GECO Evolutionary and Computational Genomics

A eukaryotic-like sulfiredoxin involved in oxidative stress responses and in the reduction of the sulfinic form of 2 Cys-peroxiredoxin in the cyanobacterium Anabaena PCC 7120

C. Boileau, L. Eme, Céline Brochier-Armanet, A. Janicki, C-C. Zhang, A. Latifi

New Phytologist . 191 : 1108-1118

DOI: 10.1111/j.1469-8137.2011.03774.x

2011

Journal article

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Specificity shifts in the rRNA and tRNA nucleotide targets of archaeal and bacterial m5U methyltransferases.

Sylvie Auxilien, Anette Rasmussen, Simon Rose, Céline Brochier-Armanet, Clotilde Husson, Dominique Fourmy...

RNA . 17 ( 1 ) : 45-53

DOI: 10.1261/rna.2323411

2011

Journal article

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Characteristics of a phylogenetically ambiguous, arsenic-oxidizing Thiomonas sp., Thiomonas arsenitoxydans strain 3As(T) sp. nov.

D. Slyemi, D. Moinier, Céline Brochier-Armanet, V. Bonnefoy, D. B. Johnson

Archives of Microbiology . 193 : 439-449

DOI: 10.1007/s00203-011-0684-y

2011

Journal article

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Phylogenetic and genetic variation among Fe(II)-oxidizing acidithiobacilli supports the view that these comprise multiple species with different ferrous iron oxidation pathways

A. Amouric, Céline Brochier-Armanet, D. B. Johnson, V. Bonnefoy, K. B. Hallberg

Microbiology . 155 : 111-122

DOI: 10.1099/mic.0.044537-0

2011

Journal article

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An oxygen reduction chain in the hyperthermophilic anaerobe Thermotoga maritima highlights horizontal gene transfer between Thermococcales and Thermotogales

C. Le Fourn, G. Brasseur, Céline Brochier-Armanet, L. Pieulle, A. Brioukhanov, B. Ollivier...

Environmental Microbiology . 13 : 2132-45

DOI: 10.1111/j.1462-2920.2011.02439.x

2011

Journal article

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Comparative analysis of transposable elements in the melanogaster subgroup sequenced genomes.

Emmanuelle Lerat, Nelly Burlet, Christian Biémont, Cristina Vieira

Gene . 473 ( 2 ) : 100-9

DOI: 10.1016/j.gene.2010.11.009

2011

Journal article

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Characterization of heterotrophic prokaryote subgroups in the Sfax coastal solar salterns by combining flow cytometry cell sorting and phylogenetic analysis

Hana Trigui, Salma Masmoudi, Céline Brochier-Armanet, Aude Barani, Gérald Grégori, Michel Denis...

Extremophiles . 15 : 347-358

DOI: 10.1007/s00792-011-0364-5

2011

Journal article

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Specificity shifts in the rRNA and tRNA nucleotide targets of archaeal and bacterial m5U methyltransferases.

Sylvie Auxilien, Anette Rasmussen, Simon Rose, Céline Brochier-Armanet, Clotilde Husson, Dominique Fourmy...

RNA . 17 ( 1 ) : 45-53

DOI: 10.1261/rna.2323411

2011

Journal article

see the publication

Using the “CycADS” annotation management system to develop a BioCyc metabolic network database for sequenced arthropods genomes: first steps towards “ArthropodsCyc”

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

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

2011

Poster

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Absence of a core metabolic network common to symbiotic bacteria

Cecilia Coimbra Klein, Ludovic Cottret, Hubert Charles, Christian Gautier, Ana Tereza Ribeiro de Vasconcelos, Vincent Lacroix...

6. Meeting GDRE-RA Comparative genomics . : 33 diapositives

2011

Conference paper

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CycADS: an annotation database system to ease the development and update of BioCyc databases.

Augusto F Vellozo, Amélie S Véron, Patrice Baa-Puyoulet, Jaime Huerta-Cepas, Ludovic Cottret, Gérard Febvay...

Database - The journal of Biological Databases and Curation . 2011 : bar008

DOI: 10.1093/database/bar008

2011

Journal article

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Bacterial syntenies: an exact approach with gene quorum.

