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 61 to 90 publications on 1378 in total

The evolution of GC-biased gene conversion by means of natural selection

Nicolas Lartillot, Julien Joseph, Augustin Clessin

ETEE'2023: Empiricism & Theory in Ecology and Evolution .

Conference paper

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Geographic origin and social status of the Gallic warriors from Ribemont‐sur‐Ancre (France) studied through isotope systematics of bone remains

Thibault Clauzel, Pascale Richardin, Jannick Ricard, Gilles Prilaux, Jeremy E. Martin, Romain Amiot...

International Journal of Osteoarchaeology . 33 ( 1 ) : 39-50

DOI: 10.1002/oa.3172

Journal article

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Experimental analysis of diverse actin-like proteins from various magnetotactic bacteria by functional expression in Magnetospirillum gryphiswaldense

Ram Prasad Awal, Frank D Müller, Daniel Pfeiffer, Caroline L Monteil, Guy Perrière, Christopher T Lefèvre...

mBio . 14 ( 5 )

DOI: 10.1128/mbio.01649-23

Journal article

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A first step towards the characterization of endogenous retroviruses’ evolutionary history and impact on small ruminant genomes

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

CNET 2023 : 24th National Congress on Transposable Elements 2023 .

Conference paper

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OVINE β-ENDOGENOUS RETROVIRUSES : FROM INTEGRATION TO COPY-SPECIFIC TRANSCRIPTION

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

XXVèmes Journées Francophones de Virologie .

Poster

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De novo analysis of splicing from RNA-seq data: models, algorithms and applications

Vincent Lacroix

HDR

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Mitigation of the diagenesis risk in biological apatite δ18O interpretation

Christophe Lécuyer, Jean-Pierre Flandrois

Palaeogeography, Palaeoclimatology, Palaeoecology . 630 : 111812

DOI: 10.1016/j.palaeo.2023.111812

Journal article

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δ2H and δ18O of river water from a high-altitude humid plain of the southern Alps: Implications for the interpretation of the isotopic compositions of bioapatite from humans living close to mountain areas

Christophe Lécuyer, François Atrops, François Fourel, Thibault Clauzel, Jean-Pierre Flandrois

Journal of Archaeological Science: Reports . 49 : 104020

DOI: 10.1016/j.jasrep.2023.104020

Journal article

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Evolution of sex-biased gene expression during transitions to separate sexes in the Silene genus

Djivan Prentout, Aline Muyle, Niklaus Zemp, Adil El Filali, Bastien Boussau, Pascal Touzet...

DOI: 10.1101/2023.10.02.560480

Preprint

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IFB/ELIXIR-FR, the french node of ELIXIR

Anne-Françoise Adam-Blondon, Jacques van Helden, Gildas Le Corguillé, Christophe Blanchet, Hélène Chiapello, Christine Gaspin...

ISMB ECCB 2023 .

Conference paper

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Genomic portrait and relatedness patterns of the Iron Age Log Coffin culture in northwestern Thailand

Selina Carlhoff, Wibhu Kutanan, Adam B Rohrlach, Cosimo Posth, Mark Stoneking, Kathrin Nägele...

Nature Communications . 14 ( 1 ) : 8527

DOI: 10.1038/s41467-023-44328-2

Journal article

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Genome-wide variation in the Angolan Namib Desert reveals unique pre-Bantu ancestry

Sandra Oliveira, Anne-Maria Fehn, Beatriz Amorim, Mark Stoneking, Jorge Rocha

Science Advances . 9 ( 38 )

DOI: 10.1126/sciadv.adh3822

Journal article

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South Asian maternal and paternal lineages in southern Thailand and the role of sex-biased admixture

Wipada Woravatin, Mark Stoneking, Metawee Srikummool, Jatupol Kampuansai, Leonardo Arias, Wibhu Kutanan

PLoS ONE . 18 ( 9 ) : e0291547

DOI: 10.1371/journal.pone.0291547

Journal article

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The genomic diversity of Taiwanese Austronesian groups: Implications for the “Into- and Out-of-Taiwan” models

Dang Liu, Albert Min-Shan Ko, Mark Stoneking

PNAS Nexus . 2 ( 5 )

DOI: 10.1093/pnasnexus/pgad122

Journal article

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Genomic perspectives on human dispersals during the Holocene

Mark Stoneking, Leonardo Arias, Dang Liu, Sandra Oliveira, Irina Pugach, Jae Joseph Russell B Rodriguez

Proceedings of the National Academy of Sciences of the United States of America . 120 ( 4 )

DOI: 10.1073/pnas.2209475119

Journal article

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Minimal Cut Sets of a Consortium Model of P. aeruginosa and S. aureus Reveal New Cross-Feeding Interactions

Maxime Mahout, Sabine Peres

Metabolic Pathway Analysis 2023 .

