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Recurrent insertion and duplication generate networks of transposable element sequences in the Drosophila melanogaster genome
Casey M Bergman, Hadi Quesneville, Dominique Anxolabéhère, Michael Ashburner
Genome Biol. 2006; 7(11): R112. Published online 2006 November 29. doi: 10.1186/gb-2006-7-11-r112
PMCID:
PMC1794594
Abstract Full Text PDF–1.0M
 Is Cited by the Following 29 Articles in this Archive:
Sequencing of Pooled DNA Samples (Pool-Seq) Uncovers Complex Dynamics of Transposable Element Insertions in Drosophila melanogaster
Robert Kofler, Andrea J. Betancourt, Christian Schlötterer
PLoS Genet. 2012 January; 8(1): e1002487. Published online 2012 January 26. doi: 10.1371/journal.pgen.1002487
PMCID:
PMC3266889
Abstract Full Text PDF–517K Supplementary Material
Drosophila Duplication Hotspots Are Associated with Late-Replicating Regions of the Genome
Margarida Cardoso-Moreira, J. J. Emerson, Andrew G. Clark, Manyuan Long
PLoS Genet. 2011 November; 7(11): e1002340. Published online 2011 November 3. doi: 10.1371/journal.pgen.1002340
PMCID:
PMC3207856
Abstract Full Text PDF–355K Supplementary Material
The struggle for life of the genome's selfish architects
Aurélie Hua-Van, Arnaud Le Rouzic, Thibaud S Boutin, Jonathan Filée, Pierre Capy
Biol Direct. 2011; 6: 19. Published online 2011 March 17. doi: 10.1186/1745-6150-6-19
PMCID:
PMC3072357
Abstract Full Text PDF–1.0M Supplementary Material
Considering Transposable Element Diversification in De Novo Annotation Approaches
Timothée Flutre, Elodie Duprat, Catherine Feuillet, Hadi Quesneville
PLoS One. 2011; 6(1): e16526. Published online 2011 January 31. doi: 10.1371/journal.pone.0016526
PMCID:
PMC3031573
Abstract Full Text PDF–515K Supplementary Material
An in vivo RNAi assay identifies major genetic and cellular requirements for primary piRNA biogenesis in Drosophila
Daniel Olivieri, Martina M Sykora, Ravi Sachidanandam, Karl Mechtler, Julius Brennecke
EMBO J. 2010 October 6; 29(19): 3301–3317. Published online 2010 September 3. doi: 10.1038/emboj.2010.212
PMCID:
PMC2957214
Abstract Full Text PDF–3.4M Supplementary Material
Evolution of a Distinct Genomic Domain in Drosophila: Comparative Analysis of the Dot Chromosome in Drosophila melanogaster and Drosophila virilis
Wilson Leung, Christopher D. Shaffer, Taylor Cordonnier, Jeannette Wong, Michelle S. Itano, Elizabeth E. Slawson Tempel, Elmer Kellmann, David Michael Desruisseau, Carolyn Cain, Robert Carrasquillo, Tien M. Chusak, Katazyna Falkowska, Kelli D. Grim, Rui Guan, Jacquelyn Honeybourne, Sana Khan, Louis Lo, Rebecca McGaha, Jevon Plunkett, Justin M. Richner, Ryan Richt, Leah Sabin, Anita Shah, Anushree Sharma, Sonal Singhal, Fine Song, Christopher Swope, Craig B. Wilen, Jeremy Buhler, Elaine R. Mardis, Sarah C. R. Elgin
Genetics. 2010 August; 185(4): 1519–1534. doi: 10.1534/genetics.110.116129
PMCID:
PMC2927774
Abstract Full Text PDF–3.9M
The Evolution of tRNA Genes in Drosophila
Hubert H. Rogers, Casey M. Bergman, Sam Griffiths-Jones
Genome Biol Evol. 2010; 2: 467–477. Published online 2010 June 23. doi: 10.1093/gbe/evq034
PMCID:
PMC2997554
Abstract Full Text PDF–535K
Transposable elements in natural populations of Drosophila melanogaster
Yuh Chwen G. Lee, Charles H. Langley
Philos Trans R Soc Lond B Biol Sci. 2010 April 27; 365(1544): 1219–1228. doi: 10.1098/rstb.2009.0318
PMCID:
PMC2871824
Abstract Full Text PDF–475K
Mutational bias shaping fly copy number variation: implications for genome evolution
Margarida M. Cardoso-Moreira, Manyuan Long
Trends Genet. Author manuscript; available in PMC 2011 June 1.
