UMR CNRS 5558 Laboratoire de Biométrie et Biologie Évolutive

Anselmetti Y, Duchemin W, Tannier E, Chauve C, Bérard S (2018)
Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes, BMC Genomics, vol. 19 pp.96-96.

Anselmetti Y, Luhmann N, Bérard S, Tannier E, Chauve C (2018)
Comparative Methods for Reconstructing Ancient Genome Organization
in: Methods in Molecular Biology, , pp.343-362.

Aouad M, Taib N, Oudart A, Lecocq M, Gouy M, Brochier-Armanet C (2018)
Extreme halophilic archaea derive from two distinct methanogen Class II lineages, Molecular phylogenetics and evolution, vol. 127 pp.46-54.

Branco S, Carpentier F, Rodriguez de la Vega RC, Badouin H, Snirc A, Le Prieur S, Coelho M A, de Vienne DM, Hartmann FE, Begerow D, Hood ME, Giraud T (2018)
Multiple convergent supergene evolution events in mating-type chromosomes, Nature communications, vol. 9 pp.2000-2000.

Collet M, Amat I, Sauzet S, Auguste A, Fauvergue X, Mouton L, Desouhant E (2018)
Insects and incest: sib-mating tolerance in natural populations of a parasitoid wasp, Peer Community in Evolutionary Biology, vol. pp.1-19.

Davin AA, Tannier E, Williams TA, Boussau B, Daubin V, Szollosi GJ (2018)
Gene transfers can date the tree of life, Nature ecology & evolution, vol. pp.1-8.

Diagouraga B, Clement JAJ, Duret L, Kadlec J, De Massy B, Baudat F (2018)
PRDM9 Methyltransferase Activity Is Essential for Meiotic DNA Double-Strand Break Formation at Its Binding Sites, Molecular cell, vol. 69 pp.853-865.

Dumas JG, Roch JA, Tannier E, Varrette S (2018) Théorie des codes, , 2018

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Esteve C, Francescatto L, Tan PL, Bourchany A, De Leusse C, Marinier E, Blanchard A, Bourgeois P, Brochier-Armanet C, Bruel AL, Delarue A, Duffourd Y, Ecochard-Dugelay E, Hery G, Huet F, Gauchez P, Gonzales E, Guettier-Bouttier C, Komuta M, Lacoste C, Maudinas R, Mazodier K, Rimet Y, Rivière JB, Roquelaure B, Sigaudy S, Stephenne X, Thauvin-Robinet C, Thevenon J, Sarles J, Levy N, Badens C, Goulet O, Hugot J P, Katsanis N, Faivre L, Fabre A (2018)
Loss-of-Function Mutations in UNC45A Cause a Syndrome Associating Cholestasis Diarrhea Impaired Hearing and Bone Fragility, American journal of human genetics, vol. 102 pp.364-374.

Fadhlaoui K, Ben Hania W, Armougom F, Bartoli M, Fardeau ML, Erauso G, Brasseur G, Aubert C, Hamdi M, Brochier-Armanet C, Dolla A, Ollivier B (2018)
Obligate sugar oxidation in Mesotoga spp. phylum Thermotogae in the presence of either elemental sulfur or hydrogenotrophic sulfate-reducers as electron acceptor, Environmental microbiology, vol. 20 pp.281-292.

Galtier N, Roux C, Rousselle M, Romiguier J, Figuet E, Glémin S, Bierne N, Duret L (2018)
Codon Usage Bias in Animals: Disentangling the Effects of Natural Selection Effective Population Size and GC-Biased Gene Conversion, Molecular Biology and Evolution, vol. 35 pp.1092-1103.

Guéguen L, Duret L (2018)
Unbiased estimate of synonymous and non-synonymous substitution rates with non-stationary base composition, Molecular biology and evolution, vol. 35 pp.734-742.

Parto S, Lartillot N (2018)
Molecular adaptation in Rubisco: Discriminating between convergent evolution and positive selection using mechanistic and classical codon models, PLoS one, vol. 13 pp.e0192697-e0192697.

Zucchini L, Mercy C, Garcia PS, Cluzel C, Gueguen-Chaignon V, Galisson F, Freton C, Guiral S, Brochier-Armanet C, Gouet P, Grangeasse C (2018)
PASTA repeats of the protein kinase StkP interconnect cell constriction and separation of Streptococcus pneumoniae, Nature microbiology, vol. 3 pp.197-209.

Adam PS, Borrel G, Brochier-Armanet C, Gribaldo S (2017)
The growing tree of Archaea: new perspectives on their diversity evolution and ecology, ISME Journal, vol. 11 pp.2407-2425.

Bailly-Bechet M, Martins-Simoes P, Szollosi GJ, Mialdea G, Sagot MF, Charlat S (2017)
How Long Does Wolbachia Remain on Board?, Molecular Biology and Evolution, vol. 34 pp.1183-1193.

Boldanova T, Suslov A, Heim MH, Necsulea A (2017)
Transcriptional response to hepatitis C virus infection and interferon-alpha treatment in the human liver, EMBO Molecular Medicine, vol. 9 pp.816-834.

Boutin H, de Vienne DM (2017)
Sonification of phylogenetic trees: listening to evolution, Journées d`Informatique Musicale 2017, pp.1-4.

Cariou M, Duret L, Charlat S (2017)
The global impact of Wolbachia on mitochondrial diversity and evolution, Journal of Evolutionary Biology, vol. 30 pp.2204-2210.

Chauve C, Rafiey A, Davin AA, Scornavacca C, Veber P, Boussau B, Szollosi G, Daubin V, Tannier E (2017)
MaxTiC: Fast ranking of a phylogenetic tree by Maximum Time Consistency with lateral gene transfers, Peer Community In Evolutionary Biology, vol. pp.1-18.

Collet M (2017)
Evolution et mécanismes d’évitement de la consanguinité chez un hyménoptère parasitoïde Venturia canescens .

Duchemin W (2017)
Phylogénie des dépendances et dépendances des phylogénies dans les gènes et les génomes .

Duchemin W, Anselmetti Y, Patterson M, Ponty Y, Berard S, Chauve C, Scornavacca C, Daubin V, Tannier E (2017)
DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies, Genome Biology and Evolution, vol. 9 pp.1312-1319.

Elsensohn MH, Leblay N, Dimassi S, Campan-Fournier A, Labalme A, Roucher-Boulez F, Sanlaville D, Lesca G, Bardel C, Roy P (2017)
Statistical method to compare massive parallel sequencing pipelines, BMC Bioinformatics, vol. 18 pp.139-139.

Fertin G, Jean G, Tannier E (2017)
Algorithms for computing the double cut and join distance on both gene order and intergenic sizes, Algorithms for Molecular Biology, vol. 12 pp.16-16.

Feuda R, Dohrmann M, Pett W, Philippe H, Rota-Stabelli O, Lartillot N, Worheide G, Pisani D (2017)
Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals, Current biology, vol. 27 pp.3864-3870.

Grey C, Clement JA, Buard J, Leblanc B, Gut I, Gut M, Duret L, de Massy B (2017)
In vivo binding of PRDM9 reveals interactions with noncanonical genomic sites, Genome research, vol. 27 pp.580-590.

Gueeguen L, Duret L (2017)
Unbiased estimate of synonymous and non-synonymous substitution rates with non-stationary base composition, Mol Biol Evol, vol. pp.57-62.

Jacox E, Weller M, Tannier E, Scornavacca C (2017)
Resolution and reconciliation of non-binary gene trees with transfers duplications and losses, Bioinformatics, vol. 33 pp.980-987.

Latrille T, Duret L, Lartillot N (2017)
The Red Queen model of recombination hot-spot evolution: a theoretical investigation, Philosophical transactions of the Royal Society B Biological sciences, vol. 372 pp.20160463-20160463.

Lefebure T, Morvan C, Malard F, Francois C, Konecny-Dupre L, Gueguen L, Weiss-Gayet M, Seguin-Orlando A, Ermini L, Sarkissian C, Charrier N P, Eme D, Mermillod-Blondin F, Duret L, Vieira C, Orlando L, Douady CJ (2017)
Less effective selection leads to larger genomes, Genome research, vol. 27 pp.1016-1028.

Pantalacci S, Guéguen L, Petit C, Lambert A, Peterkova R, Sémon M (2017)
Transcriptomic signatures shaped by cell proportions shed light on comparative developmental biology, Genome biology, vol. 18 pp.29-29.

Parto S, Lartillot N (2017)
Detecting consistent patterns of directional adaptation using differential selection codon models, BMC evolutionary biology, vol. 17 pp.147-147.

Philippe H, de Vienne DM, Ranwez V, Roure B, Baurain D, Delsuc F (2017)
Pitfalls in supermatrix phylogenomics, European Journal of Taxonomy, vol. 283 pp.1-25.

Philippon H, Souvane A, Brochier-Armanet C, Perriere G (2017)
IsoSel: Protein Isoform Selector for phylogenetic reconstructions, PLoS One, vol. 12 pp.e0174250-e0174250.

Pouyet F, Mouchiroud D, Duret L, Sémon M (2017)
Recombination meiotic expression and human codon usage, eLife, vol. 6 pp.e27344-e27344.

Repizo GD, Viale AM, Borges V, Cameranesi MM, Taib N, Espariz M, Brochier-Armanet C, Gomes JP, Salcedo SP (2017)
The Environmental Acinetobacter baumannii Isolate DSM30011 Reveals Clues into the Preantibiotic Era Genome Diversity Virulence Potential and Niche Range of a Predominant Nosocomial Pathogen, Genome biology and evolution, vol. 9 pp.2292-2307.

Rodrigue N, Lartillot N (2017)
Detecting Adaptation in Protein-Coding Genes Using a Bayesian Site-Heterogeneous Mutation-Selection Codon Substitution Model, Molecular biology and evolution, vol. 34 pp.204-214.

Saudemont B, Popa A, Parmley JL, Rocher V, Blugeon C, Necsulea A, Meyer E, Duret L (2017)
The fitness cost of mis-splicing is the main determinant of alternative splicing patterns, Genome biology, vol. 18 pp.208-208.

Schlapfer P, Zhang P, Wang C, Kim T, Banf M, Chae L, Dreher K, Chavali AK, Nilo-Poyanco R, Bernard T, Kahn D, Rhee SY (2017)
Genome-Wide Prediction of Metabolic Enzymes Pathways and Gene Clusters in Plants, Plant physiology, vol. 173 pp.2041-2059.

Siberchicot A, Bessy A, Gueguen L, Marais GAB (2017)
MareyMap Online: A User-Friendly Web Application and Database Service for Estimating Recombination Rates Using Physical and Genetic Maps, Genome biology and evolution, vol. 9 pp.2506-2509.

