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Michel Lecocq, Mathieu Groussin, Manolo Gouy, Celine Brochier-Armanet. The Molecular Determinants of Thermoadaptation: Methanococcales as a Case Study. Molecular Biology and Evolution, Oxford University Press (OUP), 2020, ⟨10.1093/molbev/msaa312⟩. ⟨hal-03118165⟩

Nicolas Comte, Benoît Morel, Damir Hasic, Laurent Guéguen, Bastien Boussau, et al.. Treerecs: an integrated phylogenetic tool, from sequences to reconciliations.. Bioinformatics, Oxford University Press (OUP), 2020, 36 (18), pp.4822-4824. ⟨10.1093/bioinformatics/btaa615⟩. ⟨hal-02883386⟩

Monique Aouad, Najwa Taïb, Anne Oudart, Michel Lecocq, Manolo Gouy, et al.. Extreme halophilic archaea derive from two distinct methanogen Class II lineages. Molecular Phylogenetics and Evolution, Elsevier, 2018, 127, pp.46-54. ⟨10.1016/j.ympev.2018.04.011⟩. ⟨hal-01799910⟩

Mathieu Groussin, Bastien Boussau, Gergely Szollosi, Laura Eme, Manolo Gouy, et al.. Gene Acquisitions from Bacteria at the Origins of Major Archaeal Clades Are Vastly Overestimated. Molecular Biology and Evolution, Oxford University Press (OUP), 2016, 33 (2), pp.305 - 310. ⟨10.1093/molbev/msv249⟩. ⟨hal-01913926⟩

Frédéric Jauffrit, Simon Penel, Stéphane Delmotte, Carine Rey, Damien de Vienne, et al.. RiboDB database: a comprehensive resource for prokaryotic systematics. Molecular Biology and Evolution, Oxford University Press (OUP), 2016, 33 (8), pp.2170--2172. ⟨10.1093/molbev/msw088⟩. ⟨hal-01800061⟩

Jean-Pierre Flandrois, G. Perrière, Manolo Gouy. leBIBIQBPP: a set of databases and a webtool for automatic phylogenetic analysis of prokaryotic sequences. BMC Bioinformatics, BioMed Central, 2015, 16 (1), pp.251. ⟨10.1186/s12859-015-0692-z⟩. ⟨hal-02044751⟩

M. Groussin, J. K. Hobbs, G. J. Szollosi, S. Gribaldo, V. L. Arcus, et al.. Toward more accurate ancestral protein genotype-phenotype reconstructions with the use of species tree-aware gene trees. Molecular Biology and Evolution, Oxford University Press (OUP), 2015, 32, pp.13-22. ⟨10.1093/molbev/msu305⟩. ⟨hal-02044770⟩

Nc. Rochette, Céline Brochier-Armanet, M. Gouy. Phylogenomic test of the hypotheses for the evolutionary origin of eukaryotes. Molecular Biology and Evolution, Oxford University Press (OUP), 2014, 31 (4), pp.832-45. ⟨10.1093/molbev/mst272⟩. ⟨hal-02045522⟩

M. Groussin, Bastien Boussau, Manolo Gouy. A Branch-Heterogeneous Model of Protein Evolution for Efficient Inference of Ancestral Sequences. Systematic Biology, Oxford University Press (OUP), 2013, 62 (4), pp.523-538. ⟨10.1093/sysbio/syt016⟩. ⟨hal-02320419⟩

Mathieu Groussin, Bastien Boussau, Sandrine Charles, Samuel Blanquart, Manolo Gouy. The molecular signal for the adaptation to cold temperature during early life on Earth. Biology Letters, Royal Society, The, 2013, 9 (5), pp.20130608. ⟨hal-00918283⟩

M. Gouy, Y. Rousselle, Denis Bastianelli, Philippe Lecomte, L. Bonnal, et al.. Experimental assessment of the accuracy of genomic selection in sugarcane. TAG Theoretical and Applied Genetics, Springer Verlag, 2013, 126 (10), pp.2575-2586. ⟨10.1007/s00122-013-2156-z⟩. ⟨hal-02648497⟩

Laurent Gueguen, Sylvain Gaillard, Bastien Boussau, Manolo Gouy, Mathieu Groussin, et al.. Bio++ : Efficient Extensible Libraries and Tools for Computational Molecular Evolution. Molecular Biology and Evolution, Oxford University Press (OUP), 2013, 30 (8), pp.1745 - 1750. ⟨10.1093/molbev/mst097⟩. ⟨hal-01209906⟩

