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Items: 28

1.

SNP discovery in nonmodel organisms: strand bias and base-substitution errors reduce conversion rates.

Gonçalves da Silva A, Barendse W, Kijas JW, Barris WC, McWilliam S, Bunch RJ, McCullough R, Harrison B, Hoelzel AR, England PR.

Mol Ecol Resour. 2015 Jul;15(4):723-36. doi: 10.1111/1755-0998.12343. Epub 2014 Nov 23.

PMID:
25388640
2.

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.

3.

Genome-wide association studies of female reproduction in tropically adapted beef cattle.

Hawken RJ, Zhang YD, Fortes MR, Collis E, Barris WC, Corbet NJ, Williams PJ, Fordyce G, Holroyd RG, Walkley JR, Barendse W, Johnston DJ, Prayaga KC, Tier B, Reverter A, Lehnert SA.

J Anim Sci. 2012 May;90(5):1398-410. doi: 10.2527/jas.2011-4410. Epub 2011 Nov 18.

PMID:
22100599
4.

Analysis of copy number variants in the cattle genome.

Kijas JW, Barendse W, Barris W, Harrison B, McCulloch R, McWilliam S, Whan V.

Gene. 2011 Aug 15;482(1-2):73-7. doi: 10.1016/j.gene.2011.04.011. Epub 2011 May 18.

PMID:
21620936
5.

A single nucleotide polymorphism-derived regulatory gene network underlying puberty in 2 tropical breeds of beef cattle.

Fortes MR, Reverter A, Nagaraj SH, Zhang Y, Jonsson NN, Barris W, Lehnert S, Boe-Hansen GB, Hawken RJ.

J Anim Sci. 2011 Jun;89(6):1669-83. doi: 10.2527/jas.2010-3681. Epub 2011 Feb 25.

PMID:
21357453
6.

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.

7.

Association weight matrix for the genetic dissection of puberty in beef cattle.

Fortes MR, Reverter A, Zhang Y, Collis E, Nagaraj SH, Jonsson NN, Prayaga KC, Barris W, Hawken RJ.

Proc Natl Acad Sci U S A. 2010 Aug 3;107(31):13642-7. doi: 10.1073/pnas.1002044107. Epub 2010 Jul 19.

8.

Transcription profiling provides insights into gene pathways involved in horn and scurs development in cattle.

Mariasegaram M, Reverter A, Barris W, Lehnert SA, Dalrymple B, Prayaga K.

BMC Genomics. 2010 Jun 11;11:370. doi: 10.1186/1471-2164-11-370.

9.

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.

10.

The bovine lactation genome: insights into the evolution of mammalian milk.

Lemay DG, Lynn DJ, Martin WF, Neville MC, Casey TM, Rincon G, Kriventseva EV, Barris WC, Hinrichs AS, Molenaar AJ, Pollard KS, Maqbool NJ, Singh K, Murney R, Zdobnov EM, Tellam RL, Medrano JF, German JB, Rijnkels M.

Genome Biol. 2009;10(4):R43. doi: 10.1186/gb-2009-10-4-r43. Epub 2009 Apr 24.

11.

The genome sequence of taurine cattle: a window to ruminant biology and evolution.

