GECO Génomique Computationnelle et Evolutive

A comprehensive evaluation of binning methods to recover human gut microbial species from a non-redundant reference gene catalog

Marianne Borderes, Cyrielle Gasc, Emmanuel Prestat, Mariana Ferrarini, Susana Vinga, Lilia Boucinha...

NAR Genomics and Bioinformatics . 3 ( 1 )

DOI: 10.1093/nargab/lqab009

2021

Article dans une revue

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DILS: Demographic inferences with linked selection by using ABC

Christelle Fraïsse, Iva Popovic, Clément Mazoyer, Bruno Spataro, Stephane Delmotte, Jonathan Romiguier...

Molecular Ecology Resources .

DOI: 10.1111/1755-0998.13323

2021

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Complete genome of Bradyrhizobium sp. strain BDV5419, representative of Australian genospecies L

Christine Oger-Desfeux, Jerome Briolay, P. Oger, Bénédicte Lafay

Microbiology Resource Announcements . 10 ( 8 ) : e00042-21

DOI: 10.1128/MRA.00042-21

2021

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Complete Genome Sequence of Bradyrhizobium sp. Strain BDV5040, Representative of Widespread Genospecies B in Australia

Christine Oger-Desfeux, Jérôme Briolay, Philippe Oger, Bénédicte Lafay

Microbiology Resource Announcements . 10 ( 3 ) : e01326-20

DOI: 10.1128/MRA.01326-20

2021

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The Molecular Determinants of Thermoadaptation: Methanococcales as a Case Study

Michel Lecocq, Mathieu Groussin, Manolo Gouy, Celine Brochier-Armanet

Molecular Biology and Evolution . 38 ( 5 ) : 1761–1776

DOI: 10.1093/molbev/msaa312

2021

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Seaview Version 5: A Multiplatform Software for Multiple Sequence Alignment, Molecular Phylogenetic Analyses, and Tree Reconciliation

Manolo Gouy, Eric Tannier, Nicolas Comte, David Parsons

Multiple Sequence Alignment . 2231 : 241-260

DOI: 10.1007/978-1-0716-1036-7_15

2021

Chapitre d'ouvrage

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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

2020

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

Celine Brochier-Armanet

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

DOI: 10.1016/j.jhepr.2020.100144

2020

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Evolutionary relationships between Archaea and eukaryotes

Simonetta Gribaldo, Celine Brochier-Armanet

Nature Ecology & Evolution . 4 : 20-21

DOI: 10.1038/s41559-019-1073-1

2020

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Probabilistic programming: a powerful new approach to statistical phylogenetics

Fredrik Ronquist, Jan Kudlicka, Viktor Senderov, Johannes Borgström, Nicolas Lartillot, Daniel Lundén...

DOI: 10.1101/2020.06.16.154443

2020

Pré-publication

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Detecting sex-linked genes using genotyped individuals sampled in natural populations

Jos Käfer, Nicolas Lartillot, Gabriel Marais, Franck Picard

DOI: 10.1101/2020.01.31.928291

2020

Pré-publication

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Evolutionary plasticity of mating-type determination mechanisms in Paramecium aurelia sibling species

Natalia Sawka-Gądek, Alexey Potekhin, Deepankar Pratap Singh, Inessa Grevtseva, Olivier Arnaiz, Simon Penel...

Genome Biology and Evolution . ( evaa258 )

DOI: 10.1093/gbe/evaa258

2020

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

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

Genes . 11 ( 7 ) : 787

DOI: 10.3390/genes11070787

2020

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

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

eLife . 9

DOI: 10.7554/eLife.54795

2020

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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 )

DOI: 10.1128/JCM.00060-20

2020

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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

2020

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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

2020

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Efficient hybrid de novo assembly of human genomes with WENGAN

Alex Genova, Elena Buena-Atienza, Stephan Ossowski, Marie-France Sagot

Nature Biotechnology . 39 : 422–430

DOI: 10.1038/s41587-020-00747-w

2020

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Niche specialization and spread of Staphylococcus capitis involved in neonatal sepsis

Thierry Wirth, Marine Bergot, Jean-Philippe Rasigade, Bruno Pichon, Maxime Barbier, Patricia Martins-Simoes...

Nature Microbiology . 5 ( 5 ) : 735-745

DOI: 10.1038/s41564-020-0676-2

2020

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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

2020

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Accumulation of amyloid precursor protein C-terminal fragments triggers mitochondrial structure, function, and mitophagy defects in Alzheimer's disease models and human brains

Loan Vaillant-Beuchot, Arnaud Mary, Raphaëlle Pardossi-Piquard, Alexandre Bourgeois, Inger Lauritzen, Fanny Eysert...

Acta Neuropathologica .

DOI: 10.1007/s00401-020-02234-7

2020

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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

2020

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How consistent is RAD‐seq divergence with DNA‐barcode based clustering in insects?

Marie Cariou, Hélène Henri, Sonia Martinez, Laurent Duret, Sylvain Charlat

Molecular Ecology Resources . 20 ( 5 ) : 1294-1298

DOI: 10.1111/1755-0998.13178

2020

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Controlling technical variation amongst 6693 patient microarrays of the randomized MINDACT trial

Laurent Jacob, Anke Witteveen, Inès Beumer, Leonie Delahaye, Diederik Wehkamp, Jeroen van den Akker...

