GECO Evolutionary and Computational Genomics

Molecular diversity of rhizobia nodulating the invasive legume Cytisus scoparius in Australia.

Bénédicte Lafay, Jeremy J. Burdon

Journal of Applied Microbiology . 100 ( 6 ) : 1228-38

DOI: 10.1111/j.1365-2672.2006.02902.x

2006

Journal article

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Bradyrhizobia isolated from root nodules of Parasponia (Ulmaceae) do not constitute a separate coherent lineage.

Bénédicte Lafay, Erika Bullier, Jeremy J. Burdon

International Journal of Systematic and Evolutionary Microbiology . 56 ( Pt 5 ) : 1013-8

DOI: 10.1099/ijs.0.63897-0

2006

Journal article

see the publication

Multipolar Consensus for Phylogenetic Trees

Cécile Bonnard, Vincent Berry, Nicolas Lartillot

Systematic Biology . 55 ( 5 ) : 837-843

DOI: 10.1080/10635150600969880

2006

Journal article

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A maximum likelihood framework for protein design

Claudia Kleinman, Nicolas Rodrigue, Cécile Bonnard, Hervé Philippe, Nicolas Lartillot

BMC Bioinformatics . 7 : 326-336

DOI: 10.1186/1471-2105-7-326

2006

Journal article

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Computing Bayes Factors using Thermodynamilmc Integration

Nicolas Lartillot, Hervé Philippe

Systematic Biology . 55 ( 2 ) : 195-207

DOI: 10.1080/10635150500433722

2006

Journal article

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Quantitative prediction for two-dimensional bacterial genomic displays

Jean-François Mercier, Bénédicte Lafay, Gary W. Slater

American Physical Society Meeting .

2006

Conference paper

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No Evidence for Tissue-Specific Adaptation of Synonymous Codon Usage in Humans

M. Sémon, J.R. Lobry, L. Duret

Molecular Biology and Evolution . 23 : 523-529

2006

Journal article

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Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia.

Jean-Marc Aury, Olivier Jaillon, L. Duret, Benjamin Noel, Claire Jubin, Betina M Porcel...

Nature . 444 ( 7116 ) : 171-8

DOI: 10.1038/nature05230

2006

Journal article

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The GC Content of Primates and Rodents Genomes Is Not at Equilibrium : a Reply to Antezana

L. Duret

Journal of Molecular Evolution . -- : 803-806

2006

Journal article

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The Xist RNA Gene Evolved in Eutherians by Pseudogenization of a Protein-Coding Gene

L. Duret, C. Chureau, S. Samain, J. Weissenbach, P. Avner

Science . 312 : 1653-1655

2006

Journal article

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Evolutionary origin and maintenance of coexpressed gene clusters in mammals.

M. Sémon, L. Duret

Molecular Biology and Evolution . 23 : 1715-1723

2006

Journal article

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RISOTTO: Fast extraction of motifs with mismatches

N. Pisanti, A. Carvalho, L. Marsan, M.-F. Sagot

Latin American Symposium on Theoretical Informatics . 3887 : 757-768

DOI: 10.1007/11682462_69

2006

Conference paper

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The Gapped-Factor Tree

Pierre Peterlongo, Julien Allali, Marie-France Sagot

Prague Stringology Conference 2006 . : 182--196

2006

Conference paper

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An efficient algorithm for the identification of structured motifs in DNA promoter sequences

A.M. Carvalho, A.T. Freitas, A.L. Oliveira, M.-F. Sagot

IEEE/ACM Transactions on Computational Biology and Bioinformatics . 3 : 126-140

2006

Journal article

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Lossless Filter for Long Multiple Repetitions with Edit Distance

Pierre Peterlongo, Nadia Pisanti, Alair Peirera Do Lago, Marie-France Sagot

2006

Report

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Physiological oxygenation status is required for fully differentiated phenotype in kidney cortex proximal tubules.

Elodie de Laplanche, Karine Gouget, Guilhem Cléris, Franck Dragounoff, Jocelyne Demont, Anne Morales...

AJP Renal Physiology . 291 ( 4 ) : F750-60

DOI: 10.1152/ajprenal.00022.2006

2006

Journal article

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HoSeql : automated homologous sequence identification in gene family databases

Anne-Muriel Arigon Chifolleau, G. Perrière, Manolo Gouy

Bioinformatics . 22 ( 14 ) : 1786-1787

DOI: 10.1093/bioinformatics/btl179

2006

Journal article

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Relationship between morphological taxonomy and molecular divergence within Crustacea : Proposal of a molecular threshold to help species delimitation

T. Lefébure, C.J. Douady, Manolo Gouy, J. Gibert

Molecular Phylogenetics and Evolution . 40 ( 2 ) : 435-447

DOI: 10.1016/j.ympev.2006.03.014

2006

Journal article

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Use of PCR-Restriction Enzyme Pattern Analysis and Sequencing Database for hsp65 Gene-Based Identification of Nocardia Species

V. Rodriguez-Nava, A. Couble, G. Devulder, Jean-Pierre Flandrois, P. Boiron, F. Laurent

Journal of Clinical Microbiology . 44 ( 2 ) : 536-546

DOI: 10.1128/JCM.44.2.536-546.2006

2006

Journal article

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16S rRNA sequencing in routine bacterial identification : A 30-month experiment

