Publications - Published papers

Please find below publications of our group. Currently, we list 496 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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Orthology Relations, Symbolic Ultrametrics, and Cographs

Marc Hellmuth, Maribel Hernandez-Rosales, Katharina T. Huber, Vincent Moulton, Peter F. Stadler, Nicolas Wieseke

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J.Math.Biol. 66: 399-420 (2013)

Abstract


Orthology detection is an important problem in comparative and evolutionary genomics and, consequently, a variety of orthology detection methods have been devised in recent years. Although many of these methods are dependent on generating gene and/or species trees, it has been shown that orthology can be estimated at acceptable levels of accuracy without having to infer gene trees and/or reconciling gene trees with species trees. Thus, it is of interest to understand how much information about the gene tree, the species tree, and their reconciliation is already contained in the orthology relation on the underlying set of genes. Here we shall show that a result by Böcker and Dress concerning symbolic ultrametrics, and subsequent algorithmic results by Semple and Steel for processing these structures can throw a considerable amount of light on this problem. More specifically, building upon these authors' results, we present some new characterizations for symbolic ultrametrics and new algorithms for recovering the associated trees, with an emphasis on how these algorithms could be potentially extended to deal with arbitrary orthology relations. In so doing we shall also show that, somewhat surprisingly, symbolic ultrametrics are very closely related to cographs,graphs that do not contain an induced path on any subset of four vertices. We conclude with a discussion on how our results might be applied in practice to orthology detection.

Keywords


orthology, symbolic ultrametric, Cograph, cotree, rooted triples