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51

Symposium review: Advances in sequencing technology herald a new frontier in cattle genomics and genome-enabled selection

Bickhart, D.M., McClure, J.C., Schnabel, R.D., Rosen, B.D., Medrano, J.F., Smith, T.P.L.

Journal:

Journal of Dairy Science

Year:

2020

File:

PDF, 506 KB

2020

52

Copy number variation in the cattle genome

George E. Liu, Derek M. Bickhart

Journal:

Functional & Integrative Genomics

Year:

2012

Language:

english

File:

PDF, 338 KB

english, 2012

53

The Biology of Frankia sp. Strains in the Post-Genome Era

Benson, David R., Brooks, James M., Huang, Ying, Bickhart, Derek M., Mastronunzio, Juliana E.

Journal:

Molecular Plant-Microbe Interactions

Year:

2011

Language:

english

File:

PDF, 543 KB

english, 2011

54

A genome-wide association study of calf birth weight in Holstein cattle using single nucleotide polymorphisms and phenotypes predicted from auxiliary traits

Cole, J.B., Waurich, B., Wensch-Dorendorf, M., Bickhart, D.M., Swalve, H.H.

Journal:

Journal of Dairy Science

Year:

2014

Language:

english

File:

PDF, 549 KB

english, 2014

55

A high-resolution whole-genome map of the distinctive epigenomic landscape induced by butyrate in bovine cells

Shin, J. H., Xu, L., Li, R. W., Gao, Y., Bickhart, D., Liu, G. E., Baldwin, R., Li, C.-J.

Journal:

Animal Genetics

Year:

2014

Language:

english

File:

PDF, 2.03 MB

english, 2014

56

The evolution of the natural killer complex; a comparison between mammals using new high-quality genome assemblies and targeted annotation

Schwartz, John C., Gibson, Mark S., Heimeier, Dorothea, Koren, Sergey, Phillippy, Adam M., Bickhart, Derek M., Smith, Timothy P. L., Medrano, Juan F., Hammond, John A.

Journal:

Year:

2017

Language:

english

File:

PDF, 1.67 MB

english, 2017

57

Determination of quantitative trait nucleotides by concordance analysis between quantitative trait loci and marker genotypes of US Holsteins

Weller, J.I., Bickhart, D.M., Wiggans, G.R., Tooker, M.E., O'Connell, J.R., Jiang, J., Ron, M., VanRaden, P.M.

Journal:

Journal of Dairy Science

Year:

2018

File:

PDF, 628 KB

2018

58

Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle

Low, Wai Yee, Tearle, Rick, Liu, Ruijie, Koren, Sergey, Rhie, Arang, Bickhart, Derek M., Rosen, Benjamin D., Kronenberg, Zev N., Kingan, Sarah B., Tseng, Elizabeth, Thibaud-Nissen, FranÃ§oise, Martin,

Journal:

Nature Communications

Year:

2020

File:

PDF, 2.95 MB

2020

59

Tet-mediated imprinting erasure in H19 locus following reprogramming of spermatogonial stem cells to induced pluripotent stem cells

Bermejo-Álvarez, P., Ramos-Ibeas, P., Park, K.E., Powell, A. P., Vansandt, L., Derek, Bickhart, Ramirez, M. A., Gutiérrez-Adán, A., Telugu, B. P.

Journal:

Scientific Reports

Year:

2015

Language:

english

File:

PDF, 1.83 MB

english, 2015

60

Genomic evaluation of age at first calving

Hutchison, J.L., VanRaden, P.M., Null, D.J., Cole, J.B., Bickhart, D.M.

Journal:

Journal of Dairy Science

Year:

2017

Language:

english

File:

PDF, 518 KB

english, 2017

61

The antibody loci of the domestic goat (Capra hircus)

Schwartz, John C., Philp, Rebecca L., Bickhart, Derek M., Smith, Timothy P. L., Hammond, John A.

