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Items: 1 to 50 of 132

1.

A Helitron transposon reconstructed from bats reveals a novel mechanism of genome shuffling in eukaryotes.

Grabundzija I, Messing SA, Thomas J, Cosby RL, Bilic I, Miskey C, Gogol-Döring A, Kapitonov V, Diem T, Dalda A, Jurka J, Pritham EJ, Dyda F, Izsvák Z, Ivics Z.

Nat Commun. 2016 Mar 2;7:10716. doi: 10.1038/ncomms10716.

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.

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.

Green RE, Braun EL, Armstrong J, Earl D, Nguyen N, Hickey G, Vandewege MW, St John JA, Capella-Gutiérrez S, Castoe TA, Kern C, Fujita MK, Opazo JC, Jurka J, Kojima KK, Caballero J, Hubley RM, Smit AF, Platt RN, Lavoie CA, Ramakodi MP, Finger JW Jr, Suh A, Isberg SR, Miles L, Chong AY, Jaratlerdsiri W, Gongora J, Moran C, Iriarte A, McCormack J, Burgess SC, Edwards SV, Lyons E, Williams C, Breen M, Howard JT, Gresham CR, Peterson DG, Schmitz J, Pollock DD, Haussler D, Triplett EW, Zhang G, Irie N, Jarvis ED, Brochu CA, Schmidt CJ, McCarthy FM, Faircloth BC, Hoffmann FG, Glenn TC, Gabaldón T, Paten B, Ray DA.

Science. 2014 Dec 12;346(6215):1254449. doi: 10.1126/science.1254449. Epub 2014 Dec 11.

4.

Multiple lineages of ancient CR1 retroposons shaped the early genome evolution of amniotes.

Suh A, Churakov G, Ramakodi MP, Platt RN 2nd, Jurka J, Kojima KK, Caballero J, Smit AF, Vliet KA, Hoffmann FG, Brosius J, Green RE, Braun EL, Ray DA, Schmitz J.

Genome Biol Evol. 2014 Dec 11;7(1):205-17. doi: 10.1093/gbe/evu256.

5.

Evolution and gene capture in ancient endogenous retroviruses - insights from the crocodilian genomes.

Chong AY, Kojima KK, Jurka J, Ray DA, Smit AF, Isberg SR, Gongora J.

Retrovirology. 2014 Dec 12;11:71. doi: 10.1186/s12977-014-0071-2.

6.

The ctenophore genome and the evolutionary origins of neural systems.

Moroz LL, Kocot KM, Citarella MR, Dosung S, Norekian TP, Povolotskaya IS, Grigorenko AP, Dailey C, Berezikov E, Buckley KM, Ptitsyn A, Reshetov D, Mukherjee K, Moroz TP, Bobkova Y, Yu F, Kapitonov VV, Jurka J, Bobkov YV, Swore JJ, Girardo DO, Fodor A, Gusev F, Sanford R, Bruders R, Kittler E, Mills CE, Rast JP, Derelle R, Solovyev VV, Kondrashov FA, Swalla BJ, Sweedler JV, Rogaev EI, Halanych KM, Kohn AB.

Nature. 2014 Jun 5;510(7503):109-14. doi: 10.1038/nature13400. Epub 2014 May 21.

7.

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.

8.

Homologues of bacterial TnpB_IS605 are widespread in diverse eukaryotic transposable elements.

Bao W, Jurka J.

Mob DNA. 2013 Apr 1;4(1):12. doi: 10.1186/1759-8753-4-12.

9.

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.

10.

Genomic impact of eukaryotic transposable elements.

Arkhipova IR, Batzer MA, Brosius J, Feschotte C, Moran JV, Schmitz J, Jurka J.

Mob DNA. 2012 Nov 21;3(1):19. doi: 10.1186/1759-8753-3-19.

11.

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.

12.

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.

13.

Horizontal transfers of Mariner transposons between mammals and insects.

Oliveira SG, Bao W, Martins C, Jurka J.

Mob DNA. 2012 Sep 26;3(1):14. doi: 10.1186/1759-8753-3-14.

14.

Crypton transposons: identification of new diverse families and ancient domestication events.

Kojima KK, Jurka J.

Mob DNA. 2011 Oct 19;2(1):12. doi: 10.1186/1759-8753-2-12.

15.

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.

16.

Next generation sequencing provides rapid access to the genome of Puccinia striiformis f. sp. tritici, the causal agent of wheat stripe rust.

Cantu D, Govindarajulu M, Kozik A, Wang M, Chen X, Kojima KK, Jurka J, Michelmore RW, Dubcovsky J.

PLoS One. 2011;6(8):e24230. doi: 10.1371/journal.pone.0024230. Epub 2011 Aug 31.

17.

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.

18.

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.

19.

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.

20.

The genome of the Western clawed frog Xenopus tropicalis.

Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J, Kapitonov V, Ovcharenko I, Putnam NH, Shu S, Taher L, Blitz IL, Blumberg B, Dichmann DS, Dubchak I, Amaya E, Detter JC, Fletcher R, Gerhard DS, Goodstein D, Graves T, Grigoriev IV, Grimwood J, Kawashima T, Lindquist E, Lucas SM, Mead PE, Mitros T, Ogino H, Ohta Y, Poliakov AV, Pollet N, Robert J, Salamov A, Sater AK, Schmutz J, Terry A, Vize PD, Warren WC, Wells D, Wills A, Wilson RK, Zimmerman LB, Zorn AM, Grainger R, Grammer T, Khokha MK, Richardson PM, Rokhsar DS.

Science. 2010 Apr 30;328(5978):633-6. doi: 10.1126/science.1183670.

21.

Ginger DNA transposons in eukaryotes and their evolutionary relationships with long terminal repeat retrotransposons.

Bao W, Kapitonov VV, Jurka J.

Mob DNA. 2010 Jan 25;1(1):3. doi: 10.1186/1759-8753-1-3.

22.

Genome sequence, comparative analysis, and population genetics of the domestic horse.

Wade CM, Giulotto E, Sigurdsson S, Zoli M, Gnerre S, Imsland F, Lear TL, Adelson DL, Bailey E, Bellone RR, Blöcker H, Distl O, Edgar RC, Garber M, Leeb T, Mauceli E, MacLeod JN, Penedo MC, Raison JM, Sharpe T, Vogel J, Andersson L, Antczak DF, Biagi T, Binns MM, Chowdhary BP, Coleman SJ, Della Valle G, Fryc S, Guérin G, Hasegawa T, Hill EW, Jurka J, Kiialainen A, Lindgren G, Liu J, Magnani E, Mickelson JR, Murray J, Nergadze SG, Onofrio R, Pedroni S, Piras MF, Raudsepp T, Rocchi M, Røed KH, Ryder OA, Searle S, Skow L, Swinburne JE, Syvänen AC, Tozaki T, Valberg SJ, Vaudin M, White JR, Zody MC; Broad Institute Genome Sequencing Platform; Broad Institute Whole Genome Assembly Team, Lander ES, Lindblad-Toh K.

Science. 2009 Nov 6;326(5954):865-7. doi: 10.1126/science.1178158.

23.

"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.

24.

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.

25.

Evolutionary breakpoints in the gibbon suggest association between cytosine methylation and karyotype evolution.

Carbone L, Harris RA, Vessere GM, Mootnick AR, Humphray S, Rogers J, Kim SK, Wall JD, Martin D, Jurka J, Milosavljevic A, de Jong PJ.

PLoS Genet. 2009 Jun;5(6):e1000538. doi: 10.1371/journal.pgen.1000538. Epub 2009 Jun 26.

26.

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.

27.

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.

28.

The amphioxus genome and the evolution of the chordate karyotype.

Putnam NH, Butts T, Ferrier DE, Furlong RF, Hellsten U, Kawashima T, Robinson-Rechavi M, Shoguchi E, Terry A, Yu JK, Benito-Gutiérrez EL, Dubchak I, Garcia-Fernàndez J, Gibson-Brown JJ, Grigoriev IV, Horton AC, de Jong PJ, Jurka J, Kapitonov VV, Kohara Y, Kuroki Y, Lindquist E, Lucas S, Osoegawa K, Pennacchio LA, Salamov AA, Satou Y, Sauka-Spengler T, Schmutz J, Shin-I T, Toyoda A, Bronner-Fraser M, Fujiyama A, Holland LZ, Holland PW, Satoh N, Rokhsar DS.

Nature. 2008 Jun 19;453(7198):1064-71. doi: 10.1038/nature06967.

PMID:
18563158
29.

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
30.

Transposition of a reconstructed Harbinger element in human cells and functional homology with two transposon-derived cellular genes.

Sinzelle L, Kapitonov VV, Grzela DP, Jursch T, Jurka J, Izsvák Z, Ivics Z.

Proc Natl Acad Sci U S A. 2008 Mar 25;105(12):4715-20. doi: 10.1073/pnas.0707746105. Epub 2008 Mar 13.

31.

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
32.

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
33.

Tracing genetic history of modern humans using X-chromosome lineages.

Yotova V, Lefebvre JF, Kohany O, Jurka J, Michalski R, Modiano D, Utermann G, Williams SM, Labuda D.

Hum Genet. 2007 Dec;122(5):431-43. Epub 2007 Aug 7.

PMID:
17680273
34.

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.

35.

Repetitive sequences in complex genomes: structure and evolution.

Jurka J, Kapitonov VV, Kohany O, Jurka MV.

Annu Rev Genomics Hum Genet. 2007;8:241-59. Review.

PMID:
17506661
36.

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences.

Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, Duke S, Garber M, Gentles AJ, Goodstadt L, Heger A, Jurka J, Kamal M, Mauceli E, Searle SM, Sharpe T, Baker ML, Batzer MA, Benos PV, Belov K, Clamp M, Cook A, Cuff J, Das R, Davidow L, Deakin JE, Fazzari MJ, Glass JL, Grabherr M, Greally JM, Gu W, Hore TA, Huttley GA, Kleber M, Jirtle RL, Koina E, Lee JT, Mahony S, Marra MA, Miller RD, Nicholls RD, Oda M, Papenfuss AT, Parra ZE, Pollock DD, Ray DA, Schein JE, Speed TP, Thompson K, VandeBerg JL, Wade CM, Walker JA, Waters PD, Webber C, Weidman JR, Xie X, Zody MC; Broad Institute Genome Sequencing Platform; Broad Institute Whole Genome Assembly Team, Graves JA, Ponting CP, Breen M, Samollow PB, Lander ES, Lindblad-Toh K.

Nature. 2007 May 10;447(7141):167-77.

PMID:
17495919
37.

Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica.

Gentles AJ, Wakefield MJ, Kohany O, Gu W, Batzer MA, Pollock DD, Jurka J.

Genome Res. 2007 Jul;17(7):992-1004. Epub 2007 May 10.

38.

SINEs, evolution and genome structure in the opossum.

Gu W, Ray DA, Walker JA, Barnes EW, Gentles AJ, Samollow PB, Jurka J, Batzer MA, Pollock DD.

Gene. 2007 Jul 1;396(1):46-58. Epub 2007 Mar 19.

PMID:
17442506
39.

Evolutionary diversification of SPANX-N sperm protein gene structure and expression.

Kouprina N, Noskov VN, Pavlicek A, Collins NK, Schoppee Bortz PD, Ottolenghi C, Loukinov D, Goldsmith P, Risinger JI, Kim JH, Westbrook VA, Solomon G, Sounders H, Herr JC, Jurka J, Lobanenkov V, Schlessinger D, Larionov V.

PLoS One. 2007 Apr 4;2(4):e359.

40.

Evolutionary history of 7SL RNA-derived SINEs in Supraprimates.

Kriegs JO, Churakov G, Jurka J, Brosius J, Schmitz J.

Trends Genet. 2007 Apr;23(4):158-61. Epub 2007 Feb 20. Review.

PMID:
17307271
41.

Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor.

Kohany O, Gentles AJ, Hankus L, Jurka J.

BMC Bioinformatics. 2006 Oct 25;7:474.

42.

Introduction for the Gene special issue dedicated to the meeting "Genomic impact of eukaryotic transposable elements" at Asilomar.

Batzer MA, Deininger PL, Jurka J, Moran JV.

Gene. 2007 Apr 1;390(1-2):1-2. Epub 2006 Aug 23. No abstract available.

PMID:
17027200
43.

Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation.

Qi Y, He X, Wang XJ, Kohany O, Jurka J, Hannon GJ.

Nature. 2006 Oct 26;443(7114):1008-12. Epub 2006 Sep 24.

PMID:
16998468
44.

Identification of sequence motifs at the breakpoint junctions in three t(1;9)(p36.3;q34) and delineation of mechanisms involved in generating balanced translocations.

Gajecka M, Pavlicek A, Glotzbach CD, Ballif BC, Jarmuz M, Jurka J, Shaffer LG.

Hum Genet. 2006 Nov;120(4):519-26. Epub 2006 Jul 18.

PMID:
16847692
45.
46.

Self-synthesizing DNA transposons in eukaryotes.

Kapitonov VV, Jurka J.

Proc Natl Acad Sci U S A. 2006 Mar 21;103(12):4540-5. Epub 2006 Mar 14.

47.

Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae.

Galagan JE, Calvo SE, Cuomo C, Ma LJ, Wortman JR, Batzoglou S, Lee SI, Baştürkmen M, Spevak CC, Clutterbuck J, Kapitonov V, Jurka J, Scazzocchio C, Farman M, Butler J, Purcell S, Harris S, Braus GH, Draht O, Busch S, D'Enfert C, Bouchier C, Goldman GH, Bell-Pedersen D, Griffiths-Jones S, Doonan JH, Yu J, Vienken K, Pain A, Freitag M, Selker EU, Archer DB, Peñalva MA, Oakley BR, Momany M, Tanaka T, Kumagai T, Asai K, Machida M, Nierman WC, Denning DW, Caddick M, Hynes M, Paoletti M, Fischer R, Miller B, Dyer P, Sachs MS, Osmani SA, Birren BW.

Nature. 2005 Dec 22;438(7071):1105-15.

PMID:
16372000
48.

Retroposition of processed pseudogenes: the impact of RNA stability and translational control.

Pavlicek A, Gentles AJ, Paces J, Paces V, Jurka J.

Trends Genet. 2006 Feb;22(2):69-73. Epub 2005 Dec 13. Review.

49.

Origin and diversification of minisatellites derived from human Alu sequences.

Jurka J, Gentles AJ.

Gene. 2006 Jan 3;365:21-6. Epub 2005 Dec 15.

PMID:
16343813
50.

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