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Genome to Phenome: Improving Animal Health, Production, and Well-Being - A New USDA Blueprint for Animal Genome Research 2018-2027.

Rexroad C, Vallet J, Matukumalli LK, Reecy J, Bickhart D, Blackburn H, Boggess M, Cheng H, Clutter A, Cockett N, Ernst C, Fulton JE, Liu J, Lunney J, Neibergs H, Purcell C, Smith TPL, Sonstegard T, Taylor J, Telugu B, Eenennaam AV, Tassell CPV, Wells K.

Front Genet. 2019 May 16;10:327. doi: 10.3389/fgene.2019.00327. eCollection 2019.


Identification of genes directly responding to DLK1 signaling in Callipyge sheep.

Yu H, Waddell JN, Kuang S, Tellam RL, Cockett NE, Bidwell CA.

BMC Genomics. 2018 Apr 24;19(1):283. doi: 10.1186/s12864-018-4682-1.


Sheep genome functional annotation reveals proximal regulatory elements contributed to the evolution of modern breeds.

Naval-Sanchez M, Nguyen Q, McWilliam S, Porto-Neto LR, Tellam R, Vuocolo T, Reverter A, Perez-Enciso M, Brauning R, Clarke S, McCulloch A, Zamani W, Naderi S, Rezaei HR, Pompanon F, Taberlet P, Worley KC, Gibbs RA, Muzny DM, Jhangiani SN, Cockett N, Daetwyler H, Kijas J.

Nat Commun. 2018 Feb 28;9(1):859. doi: 10.1038/s41467-017-02809-1.


EXTENSION EDUCATION SYMPOSIUM: Getting the most out of your extension appointment and still having a life.

Powers W, Cockett N, Lardy G.

J Anim Sci. 2017 Apr;95(4):1827-1835. doi: 10.2527/jas.2016.1266.


Copy number variants in the sheep genome detected using multiple approaches.

Jenkins GM, Goddard ME, Black MA, Brauning R, Auvray B, Dodds KG, Kijas JW, Cockett N, McEwan JC.

BMC Genomics. 2016 Jun 8;17:441. doi: 10.1186/s12864-016-2754-7.


Genome-wide association reveals the locus responsible for four-horned ruminant.

Kijas JW, Hadfield T, Naval Sanchez M, Cockett N.

Anim Genet. 2016 Apr;47(2):258-62. doi: 10.1111/age.12409. Epub 2016 Jan 14.


Ectopic Expression of Retrotransposon-Derived PEG11/RTL1 Contributes to the Callipyge Muscular Hypertrophy.

Xu X, Ectors F, Davis EE, Pirottin D, Cheng H, Farnir F, Hadfield T, Cockett N, Charlier C, Georges M, Takeda H.

PLoS One. 2015 Oct 16;10(10):e0140594. doi: 10.1371/journal.pone.0140594. eCollection 2015.


Experimental evaluation does not reveal a direct effect of microRNA from the callipyge locus on DLK1 expression.

Cheng H, Xu X, Hadfield T, Cockett N, Charlier C, Georges M, Takeda H.

BMC Genomics. 2014 Oct 30;15:944. doi: 10.1186/1471-2164-15-944.


New insights into polar overdominance in callipyge sheep.

Bidwell CA, Waddell JN, Taxis TM, Yu H, Tellam RL, Neary MK, Cockett NE.

Anim Genet. 2014 Aug;45 Suppl 1:51-61. doi: 10.1111/age.12132. Epub 2014 Jul 2.


Impacts of the Callipyge mutation on ovine plasma metabolites and muscle fibre type.

Li J, Greenwood PL, Cockett NE, Hadfield TS, Vuocolo T, Byrne K, White JD, Tellam RL, Schirra HJ.

PLoS One. 2014 Jun 17;9(6):e99726. doi: 10.1371/journal.pone.0099726. eCollection 2014.


The sheep genome illuminates biology of the rumen and lipid metabolism.

Jiang Y, Xie M, Chen W, Talbot R, Maddox JF, Faraut T, Wu C, Muzny DM, Li Y, Zhang W, Stanton JA, Brauning R, Barris WC, Hourlier T, Aken BL, Searle SMJ, Adelson DL, Bian C, Cam GR, Chen Y, Cheng S, DeSilva U, Dixen K, Dong Y, Fan G, Franklin IR, Fu S, Guan R, Highland MA, Holder ME, Huang G, Ingham AB, Jhangiani SN, Kalra D, Kovar CL, Lee SL, Liu W, Liu X, Lu C, Lv T, Mathew T, McWilliam S, Menzies M, Pan S, Robelin D, Servin B, Townley D, Wang W, Wei B, White SN, Yang X, Ye C, Yue Y, Zeng P, Zhou Q, Hansen JB, Kristensen K, Gibbs RA, Flicek P, Warkup CC, Jones HE, Oddy VH, Nicholas FW, McEwan JC, Kijas J, Wang J, Worley KC, Archibald AL, Cockett N, Xu X, Wang W, Dalrymple BP.

