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:

©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.

Discovering cis-regulatory modules by optimizing barbecues

Axel Mosig, Türker Biyikoglu, Sonja J. Prohaska, Peter F. Stadler


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Discr. Appl. Math. 157: 2458-2468 (2009)


Taking a geometric view on a problem occurring in the context of phylogenetic footprinting, we study the so-called Best Barbeque Problem. The Best Barbeque Problem asks for simultaneously stabbing a maximum number of differently colored intervals from $K$ arrangements of colored intervals. This geometric problem leads to a combinatorial optimization problem, a decision version of which is shown to be NP-complete. Due to its relevance in biological applications, we propose two branch-and-bound algorithms to detect footprint clusters in some real world instances of phylogenetic footprints. Finally, we point out other geometric and combinatorial scenarios where optimizing barbeques might be of practical relevance.