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Radboud University, Toernooiveld 1, P.O. Box 9010, 6500 GL Nijmegen, +31 (0)24-3653391, postmaster@cmbi.ru.nl
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Centre for Molecular and Biomolecular Informatics Radboud University, Toernooiveld 1, P.O. Box 9010, 6500 GL Nijmegen, +31 (0)24-3653391, postmaster@cmbi.ru.nl |
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| Computational Genomics |
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The sequencing of complete genomes raises the question: how do we show that a genome is more than the sum of its genes ?, or, how do the proteins encoded in these genomes interact with each other to produce cells and phenotypes ? The core research focus of the Huynen group is to predict such functional interactions between proteins as there exist e.g. in metabolic pathways, signalling pathways or protein complexes. On the one hand we develop computational genomics techniques that exploit the information in sequenced genomes and functional genomics data, like mRNA expression and protein-protein interactions, to make such predictions. Techniques that are used for this are sequence analysis tools for the prediction of homology and orthology, in combination with scripts that combine the data for various sequenced genomes and functional genomics datasets with each other to make predictions about specific pathways. In this we collaborate with the computational biology department at the EMBL (Bork group). On the other hand we make specific, testable predictions about pathways and the functions of proteins therein. For the latter we are directing our attention to systems that are relevant to the research at the KUN/UMC, thus exploiting the possibilities there are for experimental testing of our predictions. As part of this we are presently using computational genomics to predict pathways and protein functions in the mitochondria. A specific example is a recent study on the likely interaction partners of frataxin. Frataxin is a well-known disease gene (Friedreich's ataxia) whose function has remained elusive despite more than six years of intensive experimental research. Using computational genomics we have shown that frataxin is likely involved in iron-sulfur cluster assembly in conjunction with the co-chaperone HscB/JAC1. We have also identified the complete eukaryotic protein set that has been derived from the alpha-proteobacteria, and that are mainly functioning in the mitochondria to predict pathways among these.
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| Recent Publications |
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