/10.1038/s41467-018-08260-0.
    
  • Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation-(Abstract Only)
    
    
  • Calling known variants and identifying new variants while rapidly aligning sequence data -(Peer Reviewed Journal)
    Van Raden, P.M., Bickhart, D.M., O'Connell, J.R. 2019. Calling known variants and identifying new variants while rapidly aligning sequence data. Journal of Dairy Science. 102(4):3216–3229. https://doi.org/10.3168/jds.2018-15172.
    
  • Selection of cattle SNP markers using selective-sequencing experimental design and statistical learning-(Abstract Only)
    
    
  • Transcriptomics analysis of host liver and meta-transcriptome analysis of rumen epimural microbial community in young calves treated with artificial dosing of rumen content from adult donor cow -(Peer Reviewed Journal)
    Li, W., Edwards, A., Riehle, C., Cox, M., Raabis, S., Steinberger, A., Skarlupka, J., Walling, J.G., Bickhart, D.M., Suen, G. 2019. Transcriptomics analysis of host liver and meta-transcriptome analysis of rumen epimural microbial community in young calves treated with artificial dosing of rumen content from adult donor cow. Scientific Reports. 9. Article 790. https://doi.org/10.1038/s41598-018-37033-4.
    
  • Microbiome – Improving production and controlling disease-(Proceedings)
    
    
  • Microbiome – improving production and controlling disease-(Abstract Only)
    
    
  • The application of long-read sequencing and assembly to livestock genomics and metagenomics-(Abstract Only)
    
    
  • Contiguity of the goat genome assembly enables comparative analyses and gene discovery within the repetitive immune-related regions-(Abstract Only)
    
    
  • Goat and sheep KIR have independently expanded compared to cattle and a unique subtype is unusually expressed-(Abstract Only)
    
    
  • Misidentification of runs of homozygosity islands in cattle caused by interference with copy number variation or large intermarker distances -(Peer Reviewed Journal)
    Nandolo, W., Utsunomiya, Y.T., Meszaros, G., Wurzinger, M., Khayadzadeh, N., Torrecilha, R.B., Mulindwa, H., Gondwe, T., Waldmann, P., Ferencakovic, M., Garcia, J.F., Rosen, B.D., Bickhart, D.M., Van Tassell, C.P., Curik, I., Solkner, J. 2018. Misidentification of runs of homozygosity islands in cattle caused by interference with copy number variation or large intermarker distances. Genetic Selection Evolution. 50(1):43. https://doi.org/10.1186/s12711-018-0414-x.
    
  • Examination of the xanthosine response on gene expression of mammary epithelial cells using RNA-seq technology -(Peer Reviewed Journal)
    Choudhary, S., Li, W., Bickhart, D.M., Ramneek, V., Sethi, R.S., Mukhopadhyay, C.S., Choudhary, R.K. 2018. Examination of the xanthosine response on gene expression of mammary epithelial cells using RNA-seq technology. Journal of Animal Science and Technology. 60. Article 18. https://doi.org/10.1186/s40781-018-0177-5.
    
  • Effect of consuming endophyte-infected fescue seed on transcript abundance in the mammary gland of lactating and dry cows, as assessed by RNA sequencing -(Peer Reviewed Journal)
    Capuco, A.V., Bickhart, D.M., Li, C., Clover, C.M., Choudhary, R., Grossi, P., Bertoni, G., Trevisi, E., Aiken, G.E., Mcleod, K.R., Baldwin, R.L. 2018. Effect of consuming endophyte-infected fescue seed on transcript abundance in the mammary gland of lactating and dry cows, as assessed by RNA sequencing. Journal of Dairy Science. 101(11):10478–10494. https://doi.org/10.3168/jds.2018-14735.
    
  • Use of RAPTR-SV to identify SVs from read pairing and split read signatures-(Book / Chapter)
    
    
  • Determination of quantitative trait nucleotides by concordance analysis between quantitative trait loci and marker genotypes of US Holsteins -(Peer Reviewed Journal)
    Weller, J.I., Bickhart, D.M., Wiggans, G.R., Tooker, M.E., O'Connell, J.R., Jiang, J., Ron, M., Van Raden, P.M. 2018. Determination of quantitative trait nucleotides by concordance analysis between quantitative trait loci and marker genotypes of US Holsteins. Journal of Dairy Science. 101(10):9089–9107. https://doi.org/10.3168/jds.2018-14816.
    
  • Genomic predictions combining SNP markers and copy number variations in Nellore cattle -(Peer Reviewed Journal)
    Hay, E.A., Utsunomiya, Y.T., Xu, L., Neves, H.H., Carvalheiro, R., Bickhart, D.M., Ma, L., Garcia, J.F., Liu, G. 2018. Genomic predictions combining SNP markers and copy number variations in Nellore cattle. BMC Genomics. 19(1):441-449. https://doi.org/10.1186/s12864-018-4787-6.
    
  • Genomic predictions combining SNP markers and copy number variations in Nellore cattle -(Peer Reviewed Journal)
    Hay, E.A., Utsunomiya, Y.T., Xu, L., Zhou, Y., Neves, H.H., Carvalheiro, R., Bickhart, D.M., Garcia, J., Liu, G. 2018. Genomic predictions combining SNP markers and copy number variations in Nellore cattle. Biomed Central (BMC) Genomics. 19(1):441. https://doi.org/10.1186/s12864-018-4787-6.
    
  • Haplotype resolution of MHC in cattle through targeted enrichment and SMRT sequencing-(Abstract Only)
    
    
  • Genomic structural differences between cattle and river buffalo identified through a combination and genomic and transcriptomic analysis-(Peer Reviewed Journal)
    Li, W., Bickhart, D.M., Ramunno, L., Lamartino, D., Williams, J., Liu, G. 2018. Genomic structural differences between cattle and river buffalo identified through a combination and genomic and transcriptomic analysis. Data in Brief. 19:236-239.
    
  • Buccal swabs as a noninvasive proxy for rumen microbial content -(Abstract Only)
    
    
  • Comparative whole genome DNA methylation profiling of cattle sperm and somatic tissues reveals striking hypomethylated patterns in sperm -(Peer Reviewed Journal)
    Zhou, Y., Connor, E.E., Bickhart, D.M., Li, C., Baldwin, R.L., Schroeder, S.G., Rosen, B.D., Yang, L., Van Tassell, C.P., Liu, G. 2018. Comparative whole genome DNA methylation profiling of cattle sperm and somatic tissues reveals striking hypomethylated patterns in sperm. Gigascience. 7(5):1-13. https://doi.org/10.1093/gigascience/giy039.
    
