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 243 au total

Gene tree correction guided by orthology

Manuel Lafond, Magali Semeria, Krister M. Swenson, Eric Tannier, Nadia El-Mabrouk

BMC Bioinformatics . 14 ( Suppl 15 ) : S5

Article dans une revue

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Duplication, Rearrangement and Reconciliation: A Follow-Up 13 Years Later

Cedric Chauve, Nadia El-Mabrouk, Laurent Gueguen, Magali Semeria, Eric Tannier

Models and Algorithms for Genome Evolution . 19 : 47-62

Chapitre d'ouvrage

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Efficient Exploration of the Space of Reconciled Gene Trees.

Gergely J Szöllosi, Wojciech Rosikiewicz, Bastien Boussau, Eric Tannier, Vincent Daubin

Systematic Biology . 62 ( 6 ) : 901-912

DOI: 10.1093/sysbio/syt054

Article dans une revue

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Genome-scale coestimation of species and gene trees.

Bastien Boussau, Gergely J Szöllosi, L. Duret, Manolo Gouy, Eric Tannier, Vincent Daubin

Genome Research . 23 ( 2 ) : 323-330

DOI: 10.1101/gr.141978.112

Article dans une revue

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Models and Algorithms for Genome Evolution

Cedric Chauve, Nadia El-Mabrouk, Eric Tannier

978-1-4471-5297-2 : 318

Ouvrage

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Bio++ : Efficient Extensible Libraries and Tools for Computational Molecular Evolution

Laurent Gueguen, Sylvain Gaillard, Bastien Boussau, Manolo Gouy, Mathieu Groussin, Nicolas C. Rochette...

Molecular Biology and Evolution . 30 ( 8 ) : 1745 - 1750

DOI: 10.1093/molbev/mst097

Article dans une revue

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An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions

Annabelle A. Haudry, Adrian Platts, Emilio Vello, Douglas Hoen, Mickael Leclercq, Robert Williamson...

Nature Genetics . 45 ( 8 ) : 891 - 898

DOI: 10.1038/ng.2684

Article dans une revue

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TPMS: a set of utilities for querying collections of gene trees.

Thomas Bigot, Vincent Daubin, Florent Lassalle, Guy Perrière

BMC Bioinformatics . 14 : 109

DOI: 10.1186/1471-2105-14-109

Article dans une revue

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Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations.

Gergely J Szöllosi, Bastien Boussau, Sophie S Abby, Eric Tannier, Vincent Daubin

Proceedings of the National Academy of Sciences of the United States of America . 109 ( 43 ) : 17513-17518

DOI: 10.1073/pnas.1202997109

Article dans une revue

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Modeling Gene Family Evolution and Reconciling Phylogenetic Discord

G.J. Szollosi, Vincent Daubin

Methods in Molecular Biology . 856 : 29-51

Article dans une revue

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Preserving Inversion Phylogeny Reconstruction

Matthias Bernt, Kun-Mao Chao, Jyun-Wei Kao, Martin Middendorf, Eric Tannier

WABI 2012 - 12th International Workshop on Algorithms in Bioinformatics . : 1-13

DOI: 10.1007/978-3-642-33122-0_1

Acte de congrès

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Phylo-MCOA: a fast and efficient method to detect outlier genes and species in phylogenomics using multiple co-inertia analysis

Damien M. de Vienne, Sébastien Ollier, Gabriela Aguileta

Molecular Biology and Evolution . 29 ( 6 ) : 1587--1598

DOI: 10.1093/molbev/msr317

Article dans une revue

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Linkage to the mating-type locus across the genus microbotryum: insights into nonrecombining chromosomes

Elsa Petit, Tatiana Giraud, Damien M. de Vienne, Marco A Coelho, Gabriela Aguileta, Joelle J. Amselem...

Evolution - International Journal of Organic Evolution . 66 ( 11 ) : 3519-3533

DOI: 10.1111/j.1558-5646.2012.01703.x

Article dans une revue

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Evolution of Prokaryotic Pangenomes

Florent Lassalle, Vincent Daubin

Horizontal Gene Transfer in Microorganisms . 978-1-908230-10-2 : 23-32

Chapitre d'ouvrage

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Disentangling the effects of breakdown of self-incompatibility and transition to selfing in North-American Arabidopsis lyrata

A. Haudry, H.G. Zha, M. Stift, B.K. Mable

Molecular Ecology . 21 : 1130-1142

DOI: 10.1111/j.1365-294X.2011.05435.x

Article dans une revue

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Linearization of ancestral multichromosomal genomes

Ján Maňuch, Murray Patterson, Roland Wittler, Cedric Chauve, Eric Tannier

BMC Bioinformatics . 13 ( Suppl 19 ) : S11

DOI: 10.1186/1471-2105-13-S19-S11

Article dans une revue

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Evolution of gene neighborhoods within reconciled phylogenies

Sèverine Bérard, Coralie Gallien, Bastien Boussau, Gergely J Szöllosi, Vincent Daubin, Eric Tannier

Bioinformatics . 28 ( 18 ) : i382-i388

DOI: 10.1093/bioinformatics/bts374

Article dans une revue

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Lateral gene transfer as a support for the tree of life.

Sophie S Abby, Eric Tannier, Manolo Gouy, Vincent Daubin

Proceedings of the National Academy of Sciences of the United States of America . 109 ( 13 ) : 4962-4967

DOI: 10.1073/pnas.1116871109

Article dans une revue

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High-quality sequence clustering guided by network topology and multiple alignment likelihood.

Vincent Miele, Simon Penel, Vincent Daubin, Franck Picard, Daniel Kahn, L. Duret

Bioinformatics . 28 ( 8 ) : 1078-85

DOI: 10.1093/bioinformatics/bts098

Article dans une revue

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Genomic Species Are Ecological Species as Revealed by Comparative Genomics in Agrobacterium tumefaciens

Florent Lassalle, Tony Campillo, Ludovic Vial, Jessica Baude, Denis Costechareyre, David Chapulliot...

Genome Biology and Evolution . 3 ( 3 ) : 762-781

DOI: 10.1093/gbe/evr070

Article dans une revue

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Models, algorithms, and programs for phylogeny reconciliation

Jean-Philippe Doyon, Vincent Ranwez, Vincent Daubin, Vincent Berry

Briefings in Bioinformatics . 12 ( 5 ) : 392-400

DOI: 10.1093/bib/bbr045

Article dans une revue

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Multiple Nuclear Gene Phylogenetic Analysis of the Evolution of Dioecy and Sex Chromosomes in the Genus Silene

Gabriel Marais, A. Forrest, E. Kamau, Jos Käfer, Vincent Daubin, D. Charlesworth

PLoS ONE . 6 : e21915

DOI: 10.1371/journal.pone.0021915

Article dans une revue

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HDR - Evolution combinatoire Algorithmique des chromosomes

Eric Tannier

incollection . -- : 54-56

Article dans une revue

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Euclidean nature of phylogenetic distance matrices

Damien M. de Vienne, Gabriela Aguileta, Sébastien Ollier

Systematic Biology . 60 ( 6 ) : 826--832

DOI: 10.1093/sysbio/syr066

Article dans une revue

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