Research Project: Accelerating Genetic Improvement of Ruminants Through Enhanced Genome Assembly, Annotation, and Selection

Location: Animal Genomics and Improvement Laboratory

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

Finishing complete genomes from telomere to telomere with Verkko-Fillet - (Peer Reviewed Journal)

Telomere to Telomere (T2T) genomes for the pig - (Proceedings)

Genomic signatures of selection revealed by SNPs and structural variants in unselected and contemporary Holstein cattle - (Proceedings)

Liver transcriptome dynamics in holstein cows during the periparturient transition - (Peer Reviewed Journal)
Bhowmik, N., da Silva, M., Castaneda, A., Miles, A.M., Li, C., Van Tassell, C.P., Baldwin, R.L., Rico, E., Liu, G. 2026. Liver transcriptome dynamics in holstein cows during the periparturient transition. Scientific Reports. 16:16227. https://doi.org/10.1038/s41598-026-46925-9.

Reassessing Wiggans’ method for estimating daily yields in 3× milking systems over four decades: what have we learned? - (Proceedings)

Diploid dual assemblies reveal the telocentric structure and extensive allelic heterogeneity of canine genomes - (Peer Reviewed Journal)
Kidd, J.M., Souilmi, Y., Rosen, B.D., Khan, R., Weisz, D., Dudchenko, O., Aiden, E.L., Zammit, R., Ballard, J.O. 2026. Diploid dual assemblies reveal the telocentric structure and extensive allelic heterogeneity of canine genomes. NAR Genomics and Bioinformatics. 8(2):lqag035. https://doi.org/10.1093/nargab/lqag035.

Participatory selection of breeding bucks in community-based goat breeding programs by combining scientific evidence with farmers’ preferences and local knowledge - (Peer Reviewed Journal)
Ouedraogo, D., Akounda, B., Burger, P.A., Rosen, B.D., Van Tassell, C.P., Solkner, J., Soudre, A. 2026. Participatory selection of breeding bucks in community-based goat breeding programs by combining scientific evidence with farmers’ preferences and local knowledge. Discover Agriculture. 4:86. https://doi.org/10.1007/s44279-026-00527-1.

Gene variants in the pheromone vomeronasal receptors and QTLs around behavioral and fat metabolism genes associated with altered feed efficiency in cattle - (Peer Reviewed Journal)
Shirak, A., Yang, L., Bhowmik, N., Ben-Meir, Y., Shabtay, A., Cohen-Zinder, M., Baldwin, R.L., Seroussi, E., Liu, G., Gershoni, M. 2026. Gene variants in the pheromone vomeronasal receptors and QTLs around behavioral and fat metabolism genes associated with altered feed efficiency in cattle. Scientific Reports. 16:7430. https://doi.org/10.1038/s41598-026-37314-3.

Phased-assembly-driven pangenome graphs for structural variant genotyping and complex trait mapping in dairy cattle - (Peer Reviewed Journal)
Yang, L., Gao, Y., Kuhn, K.L., Bhowmik, N., Li, W., Zanton, G.I., Fang, L., Cole, J.B., Li, C., Baldwin, R.L., Van Tassell, C.P., Rosen, B.D., Ma, L., Smith, T.P., Liu, G. 2026. Phased-assembly-driven pangenome graphs for structural variant genotyping and complex trait mapping in dairy cattle. Nature Communications. https://doi.org/10.1038/s41467-026-68807-4.

Population structure and domestication history of the Javan banteng - (Peer Reviewed Journal)
Wang, X., Aninta, S.G., Garcia-Erill, G., Li, Z., Khan, A., Liu, X., Bertola, L.D., Dharmayanthi, A.B., Yulianto, Yonathan, Rossi, C., Cauble-Sims, R., Rosen, B.D., Hagen, D.E., Heaton, M.P., Smith, T.P., Lenstra, J.A., Martins, N.F., Sinding, M.S., Agil, M., Heller, R. 2026. Population structure and domestication history of the Javan banteng. Current Biology. 36(2):458-473. https://doi.org/10.1016/j.cub.2025.11.076.

