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.
- 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.
- 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.
Display of 1 to 30 publications on 294 in total
An evolutionary timescale for Bacteria calibrated using the Great Oxidation Event
Evaluation of Methods to Detect Shifts in Directional Selection at the Genome Scale
Molecular Biology and Evolution . 40 ( 2 )
Approche globale des éthiques dans les relations sociétés/nature
Dual control of host actin polymerization by a Legionella effector pair
Endoparasitoid lifestyle promotes endogenization and domestication of dsDNA viruses
eLife . 12 : e85993
Back to the trees: Identifying plants with Human Intelligence
LIMITS 2023 - Ninth Workshop on Computing within Limits . : 1-11
Se réapproprier la production de connaissance
AOC [Analyse Opinion Critique] . : https://aoc.media/opinion/2023/05/17/se-reapproprier-la-production-de-connaissance/
PhylteR: efficient identification of outlier sequences in phylogenomic datasets
Molecular Biology and Evolution .
Host-symbiont-gene phylogenetic reconciliation
Peer Community Journal . : 1-22
The crisis of the scientific mind : an investigation, a tragedy and a collective redistribution of roles
Les Cahiers de Framespa : e-Storia . ( 40 )
Calculs d’inférence dans les arbres phylogénétiques
Modèles et méthodes pour l’évolution biologique . 9781789480696 : 177-202
Diversity and evolution of pigment types in marine $Synechococcus$ cyanobacteria
Genome Biology and Evolution . 14 ( 4 ) : evac035
Adaptation to host cell environment during experimental evolution of Zika virus
Communications Biology . 5 ( 1 ) : 1115
Evaluation of methods to detect shifts in directional selection at the genome scale
Polymorphism‐aware estimation of species trees and evolutionary forces from genomic sequences with RevBayes
Methods in Ecology and Evolution . 13 ( 11 ) : 2339-2346
Relative Time Constraints Improve Molecular Dating
Systematic Biology . 71 ( 4 ) : 797-809
Vers une représentation sonore des arbres phylogénétiques
16ème Congrès Français d'Acoustique, CFA2022 .
tidy tree : A New Layout for Phylogenetic Trees
Molecular Biology and Evolution . 39 ( 10 ) : msac204
Ghost lineages can invalidate or even reverse findings regarding gene flow
PLoS Biology . 20 ( 9 ) : e3001776
GOntact: using chromatin contacts to infer Gene Ontology enrichments for cis -regulatory elements
Distinct 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 )
Extreme mitochondrial DNA divergence underlies genetic conflict over sex determination
Current Biology - CB . 32 ( 10 ) : 2325-2333.e1-e6
Phyloformer: towards fast and accurate phylogeny estimation with self-attention networks
Bayesian investigation of SARS-CoV-2-related mortality in France
Peer Community Journal . 2 ( e6 )
A hapless mathematical contribution to biology
History and Philosophy of the Life Sciences . 44 ( 34 )
Thirdkind: displaying phylogenetic encounters beyond 2-level reconciliation
Bioinformatics . 38 ( 8 ) : 2350–2352
PLoS Computational Biology . 18 ( 11 ) : e1010621
Long-range promoter–enhancer contacts are conserved during evolution and contribute to gene expression robustness
Genome Research . 32 ( 2 ) : 280-296
Ghost lineages highly influence the interpretation of introgression tests
Systematic Biology . 71 ( 5 ) : 1147–1158