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

Phone: (301) 504-9843
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.)

Projects
Accelerating Genetic Improvement of Ruminants Through Enhanced Genome Assembly, Annotation, and Selection
In-House Appropriated (D)
  Accession Number: 442481
Incorporate Functional Annotation Data in Cattle GWAS and Genomic Selection
Reimbursable Cooperative Agreement (R)
  Accession Number: 439617

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)
Effects of rumen metabolite butyric acid on bovine skeletal muscle satellite cells proliferation, apoptosis, and transcriptional states during myogenic differentiation Reprint Icon - (Peer Reviewed Journal)
Wang, X., Ding, Y., Li, C., Ma, Q., Shi, Y., Liu, G., Li, C., Kang, X. 2024. Effects of rumen metabolite butyric acid on bovine skeletal muscle satellite cells proliferation, apoptosis, and transcriptional states during myogenic differentiation. Domestic Animal Endocrinology. https://doi.org/10.1016/j.domaniend.2024.106892.
Genetic advancements and future directions in ruminant livestock breeding: from reference genomes to multiomics innovations - (Review Article)
A pilot detection and associate study of gene presence-absence variation in Holstein cattle Reprint Icon - (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. 14(13):1921. https://doi.org/10.3390/ani14131921.
Transcriptomic profiling of gastrointestinal tracts in dairy cattle during lactation reveals molecular adaptations for milk synthesis Reprint Icon - (Peer Reviewed Journal)
Gao, Y., Liu, G., Ma, L., Fang, L., Li, C., Baldwin, R.L. 2024. Transcriptomic profiling of gastrointestinal tracts in dairy cattle during lactation reveals molecular adaptations for milk synthesis. Journal of Advanced Research. https://doi.org/10.1016/j.jare.2024.06.020.
Systemic interindividual DNA methylation variants in cattle share major hallmarks with those in humans Reprint Icon - (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.
Mapping and functional characterization of structural variation in 1060 pig genomes Reprint Icon - (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.
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 Reprint Icon - (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.
Integrated meta-omics reveals the regulatory landscape involved in lipid metabolism between pig breeds Reprint Icon - (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.
Unraveling the genetic basis of feed efficiency in cattle through integrated DNA methylation and CattleGTEx analysis Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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.
Building an atlas of transposable elements reveals the extensive roles of young sine in gene regulation, genetic diversity and complex traits in pigs Reprint Icon - (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 Reprint Icon - (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.
Genome-wide acetylation modification of H3K27ac in bovine rumen cell following butyrate exposure Reprint Icon - (Peer Reviewed Journal)
Kang, X., Li, C., Liu, S., Baldwin, R.L., Liu, G., Li, C.-J. 2023. Genome-wide acetylation modification of H3K27ac in bovine rumen cell following butyrate exposure. Biomolecules. 13(7):1137. https://doi.org/10.3390/biom13071137.
The single-cell transcriptome and chromatin accessibility datasets of peripheral blood mononuclear cells in Chinese Holstein cattle Reprint Icon - (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.
Taming transposable elements in livestock and poultry: a review of their roles and applications Reprint Icon - (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.
Harnessing male germline epigenomics for the genetic improvement in cattle Reprint Icon - (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.
Mediating a host cell signaling pathway linked to the overwinter mortality offers a promising therapeutic approach for improving bee health Reprint Icon - (Peer Reviewed Journal)
Zhang, Y., Liu, A., Huang, S., Evans, J.D., Cook, S.C., Palmer-Young, E., Corona, M.V., Alburaki, M., Liu, G., Han, R., Li, W., Hao, Y., Li, J., Gilligan, T., Smith-Pardo, A.H., Banmeke, O., Posada-Florez, F.J., Gao, Y.H., Hoffman, G.D., Xie, H., Chen, Y. 2022. Mediating a host cell signaling pathway linked to the overwinter mortality offers a promising therapeutic approach for improving bee health. Journal of Advanced Research. https://doi.org/10.1016/j.jare.2022.12.011.
Cis-eQTL analysis and functional validation of candidate genes for carcass yield traits in beef cattle Reprint Icon - (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.
The conservation of human functional variants and their effects across livestock species Reprint Icon - (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.
Genetic diversity and selection signatures in Jianchang Black goats revealed by whole-genome sequencing data Reprint Icon - (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.
Butyrate induces modifications of the CTCF-binding landscape in cattle cells Reprint Icon - (Peer Reviewed Journal)
Boschiero, C., Gao, Y., Baldwin, R.L., Ma, L., Li, C., Liu, G. 2022. Butyrate induces modifications of the CTCF-binding landscape in cattle cells. Biomolecules. 12(9):1177. https://doi.org/10.3390/biom12091177.
Differentially CTCF-binding sites in cattle rumen tissue during weaning Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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.
A 13.42-kb tandem duplication at the ASIP locus is strongly associated with the pigmentation phenotype of Swiss markings in goats Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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.
Single-cell transcriptomic and chromatin accessibility analyses of dairy cattle peripheral blood mononuclear cells and their responses to lipopolysaccharide Reprint Icon - (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 Reprint Icon - (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.
Characterization of accessible chromatin regions in cattle rumen epithelial tissue during weaning Reprint Icon - (Peer Reviewed Journal)
Boschiero, C., Gao, Y., Baldwin, R.L., Ma, L., Liu, G.E., Li, C.-J. 2022. Characterization of accessible chromatin regions in cattle rumen epithelial tissue during weaning. Genes. 13:535. https://doi.org/10.3390/genes13030535.
Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle Reprint Icon - (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.
Large-scale cis-eQTL analysis of gene expression in blood of young healthy pigs using PigGTEx Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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.
Genome-wide recombination map construction from single sperm sequencing in cattle Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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.
Transcriptional reprogramming in rumen epithelium during the developmental transition of pre-ruminant to the ruminant in cattle Reprint Icon - (Peer Reviewed Journal)
Baldwin, R.L., Liu, M., Connor, E.E., Ramsay, T.G., Liu, G., Li, C. 2021. Transcriptional reprogramming in rumen epithelium during the developmental transition of pre-ruminant to the ruminant in cattle. Animals. 11(10):2870. https://doi.org/10.3390/ani11102870.
Comprehensive transcriptome and methylome analysis delineates the biological basis of hair follicle development and wool-related traits in Merino sheep Reprint Icon - (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.
Effect of temperature and maternal age on recombination rate in cattle Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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).
Identification and population genetic analyses of copy number variations in six domestic goat breeds and Bezoar ibexes using next-generation sequencing Reprint Icon - (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.
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.
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.
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.
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.
A LINE-1 derived promoter driving over-expression of the ASIP gene is responsible for white color in swamp buffalo Reprint Icon - (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.
Comparative analyses of copy number variations between Bos taurus and Bos indicus Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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.
Establishment and transcriptomic analyses of a cattle rumen epithelial primary cells (REPC) culture by bulk and single-cell RNA sequencing to elucidate interactions of butyrate and rumen development Reprint Icon - (Peer Reviewed Journal)
Lin, S., Fang, L., Kang, X., Liu, S., Liu, M., Connor, E.E., Baldwin, R.L., Liu, G., Li, C. 2020. Establishment and transcriptomic analyses of a cattle rumen epithelial primary cells (REPC) culture by bulk and single-cell RNA sequencing to elucidate interactions of butyrate and rumen development. Heliyon. 6(6):e041123. https://doi.org/10.1016/j.heliyon.2020.e04112.
Epigenomics and genotype-phenotype association analyses reveal conserved genetic architecture of complex traits in cattle and human Reprint Icon - (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 Reprint Icon - (Peer Reviewed Journal)
Zhou, Y., Liu, S., Hu, Y., Fang, L., Gao, Y., Xia, H., Schroeder, S.G., Rosen, B.D., Connor, E.E., Li, C., Baldwin, R.L., Cole, J.B., Van Tassell, C.P., Yang, L., Ma, L., Liu, G. 2020. Comparative whole genome DNA methylation profiling of cattle tissues reveals global and tissue-specific methylation patterns. BMC Biology. 18(1):85. https://doi.org/10.1186/s12915-020-00793-5.
Comprehensive analyses of 723 transcriptomes enhance biological interpretation and genomic prediction for complex traits in cattle Reprint Icon - (Peer Reviewed Journal)
Fang, L., Cai, W., Liu, S., Canela-Xandri, O., Gao, Y., Jiang, J., Rawlik, K., Li, B., Schroeder, S.G., Rosen, B.D., Li, C., Sonstegard, T.S., Alexander, L.J., Van Tassell, C.P., Van Raden, P.M., Cole, J.B., Yu, Y., Zhang, S., Tenesa, A., Ma, L., Liu, G. 2019. Comprehensive analyses of 723 transcriptomes enhance biological interpretation and genomic prediction for complex traits in cattle. Genome Research. 30(5):790-801. https://doi.org/10.1101/gr.250704.119.
Gamevar.f90: A software package for calculating individual gametic diversity Reprint Icon - (Peer Reviewed Journal)
Santos, D.J., Cole, J.B., Liu, G., Van Raden, P.M., Ma, L. 2020. Gamevar.f90: A software package for calculating individual gametic diversity. BMC Bioinformatics. 21:100. https://doi.org/10.1186/s12859-020-3417-x.
De novo assembly of the cattle reference genome with single-molecule sequencing Reprint Icon - (Peer Reviewed Journal)
Rosen, B.D., Bickhart, D.M., Schnabel, R.D., Koren, S., Elsik, C.G., Tseng, E., Rowan, T.N., Low, W.Y., Zimin, A., Couldrey, C., Hall, R., Li, W., Rhie, A., Ghurye, J., McKay, S.D., Thibaud-Nissen, F., Hoffman, J., Murdoch, B.M., Snelling, W.M., McDaneld, T.G., Hammond, J.A., Schwartz, J.C., Nandolo, W., Hagen, D.E., Dreischer, C., Schultheiss, S.J., Schroeder, S.G., Phillippy, A.M.,Cole, J.B., Van Tassell, C.P., Liu, G., Smith, T.P.L., Medrano, J.F. 2020. De novo assembly of the cattle reference genome with single-molecule sequencing. GigaScience. 9(3):1-9. https://doi.org/10.1093/gigascience/giaa021.
GWAS and fine-mapping of livability and six disease traits in Holstein cattle Reprint Icon - (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.
Epigenomic profiling of histone marks and CTCF binding sites in bovine rumen epithelial primary cells before and after butyrate treatment Reprint Icon - (Peer Reviewed Journal)
Kang, X., Liu, S., Fang, L., Lin, S., Liu, M., Baldwin, R.L., Liu, G., Li, C. 2020. Epigenomic profiling of histone marks and CTCF binding sites in bovine rumen epithelial primary cells before and after butyrate treatment. Data in Brief. 28:104983. https://doi.org/10.1016/j.dib.2019.104983.
