Publications - Published papers
Please find below publications of our group. Currently, we list 565 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 (
) is restricted to our local network and chosen collaborators.
If you have problems accessing electronic information, please let us know:
) 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.
Visualization of Barrier Tree Sequences
Christian Heine, Gerik Scheuermann, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
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Status: Published
IEEE Trans. Vis. Comp. Graphics 12: 781-788 (2006)
Abstract
Dynamical models that explain the formation of spatial structures of RNA molecules have reached a complexity that
requires novel visualization methods that help to analyze the validity of these models. Here, we focus on the visualization of so-called
folding landscapes of a growing RNA molecule. Folding landscapes describe the energy of a molecule as a function of its spatial
configuration; thus they are huge and high dimensional. Their most salient features, however, are encapsulated by their so-called
barrier tree that reflects the local minima and their connecting saddle points. For each length of the growing RNA chain there exists a
folding landscape. We visualize the sequence of folding landscapes by an animation of the corresponding barrier trees. To generate
the animation, we adapt the foresight layout with tolerance algorithm for general dynamic graph layout problems. Since it is very
general, we give a detailed description of each phase: constructing a supergraph for the trees, layout of that supergraph using a
modified DOT algorithm, and presentation techniques for the final animation.