Science. 2014 Jun 6;344(6188):1168-1173. doi: 10.1126/science.1252806.


Genomic architecture of histone 3 lysine 27 trimethylation during late ovine skeletal muscle development.

Byrne K, McWilliam S, Vuocolo T, Gondro C, Cockett NE, Tellam RL.

Anim Genet. 2014 Jun;45(3):427-38. doi: 10.1111/age.12145. Epub 2014 Mar 27.


Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus).

Dong Y, Xie M, Jiang Y, Xiao N, Du X, Zhang W, Tosser-Klopp G, Wang J, Yang S, Liang J, Chen W, Chen J, Zeng P, Hou Y, Bian C, Pan S, Li Y, Liu X, Wang W, Servin B, Sayre B, Zhu B, Sweeney D, Moore R, Nie W, Shen Y, Zhao R, Zhang G, Li J, Faraut T, Womack J, Zhang Y, Kijas J, Cockett N, Xu X, Zhao S, Wang J, Wang W.

Nat Biotechnol. 2013 Feb;31(2):135-41. doi: 10.1038/nbt.2478. Epub 2012 Dec 23.


Genes contributing to genetic variation of muscling in sheep.

Tellam RL, Cockett NE, Vuocolo T, Bidwell CA.

Front Genet. 2012 Aug 29;3:164. doi: 10.3389/fgene.2012.00164. eCollection 2012.


Tracking the emergence of a new breed using 49,034 SNP in sheep.

Kijas JW, Miller JE, Hadfield T, McCulloch R, Garcia-Gamez E, Porto Neto LR, Cockett N.

PLoS One. 2012;7(7):e41508. doi: 10.1371/journal.pone.0041508. Epub 2012 Jul 27.


Assessing the effect of the CLPG mutation on the microRNA catalog of skeletal muscle using high-throughput sequencing.

Caiment F, Charlier C, Hadfield T, Cockett N, Georges M, Baurain D.

Genome Res. 2010 Dec;20(12):1651-62. doi: 10.1101/gr.108787.110. Epub 2010 Oct 13.


The sheep genome reference sequence: a work in progress.

International Sheep Genomics Consortium, Archibald AL, Cockett NE, Dalrymple BP, Faraut T, Kijas JW, Maddox JF, McEwan JC, Hutton Oddy V, Raadsma HW, Wade C, Wang J, Wang W, Xun X.

Anim Genet. 2010 Oct;41(5):449-53. doi: 10.1111/j.1365-2052.2010.02100.x. Review.


A gene network switch enhances the oxidative capacity of ovine skeletal muscle during late fetal development.

Byrne K, Vuocolo T, Gondro C, White JD, Cockett NE, Hadfield T, Bidwell CA, Waddell JN, Tellam RL.

BMC Genomics. 2010 Jun 15;11:378. doi: 10.1186/1471-2164-11-378.


The imprinted retrotransposon-like gene PEG11 (RTL1) is expressed as a full-length protein in skeletal muscle from Callipyge sheep.

Byrne K, Colgrave ML, Vuocolo T, Pearson R, Bidwell CA, Cockett NE, Lynn DJ, Fleming-Waddell JN, Tellam RL.

PLoS One. 2010 Jan 8;5(1):e8638. doi: 10.1371/journal.pone.0008638.


Molecular cytogenetics and gene mapping in sheep (Ovis aries, 2n = 54).

Goldammer T, Di Meo GP, Lühken G, Drögemüller C, Wu CH, Kijas J, Dalrymple BP, Nicholas FW, Maddox JF, Iannuzzi L, Cockett NE.

Cytogenet Genome Res. 2009;126(1-2):63-76. doi: 10.1159/000245907. Epub 2009 Dec 9.


Effect of DLK1 and RTL1 but not MEG3 or MEG8 on muscle gene expression in Callipyge lambs.

Fleming-Waddell JN, Olbricht GR, Taxis TM, White JD, Vuocolo T, Craig BA, Tellam RL, Neary MK, Cockett NE, Bidwell CA.

PLoS One. 2009 Oct 9;4(10):e7399. doi: 10.1371/journal.pone.0007399.


A high-resolution radiation hybrid map of sheep chromosome X and comparison with human and cattle.

Goldammer T, Brunner RM, Rebl A, Wu CH, Nomura K, Hadfield T, Gill C, Dalrymple BP, Womack JE, Cockett NE.

