Research Project: Enhancing Genetic Merit of Ruminants Through Improved Genome Assembly, Annotation, and Selection

Location: Animal Genomics and Improvement Laboratory

Publications (Clicking on the reprint icon will take you to the publication reprint.)

Mapping and functional characterization of structural variation in 1060 pig genomes - (Peer Reviewed Journal)
Yang, L., Yin, H., Bai, L., Yao, W., Tao, T., Zhao, Q., Gao, Y., Teng, J., Xu, Z., Lin, Q., Diao, S., Pan, Z., Guan, D., Li, B., Zhou, H., Zhou, Z., Zhao, F., Wang, Q., Pan, Y., Zhang, Z., Li, K., Fang, L., Liu, G. 2024. Mapping and functional characterization of structural variation in 1060 pig genomes. Genome Biology. 25. Article e116. https://doi.org/10.1186/s13059-024-03253-3.

Building an atlas of transposable elements reveals the extensive roles of young sine in gene regulation, genetic diversity and complex traits in pigs - (Peer Reviewed Journal)
Zhao, P., Gu, L., Gao, Y., Pan, Z., Liu, L., Li, X., Zhou, H., Han, X., Qian, L., Liu, G., Fang, L., Wang, Z. 2023. Building an atlas of transposable elements reveals the extensive roles of young sine in gene regulation, genetic diversity and complex traits in pigs. Communications Biology. 6(1):894. https://doi.org/10.1038/s42003-023-05234-x.

Gene expression and RNA splicing explain large proportions of the heritability for complex traits in cattle - (Peer Reviewed Journal)
Xiang, R., Fang, L., Liu, S., Macleod, I.M., Liu, Z., Breen, E.J., Gao, Y., Liu, G., Tenesa, A., Consortium, C., Mason, B., Chamberlain, A.J., Wray, N.R., Goddard, M.E. 2023. Gene expression and RNA splicing explain large proportions of the heritability for complex traits in cattle. Cell Genomics. 100385. https://doi.org/10.1016/j.xgen.2023.100385.

Invited review: Reliability computation from the animal model era to the single-step genomic model era - (Peer Reviewed Journal)
Zaabza, H.B., Van Tassell, C.P., Vandenplas, J., Van Raden, P.M., Liu, Z., Eding, H., Mckay, S., Haugaard, K., Lidauer, M.H., Mäntysaari, E.A., Strandén, I. 2023. Invited review: Reliability computation from the animal model era to the single-step genomic model era. Journal of Dairy Science. 106(3):1518–1532. https://doi.org/10.3168/jds.2022-22629.

Adding and reporting genomically discovered ancestors in US evaluations - (Proceedings)
Carrillo, J., Van Raden, P.M., Ogwo, E.O., Mota, R.R., Wiggans, G.R., Bacheller, L.R., Fok, G.C., Null, D.J. 2022. Adding and reporting genomically discovered ancestors in US evaluations. Interbull Bulletin. 57:23-27.

Genetic diversity and selection signatures in Jianchang Black goats revealed by whole-genome sequencing data - (Peer Reviewed Journal)
Sun, X., Guo, J., Li, L., Zhong, T., Wang, L., Zhan, S., Dai, D., Lu, J., Wang, D., Liu, G., Zheng, H. 2022. Genetic diversity and selection signatures in Jianchang Black goats revealed by whole-genome sequencing data. Animals. 12(18):2365. https://doi.org/10.3390/ani12182365.

Changes in genetic trends in US dairy cattle since the implementation of genomic evaluations - (Peer Reviewed Journal)
Guinan, F.L., Wiggans, G.R., Norman, H.D., Durr, J.W., Cole, J.B., Van Tassell, C.P., Misztal, I., Lourenco, D. 2023. Changes in genetic trends in US dairy cattle since the implementation of genomic evaluations. Journal of Dairy Science. 106(2):1110–1129. https://doi.org/10.3168/jds.2022-22205.

Differentially CTCF-binding sites in cattle rumen tissue during weaning - (Peer Reviewed Journal)
Boschiero, C., Gao, Y., Baldwin, R.L., Ma, L., Li, C., Liu, G. 2022. Differentially CTCF-binding sites in cattle rumen tissue during weaning. International Journal of Molecular Sciences. 23(16):9070. https://doi.org/10.3390/ijms23169070.

