GECO Génomique Computationnelle et Evolutive

Two Host Clades, Two Bacterial Arsenals: Evolution through Gene Losses in Facultative Endosymbionts.

Pierre-Antoine Rollat-Farnier, Diego Santos-Garcia, Qiong Rao, Marie-France Sagot, Francisco J Silva, Hélène Henri...

Genome Biology and Evolution . 7 ( 3 ) : 839-855

DOI: 10.1093/gbe/evv030

2015

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MeDuSa: A multi-draft based scaffolder.

Emanuele Bosi, Beatrice Donati, Marco Galardini, Sara Brunetti, Marie-France Sagot, Pietro Lió...

Bioinformatics . : pii: btv171 [Epub ahead of print]

DOI: 10.1093/bioinformatics/btv171

2015

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A polynomial delay algorithm for the enumeration of bubbles with length constraints in directed graphs

Gustavo Sacomoto, Vincent Lacroix, Marie‑france Sagot

Algorithms for Molecular Biology . : 10

DOI: 10.1186/s13015-015-0046-4

2015

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Mitochondrial respiration and genomic analysis provide insight into the influence of the symbiotic bacterium on host trypanosomatid oxygen consumption.

Allan C. Azevedo-Martins, A. C. L. Machado, Cecilia Coimbra Klein, L. Ciapina, Luiz Gonzaga, Ana Tereza Ribeiro Vasconcelos...

Parasitology . 142 ( 2 ) : 352-362

DOI: 10.1017/S0031182014001139

2015

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Polynomial Delay Algorithm for Listing Minimal Edge Dominating Sets in Graphs

Mamadou Moustapha Kanté, Vincent Limouzy, Arnaud Mary, Lhouari Nourine, Takeaki Uno

Algorithms and Data Structures (WADS) . 9214 : 446-457

2015

Acte de congrès

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Assessment of polycarbonate filter in a molecular analytical system for the microbiological quality monitoring of recycled waters onboard ISS

Anne-Laure Bechy-Loizeau, Jean-Pierre Flandrois, Hafid Abaibou

Life Sciences in Space Research . 6 : 29-35

DOI: 10.1016/j.lssr.2015.06.002

2015

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Nontuberculous Mycobacteria: An Underestimated Cause of Bioprosthetic Valve Infective Endocarditis

C. Bouchiat, J. Saison, S. Boisset, Jean-Pierre Flandrois, B. Issartel, O. Dauwalder...

Open Forum Infectious Diseases . 2 ( 2 )

DOI: 10.1093/ofid/ofv047

2015

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Adaptation in toxic environments: arsenic Genomic Islands in the bacterial genus $Thiomonas$

Kelle Freel, Martin Krueger, Julien Farasin, Céline Brochier-Armanet, Valérie Barbe, Jérémy Andres...

PLoS ONE . 10 ( 9 ) : 0139011

DOI: 10.1371/journal.pone.0139011

2015

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GC-Content evolution in bacterial genomes: The biased gene conversion hypothesis expands

Florent Lassalle, Séverine Périan, Thomas Bataillon, Xavier Nesme, L. Duret, Vincent Daubin

PLoS Genetics . 11 ( 2 ) : 1-20

DOI: 10.1371/journal.pgen.1004941

2015

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Quantification of GC-biased gene conversion in the human genome

Sylvain Glemin, Peter F. Arndt, Messer W. Philip, Petrov M. Dmitri, Nicolas Galtier, L. Duret

Genome Research . 25 ( 8 ) : 1215 - 1228

DOI: 10.1101/gr.185488.114

2015

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Optimization of multiplexed RADseq libraries using low-cost adaptors

Hélène Henri, Marie Cariou, Gabriel Terraz, Sonia Martinez, Adil El Filali, Marine Veyssière...