Analyses of inter-individual variations in sperm DNA methylation reveal their regulatory role in gene expression and association with reproduction traits in cattle Reprint Icon - (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.
Divergence analyses of sperm DNA methylomes between monozygotic twin AI bulls Reprint Icon - (Peer Reviewed Journal)
Liu, S., Cai, W., Yin, H., Liu, A., Li, Y., Wang, Y., Liu, G., Yu, Y., Zhang, S. 2019. Divergence analyses of sperm DNA methylomes between monozygotic twin AI bulls. Epigenomes. 3(4):21. https://doi.org/10.3390/epigenomes3040021.
Bos taurus-indicus hybridization correlates with intralocus sexual-conflicting effects of PRDM9 on male and female fertility in Holstein cattle Reprint Icon - (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.
Genome-wide CNV analysis revealed variants associated with growth traits in African indigenous goats Reprint Icon - (Peer Reviewed Journal)
Liu, M., Woodward Greene, M.J., Kang, X., Pan, M.G., Rosen, B.D., Van Tassell, C.P., Chen, H., Liu, G. 2020. Genome-wide CNV analysis revealed variants associated with growth traits in African indigenous goats. Genomics. 112(2):1477-1480. https://doi.org/10.1016/j.ygeno.2019.08.018.
Genomic patterns of homozygosity in Chinese local cattle Reprint Icon - (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.
Functional annotation of the cattle genome through systematic discovery and characterization of chromatin states and butyrate-induced variations Reprint Icon - (Peer Reviewed Journal)
Fang, L., Liu, S., Liu, M., Kang, X., Lin, S., Li, B., Connor, E.E., Baldwin, R.L., Tenesa, A., Ma, L., Liu, G., Li, C. 2019. Functional annotation of the cattle genome through systematic discovery and characterization of chromatin states and butyrate-induced variations. BMC Biology. 17(1):68. https://doi.org/10.1186/s12915-019-0687-8.
Genomic analysis reveals specific patterns of homozygosity in inbred pigs Reprint Icon - (Peer Reviewed Journal)
Wang, L., Xu, L., Mu, Y., Li, K., Han, J., Wu, T., Liu, L., Gao, Q., Xia, Y., Dong, K., Hou, G., Huang, L., Tang, F., Cheng, Y., Liu, Y., Wang, C., Wang, Z., Yang, S., He, X., Qian, L., Liu, G., Feng, S. 2019. Genomic analysis reveals specific patterns of homozygosity in inbred pigs. Animals. 9(6):314. https://doi.org/10.3390/ani9060314.
Timing and extent of inbreeding in African goats Reprint Icon - (Peer Reviewed Journal)
Nandolo, W., Meszaros, G., Banda, L.J., Gondwe, T.N., Lamuno, D., Mulindwa, H., Nakimbugwe, H.N., Wurzinger, M., Utsunomiya, Y.T., Woodward Greene, M.J., Liu, M., Liu, G., Van Tassell, C.P., Curik, I., Rosen, B.D., Solkner, J. 2019. Timing and extent of inbreeding in African goats. Frontiers in Genetics. 10:57. https://doi.org/10.3389/fgene.2019.00537.
Integrating signals from sperm methylome analysis and genome-wide association study for a better understanding of male fertility in cattle Reprint Icon - (Peer Reviewed Journal)
Fang, L., Zhou, Y., Liu, S., Jiang, J., Bickhart, D.M., Null, D.J., Li, B., Schroeder, S.G., Rosen, B.D., Cole, J.B., Van Tassell, C.P., Ma, L., Liu, G. 2019. Integrating signals from sperm methylome analysis and genome-wide association study for a better understanding of male fertility in cattle. Epigenomes. 3(2):10. https://doi.org/10.3390/epigenomes3020010.
Copy number variation of bovine SHH gene is associated with body conformation traits in Chinese beef cattle Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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.
Genetic and epigenetic architecture of paternal origin contribute to gestation length in cattle Reprint Icon - (Peer Reviewed Journal)
Fang, L., Jiang, J., Li, B., Zhou, Y., Freebern, E., Van Raden, P.M., Cole, J.B., Liu, G., Ma, L. 2019. Genetic and epigenetic architecture of paternal origin contribute to gestation length in cattle. Communications Biology. 2:100. https://doi.org/10.1038/s42003-019-0341-6.
Comparative analyses of sperm DNA methylomes among human, mouse and cattle provide insights into epigenomic evolution and complex traits Reprint Icon - (Peer Reviewed Journal)
Fang, L., Zhou, Y., Liu, S., Jiang, J., Bickhart, D.M., Null, D.J., Li, B., Schroeder, S.G., Rosen, B.D., Cole, J.B., Van Tassell, C.P., Ma, L., Liu, G. 2019. Comparative analyses of sperm DNA methylomes among human, mouse and cattle provide insights into epigenomic evolution and complex traits. Epigenetics. 14(3):260-276. https://doi.org/10.1080/15592294.2019.1582217.
Genome changes due to artificial selection in U.S. Holstein cattle Reprint Icon - (Peer Reviewed Journal)
Ma, L., Sonstegard, T.S., Cole, J.B., Van Tassell, C.P., Wiggans, G.R., Crooker, B.A., Tan, C., Prakapenka, D., Liu, G., Da, Y. 2019. Genome changes due to artificial selection in U.S. Holstein cattle. BMC Genomics. 20:128. https://doi.org/10.1186/s12864-019-5459-x.
Computational detection and experimental validation of segmental duplications and associated copy number variations in water buffalo (Bubalus bubalis) Reprint Icon - (Peer Reviewed Journal)
Liu, S., Kang, X., Catacchio, C.R., Liu, M., Fang, L., Schroeder, S.G., Li, W., Rosen, B.D., Iamartino, D., Iannuzzi, L., Sonstegard, T.S., Van Tassell, C.P., Ventura, M., Low, W., Williams, J.L., Bickhart, D.M., Liu, G. 2019. Computational detection and experimental validation of segmental duplications and associated copy number variations in water buffalo (Bubalus bubalis). Functional and Integrative Genomics. 19(3):409–419. https://doi.org/10.1007/s10142-019-00657-4.
Probe-based association analysis identifies several deletions associated with average daily gain in beef cattle Reprint Icon - (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.
Epigenetics and heritable phenotypic variations in livestock Reprint Icon - (Book / Chapter)
Lin, S., Fang, L., Li, C., Liu, G. 2019. Epigenetics and heritable phenotypic variations in livestock. In: Tollefsbol T. (editor). Transgenerational Epigenetics. 2nd edition. Amsterdam, Netherlands: Elsevier, p. 283-313
A genome-wide association study for mastitis resistance in phenotypically well-characterized Holstein dairy cattle using a selective genotyping approach Reprint Icon - (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 Reprint Icon - (Peer Reviewed Journal)
Liu, M., Zhou, Y., Rosen, B.D., Van Tassell, C.P., Stella, A., Tosser, G., Rupp, R., Palhiere, I., Colli, L., Sayre, B., Crepaldi, P., Fang, L., Meszaros, G., Chen, H., Liu, G., Adaptmap Consortium. 2018. Diversity of copy number variation in the worldwide goat population. Heredity. 122:636–646. https://doi.org/10.1038/s41437-018-0150-6.
Integrative analysis of transcriptome and epigenome data enhances the understanding of the genetic basis underlying rumen development - (Abstract Only)
Genetic assessment of inbred chicken lines indicates genomic signatures of resistance to Marek’s disease Reprint Icon - (Peer Reviewed Journal)
Xu, L., He, Y., Ding, Y., Liu, G., Zhang, H., Cheng, H.H., Taylor, R.L., Song, J. 2018. Genetic assessment of inbred chicken lines indicates genomic signatures of resistance to Marek’s disease. Journal of Animal Science and Biotechnology. 9:65. https://doi.org/10.1186/s40104-018-0281-x.
MicroRNA-guided prioritization of genome-wide association signals reveals the importance of microRNA-target gene networks for complex traits in cattle Reprint Icon - (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.
Genomic predictions combining SNP markers and copy number variations in Nellore cattle Reprint Icon - (Peer Reviewed Journal)
Hay, E.A., Utsunomiya, Y.T., Xu, L., Zhou, Y., Neves, H.H., Carvalheiro, R., Bickhart, D.M., Garcia, J., Liu, G. 2018. Genomic predictions combining SNP markers and copy number variations in Nellore cattle. Biomed Central (BMC) Genomics. 19(1):441. https://doi.org/10.1186/s12864-018-4787-6.
Genomic predictions combining SNP markers and copy number variations in Nellore cattle Reprint Icon - (Peer Reviewed Journal)
Hay, E.A., Utsunomiya, Y.T., Xu, L., Neves, H.H., Carvalheiro, R., Bickhart, D.M., Ma, L., Garcia, J.F., Liu, G. 2018. Genomic predictions combining SNP markers and copy number variations in Nellore cattle. BMC Genomics. 19(1):441-449. https://doi.org/10.1186/s12864-018-4787-6.
Evidence of evolutionary history and selective sweeps in the genome of Meishan pig reveals its genetic and phenotypic characterization Reprint Icon - (Peer Reviewed Journal)
Zhao, P., Yu, Y., Feng, W., Du, H., Yu, J., Kang, H., Zheng, X., Wang, Z., Liu, G., Ernst, C.W., Ran, X., Wang, J., Liu, J. 2018. Evidence of evolutionary history and selective sweeps in the genome of Meishan pig reveals its genetic and phenotypic characterization. Gigascience. 7(5):1-12. https://doi.org/10.1093/gigascience/giy058.
Genomic structural differences between cattle and river buffalo identified through a combination and genomic and transcriptomic analysis - (Peer Reviewed Journal)
Li, W., Bickhart, D.M., Ramunno, L., Lamartino, D., Williams, J., Liu, G. 2018. Genomic structural differences between cattle and river buffalo identified through a combination and genomic and transcriptomic analysis. Data in Brief. 19:236-239.
Characterization of recombination features and the genetic basis in multiple cattle breeds Reprint Icon - (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.
Genome-wide copy number variant analysis reveals variants associated with 10 diverse production traits in Holstein cattle Reprint Icon - (Peer Reviewed Journal)
Zhou, Y., Connor, E.E., Wiggans, G.R., Lu, Y., Tempelman, R., Schroeder, S.G., Chen, H., Liu, G. 2018. Genome-wide copy number variant analysis reveals variants associated with 10 diverse production traits in Holstein cattle. BMC Genomics. 19(1):314. https://doi.org/10.1186/s12864-018-4699-5.