  • Potential benefits from using a new reference map in genomic prediction-(Abstract Only)
    Null, D.J., Van Raden, P.M., Bickhart, D.M., Cole, J.B., O'Connell, J.R., Rosen, B.D. 2018. Potential benefits from using a new reference map in genomic prediction. Journal of Dairy Science. 101 (Suppl. 2):181-182(abstr. 168).
    
  • Comparative sequence alignment reveals River Buffalo genomic structural differences compared with cattle-(Peer Reviewed Journal)
    Li, W., Bickhart, D.M., Ramunno, L., Iamartino, D., Williams, J., Liu, G. 2018. Comparative sequence alignment reveals River Buffalo genomic structural differences compared with cattle. Genomics. https://doi.org/10.1016/j.ygeno.2018.02.018.
    
  • Convergent evolution of slick coat in cattle through truncation mutations in the prolactin receptor -(Peer Reviewed Journal)
    Porto-Neto, L.R., Bickhart, D.M., Landaeta-Hernandez, A.J., Utsunomiya, Y.T., Morales, M.P., Caban-Jimenez, E., Hansen, P.J., Dikmen, S., Schroeder, S.G., Sun, J., Crespo, E., Amati, N., Cole, J.B., Null, D.J., Garcia, J.F., Reverter, A., Barendse, W., Sonstegard, T.S. 2018. Convergent evolution of slick coat in cattle through truncation mutations in the prolactin receptor. Frontiers in Genetics. 9:57. https://doi.org/10.3389/fgene.2018.00057
    
  • Long-read sequencing enables the accurate annotation of immune gene clusters in goat-(Abstract Only)
    
    
  • Chromosome-level assembly of the water buffalo genome-(Abstract Only)
    
    
  • New-world quail population genomics reveal structure, divergence, and evidence for selection-(Abstract Only)
    
    
  • Copy number variation in dairy cattle using next-generation sequencing-(Abstract Only)
    
    
  • Reassembly of cattle immune gene clusters for quantitative analysis-(Abstract Only)
    
    
  • Breeding cattle for improved disease resistance-(Abstract Only)
    
    
  • A haplotype spanning PLAG1 contributed to stature recovery in modern cattle -(Peer Reviewed Journal)
    Utsunomiya, Y., Milanesi, M., Utsunomiya, A., Torrecilha, R., Kim, E., Silva, M., Do Carmo, A.S., Carvalheiro, R., De Rezende Neves, H.H., Padula, R., Sussai, T., Zavarez, L.B., Cipriano, R.S., Caminhas, M., Hambrecht, G., Colli, L., Eufemi, E., Ajmone-Marsan, P., Buora, M., Liu, G., Bickhart, D.M., Van Tassell, C.P., Solkner, J., Sonstegard, T.S., Garcia, J.F. 2017. A haplotype spanning PLAG1 contributed to stature recovery in modern cattle. Scientific Reports. 7(1):17140. https://doi.org/10.1038/s41598-017-17127-1.
    
  • Comparative sequence alignment reveals River Buffalo genomic structural differences compared with cattle-(Abstract Only)
    
    
  • Genome-wide sequencing and comparative profiling of cattle sperm DNA methylome reveals its hypomethylated patterns-(Abstract Only)
    
    
  • The antibody loci of the domestic goat (Capra hircus) -(Peer Reviewed Journal)
    Schwartz, J.C., Philp, R.L., Bickhart, D.M., Smith, T.P., Hammond, J.A. 2018. The antibody loci of the domestic goat (Capra hircus). Immunogenetics. 70: 317-326. doi: https://doi.org/10.1007/s00251-017-1033-3).
    
  • Bovine rumen metagenomics – moving beyond microbial diversity-(Review Article)
    Bickhart, D.M., Weimer, P.J. 2017. Bovine rumen metagenomics – moving beyond microbial diversity. Journal of Dairy Science. 101:1-10.
    
  • Annotated draft genome assemblies for the northern bobwhite (Colinus virginianus) and the scaled quail (Callipepla squamata) reveal disparate estimates of modern genome diversity and historic effective population size -(Peer Reviewed Journal)
    Oldeschulte, D.L., Halley, Y.A., Wilson, M.L., Bhattarai, E.K., Brashear, W., Hill, J., Metz, R.P., Johnson, C.D., Rollins, D., Peterson, M.J., Bickhart, D.M., Decker, J.E., Sewell, J.F., Seabury, C.M. 2017. Annotated draft genome assemblies for the northern bobwhite (Colinus virginianus) and the scaled quail (Callipepla squamata) reveal disparate estimates of modern genome diversity and historic effective population size. Genes, Genomes, and Genomics. https://doi.org/10.1534/g3.117.043083.
    
  • Scaffolding of long read assemblies using long range contact information -(Peer Reviewed Journal)
    Ghurye, J., Pop, M., Koren, S., Bickhart, D.M., Chin, C. 2017. Scaffolding of long read assemblies using long range contact information. Biomed Central (BMC) Genomics. 18(1):527. https://doi.org/10.1186/s12864-017-3879-z.
    
  • Genomic evaluation of age at first calving -(Peer Reviewed Journal)
    Hutchison, J.L., Van Raden, P.M., Null, D.J., Cole, J.B., Bickhart, D.M. 2017. Genomic evaluation of age at first calving. Journal of Dairy Science. 100(8):6853-6861. https://doi.org/10.3168/jds.2016-12060.
    
  • The evolution of the natural killer complex; a comparison between mammals using new high-quality genome assemblies and targeted annotation-(Peer Reviewed Journal)
    Schwartz, J.C., Gibson, M.S., Heimeier, D., Koren, S., Phillippy, A.M., Bickhart, D.M., Smith, T.P., Medrano, J.F., Hammond, J.A. 2017. The evolution of the natural killer complex; a comparison between mammals using new high-quality genome assemblies and targeted annotation. Immunogenetics. 69(2):255-269.
    
  • Haplotype resolution of leukocyte receptor complex in cattle through targeted enrichment and SMRT sequencing-(Abstract Only)
    
    
  • Comparison of the cattle leukocyte receptor complex with related livestock species-(Abstract Only)
    
    
  • Effects of xanthosine on gene expression of mammary epithelial cells using RNA sequencing of goat milk fat globules-(Abstract Only)
    
    
  • Determination of quantitative trait variants by concordance via application of the a posteriori granddaughter design to the U.S. Holstein population-(Abstract Only)
    Weller, J.I., Bickhart, D.M., Wiggans, G.R., Tooker, M.E., O'Connell, J.R., Jiang, J., Van Raden, P.M. 2017. Determination of quantitative trait variants by concordance via application of the a posteriori granddaughter design to the U.S. Holstein population. Journal of Dairy Science. 100(Suppl. 2):410–411(abstr. 464).
    
