Functionnal Evolutionary Genomics Group

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Publications

Display of 1 to 30 publications on 136 in total

Search for photosynthesis-related protein sites through chloroplast phylogenomics

Pierre Gérenton, Philippe Veber, Vincent Lacroix, Bastien Boussau

ALPHY/AIEM 2025 .

Poster

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Convergent transcriptomic and genomic adaptation in xeric rodents

Chalopin Domitille, Rey Carine, Ganofsky Jeremy, Blin Juliana, Chevret Pascale, Mouginot Marion...

DOI: 10.1101/2024.10.02.616319

Preprint

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Phyloformer: Fast, accurate and versatile phylogenetic reconstruction with deep neural networks

Luca Nesterenko, Luc Blassel, Philippe Veber, Bastien Boussau, Laurent Jacob

DOI: 10.1101/2024.06.17.599404

Preprint

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Simulations of Sequence Evolution: How (Un)realistic They Are and Why

Johanna Trost, Julia Haag, Dimitri Höhler, Laurent Jacob, Alexandros Stamatakis, Bastien Boussau

Molecular Biology and Evolution . 41 ( 1 )

DOI: 10.1093/molbev/msad277

Journal article

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Evolution and functional relevance of non-coding elements in vertebrate genomes

Anamaria Necsulea

HDR

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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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Meta-analysis reveals limited reproducibility of lncRNA-related findings in hepatocellular carcinoma research

Anamaria Necsulea, Philippe Veber, Tuyana Boldanova, Charlotte Ky Ng, Stefan Wieland, Markus H Heim

DOI: 10.1101/2024.08.17.608405

Preprint

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SAMD9L acts as an antiviral factor against HIV-1 and primate lentiviruses by restricting viral and cellular translation

Alexandre Legrand, Clara Dahoui, Clément de la Myre Mory, Kodie Noy, Laura Guiguettaz, Margaux Versapuech...

PLoS Biology . 22 ( 7 ) : e3002696

DOI: 10.1371/journal.pbio.3002696

Journal article

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GTDrift: a resource for exploring the interplay between genetic drift, genomic and transcriptomic characteristics in eukaryotes

Florian Bénitière, Laurent Duret, Anamaria Necsulea

NAR Genomics and Bioinformatics . 6 ( 2 ) : lqae064

DOI: 10.1093/nargab/lqae064

Journal article

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LncRNA analyses reveal increased levels of non-coding centromeric transcripts in hepatocellular carcinoma

Anamaria Necsulea, Philippe Veber, Tuyana Boldanova, Charlotte K Y Ng, Stefan Wieland, Markus H Heim

DOI: 10.1101/2021.03.03.433778

Preprint

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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...

Peer Community Journal . 4 ( e89 )

DOI: 10.24072/pcjournal.457

Journal article

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

Florian Bénitière, Anamaria Necsulea, Laurent Duret

eLife . 13 : RP93629

DOI: 10.7554/eLife.93629.3

Journal article

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Transposable element expression with variation in sex chromosome number: insights into a toxic Y effect on human longevity

Jordan Teoli, Miriam Merenciano, Marie Fablet, Anamaria Necsulea, Daniel Siqueira-De-Oliveira, Alessandro Brandulas-Cammarata...

Peer Community In Genomics .

DOI: 10.1101/2023.08.03.550779

Journal article

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An evolutionary timescale for Bacteria calibrated using the Great Oxidation Event

Adrián Davín, Ben Woodcroft, Rochelle Soo, Benoit Morel, Ranjani Murali, Dominik Schrempf...

DOI: 10.1101/2023.08.08.552427

Preprint

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Evaluation of Methods to Detect Shifts in Directional Selection at the Genome Scale

Louis Duchemin, Vincent Lanore, Philippe Veber, Bastien Boussau

Molecular Biology and Evolution . 40 ( 2 )

DOI: 10.1093/molbev/msac247

Journal article

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Endoparasitoid lifestyle promotes endogenization and domestication of dsDNA viruses

Benjamin Guinet, D. Lepetit, S. Charlat, Peter N Buhl, David G Notton, Astrid Cruaud...

eLife . 12 : e85993

DOI: 10.7554/eLife.85993

Journal article

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Adaptation to host cell environment during experimental evolution of Zika virus

Vincent Grass, Emilie Hardy, Kassian Kobert, Soheil Rastgou Talemi, Elodie Décembre, Coralie Guy...

Communications Biology . 5 ( 1 ) : 1115

DOI: 10.1038/s42003-022-03902-y

Journal article

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Calculs d’inférence dans les arbres phylogénétiques

Laurent Guéguen

Modèles et méthodes pour l’évolution biologique . 9781789480696 : 177-202

DOI: 10.51926/ISTE.9069.ch7

Book chapter

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Adaptation to host cell environment during experimental evolution of Zika virus

Vincent Grass, Emilie Hardy, Kassian Kobert, Soheil Rastgou Talemi, Elodie Décembre, Coralie Guy...

Communications Biology . 5 ( 1 ) : 1115

DOI: 10.1038/s42003-022-03902-y

Journal article

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Polymorphism‐aware estimation of species trees and evolutionary forces from genomic sequences with RevBayes

Rui Borges, Bastien Boussau, Sebastian Höhna, Ricardo Pereira, Carolin Kosiol

Methods in Ecology and Evolution . 13 ( 11 ) : 2339-2346

DOI: 10.1111/2041-210X.13980

Journal article

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Relative Time Constraints Improve Molecular Dating

Gergely Szöllõsi, Sebastian Höhna, Tom Williams, Dominik Schrempf, Vincent Daubin, Bastien Boussau

Systematic Biology . 71 ( 4 ) : 797-809

DOI: 10.1093/sysbio/syab084

Journal article

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GOntact: using chromatin contacts to infer Gene Ontology enrichments for cis -regulatory elements

Alexandre Laverré, Eric Tannier, Philippe Veber, Anamaria Necsulea

DOI: 10.1101/2022.06.13.495495

Preprint

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Distinct evolutionary trajectories of SARS-CoV-2-interacting proteins in bats and primates identify important host determinants of COVID-19

Marie Cariou, Léa Picard, Laurent Guéguen, Stéphanie Jacquet, Andrea Cimarelli, Oliver Fregoso...

Proceedings of the National Academy of Sciences of the United States of America . 119 ( 35 )

DOI: 10.1073/pnas.2206610119

Journal article

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Extreme mitochondrial DNA divergence underlies genetic conflict over sex determination

Patrice David, Cyril Degletagne, Nathanaelle Saclier, Aurel Jennan, Philippe Jarne, Sandrine Plénet...

Current Biology . 32 ( 10 ) : 2325-2333.e1-e6

DOI: 10.1016/j.cub.2022.04.014

Journal article

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