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 241 à 270 sur 309 au total

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

Article dans une revue

voir la publication

Precise detection of rearrangement breakpoints in mammalian chromosomes

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

: 26

Rapport

voir la publication

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

Acte de congrès

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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

Acte de congrès

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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

Acte de congrès

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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

Acte de congrès

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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

Article dans une revue

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

Eric Tannier

incollection . -- : 860-863

Article dans une revue

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The heterochromatic copies of the LTR retrotransposons as a record of the genomic events that have shaped the Drosophila melanogaster genome

N. Mugnier, Laurent Guéguen, Cristina Vieira, C. Biémont

Gene . 411 : 87-93

Article dans une revue

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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

Article dans une revue

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Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota.

Céline Brochier-Armanet, Bastien Boussau, Simonetta Gribaldo, Patrick Forterre

Nature Reviews Microbiology . 6 ( 3 ) : 245-252

DOI: 10.1038/nrmicro1852

Article dans une revue

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Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria

Bastien Boussau, Laurent Guéguen, Manolo Gouy

BMC Evolutionary Biology . 8 : 272-272

DOI: 10.1186/1471-2148-8-272

Article dans une revue

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Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs

J. Dutheil, Bastien Boussau

BMC Evolutionary Biology . 8:255 : 31-42

Article dans une revue

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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

Article dans une revue

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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

Acte de congrès

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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

Article dans une revue

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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

Article dans une revue

voir la publication

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

Acte de congrès

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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

Rapport

voir la publication

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

Article dans une revue

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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

Article dans une revue

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Parallel Adaptations to High Temperatures in the Archean Eon

Bastien Boussau, Samuel Blanquart, Anamaria Necsulea, Nicolas Lartillot, Manolo Gouy

Nature . 456 ( 7224 ) : 942-945

DOI: 10.1038/nature07393

Article dans une revue

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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

Acte de congrès

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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

Article dans une revue

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Advances on sorting by reversals

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

Discrete Applied Mathematics . 155 : 881-888

Article dans une revue

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Théorie des Codes : compression, cryptage, correction

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

9782100506927 : 352

Ouvrage

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

Annabelle Haudry, Alberto Cenci, C. Ravel, Thomas Bataillon, Dominique Brunel, C. Poncet...

Molecular Biology and Evolution . 24 ( 7 ) : 1506-1517

DOI: 10.1093/molbev/msm077

Article dans une revue

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Horizontal Gene Transfer Regulation in Bacteria as a ‘‘Spandrel'' of DNA Repair Mechanisms

Saliou Fall, Anne Mercier, Franck Bertolla, Alexandra Calteau, Laurent Gueguen, Guy Perrière...

PLoS ONE . 2 ( 10 ) : e1055-e1066

DOI: 10.1371/journal.pone.0001055

Article dans une revue

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A congruence index for testing topological similarity between trees

Damien M de Vienne, Tatiana Giraud, Olivier C Martin

Bioinformatics . 23 ( 23 ) : 3119--3124

DOI: 10.1093/bioinformatics/btm500

Article dans une revue

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