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 121 à 150 sur 311 au total

Strong phylogenetic inertia on genome size and transposable element content among 26 species of flies

Camille Sessegolo, Nelly Burlet, Annabelle A. Haudry

Biology Letters . 12 ( 8 )

DOI: 10.1098/rsbl.2016.0407

Article dans une revue

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RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language

S. Hohna, M. J. Landis, T. A. Heath, Bastien Boussau, Nicolas Lartillot, B. R. Moore...

Systematic Biology . 65 : 726-36

DOI: 10.1093/sysbio/syw021

Article dans une revue

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The transposable element environment of human genes is associated with histone and expression changes in cancer

Laura Grégoire, Annabelle A. Haudry, Emmanuelle Lerat

BMC Genomics . 17 ( 1 )

DOI: 10.1186/s12864-016-2970-1

Article dans une revue

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Response to Comment on "Statistical binning enables an accurate coalescent-based estimation of the avian tree

S. Mirarab, M. Bayzid, B. Boussau, T. Warnow

Science . 350 ( 6257 ) : 171-171

DOI: 10.1126/science.aaa7719

Article dans une revue

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The inference of gene trees with species trees

Gergely Szöllősi, Eric Tannier, Vincent Daubin, Bastien Boussau

Systematic Biology . 64 ( 1 ) : e42-e62

DOI: 10.1093/sysbio/syu048

Article dans une revue

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Reconstruction of an ancestral Yersinia pestis genome and comparison with an ancient sequence

Wandrille Duchemin, Vincent Daubin, Eric Tannier

BMC Genomics . 16 ( Suppl 10 ) : S9

DOI: 10.1007/978-3-319-19048-8_16

Article dans une revue

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Sex and evolution

Pierre-Henri Gouyon, Damien De Vienne, Tatiana Giraud

Handbook of Evolutionary Thinking in the Sciences . 978-94-017-9013-0 : 499--507

Chapitre d'ouvrage

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Degeneration of the Nonrecombining Regions in the Mating-Type Chromosomes of the Anther-Smut Fungi

Eric Fontanillas, Michael E Hood, Hélène Badouin, Elsa Petit, Valérie Barbe, Jerome Gouzy...

Molecular Biology and Evolution . 32 ( 4 ) : 928-943

DOI: 10.1093/molbev/msu396

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GC-Content evolution in bacterial genomes: The biased gene conversion hypothesis expands

Florent Lassalle, Séverine Périan, Thomas Bataillon, Xavier Nesme, L. Duret, Vincent Daubin

PLoS Genetics . 11 ( 2 ) : 1-20

DOI: 10.1371/journal.pgen.1004941

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Karyotype and Gene Order Evolution from ReconstructedExtinct Ancestors Highlight Contrasts in Genome Plasticity ofModern Rosid Crops

Florent Murat, Rongzhi R. Zhang, Sébastien Guizard, Haris Gavranovic, Raphael Flores, Delphine Steinbach...

Genome Biology and Evolution . 7 ( 3 ) : 735-749

DOI: 10.1093/gbe/evv014

Article dans une revue

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Foundations of Coding: Compression, Encryption, Error-Correction

Jean-Guillaume Dumas, Jean-Louis Roch, Eric Tannier, Sébastien Varrette

978-1-118-88144-6 : 376

Ouvrage

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Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses

Md Shamsuzzoha Bayzid, Siavash Mirarab, Bastien Boussau, Tandy Warnow

PLoS ONE . 10 ( 6 ) : e0129183

DOI: 10.1371/journal.pone.0129183

Article dans une revue

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Assessing Approaches for Inferring Species Trees from Multi-Copy Genes

Ruchi Chaudhary, Bastien Boussau, J. Gordon Burleigh, David Fernández-Baca

Systematic Biology . 64 ( 2 ) : 325-339

DOI: 10.1093/sysbio/syu128

Article dans une revue

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Ancestral gene synteny reconstruction improves extant species scaffolding

Yoann Anselmetti, Vincent Berry, Cedric Chauve, Annie Chateau, Eric Tannier, Sèverine Bérard

BMC Genomics . 16 ( Suppl 10 ) : S11

DOI: 10.1186/1471-2164-16-S10-S11

Article dans une revue

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Probabilistic modeling of the evolution of gene synteny within reconciled phylogenies

