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 691 to 720 publications on 1098 in total
In search of polymorphic Alu insertions with restricted geographic distributions
Genomics . 90 : 154-158
Journal article
see the publicationMating patterns amongst Siberian reindeer herders: Inferences from mtDNA and Y-chromosomal analyses
American Journal of Physical Anthropology . 133 ( 3 ) : 1013-1027
DOI: 10.1002/ajpa.20590
Journal article
see the publicationUnexpected observations after mapping LongSAGE tags to the human genome
BMC Bioinformatics . 8 : 1-11
Journal article
see the publicationIdentification of Mycobacterium using the EF-Tu encoding (tuf) gene and the tmRNA encoding (ssrA) gene
Journal of Medical Microbiology . 56 ( 8 ) : 1033-1041
Journal article
see the publicationIn vitro detection of the enzymatic activity of folate-dependent tRNA(U54 C5)methyltransferase
Methods in Enzymology . 25 : 103-19
Journal article
see the publicationIn vitro detection of the enzymatic activity of folate-dependent tRNA (Uracil-54,-C5)-methyltransferase: evolutionary implications.
Methods in Enzymology . 425 : 103-19
Journal article
see the publicationComparative RNomics and modomics in mollicutes: prediction of gene function and evolutionary implications
IUBMB Life . 59 : 634-58
Journal article
see the publicationA General Comparison of Relaxed Molecular Clock Models
Molecular Biology and Evolution . 24 ( 12 ) : 2669-2680
Journal article
see the publicationExploring Fast Computational Strategies for Probabilistic Phylogenetic analysis
Systematic Biology . 56 : 711-726
Journal article
see the publicationA New Method for Assessing the Effect of Replication on DNA Base Composition Asymmetry
Molecular Biology and Evolution . 24 : 2169-2179
Journal article
see the publicationInfluence of the transposable element neighborhood on human gene expression in normal and tumor tissues
Gene . 396 : 303-311
Journal article
see the publicationHorizontal Gene Transfer Regulation in Bacteria as a ‘‘Spandrel'' of DNA Repair Mechanisms
PLoS ONE . 2 ( 10 ) : e1055-e1066
Journal article
see the publicationMareyMap: an R-based tool with graphical interface for estimating recombination rates
Bioinformatics . 23 : 2188-2189
Journal article
see the publicationAdaptation or biased gene conversion? Extending the null hypothesis of molecular evolution
Trends in Genetics . 23 ( 6 ) : 273-277
Journal article
see the publicationUnexpected observations after mapping LongSAGE tags to the human genome.
BMC Bioinformatics . 8 : 154
Journal article
see the publicationIntegrating transcription factor binding site information with gene expression datasets
Bioinformatics . 23 : 298-305
Journal article
see the publicationAn archaeal orthologue of the universal protein Kae1 is an iron metalloprotein which exhibits atypical DNA-binding properties and apurinic-endonuclease activity in vitro.
Nucleic Acids Research . 35 ( 18 ) : 6042-51
DOI: 10.1093/nar/gkm554
Journal article
see the publicationEarly archives of genetically-restricted proviral DNA in the female genital tract after heterosexual transmission of HIV-1
AIDS. Official journal of the international AIDS Society . 21 : 153--162
Journal article
see the publicationPhylogenomics of the archaeal flagellum: rare horizontal gene transfer in a unique motility structure
BMC Evolutionary Biology . 7 : 53-70
Journal article
see the publicationIdentification and molecular characterization of new STLV-1 and STLV-3 strains in wild-caught nonhuman primates in Cameroon
Virology . 371 ( 2 ) : 405-417
Journal article
see the publicationEvaluation of the models handling heterotachy in phylogenetic inference
BMC Evolutionary Biology . 7 : 206-219
Journal article
see the publicationSuppression of Long-Branch Attraction Artefacts in the Animal Phylogeny Using a Site-Heterogeneous Model
BMC Evolutionary Biology . 7 ( Suppl 1 ) : S4
Journal article
see the publicationA New Method for Assessing the Effect of Replication on DNA Base Composition Asymmetry
incollection . 7 : 379-381
Journal article
see the publicationMaintenance in the chicken genome of the retroviral-like cENS gene family specifically expressed in early embryos
Journal of Molecular Evolution . 65 ( 3 ) : 215-227
Journal article
see the publicationPredictions for whole genome 2D display according to size and sequence composition
3rd SCOPE meeting on Microbial Environmental Genomics (MicroEnGenIII ) .
Conference paper
see the publicationGenetic diversity and phylogeographic clustering of SIVcpzPtt in wild chimpanzees in Cameroon.
Virology . 368 ( 1 ) : 155-71
Journal article
see the publicationPrevalence and genetic diversity of simian immunodeficiency virus infection in wild red colobus Monkeys (Piliocolobus badius badius) from the Taï Forest, Côte d'Ivoire
2nd Congress of the European Federation of Primatology .
Conference paper
see the publicationMolecular characterization of a simian immunodeficiency virus lineage (SIVwrc) from western red colobus (Piliocolobus badius badius)
14th International Workshop of HIV Dynamics & Evolution .
Conference paper
see the publicationSimian immunodeficiency virus infection in wildliving red colobus monkey (Piliocolobus badius badius) from the Taï forest, Côte D'Ivoire
14th International Workshop of HIV Dynamics & Evolution .
Conference paper
see the publicationMolecular diversity of legume root-nodule bacteria in Kakadu National Park, Northern Territory, Australia.
PLoS ONE . 2 ( 3 ) : e277
Journal article
see the publication