Construction of a multi-tissue cell atlas reveals cell-type-specific regulation of molecular and complex phenotypes in pigs - (Peer Reviewed Journal)
Chen, L., Li, H., Teng, J., Wang, Z., Qu, X., Chen, Z., Cai, X., Zeng, H., Bai, Z., Li, J., Pan, X., Yan, L., Wang, F., Lin, L., Luo, Y., Sahana, G., Lund, M., Ballester, M., Crespo-Piazuelo, D., Karlskov-Mortensen, P., Fredholm, M., Clop, A., Amills, M., Loving, C.L., Tuggle, C.K., Madsen, O., Li, J., Zhang, Z., Liu, G., Jiang, J., Fang, L., Yi, G. 2025. Construction of a multi-tissue cell atlas reveals cell-type-specific regulation of molecular and complex phenotypes in pigs. Advanced Science. 13(8):e04961. https://doi.org/10.1002/advs.202504961.

Insights into natural neocentromere evolution from a cattle T2T X chromosome - (Peer Reviewed Journal)
Pineda, P.S., MacPhillamy, C., Ren, Y., Chen, T., Zhong, L., Adelson, D.L., Dessaix, C., Perez-Silva, J., Haggerty, L., Martin, F.J., Bottema, C., Pitchford, W.S., Rosen, B.D., Smith, T.P., Low, W.Y. 2025. Insights into natural neocentromere evolution from a cattle T2T X chromosome. Nature Communications. 16:10745. https://doi.org/10.1038/s41467-025-65778-w.

Exploring cattle structural variation in the era of long reads, pangenome graphs, and nearly complete assemblies - (Review Article)
Liu, G. 2025. Exploring cattle structural variation in the era of long reads, pangenome graphs, and nearly complete assemblies. Journal of Animal Science and Biotechnology. 16(1):158. https://doi.org/10.1186/s40104-025-01294-7.

Inferring domestic goat demographic history through ancient genome imputation - (Peer Reviewed Journal)
Erven, J.A., Etourneau, A., Mashkour, M., Neupane, M., Bardou, P., Stella, A., Talenti, A., Masiga, C.W., Van Tassell, C.P., Clark, E., Pompanon, F., Colli, L., Amillis, M., Milanesi, M., Crepaldi, P., Consortium, T., Servin, B., Rosen, B.D., Tosser-Klopp, G., Daly, K.G. 2025. Inferring domestic goat demographic history through ancient genome imputation. Genome Biology and Evolution. 17(11):evaf181. https://doi.org/10.1093/gbe/evaf181.

Whole-genome sequencing reveals complex structural variations at a major locus linked to pigmented spot sizes in Tianfu goats - (Peer Reviewed Journal)
Guo, J., Huang, Q., Xiang, Q., Wu, G., Bian, P., Wang, X., Li, L., Liu, G., Zhang, H. 2025. Whole-genome sequencing reveals complex structural variations at a major locus linked to pigmented spot sizes in Tianfu goats. BMC Genomics. https://doi.org/10.1186/s12864-025-12055-1.

Immunogenomics approaches to studying antibody repertoires and vaccine responses in ruminants - (Review Article)
Safonova, Y., Collins, A., Murdoch, B.M., Rosen, B.D., Smith, T.P., Watson, C.T. 2025. Immunogenomics approaches to studying antibody repertoires and vaccine responses in ruminants. Annual Review of Animal Biosciences. 14:49-65. https://doi.org/10.1146/annurev-animal-030424-091103.

