Equipe Le Cocon
Membres
Post-doc
CNRS
Tél : 04 72 44 81 42
Directeur de recherche
CNRS
Tél : 04 26 23 44 74
Stagiaire
UCBL
Stagiaire
UCBL
Directeur de recherche
CNRS
Tél : 33 04 26 23 44 74
Technicien CDD
CNRS
Chargé de recherche
CNRS
Tél : 04 72 43 29 09
Maître de conférences
UCBL
Tél : 04 72 43 13 44
Maîtresse de conférences
UCBL
Tél : 33 04 72 43 29 18
Post-doc
CNRS
Tél : 04 72 44 81 42
Doctorant
CNRS
Tél : 04 72 44 81 42
Doctorant
UCBL
Tél : 04 72 44 81 42
Directeur de recherche
INRIA
Tél : 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
Affichage des publications 241 à 270 sur 295 au total
Speciation in fungi
Fungal Genetics and Biology . 45 ( 6 ) : 791--802
Article dans une revue
voir la 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
Acte de congrès
voir la publicationDealing with incongruence in phylogenomic analyses
Philosophical Transactions of the Royal Society B: Biological Sciences . -- : 1233-1241
Article dans une revue
voir la publicationPrecise detection of rearrangement breakpoints in mammalian chromosomes
BMC Bioinformatics . 9 ( 1 ) : 286
Article dans une revue
voir la publicationReactive Stochastic Local Search Algorithms for the Genomic Median Problem
European Conference on Evolutionary Computation in Combinatorial Optimization (EvoCOP) . 4972 : 266-276
Acte de congrès
voir la publicationA Methodological Framework for the Reconstruction of Contiguous Regions of Ancestral Genomes and its Application to Mammalian Genomes
: 26
Rapport
voir la publicationMating system and recombination affect molecular evolution in four Triticeae species
Genetics Research . 90 : 97-109
Article dans une revue
voir la publicationMating system and recombination affect molecular evolution in four Triticeae species
Genetics Research . 90 ( 1 ) : 97-109
Article dans une revue
voir la publicationParallel Adaptations to High Temperatures in the Archean Eon
Nature . 456 ( 7224 ) : 942-945
DOI: 10.1038/nature07393
Article dans une revue
voir la publicationThe solution space of sorting by reversals
3rd International Symposium on Bioinformatics Research and Applications (ISBRA 2007) . 4463 : 293-304
Acte de congrès
voir la publicationEvolution under Reversals: Parsimony and Conservation of Common Intervals
IEEE/ACM Transactions on Computational Biology and Bioinformatics . 4 : 301-309
Article dans une revue
voir la publicationAdvances on sorting by reversals
Discrete Applied Mathematics . 155 : 881-888
Article dans une revue
voir la publicationThéorie des Codes : compression, cryptage, correction
9782100506927 : 352
Ouvrage
voir la publicationGrinding up wheat: A massive loss of nucleotide diversity since domestication
Molecular Biology and Evolution . 24 ( 7 ) : 1506-1517
Article dans une revue
voir la publicationHorizontal Gene Transfer Regulation in Bacteria as a ‘‘Spandrel'' of DNA Repair Mechanisms
PLoS ONE . 2 ( 10 ) : e1055-e1066
Article dans une revue
voir la publicationA congruence index for testing topological similarity between trees
Bioinformatics . 23 ( 23 ) : 3119--3124
Article dans une revue
voir la publicationMareyMap: an R-based tool with graphical interface for estimating recombination rates
Bioinformatics . 23 : 2188-2189
Article dans une revue
voir la publicationWhen can host shifts produce congruent host and parasite phylogenies? A simulation approach
Journal of Evolutionary Biology . 20 ( 4 ) : 1428--1438
Article dans une revue
voir la publicationComparative genomics and the evolution of prokaryotes
Trends in Microbiology . 15 : 135-141
Article dans une revue
voir la 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
Article dans une revue
voir la publicationGrinding up wheat: a massive loss of nucleotide diversity since domestication
Molecular Biology and Evolution . 24 : 1506-1517
Article dans une revue
voir la publicationEffective Stochastic Local Search Algorithms for the Genomic Median Problem
Doctoral Symposium on Engineering Stochastic Local Search Algorithms (SLS-DS) . : 1-5
Acte de congrès
voir la 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
Article dans une revue
voir la publicationA Markovian Approach for the Analysis of the Gene Structure
Prague stringology conference . 19 ( 1 ) : 19-35
Acte de congrès
voir la publicationA computational prediction of isochores based on hidden Markov models
Gene . 385 : 41-49
Article dans une revue
voir la publicationEfficient Likelihood Computations with Nonreversible Models of Evolution
Systematic Biology . 55 ( 5 ) : 756-768
Article dans une revue
voir la 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
Article dans une revue
voir la publicationUV-Targeted Dinucleotides Are Not Depleted in Light-Exposed Prokaryotic Genomes
Molecular Biology and Evolution . 23 : 2214-2219
Article dans une revue
voir la publicationGlobal trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia.
Nature . 444 ( 7116 ) : 171-8
DOI: 10.1038/nature05230
Article dans une revue
voir la publicationSarment: Python modules for HMM analysis and partitioning of sequences
Bioinformatics . 21 : 3427-3428
Article dans une revue
voir la publication