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 1 to 30 publications on 1377 in total

Neanderthal adaptive introgression shaped LCT enhancer region diversity without linking to lactase persistence in East Asian populations

Xixian Ma, Yan Lu, Mark Stoneking, Shuhua Xu

Proceedings of the National Academy of Sciences of the United States of America . 122 ( 11 ) : e2404393122

DOI: 10.1073/pnas.2404393122

Journal article

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Faithful Interpretation of Protein Structures through Weighted Persistent Homology Improves Evolutionary Distance Estimation

Léa Bou Dagher, Dominique Madern, Philippe Malbos, Céline Brochier-Armanet

Molecular Biology and Evolution . 42 ( 2 )

DOI: 10.1093/molbev/msae271

Journal article

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Exploring endogenous retroviruses in ruminant genomes: They might not be all dead after all

Marie Verneret, Caroline Leroux, Thomas Faraut, Vincent Navratil, Emmanuelle Lerat, Jocelyn Turpin

Bioinformatics and Evolutionary Genomics (ALPHY = ALignments and PHYlogeny) .

Poster

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A genome-wide study of ruminants uncovers two endogenous retrovirus families recently active in goats

Marie Verneret, Caroline Leroux, Thomas Faraut, Vincent Navratil, Emmanuelle Lerat, Jocelyn Turpin

Mobile DNA . 16 ( 1 ) : 4

DOI: 10.1186/s13100-024-00337-6

Journal article

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Exploring the role of transposable elements to sex gap in longevity in Drosophila species

Miriam Merenciano, Sonia Janillon, Camille Mermet-Bouvier, Nelly Burlet, Valentina Rodriguez-Rada, Victor Ronget...

DOI: 10.1101/2025.01.22.634250

Preprint

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Allostery and Evolution: A Molecular Journey Through the Structural and Dynamical Landscape of an Enzyme Super Family

Sandrine Coquille, Caroline Simões Pereira, Jennifer Roche, Gianluca Santoni, Sylvain Engilberge, Céline Brochier-Armanet...

Molecular Biology and Evolution . 42 ( 1 )

DOI: 10.1093/molbev/msae265

Journal article

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PRDM9 drives the location and rapid evolution of recombination hotspots in salmonids fish

Marie Raynaud, Paola Sanna, Julien Joseph, Julie A. J. Clément, Yukiko Imai, Jean-Jacques Lareyre...

PLoS Biology . 23 ( 1 ) : e3002950

DOI: 10.1371/journal.pbio.3002950

Journal article

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Variation in the fitness impact of translationally optimal codons among animals

Florian Bénitière, Tristan Lefébure, Laurent Duret

Genome Research . 35 ( 3 ) : 446-458

DOI: 10.1101/gr.279837.124

Journal article

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The Silene latifolia genome and its giant Y chromosome

Carol Moraga, Catarina Branco, Quentin Rougemont, Paris Veltsos, Pavel Jedlička, Aline Muyle...

Science . 387 ( 6734 ) : 630-636

DOI: 10.1126/science.adj7430

Journal article

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Out-of-Africa migration and clonal expansion of a recombinant Epstein-Barr virus drives frequent nasopharyngeal carcinoma in southern China

Xinyi Zhang, Yanhong Chen, Jingtong Liang, Yue Yang, Hui Chen, Zehui Chen...

National Science Review . 12

DOI: 10.1093/nsr/nwae438

Journal article

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Genome Streamlining: Effect of Mutation Rate and Population Size on Genome Size Reduction

Juliette Luiselli, Jonathan Rouzaud-Cornabas, Nicolas Lartillot, Guillaume Beslon

Genome Biology and Evolution . 16

DOI: 10.1093/gbe/evae250

Journal article

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Efficient enumeration of maximal split subgraphs and induced sub-cographs and related classes

Caroline Brosse, Aurélie Lagoutte, Vincent Limouzy, Arnaud Mary, Lucas Pastor

Discrete Applied Mathematics . 345 : 34-51

DOI: 10.1016/j.dam.2023.10.025

Journal article

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Metabolic modelling links Warburg effect to collagen formation, angiogenesis and inflammation in the tumoral stroma

