GECO Génomique Computationnelle et Evolutive

Protein conformational space at the edge of allostery: turning a nonallosteric malate dehydrogenase into an “allosterized” enzyme using evolution-guided punctual mutations

Antonio Iorio, Céline Brochier-Armanet, Caroline Mas, Fabio Sterpone, Dominique Madern

Molecular Biology and Evolution . 39 ( 9 ) : msac186

DOI: 10.1093/molbev/msac186

2022

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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

2022

Pré-publication

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An Improved Codon Modeling Approach for Accurate Estimation of the Mutation Bias

Thibault Latrille, Nicolas Lartillot

Molecular Biology and Evolution . 39

DOI: 10.1093/molbev/msac005

2022

Article dans une revue

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Compositionally constrained sites drive long branch attraction

Lenard L Szantho, Nicolas Lartillot, Gergely Szöllősi, Dominik Schrempf

DOI: 10.1101/2022.03.03.482715

2022

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Identifying the best approximating model in Bayesian phylogenetics: Bayes factors, cross-validation or wAIC?

Nicolas Lartillot

DOI: 10.1101/2022.04.22.489153

2022

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Phyloformer: towards fast and accurate phylogeny estimation with self-attention networks

Luca Nesterenko, Bastien Boussau, Laurent Jacob

DOI: 10.1101/2022.06.24.496975

2022

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Efficiently sparse listing of classes of optimal cophylogeny reconciliations

Yishu Wang, Arnaud Mary, Marie-France Sagot, Blerina Sinaimeri

Algorithms for Molecular Biology . 17 ( 1 ) : 1-16

DOI: 10.1186/s13015-022-00206-y

2022

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Totoro: Identifying Active Reactions During the Transient State for Metabolic Perturbations

Mariana Galvão Ferrarini, Irene Ziska, Ricardo Andrade, Alice Julien-Laferrière, Louis Duchemin, Roberto Marcondes César...

Frontiers in Genetics . 13 : 1-12

DOI: 10.3389/fgene.2022.815476

2022

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Labile sex expression in angiosperm species with sex chromosomes

Jos Käfer, Marcos Méndez, Sylvain Mousset

Philosophical Transactions of the Royal Society B: Biological Sciences . 377 ( 1850 )

DOI: 10.1098/rstb.2021.0216

2022

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Recent Bioinformatic Progress to Identify Epigenetic Changes Associated to Transposable Elements

Emmanuelle Lerat

Frontiers in Genetics . 13

DOI: 10.3389/fgene.2022.891194

2022

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How sex chromosomes get trapped into nonrecombination

Jos Käfer

Plos Biology . 20 ( 7 ) : e3001718

DOI: 10.1371/journal.pbio.3001718

2022

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CALDERA: Finding all significant de Bruijn subgraphs for bacterial GWAS

Hector Roux de Bézieux, Leandro Lima, Fanny Perraudeau, Arnaud Mary, Sandrine Dudoit, Laurent Jacob

Bioinformatics .

DOI: 10.1093/bioinformatics/btac238

2022

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A divide-and-conquer phylogenomic approach based on character supermatrices resolves early steps in the evolution of the Archaea

Monique Aouad, Jean-Pierre Flandrois, Frédéric Jauffrit, Manolo Gouy, Simonetta Gribaldo, Celine Brochier-Armanet

BMC Ecology and Evolution . 22 ( 1 ) : 1-12

DOI: 10.1186/s12862-021-01952-0

2022

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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

2022

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A derived ZW chromosome system in Amborella trichopoda, representing the sister lineage to all other extant flowering plants

Jos Käfer, Adam Bewick, Amélie Andres‐robin, Garance Lapetoule, Alex Harkess, José Caïus...

New Phytologist . 233 : 1636-1642

DOI: 10.1111/nph.17662

2022

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The human gut microbiome and health inequities

Katherine Amato, Marie-Claire Arrieta, Meghan Azad, Michael Bailey, Josiane Broussard, Carlijn Bruggeling...

Proceedings of the National Academy of Sciences of the United States of America . 118 ( 25 ) : e2017947118

DOI: 10.1073/pnas.2017947118

2021

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No evidence for female kin association, indications for extragroup paternity, and sex‐biased dispersal patterns in wild western gorillas

Shelly Masi, Frédéric Austerlitz, Chloé Chabaud, Sophie Lafosse, Nina Marchi, Myriam Georges...

Ecology and Evolution . 11 ( 12 ) : 7634-7646

DOI: 10.1002/ece3.7596

2021

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Elevated rates of horizontal gene transfer in the industrialized human microbiome

Mathieu Groussin, Mathilde Poyet, Ainara Sistiaga, Sean Kearney, Katya Moniz, Mary Noel...

Cell . 184 ( 8 ) : 2053-2067.e18

DOI: 10.1016/j.cell.2021.02.052

2021

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Changes in the Human Gut Microbiota Associated With Colonization by Blastocystis sp. and Entamoeba spp. in Non-Industrialized Populations

Gaël Even, Ana Lokmer, Jules Rodrigues, Christophe Audebert, Eric Viscogliosi, Laure L. Segurel...

Frontiers in Cellular and Infection Microbiology . 11 : 533528

DOI: 10.3389/fcimb.2021.533528

2021

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The Molecular Determinants of Thermoadaptation: Methanococcales as a Case Study

Michel Lecocq, Mathieu Groussin, Manolo Gouy, Celine Brochier-Armanet

Molecular Biology and Evolution . 38 ( 5 ) : 1761–1776

DOI: 10.1093/molbev/msaa312

2021

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Within-host genetic micro-diversity of Mycobacterium tuberculosis and the link with tuberculosis disease features

Charlotte Genestet, Elisabeth Hodille, François Massol, Guislaine Refrégier, Alexia Barbry, Emilie Westeel...