Bastien Boussau, Gergely J Szöllosi, L. Duret, Manolo Gouy, Eric Tannier, et al.. Genome-scale coestimation of species and gene trees.. Genome Research, Cold Spring Harbor Laboratory Press, 2013, 23 (2), pp.323-330. ⟨10.1101/gr.141978.112⟩. ⟨hal-00750148⟩

Bastien Boussau, Manolo Gouy. What genomes have to say about the evolution of the Earth. Gondwana Research, Elsevier, 2012, 21, pp.483-494. ⟨10.1016/j.gr.2011.08.002⟩. ⟨hal-00698400⟩

J.C. Bertrand, Céline Brochier-Armanet, Manolo Gouy, F. Westall. Pendant trois milliards d'années les micro-organismes sont les seuls habitants de la terre. incollection, 2012, --, pp.94-U259. ⟨hal-00698386⟩

Sophie S Abby, Eric Tannier, Manolo Gouy, Vincent Daubin. Lateral gene transfer as a support for the tree of life.. Proceedings of the National Academy of Sciences of the United States of America , National Academy of Sciences, 2012, 109 (13), pp.4962-4967. ⟨10.1073/pnas.1116871109⟩. ⟨hal-00752055⟩

Marie Bergeron, Olivier Dauwalder, Manolo Gouy, Anne-Marie Freydiere, Michèle Bes, et al.. 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.. European Journal of Clinical Microbiology and Infectious Diseases, Springer Verlag, 2011, 30 (3), pp.343-54. ⟨10.1007/s10096-010-1091-z⟩. ⟨hal-00698367⟩

M. Groussin, Manolo Gouy. Adaptation to Environmental Temperature Is a Major Determinant of Molecular Evolutionary Rates in Archaea. Molecular Biology and Evolution, Oxford University Press (OUP), 2011, 28, pp.2661-2674. ⟨10.1093/molbev/msr098⟩. ⟨hal-00697929⟩

Anne-Muriel Arigon Chifolleau, Guy Perrière, Manolo Gouy. Proposals for classification methods dedicated to biological data. International Journal of Biomedical Engineering and Technology (IJBET), Inderscience, 2010, 3 (1/2), pp.4-21. ⟨10.1504/IJBET.2010.029649⟩. ⟨lirmm-00830931⟩

M. Bergeron, O. Dauwalder, M. Gouy, A.-M. Freydiere, M. Bes, et al.. 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. European Journal of Clinical Microbiology and Infectious Diseases, Springer Verlag, 2010, pp.343-354. ⟨10.1007/s10096-010-1091-z⟩. ⟨hal-00634698⟩

Sophie Abby, Eric Tannier, Manolo Gouy, Vincent Daubin. Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests. BMC Bioinformatics, BioMed Central, 2010, 11 (324), pp.13. ⟨10.1186/1471-2105-11-324⟩. ⟨inria-00527151⟩

Manolo Gouy, Stéphane Guindon, Olivier Gascuel. SeaView Version 4: a Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building. Molecular Biology and Evolution, Oxford University Press (OUP), 2010, 27, pp.221-224. ⟨10.1093/molbev/msp259⟩. ⟨lirmm-00511794v2⟩

Dan Graur, Manolo Gouy, David Wool. In Retrospect: Lamarck's treatise at 200. Nature, Nature Publishing Group, 2009, 460 (7256), pp.688-689. ⟨10.1038/460688a⟩. ⟨hal-02320435⟩

Simon Penel, Anne-Muriel Arigon Chifolleau, Jean-François Dufayard, Anne-Sophie Sertier, Vincent Daubin, et al.. Databases of Homologous Gene Families for Comparative Genomics. BMC Bioinformatics, BioMed Central, 2009, 10 (Suppl.6) :S3, pp.13. ⟨10.1186/1471-2105-10-S6-S3⟩. ⟨lirmm-00400099⟩

Bastien Boussau, Laurent Guéguen, Manolo Gouy. A Mixture Model and a Hidden Markov Model to Simultaneously Detect Recombination Breakpoints and Reconstruct Phylogenies. Evolutionary Bioinformatics, Libertas Academica (New Zealand), 2009, 5, pp.67-79. ⟨hal-00428395⟩

O. Dumitrescu, A. Tristan, H. Meugnier, M. Bes, Manolo Gouy, et al.. Polymorphism of the Staphylococcus aureus Panton-Valentine LeukocidinGenes and Its Possible Link with the Fitness of Community-Associated Methicillin-Resistant S. aureus. Journal of Infectious Diseases, Oxford University Press (OUP), 2008, 198(5), pp.792-794. ⟨hal-00428303⟩

