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/
Group leader
Post-docs
- Dr. Tina Begum
- Dr. Sara Fonseca Costa (Bgee)
- Dr Darren Parker (Co-supervised by Prof. Tanja Schwander)
- Dr. Giulia Zancolli
Graduate students
- Amina Echchiki
- David Laloum
- Jialin Liu
- Victor Rossier (Co supervised by Prof. C. Dessimoz)
Embedded Bioinformatician
Staff
Trainees
- Bastien Vallat
Former group members
- Grigouris Amoutzias
- Briseïs Castella (Bgee)
- Joaquim Claivaz
- Aurélie Comte (Bgee)
- Fernando Cruz
- Joséphine Daub (Main advisor: Prof. Excoffier)
- Dr. Iakov Davydov (co-supervised by Prof. N. Salamin)
- Jelisaveta Djordjevic
- Pavel Dobrokhotov
- Angelique Escoriza
- Jose Rodrigo Flores Espinosa
- Walid Gharib
- Dr. Elsa Guillot
- Janna Hastings
- Vidhya Jagannathan
- Kamil Jaron (co-supervised by Prof. T. Schwander)
- Yohan Jarosz (Bgee)
- Alice Koechlin
- Andrea Komljenovic
- Nadezda Kryuchkova
- Arnold Kuzniar (co-supervised by Prof. N. Salamin)
- Titouan Laessle
- 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)
- Namrata Sarkar (Main advisor: Prof. Reymond)
- Hannes Schabauer (co-supervised by Prof. Salamin)
- Omid Shahmirzadi
- Romain Studer
- Patrick Tran Van
- Laurie Vuillet