Bioinformatics, Phylogeny and Evolutionary Genomics Group
Members
Maîtresse de conférences
UCBL
Tel: 04 72 44 84 87
Stagiaire
UCBL

Professeure des universités
UCBL
Tel: 33 04 26 23 44 76

Doctorante
UCBL
Enseignant-chercheur CPJ
UCBL

Directeur de recherche
CNRS
Tel: 33 04 72 44 62 97

Professeur d'université émérite
UCBL
Tel: 04 72 44 85 60
Ingénieur d'études CDD
CNRS

Directeur de recherche
CNRS
Tel: 33 04 72 43 11 67
Doctorante
UCBL

Chargée de recherche
CNRS
Tel: 33 04 72 44 85 60

Directeur de recherche
CNRS
Tel: 04 72 44 84 87
Doctorant
UCBL

Chargée de recherche
CNRS
Tel: 04 72 43 13 44

Directeur de recherche
CNRS

Professeure des universités émérite
UCBL
Tel: 04 72 44 81 42

Maître de conférences
UCBL
Tel: 04 72 43 35 83

Chargée de recherche
CNRS
Tel: 04 72 44 81 42
Doctorant
CNRS

Chargée de recherche
CNRS
Tel: 04 72 43 35 82

Directeur de recherche
CNRS
Tel: 33 04 72 44 62 96

Chargée de recherche
CNRS
Tel: 04 72 43 26 28
Doctorant
UCBL

Chercheur invité
UCBL
Ingénieur de recherche CDD
CNRS
Tel: 04 72 44 81 42
Our group focuses on two main axes: phylogenomics (i.e. the inference of evolutionary history based on genomics data) and evolutionary genomics (understanding the molecular and population processes that drive genome evolution). We see genomes both as a subject of research (how do genomes evolve, why are they structured the way they are?), but also as a main source of empirical knowledge about the macroevolutionary patterns (what do they tell us about the history of life on Earth?), or about the phenotypes and life-history strategies of organisms. Our works heavily rely on methodological developments (bioinformatics, modeling and statistical inference).
Evolution of genome architecture and expression
Genomes are the result of a long-term evolutionary process, shaped by multiple evolutionary forces. Some genomic features are adaptive (i.e. are beneficial for the fitness of organisms), others result from non-adaptive processes (random drift and biased gene conversion - BGC) or are caused by conflicts between multiple levels of selection (e.g. meiotic drive or the spread of selfish genetic elements). We explore different aspects of genome architecture (base composition landscapes, genome structure and size, impact of transposable elements, …) or functioning (gene expression, lncRNAs, epigenetic landscapes, …), and try to disentangle the relative contribution of adaptive and non-adaptive processes to their evolution. For this purpose, we consider both the molecular mechanisms (mutation, repair, recombination) and the population processes (selection, drift, BGC, …) that shape genetic variation.
Phylogenomics
We are interested in reconstructing the history of life on Earth. This research unfolds along several axes. First, we develop phylogenomic databases of aligned genetic sequences (e.g. BIBI, RiboDB or HOGENOM). Second, we conduct methodological research on how to accurately reconstruct deep phylogenies, infer divergence times, reconstruct ancestral genetic sequences, gene repertoires and life-history traits. This methodological work is translated into publicly available software programs (e.g. SeaView, PhyloBayes, Coevol). Finally, we apply these approaches to several important problems, among which: reconstructing the phylogeny of animals, of archaea, or the global tree of life; using phylogenies and ancestral gene repertoires to investigate the evolution of complex systems and the emergence of molecular and cellular functions in the three domains of life; reconstructing ancestral genetic sequences, a research activity that has industrial and biotechnological applications.
Teaching and outreach
We teach at University Lyon 1 (Master Bioinfo@Lyon), INSA, ENS Lyon, we organize bioinformatics internships. We regularly give conferences on evolution (tree of life, human evolution, genetic diversity, …).
Prospective students and postdocs are invited to apply, as we often welcome visitors for internships or research projects.
Keywords: Molecular evolution and Population Genomics; Phylogenomics; Computational Genomics; Comparative genomics; Bioinformatics; Statistical inference.
Publications
Display of 271 to 300 publications on 1098 in total
A Survey and a Positive Psychology Intervention on French PhD Student Well-being
International Journal of Doctoral Studies . 13 : 109-138
DOI: 10.28945/3948
Journal article
see the publicationGenomic imprinting mediates dosage compensation in a young plant XY system
Nature Plants . 4 ( 9 ) : 677-680
Journal article
see the publicationIntegrative Mobilizable Element (IMEs): a reservoir of antibiotic resistance genes in the zoonotic pathogen Streptococcus suis
GDR 3546 - Les elements mobiles du mécanisme aux populations, une approche intégrative .
Conference paper
