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United States Department of Agriculture

Agricultural Research Service

Research Project: ENHANCING GENETIC MERIT OF DAIRY CATTLE THROUGH GENOME SELECTION AND ANALYSIS Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)

Detecting Loci under recent positive selection in dairy and beef cattle by combining different genome-wide scan methods - (Peer Reviewed Journal)
Utsunomiya, Y.T., O'Brien, A.P., Sonstegard, T.S., Van Tassell, C.P., Santana Do Carmo, A.D., Meszaros, G., Solkner, J., Garcia, J.F. 2013. Detecting Loci under recent positive selection in dairy and beef cattle by combining different genome-wide scan methods. PLoS One. 8(5):e64280.
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.
Gene expression analysis of copper tolerance and wood decay in the brown rot fungus Fibroporia radiculosa - (Peer Reviewed Journal)
Tang, J.D., Perkins, A.D., Sonstegard, T.S., Schroeder, S.G., Nicholas, D.D., Diehl, S.V. 2012. Gene expression analysis of copper tolerance and wood decay in the brown rot fungus Fibroporia radiculosa. Applied and Environmental Microbiology. 79(5):1523-33.
A novel analytical method detects response of the Angus (Bos taurus) genome to artificial selection on complex traits - (Peer Reviewed Journal)
Mcclure, M.C., Decker, J.E., Vasco, D.A., Mckay, S.D., Rolf, M.M., Kim, J., Northcutt, S.J., Bauck, S., Woodward, B., Schnabel, R.D., Taylor, J.F. 2012. A novel analytical method detects response of the Angus (Bos taurus) genome to artificial selection on complex traits. Genome Biology. DOI: 10.1186/1471-2164-13-606.
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.
Imputation of microsatellite allele from dense SNP genotypes for parentage verification - (Peer Reviewed Journal)
Mcclure, M.C., Sonstegard, T.S., Van Tassell, C.P., Wiggans, G.R. 2012. Imputation of Microsatellite Allele from Dense SNP Genotypes for Parentage Verification. Frontiers in Livestock Genomics. 3:140.
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.
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
Cooling of heat-stressed cows during the dry period alters lymphocyte but not mammary gland gene expression - (Abstract Only)
Tao, S., Connor, E.E., Bubolz, J.W., Thompson, I.M., Do Amaral, B.C., Hayen, M.J., Dahl, G.E. 2012. Cooling of heat-stressed cows during the dry period alters lymphocyte but not mammary gland gene expression [abstract]. Journal of Animal Science. 90(suppl. 3):303. Paper No. T140.
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.
Growth and Development Symposium: Understanding and Mitigating the Impacts of Inflammation on Animal Growth and Development - (Proceedings)
Connor, E.E., Baldwin, R.L., Blanton Jr., J.R., Johnson, S.E., Poulos, S., Welsh Jr., T.H. 2012. GROWTH AND DEVELOPMENT SYMPOSIUM: Understanding and mitigating the impacts of inflammation on animal growth and development. Journal of Animal Science. 90(5):1436-1437.
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.
Short read sequencing for Genomic Analysis of the brown rot fungus Fibroporia radiculosa - (Peer Reviewed Journal)
Tang, J.D., Perkins, A.D., Sonstegard, T.S., Schroeder, S.G., Burgess, S.C., Diehl, S.V. 2012. Short read sequencing for Genomic Analysis of the brown rot fungus Fibroporia radiculosa. Applied and Environmental Microbiology. 78(7):2272-81.
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.
Characterization of microsatellite loci in the SLA class I region     Reprint Icon - (Peer Reviewed Journal)
Chung, H.Y., Mcclure, M.C. 2011. Characterization of microsatellite loci in the SLA class I region. Genomics. Genomics 97(1):223-234.
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.