DOI: 10.1101/2021.04.07.438754

2021

Pré-publication

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DILS: Demographic inferences with linked selection by using ABC

Christelle Fraïsse, Iva Popovic, Clément Mazoyer, Bruno Spataro, Stephane Delmotte, Jonathan Romiguier...

Molecular Ecology Resources .

DOI: 10.1111/1755-0998.13323

2021

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Massive colonization of protein-coding exons by selfish genetic elements in Paramecium germline genomes

Diamantis Sellis, Frédéric Guérin, Olivier Arnaiz, Walker Pett, Emmanuelle Lerat, Nicole Boggetto...

Plos Biology . 19 ( 7 ) : e3001309

DOI: 10.1371/journal.pbio.3001309

2021

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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

2021

Chapitre d'ouvrage

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Resurrection of Ancestral Malate Dehydrogenases Reveals the Evolutionary History of Halobacterial Proteins : Deciphering Gene Trajectories and Changes in Biochemical Properties

Samuel Blanquart, Mathieu Groussin, Aline Le Roy, Gergely J Szöllosi, Eric Girard, Bruno Franzetti...

Molecular Biology and Evolution . : 1-44

DOI: 10.1093/molbev/msab146

2021

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Structural and functional analysis of the Francisella lysine decarboxylase as a key actor in oxidative stress resistance

Jan Felix, Claire Siebert, Juila Novion Ducassou, Jérôme Nigou, Pierre Simon Garcia, Angélique Fraudeau...

Scientific Reports . 11 ( 1 ) : 972

DOI: 10.1038/s41598-020-79611-5

2021

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Natural Selection beyond Life? A Workshop Report

Sylvain Charlat, André Ariew, Pierrick Bourrat, María Ferreira Ruiz, Thomas Heams, Philippe Huneman...

Life . 11 ( 10 ) : 1051

DOI: 10.3390/life11101051

2021

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Quantifying the impact of changes in effective population size and expression level on the rate of coding sequence evolution

Thibault Latrille, Nicolas Lartillot

Theoretical Population Biology . 142 : 57-66

DOI: 10.1016/j.tpb.2021.09.005

2021

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Inferring Long-Term Effective Population Size with Mutation–Selection Models

Thibault Latrille, Vincent Lanore, Nicolas Lartillot

Molecular Biology and Evolution . 38 ( 10 ) : 4573-4587

DOI: 10.1093/molbev/msab160

2021

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Long-Lived Species of Bivalves Exhibit Low MT-DNA Substitution Rates

Mathieu Mortz, Aurore Levivier, Nicolas Lartillot, France Dufresne, Pierre Blier

Frontiers in Molecular Biosciences . 8

DOI: 10.3389/fmolb.2021.626042

2021

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GECO Génomique Computationnelle et Evolutive

Equipe Bioinformatique, Phylogénie et Génomique Évolutive

Equipe Baobab

Equipe Sexe et Evolution

Publications

Protein conformational space at the edge of allostery: turning a nonallosteric malate dehydrogenase into an “allosterized” enzyme using evolution-guided punctual mutations

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

An Improved Codon Modeling Approach for Accurate Estimation of the Mutation Bias

Compositionally constrained sites drive long branch attraction

Identifying the best approximating model in Bayesian phylogenetics: Bayes factors, cross-validation or wAIC?

Phyloformer: towards fast and accurate phylogeny estimation with self-attention networks

Efficiently sparse listing of classes of optimal cophylogeny reconciliations

Totoro: Identifying Active Reactions During the Transient State for Metabolic Perturbations

Labile sex expression in angiosperm species with sex chromosomes

Recent Bioinformatic Progress to Identify Epigenetic Changes Associated to Transposable Elements

How sex chromosomes get trapped into nonrecombination

CALDERA: Finding all significant de Bruijn subgraphs for bacterial GWAS

A divide-and-conquer phylogenomic approach based on character supermatrices resolves early steps in the evolution of the Archaea

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

A derived ZW chromosome system in Amborella trichopoda, representing the sister lineage to all other extant flowering plants

The human gut microbiome and health inequities

No evidence for female kin association, indications for extragroup paternity, and sex‐biased dispersal patterns in wild western gorillas

Elevated rates of horizontal gene transfer in the industrialized human microbiome

Changes in the Human Gut Microbiota Associated With Colonization by Blastocystis sp. and Entamoeba spp. in Non-Industrialized Populations

The Molecular Determinants of Thermoadaptation: Methanococcales as a Case Study

Within-host genetic micro-diversity of Mycobacterium tuberculosis and the link with tuberculosis disease features

DILS: Demographic inferences with linked selection by using ABC

Massive colonization of protein-coding exons by selfish genetic elements in Paramecium germline genomes

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

Resurrection of Ancestral Malate Dehydrogenases Reveals the Evolutionary History of Halobacterial Proteins : Deciphering Gene Trajectories and Changes in Biochemical Properties

Structural and functional analysis of the Francisella lysine decarboxylase as a key actor in oxidative stress resistance

Natural Selection beyond Life? A Workshop Report

Quantifying the impact of changes in effective population size and expression level on the rate of coding sequence evolution

Inferring Long-Term Effective Population Size with Mutation–Selection Models

Long-Lived Species of Bivalves Exhibit Low MT-DNA Substitution Rates