Professor at Strasbourg University
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 email@example.com
Current research activities
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. 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.
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.
- 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.
- PhD theses
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)
2015-2018 Y. Nevers Exploitation of evolutionary markers to study genotype-phenotype relationships: application to ciliopathies.
2017-2020 A. Defosset Multilevel evolutionary study of multiciliation genes in metazoans
2020- C. Rutz European freshwater crayfish genomes, evolutionary history and defence mechanism against crayfish plague
2021- LL. Boštjančić Host-pathogen coevolution: molecular characterisation of the noble crayfish immune response to crayfish plague disease agent
2022- L. Bonassin Evolution of genome organization in European crayfish species
2022- D. Merlat Comparative genomics in soil invertebrates: genome exploration of myriapods and Oribatida mites
- Master's degree internships
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), C Rutz (2020), D Merlat (2022)
- Courses (responsible for 7 Teaching Units)
- Sequence analysis
- Comparative genomics
- Data Science for health
- Advanced topics in omics
- Co-leader of a master program (Biotechnology and data science)
- Responsible of the summer chool « Practical courses in Bioinformatics » for PhD students
- Elected member of the ESBS Council
Other professional activities
- Editorial board member for Genes
- Reviewer for international journals
- Member of the steering committee for mentoring in Alsace (University of Strasbourg - University of Haute-Alsace)
- Participation in evaluation committees for the High Council for the Evaluation of Research and Higher Education (France)
- Grant peer reviewer for international funding agencies
- Member of the Specialized Scientific Committee 1 of INSERM (2018-2021)
- Member of the international consortium Quest For Orthologs
- Member of the ERGA (European Reference Genome Atlas) initiative.