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United States Department of Agriculture

Agricultural Research Service

Related Topics

Derek M Bickhart
Animal Genomics and Improvement Laboratory
Genetics

Phone: (301) 504-8679
Fax: (301) 504-8092
Room 318

10300 BALTIMORE AVENUE
BLDG 005 BARC-WEST
BELTSVILLE , MD 20705

Projects
Improving Genetic Predictions in Dairy Animals Using Phenotypic and Genomic Information
Appropriated (D)
  Accession Number: 423282
ENHANCING GENETIC MERIT OF RUMINANTS THROUGH GENOME SELECTION AND ANALYSIS
Appropriated (D)
  Accession Number: 423740
Reassembly of Cattle Immune Gene Clusters for Quantitative Analysis
Interagency Reimbursable Agreement (I)
  Accession Number: 428155
National Dairy Genetic Evaluation Program
Nonfunded Cooperative Agreement (N)
  Accession Number: 424155
1000 Bull Genomes Project
Nonfunded Cooperative Agreement (N)
  Accession Number: 426790
Sequence-Based Big Data Genomic Discovery and Application to Improve Dairy Fertility
Reimbursable (R)
  Accession Number: 430498
Improvement of Algorithms and Software to Process Very Large Genomic Datasets
Specific Cooperative Agreement (S)
  Accession Number: 426953
Determination of Actual Polymorphisms Responsible for Economic Trait Variation in Dairy Cattle
Trust (T)
  Accession Number: 429077

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)
Revealing misassembled segments in the bovine reference genome by high resolution linkage disequilibrium scan -
Utsunomiya, A., De Abreu Santos, D.J., Boison, S.A., Utsunomiya, Y.T., Milanesi, M., Bickhart, D.M., Ajmone-Marsan, P., Solkner, J., Garcia, J.F., Fonseca, R., Da Silva, M.V. 2016. Revealing misassembled segments in the bovine reference genome by high resolution linkage disequilibrium scan. BMC Genomics. 17:705.
Comparative analyses across cattle breeds reveal the pitfalls caused by artificial and lineage-differential copy number variations -
Zhou, Y., Utsunomiya, Y.T., Xu, L., Hay, E.A., Bickhart, D.M., Carvalheiro, R., Neves, H.H., Van Tassell, C.P., Songstegard, T.S., Garcia, J., Liu, G. 2016. Comparative analyses across cattle breeds reveal the pitfalls caused by artificial and lineage-differential copy number variations. Scientific Reports. 6:29219.
Reduced representation bisulphite sequencing of the ten bovine somatic tissues reveals DNA methylation patterns -
Zhou, Y., Xu, L., Hay, E., Bickhart, D.M., Sonstegard, T., Van Tassell, C.P., Chen, H., Liu, G. 2016. Reduced representation bisulphite sequencing of the ten bovine somatic tissues reveals DNA methylation patterns [abstract]. In: Proceedings of 2016 BARC Poster Day, April 27, 2016, Beltsville, Maryland. P63.
Exploring the feasibility of using copy number variants as genetic markers through large-scale whole genome sequencing experiments -
Bickhart, D.M., Xu, L., Hutchison, J.L., Cole, J.B., Null, D.J., Schroeder, S.G., Song, J., Garcia, J.F., Sonstegardq, T.S., Van Tassell, C.P., Schnabel, R.D., Taylor, J.F., Lewin, H.A., Liu, G. 2016. Exploring the feasibility of using copy number variants as genetic markers through large-scale whole genome sequencing experiments. Journal of Dairy Science. 99(E-Suppl. 1)/Journal of Animal Science. 94(E-Suppl. 5):142(abstr. 0306).
Identifying and calling insertions, deletions, and single-base mutations efficiently from sequence data -
Van Raden, P.M., Bickhart, D.M., O'Connell, J.R. 2016. Identifying and calling insertions, deletions, and single-base mutations efficiently from sequence data. Journal of Dairy Science. 99(E-Suppl. 1)/Journal of Animal Science. 94(E-Suppl. 5):140(abstr. 0302).