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 Reprint Icon - (Peer Reviewed Journal)
Zhou, Y., Connor, E.E., Bickhart, D.M., Li, C., Baldwin, R.L., Schroeder, S.G., Rosen, B.D., Yang, L., Van Tassell, C.P., Liu, G. 2018. Comparative whole genome DNA methylation profiling of cattle sperm and somatic tissues reveals striking hypomethylated patterns in sperm. Gigascience. 7(5):1-13. https://doi.org/10.1093/gigascience/giy039.
Comparative sequence alignment reveals River Buffalo genomic structural differences compared with cattle - (Peer Reviewed Journal)
Li, W., Bickhart, D.M., Ramunno, L., Iamartino, D., Williams, J., Liu, G. 2018. Comparative sequence alignment reveals River Buffalo genomic structural differences compared with cattle. Genomics. https://doi.org/10.1016/j.ygeno.2018.02.018.
A haplotype spanning PLAG1 contributed to stature recovery in modern cattle Reprint Icon - (Peer Reviewed Journal)
Utsunomiya, Y., Milanesi, M., Utsunomiya, A., Torrecilha, R., Kim, E., Silva, M., Do Carmo, A.S., Carvalheiro, R., De Rezende Neves, H.H., Padula, R., Sussai, T., Zavarez, L.B., Cipriano, R.S., Caminhas, M., Hambrecht, G., Colli, L., Eufemi, E., Ajmone-Marsan, P., Buora, M., Liu, G., Bickhart, D.M., Van Tassell, C.P., Solkner, J., Sonstegard, T.S., Garcia, J.F. 2017. A haplotype spanning PLAG1 contributed to stature recovery in modern cattle. Scientific Reports. 7(1):17140. https://doi.org/10.1038/s41598-017-17127-1.
Comparative sequence alignment reveals River Buffalo genomic structural differences compared with cattle - (Abstract Only)
Genome-wide sequencing and comparative profiling of cattle sperm DNA methylome reveals its hypomethylated patterns - (Abstract Only)
Construction of PRDM9 allele-specific recombination maps in cattle using large-scale pedigree analysis and genome-wide single sperm genomics Reprint Icon - (Peer Reviewed Journal)
Zhou, Y., Shen, B., Jiang, J., Padhi, A., Park, K., Oswalt, A., Sattler, C., Telugu, B.P., Chen, H., Cole, J.B., Liu, G., Ma, L. 2017. Construction of PRDM9 allele-specific recombination maps in cattle using large-scale pedigree analysis and genome-wide single sperm genomics. DNA Research. 25(2):183–194. https://doi.org/10.1093/dnares/dsx048.
The essence of appetite: Does olfactory receptor variation play a role? Reprint Icon - (Review Article)
Connor, E.E., Yang, Z., Liu, G. 2018. The essence of appetite: Does olfactory receptor variation play a role? Journal of Animal Science. 96(4):1551-1558. https://doi.org/10.1093/jas/sky068.
Characterization of candidate genes for bovine adipogenesis reveals differences of TUSC5 isoforms caused by novel alternative splicing Reprint Icon - (Peer Reviewed Journal)
Zhang, Z., Li, M., Hu, X., Cai, H., Liu, M., Sun, Y., Huang, Y., Dang, R., Lan, X., Lei, C., Liu, G., Li, C., Hong, C. 2018. Characterization of candidate genes for bovine adipogenesis reveals differences of TUSC5 isoforms caused by novel alternative splicing. Oncotarget. 9(1): s287-s298. https://doi.org/10.18632/oncotarget.23482.
Diversity of copy number variation in a worldwide population of sheep Reprint Icon - (Peer Reviewed Journal)
Yang, L., Xu, L., Zhou, Y., Liu, M., Wang, L., Kijas, J.W., Zhang, H., Li, L., Liu, G. 2017. Diversity of copy number variation in a worldwide population of sheep. Genomics. 110(3):143-148. https://doi.org/10.1016/j.ygeno.2017.09.005.
Characterization of copy number variation's potential Role in Marek’s disease Reprint Icon - (Peer Reviewed Journal)
Xu, L., He, Y., Ding, Y., Sun, G., Carrillo, J., Li, Y., Ghaly, M.M., Ma, L., Zhang, H., Liu, G., Song, J. 2017. Characterization of copy number variation's potential Role in Marek’s disease. International Journal of Molecular Sciences. Available:http://wwww.mdpi.com/1422-0067/18/5/1020/pdf.
CNV discovery for milk composition traits in dairy cattle using whole genome resequencing - (Peer Reviewed Journal)
Sun, D., Gao, Y., Jiang, S., Yang, S., Hou, Y., Liu, G., Zhang, S., Zhang, Q. 2017. CNV discovery for milk composition traits in dairy cattle using whole genome resequencing. Biomed Central (BMC) Genomics. 18(1):265.
Genome-wide copy number variant analysis in Holstein cattle reveals variants associated with 10 production traits including residual feed intake and dry matter intake - (Abstract Only)
Connor, E.E., Zhou, Y., Wiggans, G.R., Lu, Y., Tempelman, R., Schroeder, S.G., Chen, H., Liu, G. 2017. Genome-wide copy number variant analysis in Holstein cattle reveals variants associated with 10 production traits including residual feed intake and dry matter intake. Journal of Dairy Science. 100(Suppl. 2):43 (abstr. M103).
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.
Ruminant-specific multiple duplication events of PRDM9 before speciation - (Peer Reviewed Journal)
Padhi, A., Shen, B., Jiang, J., Zhou, Y., Liu, G., Ma, L. 2017. Ruminant-specific multiple duplication events of PRDM9 before speciation. BMC Evolutionary Biology. 17:79.
Systematic profiling of bovine short tandem repeats using whole genome sequencing data - (Peer Reviewed Journal)
Xu, L., Haasl, R.J., Sun, J., Zhou, Y., Bickhart, D.M., Son, J., Van Tassell, C.P., Lwein, H.A., Liu, G. 2016. Systematic profiling of bovine short tandem repeats using whole genome sequencing data. Genome Biology and Evolution. 9(1):20-31.
Reduced representation bisulphite sequencing of the cattle genome reveals DNA methylation patterns - (Peer Reviewed Journal)
Zhou, Y., Xu, L., Bickhart, D.M., Hay, E., Schroeder, S.G., Connor, E.E., Leeson, A.J., Sonstegard, T., Van Tassell, C.P., Hong, C., Liu, G. 2016. Reduced representation bisulphite sequencing of the cattle genome reveals DNA methylation patterns. BMC Genomics. 17(1):779.
Initial analysis of sperm DNA methylome in Holstein bulls - (Abstract Only)
Liu, G. 2016. Initial analysis of sperm DNA methylome in Holstein bulls. In: Proceedings of the 35th International Society for Animal Genetics (ISAG) Conference. 7/23-27/16, Salt Lake City, Utah. P2009.
Comparative analyses across cattle breeds reveal the pitfalls caused by artificial and lineage-differential copy number variations - (Peer Reviewed Journal)
Zhou, Y., Utsunomiya, Y.T., Xu, L., Hay, E.A., Bickhart, D.M., Carvalheiro, R., Neves, H.H., Van Tassell, C.P., Sonstegard, T.S., Garcia, J., Liu, G. 2016. Comparative analyses across cattle breeds reveal the pitfalls caused by artificial and lineage-differential copy number variations. Scientific Reports. 6:29219.
Reduced representation bisulphite sequencing of the ten bovine somatic tissues reveals DNA methylation patterns - (Abstract Only)
Zhou, Y., Xu, L., Hay, E., Bickhart, D.M., Sonstegard, T., Van Tassell, C.P., Chen, H., Liu, G. 2016. Reduced representation bisulphite sequencing of the ten bovine somatic tissues reveals DNA methylation patterns [abstract]. In: Proceedings of 2016 BARC Poster Day, April 27, 2016, Beltsville, Maryland. P63.
Exploring the feasibility of using copy number variants as genetic markers through large-scale whole genome sequencing experiments - (Abstract Only)
Bickhart, D.M., Xu, L., Hutchison, J.L., Cole, J.B., Null, D.J., Schroeder, S.G., Song, J., Garcia, J.F., Sonstegardq, T.S., Van Tassell, C.P., Schnabel, R.D., Taylor, J.F., Lewin, H.A., Liu, G. 2016. Exploring the feasibility of using copy number variants as genetic markers through large-scale whole genome sequencing experiments. Journal of Dairy Science. 99(E-Suppl. 1)/Journal of Animal Science. 94(E-Suppl. 5):142(abstr. 0306).
Whole-genome sequencing reveals the diversity of cattle copy number variations and multicopy genes - (Peer Reviewed Journal)
Bickhart, D.M., Xu, L., Hutchison, J.L., Cole, J.B., Schroeder, S.G., Song, J., Garcia, J., Van Tassell, C.P., Sonstegard, T.S., Schnabel, R.D., Taylor, J.F., Lewin, H.A., Liu, G. 2016. Whole-genome sequencing reveals the diversity of cattle copy number variations and multicopy genes. DNA Research. 23(3):253-62.
Population-genetic properties of differentiated copy number variations in cattle - (Peer Reviewed Journal)
Xu, L., Hou, Y., Bickhart, D.M., Zhou, Y., Hay, E.A., Song, J., Sonstegard, T., Van Tassell, C.P., Liu, G. 2016. Population-genetic properties of differentiated copy number variations in cattle. Scientific Reports. 6:23161.
Genome-wide CNV analysis reveals variants associated with growth traits in Bos indicus - (Peer Reviewed Journal)
Zhou, Y., Utsunomiya, Y.T., Xu, L., Hay, E.A., Bickhart, D.M., Carvalheiro, R., Neves, H.E., Sonstegard, T., Van Tassell, C.P., Garcia, J., Liu, G. 2016. Genome-wide CNV analysis reveals variants associated with growth traits in Bos indicus. Biomed Central (BMC) Genomics. 17(1):419.2016.
CNV analysis of host responses to porcine reproductive and respiratory syndrome virus infection - (Peer Reviewed Journal)
Hay, E.A., Choi, I., Xu, L., Zhou, Y., Rowland, R., Lunney, J.K., Liu, G. 2017. CNV analysis of host responses to porcine reproductive and respiratory syndrome virus infection. Journal of Genomics. 5:58-63.
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.
Diversity and population-genetic properties of copy number variations and multicopy genes in cattle - (Abstract Only)
Bickhart, D.M., Xu, L., Hutchison, J.L., Cole, J.B., Null, D.J., Schroeder, S.G., Song, J., Garcia, J., Van Tassell, C.P., Sonstegard, T.S., Schnabel, R.D., Taylor, J.F., Lewin, H.A., Liu, G. 2016. Diversity and population-genetic properties of copy number variations and multicopy genes in cattle [abstract]. USDA NIFA Animal Genome Program PD Meeting, January 8, 2016, San Diego, California.