  • Host-rumen microbe interactions may be leveraged to improve the productivity of dairy cows-(Abstract Only)
    Bickhart, D.M., Weimer, P.J. 2017. Host-rumen microbe interactions may be leveraged to improve the productivity of dairy cows. American Dairy Science Association Abstracts. 101:1-10. doi: 10.3168/jds.2017-13328
    
  • Discovery of a haplotype affecting fertility in Ayrshire dairy dattle and identification of a putative causal variant-(Abstract Only)
    Null, D.J., Hutchison, J.L., Bickhart, D.M., Van Raden, P.M., Cole, J.B. 2017. Discovery of a haplotype affecting fertility in Ayrshire dairy dattle and identification of a putative causal variant. Journal of Dairy Science. 100(Suppl. 2):199(abstr. 205).
    
  • Selecting sequence variants to improve genomic predictions for dairy cattle-(Peer Reviewed Journal)
    Van Raden, P.M., Tooker, M.E., O'Connell, J.O., Cole, J.B., Bickhart, D.M. 2017. Selecting sequence variants to improve genomic predictions for dairy cattle. Genetics Selection Evolution. 49:32.
    
  • Single-molecule sequencing and conformational capture enable de novo mammalian reference genomes-(Peer Reviewed Journal)
    Bickhart, D.M., Rosen, B.D., Koren, S., Sayre, B.L., Hastie, A.R., Chan, S., Lee, J., Lam, E.T., Liachko, I., Sullivan, S.T., Burton, J., Huson, H.J., Kelley, C.M., Hutchison, J.L., Zhou, Y., Sun, J., Crisa, A., Ponce De Leon, F.A., Schwartz, J.C., Hammond, J.A., Waldbieser, G.C., Schroeder, S.G., Liu, G., Dunham, M., Shendure, J., Sonstegard, T.S., Phillippy, A.M., Van Tassell, C.P., Smith, T.P. 2017. Single-molecule sequencing and conformational capture enable de novo mammalian reference genomes. Nature Genetics. 49(4):643-650.
    
  • Exploiting long read sequencing technologies to establish high quality highly contiguous pig reference genome assemblies-(Abstract Only)
    Warr, A., Hall, R., Kim, K., Tseng, E., Koren, S., Phillippy, A.M., Bickhart, D.M., Rosen, B.D., Schroeder, S.G., Hume, D.A., Talbot, R., Rund, L., Schook, L.B., Chow, W., Howe, K., Nonneman, D.J., Rohrer, G.A., Putnam, N., Green, E., Watson, M., Smith, T.P., Archibald, A.L. 2017. Exploiting long read sequencing technologies to establish high quality highly contiguous pig reference genome assemblies [abstract]. Plant and Animal Genome Conference XX, January 14-18, 2017, San Diego, California. Paper No. 25025.
    
  • Systematic profiling of bovine short tandem repeats using whole genome sequencing data-(Peer Reviewed Journal)
    Xu, L., Haasl, R.J., Sun, J., Zhou, Y., Bickhart, D.M., Son, J., Van Tassell, C.P., Lwein, H.A., Liu, G. 2016. Systematic profiling of bovine short tandem repeats using whole genome sequencing data. Genome Biology and Evolution. 9(1):20-31.
    
  • Reduced representation bisulphite sequencing of the cattle genome reveals DNA methylation patterns-(Peer Reviewed Journal)
    Zhou, Y., Xu, L., Bickhart, D.M., Hay, E., Schroeder, S.G., Connor, E.E., Leeson, A.J., Sonstegard, T., Van Tassell, C.P., Hong, C., Liu, G. 2016. Reduced representation bisulphite sequencing of the cattle genome reveals DNA methylation patterns. BMC Genomics. 17(1):779.
    
  • Revealing misassembled segments in the bovine reference genome by high resolution linkage disequilibrium scan-(Peer Reviewed Journal)
    Utsunomiya, A., De Abreu Santos, D.J., Boison, S.A., Utsunomiya, Y.T., Milanesi, M., Bickhart, D.M., Ajmone-Marsan, P., Solkner, J., Garcia, J.F., Fonseca, R., Da Silva, M.V. 2016. Revealing misassembled segments in the bovine reference genome by high resolution linkage disequilibrium scan. BMC Genomics. 17:705.
    
  • Comparative analyses across cattle breeds reveal the pitfalls caused by artificial and lineage-differential copy number variations-(Peer Reviewed Journal)
    Zhou, Y., Utsunomiya, Y.T., Xu, L., Hay, E.A., Bickhart, D.M., Carvalheiro, R., Neves, H.H., Van Tassell, C.P., Sonstegard, T.S., Garcia, J., Liu, G. 2016. Comparative analyses across cattle breeds reveal the pitfalls caused by artificial and lineage-differential copy number variations. Scientific Reports. 6:29219.
    
  • Reduced representation bisulphite sequencing of the ten bovine somatic tissues reveals DNA methylation patterns -(Abstract Only)
    Zhou, Y., Xu, L., Hay, E., Bickhart, D.M., Sonstegard, T., Van Tassell, C.P., Chen, H., Liu, G. 2016. Reduced representation bisulphite sequencing of the ten bovine somatic tissues reveals DNA methylation patterns [abstract]. In: Proceedings of 2016 BARC Poster Day, April 27, 2016, Beltsville, Maryland. P63.
    
  • Exploring the feasibility of using copy number variants as genetic markers through large-scale whole genome sequencing experiments-(Abstract Only)
    Bickhart, D.M., Xu, L., Hutchison, J.L., Cole, J.B., Null, D.J., Schroeder, S.G., Song, J., Garcia, J.F., Sonstegardq, T.S., Van Tassell, C.P., Schnabel, R.D., Taylor, J.F., Lewin, H.A., Liu, G. 2016. Exploring the feasibility of using copy number variants as genetic markers through large-scale whole genome sequencing experiments. Journal of Dairy Science. 99(E-Suppl. 1)/Journal of Animal Science. 94(E-Suppl. 5):142(abstr. 0306).
    
  • Identifying and calling insertions, deletions, and single-base mutations efficiently from sequence data-(Abstract Only)
    Van Raden, P.M., Bickhart, D.M., O'Connell, J.R. 2016. Identifying and calling insertions, deletions, and single-base mutations efficiently from sequence data. Journal of Dairy Science. 99(E-Suppl. 1)/Journal of Animal Science. 94(E-Suppl. 5):140(abstr. 0302).
    
  • Sexed-semen usage for Holstein AI in the United States-(Abstract Only)
    Hutchison, J.L., Bickhart, D.M. 2016. Sexed-semen usage for Holstein AI in the United States. Journal of Dairy Science. 99(E-Suppl. 1)/Journal of Animal Science. 94(E-Suppl. 5):176(abstr. 0372).
    