Whole genome analysis for backfat thickness in a tropically adapted, composite cattle breed from Brazil - (Peer Reviewed Journal)
Veneroni- Gouveia, G., Meirelles, S.L., Grossi, D.A., Santiago, A.C., Sonstegard, T.S., Yamagishi, M.B., Matukumalli, L.K., Coutinho, L.L., Alencar, M.M., Oliveira, H.N., Regitano, L.A. 2011. Whole genome analysis for backfat thickness in a tropically adapted, composite cattle breed from Brazil. Animal Genetics. DOI: 10.1111/j.1365-2052.2011.02286.x.
Genome Wide Scan for Loci influencing Warner Bratzler Shear Force in Five Bos taurus Breeds - (Peer Reviewed Journal)
Mcclure, M.C., Ramey, H.R., Rolf, M.M., Mckay, S.D., Weaber, R.L., Schnabel, R.D., Taylor, J.F. 2012. Genome Wide Scan for Loci influencing Warner Bratzler Shear Force in Five Bos taurus Breeds. Animal Genetics. DOI: 10.1111/j.1365-2052.2012.02323.x.
Applications of Genomics to Genetic Improvement of Dairy Cattle - (Proceedings)
Van Tassell, C.P., Wiggins, G.R., Vanraden, P.M., Cooper, T.A., Sonstegard, T.S. 2011. Applications of Genomics to Genetic Improvement of Dairy Cattle. Cornell Nutrition Conference for Feed Manufacturers. p. 57-68.
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.
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.
Cattle from the Isle of Jersey: A perfect storm for change - (Government Publication)
Sonstegard, T.S., Van Tassell, C.P., Wolfe, C. 2011. Cattle from the Isle of Jersey: A perfect storm for change. GlobalDiv Newsletter. vol. 19 p. 15-18.
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.
Phylogenetic analysis of the swine leukocyte antigen - 2 gene for Korean native pigs - (Peer Reviewed Journal)
Chung, H., Mcclure, M.C., Kim, J. 2011. Phylogenetic analysis of the swine leukocyte antigen - 2 gene for Korean native pigs. Genes and Genomics. 33:345-351.
Bovine Genetic Diversity Revealed By mtDNA Sequence Variation - (Abstract Only)
Sonstegard, T.S., Van Tassell, C.P., Mcclure, M.C., Chung, H. 2011. Bovine Genetic Diversity Revealed By mtDNA Sequence Variation [abstrac]. BARC Poster Day. No. 15.
Discovery of Genetic Variation that Enhances Improvement of Dairy Production and Health in Cattle and Buffalos - (Abstract Only)
(14-Mar-11)
A Probabilistic Approach for Improved Sequence Mapping in Metatranscriptomic Studies - (Abstract Only)
(11-Mar-11)
A Statistical Approach for Ambiguous Sequence Mappings - (Abstract Only)
(11-Mar-11)
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.
Next Generation Sequencing of a Bos taurus indicus (Nellore) animal: Genome Assembly and SNP Analysis - (Abstract Only)
(08-Mar-11)
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.
Identification of quantitative trait loci affecting resistance to gastro-intestinal parasites in a double backcross population of Red Maasai and Dorper sheep - (Peer Reviewed Journal)
Silva, M.V., Sonstegard, T.S., Hanotte, O., Mugambi, J., Garcia, J.F., Nagda, S., Gibson, J., Iraqi, F., Mcclintock, A.E., Kemp, S., Boettcher, P., Malek, M., Van Tassell, C.P., Baker, R.L. 2012. Identification of quantitative trait loci affecting resistance to gastro-intestinal parasites in a double backcross population of Red Maasai and Dorper sheep. Animal Genetics. 43(1):63-71.
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.
Effects of SNPs from the differentially expressed swine odorant binding protein (OBP) gene on average daily gain - (Peer Reviewed Journal)
Chung, H.Y., Mcclure, M.C. 2011. Effects of SNPs from the differentially expressed swine odorant binding protein (OBP) gene on average daily gain. Journal of Applied Animal Research. 39(1):1-4.
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.