Published in final edited form as: Trends Genet. 2010 June; 26(6): 243–247. Published online 2010 April 21. doi: 10.1016/j.tig.2010.03.002
PMCID:
PMC2878862
Abstract Full Text PDF–545K Supplementary Material
Large-scale discovery of insertion hotspots and preferential integration sites of human transposed elements
Asaf Levy, Schraga Schwartz, Gil Ast
Nucleic Acids Res. 2010 March; 38(5): 1515–1530. Published online 2010 March. doi: 10.1093/nar/gkp1134
PMCID:
PMC2836564
Abstract Full Text PDF–4.6M Supplementary Material
Population dynamics of PIWI-interacting RNAs (piRNAs) and their targets in Drosophila
Jian Lu, Andrew G. Clark
Genome Res. 2010 February; 20(2): 212–227. doi: 10.1101/gr.095406.109
PMCID:
PMC2813477
Abstract Full Text PDF–508K
The Transposon Galileo Generates Natural Chromosomal Inversions in Drosophila by Ectopic Recombination
Alejandra Delprat, Bàrbara Negre, Marta Puig, Alfredo Ruiz
PLoS One. 2009; 4(11): e7883. Published online 2009 November 18. doi: 10.1371/journal.pone.0007883
PMCID:
PMC2775673
Abstract Full Text PDF–714K Supplementary Material
Population Genomic Inferences from Sparse High-Throughput Sequencing of Two Populations of Drosophila melanogaster
Timothy B. Sackton, Rob J. Kulathinal, Casey M. Bergman, Aaron R. Quinlan, Erik B. Dopman, Mauricio Carneiro, Gabor T. Marth, Daniel L. Hartl, Andrew G. Clark
Genome Biol Evol. 2009; 1: 449–465. Published online 2009 November 18. doi: 10.1093/gbe/evp048
PMCID:
PMC2839279
Abstract Full Text PDF–762K Supplementary Material
Fine-grained annotation and classification of de novo predicted LTR retrotransposons
Sascha Steinbiss, Ute Willhoeft, Gordon Gremme, Stefan Kurtz
Nucleic Acids Res. 2009 November; 37(21): 7002–7013. Published online 2009 November. doi: 10.1093/nar/gkp759
PMCID:
PMC2790888
Abstract Full Text PDF–1.9M Supplementary Material
Exploring Repetitive DNA Landscapes Using REPCLASS, a Tool That Automates the Classification of Transposable Elements in Eukaryotic Genomes
Cédric Feschotte, Umeshkumar Keswani, Nirmal Ranganathan, Marcel L. Guibotsy, David Levine
Genome Biol Evol. 2009; 1: 205–220. Published online 2009 July 23. doi: 10.1093/gbe/evp023
PMCID:
PMC2817418
Abstract Full Text PDF–516K Supplementary Material
General gene movement off the X chromosome in the Drosophila genus
Maria D. Vibranovski, Yong Zhang, Manyuan Long
Genome Res. 2009 May; 19(5): 897–903. doi: 10.1101/gr.088609.108
PMCID:
PMC2675978
Abstract Full Text PDF–199K
Small RNAs as Guardians of the Genome
Colin D. Malone, Gregory J. Hannon
Cell. Author manuscript; available in PMC 2009 December 14.
