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Publications

Selected peer reviewed articles

  1. Yano N, Chong PF, Kojima KK, Miyoshi T, Luqman-Fatah A, Kimura Y, Kora K, Kayaki T, Maizuru K, Hayashi T, Yokoyama A, Ajiro M, Hagiwara M, Kondo T, Kira R, Takita J, Yoshida T
    Long-read sequencing identifies an SVA_D retrotransposon insertion deep within the intron of ATP7A as a novel cause of occipital horn syndrome.
    J Med Genet, 2024 Sep 24;61(10):950-958

  2. Kojima KK
    Helenus and Ajax, Two Groups of Non-Autonomous LTR Retrotransposons, Represent a New Type of Small RNA Gene-Derived Mobile Elements.
    Biology (Basel), 2024 Feb 13;13(2)

  3. Jiang K, Lim J, Sgrizzi S, Trinh M, Kayabolen A, Yutin N, Bao W, Kato K, Koonin EV, Gootenberg JS, Abudayyeh OO
    Programmable RNA-guided DNA endonucleases are widespread in eukaryotes and their viruses.
    Sci Adv, 2023 Sep 29;9(39):eadk0171

  4. Kojima KK
    Daidara: A gigantic Gypsy LTR retrotransposon lineage in the springtail Allacma fusca genome.
    Genes Cells, 2023 Oct;28(10):746-752

  5. Kojima KK, Kobayashi I
    Base-excision restriction enzymes: expanding the world of epigenetic immune systems.
    DNA Res, 2023 Aug 1;30(4)

  6. Kojima KK, Bao W
    IS481EU Shows a New Connection between Eukaryotic and Prokaryotic DNA Transposons.
    Biology (Basel), 2023 Feb 25;12(3)

  7. Kojima KK, Bao W
    A unique eukaryotic lineage of composite-like DNA transposons encoding a DDD/E transposase and a His-Me finger homing endonuclease.
    Mob DNA, 2022 Oct 22;13(1):24

  8. Kojima KK
    Diversity and Evolution of DNA Transposons Targeting Multicopy Small RNA Genes from Actinopterygian Fish.
    Biology (Basel), 2022 Jan 20;11(2)

  9. Kojima KK
    Hagfish genome reveals parallel evolution of 7SL RNA-derived SINEs.
    Mob DNA, 2020;11:18

  10. Sultana N, Menzel G, Heitkam T, Kojima KK, Bao W, Serçe S
    Bioinformatic and Molecular Analysis of Satellite Repeat Diversity in Vaccinium Genomes.
    Genes (Basel), 2020 May 9;11(5)

  11. Kojima KK
    AcademH, a lineage of Academ DNA transposons encoding helicase found in animals and fungi.
    Mob DNA, 2020;11:15

  12. Bao W, Tang KFJ, Alcivar-Warren A
    The Complete Genome of an Endogenous Nimavirus (Nimav-1_LVa) From the Pacific Whiteleg Shrimp Penaeus (Litopenaeus) Vannamei.
    Genes (Basel), 2020 Jan 14;11(1)

  13. Kojima KK
    Structural and sequence diversity of eukaryotic transposable elements.
    Genes Genet Syst, 2020 Jan 30;94(6):233-252

  14. Kojima KK
    LINEs Contribute to the Origins of Middle Bodies of SINEs besides 3' Tails.
    Genome Biol Evol, 2018 Jan 1;10(1):370-379

  15. Kojima KK
    Human transposable elements in Repbase: genomic footprints from fish to humans.
    Mob DNA, 2018;9:2

  16. Wan TW, Higuchi W, Khokhlova OE, Hung WC, Iwao Y, Wakayama M, Inomata N, Takano T, Lin YT, Peryanova OV, Kojima KK, Salmina AB, Teng LJ, Yamamoto T
    Genomic comparison between Staphylococcus aureus GN strains clinically isolated from a familial infection case: IS1272 transposition through a novel inverted repeat-replacing mechanism.
    PLoS One, 2017;12(11):e0187288