Sequence analysis for a de novo genome assembly of Bos indicus (Nelore) cattle - (Abstract Only)
Sonstegard, T.S., Schroeder, S.G., Smith, T.P., Zimin, A., Matukumalli, L.K., Ajmone-Marsan, P., Wiedmann, R.T., Negrini, R., Yorke, J., Van Tassell, C.P., Garcia, J.F. 2010. Sequence analysis for a de novo genome assembly of Bos indicus (Nelore) cattle. Animal Genetics International Conference Proceedings.
Genome-Wide Association Analysis to Identify Loci for Milk Yield in Gyr Breed - (Abstract Only)
Silva, M., Verneque, R.S., Machado, M.A., Peixota, M.G., Guimaraes, M.M., Arbex, W.A., Guedes, E., Van Tassell, C.P., Sonstegard, T.S. 2010. Genome-Wide Association Analysis to Identify Loci for Milk Yield in Gyr Breed. Animal Genetics International Conference Proceedings.
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.
The use of SNP data for the monitoring of genetic diversity in cattle breeds - (Proceedings)
Flury, C., Tapio, M., Sonstegard, T.S., Drogemuller, C., Leeb, T., Hanotte, O., Simianer, H., Rieder, S. 2010. The use of SNP data for the monitoring of genetic diversity in cattle breeds. World Congress of Genetics Applied in Livestock Production.
Whole Genome Association Analysis Identifies Susceptibility Alleles for Parasitic Infection in Bos Taurus Cattle - (Abstract Only)
Sonstegard, T.S., Silva, M.V., Kim, E., Matukumalli, L.K., Schroeder, S.G., Gasbarre, L.C., Van Tassell, C.P. 2010. Whole genome association analysis identifies susceptibility alleles for parasitic infection in Bos taurus cattle. International Symposium on Animal Genomics for Animal Health.
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.
High Throughput Sequence Analysis for Disease Resistance in Maize - (Abstract Only)
Gautam, D., Johnston, I., Bhowmik, T., Ankala, A., Sonstegard, T.S., Schroeder, S.G., Wilkinson, J., Perkins, A.D. 2010. High Throughput Sequence Analysis for Disease Resistance in Maize. International Conference on Bioinformatics and Computational Biology.
Effective population size of an indigenous Swiss cattle breed estimated from linkage disequilibrium - (Peer Reviewed Journal)
Flury, C., Tapio, M., Sonstegard, T.S., Drogemuller, C., Leeb, T., Simianer, H., Hanotte, O., Rieder, S. 2010. Effective population size of an indigenous Swiss cattle breed estimated from linkage disequilibrium. Journal of Animal Breeding and Genetics. 127:339-347.
Information Theoretical Analysis of a Bovine Gene Atlas Reveals Chromosomal Regions with Tissue Specific Gene Expression. - (Abstract Only)
Sonstegard, T.S., Harhay, G.P., Alexander, L.J., Schroeder, S.G., Keele, J.W., Matukumalli, L., Bridges, S., Burgess, S., Van Tassell, C.P., Smith, T.P. 2010. Information Theoretical Analysis of a Bovine Gene Atlas Reveals Chromosomal Regions with Tissue Specific Gene Expression. Plant and Animal Genome VX Conference Abstracts.
Estimation of Genomic Inbreeding Coefficients Using BovineSNP50 genotypes from U.S. Jersey Cattle - (Abstract Only)
Kim, E., Van Tassell, C.P., Sonstegard, T.S. 2010. Estimation of Genomic Inbreeding Coefficients Using BovineSNP50 genotypes from U.S. Jersey Cattle. Plant and Animal Genome Conference Proceedings.
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.
A validated genome wide association study to breed cattle adapted to an environment altered by climate change     Reprint Icon - (Peer Reviewed Journal)
Hayes, B.J., Bowman, A.J., Chamberlain, A.J., Savin, K., Van Tassell, C.P., Sonstegard, T.S., Goddard, M.E. 2009. A validated genome wide association study to breed cattle adapted to an environment altered by climate change. PLoS One. Aug 18:4(8)e:6676.