Sexed-semen usage for Holstein AI in the United States -
Hutchison, J.L., Bickhart, D.M. 2016. Sexed-semen usage for Holstein AI in the United States. Journal of Dairy Science. 99(E-Suppl. 1)/Journal of Animal Science. 94(E-Suppl. 5):176(abstr. 0372).
Selection of sequence variants to improve dairy cattle genomic predictions -
Tooker, M.E., Van Raden, P.M., Bickhart, D.M., O'Connell, J.R. 2016. Selection of sequence variants to improve dairy cattle genomic predictions. Journal of Dairy Science. 99(E-Suppl. 1)/Journal of Animal Science. 94(E-Suppl. 5):138(abstr. 298).
Strategy for incorporating newly discovered causative genetic variants into genomic evaluations -
Wiggans, G.R., Van Raden, P.M., Bickhart, D.M., Tooker, M.E. 2016. Strategy for incorporating newly discovered causative genetic variants into genomic evaluations. Journal of Dairy Science. 99(E–Suppl. 1)/Journal of Animal Science. 94(E–Suppl. 5):137(abstr. 296).
Whole-genome sequencing reveals the diversity of cattle copy number variations and multicopy genes -
Bickhart, D.M., Xu, L., Hutchison, J.L., Cole, J.B., Schroeder, S.G., Song, J., Garcia, J., Van Tassell, C.P., Sonstegard, T.S., Schnabel, R.D., Taylor, J.F., Lewin, H.A., Liu, G. 2016. Whole-genome sequencing reveals the diversity of cattle copy number variations and multicopy genes. DNA Research. 23(3):253-62.
Population-genetic properties of differentiated copy number variations in cattle -
Xu, L., Hou, Y., Bickhart, D.M., Zhou, Y., Hay, E.A., Song, J., Sonstegard, T., Van Tassell, C.P., Liu, G. 2016. Population-genetic properties of differentiated copy number variations in cattle. Scientific Reports. 6:23161.
Increasing the number of single nucleotide polymorphisms used in genomic evaluation of dairy cattle -
Wiggans, G.R., Cooper, T.A., Van Raden, P.M., Van Tassell, C.P., Bickhart, D.M., Sonstegard, T.S. 2016. Increasing the number of single nucleotide polymorphisms used in genomic evaluation of dairy cattle. Journal of Dairy Science. 99(6):4504-4511.
Genome-wide CNV analysis reveals variants associated with growth traits in Bos indicus -
Zhou, Y., Utsunomiya, Y.T., Xu, L., Hay, E.A., Bickhart, D.M., Carvalheiro, R., Neves, H.E., Sonstegard, T., Van Tassell, C.P., Garcia, J., Liu, G. 2016. Genome-wide CNV analysis reveals variants associated with growth traits in Bos indicus. Biomed Central (BMC) Genomics. 17(1):419.2016.
Improving the goat long-read assembly with optical mapping -
Bickhart, D.M., Smith, T.P., Rosen, B.D., Koren , S., Phillippy, A., Hastie, A.R., Sullivan, S.T., Liachko, I., Burton, J.N., Sayre, B.L., Liu, G., Schroeder, S.G., Sonstegard, T.S., Van Tassell, C.P. 2016. Improving the goat long-read assembly with optical mapping. Plant and Animal Genome Conference Proceedings. San Diego, CA, Jan. 9–13.
Diversity and population-genetic properties of copy number variations and multicopy genes in cattle -
Bickhart, D.M., Xu, L., Hutchison, J.L., Cole, J.B., Null, D.J., Schroeder, S.G., Song, J., Garcia, J., Van Tassell, C.P., Sonstegard, T.S., Schnabel, R.D., Taylor, J.F., Lewin, H.A., Liu, G. 2016. Diversity and population-genetic properties of copy number variations and multicopy genes in cattle [abstract]. USDA NIFA Animal Genome Program PD Meeting, January 8, 2016, San Diego, California.
