The Cocoon Group
Members
Post-doc
INRIA
Tel: 04 72 44 81 42
Stagiaire
UCBL
Tel: 04 72 44 81 42

Chargé de recherche
CNRS
Tel: 04 26 23 44 74
Stagiaire
UCBL
Tel: 04 72 44 81 42

Directeur de recherche
CNRS
Tel: 33 04 26 23 44 74

Ingénieur d'études CDD
CNRS
Tel: 04 72 44 81 42

Chargé de recherche
CNRS
Tel: 04 72 43 29 09

Doctorant
UCBL
Tel: 04 26 23 44 74

Maître de conférences
UCBL
Tel: 04 72 43 13 44

Maîtresse de conférences
UCBL
Tel: 33 04 72 43 29 18
Stagiaire
UCBL
Tel: 04 72 44 81 42

Chargé de recherche
CNRS
Tel: 04 72 44 79 32

Stagiaire
UCBL
Tel: 04 72 44 81 42
Stagiaire
UCBL
Tel: 04 72 44 81 42
Post-doc
CNRS
Tel: 04 72 44 81 42
Doctorant
CNRS
Tel: 04 72 44 81 42

Doctorante
UCBL
Tel: 04 26 23 44 72
Stagiaire
UCBL
Tel: 04 72 44 81 42
Doctorant
UCBL
Tel: 04 72 44 81 42

