The Cocoon Group
Members
Post-doc
CNRS
Tel: 04 72 44 81 42
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 61 to 90 publications on 295 in total
Coexistence of two sympatric cryptic bat species in French Guiana: insights from genetic, acoustic and ecological data
BMC Evolutionary Biology . 18 ( 1 )
Journal article
see the publicationCoexistence de deux espèces cryptiques de chauves-souris en Guyane française : apprentissages à partir de la génétique de l’acoustique et de l’écologie
Plume de Naturalistes . 2 : 169-190
Journal article
see the publicationCo-occurrence among three divergent plant-castrating fungi in the same Silene host species
Molecular Ecology . 27 ( 16 ) : 3357 - 3370
DOI: 10.1111/mec.14805
Journal article
see the publicationGearing up to handle the mosaic nature of life in the quest for orthologs
Bioinformatics . 34 ( 2 ) : 323-329
Journal article
see the publicationUnbiased Estimate of Synonymous and Nonsynonymous Substitution Rates with Nonstationary Base Composition
Molecular Biology and Evolution . 35 ( 3 ) : 734-742
Journal article
see the publicationRecPhyloXML: a format for reconciled gene trees
Bioinformatics . 34 ( 21 ) : 3646-3652
Journal article
see the publicationOvertraining often results in topologically incorrect species trees with maximum likelihood methods
DOI: 10.1101/140780
Preprint
see the publicationMultiple convergent supergene evolution events in mating-type chromosomes
Nature Communications . 9 ( 1 ) : 2000
Journal article
see the publicationPhylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes
BMC Genomics . 19 ( S2 ) : 1-15
Journal article
see the publicationHelena and BS: two travellers between the genera Drosophila and Zaprionus
Genome Biology and Evolution .
DOI: 10.1093/gbe/evy184
Journal article
see the publicationLife History Traits Impact the Nuclear Rate of Substitution but Not the Mitochondrial Rate in Isopods
Molecular Biology and Evolution . 35 ( 12 ) : 2900-2912
Journal article
see the publicationBiodiversité, évolution et fonctionnement des écosystèmes
Les Cahiers des prospectives . hors série : 25-33.
Book chapter
see the publicationMareyMap online: A user-friendly web application and database service for estimating recombination rates using physical and genetic maps
Genome Biology and Evolution . 9 ( 10 ) : 2506-2509
DOI: 10.1093/gbe/evx178
Journal article
see the publicationPitfalls in supermatrix phylogenomics
European Journal of Taxonomy . 283 : 1-25
DOI: 10.5852/ejt.2017.283
Journal article
see the publicationTranscriptomic signatures shaped by cell proportions shed light on comparative developmental biology
Genome Biology . 18 : 29
Journal article
see the publicationSONIFICATION OF PHYLOGENETIC TREES: LISTENING TO EVOLUTION
Journées d'Informatique Musicale (JIM) 2017 .
Conference paper
see the publicationDeCoSTAR: Reconstructing the ancestral organization of genes or genomes using reconciled phylogenies
Genome Biology and Evolution . 9 ( 5 ) : 1312-1319
DOI: 10.1093/gbe/evx069
Journal article
see the publicationAlgorithms for computing the double cut and join distance on both gene order and intergenic sizes
Algorithms for Molecular Biology . 12 : 16 (11 pages)
Journal article
see the publicationResolution and reconciliation of non-binary gene trees with transfers, duplications and losses
Bioinformatics . 33 ( 7 ) : 980-987
Journal article
see the publicationEcological networks to unravel the routes to horizontal transposon transfers
PLoS Biology . 15 ( 2 ) : np
Journal article
see the publicationAncestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium
Genome Biology and Evolution . 9 ( 12 ) : 3413 - 3431
DOI: 10.1093/gbe/evx255
Journal article
see the publicationComparative Methods for Reconstructing Ancient Genome Organization
Comparative Genomics: Methods and Protocols . : 343 - 362
Book chapter
see the publicationMaxTiC: Fast Ranking Of A Phylogenetic Tree By Maximum Time Consistency With Lateral Gene Transfers
DOI: 10.1101/127548
Other publication
see the publicationIntegrative modeling of gene and genome evolution roots the archaeal tree of life
Proceedings of the National Academy of Sciences of the United States of America . 114 ( 23 ) : E4602-E4611
Journal article
see the publicationLess effective selection leads to larger genomes
Genome Research . 27 : 1016-1028
Journal article
see the publicationDating with transfers
Journées Ouvertes Biologie Informatique Mathématiques .
Conference paper
see the publicationAncestral Reconstruction: Theory and Practice
Encyclopedia of Evolutionary Biology . : 70–77
Book chapter
see the publicationHorizontal Gene Transfer and the History of Life
Cold Spring Harbor Perspectives in Biology . 8 ( 4 ) : 1312 - 1319
Journal article
see the publication