Equipe Le Cocon

Membres

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 31 à 60 sur 314 au total

Evaluation of methods to detect shifts in directional selection at the genome scale

Louis Duchemin, Vincent Lanore, Philippe Veber, Bastien Boussau

DOI: 10.1101/2022.06.22.497174

Pré-publication

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Nucleotide Usage Biases Distort Inferences of the Species Tree

Rui Borges, Bastien Boussau, Gergely Szöllősi, Carolin Kosiol

DOI: 10.1093/gbe/evab290

Pré-publication

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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

Article dans une revue

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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

Article dans une revue

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Vers une représentation sonore des arbres phylogénétiques

Arthur Paté, Henri Boutin, Damien de Vienne

16ème Congrès Français d'Acoustique, CFA2022 .

Acte de congrès

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tidy tree : A New Layout for Phylogenetic Trees

Simon Penel, Damien de Vienne

Molecular Biology and Evolution . 39 ( 10 ) : msac204

DOI: 10.1093/molbev/msac204

Article dans une revue

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Ghost lineages can invalidate or even reverse findings regarding gene flow

Théo Tricou, Eric Tannier, Damien M. de Vienne

PLoS Biology . 20 ( 9 ) : e3001776

DOI: 10.1371/journal.pbio.3001776

Article dans une revue

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GOntact: using chromatin contacts to infer Gene Ontology enrichments for cis -regulatory elements

Alexandre Laverré, Eric Tannier, Philippe Veber, Anamaria Necsulea

DOI: 10.1101/2022.06.13.495495

Pré-publication

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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

Article dans une revue

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Extreme mitochondrial DNA divergence underlies genetic conflict over sex determination

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

Current Biology . 32 ( 10 ) : 2325-2333.e1-e6

DOI: 10.1016/j.cub.2022.04.014

Article dans une revue

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Thirdkind: displaying phylogenetic encounters beyond 2-level reconciliation

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

Bioinformatics . 38 ( 8 ) : 2350–2352

DOI: 10.1093/bioinformatics/btac062

Article dans une revue

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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

Article dans une revue

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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

Article dans une revue

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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

Pré-publication

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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

Pré-publication

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Seaview Version 5: A Multiplatform Software for Multiple Sequence Alignment, Molecular Phylogenetic Analyses, and Tree Reconciliation

Manolo Gouy, Eric Tannier, Nicolas Comte, David Parsons

Multiple Sequence Alignment . 2231 : 241-260

DOI: 10.1007/978-1-0716-1036-7_15

Chapitre d'ouvrage

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A Codon Model for Associating Phenotypic Traits with Altered Selective Patterns of Sequence Evolution

Keren Halabi, Eli Levy Karin, Laurent Guéguen, Itay Mayrose

Systematic Biology . 70 ( 3 ) : 608-622

DOI: 10.1093/sysbio/syaa087

Article dans une revue

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Predicted effects of summer holidays and seasonality on the SARS-Cov-2 epidemic in France

Louis Duchemin, Mathilde Paris, Bastien Boussau

medRxiv : the preprint server for health sciences .

DOI: 10.1101/2020.07.06.20147660

Pré-publication

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Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses

Martin Kapun, Maite G Barrón, Fabian Staubach, Darren J Obbard, R Axel W Wiberg, Jorge Vieira...

Molecular Biology and Evolution . 37 ( 9 ) : 2661-2678

DOI: 10.1093/molbev/msaa120

Article dans une revue

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Treerecs: an integrated phylogenetic tool, from sequences to reconciliations.

Nicolas Comte, Benoît Morel, Damir Hasic, Laurent Guéguen, Bastien Boussau, Vincent Daubin...

Bioinformatics . 36 ( 18 ) : 4822-4824

DOI: 10.1093/bioinformatics/btaa615

Article dans une revue

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Reconciling Gene trees with Species Trees

Bastien Boussau, Celine Scornavacca

Phylogenetics in the Genomic Era . : 3.2:1--3.2:23

Chapitre d'ouvrage

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Ancestral Genome Organization as a Diagnosis Tool for Phylogenomics

Eric Tannier, Adelme Bazin, Adrián Davín, Laurent Guéguen, Sèverine Bérard, Cedric Chauve

Phylogenetics in the Genomic Era . : 2.5:1--2.5:19

Chapitre d'ouvrage

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DGINN, an automated and highly-flexible pipeline for the detection of genetic innovations on protein-coding genes

Lea Picard, Quentin Ganivet, Omran Allatif, Andrea Cimarelli, Laurent Guéguen, Lucie Etienne

Nucleic Acids Research . 48 ( 18 ) : e103-e103

DOI: 10.1093/nar/gkaa680

Article dans une revue

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