A multi-tissue single-cell expression atlas in cattle - (Peer Reviewed Journal)
Han, B., Li, H., Zheng, W., Zhang, Q., Chen, A., Zhu, S., Shi, T., Wang, F., Zou, D., Song, Y., Ye, W., Du, A., Fu, Y., Jia, M., Bai, Z., Yuan, Z., Liu, W., Tuo, W., Hope, J.C., MacHugh, D.E., O’Grady, J.F., Madsen, O., Sahana, G., Luo, Y., Lin, L., Li, C., Cai, Z., Li, B., Huang, J., Liu, L., Zhang, Z., Ma, Z., Hou, Y., Liu, G., Jiang, Y., Sun, H., Fang, L., Sun, D. 2025. A multi-tissue single-cell expression atlas in cattle. Nature Genetics. https://doi.org/10.1038/s41588-025-02329-5.

Global pangenome analysis highlights the critical role of structural variants in cattle improvement and identifies a unique event as a novel enhancer in IGFBP7+ cells - (Peer Reviewed Journal)
Dai, S., Zhao, P., Li, W., Peng, L., Jiang, E., Du, Y., Zhang, W., Dai, X., Yang, L., Li, Z., Xu, L., Lan, X., Lyu, W., Yang, L., Fang, L., Liu, G., Zhou, Y. 2025. Global pangenome analysis highlights the critical role of structural variants in cattle improvement and identifies a unique event as a novel enhancer in IGFBP7+ cells. Molecular Biology and Evolution. https://doi.org/10.1093/molbev/msaf205.

Selection signature analysis of whole-genome sequences to identify genome differences between selected and unselected Holstein cattle - (Peer Reviewed Journal)
Cai, J., Yang, L., Gao, Y., Liu, G., Da, Y., Ma, L. 2025. Selection signature analysis of whole-genome sequences to identify genome differences between selected and unselected Holstein cattle. Animals. https://doi.org/10.3390/ani15152247.

Comprehensive multi-omics analysis of regulatory variants for body weight in cattle - (Peer Reviewed Journal)
Niu, Q., Wu, J., Wu, T., Zhang, T., Wang, T., Xu, Z., Zhao, Z., Xu, L., Wang, Z., Zhu, B., Zhang, L., Gao, H., Liu, G., Li, J., Xu, L. 2025. Comprehensive multi-omics analysis of regulatory variants for body weight in cattle. Genomics, Proteomics and Bioinformatics. https://doi.org/10.1093/gpbjnl/qzaf067.

Haplotype-resolved genome and pan-genome graphs reveal the impacts of structural variation on functional genome and feather colors in chickens - (Peer Reviewed Journal)
Gu, L., Peng, C., Chen, A., Chen, K., Zheng, X., Yu, D., Wang, Z., Fang, L., Liu, G., Zhao, P. 2025. Haplotype-resolved genome and pan-genome graphs reveal the impacts of structural variation on functional genome and feather colors in chickens. iMetaOmics. https://doi.org/10.1002/imo2.70027.

Genomic analysis of hair sheep from West/Central Africa reveals unique genetic diversity and ancestral links to breed formation in the Caribbean - (Peer Reviewed Journal)
Wiener, P., Friedrich, J., Marr, M., Simo, G., Tanya, V., Ballingall, K., Flegontov, P., Rosen, B.D., Salle, G., Spangler, G., Van Tassell, C.P., Salavati, M., Meutchieye, F., Clark, E. 2025. Genomic analysis of hair sheep from West/Central Africa reveals unique genetic diversity and ancestral links to breed formation in the Caribbean. Molecular Ecology. https://doi.org/10.1111/mec.17796.

Exploring tissue- and sex-specific DNA methylation in cattle using a pan-mammalian infinium array - (Peer Reviewed Journal)
Hu, Z., Boschiero, C., Neupane, M., Bhowmik, N., Yang, L., Kilian, L., Dejarnette, M., Sargolzaei, M., Harstine, B., Li, C., Tuo, W., Baldwin, R.L., Van Tassell, C.P., Sattler, C.G., Liu, G.E. 2025. Exploring tissue- and sex-specific DNA methylation in cattle using a pan-mammalian infinium array. International Journal of Molecular Sciences. 26(9).Article e4284. https://doi.org/10.3390/ijms26094284.