Anne-Muriel Arigon Chifolleau, Guy Perrière, Manolo Gouy. Automatic Identification of Large Collections of Protein-Coding or rRNA Sequences. Biochimie, Elsevier, 2008, 90 (4), pp.609-614. ⟨10.1016/j.biochi.2007.08.006⟩. ⟨lirmm-00366131⟩

Manolo Gouy, Stephane Delmotte. Remote access to ACNUC nucleotide and protein sequence databases at PBIL. Biochimie, Elsevier, 2008, 90, pp.555-562. ⟨10.1016/j.biochi.2007.07.003⟩. ⟨hal-00428117⟩

Bastien Boussau, Samuel Blanquart, Anamaria Necsulea, Nicolas Lartillot, Manolo Gouy. Parallel Adaptations to High Temperatures in the Archean Eon. Nature, Nature Publishing Group, 2008, 456 (7224), pp.942-945. ⟨10.1038/nature07393⟩. ⟨lirmm-00324159⟩

Bastien Boussau, Laurent Guéguen, Manolo Gouy. Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria. BMC Evolutionary Biology, BioMed Central, 2008, 8, pp.272-272. ⟨hal-00428101⟩

M. Gouy, M. Chaussidon. Ancient bacteria liked it hot. Nature, Nature Publishing Group, 2008, 451, pp.635-636. ⟨hal-00345924⟩

Anne-Muriel Arigon Chifolleau, G. Perrière, Manolo Gouy. HoSeql : automated homologous sequence identification in gene family databases. Bioinformatics, Oxford University Press (OUP), 2006, 22, pp.1786-1787. ⟨hal-00427893⟩

Bastien Boussau, Manolo Gouy. Efficient Likelihood Computations with Nonreversible Models of Evolution. Systematic Biology, Oxford University Press (OUP), 2006, 55, pp.756-768. ⟨hal-00427908⟩

T. Lefébure, C.J. Douady, Manolo Gouy, P. Trontel, J. Briolay, et al.. Phylogeography of a subterranean amphipod reveals cryptic diversity and dynamic evolution in extreme environments. Molecular Ecology, Wiley, 2006, 15, pp.1797-1806. ⟨10.1111/j.1365-294X.2006.02888.x⟩. ⟨hal-00427985⟩

T. Lefébure, C.J. Douady, Manolo Gouy, J. Gibert. Relationship between morphological taxonomy and molecular divergence within Crustacea : Proposal of a molecular threshold to help species delimitation. Molecular Phylogenetics and Evolution, Elsevier, 2006, 40, pp.435-447. ⟨10.1016/j.ympev.2006.03.014⟩. ⟨hal-00427988⟩

Julien Grassot, Manolo Gouy, Guy Perrière, Guy Mouchiroud. Origin and molecular evolution of receptor tyrosine kinases with immunoglobulin-like domains.. Molecular Biology and Evolution, Oxford University Press (OUP), 2006, 23 (6), pp.1232-41. ⟨10.1093/molbev/msk007⟩. ⟨hal-00192848⟩

J. Grassot, M. Gouy, G. Perrière, G. Mouchiroud. Origin and molecular evolultion of receptor tyrosine kinases with immunglobulin-like domains.. Molecular Biology and Evolution, Oxford University Press (OUP), 2006, pp.1232-1241. ⟨hal-00146962⟩

A. Calteau, Manolo Gouy, G. Perrière. Horizontal transfer of two operons coding for hydrogenases between bacteria and archaea.. Journal of Molecular Evolution, Springer Verlag, 2005, 60 (5), pp.557-65. ⟨10.1007/s00239-004-0094-8⟩. ⟨hal-00427722⟩

Jean-François Dufayard, L. Duret, S. Penel, Manolo Gouy, F. Rechenmann, et al.. Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases.. Bioinformatics, Oxford University Press (OUP), 2005, 21 (11), pp.2596-603. ⟨10.1093/bioinformatics/bti325⟩. ⟨hal-00427861⟩

H. Aurell, Pierre Farge, H. Meugnier, Manolo Gouy, F. Forey, et al.. Clinical and environmental isolates of Legionella pneumophila serogroup 1 cannot be distinguished by sequence analysis of two surface protein genes and three housekeeping genes. Applied and Environmental Microbiology, American Society for Microbiology, 2005, 71, pp.282-289. ⟨10.1128/AEM.71.1.282-289.2005⟩. ⟨hal-00427706⟩

