GECO Génomique Computationnelle et Evolutive

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 . : 1-28

DOI: 10.1371/journal.pgen.1007758

2018

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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

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Reconstruction of body mass evolution in the Cetartiodactyla and mammals using phylogenomic data.

Emeric Figuet, Marion Ballenghien, Nicolas Lartillot, Nicolas Galtier

Peer Community in Evolutionary Biology .

DOI: 10.1101/139147

2017

Autre 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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Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals

Roberto Feuda, Martin Dohrmann, Walker Pett, Herve Philippe, Omar Rota-Stabelli, Nicolas Lartillot...

Current Biology - CB . 27 ( 24 ) : 3864-3870.e4

DOI: 10.1016/j.cub.2017.11.008

2017

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Evolutionary history of LTR-retrotransposons among 20 Drosophila species

N. Bargues, Emmanuelle Lerat

Mobile DNA . 8 : 7

DOI: 10.1186/s13100-017-0090-3

2017

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Transcriptional response to hepatitis C virus infection and interferon-alpha treatment in the human liver

T. Boldanova, A. Suslov, M.H. Heim, A. Necsulea

EMBO Molecular Medicine . 9 : 816-834

DOI: 10.15252/emmm.201607006

2017

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Evolutionary strata on young mating-type chromosomes despite the lack of sexual antagonism

Sara Branco, Hélène Badouin, Ricardo Rodríguez de la Vega, Jerome Gouzy, Fantin Carpentier, Gabriela Aguileta...

Proceedings of the National Academy of Sciences of the United States of America . 114 ( 27 ) : 7067-7072

DOI: 10.1073/pnas.1701658114

2017

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Widespread selective sweeps throughout the genome of model plant pathogenic fungi and identification of effector candidates

Helene Badouin, Pierre Gladieux, Jerome Gouzy, Sophie Siguenza, Gabriela Aguileta, Alodie Snirc...

Molecular Ecology . 26 ( 7 )

DOI: 10.1111/mec.13976

2017

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Continental-level population differentiation and environmental adaptation in the mushroom Suillus brevipes

Sara Branco, Ke Bi, Hui-Ling Liao, Pierre Gladieux, Helene Badouin, Christopher E Ellison...

Molecular Ecology . 26 ( 7 ) : 2063-2076

DOI: 10.1111/mec.13892

2017

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The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution

Hélène Badouin, Jerome Gouzy, Christopher Grassa, Florent Murat, S Evan Staton, Ludovic Cottret...

Nature . 546 ( 7656 ) : 148-152

DOI: 10.1038/nature22380

2017

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Environmental assessment of urban mobility: Combining life cycle assessment with land-use and transport interaction modelling—Application to Lyon (France)

Cyrille François, Natacha Gondran, Jean-Pierre Nicolas, David Parsons

Ecological Indicators . 72 : Pages 597–604

DOI: 10.1016/j.ecolind.2016.07.014

2017

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Identification of misexpressed genetic elements in hybrids between Drosophila-related species

Hélène Lopez-Maestre, Elias A. G. Carnelossi, Vincent Lacroix, Nelly Burlet, Bruno Mugat, Séverine Chambeyron...

Scientific Reports . 7 : 40618

DOI: 10.1038/srep40618

2017

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Record of Nile seasonality in Nubian neonates.

Céline Martin, Bruno Maureille, Romain Amiot, Alexandra Touzeau, Aurélien Royer, François Fourel...

Isotopes in Environmental and Health Studies . 53 ( 3 ) : 223-242

DOI: 10.1080/10256016.2016.1229667

2017

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d18O-Derived incubation temperatures of oviraptorosaur eggs.

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

Palaeontology . : 1-15

DOI: 10.1111/pala.12311

2017

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Strain-specific estimation of epidemic success provides insights into the transmission dynamics of tuberculosis

Jean-Philippe Rasigade, Maxime Barbier, Oana Dumitrescu, Catherine Pichat, Gérard Carret, Anne-Sophie Ronnaux-Baron...

Scientific Reports . 7 : 45326

DOI: 10.1038/srep45326

2017

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IsoSel: Protein Isoform Selector for phylogenetic reconstructions

H. Philippon, A. Souvane, Céline Brochier-Armanet, G. Perriere

PLoS ONE . 12 : e0174250

DOI: 10.1371/journal.pone.0174250

2017

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On the rarity of dioecy in flowering plants

Jos Käfer, Gabriel Marais, Jr. Pannell

Molecular Ecology . 26 : 1225-1241

DOI: 10.1111/mec.14020

2017

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Token Jumping in minor-closed classes

Nicolas Bousquet, Arnaud Mary, Aline Parreau

International symposium on fundamentals of computer theory (FCT 2017) . 10472 : 136-149

DOI: 10.1007/978-3-662-55751-8_12

2017

Acte de congrès

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Algorithms for k-meet-semidistributive lattices

Laurent Beaudou, Arnaud Mary, Lhouari Nourine

Theoretical Computer Science . 658 : 391 - 398

DOI: 10.1016/j.tcs.2015.10.029

2017

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GECO Génomique Computationnelle et Evolutive

Equipe Bioinformatique, Phylogénie et Génomique Évolutive

Equipe Baobab

Equipe Sexe et Evolution

Publications

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

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

Reconstruction of body mass evolution in the Cetartiodactyla and mammals using phylogenomic data.

δ 18 O-derived incubation temperatures of oviraptorosaur eggs

Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals

Evolutionary history of LTR-retrotransposons among 20 Drosophila species

Transcriptional response to hepatitis C virus infection and interferon-alpha treatment in the human liver

Evolutionary strata on young mating-type chromosomes despite the lack of sexual antagonism

Widespread selective sweeps throughout the genome of model plant pathogenic fungi and identification of effector candidates

Continental-level population differentiation and environmental adaptation in the mushroom Suillus brevipes

The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution

Environmental assessment of urban mobility: Combining life cycle assessment with land-use and transport interaction modelling—Application to Lyon (France)

Identification of misexpressed genetic elements in hybrids between Drosophila-related species

Record of Nile seasonality in Nubian neonates.

d18O-Derived incubation temperatures of oviraptorosaur eggs.

Strain-specific estimation of epidemic success provides insights into the transmission dynamics of tuberculosis

IsoSel: Protein Isoform Selector for phylogenetic reconstructions

On the rarity of dioecy in flowering plants

Token Jumping in minor-closed classes

Algorithms for k-meet-semidistributive lattices