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Publications

Selected peer reviewed articles

  1. Kohany O, Gentles AJ, Hankus L, Jurka J. Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinformatics. 2006,7:474 [PubMed][Full text]

  2. 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. 443(7114):1008-12 [Epub 2006 Sep 24] [PubMed]

  3. 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. 2006 Aug 23; [Epub ahead of print] [PubMed]

  4. 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).

  5. 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 Jul 18; [Epub ahead of print] [PubMed]

  6. Pavlicek A, Jurka J. Positive selection on the nonhomologous end-joining factor Cernunnos-XLF in the human lineage. Biol Direct. 2006 Jun 2;1(1):15 [Epub ahead of print] [PubMed]

  7. Kapitonov VV, Jurka J. Self-synthesizing DNA transposons in eukaryotes. Proc. Natl. Acad. Sci. USA 103(12): 4540-4545 (2006). March 14, [Epub ahead of print] [PubMed]

  8. 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)

  9. Galagan JE, Calvo SE, Cuomo C, Ma LJ, Wortman JR, Batzoglou S, Lee SI, Basturkmen 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, Penalva 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 438(7071):1105-15 (2005) [PubMed]

  10. Pavlicek A, Gentles AJ, Paces J, Paces V, Jurka J. Retroposition of processed pseudogenes: the impact of RNA stability and translational control. Trends Genet. 22(2):69-73 (2005) [PubMed]

  11. Jurka, J., Gentles, A. Origin and diversification of minisatellites derived from human Alu sequences. Gene 365:21-26 (2005) [PubMed]

  12. Pavlicek, A., House, R., Gentles, A., Jurka, J., Morrow, B. Traffic of genetic information between segmental duplications flanking the typical 22q11.2 deletion in velo-cardio-facial syndrome/DiGeorge syndrome. Genome Res. 15:1477-1486 (2005) [PubMed]

  13. Kouprina N., Pavlicek A, Noskov, V.N., Solomon G., Otstot, J., Isaacs, W., Carpten, J.D., Trent, J.M., Barrett C., Jurka J., Larionov, V. Dynamic structure of the SPANX gene cluster mapped to the prostate cancer susceptibility locus HPCX at Xq27. Genome Res. 15:1487-1495 (2005) [PubMed]

  14. Gentles, A., Kohany, O., Jurka, J. Evolutionary diversity and potential recombinogenic role of integration targets of non-LTR retrotransposons. Mol. Biol. Evol. 22:1983-1991 (2005) [pubMed]

  15. Kouprina N., Pavlicek A, Collins NK, Nakano M., Noskov, V.N., Ohzeki J.-I., Mochida G.H., Risinger J.I., Goldsmith P., Gunsior M., Solomon G., Gersch W., Kim, J.-H., Barrett C., Walsh C.A., Jurka J., Masumoto H., Larionov, V. The microcephaly ASPM gene is expressed in proliferating tissues and encodes for a mitotic spindle protein. Human Molecular Genetics 14:2155-2165 (2005) [PubMed]

  16. Jurka, J., Kapitonov, V.V., Pavlicek, A., Klonowski, P., Kohany, O., Walichiewicz, J. Repbase Update, a database of eukaryotic repetitive elements Cytogenetic and Genome Research 110:462-467 (2005) [PubMed]

  17. Jurka, J ., Kohany, O., Pavlicek, A., Kapitonov, V.V., Jurka, M.V. Clustering, duplication and chromosomal distribution of mouse SINE retrotransposons. Cytogenetic and Genome Research 110:117-123 (2005) [PubMed]

  18. Kapitonov, V.V., Jurka, J. RAG1 Core and V(D)J recombination signal sequences were derived from Transib Transposons. PloS Biology, 3(6):e181 (2005) [PubMed]

  19. Salem A.H., Ray D.A., Hedges D.J., Jurka J., Batzer M.A. Analysis of the human Alu Ye lineage.BMC Evol Biol. 5: 18 (2005) [PubMed]

  20. 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).