Effect of sex, age, and breed on genetic recombination features in cattle - (Abstract Only)
Shen, B., Wang, Z., Jiang, J., Cole, J.B., Bickhart, D.M., Wiggans, G.R., Liu, G., Ma, L. 2016. Effect of sex, age, and breed on genetic recombination features in cattle. Plant and Animal Genome Conference Proceedings. San Diego, CA, Jan. 9–13, P0522.
Progress toward a low budget reference grade genome assembly Reprint Icon - (Abstract Only)
Rosen, B.D., Bickhart, D.M., Koren, S., Hastie, A.R., Schroeder, S.G., Smith, T.P., Sullivan, S.T., Liachko, I., Burton, J.N., Dunham, M.J., Sendure, J., Sayre, B.L., Huson, H.J., Liu, G., Connor, E.E., Sonstegard, T.S., Phillippy, A., Van Tassell, C.P. 2016. Progress toward a low budget reference grade genome assembly. Plant and Animal Genome Conference Proceedings. San Diego, CA, Jan. 9–13, P0612.
Population-genetic properties of differentiated copy number variations in cattle - (Abstract Only)
Liu, G. 2015. Population-genetic properties of differentiated copy number variations in cattle [abstract]. China Agriculture University, November 12, 2015, Beijing, China.
Co-expression analysis of fetal weight-related genes in ovine skeletal muscle during mid and late fetal development stages - (Peer Reviewed Journal)
Xu, L., Zhao, F., Ren, H., Li, L., Lu, J., Liu, J., Zhang, S., Liu, G., Song, J., Zhang, L., Wei, C., Du, L. 2014. Co-expression analysis of fetal weight-related genes in ovine skeletal muscle during mid and late fetal development stages. International Journal of Medical Sciences. 10(9):1039-50.
CNV-based genome wide association study reveals additional variants contributing to meat quality in swine - (Peer Reviewed Journal)
Wang, L., Xu, L., Liu, X., Zhang, T., Li, N., Zhang, Y., Yan, H., Zhao, K., Liu, G., Zhang, L., Wang, L. 2015. CNV-based genome wide association study reveals additional variants contributing to meat quality in swine. Scientific Reports. 5:12535.
Transcriptomic profiling of spleen in grass-fed and grain-fed Angus cattle - (Peer Reviewed Journal)
Li, Y., Carrillo, J.A., Ding, Y., He, Y., Zhao, C., Lui, J., Liu, G., Zan, L., Song, J. 2015. Transcriptomic profiling of spleen in grass-fed and grain-fed Angus cattle. PLoS One. 10(9):e0135670.
Cattle sex-specific recombination and genetic control from a very large pedigree - (Peer Reviewed Journal)
Ma, L., O'Connell, J.R., Van Raden, P.M., Shen, B., Padhi, A., Sun, C., Bickhart, D.M., Cole, J.B., Null, D.J., Liu, G., Da, Y., Wiggans, G.R. 2015. Cattle sex-specific recombination and genetic control from a very large pedigree. PLoS Genetics. 11(11):e1005387.
Identification of copy number variable gene families in Holstein and Jersey cattle - (Abstract Only)
Bickhart, D.M., Xu, L., Hutchison, J.L., Liu, G., Lewin, H.A. 2015. Identification of copy number variable gene families in Holstein and Jersey cattle. Journal of Dairy Science. 98(Suppl. 2)/Journal of Animal Science 93(Suppl. 3):648(abstr. W84).
RAPTR-SV: a hybrid method for the detection of structural variants Reprint Icon - (Peer Reviewed Journal)
Bickhart, D.M., Hutchison, J.L., Xu, L., Schnabel, R.D., Taylor, J.F., Reecy, J.M., Schroeder, S.G., Van Tassell, C.P., Sonstegard, T.S., Liu, G. 2015. RAPTR-SV: a hybrid method for the detection of structural variants. Bioinformatics. 31(13):2084-2090.
Comparison of CNVs in Buffalo with other species - (Abstract Only)
Bickhart, D.M., Liu, G., International Water, B.A. 2015. Comparison of CNVs in Buffalo with other species. Plant and Animal Genome Conference Proceedings. San Diego, CA, January 10–14, W107.
Genome changes due to forty years of artificial selection associated with divergent dairy production and reproduction - (Abstract Only)
Sonstegard, T.S., Ma, L., Kim, E., Van Tassell, C.P., Wiggans, G.R., Crooker, B.A., Cole, J.B., Liu, G., Garbe, J.R., Fahrenkug, S.C., Ponce De Leon, F., Da, Y. 2015. Genome changes due to forty years of artificial selection associated with divergent dairy production and reproduction. Plant and Animal Genome Conference. San Diego, CA, January 10–14, W150.
Genomic signatures reveal geographic adaption and human selection in cattle - (Peer Reviewed Journal)
Xu, L., Bickhart, D.M., Cole, J.B., Schroeder, S.G., Song, J., Van Tassell, C.P., Sonstegard, T.S., Liu, G. 2014. Genomic signatures reveal geographic adaption and human selection in cattle. Molecular Biology and Evolution. 32(3):711-25.
Genome wide CNV analysis reveals additional variants associated with milk production traits in Holsteins - (Peer Reviewed Journal)
Xu, L., Cole, J.B., Bickhart, D.M., Hou, Y., Song, J., Van Raden, P.M., Sonstegard, T.S., Van Tassell, C.P., Liu, G. 2014. Genome wide CNV analysis reveals additional variants associated with milk production traits in Holsteins. Biomed Central (BMC) Genomics. 15:683.
Recent advances in studying of copy number variation and gene expression - (Peer Reviewed Journal)
Liu, G., Xu, L., Huang, K.S. 2014. Recent advances in studying of copy number variation and gene expression. Gene Expression. 7:1-5 DOI:10.4137/GGG.S14286.
The hunt for a functional mutation affecting conformation and calving traits on chromosome 18 in Holstein cattle - (Proceedings)
Cole, J.B., Hutchison, J.L., Null, D.J., Van Raden, P.M., Liu, G., Schroeder, S.G., Smith, T.P., Sonstegard, T.S., Van Tassell, C.P., Bickhart, D.M. 2014. The hunt for a functional mutation affecting conformation and calving traits on chromosome 18 in Holstein cattle. World Congress of Genetics Applied in Livestock Production. Vancouver, Canada, Aug. 17–22. 3 pp.
Using the whole read: structural variant detection using NGS data - (Proceedings)
Bickhart, D.M., Cole, J.B., Hutchison, J.L., Xu, L., Liu, G. 2014. Using the whole read: structural variant detection using NGS data. World Congress of Genetics Applied in Livestock Production. Vancouver, Canada, Aug. 17–22. 5 pp.
Genome wide CNV analysis reveals additional variants associated with milk production traits in Holsteins - (Abstract Only)
Xu, L., Cole, J.B., Bickhart, D.M., Hou, Y., Song, J., Van Raden, P.M., Sonstegard, T.S., Van Tassell, C.P., Liu, G. 2014. Genome wide CNV analysis reveals additional variants associated with milk production traits in Holsteins. BARC Poster Day. BARC Poster Day.p.67, abstract 54.
Population sequencing reveals breed and sub-species specific CNVs in cattle - (Abstract Only)
Bickhart, D.M., Xu, L., Hutchison, J.L., Sonstegard, T.S., Van Tassell, C.P., Schroeder, S.G., Fernando Garcia, J., Taylor, J.F., Schnabel, R.D., Lewin, H.A., Liu, G. 2014. Population sequencing reveals breed and sub-species specific CNVs in cattle. CONFERENCE ON THE BIOLOGY OF GENOMES. Conference on the Biology of Genomes, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. p199.
Bovine exome sequence analysis and targeted SNP genotyping of recessive fertility defects HH2, HH3, and BH1 reveals causative mutation in SMC2 for HH3 Reprint Icon - (Peer Reviewed Journal)
Mc Clure, M., Bickhart, D.M., Null, D.J., Van Raden, P.M., Xu, L., Wiggans, G.R., Liu, G., Schroeder, S.G., Glasscock, J., Armstrong, J., Cole, J.B., Sonstegard, T.S., Van Tassell, C.P. 2014. Bovine exome sequence analysis and targeted SNP genotyping of recessive fertility defects HH2, HH3, and BH1 reveals causative mutation in SMC2 for HH3. PLoS One. 9(3):e92769.
A high-resolution whole-genome map of the distinctive epigenomic landscape induced by butyrate in bovine cells - (Peer Reviewed Journal)
Shin, J., Xu, L., Li, R.W., Gao, Y., Bickhart, D.M., Liu, G., Baldwin, R.L., Li, C. 2014. A high-resolution whole-genome map of the distinctive epigenomic landscape induced by butyrate in bovine cells. Animal Genetics. 45:40–50. DOI:10.1111.age.12147.
An atlas of DNA methylation in diverse bovine tissues - (Abstract Only)
Liu, G. 2013. An atlas of DNA methylation in diverse bovine tissues. Meeting Abstract. The Clinical Epigenome Conference Program Guide. p.17.
A genome-wide survey reveals a deletion polymorphism associated with resistance to gastrointestinal nematodes in Angus cattle - (Peer Reviewed Journal)
Xu, L., Hou, Y., Bickhart, D.M., Song, J., Van Tassell, C.P., Sonstegard, T.S., Liu, G. 2014. A genome-wide survey reveals a deletion polymorphism associated with resistance to gastrointestinal nematodes in Angus cattle. Functional and Integrative Genomics. DOI:14(2):333-9.
Gene expression profiles of bovine mammary epithelial cells and association with milk composition traits using RNA-seq - (Peer Reviewed Journal)
Cui, X., Hou, Y., Sun, D., Zhang, S., Lv, X., Liu, G., Zhang, Y., Zhang, Q. 2014. Gene expression profiles of bovine mammary epithelial cells and association with milk composition traits using RNA-seq. Biomed Central (BMC) Genomics 15:226.
The challenges and importance of structural variation detection in livestock - (Review Article)
Bickhart, D.M., Liu, G. 2014. The challenges and importance of structural variation detection in livestock. Frontiers in Genetics. 5:37.
Candidate causative mutation on BTA18 associated with calving and conformation traits in Holstein bulls - (Abstract Only)
Cole, J.B., Hutchison, J.L., Null, D.J., Van Raden, P.M., Liu, G., Schroeder, S.G., Sonstegard, T.S., Van Tassell, C.P., Bickhart, D.M. 2014. Candidate causative mutation on BTA18 associated with calving and conformation traits in Holstein bulls. Plant and Animal Genome Conference Proceedings. Plant Animal Genome XXII, San Diego, CA, Jan. 11–15, P1097.
