Publications - Published papers

Please find below publications of our group. Currently, we list 500 papers. Some of the publications are in collaboration with the group of Sonja Prohaska and are also listed in the publication list for her individual group. Access to published papers (access) is restricted to our local network and chosen collaborators. If you have problems accessing electronic information, please let us know:

©NOTICE: All papers are copyrighted by the authors; If you would like to use all or a portion of any paper, please contact the author.

Tanimoto's Best Barbecue: Discovering Regulatory Modules using Tanimoto Scores

Peter Menzel, Peter F. Stadler, Axel Mosig

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PREPRINT 07-016: [ PDF ]

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In "German Confernce on Biocomputing (GCB 2007)", C.Falter, A.Schliep, J.Selbig, M.Vingron, D.Walther (eds), Lect.Notes Informatik 115: 68-77 (2007)

Abstract


We present a combinatorial method for discovering <em>cis</em>-regulatory modules in promoter sequences. Our approach combines ``sliding window&#039;&#039; approaches with a scoring function based on the so-called Tanimoto score. This allows to identify sets of binding sites that tend to occur preferentially in the vicinity of each other in a given set of promoter sequences belonging to co-expressed or orthologous genes. We benchmark our method on a data set derived from muscle-specific genes, demonstrating that our approach is capable of identifying modules that were identified as functional in previous studies.