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 271 to 300 publications on 309 in total

MareyMap: an R-based tool with graphical interface for estimating recombination rates

C. Rezvoy, D. Charif, Laurent Guéguen, Gabriel Marais

Bioinformatics . 23 : 2188-2189

Journal article

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When can host shifts produce congruent host and parasite phylogenies? A simulation approach

Damien M de Vienne, Tatiana Giraud, J A Shykoff

Journal of Evolutionary Biology . 20 ( 4 ) : 1428--1438

Journal article

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Comparative genomics and the evolution of prokaryotes

Sophie S. Abby, Vincent Daubin

Trends in Microbiology . 15 : 135-141

Journal article

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Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography

Philippe Normand, Pascal Lapierre, Louis S. Tisa, Johann Peter Gogarten, Nicole Alloisio, Emilie Bagnarol...

Genome Research . 17 : 7-15

DOI: 10.1101/gr.5798407

Journal article

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Grinding up wheat: a massive loss of nucleotide diversity since domestication

A. Haudry, A. Cenci, C. Ravel, T. Bataillon, D. Brunel, C. Poncet...

Molecular Biology and Evolution . 24 : 1506-1517

Journal article

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Effective Stochastic Local Search Algorithms for the Genomic Median Problem

Renaud Lenne, Christine Solnon, Thomas Stützle, Eric Tannier, Mauro Birattari

Doctoral Symposium on Engineering Stochastic Local Search Algorithms (SLS-DS) . : 1-5

Conference paper

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Impacts d’événements démographiques et sélectifs sur la diversité des plantes cultivées: apports de l’analyse du polymorphisme alliée à la théorie de la coalescence

Thomas Bataillon, Nathalie N. Chantret, Alberto Cenci, Marie-Françoise Gautier, Philippe Joudrier, Annabelle Haudry...

Actes du BRG . 6 : 243-257

Journal article

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A Markovian Approach for the Analysis of the Gene Structure

C. Melodelima, Laurent Guéguen, Christian Gautier, D. Piau

Prague stringology conference . 19 ( 1 ) : 19-35

Conference paper

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A computational prediction of isochores based on hidden Markov models

C. Melodelima, Laurent Guéguen, D. Piau, Christian Gautier

Gene . 385 : 41-49

Journal article

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Global trends of whole genome duplications revealed by the genome sequence of the ciliate Paramecium tetraurelia

Jean-Marc Aury, Olivier Jaillon, * Laurent Duret, Benjamin Noel, Claire Jubin, Betina M. Porcel...

Nature . 444 ( 7116 ) : 171-178

DOI: 10.1038/nature05230

Journal article

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UV-Targeted Dinucleotides Are Not Depleted in Light-Exposed Prokaryotic Genomes

L. Palmeira, Laurent Guéguen, J.R. Lobry

Molecular Biology and Evolution . 23 : 2214-2219

Journal article

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Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia.

Jean-Marc Aury, Olivier Jaillon, L. Duret, Benjamin Noel, Claire Jubin, Betina M Porcel...

Nature . 444 ( 7116 ) : 171-8

DOI: 10.1038/nature05230

Journal article

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Sarment: Python modules for HMM analysis and partitioning of sequences

Laurent Guéguen

Bioinformatics . 21 : 3427-3428

Journal article

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Evolutionary origins of genomic repertoires in bacteria

E. Lerat, Vincent Daubin, H. Ochman, N.A. Moran

PLoS Biology . 3 : 0807-0814

Journal article

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Perfect Sorting by Reversals

Marie-France Sagot, Eric Tannier

: 13

Report

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A bunch of fun-guys: the whole-genome view of yeast evolution

H. Ochman, Vincent Daubin, E. Lerat

Trends in Genetics . 21 : 1-3

Journal article

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Examining bacterial species under the specter of gene transfer and exchange

H. Ochman, E. Lerat, Vincent Daubin

Proceedings of the National Academy of Sciences of the United States of America . 102 : 6595-6599

Journal article

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Perfect sorting by reversals

M.-F. Sagot, Eric Tannier

International Computing and Combinatorics Conference . 3595 : 42-51

DOI: 10.1007/11533719_7

Conference paper

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Phylogenetic dating and characterization of gene duplications in vertebrates: the cartilaginous fish reference

M. Robinson-Rechavi, Bastien Boussau, V. Laudet

Molecular Biology and Evolution . 21 : 580-586

Journal article

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Phylogenetic dating and characterization of gene duplications in vertebrates: the cartilaginous fish reference

M. Robinson-Rechavi, B. Boussau, V. Laudet

Molecular Biology and Evolution . 21 ( 3 ) : 580-586

Journal article

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Comment on "The origins of genome complexity

Vincent Daubin, N.A. Moran

Science . 306 : 978a-978a

Journal article

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Detecting phylogenetic incongruence using BIONJ: an improvement of the ILD test

M. Zelwer, Vincent Daubin

Molecular Phylogenetics and Evolution . 33 : 687-693

Journal article

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On Metric Generators of Graphs

András Sebő, Eric Tannier

Mathematics of Operations Research . 29 : 383-393

Journal article

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Computational inference of scenarios for alpha-proteobacterial genome evolution

Bastien Boussau, E.O. Karlberg, A.C. Frank, B.A. Legault, S.G. Andersson

Proceedings of the National Academy of Sciences of the United States of America . 101 : 9722-9727

Journal article

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Bacterial genomes as new gene homes: the genealogy of ORFans in E. coli

Vincent Daubin, H. Ochman

Genome Research . 14 : 1036-1042

Journal article

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Start-up entities in the origin of new genes

Vincent Daubin, H. Ochman

Current Opinion in Genetics and Development . 14 : 616-619

Journal article

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Quartet mapping and the extent of lateral transfer in bacterial genomes

Vincent Daubin, H. Ochman

Molecular Biology and Evolution . 21 : 86-89

Journal article

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Sorting by reversals in subquadratic time

Eric Tannier, Marie-France Sagot

Report

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