  21. Armbrust, E.V., Berges, J.A.,Chris Bowler, C., Green, B.R.,Martinez, D., Putnam, N.H., Zhou, S., Allen, A.E., Apt, K.E., Bechner, M., Brzezinski, M.A., Balbir K., Chaal, B.K., Chiovitti, A., Davis, A.K., Demarest,M.S., Detter, J.C., Glavina, T., Goodstein, D., Hadi, M.Z., Hellsten, U., Hildebrand, M., Jenkins, B.D., Jurka, J., Kapitonov, V.V., Kröger, N., Lau, W.W.Y., Lane, T.W., Larimer, F.W., Lippmeier, J.C., Lucas, S., Medina, M., Monstant, A., Obornik, M., Schnizler Parker, M., Palenik, B., Pazour, G.J.,Richardson, P.M., Rynearson, T.A., Saito, M.A., Schwartz, D.C., Thamatrakoln, K., Valentin K., Vardi, A., Wilkerson, F.P., Rokhsar, D.S. The genome of the diatom Thalassiosira pseudonana: Ecology, evolution, and metabolism. Science 306:79-86(2004) [PubMed]

  22. Pavlicek, A., Noskov, V.N., Kouprina, N., Barrett, J.C., Jurka, J., Larionov, V., Evolution of the tumor suppressor BRCA1 locus in primates: implications for cancer predisposition. Hum. Mol. Genetics. 13:2737-2751 (2004) [PubMed]

  23. Jurka, J ., Evolutionary impact of human Alu repetitive elements. Curr. Opin. Genet. Dev. 14: 603-608 (2004) [PubMed]

  24. Kouprina, N., Pavlicek, A., Mochida, G., Solomon, G.,Ostot, J., Yoon, Y.-H., Collura, R., Ruvolo, M., Barrett, J.C., Woods, G., Walsh, C., Jurka, J ., Larionov, V. Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansion. PloS Biology, 5:1-11 (2004) [PubMed]

  25. Kapitonov, V.V., Jurka, J. Harbinger transposons and an ancient HARBI1 gene derived from a transposase. DNA and Cell Biol, 23:311-324(2004) [PubMed]

  26. Jurka, J ., Kohany, O., Pavlicek, A., Kapitonov, V.V., Jurka, M.V. Duplication, coclustering and selection of human Alu retrotransposons. Proc. Natl. Acad. Sci. USA 101: 1268-1272 (2004) [PubMed]

  27. Paces, J., Pavlicek, A., Zika, R., Kapitonov, V.V., Jurka, J., Paces, V. HERVd: the human endogenous retrovirus database: updat Nucleic Acids Res. Database issue:D50 Jan 1;32 (2004) [PubMed]

  28. Babcock, M., Pavlicek, A., Spiteri, E., Kashork, C.D.,Ioshikhes, I., Shaffer, L.G., Jurka, J. & Morrow, B.E. Shuffling of genes within low-copy repeats on 22q11 (LCR22) by Alu-mediated recombination events during evolution. Genome Res. 13:2519-2532(2003) [PubMed]

  29. 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).

  30. Jurka, J., Kapitonov, V.V., Smit, A.F.A. Repetitive elements: detection. Nature Encyclopedia of the Human Genome (Cooper, N.D., ed.), vol. 5, pp. 9-14, Nature Publishing Group, London, New York and Tokyo (2003).

  31. Kapitonov, V.V., Jurka, J. Molecular palentology of transposable elements in the Drosophila melanogaster genome. Proc. Natl. Acad. Sci. USA 100:6569-6574 (2003) [PubMed]

  32. Kapitonov, V.V. & Jurka, J. 5SRNA-derived SINE elements Mol Biol Evol. 20:694-702 (2003).

  33. Johanning, K., Stevenson, C.A., Oyeniran, O.O., Gozal, Y.M., Roy-Engel, A.M., Jurka, J. Deininger, P.L. Potential for retroposition by old Alu subfamilies J. Mol. Evol. Potential for retroposition by old Alu subfamilies. J Mol Evol. 56:658-664 (2003).

  34. Xing, J., A.-H. Salem, Hedges, D.J., Kilroy, G.E., Watkins W.S., Schienman, J.E., Stewart, C.-B., Jurka, J., Jorde, L.B., Batzer, M.A. Comprehensive analysis\ of two AluYd subfamilies J. Mol. Evol. 57:S76-S89 (2003).

