Manolo Gouy

117

Documents

Publications

	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 BMC Ecology and Evolution, 2022, 22 (1), pp.1-12. ⟨10.1186/s12862-021-01952-0⟩ Journal articles hal-03514913v1
	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 Molecular Biology and Evolution, 2021, 38 (9), pp.3754-3774. ⟨10.1093/molbev/msab146⟩ Journal articles hal-03231689v1
	The Molecular Determinants of Thermoadaptation: Methanococcales as a Case Study Michel Lecocq , Mathieu Groussin , Manolo Gouy , Celine Brochier-Armanet Molecular Biology and Evolution, 2021, 38 (5), pp.1761-1776. ⟨10.1093/molbev/msaa312⟩ Journal articles hal-03118165v1
	Treerecs: an integrated phylogenetic tool, from sequences to reconciliations. Nicolas Comte , Benoît Morel , Damir Hasic , Laurent Guéguen , Bastien Boussau Bioinformatics, 2020, 36 (18), pp.4822-4824. ⟨10.1093/bioinformatics/btaa615⟩ Journal articles hal-02883386v1
	Extreme halophilic archaea derive from two distinct methanogen Class II lineages Monique Aouad , Najwa Taïb , Anne Oudart , Michel Lecocq , Manolo Gouy Molecular Phylogenetics and Evolution, 2018, 127, pp.46-54. ⟨10.1016/j.ympev.2018.04.011⟩ Journal articles hal-01799910v1
	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 Molecular Biology and Evolution, 2016, 33 (2), pp.305 - 310. ⟨10.1093/molbev/msv249⟩ Journal articles hal-01913926v1
	RiboDB database: a comprehensive resource for prokaryotic systematics Frédéric Jauffrit , Simon Penel , Stéphane Delmotte , Carine Rey , Damien M de Vienne Molecular Biology and Evolution, 2016, 33 (8), pp.2170--2172. ⟨10.1093/molbev/msw088⟩ Journal articles hal-01800061v1
	leBIBIQBPP: a set of databases and a webtool for automatic phylogenetic analysis of prokaryotic sequences Jean-Pierre Flandrois , G. Perrière , Manolo Gouy BMC Bioinformatics, 2015, 16 (1), pp.251. ⟨10.1186/s12859-015-0692-z⟩ Journal articles hal-02044751v1
	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 Molecular Biology and Evolution, 2015, 32, pp.13-22. ⟨10.1093/molbev/msu305⟩ Journal articles hal-02044770v1
	Phylogenomic test of the hypotheses for the evolutionary origin of eukaryotes Nc. Rochette , Céline Brochier-Armanet , M. Gouy Molecular Biology and Evolution, 2014, 31 (4), pp.832-45. ⟨10.1093/molbev/mst272⟩ Journal articles hal-02045522v1
	Genome-scale coestimation of species and gene trees. Bastien Boussau , Gergely J Szöllosi , L. Duret , Manolo Gouy , Eric Tannier Genome Research, 2013, 23 (2), pp.323-330. ⟨10.1101/gr.141978.112⟩ Journal articles hal-00750148v1
	A Branch-Heterogeneous Model of Protein Evolution for Efficient Inference of Ancestral Sequences M. Groussin , Bastien Boussau , Manolo Gouy Systematic Biology, 2013, 62 (4), pp.523-538. ⟨10.1093/sysbio/syt016⟩ Journal articles hal-02320419v1
	Experimental assessment of the accuracy of genomic selection in sugarcane M. Gouy , Y. Rousselle , Denis Bastianelli , Philippe Lecomte , Laurent Bonnal TAG Theoretical and Applied Genetics, 2013, 126 (10), pp.2575-2586. ⟨10.1007/s00122-013-2156-z⟩ Journal articles hal-02648497v1
	Bio++ : Efficient Extensible Libraries and Tools for Computational Molecular Evolution Laurent Gueguen , Sylvain Gaillard , Bastien Boussau , Manolo Gouy , Mathieu Groussin Molecular Biology and Evolution, 2013, 30 (8), pp.1745 - 1750. ⟨10.1093/molbev/mst097⟩ Journal articles hal-01209906v1
	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, 2013, 9 (5), pp.20130608. ⟨10.1098/rsbl.2013.0608⟩ Journal articles hal-00918283v1
	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, 2012, 109 (13), pp.4962-4967. ⟨10.1073/pnas.1116871109⟩ Journal articles hal-00752055v1
	What genomes have to say about the evolution of the Earth Bastien Boussau , Manolo Gouy Gondwana Research, 2012, 21, pp.483-494. ⟨10.1016/j.gr.2011.08.002⟩ Journal articles hal-00698400v1
	Adaptation to Environmental Temperature Is a Major Determinant of Molecular Evolutionary Rates in Archaea M. Groussin , Manolo Gouy Molecular Biology and Evolution, 2011, 28, pp.2661-2674. ⟨10.1093/molbev/msr098⟩ Journal articles hal-00697929v1
	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 European Journal of Clinical Microbiology and Infectious Diseases, 2011, 30 (3), pp.343-54. ⟨10.1007/s10096-010-1091-z⟩ Journal articles hal-00698367v1
	Proposals for classification methods dedicated to biological data Anne-Muriel Arigon Chifolleau , Guy Perrière , Manolo Gouy International Journal of Biomedical Engineering and Technology (IJBET), 2010, 3 (1/2), pp.4-21. ⟨10.1504/IJBET.2010.029649⟩ Journal articles lirmm-00830931v1
