GECO Evolutionary and Computational Genomics

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

M. Bergeron, O. Dauwalder, M. Gouy, A.-M. Freydiere, M. Bes, H. Meugnier...

European Journal of Clinical Microbiology and Infectious Diseases . : 343-354

2010

Journal article

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Biosynthesis of wyosine derivatives in tRNA: an ancient and highly diverse pathway in Archaea.

Valérie de Crécy-Lagard, Céline Brochier-Armanet, Jaunius Urbonavicius, Bernard Fernandez, Gabriela Phillips, Benjamin Lyons...

Molecular Biology and Evolution . 27 ( 9 ) : 2062-77

DOI: 10.1093/molbev/msq096

2010

Journal article

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The Pseudomonas aeruginosa patatin-like protein PlpD is the archetype of a novel Type V secretion system

R. Salacha, F. Kovacic, Céline Brochier-Armanet, S. Wilhelm, J. Tommassen, A. Filloux...

Environmental Microbiology . 12 ( 6 ) : 1498-512

DOI: 10.1111/j.1462-2920.2010.02174.x

2010

Journal article

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Enumerating Chemical Organisations in Consistent Metabolic Networks: Complexity and Algorithms

Paulo Vieira Milreu, Vicente Acuña, Etienne E. Birmelé, Pierluigi Crescenzi, Alberto Marchetti-Spaccamela, Marie-France Sagot...

Algorithms in Bioinformatics . 6293 : 226-237

DOI: 10.1007/978-3-642-15294-8_19

2010

Conference paper

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

Augusto Vellozo, Patrice Baa-Puyoulet, Jaime Huerta-Cepas, Gérard Febvay, Federica Calevro, Yvan Rahbé...

4. Annual Arthropod Genomics Symposium on “Arthropod Genomics: New Approaches and Outcomes” . : 45 p.

2010

Poster

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Statistical Potentials for Improved Structurally Constrained Evolutionary Models

Claudia L Kleinman, Nicolas Rodrigue, Nicolas Lartillot, Hervé Philippe

Molecular Biology and Evolution . 27 ( 7 ) : 1546 - 1560

DOI: 10.1093/molbev/msq047

2010

Journal article

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Genes devoid of full-length transposable element insertions are involved in development and in the regulation of transcription in human and closely related species.

Hussein Mortada, Cristina Vieira, Emmanuelle Lerat

Journal of Molecular Evolution . 71 ( 3 ) : 180-91

DOI: 10.1007/s00239-010-9376-5

2010

Journal article

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Detecting positive selection within genomes: the problem of biased gene conversion

A. Ratnakumar, Sylvain Mousset, S. Glémin, J. Berglund, N. Galtier, L. Duret...

Philosophical Transactions of the Royal Society B: Biological Sciences . 365 ( 1552 ) : 2571-2580

DOI: 10.1098/rstb.2010.0007

2010

Journal article

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Paramecium tetraurelia: The Renaissance of an Early Unicellular Model

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

Emerging Model Organisms . 2010 : 1-55

2010

Journal article

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Identifying SNPs without a reference genome by comparing raw reads

Pierre Peterlongo, Nicolas Schnel, Nadia Pisanti, Marie-France Sagot, Vincent Lacroix

String Processing and Information Retrieval . 6393 : 147-158

DOI: 10.1007/978-3-642-16321-0_14

2010

Conference paper

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Cassis: detection of genomic rearrangement breakpoints.

Christian Baudet, Claire Lemaitre, Zanoni Dias, Christian Gautier, Eric Tannier, Marie-France Sagot

Bioinformatics . 26 ( 15 ) : 1897-8

DOI: 10.1093/bioinformatics/btq301

2010

Journal article

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Genome Sequence of the Pea Aphid Acyrthosiphon pisum

Iagc The International Aphid Genomics Consortium, Federica Calevro, Hubert Charles, Stefano Colella, Gérard Febvay, Caroline Anselme...

PLoS Biology . 8 ( 2 ) : e1000313

DOI: 10.1371/journal.pbio.1000313

2010

Journal article

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Repetition-free longest common subsequence

S.S Adi, M. Braga, C.G. Fernandes, C.E. Ferreira, F.V. Martinez, M.-F. Sagot...

