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Finishing a whole-genome shotgun: Release 3 of the Drosophila melanogaster euchromatic genome sequence
Susan E Celniker, David A Wheeler, Brent Kronmiller, Joseph W Carlson, Aaron Halpern, Sandeep Patel, Mark Adams, Mark Champe, Shannon P Dugan, Erwin Frise, Ann Hodgson, Reed A George, Roger A Hoskins, Todd Laverty, Donna M Muzny, Catherine R Nelson, Joanne M Pacleb, Soo Park, Barret D Pfeiffer, Stephen Richards, Erica J Sodergren, Robert Svirskas, Paul E Tabor, Kenneth Wan, Mark Stapleton, Granger G Sutton, Craig Venter, George Weinstock, Steven E Scherer, Eugene W Myers, Richard A Gibbs, Gerald M Rubin
Genome Biol. 2002; 3(12): research0079.1–79.14. Published online 2002 December 23. doi: 10.1186/gb-2002-3-12-research0079
PMCID:
PMC151181
Abstract Full Text PDF–171K

Is Cited by the Following 79 Articles in this Archive:

LOESS correction for length variation in gene set-based genomic sequence analysis
Anton Aboukhalil, Martha L. Bulyk
Bioinformatics. 2012 June 1; 28(11): 1446–1454. Published online 2012 April 5. doi: 10.1093/bioinformatics/bts155
PMCID:
PMC3356840
Free in PMC on 2013/06/01
APRIN is a cell cycle specific BRCA2-interacting protein required for genome integrity and a predictor of outcome after chemotherapy in breast cancer
Rachel Brough, Ilirjana Bajrami, Radost Vatcheva, Rachael Natrajan, Jorge S Reis-Filho, Christopher J Lord, Alan Ashworth
EMBO J. 2012 March 7; 31(5): 1160–1176. Published online 2012 January 31. doi: 10.1038/emboj.2011.490
PMCID:
PMC3297997
Free in PMC on 2013/03/07
Hundreds of putatively functional small open reading frames in Drosophila
Emmanuel Ladoukakis, Vini Pereira, Emile G Magny, Adam Eyre-Walker, Juan Pablo Couso
Genome Biol. 2011; 12(11): R118. Published online 2011 November 25. doi: 10.1186/gb-2011-12-11-r118
PMCID:
PMC3334604
Abstract Full Text PDF–939K Supplementary Material
Intron retention in the Drosophila melanogaster Rieske iron sulphur protein gene generated a new protein
Alisson M. Gontijo, Veronica Miguela, Michael F. Whiting, R.C. Woodruff, Maria Dominguez
Nat Commun. 2011 May; 2: 323. Published online 2011 May 24. doi: 10.1038/ncomms1328
PMCID:
PMC3113295
Abstract Full Text PDF–1.9M Supplementary Material
The 19 Genomes of Drosophila: A BAC Library Resource for Genus-Wide and Genome-Scale Comparative Evolutionary Research
Xiang Song, Jose Luis Goicoechea, Jetty S. S. Ammiraju, Meizhong Luo, Ruifeng He, Jinke Lin, So-Jeong Lee, Nicholas Sisneros, Tom Watts, David A. Kudrna, Wolfgang Golser, Elizabeth Ashley, Kristi Collura, Michele Braidotti, Yeisoo Yu, Luciano M. Matzkin, Bryant F. McAllister, Therese Ann Markow, Rod A. Wing
Genetics. 2011 April; 187(4): 1023–1030. doi: 10.1534/genetics.111.126540
PMCID:
PMC3070512
Abstract Full Text PDF–610K
Conservation of an RNA regulatory map between Drosophila and mammals
Angela N. Brooks, Li Yang, Michael O. Duff, Kasper D. Hansen, Jung W. Park, Sandrine Dudoit, Steven E. Brenner, Brenton R. Graveley
Genome Res. 2011 February; 21(2): 193–202. doi: 10.1101/gr.108662.110
PMCID:
PMC3032923
Abstract Full Text PDF–758K
A Molecularly Defined Duplication Set for the X Chromosome of Drosophila melanogaster
Koen J. T. Venken, Ellen Popodi, Stacy L. Holtzman, Karen L. Schulze, Soo Park, Joseph W. Carlson, Roger A. Hoskins, Hugo J. Bellen, Thomas C. Kaufman
