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Items: 1 to 20 of 33

1.

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 Jul 17. pii: g3.117.043083. doi: 10.1534/g3.117.043083. [Epub ahead of print]

PMID:
28717047
2.

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.

3.

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.

PMID:
28263316
4.

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.

5.

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.

6.

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.

7.

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.

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.

9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

PMID:
25686638
14.

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.

15.

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.

16.

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.

PMID:
24718732
17.

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.

18.

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.

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.

20.

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.

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