  17. Kojima KK, Seto Y, Fujiwara H
    The Wide Distribution and Change of Target Specificity of R2 Non-LTR Retrotransposons in Animals.
    PLoS One, 2016;11(9):e0163496

  18. Kojima KK, Furuta Y, Yahara K, Fukuyo M, Shiwa Y, Nishiumi S, Yoshida M, Azuma T, Yoshikawa H, Kobayashi I
    Population Evolution of Helicobacter pylori through Diversification in DNA Methylation and Interstrain Sequence Homogenization.
    Mol Biol Evol, 2016 Nov;33(11):2848-2859

  19. Uchiyama I, Albritton J, Fukuyo M, Kojima KK, Yahara K, Kobayashi I
    A Novel Approach to Helicobacter pylori Pan-Genome Analysis for Identification of Genomic Islands.
    PLoS One, 2016;11(8):e0159419

  20. 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
    A Helitron transposon reconstructed from bats reveals a novel mechanism of genome shuffling in eukaryotes.
    Nat Commun, 2016 Mar 2;7:10716

  21. Lescot M, Hingamp P, Kojima KK, Villar E, Romac S, Veluchamy A, Boccara M, Jaillon O, Iudicone D, Bowler C, Wincker P, Claverie JM, Ogata H
    Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages.
    ISME J, 2016 May;10(5):1134-46

  22. Hubley R, Finn RD, Clements J, Eddy SR, Jones TA, Bao W, Smit AF, Wheeler TJ
    The Dfam database of repetitive DNA families.
    Nucleic Acids Res, 2016 Jan 4;44(D1):D81-9

  23. Kojima KK, Jurka J
    Ancient Origin of the U2 Small Nuclear RNA Gene-Targeting Non-LTR Retrotransposons Utopia.
    PLoS One, 2015;10(11):e0140084

  24. Kojima KK, Kobayashi I
    Transmission of the PabI family of restriction DNA glycosylase genes: mobility and long-term inheritance.
    BMC Genomics, 2015 Oct 19;16:817

  25. Bao W, Kojima KK, Kohany O
    Repbase Update, a database of repetitive elements in eukaryotic genomes.
    Mob DNA, 2015;6:11

  26. Kojima KK
    A New Class of SINEs with snRNA Gene-Derived Heads.
    Genome Biol Evol, 2015 May 27;7(6):1702-12

  27. 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
    Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.
    Science, 2014 Dec 12;346(6215):1254449

  28. 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
    Multiple lineages of ancient CR1 retroposons shaped the early genome evolution of amniotes.
    Genome Biol Evol, 2014 Dec 11;7(1):205-17

  29. Chong AY, Kojima KK, Jurka J, Ray DA, Smit AF, Isberg SR, Gongora J
    Evolution and gene capture in ancient endogenous retroviruses - insights from the crocodilian genomes.
    Retrovirology, 2014 Dec 12;11:71

  30. 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
    The ctenophore genome and the evolutionary origins of neural systems.
    Nature, 2014 Jun 5;510(7503):109-14

  31. Kojima KK, Jurka J
    A superfamily of DNA transposons targeting multicopy small RNA genes.
    PLoS One, 2013;8(7):e68260

  32. Bao W, Jurka J
    Homologues of bacterial TnpB_IS605 are widespread in diverse eukaryotic transposable elements.
    Mob DNA, 2013 Apr 1;4(1):12

  33. Wheeler TJ, Clements J, Eddy SR, Hubley R, Jones TA, Jurka J, Smit AF, Finn RD
    Dfam: a database of repetitive DNA based on profile hidden Markov models.
    Nucleic Acids Res, 2013 Jan;41(Database issue):D70-82

  34. Arkhipova IR, Batzer MA, Brosius J, Feschotte C, Moran JV, Schmitz J, Jurka J
    Genomic impact of eukaryotic transposable elements.
    Mob DNA, 2012 Nov 21;3(1):19

