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.

Non-coding RNAs in <i>Ciona intestinalis</i>

Kristin Missal, Dominic Rose, Peter F. Stadler


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Bioinformatics, 21(S2): i77-i78 (2005)


<b>Motivation:</b><br/> The analysis of animal genomes showed that only a minute part of their DNA codes for proteins. Recent experimental results agree, however, that a large fraction of these genomes is transcribed and hence is probably functional at the RNA level. A computational survey of vertebrate genomes has predicted thousands of previously unknown ncRNAs with evolutionary conserved secondary structures. An extension of these comparative studies beyond vertebrates is difficult, however, since most ncRNAs evolve relatively fast at the sequence level while conserving their characteristic secondary structures.<br/> <b>Results:</b><br/> Here we report on a computational screen of structured ncRNAs in the urochordate lineage based on a comparison of the genomic data from Ciona intestinalis, Ciona savignyi, and Oikopleura dioica. We predict more than 1000 ncRNAs with an evolutionarily conserved RNA secondary structure. Of these, about a quarter is located in introns of known protein coding sequences. Only a small fraction of the RNA motifs can be identified as known RNAs, including about 300 tRNAs, some 100 snRNA genes, and a few microRNAs and snoRNAs.


non-coding RNAs, microRNA, snRNA, urochordates


ECCB/JBI'05, Madrid