GECO Génomique Computationnelle et Evolutive

The sunflower genome provides insights into Asterid evolution and relationships between paleoploidization and the genetic architecture of a major breeding trait

Hélène Badouin

Second Joint Congress on Evolutionary Biology .

2018

Acte de congrès

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The Rosa genome provides new insights into the domestication of modern roses

Olivier Raymond, Jerome Gouzy, Jérémy Just, Hélène Badouin, Marion Verdenaud, Arnaud Lemainque...

Nature Genetics . 50 ( 6 ) : 772-777

DOI: 10.1038/s41588-018-0110-3

2018

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Conditional Approximate Bayesian Computation: A New Approach for Across-Site Dependency in High-Dimensional Mutation–Selection Models

Simon Laurin-Lemay, Nicolas Rodrigue, Nicolas Lartillot, Herve Philippe

Molecular Biology and Evolution . 35 ( 11 ) : 2819-2834

DOI: 10.1093/molbev/msy173

2018

Article dans une revue

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Complementarity of assembly-first and mapping-first approaches for alternative splicing annotation and differential analysis from RNAseq data

Clara Benoit-Pilven, Camille Marchet, Emilie Chautard, Leandro Lima, Marie-Pierre Lambert, Gustavo Sacomoto...

Scientific Reports . 8 ( 1 )

DOI: 10.1038/s41598-018-21770-7

2018

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Highly Reduced Genome of the New Species Mycobacterium uberis, the Causative Agent of Nodular Thelitis and Tuberculoid Scrotitis in Livestock and a Close Relative of the Leprosy Bacilli

Andrej Benjak, Charlotte Avanzi, Yvonne Benito, Franck Breysse, Christophe Chartier, Maria-Laura Boschiroli...

MSphere . 3 ( 5 ) : e00405-18

DOI: 10.1128/mSphere.00405-18

2018

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Changing patterns of human migrations shaped the global population structure of Mycobacterium tuberculosis in France

Maxime Barbier, Oana Dumitrescu, Catherine Pichat, Gérard Carret, Anne-Sophie Ronnaux-Baron, Ghislaine Blasquez...

Scientific Reports . 8 ( 1 ) : 5855

DOI: 10.1038/s41598-018-24034-6

2018

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Tsunami sedimentary deposits of Crete records climate during the ‘Minoan Warming Period’ (≈3350 yr BP)

Christophe Lécuyer, François Atrops, Romain Amiot, Delphine Angst, Valérie Daux, Jean-Pierre Flandrois...

The Holocene .

DOI: 10.1177/0959683617752840

2018

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Population specific dynamics and selection patterns of transposable element insertions in European natural populations

Emmanuelle Lerat, Clément Goubert, Sara Guirao-Rico, Miriam Merenciano, Anne-Béatrice Dufour, Cristina Vieira...

Molecular Ecology . : 1-17

DOI: 10.1111/mec.14963

2018

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Extreme halophilic archaea derive from two distinct methanogen Class II lineages

Monique Aouad, Najwa Taïb, Anne Oudart, Michel Lecocq, Manolo Gouy, Céline Brochier-Armanet

Molecular Phylogenetics and Evolution . 127 : 46-54

DOI: 10.1016/j.ympev.2018.04.011

2018

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Genomic study of a novel magnetotactic Alphaproteobacteria uncovers the multiple ancestry of magnetotaxis

Caroline Monteil, Guy Perrière, Nicolas Menguy, Nicolas Ginet, Béatrice Alonso, Nicolas Waisbord...

Environmental Microbiology .

DOI: 10.1111/1462-2920.14364

2018

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Progress and Prospects in Gender Visibility at SMBE Annual Meetings

Jos Käfer, Andrea Betancourt, Avelyne Villain, Marie Fernandez, Clémentine Vignal, Gabriel Marais...

