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Items: 1 to 20 of 47

1.

The Dfam database of repetitive DNA families.

Hubley R, Finn RD, Clements J, Eddy SR, Jones TA, Bao W, Smit AF, Wheeler TJ.

Nucleic Acids Res. 2016 Jan 4;44(D1):D81-9. doi: 10.1093/nar/gkv1272. Epub 2015 Nov 26.

2.

Ancient Origin of the U2 Small Nuclear RNA Gene-Targeting Non-LTR Retrotransposons Utopia.

Kojima KK, Jurka J.

PLoS One. 2015 Nov 10;10(11):e0140084. doi: 10.1371/journal.pone.0140084. eCollection 2015.

3.

A New Class of SINEs with snRNA Gene-Derived Heads.

Kojima KK.

Genome Biol Evol. 2015 May 27;7(6):1702-12. doi: 10.1093/gbe/evv100.

4.

A superfamily of DNA transposons targeting multicopy small RNA genes.

Kojima KK, Jurka J.

PLoS One. 2013 Jul 9;8(7):e68260. doi: 10.1371/journal.pone.0068260. Print 2013.

5.

Dfam: a database of repetitive DNA based on profile hidden Markov models.

Wheeler TJ, Clements J, Eddy SR, Hubley R, Jones TA, Jurka J, Smit AF, Finn RD.

Nucleic Acids Res. 2013 Jan;41(Database issue):D70-82. doi: 10.1093/nar/gks1265. Epub 2012 Nov 30.

6.

Analyses of pig genomes provide insight into porcine demography and evolution.

Groenen MA, Archibald AL, Uenishi H, Tuggle CK, Takeuchi Y, Rothschild MF, Rogel-Gaillard C, Park C, Milan D, Megens HJ, Li S, Larkin DM, Kim H, Frantz LA, Caccamo M, Ahn H, Aken BL, Anselmo A, Anthon C, Auvil L, Badaoui B, Beattie CW, Bendixen C, Berman D, Blecha F, Blomberg J, Bolund L, Bosse M, Botti S, Bujie Z, Bystrom M, Capitanu B, Carvalho-Silva D, Chardon P, Chen C, Cheng R, Choi SH, Chow W, Clark RC, Clee C, Crooijmans RP, Dawson HD, Dehais P, De Sapio F, Dibbits B, Drou N, Du ZQ, Eversole K, Fadista J, Fairley S, Faraut T, Faulkner GJ, Fowler KE, Fredholm M, Fritz E, Gilbert JG, Giuffra E, Gorodkin J, Griffin DK, Harrow JL, Hayward A, Howe K, Hu ZL, Humphray SJ, Hunt T, Hornshøj H, Jeon JT, Jern P, Jones M, Jurka J, Kanamori H, Kapetanovic R, Kim J, Kim JH, Kim KW, Kim TH, Larson G, Lee K, Lee KT, Leggett R, Lewin HA, Li Y, Liu W, Loveland JE, Lu Y, Lunney JK, Ma J, Madsen O, Mann K, Matthews L, McLaren S, Morozumi T, Murtaugh MP, Narayan J, Nguyen DT, Ni P, Oh SJ, Onteru S, Panitz F, Park EW, Park HS, Pascal G, Paudel Y, Perez-Enciso M, Ramirez-Gonzalez R, Reecy JM, Rodriguez-Zas S, Rohrer GA, Rund L, Sang Y, Schachtschneider K, Schraiber JG, Schwartz J, Scobie L, Scott C, Searle S, Servin B, Southey BR, Sperber G, Stadler P, Sweedler JV, Tafer H, Thomsen B, Wali R, Wang J, Wang J, White S, Xu X, Yerle M, Zhang G, Zhang J, Zhang J, Zhao S, Rogers J, Churcher C, Schook LB.

Nature. 2012 Nov 15;491(7424):393-8. doi: 10.1038/nature11622.

7.

Distinct groups of repetitive families preserved in mammals correspond to different periods of regulatory innovations in vertebrates.

Jurka J, Bao W, Kojima KK, Kohany O, Yurka MG.

