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Heterochromatic sequences in a Drosophila whole-genome shotgun assembly
Roger A Hoskins, Christopher D Smith, Joseph W Carlson, A Bernardo Carvalho, Aaron Halpern, Joshua S Kaminker, Cameron Kennedy, Chris J Mungall, Beth A Sullivan, Granger G Sutton, Jiro C Yasuhara, Barbara T Wakimoto, Eugene W Myers, Susan E Celniker, Gerald M Rubin, Gary H Karpen
Genome Biol. 2002; 3(12): research0085.1–85.16. Published online 2002 December 31. doi: 10.1186/gb-2002-3-12-research0085
PMCID:
PMC151187
Abstract Full Text PDF–280K Supplementary Material

Is Cited by the Following 41 Articles in this Archive:

Transcriptional analysis of the HeT-A retrotransposon in mutant and wild type stocks reveals high sequence variability at Drosophila telomeres and other unusual features
David Piñeyro, Elisenda López-Panadès, María Lucena-Pérez, Elena Casacuberta
BMC Genomics. 2011; 12: 573. Published online 2011 November 23. doi: 10.1186/1471-2164-12-573
PMCID:
PMC3235214
Abstract Full Text PDF–1.4M Supplementary Material
Imaginal Discs – A New Source of Chromosomes for Genome Mapping of the Yellow Fever Mosquito Aedes aegypti
Maria V. Sharakhova, Vladimir A. Timoshevskiy, Fan Yang, Sergei Iu. Demin, David W. Severson, Igor V. Sharakhov
PLoS Negl Trop Dis. 2011 October; 5(10): e1335. Published online 2011 October 4. doi: 10.1371/journal.pntd.0001335
PMCID:
PMC3186762
Abstract Full Text PDF–2.7M
Retrotransposon-Induced Heterochromatin Spreading in the Mouse Revealed by Insertional Polymorphisms
Rita Rebollo, Mohammad M. Karimi, Misha Bilenky, Liane Gagnier, Katharine Miceli-Royer, Ying Zhang, Preeti Goyal, Thomas M. Keane, Steven Jones, Martin Hirst, Matthew C. Lorincz, Dixie L. Mager
PLoS Genet. 2011 September; 7(9): e1002301. Published online 2011 September 29. doi: 10.1371/journal.pgen.1002301
PMCID:
PMC3183085
Abstract Full Text PDF–1.6M Supplementary Material
Conservation and Purifying Selection of Transcribed Genes Located in a Rice Centromere
Chuanzhu Fan, Jason G. Walling, Jianwei Zhang, Cory D. Hirsch, Jiming Jiang, Rod A. Wing
Plant Cell. 2011 August; 23(8): 2821–2830. Published online 2011 August 19. doi: 10.1105/tpc.111.085605
PMCID:
PMC3180794
Free in PMC on 2012/08/01
Genomic Organization of H2Av Containing Nucleosomes in Drosophila Heterochromatin
Zhenhai Zhang, B. Franklin Pugh
PLoS One. 2011; 6(6): e20511. Published online 2011 June 27. doi: 10.1371/journal.pone.0020511
PMCID:
PMC3124471
Abstract Full Text PDF–813K Supplementary Material
Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin
Nicole C. Riddle, Aki Minoda, Peter V. Kharchenko, Artyom A. Alekseyenko, Yuri B. Schwartz, Michael Y. Tolstorukov, Andrey A. Gorchakov, Jacob D. Jaffe, Cameron Kennedy, Daniela Linder-Basso, Sally E. Peach, Gregory Shanower, Haiyan Zheng, Mitzi I. Kuroda, Vincenzo Pirrotta, Peter J. Park, Sarah C.R. Elgin, Gary H. Karpen
Genome Res. 2011 February; 21(2): 147–163. doi: 10.1101/gr.110098.110
PMCID:
PMC3032919
Abstract Full Text PDF–2.1M
Functional antagonism between histone H3K4 demethylases in vivo
Luisa Di Stefano, James A. Walker, Giosalba Burgio, Davide F.V. Corona, Peter Mulligan, Anders M. Näär, Nicholas J. Dyson
Genes Dev. 2011 January 1; 25(1): 17–28. doi: 10.1101/gad.1983711
PMCID:
PMC3012933
Abstract Full Text PDF–1.2M
Genome mapping and characterization of the Anopheles gambiae heterochromatin
Maria V Sharakhova, Phillip George, Irina V Brusentsova, Scotland C Leman, Jeffrey A Bailey, Christopher D Smith, Igor V Sharakhov
BMC Genomics. 2010; 11: 459. Published online 2010 August 4. doi: 10.1186/1471-2164-11-459
PMCID:
PMC3091655
Abstract Full Text PDF–2.8M Supplementary Material
The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation
Sandra N Loevenich, Erich Brunner, Nichole L King, Eric W Deutsch, Stephen E Stein, The FlyBase Consortium, Ruedi Aebersold, Ernst Hafen
BMC Bioinformatics. 2009; 10: 59. Published online 2009 February 11. doi: 10.1186/1471-2105-10-59
PMCID:
PMC2648944
Abstract Full Text PDF–665K Supplementary Material
ReRep: Computational detection of repetitive sequences in genome survey sequences (GSS)
Thomas D Otto, Leonardo HF Gomes, Marcelo Alves-Ferreira, Antonio B de Miranda, Wim M Degrave
BMC Bioinformatics. 2008; 9: 366. Published online 2008 September 9. doi: 10.1186/1471-2105-9-366
PMCID:
PMC2559850
Abstract Full Text PDF–1016K Supplementary Material
Rudra Interrupts Receptor Signaling Complexes to Negatively Regulate the IMD Pathway
Kamna Aggarwal, Florentina Rus, Christie Vriesema-Magnuson, Deniz Ertürk-Hasdemir, Nicholas Paquette, Neal Silverman
PLoS Pathog. 2008 August; 4(8): e1000120. Published online 2008 August 8. doi: 10.1371/journal.ppat.1000120
PMCID:
PMC2483946
Abstract Full Text PDF–488K Supplementary Material
Two New Y-Linked Genes in Drosophila melanogaster
Maria D. Vibranovski, Leonardo B. Koerich, A. Bernardo Carvalho
Genetics. 2008 August; 179(4): 2325–2327. doi: 10.1534/genetics.108.086819
PMCID:
PMC2516102
Abstract Full Text PDF–71K
A Competition between Stimulators and Antagonists of Upf Complex Recruitment Governs Human Nonsense-Mediated mRNA Decay
Guramrit Singh, Indrani Rebbapragada, Jens Lykke-Andersen
PLoS Biol. 2008 April; 6(4): e111. Published online 2008 April 29. doi: 10.1371/journal.pbio.0060111
PMCID:
PMC2689706
Abstract Full Text PDF–646K Supplementary Material
Analysis of repetitive DNA distribution patterns in the Tribolium castaneum genome
Suzhi Wang, Marcé D Lorenzen, Richard W Beeman, Susan J Brown
Genome Biol. 2008; 9(3): R61. Published online 2008 March 26. doi: 10.1186/gb-2008-9-3-r61
PMCID:
PMC2397513
Abstract Full Text PDF–582K Supplementary Material
Phosphoproteome Analysis of Drosophila melanogaster Embryos
Bo Zhai, Judit Villén, Sean A. Beausoleil, Julian Mintseris, Steven P. Gygi
J Proteome Res. Author manuscript; available in PMC 2011 March 25.
Published in final edited form as: J Proteome Res. 2008 April; 7(4): 1675–1682. Published online 2008 March 8. doi: 10.1021/pr700696a
PMCID:
PMC3063950
Abstract Full Text PDF–1.6M Supplementary Material
Analysis of Drosophila Species Genome Size and Satellite DNA Content Reveals Significant Differences Among Strains as Well as Between Species
Giovanni Bosco, Paula Campbell, Joao T. Leiva-Neto, Therese A. Markow
Genetics. 2007 November; 177(3): 1277–1290. doi: 10.1534/genetics.107.075069
PMCID:
PMC2147996
Abstract Full Text PDF–1.0M
The ribosomal protein genes and Minute loci of Drosophila melanogaster
Steven J Marygold, John Roote, Gunter Reuter, Andrew Lambertsson, Michael Ashburner, Gillian H Millburn, Paul M Harrison, Zhan Yu, Naoya Kenmochi, Thomas C Kaufman, Sally J Leevers, Kevin R Cook
Genome Biol. 2007; 8(10): R216. Published online 2007 October 10. doi: 10.1186/gb-2007-8-10-r216
PMCID:
PMC2246290
Abstract Full Text PDF–1.7M 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
Sequence Finishing and Mapping of Drosophila melanogaster Heterochromatin
Roger A. Hoskins, Joseph W. Carlson, Cameron Kennedy, David Acevedo, Martha Evans-Holm, Erwin Frise, Kenneth H. Wan, Soo Park, Maria Mendez-Lago, Fabrizio Rossi, Alfredo Villasante, Patrizio Dimitri, Gary H. Karpen, Susan E. Celniker
Science. Author manuscript; available in PMC 2010 February 19.