Journal:

Year:

2017

Language:

english

File:

PDF, 1.37 MB

english, 2017

62

Annotated Draft Genome Assemblies for the Northern Bobwhite ( Colinus virginianus ) and the Scaled Quail ( Callipepla squamata ) Reveal Disparate Estimates of Modern Genome Diversity and Historic Effective Population Size

Oldeschulte, David L., Halley, Yvette A., Wilson, Miranda L., Bhattarai, Eric K., Brashear, Wesley, Hill, Joshua, Metz, Richard P., Johnson, Charles D., Rollins, Dale, Peterson, Markus J., Bickhart, D

Journal:

G3 Genes|Genome|Genetics

Year:

2017

Language:

english

File:

PDF, 1.27 MB

english, 2017

63

[Methods in Molecular Biology] Copy Number Variants Volume 1833 (Methods and Protocols) || Split-Read Indel and Structural Variant Calling Using PINDEL

Bickhart, Derek M.

Year:

2018

Language:

english

File:

PDF, 349 KB

english, 2018

64

[Methods in Molecular Biology] Copy Number Variants Volume 1833 (Methods and Protocols) || Use of RAPTR-SV to Identify SVs from Read Pairing and Split Read Signatures

Bickhart, Derek M.

Year:

2018

Language:

english

File:

PDF, 221 KB

english, 2018

65

Calling known variants and identifying new variants while rapidly aligning sequence data

VanRaden, P.M., Bickhart, D.M., O'Connell, J.R.

Journal:

Journal of Dairy Science

Year:

2019

Language:

english

File:

PDF, 644 KB

english, 2019

66

The Structure, Evolution, and Gene Expression Within the Caprine Leukocyte Receptor Complex

Schwartz, John C., Sanderson, Nicholas D., Bickhart, Derek M., Smith, Timothy P. L., Hammond, John A.

Journal:

Frontiers in Immunology

Year:

2019

File:

PDF, 2.07 MB

2019

67

An improved pig reference genome sequence to enable pig genetics and genomics research

Warr, Amanda, Affara, Nabeel, Aken, Bronwen, Beiki, Hamid, Bickhart, Derek M, Billis, Konstantinos, Chow, William, Eory, Lel, Finlayson, Heather A, Flicek, Paul, GirÃ³n, Carlos G, Griffin, Darren K, H

Journal:

Year:

2020

File:

PDF, 2.43 MB

2020

68

Random Forests approach for identifying additive and epistatic single nucleotide polymorphisms associated with residual feed intake in dairy cattle

Yao, C., Spurlock, D.M., Armentano, L.E., Page, C.D., VandeHaar, M.J., Bickhart, D.M., Weigel, K.A.

Journal:

Journal of Dairy Science

Year:

2013

Language:

english

File:

PDF, 847 KB

english, 2013

69

RAPTR-SV: a hybrid method for the detection of structural variants

Bickhart, D. M., Hutchison, J. L., Xu, L., Schnabel, R. D., Taylor, J. F., Reecy, J. M., Schroeder, S., Van Tassell, C. P., Sonstegard, T. S., Liu, G. E.

Journal:

Year:

2015

Language:

english

File:

PDF, 496 KB

english, 2015

70

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome

Bickhart, Derek M, Rosen, Benjamin D, Koren, Sergey, Sayre, Brian L, Hastie, Alex R, Chan, Saki, Lee, Joyce, Lam, Ernest T, Liachko, Ivan, Sullivan, Shawn T, Burton, Joshua N, Huson, Heather J, Nystro

Journal:

Nature Genetics

Year:

2017

Language:

english

File:

PDF, 1.65 MB

english, 2017

71

Identification of Candidate Transcription Factor Binding Sites in the Cattle Genome

Bickhart, Derek M., Liu, George E.

Journal:

Genomics, Proteomics & Bioinformatics

Year:

2013

Language:

english

File:

PDF, 475 KB

english, 2013

72

Examination of the xanthosine response on gene expression of mammary epithelial cells using RNA-seq technology

Choudhary, Shanti, Li, Wenli, Bickhart, Derek, Verma, Ramneek, Sethi, R. S., Mukhopadhyay, C. S., Choudhary, Ratan K.