  • Selection of sequence variants to improve dairy cattle genomic predictions-(Abstract Only)
    Tooker, M.E., Van Raden, P.M., Bickhart, D.M., O'Connell, J.R. 2016. Selection of sequence variants to improve dairy cattle genomic predictions. Journal of Dairy Science. 99(E-Suppl. 1)/Journal of Animal Science. 94(E-Suppl. 5):138(abstr. 298).
    
  • Strategy for incorporating newly discovered causative genetic variants into genomic evaluations-(Abstract Only)
    Wiggans, G.R., Van Raden, P.M., Bickhart, D.M., Tooker, M.E. 2016. Strategy for incorporating newly discovered causative genetic variants into genomic evaluations. Journal of Dairy Science. 99(E–Suppl. 1)/Journal of Animal Science. 94(E–Suppl. 5):137(abstr. 296).
    
  • Calculation of genomic predicted transmitting abilities for bovine respiratory disease complex in Holsteins-(Abstract Only)
    Van Tassell, C.P., Spangler, G.L., Bickhart, D.M., Wiggans, G.R., Cole, J.B., Taylor, J.F., Neibergs, H.L., Seabury, C., Van Eenennaam, A.L., Womack, J.E., Brd Consortium 2016. Calculation of genomic predicted transmitting abilities for bovine respiratory disease complex in Holsteins. Journal of Dairy Science. 99(E-Suppl. 1)/Journal of Animal Science. 94(E-Suppl. 5):133(abstr. 0288).
    
  • Consumption of endophyte-infected fescue seed during the dry period and lactation affects mammary gland gene expression in dairy cows-(Abstract Only)
    Baldwin, R.L., Li, C., Bickhart, D.M., Clover, C.M., Grossi, P., Choudhary, R.K., Elsasser, T.H., Bertoni, G., Trevisi, E., Aiken, G.E., Mcleod, K.R., Capuco, A.V. 2016. Consumption of endophyte-infected fescue seed during the dry period and lactation affects mammary gland gene expression in dairy cows. Journal of Dairy Science. Vol. 99 (E-Supplement 1):401.
    
  • Resolving misassembled cattle immune gene clusters with hierarchical, long read sequencing-(Abstract Only)
    Bickhart, D.M., Hammond, J.A., Schwartz, J.C., Heimeier, D., Smith, T.P. 2016. Resolving misassembled cattle immune gene clusters with hierarchical, long read sequencing. International Society for Animal Genetics (ISAG). Salt Lake City, UT, July 23-27. p. 105–106 (P4054).
    
  • Whole-genome sequencing reveals the diversity of cattle copy number variations and multicopy genes-(Peer Reviewed Journal)
    Bickhart, D.M., Xu, L., Hutchison, J.L., Cole, J.B., Schroeder, S.G., Song, J., Garcia, J., Van Tassell, C.P., Sonstegard, T.S., Schnabel, R.D., Taylor, J.F., Lewin, H.A., Liu, G. 2016. Whole-genome sequencing reveals the diversity of cattle copy number variations and multicopy genes. DNA Research. 23(3):253-62.
    
  • Population-genetic properties of differentiated copy number variations in cattle-(Peer Reviewed Journal)
    Xu, L., Hou, Y., Bickhart, D.M., Zhou, Y., Hay, E.A., Song, J., Sonstegard, T., Van Tassell, C.P., Liu, G. 2016. Population-genetic properties of differentiated copy number variations in cattle. Scientific Reports. 6:23161.
    
  • Increasing the number of single nucleotide polymorphisms used in genomic evaluation of dairy cattle-(Peer Reviewed Journal)
    Wiggans, G.R., Cooper, T.A., Van Raden, P.M., Van Tassell, C.P., Bickhart, D.M., Sonstegard, T.S. 2016. Increasing the number of single nucleotide polymorphisms used in genomic evaluation of dairy cattle. Journal of Dairy Science. 99(6):4504-4511.
    
  • Genome-wide CNV analysis reveals variants associated with growth traits in Bos indicus-(Peer Reviewed Journal)
    Zhou, Y., Utsunomiya, Y.T., Xu, L., Hay, E.A., Bickhart, D.M., Carvalheiro, R., Neves, H.E., Sonstegard, T., Van Tassell, C.P., Garcia, J., Liu, G. 2016. Genome-wide CNV analysis reveals variants associated with growth traits in Bos indicus. Biomed Central (BMC) Genomics. 17(1):419.2016.
    
  • Improving the goat long-read assembly with optical mapping-(Abstract Only)
    Bickhart, D.M., Smith, T.P., Rosen, B.D., Koren , S., Phillippy, A., Hastie, A.R., Sullivan, S.T., Liachko, I., Burton, J.N., Sayre, B.L., Liu, G., Schroeder, S.G., Sonstegard, T.S., Van Tassell, C.P. 2016. Improving the goat long-read assembly with optical mapping. Plant and Animal Genome Conference Proceedings. San Diego, CA, Jan. 9–13.
    
  • Diversity and population-genetic properties of copy number variations and multicopy genes in cattle-(Abstract Only)
    Bickhart, D.M., Xu, L., Hutchison, J.L., Cole, J.B., Null, D.J., Schroeder, S.G., Song, J., Garcia, J., Van Tassell, C.P., Sonstegard, T.S., Schnabel, R.D., Taylor, J.F., Lewin, H.A., Liu, G. 2016. Diversity and population-genetic properties of copy number variations and multicopy genes in cattle [abstract]. USDA NIFA Animal Genome Program PD Meeting, January 8, 2016, San Diego, California.
    
  • Comparative ruminant genomics highlights segmental duplication and mobile element insertion diversity-(Abstract Only)
    Bickhart, D.M., Rosen, B.D., Schroeder, S.G., Van Tassell, C.P. 2016. Comparative ruminant genomics highlights segmental duplication and mobile element insertion diversity. Plant and Animal Genome Conference Proceedings. San Diego, CA, Jan. 9–13, W109.
    
  • Fast single-pass alignment and variant calling using sequencing data-(Abstract Only)
    Van Raden, P.M., Bickhart, D.M. 2016. Fast single-pass alignment and variant calling using sequencing data. Plant and Animal Genome Conference Proceedings. San Diego, CA, Jan. 9–13, W161.
    
  • Progress toward a low budget reference grade genome assembly -(Abstract Only)
    Rosen, B.D., Bickhart, D.M., Koren, S., Hastie, A.R., Schroeder, S.G., Smith, T.P., Sullivan, S.T., Liachko, I., Burton, J.N., Dunham, M.J., Sendure, J., Sayre, B.L., Huson, H.J., Liu, G., Connor, E.E., Sonstegard, T.S., Phillippy, A., Van Tassell, C.P. 2016. Progress toward a low budget reference grade genome assembly. Plant and Animal Genome Conference Proceedings. San Diego, CA, Jan. 9–13, P0612.
    