Timm J, Brochier-Armanet C, Perard J, Zambelli B, Ollagnier-de-Choudens S, Ciurli S, Cavazza C (2017)
The CO dehydrogenase accessory protein CooT is a novel nickel-binding protein, Metallomics, vol. 9 pp.575-583.

Venner S, Miele V, Terzian C, Biemont C, Daubin V, Feschotte C, Pontier D (2017)
Ecological networks to unravel the routes to horizontal transposon transfers, PLoS Biology, vol. 15 pp.e2001536-e2001536.

Williams TA, Szollosi GJ, Spang A, Foster PG, Heaps SE, Boussau B, Ettema TJG, Embley MT (2017)
Integrative modeling of gene and genome evolution roots the archaeal tree of life, Proceedings of the National Academy of Sciences of the United States of America, vol. 114 pp.E4602-E4602.

Amandio AR, Necsulea A, Joye E, Mascrez B, Duboule D (2016)
Hotair Is Dispensible for Mouse Development, PLoS Genetics, vol. 12 pp.e1006232-e1006232.

Antunes LC, Poppleton D, Klingl A, Criscuolo A, Dupuy B, Brochier-Armanet C, Beloin C, Gribaldo S (2016)
Phylogenomic analysis supports the ancestral presence of LPS-outer membranes in the Firmicutes, eLife, vol. 5 pp.e14589-e14589.

Attaiech L, Boughammoura A, Brochier-Armanet C, Allatif O, Peillard-Fiorente F, Edwards RA, Omar AR, MacMillan AM, Glover M, Charpentier X (2016)
Silencing of natural transformation by an RNA chaperone and a multitarget small RNA, Proceedings of the National Academy of Sciences of the United States of America, vol. 113 pp.8813-8818.

Beccari L, Yakushiji-Kaminatsui N, Woltering J M, Necsulea A, Lonfat N, Rodriguez-Carballo E, Mascrez B, Yamamoto S, Kuroiwa A, Duboule D (2016)
A role for HOX13 proteins in the regulatory switch between TADs at the HoxD locus, Genes & development, vol. 30 pp.1172-86.

Biller P, Gueguen L, Knibbe C, Tannier E (2016)
Breaking Good: Accounting for Fragility of Genomic Regions in Rearrangement Distance Estimation, Genome Biology and Evolution, vol. 8 pp.1427-39.

Biller P, Knibbe C, Beslon G, Tannier E (2016)
Comparative Genomics on Artifical Life, Computability in Europe, pp.1-10.

Boccara M, Fedala Y, Bryan Venien C, Bailly-Bechet M, Bowler C, Boccara AC (2016)
Full-field interferometry for counting and differentiating aquatic biotic nanoparticles: from laboratory to Tara Oceans, Biomedical Optics Express, vol. 7 pp.3736-3736.

Bulteau L, Fertin G, Tannier E (2016)
Genome rearrangements with indels in intergenes restrict the scenario space, BMC Bioinformatics, vol. 17 pp.225-231.

Cariou M, Duret L, Charlat S (2016)
How and how much does RAD-seq bias genetic diversity estimates?, BMC evolutionary biology, vol. 16 pp.240-240.

Collet M, Vayssade C, Auguste A, Mouton L, Desouhant E, Malausa T, Fauvergue X (2016)
Diploid male production correlates with genetic diversity in the parasitoid wasp Venturia canescens : a genetic approach with new microsatellite markers, Ecology and Evolution, vol. 6 pp.6721-6734.

Dacks JB, Field MC, Buick R, Eme L, Gribaldo S, Roger AJ, Brochier-Armanet C, Devos DP (2016)
The changing view of eukaryogenesis - fossils cells lineages and how they all come together, Journal of Cell Science, vol. 129 pp.3695-3703.

de Vienne DM (2016)
Lifemap: Exploring the Entire Tree of Life, PLoS Biology, vol. 14 pp.e2001624-e2001624.

Duprey A, Nasser W, Leonard S, Brochier-Armanet C, Reverchon S (2016)
Transcriptional start site turnover in the evolution of bacterial paralogous genes - the pelE-pelD virulence genes in Dickeya, FEBS journal, vol. 283 pp.4192-4207.

Fertin G, Jean G, Tannier E (2016)
Genome Rearrangements on Both Gene Order and Intergenic Regions, WABI, , vol. 9838 pp.162-173.

Francois CM, Duret L, Simon L, Mermillod-Blondin F, Malard F, Konecny-Dupre L, Planel R, Penel S, Douady CJ, Lefebure T (2016)
No Evidence That Nitrogen Limitation Influences the Elemental Composition of Isopod Transcriptomes and Proteomes, Molecular Biology and Evolution, vol. 33 pp.2605-20.

Fraune J, Brochier-Armanet C, Alsheimer M, Volff J N, Schucker K, Benavente R (2016)
Evolutionary history of the mammalian synaptonemal complex, Chromosoma, vol. 125 pp.355-60.

Freyermuth F, Rau F, Kokunai Y, Linke T, Sellier C, Nakamori M, Kino Y, Arandel L, Jollet A, Thibault C, Philipps M, Vicaire S, Jost B, Udd B, Day JW, Duboc D, Wahbi K, Matsumura T, Fujimura H, Mochizuki H, Deryckere F, Kimura T, Nukina N, Ishiura S, Lacroix V, Campan-Fournier A, Navratil V, Chautard E, Auboeuf D, Horie M, Imoto K, Lee KY, Swanson MS, Lopez de Munain A, Inada S, Itoh H, Nakazawa K, Ashihara T, Wang E, Zimmer T, Furling D, Takahashi MP, Charlet-Berguerand N (2016)
Splicing misregulation of SCN5A contributes to cardiac-conduction delay and heart arrhythmia in myotonic dystrophy, Nature communications, vol. 7 pp.11067-11067.

Garcia PS, Simorre JP, Brochier-Armanet C, Grangeasse C (2016)
Cell division of Streptococcus pneumoniae: think positive!, Current opinion in microbiology, vol. 34 pp.18-23.

Groussin M, Boussau B, Szollosi G, Eme L, Gouy M, Brochier-Armanet C, Daubin V (2016)
Gene Acquisitions from Bacteria at the Origins of Major Archaeal Clades Are Vastly Overestimated, Molecular Biology and Evolution, vol. 33 pp.305-10.

Groussin M, Daubin V, Gouy M, Tannier E (2016)
Ancestral Reconstruction: Theory and Practice
in: The Encyclopedia of Evolutionary Biology, , pp.70-77.

Hohna S, Landis MJ, Heath T A, Boussau B, Lartillot N, Moore BR, Huelsenbeck JP, Ronquist F (2016)
RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language, Systematic biology, vol. 65 pp.726-36.

Jauffrit F, Penel S, Delmotte S, Rey C, De Vienne DM, Gouy M, Charrier JP, Flandrois JP, Brochier-Armanet C (2016)
RiboDB Database: A Comprehensive Resource for Prokaryotic Systematics, Molecular Biology and Evolution, vol. 33 pp.2170-2172.

Karaki L, Da Silva P, Rizk F, Chouabe C, Chantret N, Eyraud V, Gressent F, Sivignon C, Rahioui I, Kahn D, Brochier-Armanet C, Rahbe Y, Royer C (2016)
Genome-wide analysis identifies gain and loss/change of function within the small multigenic insecticidal Albumin 1 family of Medicago truncatula, BMC plant biology, vol. 16 pp.63-63.

Lartillot N, Phillips M J, Ronquist F (2016)
A mixed relaxed clock model, Philosophical transactions of the Royal Society B-Biological sciences, vol. 371 pp.20150132-20150132.

Lays C, Tannier E, Henry T (2016)
Francisella IglG protein and the DUF4280 proteins: PAAR-like proteins in non-canonical Type VI secretion systems?, Microbial Cell, vol. 3 pp.445-447.

Lazzerini N, Lecuyer C, Amiot R, Angst D, Buffetaut E, Fourel F, Daux V, Betancort JF, Flandrois JP, Marco AS, Lomoschitz A (2016)
Oxygen isotope fractionation between bird eggshell calcite and body water: application to fossil eggs from Lanzarote (Canary Islands), Naturwissenschaften, vol. 103 pp.81-81.

Lopez-Maestre H, Brinza L, Marchet C, Kielbassa J, Bastien S, Boutigny M, Monnin D, El Filali A, Carareto CM, Vieira C, Picard F, Kremer N, Vavre F, Sagot MF, Lacroix V (2016)
SNP calling from RNA-seq data without a reference genome: identification quantification differential analysis and impact on the protein sequence, Nucleic Acids Research, vol. 44 pp.e148-e148.

Martin C, Maureille B, Amiot R, Touzeau A, Royer A, Fourel F, Panczer G, Flandrois JP, Lécuyer C (2016)
Record of Nile seasonality in Nubian neonates, Isotopes in Environmental and Health Studies, vol. 53 pp.223-242.

Noutahi E, Semeria M, Lafond M, Seguin J, Boussau B, Gueguen L, El-Mabrouk N, Tannier E (2016)
Efficient Gene Tree Correction Guided by Genome Evolution, PLoS One, vol. 11 pp.e0159559-e0159559.

Philippon H (2016)
Étude de l`histoire évolutive des PI3K et des voies de signalisation associées .

Pichat C, Couvin D, Carret G, Fredenucci I, Jacomo V, Carricajo A, Boisset S, Dumitrescu O, Flandrois JP, Lina G, Rastogi N (2016)
Combined Genotypic Phylogenetic and Epidemiologic Analyses of Mycobacterium tuberculosis Genetic Diversity in the Rhone Alpes Region France, PLoS One, vol. 11 pp.e0153580-e0153580.

Pisani D, Pett W, Dohrmann M, Feuda R, Rota-Stabelli O, Philippe H, Lartillot N, Worheide G (2016)
Reply to Halanych et al.: Ctenophore misplacement is corroborated by independent datasets, Proceedings of the National Academy of Sciences of the United States of America, vol. 113 pp.E948-9.

Pouyet F (2016)
Etude bioinformatique de l`evolution de l`usage du code génétique .

Pouyet F, Bailly-Bechet M, Mouchiroud D, Gueguen L (2016)
SENCA: A Multilayered Codon Model to Study the Origins and Dynamics of Codon Usage, Genome Biology and Evolution, vol. 8 pp.2427-41.

Ronquist F, Lartillot N, Phillips MJ (2016)
Closing the gap between rocks and clocks using total-evidence dating, Philosophical transactions of the Royal Society B-Biological sciences, vol. 371 pp.20150136-20150136.

Safa E, Barreau JB, Gaugne R, Duchemin W, Talma JD, Arnaldi B, Dumont G, Gouranton V (2016)
Digital and Handcrafting Processes Applied to Sound-Studies of Archaeological Bone Flutes, International conference on digital heritage EUROMED 2016, pp.184-195.

