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 241 to 270 publications on 295 in total
Speciation in fungi
Fungal Genetics and Biology . 45 ( 6 ) : 791--802
Journal article
see the publicationDémasquage des gènes spécifiques d'une espèce génomique du complexeAgrobacterium tumefaciens par AFLP et multicapteur à ADN
7. Colloque national du Bureau des Ressources Génétiques . 7
Conference paper
see the publicationDealing with incongruence in phylogenomic analyses
Philosophical Transactions of the Royal Society B: Biological Sciences . -- : 1233-1241
Journal article
see the publicationPrecise detection of rearrangement breakpoints in mammalian chromosomes
BMC Bioinformatics . 9 ( 1 ) : 286
Journal article
see the publicationReactive Stochastic Local Search Algorithms for the Genomic Median Problem
European Conference on Evolutionary Computation in Combinatorial Optimization (EvoCOP) . 4972 : 266-276
Conference paper
see the publicationA Methodological Framework for the Reconstruction of Contiguous Regions of Ancestral Genomes and its Application to Mammalian Genomes
: 26
Report
see the publicationMating system and recombination affect molecular evolution in four Triticeae species
Genetics Research . 90 : 97-109
Journal article
see the publicationMating system and recombination affect molecular evolution in four Triticeae species
Genetics Research . 90 ( 1 ) : 97-109
Journal article
see the publicationParallel Adaptations to High Temperatures in the Archean Eon
Nature . 456 ( 7224 ) : 942-945
DOI: 10.1038/nature07393
Journal article
see the publicationThe solution space of sorting by reversals
3rd International Symposium on Bioinformatics Research and Applications (ISBRA 2007) . 4463 : 293-304
Conference paper
see the publicationEvolution under Reversals: Parsimony and Conservation of Common Intervals
IEEE/ACM Transactions on Computational Biology and Bioinformatics . 4 : 301-309
Journal article
see the publicationAdvances on sorting by reversals
Discrete Applied Mathematics . 155 : 881-888
Journal article
see the publicationGrinding up wheat: A massive loss of nucleotide diversity since domestication
Molecular Biology and Evolution . 24 ( 7 ) : 1506-1517
Journal article
see the publicationHorizontal Gene Transfer Regulation in Bacteria as a ‘‘Spandrel'' of DNA Repair Mechanisms
PLoS ONE . 2 ( 10 ) : e1055-e1066
Journal article
see the publicationA congruence index for testing topological similarity between trees
Bioinformatics . 23 ( 23 ) : 3119--3124
Journal article
see the publicationMareyMap: an R-based tool with graphical interface for estimating recombination rates
Bioinformatics . 23 : 2188-2189
Journal article
see the publicationWhen can host shifts produce congruent host and parasite phylogenies? A simulation approach
Journal of Evolutionary Biology . 20 ( 4 ) : 1428--1438
Journal article
see the publicationComparative genomics and the evolution of prokaryotes
Trends in Microbiology . 15 : 135-141
Journal article
see the publicationGenome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography
Genome Research . 17 : 7-15
DOI: 10.1101/gr.5798407
Journal article
see the publicationGrinding up wheat: a massive loss of nucleotide diversity since domestication
Molecular Biology and Evolution . 24 : 1506-1517
Journal article
see the publicationEffective Stochastic Local Search Algorithms for the Genomic Median Problem
Doctoral Symposium on Engineering Stochastic Local Search Algorithms (SLS-DS) . : 1-5
Conference paper
see the publicationImpacts d’événements démographiques et sélectifs sur la diversité des plantes cultivées: apports de l’analyse du polymorphisme alliée à la théorie de la coalescence
Actes du BRG . 6 : 243-257
Journal article
see the publicationA Markovian Approach for the Analysis of the Gene Structure
Prague stringology conference . 19 ( 1 ) : 19-35
Conference paper
see the publicationA computational prediction of isochores based on hidden Markov models
Gene . 385 : 41-49
Journal article
see the publicationEfficient Likelihood Computations with Nonreversible Models of Evolution
Systematic Biology . 55 ( 5 ) : 756-768
Journal article
see the publicationGlobal trends of whole genome duplications revealed by the genome sequence of the ciliate Paramecium tetraurelia
Nature . 444 ( 7116 ) : 171-178
DOI: 10.1038/nature05230
Journal article
see the publicationUV-Targeted Dinucleotides Are Not Depleted in Light-Exposed Prokaryotic Genomes
Molecular Biology and Evolution . 23 : 2214-2219
Journal article
see the publicationGlobal trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia.
Nature . 444 ( 7116 ) : 171-8
DOI: 10.1038/nature05230
Journal article
see the publicationSarment: Python modules for HMM analysis and partitioning of sequences
Bioinformatics . 21 : 3427-3428
Journal article
see the publication