Website Dessimoz lab
Computational Evolutionary Biology
2018 Research Highlights
We published a new method to help identify causal genes in Quantitative Locus Trait (QTLs) analyses by leveraging evolutionary links. Paper. Blog post.
To integrate evolutionary and function information on protein coding genes across many species, we have been strong proponents of the concept of hierarchical orthologous groups—or HOGs for those in the know (brief introductory video). After improving our HOG algorithm in 2017, we have released tools to facilitate interactive exploration and programmatic “slicing and dicing” of HOGs. Paper. Blog post. Video.
A third highlight was the publication of a method to detect erroneously fragmented genes in draft assemblies, with application the the notoriously challenging wheat genome. Paper. (Blog post forthcoming!)
Finally, we are proud that team member Jeremy Levy successfully completed his PhD. One of his main papers is available on BioRxiv, and stay tuned for another one to hopefully appear in 2019!
2017 Research Highlights
It was a big year for the OMA (Orthologous Matrix) project. We introduced changes to the algorithm to make it more robust to duplicated genes evolving at different rates, and to make it more scalable (http://doi.org/10.1093/bioinformatics/btx229 ). We also released numerous improvements for our end users in form of better web and programmatic interfaces (http://doi.org/10.1093/nar/gkx1019 ).
Among several collaborative works published this year, we systematically surveyed structural variations within the known world population of fission yeast (Jeffares et al, Nat Comm, http://doi.org/10.1038/ncomms14061 ). We observed a surprisingly rapid turnover of duplications within the population, and strong association with several quantitative traits and reproductive isolation. Blog post: http://lab.dessimoz.org/blog/2017/02/08/sex-alcohol-and-structural-variants-in-fission-yeast.