Gouy Manolo

A divide-and-conquer phylogenomic approach based on character supermatrices resolves early steps in the evolution of the Archaea

Monique Aouad, Jean-Pierre Flandrois, Frédéric Jauffrit, Manolo Gouy, Simonetta Gribaldo, Celine Brochier-Armanet

BMC Ecology and Evolution . 22 ( 1 ) : 1-12

DOI: 10.1186/s12862-021-01952-0

2022

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The Molecular Determinants of Thermoadaptation: Methanococcales as a Case Study

Michel Lecocq, Mathieu Groussin, Manolo Gouy, Celine Brochier-Armanet

Molecular Biology and Evolution . 38 ( 5 ) : 1761–1776

DOI: 10.1093/molbev/msaa312

2021

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Seaview Version 5: A Multiplatform Software for Multiple Sequence Alignment, Molecular Phylogenetic Analyses, and Tree Reconciliation

Manolo Gouy, Eric Tannier, Nicolas Comte, David Parsons

Multiple Sequence Alignment . 2231 : 241-260

DOI: 10.1007/978-1-0716-1036-7_15

2021

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Resurrection of Ancestral Malate Dehydrogenases Reveals the Evolutionary History of Halobacterial Proteins : Deciphering Gene Trajectories and Changes in Biochemical Properties

Samuel Blanquart, Mathieu Groussin, Aline Le Roy, Gergely J Szöllosi, Eric Girard, Bruno Franzetti...

Molecular Biology and Evolution . 38 ( 9 ) : 3754-3774

DOI: 10.1093/molbev/msab146

2021

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Bioinformatique - 3e édition

Gilbert Deléage, Manolo Gouy, Alexandre de Brevern

978-2-10-081515-9

2021

Ouvrage

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Treerecs: an integrated phylogenetic tool, from sequences to reconciliations.

Nicolas Comte, Benoît Morel, Damir Hasic, Laurent Guéguen, Bastien Boussau, Vincent Daubin...

Bioinformatics . 36 ( 18 ) : 4822-4824

DOI: 10.1093/bioinformatics/btaa615

2020

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Extreme halophilic archaea derive from two distinct methanogen Class II lineages

Monique Aouad, Najwa Taïb, Anne Oudart, Michel Lecocq, Manolo Gouy, Céline Brochier-Armanet

Molecular Phylogenetics and Evolution . 127 : 46-54

DOI: 10.1016/j.ympev.2018.04.011

2018

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Ancestral Reconstruction: Theory and Practice

Mathieu Groussin, Vincent Daubin, Eric Tannier, Manolo Gouy

Encyclopedia of Evolutionary Biology . : 70–77

DOI: 10.1016/B978-0-12-800049-6.00166-9

2016

Chapitre d'ouvrage

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Gene Acquisitions from Bacteria at the Origins of Major Archaeal Clades Are Vastly Overestimated

Mathieu Groussin, Bastien Boussau, Gergely J Szollosi, Laura Eme, Manolo Gouy, Céline Brochier-Armanet...

Molecular Biology and Evolution . 33 ( 2 ) : 305 - 310

DOI: 10.1093/molbev/msv249

2016

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RiboDB database: a comprehensive resource for prokaryotic systematics

Frédéric Jauffrit, Simon Penel, Stéphane Delmotte, Carine Rey, Damien M de Vienne, Manolo Gouy...

Molecular Biology and Evolution . 33 ( 8 ) : 2170--2172

DOI: 10.1093/molbev/msw088

2016

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leBIBIQBPP: a set of databases and a webtool for automatic phylogenetic analysis of prokaryotic sequences

Jean-Pierre Flandrois, G. Perrière, Manolo Gouy

BMC Bioinformatics . 16 ( 1 ) : 251

DOI: 10.1186/s12859-015-0692-z

2015

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Toward more accurate ancestral protein genotype-phenotype reconstructions with the use of species tree-aware gene trees

M. Groussin, J. K. Hobbs, G. J. Szollosi, S. Gribaldo, V. L. Arcus, Manolo Gouy

Molecular Biology and Evolution . 32 : 13-22

DOI: 10.1093/molbev/msu305

2015

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Phylogenomic test of the hypotheses for the evolutionary origin of eukaryotes

Nc. Rochette, Céline Brochier-Armanet, M. Gouy

Molecular Biology and Evolution . 31 ( 4 ) : 832-45

DOI: 10.1093/molbev/mst272

2014

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Bioinformatique : cours et cas pratique

Gilbert Deléage, Manolo Gouy

978-2-10-058751-3

2013

Ouvrage

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The molecular signal for the adaptation to cold temperature during early life on Earth

Mathieu Groussin, Bastien Boussau, Sandrine Charles, Samuel Blanquart, Manolo Gouy

Biology Letters . 9 ( 5 ) : 20130608

DOI: 10.1098/rsbl.2013.0608

2013

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Genome-scale coestimation of species and gene trees.