Comparative ruminant genomics highlights segmental duplication and mobile element insertion diversity -
Bickhart, D.M., Rosen, B.D., Schroeder, S.G., Van Tassell, C.P. 2016. Comparative ruminant genomics highlights segmental duplication and mobile element insertion diversity. Plant and Animal Genome Conference Proceedings. San Diego, CA, Jan. 9–13, W109.
Fast single-pass alignment and variant calling using sequencing data -
Van Raden, P.M., Bickhart, D.M. 2016. Fast single-pass alignment and variant calling using sequencing data. Plant and Animal Genome Conference Proceedings. San Diego, CA, Jan. 9–13, W161.
Effect of sex, age, and breed on genetic recombination features in cattle -
Shen, B., Wang, Z., Jiang, J., Cole, J.B., Bickhart, D.M., Wiggans, G.R., Liu, G., Ma, L. 2016. Effect of sex, age, and breed on genetic recombination features in cattle. Plant and Animal Genome Conference Proceedings. San Diego, CA, Jan. 9–13, P0522.
Reducing animal sequencing redundancy by preferentially selecting animals with low-frequency haplotypes -
Bickhart, D.M., Hutchison, J.L., Null, D.J., Van Raden, P.M., Cole, J.B. 2016. Reducing animal sequencing redundancy by preferentially selecting animals with low-frequency haplotypes. Journal of Dairy Science. 99(7):5526-5534.
Tet-mediated imprinting erasure in H19 locus following reprogramming of spermatogonial stem cells to induced pluripotent stem cells -
Bermejo-Alvarez, P., Ramos-Ibeas, P., Park, K., Powell, A.M., Vansandt, L., Bickhart, D.M., Ramirez, M.A., Gutierrez-Adan, A., Telugu, B. 2015. Tet-mediated imprinting erasure in H19 locus following reprogramming of spermatogonial stem cells to induced pluripotent stem cells. Scientific Reports. 5:13691.
Cattle sex-specific recombination and genetic control from a very large pedigree -
Ma, L., O'Connell, J.R., Van Raden, P.M., Shen, B., Padhi, A., Sun, C., Bickhart, D.M., Cole, J.B., Null, D.J., Liu, G., Da, Y., Wiggans, G.R. 2015. Cattle sex-specific recombination and genetic control from a very large pedigree. PLoS Genetics. 11(11):e1005387.
Animal selection for whole genome sequencing by quantifying the unique contribution of homozygous haplotypes sequenced -
Bickhart, D.M., Cole, J.B., Hutchison, J.L. 2015. Animal selection for whole genome sequencing by quantifying the unique contribution of homozygous haplotypes sequenced. Journal of Dairy Science. 98(Suppl. 2)/Journal of Animal Science 93(Suppl. 3):649(abstr. W86).
Identification of copy number variable gene families in Holstein and Jersey cattle -
Bickhart, D.M., Xu, L., Hutchison, J.L., Liu, G., Lewin, H.A. 2015. Identification of copy number variable gene families in Holstein and Jersey cattle. Journal of Dairy Science. 98(Suppl. 2)/Journal of Animal Science 93(Suppl. 3):648(abstr. W84).
Effect of increasing the number of single-nucleotide polymorphisms from 60,000 to 85,000 in genomic evaluation of Holsteins -
Wiggans, G.R., Cooper, T.A., Van Raden, P.M., Pomp, D., Van Tassell, C.P., Bickhart, D.M., Sonstegard, T.S. 2015. Effect of increasing the number of single-nucleotide polymorphisms from 60,000 to 85,000 in genomic evaluation of Holsteins. Journal of Dairy Science. 98(Suppl. 2)/Journal of Animal Science 93(Suppl. 3):578(abstr. 537).
RAPTR-SV: a hybrid method for the detection of structural variants Reprint Icon -
Bickhart, D.M., Hutchison, J.L., Xu, L., Schnabel, R.D., Taylor, J.F., Reecy, J.M., Schroeder, S.G., Van Tassell, C.P., Sonstegard, T.S., Liu, G. 2015. RAPTR-SV: a hybrid method for the detection of structural variants. Bioinformatics. 31(13):2084-2090.
