GECO Génomique Computationnelle et Evolutive

Efficient enumeration of solutions produced by closure operations

Arnaud Mary, Yann Strozecki

Discrete Mathematics and Theoretical Computer Science . : 1-30

DOI: 10.23638/DMTCS-21-3-22

2019

Article dans une revue

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The phytopathogenic nature of Dickeya aquatica 174/2 and the dynamic early evolution of Dickeya pathogenicity

Alexandre Duprey, Najwa Taïb, Simon Leonard, Tiffany Garin, Jean-Pierre Flandrois, William Nasser...

Environmental Microbiology . 21 ( 8 ) : 2809-2835

DOI: 10.1111/1462-2920.14627

2019

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New insights into minor splicing-a transcriptomic analysis of cells derived from TALS patients

Audric Cologne, Clara Benoit-Pilven, Alicia Besson, Audrey Putoux, Amandine Campan-Fournier, Michael B Bober...

RNA . : 1-21

DOI: 10.1261/rna.071423.119

2019

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Advances in Analyzing Virus-Induced Alterations of Host Cell Splicing

Usama Ashraf, Clara Benoit-Pilven, Vincent Lacroix, Vincent Navratil, Nadia Naffakh

Trends in Microbiology . 27 ( 3 ) : 268-281

DOI: 10.1016/j.tim.2018.11.004

2019

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Francisella tularensis: FupA mutation contributes tofluoroquinolone resistance by increasing vesicle secretion and biofilm formation

Claire Siebert, Helena Lindgren, Sabrina Ferré, Corinne Villers, Sandrine Boisset, Julien Pérard...

Emerging microbes & infections . 8 ( 1 ) : 808-822

DOI: 10.1080/22221751.2019.1615848

2019

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Comparative genomics and proteogenomics highlight key molecular players involved in Frankia sporulation

Lorine Bethencourt, Hasna Boubakri, Najwa Taïb, Philippe Normand, J. Armengaud, Pascale P Fournier...

Research in Microbiology . 170 ( 4-5 ) : 202-213

DOI: 10.1016/j.resmic.2019.04.002

2019

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Evolutionary placement of Methanonatronarchaeia

Monique Aouad, Guillaume Borrel, Céline Brochier-Armanet, Simonetta Gribaldo

Nature Microbiology .

DOI: 10.1038/s41564-019-0359-z

2019

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GeneSpy, a user-friendly and flexible genomic context visualizer

Pierre Simon Garcia, Frédéric Jauffrit, Christophe Grangeasse, Céline Brochier-Armanet

Bioinformatics . 35 ( 2 ) : 329-331

DOI: 10.1093/bioinformatics/bty459

2019

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Article 5. L’émergence des eucaryotes : une mosaïque d’ADN

Dominique D. Joly, Celine Brochier-Armanet

101 secrets de l’ADN. CNRS Éditions, Paris, pp 39-41 . : 39-41

2019

Chapitre d'ouvrage

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Neo-formation of chromosomes in bacteria.

Olivier Poirion, Bénédicte Lafay

DOI: 10.1101/264945

2019

Pré-publication

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Repeat in genomes: how and why you should consider them in genome analyses

Emmanuelle Lerat

Encyclopedia of Bioinformatics and Computational Biology . 2 : 210-220

DOI: 10.1016/B978-0-12-809633-8.20227-6

2019

Chapitre d'ouvrage

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Detecting adaptive convergent amino acid evolution

Carine Rey, Vincent Lanore, Philippe Veber, Laurent Guéguen, Nicolas Lartillot, Marie Sémon...

Philosophical Transactions of the Royal Society B: Biological Sciences . 374 ( 1777 ) : 1-11

DOI: 10.1098/rstb.2018.0234

2019

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Transcriptome profiling of mouse samples using nanopore sequencing of cDNA and RNA molecules

Camille Sessegolo, Corinne Cruaud, Corinne da Silva, Audric Cologne, Marion Dubarry, Thomas Derrien...

Scientific Reports . 9 ( 1 ) : 14908

DOI: 10.1038/s41598-019-51470-9

2019

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Metabolic Games

Taneli Pusa, Martin Wannagat, Marie-France Sagot

Frontiers in Applied Mathematics and Statistics . 5 : 1-13

DOI: 10.3389/fams.2019.00018

2019

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Close inbreeding and low genetic diversity in Inner Asian human populations despite geographical exogamy

Nina Marchi, Philippe Mennecier, Myriam Georges, Sophie Lafosse, Tatyana Hegay, Choduraa Dorzhu...

