Publications - Published papers

Please find below publications of our group. Currently, we list 501 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:

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<tt>RNAsnoop</tt>: efficient target prediction for box H/ACA snoRNAs. Submitted.

Hakim Tafer, Stephanie Kehr, Jana Hertel, Ivo L. Hofacker, Peter F. Stadler

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Bioinformatics. 26: 610-616 (2010)

Abstract


<b>Motivation:</b> all nucleolar RNAs are an abundant class of non-coding RNAs that guide chemical modifications of rRNAs, snRNAs, and some mRNAs. In the case of many "orphan" snoRNAs, the targeted nucleotides remain unknown, however. The box H/ACA subclass determines uridine residues that are to be converted into pseudouridines via specific complementary binding of in a well-defined secondary structure configuration that is outside the scope of common RNA (co-)folding algorithms. <br> <b>Results:</b> implements a dynamic programming algorithm that computes thermodynamically optimal H/ACA-RNA interactions in an efficient scanning variant. Complemented by an SVM-based machine-learning approach to distinguish true binding sites from spurious solutions and a system to evaluate comparative information, it presents an efficient and reliable tool for the prediction of H/ACA snoRNA target sites. We apply <tt>RNAsnoop</tt> to identify the snoRNAs that are responsible for several of the remaining ``orphan&#039;&#039; pseudouridine modifications in human rRNAs, and we assign a target to one of the five orphan H/ACA snoRNAs in <e>Drosophila</e>. <br> <b>Availability:</b> The C source code of <tt>RNAsnoop</tt> can be obtained under the GPL from <a href="http://www.tbi.univie.ac.at/~htafer/RNAsnoop"><tt>http://www.tbi.univie.ac.at/~htafer/RNAsnoop</tt></a> <tt>RNAsnoop</tt>

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doi:10.1093/bioinformatics/btp680