UMR CNRS 5558 Laboratoire de Biométrie et Biologie Évolutive

article :
Abby S S, Tannier E, Gouy M, Daubin V (2012)
Lateral gene transfer as a support for the tree of life, Proc Natl Acad Sci U S A, vol. 109 pp.4962-4967

Boussau B, Gouy M (2012)
What genomes have to say about the evolution of the Earth, Gondwana Research, vol. 21 pp.483-494

Bergeron M, Dauwalder O, Gouy M, Freydiere A-M, Bes M, Meugnier H, Benito Y, Etienne J, Lina G, Vandenesch F, Boisset S (2011)
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 & Infectious Diseases, vol. 30(3) pp.343-354

Groussin M, Gouy M (2011)
Adaptation to Environmental Temperature Is a Major Determinant of Molecular Evolutionary Rates in Archaea, Molecular Biology and Evolution, vol. 28 pp.2661-2674

Abby S, Tannier E, Gouy M, Daubin V (2010)
Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests, BMC Bioinformatics, vol. 11(324) pp.1-13

Arigon A M, Perrière G, Gouy M (2010)
Proposals for classification methods dedicated to biological data, International Journal of Biomedical Engineering and Technology, vol. 3(1) pp.4-21

Gouy M, Guindon S, Gascuell O (2010)
SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building, Molecular Biology and Evolution, vol. 27(2) pp.221-224

Boussau B, Guéguen L, Gouy M (2009)
A Mixture Model and a Hidden Markov Model to Simultaneously Detect Recombination Breakpoints and Reconstruct Phylogenies, Evolutionary Bioinformatics, vol. 5 pp.67-79

Penel S, Arigon A-M, Dufayard J-F, Sertier A-S, Daubin V, Duret L, Gouy M, Perrière G (2009)
Databases of homologous gene families for comparative genomics, BMC Bioinformatics, vol. 10 pp.1-13

Arigon A-M, Perrière G, Gouy M (2008)
Automatic identification of large collections of protein-coding or rRNA sequences, Biochimie, vol. 90 pp.609-614

Boussau B, Blanquart S, Necsulea A, Lartillot N, Gouy M (2008)
Parallel adaptations to high temperatures in the Archaean eon, Nature, vol. 456 pp.942-945

Boussau B, Guéguen L, Gouy M (2008)
Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria, BMC Evolutionary Biology, vol. 8 pp.272-272

Dumitrescu O, Tristan A, Meugnier H, Bes M, Gouy M, Etienne J, Lina G (2008)
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, vol. 198(5) pp.792-794

Gouy M, Chaussidon M (2008)
Ancient bacteria liked it hot, Nature, vol. 451 pp.635-636

Gouy M, Delmotte S (2008)
Remote access to ACNUC nucleotide and protein sequence databases at PBIL, Biochimie, vol. 90 pp.555-562

Arigon A-M, Perrière G, Gouy M (2006)
HoSeql : automated homologous sequence identification in gene family databases, Bioinformatics, vol. 22 pp.1786-1787

Boussau B, Gouy M (2006)
Efficient Likelihood Computations with Nonreversible Models of Evolution, Systematic Biology, vol. 55 pp.756-768

Grassot J, Gouy M, Perrière G, Mouchiroud G (2006)
Origin and Molecular Evolution of Receptor Tyrosine Kinases with Immunoglobulin-Like Domains., Molecular Biology and Evolution, vol. 23 pp.1232-1241

Lefébure T, Douady CJ, Gouy M, Gibert J (2006)
Relationship between morphological taxonomy and molecular divergence within Crustacea : Proposal of a molecular threshold to help species delimitation, Molecular Phylogenetics and Evolution, vol. 40 pp.435-447

Lefébure T, Douady CJ, Gouy M, Trontel P, Briolay J, Gibert J (2006)
Phylogeography of a subterranean amphipod reveals cryptic diversity and dynamic evolution in extreme environments, Molecular Ecology, vol. 15 pp.1797-1806

Aouacheria A, Brunet F, Gouy M (2005)
Phylogenomics of Life-or-Death Switches in Multicellular Animals: Bcl-2 BH3-, Molecular Biology and Evolution, vol. 22 pp.2395-2416

Aouacheria A, Navratil V, Wen W, Jiang M, Mouchiroud D, Gautier C, Gouy M, Zhang M (2005)
In silico whole-genome scanning of cancer-associated nonsynonymous SNPs and molecular characterization of a dynein light chain tumour variant, Oncogene, vol. 24 pp.6133-6142

Aurell H, Farge P, Meugnier H, Gouy M, Forey F, Lina G, Vandenesch F, Etienne J, Jarraud S (2005)
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, vol. 71 pp.282-289

Calteau A, Gouy M, Perrière G (2005)
Horizontal transfer of two operons coding for hydrogenases between bacteria and archaea, Journal of Molecular Evolution, vol. 60 pp.557-565

