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:

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Hairpins in a Haystack: Recognizing microRNA Precursors in Comparative Genomics Data

Jana Hertel, Peter F. Stadler

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Bioinformatics 22: e197-e202 (2006)

Abstract


Recently, genome wide surveys for non-coding RNAs have provided evidence for tens of thousands of previously undescribed evolutionary conserved RNAs with distinctive secondary structures. The annotation of these putative ncRNAs, however, remains a difficult problem. Here we describe a SVM-based approach that, in conjunction with a non-stringent filter for consensus secondary structures, is capable of efficiently recognizing microRNA precursors in multiple sequence alignments. The software was applied to recent genome-wide \texttt{RNAz} surveys of mammals, urochordates, and nematodes.

Keywords


miRNA detection, support vector machine classification, miRNA precursor