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.
High-Throughput Phylogenomics: from Ancient DNA to Signatures of Human Animal Husbandry - (Abstract Only)
Decker, J.E., Pires, J.C., Conant, G.C., Mckay, S.D., Heaton, M.P., Vilkki, J., Seabury, C.M., Caetano, A.R., Johnson, G.S., Brenneman, R.A., Hanotte, O., Eggert, L.S., Wiener, P., Kim, J., Kim, K.S., Sonstegard, T.S., Van Tassell, C.P., Neibergs, H.L., Chen, K., Cooper, A., Mcewan, J.C., Brauning, R., Coutinho, L.L., Babar, M.E., Wilson, G.A., Mcclure, M.C., Rolf, M.M., Kim, J., Schnabel, R.D., Taylor, J.F. 2009. HIGH-THROUGHPUT PHYLOGENOMICS: FROM ANCIENT DNA TO SIGNATURES OF HUMAN ANIMAL HUSBANDRY. Cold Spring Harbor Meeting.
High-resolution haplotype block structure in the cattle genome     Reprint Icon - (Peer Reviewed Journal)
Villa-Angulo, R., Matukumalli, L.K., Gill, C.A., Choi, J., Van Tassell, C.P., Grefenstette, J.J. 2009. High-resolution haplotype block structure in the cattle genome. Journal of Animal Breeding and Genetics. 24(10):19.
Unlocking the bovine genome     Reprint Icon - (Peer Reviewed Journal)
Tellam, R.L., Lemay, D.G., Van Tassell, C.P., Lewin, H.A., Worley, K.C., Elsik, C.G. 2009. Unlocking the bovine genome. BioMed Central (BMC) Genetics. 24(10):193.
A whole-genome assembly of the domestic cow, Bos taurus - (Peer Reviewed Journal)
Zimin, A.V., Delcher, A.L., Florea, L., Kelley, D.R., Schatz, M.C., Puiu, D., Hanrahan, F., Pertea, G., Van Tassell, C.P., Sonstegard, T.S., Marcais, G., Roberts, M., Subramanian, P., Yorke, J.A., Salzberg, S.L. 2009. A whole-genome assembly of the domestic cow, Bos taurus. Genome Biology. 10(4):R42.
Análise de Associação por Todo o Genoma para Identificar Locos Relacionados ao Lucro Líquido, à Vida Produtiva e ao Escore de Células Somáticas na raça Jersey1 - (Peer Reviewed Journal)
Silva, M., Van Raden, P.M., Van Tassell, C.P., Sonstegard, T.S., Matukumalli, L.K., Schroeder, S.G., Kim, E., Wiggans, G.R. 2009. Análise de Associação por Todo o Genoma para Identificar Locos Relacionados ao Lucro Líquido, à Vida Produtiva e ao Escore de Células Somáticas na raça Jersey1. Brazilian Animal Science Society.
Whole Genome-Wide Snp Association: Identification of Susceptibility Alleles for Parasitic Infection - (Abstract Only)
Silva, M.V., Van Tassell, C.P., Sonstegard, T.S., Matukumalli, L.K., Schroeder, S.G., Kim, E., Gasbarre, L.C. 2009. WHOLE GENOME-WIDE SNP ASSOCIATION: IDENTIFICATION OF SUSCEPTIBILITY ALLELES FOR PARASITIC INFECTION. BARC Poster Day.
Development and Characterization of a High Density SNP Genotyping Assay for Cattle     Reprint Icon - (Peer Reviewed Journal)
Matukumalli, L.K., Lawley, C.T., Schnabel, R.D., Taylor, J.F., Allan, M.F., Heaton, M.P., O'Connell, J., Moore, S.S., Smith, T.P., Sonstegard, T.S., Van Tassell, C.P. 2009. Development and Characterization of a High Density SNP Genotyping Assay for Cattle. PLoS One. 4(4):e5350. Available: http://dx.doi.org/10.1371/journal.pone.0005350.