V. Huguet, Manolo Gouy, P. Normand, J.F. Zimpfer, M.P. Fernandez. Molecular phylogeny of Myricaceae: a reexamination of host-symbiont specificity. Molecular Phylogenetics and Evolution, Elsevier, 2005, 34, pp.557-568. ⟨hal-00427839⟩

A. Aouacheria, V. Navratil, W. Wen, M. Jiang, Dominique Mouchiroud, et al.. In silico whole-genome scanning of cancer-associated nonsynonymous SNPs and molecular characterization of a dynein light chain tumour variant. Oncogene, Nature Publishing Group, 2005, 24, pp.6133-6142. ⟨hal-00427704⟩

A. Aouacheria, F. Brunet, Manolo Gouy. Phylogenomics of Life-or-Death Switches in Multicellular Animals: Bcl-2 BH3-. Molecular Biology and Evolution, Oxford University Press (OUP), 2005, 22, pp.2395-2416. ⟨hal-00427703⟩

Frédérique Le Roux, Mélanie Gay, Christophe Lambert, Jean-Louis Nicolas, Manolo Gouy, et al.. Phylogenetic study and identification of Vibrio splendidus-related strains based on gyrB gene sequences.. Diseases of Aquatic Organisms, Inter Research, 2004, 58 (2-3), pp.143-150. ⟨hal-00458183⟩

Abdel Aouacheria, Caroline Cluzel, Claire Lethias, Manolo Gouy, Robert Garrone, et al.. Invertebrate Data Predict an Early Emergence of Vertebrate Fibrillar Collagen Clades and an Anti-incest Model. Journal of Biological Chemistry, American Society for Biochemistry and Molecular Biology, 2004, 260, pp.15352 - 47719. ⟨10.1007/978-3-642-86659-3⟩. ⟨hal-00427534v2⟩

F. Thomarat, Christian Vivarès, Manolo Gouy. 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. Journal of Molecular Evolution, Springer Verlag, 2004, 59, pp.780-791. ⟨10.1007/s00239-004-2673-0⟩. ⟨hal-00427661⟩

G. Perriere, C. Combet, S. Penel, C. Blanchet, J. Thioulouse, et al.. Integrated databanks access and sequence/structure analysis services at the PBIL.. Nucleic Acids Research, Oxford University Press, 2003, pp.3393-3399. ⟨hal-00146928⟩

G. Perriere, C. Combet, S. Penel, C. Blanchet, J. Thioulouse, et al.. Integrated databanks access and sequence/structure analysis services at the PBIL.. Nucleic Acids Research, Oxford University Press, 2003, 31, pp.3393-3399. ⟨hal-00313743⟩

F. Tahi, Manolo Gouy, M. Regnier. Automatic RNA secondary structure prediction with a comparative approach. Journal of Computational Chemistry, Wiley, 2002, 26, pp.521-530. ⟨hal-00427303⟩

Vincent Daubin, Manolo Gouy, G. Perrière. A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history. Genome Research, Cold Spring Harbor Laboratory Press, 2002, 12, pp.1080-1090. ⟨hal-00427259⟩

C. Rizzon, Gabriel Marais, Manolo Gouy, C. Biémont. Recombination rate and the distribution of transposable elements in the Drosophila melanogaster genome. Genome Research, Cold Spring Harbor Laboratory Press, 2002, 12, pp.400-407. ⟨hal-00427298⟩

Christian Vivarès, Manolo Gouy, F. Thomarat, G. Metenier. Functional and evolutionary analysis of a eukaryotic parasitic genome. Current Opinion in Microbiology, Elsevier, 2002, 5, pp.499-505. ⟨hal-00427309⟩

O. Pierrugues, C. Brutesco, J. Oshiro, Manolo Gouy, Y. Deveaux, et al.. Lipid phosphate phosphatases in Arabidopsis. Regulation of the AtLPP1 gene in response to stress. Journal of Biological Chemistry, American Society for Biochemistry and Molecular Biology, 2001, 276, pp.20300-20308. ⟨hal-00427174⟩

F. Le Roux, G. Lorenzo, P. Peyret, C. Audemard, A. Figueras, et al.. Molecular evidence for the existence of two species of Marteilia in Europe. Journal of Eukaryotic Microbiology, Wiley, 2001, 48(4), pp.449-454. ⟨hal-00427181⟩