Comparative transcriptome in large-scale human and cattle populations - (Peer Reviewed Journal)
Yao, Y., Liu, S., Xia, C., Gao, Y., Pan, Z., Canela-Xandri, O., Khamesh, A., Rawlik, K., Wang, S., Li, B., Zhang, Y., Pairo-Castineira, E., D'Mellow, K., Li, X., Yan, Z., Li, C., Yu, Y., Zhang, S., Ma, L., Cole, J.B., Ross, P.J., Zhou, H., Haley, C., Liu, G., Fang, L., Tenesa, A. 2022. Comparative transcriptome in large-scale human and cattle populations. Genome Biology. 23:176. https://doi.org/10.1186/s13059-022-02745-4.

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.

Investigation of rumen long noncoding RNA before and after weaning in cattle - (Peer Reviewed Journal)
Marceau, A., Gao, Y., Baldwin, R.L., Li, C., Jiang, J., Ma, L., Liu, G. 2022. Investigation of rumen long noncoding RNA before and after weaning in cattle. BMC Genomics. 23:531. https://doi.org/10.1186/s12864-022-08758-4.

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.

A 13.42-kb tandem duplication at the ASIP locus is strongly associated with the pigmentation phenotype of Swiss markings in goats - (Peer Reviewed Journal)
Guo, J., Sun, X., Mao, A., Liu, H., Zhan, S., Li, L., Zhong, T., Wang, L., Cao, J., Liu, G., Zheng, H. 2022. A 13.42-kb tandem duplication at the ASIP locus is strongly associated with the pigmentation phenotype of Swiss markings in goats. BMC Genomics. 23:437. https://doi.org/10.1186/s12864-022-08672-9.

The dynamics of chromatin accessibility prompted by butyrate-induced chromatin modification in bovine cells - (Peer Reviewed Journal)
Boschiero, C., Gao, Y., Liu, M., Baldwin, R.L., Ma, L., Li, C., Liu, G. 2022. The dynamics of chromatin accessibility prompted by butyrate-induced chromatin modification in bovine cells. Ruminants. 2(2):226-243. https://doi.org/10.3390/ruminants2020015.

Editorial: Epigenetic variation influences on livestock production and disease traits - (Other)
Ibeagha-Awemu, E.M., Kiefer, H., Mckay, S., Liu, G. 2022. Editorial: Epigenetic variation influences on livestock production and disease traits. Frontiers in Genetics. 13:942747. https://doi.org/10.3389/fgene.2022.942747.

Initial analysis of structural variation detections in cattle using long-read sequencing methods - (Peer Reviewed Journal)
Gao, Y., Ma, L., Liu, G. 2022. Initial analysis of structural variation detections in cattle using long-read sequencing methods. Genes. 13(5):828. https://doi.org/10.3390/genes13050828.

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.

Single-cell transcriptomic and chromatin accessibility analyses of dairy cattle peripheral blood mononuclear cells and their responses to lipopolysaccharide - (Peer Reviewed Journal)
Gao, Y., Li, J., Cai, G., Wang, Y., Yang, W., Li, Y., Zhao, X., Li, R., Gao, Y., Tuo, W., Baldwin, R.L., Li, C., Fang, L., Liu, G.E. 2022. Single-cell transcriptomic and chromatin accessibility analyses of dairy cattle peripheral blood mononuclear cells and their responses to lipopolysaccharide. BMC Genomics. 23:338. https://doi.org/10.1186/s12864-022-08562-0.

Comparative transcriptomic analysis reveals region-specifc expression patterns in diferent beef cuts - (Peer Reviewed Journal)
Zhang, T., Wang, T., Niu, Q., Zheng, X., Li, H., Gao, X., Chen, Y., Gao, H., Zhang, L., Liu, G., Li, J., Xu, L. 2022. Comparative transcriptomic analysis reveals region-specifc expression patterns in diferent beef cuts. Biomed Central (BMC) Genomics. 23(1):387. https://doi.org/10.1186/s12864-022-08527-3.

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.

Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle - (Peer Reviewed Journal)
Zhang, T., Wang, T., Niu, Q., Xu, L., Chen, Y., Gao, X., Gao, H., Zhang, L., Liu, G., Li, J., Xu, L. 2022. Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle. BMC Biology. 20(1):79. https://doi.org/10.1186/s12915-022-01269-4.

