Bioinformatics, Phylogeny and Evolutionary Genomics Group
Members
Maîtresse de conférences
UCBL
Tel: 04 72 44 84 87
Stagiaire
CNRS
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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
Stagiaire
UCBL
Stagiaire
UCBL
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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
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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
Stagiaire
UCBL
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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
Stagiaire
UCBL
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Chercheur invité
UCBL
Stagiaire
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 952 in total
CAT : Un Modèle Phylogénétique Bayésien permettant de prendre en compte l'Hétérogénéité des Processus de Substitution entre Sites dans les Alignements Protéiques
Biosystema 22 . 22 : 97-104
Book chapter
see the publication$Psi$-$Phi$: Exploring the outer limits of bacterial pseudogenes
Genome Research . 14 : 2273-2278
Journal article
see the publicationInvertebrate Data Predict an Early Emergence of Vertebrate Fibrillar Collagen Clades and an Anti-incest Model
Journal of Biological Chemistry . 279 ( 46 ) : 47711-47719
Journal article
see the publicationPhysical and transcript map of the autosomal dominant colobomatous microphthalmia locus on chromosome 15q12-q15 and refinement to a 4.4 Mb region.
European Journal of Human Genetics . ( 12 ) : 574-578
Journal article
see the publicationEvidence of a high rate of selective sweeps in African Drosophila melanogaster
Genetics . 163 : 599-609
Journal article
see the publicationDemography and natural selection have shaped genetic variation in Drosophila melanogaster: a multi-locus approach
Genetics . 165 : 1269-1278
Journal article
see the publicationPower of neutrality tests to detect bottlenecks and hitchhiking
Journal of Molecular Evolution . 57 : S190-S200
Journal article
see the publicationMitochondrial DNA evidence for admixed origins of central Siberian populations
American Journal of Physical Anthropology . 120 ( 3 ) : 211-224
Journal article
see the publicationNeutral effect of recombination on base composition in Drosophila
Genetical Research . 81 : 79-89
Journal article
see the publicationPlacenta-Specific INSL4 Expression Is Mediated by a Human Endogenous Retrovirus Element
Biology of Reproduction . 68 : 1422-1429.
Journal article
see the publicationPatterns of selection against transposons inferred from the distribution of Tc1 Tc3 and Tc5 insertions in the mut-7 line of the nematode Caenorhabditis elegans
Genetics . 165 : 1127-1135
Journal article
see the publicationG+C3 structuring along the genome: a common feature in prokaryotes
Molecular Biology and Evolution . 20 : 471-483
Journal article
see the publicationThe source of laterally transferred genes in bacterial genomes
Genome Biology . 4 : R57.1-R57.12
Journal article
see the publicationRTKdb: database of Receptor Tyrosine Kinase
Nucleic Acids Research . 31 : 353-358
Journal article
see the publicationQuelques problèmes statistiques rencontrés dans l`estimation de la température minimale de croissance de Listeria monocytogenes
Revue de Statistique Appliquée . LI : 59-71
Journal article
see the publicationMgtC as a horizontally-acquired virulence factor of intracellular bacterial pathogens: evidence from molecular phylogeny and comparative genomics.
Journal of Molecular Evolution . 57 ( 4 ) : 479-86
Journal article
see the publicationFrom gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria
PLoS Biology . 1 ( 1 ) : 101-109
Journal article
see the publicationSequence divergence within transposable element families in the Drosophila melanogaster genome
Genome Research . 13 : 1889-1896
Journal article
see the publicationIntegrated databanks access and sequence/structure analysis services at the PBIL.
Nucleic Acids Research . 31 ( 13 ) : 3393-3399
DOI: 10.1093/nar/gkg530
Journal article
see the publicationPatterns of selection against transposons inferred from the distribution of Tc1, Tc3 and Tc5 insertions in the mut-7 line of the nematode Caenorhabditis elegans.
Genetics . 165 ( 3 ) : 1127-35
Journal article
see the publicationROSO: a software to search optimized oligonucleotide probes for microarrays
14. Rencontres Régionales de la Recherche .
Poster
see the publicationSubcellular localization of 14-3-3 proteins in Toxoplasma gondii tachyzoites and evidence for a lipid raft-associated form
FEMS Microbiology Letters . 224 ( 2 ) : 161-168
Journal article
see the publicationSubcellular localization of 14-3-3 proteins in Toxoplasma gondii tachyzoites and evidence for a lipid raft-associated form
FEMS Microbiology Letters . 224 : 161-168.
Journal article
see the publicationPatterns of selection against transposons inferred from the distribution of Tcl, Tc3 and Tc5 insertions in the mut-7 line of the nematode Caenorhabditis elegans.
Genetics . ( 165 ) : 1127-1135
Journal article
see the publicationUse of Correspondence Discriminant Analysis to predict the subcellular location of bacterial proteins
Computer Methods and Programs in Biomedicine . 70 : 99-105
Journal article
see the publicationCross-platform comparison and visualisation of gene expression data using co-inertia analysis
BMC Bioinformatics . 4 : 1-15
Journal article
see the publicationBIBI a bioinformatics bacterial identification tool
Journal of Clinical Microbiology . 41 : 1785-1787
Journal article
see the publicationRTKdb: database of Receptor Tyrosine Kinase.
Nucleic Acids Research . 31 ( 1 ) : 353-8
Journal article
see the publicationA method to study the microscale 3-D spatial distribution of Bacteria in soil.
Mycological Research . 107 : 1221-1230
Journal article
see the publicationPhylogenetic analysis of proteins homologous to the Salmonella MgtC virulence factor
ASM Conference on Salmonella: Pathogenesis, Epidemiology, and Vaccine Development .
Conference paper
see the publication