Dufayard JF, Duret L, Penel S, Gouy M, Rechenmann F, Perrière G (2005)
Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases, Bioinformatics, vol. 21 pp.2596-2603

Huguet V, Gouy M, Normand P, Zimpfer JF, Fernandez MP (2005)
Molecular phylogeny of Myricaceae: a reexamination of host-symbiont specificity, Molecular Phylogenetics and Evolution, vol. 34 pp.557-568

Aouacheria A, Cluzel C, Lethias C, Gouy M, Garrone R, Exposito JY (2004)
Invertebrate data predict an early emergence of vertebrate fibrillar collagen clades and an anti-incest model, Journal of Biological Chemistry, vol. 279 pp.47711-47719

Le Roux F, Gay M, Lambert C, Nicolas JL, Gouy M, Berthe F (2004)
Phylogenetic study and identification of Vibrio splendidus-related strains based on gyrB gene sequences, Diseases of Aquatic Organisms, vol. 58 pp.143-150

Thomarat F, Vivares CP, Gouy M (2004)
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, vol. 59 pp.780-791

Perrière G, Combet C, Penel S, Blanchet C, Thioulouse J, Geourjon C, Grassot J, Charavay C, Gouy M, Duret L, Deléage G (2003)
Integrated databanks access and sequence/structure analysis services at the PBIL., Nucleic Acids Research, vol. 31 pp.3393-3399

Daubin V, Gouy M, Perrière G (2002)
A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history, Genome Research, vol. 12 pp.1080-1090

Rizzon C, Marais GAB, Gouy M, Biémont C (2002)
Recombination rate and the distribution of transposable elements in the Drosophila melanogaster genome, Genome Research, vol. 12 pp.400-407

Tahi F, Gouy M, Regnier M (2002)
Automatic RNA secondary structure prediction with a comparative approach, Journal of Computational Chemistry, vol. 26 pp.521-530

Vivares CP, Gouy M, Thomarat F, Metenier G (2002)
Functional and evolutionary analysis of a eukaryotic parasitic genome, Current Opinion in Microbiology, vol. 5 pp.499-505

Aouacheria A, Arnaud E, Venet S, Lalle P, Gouy M, Rigal D, Gillet G (2001)
Nrh a human homologue of Nr-13 associates with Bcl-Xs and is an inhibitor of apoptosis, Oncogene, vol. 20 pp.5846-5855

Katinka M D, Duprat S, Cornillot E, Metenier G, Thomarat F, Prensier G, Barbe V, Peyretaillade E, Brottier P, Wincker P, Delbac F, El Alaoui H, Peyret P, Saurin W, Gouy M, Weissenbach J, Vivares C P (2001)
Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi, Nature, vol. 414 pp.450-453

Le Roux F, Lorenzo G, Peyret P, Audemard C, Figueras A, Vivares C, Gouy M, Berthe F (2001)
Molecular evidence for the existence of two species of Marteilia in Europe, Journal of Eukaryotic Microbiology, vol. 48(4) pp.449-454

Pierrugues O, Brutesco C, Oshiro J, Gouy M, Deveaux Y, Carman G M, Thuriaux P, Kazmaier M (2001)
Lipid phosphate phosphatases in Arabidopsis. Regulation of the AtLPP1 gene in response to stress, Journal of Biological Chemistry, vol. 276 pp.20300-20308

Berthe FC, Le Roux F, Peyretaillade E, Peyret P, Rodriguez D, Gouy M, Vivares C P (2000)
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, vol. 47 pp.288-293

Figueras A, Lorenzo G, Ordas M C, Gouy M, Novoa B (2000)
Sequence of the Small Subunit Ribosomal RNA Gene of Perkinsus atlanticus-like Isolated from Carpet Shell Clam in Galicia Spain, Marine Biotechnology, vol. 2 pp.419-428

Perrière G, Duret L, Gouy M (2000)
HOBACGEN: database system for comparative genomics in bacteria, Genome Research, vol. 10 pp.379-385

Galtier N, Tourasse N, Gouy M (1999)
A nonhyperthermophilic common ancestor to extant life forms, Science, vol. 283 pp.220-221

Tourasse NJ, Gouy M (1999)
Accounting for evolutionary rate variation among sequence sites consistently changes universal phylogenies deduced from rRNA and protein-coding genes, Molecular Phylogenetics and Evolution, vol. 13 pp.159-168

Courties C, Perasso R, Chrétiennot-Dinet M-J, Gouy M, Guillou L, Troussellier M (1998)
Phylogenetic analysis and genome size of Ostreococcus tauri (Chlorophyta Prasinophyceae), Journal of Phycology, vol. 34 pp.844-849