Genetics. 2010 December; 186(4): 1111–1125. doi: 10.1534/genetics.110.121285
PMCID:
PMC2998297
Abstract Full Text PDF–2.6M
The Drosophila Anion Exchanger (DAE) lacks a detectable interaction with the spectrin cytoskeleton
Ronald R Dubreuil, Amlan Das, Christine Base, G Harper Mazock
J Negat Results Biomed. 2010; 9: 5. Published online 2010 June 23. doi: 10.1186/1477-5751-9-5
PMCID:
PMC2901199
Abstract Full Text PDF–1.1M
Regulatory divergence in Drosophila revealed by mRNA-seq
C. Joel McManus, Joseph D. Coolon, Michael O. Duff, Jodi Eipper-Mains, Brenton R. Graveley, Patricia J. Wittkopp
Genome Res. 2010 June; 20(6): 816–825. doi: 10.1101/gr.102491.109
PMCID:
PMC2877578
Abstract Full Text PDF–788K
Linear plasmid vector for cloning of repetitive or unstable sequences in Escherichia coli
Ronald Godiska, David Mead, Vinay Dhodda, Chengcang Wu, Rebecca Hochstein, Attila Karsi, Karen Usdin, Ali Entezam, Nikolai Ravin
Nucleic Acids Res. 2010 April; 38(6): e88. Published online 2010 April. doi: 10.1093/nar/gkp1181
PMCID:
PMC2847241
Abstract Full Text PDF–7.7M
Gag Proteins of Drosophila Telomeric Retrotransposons: Collaborative Targeting to Chromosome Ends
Adelaide M. Fuller, Elizabeth G. Cook, Kerry J. Kelley, Mary-Lou Pardue
Genetics. 2010 March; 184(3): 629–636. doi: 10.1534/genetics.109.109744
PMCID:
PMC2845333
Abstract Full Text PDF–1.4M
Vasa promotes Drosophila germline stem cell differentiation by activating mei-P26 translation by directly interacting with a (U)-rich motif in its 3′ UTR
Niankun Liu, Hong Han, Paul Lasko
Genes Dev. 2009 December 1; 23(23): 2742–2752. doi: 10.1101/gad.1820709
PMCID:
PMC2788330
Abstract Full Text PDF–970K
Regulation of the Drosophila Enhancer of split and invected-engrailed Gene Complexes by Sister Chromatid Cohesion Proteins
Cheri A. Schaaf, Ziva Misulovin, Gurmukh Sahota, Akbar M. Siddiqui, Yuri B. Schwartz, Tatyana G. Kahn, Vincenzo Pirrotta, Maria Gause, Dale Dorsett
PLoS One. 2009; 4(7): e6202. Published online 2009 July 9. doi: 10.1371/journal.pone.0006202
PMCID:
PMC2703808
Abstract Full Text PDF–778K Supplementary Material
Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome
Elizabeth A Rach, Hsiang-Yu Yuan, William H Majoros, Pavel Tomancak, Uwe Ohler
Genome Biol. 2009; 10(7): R73. Published online 2009 July 9. doi: 10.1186/gb-2009-10-7-r73
PMCID:
PMC2728527
Abstract Full Text PDF–1.6M Supplementary Material
Chromosome level assembly of the hybrid Trypanosoma cruzi genome
D Brent Weatherly, Courtney Boehlke, Rick L Tarleton
BMC Genomics. 2009; 10: 255. Published online 2009 June 1. doi: 10.1186/1471-2164-10-255
PMCID:
PMC2698008
Abstract Full Text PDF–2.3M Supplementary Material
A whole-genome assembly of the domestic cow, Bos taurus
Aleksey V Zimin, Arthur L Delcher, Liliana Florea, David R Kelley, Michael C Schatz, Daniela Puiu, Finnian Hanrahan, Geo Pertea, Curtis P Van Tassell, Tad S Sonstegard, Guillaume Marçais, Michael Roberts, Poorani Subramanian, James A Yorke, Steven L Salzberg
Genome Biol. 2009; 10(4): R42. Published online 2009 April 24. doi: 10.1186/gb-2009-10-4-r42
PMCID:
PMC2688933
Abstract Full Text PDF–454K Supplementary Material
Quantitative measures for the management and comparison of annotated genomes
Karen Eilbeck, Barry Moore, Carson Holt, Mark Yandell
BMC Bioinformatics. 2009; 10: 67. Published online 2009 February 23. doi: 10.1186/1471-2105-10-67
