Publications by authors named "Jerzy Jurka"

68Publications

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

PLoS One 2015 10;10(11):e0140084. Epub 2015 Nov 10.

Genetic Information Research Institute, Los Altos, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0140084PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4640811PMC
June 2016

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.

Science 2014 Dec 11;346(6215):1254449. Epub 2014 Dec 11.

Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA.

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http://jarvislab.net/wp-content/uploads/2012/02/Green-et-al-
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http://www.sciencemag.org/cgi/doi/10.1126/science.1254449
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http://dx.doi.org/10.1126/science.1254449DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4386873PMC
December 2014

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

Retrovirology 2014 Dec 12;11:71. Epub 2014 Dec 12.

Faculty of Veterinary Science, University of Sydney, Sydney, NSW, 2006, Australia.

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http://dx.doi.org/10.1186/s12977-014-0071-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299795PMC
December 2014

A superfamily of DNA transposons targeting multicopy small RNA genes.

PLoS One 2013 9;8(7):e68260. Epub 2013 Jul 9.

Genetic Information Research Institute, Mountain View, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0068260PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3706591PMC
February 2014

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

Mob DNA 2013 Apr 1;4(1):12. Epub 2013 Apr 1.

Genetic Information Research Institute, 1925 Landings Drive, Mountain View, CA, 94043, USA.

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http://dx.doi.org/10.1186/1759-8753-4-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3627910PMC
April 2013

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

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

HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA.

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http://dx.doi.org/10.1093/nar/gks1265DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531169PMC
January 2013

Genomic impact of eukaryotic transposable elements.

Mob DNA 2012 Nov 21;3(1):19. Epub 2012 Nov 21.

Institute of Experimental Pathology, ZMBE, University of Münster, Münster D-48149, Germany.

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http://dx.doi.org/10.1186/1759-8753-3-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3520738PMC
November 2012

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

Authors:
Martien A M Groenen Alan L Archibald Hirohide Uenishi Christopher K Tuggle Yasuhiro Takeuchi Max F Rothschild Claire Rogel-Gaillard Chankyu Park Denis Milan Hendrik-Jan Megens Shengting Li Denis M Larkin Heebal Kim Laurent A F Frantz Mario Caccamo Hyeonju Ahn Bronwen L Aken Anna Anselmo Christian Anthon Loretta Auvil Bouabid Badaoui Craig W Beattie Christian Bendixen Daniel Berman Frank Blecha Jonas Blomberg Lars Bolund Mirte Bosse Sara Botti Zhan Bujie Megan Bystrom Boris Capitanu Denise Carvalho-Silva Patrick Chardon Celine Chen Ryan Cheng Sang-Haeng Choi William Chow Richard C Clark Christopher Clee Richard P M A Crooijmans Harry D Dawson Patrice Dehais Fioravante De Sapio Bert Dibbits Nizar Drou Zhi-Qiang Du Kellye Eversole João Fadista Susan Fairley Thomas Faraut Geoffrey J Faulkner Katie E Fowler Merete Fredholm Eric Fritz James G R Gilbert Elisabetta Giuffra Jan Gorodkin Darren K Griffin Jennifer L Harrow Alexander Hayward Kerstin Howe Zhi-Liang Hu Sean J Humphray Toby Hunt Henrik Hornshøj Jin-Tae Jeon Patric Jern Matthew Jones Jerzy Jurka Hiroyuki Kanamori Ronan Kapetanovic Jaebum Kim Jae-Hwan Kim Kyu-Won Kim Tae-Hun Kim Greger Larson Kyooyeol Lee Kyung-Tai Lee Richard Leggett Harris A Lewin Yingrui Li Wansheng Liu Jane E Loveland Yao Lu Joan K Lunney Jian Ma Ole Madsen Katherine Mann Lucy Matthews Stuart McLaren Takeya Morozumi Michael P Murtaugh Jitendra Narayan Dinh Truong Nguyen Peixiang Ni Song-Jung Oh Suneel Onteru Frank Panitz Eung-Woo Park Hong-Seog Park Geraldine Pascal Yogesh Paudel Miguel Perez-Enciso Ricardo Ramirez-Gonzalez James M Reecy Sandra Rodriguez-Zas Gary A Rohrer Lauretta Rund Yongming Sang Kyle Schachtschneider Joshua G Schraiber John Schwartz Linda Scobie Carol Scott Stephen Searle Bertrand Servin Bruce R Southey Goran Sperber Peter Stadler Jonathan V Sweedler Hakim Tafer Bo Thomsen Rashmi Wali Jian Wang Jun Wang Simon White Xun Xu Martine Yerle Guojie Zhang Jianguo Zhang Jie Zhang Shuhong Zhao Jane Rogers Carol Churcher Lawrence B Schook