Bovine Genome Sequencing and Analysis Consortium, Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny DM, Weinstock GM, Adelson DL, Eichler EE, Elnitski L, Guigó R, Hamernik DL, Kappes SM, Lewin HA, Lynn DJ, Nicholas FW, Reymond A, Rijnkels M, Skow LC, Zdobnov EM, Schook L, Womack J, Alioto T, Antonarakis SE, Astashyn A, Chapple CE, Chen HC, Chrast J, Câmara F, Ermolaeva O, Henrichsen CN, Hlavina W, Kapustin Y, Kiryutin B, Kitts P, Kokocinski F, Landrum M, Maglott D, Pruitt K, Sapojnikov V, Searle SM, Solovyev V, Souvorov A, Ucla C, Wyss C, Anzola JM, Gerlach D, Elhaik E, Graur D, Reese JT, Edgar RC, McEwan JC, Payne GM, Raison JM, Junier T, Kriventseva EV, Eyras E, Plass M, Donthu R, Larkin DM, Reecy J, Yang MQ, Chen L, Cheng Z, Chitko-McKown CG, Liu GE, Matukumalli LK, Song J, Zhu B, Bradley DG, Brinkman FS, Lau LP, Whiteside MD, Walker A, Wheeler TT, Casey T, German JB, Lemay DG, Maqbool NJ, Molenaar AJ, Seo S, Stothard P, Baldwin CL, Baxter R, Brinkmeyer-Langford CL, Brown WC, Childers CP, Connelley T, Ellis SA, Fritz K, Glass EJ, Herzig CT, Iivanainen A, Lahmers KK, Bennett AK, Dickens CM, Gilbert JG, Hagen DE, Salih H, Aerts J, Caetano AR, Dalrymple B, Garcia JF, Gill CA, Hiendleder SG, Memili E, Spurlock D, Williams JL, Alexander L, Brownstein MJ, Guan L, Holt RA, Jones SJ, Marra MA, Moore R, Moore SS, Roberts A, Taniguchi M, Waterman RC, Chacko J, Chandrabose MM, Cree A, Dao MD, Dinh HH, Gabisi RA, Hines S, Hume J, Jhangiani SN, Joshi V, Kovar CL, Lewis LR, Liu YS, Lopez J, Morgan MB, Nguyen NB, Okwuonu GO, Ruiz SJ, Santibanez J, Wright RA, Buhay C, Ding Y, Dugan-Rocha S, Herdandez J, Holder M, Sabo A, Egan A, Goodell J, Wilczek-Boney K, Fowler GR, Hitchens ME, Lozado RJ, Moen C, Steffen D, Warren JT, Zhang J, Chiu R, Schein JE, Durbin KJ, Havlak P, Jiang H, Liu Y, Qin X, Ren Y, Shen Y, Song H, Bell SN, Davis C, Johnson AJ, Lee S, Nazareth LV, Patel BM, Pu LL, Vattathil S, Williams RL Jr, Curry S, Hamilton C, Sodergren E, Wheeler DA, Barris W, Bennett GL, Eggen A, Green RD, Harhay GP, Hobbs M, Jann O, Keele JW, Kent MP, Lien S, McKay SD, McWilliam S, Ratnakumar A, Schnabel RD, Smith T, Snelling WM, Sonstegard TS, Stone RT, Sugimoto Y, Takasuga A, Taylor JF, Van Tassell CP, Macneil MD, Abatepaulo AR, Abbey CA, Ahola V, Almeida IG, Amadio AF, Anatriello E, Bahadue SM, Biase FH, Boldt CR, Carroll JA, Carvalho WA, Cervelatti EP, Chacko E, Chapin JE, Cheng Y, Choi J, Colley AJ, de Campos TA, De Donato M, Santos IK, de Oliveira CJ, Deobald H, Devinoy E, Donohue KE, Dovc P, Eberlein A, Fitzsimmons CJ, Franzin AM, Garcia GR, Genini S, Gladney CJ, Grant JR, Greaser ML, Green JA, Hadsell DL, Hakimov HA, Halgren R, Harrow JL, Hart EA, Hastings N, Hernandez M, Hu ZL, Ingham A, Iso-Touru T, Jamis C, Jensen K, Kapetis D, Kerr T, Khalil SS, Khatib H, Kolbehdari D, Kumar CG, Kumar D, Leach R, Lee JC, Li C, Logan KM, Malinverni R, Marques E, Martin WF, Martins NF, Maruyama SR, Mazza R, McLean KL, Medrano JF, Moreno BT, Moré DD, Muntean CT, Nandakumar HP, Nogueira MF, Olsaker I, Pant SD, Panzitta F, Pastor RC, Poli MA, Poslusny N, Rachagani S, Ranganathan S, Razpet A, Riggs PK, Rincon G, Rodriguez-Osorio N, Rodriguez-Zas SL, Romero NE, Rosenwald A, Sando L, Schmutz SM, Shen L, Sherman L, Southey BR, Lutzow YS, Sweedler JV, Tammen I, Telugu BP, Urbanski JM, Utsunomiya YT, Verschoor CP, Waardenberg AJ, Wang Z, Ward R, Weikard R, Welsh TH Jr, White SN, Wilming LG, Wunderlich KR, Yang J, Zhao FQ.

