U.S. flagAn official website of the United States government
                    Here's how you know **Official websites use .gov**
                            
                            A **.gov** website belongs to an official government organization in the United States.
 **Secure .gov websites use HTTPS**
                            
                            A **lock** (                            
                              A locked padlock                                                      
                            
                            ) or **https://** means you’ve safely connected to the .gov website. Share sensitive information only on official, secure websites.


Menu Agricultural Research Service
						
                    U.S. DEPARTMENT OF AGRICULTURE
 Animal Genomics and Improvement Laboratory: Beltsville, MD
 close



    Research

                    Research Projects
                                    Publications
                                    Collaborations
                                    News
                                    Software
                People

                    Staff Listing
                                    Careers


        


                    AIP
                        Home
                                    About
                                    Publications
                                    Software
                                    People
                                    Collaborations
                                    Careers
                                    Centennial
                                    Contact
                                    Dairy industry links
                    DirectionsSearch small
                    Search
            
            ARS Home
                                About ARS
                                Contact Us




ARS Home Northeast Area Beltsville, Maryland (BARC) Beltsville Agricultural Research Center Animal Genomics and Improvement Laboratory People & Locations







Benjamin D Rosen

(Ben)
                        Animal Genomics and Improvement Laboratory

                        




                        
                        Research Biologist
                        Phone: (301) 504-8416
                        
                        
                        Fax: (301) 504-8414(Employee information on this page comes from the REE Directory. Please contact your front office staff to update the REE Directory.)
                            ProjectsAccelerating Genetic Improvement of Ruminants Through Enhanced Genome Assembly, Annotation, and Selection
                                                    In-House Appropriated
                                                                    (D)Accession Number: 442481Increasing Accuracy of Genomic Prediction, Developing Algorithms, Selecting Markers, and Evaluating New Traits to Improve Dairy Cattle
                                                    In-House Appropriated
                                                                    (D)Accession Number: 442491**Publications**
                                                (Clicking on the reprint icon
                                                    Reprint Icon
                                                    will take you to the publication reprint.)Participatory investigation of goat farmers’ breeding practices, trait preference, and selection criteria in Burkina Faso
                                                        

- (Peer Reviewed Journal)Badjibassa, A., Ouedraogo, D., Burger, P.A., Rosen, B.D., Van Tassell, C.P., Solkner, J., Soudre, A. 2024. Participatory investigation of goat farmers’ breeding practices, trait preference, and selection criteria in Burkina Faso. Tropical Animal Health and Production. 56:35. https://doi.org/10.1007/s11250-023-03869-w.The African Goat Improvement Network: A scientific group empowering smallholder farmers
                                                        

- (Peer Reviewed Journal)Van Tassell, C.P., Rosen, B.D., Woodward Greene, M.J., Silverstein, J., Huson, H.J., Solkner, J., Boettcher, P., Rothschild, M.F., Meszaros, G., Nakimbugwe, H., Gondwe, T., Muchadeyi, F.C., Nandolo, W., Mulindwa, H.A., Banda, L.J., Kaumbata, W., Getachew, T., Haile, A., Soudre, A., Ouedraogo, D., Rischkowsky, B.A., Mwai, A.O., Dzomba, E.F., Nash, O., Abegaz, S., Masiga, C.W., Wurzinger, M., Sayre, B.L., Stella, A., Tosser-Klopp, G., Sonstegard, T.S. 2023. The African Goat Improvement Network: A scientific group empowering smallholder farmers. Frontiers in Genetics. 14:1183240. https://doi.org/10.3389/fgene.2023.1183240.Using the community-based breeding program (CBBP) model as a collaborative platform to develop the African Goat Improvement Network—Image collection protocol (AGIN-ICP) with mobile technology for data collection
                                                        

