GECO Evolutionary and Computational Genomics

Species identification of staphylococci by amplification and sequencing of the tuf gene compared to the gap gene and by matrix-assisted laser desorption ionization time-of-flight mass spectrometry.

Marie Bergeron, Olivier Dauwalder, Manolo Gouy, Anne-Marie Freydiere, Michèle Bes, Hélène Meugnier...

European Journal of Clinical Microbiology and Infectious Diseases . 30 ( 3 ) : 343-54

DOI: 10.1007/s10096-010-1091-z

2011

Journal article

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Species-driven interpretation guidelines in case of a single-sampling strategy for blood culture

D. Leyssene, S. Gardes, P. Vilquin, Jp. Flandrois, Gérard Carret, B. Lamy

European Journal of Clinical Microbiology and Infectious Diseases . 30 : 1537-1541

DOI: 10.1007/s10096-011-1257-3

2011

Journal article

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Phylogeny and evolution of the Archaea: one hundred genomes later.

Celine Brochier-Armanet, Patrick Forterre, Simonetta Gribaldo

Current Opinion in Microbiology . : epub ahead of print

DOI: 10.1016/j.mib.2011.04.015

2011

Journal article

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Genome sequence of the stramenopile Blastocystis, a human anaerobic parasite.

France Denoeud, Michaël Roussel, Benjamin Noel, Ivan Wawrzyniak, Corinne da Silva, Marie Diogon...

Genome Biology . 12 ( 3 ) : R29

DOI: 10.1186/gb-2011-12-3-r29

2011

Journal article

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Cultivation of the first mesophilic representative ("mesotoga") within the order Thermotogales

Wajdi Ben Hania, Ramzi Ghodbane, Anne Postec, Celine Brochier-Armanet, Moktar Hamdi, Marie Laure Fardeau...

Systematic and Applied Microbiology . 34 : 581-585

DOI: 10.1016/j.syapm.2011.04.001

2011

Journal article

see the publication

The GTPase Function of YvcJ and Its Subcellular Relocalization Are Dependent on Growth Conditions in Bacillus subtilis

F. Pompeo, J. Luciano, Céline Brochier-Armanet, A. Galinier

Journal of Molecular Microbiology and Biotechnology . 20 : 156-67

2011

Journal article

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Survival of extremely and moderately halophilic isolates of Tunisian solar salterns after UV-B or oxidative stress

H. Trigui, Salma Masmoudi, Céline Brochier-Armanet, S. Maalej, S. Dukan

Canadian Journal of Microbiology . 57(11) : 923-33

2011

Journal article

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The phylogenomic analysis of the anaphase promoting complex and its targets points to complex and modern-like control of the cell cycle in the last common ancestor of eukaryotes

L. Eme, A. Trilles, D. Moreira, Céline Brochier-Armanet

BMC Evolutionary Biology . 11 : 923-33

DOI: 10.1186/1471-2148-11-265

2011

Journal article

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The Assembly Mode of the Pseudopilus: a hallmark to distinguish a novel secretion system subtype

E. Durand, S. Alphonse, Céline Brochier-Armanet, G. Ball, Badreddine Douzi, A. Filloux...

Journal of Biological Chemistry . 286 ( 27 ) : 24407-24416

DOI: 10.1074/jbc.M111.234278

2011

Journal article

see the publication

Taxonomie et phylogénie des procaryotes. Chapitre 6

Pierre Caumette, Céline Brochier-Armanet, Philippe Normand

Ecologie Microbienne : Microbiologie des milieux naturels et anthropisés . 2-35311-022-3 9782353110223 : 1004 p.

2011

Book chapter

see the publication

Ultra-fast sequence clustering from similarity networks with SiLiX

V. Miele, Simon Penel, L. Duret

BMC Bioinformatics . 12(116) : 1-9

DOI: 10.1186/1471-2105-12-116

2011

Journal article

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Ftx is a non-coding RNA which affects Xist expression and chromatin structure within the X-inactivation center region

C. Chureau, S. Chantalat, A. Romito, A. Galvani, Laurent Duret, P. Avner...

Human Molecular Genetics . 20 : 705-718

DOI: 10.1093/hmg/ddq516

2011

Journal article

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Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations

T. Rouxel, J. Grandaubert, Jk. Hane, Claire Hoede, Angela P. van de Wouw, A. Couloux...

Nature Communications . 2 : 202

DOI: 10.1038/ncomms1189

2011

Journal article

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Wolbachia detection: an assessment of standard PCR protocols.

