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

Monitoring biodiversity of an alpine watershed using eDNA metabarcoding and ecological surveys: a collaborative work between students, scientists and citizens

Florian Blanchard, Abigaël Chieux, Samuel Delorme, Quentin Derian, Uma Disdier, Flora Mottet...

Biennial meeting of the French Society of Ecology and Evolution .

Poster

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Phyloformer: Fast, accurate and versatile phylogenetic reconstruction with deep neural networks

Luca Nesterenko, Luc Blassel, Philippe Veber, Bastien Boussau, Laurent Jacob

DOI: 10.1101/2024.06.17.599404

Preprint

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Simulations of Sequence Evolution: How (Un)realistic They Are and Why

Johanna Trost, Julia Haag, Dimitri Höhler, Laurent Jacob, Alexandros Stamatakis, Bastien Boussau

Molecular Biology and Evolution . 41 ( 1 )

DOI: 10.1093/molbev/msad277

Journal article

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Effective population size does not explain long-term variation in genome size and transposable element content in animals

Alba Marino, Gautier Debaecker, Anna-Sophie Fiston-Lavier, Annabelle Haudry, Benoit Nabholz

eLife .

DOI: 10.7554/eLife.100574.1

Journal article

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Accurate Detection of Convergent Mutations in Large Protein Alignments With ConDor

Marie Morel, Anna Zhukova, Frédéric Lemoine, Olivier Gascuel

Genome Biology and Evolution . 16 ( 4 ) : evae040

DOI: 10.1093/gbe/evae040

Journal article

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Dual Control of Host Actin Polymerization by a Legionella Effector Pair

Margaux Pillon, Céline Michard, Nathalie Baïlo, Juliette Bougnon, Kévin Picq, Oceane Dubois...

Cellular Microbiology . 2024 : 1-19

DOI: 10.1155/2024/8896219

Journal article

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Aevol 4b: Bridging the gap between artificial life and bioinformatics

Hugo Daudey, David P Parsons, David P. Parsons, Eric Tannier, Vincent Daubin, Bastien Boussau...

ALIFE 2024 - International Conference for Artificial Life . : 41-49

DOI: 10.1162/isal_a_00716

Conference paper

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SAMD9L acts as an antiviral factor against HIV-1 and primate lentiviruses by restricting viral and cellular translation

Alexandre Legrand, Clara Dahoui, Clément de la Myre Mory, Kodie Noy, Laura Guiguettaz, Margaux Versapuech...

PLoS Biology . 22 ( 7 ) : e3002696

DOI: 10.1371/journal.pbio.3002696

Journal article

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Proteome allocation and the evolution of metabolic cross-feeding

Florian Labourel, Vincent Daubin, Frédéric Menu, Etienne Rajon

Evolution - International Journal of Organic Evolution .

DOI: 10.1093/evolut/qpae008

Journal article

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Response to “On the impact of incomplete taxon sampling on the relative timing of gene transfer events”

Théo Tricou, Eric Tannier, Damien de Vienne

PLoS Biology . 22 ( 3 ) : e3002557

DOI: 10.1371/journal.pbio.3002557

Journal article

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Dual control of host actin polymerization by a Legionella effector pair

Margaux Pillon, Céline Michard, Nathalie Baïlo, Juliette Bougnon, Kévin Picq, Océane Dubois...

Cellular Microbiology .

DOI: 10.1155/2024/8896219

Journal article

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The Silene latifolia genome and its giant Y chromosome

Carol Moraga, Catarina Branco, Quentin Rougemont, Paris Veltsos, Pavel Jedlička, Aline Muyle...

: 1-23

DOI: 10.1101/2023.09.21.558754

Preprint

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An evolutionary timescale for Bacteria calibrated using the Great Oxidation Event

Adrián Davín, Ben Woodcroft, Rochelle Soo, Benoit Morel, Ranjani Murali, Dominik Schrempf...

DOI: 10.1101/2023.08.08.552427

Preprint

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Evaluation of Methods to Detect Shifts in Directional Selection at the Genome Scale

Louis Duchemin, Vincent Lanore, Philippe Veber, Bastien Boussau

Molecular Biology and Evolution . 40 ( 2 )

DOI: 10.1093/molbev/msac247

Journal article

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Approche globale des éthiques dans les relations sociétés/nature

Rémi Beau, Catherine Aubertin, Annabelle Aish, Anne Atlan, Sébastien Barot, Olivier Barrière...

: 211-219

Report

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Endoparasitoid lifestyle promotes endogenization and domestication of dsDNA viruses

Benjamin Guinet, D. Lepetit, S. Charlat, Peter N Buhl, David G Notton, Astrid Cruaud...

eLife . 12 : e85993

DOI: 10.7554/eLife.85993

Journal article

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Back to the trees: Identifying plants with Human Intelligence

Simon Castellan, Jos Käfer, Eric Tannier

LIMITS 2023 - Ninth Workshop on Computing within Limits . : 1-11

DOI: 10.21428/bf6fb269.265c52ce

see the publication

Se réapproprier la production de connaissance

Alexandre Monnin, Eric Tannier, Maël Thomas

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

Journal article

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PhylteR: Efficient Identification of Outlier Sequences in Phylogenomic Datasets

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

Molecular Biology and Evolution . 40 ( 11 ) : msad234

DOI: 10.1093/molbev/msad234

Journal article

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Host-symbiont-gene phylogenetic reconciliation

Hugo Menet, Alexia Nguyen Trung, Vincent Daubin, Eric Tannier

Peer Community Journal . : 1-22

DOI: 10.24072/pcjournal.273

Journal article

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Approches bioinformatiques pour la détection de l'évolution convergente dans les génomes viraux, application à la résistance aux traitements.

Marie Morel

Thesis

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The crisis of the scientific mind : an investigation, a tragedy and a collective redistribution of roles

Eric Tannier, Vincent Daubin, Sophie Quinton

Les Cahiers de Framespa : e-Storia . ( 40 )

DOI: 10.4000/framespa.13150

Journal article

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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

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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

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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

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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

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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

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