  35. 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
    Analyses of pig genomes provide insight into porcine demography and evolution.
    Nature, 2012 Nov 15;491(7424):393-8

  36. Jurka J, Bao W, Kojima KK, Kohany O, Yurka MG
    Distinct groups of repetitive families preserved in mammals correspond to different periods of regulatory innovations in vertebrates.
    Biol Direct, 2012 Oct 25;7:36

  37. Oliveira SG, Bao W, Martins C, Jurka J
    Horizontal transfers of Mariner transposons between mammals and insects.
    Mob DNA, 2012 Sep 26;3(1):14

  38. Kojima KK, Jurka J
    Crypton transposons: identification of new diverse families and ancient domestication events.
    Mob DNA, 2011 Oct 19;2(1):12

  39. Jurka J, Bao W, Kojima KK
    Families of transposable elements, population structure and the origin of species.
    Biol Direct, 2011 Sep 19;6:44

  40. Cantu D, Govindarajulu M, Kozik A, Wang M, Chen X, Kojima KK, Jurka J, Michelmore RW, Dubcovsky J
    Next generation sequencing provides rapid access to the genome of Puccinia striiformis f. sp. tritici, the causal agent of wheat stripe rust.
    PLoS One, 2011;6(8):e24230

  41. Kojima KK, Kapitonov VV, Jurka J
    Recent expansion of a new Ingi-related clade of Vingi non-LTR retrotransposons in hedgehogs.
    Mol Biol Evol, 2011 Jan;28(1):17-20

  42. 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
    Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri.
    Science, 2010 Jul 9;329(5988):223-6

  43. Bao W, Jurka J
    Origin and evolution of LINE-1 derived "half-L1" retrotransposons (HAL1).
    Gene, 2010 Oct 1;465(1-2):9-16

  44. 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
    The genome of the Western clawed frog Xenopus tropicalis.
    Science, 2010 Apr 30;328(5978):633-6

  45. Bao W, Kapitonov VV, Jurka J
    Ginger DNA transposons in eukaryotes and their evolutionary relationships with long terminal repeat retrotransposons.
    Mob DNA, 2010 Jan 25;1(1):3

  46. 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, Lander ES, Lindblad-Toh K
    Genome sequence, comparative analysis, and population genetics of the domestic horse.
    Science, 2009 Nov 6;326(5954):865-7

  47. Jurka J
    "Genomic Impact of Eukaryotic Transposable Elements", Pacific Grove, California, February 6-10, 2009.
    Gene, 2009 Dec 15;448(2):103

  48. Kapitonov VV, Tempel S, Jurka J
    Simple and fast classification of non-LTR retrotransposons based on phylogeny of their RT domain protein sequences.
    Gene, 2009 Dec 15;448(2):207-13

  49. 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
    Evolutionary breakpoints in the gibbon suggest association between cytosine methylation and karyotype evolution.
    PLoS Genet, 2009 Jun;5(6):e1000538

  50. Bao W, Jurka MG, Kapitonov VV, Jurka J
    New superfamilies of eukaryotic DNA transposons and their internal divisions.
    Mol Biol Evol, 2009 May;26(5):983-93

  51. Tempel S, Jurka M, Jurka J
    VisualRepbase: an interface for the study of occurrences of transposable element families.
    BMC Bioinformatics, 2008 Aug 18;9:345

  52. 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
    The amphioxus genome and the evolution of the chordate karyotype.
    Nature, 2008 Jun 19;453(7198):1064-71

  53. Kapitonov VV, Jurka J
    A universal classification of eukaryotic transposable elements implemented in Repbase.
    Nat Rev Genet, 2008 May;9(5):411-2; author reply 414

  54. Sinzelle L, Kapitonov VV, Grzela DP, Jursch T, Jurka J, Izsvák Z, Ivics Z
    Transposition of a reconstructed Harbinger element in human cells and functional homology with two transposon-derived cellular genes.
    Proc Natl Acad Sci U S A, 2008 Mar 25;105(12):4715-20

