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Across-Experiment Transcriptomics of Sheep Rumen Identifies Expression of Lipid/Oxo-Acid Metabolism and Muscle Cell Junction Genes Associated With Variation in Methane-Related Phenotypes.

Xiang R, McNally J, Bond J, Tucker D, Cameron M, Donaldson AJ, Austin KL, Rowe S, Jonker A, Pinares-Patino CS, McEwan JC, Vercoe PE, Oddy VH, Dalrymple BP.

Front Genet. 2018 Aug 20;9:330. doi: 10.3389/fgene.2018.00330. eCollection 2018.


Mammalian genomic regulatory regions predicted by utilizing human genomics, transcriptomics, and epigenetics data.

Nguyen QH, Tellam RL, Naval-Sanchez M, Porto-Neto LR, Barendse W, Reverter A, Hayes B, Kijas J, Dalrymple BP.

Gigascience. 2018 Mar 1;7(3):1-17. doi: 10.1093/gigascience/gix136.


A comparison of transcriptomic patterns measured in the skin of Chinese fine and coarse wool sheep breeds.

Zhang L, Sun F, Jin H, Dalrymple BP, Cao Y, Wei T, Vuocolo T, Zhang M, Piao Q, Ingham AB.

Sci Rep. 2017 Oct 30;7(1):14301. doi: 10.1038/s41598-017-14772-4.


TRIENNIAL GROWTH AND DEVELOPMENT SYMPOSIUM: Intramuscular fat deposition in ruminants and pigs: A transcriptomics perspective.

Dalrymple BP, Guo B.

J Anim Sci. 2017 May;95(5):2272-2283. doi: 10.2527/jas.2016.1112.


Gene network analysis identifies rumen epithelial cell proliferation, differentiation and metabolic pathways perturbed by diet and correlated with methane production.

Xiang R, McNally J, Rowe S, Jonker A, Pinares-Patino CS, Oddy VH, Vercoe PE, McEwan JC, Dalrymple BP.

Sci Rep. 2016 Dec 14;6:39022. doi: 10.1038/srep39022.


Epithelial, metabolic and innate immunity transcriptomic signatures differentiating the rumen from other sheep and mammalian gastrointestinal tract tissues.

Xiang R, Oddy VH, Archibald AL, Vercoe PE, Dalrymple BP.

PeerJ. 2016 Mar 8;4:e1762. doi: 10.7717/peerj.1762. eCollection 2016.


Beta-globin gene evolution in the ruminants: evidence for an ancient origin of sheep haplotype B.

Jiang Y, Wang X, Kijas JW, Dalrymple BP.

Anim Genet. 2015 Oct;46(5):506-14. doi: 10.1111/age.12318. Epub 2015 Jun 19.


Transcriptome analysis of cattle muscle identifies potential markers for skeletal muscle growth rate and major cell types.

Guo B, Greenwood PL, Cafe LM, Zhou G, Zhang W, Dalrymple BP.

BMC Genomics. 2015 Mar 13;16:177. doi: 10.1186/s12864-015-1403-x.


Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project.

Andersson L, Archibald AL, Bottema CD, Brauning R, Burgess SC, Burt DW, Casas E, Cheng HH, Clarke L, Couldrey C, Dalrymple BP, Elsik CG, Foissac S, Giuffra E, Groenen MA, Hayes BJ, Huang LS, Khatib H, Kijas JW, Kim H, Lunney JK, McCarthy FM, McEwan JC, Moore S, Nanduri B, Notredame C, Palti Y, Plastow GS, Reecy JM, Rohrer GA, Sarropoulou E, Schmidt CJ, Silverstein J, Tellam RL, Tixier-Boichard M, Tosser-Klopp G, Tuggle CK, Vilkki J, White SN, Zhao S, Zhou H; FAANG Consortium.

Genome Biol. 2015 Mar 25;16:57. doi: 10.1186/s13059-015-0622-4.


Longitudinal muscle gene expression patterns associated with differential intramuscular fat in cattle.

Hudson NJ, Reverter A, Greenwood PL, Guo B, Cafe LM, Dalrymple BP.

Animal. 2015 Apr;9(4):650-9. doi: 10.1017/S1751731114002754. Epub 2014 Nov 13.


A gene expression estimator of intramuscular fat percentage for use in both cattle and sheep.

Guo B, Kongsuwan K, Greenwood PL, Zhou G, Zhang W, Dalrymple BP.

J Anim Sci Biotechnol. 2014 Jun 16;5(1):35. doi: 10.1186/2049-1891-5-35. 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.


