GECO Evolutionary and Computational Genomics

Bioinformatics, Phylogeny and Evolutionary Genomics Group

Baobab Group

The main goal of the GECO department is to foster integration and synergies between theoretical and methodological research relevant for the analysis of genomes (computational genomics) and empirical analysis of genomic and multi-omic data (evolutionary and functional genomics). The department is structured in two teams, BAOBAB and BPGE:

BAOBAB is deeply rooted in computer science. Its strengths are in algorithms, models, and mathematical analysis of graphs and networks, with applications to transcriptomics and metabolic networks.

BPGE is oriented towards bioinformatics, phylogenetics and evolutionary genomics. Its research projects cover a broad range of subjects, such as methodological developments for phylogenetic inference, their applications to the reconstruction of the evolutionary history of bacteria and archaea, the role of mobile genetic elements in the evolution of bacteria and of antibioresistance, or the role of recombination, of genomic rearrangements and of transposable elements in the evolution of eukaryotic genomes.

As detailed on their pages, the research conducted in both teams integrates deep and long-ranging theoretical and methodological (algorithmic and computational) developments with data analysis driven by empirical questions. This integration is bi-directional: methodological developments are guided by empirical questions and then used in empirical applications, while theoretical modeling helps clarify the conceptual basis of subsequent empirical analyses.

Publications

Display of 151 to 180 publications on 1378 in total

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

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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 . 38 ( 9 ) : 3754-3774

DOI: 10.1093/molbev/msab146

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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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

Conference paper

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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

Journal article

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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

Journal article

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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

Journal article

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Bioinformatique - 3e édition

Gilbert Deléage, Manolo Gouy, Alexandre de Brevern

978-2-10-081515-9

Book

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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

Journal article

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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

Journal article

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

Christine Oger-Desfeux, Jerome Briolay, Phil M. Oger, Bénédicte Lafay

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

DOI: 10.1128/MRA.00042-21

Journal article

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

Christine Oger-Desfeux, Jérôme Briolay, Phil M. Oger, Bénédicte Lafay

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

DOI: 10.1128/MRA.01326-20

Journal article

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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

Journal article

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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

Journal article

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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 ) : 244

DOI: 10.1038/s42003-021-01753-7

Journal article

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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

Journal article

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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

Conference paper

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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

Journal article

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Epigenetics drive the evolution of sex chromosomes in animals and plants

Aline Muyle, Doris Bachtrog, Gabriel Marais, James Turner

Philosophical Transactions of the Royal Society B: Biological Sciences . 376 ( 1826 ) : 20200124

DOI: 10.1098/rstb.2020.0124

Journal article

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Mindfulness-based programs improve psychological flexibility, mental health, well-being and time management in academics

Gabriel Marais, Sophie Lantheaume, Robin Fiault, Rebecca Shankland

European Journal of Investigation in Health, Psychology and Education .

DOI: 10.31234/osf.io/9w4zp

Journal article

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Answer Set Programming for Computing Constraints-Based Elementary Flux Modes: Application to Escherichia coli Core Metabolism

Maxime Mahout, Ross Carlson, Sabine Peres

Processes . 8 ( 12 ) : 1649

DOI: 10.3390/pr8121649

Journal article

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Chromosomal Conjugative and Mobilizable Elements in Streptococcus suis: Major Actors in the Spreading of Antimicrobial Resistance and Bacteriocin Synthesis Genes

Virginie Libante, Yves Nombre, Charles Coluzzi, Johan Staub, Gérard Guédon, Marcelo Gottschalk...

Pathogens . 9 ( 1 ) : 22

DOI: 10.3390/pathogens9010022

Journal article

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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 ) : 1-12

DOI: 10.1073/pnas.2022112118

Journal article

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