Bioinformatics, Phylogeny and Evolutionary Genomics Group
Members
Maîtresse de conférences
UCBL
Tel: 04 72 44 84 87
Stagiaire
UCBL

Professeure des universités
UCBL
Tel: 33 04 26 23 44 76

Doctorante
UCBL
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

Directeur de recherche
CNRS

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 331 to 360 publications on 1098 in total
A mixed relaxed clock model
Philosophical Transactions of the Royal Society B: Biological Sciences . 371 : 20150132
Journal article
see the publicationPolymorphic Microsatellite Markers for the Tetrapolar Anther-Smut Fungus Microbotryum saponariae Based on Genome Sequencing
PLoS ONE . 11 ( 11 ) : e0165656
Journal article
see the publicationQualité des données NGS : de la séquence aux bases de données
La génomique environnementale . 978-1-78405-151-8 : 180 p.
Book chapter
see the publicationGene Acquisitions from Bacteria at the Origins of Major Archaeal Clades Are Vastly Overestimated
Molecular Biology and Evolution . 33 ( 2 ) : 305 - 310
Journal article
see the publicationRiboDB database: a comprehensive resource for prokaryotic systematics
Molecular Biology and Evolution . 33 ( 8 ) : 2170--2172
Journal article
see the publicationCombined Genotypic, Phylogenetic, and Epidemiologic Analyses of Mycobacterium tuberculosis Genetic Diversity in the Rhône Alpes Region, France
PLoS ONE . 11 ( 4 ) : e0153580
Journal article
see the publicationSilencing of natural transformation by an RNA chaperone and a multitarget small RNA
Proceedings of the National Academy of Sciences of the United States of America . 113 ( 31 ) : 8813-8818
Journal article
see the publicationTranscriptional start site turnover in the evolution of bacterial paralogous genes - the pelE-pelD virulence genes in Dickeya
FEBS Journal . 283 ( 22 ) : 4192-4207
Journal article
see the publicationControl of Hoxd gene transcription in the mammary bud by hijacking a preexisting regulatory landscape
Proceedings of the National Academy of Sciences of the United States of America . 113 ( 48 ) : e7720-e7729
Journal article
see the publicationSEX-DETector: a probabilistic approach to study sex chromosomes in non-model organisms
Genome Biology and Evolution . 8 : 2530-2543
DOI: 10.1093/gbe/evw172
Journal article
see the publicationPhylogenomic analysis supports the ancestral presence of LPS-outer membranes in the Firmicutes.
eLife . 5 : e14589
Journal article
see the publicationCell division of Streptococcus pneumoniae: think positive!
Current Opinion in Microbiology . 34 : 18-23
Journal article
see the publicationReply to Halanych et al.
Proceedings of the National Academy of Sciences of the United States of America . 113 ( 8 ) : E948-E949
Journal article
see the publicationHotair Is Dispensible for Mouse Development
PLoS Genetics . 12 : e1006232
Journal article
see the publicationA role for HOX13 proteins in the regulatory switch between TADs at the HoxD locus
Genes and Development . 30 : 1172-86
Journal article
see the publicationRevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language
Systematic Biology . 65 : 726-36
Journal article
see the publicationThe transposable element environment of human genes is associated with histone and expression changes in cancer
BMC Genomics . 17 ( 1 )
Journal article
see the publicationLife Histories, Axes of Variation in
The Encyclopedia of Evolutionary Biology . 2 : 480-492
Book chapter
see the publicationEvolution of sex-biased gene expression in a dioecious plant
Nature Plants . 2 : 16168
Journal article
see the publicationNo Evidence That Nitrogen Limitation Influences the Elemental Composition of Isopod Transcriptomes and Proteomes
Molecular Biology and Evolution . 33 ( 10 ) : 2605–2620
Journal article
see the publicationRecombination Rate Variation Modulates Gene Sequence Evolution Mainly via GC-Biased Gene Conversion, Not Hill–Robertson Interference, in an Avian System
Molecular Biology and Evolution . 33 ( 1 ) : 216-227
Journal article
see the publicationGC‐biased gene conversion links the recombination landscape and demography to genomic base composition
BioEssays . 37 ( 12 ) : 1317-1326
Journal article
see the publicationLinked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers
Genome Research . 25 ( 11 ) : 1656-1665
Journal article
see the publicationEvolutionary Consequences of DNA Methylation on the GC Content in Vertebrate Genomes
G3 . 5 ( 3 ) : 441-447
Journal article
see the publicationVariation in Rural African Gut Microbiota Is Strongly Correlated with Colonization by Entamoeba and Subsistence
PLoS Genetics . 11 ( 11 ) : e1005658
Journal article
see the publicationIdentifying new sex-linked genes through BAC sequencing in the dioecious plant Silene latifolia
BMC Genomics . 16 : 546
Journal article
see the publicationAssessment of polycarbonate filter in a molecular analytical system for the microbiological quality monitoring of recycled waters onboard ISS
Life Sciences in Space Research . 6 : 29-35
Journal article
see the publicationNontuberculous Mycobacteria: An Underestimated Cause of Bioprosthetic Valve Infective Endocarditis
Open Forum Infectious Diseases . 2 ( 2 )
DOI: 10.1093/ofid/ofv047
Journal article
see the publicationAdaptation in toxic environments: arsenic Genomic Islands in the bacterial genus $Thiomonas$
PLoS ONE . 10 ( 9 ) : 0139011
Journal article
see the publicationGC-Content evolution in bacterial genomes: The biased gene conversion hypothesis expands
PLoS Genetics . 11 ( 2 ) : 1-20
Journal article
see the publication