Long read and preliminary pangenome analyses reveal breed-specific structural variations and novel sequences in Holstein and Jersey cattle - (Peer Reviewed Journal)
Gao, Y., Yang, L., Kuhn, K.L., Li, W., Zanton, G.I., Bowman, M.E., Zhao, P., Zhou, Y., Fang, L., Cole, J.B., Rosen, B.D., Ma, L., Li, C., Baldwin, R.L., Van Tassell, C.P., Zhang, Z., Smith, T.P., Liu, G. 2025. Long read and preliminary pangenome analyses reveal breed-specific structural variations and novel sequences in Holstein and Jersey cattle. Journal of Advanced Research. https://doi.org/10.1016/j.jare.2025.04.014.

Constructing a draft Indian cattle pangenome using short-read sequencing - (Peer Reviewed Journal)
Azam, S., Sahu, A., Pandey, N.K., Neupane, M., Van Tassell, C.P., Rosen, B.D., Gandham, R.K., Rath, S.N., Majumdar, S.S. 2025. Constructing a draft Indian cattle pangenome using short-read sequencing. Communications Biology. 8. Article e605. https://doi.org/10.1038/s42003-025-07978-0.

Liver transcriptome dynamics in Holstein cows during the periparturient transition - (Abstract Only)
Bhowmik, N., da Silva, M., Castaneda, A., Miles, A.M., Li, C., Van Tassell, C.P., Baldwin, R.L., Rico, E., Liu, G. 2025. Liver transcriptome dynamics in Holstein cows during the periparturient transition [abstract]. Journal of Dairy Science. 108(Suppl 1):214-215(abstr 2235).

Genetic regulation of gene expression across multiple tissues in chickens - (Peer Reviewed Journal)
Guan, D., Bai, Z., Zhu, X., Zhong, C., Hou, Y., Zhu, D., Chickengtex, C., Li, H., Lan, F., Diao, S., Yao, Y., Zhao, B., Li, X., Pan, Z., Gao, Y., Wang, Y., Zou, D., Wang, R., Xu, T., Sun, C., Yin, H., Teng, J., Xu, Z., Lin, Q., Shi, S., Shao, D., Degalez, F., Lagarrigue, S., Wang, Y., Wang, M., Peng, M., Rocha, D., Charles, M., Smith, J., Watson, K., Buitenhuis, J.A., Sahana, G., Lund, M.S., Warren, W., Frantz, L., Larson, G., Lamont, S. ., Si, W., Zhao, X., Li, B., Zhang, H., Luo, C., Shu, D., Qu, H., Luo, W., Li, Z., Nie, Q., Zhang, X., Xiang, R., Liu, S., Zhang, Z., Zhang, Z., Liu, G., Cheng, H.H., Yang, N., Hu, X., Zhou, H., Fang, L. 2025. Genetic regulation of gene expression across multiple tissues in chickens. Nature Genetics. 57:1298–1308. https://doi.org/10.1038/s41588-025-02155-9.