A. Aouacheria, E. Arnaud, S. Venet, P. Lalle, M. Gouy, et al.. Nrh, a human homologue of Nr-13 associates with Bcl-Xs and is an inhibitor of apoptosis.. Oncogene, Nature Publishing Group, 2001, 20, pp.5846-5855. ⟨hal-00314329⟩

A. Aouacheria, E. Arnaud, S. Venet, P. Lalle, Manolo Gouy, et al.. Nrh a human homologue of Nr-13 associates with Bcl-Xs and is an inhibitor of apoptosis. Oncogene, Nature Publishing Group, 2001, 20, pp.5846-5855. ⟨hal-00427154⟩

M.D. Katinka, S. Duprat, E. Cornillot, G. Metenier, F. Thomarat, et al.. Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi. Nature, Nature Publishing Group, 2001, 414, pp.450-453. ⟨10.1038/35106579⟩. ⟨hal-00427201⟩

A. Figueras, G. Lorenzo, M.C. Ordas, Manolo Gouy, B. Novoa. Sequence of the Small Subunit Ribosomal RNA Gene of Perkinsus atlanticus-like Isolated from Carpet Shell Clam in Galicia Spain. Marine Biotechnology, Springer Verlag, 2000, 2, pp.419-428. ⟨hal-00427078⟩

F.C. Berthe, F. Le Roux, E. Peyretaillade, P. Peyret, D. Rodriguez, et al.. Phylogenetic analysis of the small subunit ribosomal RNA of Marteilia refringens validates the existence of phylum Paramyxea (Desportes and Perkins 1990). Journal of Eukaryotic Microbiology, Wiley, 2000, 47, pp.288-293. ⟨hal-00427063⟩

G. Perrière, L. Duret, Manolo Gouy. HOBACGEN: database system for comparative genomics in bacteria. Genome Research, Cold Spring Harbor Laboratory Press, 2000, 10, pp.379-385. ⟨hal-00427099⟩

L. Duret, G. Perrière, Manolo Gouy. HOVERGEN: comparative analysis of homologous vertebrate genes. incollection, 1999, --, pp.21-35. ⟨hal-00428428⟩

N. Galtier, N. Tourasse, Manolo Gouy. A nonhyperthermophilic common ancestor to extant life forms. Science, American Association for the Advancement of Science, 1999, 283, pp.220-221. ⟨10.1126/science.283.5399.220⟩. ⟨hal-00428447⟩

N.J. Tourasse, Manolo Gouy. Accounting for evolutionary rate variation among sequence sites consistently changes universal phylogenies deduced from rRNA and protein-coding genes. Molecular Phylogenetics and Evolution, Elsevier, 1999, 13, pp.159-168. ⟨10.1006/mpev.1999.0675⟩. ⟨hal-00428462⟩

F. Jeanmougin, J.D. Thompson, Manolo Gouy, D.G. Higgins, T.J. Gibson. Multiple sequence alignment with Clustal X. Trends in Biochemical Sciences, Elsevier, 1998, 23, pp.403-405. ⟨hal-00428491⟩

E. Peyretaillade, V. Broussolle, P. Peyret, G. Metenier, Manolo Gouy, et al.. Microsporidia amitochondrial protists possess a 70-kDa heat shock protein gene of mitochondrial evolutionary origin. Molecular Biology and Evolution, Oxford University Press (OUP), 1998, 15, pp.683-689. ⟨hal-00428498⟩

E. Peyretaillade, C. Biderre, P. Peyret, F. Duffieux, G. Metenier, et al.. Microsporidian Encephalitozoon cuniculi a unicellular eukaryote with an unusual chromosomal dispersion of ribosomal genes and a LSU rRNA reduced to the universal core. Nucleic Acids Research, Oxford University Press, 1998, 26, pp.3513-3520. ⟨hal-00428508⟩

G. Perrière, Manolo Gouy, T. Gojobori. The non-redundant Bacillus subtilis (NRSub) database: update 1998. Nucleic Acids Research, Oxford University Press, 1998, 26, pp.60-62. ⟨hal-00428499⟩

M. Robinson, Manolo Gouy, Christian Gautier, Dominique Mouchiroud. Sensitivity of the relative-rate test to taxonomic sampling. Molecular Biology and Evolution, Oxford University Press (OUP), 1998, 15, pp.1091-1098. ⟨hal-00428501⟩

N. Galtier, Manolo Gouy. Inferring pattern and process: maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis. Molecular Biology and Evolution, Oxford University Press (OUP), 1998, 15, pp.871-879. ⟨hal-00428472⟩

