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The SIB recognizes the next generation of bioinformaticians

The SIB Swiss Institute of Bioinformatics today announced the winners of the 2009 SIB Best Graduate Paper and the SIB Young Bioinformatician Award at the 7th annual [BC]2 Basel Computational Biology Conference.

**2009 SIB Young Bioinformatician Award **

The winner of the 2009 SIB Young Bioinformatician Award is SIB Member Lukas Burger, 29, who has been working for the past four years with the SIB in the Bioinformatics and Systems Biology Group led by Prof. Erik van Nimwegen at the Biozentrum of the University of Basel. In his recently obtained PhD thesis, he studied how to predict physical interactions between protein residues entirely based on sequence data, using multiple sequence alignments of similar proteins.

Dr. Burger has developed a new Bayesian network methodology for the characterization of protein sequences that is extremely powerful and allows the prediction of intra- and interprotein interactions with greatly improved accuracy. Dr. Burger explains the importance of such a methodology, "As the number of sequenced genomes has grown exponentially over the last years, multiple alignments of many protein families now contain more than 100 homologous sequences(and some even several thousand), which makes it possible to investigate the evolutionary constraints that act on particular residues in much detail. Such analyses reveal that protein residues are constrained in very complicated ways, with interacting residues forming chains or networks that even connect residues that are distant in the 3-dimensional structure of the protein.

The introduced methodology provides a way of describing these interdependencies in a statistically sound and efficient way and thus provides a generalization of currently used models for the characterization of protein sequences. A key feature of the method is that it is able to disentangle direct interactions from indirect interactions that are mediated via other residues. As such the method greatly improves the prediction of contacting amino acids in the 3-dimensional structure of proteins and is thus expected to be of help in protein structure prediction. In an extended form, the same methodology can be used to infer protein-protein interactions directly from sequence alignments with high accuracy.

SIB 2009 Young Bioinformatician Award was funded by the Swiss National Science Foundation

**2009 SIB Best Graduate Paper**

The winner of the 2009 SIB Best Graduate Paper is SIB Member Julien Roux, 25, PhD student for the past two and a half years in the Evolutionary Bioinformatics Group led by Prof. Marc Robinson-Rechavi at the University of Lausanne. The topic of his paper Developmental Constraints on Vertebrate Genome Evolution (PLoS Genetics, December 2008) focused on the impact of developmental processes on evolution.

Mr. Roux looked at how evolutionary changes are limited by the extent they affect the development of an organism, and focused specifically on how the timing of expression in development affects selective pressure on genes. In his own words: "Because embryonic development must proceed correctly for an animal to survive, changes in evolution are constrained according to their effects on development. Changes that disrupt development too dramatically are thus rare in evolution."

While this has been long observed at the morphological level, it has been more difficult to characterise the impact of such constraints on the genome. Mr. Roux studied the effect of gene expression over vertebrate developmental time (from early to late development) in both zebrafish and mice. Results indicate "a strong effect of constraints, which are progressively weaker towards late development, in early development on the genome", which contradicts the "hourglass" model that is generally used to describe vertebrate developmental constraint.

Once published, this paper was immediately recognised as an important contribution to the general understanding of evolution, and was highlighted in Nature Reviews Genetics and Faculty of 1000.


Contact: Janice Blondeau
Swiss Institute of Bioinoformatics

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