The use of PacBio and Hi-C data in denovo assembly of the goat genome -
Bickhart, D.M., Koren, S., Phillippy, A.M., Smith, T.P., Burton, J.N., Llachko, I., Sayre, B.L., Huson, H.J., Schroeder, S.G., Van Tassell, C.P., Sonstegard, T.S. 2015. The use of PacBio and Hi-C data in denovo assembly of the goat genome. Plant and Animal Genome Conference Proceedings. San Diego, CA, January 10–14, W144.
Comparison of CNVs in Buffalo with other species -
Bickhart, D.M., Liu, G., International Water, B.A. 2015. Comparison of CNVs in Buffalo with other species. Plant and Animal Genome Conference Proceedings. San Diego, CA, January 10–14, W107.
Genomic signatures reveal geographic adaption and human selection in cattle -
Xu, L., Bickhart, D.M., Cole, J.B., Schroeder, S.G., Song, J., Van Tassell, C.P., Sonstegard, T.S., Liu, G. 2014. Genomic signatures reveal geographic adaption and human selection in cattle. Molecular Biology and Evolution. 32(3):711-25.
Genome wide CNV analysis reveals additional variants associated with milk production traits in Holsteins -
Xu, L., Cole, J.B., Bickhart, D.M., Hou, Y., Song, J., Van Raden, P.M., Sonstegard, T.S., Van Tassell, C.P., Liu, G. 2014. Genome wide CNV analysis reveals additional variants associated with milk production traits in Holsteins. Biomed Central (BMC) Genomics. 15:683.
The identification of a putative mutation for SLICK hair coat in Senepol cattle -
Using the whole read: structural variant detection using NGS data -
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.
The hunt for a functional mutation affecting conformation and calving traits on chromosome 18 in Holstein cattle -
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.
Genome wide CNV analysis reveals additional variants associated with milk production traits in Holsteins -
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 -
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 -
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 -
Shin, J., Xu, L., Li, R.W., Gao, Y., Bickhart, D.M., Liu, G., Baldwin, R.L., Li, C. 2014. A high-resolution whole-genome map of the distinctive epigenomic landscape induced by butyrate in bovine cells. Animal Genetics. 45:40–50. DOI:10.1111.age.12147.
A genome-wide survey reveals a deletion polymorphism associated with resistance to gastrointestinal nematodes in Angus cattle -
Xu, L., Hou, Y., Bickhart, D.M., Song, J., Van Tassell, C.P., Sonstegard, T.S., Liu, G. 2014. A genome-wide survey reveals a deletion polymorphism associated with resistance to gastrointestinal nematodes in Angus cattle. Functional and Integrative Genomics. DOI:14(2):333-9.
The challenges and importance of structural variation detection in livestock -
Bickhart, D.M., Liu, G. 2014. The challenges and importance of structural variation detection in livestock. Frontiers in Genetics. 5:37.
A genome-wide association study of calf birth weight in Holstein cattle using single nucleotide polymorphisms and phenotypes predicted from auxiliary traits Reprint Icon -
Cole, J.B., Waurich, B., Wensch-Dorendorf, M., Bickhart, D.M., Swalve, H.H. 2014. A genome-wide association study of calf birth weight in Holstein cattle using single nucleotide polymorphisms and phenotypes predicted from auxiliary traits. Journal of Dairy Science. 97(5):3156-3172.
The use of population-scale sequencing to identify CNVs impacting productive traits in different cattle breeds -
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.
Candidate causative mutation on BTA18 associated with calving and conformation traits in Holstein bulls -
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.
Assessing signatures of selection through variation in linkage disequilibrium between taurine and indicine cattle -
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.
Short communication: Use of young bulls in the United States Reprint Icon -
Hutchison, J.L., Cole, J.B., Bickhart, D.M. 2014. Short communication: Use of young bulls in the United States. Journal of Dairy Science. 97(5):3213-3220.
Population sequencing reveals breed and sub-species specific CNVs in cattle -
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.
A genome-wide survey reveals a deletion polymorphism associated with resistance to gastrointestinal nematodes in Angus cattle -
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.
