GECO Evolutionary and Computational Genomics

Bioinformatics, Phylogeny and Evolutionary Genomics Group

Baobab Group

Publications

Display of 181 to 210 publications on 1308 in total

Exploring protein space: From hydrolase to ligase by substitution

Nir Hecht, Caroline Monteil, Guy Perriere, Marina Vishkautzan, Eyal Gur

Molecular Biology and Evolution .

DOI: 10.1093/molbev/msaa215

Journal article

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Repeated horizontal gene transfers triggered parallel evolution of magnetotaxis in two evolutionary divergent lineages of magnetotactic bacteria

Caroline Monteil, Denis Grouzdev, Guy Perriere, Béatrice Alonso, Zoé Rouy, Stéphane Cruveiller...

The International Society of Microbiologial Ecology Journal .

DOI: 10.1038/s41396-020-0647-x

Journal article

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Treerecs: an integrated phylogenetic tool, from sequences to reconciliations.

Nicolas Comte, Benoît Morel, Damir Hasic, Laurent Guéguen, Bastien Boussau, Vincent Daubin...

Bioinformatics . 36 ( 18 ) : 4822-4824

DOI: 10.1093/bioinformatics/btaa615

Journal article

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Influenza virus infection induces widespread alterations of host cell splicing

Usama Ashraf, Clara Benoit-Pilven, Vincent Navratil, Cécile Ligneau, Guillaume Fournier, Sandie Munier...

NAR Genomics and Bioinformatics . 2 ( 4 )

DOI: 10.1093/nargab/lqaa095

Journal article

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The TERB1-TERB2-MAJIN complex of mouse meiotic telomeres dates back to the common ancestor of metazoans

Irene da Cruz, Celine Brochier-Armanet, Ricardo Benavente

BMC Evolutionary Biology . 20 ( 1 )

DOI: 10.1186/s12862-020-01612-9

Journal article

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Hepatitis B virus preS2Δ38–55 variants: A newly identified risk factor for hepatocellular carcinoma

Damien Cohen, Sumantra Ghosh, Yusuke Shimakawa, Njie Ramou, Pierre Simon Garcia, Anaëlle Dubois...

JHEP Reports Innovation in Hepatology . 2 ( 5 ) : 100144

DOI: 10.1016/j.jhepr.2020.100144

Journal article

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The Bayesian Approach to Molecular Phylogeny

Nicolas Lartillot

Phylogenetics in the Genomic Era . : 1.4:1--1.4:17

Book chapter

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PhyloBayes: Bayesian Phylogenetics Using Site-heterogeneous Models

Nicolas Lartillot

Phylogenetics in the Genomic Era . : 1.5:1--1.5:16

Book chapter

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An efficient RNA-seq-based segregation analysis identifies the sex chromosomes of Cannabis sativa

Djivan Prentout, Olga Razumova, Benedicte Rhone, Hélène Badouin, Hélène Henri, Cong Feng...

Genome Research . 30 ( 2 ) : 164-172

DOI: 10.1101/gr.251207.119

Journal article

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The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication

Hélène E Badouin, Amandine Velt, François Gindraud, Timothée Flutre, Vincent Dumas, Sonia Vautrin...

Genome Biology . 21 ( 1 ) : 223

DOI: 10.1186/s13059-020-02131-y

Journal article

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An Overview of Duplicated Gene Detection Methods: Why the Duplication Mechanism Has to Be Accounted for in Their Choice

Tanguy Lallemand, Martin Leduc, Claudine Landès, Carène Rizzon, Emmanuelle Lerat

Genes . 11 ( 9 ) : 1046

DOI: 10.3390/genes11091046

Journal article

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A Sample-to-Report Solution for Taxonomic Identification of Cultured Bacteria in the Clinical Setting Based on Nanopore Sequencing

Stefan Moritz Neuenschwander, Miguel Angel Terrazos Miani, Heiko Amlang, Carmen Perroulaz, Pascal Bittel, Carlo Casanova...

Journal of Clinical Microbiology . 58 ( 6 ) : 1128

DOI: 10.1128/JCM.00060-20

Journal article

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Evidence for Dosage Compensation in Coccinia grandis, a Plant with a Highly Heteromorphic XY System

Cécile Fruchard, Hélène E Badouin, David Latrasse, Ravi S Devani, Aline Muyle, Bénédicte Rhoné...

