Bioinformatics, Phylogeny and Evolutionary Genomics Group
Members
Maîtresse de conférences
UCBL
Tel: 04 72 44 84 87
Doctorante
UCBL
Tel: 04 72 44 81 42
Ingénieur de recherche CDD
CNRS
Doctorante
autre
Tel: 04 72 44 81 42
Professeure des universités
UCBL
Tel: 33 04 26 23 44 76
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
Chargée de recherche
CNRS
Tel: 04 72 43 13 44
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 871 to 900 publications on 962 in total
Phylogenetic position of foraminifera inferred from LSU rRNA gene sequences
Molecular Biology and Evolution . 11 ( 6 ) : 929-938
Journal article
see the publicationHOVERGEN: a database of homologous vertebrate genes
Nucleic Acids Research . 22 ( 12 ) : 2360-2365
Journal article
see the publicationMolecular Phylogenetic Analysis of Nitrobacter spp
International Journal of Systematic Bacteriology . 44 ( 1 ) : 83-86
Journal article
see the publicationHeterogeneity of hepatitis C virus genotypes in France
Journal of General Virology . 75 ( Pt 5) : 1063-1070
Journal article
see the publicationPhylogenetic analysis and assessment of the genera Vibrio, Photobacterium, Aeromonas, and Plesiomonas deduced from small-subunit rRNA sequences.
International Journal of Systematic Bacteriology . 44 ( 3 ) : 416-26
Journal article
see the publicationMathematical model of the interactions between Micrococcus spp. and Pseudomonas aeruginosa on agar surface
The Journal of applied bacteriology . 77 ( 6 ) : 727-732
Journal article
see the publication[Post-antibiotic effect of three aminoglycosides against Klebsiella pneumoniae].
Pathologie Biologie . 42 ( 5 ) : 419-24
Journal article
see the publicationAn accurate diffusion method for determining bacterial sensitivity to antibiotics
Journal of Antimicrobial Chemotherapy . 34 ( 1 ) : 73-81
DOI: 10.1093/jac/34.1.73
Journal article
see the publicationMolecular phylogeny of Eubacteria: a new multiple tree analysis method applied to 15 sequence data sets questions the monophyly of Gram-positive bacteria
Research in Microbiology . 145 ( 7 ) : 531-541
Journal article
see the publicationColiGene: object-centered representation for the study of E coli gene expressivity by sequence analysis
Biochimie . 75 : 415-422
Journal article
see the publicationBuilding large knowledge bases in molecular biology
In Proceedings of the First International Conference on Intelligent Systems for Molecular Biology . 1 : 345-353
Journal article
see the publicationMorphological and molecular phylogeny of ophiuroids
Eigth International Echinoderm Conference .
Conference paper
see the publicationAn analysis of partial 28S ribosomal RNA sequence suggests early radiations within the phylum Porifera
4th International Porifera Congress "Sponges in Time and Space" .
Conference paper
see the publicationSequence analysis reveals that the BTG1 anti-proliferative gene is conserved throughout evolution in its coding and 3' non-coding regions
Gene . 129 ( 2 ) : 303-306
Journal article
see the publicationObject-oriented knowledge bases for the analysis of prokaryotic and eukaryotic genomes
In Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology . 1 : 319-327
Journal article
see the publicationAn unexpected correlation between cardinal temperatures of microbial growth highlighted by a new model
Journal of Theoretical Biology . 162 : 447-463
Journal article
see the publicationActinomyces pyogenes: susceptibility of 103 clinical animal isolates to 22 antimicrobial agents
Veterinary Research . 24 ( 3 ) : 251-259
Journal article
see the publicationMathematical model for comparison of time-killing curves.
Antimicrobial Agents and Chemotherapy . 37 ( 8 ) : 1685-1689
Journal article
see the publicationAntimicrobial susceptibility testing of actinomyces pyogenes: Comparison of disk diffusion test and Api ATB Strep system with the Agar dilution method
Zentralblatt fur Bakteriologie, Mikrobiologie, und Hygiene. Series A, Medical microbiology, infectious diseases, virology, parasitology . 279 ( 3 ) : 377-386
Journal article
see the publicationA statistical evaluation of the bactericidal effects of ceftibuten in combination with aminoglycosides and ciprofloxacin
Journal of Antimicrobial Chemotherapy . 32 ( 5 ) : 685-694
DOI: 10.1093/jac/32.5.685
Journal article
see the publicationMolecular phylogeny of the symbiotic actinomycetes of the genus Frankia matches host-plant infection processes.
Molecular Biology and Evolution .
Journal article
see the publicationNucleotide sequence of nifD from Frankia alni strain ArI3: phylogenetic inferences
Molecular Biology and Evolution . 9 ( 3 ) : 495-506
Journal article
see the publication[Comparative study of two systems for the determination of the sensitivity of yeasts to antifungal agents].
Pathologie Biologie . 40 ( 5 ) : 495-9
Journal article
see the publicationGram-positive infections in neutropenic patients: glycopeptide antibiotic choice
Journal of Antimicrobial Chemotherapy . 29 ( 4 ) : 462-463
DOI: 10.1093/jac/29.4.462
Journal article
see the publicationComparative variation of morphological and molecular evolution through geologic time: 28S ribosomal RNA versus morphology in echinoids.
Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences (1934–1990) . 338 ( 1286 ) : 365-82
Journal article
see the publicationPhylogenetic analysis of the pathogenic anaerobe Clostridium perfringens using the 16S rRNA nucleotide sequence.
International Journal of Systematic Bacteriology . 42 ( 2 ) : 312-4
Journal article
see the publicationBTG1, a member of a new family of antiproliferative genes.
EMBO Journal . 11 ( 4 ) : 1663-1670
Journal article
see the publicationInsect muscle actins differ distinctly from invertebrate and vertebrate cytoplasmic actins
Journal of Molecular Evolution . 34 : 406-415
DOI: 10.1007/BF00162997
Journal article
see the publicationEvolution of the primate beta-globin gene region: nucleotide sequence of the delta-beta-globin intergenic region of gorilla and phylogenetic relationships between African apes and man
Journal of Molecular Evolution . 34 : 17-30
DOI: 10.1007/BF00163849
Journal article
see the publicationMonod's bacterial growth model revisited
Bulletin of Mathematical Biology . 54(1) : 117-122
Journal article
see the publication