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The regulatory content of intergenic DNA shapes genome architecture

Craig E Nelson*†, Bradley M Hersh† and Sean B Carroll

Genome Biology 2004, 5:R25 doi:

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BioMed Central: 8 citations

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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 Biology 2009, 10:R73 (9 July 2009)

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A map of transcription start sites across the Drosophila genome, providing insights into initiation patterns and spatiotemporal conditions.

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Selective maintenance of Drosophila tandemly arranged duplicated genes during evolution

Carlos Quijano, Pavel Tomancak, Jesus Lopez-Marti, Mikita Suyama, Peer Bork, Marco Milan, David Torrents, Miguel Manzanares Genome Biology 2008, 9:R176 (16 December 2008)

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Genes occurring in conserved, tandemly-arrayed clusters in Drosophila melanogaster are co-expressed to a much higher extent than other duplicated genes.

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The effects of protein interactions, gene essentiality and regulatory regions on expression variation

Linqi Zhou, Xiaotu Ma, Fengzhu Sun BMC Systems Biology 2008, 2:54 (26 June 2008)

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Coordinated evolution of co-expressed gene clusters in the Drosophila transcriptome

Jason G Mezey, Sergey V Nuzhdin, Fangfei Ye, Corbin D Jones BMC Evolutionary Biology 2008, 8:2 (7 January 2008)

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Comprehensive characterization of the cis-regulatory code responsible for the spatio-temporal expression of olSix3.2 in the developing medaka forebrain

Ivan Conte, Paola Bovolenta Genome Biology 2007, 8:R137 (6 July 2007)

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A cluster of highly conserved non-coding sequences surrounding the Six3 gene were identified in fish genomes, and transgenesis in medaka fish demonstrates that these sequences have enhancer, silencer and silencer blocker activities that are differentially combined to control the distribution of Six3.

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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)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central | F1000 Biology | Editor’s summary

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

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Towards the identification of essential genes using targeted genome sequencing and comparative analysis

Adam M Gustafson, Evan S Snitkin, Stephen CJ Parker, Charles DeLisi, Simon Kasif BMC Genomics 2006, 7:265 (19 October 2006)

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Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila

Saurabh Sinha, Mark D Schroeder, Ulrich Unnerstall, Ulrike Gaul, Eric D Siggia BMC Bioinformatics 2004, 5:129 (9 September 2004)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central | F1000 Biology

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