Random forests approach for identifying additive and epistatic single nucleotide polymorphisms associated with residual feed intake in dairy cattle -
Yao, C., Spurlock, D., Armentano, L., Page, D., Vandehaar, M., Bickhart, D.M., Weigel, K. 2013. Random forests approach for identifying additive and epistatic single nucleotide polymorphisms associated with residual feed intake in dairy cattle. Journal of Dairy Science. 96(10):6716-6729.
Structural and functional impacts of copy number variations on the cattle genome -
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 -
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 -
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 -
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.
Genomic divergence of indicine and taurine cattle identified through high-density SNP genotyping -
Porto-Neto, L.R., Sonstegard, T.S., Mcclure, M.C., Bickhart, D.M., Gondro, C., Da Silva, M., Utsunomiya, Y.T., Garcia, J.F., Van Tassell, C.P. 2013. Genomic divergence of indicine and taurine cattle identified through high-density SNP genotyping. J. Anim. Sci. Vol. 91, E-Suppl. 2/J. Dairy Sci. Vol. 96, E-Suppl. 1, paper 314, pp. 314.
Tools to exploit sequence data to find new markers and disease loci in dairy cattle -
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).
Optimal age at first calving for U.S. dairy cattle -
Cole, J.B., Hutchison, J.L., Bickhart, D.M., Null, D.J. 2013. Optimal age at first calving for U.S. dairy cattle. Journal of Dairy Science. 96(E-Suppl. 1):289–290 (abstr. W188).
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 Reprint Icon -
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 -
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 -
Bickhart, D.M., Liu, G. 2013. Combined arms: a full spectrum approach to structural variant discovery in livestock populations. Meeting Abstract. W145.
Bos taurus indicus (Nelore) hybrid assembly improvement using PacBio reads -
Schroeder, S.G., Zimin, A., Bickhart, D.M., Sonstegard, T.S., Van Tassell, C.P., Garcia, F.J. 2013. Bos taurus indicus (Nelore) hybrid assembly improvement using PacBio reads. Poster P0523, pp.237.
Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping -
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.
Identification of a nonsense mutation in CWC15 associated with decreased reproductive efficiency in Jersey cattle Reprint Icon -
Sonstegard, T.S., Cole, J.B., Van Raden, P.M., Van Tassell, C.P., Null, D.J., Schroeder, S.G., Bickhart, D.M., Mcclure, M.C. 2013. Identification of a nonsense mutation in CWC15 associated with decreased reproductive efficiency in Jersey cattle. PLoS One. 8(1):e54872.
Bos taurus indicus (Nelore) hybrid assembly improvement using PacBio reads -
Identification of candidate transcription factor binding sites in the cattle genome -
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 -
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 Reprint Icon -
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 -
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.
Copy Number Variation in the Cattle Genome Reprint Icon -
Liu, G., Bickhart, D.M. 2012. Copy Number Variation in the Cattle Genome. Functional and Integrative Genomics. DOI: 10.1007/S10142-012-0289-9.
Butyrate induced IGF2 activation correlated with distinct chromatin landscapes due to histone modification Reprint Icon -
Shin, J., Li, R.W., Goa, Y., Bickhart, D.M., Liu, G., Li, W., Wu, S., Li, C. 2013. Butyrate induced IGF2 activation correlated with distinct chromatin landscapes due to histone modification. PLoS Genetics. DOI:10.4137/GRSB.S11243.
Copy number variation detection in cattle reveals potential breed specific differences -
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
Copy number variation of individual cattle genomes using next-generation sequencing Reprint Icon -
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.
Copy number variation of individual cattle genomes using next-generation sequencing -
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.
Copy number variations related to reproduction traits in Holstein cattle -
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.
Genomic regions showing copy number variations associate with resistance or susceptibility to gastrointestinal nematodes in Angus cattle -
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.
Individualized cattle copy number and segmental duplication maps using next generation sequencing -
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 Reprint Icon -
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A high-resolution cattle CNV map by population-scale genome sequencing -
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Genomic characteristics of cattle copy number variations Reprint Icon -
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