Biol Direct. 2012 Oct 25;7:36. doi: 10.1186/1745-6150-7-36.

8.

Families of transposable elements, population structure and the origin of species.

Jurka J, Bao W, Kojima KK.

Biol Direct. 2011 Sep 19;6:44. doi: 10.1186/1745-6150-6-44.

9.

Modeling the asymmetric evolution of a mouse and rat-specific microRNA gene cluster intron 10 of the Sfmbt2 gene.

Lehnert S, Kapitonov V, Thilakarathne PJ, Schuit FC.

BMC Genomics. 2011 May 23;12:257. doi: 10.1186/1471-2164-12-257.

10.

Recent expansion of a new Ingi-related clade of Vingi non-LTR retrotransposons in hedgehogs.

Kojima KK, Kapitonov VV, Jurka J.

Mol Biol Evol. 2011 Jan;28(1):17-20. doi: 10.1093/molbev/msq220. Epub 2010 Aug 17.

11.

Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri.

Prochnik SE, Umen J, Nedelcu AM, Hallmann A, Miller SM, Nishii I, Ferris P, Kuo A, Mitros T, Fritz-Laylin LK, Hellsten U, Chapman J, Simakov O, Rensing SA, Terry A, Pangilinan J, Kapitonov V, Jurka J, Salamov A, Shapiro H, Schmutz J, Grimwood J, Lindquist E, Lucas S, Grigoriev IV, Schmitt R, Kirk D, Rokhsar DS.

Science. 2010 Jul 9;329(5988):223-6. doi: 10.1126/science.1188800.

12.

Origin and evolution of LINE-1 derived "half-L1" retrotransposons (HAL1).

Bao W, Jurka J.

Gene. 2010 Oct 1;465(1-2):9-16. doi: 10.1016/j.gene.2010.06.005. Epub 2010 Jun 21.

13.

"Genomic Impact of Eukaryotic Transposable Elements", Pacific Grove, California, February 6-10, 2009.

Jurka J.

Gene. 2009 Dec 15;448(2):103. doi: 10.1016/j.gene.2009.08.001. Epub 2009 Aug 12. No abstract available.

14.

Simple and fast classification of non-LTR retrotransposons based on phylogeny of their RT domain protein sequences.

Kapitonov VV, Tempel S, Jurka J.

Gene. 2009 Dec 15;448(2):207-13. doi: 10.1016/j.gene.2009.07.019. Epub 2009 Aug 3.

15.

New superfamilies of eukaryotic DNA transposons and their internal divisions.

Bao W, Jurka MG, Kapitonov VV, Jurka J.

Mol Biol Evol. 2009 May;26(5):983-93. doi: 10.1093/molbev/msp013. Epub 2009 Jan 27.

16.

VisualRepbase: an interface for the study of occurrences of transposable element families.

Tempel S, Jurka M, Jurka J.

BMC Bioinformatics. 2008 Aug 18;9:345. doi: 10.1186/1471-2105-9-345.

17.

A universal classification of eukaryotic transposable elements implemented in Repbase.

Kapitonov VV, Jurka J.

Nat Rev Genet. 2008 May;9(5):411-2; author reply 414. doi: 10.1038/nrg2165-c1. No abstract available.

PMID:
18421312
18.

Conserved eukaryotic transposable elements and the evolution of gene regulation.

Jurka J.

Cell Mol Life Sci. 2008 Jan;65(2):201-4. Review.

PMID:
18030428
19.

Helitrons on a roll: eukaryotic rolling-circle transposons.

Kapitonov VV, Jurka J.

Trends Genet. 2007 Oct;23(10):521-9. Epub 2007 Sep 11. Review.

PMID:
17850916
20.

Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization.

Putnam NH, Srivastava M, Hellsten U, Dirks B, Chapman J, Salamov A, Terry A, Shapiro H, Lindquist E, Kapitonov VV, Jurka J, Genikhovich G, Grigoriev IV, Lucas SM, Steele RE, Finnerty JR, Technau U, Martindale MQ, Rokhsar DS.

Science. 2007 Jul 6;317(5834):86-94.

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