UMR CNRS 5558 Laboratoire de Biométrie et Biologie Évolutive

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.

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.

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.

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

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.

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.

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.

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

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.

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.

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.

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.

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.1-11.

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.

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.

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.

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.

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

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.

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.

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

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.

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.

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

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.

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.

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.1-13.

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

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.

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.

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.

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

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.

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

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

Wiberg RA, Halligan DL, Ness RW, Necsulea A, Kaessmann H, Keightley PD (2015)
Assessing Recent Selection and Functionality at Long Noncoding RNA Loci in the Mouse Genome, Genome Biology and Evolution, vol. 7 pp.2432-44.

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.

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.

Semeria M, Tannier E, Gueguen L (2015)
Probabilistic modeling of the evolution of gene synteny within reconciled phylogenies, BMC Bioinformatics, vol. 16 Suppl 14 pp.S5-S5.

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.

Pisani D, Pett W, Dohrmann M, Feuda R, Rota Stabelli O, Philippe H, Lartillot N, Worheide G (2015)
Genomic data do not support comb jellies as the sister group to all other animals, Proceedings of the National Academy of Sciences of The United States of America, vol. 112 pp.15402-15407.

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.

Murat F, Zhang R, Guizard S, Gavranovic H, Flores R, Steinbach D, Quesneville H, Tannier E, Salse J (2015)
Karyotype and gene order evolution from reconstructed extinct ancestors highlight contrasts in genome plasticity of modern rosid crops, Genome biology and evolution, vol. 7 pp.735-49.

Philippon H, Brochier-Armanet C, Perriere G (2015)
Evolutionary history of phosphatidylinositol- 3-kinases: ancestral origin in eukaryotes and complex duplication patterns, BMC evolutionary biology, vol. 15 pp.226-226.

Mitchell A, Chang H Y, Daugherty L, Fraser M, Hunter S, Lopez R, McAnulla C, McMenamin C, Nuka G, Pesseat S, Sangrador-Vegas A, Scheremetjew M, Rato C, Yong SY, Bateman A, Punta M, Attwood TK, Sigrist CJ, Redaschi N, Rivoire C, Xenarios I, Kahn D, Guyot D, Bork P, Letunic I, Gough J, Oates M, Haft D, Huang H, Natale DA, Wu CH, Orengo C, Sillitoe I, Mi H, Thomas PD, Finn RD (2015)
The InterPro protein families database: the classification resource after 15 years, Nucleic Acids Research, vol. 43 pp.D213-D221.

Patten SA, Margaritte-Jeannin P, Bernard JC, Alix E, Labalme A, Besson A, Girard SL, Fendri K, Fraisse N, Biot B, Poizat C, Campan-Fournier A, Abelin-Genevois K, Cunin V, Zaouter C, Liao M, Lamy R, Lesca G, Menassa R, Marcaillou C, Letexier M, Sanlaville D, Berard J, Rouleau GA, Clerget-Darpoux F, Drapeau P, Moldovan F, Edery P (2015)
Functional variants of POC5 identified in patients with idiopathic scoliosis, Journal of Clinical Investigation, vol. 125 pp.1124-1128.

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.

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.

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.

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.

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.

Lassalle F, Perian S, Bataillon T, Nesme X, Duret L, Daubin V (2015)
GC-Content Evolution in Bacterial Genomes: The Biased Gene Conversion Hypothesis Expands, PLoS genetics, vol. 11 pp.e1004941-e1004941.

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.

Lartillot N (2015)
Probabilistic models of eukaryotic evolution: time for integration, Philosophical transactions of the Royal Society B-Biological sciences, vol. 370 pp.20140338-20140338.

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.

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.

Petitjean C, Deschamps P, Lopez-Garcia P, Moreira D, Brochier-Armanet C (2015)
Extending the conserved phylogenetic core of archaea disentangles the evolution of the third domain of life, Molecular biology and evolution, vol. 32 pp.1242-54.

Szollosi G J, Tannier E, Daubin V, Boussau B (2015)
The Inference of Gene Trees with Species Trees, Systematic biology, vol. 64 pp.e42-e62.

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.

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.

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.

Szollosi GJ, Arellano Davin A, Tannier E, Daubin V, Boussau B (2015)
Genome-scale phylogenetic analysis finds extensive gene transfer among fungi, Philosophical transactions of the Royal Society B-Biological sciences, vol. 370 pp.201403335-201403335.