Bastien Boussau, Gergely J Szöllosi, L. Duret, Manolo Gouy, Eric Tannier, Vincent Daubin

Genome Research . 23 ( 2 ) : 323-330

DOI: 10.1101/gr.141978.112

2013

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Bio++ : Efficient Extensible Libraries and Tools for Computational Molecular Evolution

Laurent Gueguen, Sylvain Gaillard, Bastien Boussau, Manolo Gouy, Mathieu Groussin, Nicolas C. Rochette...

Molecular Biology and Evolution . 30 ( 8 ) : 1745 - 1750

DOI: 10.1093/molbev/mst097

2013

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Experimental assessment of the accuracy of genomic selection in sugarcane

M. Gouy, Y. Rousselle, Denis Bastianelli, Philippe Lecomte, Laurent Bonnal, D. Roques...

TAG Theoretical and Applied Genetics . 126 ( 10 ) : 2575-2586

DOI: 10.1007/s00122-013-2156-z

2013

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A Branch-Heterogeneous Model of Protein Evolution for Efficient Inference of Ancestral Sequences

M. Groussin, Bastien Boussau, Manolo Gouy

Systematic Biology . 62 ( 4 ) : 523-538

DOI: 10.1093/sysbio/syt016

2013

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What genomes have to say about the evolution of the Earth

Bastien Boussau, Manolo Gouy

Gondwana Research . 21 : 483-494

DOI: 10.1016/j.gr.2011.08.002

2012

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Lateral gene transfer as a support for the tree of life.

Sophie S Abby, Eric Tannier, Manolo Gouy, Vincent Daubin

Proceedings of the National Academy of Sciences of the United States of America . 109 ( 13 ) : 4962-4967

DOI: 10.1073/pnas.1116871109

2012

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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

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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

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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

Chapitre d'ouvrage

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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

DOI: 10.1007/s10096-010-1091-z

2010

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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

Chapitre d'ouvrage

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Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests

Sophie S. Abby, Eric Tannier, Manolo Gouy, Vincent Daubin

BMC Bioinformatics . 11 ( 324 ) : 13

DOI: 10.1186/1471-2105-11-324

2010

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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

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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

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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

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Publications

A divide-and-conquer phylogenomic approach based on character supermatrices resolves early steps in the evolution of the Archaea

The Molecular Determinants of Thermoadaptation: Methanococcales as a Case Study

Seaview Version 5: A Multiplatform Software for Multiple Sequence Alignment, Molecular Phylogenetic Analyses, and Tree Reconciliation

Resurrection of Ancestral Malate Dehydrogenases Reveals the Evolutionary History of Halobacterial Proteins : Deciphering Gene Trajectories and Changes in Biochemical Properties

Bioinformatique - 3e édition

Treerecs: an integrated phylogenetic tool, from sequences to reconciliations.

Extreme halophilic archaea derive from two distinct methanogen Class II lineages

Ancestral Reconstruction: Theory and Practice

Gene Acquisitions from Bacteria at the Origins of Major Archaeal Clades Are Vastly Overestimated

RiboDB database: a comprehensive resource for prokaryotic systematics

leBIBIQBPP: a set of databases and a webtool for automatic phylogenetic analysis of prokaryotic sequences

Toward more accurate ancestral protein genotype-phenotype reconstructions with the use of species tree-aware gene trees

Phylogenomic test of the hypotheses for the evolutionary origin of eukaryotes

Bioinformatique : cours et cas pratique

The molecular signal for the adaptation to cold temperature during early life on Earth

Genome-scale coestimation of species and gene trees.

Bio++ : Efficient Extensible Libraries and Tools for Computational Molecular Evolution

Experimental assessment of the accuracy of genomic selection in sugarcane

A Branch-Heterogeneous Model of Protein Evolution for Efficient Inference of Ancestral Sequences

What genomes have to say about the evolution of the Earth

Lateral gene transfer as a support for the tree of life.

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.

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

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

Evolution Moléculaire

Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests

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

Proposals for classification methods dedicated to biological data

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