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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Conserved RNA Secondary Structures in Flaviviridae Genomes

Caroline Thurner, Christina Witwer, Ivo L. Hofacker, Peter F. Stadler


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J Gen Virol 85 (2004), 1113-1124


We report here on a comprehensive computational survey of evolutionarily conserved secondary structure motifs in the genomic RNAs of the family Flaviviridae. This virus family consists of the three genera Flavivirus, Pestivirus, Hepacivirus and the group of \emph{Hepatitis G Viruses} with a currently uncertain taxonomic classification. Based on the control of replication and translation, two subgroups were considered separately: The genus Flavivirus with its type I cap structure at the 5' untranslated region (UTR) and a highly structured 3'UTR, and the remaining three groups that exhibit translation control by means of a Internal Ribosomal Entry Site (IRES) in the 5'UTR and a much shorter less structured 3'UTR. The main findings of our survey are: strong evidence for the possibility of genome cyclization in Hepatitis C and G viruses in addition to the Flaviviruses; a surprisingly large number of conserved RNA motifs in the coding regions; and a lower level of detailed structural conservation in the IRES and 3'UTR motifs than reported in the literature. An electronic atlas organizes the information on the more than 150 conserved, and therefore putatively functional, RNA secondary structure elements.


Flaviviridae, RNA secondary structure, Internal Ribosomal Entry Site (IRES), Genome Cyclization.