GECO Génomique Computationnelle et Evolutive

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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The Transposable Element Environment of Human Genes Differs According to Their Duplication Status and Essentiality

Margot Correa, Emmanuelle Lerat, Etienne E. Birmelé, Franck Samson, Bérengère Bouillon, Kévin Normand...

Genome Biology and Evolution . 13 ( 5 )

DOI: 10.1093/gbe/evab062

2021

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A General Framework for Enumerating Equivalence Classes of Solutions

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

ESA 2021 - 29th Annual European Symposium on Algorithms . : 1-14

DOI: 10.4230/LIPIcs.ESA.2021.80

2021

Acte de congrès

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Dichloroacetate and Pyruvate Metabolism: Pyruvate Dehydrogenase Kinases as Targets Worth Investigating for Effective Therapy of Toxoplasmosis

Mariana Galvão Ferrarini, Lindice Mitie Nisimura, Richard Marcel Bruno Moreira Girard, Mayke Bezerra Alencar, Mariana Sayuri Ishikawa Fragoso, Carlla Assis Araújo-Silva...

MSphere . 6 ( 1 )

DOI: 10.1128/mSphere.01002-20

2021

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A family of tree-based generators for bubbles in directed graphs

Vicente Acuña, Leandro Ishi Soares de Lima, Giuseppe F Italiano, Luca Pepè Sciarria, Marie-France Sagot, Blerina Sinaimeri

Journal of Graph Algorithms and Applications . 25 ( 1 ) : 549-562

DOI: 10.7155/jgaa.00572

2021

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A comprehensive evaluation of binning methods to recover human gut microbial species from a non-redundant reference gene catalog

Marianne Borderes, Cyrielle Gasc, Emmanuel Prestat, Mariana Galvão Ferrarini, Susana Vinga, Lilia Boucinha...

NAR Genomics and Bioinformatics . 3 ( 1 )

DOI: 10.1093/nargab/lqab009

2021

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Bioinformatique - 3e édition

Gilbert Deléage, Manolo Gouy, Alexandre de Brevern

978-2-10-081515-9

2021

Ouvrage

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A Comprehensive Evolutionary Scenario of Cell Division and Associated Processes in the Firmicutes

Pierre Garcia, Wandrille Duchemin, Jean-Pierre Flandrois, Simonetta Gribaldo, Christophe Grangeasse, Céline Brochier-Armanet

Molecular Biology and Evolution . 38 ( 6 ) : 2396-2412

DOI: 10.1093/molbev/msab034

2021

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Plant genera Cannabis and Humulus share the same pair of well-differentiated sex chromosomes

Djivan Prentout, Natasa Stajner, Andreja Cerenak, Theo Tricou, Celine Brochier-Armanet, Jernej Jakse...

New Phytologist . 231 ( 4 ) : 1599-1611

DOI: 10.1111/nph.17456

2021

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Complete genome of Bradyrhizobium sp. strain BDV5419, representative of Australian genospecies L

Christine Oger-Desfeux, Jerome Briolay, P. Oger, Bénédicte Lafay

Microbiology Resource Announcements . 10 ( 8 ) : e00042-21

DOI: 10.1128/MRA.00042-21

2021

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Complete Genome Sequence of Bradyrhizobium sp. Strain BDV5040, Representative of Widespread Genospecies B in Australia

Christine Oger-Desfeux, Jérôme Briolay, Philippe Oger, Bénédicte Lafay

Microbiology Resource Announcements . 10 ( 3 ) : e01326-20

DOI: 10.1128/MRA.01326-20

2021

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Reconstruction of body mass evolution in the Cetartiodactyla and mammals using phylogenomic data.

Emeric Figuet, Marion Ballenghien, Nicolas Lartillot, Nicolas Galtier

Peer Community Journal . 1 : e42

DOI: 10.24072/pcjournal.42

2021

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Transposable element activity in the transcriptomic analysis of mouse pancreatic tumors

Emmanuelle Lerat, Nelly Burlet, Vincent Navratil, Camilles Noûs

DOI: 10.1101/2021.07.16.452652

2021

Pré-publication

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A new tool to cross and analyze TE and gene annotations

Emmanuelle Lerat

Peer Community In Genomics . : 100010

DOI: 10.24072/pci.genomics.100010

2021

Autre publication

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A Bayesian Mutation–Selection Framework for Detecting Site-Specific Adaptive Evolution in Protein-Coding Genes

Nicolas Rodrigue, Thibault Latrille, Nicolas Lartillot

Molecular Biology and Evolution . 38 ( 3 ) : 1199-1208

DOI: 10.1093/molbev/msaa265

2021

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Universal probabilistic programming offers a powerful approach to statistical phylogenetics

Fredrik Ronquist, Jan Kudlicka, Viktor Senderov, Johannes Borgström, Nicolas Lartillot, Daniel Lundén...

Communications Biology . 4 ( 1 )

DOI: 10.1038/s42003-021-01753-7

2021

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Reconstructing the History of Variation in Effective Population Size along Phylogenies

Mathieu Brevet, Nicolas Lartillot

Genome Biology and Evolution . 13 ( 8 )

DOI: 10.1093/gbe/evab150

2021

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Making Sense of a Cophylogeny Output: Efficient Listing of Representative Reconciliations

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

WABI 2021 - 21st International Workshop on Algorithms in Bioinformatics . : 1-18

DOI: 10.4230/LIPIcs.WABI.2021.3

2021

Acte de congrès

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Climatic change and diet of the pre-Hispanic population of Gran Canaria (Canary Archipelago, Spain) during the Medieval Warm Period and Little Ice Age

Christophe Lécuyer, Jean Goedert, Johanne Klee, Thibault Clauzel, Pascale Richardin, François Fourel...

