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Auflistung nach Autor:in "Bernhart, Stephan H."

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  • Konferenzbeitrag
    RNALfoldz: efficient prediction of thermodynamically stable, local secondary structures
    (German Conference on Bioinformatics 2010, 2010) Gruber, Andreas R.; Bernhart, Stephan H.; Zhou, You; Hofacker, Ivo L.
    The search for local RNA secondary structures and the annotation of unusually stable folding regions in genomic sequences are two well motivated bioinformatic problems. In this contribution we introduce RNALfoldz an efficient solution two tackle both tasks. It is an extension of the RNALfold algorithm augmented by support vector regression for efficient calculation of a structure's thermodynamic stability. We demonstrate the applicability of this approach on the genome of E. coli and investigate a potential strategy to determine z-score cutoffs given a predefined false discovery rate.
  • Konferenzbeitrag
    Thermodynamics of RNA-RNA binding
    (German Conference on Bioinformatics 2005 (GCB 2005), 2005) Mückstein, Ulrike; Tafer, Hakim; Hackermüller, Jörg; Bernhart, Stephan H.; Stadler, Peter F.; Hofacker, Ivo L.
    We present an extension of the standard partition function approach to RNA secondary structures that computes the probabilities Pu[i, j] that a sequence interval [i, j] is unpaired. Comparison with experimental data shows that Pu[i, j] can be applied as a significant determinant of local target site accessibility for RNA interference (RNAi). Furthermore, these quantities can be used to rigorously determine binding free energies of short oligomers to large mRNA targets. The resource consumption is comparable to a single partition function computation for the large target molecule. We can show that RNAi efficiency correlates well with the binding probabilities of siRNAs to their respective mRNA target.