Research in our group is mainly focused on linking the evolution of animal development to genome evolution. The group develops database for evolutionary biology, and studies genome evolution in vertebrates. The group is also involved in targeted projects in functional genomics.
Bgee is a database to compare expression patterns between animal species. Bgee addresses difficulties such as complex anatomies and diverse sources of data by the use of ontologies and the explicit representation of homology. Homology relationships are defined both between genes and between anatomical features. The main efforts are the annotation of anatomical and developmental terms and their homology relationships, and the annotation and statistical treatment of transcriptome data. Such efforts provide an answer to the question "Where is this gene expressed?" from the analysis of data as diverse as ESTs, microarrays, and in situ hybridization. We have the aim of producing a database useful to disciplines such as comparative genomics, Evo-Devo, or transcriptome studies, whilst providing an improved integration of homology and related concepts into bioinformatics through ontologies and ontology tools.
Bgee is available at http://bgee.unil.ch/
A main use of Bgee in the lab is the integrated study of genome evolution and of Evo-Devo.
Gene and genome duplication are considered major mechanisms in the creation of new functions in genomes, or in the refinement of networks by the division of function among more genes. We are especially interested in the genome duplications which occurred in the Paleozoic, in the ancestor of vertebrates and in the ancestor of teleost fishes.
We are also interested in characterizing patterns of positive selection, especially ancient and rare events. For this we develop the database Selectome: http://selectome.unil.ch/
We collaborate with experimental biology laboratories, bringing expertise in comparative and functional genomics. We most notably have a long term interest in nuclear hormone receptors.
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We have two positions open on our new SNSF project "Selection on gene expression at different time scales and vertebrate EvoDevo":
A postdoc in evolutionary genomics, who will take the lead on general patterns of selection and variability in animal evolution: https://bit.ly/3zccixs
A PhD student in bioinformatics, who will take the lead on on new method development and data integration: https://bit.ly/3PRA4Vp
We also have a bioinformatics postdoc position open to work on data integration and a database of arthropod molting characteristics, and collaborate with an interdisciplinary team (paleo + evodevo + genomics) on arthropod evolution: https://bit.ly/3aOJaSZ