Genes . 11 ( 7 ) : 787

DOI: 10.3390/genes11070787

Journal article

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Population genomics supports clonal reproduction and multiple independent gains and losses of parasitic abilities in the most devastating nematode pest

Georgios Koutsovoulos, Eder Marques, Marie Jeanne Arguel, Laurent Duret, Andressa C. Z. Machado, Regina M. D. G. Carneiro...

Evolutionary Applications . 13 : 442-457

DOI: 10.1111/eva.12881

Journal article

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Capybara: equivalence ClAss enumeration of coPhylogenY event-BAsed ReconciliAtions

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

Bioinformatics . 36 ( 14 ) : 4197-4199

DOI: 10.1093/bioinformatics/btaa498

Journal article

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Algorithms for the quantitative Lock/Key model of cytoplasmic incompatibility

Tiziana Calamoneri, Mattia Gastaldello, Arnaud Mary, Marie-France Sagot, Blerina Sinaimeri

Algorithms for Molecular Biology . : 1-16

DOI: 10.1186/s13015-020-00174-1

Journal article

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From conservation to structure, studies of magnetosome associated cation diffusion facilitators (CDF) proteins in Proteobacteria

Keren-Khadmy Noa, Natalie Zeytuni, Nitzan Kutnowski, Guy Perriere, Caroline Monteil, Raz Zarivachid

PLoS ONE . 15 ( 4 ) : e0231839

DOI: 10.1371/journal.pone.0231839

Journal article

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Isotopic systematics point to wild origin of mummified birds in Ancient Egypt

Marie Linglin, Romain Amiot, Pascale Richardin, Stéphanie Porcier, Ingrid Antheaume, Didier Berthet...

Scientific Reports . 10 ( 1 )

DOI: 10.1038/s41598-020-72326-7

Journal article

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The Gauls experienced the Roman Warm Period: Oxygen isotope study of the Gallic site of Thézy-Glimont, Picardie, France

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

Journal of Archaeological Science: Reports . 34 : 102595

DOI: 10.1016/j.jasrep.2020.102595

Journal article

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Metapopulation ecology links antibiotic resistance, consumption, and patient transfers in a network of hospital wards

Julie Teresa Shapiro, Gilles Leboucher, Anne-Florence Myard-Dury, Pascale Girardo, Anatole Luzzati, Mélissa Mary...

eLife . 9

DOI: 10.7554/eLife.54795

Journal article

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Dickeya poaceiphila sp. nov., a plant-pathogenic bacterium isolated from sugar cane (Saccharum officinarum)

Nicole Hugouvieux-Cotte-Pattat, Celine Brochier-Armanet, Jean-Pierre Flandrois, Sylvie Reverchon

International Journal of Systematic and Evolutionary Microbiology . 70 ( 8 ) : 4508-4514

DOI: 10.1099/ijsem.0.004306

Journal article

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δ18O and δ13C of diagenetic land snail shells from the Pliocene (Zanclean) of Lanzarote, Canary Archipelago: Do they still record some climatic parameters?

Christophe Lécuyer, Antonio Sanchez Marco, Alejandro Lomoschitz, Juan-Francisco Betancort, François Fourel, Romain Amiot...

Journal of African Earth Sciences . 162 : 103702

DOI: 10.1016/j.jafrearsci.2019.103702

Journal article

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Clinical interpretation of variants identified in RNU4ATAC, a non-coding spliceosomal gene

Clara Benoit-Pilven, Alicia Besson, Audrey Putoux, Claire Benetollo, Clément Saccaro, Justine Guguin...

PLoS ONE . 15 ( 7 ) : e0235655

DOI: 10.1371/journal.pone.0235655

Journal article

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Phylogenomics and Genome Annotation

Anamaria Necsulea

Phylogenetics in the Genomic Era . : 4.1:1--4.1:26

Book chapter

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Bedrock radioactivity influences the rate and spectrum of mutation

Nathanaëlle Saclier, Patrick Chardon, Florian Malard, Lara Konecny-Dupré, David Eme, Arnaud Bellec...

eLife . 9 : e56830

DOI: 10.7554/eLife.56830

Journal article

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Development of a dual RNA-seq strategy to unravel the molecular bases of host-symbiont interactions

Nicolas Parisot, Agnès Vallier, Justin Maire, Mariana G. Ferrarini, Benjamin Gillet, Sandrine Hughes...

Journée scientifique de la FR BioEnviS .

Poster

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Key role of chromosomal mobile genetic elements transferred by conjugation in the dissemination of antimicrobial resistance in S. suis

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

4th International Workshop on Streptococcus suis .

Conference paper

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