The Cocoon Group

Members

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 1 to 30 publications on 313 in total

Se réapproprier la production de connaissance

Alexandre Monnin, Eric Tannier, Maël Thomas

AOC [Analyse Opinion Critique] . : https://aoc.media/opinion/2023/05/17/se-reapproprier-la-production-de-connaissance/

Journal article

see the publication

Opposing effects of plant traits on diversification

B. Anderson, J. Pannell, S. Billiard, C. Burgarella, H. de Boer, M. Dufay...

Iscience . 26 ( 4 ) : 106362

DOI: 10.1016/j.isci.2023.106362

Journal article

see the publication

Trait-dependent diversification in angiosperms: Patterns, models and data

Andrew J. Helmstetter, Rosana Zenil-Ferguson, Hervé Sauquet, Sarah P Otto, Marcos Méndez, Mario Vallejo-Marín...

Ecology Letters . 26 ( 4 ) : 640-657

DOI: 10.1111/ele.14170

Journal article

see the publication

PhylteR: efficient identification of outlier sequences in phylogenomic datasets

Aurore Comte, Théo Tricou, Eric Tannier, Julien Joseph, Aurélie Siberchicot, Simon Penel...

DOI: 10.1101/2023.02.02.526888

Preprint

see the publication

Calculs d’inférence dans les arbres phylogénétiques

Laurent Guéguen

Modèles et méthodes pour l’évolution biologique . 9781789480696 : 177-202

DOI: 10.51926/ISTE.9069.ch7

Book chapter

see the publication

Diversity and evolution of pigment types in marine $Synechococcus$ cyanobacteria

Théophile Grébert, Laurence Garczarek, Vincent Daubin, Florian Humily, Dominique Marie, Morgane Ratin...

Genome Biology and Evolution . 14 ( 4 ) : evac035

DOI: 10.1093/gbe/evac035

Journal article

see the publication

Adaptation to host cell environment during experimental evolution of Zika virus

Vincent Grass, Emilie Hardy, Kassian Kobert, Soheil Rastgou Talemi, Elodie Décembre, Coralie Guy...

Communications Biology . 5 ( 1 ) : 1115

DOI: 10.1038/s42003-022-03902-y

Journal article

see the publication

Polymorphism‐aware estimation of species trees and evolutionary forces from genomic sequences with RevBayes

Rui Borges, Bastien Boussau, Sebastian Höhna, Ricardo Pereira, Carolin Kosiol

Methods in Ecology and Evolution . 13 ( 11 ) : 2339-2346

DOI: 10.1111/2041-210X.13980

Journal article

see the publication

Relative Time Constraints Improve Molecular Dating

Gergely Szöllõsi, Sebastian Höhna, Tom Williams, Dominik Schrempf, Vincent Daubin, Bastien Boussau

Systematic Biology . 71 ( 4 ) : 797-809

DOI: 10.1093/sysbio/syab084

Journal article

see the publication

Vers une représentation sonore des arbres phylogénétiques

Arthur Paté, Henri Boutin, Damien de Vienne

16ème Congrès Français d'Acoustique, CFA2022 .

Conference paper

see the publication

Distinct evolutionary trajectories of SARS-CoV-2-interacting proteins in bats and primates identify important host determinants of COVID-19

Marie Cariou, Léa Picard, Laurent Guéguen, Stéphanie Jacquet, Andrea Cimarelli, Oliver Fregoso...

Proceedings of the National Academy of Sciences of the United States of America . 119 ( 35 )

DOI: 10.1073/pnas.2206610119

Journal article

see the publication

Extreme mitochondrial DNA divergence underlies genetic conflict over sex determination

Patrice David, Cyril Degletagne, Nathanaelle Saclier, Aurel Jennan, Philippe Jarne, Sandrine Plénet...

Current Biology - CB . 32 ( 10 ) : 2325-2333.e6

DOI: 10.1016/j.cub.2022.04.014

Journal article

see the publication

A hapless mathematical contribution to biology: Chromosome inversions in Drosophila 1937-1941

Eric Tannier

History and Philosophy of the Life Sciences .

DOI: 10.1007/s40656-022-00514-x

Journal article

see the publication

Labile sex expression in angiosperm species with sex chromosomes

Jos Käfer, Marcos Méndez, Sylvain Mousset

Philosophical Transactions of the Royal Society B: Biological Sciences . 377 ( 1850 )

DOI: 10.1098/rstb.2021.0216

Journal article

see the publication

Pulled Diversification Rates, Lineages-Through-Time Plots, and Modern Macroevolutionary Modeling

Andrew J. Helmstetter, Sylvain Glémin, Jos Käfer, Rosana Zenil-Ferguson, Hervé Sauquet, Hugo J de Boer...

Systematic Biology . 71 ( 3 ) : 758-773

DOI: 10.1093/sysbio/syab083

Journal article

see the publication

Thirdkind: displaying phylogenetic encounters beyond 2-level reconciliation

Simon Penel, Hugo Menet, Théo Tricou, Vincent Daubin, Eric Tannier

Bioinformatics . : 1-3

DOI: 10.1093/bioinformatics/btac062

Journal article

see the publication

Long-range promoter–enhancer contacts are conserved during evolution and contribute to gene expression robustness

Alexandre Laverré, Eric Tannier, Anamaria Necsulea

Genome Research . 32 ( 2 ) : 280-296

DOI: 10.1101/gr.275901.121

Journal article

see the publication

Ghost lineages highly influence the interpretation of introgression tests

Théo Tricou, Eric Tannier, Damien M. de Vienne

Systematic Biology . 71 ( 5 ) : 1147–1158

DOI: 10.1093/sysbio/syac011

Journal article

see the publication

A derived ZW chromosome system in Amborella trichopoda, representing the sister lineage to all other extant flowering plants

Jos Käfer, Adam Bewick, Amélie Andres‐robin, Garance Lapetoule, Alex Harkess, José Caïus...

New Phytologist . 233 : 1636-1642

DOI: 10.1111/nph.17662

Journal article

see the publication

Comparison of developmental genome expression in rodent molars reveals extensive developmental system drift

Marie Sémon, Laurent Guéguen, Coraline Petit, Carine Rey, Anne Lambert, Manon Peltier...

DOI: 10.1101/2020.04.22.043422

Preprint

see the publication

Relative time constraints improve molecular dating

Gergely J Szöllősi, Sebastian Höhna, Tom A Williams, Dominik Schrempf, Vincent Daubin, Bastien Boussau

DOI: 10.1101/2020.10.17.343889

Preprint

see the publication