Schep R, Necsulea A, Rodriguez-Carballo E, Guerreiro I, Andrey G, Nguyen Huynh TH, Marcet V, Zakany J, Duboule D, Beccari L (2016)
Control of Hoxd gene transcription in the mammary bud by hijacking a preexisting regulatory landscape, Proceedings of the National Academy of Sciences of the United States of America, vol. 113 pp.e7720-e7729.

Sellis D, Kvitek D J, Dunn B, Sherlock G, Petrov DA (2016)
Heterozygote Advantage Is a Common Outcome of Adaptation in Saccharomyces cerevisiae, Genetics, vol. 203 pp.1401-1413.

Thiaville JJ, Kellner SM, Yuan Y, Hutinet G, Thiaville PC, Jumpathong W, Mohapatra S, Brochier-Armanet C, Letarov AV, Hillebrand R, Malik CK, Rizzo CJ, Dedon PC, de Crécy-Lagard V (2016)
Novel genomic island modifies DNA with 7-deazaguanine derivatives, Proceedings of the National Academy of Sciences of the United States of America, vol. 113 pp.e1452-e1459.

Agrebi R, Wartel M, Brochier-Armanet C, Mignot T (2015)
An evolutionary link between capsular biogenesis and surface motility in bacteria, Nature Reviews Microbiology, vol. 13 pp.318-326.

Anselmetti Y, Berry V, Chauve C, Chateau A, Tannier E, Berard S (2015)
Ancestral gene synteny reconstruction improves extant species scaffolding, BMC Genomics, vol. 16 Suppl 10 pp.S11-S11.

Baty F, Ritz C, Charles S, Brutsche M, Flandrois JP, Delignette-Muller ML (2015)
A Toolbox for Nonlinear Regression in R: The Package nistools, Journal of Statistical Software, vol. 66 pp.1-21.

Ben Hania W, Fadhlaoui K, Brochier-Armanet C, Persillon C, Postec A, Hamdi M, Dolla A, Ollivier B, Fardeau ML, Le Mer J, Erauso G (2015)
Draft genome sequence of Mesotoga strain PhosAC3 a mesophilic member of the bacterial order Thermotogales isolated from a digestor treating phosphogypsum in Tunisia, Standards in genomic sciences, vol. 10 pp.12-12.

Biller P, Gueguen L, Tannier E (2015)
Moments of genome evolution by Double Cut-and-Join, BMC Bioinformatics, vol. 16 Suppl 14 pp.S7-S7.

Borland S, Oudart A, Prigent-Combaret C, Brochier-Armanet C, Wisniewski-Dye F (2015)
Genome-wide survey of two-component signal transduction systems in the plant growth-promoting bacterium Azospirillum, BMC Genomics, vol. 16 pp.833-833.

Bouchiat C, Saison J, Boisset S, Flandrois JP, Issartel B, Dauwalder O, Benito Y, Jarraud S, Grando J, Boibieux A, Dumitrescu O, Delahaye F, Farhat F, Thivolet-Bejui F, Frieh J P, Vandenesch F (2015)
Nontuberculous Mycobacteria: An Underestimated Cause of Bioprosthetic Valve Infective Endocarditis, Open Forum Infectious Diseases, vol. 2 pp.ofv047-ofv047.

Campan-Fournier A, Oger C, Ginevra C, Navratil V, Ranc AG, Perrière G, Jarraud S (2015)
Analyse de 32 souches de Legionella pneumophila de sévérités variables afin d`identifier les déterminants de la pathogénicité, JOBIM, pp.89-89.

Dimassi S, Simonet T, Labalme A, Boutry-Kryza N, Campan-Fournier A, Lamy R, Bardel C, Elsensohn M H, Roucher-Boulez F, Chatron N, Putoux A, de Bellescize J, Ville D, Schaeffer L, Roy P, Mougou-Zerelli S, Saad A, Calender A, Sanlaville D, Lesca G (2015)
Comparison of two next-generation sequencing kits for diagnosis of epileptic disorders with a user-friendly tool for displaying gene coverage DeCovA, Applied and translational genomics, vol. 7 pp.19-25.

Duchemin W, Daubin V, Tannier E (2015)
Reconstruction of an ancestral Yersinia pestis genome and comparison with an ancient sequence, BMC Genomics, vol. 16 Suppl 10 pp.S9-S9.

Duchemin W, Dupont P Y, Campbell M A, Ganley A, Cox M P (2015)
HyLiTE: accurate and flexible analysis of gene expression in hybrid and allopolyploid species, BMC Bioinformatics, vol. 16 pp.8-8.

Dumas JG, Roch JL, Tannier E, Varrette S (2015) Foundations of coding. Compression Encryption Error Correction, Wiley, 2015

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Ferrandiz-Rovira M, Bigot T, Allaine D, Callait-Cardinal MP, Cohas A (2015)
Large-scale genotyping of highly polymorphic loci by next-generation sequencing: how to overcome the challenges to reliably genotype individuals?, Heredity, vol. 114 pp.485-93.

Fischer MJ, Rustenhloz C, Leh-Louis V, Perriere G (2015)
Molecular and functional evolution of the fungal diterpene synthase genes, BMC microbiology, vol. 15 pp.221-221.

Flandrois JP, Perrière G, Gouy M (2015)
leBIBIQBPP: a set of databases and a webtool for automatic phylogenetic analysis of prokaryotic sequences, BMC Bioinformatics, vol. 16 pp.251-251.

Freel KC, Krueger MC, Farasin J, Brochier-Armanet C, Barbe V, Andrès J, Cholley P-E, Dillies M-A, Jagla B, Koechler S, Leva Y, Magdelenat G, Plewniak F, Proux C, Coppée J-Y, Bertin PN, Heipieper HJ, Arsène-Ploetze F (2015)
Adaptation in Toxic Environments: Arsenic Genomic Islands in the Bacterial Genus Thiomonas, PLoS One, vol. 10 pp.e0139011-e0139011.

Glemin S, Arndt P F, Messer P W, Petrov D, Galtier N, Duret L (2015)
Quantification of GC-biased gene conversion in the human genome, Genome research, vol. 25 pp.1215-28.

Groussin M, Hobbs J K, Szollosi G J, Gribaldo S, Arcus V L, Gouy M (2015)
Toward more accurate ancestral protein genotype-phenotype reconstructions with the use of species tree-aware gene trees, Molecular Biology and Evolution, vol. 32 pp.13-22.

Guzzo M, Agrebi R, Espinosa L, Baronian G, Molle V, Mauriello E M, Brochier-Armanet C, Mignot T (2015)
Evolution and Design Governing Signal Precision and Amplification in a Bacterial Chemosensory Pathway, PLoS genetics, vol. 11 pp.e1005460-e1005460.

Henri H, Cariou M, Terraz G, Martinez S, El Filali A, Veyssiere M, Duret L, Charlat S (2015)
Optimization of multiplexed RADseq libraries using low-cost adaptors, Genetica, vol. 143 pp.139-43.

Koechler S, Arsene-Ploetze F, Brochier-Armanet C, Goulhen-Chollet F, Heinrich-Salmeron A, Jost B, Lievremont D, Philipps M, Plewniak F, Bertin P N, Lett M C (2015)
Constitutive arsenite oxidase expression detected in arsenic-hypertolerant Pseudomonas xanthomarina S11, Research in microbiology, vol. 166 pp.205-14.

Kondili M, Roux M, Vabret N, Bailly-Bechet M (2015)
Innate immune system activation by viral RNA: How to predict it?, Virology, vol. 488 pp.169-178.

Lartillot N (2015)
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Bernt M, Chao K-M, Kao J-W, Middendorf M, Tannier E (2012)
Preserving Inversion Phylogeny Reconstruction, WABI 2012, Springer-Verlag, vol. 7534 pp.1-13.

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

Brochier-Armanet C, Gribaldo S (2012)
Les défis de la systématique face au monde microbien, Biofutur, vol. 328 pp.49-52.

Brochier-Armanet C, Gribaldo S, Forterre P (2012)
Spotlight on the Thaumarchaeota, Isme Journal, vol. 6 pp.227-230.

Brochier-Armanet C, Moreira D (2012)
Transferts horizontaux de gènes dans les écosystèmes microbiens
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Caumette P, Brochier C, Normand P (2012)
Taxonomie et phylogénie des procaryotes
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Daubin V (2012)
HDR - Phylogénie Moléculaire 2.0 .

Daubin V, Abby S (2012)
Les transferts horizontaux de gènes et l’arbre de la vie, M S-Médecine Sciences, vol. 28 pp.695-698.

De Crécy-Lagard V, Forouhar F, Brochier-Armanet C, Tong L, Hunt JF (2012)
Comparative genomic analysis of the DUF71/COG2102 family predicts roles in diphthamide biosynthesis and B12 salvage, Biology Direct, vol. 7 pp.1-13.

de Vienne D M, Azé J (2012)
Efficient Prediction of Co-Complexed Proteins Based on Coevolution, PLoS one, vol. 7 pp.e48728-e48728.

de Vienne D M, Ollier S, Aguileta G (2012)
Phylo-MCOA: a fast and efficient method to detect outlier genes and species in phylogenomics using multiple co-inertia analysis, Molecular biology and evolution, vol. 29 pp.1587-1598.

Dutheil J Y, Galtier N, Romiguier J, Douzery E J P, Ranwez V, Boussau B (2012)
Efficient Selection of Branch-Specific Models of Sequence Evolution, Molecular Biology and Evolution, vol. 29 pp.1861-1874.

Fong JJ, Brown JM, Fujita MK, Boussau B (2012)
A Phylogenomic Approach to Vertebrate Phylogeny Supports a Turtle-Archosaur Affinity and a Possible Paraphyletic Lissamphibia, PLoS one, vol. 7 pp.e48990-e48990.

Gribaldo S, Brochier-Armanet C (2012)
Time for order in microbial systematics, Trends in Microbiology, vol. 20 pp.209-210.

Hunter S, Jones P, Mitchell A, Apweiler R, Attwood T K, Bateman A, Bernard T, Binns D, Bork P, Burge S, de Castro E, Coggill P, Corbett M, Das U, Daugherty L, Duquenne L, Finn R D, Fraser M, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, McMenamin C, Mi H, Mutowo-Muellenet P, Mulder N, Natale D, Orengo C, Pesseat S, Punta M, Quinn A F, Rivoire C, Sangrador-Vegas A, Selengut J D, Sigrist C J A, Scheremetjew M, Tate J, Thimmajanarthanan M, Thomas P D, Wu C H, Yeats C, Yong S-Y (2012)
InterPro in 2011: new developments in the family and domain prediction database, Nucleic Acids Research, vol. 40 pp.D306-D312.

