My NCBISign In
Annotation of the Drosophila melanogaster euchromatic genome: a systematic review
Sima Misra, Madeline A Crosby, Christopher J Mungall, Beverley B Matthews, Kathryn S Campbell, Pavel Hradecky, Yanmei Huang, Joshua S Kaminker, Gillian H Millburn, Simon E Prochnik, Christopher D Smith, Jonathan L Tupy, Eleanor J Whitfield, Leyla Bayraktaroglu, Benjamin P Berman, Brian R Bettencourt, Susan E Celniker, Aubrey DNJ de Grey, Rachel A Drysdale, Nomi L Harris, John Richter, Susan Russo, Andrew J Schroeder, ShengQiang Shu, Mark Stapleton, Chihiro Yamada, Michael Ashburner, William M Gelbart, Gerald M Rubin, Suzanna E Lewis
Genome Biol. 2002; 3(12): research0083.1–83.22. Published online 2002 December 31. doi: 10.1186/gb-2002-3-12-research0083
PMCID:
PMC151185
Abstract Full Text PDF–1.1M Supplementary Material

Is Cited by the Following 81 Articles in this Archive:

The Role of Background Selection in Shaping Patterns of Molecular Evolution and Variation: Evidence from Variability on the Drosophila X Chromosome
Brian Charlesworth
Genetics. 2012 May; 191(1): 233–246. doi: 10.1534/genetics.111.138073
PMCID:
PMC3338263
Free in PMC on 2013/05/01
Poly(ADP-ribose) controls DE-cadherin-dependent stem cell maintenance and oocyte localization
Yingbiao Ji, Alexei V. Tulin
Nat Commun. Author manuscript; available in PMC 2013 March 27.
Published in final edited form as: Nat Commun. 2012 March 27; 3: 760. doi: 10.1038/ncomms1759
PMCID:
PMC3319983
Free in PMC on 2013/03/27
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
Approaches to Fungal Genome Annotation
Brian J. Haas, Qiandong Zeng, Matthew D. Pearson, Christina A. Cuomo, Jennifer R. Wortman
Mycology. Author manuscript; available in PMC 2012 October 3.
Published in final edited form as: Mycology. 2011 October 3; 2(3): 118–141. doi: 10.1080/21501203.2011.606851
PMCID:
PMC3207268
Free in PMC on 2012/10/03
Somatic sex-specific transcriptome differences in Drosophila revealed by whole transcriptome sequencing
Peter L Chang, Joseph P Dunham, Sergey V Nuzhdin, Michelle N Arbeitman
BMC Genomics. 2011; 12: 364. Published online 2011 July 14. doi: 10.1186/1471-2164-12-364
PMCID:
PMC3152543
Abstract Full Text PDF–4.5M Supplementary Material
The Drosophila Gene Disruption Project: Progress Using Transposons With Distinctive Site Specificities
Hugo J. Bellen, Robert W. Levis, Yuchun He, Joseph W. Carlson, Martha Evans-Holm, Eunkyung Bae, Jaeseob Kim, Athanasios Metaxakis, Charalambos Savakis, Karen L. Schulze, Roger A. Hoskins, Allan C. Spradling
Genetics. 2011 July; 188(3): 731–743. doi: 10.1534/genetics.111.126995
PMCID:
PMC3176542
Free in PMC on 2012/07/01
Synergistic use of plant-prokaryote comparative genomics for functional annotations
Svetlana Gerdes, Basma El Yacoubi, Marc Bailly, Ian K Blaby, Crysten E Blaby-Haas, Linda Jeanguenin, Aurora Lara-Núñez, Anne Pribat, Jeffrey C Waller, Andreas Wilke, Ross Overbeek, Andrew D Hanson, Valérie de Crécy-Lagard
BMC Genomics. 2011; 12(Suppl 1): S2. Published online 2011 June 15. doi: 10.1186/1471-2164-12-S1-S2
PMCID:
PMC3223725
Abstract Full Text PDF–718K Supplementary Material
Convergent transcription confers a bistable switch in Enterococcus faecalis conjugation
Anushree Chatterjee, Christopher M. Johnson, Che-Chi Shu, Yiannis N. Kaznessis, Doraiswami Ramkrishna, Gary M. Dunny, Wei-Shou Hu
Proc Natl Acad Sci U S A. 2011 June 7; 108(23): 9721–9726. Published online 2011 May 23. doi: 10.1073/pnas.1101569108
PMCID:
PMC3111305
Abstract Full Text PDF–743K Supplementary Material
Genome-wide analysis of promoter architecture in Drosophila melanogaster
Roger A. Hoskins, Jane M. Landolin, James B. Brown, Jeremy E. Sandler, Hazuki Takahashi, Timo Lassmann, Charles Yu, Benjamin W. Booth, Dayu Zhang, Kenneth H. Wan, Li Yang, Nathan Boley, Justen Andrews, Thomas C. Kaufman, Brenton R. Graveley, Peter J. Bickel, Piero Carninci, Joseph W. Carlson, Susan E. Celniker