Galtier N, Gouy M (1998)
Inferring pattern and process: maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis, Molecular Biology and Evolution, vol. 15 pp.871-879

Jeanmougin F, Thompson J D, Gouy M, Higgins D G, Gibson T J (1998)
Multiple sequence alignment with Clustal X, Trends in Biochemical Sciences, vol. 23 pp.403-405

Perrière G, Gouy M, Gojobori T (1998)
The non-redundant Bacillus subtilis (NRSub) database: update 1998, Nucleic Acids Research, vol. 26 pp.60-62

Peyretaillade E, Biderre C, Peyret P, Duffieux F, Metenier G, Gouy M, Michot B, Vivares C P (1998)
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, vol. 26 pp.3513-3520

Peyretaillade E, Broussolle V, Peyret P, Metenier G, Gouy M, Vivares C P (1998)
Microsporidia amitochondrial protists possess a 70-kDa heat shock protein gene of mitochondrial evolutionary origin, Molecular Biology and Evolution, vol. 15 pp.683-689

Robinson M, Gouy M, Gautier C, Mouchiroud D (1998)
Sensitivity of the relative-rate test to taxonomic sampling, Molecular Biology and Evolution, vol. 15 pp.1091-1098

Graur D, Gouy M, Duret L (1997)
Evolutionary affinities of the order Perissodactyla and the phylogenetic status of the superordinal taxa Ungulata and Altungulata, Molecular Phylogenetics and Evolution, vol. 7 pp.195-200

Pawlowski J, Bolivar I, Fahrni J F, de Vargas C, Gouy M, Zaninetti L (1997)
Extreme differences in rates of molecular evolution of foraminifera revealed by comparison of ribosomal DNA sequences and the fossil record, Molecular Biology and Evolution, vol. 14 pp.498-505

Tourasse NJ, Gouy M (1997)
Evolutionary distances between nucleotide sequences based on the distribution of substitution rates among sites as estimated by parsimony, Molecular Biology and Evolution, vol. 14 pp.287-298

Galtier N, Gouy M, Gautier C (1996)
SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny, Bioinformatics, vol. 12 pp.543-548

Graur D, Duret L, Gouy M (1996)
Phylogenetic position of the order Lagomorpha (rabbits hares and allies), Nature, vol. 379 pp.333-335

Pawlowski J, Bolivar I, Fahrni J F, Cavalier-Smith T, Gouy M (1996)
Early origin of foraminifera suggested by SSU rRNA gene sequences, Molecular Biology and Evolution, vol. 13 pp.445-450

Perrière G, Gouy M (1996)
WWW-query: an on-line retrieval system for biological sequence banks, Biochimie, vol. 78 pp.364-369

Galtier N, Gouy M (1995)
Inferring phylogenies from DNA sequences of unequal base compositions, Proceedings of The National Academy of Sciences of The United States of America, vol. 92 pp.11317-11321

Michaille J J, Gouy M, Blanchet S, Duret L (1995)
Isolation and characterization of a cDNA encoding a chicken actin-like protein, Gene, vol. 154 pp.205-209

Duret L, Mouchiroud D, Gouy M (1994)
HOVERGEN: a database of homologous vertebrate genes, Nucleic Acids Research, vol. 22 pp.2360-2365

Galtier N, Gouy M (1994)
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, vol. 145 pp.531-541

Orso S, Gouy M, Navarro E, Normand P (1994)
Molecular Phylogenetic Analysis of Nitrobacter spp, International Journal of Systematic Bacteriology, vol. 44 pp.83-86

Pawlowski J, Bolivar I, Guiard-Maffia J, Gouy M (1994)
Phylogenetic position of foraminifera inferred from LSU rRNA gene sequences, Molecular Biology and Evolution, vol. 11 pp.929-938

Perrière G, Gouy M, Gojobori T (1994)
NRSub: a non-redundant data base for the Bacillus subtilis genome, Nucleic Acids Research, vol. 22 pp.5525-5529

Qu D, Hantz O, Gouy M, Vitvitski L, Li J S, Berby F, Tong S P, Trepo C (1994)
Heterogeneity of hepatitis C virus genotypes in France, Journal of General Virology, vol. 75 ( Pt 5) pp.1063-1070

Cournoyer B, Gouy M, Normand P (1993)
Molecular phylogeny of the symbiotic actinomycetes of the genus Frankia matches host-plant infection processes, Molecular Biology and Evolution, vol. 10 pp.1303-1316

Mounier N, Gouy M, Mouchiroud D, Prudhomme J C (1992)
Insect muscle actins differ distinctly from invertebrate and vertebrate cytoplasmic actins, Journal of Molecular Evolution, vol. 34 pp.406-415

Normand P, Gouy M, Cournoyer B, Simonet P (1992)
Nucleotide sequence of nifD from Frankia alni strain ArI3: phylogenetic inferences, Molecular Biology and Evolution, vol. 9 pp.495-506