Jones BR, Rajaraman A, Tannier E, Chauve C (2012)
ANGES: reconstructing ANcestral GEnomeS maps, Bioinformatics, vol. 28 pp.2388-90.

Junillon T, Vimont A, Mosticone D, Mallen B, Baril F, Rozand C, Flandrois JP (2012)
Simplified detection of food-borne pathogens: An in situ high affinity capture and staining concept, Journal of Microbiological Methods, vol. 91 pp.501-505.

Lartillot N, Delsuc F (2012)
Joint reconstruction of divergence times and life-history evolution in placental mammals using a phylogenetic covariance model, Evolution, vol. 66 pp.1773-1787.

Lesecque Y, Keightley PD, Eyre-Walker A (2012)
A Resolution of the Mutation Load Paradox in Humans, Genetics, vol. 191 pp.1321-1330.

Manuch J, Patterson M, Wittler R, Chauve C, Tannier E (2012)
Linearization of ancestral multichromosomal genomes, BMC Bioinformatics, vol. 13 pp.11-11.

Miele V, Penel S, Daubin V, Picard F, Kahn D, Duret L (2012)
High-quality sequence clustering guided by network topology and multiple alignment likelihood, Bioinformatics, vol. 28 pp.1078-1085.

Miklos I, Tannier E (2012)
Approximating the number of Double Cut-and-Join scenarios, Theoretical Computer Science, vol. 439 pp.30-40.

Morin L, Lobry JR, Peyron F, Wallon M (2012)
Seasonal variations in acute toxoplasmosis in pregnant women in the Rhône-Alpes region (France), Clinical Microbiology and Infection, vol. 18 pp.E401-E403.

Narasingarao P, Podell S, Ugalde J A, Brochier-Armanet C, B Emerson J, Brocks J J, Heidelberg K B, Banfield J F, Allen E E (2012)
De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities, ISME Journal, vol. 6 pp.81-93.

Paganini J, Campan-Fournier A, Da Rocha M, Gouret P, Pontarotti P, Wajnberg E, Abad P, Danchin E G (2012)
Contribution of Lateral Gene Transfers to the Genome Composition and Parasitic Ability of Root-Knot Nematodes, PLoS one, vol. 7 pp.e50875-e50875.

Perrière G (2012)
ReNaBi-IFB : The French Bioinformatics Infrastructure, EMBNet.journal, vol. 18 pp.12-13.

Pessia E, Makino T, Bailly-Bechet M, McLysaght A, Marais GAB (2012)
Mammalian X chromosome inactivation evolved as a dosage-compensation mechanism for dosage-sensitive genes on the X chromosome, Proceedings of the National Academy of Sciences of the United States of America, vol. 109 pp.5346-5351.

Pessia E, Popa A, Mousset S, Rezvoy C, Duret L, Marais G (2012)
Evidence for Widespread GC-biased Gene Conversion in Eukaryotes, Genome Biology and Evolution, vol. 4 pp.787-794.

Petit E, Giraud T, de Vienne D M, Coelho M A, Aguileta G, Amselem J, Kreplak J, Poulain J, Gavory F, Wincker P, Young S K, Cuomo C, Perlin M H, Hood M E (2012)
Linkage to the mating-type locus across the genus Microbotryum: insights into nonrecombining chromosomes, Evolution, vol. 66 pp.3519-3533.

Petitjean C, Moreira D, Lopez-Garcia P, Brochier-Armanet C (2012)
Horizontal gene transfer of a chloroplast DnaJ-Fer protein to Thaumarchaeota and the evolutionary history of the DnaK chaperone system in Archea, BMC Evolutionary Biology, vol. 12 pp.226-226.

Popa A, Samollow P, Gautier C, Mouchiroud D (2012)
The sex-specific impact of meiotic recombination on nucleotide composition, Genome Biology and Evolution, vol. 4 pp.412-422.

Py B, Gerez C, Angelini S, Planel R, Vinella D, Loiseau L, Talla E, Brochier-Armanet C, Garcia Serres R, Latour J M, Ollagnier-de Choudens S, Fontecave M, Barras F (2012)
Molecular organization biochemical function cellular role and evolution of NfuA an atypical Fe-S carrier, Molecular microbiology, vol. 86 pp.155-71.

Romiguier J, Figuet E, Galtier N, Douzery E J P, Boussau B, Dutheil J Y, Ranwez V (2012)
Fast and Robust Characterization of Time Heterogeneous Sequence Evolutionary Processes Using Substitution Mapping, PLos One, vol. 7 pp.e33852-e33852.

Szollosi GJ, Boussau B, Abby SS, Tannier E, Daubin V (2012)
Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations, Proceedings of the National Academy of Sciences of The United States of America, vol. 109 pp.17513-17518.

Szollosi GJ, Daubin V (2012)
Modeling Gene Family Evolution and Reconciling Phylogenetic Discord, Methods in Molecular Biology, vol. 856 pp.29-51.

Vabret N, Bailly-Bechet M, Najburg V, Müller-Trutwin M, Verrier B, Tangy F (2012)
The Biased Nucleotide Composition of HIV-1 Triggers Type I Interferon Response and Correlates with Subtype D Increased Pathogenicity, PLoS one, vol. 7 pp.e33502-e33502.

Amouric A, Brochier-Armanet C, Johnson D B, Bonnefoy V, Hallberg K B (2011)
Phylogenetic and genetic variation among Fe(II)-oxidizing acidithiobacilli supports the view that these comprise multiple species with different ferrous iron oxidation pathways, Microbiology, vol. 155 pp.111-122.

Arguel MJ, Campan-Fournier A, Perfus-Barbeoch L, Danchin EG, Rosso MN, Da Silva C, Labadie K, Marteu N, Artiguenave F, Abad P (2011)
Identification of plant-parasitism genes in nematodes in silico screening and in vivo validation in Meloidogyne incognita., Communications in agricultural and applied biological sciences, vol. 76 pp.409-412.

Auxilien S, Rasmussen A, Rose S, Brochier-Armanet C, Husson C, Fourmy D, Grosjean H, Douthwaite S (2011)
Specificity shifts in the rRNA and tRNA nucleotide targets of archaeal and bacterial m5U methyltransferases, RNA, vol. 17 pp.45-53.

Bailly-Bechet M, Benecke A, Hardt WD, Lanza V, Sturm A, Zecchina R (2011)
An externally modulated noise-driven switch for the regulation of SPI1 in Salmonella enterica serovar Typhimurium, Journal of Mathematical Biology, vol. 63 pp.637-662.

Bailly-Bechet M, Borgs C, Braunstein A, Chayes J, Dagkessamanskaia A, François JM, Zecchina R (2011)
Finding undetected protein associations in cell signaling by belief propagation, Proceedings of The National Academy of Sciences of The United States of America, vol. 108 pp.882-887.

Ben Hania W, Ghodbane R, Postec A, Brochier-Armanet C, Hamdi M, Fardeau M-L, Ollivier B (2011)
Cultivation of the first mesophilic representative ("mesotoga") within the order Thermotogales, Systematic and Applied Microbiology, vol. 34 pp.581-585.

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 pp.343-354.

Berthoumieux S, Brilli M, de Jong H, Kahn D, Cinquemani E (2011)
Identification of metabolic network models from incomplete high-throughput datasets, Bioinformatics, vol. 27 pp.i186-i195.

Bigot T, Daubin V, Perrière G (2011)
Tpms: a Tree Pattern-matching Utility for Querying Gene Trees Collections, Journées Ouvertes Biologie Informatique Mathématiques (JOBIM), pp.111-112.

Boileau C, Eme L, Brochier-Armanet C, Janicki A, Zhang C-C, Latifi A (2011)
A eukaryotic-like sulfiredoxin involved in oxidative stress responses and in the reduction of the sulfinic form of 2 Cys-peroxiredoxin in the cyanobacterium Anabaena PCC 7120, New phytologist, vol. 191 pp.1108-1118.

Boussau B, Brown J M, Fujita M K (2011)
Nonadaptive evolution of mitochondrial genome size, Evolution, vol. 65 pp.2706-2711.

Brochier-Armanet C, Deschamps P, Lopez-Garcia P, Zivanovic Y, Rodriguez-Valera F, Moreira D (2011)
Complete-fosmid and fosmid-end sequences reveal frequent horizontal gene transfers in marine uncultured planktonic Thaumarchaeota and Euryarchaeota, ISME, vol. 5 pp.1291-302.

Brochier-Armanet C, Forterre P, Gribaldo S (2011)
Phylogeny and Evolution of the Archaea: one Hundred Genomes Later, Current opinion in microbiology, vol. 14 pp.274-281.

Campan-Fournier A, Perfus-Barbeoch L, Rosso MN, Arguel MJ, Da Silva C, Vens C, Marteu N, Labadie K, Artiguenave F, Abad P, Danchin EG (2011)
Identification of Putative Parasitism Genes in Plant-Parasitic Nematodes - In silico Screening of Whole Genomes and Transcriptomes, Journées Ouvertes en Biologie Informatique et Mathématiques (JOBIM), pp.1-8.

Chureau C, Chantalat S, Romito A, Galvani A, Duret L, Avner P, Rougeulle C (2011)
Ftx is a non-coding RNA which affects Xist expression and chromatin structure within the X-inactivation center region, Human Molecular Genetics, vol. 20 pp.705-718.

Coumes-Florens S, Brochier-Armanet C, Guiseppi A, Denizot F, Foglino M (2011)
A New Highly Conserved Antibiotic Sensing/Resistance Pathway in Firmicutes Involves an ABC Transporter Interplaying with a Signal Transduction System, PLoS one, vol. 6 pp.e15951-e15951.

Cusack BP, Arndt PF, Duret L, Roest Crollius H (2011)
Preventing Dangerous Nonsense: Selection for Robustness to Transcriptional Error in Human Genes, PLoS Genetics, vol. 7 pp.e1002276-e1002276.

de Vienne D M, Aguileta G, Ollier S (2011)
Euclidean Nature of Phylogenetic Distance Matrices, Systematic Biology, vol. 60 pp.826-832.

Debernardi A, Suzanne E, Formant A, Pène L, Dufour A-B, Lobry JR (2011)
One year variability of peak heights heterozygous balance and inter-locus balance for the DNA positive control of AmpFlSTR Identifiler STR kit, Forensic Science International: Genetics, vol. 5 pp.43-49.

Denoeud F, Roussel, Noel B, Wawrzyniak I, Da Silva C, Diogon M, Viscogliosi E, Brochier-Armanet C, Couloux A, Poulain J, Segurens B, Anthouard V, Texier C, Blot N, Poirier P, Choo Ng G, Tan K S W, Artiguenave F, Jaillon O, Aury J-M, Delbac F, Wincker P, Vivarès C P, El Alaoui H (2011)
Genome sequence of the stramenopile Blastocystis a human anaerobic parasite, Genome Biology, vol. 12 pp.R29-R29.