Journal of Archaeological Science . 128 : 105336

DOI: 10.1016/j.jas.2021.105336

2021

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Ancient DNA from Guam and the peopling of the Pacific

Irina Pugach, Alexander Hübner, Hsiao-Chun Hung, Matthias Meyer, Mike Carson, Mark Stoneking

Proceedings of the National Academy of Sciences of the United States of America . 118 ( 1 )

DOI: 10.1073/pnas.2022112118

2020

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Expanding the Geographic Characterisation of Epstein–Barr Virus Variation through Gene-Based Approaches

Marco Telford, David Hughes, David Juan, Mark Stoneking, Arcadi Navarro, Gabriel Santpere

Microorganisms . 8 ( 11 ) : 1686

DOI: 10.3390/microorganisms8111686

2020

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Ancient DNA indicates human population shifts and admixture in northern and southern China

Melinda Yang, Xuechun Fan, Bo Sun, Chungyu Chen, Jianfeng Lang, Ying-Chin Ko...

Science . 369 ( 6501 ) : 282-288

DOI: 10.1126/science.aba0909

2020

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Cultural variation impacts paternal and maternal genetic lineages of the Hmong-Mien and Sino-Tibetan groups from Thailand

Wibhu Kutanan, Rasmi Shoocongdej, Metawee Srikummool, Alexander Hübner, Thanatip Suttipai, Suparat Srithawong...

European Journal of Human Genetics . 28 : 1563 - 1579

DOI: 10.1038/s41431-020-0693-x

2020

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Papuan mitochondrial genomes and the settlement of Sahul

Nicole Pedro, Nicolas Brucato, Verónica Fernandes, Mathilde André, Lauri Saag, William Pomat...

Journal of Human Genetics .

DOI: 10.1038/s10038-020-0781-3

2020

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The paternal and maternal genetic history of Vietnamese populations

Enrico Macholdt, Leonardo Arias, Nguyen Thuy Duong, Nguyen Dang Ton, Nguyen Van Phong, Roland Schröder...

European Journal of Human Genetics . 28 ( 5 ) : 636-645

DOI: 10.1038/s41431-019-0557-4

2020

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Extensive Ethnolinguistic Diversity in Vietnam Reflects Multiple Sources of Genetic Diversity

Dang Liu, Nguyen Thuy Duong, Nguyen Dang Ton, Nguyen van Phong, Brigitte Pakendorf, Nong van Hai...

Molecular Biology and Evolution . 37 ( 9 ) : 2503 - 2519

DOI: 10.1093/molbev/msaa099

2020

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GECO Génomique Computationnelle et Evolutive

Equipe Bioinformatique, Phylogénie et Génomique Évolutive

Equipe Baobab

Publications

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

The Transposable Element Environment of Human Genes Differs According to Their Duplication Status and Essentiality

A General Framework for Enumerating Equivalence Classes of Solutions

Dichloroacetate and Pyruvate Metabolism: Pyruvate Dehydrogenase Kinases as Targets Worth Investigating for Effective Therapy of Toxoplasmosis

A family of tree-based generators for bubbles in directed graphs

A comprehensive evaluation of binning methods to recover human gut microbial species from a non-redundant reference gene catalog

Bioinformatique - 3e édition

A Comprehensive Evolutionary Scenario of Cell Division and Associated Processes in the Firmicutes

Plant genera Cannabis and Humulus share the same pair of well-differentiated sex chromosomes

Complete genome of Bradyrhizobium sp. strain BDV5419, representative of Australian genospecies L

Complete Genome Sequence of Bradyrhizobium sp. Strain BDV5040, Representative of Widespread Genospecies B in Australia

Reconstruction of body mass evolution in the Cetartiodactyla and mammals using phylogenomic data.

Transposable element activity in the transcriptomic analysis of mouse pancreatic tumors

A new tool to cross and analyze TE and gene annotations

A Bayesian Mutation–Selection Framework for Detecting Site-Specific Adaptive Evolution in Protein-Coding Genes

Universal probabilistic programming offers a powerful approach to statistical phylogenetics

Reconstructing the History of Variation in Effective Population Size along Phylogenies

Making Sense of a Cophylogeny Output: Efficient Listing of Representative Reconciliations

Climatic change and diet of the pre-Hispanic population of Gran Canaria (Canary Archipelago, Spain) during the Medieval Warm Period and Little Ice Age

Ancient DNA from Guam and the peopling of the Pacific

Expanding the Geographic Characterisation of Epstein–Barr Virus Variation through Gene-Based Approaches

Ancient DNA indicates human population shifts and admixture in northern and southern China

Cultural variation impacts paternal and maternal genetic lineages of the Hmong-Mien and Sino-Tibetan groups from Thailand

Papuan mitochondrial genomes and the settlement of Sahul

The paternal and maternal genetic history of Vietnamese populations

Extensive Ethnolinguistic Diversity in Vietnam Reflects Multiple Sources of Genetic Diversity