see the publicationL'exploration des génomes par l'outil ICEFinder révèle la forte prévalence et l'extrême diversité des ICE et des IME de streptocoques
Thesis
see the publicationA Glimpse into the World of Integrative and Mobilizable Elements in Streptococci Reveals an Unexpected Diversity and Novel Families of Mobilization Proteins
Frontiers in Microbiology . 8 : 16
Journal article
see the publicationThe obscure world of integrative and mobilizable elements
Genes . 8 ( 11 ) : 337
DOI: 10.3390/genes8110337
Journal article
see the publicationThe palaeolatitudinal distribution of fossil wood genera as a proxy for European Jurassic terrestrial climate
Palaeogeography, Palaeoclimatology, Palaeoecology . 466 ( 373–381 )
Journal article
see the publicationGenomic landscape of human diversity across Madagascar
Proceedings of the National Academy of Sciences of the United States of America . 114 ( 32 ) : E6498-E6506
Journal article
see the publicationWhole‐genome patterns of linkage disequilibrium across flycatcher populations clarify the causes and consequences of fine‐scale recombination rate variation in birds
Molecular Ecology . 26 ( 16 ) : 4158-4172
DOI: 10.1111/mec.14197
Journal article
see the publicationCovariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting
Proceedings of the Royal Society B: Biological Sciences . 284 ( 1849 ) : 20162756
Journal article
see the publicationGenomic distribution and estimation of nucleotide diversity in natural populations: perspectives from the collared flycatcher ( Ficedula albicollis ) genome
Molecular Ecology Resources . 17 ( 4 ) : 586-597
Journal article
see the publicationSimulation-based estimation of branching models for LTR retrotransposons
Bioinformatics . 33 ( 3 ) : 320 - 326
Journal article
see the publicationGut Protozoa: Friends or Foes of the Human Gut Microbiota?
Trends in Parasitology . 33 ( 12 ) : 925-934
Journal article
see the publicationMicrobiome intestinal ancien et problématiques médicales contemporaines
Médecine/Sciences . 33 : 984-990
Other publication
see the publicationOn the Evolution of Lactase Persistence in Humans
Annual Review of Genomics and Human Genetics . 18 ( 1 ) : 297-319
Journal article
see the publicationSex-specific genetic diversity is shaped by cultural factors in Inner Asian human populations
American Journal of Physical Anthropology . 162 ( 4 ) : 627-640
DOI: 10.1002/ajpa.23151
Journal article
see the publicationLatitude as a co-driver of human gut microbial diversity?
BioEssays . 39 ( 3 ) : 1600145
Journal article
see the publicationMareyMap online: A user-friendly web application and database service for estimating recombination rates using physical and genetic maps
Genome Biology and Evolution . 9 ( 10 ) : 2506-2509
DOI: 10.1093/gbe/evx178
Journal article
see the publicationThe global impact of Wolbachia on mitochondrial diversity and evolution
Journal of Evolutionary Biology . 30 ( 12 ) : 2204-2210
DOI: 10.1111/jeb.13186
Journal article
see the publicationThe Red Queen model of recombination hot-spot evolution: a theoretical investigation
Philosophical Transactions of the Royal Society B: Biological Sciences .
Journal article
see the publicationd18O-Derived incubation temperatures of oviraptorosaur eggs.
Palaeontology . : 1-15
DOI: 10.1111/pala.12311
Journal article
see the publicationThe growing tree of Archaea: new perspectives on their diversity, evolution and ecology
The International Society of Microbiologial Ecology Journal . 11 ( 11 ) : 2407-2425
Journal article
see the publicationImproved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals
Current Biology . 27 ( 24 ) : 3864-3870.e4
Journal article
see the publicationEvolutionary strata on young mating-type chromosomes despite the lack of sexual antagonism
Proceedings of the National Academy of Sciences of the United States of America . 114 ( 27 ) : 7067-7072
Journal article
see the publicationWidespread selective sweeps throughout the genome of model plant pathogenic fungi and identification of effector candidates
Molecular Ecology . 26 ( 7 )
DOI: 10.1111/mec.13976
Journal article
see the publicationTranscriptional response to hepatitis C virus infection and interferon-alpha treatment in the human liver
EMBO Molecular Medicine . 9 : 816-834
Journal article
see the publicationTEtools facilitates big data expression analysis of transposable elements and reveals an antagonism between their activity and that of piRNA genes
Nucleic Acids Research . 45 : 13
DOI: 10.1093/nar/gkw953
Journal article
see the publicationOn the rarity of dioecy in flowering plants
Molecular Ecology . 26 : 1225-1241
DOI: 10.1111/mec.14020
Journal article
see the publicationIn vivo binding of PRDM9 reveals interactions with noncanonical genomic sites
Genome Research . 27 ( 4 ) : 580-590
Journal article
see the publicationRecombination, meiotic expression and human codon usage
eLife . 6 : e27344
Journal article
see the publication