Magali Semeria, Eric Tannier, Laurent Guéguen

BMC Bioinformatics . 16 ( Suppl 14 ) : S5

DOI: 10.1186/1471-2105-16-S14-S5

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Genome-scale phylogenetic analysis finds extensive gene transfer among fungi

G.J. Szollosi, Adrián Arellano Davin, Eric Tannier, Vincent Daubin, Bastien Boussau

Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences (1934–1990) . 370 : 20140335 (11 pages)

DOI: 10.1098/rstb.2014.0335

Article dans une revue

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Probabilistic Graphical Model Representation in Phylogenetics

S. Höhna, Ta. Heath, Bastien Boussau

Systematic Biology . 63 ( 5 ) : 753-771

DOI: 10.1093/sysbio/syu039

Article dans une revue

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Phylogeny of the class Actinobacteria revisited in the light of complete genomes. The orders 'Frankiales' and Micrococcales should be split into coherent entities: proposal of Frankiales ord. nov., Geodermatophilales ord. nov., Acidothermales ord. nov. an

A. Sen, Vincent Daubin, D. Abrouk, I. Gifford, A. M. Berry, P. Normand

International Journal of Systematic and Evolutionary Microbiology . 64 ( Pt 11 ) : 3821-32

DOI: 10.1099/ijs.0.063966-0

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Counting and sampling SCJ small parsimony solutions

István Miklós, Sándor Z. Kiss, Eric Tannier

Theoretical Computer Science . 552 : 83-98

DOI: 10.1016/j.tcs.2014.07.027

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Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes

Pierre P. Gladieux, Jeanne Ropars, Helene Badouin, Antoine Branca, Gabriela G. Aguileta, Damien M. de Vienne...

Molecular Ecology . 23 ( 4 ) : 753-773

DOI: 10.1111/mec.12631

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Whole-genome analyses resolve early branches in the tree of life of modern birds.

Erich Jarvis, Siavash Mirarab, Andre Aberer, Bo Li, Peter Houde, Cai Li...

Science . 346 ( 6215 ) : 1320-31

DOI: 10.1126/science.1253451

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Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition

Claudia C. Weber, Bastien Boussau, Jonathan Romiguier, Erich D. Jarvis, H. Ellegren

Genome Biology . 15 : 549

DOI: 10.1186/s13059-014-0549-1

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Statistical binning enables an accurate coalescent-based estimation of the avian tree

S. Mirarab, M. S. Bayzid, Bastien Boussau, T. Warnow

Science . 346 : 1250463

Article dans une revue

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Strepsiptera, Phylogenomics and the Long Branch Attraction Problem

Bastien Boussau, Z. Walton, Ja. Delgado, F. Collantes, L. Beani, Ij. Stewart...

PLoS ONE . 9 : e107709

DOI: 10.6084/m9.figshare.1040412

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Massive gene swamping among cheese-making Penicillium fungi

Jeanne Ropars, Gabriela Aguileta, Damien M. de Vienne, Tatiana Giraud

Microbial Cell .

DOI: 10.15698/mic2014.01.135

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High Variability of Mitochondrial Gene Order among Fungi

Gabriela Aguileta, Damien M. de Vienne, Oliver N. Ross, Michael E Hood, Tatiana Giraud, Elsa Petit...

Genome Biology and Evolution . 6 ( 2 ) : 451-465

DOI: 10.1093/gbe/evu028

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Reductive genome evolution at both ends of bacterial population size spectrum

Bérénice Batut, Carole Knibbe, Gabriel Marais, Vincent Daubin

Nature Reviews Microbiology . 12 ( 12 ) : 841-850

DOI: 10.1038/nrmicro3331

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Ribosomal proteins: Toward a next generation standard for prokaryotic systematics?

Hemalatha Golaconda Ramulu, Mathieu Groussin, Emmanuel Talla, Rémi Planel, Vincent Daubin, Céline Brochier-Armanet

Molecular Phylogenetics and Evolution . 75 : 103 - 117

DOI: 10.1016/j.ympev.2014.02.013

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Single acquisition of protelomerase gave rise to speciation of a large and diverse clade within the Agrobacterium/Rhizobium supercluster characterized by the presence of a linear chromid

Martha H. Ramírez-Bahena, Ludovic Vial, Florent Lassalle, Benjamin Diel, David Chapulliot, Vincent Daubin...

Molecular Phylogenetics and Evolution . 73 : 202-207

DOI: 10.1016/j.ympev.2014.01.005

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