Discrete Applied Mathematics . 158 ( 12 ) : 1315-1324

DOI: 10.1016/j.dam.2009.04.023

2010

Journal article

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Combination of measures distinguishes pre-miRNAs from other stem-loops in the genome of the newly sequenced Anopheles darlingi

Nuno Mendes, Ana Freitas, Ana Vasconcelos, Marie-France Sagot

BMC Genomics . 11 ( 1 ) : 529

DOI: 10.1186/1471-2164-11-529

2010

Journal article

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SeaView Version 4: a Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

Manolo Gouy, Stéphane Guindon, Olivier Gascuel

Molecular Biology and Evolution . 27 : 221-224

DOI: 10.1093/molbev/msp259

2010

Journal article

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The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse?

Simonetta Gribaldo, Anthony M. Poole, Vincent Daubin, Patrick Forterre, C. Brochier-Armanet

Nature Reviews Microbiology . 8 ( 10 ) : 743-753

DOI: 10.1038/nrmicro2426

2010

Journal article

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Distinct gene set in two different lineages of ammoniaoxidizing archaea supports the phylum Thaumarchaeota

A. Spang, R. Hatzenpichler, Céline Brochier-Armanet, T. Rattei, P. Tischler, E. Spieck...

Trends Microbiol . 18(8) : 331-40

2010

Journal article

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Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea

C.B. Walker, J.R. La Torre, M.G. Klotz, H. Urakawa, N. Pinel, D.J. Arp...

Proceedings of the National Academy of Sciences of the United States of America . 107 ( 19 ) : 8818-23

DOI: 10.1073/pnas.0913533107

2010

Journal article

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Structure, function, and evolution of the Thiomonas spp. genome.

Florence Arsène-Ploetze, Sandrine Koechler, Marie Marchal, Jean-Yves Coppée, Michael Chandler, Violaine Bonnefoy...

PLoS Genetics . 6 ( 2 ) : e1000859

DOI: 10.1371/journal.pgen.1000859

2010

Journal article

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A Phylogenetic Model for Investigating Correlated Evolution of Substitution Rates and Continuous Phenotypic Characters

Nicolas Lartillot, Raphaël Poujol

Molecular Biology and Evolution . 28 ( 1 ) : 729 - 744

DOI: 10.1093/molbev/msq244

2010

Journal article

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A Dirichlet Process Covarion Mixture Model and Its Assessments Using Posterior Predictive Discrepancy Tests

Yan Zhou, Henner Brinkmann, Nicolas Rodrigue, Nicolas Lartillot, Herve Philippe

Molecular Biology and Evolution . 27 ( 2 ) : 371-384

DOI: 10.1093/molbev/msp248

2010

Journal article

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Proposals for classification methods dedicated to biological data

Anne-Muriel Arigon Chifolleau, Guy Perrière, Manolo Gouy

International Journal of Biomedical Engineering and Technology (IJBET) . 3 ( 1/2 ) : 4-21

DOI: 10.1504/IJBET.2010.029649

2010

Journal article

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Specialization of a Drosophila capping protein essential for the protection of sperm telomeres.

Raphaëlle Dubruille, Guillermo A Orsi, Lætitia Delabaere, Elisabeth Cortier, Pierre Couble, Gabriel A.B. Marais...

Current Biology . 20 ( 23 ) : 2090-9

DOI: 10.1016/j.cub.2010.11.013

2010

Journal article

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Can Intra-Y Gene Conversion Oppose the Degeneration of the Human Y Chromosome? A Simulation Study

Gabriel Marais, P.R.A. Campos, I. Gordo

Genome Biology and Evolution . 2 : 347-357

2010

Journal article

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Structure and evolution of Apetala3 a sex-linked gene in Silene latifolia

R. Cegan, Gabriel Marais, H. Kubekova, N. Blavet, A. Widmer, B. Vyskot...

BMC Plant Biology . 10 : 1-10

2010

Journal article

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Chromosomal Redistribution of Male-Biased Genes in Mammalian Evolution with Two Bursts of Gene Gain on the X Chromosome