- (Peer Reviewed Journal)Woodward Greene, M.J., Kinser, J.M., Huson, H.J., Sonstegard, T.S., Solkner, J., Vaisman, I.I., Boettcher, P., Masiga, C., Mukasa, C., Abegaz, S., Agaba, M., Ahmed, S.S., Fridolin, M., Getachew, T., Gondowe, T., Haile, A., Hassan, Y., Kihara, A., Kouriba, A., Mruttu, H.A., Mujibi, D., Nandolo, W., Rischkowsky, B., Rosen, B.D., Sayre, B., Van Tassell, C.P. 2023. Using the community-based breeding program (CBBP) model as a collaborative platform to develop the African Goat Improvement Network—Image collection protocol (AGIN-ICP) with mobile technology for data collection and management of livestock phenotypes. Frontiers in Genetics. 14:1200770. https://doi.org/10.3389/fgene.2023.1200770.A Chinese indicine pan-genome reveals a wealth of novel structural variants introgressed from other Bos species
                                                        

- (Peer Reviewed Journal)Dai, X., Bian, P., Hu, D., Luo, F., Huang, Y., Jiao, S., Wang, X., Gong, M., Li, R., Cai, Y., Wen, J., Yang, Q., Deng, W., Nanaei, H.A., Wang, Y., Wang, F., Zhang, Z., Rosen, B.D., Heller, R., Jiang, Y. 2023. A Chinese indicine pan-genome reveals a wealth of novel structural variants introgressed from other Bos species. Genome Research. 33(8):1284–1298. https://doi.org/10.1101/gr.277481.122.Morphometric characterization of local goat breeds in two agroecological zones of Burkina Faso, West Africa
                                                        

- (Peer Reviewed Journal)Akounda, B., Ouedraogo, D., Soudre, A., Burger, P.A., Rosen, B.D., Van Tassell, C.P., Solkner, J. 2023. Morphometric characterization of local goat breeds in two agroecological zones of Burkina Faso, West Africa. Animals. 13(12):1931. https://doi.org/10.3390/ani13121931.The Bovine Pangenome Consortium: Democratizing production and accessibility of genome assemblies for global cattle breeds and other bovine species
                                                        

- (Peer Reviewed Journal)Smith, T.P.L., Bickhart, D.M., Boichard, D., Chamberlain, A.J., Djikeng, A., Jiang, Y., Low, W., Pausch, H., Demyda-Peyras, S., Prendergast, J., Schnabel, R.D., Rosen, B.D. 2023. The Bovine Pangenome Consortium: democratizing production and accessibility of genome assemblies for global cattle breeds and other bovine species. Genome Biology. 24. Article 139. https://doi.org/10.1186/s13059-023-02975-0.The Australasian dingo archetype: de novo chromosome-length genome assembly, DNA methylome, and cranial morphology
                                                        

- (Peer Reviewed Journal)Ballard, J.O., Field, M.A., Edwards, R.J., Wilson, L.A., Koungoulos, L.G., Rosen, B.D., Chernoff, B., Dudchenko, O., Omer, A., Keilwagen, J., Skvortsova, K., Bogdanovic, O., Chan, E.K., Zammit, R.A., Hayes, V., Aiden, E.L. 2023. The Australasian dingo archetype: de novo chromosome-length genome assembly, DNA methylome, and cranial morphology. GigaScience. https://doi.org/10.1093/gigascience/giad018.A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes
                                                        

- (Peer Reviewed Journal)Li, R., Gong, M., Zhang, X., Wang, F., Liu, Z., Zhang, L., Yang, Q., Xu, Y., Xu, M., Zhang, H., Zhang, Y., Dai, X., Zhang, Z., Fang, W., Yang, Y., Fu, W., Cao, C., Yang, P., Ghanatsaman, Z.A., Negari, N.J., Nanaei, H.A., Yue, X., Song, Y., Lan, X., Deng, W., Wang, X., Pan, C., Xiang, R., Ibeagha-Awemu, E.M., Heslop-Harrison, P.J., Rosen, B.D., Lenstra, J.A., Gan, S., Jiang, Y. 2023. A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes. Genome Research. 33:463-477. https://doi.org/10.1101/gr.277372.122.polishCLR: a Nextflow workflow for polishing PacBio CLR genome assemblies
                                                        

- (Peer Reviewed Journal)Chang, J., Stahlke, A.R., Chudalayandi, S., Rosen, B.D., Childers, A.K., Severin, A. 2023. polishCLR: a Nextflow workflow for polishing PacBio CLR genome assemblies. Genome Biology and Evolution. 15(3): Article evad020. https://doi.org/10.1093/gbe/evad020.Favored single nucleotide variants identified using whole genome re-sequencing of Austrian and Chinese cattle breeds
                                                        