Journal:

Journal of Animal Science and Technology

Year:

2018

Language:

english

File:

PDF, 4.49 MB

english, 2018

73

Comparative analyses of sperm DNA methylomes among human, mouse and cattle provide insights into epigenomic evolution and complex traits

Fang, Lingzhao, Zhou, Yang, Liu, Shuli, Jiang, Jicai, Bickhart, Derek M, Null, Daniel J., Li, Bingjie, Schroeder, Steven G., Rosen, Benjamin D., Cole, John B., Van Tassell, Curtis P., Ma, Li, Liu, Geo

Journal:

Year:

2019

File:

PDF, 5.52 MB

2019

74

Genomic Signatures Reveal New Evidences for Selection of Important Traits in Domestic Cattle

Xu, L., Bickhart, D. M., Cole, J. B., Schroeder, S. G., Song, J., Tassell, C. P. V., Sonstegard, T. S., Liu, G. E.

Journal:

Molecular Biology and Evolution

Year:

2015

Language:

english

File:

PDF, 1.13 MB

english, 2015

75

Continuous chromosome-scale haplotypes assembled from a single interspecies F1 hybrid of yak and cattle

Rice, Edward S, Koren, Sergey, Rhie, Arang, Heaton, Michael P, Kalbfleisch, Theodore S, Hardy, Timothy, Hackett, Peter H, Bickhart, Derek M, Rosen, Benjamin D, Ley, Brian Vander, Maurer, Nicholas W, G

Journal:

Year:

2020

File:

PDF, 1.40 MB

2020

76

Comparative Analysis of CNV Calling Algorithms: Literature Survey and a Case Study Using Bovine High-Density SNP Data

Xu, Lingyang, Hou, Yali, Bickhart, Derek, Song, Jiuzhou, Liu, George

Journal:

Year:

2013

Language:

english

File:

PDF, 283 KB

english, 2013

77

Comparative analyses across cattle genders and breeds reveal the pitfalls caused by false positive and lineage-differential copy number variations

Zhou, Yang, Utsunomiya, Yuri T., Xu, Lingyang, Hay, El Hamidi abdel, Bickhart, Derek M., Sonstegard, Tad S., Van Tassell, Curtis P., Garcia, Jose Fernando, Liu, George E.

Journal:

Scientific Reports

Year:

2016

Language:

english

File:

PDF, 1.04 MB

english, 2016

78

Genomic characteristics of cattle copy number variations

Yali Hou, George E Liu, Derek M Bickhart, Maria Francesca Cardone, Kai Wang, Eui-soo Kim, Lakshmi K Matukumalli, Mario Ventura, Jiuzhou Song, Paul M VanRaden, Tad S Sonstegard, Curt P Van Tassell

Journal:

Year:

2011

Language:

english

File:

PDF, 779 KB

english, 2011

79

Transcriptomes ofFrankiasp. strain CcI3 in growth transitions

Derek M Bickhart, David R Benson

Journal:

BMC Microbiology

Year:

2011

Language:

english

File:

PDF, 342 KB

english, 2011

80

On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales

Zhaxybayeva, O., Swithers, K. S., Lapierre, P., Fournier, G. P., Bickhart, D. M., DeBoy, R. T., Nelson, K. E., Nesbo, C. L., Doolittle, W. F., Gogarten, J. P.

Journal:

Proceedings of the National Academy of Sciences

Year:

2009

Language:

english

File:

PDF, 702 KB

english, 2009

81

Reducing animal sequencing redundancy by preferentially selecting animals with low-frequency haplotypes

Bickhart, D.M., Hutchison, J.L., Null, D.J., VanRaden, P.M., Cole, J.B.

Journal:

Journal of Dairy Science

Year:

2016

Language:

english

File:

PDF, 705 KB

english, 2016

82

P4027 Systematic profiling of short tandem repeats in the cattle genome

Xu, L., Haasl, R., Sun, J., Zhou, Y., Bickhart, D., Li, J., Song, J., Sonstegard, T., VanTassell, C. P., Lewin, H., Liu, G. E.

