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Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools

Weichun Huang*, Joseph R Nevins and Uwe Ohler*

Genome Biology 2007, 8:R225 doi:10.1186/gb-2007-8-10-r225

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Towards realistic benchmarks for multiple alignments of non-coding sequences

Jaebum Kim, Saurabh Sinha BMC Bioinformatics 2010, 11:54 (26 January 2010)

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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)

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

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

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Tools for simulating evolution of aligned genomic regions with integrated parameter estimation

Avinash Varadarajan, Robert K Bradley, Ian H Holmes Genome Biology 2008, 9:R147 (8 October 2008)

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Three tools for simulating genome evolution are presented: for neutrally evolving DNA, for phylogenetic context-free grammars and for richly structured syntenic blocks of genome sequence.

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