- (Peer Reviewed Journal)Naji, M.M., Jiang, Y., Utsunomiya, Y.T., Rosen, B.D., Solkner, J., Wang, C., Jiang, L., Zhang, Q., Zhang, Y., Ding, X., Meszaros, G. 2022. Favored single nucleotide variants identified using whole genome re-sequencing of Austrian and Chinese cattle breeds. Frontiers in Genetics. https://doi.org/10.3389/fgene.2022.974787.Assembly of a pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history
                                                        

- (Peer Reviewed Journal)Zhou, Y., Yang, L., Han, X., Han, J., Hu, Y., Li, F., Xia, H., 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 pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history. Genome Research. 32(8):1585-1601. https://doi.org/10.1101/gr.276550.122.A multi-tissue atlas of regulatory variants in cattle
                                                        

- (Peer Reviewed Journal)Liu, S., Gao, Y., Canela-Xandri, O., Wang, S., Yu, Y., Cai, W., Li, B., Pairo-Castineira, E., D'Mellow, K., Rawlik, K., Xia, C., Yao, Y., Li, X., Yan, Z., Li, C., Rosen, B.D., Van Tassell, C.P., Van Raden, P.M., Zhang, S., Ma, L., Cole, J.B., Liu, G., Tenesa, A., Fang, L. 2022. A multi-tissue atlas of regulatory variants in cattle. Nature Genetics. 54(9):1438-1447. https://doi.org/10.1038/s41588-022-01153-5.Geographic contrasts of Y-chromosomal haplogroups from wild and domestic goats reveals ancient migrations and recent introgressions
                                                        

- (Peer Reviewed Journal)Vargoats Consortium, Nijman, I.J., Rosen, B.D., Bardou, P., Faraut, T., Cumer, T., Daly, K., Zheng, Z., Le, C., Cai, Y., Asadollahpour, H., Kul, B.C., Zhang, W., E, G., Ayin, A., Bakhtin, M., Balteanu, V.A., Barfield, D., Beard, H., Berger, B., Blichfeldt, T., Boink, G., Bugiwati, S.R., Cai, Z., Carolan, S., Cubric-Curik, V., Dagong, I.A., Dorji, T., Drew, L., Guo, J., Hallsson, J., Kantanen, J., Kawaguchi, F., Kazymbet, P., Khayatzadeh, N., Kim, N., Kumar, S., Liao, Y., Martinez, A., Masangkay, J.S., Masaoka, M., Mazza, R., Mcewan, J., Milanesi, M., Omar, F., Nomura, Y., Ouchene-Khelifi, N., Pereira, F., Sahana, G., Sasazaki, S., Da Silva, A., Simcic, M., Solkner, J., Sutherland, A., Tigchelaar, J., Zhang, H., Ajmone-Marsan, P., Bradley, D.G., Colli, L., Drogemuller, C., Mannen, H., Pompanon, F., Tosser-Klopp, G., Yu, J., Lenstra, J.A. 2022. Geographic contrasts of Y-chromosomal haplogroups from wild and domestic goats reveals ancient migrations and recent introgressions. Molecular Ecology.  https://doi.org/10.1111/mec.16579.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. Article 344. https://doi.org/10.1186/s12864-022-08561-1.The Australian dingo is an early offshoot of modern breed dogs
                                                        

- (Peer Reviewed Journal)Field, M.A., Yadav, S., Dudchenko, O., Esvaran, M., Rosen, B.D., Skvortsova, K., Edwards, R.J., Keilwagen, J., Cochran, B.J., Manandhar, B., Bustamante, S., Rasmussen, J.A., Melvin, R.G., Chernoff, B., Omer, A., Colaric, Z., Chan, E.K., Minoche, A.E., Smith, T.P., Gilbert, T.P., Bogdanovic, O., Zammit, R.A., Thomas, T., Aien, E.L., Ballard, J.W. 2022. The Australian dingo is an early offshoot of modern breed dogs. Science Advances. 8(16):eabm5944. https://doi.org/10.1126/sciadv.abm5944.Inbreeding and effective population size of United States Katahdin sheep
                                                        