  • Effect of sex, age, and breed on genetic recombination features in cattle-(Abstract Only)
    Shen, B., Wang, Z., Jiang, J., Cole, J.B., Bickhart, D.M., Wiggans, G.R., Liu, G., Ma, L. 2016. Effect of sex, age, and breed on genetic recombination features in cattle. Plant and Animal Genome Conference Proceedings. San Diego, CA, Jan. 9–13, P0522.
    
  • Reducing animal sequencing redundancy by preferentially selecting animals with low-frequency haplotypes-(Peer Reviewed Journal)
    Bickhart, D.M., Hutchison, J.L., Null, D.J., Van Raden, P.M., Cole, J.B. 2016. Reducing animal sequencing redundancy by preferentially selecting animals with low-frequency haplotypes. Journal of Dairy Science. 99(7):5526-5534.
    
  • Tet-mediated imprinting erasure in H19 locus following reprogramming of spermatogonial stem cells to induced pluripotent stem cells -(Peer Reviewed Journal)
    Bermejo-Alvarez, P., Ramos-Ibeas, P., Park, K., Powell, A.M., Vansandt, L., Bickhart, D.M., Ramirez, M.A., Gutierrez-Adan, A., Telugu, B. 2015. Tet-mediated imprinting erasure in H19 locus following reprogramming of spermatogonial stem cells to induced pluripotent stem cells. Scientific Reports. 5:13691.
    
  • Cattle sex-specific recombination and genetic control from a very large pedigree-(Peer Reviewed Journal)
    Ma, L., O'Connell, J.R., Van Raden, P.M., Shen, B., Padhi, A., Sun, C., Bickhart, D.M., Cole, J.B., Null, D.J., Liu, G., Da, Y., Wiggans, G.R. 2015. Cattle sex-specific recombination and genetic control from a very large pedigree. PLoS Genetics. 11(11):e1005387.
    
  • Animal selection for whole genome sequencing by quantifying the unique contribution of homozygous haplotypes sequenced-(Abstract Only)
    Bickhart, D.M., Cole, J.B., Hutchison, J.L. 2015. Animal selection for whole genome sequencing by quantifying the unique contribution of homozygous haplotypes sequenced. Journal of Dairy Science. 98(Suppl. 2)/Journal of Animal Science 93(Suppl. 3):649(abstr. W86).
    
  • Identification of copy number variable gene families in Holstein and Jersey cattle-(Abstract Only)
    Bickhart, D.M., Xu, L., Hutchison, J.L., Liu, G., Lewin, H.A. 2015. Identification of copy number variable gene families in Holstein and Jersey cattle. Journal of Dairy Science. 98(Suppl. 2)/Journal of Animal Science 93(Suppl. 3):648(abstr. W84).
    
  • Effect of increasing the number of single-nucleotide polymorphisms from 60,000 to 85,000 in genomic evaluation of Holsteins-(Abstract Only)
    Wiggans, G.R., Cooper, T.A., Van Raden, P.M., Pomp, D., Van Tassell, C.P., Bickhart, D.M., Sonstegard, T.S. 2015. Effect of increasing the number of single-nucleotide polymorphisms from 60,000 to 85,000 in genomic evaluation of Holsteins. Journal of Dairy Science. 98(Suppl. 2)/Journal of Animal Science 93(Suppl. 3):578(abstr. 537).
    
  • RAPTR-SV: a hybrid method for the detection of structural variants -(Peer Reviewed Journal)
    Bickhart, D.M., Hutchison, J.L., Xu, L., Schnabel, R.D., Taylor, J.F., Reecy, J.M., Schroeder, S.G., Van Tassell, C.P., Sonstegard, T.S., Liu, G. 2015. RAPTR-SV: a hybrid method for the detection of structural variants. Bioinformatics. 31(13):2084-2090.
    
  • The use of PacBio and Hi-C data in denovo assembly of the goat genome-(Abstract Only)
    Bickhart, D.M., Koren, S., Phillippy, A.M., Smith, T.P., Burton, J.N., Llachko, I., Sayre, B.L., Huson, H.J., Schroeder, S.G., Van Tassell, C.P., Sonstegard, T.S. 2015. The use of PacBio and Hi-C data in denovo assembly of the goat genome. Plant and Animal Genome Conference Proceedings. San Diego, CA, January 10–14, W144.
    
  • Comparison of CNVs in Buffalo with other species-(Abstract Only)
    Bickhart, D.M., Liu, G., International Water, B.A. 2015. Comparison of CNVs in Buffalo with other species. Plant and Animal Genome Conference Proceedings. San Diego, CA, January 10–14, W107.
    
  • Genomic signatures reveal geographic adaption and human selection in cattle-(Peer Reviewed Journal)
    Xu, L., Bickhart, D.M., Cole, J.B., Schroeder, S.G., Song, J., Van Tassell, C.P., Sonstegard, T.S., Liu, G. 2014. Genomic signatures reveal geographic adaption and human selection in cattle. Molecular Biology and Evolution. 32(3):711-25.
    
  • Genome wide CNV analysis reveals additional variants associated with milk production traits in Holsteins-(Peer Reviewed Journal)
    Xu, L., Cole, J.B., Bickhart, D.M., Hou, Y., Song, J., Van Raden, P.M., Sonstegard, T.S., Van Tassell, C.P., Liu, G. 2014. Genome wide CNV analysis reveals additional variants associated with milk production traits in Holsteins. Biomed Central (BMC) Genomics. 15:683.
    
  • The identification of a putative mutation for SLICK hair coat in Senepol cattle-(Abstract Only)
    
    
  • Using the whole read: structural variant detection using NGS data-(Proceedings)
    Bickhart, D.M., Cole, J.B., Hutchison, J.L., Xu, L., Liu, G. 2014. Using the whole read: structural variant detection using NGS data. World Congress of Genetics Applied in Livestock Production. Vancouver, Canada, Aug. 17–22. 5 pp.
    
  • The hunt for a functional mutation affecting conformation and calving traits on chromosome 18 in Holstein cattle-(Proceedings)
    Cole, J.B., Hutchison, J.L., Null, D.J., Van Raden, P.M., Liu, G., Schroeder, S.G., Smith, T.P., Sonstegard, T.S., Van Tassell, C.P., Bickhart, D.M. 2014. The hunt for a functional mutation affecting conformation and calving traits on chromosome 18 in Holstein cattle. World Congress of Genetics Applied in Livestock Production. Vancouver, Canada, Aug. 17–22. 3 pp.
    