Yves-Pol Deniélou, Marie-France Sagot, Frédéric Boyer, Alain Viari

BMC Bioinformatics . 12 : 193

DOI: 10.1186/1471-2105-12-193

2011

Journal article

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An efficient method to find potentially universal population genetic markers applied to metazoans

A. Chenuil, Thierry B. Hoareau, E. Egea, G. Penant, C. Rocher, D. Aurelle...

BMC Evolutionary Biology . 10 ( 276 ) : 1-17

DOI: 10.1186/1471-2148-10-276

2010

Journal article

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Genetic perspectives on forager-farmer interaction in the Luangwa Valley of Zambia

Cesare de Filippo, Patricia Heyn, Lawrence Barham, Mark Stoneking, Brigitte Pakendorf

American Journal of Physical Anthropology . 141 ( 3 ) : 382-394

DOI: 10.1002/ajpa.21155

2010

Journal article

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Conservation of Neutral Substitution Rate and Substitutional Asymmetries in Mammalian Genes

Carina Mugal, J. Wolf, H. von Grünberg, H. Ellegren

Genome Biology and Evolution . 2 : 19-28

DOI: 10.1093/gbe/evp056

2010

Journal article

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Molecular evolution of genes in avian genomes

Ki Woong Nam, Carina Mugal, Benoit Nabholz, Holger Schielzeth, Jochen B W Wolf, Niclas Backström...

Genome Biology . 11 ( 6 ) : 17 p.

DOI: 10.1186/gb-2010-11-6-r68

2010

Journal article

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Phylogénie moléculaire

Samuel Blanquart, Alexis Criscuolo, Christophe J Douady, Emmanuel Douzery, Nicolas Lartillot, Herve Philippe...

Biologie évolutive . 9782804101619

2010

Book chapter

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Towards a multi-scale and formalized representation of protein sequence-structure-function relationships : the nsLTP family as a case of study

Cécile Fleury, Marie Francoise M. F. Gautier, Pierre Larmande, Sabine Pérès, Frédéric F. de Lamotte, Franck Molina...

JOBIM2010 .

2010

Conference paper

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Towards a multi-scale and formalized representation of protein sequence-structure-function relationships : the nsLTP family as a case of study

Cécile Fleury, Marie Francoise M. F. Gautier, Pierre Larmande, Sabine Pérès, Frédéric F. de Lamotte, Franck Molina...

18. Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) .

2010

Conference paper

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Towards a multi-scale and formalized representation of protein sequence-structure-function relationships : the nsLTP family as a case of study

Cécile Fleury, Marie Francoise M. F. Gautier, Pierre Larmande, Sabine Pérès, Frédéric F. de Lamotte, Franck Molina...

Séminaire Génomique Végétale .

2010

Conference paper

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Géographie des interfaces. Une nouvelle vision du territoire

C. Lampin-Maillet, Sabine Pérès, J.P. Ferrier, P. Allard

978-2-7592-0857-9 : 168

2010

Book

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In the heartland of Eurasia: the multilocus genetic landscape of Central Asian populations

Evelyne Heyer, Begoña Martínez-Cruz, Renaud Vitalis, Laure Ségurel, Frédéric Austerlitz, Myriam Georges...

European Journal of Human Genetics .

DOI: 10.1038/ejhg.2010.153

2010

Journal article

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Mode de vie et diversité génétique dans les populations humaines d'Asie Centrale

Laure Ségurel

2010

Thesis

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Frequency of the AGT Pro11Leu polymorphism in humans: Does diet matter?

Laure Ségurel, Sophie Lafosse, Evelyne Heyer, Renaud Vitalis

Annals of Human Genetics . 74 ( 1 ) : 57-64

DOI: 10.1111/j.1469-1809.2009.00549.x

2010

Journal article

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Looking for signatures of sex-specific demography and local adaptation on the X chromosome.

Evelyne Heyer, Laure Segurel

Genome Biology . 11 ( 1 ) : 203

DOI: 10.1186/gb-2010-11-1-203

2010

Journal article

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Evolution Moléculaire

L. Duret, T. Bataillon, N. Bierne, Vincent Daubin, J. Dutheil, Christian Gautier...

Biologie évolutive . 978-2-8041-0161-9 : 114-173

2010

Book chapter

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Paramecium tetraurelia: The Renaissance of an Early Unicellular Model

J. Beisson, M. Bétermier, M.-H. Bré, J. Cohen, S. Duharcourt, L. Duret...

Emerging Model Organisms . 2010(1) : 1-55

2010

Journal article

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Gene expression in a paleopolyploid: a transcriptome resource for the ciliate Paramecium tetraurelia.