C. Courties, R. Perasso, M.-J. Chrétiennot-Dinet, Manolo Gouy, Laure Guillou, et al.. Phylogenetic analysis and genome size of Ostreococcus tauri (Chlorophyta Prasinophyceae). Journal of Phycology, Wiley, 1998, 34, pp.844-849. ⟨hal-00428471⟩

J. Pawlowski, I. Bolivar, J.F. Fahrni, C. de Vargas, Manolo Gouy, et al.. Extreme differences in rates of molecular evolution of foraminifera revealed by comparison of ribosomal DNA sequences and the fossil record. Molecular Biology and Evolution, Oxford University Press (OUP), 1997, 14, pp.498-505. ⟨hal-00434978⟩

N.J. Tourasse, Manolo Gouy. Evolutionary distances between nucleotide sequences based on the distribution of substitution rates among sites as estimated by parsimony. Molecular Biology and Evolution, Oxford University Press (OUP), 1997, 14, pp.287-298. ⟨hal-00434995⟩

D. Graur, Manolo Gouy, L. Duret. Evolutionary affinities of the order Perissodactyla and the phylogenetic status of the superordinal taxa Ungulata and Altungulata. Molecular Phylogenetics and Evolution, Elsevier, 1997, 7, pp.195-200. ⟨hal-00434984⟩

D. Graur, L. Duret, Manolo Gouy. Phylogenetic position of the order Lagomorpha (rabbits hares and allies). Nature, Nature Publishing Group, 1996, 379, pp.333-335. ⟨hal-00435019⟩

G. Perrière, Manolo Gouy. WWW-query: an on-line retrieval system for biological sequence banks. Biochimie, Elsevier, 1996, 78, pp.364-369. ⟨hal-00435034⟩

N. Galtier, Manolo Gouy, Christian Gautier. SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. Bioinformatics, Oxford University Press (OUP), 1996, 12, pp.543-548. ⟨hal-00435028⟩

J. Pawlowski, I. Bolivar, J.F. Fahrni, T. Cavalier-Smith, Manolo Gouy. Early origin of foraminifera suggested by SSU rRNA gene sequences. Molecular Biology and Evolution, Oxford University Press (OUP), 1996, 13, pp.445-450. ⟨hal-00435033⟩

J.J. Michaille, Manolo Gouy, S. Blanchet, L. Duret. Isolation and characterization of a cDNA encoding a chicken actin-like protein. Gene, Elsevier, 1995, 154, pp.205-209. ⟨hal-00698055⟩

N. Galtier, Manolo Gouy. Inferring phylogenies from DNA sequences of unequal base compositions.. Proceedings of the National Academy of Sciences of the United States of America , National Academy of Sciences, 1995, 92 (24), pp.11317-11321. ⟨10.1073/pnas.92.24.11317⟩. ⟨hal-02320510⟩

D. Qu, O. Hantz, Manolo Gouy, L. Vitvitski, J.S. Li, et al.. Heterogeneity of hepatitis C virus genotypes in France. Journal of General Virology, Microbiology Society, 1994, 75 ( Pt 5), pp.1063-1070. ⟨hal-00698153⟩

S. Orso, Manolo Gouy, E. Navarro, P. Normand. Molecular Phylogenetic Analysis of Nitrobacter spp. International Journal of Systematic Bacteriology, Society for General Microbiology, 1994, 44, pp.83-86. ⟨hal-00698105⟩

N. Galtier, Manolo Gouy. Molecular phylogeny of Eubacteria: a new multiple tree analysis method applied to 15 sequence data sets questions the monophyly of Gram-positive bacteria. Research in Microbiology, Elsevier, 1994, 145 (7), pp.531-541. ⟨10.1016/0923-2508(94)90030-2⟩. ⟨hal-02320465⟩

G. Perrière, Manolo Gouy, T. Gojobori. NRSub: a non-redundant data base for the Bacillus subtilis genome. Nucleic Acids Research, Oxford University Press, 1994, 22, pp.5525-5529. ⟨hal-00698135⟩

L. Duret, Dominique Mouchiroud, Manolo Gouy. HOVERGEN: a database of homologous vertebrate genes. Nucleic Acids Research, Oxford University Press, 1994, 22, pp.2360-2365. ⟨hal-00698069⟩

J. Pawlowski, I. Bolivar, J. Guiard-Maffia, Manolo Gouy. Phylogenetic position of foraminifera inferred from LSU rRNA gene sequences. Molecular Biology and Evolution, Oxford University Press (OUP), 1994, 11, pp.929-938. ⟨hal-00698124⟩

