Publications - Published papers

Please find below publications of our group. Currently, we list 501 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.

Algebraic Comparison of Metabolic Networks, Phylogenetic Inference, and Metabolic Innovation

Christian V. Forst, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler

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BMC Bioinformatics, 7: 67 (2006).

Abstract


Metabolic networks are naturally represented as directed hypergraphs in such a way that metabolites are nodes and enzyme-catalyzed reactions form (hyper)edges. The familiar operations from set algebra (union, intersection, and difference) form a natural basis for both the pairwise comparison of networks and identification of distinct metabolic features of a set of algorithms. We report here on an implementation of this approach and its application to the procaryotes. We demonstrate that metabolic networks contain valuable phylogenetic information by comparing phylogenies obtained from network comparisons with 16S RNA phylogenies. We then used the same software to study metabolic innovations in two sets of organisms, free living microbes and \emph{Pyrococci}, as well as obligate intracellular pathogens.

Keywords


Set algebra, metabolic networks, phylogeny, Pyrococci, intracellular pathogens