Genome Biology

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MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model

Alan M Moses, Derek Y Chiang, Daniel A Pollard, Venky N Iyer and Michael B Eisen*

Genome Biology 2004, 5:R98 doi:10.1186/gb-2004-5-12-r98

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BioMed Central: 9 citations

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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)

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.

Research article   Open Access

A generic approach to identify Transcription Factor-specific operator motifs; Inferences for LacI-family mediated regulation in Lactobacillus plantarum WCFS1

Christof Francke, Robert Kerkhoven, Michiel Wels, Roland J Siezen BMC Genomics 2008, 9:145 (27 March 2008)

Review   Open Access

From biophysics to evolutionary genetics: statistical aspects of gene regulation

Michael Lässig BMC Bioinformatics 2007, 8(Suppl 6):S7 (27 September 2007)

Review   Open Access

Finding regulatory elements and regulatory motifs: a general probabilistic framework

Erik van Nimwegen BMC Bioinformatics 2007, 8(Suppl 6):S4 (27 September 2007)

Research   Open Access

Functional diversification of sonic hedgehog paralog enhancers identified by phylogenomic reconstruction

Yavor Hadzhiev, Michael Lang, Raymond Ertzer, Axel Meyer, Uwe Strähle, Ferenc Müller Genome Biology 2007, 8:R106 (8 June 2007)

Investigation of the ar-C midline enhancer of sonic hedgehog orthologs and paralogs from distantly related vertebrate lineages identified lineage-specific motif changes; exchanging motifs between paralog enhancers resulted in the reversal of enhancer specificity.

Research article   Open Access Highly Accessed

WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences

Giulio Pavesi, Federico Zambelli, Graziano Pesole BMC Bioinformatics 2007, 8:46 (7 February 2007)

Research   Open Access Highly Accessed

PhyloScan: identification of transcription factor binding sites using cross-species evidence

C Steven Carmack, Lee McCue, Lee A Newberg, Charles E Lawrence Algorithms for Molecular Biology 2007, 2:1 (23 January 2007)

Software   Open Access

XRate: a fast prototyping, training and annotation tool for phylo-grammars

Peter S Klosterman, Andrew V Uzilov, Yuri R Bendaña, Robert K Bradley, Sharon Chao, Carolin Kosiol, Nick Goldman, Ian Holmes BMC Bioinformatics 2006, 7:428 (3 October 2006)

Research article   Open Access

Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments

Daniel A Pollard, Alan M Moses, Venky N Iyer, Michael B Eisen BMC Bioinformatics 2006, 7:376 (14 August 2006)