The farm animal genotype-tissue expression (FarmGTEx) project - (Review Article)
Fang, L., Teng, J., Lin, Q., Bai, Z., Liu, S., Guan, D., Li, B., Gao, Y., Hou, Y., Gong, M., Pan, Z., Yu, Y., Clark, E., Smith, J., Rawlik, K., Xiang, R., Chamberlain, A.J., Goddard, M.E., Littlejohn, M., Larson, G., Machugh, D.E., O’Grady, J.F., Sorensen, P., Sahana, G., Lund, M., Jiang, Z., Pan, X., Gong, W., Zhang, H., He, X., Zhang, Y., Gao, N., He, J., Yi, G., Liu, Y., Zhao, P., Zhou, Y., Wang, X., Young, R.S., Xia, C., Cheng, H., Ma, L., Cole, J.B., Baldwin, R.L., Li, C., Van Tassell, C.P., Lunney, J.K., Liu, W., Guan, L., Zhao, X., Ibeagha-Awemu, E., Luo, O., Lin, L., Canela-Xandri, O., Derks, M., Crooijmans, R., Godia, M., Madsen, O., Groenen, M., Koltes, J.E., Tuggle, C.K., Mccarthy, F.M., Rocha, D., Amills, M., Clop, A., Ballester, M., Tosser-Klopp, G., Li, J., Fang, C., Fang, M., Wang, Q., Hou, Z., Wang, Q., Zhao, F., Jiang, L., Zhao, G., Zhou, Z., Zhou, R., Liu, H., Li, M., Mo, D., Liu, X., Chen, Y., Yuan, X., Li, J., Zhao, S., Ding, X., Sun, D., Sun, H., Li, C., Jiang, Y., Wu, D., Wang, W., Fan, X., Zhang, Q., Li, K., Yang, N., Hu, X., Liu, G. 2025. The farm animal genotype-tissue expression (FarmGTEx) project. Nature Genetics. https://doi.org/10.1038/s41588-025-02121-5.

The Farm Animal Genotype-Tissue Expression (FarmGTEx) Portal - (Database / Dataset)
Fang, L., FarmGTEx Consortium, Li, J.J., Frantz, L., Zhou, H., Zhang, Z., Liu, G.E. 2025. The Farm Animal Genotype-Tissue Expression (FarmGTEx) Portal. Nature Genetics. 57(4):786-796. https://doi.org/10.1038/s41588-025-02121-5. Available: https://www.farmgtex.org/.

Profiling genome-wide methylation patterns in cattle infected with Ostertagia ostertagi - (Peer Reviewed Journal)
Boschiero, C., Beshah, E., Zhu, X., Tuo, W., Liu, G.E. 2024. Profiling genome-wide methylation patterns in cattle infected with Ostertagia ostertagi. International Journal of Molecular Sciences. 26(1).Article e89. https://doi.org/10.3390/ijms26010089.

Advancing the Indian cattle pangenome: characterizing non-reference sequences in Bos indicus - (Peer Reviewed Journal)
Azam, S., Sahu, A., Pandey, N.K., Neupane, M., Van Tassell, C.P., Rosen, B.D., Gandam, R.K., Rath, S.N., Majumdar, S.S. 2025. Advancing the Indian cattle pangenome: characterizing non-reference sequences in Bos indicus. Journal of Animal Science and Biotechnology. https://doi.org/10.1186/s40104-024-01133-1.

Alternative polyadenylation landscape of longissimus dorsi muscle with high and low intramuscular fat content in cattle - (Peer Reviewed Journal)
Li, C., Xu, J., Zhang, Y., Ding, Y., Zhou, X., Su, Z., Qu, C., Liang, J., Han, Y., Wang, D., Shi, Y., Li, C., Liu, G., Kang, X. 2024. Alternative polyadenylation landscape of longissimus dorsi muscle with high and low intramuscular fat content in cattle. Journal of Animal Science. https://doi.org/10.1093/jas/skae357.

Multi-omics analysis reveals signatures of selection and loci associated with complex traits in pigs - (Peer Reviewed Journal)
Liu, L., Yi, G., Yao, Y., Liu, Y., Li, J., Yang, Y., Liu, M., Fang, L., Mo, D., Zhang, L., Liu, Y., Niu, Y., Wang, L., Qu, X., Pan, Z., Wang, L., Chen, M., Fan, X., Chen, Y., Zhang, Y., Li, X., Wang, Z., Tang, Y., Huang, H., Yuan, P., Liao, Y., Li, X., Yin, Z., Liu, D., Zhang, D., Zhou, Q., Wu, W., Jiang, J., Gao, Y., Liu, G., Wang, L., Chen, Y., Li, K., Groenen, M.A., Tang, Z. 2024. Multi-omics analysis reveals signatures of selection and loci associated with complex traits in pigs. iMeta. https://doi.org/10.1002/imt2.250.

