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 541 to 570 publications on 963 in total
Improvement of Molecular Phylogenetic Inference and the Phylogeny of Bilateria
Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences (1934–1990) . 363 ( 1496 ) : 1463-1472
Journal article
see the publicationUniformization for Sampling Realizations of Markov Processes: Applications to Bayesian Implementations of Codon Substitution Models
Bioinformatics . 24 ( 1 ) : 56-62
Journal article
see the publicationEtude des patrons d`évolution asymétrique dans les séquences d`ADN
incollection . -- : 476-482
Journal article
see the publicationLosing helena: The extinction of a drosophila line-like element
BMC Genomics . 9 : 1-11
Journal article
see the publicationSequence variability and phylogenetic analyses of the Complement Regulatory Protein expressed by the trypomastigote stage of Trypanosoma cruzi identify a monophyletic group of CRP-like proteins
Xth European Multicolloquium of Parasitology .
Conference paper
see the publicationPervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes
Genome Research . 18 : 1393-1402
Journal article
see the publicationAnalysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia: a somatic view of the germline.
Genome Research . 18 ( 4 ) : 585-96
Journal article
see the publicationThe Impact of Recombination on Nucleotide Substitutions in the Human Genome
PLoS Genetics . 4 : 1-19
Journal article
see the publicationNeutral Theory: The Null Hypothesis of Molecular Evolution
Nature Education . 1 ( 1 ) : 803-806
Journal article
see the publicationAnalysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia: A somatic view of the germline
Genome Research . 18 : 585-596
Journal article
see the publicationDémasquage des gènes spécifiques d'une espèce génomique du complexeAgrobacterium tumefaciens par AFLP et multicapteur à ADN
7. Colloque national du Bureau des Ressources Génétiques . 7
Conference paper
see the publicationAutomatic Identification of Large Collections of Protein-Coding or rRNA Sequences
Biochimie . 90 ( 4 ) : 609-614
Journal article
see the publicationBioinformatics in the complete genome sequence era
Biochimie . 90 : 553-554
Journal article
see the publicationAccounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria
BMC Evolutionary Biology . 8 : 272-272
Journal article
see the publicationA seven-gene multilocus genus-wide approach to the phylogeny of mycobacteria using supertrees
International Journal of Systematic and Evolutionary Microbiology . 58(part 6) : 1432-1441
Journal article
see the publicationMesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota.
Nature Reviews Microbiology . 6 ( 3 ) : 245-252
DOI: 10.1038/nrmicro1852
Journal article
see the publicationA DNA topoisomerase IB in Thaumarchaeota testifies for the presence of this enzyme in the last common ancestor of Archaea and Eucarya.
Biol Direct . 3 : 54
Journal article
see the publicationLes Archaea : évolution et diversité du troisième domaine du vivant
Bulletin - Société Française de Microbiologie . 23 ( 3 ) : 137-145
Journal article
see the publicationMetagenome Annotation Using a Distributed Grid of Undergraduate Students
PLoS Biology . 6 : 239-241
Journal article
see the publicationFull molecular characterization of a simian immunodeficiency virus, SIVwrcpbt from Temminck's red colobus (Piliocolobus badius temminckii) from Abuko Nature Reserve, The Gambia
Virology . 376 ( 1 ) : 90-100
Journal article
see the publicationPrevalence and genetic diversity of simian immunodeficiency virus infection in wild-living red colobus monkeys (Piliocolobus badius badius) from the Taï forest, Côte d'Ivoire SIVwrc in wild-living western red colobus monkeys.
Infection, Genetics and Evolution . 8 ( 1 ) : 1-14
Journal article
see the publicationA Site- and Time-Heterogeneous Model of Amino Acid Replacement
Molecular Biology and Evolution . 25 ( 5 ) : 842-858
Journal article
see the publicationAdditional molecular support for the new chordate phylogeny.
Genesis - The Journal of Genetics and Development . 46 ( 11 ) : 592-604
DOI: 10.1002/dvg.20450
Journal article
see the publicationEmpirical Profile Mixture Models for Phylogenetic Reconstruction
Bioinformatics . 29 : 2317-2323
Journal article
see the publicationParallel Adaptations to High Temperatures in the Archean Eon
Nature . 456 ( 7224 ) : 942-945
DOI: 10.1038/nature07393
Journal article
see the publicationAnalyse et exploitation de la diversité génétique des polykétides synthases de type I dans l'ADN metagénomique d'un sol
7ème colloque national "Ressources génétiques" . : 201-213
Conference paper
see the publicationGenome-wide studies highlight indirect links between human replication origins and gene regulation.
Proceedings of the National Academy of Sciences of the United States of America . 105 ( 41 ) : 15837-42
Journal article
see the publicationEvolution of the proteome of mitochondrial ribosomes: a clue for the eukaryotic tree?
Journées Ouvertes Biologie Informatique et Mathématiques JOBIM .
Conference paper
see the publicationPopulation genetic inference using a fixed number of segregating sites : a reassessment
Genetical Research . 89 : 231-244
Journal article
see the publication