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 268 in total
Ghost lineages highly influence the interpretation of introgression tests
Predicted effects of summer holidays and seasonality on the SARS-Cov-2 epidemic in France
medRxiv : the preprint server for health sciences .
Ghost lineages deceive introgression tests and call for a new null hypothesis
The curious case of a hapless mathematical contribution to biology
A Codon Model for Associating Phenotypic Traits with Altered Selective Patterns of Sequence Evolution
Systematic Biology . 70 ( 3 ) : 608-622
Seaview Version 5: A Multiplatform Software for Multiple Sequence Alignment, Molecular Phylogenetic Analyses, and Tree Reconciliation
Multiple Sequence Alignment . 2231 : 241-260
L'informatique les pieds sur Terre
La fin d'un tout petit monde
Reconciling Gene trees with Species Trees
Phylogenetics in the Genomic Era . : 3.2:1--3.2:23
DGINN, an automated and highly-flexible pipeline for the detection of genetic innovations on protein-coding genes
Nucleic Acids Research . 48 ( 18 ) : e103-e103
Genome Evolution: Mutation Is the Main Driver of Genome Size in Prokaryotes
Current Biology - CB . 30 ( 19 ) : R1083-R1085
Genomic analysis of European Drosophila melanogaster populations reveals longitudinal structure, continent-wide selection, and previously unknown DNA viruses
Molecular Biology and Evolution . 37 ( 9 ) : 2661-2678
Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies
BMC Biology . 18 ( 1 ) : 1-20
Ancestral Genome Organization as a Diagnosis Tool for Phylogenomics
Phylogenetics in the Genomic Era . : 2.5:1--2.5:19
Treerecs: an integrated phylogenetic tool, from sequences to reconciliations.
Bioinformatics . 36 ( 18 ) : 4822-4824
Quand les branches de l’arbre du vivant s’entremêlent
Pour la science .
Sciences, Environnements et Sociétés
CAARS: comparative assembly and annotation of RNA-Seq data
Bioinformatics . 35 ( 13 ) : 2199-2207
Tracing Human Ancestral Migrations Using Symbiotic Bacteria
Groupe des Méthodes Pluridisciplinaires Contribuant à l'Archéologie (GMPCA) .
Detecting adaptive convergent amino acid evolution
Philosophical Transactions of the Royal Society B: Biological Sciences . 374 ( 1777 ) : 1-11
Gene tree reconciliation including transfers with replacement is NP-hard and FPT
Journal of Combinatorial Optimization . 38 ( 2 ) : 502–544
Gene tree species tree reconciliation with gene conversion
Journal of Mathematical Biology . 78 ( 6 ) : 1981–2014
GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes
Genome Biology . 20 ( 1 )
L'arbre du vivant
101 secrets de l'adn . 978-2-271-12323-7 : 358
Tanglegrams Are Misleading for Visual Evaluation of Tree Congruence
Molecular Biology and Evolution . 36 ( 1 ) : 174-176
Zombi: A phylogenetic simulator of trees, genomes and sequences that accounts for dead lineages