Genome Biology and Evolution . 10 ( 3 ) : 901-908

DOI: 10.1093/gbe/evy056

2018

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Reconfiguration of graphs with connectivity constraints

Nicolas Bousquet, Arnaud Mary

WAOA 2018 - International Workshop on Approximation and Online Algorithms . 11312 : 295-309

DOI: 10.1007/978-3-030-04693-4_18

2018

Acte de congrès

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Bounding the Order of a Graph Using Its Diameter and Metric Dimension: A Study Through Tree Decompositions and VC Dimension

Laurent Beaudou, Peter Dankelmann, Florent Foucaud, Michael Henning, Arnaud Mary, Aline Parreau

SIAM Journal on Discrete Mathematics . 32 ( 2 ) : 902 - 918

DOI: 10.1137/16M1097833

2018

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Exploring and Visualising Spaces of Tree Reconciliations

Katharina Huber, Vincent Moulton, Marie-France Sagot, Blerina Sinaimeri

Systematic Biology . : 1-36

DOI: 10.1093/sysbio/syy075

2018

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Pierce's Disease of Grapevines: A Review of Control Strategies and an Outline of an Epidemiological Model

Ifigeneia Kyrkou, Taneli Pusa, Lea Ellegaard-Jensen, Marie-France Sagot, Lars Hansen

Frontiers in Microbiology . 9 : 1-23

DOI: 10.3389/fmicb.2018.02141

2018

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Fast-SG: an alignment-free algorithm for hybrid assembly

Alex Genova, Gonzalo Ruz, Marie-France Sagot, Alejandro Maass

GigaScience . 7 ( 5 ) : 1 - 15

DOI: 10.1093/gigascience/giy048

2018

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Hydrogen peroxide production and myo-inositol metabolism as important traits for virulence of Mycoplasma hyopneumoniae

Mariana Ferrarini, Scheila Mucha, Delphine Parrot, Guillaume Meiffren, José Fernando Ruggiero Bachega, Gilles Comte...

Molecular Microbiology . : 1-45

DOI: 10.1111/mmi.13957

2018

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Geometric medians in reconciliation spaces

Katharina Huber, Vincent Moulton, Marie-France Sagot, Blerina Sinaimeri

Information Processing Letters . 136 : 96 - 101

DOI: 10.1016/j.ipl.2018.04.001

2018

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Life History Traits Impact the Nuclear Rate of Substitution but Not the Mitochondrial Rate in Isopods

Nathanaëlle Saclier, Clémentine François, Lara Konecny-Dupré, Nicolas Lartillot, Laurent Guéguen, L. Duret...

Molecular Biology and Evolution . 35 ( 12 ) : 2900-2912

DOI: 10.1093/molbev/msy184

2018

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Codon Usage Bias in Animals: Disentangling the Effects of Natural Selection, Effective Population Size, and GC-Biased Gene Conversion

Nicolas Galtier, Camille Roux, Marjolaine Rousselle, Jonathan Romiguier, Emeric Figuet, Sylvain Glemin...

Molecular Biology and Evolution . 35 ( 5 ) : 1092 - 1103

DOI: 10.1093/molbev/msy015

2018

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PRDM9 Methyltransferase Activity Is Essential for Meiotic DNA Double-Strand Break Formation at Its Binding Sites

Boubou Diagouraga, Julie Clément, L. Duret, Jan Kadlec, Bernard de Massy, Frédéric Baudat

Molecular Cell . 69 ( 5 ) : 853 - 865.e6

DOI: 10.1016/j.molcel.2018.01.033

2018

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Unbiased Estimate of Synonymous and Nonsynonymous Substitution Rates with Nonstationary Base Composition

Laurent Guéguen, Laurent Duret

Molecular Biology and Evolution . 35 ( 3 ) : 734-742

DOI: 10.1093/molbev/msx308

2018

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Multiple convergent supergene evolution events in mating-type chromosomes

Sara Branco, Fantin Carpentier, Ricardo Rodriguez de la Vega, Hélène Badouin, Alodie Snirc, Stéphanie Le Prieur...

Nature Communications . 9 ( 1 ) : 2000

DOI: 10.1038/s41467-018-04380-9

2018

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The healthy ageing gene expression signature for Alzheimer’s disease diagnosis: a random sampling perspective

Laurent Jacob, Terence Speed

Genome Biology . 19 ( 1 )

DOI: 10.1186/s13059-018-1481-6

2018

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PEPA test: fast and powerful differential analysis from relative quantitative proteomics data using shared peptides

Laurent Jacob, Florence Combes, Thomas Burger

Biostatistics .

DOI: 10.1093/biostatistics/kxy021

2018

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A fast and agnostic method for bacterial genome-wide association studies: bridging the gap between k-mers and genetic events

Magali Jaillard, Leandro Lima, Maud Tournoud, Pierre Mahé, Alex van Belkum, Vincent Lacroix...

