Odile Lecompte
Professor at Strasbourg University
Ecole Supérieure de Biotechnologie de Strasbourg (ESBS)
Head of the Evolutionary and Medical Genomics theme of the CSTB (Complex Systems and translational Bioinformatics) team of ICUBE
Contact
CSTB - ICUBE UMR7357 Centre de Recherche en Biomédecine de Strasbourg 1 Rue Eugène Boeckel 67000 Strasbourg France Tél : +33 (0)3 68 85 32 96 odile.lecompte@unistra.fr
Research
My research activities are focused on comparative and integrative genomics. They combine the study of biological systems and data science with the development of strategies and tools necessary to extract knowledge from massive data. They are largely based on the exploitation of the evolutionary message provided by the comparison of homologous sequences.
Development of open resources for comparative genomics
We develop the OrthoInspector program for predicting orthology relationships between genes. The associated OrthoInspector website provides orthology relationships for more than 4000 species and offers tools for data exploration and visualization, allowing phylogenetic profiling or evolutionary characterization of genes associated with a function, a process or a cellular component. This work led me to join the international consortium Quest for Orthologs which aims at developing standards in comparative genomics. We are also working on the detection of differential conservations between homologous protein sequences. The PROBE program allows the automated analysis of a protein family to identify and visualize conserved blocks corresponding to domains or motifs still unknown that may have a structural and/or functional role. BLUR (BLast Unexpected Ranking) allows to compare the proteomes of 2 taxa in order to identify the divergences between species, whether they result from the loss/gain of proteins, blocks or the divergence of a homologous region.
Genotype/phenotype relationships
EvolutionWe exploit omics data to characterize genotype/phenotype relationships, in particular in the context of the study of ciliopathies which represent a large group of diseases related to dysgenesis or dysfunction of the cilium(s). Phylogenetic profiling (presence/absence of orthologs) of human genes in a wide range of eukaryotic species has allowed us to identify new ciliary genes in collaboration with the Medical Genetics Laboratory of Strasbourg. We have also defined a specific evolutionary signature of multiciliation and developed an original approach integrating comparative genomics and functional genomics to identify new genes involved in multiciliation.
Evolution and biodiversity
- Genome evolution in Decapoda
The genomes of decapods show considerable variation in size. We are working on sequencing the giant genome of the noble crayfish Astacus astacus(17 Gb), a European species currently threatened by crayfish plague. The genome coupled with complementary omics data will be used to identify the molecular basis of immunity in crayfish and to understand the differences in resistance to crayfish plague observed between populations in order to eventually allow the reintroduction of resistant individuals. This genome will also be compared to other available decapod genomes to understand the evolution of chromosome organization, gene repertoires and repeated elements. This project is carried out in collaboration with the LOEWE Centre for Translational Biodiversity Genomics in Frankfurt and is funded by ANR/DFG. It is part of the ERGA (European Reference Genome Atlas) initiative.
- Genomic exploration of Myriapod diversity
We are working on the annotation and comparison of 20 Myriapod genomes. Myriapods (millipedes and centipedes) are essential invertebrates for soil biodiversity but are still largely unknown at the genomic level. The comparative analysis of these genomes should allow us to learn more about metamerization, the ancestral genome of arthropods and the adaptation of species to more or less anthropized environments. This study is part of the MetaInvert collaborative project initiated by LOEWE Centre for Translational Biodiversity Genomics that aims to characterize the genomes of soil invertebrates and to establish correlations between genomic and ecological traits. The genomes will then serve as a reference for the identification and quantification of individuals using metagenomics approaches.
Student supervision
- PhD supervisor
2006-2009 N. Gagnière (co-supervisor: O. Poch, IGBMC) Développement d’une suite logicielle pour l’analyse et l’annotation intégrative automatiques de transcrits et de protéines. Application aux banques d’ADNc de l’annélide polychète Alvinella pompejana. (pdf)
2007-2010 Y.N. Anno (co-supervisor: P. Carbon, IBMC) Establishment of a biostatistics-based bioinformatics platform for integration and analysis of genomic, epigenetic and phylogenetic data - Application to hSTAF/ZNF143 transcription factor binding sites. (pdf)
2012-2015 A. Allot (co-supervisor: O. Poch, ICUBE) MyGeneFriends: towards a new relationship between researchers and BigData (pdf)
2015- Y. Nevers From « Big data » to genotype/phenotype relationship. Application to ciliopathies.
2017- A. Defosset Systemic and evolutionary study of multiciliation genes in Vertebrates.
- Encadrement de stage de Master M2S4
E. Perrodou (2004), N. Gagnière (2006), Y.N. Anno (2007), B. Linard (2009) A. Allot (2012), A. Nicol (2013), Y. Nevers (2015), A. Defosset (2017)
Teaching
- ESBS and Ecole Européenne de Chimie, Polymères et Matériaux (ECPM)
Bioinformatics (L3) - Engineering Students in Biotechnology and in Chembiotech
Genomics (M1) - Engineering Students in Biotechnology
UE Comparative and integrative genomics (M2) – Engineering Students in Biotechnology and M2 students from Faculty of Life Sciences
- Master Biologie Structurale, Bioinformatique, Biotechnologies (ESBS/Fac. Sciences de la Vie)
UE Macromolecular sequence analysis(M1)
UE Structure and analysis of genomes and epigenomes (M1)
UE Transcriptomes and Protéomes (M2)
- Other formations
Doctoral school of Life Sciences and Health: Practical courses in Bioinformatics (summer school)
Double Cursus Medecine-Sciences: Introduction to Bioinformatics (L2, Faculty of Medecine)
Continuing education: "From «big data» to a target gene validation"
Other professional duties
- Elected member of the ESBS Council
- Elected member of UDS Expert committee (section 64)
- Responsible of the third year of ESBS
- Responsible of 6 teaching units
- Responsible of the summer chool « Practical courses in Bioinformatics » of the Doctoral school of Life Sciences and Health (UDS)
- Responsible of the continuing educationdu course « From «big data» to a target gene validation – Practical initiation to translational bioinformatics»
- Editorial board member for three international journals
Publications
My full publication list in international pee-reviewed journals is available on PubMed. My publications since 2011 are available on the laboratoire site.
Contact
Odile Lecompte CSTB - ICUBE UMR7357 Faculté de Médecine Bâtiment 3, 5ème étage 11 rue Humann 67085 Strasbourg Tél : +33 (0)3 68 85 32 96 odile.lecompte@unistra.fr