Publications - Published papers

Please find below publications of our group. Currently, we list 508 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.

Structural profiles of human miRNA families from pairwise clustering

Bogumil Kaczkowski, Elfar Torarinsson, Kristin Reiche, Jakob Hull Havgaard, Peter F. Stadler, Jan Gorodkin


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Bioinformatics doi: 10.1093/bioinformatics/btn628


MicroRNAs are a group of small, ~21nt long, riboregulators inhibiting gene expression at a posttranscriptional level. Their most distinctive structural feature is the foldback hairpin of their precursor pre-miRNAs. Even though each pre-miRNA deposited in miRBase has its secondary structure already predicted, little is known about the patterns structural conservation among pre-miRNAs. We address this issue by clustering the human pre-miRNA sequences based on pairwise, sequence and secondary structure alignment using <tt>FoldAlign</tt>, followed by global multiple alignment of obtained clusters by WAR. As a result, the common secondary structure was successfully determined for four <tt>FoldAlign</tt> clusters: the RF00027 structural family of the Rfam database and three clusters with previously undescribed consensus structures.


microRNA, clustering, RNA secondary structure