RNF14 is a regulator of mitochondrial and immune function in muscle.

Ingham AB, Osborne SA, Menzies M, Briscoe S, Chen W, Kongsuwan K, Reverter A, Jeanes A, Dalrymple BP, Wijffels G, Seymour R, Hudson NJ.

BMC Syst Biol. 2014 Jan 29;8:10. doi: 10.1186/1752-0509-8-10.


A divergent Artiodactyl MYADM-like repeat is associated with erythrocyte traits and weight of lamb weaned in domestic sheep.

Gonzalez MV, Mousel MR, Herndon DR, Jiang Y, Dalrymple BP, Reynolds JO, Johnson WC, Herrmann-Hoesing LM, White SN.

PLoS One. 2013 Aug 30;8(8):e74700. doi: 10.1371/journal.pone.0074700. eCollection 2013.


Inferring the in vivo cellular program of developing bovine skeletal muscle from expression data.

Hudson NJ, Lyons RE, Reverter A, Greenwood PL, Dalrymple BP.

Gene Expr Patterns. 2013 Mar-Apr;13(3-4):109-25. doi: 10.1016/j.gep.2013.02.001. Epub 2013 Feb 16.


Gene expression phenotypes for lipid metabolism and intramuscular fat in skeletal muscle of cattle.

De Jager N, Hudson NJ, Reverter A, Barnard R, Cafe LM, Greenwood PL, Dalrymple BP.

J Anim Sci. 2013 Mar;91(3):1112-28. doi: 10.2527/jas.2012-5409. Epub 2013 Jan 7.


An Always Correlated gene expression landscape for ovine skeletal muscle, lessons learnt from comparison with an "equivalent" bovine landscape.

Sun W, Hudson NJ, Reverter A, Waardenberg AJ, Tellam RL, Vuocolo T, Byrne K, Dalrymple BP.

BMC Res Notes. 2012 Nov 13;5:632. doi: 10.1186/1756-0500-5-632.


Porcine tissue-specific regulatory networks derived from meta-analysis of the transcriptome.

Pérez-Montarelo D, Hudson NJ, Fernández AI, Ramayo-Caldas Y, Dalrymple BP, Reverter A.

PLoS One. 2012;7(9):e46159. doi: 10.1371/journal.pone.0046159. Epub 2012 Sep 26.


Beyond differential expression: the quest for causal mutations and effector molecules.

Hudson NJ, Dalrymple BP, Reverter A.

BMC Genomics. 2012 Jul 31;13:356.


The effect of combination treatment with trenbolone acetate and estradiol-17β on skeletal muscle expression and plasma concentrations of oxytocin in sheep.

Kongsuwan K, Knox MR, Allingham PG, Pearson R, Dalrymple BP.

Domest Anim Endocrinol. 2012 Jul;43(1):67-73. doi: 10.1016/j.domaniend.2012.02.004. Epub 2012 Mar 20.


Eukaryotic evolutionary transitions are associated with extreme codon bias in functionally-related proteins.

Hudson NJ, Gu Q, Nagaraj SH, Ding YS, Dalrymple BP, Reverter A.

PLoS One. 2011;6(9):e25457. doi: 10.1371/journal.pone.0025457. Epub 2011 Sep 23.


Phosphoinositide 3-kinase (PI3K(p110alpha)) directly regulates key components of the Z-disc and cardiac structure.

Waardenberg AJ, Bernardo BC, Ng DC, Shepherd PR, Cemerlang N, Sbroggiò M, Wells CA, Dalrymple BP, Brancaccio M, Lin RC, McMullen JR.

J Biol Chem. 2011 Sep 2;286(35):30837-46. doi: 10.1074/jbc.M111.271684. Epub 2011 Jul 11.


Binding inhibitors of the bacterial sliding clamp by design.

Wijffels G, Johnson WM, Oakley AJ, Turner K, Epa VC, Briscoe SJ, Polley M, Liepa AJ, Hofmann A, Buchardt J, Christensen C, Prosselkov P, Dalrymple BP, Alewood PF, Jennings PA, Dixon NE, Winkler DA.

J Med Chem. 2011 Jul 14;54(13):4831-8. doi: 10.1021/jm2004333. Epub 2011 Jun 7.


Chronic exposure to anabolic steroids induces the muscle expression of oxytocin and a more than fiftyfold increase in circulating oxytocin in cattle.

De Jager N, Hudson NJ, Reverter A, Wang YH, Nagaraj SH, Cafe LM, Greenwood PL, Barnard RT, Kongsuwan KP, Dalrymple BP.