- (Proceedings)Becker, G., Burke, J.M., Lewis, R.M., Miller, J.E., Morgan, J.L., Rosen, B.D., Van Tassell, C.P., Notter, D.R., Murdoch, B.M. 2023. Inbreeding and effective population size of United States Katahdin sheep. World Congress of Genetics Applied in Livestock Production. https://doi.org/10.3920/978-90-8686-940-4_706.Variants within genes EDIL3 and ADGRB3 are associated with divergent fecal egg counts in Katahdin sheep at weaning
                                                        

- (Peer Reviewed Journal)Becker, G.M., Burke, J.M., Lewis, R.M., Miller, J.E., Morgan, J.L., Rosen, B.D., Van Tassell, C.P., Notter, D.R., Murdoch, B. 2022. Variants within genes EDIL3 and ADGRB3 are associated with divergent fecal egg counts in Katahdin sheep at weaning. Frontiers in Genetics. https://doi.org/10.3389/fgene.2022.817319.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.Assessing Bos taurus introgression in the UOA Bos indicus assembly
                                                        

- (Peer Reviewed Journal)Naji, M.M., Utsunomiya, Y.T., Solkner, J., Rosen, B.D., Meszaros, G. 2021. Assessing Bos taurus introgression in the UOA Bos indicus assembly. Genetics Selection Evolution. 53:96. https://doi.org/10.1186/s12711-021-00688-1.Genome-wide recombination map construction from single sperm sequencing in cattle
                                                        

- (Peer Reviewed Journal)Yang, L., Gao, Y., Li, M., Park, K., Liu, S., Kang, X., Liu, M., Oswalt, A., Fang, L., Telugu, B.P., Sattler, C.G., Cole, J.B., Seroussi, E., Xu, L., Li, C., Li, L., Zhang, H., Rosen, B.D., Van Tassell, C.P., Ma, L., Liu, G. 2022. Genome-wide recombination map construction from single sperm sequencing in cattle. BMC Genomics. 23(1):181. https://doi.org/10.1186/s12864-022-08415-w.Towards the detection of copy number variation from single sperm sequencing in cattle
                                                        

- (Peer Reviewed Journal)Yang, L., Gao, Y., Oswalt, A., Fang, L., Boschiero, C., Neupane, M., Sattler, C.G., Seroussi, E., Xu, L., Li, C., Li, L., Zhang, H., Rosen, B.D., Van Tassell, C.P., Ma, L., Liu, G. 2022. Towards the detection of copy number variation from single sperm sequencing in cattle. BMC Genomics. 23(1):215. https://doi.org/10.1186/s12864-022-08441-8.Genomic rearrangements have consequences for introgression breeding as revealed by genome assemblies of wild and cultivated lentil species
                                                        

- (Pre-print Publication)Ramsay, L., Koh, C., Kagale, S., Gao, D., Kaur, S., Haile, T., Gela, T., Chen, L., Cao, Z., Konkin, D., Toegelova, H., Doležel, J., Rosen, B.D., Stonehouse, R., Humann, J., Main, D., Coyne, C.J., Mcgee, R.J., Cook, D., Penmetsa, V., Vandenberg, A., Chan, C., Banniza, S., Edwards, D., Bayer, P., Batley, J., Udupa, S., Bett, K.E. 2021. Genomic rearrangements have consequences for introgression breeding as revealed by genome assemblies of wild and cultivated lentil species. bioRxiv. https://doi.org/10.1101/2021.07.23.453237.VarGoats project: a dataset of 1159 whole-genome sequences to dissect Capra hircus global diversity
                                                        

- (Peer Reviewed Journal)Denoyelle, L., Talouarn, E., Bardou, P., Colli, L., Alberti, A., Danchin, C., Del Corvo, M., Engelen, S., Orvain, C., Palhiere, I., Rupp, R., Sarry, J., Salavati, M., Amills, M., Clark, E., Crepaldi, P., Faraut, T., Masiga, C., Pampanon, F., Rosen, B.D., Stella, A., Van Tassell, C.P., Tosser-Klopp, G., The Vargoats Consortium. 2021. VarGoats project: a dataset of 1159 whole-genome sequences to dissect Capra hircus global diversity. Genetic Selection Evolution. 53:86. https://doi.org/10.1186/s12711-021-00659-6.Detection of copy number variants in African goats using whole genome sequence data
                                                        