Desmond E, Brochier-Armanet C, Forterre P, Gribaldo S (2011)
On the last common ancestor and early evolution of eukaryotes: Reconstructing the history of mitochondrial ribosomes, Research in Microbiology, vol. 162 pp.53-70.

Doyon J-P, Ranwez V, Daubin V, Berry V (2011)
Models algorithms and programs for phylogeny reconciliation, Briefings in Bioinformatics, vol. 12 pp.392-400.

Durand E, Alphonse S, Brochier-Armanet C, Ball G, Douzi B, Filloux A, Bernard C, Voulhoux R (2011)
The Assembly Mode of the Pseudopilus: a hallmark to distinguish a novel secretion system subtype, Journal of Biological Chemistry, vol. 286 pp.24407-24416.

Eme L, Trilles A, Moreira D, Brochier-Armanet C (2011)
The phylogenomic analysis of the anaphase promoting complex and its targets points to complex and modern-like control of the cell cycle in the last common ancestor of eukaryotes, BMC Evolutionary Biology, vol. 11 pp.923-33.

Gavranovic H, Chauve C, Salse J, Tannier E (2011)
Mapping ancestral genomes with massive gene loss: A matrix sandwich problem, Bioinformatics, vol. 27 pp.i257-i265.

Gribaldo S, Forterre P, Brochier-Armanet C (2011)
Archaea and the tree of life, Research in microbiology, vol. 162 pp.1-4.

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.

Haned H, Pène L, Lobry JR, Dufour A-B, Pontier D (2011)
Estimating the Number of Contributors to Forensic DNA Mixtures: Does Maximum Likelihood Perform Better Than Maximum Allele Count?, Journal of Forensic Sciences, vol. 56 pp.23-28.

Heinrich-Salmeron A, Cordi A, Brochier-Armanet C, Halter D, Pagnout C, Abbaszadeh-Fard E, Montaut D, Seby F, Bertin P N, Bauda P, Arsène-Ploetze F (2011)
Unsuspected Diversity of Arsenite-Oxidizing Bacteria Revealed by a Widespread Distribution of the aoxB Gene in Prokaryotes, Applied and Environmental Microbiology, vol. 77 pp.4685-92.

Lartillot N, Poujol R (2011)
A phylogenetic model for investigating correlated evolution of substitution rates and continuous phenotypic characters, Molecular biology and evolution, vol. 28 pp.729-44.

Lassalle F, Campillo T, Vial L, Baude J, Costechareyre D, Chapulliot D, Shams M, Abrouk D, Lavire C, Oger C, Hommais F, Guéguen L, Daubin V, Muller D, Nesme X (2011)
Genomic Species Are Ecological Species as Revealed by Comparative Genomics in Agrobacterium tumefaciens, Genome Biology and Evolution, vol. 3 pp.762-781.

Le Fourn C, Brasseur G, Brochier-Armanet C, Pieulle L, Brioukhanov A, Ollivier B, Dolla A (2011)
An oxygen reduction chain in the hyperthermophilic anaerobe Thermotoga maritima highlights horizontal gene transfer between Thermococcales and Thermotogales, Environmental Microbiology, vol. 13 pp.2132-45.

Leyssene D, Gardes S, Vilquin P, Flandrois JP, Carret G, Lamy B (2011)
Species-driven interpretation guidelines in case of a single-sampling strategy for blood culture, European Journal of Clinical Microbiology & Infectious Diseases, vol. 30 pp.1537-1541.

Luciano J, Agrebi R, Le Gall AV, Wartel M, Fiegna F, Ducret A, Brochier-Armanet C, Mignot T (2011)
Emergence and Modular Evolution of a Novel Motility Machinery in Bacteria, PLoS Genetics, vol. 7 pp.e1002268-e1002268.

Marais G, Forrest A, Kamau E, Kafer J, Daubin V, Charlesworth D (2011)
Multiple Nuclear Gene Phylogenetic Analysis of the Evolution of Dioecy and Sex Chromosomes in the Genus Silene, PLoS One, vol. 6 pp.e21915-e21915.

Miele V, Penel S, Duret L (2011)
Ultra-fast sequence clustering from similarity networks with SiLiX, BMC Bioinformatics, vol. 12 pp.116-116.

Necşulea A, Popa A, Cooper DN, Stenson PD, Mouchiroud D, Gautier C, Duret L (2011)
Meiotic Recombination favors the spreading of deleterious mutations in human populations, Human Mutation, vol. 32 pp.198-206.

Ouangraoua A, Tannier E, Chauve C (2011)
Reconstructing the architecture of the ancestral amniote genome, Bioinformatics, vol. 27 pp.2664-2671.

Picard F, Perrière G (2011)
Bioinformatics developments for NGS data analysis at PRABI, EMBnet.journal, vol. 17 pp.12-12.

Pompeo F, Luciano J, Brochier-Armanet C, Galinier A (2011)
The GTPase Function of YvcJ and Its Subcellular Relocalization Are Dependent on Growth Conditions in Bacillus subtilis, Journal of Molecular Microbiology and Biotechnology, vol. 20 pp.156-167.

Popa A (2011)
The evolution of recombintion and genomic structures: a modeling approach .

Rouxel T, Grandaubert J, Hane JK, Hoede C, Van de Wouw AP, Couloux A, Dominguez V, Antouhard V, Bally P, Bourras S, Cozijnsen AJ, Ciuffetti LM, Degrave A, Dilmaghani A, Duret L, Fudal I, Goodwin SB, Gout L, Glaser N, Linglin J, GH Keman, Lapalu N, Lawrence CB, May K, Meyer M, Ollivier B, Poulain J, Schoch CL, Simon A, Spatafora JW, Stachoviak A, Turgeon BG, Tyler BM, Vincent D, Weissenbach J, Amselem J, Quesneville H, Oliver RP, Wincker P, Balesdent MH, Howlett BJ (2011)
Effector diversification with in compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations, Nature communications, vol. 2 pp.1-10.

Sertier AS (2011)
L’évolution modulaire des protéines : un point de vue phylogénétique .

Slyemi D, Moinier D, Brochier-Armanet C, Bonnefoy V, Johnson D B (2011)
Characteristics of a phylogenetically ambiguous arsenic-oxidizing Thiomonas sp. Thiomonas arsenitoxydans strain 3As(T) sp. nov., Archives of Microbiology, vol. 193 pp.439-449.

Tannier E (2011)
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Tannier E (2011)
Preface : Satellite Workshop on Comparative Genomics Research in Computational Molecular Biology (RECOMB-CG 2010), Journal of Computational Biology, vol. 18 pp.1019-1021.

Trigui H, Masmoudi S, Brochier-Armanet C, Barani A, Grégori G, Denis M, Dukan S, Maalej S (2011)
Characterization of heterotrophic prokaryote subgroups in the Sfax coastal solar salterns by combining flow cytometry cell sorting and phylogenetic analysis., Extremophiles, vol. 15 pp.347-358.

Trigui H, Masmoudi S, Brochier-Armanet C, Maalej S, Dukan S (2011)
Characterization of Halorubrum sfaxense sp. nov. a New Halophilic Archaeon Isolated from the Solar Saltern of Sfax in Tunisia, International Journal of Microbiology, vol. 2011 pp.240191-240191.

Trigui H, Masmoudi S, Brochier-Armanet C, Maalej S, Dukan S (2011)
Survival of extremely and moderately halophilic isolates of Tunisian solar salterns after UV-B or oxidative stress, Canadian Journal of Microbiology, vol. 57 pp.923-33.

Whitney K D, Boussau B, Baack J E, Garland T Jr (2011)
Drift and Genome Complexity Revisited, PLoS Genetics, vol. 7 pp.e1002092-e1002092.

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

Abrouk M, Murat F, Pont C, Messing J, Jackson S, Faraut T, Tannier E, Plomion C, Cooke R, Feuillet C, Salse J (2010)
Palaeogenomics of plants: syntenybased modelling of extinct ancestors, Trends in Plant Science, vol. 15 pp.479-487.

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.

Arnaiz O, Gout J-F, Betermier M, Bouhouche K, Cohen J, Duret L, Kapusta A, Meyer E, Sperling L (2010)
Gene expression in a paleopolyploid: a transcriptome resource for the ciliate Paramecium tetraurelia, BMC Genomics, vol. 11 pp.547-547.

Arsène-Ploetze F, Koechler S, Marchal M, Coppée J-Y, Chandler M, Bonnefoy V, Brochier-Armanet C, Barakat M, Barbe V, Battaglia-Brunet F, Bruneel O, Bryan C G, Cleiss-Arnold J, Cruveiller S, Erhardt M, Heinrich-Salmeron A, Hommais F, Joulian C, Krin E, Lieutaud A, Lièvremont D, Michel C, Muller D, Ortet P, Proux C, Siguier P, Roche D, Rouy Z, Salvignol G, Slyemi D, Talla E, Weiss S, Weissenbach J, Médigue C, Bertin P N (2010)
Structure function and evolution of the Thiomonas spp. genome, PLoS Genetics, vol. 6 pp.e100859-e100859.

Bailly-Bechet M, Braunstein A, Pagnani A, Weigt M, Zecchina R (2010)
Inference of sparse combinatorial-control networks from gene-expression data: a message passing approach, BMC Bioinformatics, vol. 11 pp.355-355.

Baldazzi V, Ropers D, Markowicz Y, Kahn D, Geiselmann J, de Jong H (2010)
The Carbon Assimilation Network in Escherichia coli Is Densely Connected and Largely Sign-Determined by Directions of Metabolic Fluxes, PLos Computational Biology, vol. 6 pp.e1000812-e1000812.

Baudet C, Lemaitre C, Dias Z, Gautier C, Tannier E, Sagot M-F (2010)
Cassis: detection of genomic rearrangement breakpoints, Bioinformatics, vol. 26(15) pp.1897-1898.

Beisson J, Bétermier M, Bré M-H, Cohen J, Duharcourt S, Duret L, Kung C, Malinsky S, Meyer E, Preer Jr JR, Sperling L (2010)
Paramecium tetraurelia: The Renaissance of an Early Unicellular Model, Emerging Model Organisms, vol. 2010 pp.1-55.

Brochier-Armanet C (2010)
Minimal cell: the biologist point of view
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Chauve C, Gavranovic H, Ouangraoua A, Tannier E (2010)
Yeast Ancestral Genome Reconstructions: The Possibilities of Computational Methods II, Journal of Computational Biology, vol. 17(9) pp.1097-1112.