	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 European Journal of Clinical Microbiology and Infectious Diseases, 2010, pp.343-354. ⟨10.1007/s10096-010-1091-z⟩ Journal articles hal-00634698v1
	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, 2010, 27, pp.221-224. ⟨10.1093/molbev/msp259⟩ Journal articles lirmm-00511794v2
	Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests Sophie S. Abby , Eric Tannier , Manolo Gouy , Vincent Daubin BMC Bioinformatics, 2010, 11 (324), pp.13. ⟨10.1186/1471-2105-11-324⟩ Journal articles inria-00527151v1
	Databases of Homologous Gene Families for Comparative Genomics Simon Penel , Anne-Muriel Arigon Chifolleau , Jean-François Dufayard , Anne-Sophie Sertier , Vincent Daubin BMC Bioinformatics, 2009, 10 (Suppl.6) :S3, pp.13. ⟨10.1186/1471-2105-10-S6-S3⟩ Journal articles lirmm-00400099v1
	In Retrospect: Lamarck's treatise at 200 Dan Graur , Manolo Gouy , David Wool Nature, 2009, 460 (7256), pp.688-689. ⟨10.1038/460688a⟩ Journal articles hal-02320435v1
	A Mixture Model and a Hidden Markov Model to Simultaneously Detect Recombination Breakpoints and Reconstruct Phylogenies Bastien Boussau , Laurent Guéguen , Manolo Gouy Evolutionary Bioinformatics, 2009, 5, pp.67-79. ⟨10.4137/EBO.S2242⟩ Journal articles hal-00428395v1
	Polymorphism of the Staphylococcus aureus Panton-Valentine LeukocidinGenes and Its Possible Link with the Fitness of Community-Associated Methicillin-Resistant S. aureus O. Dumitrescu , A. Tristan , H. Meugnier , M. Bes , Manolo Gouy Journal of Infectious Diseases, 2008, 198 (5), pp.792-794. ⟨10.1086/590914⟩ Journal articles hal-00428303v1
	Ancient bacteria liked it hot M. Gouy , M. Chaussidon Nature, 2008, 451, pp.635-636. ⟨10.1038/451635a⟩ Journal articles hal-00345924v1
	Parallel Adaptations to High Temperatures in the Archean Eon Bastien Boussau , Samuel Blanquart , Anamaria Necsulea , Nicolas Lartillot , Manolo Gouy Nature, 2008, 456 (7224), pp.942-945. ⟨10.1038/nature07393⟩ Journal articles lirmm-00324159v1
	Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria Bastien Boussau , Laurent Guéguen , Manolo Gouy BMC Evolutionary Biology, 2008, 8, pp.272-272. ⟨10.1186/1471-2148-8-272⟩ Journal articles hal-00428101v1
	Automatic Identification of Large Collections of Protein-Coding or rRNA Sequences Anne-Muriel Arigon Chifolleau , Guy Perrière , Manolo Gouy Biochimie, 2008, 90 (4), pp.609-614. ⟨10.1016/j.biochi.2007.08.006⟩ Journal articles lirmm-00366131v1
	Remote access to ACNUC nucleotide and protein sequence databases at PBIL Manolo Gouy , Stephane Delmotte Biochimie, 2008, 90 (4), pp.555-562. ⟨10.1016/j.biochi.2007.07.003⟩ Journal articles hal-00428117v1
	Efficient Likelihood Computations with Nonreversible Models of Evolution Bastien Boussau , Manolo Gouy Systematic Biology, 2006, 55 (5), pp.756-768. ⟨10.1080/10635150600975218⟩ Journal articles hal-00427908v1
	HoSeql : automated homologous sequence identification in gene family databases Anne-Muriel Arigon Chifolleau , G. Perrière , Manolo Gouy Bioinformatics, 2006, 22 (14), pp.1786-1787. ⟨10.1093/bioinformatics/btl179⟩ Journal articles hal-00427893v1
	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, 2006, 40 (2), pp.435-447. ⟨10.1016/j.ympev.2006.03.014⟩ Journal articles hal-00427988v1
	Phylogeography of a subterranean amphipod reveals cryptic diversity and dynamic evolution in extreme environments T. Lefébure , C.J. Douady , Manolo Gouy , P. Trontel , J. Briolay Molecular Ecology, 2006, 15, pp.1797-1806. ⟨10.1111/j.1365-294X.2006.02888.x⟩ Journal articles hal-00427985v1
	Origin and molecular evolution of receptor tyrosine kinases with immunoglobulin-like domains. Julien Grassot , Manolo Gouy , Guy Perrière , Guy Mouchiroud Molecular Biology and Evolution, 2006, 23 (6), pp.1232-41. ⟨10.1093/molbev/msk007⟩ Journal articles hal-00192848v1
	Clinical and environmental isolates of Legionella pneumophila serogroup 1 cannot be distinguished by sequence analysis of two surface protein genes and three housekeeping genes H. Aurell , Pierre Farge , H. Meugnier , Manolo Gouy , F. Forey Applied and Environmental Microbiology, 2005, 71, pp.282-289. ⟨10.1128/AEM.71.1.282-289.2005⟩ Journal articles hal-00427706v1