Communications Biology . 3

DOI: 10.1038/s42003-020-1111-1

2020

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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

2020

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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

2020

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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

2020

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Three-Dimensional Imaging of the Vertebral Lymphatic Vasculature and Drainage using iDISCO⁺ and Light Sheet Fluorescence Microscopy

Laurent Jacob, Jose Brito, Jean-Leon Thomas

Journal of visualized experiments : JoVE . ( 159 ) : e61099 |

DOI: 10.3791/61099

2020

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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

2020

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A Family of Tree-Based Generators for Bubbles in Directed Graphs

Vicente Acuña, Leandro Soares de Lima, Giuseppe Italiano, Luca Sciarria, Marie-France Sagot, Blerina Sinaimeri

IWOCA 2020 - 31st International Workshop on Combinatorial Algorithms . 12126 : 17-29

DOI: 10.1007/978-3-030-48966-3_2

2020

Acte de congrès

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GECO Génomique Computationnelle et Evolutive

Equipe Bioinformatique, Phylogénie et Génomique Évolutive

Equipe Baobab

Equipe Sexe et Evolution

Publications

A comprehensive evaluation of binning methods to recover human gut microbial species from a non-redundant reference gene catalog

DILS: Demographic inferences with linked selection by using ABC

Complete genome of Bradyrhizobium sp. strain BDV5419, representative of Australian genospecies L

Complete Genome Sequence of Bradyrhizobium sp. Strain BDV5040, Representative of Widespread Genospecies B in Australia

The Molecular Determinants of Thermoadaptation: Methanococcales as a Case Study

Seaview Version 5: A Multiplatform Software for Multiple Sequence Alignment, Molecular Phylogenetic Analyses, and Tree Reconciliation

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

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

Evolutionary relationships between Archaea and eukaryotes

Probabilistic programming: a powerful new approach to statistical phylogenetics

Detecting sex-linked genes using genotyped individuals sampled in natural populations

Evolutionary plasticity of mating-type determination mechanisms in Paramecium aurelia sibling species

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

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

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

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

Exploring protein space: From hydrolase to ligase by substitution

Efficient hybrid de novo assembly of human genomes with WENGAN

Niche specialization and spread of Staphylococcus capitis involved in neonatal sepsis

Bedrock radioactivity influences the rate and spectrum of mutation

Accumulation of amyloid precursor protein C-terminal fragments triggers mitochondrial structure, function, and mitophagy defects in Alzheimer's disease models and human brains

Influenza virus infection induces widespread alterations of host cell splicing

How consistent is RAD‐seq divergence with DNA‐barcode based clustering in insects?

Controlling technical variation amongst 6693 patient microarrays of the randomized MINDACT trial

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

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

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

Three-Dimensional Imaging of the Vertebral Lymphatic Vasculature and Drainage using iDISCO⁺ and Light Sheet Fluorescence Microscopy

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

A Family of Tree-Based Generators for Bubbles in Directed Graphs

Publications

A comprehensive evaluation of binning methods to recover human gut microbial species from a non-redundant reference gene catalog

DILS: Demographic inferences with linked selection by using ABC

Complete genome of Bradyrhizobium sp. strain BDV5419, representative of Australian genospecies L

Complete Genome Sequence of Bradyrhizobium sp. Strain BDV5040, Representative of Widespread Genospecies B in Australia

The Molecular Determinants of Thermoadaptation: Methanococcales as a Case Study

Seaview Version 5: A Multiplatform Software for Multiple Sequence Alignment, Molecular Phylogenetic Analyses, and Tree Reconciliation

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

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

Evolutionary relationships between Archaea and eukaryotes

Probabilistic programming: a powerful new approach to statistical phylogenetics

Detecting sex-linked genes using genotyped individuals sampled in natural populations

Evolutionary plasticity of mating-type determination mechanisms in Paramecium aurelia sibling species

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

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

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

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

Exploring protein space: From hydrolase to ligase by substitution

Efficient hybrid de novo assembly of human genomes with WENGAN

Niche specialization and spread of Staphylococcus capitis involved in neonatal sepsis

Bedrock radioactivity influences the rate and spectrum of mutation

Accumulation of amyloid precursor protein C-terminal fragments triggers mitochondrial structure, function, and mitophagy defects in Alzheimer's disease models and human brains

Influenza virus infection induces widespread alterations of host cell splicing

How consistent is RAD‐seq divergence with DNA‐barcode based clustering in insects?

Controlling technical variation amongst 6693 patient microarrays of the randomized MINDACT trial

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

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

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

Three-Dimensional Imaging of the Vertebral Lymphatic Vasculature and Drainage using iDISCO+ and Light Sheet Fluorescence Microscopy

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

A Family of Tree-Based Generators for Bubbles in Directed Graphs

Three-Dimensional Imaging of the Vertebral Lymphatic Vasculature and Drainage using iDISCO⁺ and Light Sheet Fluorescence Microscopy