Cytogenet Genome Res. 2009;125(1):40-5. doi: 10.1159/000207520. Epub 2009 Jul 14.


Cytogenetic anchoring of radiation hybrid and virtual maps of sheep chromosome X and comparison of X chromosomes in sheep, cattle, and human.

Goldammer T, Brunner RM, Rebl A, Wu CH, Nomura K, Hadfield T, Maddox JF, Cockett NE.

Chromosome Res. 2009;17(4):497-506. doi: 10.1007/s10577-009-9047-9. Epub 2009 Jul 3.


Comparative genomics of Toll-like receptor signalling in five species.

Jann OC, King A, Corrales NL, Anderson SI, Jensen K, Ait-Ali T, Tang H, Wu C, Cockett NE, Archibald AL, Glass EJ.

BMC Genomics. 2009 May 11;10:216. doi: 10.1186/1471-2164-10-216.


A radiation hybrid comparative map of ovine chromosome 1 aligned to the virtual sheep genome.

Wu CH, Jin W, Nomura K, Goldammer T, Hadfield T, Dalrymple BP, McWilliam S, Maddox JF, Cockett NE.

Anim Genet. 2009 Aug;40(4):435-55. doi: 10.1111/j.1365-2052.2009.01857.x. Epub 2009 Apr 7.


A genome wide survey of SNP variation reveals the genetic structure of sheep breeds.

Kijas JW, Townley D, Dalrymple BP, Heaton MP, Maddox JF, McGrath A, Wilson P, Ingersoll RG, McCulloch R, McWilliam S, Tang D, McEwan J, Cockett N, Oddy VH, Nicholas FW, Raadsma H; International Sheep Genomics Consortium.

PLoS One. 2009;4(3):e4668. doi: 10.1371/journal.pone.0004668. Epub 2009 Mar 3.


A map of the class III region of the sheep major histocompatibilty complex.

Qin J, Mamotte C, Cockett NE, Wetherall JD, Groth DM.

BMC Genomics. 2008 Sep 11;9:409. doi: 10.1186/1471-2164-9-409.


The sheep genome.

Cockett NE.

Genome Dyn. 2006;2:79-85. doi: 10.1159/000095096. Review.


A high-resolution comparative radiation hybrid map of ovine chromosomal regions that are homologous to human chromosome 6 (HSA6).

Wu CH, Nomura K, Goldammer T, Hadfield T, Dalrymple BP, McWilliam S, Maddox JF, Womack JE, Cockett NE.

Anim Genet. 2008 Oct;39(5):459-67. doi: 10.1111/j.1365-2052.2008.01751.x. Epub 2008 Jun 28.


A comparative radiation hybrid map of sheep chromosome 10.

Drögemüller M, Tetens J, Dalrymple B, Goldammer T, Wu CH, Cockett NE, Leeb T, Drögemüller C.

Cytogenet Genome Res. 2008;121(1):35-40. doi: 10.1159/000124379. Epub 2008 May 7.


Myoblasts isolated from hypertrophy-responsive callipyge muscles show altered growth rates and increased resistance to serum deprivation-induced apoptosis.

Lavulo LT, Uaesoontrachoon K, Mirams M, White JD, Cockett NE, Mackie EJ, Pagel CN.

Cells Tissues Organs. 2008;187(2):141-51. Epub 2007 Oct 23.


Analysis of the callipyge phenotype through skeletal muscle development; association of Dlk1 with muscle precursor cells.

White JD, Vuocolo T, McDonagh M, Grounds MD, Harper GS, Cockett NE, Tellam R.

Differentiation. 2008 Mar;76(3):283-98. Epub 2007 Aug 14.


Using comparative genomics to reorder the human genome sequence into a virtual sheep genome.

Dalrymple BP, Kirkness EF, Nefedov M, McWilliam S, Ratnakumar A, Barris W, Zhao S, Shetty J, Maddox JF, O'Grady M, Nicholas F, Crawford AM, Smith T, de Jong PJ, McEwan J, Oddy VH, Cockett NE; International Sheep Genomics Consortium.

Genome Biol. 2007;8(7):R152.


An ovine whole-genome radiation hybrid panel used to construct an RH map of ovine chromosome 9.

Wu CH, Nomura K, Goldammer T, Hadfield T, Womack JE, Cockett NE.

Anim Genet. 2007 Oct;38(5):534-6. Epub 2007 Jul 6. No abstract available.


An advanced sheep (Ovis aries, 2n = 54) cytogenetic map and assignment of 88 new autosomal loci by fluorescence in situ hybridization and R-banding.