De Crécy-Lagard V, Brochier-Armanet C, Urbonavicius J, Fernandez B, Philipps G, Lyons B, Noma A, Alvarez S, Droogmans L, Armengaud J, Grosjean H (2010)
Biosynthesis of wyosine derivatives in tRNA: an ancient and highly diverse pathway in Archaea, Molecular Biology and Evolution, vol. 27 pp.2062-77.

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)
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Gavranovic H, Tannier E (2010)
Guided genome halving: provably optimal solutions provide good insights into the preduplication ancestral genome of Saccharomyces Cerevisiae, Pacific Symposium on Biocomputing, , vol. 15 pp.21-30.

Gout J-F, Kahn D, Duret L (2010)
The Relationship among Gene Expression the Evolution of Gene Dosage and the Rate of Protein Evolution, PLoS Genetics, vol. 6 pp.e1000944-e1000944.

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 pp.221-224.

Gribaldo S, Poole A, Daubin V, Forterre P, Brochier-Armanet C (2010)
The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse?, Nature Rewiews Microbiology, vol. 8 pp.743-752.

Lopez-Villavicencio M, Aguileta G, Giraud T, de Vienne D M, Lacoste S, Couloux A, Dupont J (2010)
Sex in Penicillium: combined phylogenetic and experimental approaches, Fungal genetics and biology, vol. 47 pp.693-706.

Miklos I, Tannier E (2010)
Bayesian sampling of genomic rearrangement scenarios via double cut and join, Bioinformatics, vol. 26 pp.3012-3019.

Murat F, Xu JH, Tannier E, Abrouk M, Guilhot N, Pont C, Messing J, Salse J (2010)
Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution, Genome Research, vol. 20 pp.1545-1557.

Perrière G, Brochier-Armanet C (2010) Concepts et méthodes en phylogénie moléculaire, Springer, 2010

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HOPPSIGEN: a database of human and mouse processed pseudogenes, Nucleic Acids Research, vol. 33 pp.59-66.

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De la prévalence aux valeurs prédictives: L`antibiogramme face à l`évolution de la résistance aux antibiotiques, Annales de Biologie Clinique (Paris), vol. 63 pp.493-502.

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Nicolas M, Marais GAB, Hykelova V, Janousek B, Laporte V, Vyskot B, Mouchiroud D, Negrutiu I, Charlesworth D, Moneger F (2005)
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A bunch of fun-guys: the whole-genome view of yeast evolution, Trends in Genetics, vol. 21 pp.1-3.

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Examining bacterial species under the specter of gene transfer and exchange, Proceedings of The National Academy of Sciences of The United States of America, vol. 102 pp.6595-6599.

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The Decline of Isochores in Mammals: An Assessment of the GC Content Variation Along the Mammalian Phylogeny, Journal of Molecular Evolution, vol. 58 pp.653-660.

Bonnaud B, Bouton O, Oriol G, Cheynet V, Duret L, Mallet F (2004)
Evidence of Selection on the Domesticated ERVWE1 env Retroviral Element Involved in Placentation, Molecular Biology and Evolution, vol. 21 pp.1895-1901.

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Computational inference of scenarios for alpha-proteobacterial genome evolution, Proceedings of The National Academy of Sciences of The United States of America, vol. 101 pp.9722-9727.

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Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox, Genome Biology, vol. 5 pp.1-5.

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Horizontal gene transfer and archaeal origin of deoxyhypusine synthase homologous genes in bacteria, Gene, vol. 330 pp.169-76.

Daubin V, Moran NA (2004)
Comment on "The origins of genome complexity", Science, vol. 306 pp.978a-978a.

Daubin V, Ochman H (2004)
Bacterial genomes as new gene homes: the genealogy of ORFans in E. coli, Genome Research, vol. 14 pp.1036-1042.

Daubin V, Ochman H (2004)
Quartet mapping and the extent of lateral transfer in bacterial genomes, Molecular Biology and Evolution, vol. 21 pp.86-89.

Daubin V, Ochman H (2004)
Start-up entities in the origin of new genes, Current Opinion in Genetics and Development, vol. 14 pp.616-619.

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Nitrogen regulation in Sinorhizobium meliloti probed with whole genome arrays, FEMS Microbiology Letters, vol. 241 pp.33-40.

Dixon R, Kahn D (2004)
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Ginolhac A, Jarrin C, Gillet B, Robe P, Pujic P, Tuphile K, Bertrand H, Vogel TM, Perrière G, Simonet P, Nalin R (2004)
Phylogenetic analysis of polyketide synthase I domains from soil metagenomic libraries allows selection of promising clones., Applied and Environmental Microbiology, vol. 70 pp.5522-5527.

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Grid as a bioinformatic tool, Parallel Computing, vol. 30 pp.1093-1107.

Jaillon O, Aury J-M, Brunet F, Petit J L, Stange-Thomann N, Mauceli E, Bouneau L, Fischer C, Ozouf-Costaz C, Bernot A, Nicaud S, Jaffe D, Fisher S, Lutfalla G, Dossat C, Segurens B, Dasilva C, Salanoubat M, Levy M, Boudet N, Castellano S, Anthouard V, Jubin C, Castelli V, Katinka M, Vacherie B, Biémont C, Skalli Z, Cattolico L, Poulain J, De Berardinis V, Cruaud C, Duprat S, Brottier P, Coutanceau JP, Gouzy J, Parra G, Lardier G, Chapple C, McKernan KJ, McEwan P, Bosak S, Kellis M, Volff JN, Guigo R, Zody MC, Mesirov J, Lindblad-Toh K, Birren B, Nusbaum C, Kahn D, Robinson-Rechavi M, Laudet V, Schachter V, Quetier F, Saurin W, Scarpelli C, Wincker P, Lander E S, Weissenbach J, Roest Crollius H (2004)
Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype, Nature, vol. 431 pp.946-957.

Keime C, Damiola F, Mouchiroud D, Duret L, Gandrillon O (2004)
Identitag a relational database for SAGE tag identification and interspecies comparison of SAGE libraries, BMC Bioinformatics, vol. 5 pp.1-12.

Lamy B, Carret G, Flandrois J-P, Delignette-Muller M-L (2004)
How does susceptibility prevalence impact on the performance of disk diffusion susceptibility testing?, Diagnostic Microbiology and Infectious Disease, vol. 49 pp.131-139.

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.

Lobry JR (2004)
Life history traits and genome structure: aerobiosis and G+C content in bacteria, Lecture Notes in Computer Sciences, vol. 3039 pp.679-686.

Lopez-Garcia P, Brochier C, Moreira D, Rodriguez-Valera F (2004)
Comparative analysis of a genome fragment of an uncultivated mesopelagic crenarchaeote reveals multiple horizontal gene transfers, Environ Microbiol, vol. 6 pp.19-34.

Mallet F, Bouton O, Prudhomme S, Cheynet V, Oriol G, Bonnaud B, Lucotte G, Duret L, Mandrand B (2004)
The endogenous retroviral locus ERVWE1 is a bona fide gene involved in hominoid placental physiology, Proceedings of The National Academy of Sciences of The United States of America, vol. 101 pp.1731-1736.

Meunier J, Duret L (2004)
Recombination drives the evolution of GC-content in the human genome, Molecular Biology and Evolution, vol. 21 pp.984-990.

Michon L, Morle L, Bozon M, Duret L, Zech JC, Godet J, Plauchu H, Edery P (2004)
Physical and transcript map of the autosomal dominant colobomatous microphthalmia locus on chromosome 15q12-q15 and refinement to a 4.4 Mb region, European Journal of Human Genetics, vol. 12 pp.574-578.

Reymond N, Charles H, Duret L, Calevro F, Beslon G, Fayard J-M (2004)
ROSO : Research on Optimized Oligonucleotide Probes for Microarrays, Bioinformatics, vol. 20 pp.271-273.

Robinson-Rechavi M, Boussau B, Laudet V (2004)
Phylogenetic dating and characterization of gene duplications in vertebrates: the cartilaginous fish reference, Molecular Biology and Evolution, vol. 21 pp.580-586.

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Update of NUREBASE: nuclear hormone receptor functional genomics, Nucleic Acids Research, vol. 32 pp.D165-D167.

Sebo A, Tannier E (2004)
On Metric Generators of Graphs, Mathematics of Operations Research, vol. 29 pp.383-393.

Sémon M, Duret L (2004)
Evidence that functional transcription units cover at least half of the human genome, Trends in Genetics, vol. 20 pp.229-232.

Tannier E, Sagot M-F (2004)
Sorting by reversals in subquadratic time, Proceedings of CPM`04, Springer Verlag, Lecture Notes in Computer Science, vol. 3109 pp.1-13.

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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.

Wuyts J, Perrière G, Van De Peer Y (2004)
The European ribosomal RNA database, Nucleic Acids Research, vol. 32 pp.D101-D103.

Zelwer M, Daubin V (2004)
Detecting phylogenetic incongruence using BIONJ: an improvement of the ILD test, Molecular Phylogenetics and Evolution, vol. 33 pp.687-693.

Assossou O, Besson F, Rouault JP, Persat F, Brisson C, Duret L, Ferrandiz J, Mayencon M, Peyron F, Picot S (2003)
Subcellular localization of 14-3-3 proteins in Toxoplasma gondii tachyzoites and evidence for a lipid raft-associated form, FEMS Microbiology Letters, vol. 224 pp.161-168..

Bergès H, Lauber E, Liebe C, Batut J, Kahn D, De Bruijn FJ, Ampe F (2003)
Development of Sinorhizobium meliloti pilot macroarrays for transcriptome analysis, Applied and Environmental Microbiology, vol. 69 pp.1214-1219.

Bièche I, Laurent A, Laurendeau I, Duret L, Giovangrandi Y, Frendo JL, Olivi M, Fausser JL, Evain-brion D, Vidaud M (2003)
Placenta-Specific INSL4 Expression Is Mediated by a Human Endogenous Retrovirus Element, Biology of Reproduction, vol. 68 pp.1422-1429..

Charles S, Ney M, Mouchiroud D, Humblot L, Batier C (2003)
Un site web pour l`enseignement interdisciplinaire des Mathématiques en Biologie, EIAH (Environnement Informatique d`Apprentissage Humain), vol. pp.445-452.

Charles-Bajard S, Flandrois J-P, Tomassone R (2003)
Quelques problèmes statistiques rencontrés dans l`estimation de la température minimale de croissance de Listeria monocytogenes, Revue de Statistique Appliquée, vol. LI pp.59-71.

Claudel-Renard C, Chevalet C, Faraut T, Kahn D (2003)
Enzyme-specific profiles for genome annotation: PRIAM, Nucleic Acids Research, vol. 31 pp.6633-6639.

