GECO Evolutionary and Computational Genomics

Bioinformatics, Phylogeny and Evolutionary Genomics Group

Baobab Group

Publications

Display of 1 to 30 publications on 1140 in total

MicroAnnot: A Dedicated Workflow for Accurate Microsporidian Genome Annotation

Jérémy Tournayre, Valérie Polonais, Ivan Wawrzyniak, Reginald Florian Akossi, Nicolas Parisot, Emmanuelle Lerat...

DOI: 10.20944/preprints202310.1822.v1

Preprint

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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

DOI: 10.1101/2023.03.08.531712

Preprint

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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

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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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Random genetic drift sets an upper limit on mRNA splicing accuracy in metazoans

Florian Bénitìere, Anamaria Necsulea, Laurent Duret

Peer Community in Evolutionary Biology .

DOI: 10.1101/2022.12.09.519597

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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

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The porphyran degradation system of the human gut microbiota is complete, phylogenetically diverse and geographically structured across Asian populations

Sophie Mathieu, Mélanie Touvrey, Laurent Poulet, Sophie Drouillard, Thirumalai Selvi Ulaganathan, Laure Ségurel...

DOI: 10.1101/2023.03.30.534863

Preprint

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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

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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, Philippe M Oger

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

DOI: 10.1099/ijsem.0.005971

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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

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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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A Nearly Neutral Model of Molecular Signatures of Natural Selection after Change in Population Size

Rebekka Müller, Ingemar Kaj, Carina Mugal

Genome Biology and Evolution . 14 ( 5 )

DOI: 10.1093/gbe/evac058

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Hydrogen isotope measurements of bone and dental tissues from archaeological human and animal samples and their use as climatic and diet proxies

Thibault Clauzel, Pascale Richardin, Jannick Ricard, Yves Le Béchennec, Romain Amiot, François Fourel...

Journal of Archaeological Science . 147 : 105676

DOI: 10.1016/j.jas.2022.105676

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Climate conditions and dietary practices during the Second Iron Age studied through the multi-isotope analysis of bones and teeth from individuals of Thézy-Glimont, Picardie, France

Thibault Clauzel, Pascale Richardin, Jannick Ricard, Yves Le Béchennec, Romain Amiot, François Fourel...

Archaeological and Anthropological Sciences . 14 ( 4 ) : 61

DOI: 10.1007/s12520-022-01534-1

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Modeling the spatiotemporal spread of beneficial alleles using ancient genomes

Rasa Muktupavela, Martin Petr, Laure Ségurel, Thorfinn Korneliussen, John Novembre, Fernando Racimo

eLife . 11

DOI: 10.7554/eLife.73767

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Polynomial Delay Algorithm for Minimal Chordal Completions

Caroline Brosse, Vincent Limouzy, Arnaud Mary

49th International Colloquium on Automata, Languages, and Programming (ICALP) .

DOI: 10.4230/LIPIcs.ICALP.2022.33

Conference paper

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Mutations in the non-coding RNU4ATAC gene affect the homeostasis and function of the Integrator complex

Fatimat Almentina Ramos Shidi, Audric Cologne, Marion Delous, Alicia Besson, Audrey Putoux, Anne-Louise Leutenegger...

Nucleic Acids Research .

DOI: 10.1093/nar/gkac1182

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

Sabine Peres, Marc Dinh, Vincent Fromion

International Conference on System Biology .

Conference paper

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Special Issue on “Frontiers in Connecting Steady-State and Dynamic Approaches for Modelling Cell Metabolic Behavior”

Sabine Peres, Mario Jolicoeur

Processes . 10 ( 8 ) : 1612

DOI: 10.3390/pr10081612

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Hybrid metabolic modeling to identify new control strategies of living organisms

Sabine Peres

Hybrid models and methods in systems medicine .

Conference paper

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Mod ́elisation m ́etabolique pour identifier de nouvelles strat ́egies de contrˆole des organismes vivants

Sabine Peres

Meetochondrie .

Conference paper

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

T. Latrille, N. Rodrigue, Nicolas Lartillot

DOI: 10.1101/2022.09.23.509132

Preprint

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The era of reference genomes in conservation genomics

Giulio Formenti, Kathrin Theissinger, Carlos Fernandes, Iliana Bista, Aureliano Bombarely, Christoph Bleidorn...

Trends in Ecology and Evolution . 37 ( 3 ) : 197-202

DOI: 10.1016/j.tree.2021.11.008

Journal article

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BrumiR: A toolkit for de novo discovery of microRNAs from sRNA-seq data

Carol Moraga, Evelyn Sanchez, Mariana Galvão Ferrarini, Rodrigo A Gutierrez, Elena A Vidal, Marie-France Sagot

GigaScience . 11

DOI: 10.1093/gigascience/giac093

Journal article

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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 .

DOI: 10.1111/tan.14852

Journal article

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