Y.E. Zhang, M.D. Vibranovski, P. Landback, Gabriel Marais, M. Long

PLoS Biology . 8 ( 10 ) : 1-13

DOI: 10.1371/journal.pbio.1000494

2010

Journal article

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Meiosis: A PRDM9 Guide to the Hotspots of Recombination

A. Hochwagen, Gabriel Marais

Current Biology . 20 ( 6 ) : R271-R274

DOI: 10.1016/j.cub.2010.01.048

2010

Journal article

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Specialization of a Drosophila Capping Protein Essential for the Protection of Sperm Telomeres

R. Dubruille, G.A. Orsi, L. Delabaere, E. Cortier, P. Couble, Gabriel Marais...

Current Biology . 20 : 1-10

DOI: 10.1016/j.cub.2010.11.013

2010

Journal article

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MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks.

Ludovic Cottret, David Wildridge, Florence Vinson, Michael P Barrett, Hubert Charles, Marie-France Sagot...

Nucleic Acids Research . 38 ( Web Server issue ) : W132-7

DOI: 10.1093/nar/gkq312

2010

Journal article

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Graph-based analysis of the metabolic exchanges between two co-resident intracellular symbionts, Baumannia cicadellinicola and Sulcia muelleri, with their insect host, Homalodisca coagulata.

Ludovic Cottret, Paulo Vieira Milreu, Vicente Acuña, Alberto Marchetti-Spaccamela, Leen Stougie, Hubert Charles...

PLoS Computational Biology . 6 ( 9 ) : epub ahead of print

DOI: 10.1371/journal.pcbi.1000904

2010

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 gene compared to the gene and by matrix-assisted laser desorption ionization time-of-flight mass spectrometry

Biosynthesis of wyosine derivatives in tRNA: an ancient and highly diverse pathway in Archaea.

The Pseudomonas aeruginosa patatin-like protein PlpD is the archetype of a novel Type V secretion system

Enumerating Chemical Organisations in Consistent Metabolic Networks: Complexity and Algorithms

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

Statistical Potentials for Improved Structurally Constrained Evolutionary Models

Genes devoid of full-length transposable element insertions are involved in development and in the regulation of transcription in human and closely related species.

Detecting positive selection within genomes: the problem of biased gene conversion

Paramecium tetraurelia: The Renaissance of an Early Unicellular Model

Identifying SNPs without a reference genome by comparing raw reads

Cassis: detection of genomic rearrangement breakpoints.

Genome Sequence of the Pea Aphid Acyrthosiphon pisum

Repetition-free longest common subsequence

Combination of measures distinguishes pre-miRNAs from other stem-loops in the genome of the newly sequenced Anopheles darlingi

SeaView Version 4: a Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse?

Distinct gene set in two different lineages of ammoniaoxidizing archaea supports the phylum Thaumarchaeota

Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea

Structure, function, and evolution of the Thiomonas spp. genome.

A Phylogenetic Model for Investigating Correlated Evolution of Substitution Rates and Continuous Phenotypic Characters

A Dirichlet Process Covarion Mixture Model and Its Assessments Using Posterior Predictive Discrepancy Tests

Proposals for classification methods dedicated to biological data

Specialization of a Drosophila capping protein essential for the protection of sperm telomeres.

Can Intra-Y Gene Conversion Oppose the Degeneration of the Human Y Chromosome? A Simulation Study

Structure and evolution of Apetala3 a sex-linked gene in Silene latifolia

Chromosomal Redistribution of Male-Biased Genes in Mammalian Evolution with Two Bursts of Gene Gain on the X Chromosome

Meiosis: A PRDM9 Guide to the Hotspots of Recombination

Specialization of a Drosophila Capping Protein Essential for the Protection of Sperm Telomeres

MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks.

Graph-based analysis of the metabolic exchanges between two co-resident intracellular symbionts, Baumannia cicadellinicola and Sulcia muelleri, with their insect host, Homalodisca coagulata.