  55. Jurka J
    Conserved eukaryotic transposable elements and the evolution of gene regulation.
    Cell Mol Life Sci, 2008 Jan;65(2):201-4

  56. Kapitonov VV, Jurka J
    Helitrons on a roll: eukaryotic rolling-circle transposons.
    Trends Genet, 2007 Oct;23(10):521-9

  57. Yotova V, Lefebvre JF, Kohany O, Jurka J, Michalski R, Modiano D, Utermann G, Williams SM, Labuda D
    Tracing genetic history of modern humans using X-chromosome lineages.
    Hum Genet, 2007 Dec;122(5):431-43

  58. 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
    Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization.
    Science, 2007 Jul 6;317(5834):86-94

  59. Jurka J, Kapitonov VV, Kohany O, Jurka MV
    Repetitive sequences in complex genomes: structure and evolution.
    Annu Rev Genomics Hum Genet, 2007;8:241-59

  60. 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, Graves JA, Ponting CP, Breen M, Samollow PB, Lander ES, Lindblad-Toh K
    Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences.
    Nature, 2007 May 10;447(7141):167-77

  61. Gentles AJ, Wakefield MJ, Kohany O, Gu W, Batzer MA, Pollock DD, Jurka J
    Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica.
    Genome Res, 2007 Jul;17(7):992-1004

  62. Gu W, Ray DA, Walker JA, Barnes EW, Gentles AJ, Samollow PB, Jurka J, Batzer MA, Pollock DD
    SINEs, evolution and genome structure in the opossum.
    Gene, 2007 Jul 1;396(1):46-58

  63. 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
    Evolutionary diversification of SPANX-N sperm protein gene structure and expression.
    PLoS One, 2007 Apr 4;2(4):e359

  64. Kriegs JO, Churakov G, Jurka J, Brosius J, Schmitz J
    Evolutionary history of 7SL RNA-derived SINEs in Supraprimates.
    Trends Genet, 2007 Apr;23(4):158-61

  65. Kohany O, Gentles AJ, Hankus L, Jurka J
    Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor.
    BMC Bioinformatics, 2006 Oct 25;7:474

  66. Batzer MA, Deininger PL, Jurka J, Moran JV
    Introduction for the Gene special issue dedicated to the meeting "Genomic impact of eukaryotic transposable elements" at Asilomar.
    Gene, 2007 Apr 1;390(1-2):1-2

  67. Qi Y, He X, Wang XJ, Kohany O, Jurka J, Hannon GJ
    Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation.
    Nature, 2006 Oct 26;443(7114):1008-12

  68. Gajecka M, Pavlicek A, Glotzbach CD, Ballif BC, Jarmuz M, Jurka J, Shaffer LG
    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.
    Hum Genet, 2006 Nov;120(4):519-26

  69. Pavlicek A, Jurka J
    Positive selection on the nonhomologous end-joining factor Cernunnos-XLF in the human lineage.
    Biol Direct, 2006 Jun 2;1:15

  70. Kapitonov VV, Jurka J
    Self-synthesizing DNA transposons in eukaryotes.
    Proc Natl Acad Sci U S A, 2006 Mar 21;103(12):4540-5

  71. 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
    Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae.
    Nature, 2005 Dec 22;438(7071):1105-15

  72. Pavlicek A, Gentles AJ, Paces J, Paces V, Jurka J
    Retroposition of processed pseudogenes: the impact of RNA stability and translational control.
    Trends Genet, 2006 Feb;22(2):69-73

  73. Jurka J, Gentles AJ
    Origin and diversification of minisatellites derived from human Alu sequences.
    Gene, 2006 Jan 3;365:21-6

  74. Pavlicek A, House R, Gentles AJ, Jurka J, Morrow BE
    Traffic of genetic information between segmental duplications flanking the typical 22q11.2 deletion in velo-cardio-facial syndrome/DiGeorge syndrome.
    Genome Res, 2005 Nov;15(11):1487-95