Nature 2012 Nov;491(7424):393-8

Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708 WD, Wageningen, The Netherlands.

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http://www.umass.edu/vetimm/docs/Groenen_etal_2012.pdf
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http://www.nature.com/doifinder/10.1038/nature11622
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http://dx.doi.org/10.1038/nature11622DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3566564PMC
November 2012

Horizontal transfers of Mariner transposons between mammals and insects.

Mob DNA 2012 Sep 26;3(1):14. Epub 2012 Sep 26.

Morphology Department, Bioscience Institute, UNESP - Sao Paulo State University, Botucatu, Sao Paulo, 18618-970, Brazil.

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http://mobilednajournal.biomedcentral.com/articles/10.1186/1
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http://dx.doi.org/10.1186/1759-8753-3-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3517439PMC
September 2012

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

Mob DNA 2011 Oct 19;2(1):12. Epub 2011 Oct 19.

Genetic Information Research Institute, 1925 Landings Drive, Mountain View, CA 94043, USA.

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http://dx.doi.org/10.1186/1759-8753-2-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3212892PMC
October 2011

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

Biol Direct 2011 Sep 19;6:44. Epub 2011 Sep 19.

Genetic Information Research Institute, 1925 Landings Drive, Mountain View, CA 94043, USA.

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http://dx.doi.org/10.1186/1745-6150-6-44DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3183009PMC
September 2011

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

Gene 2010 Oct 21;465(1-2):9-16. Epub 2010 Jun 21.

Genetic Information Research Institute, Mountain View, CA 94043, USA.

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http://dx.doi.org/10.1016/j.gene.2010.06.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2923044PMC
October 2010

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

Mob DNA 2010 Jan 25;1(1). Epub 2010 Jan 25.

Genetic Information Research Institute, Mountain View, CA, USA.

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http://dx.doi.org/10.1186/1759-8753-1-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2836005PMC
January 2010

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

Gene 2009 Dec 3;448(2):207-13. Epub 2009 Aug 3.

Genetic Information Research Institute, 1925 Landings Dr, Mountain View, CA 94041, USA.

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http://dx.doi.org/10.1016/j.gene.2009.07.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2829327PMC
December 2009

New superfamilies of eukaryotic DNA transposons and their internal divisions.

Mol Biol Evol 2009 May 27;26(5):983-93. Epub 2009 Jan 27.

Genetic Information Research Institute, Mountain View, CA, USA.

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http://dx.doi.org/10.1093/molbev/msp013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2727372PMC
May 2009

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

BMC Bioinformatics 2008 Aug 18;9:345. Epub 2008 Aug 18.

Genetic Information Research Institute, 1925 Landings Dr, Mountain View, CA 94043, USA.

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http://dx.doi.org/10.1186/1471-2105-9-345DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2527617PMC
August 2008

A universal classification of eukaryotic transposable elements implemented in Repbase.

Nat Rev Genet 2008 05;9(5):411-2; author reply 414

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http://dx.doi.org/10.1038/nrg2165-c1DOI Listing
May 2008

Helitrons on a roll: eukaryotic rolling-circle transposons.

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

Genetic Information Research Institute, 1925 Landings Drive, Mountain View, CA 94043, USA.