P. M. Simões, G. Mialdea, D. Reiss, Marie-France Sagot, S. Charlat

Molecular Ecology Resources . 11 ( 3 ) : 567-72

DOI: 10.1111/j.1755-0998.2010.02955.x

2011

Journal article

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Finding Long and Multiple Repeats with Edit Distance

Maria Federico, Pierre Peterlongo, Nadia Pisanti, Marie-France Sagot

The Prague Stringology Conference 2011 .

2011

Conference paper

see the publication

ArthropodaCyc: a BioCyc database powered by CycADS to study and compare the metabolism of arthropods

Patrice Baa-Puyoulet, Augusto F Vellozo, Jaime Huerta-Cepas, Gérard Febvay, T. Gabaldon, Marie-France Sagot...

5th Annual Arthropod Genomics Symposium "Arthropod Genomics 2011: Exploring Diversity, Relating Similarity" .

2011

Conference paper

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Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny

Amélie Véron, Claire Lemaitre, Christian Gautier, Vincent Lacroix, Marie-France Sagot

BMC Genomics . 12 ( 1 ) : 303

DOI: 10.1186/1471-2164-12-303

2011

Journal article

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Initial metabolic reconstruction of Klebsiella pneumoniae Kp13, a multidrug resistant pathogen involved in nosocomial outbreaks in Brazil

P. Ivan, Cecilia C. Klein, Ludovic Cottret, Ana T Vasconcelos, Ac Gales, Marie-France Sagot...

X-meeting .

2011

Conference paper

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Tpms: a Tree Pattern-matching Utility for Querying Gene Trees Collections

Thomas Bigot, Vincent Daubin, G. Perrière

Journées Ouvertes Biologie Informatique Mathématiques (JOBIM) . : 111-112

2011

Conference paper

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Apport des nouvelles générations de séquençage pour accéder à la diversité des communautés microbiennes du sol : nécessité d’un ‘pipeline’ bio-informatique pour les biologistes

Sébastien Terrat, Richard Christen, Samuel S. Dequiedt, Pierre-Alain Maron, Christophe Mougel, Guy Perriere...

1ères Rencontres bioinformaticiens et statisticiens de l’INRA . : 1 p.

2011

Conference paper

see the publication

Adaptation to Environmental Temperature Is a Major Determinant of Molecular Evolutionary Rates in Archaea

M. Groussin, Manolo Gouy

Molecular Biology and Evolution . 28 : 2661-2674

DOI: 10.1093/molbev/msr098

2011

Journal article

see the publication

Pendant trois milliards d'années les micro-organismes sont les seuls habitants de la terre

J.C. Bertrand, Céline Brochier-Armanet, Manolo Gouy, F. Westall

incollection . 2-35311-022-3 9782353110223 : 94-U259

2011

Book chapter

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NGS without a reference genome, comparison and visualisation of non assembled data

Vincent Lacroix

Statistical Methods for Post-Genomic Data (SMPGD) .

2011

Conference paper

see the publication

Complete-fosmid and fosmid-end sequences reveal frequent horizontal gene transfers in marine uncultured planktonic archaea.

Céline Brochier-Armanet, Philippe Deschamps, Purificación López-García, Yvan Zivanovic, Francisco Rodríguez-Valera, David Moreira

The International Society of Microbiologial Ecology Journal . 5 ( 8 ) : 1291-302

DOI: 10.1038/ismej.2011.16

2011

Journal article

see the publication

A New Highly Conserved Antibiotic Sensing/Resistance Pathway in Firmicutes Involves an ABC Transporter Interplaying with a Signal Transduction System

S. Coumes-Florens, Céline Brochier-Armanet, A. Guiseppi, F. Denizot, M. Foglino

PLoS ONE . 6 : e15951

DOI: 10.1371/journal.pone.0015951

2011

Journal article

see the publication

Emergence and Modular Evolution of a Novel Motility Machinery in Bacteria

J. Luciano, R. Agrebi, A.V. Le Gall, M. Wartel, F. Fiegna, A. Ducret...

PLoS Genetics . 7 ( 9 ) : 1409-1418

DOI: 10.1371/journal.pgen.1002268

2011

Journal article

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Characterization of Halorubrum sfaxense sp. nov. a New Halophilic Archaeon Isolated from the Solar Saltern of Sfax in Tunisia

