Bioinformatics, Phylogeny and Evolutionary Genomics Group
Members
Maîtresse de conférences
UCBL
Tel: 04 72 44 84 87
Professeure des universités
UCBL
Tel: 33 04 26 23 44 76
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
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 961 to 990 publications on 1005 in total
Preparation of a Latex Reagent for the Detection of Anti-Staphylococcus aureus Ribitol Teichoic Acid Antibodies
Zentralblatt fur Bakteriologie, Mikrobiologie, und Hygiene. Series A, Medical microbiology, infectious diseases, virology, parasitology . 274 ( 1 ) : 50-60
Journal article
see the publication[Mathematical study of the sensitivity curves of Escherichia coli exposed to polymyxins].
Pathologie Biologie . 38 ( 5 ) : 441-5
Journal article
see the publicationMathematical study of the sensitivity curves of Escherichia coli exposed to polymyxins
Pathologie Biologie . 38 : 441-445
Journal article
see the publicationMolecular phylogeny of Rodentia Lagomorpha Primates Artiodactyla and Carnivora and molecular clocks
Proceedings of the National Academy of Sciences of the United States of America . 87 ( 17 ) : 6703-6707
Journal article
see the publicationIsolation ofSporosarcina ureae from a bronchial biopsy in a child with cystic fibrosis
European Journal of Clinical Microbiology and Infectious Diseases . 9 ( 4 ) : 302-303
DOI: 10.1007/bf01968068
Journal article
see the publicationMolecular phylogeny of the kingdoms Animalia Plantae and Fungi
Molecular Biology and Evolution . 6 ( 2 ) : 109-122
Journal article
see the publicationPhylogenetic analysis based on rRNA sequences supports the archaebacterial rather than the eocyte tree
Nature . 339 : 145-147
DOI: 10.1038/339145a0
Journal article
see the publication[Value of enzymuria during antibacterial therapy].
Pathologie Biologie . 37 ( 5 Pt 2 ) : 657-63
Journal article
see the publicationBacterial Strain Characterization Using Mathematical Modelling of Growth
Zentralblatt fur Bakteriologie, Mikrobiologie, und Hygiene. Series A, Medical microbiology, infectious diseases, virology, parasitology . 271 ( 1 ) : 2-10
Journal article
see the publicationDate of the monocot-dicot divergence estimated from chloroplast DNA sequence data
Proceedings of the National Academy of Sciences of the United States of America . 86 ( 16 ) : 6201-6205
Journal article
see the publication[Interpretative reading and quality control of an antibiotic sensitivity test using an expert system. Application to the API ATB system and Enterobacteriaceae].
Pathologie Biologie . 37 ( 5 Pt 2 ) : 624-8
Journal article
see the publication[Bacteriostatic and bactericidal antibiotics: differences in subinhibitory concentration effects on the growth of Escherichia coli].
Pathologie Biologie . 37 ( 5 ) : 335-40
Journal article
see the publicationMathematical modelling of growth of Escherichia coli at subinhibitory levels of chloramphenicol or tetracyclines
Research in Microbiology . 140 ( 3 ) : 243-254
Journal article
see the publicationRPA190 the gene coding for the largest subunit of yeast RNA polymerase A
Journal of Biological Chemistry . 263 ( 6 ) : 2830-2839
Journal article
see the publicationMathematical modelling of bacterial growth at subinhibitory levels of aminoglycosides
Annales de l'Institut Pasteur / Microbiologie . 139 ( 5 ) : 613-629
Journal article
see the publication[An expert system as an aid to the validation of results of the antibiogram. Feasibility study based on the example of Staphylococcus aureus].
Pathologie Biologie . 36 ( 5 ) : 381-5
Journal article
see the publication[Demonstration of an inoculum effect on the estimation of the minimal inhibitory concentration of LY 146032].
Pathologie Biologie . 36 ( 5 ) : 377-80
Journal article
see the publication[A mathematical study of the mortality curve of Escherichia coli exposed to aminoglycosides].
Pathologie Biologie . 36 ( 5 ) : 446-51
Journal article
see the publicationStudy of staphylococcus aureus teichoic acid immunodominant site by help of synthetic haptens
Zentralblatt fur Bakteriologie, Mikrobiologie, und Hygiene. Series A, Medical microbiology, infectious diseases, virology, parasitology . 267 ( 3 ) : 414-424
Journal article
see the publicationCorynebacterium JK: surgical infections in non-immunosuppressed patients
Intensive Care Medicine . 15 ( 1 )
DOI: 10.1007/bf00255631
Journal article
see the publication[Use of an expert system as a tool to carry out urinary cyto-bacteriologic tests].
Annales de Biologie Clinique . 46 ( 8 ) : 669-72
Journal article
see the publicationEarly stages of in vitro killing curve of LY146032 and vancomycin for Staphylococcus aureus.
Antimicrobial Agents and Chemotherapy . 32 ( 4 ) : 454-457
DOI: 10.1128/AAC.32.4.454
Journal article
see the publicationInterfacing similarity search software with the sequence retrieval system ACNUC
Bioinformatics . 3 ( 3 ) : 239-241
Journal article
see the publicationCodon contexts in enterobacterial and coliphage genes
Molecular Biology and Evolution . 4 : 426-444
Journal article
see the publication[Effect of subinhibitory concentrations of antibiotics on the growth level of bacteria].
Pathologie Biologie . 35 ( 5 ) : 483-93
Journal article
see the publicationBacterial growth measurement using an automated system: Mathematical modelling and analysis of growth kinetics
Annales de l'Institut Pasteur / Microbiologie . 137 ( 1 ) : 133-143
Journal article
see the publication[Evaluation of the Rapid-ATB system for testing the sensitivity of staphylococci to antibiotics. Comparison with the agar dilution reference method].
Pathologie Biologie . 34 ( 5 Pt 2 ) : 600-3
Journal article
see the publicationGelatin and collagen binding to Staphylococcus aureus strains.
Ann Inst Pasteur Microbiol . 136A : 241-245
Journal article
see the publicationNon-parametric statistics for nucleic acid sequence study
Biochimie . 67 ( 5 ) : 449-453
Journal article
see the publicationSystem analysis and nucleic acid sequence banks
Biochimie . 67 ( 5 ) : 433-436
Journal article
see the publication