Bioinformatics, Phylogeny and Evolutionary Genomics Group
Members
Maîtresse de conférences
UCBL
Tel: 04 72 44 84 87
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Doctorante
UCBL
Tel: 04 72 44 81 42
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Ingénieur de recherche CDD
CNRS
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Doctorante
autre
Tel: 04 72 44 81 42
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Professeure des universités
UCBL
Tel: 33 04 26 23 44 76
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Directeur de recherche
CNRS
Tel: 33 04 72 44 62 97
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Professeur d'université émérite
UCBL
Tel: 04 72 44 85 60
Ingénieur d'études CDD
CNRS
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Directeur de recherche
CNRS
Tel: 33 04 72 43 11 67
Doctorante
UCBL
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Chargée de recherche
CNRS
Tel: 33 04 72 44 85 60
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Directeur de recherche
CNRS
Tel: 04 72 44 84 87
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Chargée de recherche
CNRS
Tel: 04 72 43 13 44
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Professeure des universités émérite
UCBL
Tel: 04 72 44 81 42
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Maître de conférences
UCBL
Tel: 04 72 43 35 83
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Chargée de recherche
CNRS
Tel: 04 72 44 81 42
Doctorant
CNRS
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Chargée de recherche
CNRS
Tel: 04 72 43 35 82
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Directeur de recherche
CNRS
Tel: 33 04 72 44 62 96
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Chargée de recherche
CNRS
Tel: 04 72 43 26 28
Doctorant
UCBL
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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 601 to 630 publications on 963 in total
Molecular diversity of legume root-nodule bacteria in Kakadu National Park, Northern Territory, Australia.
PLoS ONE . 2 ( 3 ) : e277
Journal article
see the publicationIdentification and characterization of human Mex-3 proteins, a novel family of evolutionarily conserved RNA-binding proteins differentially localized to processing bodies.
Nucleic Acids Research . 35 ( 4 ) : 1289-300
DOI: 10.1093/nar/gkm016
Journal article
see the publicationInvestigating the effects of prehistoric migrations in Siberia: genetic variation and the origins of Yakuts
Human Genetics . 120 ( 3 ) : 334-353
Journal article
see the publicationMelanesian and Asian origins of Polynesians: mtDNA and Y chromosome gradients across the Pacific
Molecular Biology and Evolution . 23 : 2234-2244
Journal article
see the publicationGlobal trends of whole genome duplications revealed by the genome sequence of the ciliate Paramecium tetraurelia
Nature . 444 ( 7116 ) : 171-178
DOI: 10.1038/nature05230
Journal article
see the publicationGC Content Evolution of the Human and Mouse Genomes : Insights from the Study of Processed Pseudogenes in Regions of Different Recombination Rates.
Journal of Molecular Evolution . 62 : 745-752
Journal article
see the publicationInsights into social insects from the genome of the honeybee Apis mellifera
Nature . 443 : 931-949
Journal article
see the publicationOrigin and molecular evolution of receptor tyrosine kinases with immunoglobulin-like domains.
Molecular Biology and Evolution . 23 ( 6 ) : 1232-41
Journal article
see the publicationEfficient Likelihood Computations with Nonreversible Models of Evolution
Systematic Biology . 55 ( 5 ) : 756-768
Journal article
see the publicationPhylogeography of a subterranean amphipod reveals cryptic diversity and dynamic evolution in extreme environments
Molecular Ecology . 15 : 1797-1806
Journal article
see the publicationMycobacterium bovis Infection
Journal of Medical Microbiology . 56 : 1033-1041
Journal article
see the publicationMolecular diversity of rhizobia nodulating the invasive legume Cytisus scoparius in Australia.
Journal of Applied Microbiology . 100 ( 6 ) : 1228-38
Journal article
see the publicationBradyrhizobia isolated from root nodules of Parasponia (Ulmaceae) do not constitute a separate coherent lineage.
International Journal of Systematic and Evolutionary Microbiology . 56 ( Pt 5 ) : 1013-8
Journal article
see the publicationMultipolar Consensus for Phylogenetic Trees
Systematic Biology . 55 ( 5 ) : 837-843
Journal article
see the publicationA maximum likelihood framework for protein design
BMC Bioinformatics . 7 : 326-336
Journal article
see the publicationComputing Bayes Factors using Thermodynamilmc Integration
Systematic Biology . 55 ( 2 ) : 195-207
Journal article
see the publicationQuantitative prediction for two-dimensional bacterial genomic displays
American Physical Society Meeting .
Conference paper
see the publicationNo Evidence for Tissue-Specific Adaptation of Synonymous Codon Usage in Humans
Molecular Biology and Evolution . 23 : 523-529
Journal article
see the publicationGlobal trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia.
Nature . 444 ( 7116 ) : 171-8
DOI: 10.1038/nature05230
Journal article
see the publicationThe GC Content of Primates and Rodents Genomes Is Not at Equilibrium : a Reply to Antezana
Journal of Molecular Evolution . -- : 803-806
Journal article
see the publicationThe Xist RNA Gene Evolved in Eutherians by Pseudogenization of a Protein-Coding Gene
Science . 312 : 1653-1655
Journal article
see the publicationEvolutionary origin and maintenance of coexpressed gene clusters in mammals.
Molecular Biology and Evolution . 23 : 1715-1723
Journal article
see the publicationPhysiological oxygenation status is required for fully differentiated phenotype in kidney cortex proximal tubules.
AJP Renal Physiology . 291 ( 4 ) : F750-60
Journal article
see the publicationHoSeql : automated homologous sequence identification in gene family databases
Bioinformatics . 22 ( 14 ) : 1786-1787
Journal article
see the publicationRelationship between morphological taxonomy and molecular divergence within Crustacea : Proposal of a molecular threshold to help species delimitation
Molecular Phylogenetics and Evolution . 40 ( 2 ) : 435-447
Journal article
see the publicationUse of PCR-Restriction Enzyme Pattern Analysis and Sequencing Database for hsp65 Gene-Based Identification of Nocardia Species
Journal of Clinical Microbiology . 44 ( 2 ) : 536-546
Journal article
see the publication16S rRNA sequencing in routine bacterial identification : A 30-month experiment
Journal of Microbiological Methods . 67 : 574-581
Journal article
see the publicationRapid identification of Enterobacteriaceae by sequencing DNA gyrase subunit B encoding gene
Diagnostic Microbiology and Infectious Disease . 55 : 263-268
Journal article
see the publicationThe origin and evolution of Archaea: a state of the art
Philos Trans R Soc Lond B Biol Sci . 361 : 1007-22
Journal article
see the publicationA Bayesian Compound Stochastic Process for Modeling Nonstationary and Nonhomogeneous Sequence Evolution
Molecular Biology and Evolution . 23 ( 11 ) : 2058-2071
Journal article
see the publication