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 211 to 240 publications on 309 in total

Yeast ancestral genome reconstructions: the possibilities of computational methods II.

Cedric Chauve, Haris Gavranovic, Aida Ouangraoua, Eric Tannier

Journal of Computational Biology . 17 ( 9 ) : 1097-112

DOI: 10.1089/cmb.2010.0092

Journal article

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Palaeogenomics of plants: synteny-based modelling of extinct ancestors.

Michael Abrouk, Florent Murat, Caroline Pont, Joachim Messing, Scott Jackson, Thomas Faraut...

Trends in Plant Science . 15 ( 9 ) : 479-87

DOI: 10.1016/j.tplants.2010.06.001

Journal article

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Comparative genomics : international workshop, RECOMB-CG 2010, Ottawa, Canada, October 9-11, 2010 : proceedings

Eric Tannier

International Workshop on Comparative Genomics . 978-3-642-16180-3

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Le génome aux ordres des mathématiciens

Eric Tannier

La Recherche . 439 : 54-56

Journal article

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AN INTEGRATIVE TEST OF THE DEAD-END HYPOTHESIS OF SELFING EVOLUTION IN TRITICEAE (POACEAE)

Juan Escobar, Alberto Cenci, Jeremy Bolognini, Annabelle A. Haudry, Stefan Laurent, Jacques David...

Evolution - International Journal of Organic Evolution . 64 ( 10 ) : no - no

DOI: 10.1111/j.1558-5646.2010.01045.x

Journal article

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The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse?

Simonetta Gribaldo, Anthony M. Poole, Vincent Daubin, Patrick Forterre, C. Brochier-Armanet

Nature Reviews Microbiology . 8 ( 10 ) : 743-753

DOI: 10.1038/nrmicro2426

Journal article

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Cassis: detection of genomic rearrangement breakpoints.

Christian Baudet, Claire Lemaitre, Zanoni Dias, Christian Gautier, Eric Tannier, Marie-France Sagot

Bioinformatics . 26 ( 15 ) : 1897-8

DOI: 10.1093/bioinformatics/btq301

Journal article

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RECOMB Satellite Workshop on Comparative Genomics

Eric Tannier

8. Annual RECOMB Satellite Workshop on Comparative Genomics . 978-3-642-16181-0 : 303

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Comparative Genomics

Eric Tannier

incollection . 6938 : 1-12

Journal article

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RECONSTRUCTING ORIGINS OF LOSS OF SELF-INCOMPATIBILITY AND SELFING IN NORTH AMERICAN ARABIDOPSIS LYRATA: A POPULATION GENETIC CONTEXT

John Paul Foxe, Marc Stift, Andrew Tedder, Annabelle A. Haudry, Stephen Wright, Barbara Mable

Evolution - International Journal of Organic Evolution . 64 ( 12 ) : 3495 - 3510

DOI: 10.1111/j.1558-5646.2010.01094.x

Journal article

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Reconstructing origins of loss of self-incompatibility and selfing in North American Arabidopsis lyrata: a population genetic context

John Paul Foxe, Marc Stift, Andrew Tedder, Annabelle A. Haudry, Stephen Wright, Barbara Mable

Evolution - International Journal of Organic Evolution . 64 : 3495-3510

DOI: 10.1111/j.1558-5646.2010.01094.x

Journal article

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Guided genome halving: provably optimal solutions provide good insights into the preduplication ancestral genome of Saccharomyces cerevisiae.

Haris Gavranović, Eric Tannier

Pacific Symposium on Biocomputing . 15 : 21-30

DOI: 10.1142/9789814295291_0004

Conference paper

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Theory and examples of reciprocal influence between hosts and pathogens, from short-term to long term interactions: coevolution, cospeciation and pathogen speciation following host shifts

Aurélien Tellier, Damien M. de Vienne, Tatiana Giraud, Michael Hood, Guislaine Refrégier

Host-Pathogen Interactions: Genetics, Immunology, and Physiology . 978-1608762866

Book chapter

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Computing the likelihood of sequence segmentation under Markov modelling

Laurent Guéguen

Preprint

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A Mixture Model and a Hidden Markov Model to Simultaneously Detect Recombination Breakpoints and Reconstruct Phylogenies

Bastien Boussau, Laurent Guéguen, Manolo Gouy

Evolutionary Bioinformatics . 5 : 67-79

DOI: 10.4137/EBO.S2242

Journal article

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Genomes as documents of evolutionary history

Bastien Boussau, Vincent Daubin

Trends in Ecology & Evolution . 1192 : 1-9

Journal article

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Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations

Ravi D. Barabote, Gary Xie, David H. Leu, Philippe Normand, Anamaria Necsulea, Vincent Daubin...

Genome Research . ( 19 ) : 1033-1043

DOI: 10.1101/gr.084848.108

Journal article

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Footprints of Inversions at Present and Past Pseudoautosomal Boundaries in Human Sex Chromosomes

Claire Lemaitre, Marília D.V. Braga, Christian Gautier, M.-F. Sagot, Eric Tannier, Gabriel Marais

Genome Biology and Evolution . 1(1) : 56-66

Journal article

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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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The fate of the duplicated androgen receptor in fishes: a late neofunctionalization event ?

Véronique Douard, Frédéric Brunet, Bastien Boussau, Isabelle Ahrens-Fath, Virginie Vlaeminck-Guillem, Bernard Haendler...

BMC Evolutionary Biology . 8:336 : 1-19

DOI: 10.1186/1471-2148-8-336

Journal article

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