The use of population-scale sequencing to identify CNVs impacting productive traits in different cattle breeds - (Abstract Only)
Bickhart, D.M., Xu, L., Hutchison, J.L., Sonstegard, T.S., Van Tassell, C.P., Schroeder, S.G., Garcia, J.F., Taylor, J.F., Schnabel, R.D., Lewin, H., Liu, G. 2014. The use of population-scale sequencing to identify CNVs impacting productive traits in different cattle breeds. Plant and Animal Genome Conference Proceedings. Plant Animal Genome XXII, San Diego, CA, Jan. 11–15, P078.
Assessing signatures of selection through variation in linkage disequilibrium between taurine and indicine cattle - (Peer Reviewed Journal)
Perez O'Brien, A.M., Utsunomiya, Y.T., Meszaros, G., Bickhart, D.M., Liu, G., Garcia, J., Van Tassell, C.P., Sonstegard, T.S., Solkner, J. 2014. Assessing signatures of selection through variation in linkage disequilibrium between taurine and indicine cattle. Genetics Selection Evolution. 46:19.
Population sequencing reveals breed and sub-species specific CNVs in cattle - (Abstract Only)
Liu, G., Bickhart, D.M., Xu, L., Hutchison, J.L., Sonstegard, T.S., Van Tassell, C.P., Schroeder, S.G., Garcia, J., Taylor, J.F., Schnabel, R.D., Lewin, H.A. 2014. Population sequencing reveals breed and sub-species specific CNVs in cattle. Meeting Abstract. Advances in Genome Biology & Technology Conference Meeting Abstract. p.58.
Functional proteomic and interactome analysis of proteins associated with beef tenderness in angus cattle - (Peer Reviewed Journal)
Zhao, C., Zan, L., Wang, Y., Updike, M., Liu, G., Bequette, B.J., Baldwin, R.L., Song, J. 2013. Functional proteomic and interactome analysis of proteins associated with beef tenderness in angus cattle. Livestock Science. 161:201-209.
Effect of artificial selection on runs of Homozygosity in U.S. Holstein cattle Reprint Icon - (Peer Reviewed Journal)
Kim, E., Cole, J.B., Huson, H.J., Wiggans, G.R., Van Tassell, C.P., Crooker, B.A., Liu, G., Da, Y., Sonstegard, T.S. 2013. Effect of artificial selection on runs of Homozygosity in U.S. Holstein cattle. PLoS One. DOI: 10.1371/journal.pone.0080813.
A genome-wide survey reveals a deletion polymorphism associated with resistance to gastrointestinal nematodes in Angus cattle - (Abstract Only)
Liu, G., Xu, L., Hou, Y., Bickhart, D.M., Song, J., Van Tassell, C.P., Sonstegard, T.S. 2013. A genome-wide survey reveals a deletion polymorphism associated with resistance to gastrointestinal nematodes in Angus cattle. BA-UMD Symposium. The University of Maryland/Beltsville ARS 3rd Annual Symposium.
Structural and functional impacts of copy number variations on the cattle genome - (Abstract Only)
Liu, G., Bickhart, D.M. 2013. Structural and functional impacts of copy number variations on the cattle genome (abstract). Lecture. p.3.
Comparative analysis of CNV calling algorithms: literature survey and a case study using bovine high-density SNP data - (Review Article)
Xu, L., Hou, Y., Bickhart, D.M., Jiuzhou, S., Liu, G. 2013. Comparative analysis of CNV calling algorithms: literature survey and a case study using bovine high-density SNP data. Microarrays. 2(3):171-185.
Open source tools to exploit DNA sequence data from livestock species - (Proceedings)
Bickhart, D.M., Hutchison, J.L., Xu, L., Song, J., Liu, G. 2013. Open source tools to exploit DNA sequence data from livestock species. BARC Poster Day. p. 9, abstract 4.
Analysis of population structure and genetic history of cattle breeds based on high-density SNP data - (Abstract Only)
Xu, L., Huson, H.J., Hou, Y., Bickhart, D.M., Song, J., Sonstegard, T.S., Van Tassell, C.P., Liu, G. 2013. Analysis of population structure and genetic history of cattle breeds based on high-density SNP data. BARC Poster Day. p.55 Abstract 48.
Tools to exploit sequence data to find new markers and disease loci in dairy cattle - (Abstract Only)
Bickhart, D.M., Harris, L., Liu, G. 2013. Tools to exploit sequence data to find new markers and disease loci in dairy cattle. Journal of Dairy Science. 96(E-Suppl. 1):624 (abstr. 557).
Fine mapping for Weaver Syndrome in the Brown Swiss breed with the identification of possible casual mutations across NRCAM, PNPLA8, and CTTNBP2 and Developement of a diagnostic SNP haplotype - (Peer Reviewed Journal)
Mcclure, M.C., Kim, E., Bickhart, D.M., Null, D.J., Cooper, T.A., Cole, J.B., Wiggans, G.R., Marsan, P.A., Colli, L., Santus, E., Liu, G., Schroeder, S.G., Matukumalli, L., Van Tassell, C.P., Sonstegard, T.S. 2013. Fine mapping for Weaver Syndrome in the Brown Swiss breed with the identification of possible casual mutations across NRCAM, PNPLA8, and CTTNBP2 and Developement of a diagnostic SNP haplotype. PLoS One. 8(3):e59251.
Mapping cattle copy number variations in water buffalo - (Abstract Only)
Liu, G., Bickhart, D.M. 2013. Mapping cattle copy number variations in water buffalo. Meeting Abstract. W115.
Combined arms: a full spectrum approach to structural variant discovery in livestock populations - (Abstract Only)
Bickhart, D.M., Liu, G. 2013. Combined arms: a full spectrum approach to structural variant discovery in livestock populations. Meeting Abstract. W145.
Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping - (Peer Reviewed Journal)
Porto-Neto, L.R., Sonstegard, T.S., Liu, G., Bickhart, D.M., Gondro, C., Silva, M., Machado, M., Utsunomiya, Y.T., Garcia, J.F., Van Tassell, C.P. 2013. Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping. Biomed Central (BMC) Genomics. DOI:10.1186/1471-2164-14-876.
Genome-wide copy number variant analysis in inbred chickens lines with different susceptibility to Marek's disease - (Abstract Only)
Luo, J., Yu, Y., Mitra, A., Zhang, H., Liu, G., Song, J. 2013. Genome-wide copy number variant analysis in inbred chickens lines with different susceptibility to Marek's disease [abstract]. Plant and Animal Genome XXI Conference, January 12-16, 2013, San Diego, California. A-P0649. Avaliable: https://pag.confex.com/pag/xxi/webprogram/Paper5185.html.
Genome-wide copy number variant analysis in inbred chicken lines with different susceptibility to Marek’s disease - (Peer Reviewed Journal)
Luo, J., Yu, Y., Mitra, A., Chang, S., Zhang, H., Liu, G., Yang, N., Song, J. 2013. Genome-wide copy number variant analysis in inbred chicken lines with different susceptibility to Marek’s disease. Genes, Genomes, and Genomics. 3:217-223. Available: http://www.g3journal.org/lookup/suppl/doi:10.1534/g3.112.005132/-/DC1.
Identification of candidate transcription factor binding sites in the cattle genome - (Peer Reviewed Journal)
Bickhart, D.M., Liu, G. 2013. Identification of candidate transcription factor binding sites in the cattle genome. Genomics, Proteomics and Bioinformatics. 11(3):195-198.
Analysis of copy number variations in Holstein cows identify potential mechanisms contributing to differences in residual feed intake - (Peer Reviewed Journal)
Hou, Y., Bickhart, D.M., Chung, H., Hutchison, J.L., Norman, H.D., Connor, E.E., Liu, G. 2012. Analysis of copy number variations in Holstein cows identify potential mechanisms contributing to differences in residual feed intake. Functional and Integrative Genomics. 12(4):717-723.
Fine mapping of copy number variations on two cattle genome assemblies using high density SNP array - (Peer Reviewed Journal)
Hou, Y., Bickhart, D.M., Hvinden, M.L., Li, C., Song, J., Boichard, D.A., Fritz, S., Eggen, A., Denise, S., Wiggans, G.R., Sonstegard, T.S., Van Tassell, C.P., Liu, G. 2012. Fine mapping of copy number variations on two cattle genome assemblies using high density SNP array. Biomed Central (BMC) Genomics. 13:376.
The trappin gene famliy: structue, function and evolution - (Review Article)
Liu, G., Bickhart, D.M. 2013. The trappin gene famliy: structue, function and evolution. Cattle: Domestication, Disease and Environment. 1st edition. Hauppauge, NY: Nova Science Publishers, Inc. 25-38 p.
Fine mapping of copy number variations on two cattle genome assemblies using high density SNP array - (Abstract Only)
Liu, G. 2012. Fine mapping of copy number variations on two cattle genome assemblies using high density SNP array. Meeting Abstract. p. 6007.
Initial analysis of copy number variations in Holstein cattle selected for high or low feed efficiency - (Proceedings)
Hou, Y., Connor, E.E., Liu, G. 2012. Initial analysis of copy number variations in Holstein cattle selected for high or low feed efficiency. Meeting Proceedings. No. 2.
Copy Number Variation in the Cattle Genome - (Review Article)
Liu, G., Bickhart, D.M. 2012. Copy Number Variation in the Cattle Genome. Functional and Integrative Genomics. DOI: 10.1007/S10142-012-0289-9.
miRNA-dysregulation associated with tenderness variation induced by acute stress in angus cattle - (Peer Reviewed Journal)
Zhao, C., Tian, F., Yu, Y., Liu, G., Zan, L., Updike, M., Song, J. 2012. miRNA-dysregulation associated with tenderness variation induced by acute stress in angus cattle. Animal Science Biotechnol. 3(1):12.
Mapping cattle copy number variation by population-scale genome sequencing - (Abstract Only)
Liu, G. 2012. Mapping cattle copy number variation by population-scale genome sequencing. Meeting Abstract. p. 146.
Signature of forty years of artificial selection in U.S. Holstein cattle identified by long-range frequency analyses - (Proceedings)
Sonstegard, T.S., Wang, S., Van Tassell, C.P., Ma, L., Wiggans, G.R., Crooker, B., Cole, J.B., Mariani, B.D., Kim, E., Garbe, J.R., Fahrenkrug, S., Liu, G., Da, Y. 2012. Signature of forty years of artificial selection in U.S. Holstein cattle identified by long-range frequency analyses. International Conference on Quantitative Genetics: Understanding Variation in Complex Traits, Edinburgh, Scotland, June 17–22, Programme & Book of Abstracts, p. 213, abstr. P-314.
Muscle Transcriptomic Analyses in Angus Cattle with Divergent Tenderness - (Peer Reviewed Journal)
Zhao,C., Tian, F., Yu, Y., Luo, J., Hu, Q., Bequette, B.J., Baldwin, R.L., Liu, G., Zan, L., Updike, M., Song, J. 2012. Muscle Transcriptomic Analyses in Angus Cattle with Divergent Tenderness. Molecular Biology Reports. 39(4):4185-93.
