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Results: 1 to 20 of 23

1.

Convergent evolution of the genomes of marine mammals.

Foote AD, Liu Y, Thomas GW, Vinař T, Alföldi J, Deng J, Dugan S, van Elk CE, Hunter ME, Joshi V, Khan Z, Kovar C, Lee SL, Lindblad-Toh K, Mancia A, Nielsen R, Qin X, Qu J, Raney BJ, Vijay N, Wolf JB, Hahn MW, Muzny DM, Worley KC, Gilbert MT, Gibbs RA.

Nat Genet. 2015 Mar;47(3):272-5. doi: 10.1038/ng.3198. Epub 2015 Jan 26.

PMID:
25621460
2.

Fast computation of a string duplication history under no-breakpoint-reuse.

Brejová B, Kravec M, Landau GM, Vinař T.

Philos Trans A Math Phys Eng Sci. 2014 Apr 21;372(2016):20130133. doi: 10.1098/rsta.2013.0133. Print 2014 May 28.

PMID:
24751867
3.

Massive programmed translational jumping in mitochondria.

Lang BF, Jakubkova M, Hegedusova E, Daoud R, Forget L, Brejova B, Vinar T, Kosa P, Fricova D, Nebohacova M, Griac P, Tomaska L, Burger G, Nosek J.

Proc Natl Acad Sci U S A. 2014 Apr 22;111(16):5926-31. doi: 10.1073/pnas.1322190111. Epub 2014 Apr 7.

4.

Probabilistic approaches to alignment with tandem repeats.

Nánási M, Vinař T, Brejová B.

Algorithms Mol Biol. 2014 Mar 1;9(1):3. doi: 10.1186/1748-7188-9-3.

5.

Evolutionary genetics and implications of small size and twinning in callitrichine primates.

Harris RA, Tardif SD, Vinar T, Wildman DE, Rutherford JN, Rogers J, Worley KC, Aagaard KM.

Proc Natl Acad Sci U S A. 2014 Jan 28;111(4):1467-72. doi: 10.1073/pnas.1316037111. Epub 2013 Dec 30.

6.

Population genomic analysis reveals a rich speciation and demographic history of orang-utans (Pongo pygmaeus and Pongo abelii).

Ma X, Kelley JL, Eilertson K, Musharoff S, Degenhardt JD, Martins AL, Vinar T, Kosiol C, Siepel A, Gutenkunst RN, Bustamante CD.

PLoS One. 2013 Oct 23;8(10):e77175. doi: 10.1371/journal.pone.0077175. eCollection 2013.

7.

The genome of the hydatid tapeworm Echinococcus granulosus.

Zheng H, Zhang W, Zhang L, Zhang Z, Li J, Lu G, Zhu Y, Wang Y, Huang Y, Liu J, Kang H, Chen J, Wang L, Chen A, Yu S, Gao Z, Jin L, Gu W, Wang Z, Zhao L, Shi B, Wen H, Lin R, Jones MK, Brejova B, Vinar T, Zhao G, McManus DP, Chen Z, Zhou Y, Wang S.

Nat Genet. 2013 Oct;45(10):1168-75. doi: 10.1038/ng.2757. Epub 2013 Sep 8.

PMID:
24013640
8.

The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage.

Shaffer HB, Minx P, Warren DE, Shedlock AM, Thomson RC, Valenzuela N, Abramyan J, Amemiya CT, Badenhorst D, Biggar KK, Borchert GM, Botka CW, Bowden RM, Braun EL, Bronikowski AM, Bruneau BG, Buck LT, Capel B, Castoe TA, Czerwinski M, Delehaunty KD, Edwards SV, Fronick CC, Fujita MK, Fulton L, Graves TA, Green RE, Haerty W, Hariharan R, Hernandez O, Hillier LW, Holloway AK, Janes D, Janzen FJ, Kandoth C, Kong L, de Koning AP, Li Y, Literman R, McGaugh SE, Mork L, O'Laughlin M, Paitz RT, Pollock DD, Ponting CP, Radhakrishnan S, Raney BJ, Richman JM, St John J, Schwartz T, Sethuraman A, Spinks PQ, Storey KB, Thane N, Vinar T, Zimmerman LM, Warren WC, Mardis ER, Wilson RK.

Genome Biol. 2013 Mar 28;14(3):R28. doi: 10.1186/gb-2013-14-3-r28.

9.

Sequencing the genome of Marssonina brunnea reveals fungus-poplar co-evolution.

Zhu S, Cao YZ, Jiang C, Tan BY, Wang Z, Feng S, Zhang L, Su XH, Brejova B, Vinar T, Xu M, Wang MX, Zhang SG, Huang MR, Wu R, Zhou Y.

BMC Genomics. 2012 Aug 9;13:382. doi: 10.1186/1471-2164-13-382.

10.

Discovery of RNA motifs using a computational pipeline that allows insertions in paired regions and filtering of candidate sequences.

Jimenez RM, Rampášek L, Brejová B, Vinař T, Lupták A.

Methods Mol Biol. 2012;848:145-58. doi: 10.1007/978-1-61779-545-9_10.

PMID:
22315068
11.

Comparative and demographic analysis of orang-utan genomes.

Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P, Mitreva M, Cook L, Delehaunty KD, Fronick C, Schmidt H, Fulton LA, Fulton RS, Nelson JO, Magrini V, Pohl C, Graves TA, Markovic C, Cree A, Dinh HH, Hume J, Kovar CL, Fowler GR, Lunter G, Meader S, Heger A, Ponting CP, Marques-Bonet T, Alkan C, Chen L, Cheng Z, Kidd JM, Eichler EE, White S, Searle S, Vilella AJ, Chen Y, Flicek P, Ma J, Raney B, Suh B, Burhans R, Herrero J, Haussler D, Faria R, Fernando O, Darré F, Farré D, Gazave E, Oliva M, Navarro A, Roberto R, Capozzi O, Archidiacono N, Della Valle G, Purgato S, Rocchi M, Konkel MK, Walker JA, Ullmer B, Batzer MA, Smit AF, Hubley R, Casola C, Schrider DR, Hahn MW, Quesada V, Puente XS, Ordoñez GR, López-Otín C, Vinar T, Brejova B, Ratan A, Harris RS, Miller W, Kosiol C, Lawson HA, Taliwal V, Martins AL, Siepel A, Roychoudhury A, Ma X, Degenhardt J, Bustamante CD, Gutenkunst RN, Mailund T, Dutheil JY, Hobolth A, Schierup MH, Ryder OA, Yoshinaga Y, de Jong PJ, Weinstock GM, Rogers J, Mardis ER, Gibbs RA, Wilson RK.

Nature. 2011 Jan 27;469(7331):529-33. doi: 10.1038/nature09687.

12.

Evolution of linear chromosomes and multipartite genomes in yeast mitochondria.

Valach M, Farkas Z, Fricova D, Kovac J, Brejova B, Vinar T, Pfeiffer I, Kucsera J, Tomaska L, Lang BF, Nosek J.

Nucleic Acids Res. 2011 May;39(10):4202-19. doi: 10.1093/nar/gkq1345. Epub 2011 Jan 25.

13.

Reconstructing histories of complex gene clusters on a phylogeny.

Vinar T, Brejová B, Song G, Siepel A.

J Comput Biol. 2010 Sep;17(9):1267-79. doi: 10.1089/cmb.2010.0090.

PMID:
20874408
14.

CAGE: Combinatorial Analysis of Gene-cluster Evolution.

Song G, Zhang L, Vinar T, Miller W.

J Comput Biol. 2010 Sep;17(9):1227-42. doi: 10.1089/cmb.2010.0094.

15.

Positive selection on apoptosis related genes.

da Fonseca RR, Kosiol C, Vinar T, Siepel A, Nielsen R.

FEBS Lett. 2010 Feb 5;584(3):469-76. doi: 10.1016/j.febslet.2009.12.022. Epub 2009 Dec 22. Review.

16.

The sequence and de novo assembly of the giant panda genome.

Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B, Bai Y, Zhang Z, Zhang Y, Wang W, Li J, Wei F, Li H, Jian M, Li J, Zhang Z, Nielsen R, Li D, Gu W, Yang Z, Xuan Z, Ryder OA, Leung FC, Zhou Y, Cao J, Sun X, Fu Y, Fang X, Guo X, Wang B, Hou R, Shen F, Mu B, Ni P, Lin R, Qian W, Wang G, Yu C, Nie W, Wang J, Wu Z, Liang H, Min J, Wu Q, Cheng S, Ruan J, Wang M, Shi Z, Wen M, Liu B, Ren X, Zheng H, Dong D, Cook K, Shan G, Zhang H, Kosiol C, Xie X, Lu Z, Zheng H, Li Y, Steiner CC, Lam TT, Lin S, Zhang Q, Li G, Tian J, Gong T, Liu H, Zhang D, Fang L, Ye C, Zhang J, Hu W, Xu A, Ren Y, Zhang G, Bruford MW, Li Q, Ma L, Guo Y, An N, Hu Y, Zheng Y, Shi Y, Li Z, Liu Q, Chen Y, Zhao J, Qu N, Zhao S, Tian F, Wang X, Wang H, Xu L, Liu X, Vinar T, Wang Y, Lam TW, Yiu SM, Liu S, Zhang H, Li D, Huang Y, Wang X, Yang G, Jiang Z, Wang J, Qin N, Li L, Li J, Bolund L, Kristiansen K, Wong GK, Olson M, Zhang X, Li S, Yang H, Wang J, Wang J.

Nature. 2010 Jan 21;463(7279):311-7. doi: 10.1038/nature08696. Epub 2009 Dec 13. Erratum in: Nature. 2010 Feb 25;463(7284):1106.

17.

Evolutionary history reconstruction for Mammalian complex gene clusters.

Zhang Y, Song G, Vinar T, Green ED, Siepel A, Miller W.

J Comput Biol. 2009 Aug;16(8):1051-70. doi: 10.1089/cmb.2009.0040.

18.

Finding genes in Schistosoma japonicum: annotating novel genomes with help of extrinsic evidence.

Brejová B, Vinar T, Chen Y, Wang S, Zhao G, Brown DG, Li M, Zhou Y.

Nucleic Acids Res. 2009 Apr;37(7):e52. doi: 10.1093/nar/gkp052. Epub 2009 Mar 5.

19.

Patterns of positive selection in six Mammalian genomes.

Kosiol C, Vinar T, da Fonseca RR, Hubisz MJ, Bustamante CD, Nielsen R, Siepel A.

PLoS Genet. 2008 Aug 1;4(8):e1000144. doi: 10.1371/journal.pgen.1000144.

20.

Homology search for genes.

Cui X, Vinar T, Brejová B, Shasha D, Li M.

Bioinformatics. 2007 Jul 1;23(13):i97-103.

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