	Molecular phylogeny of Myricaceae: a reexamination of host-symbiont specificity V. Huguet , Manolo Gouy , P. Normand , J.F. Zimpfer , M.P. Fernandez Molecular Phylogenetics and Evolution, 2005, 34 (3), pp.557-568. ⟨10.1016/j.ympev.2004.11.018⟩ Journal articles hal-00427839v1
	In silico whole-genome scanning of cancer-associated nonsynonymous SNPs and molecular characterization of a dynein light chain tumour variant A. Aouacheria , V. Navratil , W. Wen , M. Jiang , Dominique Mouchiroud Oncogene, 2005, 24, pp.6133-6142. ⟨10.1038/sj.onc.1208745⟩ Journal articles hal-00427704v1
	Horizontal transfer of two operons coding for hydrogenases between bacteria and archaea. A. Calteau , Manolo Gouy , G. Perrière Journal of Molecular Evolution, 2005, 60 (5), pp.557-65. ⟨10.1007/s00239-004-0094-8⟩ Journal articles hal-00427722v1
	Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases. Jean-François Dufayard , L. Duret , Simon Penel , Manolo Gouy , F. Rechenmann Bioinformatics, 2005, 21 (11), pp.2596-603. ⟨10.1093/bioinformatics/bti325⟩ Journal articles hal-00427861v1
	Phylogenomics of Life-Or-Death Switches in Multicellular Animals: Bcl-2, BH3-Only, and BNip Families of Apoptotic Regulators A. Aouacheria , F. Brunet , Manolo Gouy Molecular Biology and Evolution, 2005, 22 (12), pp.2395-2416. ⟨10.1093/molbev/msi234⟩ Journal articles hal-00427703v1
	Phylogenetic analysis of the complete genome sequence of Encephalitozoon cuniculi supports the fungal origin of microsporidia and reveals a high frequency of fast-evolving genes F. Thomarat , Christian Vivarès , Manolo Gouy Journal of Molecular Evolution, 2004, 59, pp.780-791. ⟨10.1007/s00239-004-2673-0⟩ Journal articles hal-00427661v1
	Phylogenetic study and identification of Vibrio splendidus-related strains based on gyrB gene sequences. Frédérique Le Roux , Mélanie Gay , Christophe Lambert , Jean-Louis Nicolas , Manolo Gouy Diseases of Aquatic Organisms, 2004, 58 (2-3), pp.143-150. ⟨10.3354/dao058143⟩ Journal articles hal-00458183v1
	Invertebrate Data Predict an Early Emergence of Vertebrate Fibrillar Collagen Clades and an Anti-incest Model Abdel Aouacheria , Caroline Cluzel , Claire Lethias , Manolo Gouy , Robert Garrone Journal of Biological Chemistry, 2004, 279 (46), pp.47711-47719. ⟨10.1074/jbc.M408950200⟩ Journal articles hal-00427534v2
	Integrated databanks access and sequence/structure analysis services at the PBIL. G. Perriere , C. Combet , Simon Penel , Christophe Blanchet , J. Thioulouse Nucleic Acids Research, 2003, 31 (13), pp.3393-3399. ⟨10.1093/nar/gkg530⟩ Journal articles hal-00313743v1
	Automatic RNA secondary structure prediction with a comparative approach F. Tahi , Manolo Gouy , M. Regnier Journal of Computational Chemistry, 2002, 26 (5), pp.521-530. ⟨10.1016/S0097-8485(02)00012-8⟩ Journal articles hal-00427303v1
	Functional and evolutionary analysis of a eukaryotic parasitic genome Christian Vivarès , Manolo Gouy , F. Thomarat , G. Metenier Current Opinion in Microbiology, 2002, 5, pp.499-505. ⟨10.1016/S1369-5274(02)00356-9⟩ Journal articles hal-00427309v1
	Recombination rate and the distribution of transposable elements in the Drosophila melanogaster genome C. Rizzon , Gabriel Marais , Manolo Gouy , C. Biémont Genome Research, 2002, 12, pp.400-407. ⟨10.1101/gr.210802⟩ Journal articles hal-00427298v1
	A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history Vincent Daubin , Manolo Gouy , G. Perrière Genome Research, 2002, 12, pp.1080-1090. ⟨10.1101/gr.187002⟩ Journal articles hal-00427259v1
	Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi M.D. Katinka , S. Duprat , E. Cornillot , G. Metenier , F. Thomarat Nature, 2001, 414, pp.450-453. ⟨10.1038/35106579⟩ Journal articles hal-00427201v1
	Molecular evidence for the existence of two species of Marteilia in Europe F. Le Roux , G. Lorenzo , P. Peyret , C. Audemard , A. Figueras Journal of Eukaryotic Microbiology, 2001, 48 (4), pp.449-454. ⟨10.1111/j.1550-7408.2001.tb00178.x⟩ Journal articles hal-00427181v1
	Nrh, a human homologue of Nr-13 associates with Bcl-Xs and is an inhibitor of apoptosis A. Aouacheria , Estelle Arnaud , S. Venet , P. Lalle , M. Gouy Oncogene, 2001, 20, pp.5846-5855. ⟨10.1038/sj.onc.1204740⟩ Journal articles hal-00314329v1
	Lipid phosphate phosphatases in Arabidopsis. Regulation of the AtLPP1 gene in response to stress O. Pierrugues , C. Brutesco , J. Oshiro , Manolo Gouy , Y. Deveaux Journal of Biological Chemistry, 2001, 276 (23), pp.20300-20308. ⟨10.1074/jbc.M009726200⟩ Journal articles hal-00427174v1