Culhane AC, Perrière G, Higgins DG (2003)
Cross-platform comparison and visualisation of gene expression data using co-inertia analysis, BMC Bioinformatics, vol. 4 pp.1-15.

Daubin V, Lerat E, Perrière G (2003)
The source of laterally transferred genes in bacterial genomes, Genome Biology, vol. 4 pp.R57.1-R57.12.

Daubin V, Moran NA, Ochman H (2003)
Phylogenetics and the cohesion of bacterial genomes, Science, vol. 301 pp.829-832.

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G+C3 structuring along the genome: a common feature in prokaryotes, Molecular Biology and Evolution, vol. 20 pp.471-483.

Dechesne A, Pallud C, Debouzie D, Flandrois J-P, Gaudet JP, Grundmann GL (2003)
A method to study the microscale 3-D spatial distribution of Bacteria in soil., Mycological Research, vol. 107 pp.1221-1230.

Dechesne A, Pallud C, Debouzie D, Flandrois J-P, Vogel TM, Gaudet JP, Grundmann GL (2003)
A novel method for characterizing the microscale spatial distribution of bacteria in soil., Soil Biology and Biochemistry, vol. 35 pp.1537-1546.

Devulder G, Perrière G, Baty F, Flandrois J-P (2003)
BIBI a bioinformatics bacterial identification tool, Journal Clinical Microbiology, vol. 41 pp.1785-1787.

Grassot J, Mouchiroud G, Perrière G (2003)
RTKdb: database of Receptor Tyrosine Kinase, Nucleic Acids Research, vol. 31 pp.353-358.

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On a modular domination game, Theoretical Computer Science, vol. 306 pp.291-303.

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From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria, PLoS Biology, vol. 1 pp.101-109.

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Lobry JR, Louarn JM (2003)
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Marais GAB, Mouchiroud D, Duret L (2003)
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Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Barrell D, Bateman A, Binns D, Biswas M, Bradley P, Bork P, Bucher P, Copley RR, Courcelle E, Das U, Durbin R, Falquet L, Fleischmann W, Griffiths-Jones S, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lopez R, Letunic I, Lonsdale D, Silventoinen V, Orchard SE, Pagni M, Peyruc D, Ponting CP, Selengut JD, Servant F, Sigrist CJ, Vaughan R, Zdobnov EM (2003)
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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.

Perrière G, Thioulouse J (2003)
Use of Correspondence Discriminant Analysis to predict the subcellular location of bacterial proteins, Computer Methods and Programs in Biomedicine, vol. 70 pp.99-105.

Rizzon C, Martin E, Marais GAB, Duret L, Segalat L, Biémont C (2003)
Patterns of selection against transposons inferred from the distribution of Tc1 Tc3 and Tc5 insertions in the mut-7 line of the nematode Caenorhabditis elegans, Genetics, vol. 165 pp.1127-1135.

Stoesser G, Baker W, van den Broek A, Garcia-Pastor M, Kanz C, Kulikova T, Leinonen R, Lin Q, Lombard V, Lopez R, Mancuso R, Nardone F, Stoehr P, Tuli MA, Tzouvara K, Vaughan R (2003)
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Baty F, Flandrois J-P, Delignette-Muller M-L (2002)
Modeling the Lag Time of Listeria monocytogenes from Viable Count Enumeration and Optical Density Data, Applied and environmental microbiology, vol. 68 pp.5816-5825.

Brochier C, Bapteste E, Moreira D, Philippe H (2002)
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Brochier C, Philippe H (2002)
A non-hyperthermophilic ancestor for Bacteria, Nature, vol. 417 pp.50-53.

Chureau C, Prissette M, Bourdet A, Barbe V, Cattolico L, Jones L, Eggen A, Avner P, Duret L (2002)
Comparative sequence analysis of the X-inactivation center region in mouse human and bovine, Genome Research, vol. 12 pp.894-908..

Culhane AC, Perrière G, Considine E C, Cotter TG, Higgins D G (2002)
Between-group analysis of microarray data, Bioinformatics, vol. 18 pp.1600-1608.

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.

Duarte J, Perrière G, Laudet V, Robinson-Rechavi M (2002)
NUREBASE: database of nuclear hormone receptors, Nucleic Acids Research, vol. 30 pp.364-368.

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Detecting genomic features under weak selective pressure: the example of codon usage in animals and plants, Bioinformatics, vol. 18 pp.S91-S91.

Duret L (2002)
Evolution of synonymous codon usage in metazoans, Current Opinion in Genetics and Development, vol. 12 pp.640-649.

Duret L, Sémon M, Piganeau G, Mouchiroud D, Galtier N (2002)
Vanishing GC-Rich Isochores in Mammalian Genomes, Genetics, vol. 162 pp.1837-1848.

Ferrières L, Kahn D (2002)
Two distinct classes of FixJ binding sites defined by in vitro selection, FEBS Letters, vol. 517 pp.185-189.

Forterre P, Brochier C, Philippe H (2002)
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Journet EP, van Tuinen D, Gouzy J, Crespeau H, Carreau V, Farmer M J, Niebel A, Schiex T, Jaillon O, Chatagnier O, Godiard L, Micheli F, Kahn D, Gianinazzi-Pearson V, Gamas P (2002)
Exploring root symbiotic programs in the model legume Medicago truncatula using EST analysis, Nucleic Acids Research, vol. 30 pp.5579-5592.

Lamy B, Roy P, Carret G, Flandrois J-P, Delignette-Muller M-L (2002)
What is the relevance of obtaining multiple blood samples for culture? A comprehensive model to optimize the strategy for diagnosing bacteremia, Clinical Infectious Diseases, vol. 35 pp.842-850.

Lobry JR, Sueoka N (2002)
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EMBL-Align: a new public nucleotide and amino acid multiple sequence alignment database, Bioinformatics, vol. 18 pp.763-764.

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A mathematical method for determining genome divergence and species delineation using AFLP, International Journal of Systematic and Evolutionary Microbiology, vol. 52 pp.573-586.

Mulder N J, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Biswas M, Bradley P, Bork P, Bucher P, Copley R, Courcelle E, Durbin R, Falquet L, Fleischmann W, Gouzy J, Griffith-Jones S, Haft D, Hermjakob H, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lopez R, Letunic I, Orchard S, Pagni M, Peyruc D, Ponting C P, Servant F, Sigrist C J (2002)
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Perrière G, Thioulouse J (2002)
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Piganeau G, Mouchiroud D, Duret L, Gautier C (2002)
Expected Relationship Between the Silent Substitution Rate and the GC Content: Implications for the Evolution of Isochores, Journal of Molecular Evolution, vol. 54 pp.129-133..

Ponger L, Mouchiroud D (2002)
CpGProD: identifying CpG islands associated with transcription start sites in large genomic mammalian sequences, Bioinformatics, vol. 18 pp.631-633.

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.

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Molecular dynamics of the FixJ receiver domain: movement of the beta4-alpha4 loop correlates with the in and out flip of Phe101, Protein Science, vol. 11 pp.2622-2630.

Servant F, Bru C, Carrere S, Courcelle E, Gouzy J, Peyruc D, Kahn D (2002)
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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.

Tannier E (2002)
Sur quelques problèmes de recouvrement et empilement dans les graphes et les matroïdes .

Valière N, Berthier P, Mouchiroud D, Pontier D (2002)
Geminy: software for testing the effects of genotyping errors and multitubes approach for the individual identification, Molecular Ecology Notes, vol. 2 pp.83-86.

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)
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The InterPro database an integrated documentation resource for protein families domains and functional sites, Nucleic Acids Research, vol. 29 pp.37-40.

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Analysis of the chromosome sequence of the legume symbiont Sinorhizobium meliloti strain 1021, Proceedings of The National Academy of Sciences of The United States of America, vol. 98 pp.9877-9882.

Cariou ML, Silvain J F, Daubin V, Da Lage J L, Lachaise D (2001)
Divergence between Drosophila santomea and allopatric or sympatric populations of D. yakuba using paralogous amylase genes and migration scenarios along the Cameroon volcanic line, Molecular Ecology, vol. 10 pp.649-660.

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HDR - Organisation Fonctionnement et Evolution des Génomes de Métazoaires : Mais où est donc passée la sélection naturelle ? .

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Why do genes have introns? Recombination might add a new piece to the puzzle, Trends in Genetics, vol. 17 pp.172-175.

Duret L, Hurst L D (2001)
The elevated GC content at exonic third sites is not evidence against neutralist models of isochore evolution, Molecular Biology and Evolution, vol. 18 pp.757-762.

Frendo P, Jimenez M J, Mathieu C, Duret L, Gallesi D, Van de Sype G, Herouart D, Puppo A (2001)
Plant Physiol.A Medicago truncatula homoglutathione synthetase is derived from glutathione synthetase by gene duplication, Plant Physiologie, vol. 126 pp.1706-1715.

Galibert F, Finan TM, Long SR, Puhler A, Abola P, Ampe F, Barloy-Hubler F, Barnett MJ, Becker A, Boistard P, Bothe G, Boutry M, Bowser L, Buhrmester J, Cadieu E, Capela D, Chain P, Cowie A, Davis RW, Dreano S, Federspiel NA, Fisher RF, Gloux S, Godrie T, Goffeau A, Golding B, Gouzy J, Gurjal M, Hernandez-Lucas I, Hong A, Huizar L, Hyman RW, Jones T, Kahn D, Kahn ML, Kalman S, Keating DH, Kiss E, Komp C, Lelaure V, Masuy D, Palm C, Peck MC, Pohl TM, Portetelle D, Purnelle B, Ramsperger U, Surzycki R, Thébault P, Vandenbol M, Vorholter FJ, Weidner S, Wells DH, Wong K, Yeh KC, Batut J (2001)
The composite genome of the legume symbiont Sinorhizobium meliloti, Science, vol. 293 pp.668-672.

Galtier N, Piganeau G, Mouchiroud D, Duret L (2001)
GC-content evolution in mammalian genomes: the biased gene conversion hypothesis, Genetics, vol. 159 pp.907-911.

Guindon S, Perrière G (2001)
Intragenomic base content variation is a potential source of biases when searching for horizontally transferred genes, Molecular Biology and Evolution, vol. 18 pp.1838-1840.

Hughes S, Mouchiroud D (2001)
High evolutionary rates in nuclear genes of squamates, Journal of Molecular Evolution, vol. 53 pp.70-76.

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.

Lavire C, Louis D, Perrière G, Briolay J, Normand P, Cournoyer B (2001)
Analysis of pFQ31 a 8551-bp cryptic plasmid from the symbiotic nitrogen-fixing actinomycete Frankia, FEMS Microbiology Letters, vol. 197 pp.111-116.

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.

