Evolutionary Bioinformatics Group
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.
Evo-Devo and Bgee
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.
Genome duplication and positive selection
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/
Comparative functional genomics: case studies
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.
GitHub and GitLab repositories for lab projects (including collaborations):
https://github.com/BgeeDB
https://github.com/owlcollab/owltools
https://gitlab.isb-sib.ch/groups/Bgee
https://gitlab.isb-sib.ch/phylo/fastcodeml/
Publications
Group leader
Post-docs
- Dr. Tina Begum
- Dr. Iakov Davydov
- Dr. Elsa Guillot
- Dr. Tarcisio Mendes De Farias (Co supervised by Prof. C. Dessimoz)
- Dr Darren Parker (Co supervised by Prof. T. Schwander)
- Dr. Julien Wollbrett (Bgee)
Graduate students
- Amina Echchiki
- Kamil Jaron (co-supervised by Prof. T. Schwander)
- Andrea Komljenovic
- David Laloum
- Jialin Liu
- Namrata Sarkar (Main advisor: Prof. Reymond)
Staff
Embedded Bioinformatician
- Patrick Tran Van (co supervised by Prof. T. Schwander)
Former group members
- Grigouris Amoutzias
- Briseïs Castella (Bgee)
- Aurélie Comte (Bgee)
- Fernando Cruz
- Joséphine Daub (Main advisor: Prof. Excoffier)
- Pavel Dobrokhotov
- Angelique Escoriza
- Jose Rodrigo Flores Espinosa
- Walid Gharib
- Janna Hastings
- Vidhya Jagannathan
- Yohan Jarosz (Bgee)
- Alice Koechlin
- Nadezda Kryuchkova
- Arnold Kuzniar (co-supervised by Prof. N. Salamin)
- Balazs Laurenczy (Bgee)
- Antonia Mayer
- Philippe Moret (Bgee)
- Patricia Palagi
- Gilles Parmentier (Bgee)
- Barbara Piasecka
- Eyal Privman
- Frederic Ricci
- Kate Ridout
- Patrick Roelli (Bgee)
- Marta Rosikiewicz (Bgee)
- Julien Roux (Bgee)
- Dr. Sacha Laurent (co advisor: Prof. N. Salamin)
- Komal Sanjeev (Bgee)
- Hannes Schabauer (co-supervised by Prof. Salamin)
- Omid Shahmirzadi
- Romain Studer
- Laurie Vuillet