Benoit Cournoyer, Manolo Gouy, Philippe Normand. Molecular phylogeny of the symbiotic actinomycetes of the genus Frankia matches host-plant infection processes.. Molecular Biology and Evolution, Oxford University Press (OUP), 1993, ⟨10.1093/oxfordjournals.molbev.a040077⟩. ⟨hal-02320516⟩

P. Normand, Manolo Gouy, B. Cournoyer, P. Simonet. Nucleotide sequence of nifD from Frankia alni strain ArI3: phylogenetic inferences. Molecular Biology and Evolution, Oxford University Press (OUP), 1992, 9, pp.495-506. ⟨hal-00698088⟩

P. Perrin-Pecontal, Manolo Gouy, V.M. Nigon, G. Trabuchet. 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. Journal of Molecular Evolution, Springer Verlag, 1992, 34, pp.17-30. ⟨hal-00698137⟩

N. Mounier, Manolo Gouy, Dominique Mouchiroud, J.C. Prudhomme. Insect muscle actins differ distinctly from invertebrate and vertebrate cytoplasmic actins. Journal of Molecular Evolution, Springer Verlag, 1992, 34, pp.406-415. ⟨hal-00698078⟩

W.-H. Li, Manolo Gouy. Statistical tests of molecular phylogenies. Methods in Enzymology, Elsevier, 1990, 183, pp.645-659. ⟨hal-00698014⟩

W.-H. Li, Manolo Gouy, P.M. Sharp, C. O'Huigin, Y.W. Yang. Molecular phylogeny of Rodentia Lagomorpha Primates Artiodactyla and Carnivora and molecular clocks. Proceedings of the National Academy of Sciences of the United States of America , National Academy of Sciences, 1990, 87, pp.6703-6707. ⟨hal-00698389⟩

Manolo Gouy, W.-H. Li. Phylogenetic analysis based on rRNA sequences supports the archaebacterial rather than the eocyte tree. Nature, Nature Publishing Group, 1989, 339, pp.145-147. ⟨hal-00697921⟩

Manolo Gouy, W.-H. Li. Molecular phylogeny of the kingdoms Animalia Plantae and Fungi. Molecular Biology and Evolution, Oxford University Press (OUP), 1989, 6, pp.109-122. ⟨hal-00697919⟩

K.H. Wolfe, Manolo Gouy, Y.W. Yang, P.M. Sharp, W.-H. Li. Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data. Proceedings of the National Academy of Sciences of the United States of America , National Academy of Sciences, 1989, 86, pp.6201-6205. ⟨hal-00698329⟩

S. Memet, Manolo Gouy, C. Marck, A. Sentenac, J.M. Buhler. RPA190 the gene coding for the largest subunit of yeast RNA polymerase A. Journal of Biological Chemistry, American Society for Biochemistry and Molecular Biology, 1988, 263, pp.2830-2839. ⟨hal-00698053⟩

D.G. Higgins, Manolo Gouy. Interfacing similarity search software with the sequence retrieval system ACNUC. Bioinformatics, Oxford University Press (OUP), 1987, 3, pp.239-241. ⟨hal-00697947⟩

Manolo Gouy. Codon contexts in enterobacterial and coliphage genes. Molecular Biology and Evolution, Oxford University Press (OUP), 1987, 4, pp.426-444. ⟨10.1093/oxfordjournals.molbev.a040450⟩. ⟨hal-00697910⟩

R. Grantham, T. Greenland, S. Louail, Dominique Mouchiroud, J.-L. Prato, et al.. Molecular evolution of viruses as seen by nucleic acid sequence study. Bulletin de l'Institut Pasteur, 1985, 83, pp.95-148. ⟨hal-00697914⟩

Manolo Gouy, P. Marliere, C. Papanicolaou, J. Ninio. [Prediction of secondary structures of nucleic acids: algorithmic and physical aspects]. Biochimie, Elsevier, 1985, 67, pp.523-531. ⟨hal-00697912⟩

Manolo Gouy, Christian Gautier, F. Milleret. System analysis and nucleic acid sequence banks. Biochimie, Elsevier, 1985, 67, pp.433-436. ⟨hal-00697903⟩

C. Gautier, Manolo Gouy, S. Louail. Non-parametric statistics for nucleic acid sequence study. Biochimie, Elsevier, 1985, 67 (5), pp.449-453. ⟨10.1016/S0300-9084(85)80263-7⟩. ⟨hal-02320490⟩

