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Benjamin D Rosen
Animal Genomics and Improvement Laboratory
Research Biologist

Phone: (301) 504-8416
Fax: (301) 504-8414
Room 112

10300 BALTIMORE AVENUE
BLDG 306 BARC-EAST
BELTSVILLE , MD 207052350
Projects
Enhancing Genetic Merit of Ruminants Through Improved Genome Assembly, Annotation, and Selection
In-House Appropriated (D)
  Accession Number: 433411
Improving Dairy Animals by Increasing Accuracy of Genomic Prediction, Evaluating New Traits, and Redefining Selection Goals
In-House Appropriated (D)
  Accession Number: 433412
Technical Services, Collaborative Research and Cooperative Activities with the United States Agency for International Development, Phase III
Reimbursable Cooperative Agreement (R)
  Accession Number: 425991
Identification of Signatures of Selection in Locally Adapted Goats
Non-Assistance Cooperative Agreement (S)
  Accession Number: 432742

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)
Genome-wide SNP profiling of worldwide goat populations reveals a strong partitioning of diversity and highlights post-domestication migration routes -
Misidentification of runs of homozygosity islands in cattle caused by interference with copy number variation or large intermarker distances -
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.
Signatures of selection and environmental adaptation across the goat genome post domestication -
Comparative whole genome DNA methylation profiling of cattle sperm and somatic tissues reveals striking hypomethylated patterns in sperm -
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 -
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).
Long-read sequencing enables the accurate annotation of immune gene clusters in goat -
Chromosome-level assembly of the water buffalo genome -
Whole genome structural analysis of Caribbean hair sheep reveals quantitative link to West African ancestry -
Spangler, G.L., Rosen, B.D., Iiori, M.B., Hanotte, O., Kim, E.S., Sonstegard, T.S., Burke, J.M., Morgan, J.L., Notter, D.R., Van Tassell, C.P. 2017. Whole genome structural analysis of Caribbean hair sheep reveals quantitative link to West African ancestry. PLoS One. 12(6):e0179021.
Single-molecule sequencing and conformational capture enable de novo mammalian reference genomes -
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 -
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.
Improving the goat long-read assembly with optical mapping -
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.
Progress toward a low budget reference grade genome assembly Reprint Icon -
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.
Comparative ruminant genomics highlights segmental duplication and mobile element insertion diversity -
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.