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What's in your next-generation sequence data? An exploration of unmapped DNA and RNA sequence reads from the bovine reference individual.

Whitacre LK, Tizioto PC, Kim J, Sonstegard TS, Schroeder SG, Alexander LJ, Medrano JF, Schnabel RD, Taylor JF, Decker JE.

BMC Genomics. 2015 Dec 29;16(1):1114. doi: 10.1186/s12864-015-2313-7.


Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle.

Park SD, Magee DA, McGettigan PA, Teasdale MD, Edwards CJ, Lohan AJ, Murphy A, Braud M, Donoghue MT, Liu Y, Chamberlain AT, Rue-Albrecht K, Schroeder S, Spillane C, Tai S, Bradley DG, Sonstegard TS, Loftus BJ, MacHugh DE.

Genome Biol. 2015 Oct 26;16:234. doi: 10.1186/s13059-015-0790-2.


MicroRNA expression profiles of bovine milk exosomes in response to Staphylococcus aureus infection.

Sun J, Aswath K, Schroeder SG, Lippolis JD, Reinhardt TA, Sonstegard TS.

BMC Genomics. 2015 Oct 16;16(1):806. doi: 10.1186/s12864-015-2044-9.


Genome-Wide Scan for Visceral Leishmaniasis in Mixed-Breed Dogs Identifies Candidate Genes Involved in T Helper Cells and Macrophage Signaling.

Utsunomiya YT, Ribeiro ÉS, Quintal AP, Sangalli JR, Gazola VR, Paula HB, Trinconi CM, Lima VM, Perri SH, Taylor JF, Schnabel RD, Sonstegard TS, Garcia JF, Nunes CM.

PLoS One. 2015 Sep 8;10(9):e0136749. doi: 10.1371/journal.pone.0136749. eCollection 2015.


The Relationship between Runs of Homozygosity and Inbreeding in Jersey Cattle under Selection.

Kim ES, Sonstegard TS, Van Tassell CP, Wiggans G, Rothschild MF.

PLoS One. 2015 Jul 8;10(7):e0129967. doi: 10.1371/journal.pone.0129967. eCollection 2015.


Evidence of Bos javanicus x Bos indicus hybridization and major QTLs for birth weight in Indonesian Peranakan Ongole cattle.

Hartati H, Utsunomiya YT, Sonstegard TS, Garcia JF, Jakaria J, Muladno M.

BMC Genet. 2015 Jul 4;16:75. doi: 10.1186/s12863-015-0229-5.


Low levels of taurine introgression in the current Brazilian Nelore and Gir indicine cattle populations.

O'Brien AM, Höller D, Boison SA, Milanesi M, Bomba L, Utsunomiya YT, Carvalheiro R, Neves HH, da Silva MV, VanTassell CP, Sonstegard TS, Mészáros G, Ajmone-Marsan P, Garcia F, Sölkner J.

Genet Sel Evol. 2015 Apr 17;47:31. doi: 10.1186/s12711-015-0109-5.


Recent artificial selection in U.S. Jersey cattle impacts autozygosity levels of specific genomic regions.

Kim ES, Sonstegard TS, Rothschild MF.

BMC Genomics. 2015 Apr 16;16:302. doi: 10.1186/s12864-015-1500-x.


Detection of quantitative trait loci for mineral content of Nelore longissimus dorsi muscle.

Tizioto PC, Taylor JF, Decker JE, Gromboni CF, Mudadu MA, Schnabel RD, Coutinho LL, Mourão GB, Oliveira PS, Souza MM, Reecy JM, Nassu RT, Bressani FA, Tholon P, Sonstegard TS, Alencar MM, Tullio RR, Nogueira AR, Regitano LC.

Genet Sel Evol. 2015 Mar 11;47:15. doi: 10.1186/s12711-014-0083-3.


Identification of novel loci associated with gastrointestinal parasite resistance in a Red Maasai x Dorper backcross population.

Benavides MV, Sonstegard TS, Kemp S, Mugambi JM, Gibson JP, Baker RL, Hanotte O, Marshall K, Van Tassell C.

PLoS One. 2015 Apr 13;10(4):e0122797. doi: 10.1371/journal.pone.0122797. eCollection 2015.


Genome-wide scan of gastrointestinal nematode resistance in closed Angus population selected for minimized influence of MHC.

Kim ES, Sonstegard TS, da Silva MV, Gasbarre LC, Van Tassell CP.

PLoS One. 2015 Mar 24;10(3):e0119380. doi: 10.1371/journal.pone.0119380. eCollection 2015.


Genomic data as the "hitchhiker's guide" to cattle adaptation: tracking the milestones of past selection in the bovine genome.

Utsunomiya YT, Pérez O'Brien AM, Sonstegard TS, Sölkner J, Garcia JF.

Front Genet. 2015 Feb 10;6:36. doi: 10.3389/fgene.2015.00036. eCollection 2015. Review.


Altered microRNA expression in bovine skeletal muscle with age.

Sun J, Sonstegard TS, Li C, Huang Y, Li Z, Lan X, Zhang C, Lei C, Zhao X, Chen H.

Anim Genet. 2015 Jun;46(3):227-38. doi: 10.1111/age.12272. Epub 2015 Feb 20.


Assessment of autozygosity in Nellore cows (Bos indicus) through high-density SNP genotypes.

Zavarez LB, Utsunomiya YT, Carmo AS, Neves HH, Carvalheiro R, Ferenčaković M, Pérez O'Brien AM, Curik I, Cole JB, Van Tassell CP, da Silva MV, Sonstegard TS, Sölkner J, Garcia JF.

Front Genet. 2015 Jan 29;6:5. doi: 10.3389/fgene.2015.00005. eCollection 2015.


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 candidate regions for selective sweeps revealed through massive parallel sequencing of DNA across ten turkey populations.

Aslam ML, Bastiaansen JW, Megens HJ, Crooijmans RP, Nasreen F, Blomberg le A, Van Tassell CP, Sonstegard TS, Schroeder SG, Groenen MA, Long JA.

BMC Genet. 2014 Nov 25;15:117. doi: 10.1186/s12863-014-0117-4.


The genetic architecture of climatic adaptation of tropical cattle.

Porto-Neto LR, Reverter A, Prayaga KC, Chan EK, Johnston DJ, Hawken RJ, Fordyce G, Garcia JF, Sonstegard TS, Bolormaa S, Goddard ME, Burrow HM, Henshall JM, Lehnert SA, Barendse W.

PLoS One. 2014 Nov 24;9(11):e113284. doi: 10.1371/journal.pone.0113284. eCollection 2014.


Identification of genomic regions associated with feed efficiency in Nelore cattle.

de Oliveira PS, Cesar AS, do Nascimento ML, Chaves AS, Tizioto PC, Tullio RR, Lanna DP, Rosa AN, Sonstegard TS, Mourao GB, Reecy JM, Garrick DJ, Mudadu MA, Coutinho LL, Regitano LC.

BMC Genet. 2014 Sep 26;15:100. doi: 10.1186/s12863-014-0100-0.


A genome-wide scan for selection signatures in Nellore cattle.

Somavilla AL, Sonstegard TS, Higa RH, Rosa AN, Siqueira F, Silva LO, Torres Júnior RA, Coutinho LL, Mudadu MA, Alencar MM, Regitano LC.

Anim Genet. 2014 Dec;45(6):771-81. doi: 10.1111/age.12210. Epub 2014 Sep 3.

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