GECO Evolutionary and Computational Genomics

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

see the publication

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

see the publication

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

see the publication

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

see the publication

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

see the publication

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

see the publication

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

see the publication

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

The relationship among gene expression, the evolution of gene dosage, and the rate of protein evolution

Jean-François Gout, Daniel Kahn, Laurent Duret

PLoS Genetics . 6 ( 5 ) : e1000944

DOI: 10.1371/journal.pgen.1000944

2010

Journal article

see the publication

Genetic Admixture History of Eastern Indonesia as Revealed by Y-Chromosome and Mitochondrial DNA Analysis

S. Mona, K. Grunz, S. Brauer, Brigitte Pakendorf, L. Castri, H. Sudoyo...

Molecular Biology and Evolution . 26 ( 8 ) : 1865-1877

DOI: 10.1093/molbev/msp097

2009

Journal article

see the publication

Genetic diversity and the emergence of ethnic groups in Central Asia

Evelyne Heyer, Patricia Balaresque, Mark Jobling, Lluis Quintana-Murci, Raphaelle Chaix, Laure Segurel...

BMC Genetics . 10 ( 1 ) : 49

DOI: 10.1186/1471-2156-10-49

2009

Journal article

see the publication

Mutation Patterns in the Human Genome:More Variable Than Expected

L. Duret

PLoS Biology . 7(2) e1000028 : 803-806

2009

Journal article

see the publication

Monoallelic expression and tissue specificity are associated with high crossover rates

A. Necşulea, M. Sémon, L. Duret, L.D. Hurst

Trends in Genetics . 25(12) : 519-522

2009

Journal article

see the publication

GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates

N. Galtier, L. Duret, S. Glémin, Vincent Ranwez

Trends in Genetics . 25(1) : 1-5

2009

Journal article

see the publication

Systemic analysis of the symbiotic function of Buchnera aphidicola, the primary endosymbiont of the pea aphid Acyrthosiphon pisum.

Lilia Brinza, José Viñuelas, Ludovic Cottret, Federica Calevro, Yvan Rahbé, Gérard Febvay...

Comptes Rendus Biologies . 332 ( 11 ) : 1034-49

DOI: 10.1016/j.crvi.2009.09.007

2009

Journal article

see the publication

The Acyrthosiphon pisum Cyc database (AcypiCyc) created using a novel BioCyc Annotation Database System (CycADS): a useful tool to explore and study the pea aphid metabolism

Stefano Colella, A. Vellozo, Ludovic Cottret, Gérard Febvay, Federica Calevro, Yvan Rahbé...

5th Meeting of the International Aphid Genomics Consortium "Pea Aphid Genome Annotation Workshop 2, Barcelona, Espagne, juin 2009 .

2009

Conference paper

see the publication

Footprints of Inversions at Present and Past Pseudoautosomal Boundaries in Human Sex Chromosomes

Claire Lemaitre, Marília D.V. Braga, Christian Gautier, M.-F. Sagot, Eric Tannier, Gabriel Marais

Genome Biology and Evolution . 1(1) : 56-66

2009

Journal article

see the publication

Identification of expressed transposable element insertions in the sequenced genome of Drosophila melanogaster

M. Deloger, F.M.G. Cavalli, E. Lerat, C. Biémont, M.-F. Sagot, Cristina Vieira

Gene . 439 : 55-62

2009

Journal article

see the publication

Analysis of fine-scale mammalian evolutionary breakpoints provides new insight into their relation to genome organisation

Claire Lemaitre, Lamia Zaghloul, Marie-France Sagot, Christian Gautier, Alain Arneodo, Eric Tannier...

BMC Genomics . 10 ( 1 ) : 335

DOI: 10.1186/1471-2164-10-335

2009

Journal article

see the publication

A Mixture Model and a Hidden Markov Model to Simultaneously Detect Recombination Breakpoints and Reconstruct Phylogenies

Bastien Boussau, Laurent Guéguen, Manolo Gouy

Evolutionary Bioinformatics . 5 : 67-79

DOI: 10.4137/EBO.S2242

2009

Journal article

see the publication

Phylogeny of prokaryotes: does it exist and why should we care?

