GECO Génomique Computationnelle et Evolutive

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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A framework for modelling soil structure dynamics induced by biological activity

Katharina Meurer, Jennie Barron, Claire Chenu, Elsa Coucheney, Matthew Fielding, Paul Hallett...

Global Change Biology . 26 ( 10 ) : 5382-5403

DOI: 10.1111/gcb.15289

2020

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The complexity ratchet: Stronger than selection, stronger than evolvability, weaker than robustness

Vincent Liard, David Parsons, Jonathan Rouzaud-Cornabas, Guillaume Beslon

Artificial Life . 26 ( 1 ) : 38-57

DOI: 10.1162/artl_a_00312

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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Phylogenomics and Genome Annotation

Anamaria Necsulea

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

2020

Chapitre d'ouvrage

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Understanding and monitoring the evolution of the Covid-19 epidemic from medical emergency calls: the example of the Paris area

Stéphane Gaubert, Marianne Akian, Xavier Allamigeon, Marin Boyet, Baptiste Colin, Théotime Grohens...

Comptes Rendus. Mathématique . 358 ( 7 ) : 843-875

DOI: 10.5802/crmath.99

2020

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PhyloBayes: Bayesian Phylogenetics Using Site-heterogeneous Models

Nicolas Lartillot

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

2020

Chapitre d'ouvrage

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The Bayesian Approach to Molecular Phylogeny

Nicolas Lartillot

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

2020

Chapitre d'ouvrage

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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

2020

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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...

ISME Journal .

DOI: 10.1038/s41396-020-0647-x

2020

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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

2020

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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

2020

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MOMO - multi-objective metabolic mixed integer optimization: application to yeast strain engineering

Ricardo Andrade, Mahdi Doostmohammadi, João Santos, Marie-France Sagot, Nuno Mira, Susana Vinga

BMC Bioinformatics . 21 ( 1 ) : 1-13

DOI: 10.1186/s12859-020-3377-1

2020

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GECO Génomique Computationnelle et Evolutive

Equipe Bioinformatique, Phylogénie et Génomique Évolutive

Equipe Baobab

Equipe Sexe et Evolution

Publications

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

A framework for modelling soil structure dynamics induced by biological activity

The complexity ratchet: Stronger than selection, stronger than evolvability, weaker than robustness

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

Phylogenomics and Genome Annotation

Understanding and monitoring the evolution of the Covid-19 epidemic from medical emergency calls: the example of the Paris area

PhyloBayes: Bayesian Phylogenetics Using Site-heterogeneous Models

The Bayesian Approach to Molecular Phylogeny

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

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

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

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

MOMO - multi-objective metabolic mixed integer optimization: application to yeast strain engineering

Publications

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

A framework for modelling soil structure dynamics induced by biological activity

The complexity ratchet: Stronger than selection, stronger than evolvability, weaker than robustness

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

Phylogenomics and Genome Annotation

Understanding and monitoring the evolution of the Covid-19 epidemic from medical emergency calls: the example of the Paris area

PhyloBayes: Bayesian Phylogenetics Using Site-heterogeneous Models

The Bayesian Approach to Molecular Phylogeny

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

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

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

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

MOMO - multi-objective metabolic mixed integer optimization: application to yeast strain engineering

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