Genome Res. 2011 February; 21(2): 182–192. doi: 10.1101/gr.112466.110
PMCID:
PMC3032922
Abstract Full Text PDF–900K
Experimental RNomics and genomic comparative analysis reveal a large group of species-specific small non-message RNAs in the silkworm Bombyx mori
Dandan Li, Yanhong Wang, Kun Zhang, Zhujin Jiao, Xiaopeng Zhu, Geir Skogerboe, Xiangqian Guo, Viswanathan Chinnusamy, Lijun Bi, Yongping Huang, Shuanglin Dong, Runsheng Chen, Yunchao Kan
Nucleic Acids Res. 2011 May; 39(9): 3792–3805. Published online 2011 January 10. doi: 10.1093/nar/gkq1317
PMCID:
PMC3089462
Abstract Full Text PDF–6.8M Supplementary Material
The Prevalence and Regulation of Antisense Transcripts in Schizosaccharomyces pombe
Ting Ni, Kang Tu, Zhong Wang, Shen Song, Han Wu, Bin Xie, Kristin C. Scott, Shiv I. Grewal, Yuan Gao, Jun Zhu
PLoS One. 2010; 5(12): e15271. Published online 2010 December 20. doi: 10.1371/journal.pone.0015271
PMCID:
PMC3004915
Abstract Full Text PDF–522K Supplementary Material
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
TOPSAN: a collaborative annotation environment for structural genomics
Dana Weekes, S Sri Krishna, Constantina Bakolitsa, Ian A Wilson, Adam Godzik, John Wooley
BMC Bioinformatics. 2010; 11: 426. Published online 2010 August 17. doi: 10.1186/1471-2105-11-426
PMCID:
PMC2936398
Abstract Full Text PDF–2.1M
A Role for Drosophila dFoxO and dFoxO 5′UTR Internal Ribosomal Entry Sites during Fasting
Eugenia Villa-Cuesta, Brian T. Sage, Marc Tatar
PLoS One. 2010; 5(7): e11521. Published online 2010 July 9. doi: 10.1371/journal.pone.0011521
PMCID:
PMC2901383
Abstract Full Text PDF–929K
Regulation of MYCN expression in human neuroblastoma cells
Joannes FM Jacobs, Hans van Bokhoven, Frank N van Leeuwen, Christina A Hulsbergen-van de Kaa, I Jolanda M de Vries, Gosse J Adema, Peter M Hoogerbrugge, Arjan PM de Brouwer
BMC Cancer. 2009; 9: 239. Published online 2009 July 18. doi: 10.1186/1471-2407-9-239
PMCID:
PMC2720985
Abstract Full Text PDF–421K Supplementary Material
Conserved introns reveal novel transcripts in Drosophila melanogaster
Michael Hiller, Sven Findeiß, Sandro Lein, Manja Marz, Claudia Nickel, Dominic Rose, Christine Schulz, Rolf Backofen, Sonja J. Prohaska, Gunter Reuter, Peter F. Stadler
Genome Res. 2009 July; 19(7): 1289–1300. doi: 10.1101/gr.090050.108
PMCID:
PMC2704441
Abstract Full Text PDF–1.2M
An Overview of Nested Genes in Eukaryotic Genomes
Anuj Kumar
Eukaryot Cell. 2009 September; 8(9): 1321–1329. Published online 2009 June 19. doi: 10.1128/EC.00143-09
PMCID:
PMC2747821
Full Text PDF–1.2M
Large-scale analysis of antisense transcription in wheat using the Affymetrix GeneChip Wheat Genome Array
Tristan E Coram, Matthew L Settles, Xianming Chen
BMC Genomics. 2009; 10: 253. Published online 2009 May 29. doi: 10.1186/1471-2164-10-253
PMCID:
PMC2694213
Abstract Full Text PDF–411K 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
D- and L-lactate dehydrogenases during invertebrate evolution
Melania E Cristescu, David J Innes, Jonathon H Stillman, Teresa J Crease
BMC Evol Biol. 2008; 8: 268. Published online 2008 October 1. doi: 10.1186/1471-2148-8-268
PMCID:
PMC2570690
Abstract Full Text PDF–761K
Sense and antisense OsDof12 transcripts in rice
Dejun Li, Chunhua Yang, Xiaobing Li, Guobiao Ji, Lihuang Zhu
BMC Mol Biol. 2008; 9: 80. Published online 2008 September 17. doi: 10.1186/1471-2199-9-80
PMCID:
PMC2576344
Abstract Full Text PDF–441K
Non-random retention of protein-coding overlapping genes in Metazoa
Giulia Soldà, Mikita Suyama, Paride Pelucchi, Silvia Boi, Alessandro Guffanti, Ermanno Rizzi, Peer Bork, Maria Luisa Tenchini, Francesca D Ciccarelli
BMC Genomics. 2008; 9: 174. Published online 2008 April 16. doi: 10.1186/1471-2164-9-174
PMCID:
PMC2330155
Abstract Full Text PDF–1.9M Supplementary Material
Quantifying the threat of extinction from Muller's ratchet in the diploid Amazon molly (Poecilia formosa)
Laurence Loewe, Dunja K Lamatsch
BMC Evol Biol. 2008; 8: 88. Published online 2008 March 19. doi: 10.1186/1471-2148-8-88
PMCID:
PMC2292145
Abstract Full Text PDF–758K
Comparative genomic analysis of novel conserved peptide upstream open reading frames in Drosophila melanogaster and other dipteran species
Celine A Hayden, Giovanni Bosco
BMC Genomics. 2008; 9: 61. Published online 2008 February 1. doi: 10.1186/1471-2164-9-61
PMCID:
PMC2276209
Abstract Full Text PDF–323K Supplementary Material
Small RNAs and the regulation of cis-natural antisense transcripts in Arabidopsis
Hailing Jin, Vladimir Vacic, Thomas Girke, Stefano Lonardi, Jian-Kang Zhu
BMC Mol Biol. 2008; 9: 6. Published online 2008 January 14. doi: 10.1186/1471-2199-9-6
PMCID:
PMC2262095
Abstract Full Text PDF–656K Supplementary Material
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
Brian J Haas, Steven L Salzberg, Wei Zhu, Mihaela Pertea, Jonathan E Allen, Joshua Orvis, Owen White, C Robin Buell, Jennifer R Wortman
Genome Biol. 2008; 9(1): R7. Published online 2008 January 11. doi: 10.1186/gb-2008-9-1-r7
PMCID:
PMC2395244
Abstract Full Text PDF–722K Supplementary Material
Two Gr genes underlie sugar reception in Drosophila
Anupama Dahanukar, Ya-Ting Lei, Jae Young Kwon, John R. Carlson
Neuron. Author manuscript; available in PMC 2008 November 8.
Published in final edited form as: Neuron. 2007 November 8; 56(3): 503–516. doi: 10.1016/j.neuron.2007.10.024
PMCID:
PMC2096712
Abstract Full Text PDF–2.6M Supplementary Material
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures
Alexander Stark, Michael F. Lin, Pouya Kheradpour, Jakob S. Pedersen, Leopold Parts, Joseph W. Carlson, Madeline A. Crosby, Matthew D. Rasmussen, Sushmita Roy, Ameya N. Deoras, J. Graham Ruby, Julius Brennecke, Harvard FlyBase curators, Berkeley Drosophila Genome Project, Emily Hodges, Angie S. Hinrichs, Anat Caspi, Benedict Paten, Seung-Won Park, Mira V. Han, Morgan L. Maeder, Benjamin J. Polansky, Bryanne E. Robson, Stein Aerts, Jacques van Helden, Bassem Hassan, Donald G. Gilbert, Deborah A. Eastman, Michael Rice, Michael Weir, Matthew W. Hahn, Yongkyu Park, Colin N. Dewey, Lior Pachter, W. James Kent, David Haussler, Eric C. Lai, David P. Bartel, Gregory J. Hannon, Thomas C. Kaufman, Michael B. Eisen, Andrew G. Clark, Douglas Smith, Susan E. Celniker, William M. Gelbart, Manolis Kellis
Nature. Author manuscript; available in PMC 2008 November 8.
Published in final edited form as: Nature. 2007 November 8; 450(7167): 219–232. doi: 10.1038/nature06340
PMCID:
PMC2474711
Abstract Full Text PDF–3.7M Supplementary Material
Phylogenetic and Genomewide Analyses Suggest a Functional Relationship Between kayak, the Drosophila Fos Homolog, and fig, a Predicted Protein Phosphatase 2C Nested Within a kayak Intron
Stephanie G. Hudson, Matthew J. Garrett, Joseph W. Carlson, Gos Micklem, Susan E. Celniker, Elliott S. Goldstein, Stuart J. Newfeld
Genetics. 2007 November; 177(3): 1349–1361. doi: 10.1534/genetics.107.071670
PMCID:
PMC2147949
Abstract Full Text PDF–3.3M
Identification of unannotated exons of low abundance transcripts in Drosophila melanogaster and cloning of a new serine protease gene upregulated upon injury
Rafaela M Maia, Valeria Valente, Marco AV Cunha, Josane F Sousa, Daniela D Araujo, Wilson A Silva, Jr, Marco A Zago, Emmanuel Dias-Neto, Sandro J Souza, Andrew JG Simpson, Nadia Monesi, Ricardo GP Ramos, Enilza M Espreafico, Maria L Paçó-Larson
BMC Genomics. 2007; 8: 249. Published online 2007 July 24. doi: 10.1186/1471-2164-8-249
PMCID:
PMC1949825
Abstract Full Text PDF–1.0M
You are here: NCBI > Literature > PubMed Central (PMC)
Write to the Help Desk