	Sequence of the Small Subunit Ribosomal RNA Gene of Perkinsus atlanticus-like Isolated from Carpet Shell Clam in Galicia Spain A. Figueras , G. Lorenzo , M.C. Ordas , Manolo Gouy , B. Novoa Marine Biotechnology, 2000, 2, pp.419-428. ⟨10.1007/s101260000015⟩ Journal articles hal-00427078v1
	Phylogenetic analysis of the small subunit ribosomal RNA of Marteilia refringens validates the existence of phylum Paramyxea (Desportes and Perkins 1990) F.C. Berthe , F. Le Roux , E. Peyretaillade , P. Peyret , D. Rodriguez Journal of Eukaryotic Microbiology, 2000, 47 (3), pp.288-293. ⟨10.1111/j.1550-7408.2000.tb00049.x⟩ Journal articles hal-00427063v1
	HOBACGEN: database system for comparative genomics in bacteria G. Perrière , L. Duret , Manolo Gouy Genome Research, 2000, 10, pp.379-385. ⟨10.1101/gr.10.3.379⟩ Journal articles hal-00427099v1
	A nonhyperthermophilic common ancestor to extant life forms N. Galtier , N. Tourasse , Manolo Gouy Science, 1999, 283 (5399), pp.220-221. ⟨10.1126/science.283.5399.220⟩ Journal articles hal-00428447v1
	Accounting for evolutionary rate variation among sequence sites consistently changes universal phylogenies deduced from rRNA and protein-coding genes N.J. Tourasse , Manolo Gouy Molecular Phylogenetics and Evolution, 1999, 13, pp.159-168. ⟨10.1006/mpev.1999.0675⟩ Journal articles hal-00428462v1
	The non-redundant Bacillus subtilis (NRSub) database: update 1998 G. Perrière , Manolo Gouy , T. Gojobori Nucleic Acids Research, 1998, 26 (1), pp.60-62. ⟨10.1093/nar/26.1.60⟩ Journal articles hal-00428499v1
	Inferring pattern and process: maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis N. Galtier , Manolo Gouy Molecular Biology and Evolution, 1998, 15 (7), pp.871-879. ⟨10.1093/oxfordjournals.molbev.a025991⟩ Journal articles hal-00428472v1
	Phylogenetic analysis and genome size of Ostreococcus tauri (Chlorophyta Prasinophyceae) C. Courties , R. Perasso , M.-J. Chrétiennot-Dinet , Manolo Gouy , Laure Guillou Journal of Phycology, 1998, 34, pp.844-849. ⟨10.1046/j.1529-8817.1998.340844.x⟩ Journal articles hal-00428471v1
	Multiple sequence alignment with Clustal X F. Jeanmougin , J.D. Thompson , Manolo Gouy , D.G. Higgins , T.J. Gibson Trends in Biochemical Sciences, 1998, 23 (10), pp.403-405. ⟨10.1016/S0968-0004(98)01285-7⟩ Journal articles hal-00428491v1
	Microsporidian Encephalitozoon cuniculi a unicellular eukaryote with an unusual chromosomal dispersion of ribosomal genes and a LSU rRNA reduced to the universal core E. Peyretaillade , C. Biderre , P. Peyret , F. Duffieux , G. Metenier Nucleic Acids Research, 1998, 26, pp.3513-3520. ⟨10.1093/nar/26.15.3513⟩ Journal articles hal-00428508v1
	Sensitivity of the relative-rate test to taxonomic sampling M. Robinson , Manolo Gouy , Christian Gautier , Dominique Mouchiroud Molecular Biology and Evolution, 1998, 15 (9), pp.1091-1098. ⟨10.1093/oxfordjournals.molbev.a026016⟩ Journal articles hal-00428501v1
	Microsporidia amitochondrial protists possess a 70-kDa heat shock protein gene of mitochondrial evolutionary origin E. Peyretaillade , V. Broussolle , P. Peyret , G. Metenier , Manolo Gouy Molecular Biology and Evolution, 1998, 15, pp.683-689. ⟨10.1093/oxfordjournals.molbev.a025971⟩ Journal articles hal-00428498v1
	Evolutionary distances between nucleotide sequences based on the distribution of substitution rates among sites as estimated by parsimony N.J. Tourasse , Manolo Gouy Molecular Biology and Evolution, 1997, 14 (3), pp.287-298. ⟨10.1093/oxfordjournals.molbev.a025764⟩ Journal articles hal-00434995v1
	Evolutionary affinities of the order Perissodactyla and the phylogenetic status of the superordinal taxa Ungulata and Altungulata D. Graur , Manolo Gouy , L. Duret Molecular Phylogenetics and Evolution, 1997, 7 (2), pp.195-200. ⟨10.1006/mpev.1996.0391⟩ Journal articles hal-00434984v1
	Extreme differences in rates of molecular evolution of foraminifera revealed by comparison of ribosomal DNA sequences and the fossil record J. Pawlowski , I. Bolivar , J.F. Fahrni , C. de Vargas , Manolo Gouy Molecular Biology and Evolution, 1997, 14 (5), pp.498-505. ⟨10.1093/oxfordjournals.molbev.a025786⟩ Journal articles hal-00434978v1
	Early origin of foraminifera suggested by SSU rRNA gene sequences J. Pawlowski , I. Bolivar , J.F. Fahrni , T. Cavalier-Smith , Manolo Gouy Molecular Biology and Evolution, 1996, 13 (3), pp.445-450. ⟨10.1093/oxfordjournals.molbev.a025605⟩ Journal articles hal-00435033v1