Di Meo GP, Perucatti A, Floriot S, Hayes H, Schibler L, Rullo R, Incarnato D, Ferretti L, Cockett N, Cribiu E, Williams JL, Eggen A, Iannuzzi L.

Anim Genet. 2007 Jun;38(3):233-40. Epub 2007 Apr 13.


The influence of breeding intensity on above- and below-average sexual performance rams in single- and multiple-sire breeding environments.

Stellflug JN, Cockett NE, Lewis GS.

Anim Reprod Sci. 2008 Mar 3;104(2-4):248-56. Epub 2007 Feb 27.


A radiation hybrid map of sheep chromosome 23 based on ovine BAC-end sequences.

Tetens J, Goldammer T, Maddox JF, Cockett NE, Leeb T, Drögemüller C.

Anim Genet. 2007 Apr;38(2):132-40. Epub 2007 Feb 27.


Analysis of gene expression during the onset of muscle hypertrophy in callipyge lambs.

Fleming-Waddell JN, Wilson LM, Olbricht GR, Vuocolo T, Byrne K, Craig BA, Tellam RL, Cockett NE, Bidwell CA.

Anim Genet. 2007 Feb;38(1):28-36.


Postnatal changes in the expression of genes located in the callipyge region in sheep skeletal muscle.

Perkins AC, Kramer LN, Spurlock DM, Hadfield TS, Cockett NE, Bidwell CA.

Anim Genet. 2006 Dec;37(6):535-42.


Identification of a gene network contributing to hypertrophy in callipyge skeletal muscle.

Vuocolo T, Byrne K, White J, McWilliam S, Reverter A, Cockett NE, Tellam RL.

Physiol Genomics. 2007 Feb 12;28(3):253-72. Epub 2006 Oct 31.


Determination of sheep prion gene polymorphisms from paraffin-embedded tissue.

Kunkle RA, Miller JM, Alt DP, Cutlip RC, Cockett NE, Wang S, Richt JA, Thomsen BV, Hall SM.

J Vet Diagn Invest. 2006 Sep;18(5):443-7. Erratum in: J Vet Diagn Invest. 2007 Jan;19(1):133.


The callipyge mutation enhances bidirectional long-range DLK1-GTL2 intergenic transcription in cis.

Takeda H, Caiment F, Smit M, Hiard S, Tordoir X, Cockett N, Georges M, Charlier C.

Proc Natl Acad Sci U S A. 2006 May 23;103(21):8119-24. Epub 2006 May 11.


A single-base change in the tyrosine kinase II domain of ovine FGFR3 causes hereditary chondrodysplasia in sheep.

Beever JE, Smit MA, Meyers SN, Hadfield TS, Bottema C, Albretsen J, Cockett NE.

Anim Genet. 2006 Feb;37(1):66-71.


BEGAIN: a novel imprinted gene that generates paternally expressed transcripts in a tissue- and promoter-specific manner in sheep.

Smit MA, Tordoir X, Gyapay G, Cockett NE, Georges M, Charlier C.

Mamm Genome. 2005 Oct;16(10):801-14. Epub 2005 Oct 29.


Toward molecular understanding of polar overdominance at the ovine callipyge locus.

Georges M, Charlier C, Smit M, Davis E, Shay T, Tordoir X, Takeda H, Caiment F, Cockett N.

Cold Spring Harb Symp Quant Biol. 2004;69:477-83. Review. No abstract available.


Investigation of the Booroola (FecB) and Inverdale (FecX(I)) mutations in 21 prolific breeds and strains of sheep sampled in 13 countries.

Davis GH, Balakrishnan L, Ross IK, Wilson T, Galloway SM, Lumsden BM, Hanrahan JP, Mullen M, Mao XZ, Wang GL, Zhao ZS, Zeng YQ, Robinson JJ, Mavrogenis AP, Papachristoforou C, Peter C, Baumung R, Cardyn P, Boujenane I, Cockett NE, Eythorsdottir E, Arranz JJ, Notter DR.

Anim Reprod Sci. 2006 Mar;92(1-2):87-96. Epub 2005 Jun 27.


RNAi-mediated allelic trans-interaction at the imprinted Rtl1/Peg11 locus.

Davis E, Caiment F, Tordoir X, Cavaillé J, Ferguson-Smith A, Cockett N, Georges M, Charlier C.

Curr Biol. 2005 Apr 26;15(8):743-9. Erratum in: Curr Biol. 2005 May 10;15(9):884.


The callipyge mutation and other genes that affect muscle hypertrophy in sheep.

Cockett NE, Smit MA, Bidwell CA, Segers K, Hadfield TL, Snowder GD, Georges M, Charlier C.

Genet Sel Evol. 2005;37 Suppl 1:S65-81. Review.

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