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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
African Goat Improvement Network: Breed Characterization of Mongolian Cashmere Goats
Non-Assistance Cooperative Agreement (S)
  Accession Number: 436201
African Goat Improvement Network: Upscaling of Community-Based Breeding Program in Konso District, Ethiopia
Non-Assistance Cooperative Agreement (S)
  Accession Number: 437943
Design and Implementation of Community Based Goat Breeding Programs in Burkina Faso
Non-Assistance Cooperative Agreement (S)
  Accession Number: 438942

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)
Copy number variation analysis reveals variants associated with milk production traits in dairy goats - (Peer Reviewed Journal)
The Bovine Pangenome Consortium - (Abstract Only)
Comparative whole genome DNA methylation profiling of cattle tissues reveals global and tissue-specific methylation patterns Reprint Icon - (Peer Reviewed Journal)
Zhou, Y., Liu, S., Hu, Y., Fang, L., Gao, Y., Xia, H., Schroeder, S.G., Rosen, B.D., Connor, E.E., Li, C., Baldwin, R.L., Cole, J.B., Van Tassell, C.P., Yang, L., Ma, L., Liu, G. 2020. Comparative whole genome DNA methylation profiling of cattle tissues reveals global and tissue-specific methylation patterns. BMC Biology. 18(1):85. https://doi.org/10.1186/s12915-020-00793-5.
Scaling up community-based breeding programmes via multi-stakeholder collaboration Reprint Icon - (Peer Reviewed Journal)
Kaumbata, W., Nakimbugwe, H.N., Haile, A., Banda, L.J., Meszaros, G., Gondwe, T.N., Woodward Greene, M.J., Rosen, B.D., Van Tassell, C.P., Solkner, J., Wurzinger, M. 2020. Scaling up community-based breeding programmes via multi-stakeholder collaboration. Journal of Agriculture and Rural Development in the Tropics and Subtropics. 12(1):99-112. https://doi.org/10.17170/kobra-202005281298.
Comprehensive analyses of 723 transcriptomes enhance biological interpretation and genomic prediction for complex traits in cattle Reprint Icon - (Peer Reviewed Journal)
Fang, L., Cai, W., Liu, S., Canela-Xandri, O., Gao, Y., Jiang, J., Rawlik, K., Li, B., Schroeder, S.G., Rosen, B.D., Li, C., Sonstegard, T.S., Alexander, L.J., Van Tassell, C.P., Van Raden, P.M., Cole, J.B., Yu, Y., Zhang, S., Tenesa, A., Ma, L., Liu, G. 2019. Comprehensive analyses of 723 transcriptomes enhance biological interpretation and genomic prediction for complex traits in cattle. Genome Research. 30(5):790-801. https://doi.org/10.1101/gr.250704.119.
An improved pig reference genome sequence to enable pig genetics and genomics research Reprint Icon - (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.
Tangible and intangible benefits of local goats rearing in smallholder farms in Malawi Reprint Icon - (Peer Reviewed Journal)
Kaumbata, W., Banda, L.J., Meszaros, G., Gondwe, T.N., Woodward Greene, M.J., Rosen, B.D., Van Tassell, C.P., Solkner, J., Wurzinger, M. 2020. Tangible and intangible benefits of local goats rearing in smallholder farms in Malawi. Small Ruminant Research. 87:106095. https://doi.org/10.1016/j.smallrumres.2020.106095.
Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle Reprint Icon - (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.
Continuous chromosome-scale haplotypes assembled from a single interspecies F1 hybrid of yak and cattle Reprint Icon - (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.
Canfam_GSD: Denovochromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C Reprint Icon - (Peer Reviewed Journal)
Field, M.A., Rosen, B.D., Dudchenko, O., Chan, E.K.F., Minoche, A.E., Edwards, R.J., Barton, K., Lyons, R.J., Enosi Tuipulotu, D., Hayes, V.M., Omer, A.D., Colaric, Z., Keilwagen, J., Skvortsova, K., Bogdanovic, O., Smith, M.A., Aiden, E.L., Smith, T.P., Zammit, R.A., Ballard, J.O. 2020. Canfam_GSD: Denovochromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C. GigaScience. 9(4):1-12. https://doi.org/10.1093/gigascience/giaa027.
De novo assembly of the cattle reference genome with single-molecule sequencing Reprint Icon - (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 Reprint Icon ()
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 Reprint Icon - (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.
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.
Reprogramming of root cells during nitrogen-fixing symbiosis involves dynamic polysome association of coding and non-coding RNAs Reprint Icon - (Peer Reviewed Journal)
Traubenik, S., Reynoso, M.A., Hobecker, K.V., Lancia, M., Hummel, M., Rosen, B.D., Town, C., Bailey-Serres, J., Blanco, F.F., Zanetti, M.E. 2020. Reprogramming of root cells during nitrogen-fixing symbiosis involves dynamic polysome association of coding and non-coding RNAs. The Plant Cell. 32:352-373. https://doi.org/10.1105/tpc.19.00647.
