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United States Department of Agriculture

Agricultural Research Service

Ge Liu (George)
Animal Genomics and Improvement Laboratory
Research Biologist

Phone: (301) 504-9843
Fax: (301) 504-8414
Room 111
10300 BALTIMORE AVENUE
BLDG 306 BARC-EAST
ANIMAL GENOMICS AND IMPROVEMENT LAB
BELTSVILLE, MD, 20705-2350

Projects
Characterization of DNA Methylome in Livestock Genomes
General Cooperative Agreement (A)
  Accession Number: 426992
ENHANCING GENETIC MERIT OF RUMINANTS THROUGH GENOME SELECTION AND ANALYSIS
Appropriated (D)
  Accession Number: 423740
Sperm DNA Methylome and Its Impacts on Male Fertility in Dairy Cattle
Interagency Reimbursable Agreement (I)
  Accession Number: 426021
Structural and Functional Impacts of Copy Number Variations on the Cattle Genome
Reimbursable (R)
  Accession Number: 421373
Characterization of Structural Variations in Livestock Genomes
Specific Cooperative Agreement (S)
  Accession Number: 422715
Characterization of Single Sperm Cells by Whole Genome Sequencing
Specific Cooperative Agreement (S)
  Accession Number: 427062

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)
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. 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: 10.1007/s10142-014-0371-6.
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. PLoS One.2013 Nov 14;8(11):e80813.
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 Reprint Icon - (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.
Butyrate induced IGF2 activation correlated with distinct chromatin landscapes due to histone modification Reprint Icon - (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.
Muscle Transcriptomic Analyses in Angus Cattle with Divergent Tenderness - (Peer Reviewed Journal)
Zhao, Tian, Yu, Luo, Hu, Bequette, Baldwin, R.L., Liu, G., Zan, Updike, Song 2012. Muscle Transcriptomic Analyses in Angus Cattle with Divergent Tenderness. Molecular Biology Reports. 39(4):4185-93.
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) - (19-Aug-11)
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.
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.
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.
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.
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.
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.
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 Reprint Icon - (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 Reprint Icon - (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. Reprint Icon - (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. Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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) - (20-Jun-08)
Characterization of a novel microdeletion polymorphism on BTA5 in cattle Reprint Icon - (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 Reprint Icon - (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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Last Modified: 10/22/2014
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