Manolo Gouy, Christian Gautier, M. Attimonelli, C. Lanave, G. Di Paola. ACNUC--a portable retrieval system for nucleic acid sequence databases: logical and physical designs and usage. Bioinformatics, Oxford University Press (OUP), 1985, 1, pp.167-172. ⟨hal-00697905⟩

P. Savatier, G. Trabuchet, C. Faure, Y. Chebloune, M. Gouy, et al.. Evolution of the primate β-globin gene region. Journal of Molecular Biology, Elsevier, 1985, 182 (1), pp.21-29. ⟨10.1016/0022-2836(85)90024-5⟩. ⟨hal-02965509⟩

P. Savatier, G. Trabuchet, C. Faure, Y. Chebloune, Manolo Gouy, et al.. Evolution of the primate beta-globin gene region. High rate of variation in CpG dinucleotides and in short repeated sequences between man and chimpanzee. Journal of Molecular Biology, Elsevier, 1985, 182, pp.21-29. ⟨hal-00698207⟩

Manolo Gouy, F. Milleret, C. Mugnier, M. Jacobzone, Christian Gautier. ACNUC: a nucleic acid sequence data base and analysis system. Nucleic Acids Research, Oxford University Press, 1984, 12, pp.121-127. ⟨hal-00697916⟩

C. Papanicolaou, Manolo Gouy, J. Ninio. An energy model that predicts the correct folding of both the tRNA and the 5S RNA molecules. Nucleic Acids Research, Oxford University Press, 1984, 12, pp.31-44. ⟨hal-00698110⟩

Manolo Gouy, Christian Gautier. Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Research, Oxford University Press, 1982, 10, pp.7055-7074. ⟨10.1093/nar/10.22.7055⟩. ⟨hal-00697906⟩

R. Grantham, Christian Gautier, Manolo Gouy, M. Jacobzone, R. Mercier. Codon catalog usage is a genome strategy modulated for gene expressivity. Nucleic Acids Research, Oxford University Press, 1981, 9, pp.R43-R74. ⟨10.1093/nar/9.1.213-b⟩. ⟨hal-00697917⟩

Manolo Gouy, R. Grantham. Polypeptide elongation and tRNA cycling in Escherichia coli: a dynamic approach. FEBS Letters, Wiley, 1980, 115, pp.151-155. ⟨10.1016/0014-5793(80)81155-0⟩. ⟨hal-00697904⟩

R. Grantham, Christian Gautier, Manolo Gouy, R. Mercier, A. Pave. Codon catalog usage and the genome hypothesis. Nucleic Acids Research, Oxford University Press, 1980, 8, pp.R49-R62. ⟨hal-00697923⟩

R. Grantham, Christian Gautier, Manolo Gouy. Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type. Nucleic Acids Research, Oxford University Press, 1980, 8, pp.1893-1912. ⟨hal-00697920⟩

T. Lefébure, Christophe Douady, M. Gouy, P. Trontelj, J. Briolay, et al.. Phylogeography and taxonomic status of Niphargus virei (subterranean amphipod).. 2005, pp.73-74. ⟨halsde-00157705⟩

Gilbert Deléage, Manolo Gouy. Bioinformatique : cours et cas pratique. Dunod, 2013, 978-2-10-058751-3. ⟨hal-02086801⟩

Christian Gautier, Manolo Gouy, Monique Jacobzone, Richard Grantham. Nucleic acid sequences handbook. Praeger, 1-2, 1981. ⟨hal-02087468⟩

Manolo Gouy, Eric Tannier, Nicolas Comte, David Parsons. Seaview Version 5: A Multiplatform Software for Multiple Sequence Alignment, Molecular Phylogenetic Analyses, and Tree Reconciliation. Multiple Sequence Alignment, 2231, Humana, pp.241-260, 2020, Methods in Molecular Biology, ⟨10.1007/978-1-0716-1036-7_15⟩. ⟨hal-03065564⟩

Mathieu Groussin, Manolo Gouy, Vincent Daubin, Eric Tannier. Ancestral Reconstruction: Theory and Practice. Richard M. Kliman. Encyclopedia of Evolutionary Biology, Elsevier, pp.70-77, 2016. ⟨hal-01334934⟩

L. Duret, T. Bataillon, N. Bierne, Vincent Daubin, J. Dutheil, et al.. Evolution Moléculaire. sous la direction de Frédéric Thomas; Thierry Lefèvre; Michel Raymond. Biologie évolutive, De Boeck, pp.114-173, 2010, 978-2-8041-0161-9. ⟨hal-00539271⟩