Olivier Arnaiz, Jean-François Goût, Mireille Bétermier, Khaled Bouhouche, Jean Cohen, L. Duret...

BMC Genomics . 11 ( 1 ) : 547

DOI: 10.1186/1471-2164-11-547

2010

Journal article

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Mod/Resc Parsimony Inference

Igor Nor, Danny Hermelin, Sylvain Charlat, Jan Engelstadter, Max Reuter, Olivier Duron...

Combinatorial Pattern Matching . 6129 : 202--213

DOI: 10.1007/978-3-642-13509-5_19

2010

Conference paper

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A tale of genome, annotations, metabolism and phylogenomics: the pea aphid genome resources

Fabrice Legeai, Stefano Colella, Jaime Huerta-Cepas, Jean-Pierre Gauthier, Augusto Vellozo, Patrice Baa-Puyoulet...

10. Cold Spring Harbor Laboratory / Wellcome Trust conference on Genome Informatics . : 1 p.

2010

Poster

see the publication

GECO Evolutionary and Computational Genomics

Bioinformatics, Phylogeny and Evolutionary Genomics Group

Baobab Group

Publications

A eukaryotic-like sulfiredoxin involved in oxidative stress responses and in the reduction of the sulfinic form of 2 Cys-peroxiredoxin in the cyanobacterium Anabaena PCC 7120

Specificity shifts in the rRNA and tRNA nucleotide targets of archaeal and bacterial m5U methyltransferases.

Characteristics of a phylogenetically ambiguous, arsenic-oxidizing Thiomonas sp., Thiomonas arsenitoxydans strain 3As(T) sp. nov.

Phylogenetic and genetic variation among Fe(II)-oxidizing acidithiobacilli supports the view that these comprise multiple species with different ferrous iron oxidation pathways

An oxygen reduction chain in the hyperthermophilic anaerobe Thermotoga maritima highlights horizontal gene transfer between Thermococcales and Thermotogales

Comparative analysis of transposable elements in the melanogaster subgroup sequenced genomes.

Characterization of heterotrophic prokaryote subgroups in the Sfax coastal solar salterns by combining flow cytometry cell sorting and phylogenetic analysis

Specificity shifts in the rRNA and tRNA nucleotide targets of archaeal and bacterial m5U methyltransferases.

Using the “CycADS” annotation management system to develop a BioCyc metabolic network database for sequenced arthropods genomes: first steps towards “ArthropodsCyc”

Absence of a core metabolic network common to symbiotic bacteria

CycADS: an annotation database system to ease the development and update of BioCyc databases.

Bacterial syntenies: an exact approach with gene quorum.

An efficient method to find potentially universal population genetic markers applied to metazoans

Genetic perspectives on forager-farmer interaction in the Luangwa Valley of Zambia

Conservation of Neutral Substitution Rate and Substitutional Asymmetries in Mammalian Genes

Molecular evolution of genes in avian genomes

Phylogénie moléculaire

Towards a multi-scale and formalized representation of protein sequence-structure-function relationships : the nsLTP family as a case of study

Towards a multi-scale and formalized representation of protein sequence-structure-function relationships : the nsLTP family as a case of study

Towards a multi-scale and formalized representation of protein sequence-structure-function relationships : the nsLTP family as a case of study

Géographie des interfaces. Une nouvelle vision du territoire

In the heartland of Eurasia: the multilocus genetic landscape of Central Asian populations

Mode de vie et diversité génétique dans les populations humaines d'Asie Centrale

Frequency of the AGT Pro11Leu polymorphism in humans: Does diet matter?

Looking for signatures of sex-specific demography and local adaptation on the X chromosome.

Evolution Moléculaire

Paramecium tetraurelia: The Renaissance of an Early Unicellular Model

Gene expression in a paleopolyploid: a transcriptome resource for the ciliate Paramecium tetraurelia.

Mod/Resc Parsimony Inference

A tale of genome, annotations, metabolism and phylogenomics: the pea aphid genome resources