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Items: 43


Convergent Evolution of Slick Coat in Cattle through Truncation Mutations in the Prolactin Receptor.

Porto-Neto LR, Bickhart DM, Landaeta-Hernandez AJ, Utsunomiya YT, Pagan M, Jimenez E, Hansen PJ, Dikmen S, Schroeder SG, Kim ES, Sun J, Crespo E, Amati N, Cole JB, Null DJ, Garcia JF, Reverter A, Barendse W, Sonstegard TS.

Front Genet. 2018 Feb 23;9:57. doi: 10.3389/fgene.2018.00057. eCollection 2018.


Comparative sequence alignment reveals River Buffalo genomic structural differences compared with cattle.

Li W, Bickhart DM, Ramunno L, Iamartino D, Williams JL, Liu GE.

Genomics. 2018 Mar 6. pii: S0888-7543(18)30128-9. doi: 10.1016/j.ygeno.2018.02.018. [Epub ahead of print]


Host-rumen microbe interactions may be leveraged to improve the productivity of dairy cows.

Bickhart DM, Weimer PJ.

J Dairy Sci. 2017 Oct 25. pii: S0022-0302(17)30958-X. doi: 10.3168/jds.2017-13328. [Epub ahead of print]


The antibody loci of the domestic goat (Capra hircus).

Schwartz JC, Philp RL, Bickhart DM, Smith TPL, Hammond JA.

Immunogenetics. 2017 Oct 23. doi: 10.1007/s00251-017-1033-3. [Epub ahead of print]


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 DL, Halley YA, Wilson ML, Bhattarai EK, Brashear W, Hill J, Metz RP, Johnson CD, Rollins D, Peterson MJ, Bickhart DM, Decker JE, Sewell JF, Seabury CM.

G3 (Bethesda). 2017 Sep 7;7(9):3047-3058. doi: 10.1534/g3.117.043083.


Genomic evaluation of age at first calving.

Hutchison JL, VanRaden PM, Null DJ, Cole JB, Bickhart DM.

J Dairy Sci. 2017 Aug;100(8):6853-6861. doi: 10.3168/jds.2016-12060. Epub 2017 Jun 16.


Selecting sequence variants to improve genomic predictions for dairy cattle.

VanRaden PM, Tooker ME, O'Connell JR, Cole JB, Bickhart DM.

Genet Sel Evol. 2017 Mar 7;49(1):32. doi: 10.1186/s12711-017-0307-4.


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

Bickhart DM, Rosen BD, Koren S, Sayre BL, Hastie AR, Chan S, Lee J, Lam ET, Liachko I, Sullivan ST, Burton JN, Huson HJ, Nystrom JC, Kelley CM, Hutchison JL, Zhou Y, Sun J, Crisà A, Ponce de León FA, Schwartz JC, Hammond JA, Waldbieser GC, Schroeder SG, Liu GE, Dunham MJ, Shendure J, Sonstegard TS, Phillippy AM, Van Tassell CP, Smith TP.

Nat Genet. 2017 Apr;49(4):643-650. doi: 10.1038/ng.3802. Epub 2017 Mar 6.


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

Schwartz JC, Gibson MS, Heimeier D, Koren S, Phillippy AM, Bickhart DM, Smith TP, Medrano JF, Hammond JA.

Immunogenetics. 2017 Apr;69(4):255-269. doi: 10.1007/s00251-017-0973-y. Epub 2017 Feb 9.


Systematic Profiling of Short Tandem Repeats in the Cattle Genome.

Xu L, Haasl RJ, Sun J, Zhou Y, Bickhart DM, Li J, Song J, Sonstegard TS, Van Tassell CP, Lewin HA, Liu GE.

Genome Biol Evol. 2017 Jan 1;9(1):20-31. doi: 10.1093/gbe/evw256.


Reduced representation bisulphite sequencing of ten bovine somatic tissues reveals DNA methylation patterns and their impacts on gene expression.

Zhou Y, Xu L, Bickhart DM, Abdel Hay EH, Schroeder SG, Connor EE, Alexander LJ, Sonstegard TS, Van Tassell CP, Chen H, Liu GE.

BMC Genomics. 2016 Oct 6;17(1):779.


Revealing misassembled segments in the bovine reference genome by high resolution linkage disequilibrium scan.

Utsunomiya AT, Santos DJ, Boison SA, Utsunomiya YT, Milanesi M, Bickhart DM, Ajmone-Marsan P, Sölkner J, Garcia JF, da Fonseca R, da Silva MV.

BMC Genomics. 2016 Sep 5;17:705. doi: 10.1186/s12864-016-3049-8.


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

Zhou Y, Utsunomiya YT, Xu L, Hay el HA, Bickhart DM, Sonstegard TS, Van Tassell CP, Garcia JF, Liu GE.

Sci Rep. 2016 Jul 6;6:29219. doi: 10.1038/srep29219.


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

Zhou Y, Utsunomiya YT, Xu L, Hay el HA, Bickhart DM, Alexandre PA, Rosen BD, Schroeder SG, Carvalheiro R, de Rezende Neves HH, Sonstegard TS, Van Tassell CP, Ferraz JB, Fukumasu H, Garcia JF, Liu GE.

