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 181 to 210 publications on 243 in total

Analysis of fine-scale mammalian evolutionary breakpoints provides new insight into their relation to genome organisation

Claire Lemaitre, Lamia Zaghloul, Marie-France Sagot, Christian Gautier, Alain Arneodo, Eric Tannier...

BMC Genomics . 10 ( 1 ) : 335

DOI: 10.1186/1471-2164-10-335

Journal article

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Yeast Ancestral Genome Reconstructions: The Possibilities of Computational Methods

Eric Tannier

RECOMB International Workshop on Comparative Genomics . 5817 : 1-12

DOI: 10.1007/978-3-642-04744-2_1

Conference paper

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Computation of Perfect DCJ Rearrangement Scenarios with Linear and Circular Chromosomes

Sèverine Bérard, Annie Chateau, Cedric Chauve, Christophe Paul, Eric Tannier

Journal of Computational Biology . 16 ( 10 ) : 1287-1309

DOI: 10.1089/cmb.2009.0088

Journal article

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Combinatorics of Genome Rearrangements

Guillaume Fertin, Anthony Labarre, Irena Rusu, Eric Tannier, Stéphane Vialette

978-0-262-06282-4 : 312

Book

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Hybrid sterility and inviability in the parasitic fungal species complex Microbotryum

Damien de Vienne, G Refrégier, Me Hood, A Guigue, B Devier, E Vercken...

Journal of Evolutionary Biology . 22 ( 4 ) : 683--698

Journal article

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Phylogenetic determinants of potential host shifts in fungal pathogens

Damien de Vienne, Me Hood, T Giraud

Journal of Evolutionary Biology . 22 ( 12 ) : 2532--2541

Journal article

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Prediction of Contiguous Regions in the Amniote Ancestral Genome

Aïda Ouangraoua, Frédéric Boyer, Andrew Mcpherson, Eric Tannier, Cedric Chauve

ISBRA 2009, 5th International Symposium on Bioinformatics Research and Applications, . 5542

DOI: 10.1007/978-3-642-01551-9_18

Conference paper

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Multichromosomal median and halving problems under different genomic distances

Eric Tannier, Chunfang Zheng, David Sankoff

BMC Bioinformatics . 10 ( 1 ) : 120

DOI: 10.1186/1471-2105-10-120

Journal article

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High-throughput single nucleotide polymorphism genotyping in wheat (Triticum spp.)

Aurélie A. Berard, Marie-Christine Le Paslier, Mireille M. Dardevet, Florence F. Exbrayat-Vinson, Isabelle I. Bonnin, Alberto A. Cenci...

Plant Biotechnology Journal . 7 ( 4 ) : 364-374

DOI: 10.1111/j.1467-7652.2009.00404.x

Journal article

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Databases of Homologous Gene Families for Comparative Genomics

Simon Penel, Anne-Muriel Arigon Chifolleau, Jean-François Dufayard, Anne-Sophie Sertier, Vincent Daubin, L. Duret...

BMC Bioinformatics . 10 (Suppl.6) :S3 : 13

DOI: 10.1186/1471-2105-10-S6-S3

Journal article

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Exploring the Solution Space of Sorting by Reversals, with Experiments and an Application to Evolution

Marília D.V. Braga, Marie-France Sagot, Celine Scornavacca, Eric Tannier

IEEE/ACM Transactions on Computational Biology and Bioinformatics . 5 ( 3 ) : 348-356

DOI: 10.1109/TCBB.2008.16

Journal article

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Precise detection of rearrangement breakpoints in mammalian chromosomes

Claire Lemaitre, Eric Tannier, Christian Gautier, Marie-France Sagot

: 26

Report

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Prédiction de synténies dans le génome ancestral des amniotes

F. Boyer, C. Chauve, Eric Tannier

Journées Ouvertes de Biologie, Informatique et Mathématiques, JOBIM 2008 . : 141-148

Conference paper

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Perfect DCJ rearrangement

Annie Chateau, Cedric Chauve, Sèverine Bérard, Eric Tannier, Christophe Paul

RECOMB-CG: Comparative Genomics . LNCS ( 5267 ) : 158-169

DOI: 10.1007/978-3-540-87989-3_12

Conference paper

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Advances on Stochastic Local Search Algorithms for the Genomic Median Problem

