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 181 à 210 sur 220 au total

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

Eric Tannier

incollection . -- : 860-863

Article dans une revue

voir la publication

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

voir la publication

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

voir la publication

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

voir la publication

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

voir la publication

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

voir la publication

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

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

voir la publication

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

voir la publication

Advances on sorting by reversals

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

Discrete Applied Mathematics . 155 : 881-888

Article dans une revue

voir la publication

Théorie des Codes : compression, cryptage, correction

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

9782100506927 : 352

Ouvrage

voir la publication

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

voir la publication

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

Article dans une revue

voir la publication

Comparative genomics and the evolution of prokaryotes

Sophie S. Abby, Vincent Daubin

Trends in Microbiology . 15 : 135-141

Article dans une revue

voir la publication

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

Article dans une revue

voir la publication

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

Acte de congrès

voir la publication

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

Article dans une revue

voir la publication

Evolutionary origins of genomic repertoires in bacteria

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

PLoS Biology . 3 : 0807-0814

Article dans une revue

voir la publication

Perfect Sorting by Reversals

Marie-France Sagot, Eric Tannier

: 13

Rapport

voir la publication

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

H. Ochman, Vincent Daubin, E. Lerat

Trends in Genetics . 21 : 1-3

Article dans une revue

voir la publication

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

Article dans une revue

voir la publication

Perfect sorting by reversals

M.-F. Sagot, Eric Tannier

International Computing and Combinatorics Conference . 3595 : 42-51

DOI: 10.1007/11533719_7

Acte de congrès

voir la publication

Comment on "The origins of genome complexity

Vincent Daubin, N.A. Moran

Science . 306 : 978a-978a

Article dans une revue

voir la publication

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

M. Zelwer, Vincent Daubin

Molecular Phylogenetics and Evolution . 33 : 687-693

Article dans une revue

voir la publication

On Metric Generators of Graphs

András Sebő, Eric Tannier

Mathematics of Operations Research . 29 : 383-393

Article dans une revue

voir la publication

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

Vincent Daubin, H. Ochman

Genome Research . 14 : 1036-1042

Article dans une revue

voir la publication

Start-up entities in the origin of new genes

Vincent Daubin, H. Ochman

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

Article dans une revue

voir la publication

Quartet mapping and the extent of lateral transfer in bacterial genomes

Vincent Daubin, H. Ochman

Molecular Biology and Evolution . 21 : 86-89

Article dans une revue

voir la publication