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Items: 10

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1.

The genomic signature of dog domestication reveals adaptation to a starch-rich diet.

Axelsson E, Ratnakumar A, Arendt ML, Maqbool K, Webster MT, Perloski M, Liberg O, Arnemo JM, Hedhammar A, Lindblad-Toh K.

Nature. 2013 Mar 21;495(7441):360-4. doi: 10.1038/nature11837. Epub 2013 Jan 23.

PMID:
23354050
2.

Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping.

Vaysse A, Ratnakumar A, Derrien T, Axelsson E, Rosengren Pielberg G, Sigurdsson S, Fall T, Seppälä EH, Hansen MS, Lawley CT, Karlsson EK; LUPA Consortium, Bannasch D, Vilà C, Lohi H, Galibert F, Fredholm M, Häggström J, Hedhammar A, André C, Lindblad-Toh K, Hitte C, Webster MT.

PLoS Genet. 2011 Oct;7(10):e1002316. doi: 10.1371/journal.pgen.1002316. Epub 2011 Oct 13.

3.

Death of PRDM9 coincides with stabilization of the recombination landscape in the dog genome.

Axelsson E, Webster MT, Ratnakumar A; LUPA Consortium, Ponting CP, Lindblad-Toh K.

Genome Res. 2012 Jan;22(1):51-63. doi: 10.1101/gr.124123.111. Epub 2011 Oct 17. Erratum in: Genome Res. 2012 Apr;22(4):810.

4.

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.

5.

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.

6.

Detecting positive selection within genomes: the problem of biased gene conversion.

Ratnakumar A, Mousset S, Glémin S, Berglund J, Galtier N, Duret L, Webster MT.

Philos Trans R Soc Lond B Biol Sci. 2010 Aug 27;365(1552):2571-80. doi: 10.1098/rstb.2010.0007.

7.

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.

8.

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.

9.

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.

10.

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.

PMID:
16864591

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