Published in final edited form as: Cell. 2009 February 20; 136(4): 656–668. doi: 10.1016/j.cell.2009.01.045
PMCID:
PMC2792755
Abstract Full Text PDF–1.0M
Widespread evidence for horizontal transfer of transposable elements across Drosophila genomes
Carolina Bartolomé, Xabier Bello, Xulio Maside
Genome Biol. 2009; 10(2): R22. Published online 2009 February 18. doi: 10.1186/gb-2009-10-2-r22
PMCID:
PMC2688281
Abstract Full Text PDF–1.3M Supplementary Material
Automated paleontology of repetitive DNA with REANNOTATE
Vini Pereira
BMC Genomics. 2008; 9: 614. Published online 2008 December 18. doi: 10.1186/1471-2164-9-614
PMCID:
PMC2672092
Abstract Full Text PDF–521K Supplementary Material
Distribution of the transposable elements bilbo and gypsy in original and colonizing populations of Drosophila subobscura
María Pilar García Guerreiro, Blanca E Chávez-Sandoval, Joan Balanyà, Lluís Serra, Antonio Fontdevila
BMC Evol Biol. 2008; 8: 234. Published online 2008 August 14. doi: 10.1186/1471-2148-8-234
PMCID:
PMC2533020
Abstract Full Text PDF–387K Supplementary Material
The Effects of Recombination Rate on the Distribution and Abundance of Transposable Elements
Elie S. Dolgin, Brian Charlesworth
Genetics. 2008 April; 178(4): 2169–2177. doi: 10.1534/genetics.107.082743
PMCID:
PMC2323806
Abstract Full Text PDF–247K
Abundant and species-specific DINE-1 transposable elements in 12 Drosophila genomes
Hsiao-Pei Yang, Daniel A Barbash
Genome Biol. 2008; 9(2): R39. Published online 2008 February 21. doi: 10.1186/gb-2008-9-2-r39
PMCID:
PMC2374699
Abstract Full Text PDF–518K Supplementary Material
Repetitive Element-Mediated Recombination as a Mechanism for New Gene Origination in Drosophila
Shuang Yang, J. Roman Arguello, Xin Li, Yun Ding, Qi Zhou, Ying Chen, Yue Zhang, Ruoping Zhao, Frédéric Brunet, Lixin Peng, Manyuan Long, Wen Wang
PLoS Genet. 2008 January; 4(1): e3. Prepublished online 2007 November 27. Published online 2008 January 18. doi: 10.1371/journal.pgen.0040003
PMCID:
PMC2211543
Abstract Full Text PDF–521K Supplementary Material
Molecular Landscape of Modified Histones in Drosophila Heterochromatic Genes and Euchromatin-Heterochromatin Transition Zones
Jiro C Yasuhara, Barbara T Wakimoto
PLoS Genet. 2008 January; 4(1): e16. Prepublished online 2007 December 13. Published online 2008 January 18. doi: 10.1371/journal.pgen.0040016
PMCID:
PMC2211541
Abstract Full Text PDF–969K Supplementary Material
Genome Organization and Gene Expression Shape the Transposable Element Distribution in the Drosophila melanogaster Euchromatin
Pierre Fontanillas, Daniel L Hartl, Max Reuter
PLoS Genet. 2007 November; 3(11): e210. Prepublished online 2007 October 9. Published online 2007 November 30. doi: 10.1371/journal.pgen.0030210
PMCID:
PMC2098804
Abstract Full Text PDF–397K Supplementary Material
A model of segmental duplication formation in Drosophila melanogaster
Anna-Sophie Fiston-Lavier, Dominique Anxolabehere, Hadi Quesneville
Genome Res. 2007 October; 17(10): 1458–1470. doi: 10.1101/gr.6208307
PMCID:
PMC1987339
Abstract Full Text PDF–1.0M
Recent LTR retrotransposon insertion contrasts with waves of non-LTR insertion since speciation in Drosophila melanogaster
Casey M. Bergman, Douda Bensasson
Proc Natl Acad Sci U S A. 2007 July 3; 104(27): 11340–11345. Published online 2007 June 25. doi: 10.1073/pnas.0702552104
PMCID:
PMC2040900
Abstract Full Text PDF–326K Supplementary Material
The Release 5.1 Annotation of Drosophila melanogaster Heterochromatin
Christopher D. Smith, ShengQiang Shu, Christopher J. Mungall, Gary H. Karpen
Science. Author manuscript; available in PMC 2010 February 10.
Published in final edited form as: Science. 2007 June 15; 316(5831): 1586. doi: 10.1126/science.1139815
PMCID:
PMC2819280
Abstract Full Text PDF–1.3M Supplementary Material
Principles of Genome Evolution in the Drosophila melanogaster Species Group
José M Ranz, Damien Maurin, Yuk S Chan, Marcin von Grotthuss, LaDeana W Hillier, John Roote, Michael Ashburner, Casey M Bergman
PLoS Biol. 2007 June; 5(6): e152. Published online 2007 June 5. doi: 10.1371/journal.pbio.0050152
PMCID:
PMC1885836
Abstract Full Text PDF–694K Supplementary Material
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