BMC Genomics. 2016 Jun 1;17:419. doi: 10.1186/s12864-016-2461-4.


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

Bickhart DM, Hutchison JL, Null DJ, VanRaden PM, Cole JB.

J Dairy Sci. 2016 Jul;99(7):5526-5534. doi: 10.3168/jds.2015-10347. Epub 2016 Apr 13.


Diversity and population-genetic properties of copy number variations and multicopy genes in cattle.

Bickhart DM, Xu L, Hutchison JL, Cole JB, Null DJ, Schroeder SG, Song J, Garcia JF, Sonstegard TS, Van Tassell CP, Schnabel RD, Taylor JF, Lewin HA, Liu GE.

DNA Res. 2016 Jun;23(3):253-62. doi: 10.1093/dnares/dsw013. Epub 2016 Apr 15.


Increasing the number of single nucleotide polymorphisms used in genomic evaluation of dairy cattle.

Wiggans GR, Cooper TA, VanRaden PM, Van Tassell CP, Bickhart DM, Sonstegard TS.

J Dairy Sci. 2016 Jun;99(6):4504-4511. doi: 10.3168/jds.2015-10456. Epub 2016 Mar 31.


Population-genetic properties of differentiated copy number variations in cattle.

Xu L, Hou Y, Bickhart DM, Zhou Y, Hay el HA, Song J, Sonstegard TS, Van Tassell CP, Liu GE.

Sci Rep. 2016 Mar 23;6:23161. doi: 10.1038/srep23161.


Cattle Sex-Specific Recombination and Genetic Control from a Large Pedigree Analysis.

Ma L, O'Connell JR, VanRaden PM, Shen B, Padhi A, Sun C, Bickhart DM, Cole JB, Null DJ, Liu GE, Da Y, Wiggans GR.

PLoS Genet. 2015 Nov 5;11(11):e1005387. doi: 10.1371/journal.pgen.1005387. eCollection 2015 Nov.


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

Bickhart DM, Hutchison JL, Xu L, Schnabel RD, Taylor JF, Reecy JM, Schroeder S, Van Tassell CP, Sonstegard TS, Liu GE.

Bioinformatics. 2015 Jul 1;31(13):2084-90. doi: 10.1093/bioinformatics/btv086. Epub 2015 Feb 16.


Genomic signatures reveal new evidences for selection of important traits in domestic cattle.

Xu L, Bickhart DM, Cole JB, Schroeder SG, Song J, Tassell CP, Sonstegard TS, Liu GE.

Mol Biol Evol. 2015 Mar;32(3):711-25. doi: 10.1093/molbev/msu333. Epub 2014 Nov 26.


Genome wide CNV analysis reveals additional variants associated with milk production traits in Holsteins.

Xu L, Cole JB, Bickhart DM, Hou Y, Song J, VanRaden PM, Sonstegard TS, Van Tassell CP, Liu GE.

BMC Genomics. 2014 Aug 15;15:683. doi: 10.1186/1471-2164-15-683.


A genome-wide survey reveals a deletion polymorphism associated with resistance to gastrointestinal nematodes in Angus cattle.

Xu L, Hou Y, Bickhart DM, Song J, Van Tassell CP, Sonstegard TS, Liu GE.

Funct Integr Genomics. 2014 Jun;14(2):333-9. doi: 10.1007/s10142-014-0371-6. Epub 2014 Apr 10.


Short communication: Use of young bulls in the United States.

Hutchison JL, Cole JB, Bickhart DM.

J Dairy Sci. 2014 May;97(5):3213-20. doi: 10.3168/jds.2013-7525. Epub 2014 Mar 5.


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

Cole JB, Waurich B, Wensch-Dorendorf M, Bickhart DM, Swalve HH.

J Dairy Sci. 2014 May;97(5):3156-72. doi: 10.3168/jds.2013-7409. Epub 2014 Mar 5.


The challenges and importance of structural variation detection in livestock.

Bickhart DM, Liu GE.

Front Genet. 2014 Feb 18;5:37. doi: 10.3389/fgene.2014.00037. eCollection 2014. Review.


Assessing signatures of selection through variation in linkage disequilibrium between taurine and indicine cattle.

Pérez O'Brien AM, Utsunomiya YT, Mészáros G, Bickhart DM, Liu GE, Van Tassell CP, Sonstegard TS, Da Silva MV, Garcia JF, Sölkner J.

Genet Sel Evol. 2014 Mar 4;46:19. doi: 10.1186/1297-9686-46-19.


Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping.

Porto-Neto LR, Sonstegard TS, Liu GE, Bickhart DM, Da Silva MV, Machado MA, Utsunomiya YT, Garcia JF, Gondro C, Van Tassell CP.

BMC Genomics. 2013 Dec 13;14:876. doi: 10.1186/1471-2164-14-876.


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

Yao C, Spurlock DM, Armentano LE, Page CD Jr, VandeHaar MJ, Bickhart DM, Weigel KA.

J Dairy Sci. 2013 Oct;96(10):6716-29. doi: 10.3168/jds.2012-6237. Epub 2013 Aug 9.