  75. Kouprina N, Pavlicek A, Noskov VN, Solomon G, Otstot J, Isaacs W, Carpten JD, Trent JM, Schleutker J, Barrett JC, Jurka J, Larionov V
    Dynamic structure of the SPANX gene cluster mapped to the prostate cancer susceptibility locus HPCX at Xq27.
    Genome Res, 2005 Nov;15(11):1477-86

  76. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J
    Repbase Update, a database of eukaryotic repetitive elements.
    Cytogenet Genome Res, 2005;110(1-4):462-7

  77. Jurka J, Kohany O, Pavlicek A, Kapitonov VV, Jurka MV
    Clustering, duplication and chromosomal distribution of mouse SINE retrotransposons.
    Cytogenet Genome Res, 2005;110(1-4):117-23

  78. Kouprina N, Pavlicek A, Collins NK, Nakano M, Noskov VN, Ohzeki J, Mochida GH, Risinger JI, Goldsmith P, Gunsior M, Solomon G, Gersch W, Kim JH, Barrett JC, Walsh CA, Jurka J, Masumoto H, Larionov V
    The microcephaly ASPM gene is expressed in proliferating tissues and encodes for a mitotic spindle protein.
    Hum Mol Genet, 2005 Aug 1;14(15):2155-65

  79. Gentles AJ, Kohany O, Jurka J
    Evolutionary diversity and potential recombinogenic role of integration targets of Non-LTR retrotransposons.
    Mol Biol Evol, 2005 Oct;22(10):1983-91

  80. Kapitonov VV, Jurka J
    RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons.
    PLoS Biol, 2005 Jun;3(6):e181

  81. Salem AH, Ray DA, Hedges DJ, Jurka J, Batzer MA
    Analysis of the human Alu Ye lineage.
    BMC Evol Biol, 2005 Feb 22;5:18

  82. Miller WG, Pearson BM, Wells JM, Parker CT, Kapitonov VV, Mandrell RE
    Diversity within the Campylobacter jejuni type I restriction-modification loci.
    Microbiology (Reading), 2005 Feb;151(Pt 2):337-351

  83. Jurka J
    Evolutionary impact of human Alu repetitive elements.
    Curr Opin Genet Dev, 2004 Dec;14(6):603-8

  84. Armbrust EV, Berges JA, Bowler C, Green BR, Martinez D, Putnam NH, Zhou S, Allen AE, Apt KE, Bechner M, Brzezinski MA, Chaal BK, Chiovitti A, Davis AK, Demarest MS, Detter JC, Glavina T, Goodstein D, Hadi MZ, Hellsten U, Hildebrand M, Jenkins BD, Jurka J, Kapitonov VV, Kröger N, Lau WW, Lane TW, Larimer FW, Lippmeier JC, Lucas S, Medina M, Montsant A, Obornik M, Parker MS, Palenik B, Pazour GJ, Richardson PM, Rynearson TA, Saito MA, Schwartz DC, Thamatrakoln K, Valentin K, Vardi A, Wilkerson FP, Rokhsar DS
    The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism.
    Science, 2004 Oct 1;306(5693):79-86

  85. Pavlicek A, Noskov VN, Kouprina N, Barrett JC, Jurka J, Larionov V
    Evolution of the tumor suppressor BRCA1 locus in primates: implications for cancer predisposition.
    Hum Mol Genet, 2004 Nov 15;13(22):2737-51

  86. Kapitonov VV, Jurka J
    Harbinger transposons and an ancient HARBI1 gene derived from a transposase.
    DNA Cell Biol, 2004 May;23(5):311-24

  87. Kouprina N, Pavlicek A, Mochida GH, Solomon G, Gersch W, Yoon YH, Collura R, Ruvolo M, Barrett JC, Woods CG, Walsh CA, Jurka J, Larionov V
    Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansion.
    PLoS Biol, 2004 May;2(5):E126

