COEVOL Multi-Scale Coevolution

The Cocoon Group

Gueguen Laurent

Maître de conférences

UCBL

Address: 43 bd du 11 novembre 1918
69622 VILLEURBANNE cedex

Tel: 04 72 43 13 44

Email

Publications

Display of 1 to 30 publications on 38 in total

Distinct evolutionary trajectories of SARS-CoV-2-interacting proteins in bats and primates identify important host determinants of COVID-19

Marie Cariou, Léa Picard, Laurent Guéguen, Stéphanie Jacquet, Andrea Cimarelli, Oliver Fregoso...

Proceedings of the National Academy of Sciences of the United States of America . 119 ( 35 )

DOI: 10.1073/pnas.2206610119

Journal article

see the publication

Extreme mitochondrial DNA divergence underlies genetic conflict over sex determination

Patrice David, Cyril Degletagne, Nathanaelle Saclier, Aurel Jennan, Philippe Jarne, Sandrine Plénet...

Current Biology - CB . 32 ( 10 ) : 2325-2333.e6

DOI: 10.1016/j.cub.2022.04.014

Journal article

see the publication

Comparison of developmental genome expression in rodent molars reveals extensive developmental system drift

Marie Sémon, Laurent Guéguen, Coraline Petit, Carine Rey, Anne Lambert, Manon Peltier...

DOI: 10.1101/2020.04.22.043422

Preprint

see the publication

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

see the publication

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

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

see the publication

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

see the publication

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

see the publication

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

see the publication

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

see the publication

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

see the publication

MareyMap online: A user-friendly web application and database service for estimating recombination rates using physical and genetic maps

Aurélie Siberchicot, Adrien Bessy, Laurent Gueguen, Gabriel A. B. Marais

Genome Biology and Evolution . 9 ( 10 ) : 2506-2509

DOI: 10.1093/gbe/evx178

Journal article

see the publication

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

see the publication

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

see the publication

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

see the publication

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

see the publication

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

see the publication

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

see the publication

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

see the publication

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

see the publication

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

see the publication

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

see the publication

Genomic Species Are Ecological Species as Revealed by Comparative Genomics in Agrobacterium tumefaciens

Florent Lassalle, Tony Campillo, Ludovic Vial, Jessica Baude, Denis Costechareyre, David Chapulliot...

Genome Biology and Evolution . 3 ( 3 ) : 762-781

DOI: 10.1093/gbe/evr070

Journal article

see the publication

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

see the publication

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

see the publication

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

see the publication

Computing the likelihood of sequence segmentation under Markov modelling

Laurent Guéguen

Preprint

see the publication

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

see the publication

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

see the publication