Butyrate induced IGF2 activation correlated with distinct chromatin landscapes due to histone modification - (Peer Reviewed Journal)
Shin, J., Li, R.W., Goa, Y., Bickhart, D.M., Liu, G., Li, W., Wu, S., Li, C. 2013. Butyrate induced IGF2 activation correlated with distinct chromatin landscapes due to histone modification. PLoS Genetics. DOI:10.4137/GRSB.S11243.
Copy number variation detection in cattle reveals potential breed specific differences - (Abstract Only)
Bickhart, D.M., Hou, Y., Schroeder, S.G., Alkan, C., Cardone, M., Matukumalli, L.K., Song, J., Schnabel, R.D., Ventura, M., Taylor, J., Garcia, J., Van Tassell, C.P., Sonstegard, T.S., Eichler, E.E., Liu, G. 2012. Copy number variation detection in cattle reveals potential breed specific differences. BARC Poster Day. p. 13
Analysis of copy number variations among cattle breeds - (Abstract Only)
Liu, G., Hou, Y., Zhu, B., Cardone, M.F., Jiang, L., Cellamare, A., Mitra, A., Alexander, L.J., Coutinho, L.L., Gasbarre, L.C., Li, R.W., Matukumalli, L.K., Nonneman, D.J., Regitano, L.C., Smith, T.P., Song, J., Sonstegard, T.S., Van Tassell, C.P., Ventura, M., Eichler, E.E., Mcdaneld, T.G., Keele, J.W. 2012. Analysis of copy number variations among cattle breeds. [abstract] CONFERENCE ON THE BIOLOGY OF GENOMES. P. 182.
Copy number variation of individual cattle genomes using next-generation sequencing - (Peer Reviewed Journal)
Bickhart, D.M., Hou, Y., Schroeder, S.G., Alkan, C., Cardone, M., Matukumalli, L.K., Song, J., Schnabel, R.D., Ventura, M., Taylor, J., Garcia, J., Van Tassell, C.P., Sonstegard, T.S., Eichler, E.E., Liu, G. 2012. Copy number variation of individual cattle genomes using next-generation sequencing. Genome Research. 22(4):778-90.
Functional Genomic Analysis of Variation on Beef Tenderness Induced by Acute Stress in Angus Cattle - (Peer Reviewed Journal)
Zhao, C., Fei, T., Yu, Y., Luo, J., Mitra, A., Zhan, F., Hou, Y., Liu, G., Zan, L., Updike, M., Song, J. 2012. Functional Genomic Analysis of Variation on Beef Tenderness Induced by Acute Stress in Angus Cattle. Comparative and Functional Genomics. DOI: 10.1155/2012/756284.
Refinement of Bos taurus sequence assembly based on BAC-FISH experiments - (Peer Reviewed Journal)
Partipilo, G., D'Addabbo, P., Lacalandra, G.M., Liu, G., Rocchi, M. 2011. Refinement of Bos taurus sequence assembly based on BAC-FISH experiments. Biomed Central (BMC) Genomics. 12:639.
Initial analysis of copy number variations in cattle selected for resistance or susceptibility to intestinal nematodes - (Abstract Only)
Liu, G., Brown, T.E., Hebert, D.A., Cardone, M.F., Hou, Y., Choudhary, R.K., Shaffer, J.F., Amazu, C., Connor, E.E., Ventura, M., Gasbarre, L.C. 2011. Initial analysis of copy number variations in cattle selected for resistance or susceptibility to intestinal nematodes. Plant and Animal Genome Conference Proceedings. Plant and Animal Genome Conference XIX Proceedings. P542.
Analyses of cattle DNA methylation patterns in diverse tissues - (Abstract Only)
Liu, G. 2012. Analyses of cattle DNA methylation patterns in diverse tissues [abstract]. Keystone Symposia. p. 67.
Structural and functional impacts of copy member variations on the cattle genome - (Abstract Only)
Liu, G. 2012. Structural and functional impacts of copy member variations on the cattle genome [abstract]. p. 68.
Searching for copy number variations in the buffalo genome - (Abstract Only)
Liu, G. 2012. Searching for copy number variations in the buffalo genome. Meeting Proceedings [abstract]. p. 574.
Copy number variation of individual cattle genomes using next-generation sequencing - (Abstract Only)
Bickhart, D.M., Hou, Y., Schroeder, S.G., Alkan, C., Cardone, M., Matukumalli, L.K., Song, J., Schnabel, R.D., Ventura, M., Taylor, J.F., Garcia, J., Van Tassell, C.P., Sonstegard, T.S., Eichler, E.E., Liu, G. 2012. Copy number variation of individual cattle genomes using next-generation sequencing. Plant and Animal Genome Conference. p. 549.
Genomic regions showing copy number variations associate with resistance or susceptibility to gastrointestinal nematodes in Angus cattle - (Abstract Only)
Hou, Y., Liu, G., Bickhart, D.M., Matukumalli, L.K., Li, C., Song, J., Gasbarre, L.C., Van Tassell, C.P., Sonstegard, T.S. 2011. Genomic regions showing copy number variations associate with resistance or susceptibility to gastrointestinal nematodes in Angus cattle [abstract]. Paper No. 6.
Copy number variations related to reproduction traits in Holstein cattle - (Abstract Only)
Hou, Y., Bickhart, D.M., Fang, X., Song, J., Van Tassell, C.P., Sonstegard, T.S., Seroussi, E., Liu, G. 2011. Copy number variations related to reproduction traits in Holstein cattle. Meeting Abstract. No. 7.
Individualized cattle copy number and segmental duplication maps using next generation sequencing - (Abstract Only)
Bickhart, D.M., Hou, Y., Schroeder, S.G., Alkan, C., Cardone, M., Matukumalli, L., Song, J., Schnabel, R.D., Ventura, M., Taylor, J.F., Garcia, J., Eichler, E.E., Sonstegard, T.S., Van Tassell, C.P., Liu, G. 2011. Individualized cattle copy number and segmental duplication maps using next generation sequencing. Meeting Abstract. No. 8.
Innate immune response to a bovine mastitis pathogen profiled in milk and blood monocytes using a systems biology approach - (Abstract Only)
Genomic regions showing copy number variations associate with resistance or susceptibility to gastrointestinal nematodes in Angus Cattle - (Peer Reviewed Journal)
Hou, Y., Liu, G., Bickhart, D.M., Matukumalli, L.K., Li, C., Song, J., Gasbarre, L.C., Van Tassell, C.P., Sonstegard, T.S. 2011. Genomic regions showing copy number variations associate with resistance or susceptibility to gastrointestinal nematodes in Angus Cattle. Functional and Integrative Genomics. 12(1):81-92.
Recent Applications of DNA Sequencing Technologies in Food, Nutrition and Agriculture - (Review Article)
Liu, G. 2011. Recent Applications of DNA Sequencing Technologies in Food, Nutrition and Agriculture. Recent Patents on Food, Nutrition and Agriculture. 3: 187-195.
A high-resolution cattle CNV map by population-scale genome sequencing - (Abstract Only)
Bickhart, D.M., Hou, Y., Schroeder, S.G., Alkan, C., Cardone, M.F., Matukumalli, L.K., Schnabel, R.D., Ventura, M., Taylor, J.F., Eichler, E.E., Sonstegard, T.S., Van Tassell, C.P., Liu, G. 2011. A high-resolution cattle CNV map by population-scale genome sequencing [abstract]. Gordon Research Conference. No. 48.
Assessment of genome integrity in cattle transgenic cell lines using array CGH - (Peer Reviewed Journal)
Liu, G., Hou, Y., Robl, J.M., Kuroiwa, Y., Wang, Z. 2011. Assessment of genome integrity in cattle transgenic cell lines using array CGH. Genome Integrity. 2(1):6-10.
A high-resolution cattle CNV map by population-scale genome sequencing - (Abstract Only)
Bickhart, D.M., Hou, Y., Liu, G., Schroeder, S.G., Can, A., Maria, C., Matukumalli, L., Song, J., Schnabel, R., Ventura, M., Taylor, J., Eichler, E., Sonstegard, T.S., Van Tassell, C.P., Illumina Bovine Hd, C. 2011. A high-resolution cattle CNV map by population-scale genome sequencing. BARC Poster Day [abstract]. No. 5.
Genomic and functional characteristics of copy number variations in Angus cattle selected for resistance or susceptibility to gastrointestinal nematodes - (Abstract Only)
Hou, Y., Liu, G., Bickhart, D.M., Matukumalli, L., Song, J., Gasbarre, L., Van Tassell, C.P., Sonstegard, T.S. 2011. Genomic and functional characteristics of copy number variations in Angus cattle selected for resistance or susceptibility to gastrointestinal nematodes [abstract]. BARC Poster Day. No. 17.
Genomic characteristics of cattle copy number variations - (Peer Reviewed Journal)
Hou, Y., Liu, G., Bickhart, D.M., Cardone, M.F., Wang, K., Kim, E., Matukumalli, L., Ventura, M., Song, J., Van Raden, P.M., Sonstegard, T.S., Van Tassell, C.P. 2011. Genomic characteristics of cattle copy number variations. Biomed Central (BMC) Genomics. 12:127.
Studying Cattle Genomic Structural Variations in the Green Economy Era - (Abstract Only)
Liu, G. 2011. Studying Cattle Genomic Structural Variations in the Green Economy Era. Meeting Abstract. P. 086.
A high-resolution cattle CNV map by population-scale genome sequencing - (Abstract Only)
Bickhart, D.M., Hou, Y., Schroeder, S.G., Alkan, C., Cardone, M.F., Matukumalli, L.K., Schnabel, R.D., Ventura, M., Taylor, J.F., Eichler, E.E., Sonstegard, T.S., Van Tassell, C.P., Liu, G. 2011. A high-resolution cattle CNV map by population-scale genome sequencing. CONFERENCE ON THE BIOLOGY OF GENOMES [abstract]. p. 32.
Complexity and Entropy Analysis of DNMT1 Gene - (Peer Reviewed Journal)
Xie, X., Yu, Y., Liu, G., Yuan, Z., Song, J. 2010. Complexity and Entropy Analysis of DNMT1 Gene. Journal of Data Mining in Genomics & Proteomics. 1:105.
Initial analysis of copy number variations in cattle selected for resistance or susceptibility to intestinal nematodes - (Peer Reviewed Journal)
Liu, G., Brown, T.E., Hebert, D.A., Cardone, M.F., Hou, Y., Choudhary, R.K., Shaffer, J.F., Amazu, C., Connor, E.E., Ventura, M., Gasbarre, L.C. 2010. Initial analysis of copy number variations in cattle selected for resistance or susceptibility to intestinal nematodes. Mammalian Genome. 22:111-121.