  35. Kapitonov, V., Jurka, J. The esterase and PHD domains in CR1-like non-LTR retrotransposon Mol Biol Evol. 20:38-46 (2003) [PubMed]

  36. Jurka, J , Krnjajic, M., Kapitonov, V.V., Stenger, J.E., Kokhanyy, O. Active Alu elements are passed primarily through paternal germlines. Theor. Popul. Biol. 61:519-530 (2002) [PubMed]

  37. Chen, C., Gentles, A. J., Jurka, J. and Karlin, S. Genes, pseudogenes, and Alu sequence organization across human chromosomes 21 and 22. Proc. Natl. Acad. Sci. USA 99: 2930-2935 (2002) [PubMed]

  38. Jurka, J., Kapitonov, V.V. PIFs meet Tourists and Harbingers: A superfamily reunion. Proc. Natl. Acad. Sci. USA 98: 12315-12316 (2001) [PubMed]

  39. Kapitonov, V.V., Jurka, J. Rolling-circle transposons in eukaryotes. Proc. Natl. Acad. Sci. USA 98: 8714-8719 (2001) [PubMed]

  40. Kuryshev, V. Yu., Skryabin, B.V., 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. 309: 1049-1066 (2001) [PubMed]

  41. 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. 11(1):12-27 (2001) [pubMed]

  42. Jurka, J. Repbase Update: a database and an electronic journal of repetitive DNA. Trends in Genetics 16(9): 418-420 (2000) [PubMed]

  43. Toth, G., Gaspari, Z., Jurka, J. Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res. 10: 967-981 (2000) [PubMed]

  44. Lobachev, K.S., Stenger, J.E., Kozyreva, O..G., Jurka, J., Gordenin, D.A. and Resmick, M.A. Inverted Alu repeats unstable in yeast are excluded from the human genome. EMBO J. 19: 3822-3830 (2000) [PubMed]

  45. Kapitonov, V.V. and Jurka, J. Molecular paleontology of transposable elements from the Arabidopsis thaliana. Genetica 107:27-37, 1999 [PubMed]

  46. Jurka, J. and Kapitonov, V.V. Sectorial mutagenesis by transposable elements. Genetica 107:239-248, 1999 [PubMed]

  47. Kapitonov, V.V. and Jurka, J. The long terminal repeat of an endogenous retrovirus induces alternative splicing and encodes an additional carboxy-terminal sequences in human leptin receptor. J. Mol. Evol. 48(2):248-251, 1999 [PubMed]

  48. Jurka, J. Repeats in genomic DNA: mining and meaning. Curr. Opin. Struct. Biol. 8:333-337 (1998) [PubMed]

  49. Holmquist, G.P., Kapitonov, V.V. and Jurka, J. Mobile genetic elements, chiasmata, and unique organization of beta-heterochromatin. Cytogenet. Cell Genet. 80:113-116 (1998) [PubMed]

  50. Skryabin, B.V., Kremerskothen, J., Vassilacopoulou, D., Disotell, T.R., Kapitonov, V.V., Jurka, J. and Brosius, J. The BC200 RNA gene and its neural expression is conserved in the anthropoidea (primates). J. Mol. Evol. 47:677-685 (1998) [PubMed]

  51. Kapitonov, V.V., Holmquist, G. and Jurka, J. L1 repeat is a basic unit of heterochromatin satellites in cetaceans. Mol. Biol. Evol. 15(5):611-612 (1998) [PubMed]

  52. Kapitonov, V.V., Jurka, J. MER53, a non-autonomous DNA transposon associated with a variety of functionally related defense genes in the human genome. DNA Sequence —The Journal of Sequencing and Mapping 8(5):277–288 (1998).

  53. Jurka, J., Klonowski, P. and Trifonov, E.N. Mammalian retroposons integrate at kinkable DNA sites. J. Biomolecular Struct. and Dynam. 15(4):717-721 (1998) [PubMed]

  54. Jurka, J. Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons. Proc. Natl. Acad. Sci. USA 94:1872-1877 (1997) [PubMed]

  55. Bell, G.I., 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. 44(4):414-421 (1997) [PubMed]

  56. Jurka, J., Klonowski, P. Integration of retroposable elements in mammals: selection of target sites. J.Mol.Evol. 43:685-689 (1996) [PubMed]


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