Conference paper

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A General Framework for Enumerating Equivalence Classes of Solutions

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

Algorithmica . 85 ( 10 ) : 3003-3023

DOI: 10.1007/s00453-023-01131-1

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 Garza, Emmanuelle Lerat, Hani Girgis

DOI: 10.1101/2023.07.28.551030

Preprint

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Phylogenomic analysis of protein‐coding genes resolves complex gall wasp relationships

Jack Hearn, Erik Gobbo, José Luis Nieves-Aldrey, Antoine Branca, James Nicholls, Georgios Koutsovoulos...

Systematic Entomology .

DOI: 10.1111/syen.12611

Journal article

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How genomics can help biodiversity conservation

Kathrin Theissinger, Carlos Fernandes, Giulio Formenti, Iliana Bista, Paul Berg, Christoph Bleidorn...

Trends in Genetics .

DOI: 10.1016/j.tig.2023.01.005

Journal article

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Bridging the gap between the evolutionary dynamics and the molecular mechanisms of meiosis : a model based exploration of the PRDM9 intra-genomic Red Queen

Alice Genestier, Laurent Duret, Nicolas Lartillot

PLoS Genetics . 20 ( 5 ) : e1011274

DOI: 10.1371/journal.pgen.1011274

Journal article

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Compositionally Constrained Sites Drive Long-Branch Attraction

Lénárd L Szánthó, Nicolas Lartillot, Gergely J Szöllősi, Dominik Schrempf

Systematic Biology . 72 ( 4 ) : 767 - 780

DOI: 10.1093/sysbio/syad013

Journal article

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Identifying the Best Approximating Model in Bayesian Phylogenetics: Bayes Factors, Cross-Validation or wAIC?

Nicolas Lartillot

Systematic Biology . 72 : 616 - 638

DOI: 10.1093/sysbio/syad004

Journal article

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Genes and sites under adaptation at the phylogenetic scale also exhibit adaptation at the population-genetic scale

Thibault Latrille, Nicolas Rodrigue, Nicolas Lartillot

Proceedings of the National Academy of Sciences of the United States of America . 120 ( 11 ) : e2214977120

DOI: 10.1073/pnas.2214977120

Journal article

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Deciphering evolutionary trajectories of lactate dehydrogenases provides new insights into allostery.

Adeline Robin, Céline Brochier-Armanet, Quentin Bertrand, Caroline Barette, Eric Girard, Dominique Madern

Molecular Biology and Evolution . msad223

DOI: 10.1093/molbev/msad223

Journal article

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Proposed mechanism for the selection of lactase persistence in childhood

Alexandre Fabre, Anne Fabre, Céline Bon, Paul Guerry, Laure Ségurel

BioEssays . 45 ( 7 )

DOI: 10.1002/bies.202200243

Journal article

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Bradyrhizobium commune sp. nov., isolated from nodules of a wide range of native legumes across the Australian continent

Bénédicte Lafay, Elina Coquery, Phil M. Oger

International Journal of Systematic and Evolutionary Microbiology . 73 ( 7 ) : 005971

DOI: 10.1099/ijsem.0.005971

Journal article

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Cophylogeny Reconstruction Allowing for Multiple Associations Through Approximate Bayesian Computation

Blerina Sinaimeri, Laura Urbini, Marie-France Sagot, Catherine Matias

Systematic Biology . : syad058

DOI: 10.1093/sysbio/syad058

Journal article

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Hybrid modelling to Solve Optimal Concentrations of Metabolites and Enzymes in Constraint-based modelling

Sabine Peres

BIOSTEC 2023 .

Conference paper

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Population designations in biomedical research: limitations and perspectives

Caroline Gombault, Guillaume Grenet, Laure Ségurel, Laurent Duret, François Gueyffier, Pascal Cathébras...

HLA: Immune Response Genetics . 101 ( 1 ) : 3-15

DOI: 10.1111/tan.14852

Journal article

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