Genomic and evolutionary characteristics of cattle copy number variations - (Abstract Only)
Hou, Y., Liu, G., Cardone, M.F., Wang, K., Kim, E., Matukumalli, L.K., Ventura, M., Van Raden, P.M., Sonstegard, T.S., Van Tassell, C.P. 2011. Genomic and evolutionary characteristics of cattle copy number variations [abstract]. Plant and Animal Genome Conference Proceedings. p. 537.
Prediction of conserved regulatory elements in promoter regions of the cattle genome - (Abstract Only)
Liu, G. 2011. Prediction of conserved regulatory elements in promoter regions of the cattle genome. Meeting Abstract. p. 63.
Next generation sequencers: methods and applications in food-borne pathogens - (Book / Chapter)
Liu, G. 2012. Next generation sequencers: methods and applications in food-borne pathogens. Omics Technologies and Microbial Modeling in Food-borne Pathogens. p. 531-551.
Systematic identification of conserved regulatory elements in upstream promoter regions of the cattle genome - (Abstract Only)
Liu, G., Hanson, R.W., Yang, J. 2010. Systematic identification of conserved regulatory elements in upstream promoter regions of the cattle genome. Meeting Abstract. No. 10.
Forty Years Of Artificial Selection In U.S. Holstein Cattle Had Genome-wide Signatures - (Proceedings)
Sonstegard, T.S., Ma, L., Van Tassell, C.P., Kim, E., Cole, J.B., Wiggans, G.R., Crooker, B.A., Mariani, B.D., Gerber, J.R., Fahrenkrug, S.C., Liu, G., Da, Y. 2010. Forty Years Of Artificial Selection In U.S. Holstein Cattle Had Genome-wide Signatures. World Congress of Genetics Applied in Livestock Production.
Analysis of copy number variations reveals differences among cattle breeds - (Peer Reviewed Journal)
Liu, G., Hou, Y., Zhu, B., Cardone, M.F., Jiang, L., Cellamare, A., Mitra, A., Alexander, L.J., Coutinho, L.L., Gasbarre, L.C., Heaton, M.P., Li, R.W., Matukumalli, L.K., Nonneman, D.J., De A Regitano, L.C., Smith, T.P., Song, J., Sonstegard, T.S., Van Tassell, C.P., Eichler, E.E., Mcdaneld, T.G., Keele, J.W. 2010. Analysis of copy number variations among cattle breeds. Genome Research. 20:693-703.
Analysis of recent segmental duplications in the bovine genome - (Peer Reviewed Journal)
Liu, G., Ventura, M., Cellamare, A., Chen, L., Cheng, Z., Zhu, B., Song, J., Eichler, E.E. 2009. Analysis of recent segmental duplications in the bovine genome. BMC Genomics. 10:571.
A dynamic neighboring extension search algorithm for genome coordinate conversion in the presence of short sequence duplications. 2009. Gene Expression to Genetical Genomics. 2:29-36. - (Peer Reviewed Journal)
Zhu, B., Jiang, L., Liu, G. 2010. A dynamic neighboring extension search algorithm for genome coordinate conversion in the presence of short sequence duplications. Gene Expression to Genetical Genomics. 2:29-36.
Comparison of the segmental duplication pattern on two cattle genome assemblies using FISH - (Proceedings)
Liu, G., Cellamare, A., Ventura, M., Li, C., Eichler, E.E. 2010. Comparison of the segmental duplication pattern on two cattle genome assemblies using FISH. Plant and Animal Genome Conference. W178.
A genome-wide analysis of array-based comparative genomic hybridization (CGH) data to detect intra-species variations and evolutionary relationships. - (Peer Reviewed Journal)
Mitra, A., Liu, G., Song, J. A genome-wide analysis of array-based comparative genomic hybridization (CGH)data to detect intra-species variations and evolutionary relationships. PLoS One. Nov. 24; 4(11):e7978.
Activation of SIRT1 by resveratrol represses transcription of the gene for the cytosolic form of phosphoenolpyruvate carboxykinase (GTP) by deacetylating hepatic nuclear factor 4alpha - (Peer Reviewed Journal)
Yang, J., Kong, X., Martins-Santos, M.S., Aleman, G., Chaco, E., Liu, G., Wu, S., Samols, D., Hakimi, P., Chiang, C., Hanson, R.W. 2009. Activation of SIRT1 by resveratrol represses transcription of the gene for the cytosolic form of phosphoenolpyruvate carboxykinase (GTP) by deacetylating hepatic nuclear factor 4alpha. Journal of Biological Chemistry. 284(40):27042-27053.
Mucin biosynthesis in the bovine goblet cell induced by Cooperia oncophora infection - (Peer Reviewed Journal)
Li, R.W., Li, C., Elsasser, T.H., Liu, G., Garrett, W.M., Gasbarre, L.C. 2009. Mucin biosynthesis in the bovine goblet cell induced by Cooperia oncophora infection. Veterinary Parasitology. PMID 19647371.
Calibration of mutation rates reveals diverse subfamily structure of galliform CR1 repeats - (Peer Reviewed Journal)
Liu, G., Jiang, L., Tian, F., Zhu, B., Song, J. 2009. Calibration of mutation rates reveals diverse subfamily structure of galliform CR1 repeats. Genome Biology and Evolution. 2009:119-130.
Analysis of recent segmental duplications in the bovine genome - (Abstract Only)
Liu, G., Ventura, M., Cellamare, A., Chen, L., Cheng, Z., Zhu, B., Song, J., Eichler, E.E. 2009. Analysis of recent segmental duplications in the bovine genome. [abstract]. Gordon Research Conference Proceedings.
GENOME SIGNATURES OF ARTIFICIAL SELECTION IN HOLSTEIN CATTLE - (Abstract Only)
Sonstegard, T.S., Ma, L., Cole, J.B., Van Tassell, C.P., Wiggans, G.R., Crooker, B.A., Garbe, J.R., Fahrenkrug, S.C., Mariani, B.D., Liu, G., Da, Y. 2009. GENOME SIGNATURES OF ARTIFICIAL SELECTION IN HOLSTEIN CATTLE. Cold Spring Harbor Meeting.
The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution - (Peer Reviewed Journal)
Elsik, C.G., Gibbs, R., Skow, L., Tellam, R., Weinstock, G., Worley, K., Kappes, S.M., Green, R.D., Alexander, L.J., Bennett, G.L., Carroll, J.A., Chitko Mckown, C.G., Hamernik, D.L., Harhay, G.P., Keele, J.W., Liu, G., Macneil, M.D., Matukumalli, L.K., Rijnkels, M., Roberts, A.J., Smith, T.P., Snelling, W.M., Stone, R.T., Waterman, R.C., White, S.N. 2009. The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution. Science. 324:522-528.
Genome-Wide Survey of SNP Variation Uncovers the Genetic Structure of Cattle Breeds. - (Peer Reviewed Journal)
Gibbs, R., Van Tassell, C.P., Weinstock, G.M., Green, R.D., Hamernik, D.L., Kappes, S.M., Liu, G., Matukumalli, L.K., Matukumalli, A., Sonstegard, T.S., Silva, M.V. 2009. Genome-Wide Survey of SNP Variation Uncovers the Genetic Structure of Cattle Breeds. Science. 24:528-532.
Distinct turn-over patterns of common repeats correlate with genome size differences among cattle, dog and human - (Proceedings)
Liu, G. 2009. Distinct turn-over patterns of common repeats correlate with genome size differences among cattle, dog and human. In: Proceedings of the 3rd International Conference on Bioinformatics and Biomedical Engineering. 1(13):026.
Alternative Splicing Variants and DNA Methylation Status of BDNF in Inbred Chicken Lines - (Peer Reviewed Journal)
Yu, Y., Zhang, H.M., Byerly, M.S., Bacon, L.D., Porter, T.E., Liu, G.E., Song, J. 2009. Alternative Splicing Variants and DNA Methylation Status of BDNF in Inbred Chicken Lines. Brain Research. 1269(7):1-10.
CURRENT DIRECTIONS IN CATTLE GENOMICS RESEARCH - (Review Article)
Van Tassell, C.P., Sonstegard, T.S., Liu, G., Matukumalli, L.K. 2007. Current directions in cattle genomics research. Advancement of Animal Breeding & Genetics Meeting. pp. 461-470.
Applications and Case Studies of the Next-Generation Sequencing Technologies in Food, Nutrition and Agriculture. - (Review Article)
Liu, G. 2009. Applications and Case Studies of the Next-Generation Sequencing Technologies in Food, Mutrition and Agriculture. Recent Patents on Food, Nutrition & Agriculture. 1(1):75-79.
Comparative Analysis of Alu Repeats in Primate Genomes - (Peer Reviewed Journal)
Liu, G., Alkan, C., Zhao, S., Eichler, E.E. 2009. Comparative Analysis of Alu Repeats in Primate Genomes. Genome Research. 19(5):876-885.
Studies on cattle genomic structural variation provide insights into ruminant speciation and adaptation - (Abstract Only)
Liu, G., Zhu, B., Alexander, L.J., Matukumalli, L.K., Van Tassell, C.P., Sonstegard, T.S., Nonneman, D.J., Keele, J.W. 2009. Studies on cattle genomic structural variation provide insights into ruminant speciation and adaptation. [abstract]. Plant and Animal Genome Conference Proceedings. W093.
Genomic expression analysis by single-cell mRNA differential display of quiescent CD8 T cells from tumor-infiltrating lymphocytes obtained from in vivo liver tumours - (Peer Reviewed Journal)
Zhang, W., Ding, J., Qu, Y., Hu, H., Lin, M., Datta, A., Larson, A., Liu, G., Li, B. 2008. Genomic expression analysis by single-cell mRNA differential display of quiescent CD8 T cells from tumor-infiltrating lymphocytes obtained from in vivo liver tumours. Immunology. 127(1):83-90.
Genomic signatures of artificial selection in U.S. Holstein cows - (Abstract Only)
Characterization of a novel microdeletion polymorphism on BTA5 in cattle - (Peer Reviewed Journal)
Liu, G., Li, R.W., Sonstegard, T.S., Matukumalli, L.K., Silva, M.V., Van Tassell, C.P. 2008. Characterization of a novel microdeletion polymorphism on BTA5 in cattle. Animal Genetics. 39(6):655-658.
Epigenetic Case Studies in Agricultural Animals - (Abstract Only)
Liu, G. 2008. Epigenetic Case Studies in Agricultural Animals. [abstract]. International Society for Animal Genetics Conference Proceedings.