Published in final edited form as: Science. 2007 June 15; 316(5831): 1625–1628. doi: 10.1126/science.1139816
PMCID:
PMC2825053
Abstract Full Text PDF–858K Supplementary Material
Mechanism of Copper Mediated Triple Helix Formation at Neutral pH in Drosophila Satellite Repeats
C. Paris, F. Geinguenaud, C. Gouyette, J. Liquier, J. Lacoste
Biophys J. 2007 April 1; 92(7): 2498–2506. Published online 2007 January 5. doi: 10.1529/biophysj.106.099788
PMCID:
PMC1864847
Abstract Full Text PDF–199K
roX RNAs Are Required for Increased Expression of X-Linked Genes in Drosophila melanogaster Males
Xinxian Deng, Victoria H. Meller
Genetics. 2006 December; 174(4): 1859–1866. doi: 10.1534/genetics.106.064568
PMCID:
PMC1698640
Abstract Full Text PDF–1.1M
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
BAC CLONES GENERATED FROM SHEARED DNA
Kazutoyo Osoegawa, Gery M. Vessere, Chung Li Shu, Roger A. Hoskins, José P. Abad, Beatriz de Pablos, Alfredo Villasante, Pieter J. de Jong
Genomics. Author manuscript; available in PMC 2007 July 5.
Published in final edited form as: Genomics. 2007 February; 89(2): 291–299. Published online 2006 November 13. doi: 10.1016/j.ygeno.2006.10.002
PMCID:
PMC1909752
Abstract Full Text PDF–401K
FlyBase: genomes by the dozen
Madeline A. Crosby, Joshua L. Goodman, Victor B. Strelets, Peili Zhang, William M. Gelbart, The FlyBase Consortium
Nucleic Acids Res. 2007 January; 35(Database issue): D486–D491. Published online 2006 November 11. doi: 10.1093/nar/gkl827
PMCID:
PMC1669768
Abstract Full Text PDF–1.3M
Identification of transposable elements using multiple alignments of related genomes
Anat Caspi, Lior Pachter
Genome Res. 2006 February; 16(2): 260–270. doi: 10.1101/gr.4361206
PMCID:
PMC1361722
Abstract Full Text PDF–457K
Combined Evidence Annotation of Transposable Elements in Genome Sequences
Hadi Quesneville, Casey M Bergman, Olivier Andrieu, Delphine Autard, Danielle Nouaud, Michael Ashburner, Dominique Anxolabehere
PLoS Comput Biol. 2005 July; 1(2): e22. Published online 2005 July 29. doi: 10.1371/journal.pcbi.0010022
PMCID:
PMC1185648
Abstract Full Text PDF–273K
Positive Selection Drives the Evolution of rhino, a Member of the Heterochromatin Protein 1 Family in Drosophila
Danielle Vermaak, Steven Henikoff, Harmit S Malik
PLoS Genet. 2005 July; 1(1): e9. Published online 2005 July 25. doi: 10.1371/journal.pgen.0010009
PMCID:
PMC1183528
Abstract Full Text PDF–670K Supplementary Material
Evolution of heterochromatic genes of Drosophila
Jiro C. Yasuhara, Christine H. DeCrease, Barbara T. Wakimoto
Proc Natl Acad Sci U S A. 2005 August 2; 102(31): 10958–10963. Published online 2005 July 20. doi: 10.1073/pnas.0503424102
PMCID:
PMC1176909
Abstract Full Text PDF–795K Supplementary Material
DEDB: a database of Drosophila melanogaster exons in splicing graph form
Bernett TK Lee, Tin Wee Tan, Shoba Ranganathan
BMC Bioinformatics. 2004; 5: 189. Published online 2004 December 7. doi: 10.1186/1471-2105-5-189
PMCID:
PMC538278
Abstract Full Text PDF–865K
cis-Acting Determinants of Heterochromatin Formation on Drosophila melanogaster Chromosome Four
Fang-Lin Sun, Karmella Haynes, Cory L. Simpson, Susan D. Lee, Lynne Collins, Jo Wuller, Joel C. Eissenberg, S. C. R. Elgin
Mol Cell Biol. 2004 September; 24(18): 8210–8220. doi: 10.1128/MCB.24.18.8210-8220.2004
PMCID:
PMC515050
Abstract Full Text PDF–725K
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