BMC Bioinformatics

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Cis-motifs upstream of the transcription and translation initiation sites are effectively revealed by their positional disequilibrium in eukaryote genomes using frequency distribution curves

Kenneth W Berendzen, Kurt Stüber, Klaus Harter and Dierk Wanke*

BMC Bioinformatics 2006, 7:522 doi:10.1186/1471-2105-7-522

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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)

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

Research article   Open Access

The Arabidopsis thaliana response regulator ARR22 is a putative AHP phospho-histidine phosphatase expressed in the chalaza of developing seeds

Jakub Horák, Christopher Grefen, Kenneth W Berendzen, Achim Hahn, York-Dieter Stierhof, Bettina Stadelhofer, Mark Stahl, Csaba Koncz, Klaus Harter BMC Plant Biology 2008, 8:77 (15 July 2008)

The Arabidopsis response regulator ARR22, is exclusively expressed in the chalaza cells of the developing seed and interacts with histidine-containing phosphotransfer proteins 2, 3 and 5, however, loss-of-function mutants lack a discernable phenotype.

Research article   Open Access

Two different classes of co-occurring motif pairs found by a novel visualization method in human promoter regions

Katsuhiko Murakami, Tadashi Imanishi, Takashi Gojobori, Kenta Nakai BMC Genomics 2008, 9:112 (1 March 2008)

Research article   Open Access Highly Accessed

Meta-analysis of breast cancer microarray studies in conjunction with conserved cis-elements suggest patterns for coordinate regulation

David D Smith, Pål Sætrom, Ola Snøve, Cathryn Lundberg, Guillermo E Rivas, Carlotta Glackin, Garrett P Larson BMC Bioinformatics 2008, 9:63 (28 January 2008)

Research article   Open Access

Positional bias of general and tissue-specific regulatory motifs in mouse gene promoters

Nicolás Bellora, Domènec Farré, M Mar Albà BMC Genomics 2007, 8:459 (13 December 2007)

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Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice

Judith L Gómez-Porras, Diego Riaño-Pachón, Ingo Dreyer, Jorge E Mayer, Bernd Mueller-Roeber BMC Genomics 2007, 8:260 (1 August 2007)