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Items: 1 to 50 of 64

1.

Computational detection and experimental validation of segmental duplications and associated copy number variations in water buffalo ( Bubalus bubalis ).

Liu S, Kang X, Catacchio CR, Liu M, Fang L, Schroeder SG, Li W, Rosen BD, Iamartino D, Iannuzzi L, Sonstegard TS, Van Tassell CP, Ventura M, Low WY, Williams JL, Bickhart DM, Liu GE.

Funct Integr Genomics. 2019 Feb 7. doi: 10.1007/s10142-019-00657-4. [Epub ahead of print]

PMID:
30734132
2.

Transcriptomics analysis of host liver and meta-transcriptome analysis of rumen epimural microbial community in young calves treated with artificial dosing of rumen content from adult donor cow.

Li W, Edwards A, Riehle C, Cox M, Raabis S, Skarlupka J, Steinberger A, Walling J, Bickhart D, Suen G.

Sci Rep. 2019 Jan 28;9(1):790. doi: 10.1038/s41598-018-37033-4.

3.

Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity.

Low WY, Tearle R, Bickhart DM, Rosen BD, Kingan SB, Swale T, Thibaud-Nissen F, Murphy TD, Young R, Lefevre L, Hume DA, Collins A, Ajmone-Marsan P, Smith TPL, Williams JL.

Nat Commun. 2019 Jan 16;10(1):260. doi: 10.1038/s41467-018-08260-0.

4.

De novo assembly of haplotype-resolved genomes with trio binning.

Koren S, Rhie A, Walenz BP, Dilthey AT, Bickhart DM, Kingan SB, Hiendleder S, Williams JL, Smith TPL, Phillippy AM.

Nat Biotechnol. 2018 Oct 22. doi: 10.1038/nbt.4277. [Epub ahead of print]

PMID:
30346939
5.

Correction to: Analysis of Population-Genetic Properties of Copy Number Variations.

Xu L, Yang L, Bickhart DM, Li J, Liu GE.

Methods Mol Biol. 2018;1833:E1. doi: 10.1007/978-1-4939-8666-8_17.

PMID:
30178308
6.

Effect of consuming endophyte-infected fescue seed on transcript abundance in the mammary gland of lactating and dry cows, as assessed by RNA sequencing.

Capuco AV, Bickhart D, Li C, Evock-Clover CM, Choudhary RK, Grossi P, Bertoni G, Trevisi E, Aiken GE, McLeod KR, Baldwin RL 6th.

J Dairy Sci. 2018 Nov;101(11):10478-10494. doi: 10.3168/jds.2018-14735. Epub 2018 Aug 23.

PMID:
30146289
7.

Misidentification of runs of homozygosity islands in cattle caused by interference with copy number variation or large intermarker distances.

Nandolo W, Utsunomiya YT, Mészáros G, Wurzinger M, Khayadzadeh N, Torrecilha RBP, Mulindwa HA, Gondwe TN, Waldmann P, Ferenčaković M, Garcia JF, Rosen BD, Bickhart D, van Tassell CP, Curik I, Sölkner J.

Genet Sel Evol. 2018 Aug 22;50(1):43. doi: 10.1186/s12711-018-0414-x.

8.

Analysis of Population-Genetic Properties of Copy Number Variations.

Xu L, Yang L, Bickhart DM, Li J, Liu GE.

Methods Mol Biol. 2018;1833:179-186. doi: 10.1007/978-1-4939-8666-8_14. Erratum in: Methods Mol Biol. 2018;1833:E1.

PMID:
30039373
9.

Use of RAPTR-SV to Identify SVs from Read Pairing and Split Read Signatures.

Bickhart DM.

Methods Mol Biol. 2018;1833:143-153. doi: 10.1007/978-1-4939-8666-8_11.

PMID:
30039370
10.

Statistical Detection of Genome Differences Based on CNV Segments.

Zhou Y, Bickhart DM, Liu GE.

Methods Mol Biol. 2018;1833:49-59. doi: 10.1007/978-1-4939-8666-8_3.

PMID:
30039362
11.

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

Weller JI, Bickhart DM, Wiggans GR, Tooker ME, O'Connell JR, Jiang J, Ron M, VanRaden PM.

J Dairy Sci. 2018 Oct;101(10):9089-9107. doi: 10.3168/jds.2018-14816. Epub 2018 Jul 19.

PMID:
30031583
12.