Accelerating genetic improvement with SNP chips and DNA sequencing - (Abstract Only)
Van Tassell, C.P., Van Raden, P.M., Wiggans, G.R., Matukumalli, L.K., Schroeder, S.G., O'Connell, J., Schnabel, R.D., Taylor, J.F., Pollak, E.J., Munson, M., Bailey, D., Sonstegard, T.S. 2009. Accelerating genetic improvement with SNP chips and DNA sequencing. Joint Abstracts of the American Dairy Science and Society of Animal Science.
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.
Genome Signature of Artificial Selection for High Milk Yield in Holstein Cattle - (Abstract Only)
Sonstegard, T.S., Ma, L., Cole, J.B., Wiggans, G.R., Crooker, B.A., Van Tassell, C.P., Mariani, B.D., Da, Y. 2009. Genome Signature of Artificial Selection for High Milk Yield in Holstein Cattle. Plant and Animal Genome Conference Proceedings.
Genome-Wide Association Analysis Identifies Loci for Productive Traits in Jersey Breed - (Abstract Only)
Silva, M.V., Van Raden, P.M., Van Tassell, C.P., Sonstegard, T.S., Matukumalli, L.K., Schroeder, S.G., Wiggans, G.R. 2009. GENOME-WIDE ASSOCIATION ANALYSIS IDENTIFIES LOCI FOR PRODUCTIVE TRAITS IN JERSEY BREED. Plant and Animal Genome Conference.
Profiling miRNA Expression in Bovine Tissues by Deep Sequencing - (Abstract Only)
Matukumalli, L.K., Alexander, L.J., Mcdaneld, T.G., Smith, T.P., Schroeder, S.G., Sonstegard, T.S., Van Tassell, C.P. 2009. Profiling miRNA Expression in Bovine Tissues by Deep Sequencing. Plant and Animal Genome Conference.
On the search for markers of tick resistance in bovines - (Peer Reviewed Journal)
Regitano, L.C., Ibelli, A.M., Gasparin, G., Miyata, M., Azevedo, A.L., Coutinho, L.L., Teodoro, R.L., Machado, M.A., Silva, M.V., Nakata, L.C., Zaros, L.G., Sonstegard, T.S., Silva, A.M., Alencar, M.M., Oliveira, M.C. 2008. On the search for markers of tick resistance in bovines. Developments in Biologicals. 132:225-230.
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.
Serial hepatic gene expression profiling in Angus steers during feed restriction and realimentation - (Other)
Connor, E.E., Kahl, S., Elsasser, T.H., Li, R.W., Barao, S.M. 2008. Serial hepatic gene expression profiling in Angus steers during feed restriction and realimentation. NIH Gene Expression Omnibus (GEO) Database. GSE12853.
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.
Quality assessment parameters for EST-derived SNPs from catfish - (Peer Reviewed Journal)
Wang, S., Sha, Z., Sonstegard, T.S., Liu, H., Xu, P., Somridhavej, B., Peatmen, E., Kucuktas, H., Liu, Z. 2008. Quality assessment parameters for EST-derived SNPs from catfish. Biomed Central (BMC) Genomics. 30(9):450.
Prediction of total genetic value using genome-wide dense marker in Holstein breed by Bayesian method - (Abstract Only)
Silva, M.V., Van Tassell, C.P., Sonstegard, T.S., Matkumalli, L., Schroeder, S.G., Van Raden, P.M., Wiggans, G.R. 2008. Prediction of total genetic value using genome-wide dense marker in Holstein breed by Bayesian method. Congress of the Brazilian Animal Breeding Society.
A Whole-Genome Association Study of Major Determinants for Parasitic Infection in Angus Breed - (Abstract Only)
Da Silva, M., Sonstegard, T.S., Van Tassell, C.P., Matukumalli, L.K., Schroeder, S.G., Gasbarre, L.C. 2008. A WHOLE-GENOME ASSOCIATION STUDY OF MAJOR DETERMINANTS FOR PARASITIC INFECTION IN ANGUS BREED. Animal Genetics International Conference Proceedings.