Genetica . 143 ( 2 ) : 139-143

DOI: 10.1007/s10709-015-9828-3

2015

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Incremental complexity of a bi-objective hypergraph transversal problem

Ricardo Andrade, Etienne E. Birmelé, Arnaud Mary, Thomas Picchetti, Marie-France Sagot

Fundamentals of Computation Theory (FCT2015) . 9210 : 202-213

DOI: 10.1007/978-3-319-22177-9_16

2015

Acte de congrès

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EUCALYPT: efficient tree reconciliation enumerator

Beatrice Donati, Christian Baudet, Blerina Sinaimeri, Pierluigi Crescenzi, Marie-France Sagot

Algorithms for Molecular Biology . 10 ( 1 ) : 11

DOI: 10.1186/s13015-014-0031-3

2015

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Mirinho: An efficient and general plant and animal pre-miRNA predictor for genomic and deep sequencing data

Susan Higashi, Cyril Fournier, Christian Gautier, Christine Gaspin, Marie-France Sagot

BMC Bioinformatics . 16 ( 1 ) : 179

DOI: 10.1186/s12859-015-0594-0

2015

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Cophylogeny Reconstruction via an Approximate Bayesian Computation

Christian Baudet, Béatrice Donati, Blerina Sinaimeri, Pierluigi Crescenzi, Christian Gautier, Catherine Matias...

Systematic Biology . 64 ( 3 ) : 416-431

DOI: 10.1093/sysbio/syu129

2015

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An average study of hypergraphs and their minimal transversals

Julien David, Loïck Lhote, Arnaud Mary, François Rioult

Theoretical Computer Science . 596 : 124-141

DOI: 10.1016/j.tcs.2015.06.052

2015

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Analyse de 32 souches de Legionella pneumophila de sévérités variables afin d'identifier les déterminants de la pathogénicité

Amandine Campan-Fournier, Christine Oger, Christophe Ginevra, Vincent Navratil, Anne-Gaëlle Ranc, G. Perrière...

JOBIM 2015 - 16èmes Journées Ouvertes en BIologie, Informatique et Mathématiques .

2015

Poster

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Evolutionary history of phosphatidylinositol- 3-kinases: ancestral origin in eukaryotes and complex duplication patterns

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

BMC Evolutionary Biology . 15 : 226

DOI: 10.1186/s12862-015-0498-7

2015

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Molecular and functional evolution of the fungal diterpene synthase genes

Marc Fischer, Camille Rustenhloz, Véronique Leh-Louis, Guy Perrière

BMC Microbiology . 15 ( 1 ) : 221

DOI: 10.1186/s12866-015-0564-8

2015

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leBIBIQBPP: a set of databases and a webtool for automatic phylogenetic analysis of prokaryotic sequences

Jean-Pierre Flandrois, G. Perrière, Manolo Gouy

BMC Bioinformatics . 16 ( 1 ) : 251

DOI: 10.1186/s12859-015-0692-z

2015

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A Toolbox for Nonlinear Regression in R: The Package nistools

F. Baty, C. Ritz, Sandrine Charles, M. Brutsche, Jean-Pierre Flandrois, Marie Laure Delignette-Muller

Journal of Statistical Software . 66 : 1-21

2015

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Evolution of Helicobacter: Acquisition by Gastric Species of Two Histidine-Rich Proteins Essential for Colonization

Daniel Vinella, Frédéric Fischer, Egor Vorontsov, Julien Gallaud, Christian Malosse, Valérie Michel...

PLoS Pathogens . 11 ( 12 ) : e1005312

DOI: 10.1371/journal.ppat.1005312

2015

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Exploration of Frankia genomes to identify genetic determinants involved in sporogenesis: Towards promising tracks to understand in plant sporuration

Lorine Bethencourt, N. Taib, J. Briolay, P. Fournier, M.P. Fernandez, Céline Brochier-Armanet...

18th International Meeting on Frankia and Actinorhizal plants .

2015

Poster

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Evolution and Design Governing Signal Precision and Amplification in a Bacterial Chemosensory Pathway

Mathilde Guzzo, Rym Agrebi, Leon Espinosa, Gregory Baronian, Virginie Molle, Emilia M. F. Mauriello...

PLoS Genetics . 11 ( 8 ) : e1005460

DOI: 10.1371/journal.pgen.1005460

2015

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Taxonomy and Phylogeny of Prokaryotes

Pierre Caumette, Céline Brochier-Armanet, Philippe Normand

Environmental Microbiology: Fundamentals and Applications . 978-94-017-9118-2 : 145-190

DOI: 10.1007/978-94-017-9118-2_6

2015

Chapitre d'ouvrage

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Draft genome sequence of Mesotoga strain PhosAC3, a mesophilic member of the bacterial order Thermotogales, isolated from a digestor treating phosphogypsum in Tunisia

Wajdi Ben Hania, Khaled Fadhlaoui, Céline Brochier-Armanet, Cecile Persillon, Anne Postec, Moktar Hamdi...