PMCID:
PMC2653490
Abstract Full Text PDF–1.5M 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
COPI Complex Is a Regulator of Lipid Homeostasis
Mathias Beller, Carole Sztalryd, Noel Southall, Ming Bell, Herbert Jäckle, Douglas S Auld, Brian Oliver
PLoS Biol. 2008 November; 6(11): e292. Published online 2008 November 25. doi: 10.1371/journal.pbio.0060292
PMCID:
PMC2586367
Abstract Full Text PDF–2.3M 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
Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes
Pär G Engström, David Fredman, Boris Lenhard
Genome Biol. 2008; 9(2): R34. Published online 2008 February 15. doi: 10.1186/gb-2008-9-2-r34
PMCID:
PMC2374709
Abstract Full Text PDF–5.1M 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
Identification of novel regulatory factor X (RFX) target genes by comparative genomics in Drosophila species
Anne Laurençon, Raphaëlle Dubruille, Evgeni Efimenko, Guillaume Grenier, Ryan Bissett, Elisabeth Cortier, Vivien Rolland, Peter Swoboda, Bénédicte Durand
Genome Biol. 2007; 8(9): R195. Published online 2007 September 17. doi: 10.1186/gb-2007-8-9-r195
PMCID:
PMC2375033
Abstract Full Text PDF–2.0M Supplementary Material
A Maternal Screen for Genes Regulating Drosophila Oocyte Polarity Uncovers New Steps in Meiotic Progression
Vitor Barbosa, Naomi Kimm, Ruth Lehmann
Genetics. 2007 August; 176(4): 1967–1977. doi: 10.1534/genetics.106.069575
PMCID:
PMC1950606
Abstract Full Text PDF–1.7M
A 100%-complete sequence reveals unusually simple genomic features in the hot-spring red alga Cyanidioschyzon merolae
Hisayoshi Nozaki, Hiroyoshi Takano, Osami Misumi, Kimihiro Terasawa, Motomichi Matsuzaki, Shinichiro Maruyama, Keiji Nishida, Fumi Yagisawa, Yamato Yoshida, Takayuki Fujiwara, Susumu Takio, Katsunori Tamura, Sung Jin Chung, Soichi Nakamura, Haruko Kuroiwa, Kan Tanaka, Naoki Sato, Tsuneyoshi Kuroiwa
BMC Biol. 2007; 5: 28. Published online 2007 July 10. doi: 10.1186/1741-7007-5-28
PMCID:
PMC1955436
Abstract Full Text PDF–936K 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
Joint Estimates of Quantitative Trait Locus Effect and Frequency Using Synthetic Recombinant Populations of Drosophila melanogaster
Stuart J. Macdonald, Anthony D. Long
Genetics. 2007 June; 176(2): 1261–1281. doi: 10.1534/genetics.106.069641
PMCID:
PMC1894589
Abstract Full Text PDF–1.4M
Identification and characterization of insect-specific proteins by genome data analysis
Guojie Zhang, Hongsheng Wang, Junjie Shi, Xiaoling Wang, Hongkun Zheng, Gane Ka-Shu Wong, Terry Clark, Wen Wang, Jun Wang, Le Kang
BMC Genomics. 2007; 8: 93. Published online 2007 April 4. doi: 10.1186/1471-2164-8-93
PMCID:
PMC1852559
Abstract Full Text PDF–853K Supplementary Material
Complex regulation and multiple developmental functions of misfire, the Drosophila melanogaster ferlin gene
Michelle K Smith, Barbara T Wakimoto
BMC Dev Biol. 2007; 7: 21. Published online 2007 March 26. doi: 10.1186/1471-213X-7-21
PMCID:
PMC1853072
Abstract Full Text PDF–1.1M
A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome
Kerrin S Small, Michael Brudno, Matthew M Hill, Arend Sidow
Genome Biol. 2007; 8(3): R41. Published online 2007 March 20. doi: 10.1186/gb-2007-8-3-r41
PMCID:
PMC1868934
Abstract Full Text PDF–598K Supplementary Material
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