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 421 to 450 publications on 952 in total
Species-driven interpretation guidelines in case of a single-sampling strategy for blood culture
European Journal of Clinical Microbiology and Infectious Diseases . 30 : 1537-1541
Journal article
see the publicationPhylogeny and evolution of the Archaea: one hundred genomes later.
Current Opinion in Microbiology . : epub ahead of print
Journal article
see the publicationGenome sequence of the stramenopile Blastocystis, a human anaerobic parasite.
Genome Biology . 12 ( 3 ) : R29
Journal article
see the publicationCultivation of the first mesophilic representative ("mesotoga") within the order Thermotogales
Systematic and Applied Microbiology . 34 : 581-585
Journal article
see the publicationThe GTPase Function of YvcJ and Its Subcellular Relocalization Are Dependent on Growth Conditions in Bacillus subtilis
Journal of Molecular Microbiology and Biotechnology . 20 : 156-67
Journal article
see the publicationSurvival of extremely and moderately halophilic isolates of Tunisian solar salterns after UV-B or oxidative stress
Canadian Journal of Microbiology . 57(11) : 923-33
Journal article
see the publicationThe phylogenomic analysis of the anaphase promoting complex and its targets points to complex and modern-like control of the cell cycle in the last common ancestor of eukaryotes
BMC Evolutionary Biology . 11 : 923-33
Journal article
see the publicationThe Assembly Mode of the Pseudopilus: a hallmark to distinguish a novel secretion system subtype
Journal of Biological Chemistry . 286 ( 27 ) : 24407-24416
Journal article
see the publicationTaxonomie et phylogénie des procaryotes. Chapitre 6
Ecologie Microbienne : Microbiologie des milieux naturels et anthropisés . 2-35311-022-3 9782353110223 : 1004 p.
Book chapter
see the publicationUltra-fast sequence clustering from similarity networks with SiLiX
BMC Bioinformatics . 12(116) : 1-9
Journal article
see the publicationFtx is a non-coding RNA which affects Xist expression and chromatin structure within the X-inactivation center region
Human Molecular Genetics . 20 : 705-718
DOI: 10.1093/hmg/ddq516
Journal article
see the publicationEffector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations
Nature Communications . 2 : 202
DOI: 10.1038/ncomms1189
Journal article
see the publicationTpms: a Tree Pattern-matching Utility for Querying Gene Trees Collections
Journées Ouvertes Biologie Informatique Mathématiques (JOBIM) . : 111-112
Conference paper
see the publicationApport des nouvelles générations de séquençage pour accéder à la diversité des communautés microbiennes du sol : nécessité d’un ‘pipeline’ bio-informatique pour les biologistes
1ères Rencontres bioinformaticiens et statisticiens de l’INRA . : 1 p.
Conference paper
see the publicationAdaptation to Environmental Temperature Is a Major Determinant of Molecular Evolutionary Rates in Archaea
Molecular Biology and Evolution . 28 : 2661-2674
Journal article
see the publicationPendant trois milliards d'années les micro-organismes sont les seuls habitants de la terre
incollection . 2-35311-022-3 9782353110223 : 94-U259
Book chapter
see the publicationComplete-fosmid and fosmid-end sequences reveal frequent horizontal gene transfers in marine uncultured planktonic archaea.
The International Society of Microbiologial Ecology Journal . 5 ( 8 ) : 1291-302
Journal article
see the publicationA New Highly Conserved Antibiotic Sensing/Resistance Pathway in Firmicutes Involves an ABC Transporter Interplaying with a Signal Transduction System
PLoS ONE . 6 : e15951
Journal article
see the publicationEmergence and Modular Evolution of a Novel Motility Machinery in Bacteria
PLoS Genetics . 7 ( 9 ) : 1409-1418
Journal article
see the publicationCharacterization of Halorubrum sfaxense sp. nov. a New Halophilic Archaeon Isolated from the Solar Saltern of Sfax in Tunisia
Int J Microbiol . -- : 347-58
Journal article
see the publicationUnsuspected Diversity of Arsenite-Oxidizing Bacteria Revealed by a Widespread Distribution of the aoxB Gene in Prokaryotes
Applied and Environmental Microbiology . 77 : 4685-92
DOI: 10.1128/AEM.02884-10
Journal article
see the publicationArchaea and the tree of life
Research in Microbiology . 162 ( 1 ) : 1-4
Journal article
see the publicationOn the last common ancestor and early evolution of eukaryotes: reconstructing the history of mitochondrial ribosomes.
Research in Microbiology . 162 ( 1 ) : 53-70
Journal article
see the publicationA eukaryotic-like sulfiredoxin involved in oxidative stress responses and in the reduction of the sulfinic form of 2 Cys-peroxiredoxin in the cyanobacterium Anabaena PCC 7120
New Phytologist . 191 : 1108-1118
Journal article
see the publicationSpecificity shifts in the rRNA and tRNA nucleotide targets of archaeal and bacterial m5U methyltransferases.
RNA . 17 ( 1 ) : 45-53
DOI: 10.1261/rna.2323411
Journal article
see the publicationCharacteristics of a phylogenetically ambiguous, arsenic-oxidizing Thiomonas sp., Thiomonas arsenitoxydans strain 3As(T) sp. nov.
Archives of Microbiology . 193 : 439-449
Journal article
see the publicationPhylogenetic and genetic variation among Fe(II)-oxidizing acidithiobacilli supports the view that these comprise multiple species with different ferrous iron oxidation pathways
Microbiology . 155 : 111-122
Journal article
see the publicationAn oxygen reduction chain in the hyperthermophilic anaerobe Thermotoga maritima highlights horizontal gene transfer between Thermococcales and Thermotogales
Environmental Microbiology . 13 : 2132-45
Journal article
see the publicationComparative analysis of transposable elements in the melanogaster subgroup sequenced genomes.
Gene . 473 ( 2 ) : 100-9
Journal article
see the publicationCharacterization of heterotrophic prokaryote subgroups in the Sfax coastal solar salterns by combining flow cytometry cell sorting and phylogenetic analysis
Extremophiles . 15 : 347-358
Journal article
see the publication