Genetic diversity and inbreeding in US Jersey population and germplasm collection - (Proceedings)
Srikanth, K., Neupane, M., Jaafar, M.A., Wolfe, C.W., Huson, H.J., Van Tassell, C.P., Blackburn, H.D. 2022. Genetic diversity and inbreeding in US Jersey population and germplasm collection. World Congress of Genetics Applied in Livestock Production. Front Matter, Commun. 243, pp. 1029-1032. https://doi.org/10.3920/978-90-8686-940-4_243.

Impact of breed ancestry on the performance of crossbred dairy cattle - (Proceedings)
Jaafar, M.A., Heins, B.J., Dechow, C., Van Tassell, C.P., Huson, H.J. 2022. Impact of breed ancestry on the performance of crossbred dairy cattle. World Congress of Genetics Applied in Livestock Production. Front Matter, Commun. 181, pp. 777-780. https://doi.org/10.3920/978-90-8686-940-4_181.

Large-scale cis-eQTL analysis of gene expression in blood of young healthy pigs using PigGTEx - (Proceedings)
Kramer, L.M., Teng, J., Lim, K., Gao, Y., Yin, H., Bai, L., Liu, G., Zhang, Z., Fang, L., Plastow, G.S., Tuggle, C.K., Dekkers, J.C. 2022. Large-scale cis-eQTL analysis of gene expression in blood of young healthy pigs using PigGTEx. World Congress of Genetics Applied in Livestock Production. Front Matter, Commun. 560, pp. 2321-2324. https://doi.org/10.3920/978-90-8686-940-4_560.

Functional annotation of regulatory elements in cattle genome reveals the roles of extracellular interaction and dynamic change of chromatin states in rumen development during weaning - (Peer Reviewed Journal)
Gao, Y., Liu, S., Baldwin, R.L., Connor, E.E., Cole, J.B., Ma, L., Fang, L., Li, C., Liu, G. 2022. Functional annotation of regulatory elements in cattle genome reveals the roles of extracellular interaction and dynamic change of chromatin states in rumen development during weaning. Genomics. 114:110296. https://doi.org/10.1016/j.ygeno.2022.110296.

Comparative transcriptomics analysis reveals differential expression regulation underlying fatty acid composition in multiple beef cuts - (Peer Reviewed Journal)
Zhang, T., Wang, T., Niu, Q., Zheng, X., Li, H., Gao, X., Chen, Y., Gao, H., Liu, G., Zhang, L., Li, J., Xu, L. 2022. Comparative transcriptomics analysis reveals differential expression regulation underlying fatty acid composition in multiple beef cuts. Foods. 11(1):117. https://doi.org/10.3390/foods11010117.

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.

Insights from initial variant detection by sequencing single sperm in cattle - (Peer Reviewed Journal)
Yang, L., Gao, Y., Boschiero, C., Li, L., Zhang, H., Ma, L., Liu, G. 2021. Insights from initial variant detection by sequencing single sperm in cattle. Dairy. 2(4):649-657. https://doi.org/10.3390/dairy2040050.

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.

Genome-wide association study reveals 14 new SNPs and confirms two structural variants highly associated with the horned/ polled phenotype in goats - (Peer Reviewed Journal)
Guo, J., Rui, J., Mao, A., Liu, G., Zhan, S., Li, L., Zhong, T., Wang, L., Cao, J., Chen, Y., Zhang, G., Zheng, H. 2021. Genome-wide association study reveals 14 new SNPs and confirms two structural variants highly associated with the horned/polled phenotype in goats. BMC Genomics. 22:769. https://doi.org/10.1186/s12864-021-08089-w.

Comprehensive transcriptome and methylome analysis delineates the biological basis of hair follicle development and wool-related traits in Merino sheep - (Peer Reviewed Journal)
Zhao, B., Luo, H., He, J., Huang, X., Chen, S., Fu, X., Zeng, W., Li, C., Liu, G., Fang, L., Zhang, S., Tian, K. 2021. Comprehensive transcriptome and methylome analysis delineates the biological basis of hair follicle development and wool-related traits in Merino sheep. BMC Biology. 19:197. https://doi.org/10.1186/s12915-021-01127-9.

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.

Effect of temperature and maternal age on recombination rate in cattle - (Peer Reviewed Journal)
Shen, B., Freebern, E., Jiang, J., Maltecca, C., Cole, J.B., Liu, G., Ma, L. 2021. Effect of temperature and maternal age on recombination rate in cattle. Frontiers in Genetics. 12:682718. https://doi.org/10.3389/fgene.2021.682718.

