Publications - Published papers

Please find below publications of our group. Currently, we list 560 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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Target prediction and a statistical sampling algorithm for RNA-RNA interaction

Fenix Huang, Jing Qin, Christian M Reidys, Peter F Stadler


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Bioinformatics 26:175-181 (2010)


Motivation It has been proven that the accessibility of the target sites has a critical influence on RNA-RNA binding in general and the specificity and efficiency of miRNAs and siRNAs in particular. Recently, O(N6) time and O(N4) space dynamic programming algorithms have become available that compute the partition function of RNA-RNA interaction complexes, thereby providing detailed insights into their thermodynamic properties. Results: Modifications to the grammars underlying earlier approaches enables the calculation of interactions probabilities for any given interval on the target RNA. The direct computation of the “hybrid probabilities” is complemented by a stochastic backtracing algorithm that produces samples from the Boltzmann ensemble of RNA-RNA interaction structures. The sampling of k structures requires only negligible additional memory resources and runs in O(k · N3). Availability: The algorithms described here are implemented in C as part of the rip package. The source code of rip2 can be downloaded from and


RIP, RIPhybrid, RNA-RNA interaction, target prediction