PLoS Genetics . 14 ( 11 ) : 1-28

DOI: 10.1371/journal.pgen.1007758

2018

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The CO dehydrogenase accessory protein CooT is a novel nickel-binding protein.

J. Timm, C. Brochier-Armanet, J. Pérard, B. Zambelli, S. Ollagnier de Choudens, S. Ciurli...

Metallomics . 9 ( 5 ) : 575-583

DOI: 10.1039/c7mt00063d

2017

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The growing tree of Archaea: new perspectives on their diversity, evolution and ecology

Panagiotis Adam, Guillaume Borrel, Céline Brochier-Armanet, Simonetta Gribaldo

ISME Journal . 11 ( 11 ) : 2407-2425

DOI: 10.1038/ismej.2017.122

2017

Article dans une revue

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Annotation and differential analysis of alternative splicing using de novo assembly of RNAseq data

Clara Benoit-Pilven, Camille Marchet, Emilie Chautard, Leandro Lima, Marie-Pierre Lambert, Gustavo Sacomoto...

DOI: 10.1101/074807

2017

Pré-publication

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δ 18 O-derived incubation temperatures of oviraptorosaur eggs

Romain Amiot, Xu Wang, Shuo Wang, Christophe Lécuyer, Jean-Michel Mazin, Jinyou Mo...

Palaeontology . 60 ( 5 ) : 633-647

DOI: 10.1111/pala.12311

2017

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GECO Génomique Computationnelle et Evolutive

Equipe Bioinformatique, Phylogénie et Génomique Évolutive

Equipe Baobab

Equipe Sexe et Evolution

Publications

The sunflower genome provides insights into Asterid evolution and relationships between paleoploidization and the genetic architecture of a major breeding trait

The Rosa genome provides new insights into the domestication of modern roses

Conditional Approximate Bayesian Computation: A New Approach for Across-Site Dependency in High-Dimensional Mutation–Selection Models

Complementarity of assembly-first and mapping-first approaches for alternative splicing annotation and differential analysis from RNAseq data

Highly Reduced Genome of the New Species Mycobacterium uberis, the Causative Agent of Nodular Thelitis and Tuberculoid Scrotitis in Livestock and a Close Relative of the Leprosy Bacilli

Changing patterns of human migrations shaped the global population structure of Mycobacterium tuberculosis in France

Tsunami sedimentary deposits of Crete records climate during the ‘Minoan Warming Period’ (≈3350 yr BP)

Population specific dynamics and selection patterns of transposable element insertions in European natural populations

Extreme halophilic archaea derive from two distinct methanogen Class II lineages

Genomic study of a novel magnetotactic Alphaproteobacteria uncovers the multiple ancestry of magnetotaxis

Progress and Prospects in Gender Visibility at SMBE Annual Meetings

Reconfiguration of graphs with connectivity constraints

Bounding the Order of a Graph Using Its Diameter and Metric Dimension: A Study Through Tree Decompositions and VC Dimension

Exploring and Visualising Spaces of Tree Reconciliations

Pierce's Disease of Grapevines: A Review of Control Strategies and an Outline of an Epidemiological Model

Fast-SG: an alignment-free algorithm for hybrid assembly

Hydrogen peroxide production and myo-inositol metabolism as important traits for virulence of Mycoplasma hyopneumoniae

Geometric medians in reconciliation spaces

Life History Traits Impact the Nuclear Rate of Substitution but Not the Mitochondrial Rate in Isopods

Codon Usage Bias in Animals: Disentangling the Effects of Natural Selection, Effective Population Size, and GC-Biased Gene Conversion

PRDM9 Methyltransferase Activity Is Essential for Meiotic DNA Double-Strand Break Formation at Its Binding Sites

Unbiased Estimate of Synonymous and Nonsynonymous Substitution Rates with Nonstationary Base Composition

Multiple convergent supergene evolution events in mating-type chromosomes

The healthy ageing gene expression signature for Alzheimer’s disease diagnosis: a random sampling perspective

PEPA test: fast and powerful differential analysis from relative quantitative proteomics data using shared peptides

A fast and agnostic method for bacterial genome-wide association studies: bridging the gap between k-mers and genetic events

The CO dehydrogenase accessory protein CooT is a novel nickel-binding protein.

The growing tree of Archaea: new perspectives on their diversity, evolution and ecology

Annotation and differential analysis of alternative splicing using de novo assembly of RNAseq data

δ 18 O-derived incubation temperatures of oviraptorosaur eggs