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.

Translational Control by RNA-RNA Interaction: Improved Computation of RNA-RNA Binding Thermodynamics

Ulrike Mückstein, Hakim Tafer, Stephan H. Bernhart, Maribel Hernandez-Rosales, Jörg Vogel, Peter F. Stadler, Ivo L. Hofacker

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Bioinformatics Research and Development Second International Conference, BIRD 2008 Vienna, Austria, July 7-9, 2008 Proceedings;M. Elloumi, J. Küng, M. Linial, R.F. Murphy, K. Schneider, C. Toma (eds), CICS Vol 13, Springer, pp.114-127 (2008)

Abstract


The thermodynamics of RNA-RNA interaction consists of two components: the energy necessary to make a potential binding region accessible, i.e., unpaired, and the energy gained from the base pairing of the two interaction partners. We show here that both components can be efficiently computed using an improved variant of <tt>RNAup</tt>. The method is then applied to a set of bacterial small RNAs involved in translational control. In all cases of biologically active sRNA target interactions, the target sites predicted by \texttt{RNAup} is in perfect agreement with literature. In addition to prediction of target site location, <tt>RNAup</tt> can be also be used to determine the mode of sRNA action. Using information about targe site location and the accessibility change resulting form sRNA binding we can discriminate between positive and negative regulators of translation.

Keywords


RNA-RNA interaction, RNA folding, translational control, small RNAs