The Cocoon Group
Members
Post-doc
CNRS
Tel: 04 72 44 81 42
Stagiaire
UCBL
Chargé de recherche
CNRS
Tel: 04 26 23 44 74
Stagiaire
UCBL
Stagiaire
UCBL
Directeur de recherche
CNRS
Tel: 33 04 26 23 44 74
Technicien CDD
CNRS
Chargé de recherche
CNRS
Tel: 04 72 43 29 09
Maître de conférences
UCBL
Tel: 04 72 43 13 44
Maîtresse de conférences
UCBL
Tel: 33 04 72 43 29 18
Post-doc
CNRS
Tel: 04 72 44 81 42
Doctorant
CNRS
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
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 91 to 120 publications on 295 in total
Nucleotide, gene and genome evolution : a score to bind them all
Journées Ouvertes Biologie Informatique Mathématiques .
Conference paper
see the publicationGenome Rearrangements on both Gene Order and Intergenic Regions
WABI 2016 . 9838 : 162-173
Conference paper
see the publicationFrancisella IglG protein and the DUF4280 proteins: PAAR-like proteins in non-canonical Type VI secretion systems?
Microbial Cell . 3 ( 11 ) : 576-578
Journal article
see the publicationComment la reconstruction de génomes ancestraux peut aider à l'assemblage de génomes actuels
Journées Ouvertes Biologie Informatique Mathématiques .
Conference paper
see the publicationSENCA: A Multilayered Codon Model to Study the Origins and Dynamics of Codon Usage
Genome Biology and Evolution . 8 : 2427-41
DOI: 10.1093/gbe/evw165
Journal article
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 publicationEfficient gene tree correction guided by genome evolution
PLoS ONE . 11 ( 8 ) : e0159559 (22 pages)
Journal article
see the publicationLifemap: Exploring the Entire Tree of Life
PLoS Biology . 14 ( 12 )
Journal article
see the publicationRiboDB database: a comprehensive resource for prokaryotic systematics
Molecular Biology and Evolution . 33 ( 8 ) : 2170--2172
Journal article
see the publicationIn silico experimental evolution provides independent and challenging benchmarks for comparative genomics
Journées ouvertes Biologie Informatique Mathématiques . : 79-82
Conference paper
see the publicationComparative Genomics on Artificial Life
Computability in Europe . 9709 : 35-44
Conference paper
see the publicationBreaking Good: Accounting for Fragility of Genomic Regions in Rearrangement Distance Estimation
Genome Biology and Evolution . 8 ( 5 ) : 1427-1439
DOI: 10.1093/gbe/evw083
Journal article
see the publicationSorting Signed Permutations by Reversal (Reversal Sequence)
Encyclopedia of Algorithms . 978-1-4939-2863-7 : 2028-2032
Book chapter
see the publicationGenome rearrangements with indels in intergenes restrict the scenario space
BMC Bioinformatics . 17 ( Suppl 14 ) : 426 (7 pages)
Journal article
see the publicationStrong phylogenetic inertia on genome size and transposable element content among 26 species of flies
Biology Letters . 12 ( 8 )
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 publicationResponse to Comment on "Statistical binning enables an accurate coalescent-based estimation of the avian tree
Science . 350 ( 6257 ) : 171-171
Journal article
see the publicationThe inference of gene trees with species trees
Systematic Biology . 64 ( 1 ) : e42-e62
Journal article
see the publicationReconstruction of an ancestral Yersinia pestis genome and comparison with an ancient sequence
BMC Genomics . 16 ( Suppl 10 ) : S9
Journal article
see the publicationMoments of genome evolution by Double Cut-and-Join
BMC Bioinformatics . 16 ( Suppl 14 ) : S7
Journal article
see the publicationSex and evolution
Handbook of Evolutionary Thinking in the Sciences . 978-94-017-9013-0 : 499--507
Book chapter
see the publicationDegeneration of the Nonrecombining Regions in the Mating-Type Chromosomes of the Anther-Smut Fungi
Molecular Biology and Evolution . 32 ( 4 ) : 928-943
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 publicationKaryotype and Gene Order Evolution from ReconstructedExtinct Ancestors Highlight Contrasts in Genome Plasticity ofModern Rosid Crops
Genome Biology and Evolution . 7 ( 3 ) : 735-749
DOI: 10.1093/gbe/evv014
Journal article
see the publicationFoundations of Coding: Compression, Encryption, Error-Correction
978-1-118-88144-6 : 376
Book
see the publicationWeighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses
PLoS ONE . 10 ( 6 ) : e0129183
Journal article
see the publicationAssessing Approaches for Inferring Species Trees from Multi-Copy Genes
Systematic Biology . 64 ( 2 ) : 325-339
Journal article
see the publicationAncestral gene synteny reconstruction improves extant species scaffolding
BMC Genomics . 16 ( Suppl 10 ) : S11
Journal article
see the publicationProbabilistic modeling of the evolution of gene synteny within reconciled phylogenies
BMC Bioinformatics . 16 ( Suppl 14 ) : S5
Journal article
see the publication