S. Mignard, Jean-Pierre Flandrois

Journal of Microbiological Methods . 67 : 574-581

2006

Journal article

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Rapid identification of Enterobacteriaceae by sequencing DNA gyrase subunit B encoding gene

J. Delmas, F. Breysse, G. Devulder, Jean-Pierre Flandrois, M. Chomarat

Diagnostic Microbiology and Infectious Disease . 55 : 263-268

2006

Journal article

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Metabolic network visualization using constraint planar graph drawing Algorithm

Romain Bourqui, David Auber, Vincent Lacroix, Fabien Jourdan

Metabolic network visualization using constraint planar graph drawing Algorithm . : 489 - 496

2006

Conference paper

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Metabolic network visualization using constraint planar graph drawing algorithm

Romain Bourqui, D. Auber, Vincent Lacroix, F. Jourdan

incollection . -- : 489-496

2006

Journal article

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Un Algorithme Contraint de Dessin de Graphe Planaire pour la Visualisation de Réseaux Métaboliques

Romain Bourqui, David Auber, Vincent Lacroix, Fabien Jourdan

Un Algorithme Contraint de Dessin de Graphe Planaire pour la Visualisation de Réseaux Métaboliques . : électronique

2006

Conference paper

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The origin and evolution of Archaea: a state of the art

Simonetta Gribaldo, Céline Brochier-Armanet

Philos Trans R Soc Lond B Biol Sci . 361 : 1007-22

2006

Journal article

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A Bayesian Compound Stochastic Process for Modeling Nonstationary and Nonhomogeneous Sequence Evolution

Samuel Blanquart, Nicolas Lartillot

Molecular Biology and Evolution . 23 ( 11 ) : 2058-2071

DOI: 10.1093/molbev/msl091

2006

Journal article

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Assessing Site-Interdependent Phylogenetic Models of Sequence Evolution

Nicolas Rodrigue, Herve Philippe, Nicolas Lartillot

Molecular Biology and Evolution . 23 ( 9 ) : 1762-1775

DOI: 10.1093/molbev/msl041

2006

Journal article

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Conjugate Gibbs Sampling for Bayesian Phylogenetic Models

Nicolas Lartillot

Journal of Computational Biology . 13 : 1701-1722

DOI: 10.1089/cmb.2006.13.1701

2006

Journal article

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Synonymous codon usage and its potential link with optimal growth temperature in prokaryotes.

J.R. Lobry, A. Necşulea

Gene . 385 : 128-136

2006

Journal article

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Revisiting the directionnal mutation pressure theory : The analysis of a particular genomic structure in Leishmania major

A. Necşulea, J.R. Lobry

Gene . 385 : 28-40

2006

Journal article

see the publication

GECO Evolutionary and Computational Genomics

Bioinformatics, Phylogeny and Evolutionary Genomics Group

Baobab Group

Publications

Molecular diversity of rhizobia nodulating the invasive legume Cytisus scoparius in Australia.

Bradyrhizobia isolated from root nodules of Parasponia (Ulmaceae) do not constitute a separate coherent lineage.

Multipolar Consensus for Phylogenetic Trees

A maximum likelihood framework for protein design

Computing Bayes Factors using Thermodynamilmc Integration

Quantitative prediction for two-dimensional bacterial genomic displays

No Evidence for Tissue-Specific Adaptation of Synonymous Codon Usage in Humans

Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia.

The GC Content of Primates and Rodents Genomes Is Not at Equilibrium : a Reply to Antezana

The Xist RNA Gene Evolved in Eutherians by Pseudogenization of a Protein-Coding Gene

Evolutionary origin and maintenance of coexpressed gene clusters in mammals.

RISOTTO: Fast extraction of motifs with mismatches

The Gapped-Factor Tree

An efficient algorithm for the identification of structured motifs in DNA promoter sequences

Lossless Filter for Long Multiple Repetitions with Edit Distance

Physiological oxygenation status is required for fully differentiated phenotype in kidney cortex proximal tubules.

HoSeql : automated homologous sequence identification in gene family databases

Relationship between morphological taxonomy and molecular divergence within Crustacea : Proposal of a molecular threshold to help species delimitation

Use of PCR-Restriction Enzyme Pattern Analysis and Sequencing Database for hsp65 Gene-Based Identification of Nocardia Species

16S rRNA sequencing in routine bacterial identification : A 30-month experiment

Rapid identification of Enterobacteriaceae by sequencing DNA gyrase subunit B encoding gene

Metabolic network visualization using constraint planar graph drawing Algorithm

Metabolic network visualization using constraint planar graph drawing algorithm

Un Algorithme Contraint de Dessin de Graphe Planaire pour la Visualisation de Réseaux Métaboliques

The origin and evolution of Archaea: a state of the art

A Bayesian Compound Stochastic Process for Modeling Nonstationary and Nonhomogeneous Sequence Evolution

Assessing Site-Interdependent Phylogenetic Models of Sequence Evolution

Conjugate Gibbs Sampling for Bayesian Phylogenetic Models

Synonymous codon usage and its potential link with optimal growth temperature in prokaryotes.

Revisiting the directionnal mutation pressure theory : The analysis of a particular genomic structure in Leishmania major