COEVOL Multi-Scale Coevolution

The Cocoon Group

Tannier Eric

Directeur de recherche

INRIA

Address: 43 bd du 11 novembre 1918
69622 VILLEURBANNE cedex

Tel: 33 04 26 23 44 74

Email

Chercheur en biologie computationnelle, évolution, liens sciences-sociétés, permaculture

 

Recherches :

- Thèses de Alexandre Laverré (avec Anouk Necsulea), Théo Tricou (avec Damien de Vienne), Hugo Menet (avec Vincent Daubin)

- Action exploratoire "Community Garden Book" (équipe projet Inria Beagle)

- Fabrique des Questions Simples, laboratoire incubateur de recherches dans l'anthropocène

 

Enseignements :

- Cours M1 bioinformatique MADG

- Cours Ethique en video (Master et Doctorat), Video 1 et Video 2, Intégrité Scientifique Partie 1, Partie 2, Partie 3

- Cours Ethique en diapos

- Atelier Sciences Environnements Sociétés

 

Responsabilités - Animations :

- Membre du comité scientifique de la Plateforme Resetis

- Membre du comité scientifique de la boutique des sciences

- Co-fondateur et éditeur de Peer Community in Mathematical and Computational Biology

Publications

Display of 1 to 30 publications on 119 in total

Back to the trees: Identifying plants with Human Intelligence

Simon Castellan, Jos Käfer, Eric Tannier

LIMITS 2023 - Ninth Workshop on Computing within Limits . : 1-11

DOI: 10.21428/bf6fb269.265c52ce

Conference paper

see the publication

Se réapproprier la production de connaissance

Alexandre Monnin, Eric Tannier, Maël Thomas

AOC [Analyse Opinion Critique] . : https://aoc.media/opinion/2023/05/17/se-reapproprier-la-production-de-connaissance/

Journal article

see the publication

PhylteR: efficient identification of outlier sequences in phylogenomic datasets

Aurore Comte, Théo Tricou, Eric Tannier, Julien Joseph, Aurélie Siberchicot, Simon Penel...

DOI: 10.1101/2023.02.02.526888

Preprint

see the publication

Host-symbiont-gene phylogenetic reconciliation

Hugo Menet, Alexia Nguyen Trung, Vincent Daubin, Eric Tannier

Peer Community Journal . : 1-22

DOI: 10.24072/pcjournal.273

Journal article

see the publication

The crisis of the scientific mind : an investigation, a tragedy and a collective redistribution of roles

Eric Tannier, Vincent Daubin, Sophie Quinton

Les Cahiers de Framespa : e-Storia . ( 40 )

DOI: 10.4000/framespa.13150

Journal article

see the publication

GOntact: using chromatin contacts to infer Gene Ontology enrichments for cis -regulatory elements

Alexandre Laverré, Eric Tannier, Philippe Veber, Anamaria Necsulea

DOI: 10.1101/2022.06.13.495495

Preprint

see the publication

Thirdkind: displaying phylogenetic encounters beyond 2-level reconciliation

Simon Penel, Hugo Menet, Théo Tricou, Vincent Daubin, Eric Tannier

Bioinformatics . 38 ( 8 ) : 2350–2352

DOI: 10.1093/bioinformatics/btac062

Journal article

see the publication

Long-range promoter–enhancer contacts are conserved during evolution and contribute to gene expression robustness

Alexandre Laverré, Eric Tannier, Anamaria Necsulea

Genome Research . 32 ( 2 ) : 280-296

DOI: 10.1101/gr.275901.121

Journal article

see the publication

Ghost lineages highly influence the interpretation of introgression tests

Théo Tricou, Eric Tannier, Damien M. de Vienne

Systematic Biology . 71 ( 5 ) : 1147–1158

DOI: 10.1093/sysbio/syac011

Journal article

see the publication

Seaview Version 5: A Multiplatform Software for Multiple Sequence Alignment, Molecular Phylogenetic Analyses, and Tree Reconciliation

Manolo Gouy, Eric Tannier, Nicolas Comte, David Parsons

Multiple Sequence Alignment . 2231 : 241-260

DOI: 10.1007/978-1-0716-1036-7_15

Book chapter

see the publication

Treerecs: an integrated phylogenetic tool, from sequences to reconciliations.

