References of "Wiedenhoeft, John"
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See detailCocos: Constructing multi-domain protein phylogenies.
Homilius, Max; Wiedenhoeft, John; Thieme, Sebastian et al

in PLoS Currents (2011), 3

Phylogenies of multi-domain proteins have to incorporate macro-evolutionary events, which dramatically increases the complexity of their construction.We present an application to infer ancestral multi ... [more ▼]

Phylogenies of multi-domain proteins have to incorporate macro-evolutionary events, which dramatically increases the complexity of their construction.We present an application to infer ancestral multi-domain proteins given a species tree and domain phylogenies. As the individual domain phylogenies are often incongruent, we provide diagnostics for the identification and reconciliation of implausible topologies. We implement and extend a suggested algorithmic approach by Behzadi and Vingron (2006). [less ▲]

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See detailThe plexus model for the inference of ancestral multidomain proteins.
Wiedenhoeft, John; Krause, Roland UL; Eulenstein, Oliver

in IEEE/ACM Transactions on Computational Biology and Bioinformatics (2011), 8(4), 890-901

Interactions of protein domains control essential cellular processes. Thus, inferring the evolutionary histories of multidomain proteins in the context of their families can provide rewarding insights ... [more ▼]

Interactions of protein domains control essential cellular processes. Thus, inferring the evolutionary histories of multidomain proteins in the context of their families can provide rewarding insights into protein function. However, methods to infer these histories are challenged by the complexity of macroevolutionary events. Here, we address this challenge by describing an algorithm that computes a novel network-like structure, called plexus, which represents the evolution of domains and their combinations. Finally, we demonstrate the performance of this algorithm with empirical data sets. [less ▲]

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