Genome Biology

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Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome

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 and Susan E Celniker*

Genome Biology 2002, 3:research0086-0086.20 doi:10.1186/gb-2002-3-12-research0086

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Research article   Open Access

Complex organizational structure of the genome revealed by genome-wide analysis of single and alternative promoters in Drosophila melanogaster

Qianqian Zhu, Marc S Halfon BMC Genomics 2009, 10:9 (7 January 2009)

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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 Biology 2007, 8:R195 (17 September 2007)

An RFX-binding site is shown to be conserved in the promoters of a subset of ciliary genes and a subsequent screen for this site in two Drosophila species identified novel RFX target genes that are involved in sensory ciliogenesis.

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Extensive parallelism in protein evolution

Georgii A Bazykin, Fyodor A Kondrashov, Michael Brudno, Alexander Poliakov, Inna Dubchak, Alexey S Kondrashov Biology Direct 2007, 2:20 (16 August 2007)

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Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses

Long Li, Qianqian Zhu, Xin He, Saurabh Sinha, Marc S Halfon Genome Biology 2007, 8:R101 (5 June 2007)

Analysis of 280 experimentally-verified cis-regulatory modules from Drosophila reveal features both common to all and unique to distinct subclasses of modules.

Research   Open Access

Fine scale structural variants distinguish the genomes of Drosophila melanogaster and D. pseudoobscura

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

Research article   Open Access

Conserved genomic organisation of Group B Sox genes in insects.

Carol McKimmie, Gertrud Woerfel, Steven Russell BMC Genetics 2005, 6:26 (19 May 2005)

Research   Open Access

Comparison of the oxidative phosphorylation (OXPHOS) nuclear genes in the genomes of Drosophila melanogaster, Drosophila pseudoobscura and Anopheles gambiae

Gaetano Tripoli, Domenica D'Elia, Paolo Barsanti, Corrado Caggese Genome Biology 2005, 6:R11 (31 January 2005)

An analysis of nuclear-encoded oxidative phosphorylation genes in Drosophila and Anopheles reveals that pairs of duplicated genes have strikingly different expression patterns.

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The latest buzz in comparative genomics

Rob J Kulathinal, Daniel L Hartl Genome Biology 2005, 6:201 (4 January 2005)

The publication of the Drosophila pseudoobscura sequence provides a snapshot of how genomes have changed over tens of millions of years.

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Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura

Benjamin P Berman, Barret D Pfeiffer, Todd R Laverty, Steven L Salzberg, Gerald M Rubin, Michael B Eisen, Susan E Celniker Genome Biology 2004, 5:R61 (20 August 2004)

27 predicted gene-regulatory regions in the Drosophila melanogaster genome were analyzed in vivo, confirming 15 active enhancer regions. A comparison with Drosophila pseudoobscura sequences revealed that conservation of binding-site clusters accurately discriminates functional regions from non-functional ones.

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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 Caenorhabditis elegans and Drosophila melanogaster. Intergenic distance, and hence genome architecture, is shaped by regulatory information contained in noncoding DNA.

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Computational prediction of transcription-factor binding site locations

Martha L Bulyk Genome Biology 2003, 5:201 (23 December 2003)

Various experimental and computational approaches have been used to identify genomic locations of transcription-factor binding sites; methods involving computational comparisons of related genomes have been particularly successful.

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How many genes in a genome?

Brian Oliver, Benoit Leblanc Genome Biology 2003, 5:204 (22 December 2003)

A recent study of the Drosophila genome has added perhaps 2,000 genes to the predicted total, and raises a number of questions about how genome annotation data should be stored and presented.

Research article   Open Access

Statistical extraction of Drosophila cis-regulatory modules using exhaustive assessment of local word frequency

Anna G Nazina, Dmitri A Papatsenko BMC Bioinformatics 2003, 4:65 (22 December 2003)

Research article   Open Access

Genomic characterization of a repetitive motif strongly associated with developmental genes in Drosophila

Javier Costas, Cristina P Vieira, Fernando Casares, Jorge Vieira BMC Genomics 2003, 4:52 (16 December 2003)

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Multi-species sequence comparison: the next frontier in genome annotation

Inna Dubchak, Kelly Frazer Genome Biology 2003, 4:122 (27 November 2003)

Most current computational tools have been designed for pairwise comparisons of DNA sequences, and efficient extension of these tools to multiple species will require knowledge of the ideal evolutionary distance to choose and the development of new algorithms for alignment, analysis of conservation, and visualization of results.

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Impressive expressions: developing a systematic database of gene-expression patterns in Drosophila embryogenesis

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 in situ hybridization studies on whole-mount Drosophila embryos vastly increases the breadth and depth that can be reached by developmental genetics.

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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 Biology 2002, 3:research0083-0083.22 (31 December 2002)

This article is part of a collection on Release 3 of the...

The recent completion of the Drosophila melanogaster genomic sequence to high quality, and the availability of a greatly expanded set of Drosophila cDNA sequences, afforded FlyBase the opportunity to significantly improve genomic annotations.