	WWW-query: an on-line retrieval system for biological sequence banks G. Perrière , Manolo Gouy Biochimie, 1996, 78 (5), pp.364-369. ⟨10.1016/0300-9084(96)84768-7⟩ Journal articles hal-00435034v1
	Phylogenetic position of the order Lagomorpha (rabbits hares and allies) D. Graur , L. Duret , Manolo Gouy Nature, 1996, 379, pp.333-335. ⟨10.1038/379333a0⟩ Journal articles hal-00435019v1
	SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny N. Galtier , Manolo Gouy , Christian Gautier Bioinformatics, 1996, 12 (6), pp.543-548. ⟨10.1093/bioinformatics/12.6.543⟩ Journal articles hal-00435028v1
	Inferring phylogenies from DNA sequences of unequal base compositions. N. Galtier , Manolo Gouy Proceedings of the National Academy of Sciences of the United States of America, 1995, 92 (24), pp.11317-11321. ⟨10.1073/pnas.92.24.11317⟩ Journal articles hal-02320510v1
	Isolation and characterization of a cDNA encoding a chicken actin-like protein J.J. Michaille , Manolo Gouy , Simon Blanchet , L. Duret Gene, 1995, 154 (2), pp.205-209. ⟨10.1016/0378-1119(94)00865-P⟩ Journal articles hal-00698055v1
	Phylogenetic position of foraminifera inferred from LSU rRNA gene sequences J. Pawlowski , I. Bolivar , J. Guiard-Maffia , Manolo Gouy Molecular Biology and Evolution, 1994, 11 (6), pp.929-938. ⟨10.1093/oxfordjournals.molbev.a040174⟩ Journal articles hal-00698124v1
	HOVERGEN: a database of homologous vertebrate genes L. Duret , Dominique Mouchiroud , Manolo Gouy Nucleic Acids Research, 1994, 22 (12), pp.2360-2365. ⟨10.1093/nar/22.12.2360⟩ Journal articles hal-00698069v1
	Molecular phylogeny of Eubacteria: a new multiple tree analysis method applied to 15 sequence data sets questions the monophyly of Gram-positive bacteria N. Galtier , Manolo Gouy Research in Microbiology, 1994, 145 (7), pp.531-541. ⟨10.1016/0923-2508(94)90030-2⟩ Journal articles hal-02320465v1
	Molecular Phylogenetic Analysis of Nitrobacter spp S. Orso , Manolo Gouy , E. Navarro , P. Normand International Journal of Systematic Bacteriology, 1994, 44 (1), pp.83-86. ⟨10.1099/00207713-44-1-83⟩ Journal articles hal-00698105v1
	Heterogeneity of hepatitis C virus genotypes in France D. Qu , O. Hantz , Manolo Gouy , L. Vitvitski , J.S. Li Journal of General Virology, 1994, 75 ( Pt 5), pp.1063-1070. ⟨10.1099/0022-1317-75-5-1063⟩ Journal articles hal-00698153v1
	NRSub: a non-redundant data base for the Bacillus subtilis genome G. Perrière , Manolo Gouy , T. Gojobori Nucleic Acids Research, 1994, 22 (25), pp.5525-5529. ⟨10.1093/nar/22.25.5525⟩ Journal articles hal-00698135v1
	Molecular phylogeny of the symbiotic actinomycetes of the genus Frankia matches host-plant infection processes. Benoit Cournoyer , Manolo Gouy , Philippe Normand Molecular Biology and Evolution, 1993, ⟨10.1093/oxfordjournals.molbev.a040077⟩ Journal articles hal-02320516v1
	Insect muscle actins differ distinctly from invertebrate and vertebrate cytoplasmic actins N. Mounier , Manolo Gouy , Dominique Mouchiroud , J.C. Prudhomme Journal of Molecular Evolution, 1992, 34, pp.406-415. ⟨10.1007/BF00162997⟩ Journal articles hal-00698078v1
	Evolution of the primate beta-globin gene region: nucleotide sequence of the delta-beta-globin intergenic region of gorilla and phylogenetic relationships between African apes and man P. Perrin-Pecontal , Manolo Gouy , V.M. Nigon , G. Trabuchet Journal of Molecular Evolution, 1992, 34, pp.17-30. ⟨10.1007/BF00163849⟩ Journal articles hal-00698137v1
	Nucleotide sequence of nifD from Frankia alni strain ArI3: phylogenetic inferences P. Normand , Manolo Gouy , B. Cournoyer , P. Simonet Molecular Biology and Evolution, 1992, 9 (3), pp.495-506. ⟨10.1093/oxfordjournals.molbev.a040737⟩ Journal articles hal-00698088v1
	Molecular phylogeny of Rodentia Lagomorpha Primates Artiodactyla and Carnivora and molecular clocks W.-H. Li , Manolo Gouy , P.M. Sharp , C. O'Huigin , Y.W. Yang Proceedings of the National Academy of Sciences of the United States of America, 1990, 87 (17), pp.6703-6707. ⟨10.1073/pnas.87.17.6703⟩ Journal articles hal-00698389v1
	Statistical tests of molecular phylogenies W.-H. Li , Manolo Gouy Methods in Enzymology, 1990, 183, pp.645-659. ⟨10.1016/0076-6879(90)83042-8⟩ Journal articles hal-00698014v1
	Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data K.H. Wolfe , Manolo Gouy , Y.W. Yang , P.M. Sharp , W.-H. Li Proceedings of the National Academy of Sciences of the United States of America, 1989, 86 (16), pp.6201-6205. ⟨10.1073/pnas.86.16.6201⟩ Journal articles hal-00698329v1