Maxime Mahout, Laurent Schwartz, Romain Attal, Ashraf Bakkar, Sabine Peres

PLoS ONE . 19 ( 12 ) : e0313962

DOI: 10.1371/journal.pone.0313962

Journal article

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Modelling energy metabolism dysregulations in neuromuscular diseases: A case study of calpainopathy

Camille Siharath, Olivier Biondi, Sabine Peres

Heliyon . 10 ( 24 ) : e40918

DOI: 10.1016/j.heliyon.2024.e40918

Journal article

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Divergence in expression of a singing-related neuro-plasticity gene in the brains of two Ficedula flycatchers and their hybrids

David Wheatcroft, Niclas Backström, Ludovic Dutoit, S Eryn Mcfarlane, Carina Mugal, Mi Wang...

G3 .

DOI: 10.1093/g3journal/jkae293

Journal article

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Identification and quantification of transposable element transcripts using Long-Read RNA-seq in Drosophila germline tissues

Rita Rebollo, Pierre Gerenton, Eric Cumunel, Arnaud Mary, François Sabot, Nelly Burlet...

DOI: 10.1101/2023.05.27.542554

Preprint

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From Inquilines to Gall Inducers: Genomic Signature of a Life-Style Transition in Synergus Gall Wasps

Erik Gobbo, Nicolas Lartillot, Jack Hearn, Graham N Stone, Yoshihisa Abe, Christopher W Wheat...

Genome Biology and Evolution . 12 : 2060 - 2073

DOI: 10.1093/gbe/evaa204

Journal article

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Hijackers, hitchhikers, or co-drivers? The mysteries of mobilizable genetic elements

Manuel Ares-Arroyo, Charles Coluzzi, Jorge A Moura de Sousa, Eduardo P C Rocha

PLoS Biology . 22 ( 8 ) : e3002796

DOI: 10.1371/journal.pbio.3002796

Journal article

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A type IVB secretion system contributes to the pathogenicity of Yersinia pseudotuberculosis strains responsible for the Far East scarlet-like fever

Marion Lemarignier, Cyril Savin, Ines Ruedas Torres, Anne Derbise, Charles Coluzzi, Julien Burlaud-Gaillard...

DOI: 10.1101/2024.06.14.598817

Preprint

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Evo‐Scope : Fully automated assessment of correlated evolution on phylogenetic trees

Maxime Godfroid, Charles Coluzzi, Amaury Lambert, Philippe Glaser, Eduardo P C Rocha, Guillaume Achaz

Methods in Ecology and Evolution . 15 ( 2 ) : 282 - 289

DOI: 10.1111/2041-210x.14190

Journal article

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Bridging the gap between the evolutionary dynamics and the molecular mechanisms of meiosis.

Nicolas Lartillot, Alice Genestier, Laurent Duret

RecomBern .

Conference paper

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High prevalence of Prdm9-independent recombination hotspots in placental mammals

Laurent Duret, Julien Joseph, Djivan Prentout, Alexandre Laverré, Théo Tricou

Probabilistic Modeling in Genomics Conference : ProbGen 2024 .

Conference paper

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The characterization of ancient Methanococcales malate dehydrogenases reveals that strong thermal stability prevents unfolding under intense γ-irradiation

D Madern, Frédéric Halgand, Chantal Houée-Levin, A-B Dufour, S Coquille, S Ansanay-Alex...

Molecular Biology and Evolution .

DOI: 10.1093/molbev/msae231

Journal article

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Prevalence of PRDM9-dependent vs PRDM9-independent recombination hotspots in animals

Laurent Duret

RecomBern .

Conference paper

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The Inca child of the Quehuar volcano: Stable isotopes clue to geographic origin and seasonal diet, with putative seaweed consumption

Eve Poulallion, Violeta Galván, Verónica Seldes, María Fernanda Zigarán, Gabriela Recagno Browning, François Fourel...

Journal of Archaeological Science: Reports . 59 : 104784

DOI: 10.1016/j.jasrep.2024.104784

Journal article

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Look4LTRs: a Long terminal repeat retrotransposon detection tool capable of cross species studies and discovering recently nested repeats

Anthony B. Garza, Emmanuelle Lerat, Hani Z. Girgis

Mobile DNA . 15 ( 1 ) : 8

DOI: 10.1186/s13100-024-00317-w

Journal article

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