Standards in Genomic Sciences . 10

DOI: 10.1186/1944-3277-10-12

2015

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Genome-wide survey of two-component signal transduction systems in the plant growth-promoting bacterium Azospirillum

Stéphanie Borland, Anne Oudart, Claire Prigent-Combaret, Céline Brochier-Armanet, Florence Wisniewski-Dyé

BMC Genomics . 16 : 833

DOI: 10.1186/s12864-015-1962-x

2015

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Extending the conserved phylogenetic core of \textitarchaea disentangles the evolution of the third domain of life

C. Petitjean, P. Deschamps, P. Lopez-Garcia, D. Moreira, Céline Brochier-Armanet

Molecular Biology and Evolution . 32 : 1242-54

2015

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Constitutive arsenite oxidase expression detected in arsenic-hypertolerant Pseudomonas xanthomarina S11

S. Koechler, F. Arsene-Ploetze, Céline Brochier-Armanet, F. Goulhen-Chollet, A. Heinrich-Salmeron, B. Jost...

Research in Microbiology . 166 : 205-14

2015

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Degeneration of the Nonrecombining Regions in the Mating-Type Chromosomes of the Anther-Smut Fungi

Eric Fontanillas, Michael E Hood, Hélène Badouin, Elsa Petit, Valérie Barbe, Jerome Gouzy...

Molecular Biology and Evolution . 32 ( 4 ) : 928-943

DOI: 10.1093/molbev/msu396

2015

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GECO Génomique Computationnelle et Evolutive

Equipe Bioinformatique, Phylogénie et Génomique Évolutive

Equipe Baobab

Publications

Two Host Clades, Two Bacterial Arsenals: Evolution through Gene Losses in Facultative Endosymbionts.

MeDuSa: A multi-draft based scaffolder.

A polynomial delay algorithm for the enumeration of bubbles with length constraints in directed graphs

Mitochondrial respiration and genomic analysis provide insight into the influence of the symbiotic bacterium on host trypanosomatid oxygen consumption.

Polynomial Delay Algorithm for Listing Minimal Edge Dominating Sets in Graphs

Assessment of polycarbonate filter in a molecular analytical system for the microbiological quality monitoring of recycled waters onboard ISS

Nontuberculous Mycobacteria: An Underestimated Cause of Bioprosthetic Valve Infective Endocarditis

Adaptation in toxic environments: arsenic Genomic Islands in the bacterial genus $Thiomonas$

GC-Content evolution in bacterial genomes: The biased gene conversion hypothesis expands

Quantification of GC-biased gene conversion in the human genome

Optimization of multiplexed RADseq libraries using low-cost adaptors

Incremental complexity of a bi-objective hypergraph transversal problem

EUCALYPT: efficient tree reconciliation enumerator

Mirinho: An efficient and general plant and animal pre-miRNA predictor for genomic and deep sequencing data

Cophylogeny Reconstruction via an Approximate Bayesian Computation

An average study of hypergraphs and their minimal transversals

Analyse de 32 souches de Legionella pneumophila de sévérités variables afin d'identifier les déterminants de la pathogénicité

Evolutionary history of phosphatidylinositol- 3-kinases: ancestral origin in eukaryotes and complex duplication patterns

Molecular and functional evolution of the fungal diterpene synthase genes

leBIBIQBPP: a set of databases and a webtool for automatic phylogenetic analysis of prokaryotic sequences

A Toolbox for Nonlinear Regression in R: The Package nistools

Evolution of Helicobacter: Acquisition by Gastric Species of Two Histidine-Rich Proteins Essential for Colonization

Exploration of Frankia genomes to identify genetic determinants involved in sporogenesis: Towards promising tracks to understand in plant sporuration

Evolution and Design Governing Signal Precision and Amplification in a Bacterial Chemosensory Pathway

Taxonomy and Phylogeny of Prokaryotes

Draft genome sequence of Mesotoga strain PhosAC3, a mesophilic member of the bacterial order Thermotogales, isolated from a digestor treating phosphogypsum in Tunisia

Genome-wide survey of two-component signal transduction systems in the plant growth-promoting bacterium Azospirillum

Extending the conserved phylogenetic core of \textitarchaea disentangles the evolution of the third domain of life

Constitutive arsenite oxidase expression detected in arsenic-hypertolerant Pseudomonas xanthomarina S11

Degeneration of the Nonrecombining Regions in the Mating-Type Chromosomes of the Anther-Smut Fungi