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United States Department of Agriculture

Agricultural Research Service

Derek M Bickhart
Animal Genomics and Improvement Laboratory
Research Geneticist (Animals)

Phone: (301) 504-8592
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
National Dairy Genetic Evaluation Program
Nonfunded Cooperative Agreement (N)
  Accession Number: 424155
1000 Bull Genomes Project
Nonfunded Cooperative Agreement (N)
  Accession Number: 426790
Improvement of Algorithms and Software to Process Very Large Genomic Datasets
Specific Cooperative Agreement (S)
  Accession Number: 426953

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)
The identification of a putative mutation for SLICK hair coat in Senepol cattle - (Abstract Only) - (05-May-14)
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.
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.
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.
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.
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.
A genome-wide association study of calf birth weight in Holstein cattle using single nucleotide polymorphisms and phenotypes predicted from auxiliary traits Reprint Icon - (Peer Reviewed Journal)
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 - (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.
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.
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.
Short communication: Use of young bulls in the United States Reprint Icon - (Peer Reviewed Journal)
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 - (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.
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.
Random forests approach for identifying additive and epistatic single nucleotide polymorphisms associated with residual feed intake in dairy cattle - (Peer Reviewed Journal)
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 - (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.
Genomic divergence of indicine and taurine cattle identified through high-density SNP genotyping - (Abstract Only)
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 - (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).
Optimal age at first calving for U.S. dairy cattle - (Abstract Only)
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 - (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.
Bos taurus indicus (Nelore) hybrid assembly improvement using PacBio reads - (Abstract Only)
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 - (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.
Identification of a nonsense mutation in CWC15 associated with decreased reproductive efficiency in Jersey cattle - (Peer Reviewed Journal)
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 - (Abstract Only) - (27-Nov-12)
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.
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.
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.
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
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.
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.
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.
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.
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.
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.
A high-resolution cattle CNV map by population-scale genome sequencing - (Abstract Only)
Bickhart, D.M., Hou, Y., Liu, G., Schroeder, S.G., Can, A., Maria, C., Matukumalli, L., Song, J., Schnabel, R., Ventura, M., Taylor, J., Eichler, E., Sonstegard, T.S., Van Tassell, C.P., Illumina Bovine Hd, C. 2011. A high-resolution cattle CNV map by population-scale genome sequencing. BARC Poster Day [abstract]. No. 5.
Genomic and functional characteristics of copy number variations in Angus cattle selected for resistance or susceptibility to gastrointestinal nematodes - (Abstract Only)
Hou, Y., Liu, G., Bickhart, D.M., Matukumalli, L., Song, J., Gasbarre, L., Van Tassell, C.P., Sonstegard, T.S. 2011. Genomic and functional characteristics of copy number variations in Angus cattle selected for resistance or susceptibility to gastrointestinal nematodes [abstract]. BARC Poster Day. No. 17.
Genomic characteristics of cattle copy number variations - (Peer Reviewed Journal)
Hou, Y., Liu, G., Bickhart, D.M., Cardone, M.F., Wang, K., Kim, E., Matukumalli, L., Ventura, M., Song, J., Van Raden, P.M., Sonstegard, T.S., Van Tassell, C.P. 2011. Genomic characteristics of cattle copy number variations. Biomed Central (BMC) Genomics. 12:127.
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.
Last Modified: 12/21/2014
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