Directeur de recherche
INRIA
Tel: 33 04 26 23 44 74
Stagiaire
UCBL
Tel: 04 72 44 81 42
Le Cocon is both a research team and a think tank.
Research in “Le Cocon” team focuses on two main topics: multiscale evolution on one hand (i.e., studying the evolution of genetic systems while considering different levels -nucleotides, transposable elements, genes, genomes, microbiomes, organisms, populations, species, geography-), and environmental issues on the other hand. In both cases, we rely on modeling and data analysis, using a combination of statistics and computer science.
Le Cocon is also a place to think about the responsibilities of research and researchers in the anthropocene era, and about the role of non-researcher citizens in orienting and conducting research.
Multiscale evolution
- We have a long history of working on gene transfers. We develop new methods to detect these events in complex systems involving more than two levels (host, symbiont and parasites for example) and
- We use horizontal transfer detection to date species trees and to infer yet unknown biodiversity (extinct and unsampled) (Sthoriz (ANR, 2018)) .
- We have a lasting interest into convergent genomic evolution (Convergenomics - ANR, 2015)
- We question the usual way of testing bioinformatic methods (Evoluthon - ANR, 2019)
- We study the interaction between human populations, their lifestyles, and their gut microbiota (Microregal - ANR, 2015). We are notably interested in identifying cases of host-microbe coevolution and in better understanding transmission dynamics.
Environmental issues
- We develop computational methods to support an agriculture that relies on ecosystemic relationships between crops, the soil, its microbiota, and wild plants and animals (Community Garden Book - Inria, 2019)
- We develop statistical approaches to understand and predict crop yield variability with respect to meteorological conditions
Research in the anthropocene
- We participate to the science shop (UdL), the ethics platform (UdL), Labo1.5, the open science committee, Sciences Citoyennes, the shift project
- We organize a series of seminars to help us think about the position of scientific research in the history of the anthropocene, and about the position of scientists in the future of the anthropocene.
- We assemble committees of citizens to investigate to what extent scientific research can be democratized.
Teaching and outreach
- We teach at University of Lyon, University Lyon 1, INSA, Inria, ENS Lyon, we organize bioinformatics internships
- We regularly participate in the Fête de la Science, have contributed videos in the public transportation system in Lyon, give conferences at Université Populaire and contribute articles in general public journals.
- We develop the software Lifemap to explore the tree of life on computers and smartphones.
Prospective students and postdocs are invited to apply, as we often welcome visitors for internships or research projects.
Publications
Display of 1 to 30 publications on 313 in total
Se réapproprier la production de connaissance
AOC [Analyse Opinion Critique] . : https://aoc.media/opinion/2023/05/17/se-reapproprier-la-production-de-connaissance/
Journal article
see the publicationOpposing effects of plant traits on diversification
Iscience . 26 ( 4 ) : 106362
Journal article
see the publicationTrait-dependent diversification in angiosperms: Patterns, models and data
Ecology Letters . 26 ( 4 ) : 640-657
DOI: 10.1111/ele.14170
Journal article
see the publicationPhylteR: efficient identification of outlier sequences in phylogenomic datasets
Preprint
see the publicationHost-symbiont-gene phylogenetic reconciliation
Peer Community Journal .
Journal article
see the publicationCalculs d’inférence dans les arbres phylogénétiques
Modèles et méthodes pour l’évolution biologique . 9781789480696 : 177-202
Book chapter
see the publicationDiversity and evolution of pigment types in marine $Synechococcus$ cyanobacteria
Genome Biology and Evolution . 14 ( 4 ) : evac035
DOI: 10.1093/gbe/evac035
Journal article
see the publicationAdaptation to host cell environment during experimental evolution of Zika virus
Communications Biology . 5 ( 1 ) : 1115
Journal article
see the publicationEvaluation of methods to detect shifts in directional selection at the genome scale
Preprint
see the publicationNucleotide Usage Biases Distort Inferences of the Species Tree
DOI: 10.1093/gbe/evab290
Preprint
see the publicationPolymorphism‐aware estimation of species trees and evolutionary forces from genomic sequences with RevBayes
Methods in Ecology and Evolution . 13 ( 11 ) : 2339-2346
Journal article
see the publicationRelative Time Constraints Improve Molecular Dating
Systematic Biology . 71 ( 4 ) : 797-809
Journal article
see the publicationVers une représentation sonore des arbres phylogénétiques
16ème Congrès Français d'Acoustique, CFA2022 .
Conference paper
see the publicationtidy tree : A New Layout for Phylogenetic Trees
Molecular Biology and Evolution . 39 ( 10 ) : msac204
Journal article
see the publicationGhost lineages can invalidate or even reverse findings regarding gene flow
Plos Biology . 20 ( 9 ) : e3001776
Journal article
see the publicationDistinct evolutionary trajectories of SARS-CoV-2-interacting proteins in bats and primates identify important host determinants of COVID-19
Proceedings of the National Academy of Sciences of the United States of America . 119 ( 35 )
Journal article
see the publicationExtreme mitochondrial DNA divergence underlies genetic conflict over sex determination
Current Biology - CB . 32 ( 10 ) : 2325-2333.e6
Journal article
see the publicationPhyloformer: towards fast and accurate phylogeny estimation with self-attention networks
Preprint
see the publicationBayesian investigation of SARS-CoV-2-related mortality in France
Peer Community Journal . 2 ( e6 )
Journal article
see the publicationA hapless mathematical contribution to biology: Chromosome inversions in Drosophila 1937-1941
History and Philosophy of the Life Sciences .
Journal article
see the publicationLabile sex expression in angiosperm species with sex chromosomes
Philosophical Transactions of the Royal Society B: Biological Sciences . 377 ( 1850 )
Journal article
see the publicationPulled Diversification Rates, Lineages-Through-Time Plots, and Modern Macroevolutionary Modeling
Systematic Biology . 71 ( 3 ) : 758-773
Journal article
see the publicationHow sex chromosomes get trapped into nonrecombination
Plos Biology . 20 ( 7 ) : e3001718
Journal article
see the publicationThirdkind: displaying phylogenetic encounters beyond 2-level reconciliation
Bioinformatics . : 1-3
Journal article
see the publicationPhylogenetic reconciliation
PLoS Computational Biology . 18 ( 11 ) : e1010621
Journal article
see the publicationLong-range promoter–enhancer contacts are conserved during evolution and contribute to gene expression robustness
Genome Research . 32 ( 2 ) : 280-296
Journal article
see the publicationGhost lineages highly influence the interpretation of introgression tests
Systematic Biology . 71 ( 5 ) : 1147–1158
Journal article
see the publicationA derived ZW chromosome system in Amborella trichopoda, representing the sister lineage to all other extant flowering plants
New Phytologist . 233 : 1636-1642
DOI: 10.1111/nph.17662
Journal article
see the publicationComparison of developmental genome expression in rodent molars reveals extensive developmental system drift
Preprint
see the publication