Science. 2009 Apr 24;324(5926):522-8. doi: 10.1126/science.1169588.

12.

Duplication and divergence: the evolution of nematode globins.

Hunt PW, McNally J, Barris W, Blaxter ML.

J Nematol. 2009 Mar;41(1):35-51.

13.

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.

14.

Predicting genetic merit for mastitis and fertility in dairy cattle using genome wide selection and high density SNP screens.

Raadsma HW, Moser G, Crump RE, Khatkar MS, Zenger KR, Cavanagh JAL, Hawken RJ, Hobbs M, Barris W, Solkner J, Nicholas FW, Tier B.

Dev Biol (Basel). 2008;132:219-223. doi: 10.1159/000317163.

PMID:
18817305
15.

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.

16.

Extent of genome-wide linkage disequilibrium in Australian Holstein-Friesian cattle based on a high-density SNP panel.

Khatkar MS, Nicholas FW, Collins AR, Zenger KR, Cavanagh JA, Barris W, Schnabel RD, Taylor JF, Raadsma HW.

BMC Genomics. 2008 Apr 24;9:187. doi: 10.1186/1471-2164-9-187.

17.

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.

PMID:
18281269
18.

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.

19.

A validated whole-genome association study of efficient food conversion in cattle.

Barendse W, Reverter A, Bunch RJ, Harrison BE, Barris W, Thomas MB.

Genetics. 2007 Jul;176(3):1893-905. Epub 2007 May 16.

20.

A primary assembly of a bovine haplotype block map based on a 15,036-single-nucleotide polymorphism panel genotyped in holstein-friesian cattle.

Khatkar MS, Zenger KR, Hobbs M, Hawken RJ, Cavanagh JA, Barris W, McClintock AE, McClintock S, Thomson PC, Tier B, Nicholas FW, Raadsma HW.

Genetics. 2007 Jun;176(2):763-72. Epub 2007 Apr 15.

21.

Skeletal muscle extracellular matrix remodelling after aestivation in the green striped burrowing frog, Cyclorana alboguttata.

Hudson NJ, Harper GS, Allingham PG, Franklin CE, Barris W, Lehnert SA.

Comp Biochem Physiol A Mol Integr Physiol. 2007 Mar;146(3):440-5. Epub 2006 Dec 16.

PMID:
17258486
22.

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.

PMID:
16985009
23.

A first-generation metric linkage disequilibrium map of bovine chromosome 6.

Khatkar MS, Collins A, Cavanagh JA, Hawken RJ, Hobbs M, Zenger KR, Barris W, McClintock AE, Thomson PC, Nicholas FW, Raadsma HW.

Genetics. 2006 Sep;174(1):79-85. Epub 2006 Jul 2.

24.

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.

PMID:
15564293
25.

An interactive bovine in silico SNP database (IBISS).

Hawken RJ, Barris WC, McWilliam SM, Dalrymple BP.

Mamm Genome. 2004 Oct;15(10):819-27.

PMID:
15520884
26.

A rapid method for computationally inferring transcriptome coverage and microarray sensitivity.

Reverter A, McWilliam SM, Barris W, Dalrymple BP.

Bioinformatics. 2005 Jan 1;21(1):80-9. Epub 2004 Aug 12.

PMID:
15308544
27.

Gene expression profiling of the bovine gastrointestinal tract.

Hansen C, Fu A, Meng Y, Okine E, Hawken R, Barris W, Li C, Moore SS.

Genome. 2004 Aug;47(4):639-49.

PMID:
15284868
28.

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