	Phylogenetic analysis based on rRNA sequences supports the archaebacterial rather than the eocyte tree Manolo Gouy , W.-H. Li Nature, 1989, 339, pp.145-147. ⟨10.1038/339145a0⟩ Journal articles hal-00697921v1
	Molecular phylogeny of the kingdoms Animalia Plantae and Fungi Manolo Gouy , W.-H. Li Molecular Biology and Evolution, 1989, 6 (2), pp.109-122. ⟨10.1093/oxfordjournals.molbev.a040536⟩ Journal articles hal-00697919v1
	RPA190 the gene coding for the largest subunit of yeast RNA polymerase A S. Memet , Manolo Gouy , C. Marck , A. Sentenac , J.M. Buhler Journal of Biological Chemistry, 1988, 263 (6), pp.2830-2839. ⟨10.1016/S0021-9258(18)69144-6⟩ Journal articles hal-00698053v1
	Codon contexts in enterobacterial and coliphage genes Manolo Gouy Molecular Biology and Evolution, 1987, 4, pp.426-444. ⟨10.1093/oxfordjournals.molbev.a040450⟩ Journal articles hal-00697910v1
	Interfacing similarity search software with the sequence retrieval system ACNUC D.G. Higgins , Manolo Gouy Bioinformatics, 1987, 3 (3), pp.239-241. ⟨10.1093/bioinformatics/3.3.239⟩ Journal articles hal-00697947v1
	Molecular evolution of viruses as seen by nucleic acid sequence study R. Grantham , T. Greenland , S. Louail , Dominique Mouchiroud , J.-L. Prato Bulletin de l'Institut Pasteur, 1985, 83, pp.95-148 Journal articles hal-00697914v1
	Evolution of the primate β-globin gene region P. Savatier , G. Trabuchet , C. Faure , Y. Chebloune , M. Gouy Journal of Molecular Biology, 1985, 182 (1), pp.21-29. ⟨10.1016/0022-2836(85)90024-5⟩ Journal articles hal-02965509v1
	Prédiction des structures secondaires dans les acides nucléiques: aspects algorithmiques et physiques Manolo Gouy , P. Marliere , C. Papanicolaou , J. Ninio Biochimie, 1985, 67 (5), pp.523-531. ⟨10.1016/S0300-9084(85)80272-8⟩ Journal articles hal-00697912v1
	Non-parametric statistics for nucleic acid sequence study C. Gautier , Manolo Gouy , S. Louail Biochimie, 1985, 67 (5), pp.449-453. ⟨10.1016/S0300-9084(85)80263-7⟩ Journal articles hal-02320490v1
	Evolution of the primate beta-globin gene region. High rate of variation in CpG dinucleotides and in short repeated sequences between man and chimpanzee P. Savatier , G. Trabuchet , C. Faure , Y. Chebloune , Manolo Gouy Journal of Molecular Biology, 1985, 182 (1), pp.21-29. ⟨10.1016/0022-2836(85)90024-5⟩ Journal articles hal-00698207v1
	System analysis and nucleic acid sequence banks Manolo Gouy , Christian Gautier , F. Milleret Biochimie, 1985, 67 (5), pp.433-436. ⟨10.1016/S0300-9084(85)80260-1⟩ Journal articles hal-00697903v1
	ACNUC--a portable retrieval system for nucleic acid sequence databases: logical and physical designs and usage Manolo Gouy , Christian Gautier , M. Attimonelli , C. Lanave , G. Di Paola Bioinformatics, 1985, 1, pp.167-172. ⟨10.1093/bioinformatics/1.3.167⟩ Journal articles hal-00697905v1
	ACNUC: a nucleic acid sequence data base and analysis system Manolo Gouy , F. Milleret , C. Mugnier , M. Jacobzone , Christian Gautier Nucleic Acids Research, 1984, 12 (1), pp.121-127. ⟨10.1093/nar/12.1Part1.121⟩ Journal articles hal-00697916v1
	An energy model that predicts the correct folding of both the tRNA and the 5S RNA molecules C. Papanicolaou , Manolo Gouy , J. Ninio Nucleic Acids Research, 1984, 12 (1), pp.31-44. ⟨10.1093/nar/12.1Part1.31⟩ Journal articles hal-00698110v1
	Codon usage in bacteria: correlation with gene expressivity Manolo Gouy , Christian Gautier Nucleic Acids Research, 1982, 10 (22), pp.7055-7074. ⟨10.1093/nar/10.22.7055⟩ Journal articles hal-00697906v1
	Codon catalog usage is a genome strategy modulated for gene expressivity R. Grantham , Christian Gautier , Manolo Gouy , M. Jacobzone , R. Mercier Nucleic Acids Research, 1981, 9, pp.R43-R74. ⟨10.1093/nar/9.1.213-b⟩ Journal articles hal-00697917v1
	Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type R. Grantham , Christian Gautier , Manolo Gouy Nucleic Acids Research, 1980, 8 (9), pp.1893-1912. ⟨10.1093/nar/8.9.1893⟩ Journal articles hal-00697920v1
	Polypeptide elongation and tRNA cycling in Escherichia coli: a dynamic approach Manolo Gouy , R. Grantham FEBS Letters, 1980, 115, pp.151-155. ⟨10.1016/0014-5793(80)81155-0⟩ Journal articles hal-00697904v1
	Codon catalog usage and the genome hypothesis R. Grantham , Christian Gautier , Manolo Gouy , R. Mercier , A. Pave Nucleic Acids Research, 1980, 8 (1), pp.R49-R62. ⟨10.1093/nar/8.1.197-c⟩ Journal articles hal-00697923v1

