Robinson-Rechavi Group - Evolutionary Bioinformatics

Our research is mainly focused on linking patterns from animal Evo-Devo (evolution of development) to evolutionary processes on the genome. We develop databases for evolutionary biology, especially Bgee. 

The Bgee database of gene expression 

Bgee is a database for retrieval and comparison of gene expression patterns across multiple animal species. It provides an intuitive answer to the question "where is a gene expressed?" and supports research in cancer and agriculture, as well as evolutionary biology. Bgee integrates all types of expression data, from bulk to single-cell, and covers tens of animal species. All expression data is curated to be "healthy wild-type", allowing relevant comparisons between species. It is a core SIB resource and is recognized as a Global Core Biodata Resource. The team develops and maintains Bgee and related tools (e.g. R packages). 

Bgee is widely used in biomedical and evolutionary research. It is used within the group for studies of the evolution of gene expression, and as to relate gene evolution to the developmental stages or organs where genes are expressed. It also provides a motivation for methodological research in the group. 

Bgee is available at https://www.bgee.org/  

Selection on gene expression and vertebrate Evo-Devo 

The study of evolutionary and population genomics often emphasizes adaptation, while Evo-Devo emphasizes constraints and developmental mechanisms. We aim to understand how neutral and selective forces lead to the evolution of expression patterns, and how they relate to anatomical phenotypes. We study these forces under the angles of variability of expression, of selection on regulatory regions, and of evolutionary convergence. Our main focal species are ray-finned fishes, and amphioxus. We use Bgee, and develop new methods to study the evolution of expression or of regulatory sequences. We also investigate gene and genome duplications, as the impact of duplication provides an excellent window into the evolution of gene function, notably their role in development and anatomy. 

Interdisciplinary study of arthropod evolution and animal diversity 

Arthropods are the most diverse phylum on Earth. We collaborate with groups in paleontology, experimental Evo-Devo, and genome biology, to understand how the shared constraints on arthropod development (e.g., molting) can give rise to the huge diversity. Importantly in this project we focus on the full diversity of arthropods, beyond the well-studied insects. Our group leads the analysis of gene expression during molting in diverse arthropod lineages, and develops the MoultDB database which integrates genomics and phenotypic data, including from fossils. 

We also study the evolution of venom glands, notably but not only in arthropods. Venom glands are a fascinating example of convergent evolution, which allow us to link the molecular evolution of genes to adaptive anatomical innovations. 

Code and data repositories 

https://github.com/mrrlab  
https://zenodo.org/communities/mrrlab/  
https://github.com/BgeeDB  
https://github.com/obophenotype/developmental-stage-ontologies  
https://github.com/MoultDB/  
https://github.com/SelectomeDB  
https://github.com/BeeBiome-consortium/beebiome-data-portal  
https://github.com/DessimozLab/omamer  
https://github.com/DessimozLab/matreex