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

Choudhary S, Li W, Bickhart D, Verma R, Sethi RS, Mukhopadhyay CS, Choudhary RK.

J Anim Sci Technol. 2018 Jul 13;60:18. doi: 10.1186/s40781-018-0177-5. eCollection 2018.

13.

Genomic structural differences between cattle and River Buffalo identified through comparative genomic and transcriptomic analysis.

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

Data Brief. 2018 May 10;19:236-239. doi: 10.1016/j.dib.2018.05.015. eCollection 2018 Aug.

14.

Genomic predictions combining SNP markers and copy number variations in Nellore cattle.

Hay EHA, Utsunomiya YT, Xu L, Zhou Y, Neves HHR, Carvalheiro R, Bickhart DM, Ma L, Garcia JF, Liu GE.

BMC Genomics. 2018 Jun 5;19(1):441. doi: 10.1186/s12864-018-4787-6.

15.

Comparative whole genome DNA methylation profiling of cattle sperm and somatic tissues reveals striking hypomethylated patterns in sperm.

Zhou Y, Connor EE, Bickhart DM, Li C, Baldwin RL, Schroeder SG, Rosen BD, Yang L, Van Tassell CP, Liu GE.

Gigascience. 2018 May 1;7(5). doi: 10.1093/gigascience/giy039.

16.

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.

17.

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]

PMID:
29501677
18.

A PLAG1 mutation contributed to stature recovery in modern cattle.

Utsunomiya YT, Milanesi M, Utsunomiya ATH, Torrecilha RBP, Kim ES, Costa MS, Aguiar TS, Schroeder S, do Carmo AS, Carvalheiro R, Neves HHR, Padula RCM, Sussai TS, Zavarez LB, Cipriano RS, Caminhas MMT, Hambrecht G, Colli L, Eufemi E, Ajmone-Marsan P, Cesana D, Sannazaro M, Buora M, Morgante M, Liu G, Bickhart D, Van Tassell CP, Sölkner J, Sonstegard TS, Garcia JF.

Sci Rep. 2017 Dec 7;7(1):17140. doi: 10.1038/s41598-017-17127-1.

19.

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

Bickhart DM, Weimer PJ.

J Dairy Sci. 2018 Aug;101(8):7680-7689. doi: 10.3168/jds.2017-13328. Epub 2017 Nov 6. Review.

PMID:
29102146
20.

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

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

Immunogenetics. 2018 May;70(5):317-326. doi: 10.1007/s00251-017-1033-3. Epub 2017 Oct 23.

21.

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.

22.

Scaffolding of long read assemblies using long range contact information.

Ghurye J, Pop M, Koren S, Bickhart D, Chin CS.

BMC Genomics. 2017 Jul 12;18(1):527. doi: 10.1186/s12864-017-3879-z.

23.

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.

24.

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.

25.

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.

26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

PMID:
27085415
33.

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.

34.

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.

35.

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.

36.

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.

37.

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
38.

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.

39.

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.

40.

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

Shin JH, Xu L, Li RW, Gao Y, Bickhart D, Liu GE, Baldwin R, Li CJ.

Anim Genet. 2014 Aug;45 Suppl 1:40-50. doi: 10.1111/age.12147. Epub 2014 Jul 2.

PMID:
24990294
41.

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
42.

Bovine exome sequence analysis and targeted SNP genotyping of recessive fertility defects BH1, HH2, and HH3 reveal a putative causative mutation in SMC2 for HH3.

McClure MC, Bickhart D, Null D, Vanraden P, Xu L, Wiggans G, Liu G, Schroeder S, Glasscock J, Armstrong J, Cole JB, Van Tassell CP, Sonstegard TS.

PLoS One. 2014 Mar 25;9(3):e92769. doi: 10.1371/journal.pone.0092769. eCollection 2014.

43.

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.

44.

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.

45.

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.

46.

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.

47.

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.

48.

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.

PMID:
23932129
49.

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.

50.

Fine mapping for Weaver syndrome in Brown Swiss cattle and the identification of 41 concordant mutations across NRCAM, PNPLA8 and CTTNBP2.

McClure M, Kim E, Bickhart D, Null D, Cooper T, Cole J, Wiggans G, Ajmone-Marsan P, Colli L, Santus E, Liu GE, Schroeder S, Matukumalli L, Van Tassell C, Sonstegard T.

PLoS One. 2013;8(3):e59251. doi: 10.1371/journal.pone.0059251. Epub 2013 Mar 20.

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