Signatures of selection and environmental adaptation across the goat genome post-domestication Reprint Icon - (Peer Reviewed Journal)
Bertolini, F., Servin, B., Talenti, A., Rochat, E., Kim, E., Oget, C., Palhiere, I., Crisa, A., Catillo, G., Steri, R., Amills, M., Colli, L., Marras, G., Milanesi, M., Nicolazzi, E., Rosen, B.D., Van Tassell, C.P., Guldbrandtsen, B., Sonstegard, T.S., Tosser-Klopp, G., Stella, A., Rothschild, M.F., Joost, S., Crepaldi, P. 2018. Signatures of selection and environmental adaptation across the goat genome post-domestication. Genetic Selection Evolution. 50:57. https://doi.org/10.1186/s12711-018-0421-y.
Genome-wide CNV analysis revealed variants associated with growth traits in African indigenous goats Reprint Icon - (Peer Reviewed Journal)
Liu, M., Woodward Greene, M.J., Kang, X., Pan, M.G., Rosen, B.D., Van Tassell, C.P., Chen, H., Liu, G. 2020. Genome-wide CNV analysis revealed variants associated with growth traits in African indigenous goats. Genomics. 112(2):1477-1480. https://doi.org/10.1016/j.ygeno.2019.08.018.
Progress report on a plains bison-Simmental interspecies cross for genome assembly by trio binning ()
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 Reprint Icon ()
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.
Timing and extent of inbreeding in African goats Reprint Icon - (Peer Reviewed Journal)
Nandolo, W., Meszaros, G., Banda, L.J., Gondwe, T.N., Lamuno, D., Mulindwa, H., Nakimbugwe, H.N., Wurzinger, M., Utsunomiya, Y.T., Woodward Greene, M.J., Liu, M., Liu, G., Van Tassell, C.P., Curik, I., Rosen, B.D., Solkner, J. 2019. Timing and extent of inbreeding in African goats. Frontiers in Genetics. 10:57. https://doi.org/10.3389/fgene.2019.00537.
Integrating signals from sperm methylome analysis and genome-wide association study for a better understanding of male fertility in cattle Reprint Icon - (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.
Comparative analyses of sperm DNA methylomes among human, mouse and cattle provide insights into epigenomic evolution and complex traits Reprint Icon - (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) Reprint Icon - (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 Reprint Icon - (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.
Short communication: Identification of the pseudoautosomal region in the Hereford bovine reference genome assembly ARS-UCD1.2 Reprint Icon - (Peer Reviewed Journal)
Johnson, T., Keehan, M., Harland, C., Lopdell, T., Spelman, R.J., Davis, S.R., Rosen, B.D., Smith, T.P., Couldrey, C. 2019. Short communication: Identification of the pseudoautosomal region in the Hereford bovine reference genome assembly ARS-UCD1.2. Journal of Dairy Science. 102(4):3254-3258. https://doi.org/10.3168/jds.2018-15638.
AdaptMap: Exploring goat diversity and adaptation Reprint Icon - (Peer Reviewed Journal)
Stella, A., Nicolazzi, E.L., Van Tassell, C.P., Rothschild, M., Colli, L., Rosen, B.D., Sonstegard, T.S., Crepaldi, P., Tosser, G., Joost, S., Adaptmap Consortium. 2018. AdaptMap: Exploring goat diversity and adaptation. Genetic Selection Evolution. 50:61. https://doi.org/10.1186/s12711-018-0427-5.
Genome-wide SNP profiling of worldwide goat populations reveals a strong partitioning of diversity and highlights post-domestication migration routes Reprint Icon - (Peer Reviewed Journal)
Colli, L., Milanesi, M., Talenti, A., Bertolini, F., Chen, M., Crisa, A., Daly, K., Del Corvo, M., Guldbrandtsen, B., Lenstra, J.A., Rosen, B.D., Vajana, E., Catillo, G., Joost, S., Nicolazzi, E., Rochat, E., Rothschild, M.F., Servin, B., Sonstegard, T.S., Steri, R., Van Tassell, C.P., Ajmone-Marsan, P., Crepaldi, P., Stella, A. 2018. Genome-wide SNP profiling of worldwide goat populations reveals a strong partitioning of diversity and highlights post-domestication migration routes. Genetic Selection Evolution. 50:58. https://doi.org/10.1186/s12711-018-0422-x.
Diversity of copy number variation in the worldwide goat population Reprint Icon - (Peer Reviewed Journal)
Liu, M., Zhou, Y., Rosen, B.D., Van Tassell, C.P., Stella, A., Tosser, G., Rupp, R., Palhiere, I., Colli, L., Sayre, B., Crepaldi, P., Fang, L., Meszaros, G., Chen, H., Liu, G., Adaptmap Consortium. 2018. Diversity of copy number variation in the worldwide goat population. Heredity. 122:636–646. https://doi.org/10.1038/s41437-018-0150-6.
Misidentification of runs of homozygosity islands in cattle caused by interference with copy number variation or large intermarker distances Reprint Icon - (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.
Comparative whole genome DNA methylation profiling of cattle sperm and somatic tissues reveals striking hypomethylated patterns in sperm Reprint Icon - (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).
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)
Genome-wide sequencing and comparative profiling of cattle sperm DNA methylome reveals its hypomethylated patterns - (Abstract Only)
Whole genome structural analysis of Caribbean hair sheep reveals quantitative link to West African ancestry Reprint Icon - (Peer Reviewed Journal)
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 - (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.
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.
Progress toward a low budget reference grade genome assembly Reprint Icon - (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.
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.