  • Genome wide CNV analysis reveals additional variants associated with milk production traits in Holsteins-(Abstract Only)
    Xu, L., Cole, J.B., Bickhart, D.M., Hou, Y., Song, J., Van Raden, P.M., Sonstegard, T.S., Van Tassell, C.P., Liu, G. 2014. Genome wide CNV analysis reveals additional variants associated with milk production traits in Holsteins. BARC Poster Day. BARC Poster Day.p.67, abstract 54.
    
  • Population sequencing reveals breed and sub-species specific CNVs in cattle-(Abstract Only)
    Bickhart, D.M., Xu, L., Hutchison, J.L., Sonstegard, T.S., Van Tassell, C.P., Schroeder, S.G., Fernando Garcia, J., Taylor, J.F., Schnabel, R.D., Lewin, H.A., Liu, G. 2014. Population sequencing reveals breed and sub-species specific CNVs in cattle. CONFERENCE ON THE BIOLOGY OF GENOMES. Conference on the Biology of Genomes, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. p199.
    
  • Bovine exome sequence analysis and targeted SNP genotyping of recessive fertility defects HH2, HH3, and BH1 reveals causative mutation in SMC2 for HH3 -(Peer Reviewed Journal)
    Mc Clure, M., Bickhart, D.M., Null, D.J., Van Raden, P.M., Xu, L., Wiggans, G.R., Liu, G., Schroeder, S.G., Glasscock, J., Armstrong, J., Cole, J.B., Sonstegard, T.S., Van Tassell, C.P. 2014. Bovine exome sequence analysis and targeted SNP genotyping of recessive fertility defects HH2, HH3, and BH1 reveals causative mutation in SMC2 for HH3. PLoS One. 9(3):e92769.
    
  • A high-resolution whole-genome map of the distinctive epigenomic landscape induced by butyrate in bovine cells-(Peer Reviewed Journal)
    Shin, J., Xu, L., Li, R.W., Gao, Y., Bickhart, D.M., Liu, G., Baldwin, R.L., Li, C. 2014. A high-resolution whole-genome map of the distinctive epigenomic landscape induced by butyrate in bovine cells. Animal Genetics. 45:40–50. DOI:10.1111.age.12147.
    
  • A genome-wide survey reveals a deletion polymorphism associated with resistance to gastrointestinal nematodes in Angus cattle-(Peer Reviewed Journal)
    Xu, L., Hou, Y., Bickhart, D.M., Song, J., Van Tassell, C.P., Sonstegard, T.S., Liu, G. 2014. A genome-wide survey reveals a deletion polymorphism associated with resistance to gastrointestinal nematodes in Angus cattle. Functional and Integrative Genomics. DOI:14(2):333-9.
    
  • The challenges and importance of structural variation detection in livestock-(Review Article)
    Bickhart, D.M., Liu, G. 2014. The challenges and importance of structural variation detection in livestock. Frontiers in Genetics. 5:37.
    
  • A genome-wide association study of calf birth weight in Holstein cattle using single nucleotide polymorphisms and phenotypes predicted from auxiliary traits -(Peer Reviewed Journal)
    Cole, J.B., Waurich, B., Wensch-Dorendorf, M., Bickhart, D.M., Swalve, H.H. 2014. A genome-wide association study of calf birth weight in Holstein cattle using single nucleotide polymorphisms and phenotypes predicted from auxiliary traits. Journal of Dairy Science. 97(5):3156-3172.
    
  • The use of population-scale sequencing to identify CNVs impacting productive traits in different cattle breeds-(Abstract Only)
    Bickhart, D.M., Xu, L., Hutchison, J.L., Sonstegard, T.S., Van Tassell, C.P., Schroeder, S.G., Garcia, J.F., Taylor, J.F., Schnabel, R.D., Lewin, H., Liu, G. 2014. The use of population-scale sequencing to identify CNVs impacting productive traits in different cattle breeds. Plant and Animal Genome Conference Proceedings. Plant Animal Genome XXII, San Diego, CA, Jan. 11–15, P078.
    
  • Candidate causative mutation on BTA18 associated with calving and conformation traits in Holstein bulls-(Abstract Only)
    Cole, J.B., Hutchison, J.L., Null, D.J., Van Raden, P.M., Liu, G., Schroeder, S.G., Sonstegard, T.S., Van Tassell, C.P., Bickhart, D.M. 2014. Candidate causative mutation on BTA18 associated with calving and conformation traits in Holstein bulls. Plant and Animal Genome Conference Proceedings. Plant Animal Genome XXII, San Diego, CA, Jan. 11–15, P1097.
    
  • Assessing signatures of selection through variation in linkage disequilibrium between taurine and indicine cattle-(Peer Reviewed Journal)
    Perez O'Brien, A.M., Utsunomiya, Y.T., Meszaros, G., Bickhart, D.M., Liu, G., Garcia, J., Van Tassell, C.P., Sonstegard, T.S., Solkner, J. 2014. Assessing signatures of selection through variation in linkage disequilibrium between taurine and indicine cattle. Genetics Selection Evolution. 46:19.
    
  • Short communication: Use of young bulls in the United States -(Peer Reviewed Journal)
    Hutchison, J.L., Cole, J.B., Bickhart, D.M. 2014. Short communication: Use of young bulls in the United States. Journal of Dairy Science. 97(5):3213-3220.
    
  • Population sequencing reveals breed and sub-species specific CNVs in cattle-(Abstract Only)
    Liu, G., Bickhart, D.M., Xu, L., Hutchison, J.L., Sonstegard, T.S., Van Tassell, C.P., Schroeder, S.G., Garcia, J., Taylor, J.F., Schnabel, R.D., Lewin, H.A. 2014. Population sequencing reveals breed and sub-species specific CNVs in cattle. Meeting Abstract. Advances in Genome Biology & Technology Conference Meeting Abstract. p.58.
    
  • A genome-wide survey reveals a deletion polymorphism associated with resistance to gastrointestinal nematodes in Angus cattle-(Abstract Only)
    Liu, G., Xu, L., Hou, Y., Bickhart, D.M., Song, J., Van Tassell, C.P., Sonstegard, T.S. 2013. A genome-wide survey reveals a deletion polymorphism associated with resistance to gastrointestinal nematodes in Angus cattle. BA-UMD Symposium. The University of Maryland/Beltsville ARS 3rd Annual Symposium.
    
  • Random forests approach for identifying additive and epistatic single nucleotide polymorphisms associated with residual feed intake in dairy cattle-(Peer Reviewed Journal)
    Yao, C., Spurlock, D., Armentano, L., Page, D., Vandehaar, M., Bickhart, D.M., Weigel, K. 2013. Random forests approach for identifying additive and epistatic single nucleotide polymorphisms associated with residual feed intake in dairy cattle. Journal of Dairy Science. 96(10):6716-6729.
    