Genetic advancements and future directions in ruminant livestock breeding: from reference genomes to multiomics innovations - (Review Article)
Xu, S., Akhatayeva, Z., Liu, J., Feng, X., Yu, Y., Badaoui, B., Esmailizadeh, A., Kantanen, J., Amills, M., Lenstra, J.A., Johansson, A.M., Coltman, D.W., Liu, G., Curik, I., Orozco-Terwengel,, P., Paiva, S.R., Zinovieva, N.A., Zhang, L., Yang, J., Liu, Z., Wang, Y., Yu, Y., Li, M. 2024. Genetic advancements and future directions in ruminant livestock breeding: from reference genomes to multiomics innovations. Science China Life Science. 68:934-960. https://doi.org/10.1007/s11427-024-2744-4.

Telomere-to-telomere assemblies of cattle and sheep Y-chromosomes uncover divergent structure and gene content - (Peer Reviewed Journal)
Olagunju, T.A., Rosen, B.D., Neibergs, H.L., Becker, G., Davenport, K., Elsik, C., Hadfield, T., Koren, S., Rhie, A., Shira, K., Skibiel, A., Stegemiller, M., Thorne, J.W., Villamediana, P., Cockett, N.E., Murdoch, B.M., Smith, T.P. 2024. Telomere-to-telomere assemblies of cattle and sheep Y-chromosomes uncover divergent structure and gene content. Nature Communications. 15. Article e8277. https://doi.org/10.1038/s41467-024-52384-5.

A pilot detection and associate study of gene presence-absence variation in Holstein cattle - (Peer Reviewed Journal)
Boschiero, C., Neupane, M., Yang, L., Schroeder, S.G., Tuo, W., Ma, L., Baldwin, R.L., Van Tassell, C.P., Liu, G. 2024. A pilot detection and associate study of gene presence-absence variation in Holstein cattle. Animals. https://doi.org/10.3390/ani14131921.

Systemic interindividual DNA methylation variants in cattle share major hallmarks with those in humans - (Peer Reviewed Journal)
Chang, W., Baker, M., Laritsky, E., Gunasekara, C., Maduranga, U., Galliou, J.C., McFadden, J.W., Waltemyer, J.R., Berggren-Thomas, B., Tate, B.N., Zhang, H., Rosen, B.D., Van Tassell, C.P., Liu, G., Coarfa, C., Yi, A.R., Waterland, R.A. 2024. Systemic interindividual DNA methylation variants in cattle share major hallmarks with those in humans. Genome Biology. 25(1). Article e185. https://doi.org/10.1186/s13059-024-03307-6.

Variation in a Y-linked single copy gene, AMELY, was shared among modern and lost male Holstein lineages - (Abstract Only)
Yousaf, W., Liu, W., Liu, G., Lewin, H.A., Blackburn, H.D., Dechow, C.D. 2024. Variation in a Y-linked single copy gene, AMELY, was shared among modern and lost male Holstein lineages [abstract]. Journal of Dairy Science. 107(Suppl. 1):406(abstr. 2646).

Whole-genome resequencing reveals genetic diversity and wool trait-related genes in Liangshan Semi-fine Wool Sheep - (Peer Reviewed Journal)
Sun, X., Guo, J., Li, R., Zhang, H., Zhang, Y., Liu, G., Emu, Q., Zhang, H. 2024. Whole-genome resequencing reveals genetic diversity and wool trait-related genes in Liangshan Semi-fine Wool Sheep. Animals. 14(3):444. https://doi.org/10.3390/ani14030444.

