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 331 to 360 publications on 952 in total
Global phylogenomic analysis disentangles the complex evolutionary history of DNA replication in archaea.
Genome Biology and Evolution . 6 ( 1 ) : 192-212
DOI: 10.1093/gbe/evu004
Journal article
see the publication“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
Mobile DNA . 5 : 13
Journal article
see the publicationDioecy is associated with higher diversification rates in flowering plants
Journal of Evolutionary Biology . 27 : 1478-1490
DOI: 10.1111/jeb.12385
Journal article
see the publicationIdentification and Analysis of Transposable Elements in Genomic Sequences
Genome analysis, current procedures and applications . 978-1-908230-29-4
Book chapter
see the publicationFormation of chromosome in bacteria
FEBS-EMBO 2014 Conference .
Conference paper
see the publicationSpecific Activation of an I-Like Element in Drosophila Interspecific Hybrids
Genome Biology and Evolution . 6 : 1806 - 1817
DOI: 10.1093/gbe/evu141
Journal article
see the publicationGC-Biased Gene Conversion in Yeast Is Specifically Associated with Crossovers: Molecular Mechanisms and Evolutionary Significance
Molecular Biology and Evolution . 30 : 1409--19
Journal article
see the publicationXACT, a long noncoding transcript coating the active X chromosome in human pluripotent cells
Nature Genetics . 45 : 239--41
DOI: 10.1038/ng.2530
Journal article
see the publicationThe origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes
Genome Research . 23 : 749--61
Journal article
see the publicationPCR survey of 50 introns in animals: Cross-amplification of homologous EPIC loci in eight non-bilaterian, protostome and deuterostome phyla
Marine Genomics . 12 : 1-8
Journal article
see the publicationThe short-term impact of wetland restoration on the genetic diversity of a predominantly clonal plant species
Aquatic Botany . 110 : 16-23
Journal article
see the publicationAncient Substructure in Early mtDNA Lineages of Southern Africa
American Journal of Human Genetics . 92 ( 2 ) : 285-292
Journal article
see the publicationGenome-wide analysis in chicken reveals that local levels of genetic diversity are mainly governed by the rate of recombination
BMC Genomics . 14 ( 1 ) : 86
Journal article
see the publicationTwisted Signatures of GC-Biased Gene Conversion Embedded in an Evolutionary Stable Karyotype
Molecular Biology and Evolution . 30 ( 7 ) : 1700-1712
Journal article
see the publicationHuman Genetic Data Reveal Contrasting Demographic Patterns between Sedentary and Nomadic Populations That Predate the Emergence of Farming
Molecular Biology and Evolution . 30 ( 12 ) : 2629 - 2644
Journal article
see the publicationAncestry runs deeper than blood: The evolutionary history of ABO points to cryptic variation of functional importance
BioEssays . : n/a-n/a
Journal article
see the publicationMultiple Instances of Ancient Balancing Selection Shared Between Humans and Chimpanzees
Science . 339 ( 6127 ) : 1578-1582
Journal article
see the publicationPositive selection of protective variants for type 2 diabetes from the Neolithic onward: a case study in Central Asia
European Journal of Human Genetics . 21 ( 10 ) : 1146-1151
Journal article
see the publicationIs RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization
Ecology and Evolution . 3 ( 4 ) : 846-852
DOI: 10.1002/ece3.512
Journal article
see the publicationGénomes, protéomes et transcriptomes à foison
Pour la science . 433 : 38--39
Journal article
see the publicationThe molecular signal for the adaptation to cold temperature during early life on Earth
Biology Letters . 9 ( 5 ) : 20130608
Journal article
see the publicationMycobacterium bourgelatii sp. nov., a rapidly growing, non-chromogenic species isolated from the lymph nodes of cattle.
International Journal of Systematic and Evolutionary Microbiology . 63 ( Pt 12 ) : 4669-74
Journal article
see the publicationCandida albicans and non- Candida albicans fungemia in an institutional hospital during a decade
Medical Mycology . 51 ( 1 ) : 33-37
Journal article
see the publicationDiminution of 2,3,5-triphenyltetrazolium chloride toxicity on Listeria monocytogenes growth by iron source addition to the culture medium
Food Microbiology . 38 : 1--5
Journal article
see the publicationMesotoga infera sp. nov., a mesophilic member of the order Thermotogales, isolated from an underground gas storage aquifer.
International Journal of Systematic and Evolutionary Microbiology . 63 ( Pt 8 ) : 3003-8
Journal article
see the publicationMetagenomics of Kamchatkan hot spring filaments reveal two new major (hyper)thermophilic lineages related to Thaumarchaeota
Research in Microbiology . 164 : 425--38
Journal article
see the publicationUtilization of Machine-Learning Methodologies in Order to Understand Complex Evolutionary and Functional Links among Bacterial Genomes
IFCS2013 Book of abstracts . : p. 203
Conference paper
see the publication