What do we do?
At the Evolutionary Bioinformatics Group we are mainly concerned with determining the role of evolutionary innovation and constraint in animals. For this, we develop methods and databases to extract reliable information from genome and transcriptome data. These databases include Bgee, a database for gene expression evolution, Selectome, a database of positive selection. In developing these resources, we also conduct research on ontologies, biocuration, and high-performance computing. Our biological focus is to link Evo-Devo with phylogenomics. We notably study the role of gene duplication in divergence between genes and between species.
During the course of 2015, our team released new tools to analyse gene expression data in animals:
- TopAnat, a GO-like enrichment of anatomical terms mapped to genes by expression patterns, and
- Processed RNA-seq and microarray data for 17 species in Bgee. TopAnat is the first tool to provide a way of characterizing expression patterns of gene lists automatically.
The group also participated in writing two papers resulting from the master’s degree course “Sequence a genome”, a course during which master’s degree students sequence, assemble and annotate new bacterial genomes. This course is a highlight of the Molecular Life Sciences master’s degree at UNIL, and the papers are based directly on the students’ work during the class: dx.doi.org/10.3389/fmicb.2015.00101 and dx.doi.org/10.1111/1462-2920.12498.
Main publications 2015
- Bastian F.B et al. The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations. Database (Oxford) 2015;2015:bav043.
- Daub JT et al. Inference of Evolutionary Forces Acting on Human Biological Pathways. Genome Biol Evol 2015;7(6):1546-1558.
- Kryuchkova-Mostacci N et al. Tissue-Specific Evolution of Protein Coding Genes in Human and Mouse. PLOS ONE 2015;10(6):e0131673.