Vinella D, Fischer F, Vorontsov E, Gallaud J, Malosse C, Michel V, Cavazza C, Robbe-Saule M, Richaud P, Chamot-Rooke J, Brochier-Armanet C, De Reuse H (2015)
Evolution of Helicobacter : Acquisition by Gastric Species of Two Histidine-Rich Proteins Essential for Colonization, PLoS Pathogens, vol. 11 pp.e1005312-e1005312.

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.

Tannier E (2015)
Sorting Signed Permutations by Reversal (Reversal Sequence)
in: Encyclopedia of Algorithms, Springer Science+Business Media New York 2015, pp.1-5.

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.

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.

Tessereau C, Leone M, Buisson M, Duret L, Sinilnikova OM, Mazoyer S (2015)
Occurrence of a non deleterious gene conversion event in the BRCA1 gene, Genes chromosomes & cancer, vol. 54 pp.646-52.

Semeria M (2015)
Evolution de l`architecture des génomes : modélisation et reconstruction phylogénétique .

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.

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

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Raymann K, Brochier-Armanet C, Gribaldo S (2015)
The two-domain tree of life is linked to a new root for the Archaea, Proceedings of the National Academy of Sciences of The United States of America, vol. 112 pp.6670-6675.

Sen A, Daubin V, Abrouk D, Gifford I, Berry A M, Normand P (2014)
Phylogeny of the class Actinobacteria revisited in the light of complete genomes. The orders `Frankiales` and Micrococcales should be split into coherent entities: proposal of Frankiales ord. nov. Geodermatophilales ord. nov. Acidothermales ord. nov. and Nakamurellales ord. nov, International journal of systematic and evolutionary microbiology, vol. 64 pp.3821-32.

Tessereau C, Lesecque Y, Monnet N, Buisson M, Barjhoux L, Leone M, Feng B, Goldgar D E, Sinilnikova O M, Mousset S, Duret L, Mazoyer S (2014)
Estimation of the RNU2 macrosatellite mutation rate by BRCA1 mutation tracing, Nucleic Acids Research, vol. 42 pp.9121-30.

Batut B, Knibbe C, Marais G, Daubin V (2014)
Reductive genome evolution at both ends of the bacterial population size spectrum, Nature reviews Microbiology, vol. 12 pp.841-50.

Zallot R, Brochier-Armanet C, Gaston K W, Forouhar F, Limbach P A, Hunt J F, De Crecy-Lagard V (2014)
Plant animal and fungal micronutrient queuosine is salvaged by members of the DUF2419 protein family, ACS chemical biology, vol. 9 pp.1812-25.

Aguileta G, de Vienne D M, Ross O N, Hood M E, Giraud T, Petit E, Gabaldon T (2014)
High variability of mitochondrial gene order among fungi, Genome biology and evolution, vol. 6 pp.451-465.

Junillon T, Morand L, Flandrois JP (2014)
Enhanced tetrazolium violet reduction of Salmonella spp. by magnesium addition to the culture media, Food Microbiology, vol. 42 pp.132-135.

Ramulu H G, Groussin M, Talla E, Planel R, Daubin V, Brochier-Armanet C (2014)
Ribosomal proteins: Toward a next generation standard for prokaryotic systematics?, Molecular phylogenetics and evolution, vol. 75C pp.103-117.

Bailly-Bechet M, Haudry A, Lerat E (2014)
“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files, Mobile DNA, vol. 5 pp.13-13.

Mirarab S, Bayzid M S, Boussau B, Warnow T (2014)
Statistical binning enables an accurate coalescent-based estimation of the avian tree, Science, vol. 346 pp.1250463-1250463.

Flandrois JP, Lina G, Dumitrescu O (2014)
MUBII-TB-DB: a database of mutations associated with antibiotic resistance in Mycobacterium tuberculosis, BMC Bioinformatics, vol. 15 pp.107-107.

Ropars J, Aguileta G, de Vienne DM, Giraud T (2014)
Massive gene swamping among cheese-making Penicillium fungi, Microbial cell, vol. 1 pp.107-109.

Touzeau A, Amiot R, Blichert-Toft J, Flandrois JP, Fourel F, Grossi V, Martineau F, Richardin P, Lécuyer C (2014)
Diet of ancient Egyptians inferred from stable isotope systematics, Journal of Archaeological Science, vol. 46 pp.114-124.

Lesecque Y (2014)
La conversion génique biaisée : origine dynamique et intensité de la quatrième force d’évolution des génomes eucaryotes .

Rodrigue N, Lartillot N (2014)
Site-heterogeneous mutation-selection models within the PhyloBayes-MPI package, Bioinformatics, vol. 30 pp.1020-1.

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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.

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.

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

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.

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

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.

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

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

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.

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

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

Tannier E (2011)
HDR - Evolution combinatoire Algorithmique des chromosomes .