  88. Xing J, Salem AH, Hedges DJ, Kilroy GE, Watkins WS, Schienman JE, Stewart CB, Jurka J, Jorde LB, Batzer MA
    Comprehensive analysis of two Alu Yd subfamilies.
    J Mol Evol, 2003;57 Suppl 1:S76-89

  89. Jurka J, Kohany O, Pavlicek A, Kapitonov VV, Jurka MV
    Duplication, coclustering, and selection of human Alu retrotransposons.
    Proc Natl Acad Sci U S A, 2004 Feb 3;101(5):1268-72

  90. Paces J, Pavlícek A, Zika R, Kapitonov VV, Jurka J, Paces V
    HERVd: the Human Endogenous RetroViruses Database: update.
    Nucleic Acids Res, 2004 Jan 1;32(Database issue):D50

  91. Babcock M, Pavlicek A, Spiteri E, Kashork CD, Ioshikhes I, Shaffer LG, Jurka J, Morrow BE
    Shuffling of genes within low-copy repeats on 22q11 (LCR22) by Alu-mediated recombination events during evolution.
    Genome Res, 2003 Dec;13(12):2519-32

  92. Johanning K, Stevenson CA, Oyeniran OO, Gozal YM, Roy-Engel AM, Jurka J, Deininger PL
    Potential for retroposition by old Alu subfamilies.
    J Mol Evol, 2003 Jun;56(6):658-64

  93. Kapitonov VV, Jurka J
    Molecular paleontology of transposable elements in the Drosophila melanogaster genome.
    Proc Natl Acad Sci U S A, 2003 May 27;100(11):6569-74

  94. Kapitonov VV, Jurka J
    A novel class of SINE elements derived from 5S rRNA.
    Mol Biol Evol, 2003 May;20(5):694-702

  95. Kapitonov VV, Jurka J
    The esterase and PHD domains in CR1-like non-LTR retrotransposons.
    Mol Biol Evol, 2003 Jan;20(1):38-46

  96. Jurka J, Krnjajic M, Kapitonov VV, Stenger JE, Kokhanyy O
    Active Alu elements are passed primarily through paternal germlines.
    Theor Popul Biol, 2002 Jun;61(4):519-30

  97. Chen C, Gentles AJ, Jurka J, Karlin S
    Genes, pseudogenes, and Alu sequence organization across human chromosomes 21 and 22.
    Proc Natl Acad Sci U S A, 2002 Mar 5;99(5):2930-5

  98. Jurka J, Kapitonov VV
    PIFs meet Tourists and Harbingers: a superfamily reunion.
    Proc Natl Acad Sci U S A, 2001 Oct 23;98(22):12315-6

  99. Kapitonov VV, Jurka J
    Rolling-circle transposons in eukaryotes.
    Proc Natl Acad Sci U S A, 2001 Jul 17;98(15):8714-9

  100. Kuryshev VY, Skryabin BV, Kremerskothen J, Jurka J, Brosius J
    Birth of a gene: locus of neuronal BC200 snmRNA in three prosimians and human BC200 pseudogenes as archives of change in the Anthropoidea lineage.
    J Mol Biol, 2001 Jun 22;309(5):1049-66

  101. Stenger JE, Lobachev KS, Gordenin D, Darden TA, Jurka J, Resnick MA
    Biased distribution of inverted and direct Alus in the human genome: implications for insertion, exclusion, and genome stability.
    Genome Res, 2001 Jan;11(1):12-27

  102. Kapitonov VV, Jurka J
    MER53, a non-autonomous DNA transposon associated with a variety of functionally related defense genes in the human genome.
    DNA Seq, 1998;8(5):277-88

  103. Jurka J
    Repbase update: a database and an electronic journal of repetitive elements.
    Trends Genet, 2000 Sep;16(9):418-20

  104. Jurka J, Kapitonov VV
    Sectorial mutagenesis by transposable elements.
    Genetica, 1999;107(1-3):239-48

  105. Kapitonov VV, Jurka J
    Molecular paleontology of transposable elements from Arabidopsis thaliana.
    Genetica, 1999;107(1-3):27-37