Physiol Genomics. 2011 May 13;43(9):467-78. doi: 10.1152/physiolgenomics.00226.2010. Epub 2011 Feb 15.


Genome-wide patterns of promoter sharing and co-expression in bovine skeletal muscle.

Gu Q, Nagaraj SH, Hudson NJ, Dalrymple BP, Reverter A.

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


Quality control of the sheep bacterial artificial chromosome library, CHORI-243.

Ratnakumar A, Kirkness EF, Dalrymple BP.

BMC Res Notes. 2010 Dec 13;3:334. doi: 10.1186/1756-0500-3-334.


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.


Using paired-end sequences to optimise parameters for alignment of sequence reads against related genomes.

Ratnakumar A, McWilliam S, Barris W, Dalrymple BP.

BMC Genomics. 2010 Aug 3;11:458. doi: 10.1186/1471-2164-11-458.


Regulatory impact factors: unraveling the transcriptional regulation of complex traits from expression data.

Reverter A, Hudson NJ, Nagaraj SH, Pérez-Enciso M, Dalrymple BP.

Bioinformatics. 2010 Apr 1;26(7):896-904. doi: 10.1093/bioinformatics/btq051. Epub 2010 Feb 9.


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.


Inferring the transcriptional landscape of bovine skeletal muscle by integrating co-expression networks.

Hudson NJ, Reverter A, Wang Y, Greenwood PL, Dalrymple BP.

PLoS One. 2009 Oct 1;4(10):e7249. doi: 10.1371/journal.pone.0007249.


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.


A differential wiring analysis of expression data correctly identifies the gene containing the causal mutation.

Hudson NJ, Reverter A, Dalrymple BP.

PLoS Comput Biol. 2009 May;5(5):e1000382. doi: 10.1371/journal.pcbi.1000382. Epub 2009 May 1.


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.


Analysis of the complement and molecular evolution of tRNA genes in cow.

Tang DT, Glazov EA, McWilliam SM, Barris WC, Dalrymple BP.

BMC Genomics. 2009 Apr 24;10:188. doi: 10.1186/1471-2164-10-188.


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 multiway analysis for identifying high integrity bovine BACs.

Ratnakumar A, Barris W, McWilliam S, Brauning R, McEwan JC, Snelling WM, Dalrymple BP.

BMC Genomics. 2009 Jan 23;10:46. doi: 10.1186/1471-2164-10-46.


Using a 3D virtual muscle model to link gene expression changes during myogenesis to protein spatial location in muscle.

Waardenberg AJ, Reverter A, Wells CA, Dalrymple BP.

BMC Syst Biol. 2008 Oct 22;2:88. doi: 10.1186/1752-0509-2-88.


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 microRNA catalog of the developing chicken embryo identified by a deep sequencing approach.

Glazov EA, Cottee PA, Barris WC, Moore RJ, Dalrymple BP, Tizard ML.

Genome Res. 2008 Jun;18(6):957-64. doi: 10.1101/gr.074740.107. Epub 2008 May 9.


Origin, evolution, and biological role of miRNA cluster in DLK-DIO3 genomic region in placental mammals.

Glazov EA, McWilliam S, Barris WC, Dalrymple BP.

Mol Biol Evol. 2008 May;25(5):939-48. doi: 10.1093/molbev/msn045. Epub 2008 Feb 14.


A physical map of the bovine genome.

Snelling WM, Chiu R, Schein JE, Hobbs M, Abbey CA, Adelson DL, Aerts J, Bennett GL, Bosdet IE, Boussaha M, Brauning R, Caetano AR, Costa MM, Crawford AM, Dalrymple BP, Eggen A, Everts-van der Wind A, Floriot S, Gautier M, Gill CA, Green RD, Holt R, Jann O, Jones SJ, Kappes SM, Keele JW, de Jong PJ, Larkin DM, Lewin HA, McEwan JC, McKay S, Marra MA, Mathewson CA, Matukumalli LK, Moore SS, Murdoch B, Nicholas FW, Osoegawa K, Roy A, Salih H, Schibler L, Schnabel RD, Silveri L, Skow LC, Smith TP, Sonstegard TS, Taylor JF, Tellam R, Van Tassell CP, Williams JL, Womack JE, Wye NH, Yang G, Zhao S; International Bovine BAC Mapping Consortium.

Genome Biol. 2007;8(8):R165.


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.


A gene coexpression network for bovine skeletal muscle inferred from microarray data.

Reverter A, Hudson NJ, Wang Y, Tan SH, Barris W, Byrne KA, McWilliam SM, Bottema CD, Kister A, Greenwood PL, Harper GS, Lehnert SA, Dalrymple BP.