Current challenges and future of agricultural genomes to phenomes in the USA - (Peer Reviewed Journal)
Tuggle, C.K., Clarke, J.L., Murdoch, B.M., Lyons, E., Scott, N.M., Mckay, S., Lipka, A., Fulton, J., Hess, A., Lubberstedt, T., Fragomeni, B., Rowan, T., Mccarthy, F., Guadagno, C., Goddard, E., Das Choudhury, S., Sheehan, M., Kramer, L., Feldman, M.J., Daigle, C., Steibel, J.P., Benes, B., Murray, S., Riggs, P., Thompson, A., Hagen, D., Thornton-Kurth, K., Van Tassell, C.P., Campbell, J.D., Dorea, J., Chung, H., Dekkers, J.C., Ertl, D., Lawrence-Dill, C.A., Schnable, P.S. 2024. Current challenges and future of agricultural genomes to phenomes in the USA. Genome Biology. 25:8. https://doi.org/10.1186/s13059-023-03155-w.

Integrated meta-omics reveals the regulatory landscape involved in lipid metabolism between pig breeds - (Peer Reviewed Journal)
Sun, J., Xie, F., Wang, J., Luo, J., Chen, T., Jiang, Q., Xi, Q., Liu, G., Zhang, Y. 2024. Integrated meta-omics reveals the regulatory landscape involved in lipid metabolism between pig breeds. Microbiome. 12. Article e33. https://doi.org/10.1186/s40168-023-01743-3.

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.

Unraveling the genetic basis of feed efficiency in cattle through integrated DNA methylation and CcttleGTEx analysis - (Abstract Only)

Unraveling the genetic basis of feed efficiency in cattle through integrated DNA methylation and CattleGTEx analysis - (Peer Reviewed Journal)
Hu, Z., Boschiero, C., Li, C., Connor, E.E., Baldwin, R.L., Liu, G. 2023. Unraveling the genetic basis of feed efficiency in cattle through integrated DNA methylation and CattleGTEx analysis. Genes. 14(12):2121. https://doi.org/10.3390/genes14122121.

A compendium of genetic regulatory effects across pig tissues - (Peer Reviewed Journal)
Teng, J., Gao, Y., Yin, H., Bai, Z., Liu, S., Zeng, H., Consortium, T., Bai, L., Cai, Z., Zhao, B., Li, X., Xu, Z., Lin, Q., Pan, Z., Yang, W., Yu, X., Guan, D., Hou, Y., Keel-Mercer, B.N., Rohrer, G.A., Lindholm-Perry, A.K., Oliver, W.T., Ballester, M., Crespo, D., Quintanilla, R., Canela-Xandri, O., Rawlik, K., Xia, C., Yao, Y., Zhao, Q., Yao, W., Yang, L., Li, H., Zhang, H., Liao, W., Chen, T., Karlskov-Mortensen, P., Fredholm, M., Amills Eras, M., Clop, A., Giuffra, E., Wu, J., Cai, X., Diao, S., Pan, X., Wei, C., Li, J., Cheng, H., Wang, S., Su, G., Sahana, G., Lund, M., Dekkers, J., Kramer, L., Tuggle, C.K., Corbett, R., Groenen, M.A., Madsen, O., Godia, M., Rocha, D., Li, C., Pausch, H., Hu, X., Frantz, L., Luo, Y., Lin, L., Zhou, Z., Zhang, Z., Chen, Z., Cui, L., Xiang, R., Shen, X., Li, P., Huang, R., Tang, G., Li, M., Zhao, Y., Yi, G., Tang, Z., Jiang, J., Zhao, F., Yuan, X., Liu, X., Chen, Y., Xu, X., Zhao, S., Zhao, P., Haley, C., Zhou, H., Wang, Q., Pan, Y., Ding, X., Ma, L., Li, J., Navarro, P., Zhang, Q., Li, B., Tenesa, A., Liu, G. 2024. A compendium of genetic regulatory effects across pig tissues. Nature Genetics. 56:112-123. https://doi.org/10.1038/s41588-023-01585-7.