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http://dx.doi.org/10.1016/j.tig.2007.08.004DOI Listing
October 2007

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

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

Centre de Recherche, Hôpital Sainte-Justine, CHU Mère Enfant, 3175 Côte Sainte-Catherine, Montreal, QC, Canada, H3T 1C5.

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http://link.springer.com/content/pdf/10.1007/s00439-007-0413
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http://link.springer.com/10.1007/s00439-007-0413-4
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http://dx.doi.org/10.1007/s00439-007-0413-4DOI Listing
December 2007

Repetitive sequences in complex genomes: structure and evolution.

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

Genetic Information Research Institute, Mountain View, California 94043, USA.

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http://www.annualreviews.org/doi/10.1146/annurev.genom.8.080
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http://dx.doi.org/10.1146/annurev.genom.8.080706.092416DOI Listing
December 2007

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

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

Department of Radiology, School of Medicine, Stanford University, Stanford, California 94305, USA.

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http://www.genome.org/cgi/doi/10.1101/gr.6070707
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http://dx.doi.org/10.1101/gr.6070707DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899126PMC
July 2007

SINEs, evolution and genome structure in the opossum.

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

Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA.

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http://dx.doi.org/10.1016/j.gene.2007.02.028DOI Listing
July 2007

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

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

Institute of Experimental Pathology, ZMBE, University of Münster, Von-Esmarch-Str. 56, D-48149 Münster, Germany.

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http://dx.doi.org/10.1016/j.tig.2007.02.002DOI Listing
April 2007

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

BMC Bioinformatics 2006 Oct 25;7:474. Epub 2006 Oct 25.

Genetic Information Research Institute, 1925 Landings Drive, Mountain View, CA 94043, USA.

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http://dx.doi.org/10.1186/1471-2105-7-474DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1634758PMC
October 2006

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

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

Cold Spring Harbor Laboratory, Watson School of Biological Sciences and Howard Hughes Medical Institute, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.

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http://dx.doi.org/10.1038/nature05198DOI Listing
October 2006

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

Health Research and Education Center, Washington State University Spokane, Spokane, WA, 99210-1495, USA.

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http://dx.doi.org/10.1007/s00439-006-0222-1DOI Listing
November 2006

Positive selection on the nonhomologous end-joining factor Cernunnos-XLF in the human lineage.

Biol Direct 2006 Jun 2;1:15. Epub 2006 Jun 2.

Genetic Information Research Institute, Mountain View, CA 94043, USA.

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http://dx.doi.org/10.1186/1745-6150-1-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1552050PMC
June 2006

Self-synthesizing DNA transposons in eukaryotes.

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

Genetic Information Research Institute, 1925 Landings Drive, Mountain View, CA 94043, USA.

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http://dx.doi.org/10.1073/pnas.0600833103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1450207PMC
March 2006

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

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

Genetic Information Research Institute, 1925 Landings Drive, Mountain View, CA 94043, USA.

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http://dx.doi.org/10.1016/j.tig.2005.11.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1379630PMC
February 2006

Origin and diversification of minisatellites derived from human Alu sequences.

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

Genetic Information Research Institute, 1925 Landings Drive, Mountain View, CA 94043, USA.

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http://dx.doi.org/10.1016/j.gene.2005.09.029DOI Listing
January 2006

Evolutionary diversity and potential recombinogenic role of integration targets of Non-LTR retrotransposons.

Mol Biol Evol 2005 Oct 8;22(10):1983-91. Epub 2005 Jun 8.

Genetic Information Research Institute, Mountain View, California, USA.

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http://academic.oup.com/mbe/article/22/10/1983/1137956/Evolu
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http://dx.doi.org/10.1093/molbev/msi188DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1400617PMC
October 2005

RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons.

PLoS Biol 2005 Jun 24;3(6):e181. Epub 2005 May 24.

Genetic Information Research Institute, Mountain View, California, USA.

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http://dx.doi.org/10.1371/journal.pbio.0030181DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1131882PMC
June 2005

Analysis of the human Alu Ye lineage.

BMC Evol Biol 2005 Feb 22;5:18. Epub 2005 Feb 22.

