Computational Evolutionary Biology and Genomics Group
University of Lausanne
What do we do?
At the interface of biology and computer science, our laboratory seeks to better understand evolutionary and functional relationships between genes, genomes and species. A few key underlying questions are:
- How can we extrapolate to the rest of life, and in the best way possible, our current knowledge in molecular biology while concentrating on just a handful of model organisms?
- Conversely, how can we exploit the wealth and diversity of life to get a better grasp on specific organisms or systems of interest?
- Can we summarize meaningfully the evolutionary history of species by arranging them into a small number of tree topologies that capture both vertical inheritance and the most important events of non-vertical inheritance?
Our activities are divided between bioinformatics methods and resource development, and their application – typically with experimentalists.
We published a paper reporting the key achievements of the Quest for Orthologs consortium benchmarking working group, which we have been conducting for the past four years. The work established minimum standards in orthology benchmarking and reported the outcome of a community experiment including 14 leading orthology methods. For these, a battery of 20 tests was carried out on a standard set of 66 genomes crossing all kingdoms of life. This will facilitate future orthology benchmarking by offering a web-based benchmark service. (More info)
We also established a clear and tractable definition for the concept of "homoeology", i.e. evolutionary relationships which arise via hybridization–allopolyploidization of the genome. (More info)
We also edited The Gene Ontology Handbook, an open access book, which was published by Springer. The book provides a practical and self-contained overview of the Gene Ontology – an essential resource in any bioinformatician’s toolbox – with several chapters contributed by SIB members.
Altenhoff A et al., Standardized benchmarking in the quest for orthologs. Nature Methods, 2016, 13, 425–430
Glover N, Redestig H & Dessimoz C, Homoeologs: what are they and how do we infer them? Trends in Plant Science, 2016, 21, 609–621
Dessimoz C & Škunca N (Editors), The Gene Ontology Handbook. Methods in Molecular Biology, 2017, Springer (New York), Vol. 1446