Scientific Reports . 8 : 9397

DOI: 10.1038/s41598-018-27047-3

2018

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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 Antony Henning, Arnaud Mary, Aline Parreau

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

DOI: 10.1137/16M1097833

2018

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A novel subfamily of bacterial AAT-fold basic amino acid decarboxylases and functional characterization of its first representative: Pseudomonas aeruginosa LdcA

Diego Carriel, Pierre Simon Garcia, Florence Castelli, Patricia Lamourette, François Fenaille, Céline Brochier-Armanet...

Genome Biology and Evolution . 10 ( 11 ) : 3058-3075

DOI: 10.1093/gbe/evy228

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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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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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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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 Hestbjerg Hansen

Frontiers in Microbiology . 9 : 1-23

DOI: 10.3389/fmicb.2018.02141

2018

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

Mariana G. Ferrarini, Scheila Gabriele 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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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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PASTA repeats of the protein kinase StkP interconnect cell constriction and separation of Streptococcus pneumoniae

L. Zucchini, C. Mercy, Ps. Garcia, C. Cluzel, V. Gueguen-Chaignon, F. Galisson...

Nature Microbiology . 3 ( 2 ) : 197--209

2018

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Loss-of-Function Mutations in UNC45A Cause a Syndrome Associating Cholestasis, Diarrhea, Impaired Hearing, and Bone Fragility

Clothilde Esteve, Ludmila Francescatto, Perciliz Tan, Aurélie Bourchany, Cécile de Leusse, Evelyne Marinier...

American Journal of Human Genetics . 102 ( 3 ) : 364 - 374

DOI: 10.1016/j.ajhg.2018.01.009

2018

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Obligate sugar oxidation in Mesotoga spp., phylum Thermotogae , in the presence of either elemental sulfur or hydrogenotrophic sulfate-reducers as electron acceptor

Khaled Fadhlaoui, Wagdi Ben Hania, Fabrice Armougom, Manon Joseph, Marie-Laure Fardeau, Gaël Erauso...

Environmental Microbiology . 20 ( 1 ) : 281-292

DOI: 10.1111/1462-2920.13995

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

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

Laurent Jacob, Terence Paul Speed

Genome Biology . 19 ( 1 )

DOI: 10.1186/s13059-018-1481-6

2018

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GECO Génomique Computationnelle et Evolutive

Equipe Bioinformatique, Phylogénie et Génomique Évolutive

Equipe Baobab

Publications

Efficient enumeration of solutions produced by closure operations

The phytopathogenic nature of Dickeya aquatica 174/2 and the dynamic early evolution of Dickeya pathogenicity

New insights into minor splicing-a transcriptomic analysis of cells derived from TALS patients

Advances in Analyzing Virus-Induced Alterations of Host Cell Splicing

Francisella tularensis: FupA mutation contributes tofluoroquinolone resistance by increasing vesicle secretion and biofilm formation

Comparative genomics and proteogenomics highlight key molecular players involved in Frankia sporulation

Evolutionary placement of Methanonatronarchaeia

GeneSpy, a user-friendly and flexible genomic context visualizer

Article 5. L’émergence des eucaryotes : une mosaïque d’ADN

Neo-formation of chromosomes in bacteria.

Repeat in genomes: how and why you should consider them in genome analyses

Detecting adaptive convergent amino acid evolution

Transcriptome profiling of mouse samples using nanopore sequencing of cDNA and RNA molecules

Metabolic Games

Close inbreeding and low genetic diversity in Inner Asian human populations despite geographical exogamy

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

A novel subfamily of bacterial AAT-fold basic amino acid decarboxylases and functional characterization of its first representative: Pseudomonas aeruginosa LdcA

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

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

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

Exploring and Visualising Spaces of Tree Reconciliations

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

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

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

PASTA repeats of the protein kinase StkP interconnect cell constriction and separation of Streptococcus pneumoniae

Loss-of-Function Mutations in UNC45A Cause a Syndrome Associating Cholestasis, Diarrhea, Impaired Hearing, and Bone Fragility

Obligate sugar oxidation in Mesotoga spp., phylum Thermotogae , in the presence of either elemental sulfur or hydrogenotrophic sulfate-reducers as electron acceptor

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

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

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