Genome-wide association analysis of heifer livability and early first calving in Holstein cattle - (Peer Reviewed Journal)
Gao, Y., Marceau, A., Iqbal, V., Torres-Vazquez, J.A., Neupane, M., Jiang, J., Liu, G., Ma, L. 2023. Genome-wide association analysis of heifer livability and early first calving in Holstein cattle. BMC Genomics. 24:628. https://doi.org/10.1186/s12864-023-09736-0.

Investigation of lncRNA in Bos taurus mammary tissue during dry and lactation periods - (Peer Reviewed Journal)
Marceau, A., Wang, J., Iqbal, V., Jiang, J., Liu, G., Ma, L. 2023. Investigation of lncRNA in Bos taurus mammary tissue during dry and lactation periods. Genes. 14(9):1789. https://doi.org/10.3390/genes14091789.

New insights into transcriptome variation during cattle adipocyte adipogenesis by direct RNA sequencing - (Peer Reviewed Journal)
Peng, L., Zhang, X., Du, Y., Li, F., Han, J., Liu, O., Dai, S., Zhang, X., Liu, G., Yang, L., Zhou, Y. 2023. New insights into transcriptome variation during cattle adipocyte adipogenesis by direct RNA sequencing. iScience. 26(10):107753. https://doi.org/10.1016/j.isci.2023.107753.

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.

Taming transposable elements in livestock and poultry: a review of their roles and applications - (Peer Reviewed Journal)
Zhao, P., Peng, C., Fang, L., Wang, Z., Liu, G. 2023. Taming transposable elements in livestock and poultry: a review of their roles and applications. Genetic Selection Evolution. 55:50. https://doi.org/10.1186/s12711-023-00821-2.

The single-cell transcriptome and chromatin accessibility datasets of peripheral blood mononuclear cells in Chinese Holstein cattle - (Peer Reviewed Journal)
Wang, X., Gao, Y., Li, C., Fang, L., Liu, G., Zhao, X., Zhang, Y., Cai, G., Xue, G., Liu, Y., Wang, L., Zhang, F., Wang, K., Zhang, M., Li, R., Gao, Y., Li, J. 2023. The single-cell transcriptome and chromatin accessibility datasets of peripheral blood mononuclear cells in Chinese Holstein cattle. BMC Genomic Data. 24:39. https://doi.org/10.1186/s12863-023-01139-0.

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.

Harnessing male germline epigenomics for the genetic improvement in cattle - (Peer Reviewed Journal)
Wang, X., Li, W., Feng, X., Li, J., Liu, G., Fang, L., Yu, Y. 2023. Harnessing male germline epigenomics for the genetic improvement in cattle. Journal of Animal Science and Biotechnology. 14:76. https://doi.org/10.1186/s40104-023-00874-9.

Characterization and localization of within and across breed as indications of inbreeding depression and heterosis - (Abstract Only)

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.

Cis-eQTL analysis and functional validation of candidate genes for carcass yield traits in beef cattle - (Peer Reviewed Journal)
Wang, T., Niu, Q., Zhang, T., Zheng, X., Li, H., Gao, X., Chen, Y., Gao, H., Zhang, L., Liu, G., Li, J., Xu, L. 2022. Cis-eQTL analysis and functional validation of candidate genes for carcass yield traits in beef cattle. International Journal of Biological Sciences. 23(23):15055. https://doi.org/10.3390/ijms232315055.

Characterization and localization within and across breed measures of dominance as observed in inbreeding depression and heterosis - (Abstract Only)

The conservation of human functional variants and their effects across livestock species - (Peer Reviewed Journal)
Zhao, R., Talenti, A., Fang, L., Liu, S., Liu, G., Chue Hong, N.P., Tenesa, A., Hassan, M., Prendergast, J.G. 2022. The conservation of human functional variants and their effects across livestock species. Communications Biology. 5:1003. https://doi.org/10.1038/s42003-022-03961-1.

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.