Physiol Genomics. 2006 Dec 13;28(1):76-83. Epub 2006 Sep 19.


Identification of putative DnaN-binding motifs in plasmid replication initiation proteins.

Dalrymple BP, Kongsuwan K, Wijffels G.

Plasmid. 2007 Jan;57(1):82-8. Epub 2006 Sep 12.


Simultaneous identification of differential gene expression and connectivity in inflammation, adipogenesis and cancer.

Reverter A, Ingham A, Lehnert SA, Tan SH, Wang Y, Ratnakumar A, Dalrymple BP.

Bioinformatics. 2006 Oct 1;22(19):2396-404. Epub 2006 Jul 24.


The transcriptional landscape of the mammalian genome.

Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, Forrest AR, Zavolan M, Davis MJ, Wilming LG, Aidinis V, Allen JE, Ambesi-Impiombato A, Apweiler R, Aturaliya RN, Bailey TL, Bansal M, Baxter L, Beisel KW, Bersano T, Bono H, Chalk AM, Chiu KP, Choudhary V, Christoffels A, Clutterbuck DR, Crowe ML, Dalla E, Dalrymple BP, de Bono B, Della Gatta G, di Bernardo D, Down T, Engstrom P, Fagiolini M, Faulkner G, Fletcher CF, Fukushima T, Furuno M, Futaki S, Gariboldi M, Georgii-Hemming P, Gingeras TR, Gojobori T, Green RE, Gustincich S, Harbers M, Hayashi Y, Hensch TK, Hirokawa N, Hill D, Huminiecki L, Iacono M, Ikeo K, Iwama A, Ishikawa T, Jakt M, Kanapin A, Katoh M, Kawasawa Y, Kelso J, Kitamura H, Kitano H, Kollias G, Krishnan SP, Kruger A, Kummerfeld SK, Kurochkin IV, Lareau LF, Lazarevic D, Lipovich L, Liu J, Liuni S, McWilliam S, Madan Babu M, Madera M, Marchionni L, Matsuda H, Matsuzawa S, Miki H, Mignone F, Miyake S, Morris K, Mottagui-Tabar S, Mulder N, Nakano N, Nakauchi H, Ng P, Nilsson R, Nishiguchi S, Nishikawa S, Nori F, Ohara O, Okazaki Y, Orlando V, Pang KC, Pavan WJ, Pavesi G, Pesole G, Petrovsky N, Piazza S, Reed J, Reid JF, Ring BZ, Ringwald M, Rost B, Ruan Y, Salzberg SL, Sandelin A, Schneider C, Schönbach C, Sekiguchi K, Semple CA, Seno S, Sessa L, Sheng Y, Shibata Y, Shimada H, Shimada K, Silva D, Sinclair B, Sperling S, Stupka E, Sugiura K, Sultana R, Takenaka Y, Taki K, Tammoja K, Tan SL, Tang S, Taylor MS, Tegner J, Teichmann SA, Ueda HR, van Nimwegen E, Verardo R, Wei CL, Yagi K, Yamanishi H, Zabarovsky E, Zhu S, Zimmer A, Hide W, Bult C, Grimmond SM, Teasdale RD, Liu ET, Brusic V, Quackenbush J, Wahlestedt C, Mattick JS, Hume DA, Kai C, Sasaki D, Tomaru Y, Fukuda S, Kanamori-Katayama M, Suzuki M, Aoki J, Arakawa T, Iida J, Imamura K, Itoh M, Kato T, Kawaji H, Kawagashira N, Kawashima T, Kojima M, Kondo S, Konno H, Nakano K, Ninomiya N, Nishio T, Okada M, Plessy C, Shibata K, Shiraki T, Suzuki S, Tagami M, Waki K, Watahiki A, Okamura-Oho Y, Suzuki H, Kawai J, Hayashizaki Y; FANTOM Consortium; RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group).

Science. 2005 Sep 2;309(5740):1559-63. Erratum in: Science. 2006 Mar 24;311(5768):1713.


Characterisation and application of a bovine U6 promoter for expression of short hairpin RNAs.

Lambeth LS, Moore RJ, Muralitharan M, Dalrymple BP, McWilliam S, Doran TJ.

BMC Biotechnol. 2005 May 11;5:13.


Validation of alternative methods of data normalization in gene co-expression studies.

Reverter A, Barris W, McWilliam S, Byrne KA, Wang YH, Tan SH, Hudson N, Dalrymple BP.

Bioinformatics. 2005 Apr 1;21(7):1112-20. Epub 2004 Nov 25.


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