Integration of a single-step genome-wide association study with a multi-tissue transcriptome analysis provides novel insights into the genetic basis of wool and weight traits in sheep - (Peer Reviewed Journal)
Zhao, B., Luo, H., Huang, X., Wei, C., Di, J., Tian, Y., Fu, X., Li, B., Liu, G., Fang, L., Zhang, S., Tian, K. 2021. Integration of a single-step genome-wide association study with a multi-tissue transcriptome analysis provides novel insights into the genetic basis of wool and weight traits in sheep. Genetic Selection Evolution. 53:56. https://doi.org/10.1186/s12711-021-00649-8.

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.

Single-cell transcriptomic analyses of cattle ruminal epithelial cells before and after weaning - (Peer Reviewed Journal)
Gao, Y., Fang, L., Baldwin, R.L., Connor, E.E., Cole, J.B., Van Tassell, C.P., Ma, L., Li, C., Liu, G. 2021. Single-cell transcriptomic analyses of cattle ruminal epithelial cells before and after weaning. Genomics. 113(4):2045-2055. https://doi.org/10.1016/j.ygeno.2021.04.039.

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.

Identification and population genetic analyses of copy number variations in six domestic goat breeds and Bezoar ibexes using next-generation sequencing - (Peer Reviewed Journal)
Guo, J., Zhong, J., Liu, G., Yang, L., Li, L., Chen, G., Song, T., Zheng, H. 2020. Identification and population genetic analyses of copy number variations in six domestic goat breeds and Bezoar ibexes using next-generation sequencing. BMC Genomics. 21(1):840. https://doi.org/10.1186/s12864-020-07267-6.

A LINE-1 derived promoter driving over-expression of the ASIP gene is responsible for white color in swamp buffalo - (Peer Reviewed Journal)
Liang, D., Zhao, P., Si, J., Fang, L., Xu, Q., Hou, Y., Hu, X., Gong, Y., Liang, Z., Tian, B., Mao, H., Yindee, M., Faruque, M.O., Liu, G., Wu, D., Barker, J.S., Han, J., Zhang, Y. 2020. A LINE-1 derived promoter driving over-expression of the ASIP gene is responsible for white color in swamp buffalo. Molecular Biology and Evolution. 38(3):1122-1136. https://doi.org/10.1093/molbev/msaa279.

Immune cells signaling-pathway and genomic profiles for personalized immunotherapy - (Book / Chapter)
Zhang, W., Qu, Y., Lin, M., Datta, A., Liu, G., Li, B. 2020. Immune cells signaling-pathway and genomic profiles for personalized immunotherapy (Chapter 2). In: Li, B., Larson, A., Li, S. editors. Personalized Immunotherapy for Tumor Diseases and Beyond. Singapore, Singapore: Bentham Science Publishers Pte. Ltd. p. 20-42.

Molecular screening and neoantigen cloning - Fundamental of adoptive T-cell immunotherapy - (Book / Chapter)
Zhang, W., Liu, G., Devemy, E., Li, B. 2020. Molecular screening and neoantigen cloning - Fundamental of adoptive T-cell immunotherapy (Chapter 6). In: Li, B., Larson, A., Li, S. editors. Personalized Immunotherapy for Tumor Diseases and Beyond. Singapore, Singapore: Bentham Science Publishers Pte. Ltd. p. 80-96.

Bioinformatics of T-cell and primary tumor cells - Fundamental of adoptive T-cell immunotherapy - (Book / Chapter)
Liu, G., Zheng, J., Li, B. 2020. Bioinformatics of T-cell and primary tumor cells - Fundamental of adoptive T-cell immunotherapy (Chapter 8). In: Li, B., Larson, A., Li, S. editors. Personalized Immunotherapy for Tumor Diseases and Beyond. Singapore, Singapore: Bentham Science Publishers Pte. Ltd. p. 118-136.

System modeling of T-cell function - Development of adoptive T-cell immunotherapy - (Book / Chapter)
Li, B., Liu, G., Zheng, J. 2020. System modeling of T-cell function - Development of adoptive T-cell immunotherapy (Chapter 12). In: Li, B., Larson, A., Li, S. editors. Personalized Immunotherapy for Tumor Diseases and Beyond. Singapore, Singapore: Bentham Science Publishers Pte. Ltd. p. 197-223.