  • Structural and functional impacts of copy number variations on the cattle genome-(Abstract Only)
    Liu, G., Bickhart, D.M. 2013. Structural and functional impacts of copy number variations on the cattle genome (abstract). Lecture. p.3.
    
  • Comparative analysis of CNV calling algorithms: literature survey and a case study using bovine high-density SNP data-(Review Article)
    Xu, L., Hou, Y., Bickhart, D.M., Jiuzhou, S., Liu, G. 2013. Comparative analysis of CNV calling algorithms: literature survey and a case study using bovine high-density SNP data. Microarrays. 2(3):171-185.
    
  • Open source tools to exploit DNA sequence data from livestock species-(Proceedings)
    Bickhart, D.M., Hutchison, J.L., Xu, L., Song, J., Liu, G. 2013. Open source tools to exploit DNA sequence data from livestock species. BARC Poster Day. p. 9, abstract 4.
    
  • Analysis of population structure and genetic history of cattle breeds based on high-density SNP data-(Abstract Only)
    Xu, L., Huson, H.J., Hou, Y., Bickhart, D.M., Song, J., Sonstegard, T.S., Van Tassell, C.P., Liu, G. 2013. Analysis of population structure and genetic history of cattle breeds based on high-density SNP data. BARC Poster Day. p.55 Abstract 48.
    
  • Genomic divergence of indicine and taurine cattle identified through high-density SNP genotyping-(Abstract Only)
    Porto-Neto, L.R., Sonstegard, T.S., Mcclure, M.C., Bickhart, D.M., Gondro, C., Da Silva, M., Utsunomiya, Y.T., Garcia, J.F., Van Tassell, C.P. 2013. Genomic divergence of indicine and taurine cattle identified through high-density SNP genotyping. J. Anim. Sci. Vol. 91, E-Suppl. 2/J. Dairy Sci. Vol. 96, E-Suppl. 1, paper 314, pp. 314.
    
  • Tools to exploit sequence data to find new markers and disease loci in dairy cattle-(Abstract Only)
    Bickhart, D.M., Harris, L., Liu, G. 2013. Tools to exploit sequence data to find new markers and disease loci in dairy cattle. Journal of Dairy Science. 96(E-Suppl. 1):624 (abstr. 557).
    
  • Optimal age at first calving for U.S. dairy cattle-(Abstract Only)
    Cole, J.B., Hutchison, J.L., Bickhart, D.M., Null, D.J. 2013. Optimal age at first calving for U.S. dairy cattle. Journal of Dairy Science. 96(E-Suppl. 1):289–290 (abstr. W188).
    
  • Fine mapping for Weaver Syndrome in the Brown Swiss breed with the identification of possible casual mutations across NRCAM, PNPLA8, and CTTNBP2 and Developement of a diagnostic SNP haplotype-(Peer Reviewed Journal)
    Mcclure, M.C., Kim, E., Bickhart, D.M., Null, D.J., Cooper, T.A., Cole, J.B., Wiggans, G.R., Marsan, P.A., Colli, L., Santus, E., Liu, G., Schroeder, S.G., Matukumalli, L., Van Tassell, C.P., Sonstegard, T.S. 2013. Fine mapping for Weaver Syndrome in the Brown Swiss breed with the identification of possible casual mutations across NRCAM, PNPLA8, and CTTNBP2 and Developement of a diagnostic SNP haplotype. PLoS One. 8(3):e59251.
    
  • Mapping cattle copy number variations in water buffalo-(Abstract Only)
    Liu, G., Bickhart, D.M. 2013. Mapping cattle copy number variations in water buffalo. Meeting Abstract. W115.
    
  • Combined arms: a full spectrum approach to structural variant discovery in livestock populations-(Abstract Only)
    Bickhart, D.M., Liu, G. 2013. Combined arms: a full spectrum approach to structural variant discovery in livestock populations. Meeting Abstract. W145.
    
  • Bos taurus indicus (Nelore) hybrid assembly improvement using PacBio reads-(Abstract Only)
    Schroeder, S.G., Zimin, A., Bickhart, D.M., Sonstegard, T.S., Van Tassell, C.P., Garcia, F.J. 2013. Bos taurus indicus (Nelore) hybrid assembly improvement using PacBio reads. Poster P0523, pp.237.
    
  • Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping-(Peer Reviewed Journal)
    Porto-Neto, L.R., Sonstegard, T.S., Liu, G., Bickhart, D.M., Gondro, C., Silva, M., Machado, M., Utsunomiya, Y.T., Garcia, J.F., Van Tassell, C.P. 2013. Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping. Biomed Central (BMC) Genomics. DOI:10.1186/1471-2164-14-876.
    
  • Identification of a nonsense mutation in CWC15 associated with decreased reproductive efficiency in Jersey cattle-(Peer Reviewed Journal)
    Sonstegard, T.S., Cole, J.B., Van Raden, P.M., Van Tassell, C.P., Null, D.J., Schroeder, S.G., Bickhart, D.M., Mcclure, M.C. 2013. Identification of a nonsense mutation in CWC15 associated with decreased reproductive efficiency in Jersey cattle. PLoS One. 8(1):e54872.
    
  • Bos taurus indicus (Nelore) hybrid assembly improvement using PacBio reads-(Abstract Only)
    
    
  • Identification of candidate transcription factor binding sites in the cattle genome-(Peer Reviewed Journal)
    Bickhart, D.M., Liu, G. 2013. Identification of candidate transcription factor binding sites in the cattle genome. Genomics, Proteomics and Bioinformatics. 11(3):195-198.
    
  • Analysis of copy number variations in Holstein cows identify potential mechanisms contributing to differences in residual feed intake-(Peer Reviewed Journal)
    Hou, Y., Bickhart, D.M., Chung, H., Hutchison, J.L., Norman, H.D., Connor, E.E., Liu, G. 2012. Analysis of copy number variations in Holstein cows identify potential mechanisms contributing to differences in residual feed intake. Functional and Integrative Genomics. 12(4):717-723.
    
  • Fine mapping of copy number variations on two cattle genome assemblies using high density SNP array-(Peer Reviewed Journal)
    Hou, Y., Bickhart, D.M., Hvinden, M.L., Li, C., Song, J., Boichard, D.A., Fritz, S., Eggen, A., Denise, S., Wiggans, G.R., Sonstegard, T.S., Van Tassell, C.P., Liu, G. 2012. Fine mapping of copy number variations on two cattle genome assemblies using high density SNP array. Biomed Central (BMC) Genomics. 13:376.
    
  • The trappin gene famliy: structue, function and evolution-(Review Article)
    Liu, G., Bickhart, D.M. 2013. The trappin gene famliy: structue, function and evolution. Cattle: Domestication, Disease and Environment. 1st edition. Hauppauge, NY: Nova Science Publishers, Inc. 25-38 p.
    