H. Trigui, Salma Masmoudi, Céline Brochier-Armanet, S. Maalej, S. Dukan

Int J Microbiol . -- : 347-58

2011

Journal article

see the publication

Unsuspected Diversity of Arsenite-Oxidizing Bacteria Revealed by a Widespread Distribution of the aoxB Gene in Prokaryotes

A. Heinrich-Salmeron, A. Cordi, Céline Brochier-Armanet, D. Halter, C. Pagnout, E. Abbaszadeh-Fard...

Applied and Environmental Microbiology . 77 : 4685-92

DOI: 10.1128/AEM.02884-10

2011

Journal article

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Archaea and the tree of life

Simonetta Gribaldo, Patrick Forterre, Celine Brochier-Armanet

Research in Microbiology . 162 ( 1 ) : 1-4

DOI: 10.1016/j.resmic.2010.11.007

2011

Journal article

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On the last common ancestor and early evolution of eukaryotes: reconstructing the history of mitochondrial ribosomes.

Elie Desmond-Le Quéméner, Celine Brochier-Armanet, Patrick Forterre, Simonetta Gribaldo

Research in Microbiology . 162 ( 1 ) : 53-70

DOI: 10.1016/j.resmic.2010.10.004

2011

Journal article

see the publication

GECO Evolutionary and Computational Genomics

Bioinformatics, Phylogeny and Evolutionary Genomics Group

Baobab Group

Publications

Species identification of staphylococci by amplification and sequencing of the tuf gene compared to the gap gene and by matrix-assisted laser desorption ionization time-of-flight mass spectrometry.

Species-driven interpretation guidelines in case of a single-sampling strategy for blood culture

Phylogeny and evolution of the Archaea: one hundred genomes later.

Genome sequence of the stramenopile Blastocystis, a human anaerobic parasite.

Cultivation of the first mesophilic representative ("mesotoga") within the order Thermotogales

The GTPase Function of YvcJ and Its Subcellular Relocalization Are Dependent on Growth Conditions in Bacillus subtilis

Survival of extremely and moderately halophilic isolates of Tunisian solar salterns after UV-B or oxidative stress

The phylogenomic analysis of the anaphase promoting complex and its targets points to complex and modern-like control of the cell cycle in the last common ancestor of eukaryotes

The Assembly Mode of the Pseudopilus: a hallmark to distinguish a novel secretion system subtype

Taxonomie et phylogénie des procaryotes. Chapitre 6

Ultra-fast sequence clustering from similarity networks with SiLiX

Ftx is a non-coding RNA which affects Xist expression and chromatin structure within the X-inactivation center region

Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations

Wolbachia detection: an assessment of standard PCR protocols.

Finding Long and Multiple Repeats with Edit Distance

ArthropodaCyc: a BioCyc database powered by CycADS to study and compare the metabolism of arthropods

Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny

Initial metabolic reconstruction of Klebsiella pneumoniae Kp13, a multidrug resistant pathogen involved in nosocomial outbreaks in Brazil

Tpms: a Tree Pattern-matching Utility for Querying Gene Trees Collections

Apport des nouvelles générations de séquençage pour accéder à la diversité des communautés microbiennes du sol : nécessité d’un ‘pipeline’ bio-informatique pour les biologistes

Adaptation to Environmental Temperature Is a Major Determinant of Molecular Evolutionary Rates in Archaea

Pendant trois milliards d'années les micro-organismes sont les seuls habitants de la terre

NGS without a reference genome, comparison and visualisation of non assembled data

Complete-fosmid and fosmid-end sequences reveal frequent horizontal gene transfers in marine uncultured planktonic archaea.

A New Highly Conserved Antibiotic Sensing/Resistance Pathway in Firmicutes Involves an ABC Transporter Interplaying with a Signal Transduction System

Emergence and Modular Evolution of a Novel Motility Machinery in Bacteria

Characterization of Halorubrum sfaxense sp. nov. a New Halophilic Archaeon Isolated from the Solar Saltern of Sfax in Tunisia

Unsuspected Diversity of Arsenite-Oxidizing Bacteria Revealed by a Widespread Distribution of the aoxB Gene in Prokaryotes

Archaea and the tree of life

On the last common ancestor and early evolution of eukaryotes: reconstructing the history of mitochondrial ribosomes.