Comparative analyses of copy number variations between Bos taurus and Bos indicus - (Peer Reviewed Journal)
Hu, Y., Xia, H., Li, M., Xu, C., Ye, X., Su, R., Zhang, M., Guo, A., Nash, O., Sonstegard, T.S., Yang, L., Liu, G., Zhou, Y. 2020. Comparative analyses of copy number variations between Bos taurus and Bos indicus. BMC Genomics. 21(1):682. https://doi.org/10.1186/s12864-020-07097-6.

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.

Genome-wide assessment of runs of homozygosity in Chinese Wagyu beef cattle - (Peer Reviewed Journal)
Zhao, G., Zhang, T., Liu, Y., Wang, Z., Xu, L., Zhu, B., Gao, X., Zhang, L., Gao, H., Liu, G., Li, J., Xu, L. 2020. Genome-wide assessment of runs of homozygosity in Chinese Wagyu beef cattle. Animals. 10(8):E1425. https://doi.org/10.3390/ani10081425.

Integrating RNA-Seq with GWAS reveals novel insights into the molecular mechanism underpinning ketosis in cattle - (Peer Reviewed Journal)
Yan, Z., Huang, H., Freebern, E., Santos, D.J., Dai, D.D., Si, J., Ma, C., Cao, J., Guo, G., Liu, G., Ma, L., Fang, L., Zhang, Y. 2020. Integrating RNA-Seq with GWAS reveals novel insights into the molecular mechanism underpinning ketosis in cattle. BMC Genomics. 21(1):489. https://doi.org/10.1186/s12864-020-06909-z.

Epigenomics and genotype-phenotype association analyses reveal conserved genetic architecture of complex traits in cattle and human - (Peer Reviewed Journal)
Liu, S., Yu, Y., Zhang, S., Cole, J.B., Tenesa, A., Wang, T., Mcdaneld, T.G., Ma, L., Liu, G., Fang, L. 2020. Epigenomics and genotype-phenotype association analyses reveal conserved genetic architecture of complex traits in cattle and human. BMC Biology. 18(1). Article 80. https://doi.org/10.1186/s12915-020-00792-6.

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.

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.

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.

A genetic investigation of island Jersey cattle, the foundation of the Jersey breed: Comparing population structure and selection to Guernsey, Holstein, and United States Jersey cattle - (Peer Reviewed Journal)

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.

GWAS and fine-mapping of livability and six disease traits in Holstein cattle - (Peer Reviewed Journal)
Freebern, E., Santos, D.J.A., Fang, L., Jiang, J., Parker-Gaddis, K.L., Liu, G.E., Van Raden, P.M., Maltecca, C., Cole, J.B., Ma, L. 2020. GWAS and fine-mapping of livability and six disease traits in Holstein cattle. BMC Genomics. 21:41. https://doi.org/10.1186/s12864-020-6461-z.

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.

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.

Analyses of inter-individual variations in sperm DNA methylation reveal their regulatory role in gene expression and association with reproduction traits in cattle - (Peer Reviewed Journal)
Liu, S., Fang, L., Zhou, Y., Santos, D.J.A., Xiang, R., Daetwyler, H.D., Chamberlain, A.J., Cole, J.B., Li, C., Yu, Y., Ma, L., Zhang, S., Liu, G. 2019. Analyses of inter-individual variations in sperm DNA methylation reveal their regulatory role in gene expression and association with reproduction traits in cattle. BMC Genomics. 20:888. https://doi.org/10.1186/s12864-019-6228-6.

Signatures 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.

Bos taurus-indicus hybridization correlates with intralocus sexual-conflicting effects of PRDM9 on male and female fertility in Holstein cattle - (Peer Reviewed Journal)
Seroussi, E., Shirak, A., Gershoni, M., Ezra, E., Santos, D.J., Ma, L., Liu, G. 2019. Bos taurus-indicus hybridization correlates with intralocus sexual-conflicting effects of PRDM9 on male and female fertility in Holstein cattle. BMC Genetics. 20:71. https://doi.org/10.1186/s12863-019-0773-5.