Perrin-Pecontal P, Gouy M, Nigon V M, Trabuchet G (1992)
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, vol. 34 pp.17-30

Li W-H, Gouy M (1990)
Statistical tests of molecular phylogenies, Methods in Enzymology, vol. 183 pp.645-659

Li W-H, Gouy M, Sharp P M, O`Huigin C, Yang Y W (1990)
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, vol. 87 pp.6703-6707

Gouy M, Li W-H (1989)
Molecular phylogeny of the kingdoms Animalia Plantae and Fungi, Molecular Biology and Evolution, vol. 6 pp.109-122

Gouy M, Li W-H (1989)
Phylogenetic analysis based on rRNA sequences supports the archaebacterial rather than the eocyte tree, Nature, vol. 339 pp.145-147

Wolfe KH, Gouy M, Yang YW, Sharp PM, Li W-H (1989)
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, vol. 86 pp.6201-6205

Memet S, Gouy M, Marck C, Sentenac A, Buhler J M (1988)
RPA190 the gene coding for the largest subunit of yeast RNA polymerase A, Journal of Biological Chemistry, vol. 263 pp.2830-2839

Gouy M (1987)
Codon contexts in enterobacterial and coliphage genes, Molecular Biology and Evolution, vol. 4 pp.426-444

Higgins DG, Gouy M (1987)
Interfacing similarity search software with the sequence retrieval system ACNUC, Bioinformatics, vol. 3 pp.239-241

Gautier C, Gouy M, Louail S (1985)
Non-parametric statistics for nucleic acid sequence study, Biochimie, vol. 67 pp.449-453

Gouy M, Gautier C, Attimonelli M, Lanave C, di Paola G (1985)
ACNUC--a portable retrieval system for nucleic acid sequence databases: logical and physical designs and usage, Bioinformatics, vol. 1 pp.167-172

Gouy M, Gautier C, Milleret F (1985)
System analysis and nucleic acid sequence banks, Biochimie, vol. 67 pp.433-436

Gouy M, Marliere P, Papanicolaou C, Ninio J (1985)
[Prediction of secondary structures of nucleic acids: algorithmic and physical aspects], Biochimie, vol. 67 pp.523-531

Grantham R, Greenland T, Louail S, Mouchiroud D, Prato J-L, Gouy M, Gautier C (1985)
Molecular evolution of viruses as seen by nucleic acid sequence study, Bulletin de l’Institut Pasteur, vol. 83 pp.95-148

Savatier P, Trabuchet G, Faure C, Chebloune Y, Gouy M, Verdier G, Nigon V M (1985)
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, vol. 182 pp.21-29

Gouy M, Milleret F, Mugnier C, Jacobzone M, Gautier C (1984)
ACNUC: a nucleic acid sequence data base and analysis system, Nucleic Acids Research, vol. 12 pp.121-127

Papanicolaou C, Gouy M, Ninio J (1984)
An energy model that predicts the correct folding of both the tRNA and the 5S RNA molecules, Nucleic Acids Research, vol. 12 pp.31-44

Gouy M, Gautier C (1982)
Codon usage in bacteria: correlation with gene expressivity, Nucleic Acids Research, vol. 10 pp.7055-7074

Grantham R, Gautier C, Gouy M, Jacobzone M, Mercier R (1981)
Codon catalog usage is a genome strategy modulated for gene expressivity, Nucleic Acids Research, vol. 9 pp.R43-R74

Gouy M, Grantham R (1980)
Polypeptide elongation and tRNA cycling in Escherichia coli: a dynamic approach, FEBS Letters, vol. 115 pp.151-155

Grantham R, Gautier C, Gouy M (1980)
Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type, Nucleic Acids Research, vol. 8 pp.1893-1912

Grantham R, Gautier C, Gouy M, Mercier R, Pave A (1980)
Codon catalog usage and the genome hypothesis, Nucleic Acids Research, vol. 8 pp.R49-R62

book :
Gautier C, Gouy M, Jacobzone M, Grantham R (1981)
Nucleic acid sequences handbook, Praeger, 1981

inbook :
Bertrand J C, Brochier-Armanet C, Gouy M, Westall F (2012)
Pendant trois milliards d`années les micro-organismes sont les seuls habitants de la terre, , vol. pp.94-U259

Duret L, Bataillon T, Bierne N, Daubin V, Dutheil J, Gautier C, Glémin S, Gouy M, Heyer E, Marais G, Mouchiroud D, Pontarroti P, Quintana-Murci L, Robinson-Rechavi M, Galtier N (2010)
Evolution Moléculaire, , vol. pp.114-173

Duret L, Perrière G, Gouy M (1999)
HOVERGEN: comparative analysis of homologous vertebrate genes, , vol. pp.21-35