Simonetta Gribaldo, Céline Brochier-Armanet

Research in Microbiology . 160 : 513-21

2009

Journal article

see the publication

Happy together: genomic insights into the unique Nanoarchaeum/Ignicoccus association.

Patrick Forterre, Simonetta Gribaldo, Céline Brochier-Armanet

Journal of Biology . 8 ( 1 ) : 7

DOI: 10.1186/jbiol110

2009

Journal article

see the publication

Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations

Ravi D. Barabote, Gary Xie, David H. Leu, Philippe Normand, Anamaria Necsulea, Vincent Daubin...

Genome Research . ( 19 ) : 1033-1043

DOI: 10.1101/gr.084848.108

2009

Journal article

see the publication

Genomic environment influences the dynamics of the tirant LTR retrotransposon in Drosophila

M. Fablet, E. Lerat, R. Rebollo, B. Horard, N. Burlet, S. Martinez...

FASEB Journal . 23 : 54-62

2009

Journal article

see the publication

Infra- and Transspecific Clues to Understanding the Dynamics of Transposable Elements

Cristina Vieira, M. Fablet, E. Lerat

genome dyn stab . -- : 115-123

2009

Journal article

see the publication

Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs

E. Lerat

Heredity . -- : 1-14

2009

Journal article

see the publication

The relationship between DNA replication and human genome organization.

Anamaria Necsulea, Claire Guillet, Jean-Charles Cadoret, Marie-Noëlle Prioleau, L. Duret

Molecular Biology and Evolution . 26 ( 4 ) : 729-741

DOI: 10.1093/molbev/msn303

2009

Journal article

see the publication

Multiple alignment of biological networks: A flexible approach

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

Combinatorial Pattern Matching (CPM) . 5577 : 263-273

DOI: 10.1007/978-3-642-02441-2_23

2009

Conference paper

see the publication

Assessing the exceptionality of coloured motifs in networks

Sophie S. Schbath, Vincent Lacroix, Marie-France Sagot

EURASIP Journal on Bioinformatics and Systems Biology . 2009 : 9 pages on line

DOI: 10.1155/2009/616234

2009

Journal article

see the publication

Fast optimization of statistical potentials for structurally constrained phylogenetic models

Cécile Bonnard, Claudia L. Kleinman, Nicolas Rodrigue, Nicolas Lartillot

BMC Evolutionary Biology . 9 ( 1 ) : 227

DOI: 10.1186/1471-2148-9-227

2009

Journal article

see the publication

GECO Evolutionary and Computational Genomics

Bioinformatics, Phylogeny and Evolutionary Genomics Group

Baobab Group

Publications

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

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.

The relationship among gene expression, the evolution of gene dosage, and the rate of protein evolution

Genetic Admixture History of Eastern Indonesia as Revealed by Y-Chromosome and Mitochondrial DNA Analysis

Genetic diversity and the emergence of ethnic groups in Central Asia

Mutation Patterns in the Human Genome:More Variable Than Expected

Monoallelic expression and tissue specificity are associated with high crossover rates

GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates

Systemic analysis of the symbiotic function of Buchnera aphidicola, the primary endosymbiont of the pea aphid Acyrthosiphon pisum.

The Acyrthosiphon pisum Cyc database (AcypiCyc) created using a novel BioCyc Annotation Database System (CycADS): a useful tool to explore and study the pea aphid metabolism

Footprints of Inversions at Present and Past Pseudoautosomal Boundaries in Human Sex Chromosomes

Identification of expressed transposable element insertions in the sequenced genome of Drosophila melanogaster

Analysis of fine-scale mammalian evolutionary breakpoints provides new insight into their relation to genome organisation

A Mixture Model and a Hidden Markov Model to Simultaneously Detect Recombination Breakpoints and Reconstruct Phylogenies

Phylogeny of prokaryotes: does it exist and why should we care?

Happy together: genomic insights into the unique Nanoarchaeum/Ignicoccus association.

Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations

Genomic environment influences the dynamics of the tirant LTR retrotransposon in Drosophila

Infra- and Transspecific Clues to Understanding the Dynamics of Transposable Elements

Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs

The relationship between DNA replication and human genome organization.

Multiple alignment of biological networks: A flexible approach

Assessing the exceptionality of coloured motifs in networks

Fast optimization of statistical potentials for structurally constrained phylogenetic models