Genomic patterns of homozygosity in Chinese local cattle - (Peer Reviewed Journal)
Xu, L., Zhao, G., Xu, L., Wang, Z., Yang, L., Zhang, L., Gao, X., Gao, H., Liu, G., Li, J. 2019. Genomic patterns of homozygosity in Chinese local cattle. Scientific Reports. 9(1):16977. https://doi.org/10.1038/s41598-019-53274-3.

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.

Copy number variation of bovine SHH gene is associated with body conformation traits in Chinese beef cattle - (Peer Reviewed Journal)
Liu, M., Li, B., Shi, T., Huang, ., Liu, G., Lan, X., Lei, C., Chen, H. 2019. Copy number variation of bovine SHH gene is associated with body conformation traits in Chinese beef cattle. Journal of Applied Genetics. 60(2):199–207. https://doi.org/10.1007/s13353-019-00496-w.

Array CGH-based detection of CNV regions and their potential association with reproduction and other economic traits in Holsteins - (Peer Reviewed Journal)
Liu, M., Fang, L., Liu, S., Pan, M.G., Seroussi, E., Cole, J.B., Ma, L., Chen, H., Liu, G. 2019. Array CGH-based detection of CNV regions and their potential association with reproduction and other economic traits in Holsteins. BMC Genomics. 20:181. https://doi.org/10.1186/s12864-019-5552-1.

LncRNA-MEG3 promotes bovine myoblast differentiation by sponging miR-135 - (Peer Reviewed Journal)
Liu, M., Li, B., Peng, W., Ma, Y., Huang, Y., Lan, X., Lei, C., Qi, X., Liu, G., Chen, H. 2019. LncRNA-MEG3 promotes bovine myoblast differentiation by sponging miR-135. Journal of Cellular Physiology. https://doi.org/10.1002/jcp.28469.

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.

Probe-based association analysis identifies several deletions associated with average daily gain in beef cattle - (Peer Reviewed Journal)
Xu, L., Yang, L., Wang, L., Zhu, B., Chen, Y., Gao, H., Gao, X., Zhang, L., Liu, G., Li, J. 2019. Probe-based association analysis identifies several deletions associated with average daily gain in beef cattle. BMC Genomics. 20(1):31. https://doi.org/10.1186/s12864-018-5403-5.

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.

A genome-wide association study for mastitis resistance in phenotypically well-characterized Holstein dairy cattle using a selective genotyping approach - (Peer Reviewed Journal)
Kurz, J.P., Zhou, Y., Weiss, R.B., Wilson, D.J., Rood, K.J., Liu, G., Wang, Z. 2018. A genome-wide association study for mastitis resistance in phenotypically well-characterized Holstein dairy cattle using a selective genotyping approach. Immunogenetics. 71(1):35-47. https://doi.org/10.1007/s00251-018-1088-9.

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.

Predicting live weight of rural African goats using body measurements - (Peer Reviewed Journal)
Chinchilla-Vargasa, J., Woodward Greene, M.J., Van Tassell, C.P., Masiga, C.W., Rothschild, M.F. 2018. Predicting live weight of rural African goats using body measurements. Livestock Research for Rural Development. 30(7):123.

MicroRNA-guided prioritization of genome-wide association signals reveals the importance of microRNA-target gene networks for complex traits in cattle - (Peer Reviewed Journal)
Fang, L., Sorensen, P., Sahana, G., Panitz, F., Su, G., Zhang, S., Yu, Y., Li, B., Ma, L., Liu, G., Lund, M., Thomsen, B. 2018. MicroRNA-guided prioritization of genome-wide association signals reveals the importance of microRNA-target gene networks for complex traits in cattle. Scientific Reports. 8(1):9345. https://doi.org/doi:10.1038/s41598-018-27729-y.

Characterization of recombination features and the genetic basis in multiple cattle breeds - (Peer Reviewed Journal)
Shen, B., Jiang, J., Seroussi, E., Liu, G., Ma, L. 2018. Characterization of recombination features and the genetic basis in multiple cattle breeds. Biomed Central (BMC) Genomics. 19(1):304. https://doi.org/10.1186/s12864-018-4705-y.

Application of multi-omics in single cells - (Peer Reviewed Journal)
Kang, X., Liu, A., Liu, G. 2018. Application of multi-omics in single cells. Annals of Biotechnology. 2:1007.

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.

Genome-wide sequencing and comparative profiling of cattle sperm DNA methylome reveals its hypomethylated patterns - (Abstract Only)