Annotation of the Drosophila melanogaster euchromatic genome: a systematic review
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* Corresponding author: Sima Misra sima@fruitfly.org
Genome Biology 2002, 3:research0083-0083.22 doi:10.1186/gb-2002-3-12-research0083
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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 de Vries, Gosse J Adema, Peter M Hoogerbrugge, Arjan PM de Brouwer BMC Cancer 2009, 9:239 (18 July 2009) |
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Quantitative measures for the management and comparison of annotated genomes Karen Eilbeck, Barry Moore, Carson Holt, Mark Yandell BMC Bioinformatics 2009, 10:67 (23 February 2009) |
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Research article
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 Tenchini, Francesca D Ciccarelli BMC Genomics 2008, 9:174 (16 April 2008) |
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Celine A Hayden, Giovanni Bosco BMC Genomics 2008, 9:61 (1 February 2008) Conserved peptide upstream open reading frames in Drosophila preferentially associate with transcripts encoding methyltransferases and mitochondrial proteins, suggesting that Drosophila could be used to study the role of these upstream sequences in mitochondrial function and disease.
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Research article
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Method
Brian J Haas, Steven L Salzberg, Wei Zhu, Mihaela Pertea, Jonathan E Allen, Joshua Orvis, Owen White, C Robin Buell, Jennifer R Wortman Genome Biology 2008, 9:R7 (11 January 2008) EVidenceModeler (EVM) is an automated annotation tool that predicts protein-coding regions, alternatively spliced transcripts and untranslated regions of eukaryotic genes. |
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Stuart J Macdonald, Anthony D Long Genome Biology 2006, 7:R67 (27 July 2006) Comparative genomics reveals fine-scale structural variants, including microinversions, distinguishing two diverged Drosophila species |
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Joseph F Ryan, Patrick M Burton, Maureen E Mazza, Grace K Kwong, James C Mullikin, John R Finnerty Genome Biology 2006, 7:R64 (24 July 2006) The first near-complete set of homeodomains from a non-bilaterian animal is described. |
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Conserved genomic organisation of Group B Sox genes in insects. Carol McKimmie, Gertrud Woerfel, Steven Russell BMC Genetics 2005, 6:26 (19 May 2005) |
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DEDB: a database of Drosophila melanogaster exons in splicing graph form Bernett TK Lee, Tin Tan, Shoba Ranganathan BMC Bioinformatics 2004, 5:189 (7 December 2004) |
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The regulatory content of intergenic DNA shapes genome architecture Craig E Nelson, Bradley M Hersh, Sean B Carroll Genome Biology 2004, 5:R25 (15 March 2004) The relationship between regulatory complexity and gene spacing was examined in |
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Method
FlyGEM, a full transcriptome array platform for the Drosophila community Rick Johnston, Bruce Wang, Rachel Nuttall, Michael Doctolero, Pamela Edwards, Jining Lü, Marina Vainer, Huibin Yue, Xinhao Wang, James Minor, Cathy Chan, Alex Lash, Thomas Goralski, Michael Parisi, Brian Oliver, Scott Eastman Genome Biology 2004, 5:R19 (26 February 2004) An array, FlyGEM, has been constructed based on amplification of exons from |
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A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes Eugene V Koonin, Natalie D Fedorova, John D Jackson, Aviva R Jacobs, Dmitri M Krylov, Kira S Makarova, Raja Mazumder, Sergei L Mekhedov, Anastasia N Nikolskaya, B Rao, Igor B Rogozin, Sergei Smirnov, Alexander V Sorokin, Alexander V Sverdlov, Sona Vasudevan, Yuri I Wolf, Jodie J Yin, Darren A Natale Genome Biology 2004, 5:R7 (15 January 2004) We examined functional and evolutionary patterns in the recently constructed set of 5,873 clusters of predicted orthologs from seven eukaryotic genomes. The analysis reveals a conserved core of largely essential eukaryotic genes as well as major diversification and innovation associated with evolution of eukaryotic genomes. |
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Minireview
Brian Oliver, Benoit Leblanc Genome Biology 2003, 5:204 (22 December 2003) A recent study of the |