Genomic signatures of artificial selection in U.S. Holstein cows - (Abstract Only)
(20-Jun-08)
An assessment of population structure in eight breeds of cattle using a whole genome SNP panel - (Peer Reviewed Journal)
Mckay, S.E., Schnabel, R.D., Murdoch, B.M., Matukumalli, L.K., Aerts, J., Coppieters, W., Crews, D., Neto, E.D., Gill, C.A., Gao, C., Mannen, H., Wang, Z., Van Tassell, C.P., Williams, J.L., Taylor, J.F., Moore, S.S. 2008. An assessment of population structure in eight breeds of cattle using a whole genome SNP panel. Journal of Animal Breeding and Genetics. 20(9):37.
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.
Mapping Quantitative Trait Loci Associated with Parasitic Infection Using 50k Snp Chip in Angus Breed - (Abstract Only)
Silva, M.V., Van Tassell, C.P., Sonstegard, T.S., Matukumalli, L.K., Schroeder, S.G., Gasbarre, L.C. 2008. MAPPING QUANTITATIVE TRAIT LOCI ASSOCIATED WITH PARASITIC INFECTION USING 50K SNP CHIP IN ANGUS BREED. BARC Poster Day.
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.
Development and Applications of a Bovine 50,000 SNP Chip - (Abstract Only)
Taylor, J.F., Sonstegard, T.S., Van Tassell, C.P., Matukumalli, L., Smith, T.P., Allen, M.L. 2008. Development and Applications of a Bovine 50,000 SNP Chip. International Symposium of Animal Functional Genomics.
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.
A high-resolution radiation hybrid map of the bovine genome - (Peer Reviewed Journal)
Grant, J.R., Stothard, P., Wang, Z., Cai, Z., Xu, J., Lin, G., Prasad, A., Moon, D., Sonstegard, T.S., Van Tassell, C.P. 2008. A high-resolution radiation hybrid map of the bovine genome. Plant and Animal Genome Conference Proceedings.
Application of the BovineSNP50 assay for QTL mapping and prediction of genetic merit in Holstein cattle - (Abstract Only)
Schnabel, R.D., Van Tassell, C.P., Matukumalli, L., Sonstegard, T.S., Smith, T.P., Moore, S.S., Lawley, C.T., Taylor, J.F. 2008. Application of the BovineSNP50 assay for QTL mapping and prediction of genetic merit in Holstein cattle. Plant and Animal Genome Conference Proceedings.
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.
Characterization of the Cattle HapMap Population using the Illumina Bovine-50K SNP Chip - (Abstract Only)
Matukumalli, L.K., Schnabel, R.D., Lawley, C.T., Sonstegard, T.S., Smith, T.P., Moore, S.S., Taylor, J.F., Van Tassell, C.P. 2008. Characterization of the Cattle HapMap Population using the Illumina Bovine-50K SNP Chip. Plant and Animal Genome Conference.
SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries - (Peer Reviewed Journal)
Van Tassell, C.P., Smith, T.P., Matukumalli, L.K., Taylor, J.F., Schnabel, R.D., Lawley, C.T., Haudenschild, C., Moore, S.S., Warren, W.C., Sonstegard, T.S. 2008. SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nature Methods. 5:247-252.
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.
Whole genome linkage disequilibrium maps in cattle - (Peer Reviewed Journal)
Mckay, S.D., Schnabel, R.D., Murdoch, B.M., Matukumalli, L.K., Aerts, J., Coppieters, W., Crews, D., Neto, E.D., Gill, C.A., Gao, C., Mannen, H., Stothard, P., Wang, Z., Van Tassell, C.P., Williams, J.L., Taylor, J.F., Moore, S.S. 2007. Whole genome linkage disequilibrium maps in cattle. Journal of Animal Breeding and Genetics. 25(8):74.
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.
Last Modified: 4/17/2014
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