COEVOL Multi-Scale Coevolution

The Cocoon Group

Gueguen Laurent

Maître de conférences

UCBL

Address: 43 bd du 11 novembre 1918
69622 VILLEURBANNE cedex

Tel: 0472431344

Email

Publications

Display of 1 to 30 publications on 33 in total

A Codon Model for Associating Phenotypic Traits with Altered Selective Patterns of Sequence Evolution

Keren Halabi, Eli Levy Karin, Laurent Guéguen, Itay Mayrose

Systematic Biology . 70 ( 3 ) : 608-622

DOI: 10.1093/sysbio/syaa087

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

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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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DGINN, an automated and highly-flexible pipeline for the detection of genetic innovations on protein-coding genes

Lea Picard, Quentin Ganivet, Omran Allatif, Andrea Cimarelli, Laurent Guéguen, Lucie Etienne

Nucleic Acids Research . 48 ( 18 ) : e103-e103

DOI: 10.1093/nar/gkaa680

Journal article

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GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes

Paulina Bolívar, Laurent Guéguen, Laurent Duret, Hans Ellegren, Carina Mugal

Genome Biology . 20 ( 1 )

DOI: 10.1186/s13059-018-1613-z

Journal article

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Detecting adaptive convergent amino acid evolution

Carine Rey, Vincent Lanore, Philippe Veber, Laurent Guéguen, Nicolas Lartillot, Marie Sémon...

Philosophical Transactions of the Royal Society B: Biological Sciences . 374 ( 1777 ) : 1-11

DOI: 10.1098/rstb.2018.0234

Journal article

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Unbiased Estimate of Synonymous and Nonsynonymous Substitution Rates with Nonstationary Base Composition

Laurent Guéguen, Laurent Duret

Molecular Biology and Evolution . 35 ( 3 ) : 734-742

DOI: 10.1093/molbev/msx308

Journal article

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Life History Traits Impact the Nuclear Rate of Substitution but Not the Mitochondrial Rate in Isopods

Nathanaëlle Saclier, Clémentine François, Lara Konecny-Dupré, Nicolas Lartillot, Laurent Guéguen, L. Duret...

Molecular Biology and Evolution . 35 ( 12 ) : 2900-2912

DOI: 10.1093/molbev/msy184

Journal article

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Transcriptomic signatures shaped by cell proportions shed light on comparative developmental biology

S. Pantalacci, Laurent Guéguen, C. Petit, A. Lambert, R. Peterkova, M. Sémon

Genome Biology . 18 : 29

DOI: 10.1186/s13059-017-1157-7

Journal article

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Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium

Florent Lassalle, Rémi Planel, Simon Penel, David Chapulliot, Valérie Barbe, Audrey Dubost...

Genome Biology and Evolution . 9 ( 12 ) : 3413 - 3431

DOI: 10.1093/gbe/evx255

Journal article

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Less effective selection leads to larger genomes

Tristan Lefébure, Claire Morvan, Florian Malard, Clémentine François, Lara Konecny-Dupré, Laurent Guéguen...

Genome Research . 27 : 1016-1028

DOI: 10.1101/gr.212589.116

Journal article

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SENCA: A Multilayered Codon Model to Study the Origins and Dynamics of Codon Usage

F. Pouyet, M. Bailly-Bechet, Dominique Mouchiroud, Laurent Guéguen

Genome Biology and Evolution . 8 : 2427-41

DOI: 10.1093/gbe/evw165

Journal article

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Breaking Good: Accounting for Fragility of Genomic Regions in Rearrangement Distance Estimation

Priscila Biller, Laurent Guéguen, Carole Knibbe, Eric Tannier

Genome Biology and Evolution . 8 ( 5 ) : 1427-1439

DOI: 10.1093/gbe/evw083

Journal article

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Efficient gene tree correction guided by genome evolution

Emmanuel Noutahi, Magali Semeria, Manuel Lafond, Jonathan Seguin, Bastien Boussau, Laurent Guéguen...

PLoS ONE . 11 ( 8 ) : e0159559 (22 pages)

DOI: 10.1371/journal.pone.0159559

Journal article

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Probabilistic modeling of the evolution of gene synteny within reconciled phylogenies

Magali Semeria, Eric Tannier, Laurent Guéguen

BMC Bioinformatics . 16 ( Suppl 14 ) : S5

DOI: 10.1186/1471-2105-16-S14-S5

Journal article

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Duplication, Rearrangement and Reconciliation: A Follow-Up 13 Years Later

Cedric Chauve, Nadia El-Mabrouk, Laurent Gueguen, Magali Semeria, Eric Tannier

Models and Algorithms for Genome Evolution . 19 : 47-62

Book chapter

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Bio++ : Efficient Extensible Libraries and Tools for Computational Molecular Evolution

Laurent Gueguen, Sylvain Gaillard, Bastien Boussau, Manolo Gouy, Mathieu Groussin, Nicolas C. Rochette...

Molecular Biology and Evolution . 30 ( 8 ) : 1745 - 1750

DOI: 10.1093/molbev/mst097

Journal article

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Accurate Estimation of Substitution Rates with Neighbor-Dependent Models in a Phylogenetic Context

Jean Bérard, Laurent Guéguen

Systematic Biology . 61 ( 3 ) : 510-521

DOI: 10.1093/sysbio/sys024

Journal article

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La notion d'espèce en écologie microbienne

T. Campillo, Malek Shams, Sally Burr, Martha Helena Ramírez-Bahena, Florent Lassalle, Franck Bertolla...

1er Colloque National d'Ecologie Scientifique .

Conference paper

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Toward an ecological concept for bacterial species in Agrobacterium

Tony Campillo, Florent Lassalle, M. Shams, Martha Helena Ramírez-Bahena, Jessica Baude, Celine Lavire...

12th International Conference on Plant Pathogenic Bacteria .

Conference paper

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Identification de fonctions « spécifiques d'espèce » impliquées dans l'individualisation en écovar de l’espèce G8 du complexe Agrobacterium tumefaciens

Florent Lassalle, Daniel Muller, Denis Costechareyre, David Chapulliot, Celine Lavire, Laurent Guéguen...

Journées des Microbiologistes de l'INRA .

Conference paper

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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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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

Journal article

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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

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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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

Journal article

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MareyMap: an R-based tool with graphical interface for estimating recombination rates

C. Rezvoy, D. Charif, Laurent Guéguen, Gabriel Marais

Bioinformatics . 23 : 2188-2189

Journal article

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A Markovian Approach for the Analysis of the Gene Structure

C. Melodelima, Laurent Guéguen, Christian Gautier, D. Piau

Prague stringology conference . 19 ( 1 ) : 19-35

Conference paper

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