Department of Biological Sciences, Biological Computation and Visualization Center, Center for Bio-Modular Multi-scale Systems, Louisiana State University, 202 Life Sciences Building, Baton Rouge, Louisiana 70803, USA.

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http://dx.doi.org/10.1186/1471-2148-5-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC554112PMC
February 2005

Evolutionary impact of human Alu repetitive elements.

Authors:
Jerzy Jurka

Curr Opin Genet Dev 2004 Dec;14(6):603-8

Genetic Information Research Institute, 1925 Landings Drive, Mountain View, CA 94043, USA.

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http://dx.doi.org/10.1016/j.gde.2004.08.008DOI Listing
December 2004

Harbinger transposons and an ancient HARBI1 gene derived from a transposase.

DNA Cell Biol 2004 May;23(5):311-24

Genetic Information Research Institute, Mountain View, California 94040, USA.

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http://dx.doi.org/10.1089/104454904323090949DOI Listing
May 2004

Comprehensive analysis of two Alu Yd subfamilies.

J Mol Evol 2003 ;57 Suppl 1:S76-89

Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA.

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http://dx.doi.org/10.1007/s00239-003-0009-0DOI Listing
August 2004

Duplication, coclustering, and selection of human Alu retrotransposons.

Proc Natl Acad Sci U S A 2004 Feb 21;101(5):1268-72. Epub 2004 Jan 21.

Genetic Information Research Institute, 2081 Landings Drive, Mountain View, CA 94043-0815, USA.

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http://dx.doi.org/10.1073/pnas.0308084100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC337042PMC
February 2004

HERVd: the Human Endogenous RetroViruses Database: update.

Nucleic Acids Res 2004 Jan;32(Database issue):D50

Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Flemingovo 2, CZ-16637 Prague, Czech Republic.

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http://dx.doi.org/10.1093/nar/gkh075DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC308809PMC
January 2004

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

Department of Molecular Genetics, Albert Einstein College of Medicine, Bronx, New York, New York 10461, USA.

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http://dx.doi.org/10.1101/gr.1549503DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403794PMC
December 2003

Potential for retroposition by old Alu subfamilies.

J Mol Evol 2003 Jun;56(6):658-64

Tulane Cancer Center SL-66, Department of Environmental Health Sciences, Tulane University Medical Center, 1430 Tulane Avenue, New Orleans, LA 70112, USA.

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http://dx.doi.org/10.1007/s00239-002-2433-yDOI Listing
June 2003

Molecular paleontology of transposable elements in the Drosophila melanogaster genome.

Proc Natl Acad Sci U S A 2003 May 12;100(11):6569-74. Epub 2003 May 12.

Genetic Information Research Institute, 2081 Landings Drive, Mountain View, CA 94043, USA.

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http://dx.doi.org/10.1073/pnas.0732024100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC164487PMC
May 2003

A novel class of SINE elements derived from 5S rRNA.

Mol Biol Evol 2003 May 2;20(5):694-702. Epub 2003 Apr 2.

Genetic Information Research Institute, Mountain View, California, USA.

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http://dx.doi.org/10.1093/molbev/msg075DOI Listing
May 2003

The esterase and PHD domains in CR1-like non-LTR retrotransposons.

Mol Biol Evol 2003 Jan;20(1):38-46

Genetic Information Research Institute, Mountain View, California, USA.

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http://dx.doi.org/10.1093/molbev/msg011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7528939PMC
January 2003

Active Alu elements are passed primarily through paternal germlines.

Theor Popul Biol 2002 Jun;61(4):519-30

Genetic Information Research Institute, Mountain View, California 94043, USA.

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http://dx.doi.org/10.1006/tpbi.2002.1602DOI Listing
June 2002

Genes, pseudogenes, and Alu sequence organization across human chromosomes 21 and 22.

Proc Natl Acad Sci U S A 2002 Mar 26;99(5):2930-5. Epub 2002 Feb 26.

Department of Mathematics, Stanford University, Stanford, CA 94305-2125, USA.

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http://dx.doi.org/10.1073/pnas.052692099DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC122450PMC
March 2002