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M Hild, B Beckmann, SA Haas, B Koch, V Solovyev, C Busold, K Fellenberg, M Boutros, M Vingron, F Sauer, JD Hoheisel, R Paro Genome Biology 2003, 5:R3 (22 December 2003) A novel |
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Research article
Javier Costas, Cristina P Vieira, Fernando Casares, Jorge Vieira BMC Genomics 2003, 4:52 (16 December 2003) |
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Computational identification of Drosophila microRNA genes Eric C Lai, Pavel Tomancak, Robert W Williams, Gerald M Rubin Genome Biology 2003, 4:R42 (30 June 2003) An informatic procedure has been used to analyze the euchromatic sequences of |
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Minireview
Haiqiong Montalta-He, Heinrich Reichert Genome Biology 2003, 4:205 (28 January 2003) The establishment of a database of gene-expression patterns derived from systematic highthroughput |
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Research
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 Biology 2002, 3:research0085-0085.16 (31 December 2002) This article is part of a collection on Release 3 of the... Annotation of an improved whole-genome shotgun assembly of the |
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Research
Casey M Bergman, Barret D Pfeiffer, Diego E Rincón-Limas, Roger A Hoskins, Andreas Gnirke, Chris J Mungall, Adrienne M Wang, Brent Kronmiller, Joanne Pacleb, Soo Park, Mark Stapleton, Kenneth Wan, Reed A George, Pieter J de Jong, Juan Botas, Gerald M Rubin, Susan E Celniker Genome Biology 2002, 3:research0086-0086.20 (30 December 2002) This article is part of a collection on Release 3 of the... Analysis of conservation in eight genomic regions ( |
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Research
The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective Joshua S Kaminker, Casey M Bergman, Brent Kronmiller, Joseph Carlson, Robert Svirskas, Sandeep Patel, Erwin Frise, David A Wheeler, Suzanna E Lewis, Gerald M Rubin, Michael Ashburner, Susan E Celniker Genome Biology 2002, 3:research0084-0084.20 (23 December 2002) This article is part of a collection on Release 3 of the... Using Release 3 of the euchromatic genomic sequence of |
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Software
Apollo: a sequence annotation editor SE Lewis, SMJ Searle, N Harris, M Gibson, V Iyer, J Richter, C Wiel, L Bayraktaroglu, E Birney, MA Crosby, JS Kaminker, BB Matthews, SE Prochnik, CD Smith, JL Tupy, GM Rubin, S Misra, CJ Mungall, ME Clamp Genome Biology 2002, 3:research0082-0082.14 (23 December 2002) This article is part of a collection on Release 3 of the... Apollo was developed to enable curators to inspect genome annotations closely and edit them. FlyBase biologists successfully used Apollo to annotate the |
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Software
An integrated computational pipeline and database to support whole-genome sequence annotation CJ Mungall, S Misra, BP Berman, J Carlson, E Frise, N Harris, B Marshall, S Shu, JS Kaminker, SE Prochnik, CD Smith, E Smith, JL Tupy, C Wiel, GM Rubin, SE Lewis Genome Biology 2002, 3:research0081-0081.11 (23 December 2002) This article is part of a collection on Release 3 of the... In the course of annotating the |
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A Drosophila full-length cDNA resource Mark Stapleton, Joe Carlson, Peter Brokstein, Charles Yu, Mark Champe, Reed George, Hannibal Guarin, Brent Kronmiller, Joanne Pacleb, Soo Park, Ken Wan, Gerald M Rubin, Susan E Celniker Genome Biology 2002, 3:research0080-0080.8 (23 December 2002) This article is part of a collection on Release 3 of the... High-quality full-insert sequence for 8,921 putative full-length cDNA clones in the |
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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 et al. Genome Biology 2002, 3:research0079-0079.14 (23 December 2002) This article is part of a collection on Release 3 of the... The |
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Research
Computational analysis of core promoters in the Drosophila genome Uwe Ohler, Guo-chun Liao, Heinrich Niemann, Gerald M Rubin Genome Biology 2002, 3:research0087-0087.12 (20 December 2002) This article is part of a collection on Release 3 of the... Candidate transcription start sites have been identified for about 2,000 |