Butyrate Induced IGF2 Activation Correlated with Distinct Chromatin Signatures Due to Histone Modification.

Shin JH, Li RW, Gao Y, Bickhart DM, Liu GE, Li W, Wu S, Li CJ.

Gene Regul Syst Bio. 2013 Mar 26;7:57-70. doi: 10.4137/GRSB.S11243. Print 2013.


Identification of candidate transcription factor binding sites in the cattle genome.

Bickhart DM, Liu GE.

Genomics Proteomics Bioinformatics. 2013 Jun;11(3):195-8. doi: 10.1016/j.gpb.2012.10.004. Epub 2013 Feb 1.


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

Xu L, Hou Y, Bickhart DM, Song J, Liu GE.

Microarrays (Basel). 2013 Jun 25;2(3):171-85. doi: 10.3390/microarrays2030171. Review.


Analysis of copy number variations in Holstein cows identify potential mechanisms contributing to differences in residual feed intake.

Hou Y, Bickhart DM, Chung H, Hutchison JL, Norman HD, Connor EE, Liu GE.

Funct Integr Genomics. 2012 Nov;12(4):717-23. doi: 10.1007/s10142-012-0295-y. Epub 2012 Sep 19.


Fine mapping of copy number variations on two cattle genome assemblies using high density SNP array.

Hou Y, Bickhart DM, Hvinden ML, Li C, Song J, Boichard DA, Fritz S, Eggen A, DeNise S, Wiggans GR, Sonstegard TS, Van Tassell CP, Liu GE.

BMC Genomics. 2012 Aug 6;13:376. doi: 10.1186/1471-2164-13-376.


Copy number variation in the cattle genome.

Liu GE, Bickhart DM.

Funct Integr Genomics. 2012 Nov;12(4):609-24. doi: 10.1007/s10142-012-0289-9. Epub 2012 Jul 13. Review.


Copy number variation of individual cattle genomes using next-generation sequencing.

Bickhart DM, Hou Y, Schroeder SG, Alkan C, Cardone MF, Matukumalli LK, Song J, Schnabel RD, Ventura M, Taylor JF, Garcia JF, Van Tassell CP, Sonstegard TS, Eichler EE, Liu GE.

Genome Res. 2012 Apr;22(4):778-90. doi: 10.1101/gr.133967.111. Epub 2012 Feb 2.


Genomic regions showing copy number variations associate with resistance or susceptibility to gastrointestinal nematodes in Angus cattle.

Hou Y, Liu GE, Bickhart DM, Matukumalli LK, Li C, Song J, Gasbarre LC, Van Tassell CP, Sonstegard TS.

Funct Integr Genomics. 2012 Mar;12(1):81-92. doi: 10.1007/s10142-011-0252-1. Epub 2011 Sep 18.


Transcriptomes of Frankia sp. strain CcI3 in growth transitions.

Bickhart DM, Benson DR.

BMC Microbiol. 2011 Aug 25;11:192. doi: 10.1186/1471-2180-11-192.


The biology of Frankia sp. strains in the post-genome era.

Benson DR, Brooks JM, Huang Y, Bickhart DM, Mastronunzio JE.

Mol Plant Microbe Interact. 2011 Nov;24(11):1310-6. doi: 10.1094/MPMI-06-11-0150. Review.


Genomic characteristics of cattle copy number variations.

Hou Y, Liu GE, Bickhart DM, Cardone MF, Wang K, Kim ES, Matukumalli LK, Ventura M, Song J, VanRaden PM, Sonstegard TS, Van Tassell CP.

BMC Genomics. 2011 Feb 23;12:127. doi: 10.1186/1471-2164-12-127.


Insertion sequence content reflects genome plasticity in strains of the root nodule actinobacterium Frankia.

Bickhart DM, Gogarten JP, Lapierre P, Tisa LS, Normand P, Benson DR.

BMC Genomics. 2009 Oct 12;10:468. doi: 10.1186/1471-2164-10-468.


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

Zhaxybayeva O, Swithers KS, Lapierre P, Fournier GP, Bickhart DM, DeBoy RT, Nelson KE, Nesbø CL, Doolittle WF, Gogarten JP, Noll KM.

Proc Natl Acad Sci U S A. 2009 Apr 7;106(14):5865-70. doi: 10.1073/pnas.0901260106. Epub 2009 Mar 23.


Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography.

Normand P, Lapierre P, Tisa LS, Gogarten JP, Alloisio N, Bagnarol E, Bassi CA, Berry AM, Bickhart DM, Choisne N, Couloux A, Cournoyer B, Cruveiller S, Daubin V, Demange N, Francino MP, Goltsman E, Huang Y, Kopp OR, Labarre L, Lapidus A, Lavire C, Marechal J, Martinez M, Mastronunzio JE, Mullin BC, Niemann J, Pujic P, Rawnsley T, Rouy Z, Schenowitz C, Sellstedt A, Tavares F, Tomkins JP, Vallenet D, Valverde C, Wall LG, Wang Y, Medigue C, Benson DR.

Genome Res. 2007 Jan;17(1):7-15. Epub 2006 Dec 6.

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