- (Peer Reviewed Journal)Nandolo, W., Meszaros, G., Banda, L.J., Gondwe, T.N., Mulindwa, H.A., Nakimbugwe, H.N., Wurzinger, M., Clark, E., Woodward Greene, M.J., Liu, M., Liu, G., Van Tassell, C.P., Rosen, B.D., Solkner, J. 2021. Detection of copy number variants in African goats using whole genome sequence data. BMC Genomics. 22(1):398. https://doi.org/10.1186/s12864-021-07703-1.A comprehensive catalogue of regulatory variants in the cattle transcriptome

- (Abstract Only)Liu, S., Gao, Y., Canela-Xandri, O., Wang, S., Yu, Y., Cai, W., Li, B., Pairo-Castineira, E., D'Mellow, K., Rawlik, K., Xia, C., Yao, Y., Li, X., Yan, Z., Li, C., Rosen, B.D., Van Tassell, C.P., Van Raden, P.M., Zhang, S., Ma, L., Cole, J.B., Liu, G., Tenesa, A., Fang, L. 2021. A comprehensive catalogue of regulatory variants in the cattle transcriptome [abstract]. Journal of Dairy Science. 104(Suppl. 1):121(abstr. 307).Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome
                                                        

- (Peer Reviewed Journal)Edwards, R.J., Field, M.A., Ferguson, J.M., Dudchenko, O., Keilwagen, J., Rosen, B.D., Johnson, G.S., Rice, E., Hillier, L., Hammond, J.M., Towarnicki, S.G., Omer, A., Skvortsova, K., Bogdanovic, O., Zammit, R.A., Aiden, E.L., Warren, W.C., Ballard, J.W. 2021. Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome. BMC Genomics. 22(1):188. https://doi.org/10.1186/s12864-021-07493-6.Investigation of ancestral alleles in the Bovinae subfamily
                                                        

- (Peer Reviewed Journal)Naji, M.M., Utsunomiya, Y.T., Solkner, J., Rosen, B.D., Meszaros, G. 2021. Investigation of ancestral alleles in the Bovinae subfamily. Gigascience. 22(1):108. https://doi.org/10.1186/s12864-021-07412-9.Experiences from the implementation of community-based goat breeding programs in Malawi and Uganda: a potential approach for conservation and improvement of indigenous small ruminants in smallholder farms
                                                        

- (Peer Reviewed Journal)Kaumbata, W., Nakimbugwe, H.N., Nandolo, W., Banda, L.J., Meszaros, G., Gondwe, T.N., Woodward Greene, M.J., Rosen, B.D., Van Tassell, C.P., S0lkner, J., Wurzinger, M. 2021. Experiences from the implementation of community-based goat breeding programs in Malawi and Uganda: a potential approach for conservation and improvement of indigenous small ruminants in smallholder farms. Sustainability. 13(3):1494. https://doi.org/10.3390/su13031494.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.Copy number variation analysis reveals variants associated with milk production traits in dairy goats
                                                        

- (Peer Reviewed Journal)Kang, X., Liu, M., Liu, S., Pan, M.G., Li, M., Wiggans, G.R., Van Tassell, C.P., Rosen, B.D., Liu, G. 2020. Copy number variation analysis reveals variants associated with milk production traits in dairy goats. Genomics. 112(6):4934-4937. https://doi.org/10.1016/j.ygeno.2020.09.007.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.Comparative whole genome DNA methylation profiling of cattle tissues reveals global and tissue-specific methylation patterns
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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.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
                                                        

- (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.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/abstractsSignatures of selection and environmental adaptation across the goat genome post-domestication
                                                        

- (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
                                                        

- (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

- (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.Timing and extent of inbreeding in African goats
                                                        

- (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
                                                        

- (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
                                                        

- (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.Short communication: Identification of the pseudoautosomal region in the Hereford bovine reference genome assembly ARS-UCD1.2
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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.


Return to top


Connect with ARS Sign up


ARS Home
                            USDA.gov
                            Plain Writing
                            Policies & Links
                            Civil Rights Statements
                            FOIA
                            Accessibility Statement
                            Privacy Policy
                            Non-Discrimination Statement
                            Quality of Information
                            USA.gov
                            WhiteHouse.gov