  • Copy Number Variation in the Cattle Genome-(Review Article)
    Liu, G., Bickhart, D.M. 2012. Copy Number Variation in the Cattle Genome. Functional and Integrative Genomics. DOI: 10.1007/S10142-012-0289-9.
    
  • Butyrate induced IGF2 activation correlated with distinct chromatin landscapes due to histone modification-(Peer Reviewed Journal)
    Shin, J., Li, R.W., Goa, Y., Bickhart, D.M., Liu, G., Li, W., Wu, S., Li, C. 2013. Butyrate induced IGF2 activation correlated with distinct chromatin landscapes due to histone modification. PLoS Genetics. DOI:10.4137/GRSB.S11243.
    
  • Copy number variation detection in cattle reveals potential breed specific differences -(Abstract Only)
    Bickhart, D.M., Hou, Y., Schroeder, S.G., Alkan, C., Cardone, M., Matukumalli, L.K., Song, J., Schnabel, R.D., Ventura, M., Taylor, J., Garcia, J., Van Tassell, C.P., Sonstegard, T.S., Eichler, E.E., Liu, G. 2012. Copy number variation detection in cattle reveals potential breed specific differences. BARC Poster Day. p. 13
    
  • Copy number variation of individual cattle genomes using next-generation sequencing-(Peer Reviewed Journal)
    Bickhart, D.M., Hou, Y., Schroeder, S.G., Alkan, C., Cardone, M., Matukumalli, L.K., Song, J., Schnabel, R.D., Ventura, M., Taylor, J., Garcia, J., Van Tassell, C.P., Sonstegard, T.S., Eichler, E.E., Liu, G. 2012. Copy number variation of individual cattle genomes using next-generation sequencing. Genome Research. 22(4):778-90.
    
  • Copy number variation of individual cattle genomes using next-generation sequencing-(Abstract Only)
    Bickhart, D.M., Hou, Y., Schroeder, S.G., Alkan, C., Cardone, M., Matukumalli, L.K., Song, J., Schnabel, R.D., Ventura, M., Taylor, J.F., Garcia, J., Van Tassell, C.P., Sonstegard, T.S., Eichler, E.E., Liu, G. 2012. Copy number variation of individual cattle genomes using next-generation sequencing. Plant and Animal Genome Conference. p. 549.
    
  • Copy number variations related to reproduction traits in Holstein cattle-(Abstract Only)
    Hou, Y., Bickhart, D.M., Fang, X., Song, J., Van Tassell, C.P., Sonstegard, T.S., Seroussi, E., Liu, G. 2011. Copy number variations related to reproduction traits in Holstein cattle. Meeting Abstract. No. 7.
    
  • Genomic regions showing copy number variations associate with resistance or susceptibility to gastrointestinal nematodes in Angus cattle-(Abstract Only)
    Hou, Y., Liu, G., Bickhart, D.M., Matukumalli, L.K., Li, C., Song, J., Gasbarre, L.C., Van Tassell, C.P., Sonstegard, T.S. 2011. Genomic regions showing copy number variations associate with resistance or susceptibility to gastrointestinal nematodes in Angus cattle [abstract]. Paper No. 6.
    
  • Individualized cattle copy number and segmental duplication maps using next generation sequencing-(Abstract Only)
    Bickhart, D.M., Hou, Y., Schroeder, S.G., Alkan, C., Cardone, M., Matukumalli, L., Song, J., Schnabel, R.D., Ventura, M., Taylor, J.F., Garcia, J., Eichler, E.E., Sonstegard, T.S., Van Tassell, C.P., Liu, G. 2011. Individualized cattle copy number and segmental duplication maps using next generation sequencing. Meeting Abstract. No. 8.
    
  • Genomic regions showing copy number variations associate with resistance or susceptibility to gastrointestinal nematodes in Angus Cattle-(Peer Reviewed Journal)
    Hou, Y., Liu, G., Bickhart, D.M., Matukumalli, L.K., Li, C., Song, J., Gasbarre, L.C., Van Tassell, C.P., Sonstegard, T.S. 2011. Genomic regions showing copy number variations associate with resistance or susceptibility to gastrointestinal nematodes in Angus Cattle. Functional and Integrative Genomics. 12(1):81-92.
    
  • A high-resolution cattle CNV map by population-scale genome sequencing-(Abstract Only)
    Bickhart, D.M., Hou, Y., Schroeder, S.G., Alkan, C., Cardone, M.F., Matukumalli, L.K., Schnabel, R.D., Ventura, M., Taylor, J.F., Eichler, E.E., Sonstegard, T.S., Van Tassell, C.P., Liu, G. 2011. A high-resolution cattle CNV map by population-scale genome sequencing [abstract]. Gordon Research Conference. No. 48.
    
  • A high-resolution cattle CNV map by population-scale genome sequencing-(Abstract Only)
    Bickhart, D.M., Hou, Y., Liu, G., Schroeder, S.G., Can, A., Maria, C., Matukumalli, L., Song, J., Schnabel, R., Ventura, M., Taylor, J., Eichler, E., Sonstegard, T.S., Van Tassell, C.P., Illumina Bovine Hd, C. 2011. A high-resolution cattle CNV map by population-scale genome sequencing. BARC Poster Day [abstract]. No. 5.
    
  • Genomic and functional characteristics of copy number variations in Angus cattle selected for resistance or susceptibility to gastrointestinal nematodes-(Abstract Only)
    Hou, Y., Liu, G., Bickhart, D.M., Matukumalli, L., Song, J., Gasbarre, L., Van Tassell, C.P., Sonstegard, T.S. 2011. Genomic and functional characteristics of copy number variations in Angus cattle selected for resistance or susceptibility to gastrointestinal nematodes [abstract]. BARC Poster Day. No. 17.
    
  • Genomic characteristics of cattle copy number variations-(Peer Reviewed Journal)
    Hou, Y., Liu, G., Bickhart, D.M., Cardone, M.F., Wang, K., Kim, E., Matukumalli, L., Ventura, M., Song, J., Van Raden, P.M., Sonstegard, T.S., Van Tassell, C.P. 2011. Genomic characteristics of cattle copy number variations. Biomed Central (BMC) Genomics. 12:127.
    
  • A high-resolution cattle CNV map by population-scale genome sequencing-(Abstract Only)
    Bickhart, D.M., Hou, Y., Schroeder, S.G., Alkan, C., Cardone, M.F., Matukumalli, L.K., Schnabel, R.D., Ventura, M., Taylor, J.F., Eichler, E.E., Sonstegard, T.S., Van Tassell, C.P., Liu, G. 2011. A high-resolution cattle CNV map by population-scale genome sequencing. CONFERENCE ON THE BIOLOGY OF GENOMES [abstract]. p. 32.