ANALYSIS OF CATTLE COPY NUMBER VARIATION REVEALS INSIGHTS INTO THE EVOLUTION OF RUMINANTS - (Abstract Only)
Liu, G., Keele, J.W., Van Tassell, C.P., Sonstegard, T.S., Li, R.W., Alexander, L.J., Matukumalli, L.K., Smith, T.P., Gasbarre, L.C. 2008. Analysis of cattle copy number variation reveals insights into the evolution of ruminants. [abstract]. 2008 meeting on the Biology of Genomes, May 6-10, 2007, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. p197.
Applied Bovine Genomics: Chipping away at the genetics underlying disease traits. - (Abstract Only)
Sonstegard, T.S., Vanraden, P., Wiggans, G., Schnabel, S., Liu, G., Matukumalli, L.K., Silva, M.V., Mckay, S., Schroeder, S.G., Gasbarre, L.C., Taylor, J.F., Van Tassell, C.P. 2008. Applied Bovine Genomics: Chipping away at the genetics underlying disease traits.. International Symposium of Animal Functional Genomics.
SNPs to Chips: Changing the paradigm of mapping and selection in cattle - (Proceedings)
Sonstegard, T.S., Liu, G., Matukumalli, L.K., Van Tassell, C.P. 2007. Snps to chips: changing the paradigm of mapping and selection in cattle. [abstracat].Animal Breeding and Animal Genetic Resources Proceedings.
Analysis of copy number variation in the bovine genome - (Abstract Only)
Liu, G., Van Tassell, C.P., Sonstegard, T.S., Li, R.W., Alexander, L.J., Keele, J.W., Matukumalli, L.K., Brown, T., Smith, T.P., Gasbarre, L.C. 2008. Analysis of copy number variation in the bovine genome. Plant and Animal Genome (PAG) XVI Conference. San Diego, CA. p517.
A high-resolution map of copy number variation in the cattle genome - (Abstract Only)
Liu, G., Keele, J.W., Van Tassell, C.P., Sonstegard, T.S., Alexander, L.J., Li, R.W., Matukumalli, L.K., Smith, T.P., Gasbarre, L.C. 2008. A high-resolution map of copy number variation in the cattle genome. Plant and Animal Genome VX Conference Abstracts. The NRI Animal Genome PD Meeting, San Diego, CA. p84.
Detection of germline and somatic copy number variations in cattle - (Proceedings)
Liu, G., Van Tassell, C.P., Sonstegard, T.S., Li, R.W., Alexander, L.J., Keele, J.W., Matukumalli, L.K., Smith, T.P., Gasbarre, L.C. 2008. Detection of germline and somatic copy number variations in cattle. Developments in Biologicals. 132:231-237.
Effects of species combination on comparative analyses of conserved regulatory elements - (Abstract Only)
Liu, G., Yang, J., Matukumalli, L.K., Sonstegard, T.S., Van Tassell, C.P., Hanson, R.W. 2008. Effects of species combination on comparative analyses of conserved regulatory elements. [abstract]. Pacific Symposium on Biocomputing. p.100.
Description and analysis of the Bovine Gene Atlas - An extensive compendium of bovine transcript profiles - (Abstract Only)
Harhay, G.P., Keele, J.W., Smith, T.P., Alexander, L.J., Matukumalli, L.K., Schroeder, S.G., Liu, G., Van Tassell, C.P., Sonstegard, T.S. 2008. Description and analysis of the Bovine Gene Atlas - An extensive compendium of bovine transcript profiles (abstract). Plant and Animal Genome XVI Conference. Poster No. P516.
Bovine copy number variation and its implication in animal health - (Abstract Only)
Liu, G., Van Tassell, C.P., Sonstegard, T.S., Alexander, L.J., Keele, J.W., Matukumalli, L.K., Smith, T.P., Gasbarre, L.C. 2007. Bovine copy number variation and its implication in animal health. [ abstract]. International Symposium on Animal Genomics for Animal Health. pp. 32.
Initial analysis of copy number variation in the cow genome - (Abstract Only)
Liu, G., Van Tassell, C.P., Sonstegard, T.S., Li, R.W., Alexander, L.J., Keele, J.W., Matukumalli, L.K., Smith, T.P., Gasbarre, L.C. 2007. Initial analysis of copy number variation in the cow genome. [abstract}. Gordon Research Conference Proceedings.
Identification of conserved regulatory elements in upstream promoter regions of mammals at relaxed thresholds by comparative genomics - a case study using PEPCK - (Peer Reviewed Journal)
Liu, G., Weirauch, M., Van Tassell, C.P., Li, R.W., Sonstegard, T.S., Matukumalli, L.K., Connor, E.E., Hanson, R.W., Yang, J. 2008. Identification of conserved regulatory elements in mammalian promoter regions: a case study using the PCK1 promoter. Genomics, Proteomics and Bioinformatics. 6(3-4):129-143.
Construction and application of a bovine high-density SNP assay - (Abstract Only)
Van Tassell, C.P., Matukumalli, L.K., Taylor, C., Smith, T.P., Sonstegard, T.S., Schnabel, R., Silva, M.V., Wiggans, G.R., Liu, G., Moore, S., Taylor, J.F. 2007. Construction and application of a bovine high-density SNP assay. Joint Abstracts of the American Dairy Science and Society of Animal Science.
RECENT SEGMENTAL DUPLICATIONS IN THE CATTLE GENOME - (Abstract Only)
Liu, G., Matukumalli, L.K., Van Tassell, C.P., Sonstegard, T.S., Gasbarre, L.C., Eichler, E.E. 2007. Recent segmental duplications in the cattle genome. [abstract]. BARC Poster Day.Abstracat #25, p. 32.
Creation of a Gene Atlas in cattle using sequence-based transcriptional profiling - (Abstract Only)
Sonstegard, T.S., Keele, J.W., Harhay, G.P., Smith, T.P., Matukumalli, L.K., Van Tassell, C.P., Liu, G., Alexander, L.J. 2007. Creation of a Gene Atlas in cattle using sequence-based transcriptional profiling. [abstract] Joint Abstracts of the American Dairy Science and Society of Animal Science.
Protein Accumulation Changes Associated with Germination of the Uromyces appendiculatus Uredospore - (Peer Reviewed Journal)
Cooper, B., Neelan, A., Campbell, K., Lee, J., Liu, G., Garrett, W.M., Scheffler, B.E., Tucker, M.L. 2007. Protein Accumulation Changes Associated with Germination of the Uromyces appendiculatus Uredospore. Molecular Plant-Microbe Interactions. 20(7):857-866.
Identification of Weakly Conserved Regulatory Elements in Upstream Promoter Regions of Mammals - (Book / Chapter)
Liu, G., Weirauch, M., Van Tassell, C.P., Li, R.W., Sonstegard, T.S., Matukumalli, L.K., Connor, E.E., Hanson, R.W., Yang, J. 2007. Identification of Weakly Conserved Regulatory Elements in Upstream Promoter Regions of Mammals. Conference on the Biology og Genomes, pp. 218.
Stimultaneous prediction of multiple traits using dense genome-wide SNP markers - (Proceedings)
Matukumalli, L.K., Sonstegard, T.S., Silva, M.V., Liu, G., Van Tassell, C.P. 2007. Stimultaneous prediction of multiple traits using dense genome-wide SNP markers. Meeting Proceedings.
SYSTEMATIC IDENTIFICATION OF REGULATORY ELEMENTS IN CATTLE. - (Abstract Only)
Liu, G., Yang, J., Matukumalli, L.K., Sonstegard, T.S., Van Tassell, C.P., Hanson, R.W. 2006. Systematic identification of regulatory elements in cattle [abstract]. International Conference on Animal Genetics. Aug 2006, Porto Seguro, Brazil, pp C448.
GENOMIC DIVERGENCES AMONG CATTLE, DOG, AND HUMAN ESTIMATED FROM LARGE-SCALE ALIGNMENTS OF GENOMIC SEQUENCES - (Peer Reviewed Journal)
Liu, G., Van Tassell, C.P., Sonstegard, T.S., Matukumalli, L.K., Shade, L.L. 2006. Genomic divergences among cattle, dog, and human estimated from large-scale alignments of genomic sequences. Biomed Central (BMC) Genomics. 7(1):140.
DIFFERENTIAL TURN-OVER PATTERNS OF TRANSPOSABLE ELEMENTS ACCOUNT FOR THE GENOME SIZE DIFFERENCES AMONG CATTLE, DOG AND HUMAN. - (Abstract Only)
Liu, G., Matukumalli, L.K., Sonstegard, T.S., Van Tassell, C.P. 2006. Differential turn-over patterns of transposable elements account for the genome size differences among cattle, dog and human. (abstract) Conference on the Biology off Genomes, pp 187.
IN SILICO PREDICTION OF REGULATORY ELEMENTS BY PHYLOGENETIC FOOTPRINTING. - (Abstract Only)
Liu, G., Yang, J., Matukumalli, L.K., Sonstegard, T.S., Van Tassell, C.P., Hanson, R.W. 2006. In silico prediction of regulatory elements by phylogenetic footprinting. [abstract] BARC Poster Day. Beltsville, MD. pp. 32.
COMPREHENSIVE SEARCH OF BOVINE MICRORNAS EXPRESSED IN IMMUNE AND GUT TISSUES BY DEEP SEQUENCING - (Abstract Only)
Sonstegard, T.S., Matukumalli, L.K., Coutinho, L.L., Liu, G., Gasbarre, L.C., Smith, T.P. 2006. Comprehensive search of bovine micrornas expressed in immune and gut tissues by deep sequencing [abstract]. International Conference on Animal Genetics. pp. C354.
CHARACTERIZATION OF BOIVNE MICRORNAS EXPRESSED IN IMMUNE AND GUT TISSUES BY DEEP SEQUENCING - (Abstract Only)
Matukumalli, L.K., Coutinho, L.L., Sonstegard, T.S., Liu, G., Gasbarre, L.C., Smith, T.P. 2006. Characterization of boivne micrornas expressed in immune and gut tissues by deep sequencing [abstract] 17th Annual BARC Poster Day. Beltsville, MD. No 27.
GENOME RESOURCES AND COMPARATIVE ANALYSIS TOOLS FOR CARDIOVASCULAR RESEARCH - (Book / Chapter)
Liu, G., Adams, M.D. 2006. Genome resources and comparative analysis tools for cardiovascular research. IN: Methods of Molecular Medicine, Humana Press, pp. 101-123.
COMPARATIVE GENOMICS:GENOMIC VARIATION BETWEEN BOVINE AND HUMAN GENOMES. - (Abstract Only)
Liu, G., Van Tassell, C.P., Sonstegard, T.S., Matukumalli, L.K., Shade, L.L. 2005. Comparative genomics:genomic variation between bovine and human genomes [abstract]. BARC Poster Day. p. 32.
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