  106. Tóth G, Gáspári Z, Jurka J
    Microsatellites in different eukaryotic genomes: survey and analysis.
    Genome Res, 2000 Jul;10(7):967-81

  107. Lobachev KS, Stenger JE, Kozyreva OG, Jurka J, Gordenin DA, Resnick MA
    Inverted Alu repeats unstable in yeast are excluded from the human genome.
    EMBO J, 2000 Jul 17;19(14):3822-30

  108. Kapitonov VV, Jurka J
    The long terminal repeat of an endogenous retrovirus induces alternative splicing and encodes an additional carboxy-terminal sequence in the human leptin receptor.
    J Mol Evol, 1999 Feb;48(2):248-51

  109. Skryabin BV, Kremerskothen J, Vassilacopoulou D, Disotell TR, Kapitonov VV, Jurka J, Brosius J
    The BC200 RNA gene and its neural expression are conserved in Anthropoidea (Primates).
    J Mol Evol, 1998 Dec;47(6):677-85

  110. Holmquist GP, Kapitonov VV, Jurka J
    Mobile genetic elements, chiasmata, and the unique organization of beta-heterochromatin.
    Cytogenet Cell Genet, 1998;80(1-4):113-6

  111. Jurka J
    Repeats in genomic DNA: mining and meaning.
    Curr Opin Struct Biol, 1998 Jun;8(3):333-7

  112. Kapitonov VV, Holmquist GP, Jurka J
    L1 repeat is a basic unit of heterochromatin satellites in cetaceans.
    Mol Biol Evol, 1998 May;15(5):611-2

  113. Jurka J, Klonowski P, Trifonov EN
    Mammalian retroposons integrate at kinkable DNA sites.
    J Biomol Struct Dyn, 1998 Feb;15(4):717-21

  114. Bell GI, Jurka J
    The length distribution of perfect dimer repetitive DNA is consistent with its evolution by an unbiased single-step mutation process.
    J Mol Evol, 1997 Apr;44(4):414-21

  115. Jurka J
    Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons.
    Proc Natl Acad Sci U S A, 1997 Mar 4;94(5):1872-7

  116. Jurka J, Klonowski P
    Integration of retroposable elements in mammals: selection of target sites.
    J Mol Evol, 1996 Dec;43(6):685-9

  117. Jurka J, Klonowski P, Dagman V, Pelton P
    CENSOR--a program for identification and elimination of repetitive elements from DNA sequences.
    Comput Chem, 1996 Mar;20(1):119-21

  118. Jurka J, Kapitonov VV, Klonowski P, Walichiewicz J, Smit AF
    Identification of new medium reiteration frequency repeats in the genomes of Primates, Rodentia and Lagomorpha.
    Genetica, 1996-1997;98(3):235-47

Book chapters

  1. Pavlicek, A, Jurka, J. Processed pseudogenes, endogenous retroviruses and ancient transposable elements in: Genomic Disorders: The Genomic Basis of Disease (Lupski, J.R. & Stankiewicz P.T. eds.), Chapter 4, pp. 57-72. The Humana Press, Totowa, New Jersey (2006).

  2. Pavlicek, A., Kohany, O., Jurka, J. Repeat mining: basic tools for detection and analysis. In "Analytical tools for DNA, genes and genomes nuts and bolts". (Markoff, A., ed). DNA Press, Eagleville (2005)

  3. Kapitonov, V.V., Pavlicek, A., Jurka, J. Anthology of human repetitive DNA. Encyclopedia of Molecular Cell Biology and Molecular Medicine (Vol. 1, pp. 251-305). Meyers, R.A., ed., Wiley-VCH Verlag GmbH & Co. KGaA Weinheim (2004).

  4. Jurka, J. Repetitive DNA: detection, annotation and analysis. In Introduction to Bioinformatics: A Theoretical and Practical Approach. (Krawetz, S.A. and Womble D.D., eds), chapter 8, pp. 151-167, Humana Press, Totowa NJ (2003).


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