	Phylogeography and taxonomic status of Niphargus virei (subterranean amphipod). T. Lefébure , Christophe Jean Douady , M. Gouy , P. Trontelj , J. Briolay 2005, pp.73-74 Conference papers halsde-00157705v1

	Bioinformatique - 3e édition Gilbert Deléage , Manolo Gouy , Alexandre de Brevern Dunod, 2021, Collection Sciences Sup, 978-2-10-081515-9 Books hal-03356596v1
	Bioinformatique : cours et cas pratique Gilbert Deléage , Manolo Gouy Dunod, 2013, 978-2-10-058751-3 Books hal-02086801v1
	Nucleic acid sequences handbook Christian Gautier , Manolo Gouy , Monique Jacobzone , Richard Grantham Praeger, 1-2, 1981 Books hal-02087468v1

	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, Humana, pp.241-260, 2021, Methods in Molecular Biology, ⟨10.1007/978-1-0716-1036-7_15⟩ Book sections hal-03065564v1
	Ancestral Reconstruction: Theory and Practice Mathieu Groussin , Vincent Daubin , Eric Tannier , Manolo Gouy Richard M. Kliman. Encyclopedia of Evolutionary Biology, Elsevier, pp.70-77, 2016, ⟨10.1016/B978-0-12-800049-6.00166-9⟩ Book sections hal-01334934v1
	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 Ecologie microbienne : Microbiologie des milieux naturels et anthropisés, Presses Universitaires de Pau et des Pays de l'Adour, pp.94-U259, 2011, 2-35311-022-3 9782353110223 Book sections hal-00698386v1
	Evolution Moléculaire L. Duret , T. Bataillon , N. Bierne , Vincent Daubin , J. Dutheil sous la direction de Frédéric Thomas; Thierry Lefèvre; Michel Raymond. Biologie évolutive, De Boeck, pp.114-173, 2010, 978-2-8041-0161-9 Book sections hal-00539271v1
	HOVERGEN: comparative analysis of homologous vertebrate genes L. Duret , G. Perrière , Manolo Gouy Letovsky S. Bioinformatics: databases and systems, Springer, pp.21-35, 1999, 978-0-7923-8573-8. ⟨10.1007/0-306-46903-0_3⟩ Book sections hal-00428428v1

Manolo Gouy

Publications

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

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

The Molecular Determinants of Thermoadaptation: Methanococcales as a Case Study

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

Extreme halophilic archaea derive from two distinct methanogen Class II lineages

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

Genome-scale coestimation of species and gene trees.