Nicolas Comte, Benoît Morel, Damir Hasic, Laurent Guéguen, Bastien Boussau, Vincent Daubin...

Bioinformatics . 36 ( 18 ) : 4822-4824

DOI: 10.1093/bioinformatics/btaa615

Journal article

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Ancestral Genome Organization as a Diagnosis Tool for Phylogenomics

Eric Tannier, Adelme Bazin, Adrián Davín, Laurent Guéguen, Sèverine Bérard, Cedric Chauve

Phylogenetics in the Genomic Era . : 2.5:1--2.5:19

Book chapter

see the publication

Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

Robert Waterhouse, Sergey Aganezov, Yoann Anselmetti, Jiyoung Lee, Livio Ruzzante, Maarten Reijnders...

BMC Biology . 18 ( 1 ) : 1-20

DOI: 10.1186/s12915-019-0728-3

Journal article

see the publication

L'informatique les pieds sur Terre

Eric Tannier

Interstices .

Journal article

see the publication

Sciences, Environnements et Sociétés

Françoise Berthoud, Pascal Guitton, Laurent Lefèvre, Sophie Quinton, Antoine Rousseau, Jacques Sainte-Marie...

Report

see the publication

Zombi: A phylogenetic simulator of trees, genomes and sequences that accounts for dead lineages

Adrian A Davin, Theo Tricou, Eric Tannier, Damien M. de Vienne, Gergely J Szöllosi

Bioinformatics .

DOI: 10.1093/bioinformatics/btz710

Journal article

see the publication

Gene tree reconciliation including transfers with replacement is NP-hard and FPT

Damir Hasic, Eric Tannier

Journal of Combinatorial Optimization . 38 ( 2 ) : 502–544

DOI: 10.1007/s10878-019-00396-z

Journal article

see the publication

Gene transfers can date the tree of life

Adrián Davín, Eric Tannier, Tom A Williams, Bastien Boussau, Vincent Daubin, Gergely Szöllősi

Nature Ecology & Evolution . 2 ( 5 ) : 904-909

DOI: 10.1038/s41559-018-0525-3

Journal article

see the publication

Théorie des codes - 3e édition

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

9782100781096 : 416

Book

see the publication

RecPhyloXML: a format for reconciled gene trees

Wandrille Duchemin, Guillaume Gence, Anne-Muriel Arigon Chifolleau, Lars Arvestad, Mukul Bansal, Vincent Berry...

Bioinformatics . 34 ( 21 ) : 3646-3652

DOI: 10.1093/bioinformatics/bty389

Journal article

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Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes

Yoann Anselmetti, Wandrille Duchemin, Eric Tannier, Cedric Chauve, Sèverine Bérard

BMC Genomics . 19 ( S2 ) : 1-15

DOI: 10.1186/s12864-018-4466-7

Journal article

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DeCoSTAR: Reconstructing the ancestral organization of genes or genomes using reconciled phylogenies

Wandrille Duchemin, Yoann Anselmetti, Murray Patterson, Yann Ponty, Sèverine Bérard, Cedric Chauve...

Genome Biology and Evolution . 9 ( 5 ) : 1312-1319

DOI: 10.1093/gbe/evx069

Journal article

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Algorithms for computing the double cut and join distance on both gene order and intergenic sizes

Guillaume Fertin, Géraldine Jean, Eric Tannier

Algorithms for Molecular Biology . 12 : 16 (11 pages)

DOI: 10.1186/s13015-017-0107-y

Journal article

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Resolution and reconciliation of non-binary gene trees with transfers, duplications and losses

Edwin Jacox, Mathias Weller, Eric Tannier, Celine Scornavacca

Bioinformatics . 33 ( 7 ) : 980-987

DOI: 10.1093/bioinformatics/btw778

Journal article

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