Marais GAB, Duret L (2001)
Synonymous codon usage accuracy of translation and gene length in Caenorhabditis elegans, Journal of Molecular Evolution, vol. 52 pp.275-280.

Marais GAB, Mouchiroud D, Duret L (2001)
Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes, Proceedings of The National Academy of Sciences of The United States of America, vol. 98 pp.5688-5692.

Noel C, Charles S, Francon A, Flandrois J-P (2001)
A mathematical model describing the thermal virus inactivation, Vaccine, vol. 19 pp.3575-3582.

Peyrefitte S, Kahn D, Haenlin M (2001)
New members of the Drosophila Myc transcription factor subfamily revealed by a genome-wide examination for basic helix-loop-helix genes, Mechanisms of Development, vol. 104 pp.99-104.

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.

Ponger L, Duret L, Mouchiroud D (2001)
Determinants of CpG islands: expression in early embryo and isochore structure, Genome Research, vol. 11 pp.1854-1860.

Reyrat JM, Kahn D (2001)
Mycobacterium smegmatis: an absurd model for tuberculosis?, Trends in Microbiology, vol. 9 pp.472-474.

Rudnick PA, Arcondéguy T, Kennedy CK, Kahn D (2001)
glnD and mviN are genes of an essential operon in Sinorhizobium meliloti, Journal of Bacteriology, vol. 183 pp.2682-2685.

Sebo A, Tannier E (2001)
Connected Joins in Graphs, Proceedings of IPCO`01, Springer Verlag, Lecture Notes in Computer Science, vol. 2081 pp.383-391.

Stoesser G, Baker W, van den Broek A, Camon E, Garcia-Pastor M, Kanz C, Kulikova T, Lombard V, Lopez R, Parkinson H, Redaschi N, Sterk P, Stoehr P, Tuli M A (2001)
The EMBL nucleotide sequence database, Nucleic Acids Research, vol. 29 pp.17-21.

Ton-Hoang B, Salhi M, Schumacher J, Da Re S, Kahn D (2001)
Promoter-specific involvement of the FixJ receiver domain in transcriptional activation, Journal of Molecular Biology, vol. 312 pp.583-589.

Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MD, Durbin R, Falquet L, Fleischmann W, Gouzy J, Hermjakob H, Hulo N, Jonassen I, Kahn D, Kanapin A, Karavidopoulou Y, Lopez R, Marx B, Mulder NJ, Oinn TM, Pagni M, Servant F, Sigrist CJ, Zdobnov EM (2000)
InterPro--an integrated documentation resource for protein families domains and functional sites, Bioinformatics, vol. 16 pp.1145-1150.

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.

Birot A, Duret L, Bartholin L, Santalucia B, Tigaud I, Magaud J, Rouault J (2000)
Identification and molecular analysis of BANP, Gene, vol. 253 pp.189-196.

Brochier C, Philippe H (2000)
Phylogénies moléculaires et génomes
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Brochier C, Philippe H, Moreira D (2000)
The evolutionary history of ribosomal protein RpS14: horizontal gene transfer at the heart of the ribosome, Trends Genet, vol. 16 pp.529-33.

Corpet F, Servant F, Gouzy J, Kahn D (2000)
ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons, Nucleic Acids Research, vol. 28 pp.267-269.

Duret L (2000)
tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes, Trends in Genetics, vol. 16 pp.287-289.

Duret L, Abdeddaim S (2000)
Multiple alignments for structural functional or phylogenetic analyses of homologous sequences
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Duret L, Galtier N (2000)
The covariation between TpA deficiency CpG deficiency and G+C content of human isochores is due to a mathematical artifact, Molecular Biology and Evolution, vol. 17 pp.1620-1625.

Duret L, Marais GAB, Biémont C (2000)
Transposons but not retrotransposons are located preferentially in regions of high recombination rate in Caenorhabditis elegans, Genetics, vol. 156 pp.1661-1669.

Duret L, Mouchiroud D (2000)
Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate, Molecular Biology and Evolution, vol. 17 pp.68-74.

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.

Frank AC, Lobry JR (2000)
Oriloc: prediction of replication boundaries in unannotated bacterial chromosomes, Bioinformatics, vol. 16 pp.560-561.

Goncalves I, Duret L, Mouchiroud D (2000)
Nature and structure of human genes that generate retropseudogenes, Genome Research, vol. 10 pp.672-678.

Ott C, Duret L, Chemin I, Trepo C, Mandrand B, Komurian-Pradel F (2000)
Use of a TT virus ORF1 recombinant protein to detect anti-TT virus antibodies in human sera, Journal of General Virology, vol. 81 pp.2949-2958.

Perriere G (2000)
HDR - Bases de données et outils d’analyse pour la génomique bactérienne .

Perrière G, Bessieres P, Labedan B (2000)
EMGLib: the enhanced microbial genomes library (update 2000), Nucleic Acids Research, vol. 28 pp.68-71.

Perrière G, Bessieres P, Labedan B (2000)
The Enhanced Microbial Genomes Library, Nucleic Acids Research, vol. 27 pp.63-65.

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

Picardeau M, Lobry JR, Hinnebusch B J (2000)
Analyzing DNA strand compositional asymmetry to identify candidate replication origins of Borrelia burgdorferi linear and circular plasmids, Genome Research, vol. 10 pp.1594-1604.

Robinson-Rechavi M, Ponger L, Mouchiroud D (2000)
Nuclear gene LCAT supports rodent monophyly, Molecular Biology and Evolution, vol. 17 pp.1410-1412.

Voisset C, Bouton O, Bedin F, Duret L, Mandrand B, Mallet F, Paranhos-Baccala G (2000)
Chromosomal distribution and coding capacity of the human endogenous retrovirus HERV-W family, AIDS Research and Human Retroviruses, vol. 16 pp.731-740.

Birck C, Mourey L, Gouet P, Fabry B, Schumacher J, Rousseau P, Kahn D, Samama JP (1999)
Conformational changes induced by phosphorylation of the FixJ receiver domain, Structure, vol. 7 pp.1505-1515.

Blond JL, Beseme F, Duret L, Bouton O, Bedin F, Perron H, Mandrand B, Mallet F (1999)
Molecular characterization and placental expression of HERV-W a new human endogenous retrovirus family, Journal of Virology, vol. 73 pp.1175-1185.

Breand S, Fardel G, Flandrois J-P, Rosso L, Tomassone R (1999)
A model describing the relationship between regrowth lag time and mild temperature increase for Listeria monocytogenes, International Journal of Food Microbiology, vol. 46 pp.251-261.

Charles H, Mouchiroud D, Lobry JR, Goncalves I, Rahbe Y (1999)
Gene size reduction in the bacterial aphid endosymbiont Buchnera, Molecular Biology and Evolution, vol. 16 pp.1820-1822.

Cornu M, Delignette-Muller M-L, Flandrois J-P (1999)
Characterization of Unexpected Growth of Escherichia coli O157:H7 by Modeling, Applied and environmental microbiology, vol. 65 pp.5322-5327.

Corpet F, Gouzy J, Kahn D (1999)
Browsing protein families via the `Rich Family Description` format, Bioinformatics, vol. 15 pp.1020-1027.

Corpet F, Gouzy J, Kahn D (1999)
Recent improvements of the ProDom database of protein domain families., Nucleic Acids Research, vol. 27 pp.263-267.

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Phosphorylation-induced dimerization of the FixJ receiver domain, Molecular Microbiology, vol. 34 pp.504-511.

Duret L, Mouchiroud D (1999)
Expression pattern and surprisingly gene length shape codon usage in Caenorhabditis Drosophila and Arabidopsis, Proceedings of The National Academy of Sciences of The United States of America, vol. 96 pp.4482-4487.

Duret L, Perrière G, Gouy M (1999)
HOVERGEN: comparative analysis of homologous vertebrate genes
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Frank AC, Lobry JR (1999)
Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms, Gene, vol. 238 pp.65-77.

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

Goncalves I, Robinson M, Perrière G, Mouchiroud D (1999)
JaDis: computing distances between nucleic acid sequences, Bioinformatics, vol. 15 pp.424-425.

Gouet P, Fabry B, Guillet V, Birck C, Mourey L, Kahn D, Samama JP (1999)
Structural transitions in the FixJ receiver domain, Structure, vol. 7 pp.1517-1526.

Gouzy J, Corpet F, Kahn D (1999)
Whole genome protein domain analysis using a new method for domain clustering, Journal of Computational Chemistry, vol. 23 pp.333-340.

Hughes S, Zelus D, Mouchiroud D (1999)
Warm-blooded isochore structure in Nile crocodile and turtle, Molecular Biology and Evolution, vol. 16 pp.1521-1527.

Kano-Sueoka T, Lobry JR, Sueoka N (1999)
Intra-strand biases in bacteriophage T4 genome, Gene, vol. 238 pp.59-64.

Lobry JR (1999)
Genomic landscapes, Microbiology Today, vol. 26 pp.164-165.

Lobry JR (1999)
A nice wrong model for the evolution of DNA base frequencies, Physica A, vol. 273 pp.99-102.

Lobry JR, Lobry C (1999)
Evolution of DNA base composition under no-strand-bias conditions when the substitution rates are not constant, Molecular Biology and Evolution, vol. 16 pp.719-723.

Picardeau M, Lobry JR, Hinnebusch B J (1999)
Physical mapping of an origin of bidirectional replication at the centre of the Borrelia burgdorferi linear chromosome, Molecular Microbiology, vol. 32 pp.437-445.

Rouault JP, Kuwabara PE, Sinilnikova OM, Duret L, Thierry-Mieg D, Billaud M (1999)
Regulation of dauer larva development in Caenorhabditis elegans by daf-18 a homologue of the tumour suppressor PTEN, Current Biology, vol. 9 pp.329-332.

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.

Wheelan S J, Boguski M S, Duret L, Makalowski W (1999)
Human and nematode orthologs--lessons from the analysis of 1800 human genes and the proteome of Caenorhabditis elegans, Gene, vol. 238 pp.163-170.

Breand S, Fardel G, Flandrois J-P, Rosso L, Tomassone R (1998)
Model of the influence of time and mild temperature on Listeria monocytogenes nonlinear survival curves, International Journal of Food Microbiology, vol. 40 pp.185-195.

Corpet F, Gouzy J, Kahn D (1998)
The ProDom database of protein domain families, Nucleic Acids Research, vol. 26 pp.323-326.

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Phylogenetic analysis and genome size of Ostreococcus tauri (Chlorophyta Prasinophyceae), Journal of Phycology, vol. 34 pp.844-849.

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New insulin-like proteins with atypical disulfide bond pattern characterized in Caenorhabditis elegans by comparative sequence analysis and homology modeling, Genome Research, vol. 8 pp.348-353.

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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.

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