Projects

Enhancing Genetic Merit of Dairy Cattle Through Genome Selection and Analysis Appropriated (D)   Accession Number: 412388

Genome-Wide Association Study of Copy Number Variation and Qtl for Economic Traits in Holstein Cattle Reimbursable (R)   Accession Number: 416747

Bovine Copy Number Polymorphism and Its Implication in Early Embryonic Loss Reimbursable (R)   Accession Number: 411649

Characterization of Structural Variations in Livestock Genomes Specific Cooperative Agreement (S)   Accession Number: 412653

Publications

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)

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)

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/Symposium)

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)

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) - (20-Jun-08)

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) - (25-Apr-08)

analysis of Cattle Copy Number Variation Reveals Insights into the Evolution of Ruminants - (Abstract)

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)

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/Symposium)

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)

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)

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/Symposium)

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)

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)

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)

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)

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)

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)

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)

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/Symposium)

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)

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)

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)

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)

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)

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)

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.