Renaud Lenne, Christine Solnon, Thomas Stützle, Eric Tannier

International Conference on Metaheuristics and Nature Inspired Computing (META) . 4872 : 266-276

Conference paper

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Multichromosomal Genome Median and Halving Problems

Eric Tannier, C. Zheng, D. Sankoff

International Workshop on Algorithms in Bioinformatics (WABI) . 5251 : 1-13

DOI: 10.1007/978-3-540-87361-7_1

Conference paper

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A Methodological Framework for the Reconstruction of Contiguous Regions of Ancestral Genomes and Its Application to Mammalian Genomes

C. Chauve, Eric Tannier

PLoS Computational Biology . 4 : 391-410

Journal article

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Sorting Signed Permutations by Reversal (Reversal Sequence) 2004; Tannier Sagot

Eric Tannier

incollection . -- : 860-863

Journal article

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In response to comment on ‘A congruence index for testing topological similarity between trees’

Damien de Vienne, Tatiana Giraud, Olivier C Martin

Bioinformatics . 25 ( 1 ) : 150--151

DOI: 10.1093/bioinformatics/btn535

Journal article

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Speciation in fungi

Tatiana Giraud, Guislaine Refrégier, Mickaël Le Gac, Damien M. de Vienne, Michael E Hood

Fungal Genetics and Biology . 45 ( 6 ) : 791--802

DOI: 10.1016/j.fgb.2008.02.001

Journal article

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Démasquage des gènes spécifiques d'une espèce génomique du complexeAgrobacterium tumefaciens par AFLP et multicapteur à ADN

Perrine Portier, Denis Costechareyre, Daniel Muller, David Chapulliot, Christine Oger, Guy Perrière...

7. Colloque national du Bureau des Ressources Génétiques . 7

Conference paper

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Dealing with incongruence in phylogenomic analyses

N. Galtier, Vincent Daubin

Philosophical Transactions of the Royal Society B: Biological Sciences . -- : 1233-1241

Journal article

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Precise detection of rearrangement breakpoints in mammalian chromosomes

Claire Lemaitre, Eric Tannier, Christian Gautier, Marie-France Sagot

BMC Bioinformatics . 9 ( 1 ) : 286

DOI: 10.1186/1471-2105-9-286

Journal article

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Reactive Stochastic Local Search Algorithms for the Genomic Median Problem

R. Lenne, Christine Solnon, T. Stützle, Eric Tannier, M. Birattari

European Conference on Evolutionary Computation in Combinatorial Optimization (EvoCOP) . 4972 : 266-276

DOI: 10.1007/978-3-540-78604-7_23

Conference paper

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A Methodological Framework for the Reconstruction of Contiguous Regions of Ancestral Genomes and its Application to Mammalian Genomes

Eric Tannier, Cedric Chauve

: 26

Report

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Mating system and recombination affect molecular evolution in four Triticeae species

A. Haudry, A. Cenci, C. Guilhaumon, E. Paux, S. Poirier, S. Santoni...

Genetics Research . 90 : 97-109

Journal article

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Mating system and recombination affect molecular evolution in four Triticeae species

A. A. Haudry, A. A. Cenci, C C Guilhaumon, Etienne Paux, S. S. Poirier, S. S. Santoni...

Genetics Research . 90 ( 1 ) : 97-109

DOI: 10.1017/S0016672307009032

Journal article

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The solution space of sorting by reversals

Marília D.V. Braga, Marie-France Sagot, Celine Scornavacca, Eric Tannier

3rd International Symposium on Bioinformatics Research and Applications (ISBRA 2007) . 4463 : 293-304

DOI: 10.1007/978-3-540-72031-7_27

Conference paper

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Evolution under Reversals: Parsimony and Conservation of Common Intervals

Y. Diekmann, M.-F. Sagot, Eric Tannier

IEEE/ACM Transactions on Computational Biology and Bioinformatics . 4 : 301-309

Journal article

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Advances on sorting by reversals

Eric Tannier, A. Bergeron, M.-F. Sagot

Discrete Applied Mathematics . 155 : 881-888

Journal article

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