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

Experimental assessment of the accuracy of genomic selection in sugarcane

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

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

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

What genomes have to say about the evolution of the Earth

Adaptation to Environmental Temperature Is a Major Determinant of Molecular Evolutionary Rates in Archaea

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.

Proposals for classification methods dedicated to biological data

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

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

Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests

Databases of Homologous Gene Families for Comparative Genomics

In Retrospect: Lamarck's treatise at 200

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

Polymorphism of the Staphylococcus aureus Panton-Valentine LeukocidinGenes and Its Possible Link with the Fitness of Community-Associated Methicillin-Resistant S. aureus

Ancient bacteria liked it hot

Parallel Adaptations to High Temperatures in the Archean Eon

Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria

Automatic Identification of Large Collections of Protein-Coding or rRNA Sequences

Remote access to ACNUC nucleotide and protein sequence databases at PBIL

Efficient Likelihood Computations with Nonreversible Models of Evolution

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

Phylogeography of a subterranean amphipod reveals cryptic diversity and dynamic evolution in extreme environments

Origin and molecular evolution of receptor tyrosine kinases with immunoglobulin-like domains.

Clinical and environmental isolates of Legionella pneumophila serogroup 1 cannot be distinguished by sequence analysis of two surface protein genes and three housekeeping genes

Molecular phylogeny of Myricaceae: a reexamination of host-symbiont specificity

In silico whole-genome scanning of cancer-associated nonsynonymous SNPs and molecular characterization of a dynein light chain tumour variant

Horizontal transfer of two operons coding for hydrogenases between bacteria and archaea.

Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases.

Phylogenomics of Life-Or-Death Switches in Multicellular Animals: Bcl-2, BH3-Only, and BNip Families of Apoptotic Regulators

Phylogenetic analysis of the complete genome sequence of Encephalitozoon cuniculi supports the fungal origin of microsporidia and reveals a high frequency of fast-evolving genes

Phylogenetic study and identification of Vibrio splendidus-related strains based on gyrB gene sequences.

Invertebrate Data Predict an Early Emergence of Vertebrate Fibrillar Collagen Clades and an Anti-incest Model

Integrated databanks access and sequence/structure analysis services at the PBIL.

Automatic RNA secondary structure prediction with a comparative approach

Functional and evolutionary analysis of a eukaryotic parasitic genome

Recombination rate and the distribution of transposable elements in the Drosophila melanogaster genome

A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history

Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi

Molecular evidence for the existence of two species of Marteilia in Europe

Nrh, a human homologue of Nr-13 associates with Bcl-Xs and is an inhibitor of apoptosis

Lipid phosphate phosphatases in Arabidopsis. Regulation of the AtLPP1 gene in response to stress

Sequence of the Small Subunit Ribosomal RNA Gene of Perkinsus atlanticus-like Isolated from Carpet Shell Clam in Galicia Spain

Phylogenetic analysis of the small subunit ribosomal RNA of Marteilia refringens validates the existence of phylum Paramyxea (Desportes and Perkins 1990)

HOBACGEN: database system for comparative genomics in bacteria

A nonhyperthermophilic common ancestor to extant life forms

Accounting for evolutionary rate variation among sequence sites consistently changes universal phylogenies deduced from rRNA and protein-coding genes

The non-redundant Bacillus subtilis (NRSub) database: update 1998

Inferring pattern and process: maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis

Phylogenetic analysis and genome size of Ostreococcus tauri (Chlorophyta Prasinophyceae)

Multiple sequence alignment with Clustal X

Microsporidian Encephalitozoon cuniculi a unicellular eukaryote with an unusual chromosomal dispersion of ribosomal genes and a LSU rRNA reduced to the universal core

Sensitivity of the relative-rate test to taxonomic sampling

Microsporidia amitochondrial protists possess a 70-kDa heat shock protein gene of mitochondrial evolutionary origin

Evolutionary distances between nucleotide sequences based on the distribution of substitution rates among sites as estimated by parsimony

Evolutionary affinities of the order Perissodactyla and the phylogenetic status of the superordinal taxa Ungulata and Altungulata

Extreme differences in rates of molecular evolution of foraminifera revealed by comparison of ribosomal DNA sequences and the fossil record

Early origin of foraminifera suggested by SSU rRNA gene sequences

WWW-query: an on-line retrieval system for biological sequence banks

Phylogenetic position of the order Lagomorpha (rabbits hares and allies)

SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny

Inferring phylogenies from DNA sequences of unequal base compositions.

Isolation and characterization of a cDNA encoding a chicken actin-like protein

Phylogenetic position of foraminifera inferred from LSU rRNA gene sequences

HOVERGEN: a database of homologous vertebrate genes