Journal:

Journal of Animal Science

Year:

2016

Language:

english

File:

PDF, 225 KB

english, 2016

83

Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation

Bickhart, Derek M., Watson, Mick, Koren, Sergey, Panke-Buisse, Kevin, Cersosimo, Laura M., Press, Maximilian O., Van Tassell, Curtis P., Van Kessel, Jo Ann S., Haley, Bradd J., Kim, Seon Woo, Heiner,

Journal:

Year:

2019

File:

PDF, 3.56 MB

2019

84

Population-genetic properties of differentiated copy number variations in cattle

Xu, Lingyang, Hou, Yali, Bickhart, Derek M., Zhou, Yang, Hay, El Hamidi abdel, Song, Jiuzhou, Sonstegard, Tad S., Van Tassell, Curtis P., Liu, George E.

Journal:

Scientific Reports

Year:

2016

Language:

english

File:

PDF, 862 KB

english, 2016

85

[Methods in Molecular Biology] Copy Number Variants Volume 1833 (Methods and Protocols) || Versatile Identification of Copy Number Variants with Canvas

Bickhart, Derek M.

Year:

2018

Language:

english

File:

PDF, 540 KB

english, 2018

86

Insertion sequence content reflects genome plasticity in strains of the root nodule actinobacteriumFrankia

Derek M Bickhart, Johann P Gogarten, Pascal Lapierre, Louis S Tisa, Philippe Normand, David R Benson

Journal:

Year:

2009

Language:

english

File:

PDF, 1.75 MB

english, 2009

87

Short communication: Use of young bulls in the United States

Hutchison, J.L., Cole, J.B., Bickhart, D.M.

Journal:

Journal of Dairy Science

Year:

2014

Language:

english

File:

PDF, 486 KB

english, 2014

88

[Methods in Molecular Biology] Copy Number Variants Volume 1833 (Methods and Protocols) || Analysis of Population-Genetic Properties of Copy Number Variations

Bickhart, Derek M.

Year:

2018

Language:

english

File:

PDF, 226 KB

english, 2018

89

SUBJECTIVE AGE AND COGNITIVE, PHYSICAL, AND PSYCHOSOCIAL HEALTH IN OLDER ADULTS

Sprague, Briana N, Troutman, Sara B W, Bickhart, Sara E, Jiya, Nathanael, Ross, Lesley A

Journal:

Innovation in Aging

Year:

2019

Language:

english

File:

PDF, 80 KB

english, 2019

90

New insights into mammalian sex chromosome structure and evolution using high-quality sequences from bovine X and Y chromosomes

Liu, Ruijie, Low, Wai Yee, Tearle, Rick, Koren, Sergey, Ghurye, Jay, Rhie, Arang, Phillippy, Adam M., Rosen, Benjamin D., Bickhart, Derek M., Smith, Timothy P. L., Hiendleder, Stefan, Williams, John L

Journal:

Year:

2019

Language:

english

File:

PDF, 1.52 MB

english, 2019

91

[Methods in Molecular Biology] Copy Number Variants Volume 1833 (Methods and Protocols) || Validation of Genomic Structural Variants Through Long Sequencing Technologies

Bickhart, Derek M.

Year:

2018

Language:

english

File:

PDF, 220 KB

english, 2018

92

Genome-wide CNV analysis reveals variants associated with growth traits in Bos indicus

Zhou, Yang, Utsunomiya, Yuri T., Xu, Lingyang, Hay, El Hamidi abdel, Bickhart, Derek M., Alexandre, Pamela Almeida, Rosen, Benjamin D., Schroeder, Steven G., Carvalheiro, Roberto, de Rezende Neves, Ha

Journal:

Year:

2016

Language:

english

File:

PDF, 2.21 MB

english, 2016

93

New insights into mammalian sex chromosome structure and evolution using high-quality sequences from bovine X and Y chromosomes

Liu, Ruijie, Low, Wai Yee, Tearle, Rick, Koren, Sergey, Ghurye, Jay, Rhie, Arang, Phillippy, Adam M., Rosen, Benjamin D., Bickhart, Derek M., Smith, Timothy P. L., Hiendleder, Stefan, Williams, John L

Journal:

Year:

2019

File:

PDF, 1.52 MB

2019

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