Publications - Published papers

Please find below publications of our group. Currently, we list 496 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.

Prediction of Structured Non-Coding RNAs in the Genomes of the Nematodes <i>Caenorhabditis elegans</i> and <i>Caenorhabditis briggsae</i>

Kristin Missal, Xiaopeng Zhu, Dominic Rose, Wei Deng, Geir Skogerbø, Runsheng Chen, Peter F. Stadler


PREPRINT 05-023: [ PDF ]  [ PS ]  [ Supplement ]
[ Publishers's page ]  paperID


J.Exp.Zool.(Mol.Dev.Evol.) 306B: 379-392 (2006).


We present a survey for non-coding RNAs and other structured RNA motifs in the genomes of C.elegans and C.briggsae using the RNAz program. This approach explicitly evaluates comparative sequence information to detect stabilizing selection acting on RNA secondary structure. We detect 3672 structured RNA motifs, of which only 678 are known ncRNAs or clear homologs of known C.elegans ncRNAs. Most of these signals are located in introns or at a distance from known protein-coding genes. With an estimated false positive rate of about 50% and a sensitivity on the order of 50% we estimate that the nematode genomes contain between 3000 and 4000 RNAs with evolutionary conserved secondary structures. Only a small fraction of these belongs to the known RNA classes, including tRNAs, snoRNAs, snRNAs, or microRNAs. A relatively small class of ncRNA candidates is associated with previously observed RNA-specific upstream elements.