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

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

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.

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.

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.

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.

Tannier E (2011) L`époque romantique contre la peine de mort, Editions Universitaires Europeennes, 2011

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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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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

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.94-101.

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.

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.

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.

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.

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.

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.

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.

Tavares R, Cagnon M, Negrutiu L, Mouchiroud D (2010)
Testing the recent theories for the origin of the hermaphrodite flower by comparison of the transcriptomes of gymnosperms and angiosperms, BMC Evolutionary Biology, vol. 10 pp.1-7.

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.

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.

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.

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.

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.

Salacha R, Kovacic F, Brochier-Armanet C, Wilhelm S, Tommassen J, Filloux A, Voulhoux R, Bleves S (2010)
The Pseudomonas aeruginosa patatin-like protein PlpD is the archetype of a novel Type V secretion system, Environmental Microbiology, vol. 12 pp.1498-512.

Tannier E (2010)
Le génome aux ordres des mathématiciens, La Recherche, vol. 439 pp.54-56.

Tannier E (2010) Comparative Genomics, Springer, 2010

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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.

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.

Brochier-Armanet C (2010)
Minimal cell: the biologist point of view
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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.

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.

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.

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.

Spang A, Hatzenpichler R, Brochier-Armanet C, Rattei T, Tischler P, Spieck E, Streit W, Stahl D A, Wagner M, Schleper C (2010)
Distinct gene set in two different lineages of ammoniaoxidizing archaea supports the phylum Thaumarchaeota, Trends in Microbiology, vol. 18 pp.331-340.

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.

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
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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.

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.

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

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

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.

Rodrigue N, Philippe H, Lartillot N (2010)
Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles, Proceedings of the National Academy of Sciences of the United States of America, vol. 107 pp.4629-34.

Walker C B, la Torre J R, Klotz M G, Urakawa H, Pinel N, Arp D J, Brochier-Armanet C, Chain P S, Chan P P, Gollabgir A, Hemp J, Hügler M, Karr E A, Könneke M, Shin M (2010)
Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea, Proceedings of the National Academy of Sciences of The United States of America, vol. 107 pp.8818-23.

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.

Ratnakumar A, Mousset S, Glémin S, Berglund J, Galtier N, Duret L, Webster MT (2010)
Detecting positive selection within genomes: the problem of biased gene conversion, Philosophical transactions of the royal society B-Biological sciences, vol. 365 pp.2571-2580.

Duret L (2009)
Mutation Patterns in the Human Genome:More Variable Than Expected, PLoS Biology, vol. 7(2) e1000028 pp.217-219.

Lemaitre C, Zaghloul L, Sagot M-F, Gautier C, Arneodo A, Tannier E, Audit B (2009)
Analysis of fine-scale mammalian evolutionary breakpoints provides new insight into their relation to genome organisation, BMC Genomics, vol. 10:335 pp.1-12.

Forterre P, Gribaldo S, Brochier-Armanet C (2009)
Happy together: genomic insights into the unique Nanoarchaeum Ignicoccus association, Journal of Biology, vol. 8 pp.16-32.

Guyon F, Brochier-Armanet C, Guénoche A (2009)
Comparison of alignment free string distances for complete genome phylogeny, Advances in Data Analysis and Classification, vol. 3 pp.95-108.

Necşulea A, Guillet C, Cadoret J-C, Prioleau M-N, Duret L (2009)
The Relationship between DNA Replication and Human Genome Organization, Molecular Biology and Evolution, vol. 26(4) pp.729-741.

Eme L, Moreira D, Talla E, Brochier-Armanet C (2009)
A complex cell division machinery was present in the last common ancestor of eukaryotes, PloS ONE, vol. 4 pp.968-982.

Vinella D, Brochier-Armanet C, Loiseau L, Talla E, Barras F (2009)
Iron-sulfur (Fe/S) protein biogenesis: phylogenomic and genetic studies of A-type carriers, PLoS Genetics, vol. 5 pp.e1000497-e1000497.

Bérard S, Chateau A, Chauve C, Paul C, Tannier E (2009)
Computation of Perfect DCJ Rearrangement Scenarios with Linear and Circular Chromosomes, Journal of Computational Biology, vol. 16(10) pp.1287-1309.

Marais GAB, Duret L (2009)
L’évolution des chromosomes sexuels humains, Biofutur, vol. 304 pp.40-41.

Gribaldo S, Talla E, Brochier-Armanet C (2009)
Evolution of the haem copper oxidases superfamily: a rooting tale, Trends in Biochemical Sciences, vol. 34 pp.375-381.

Lepère G, Nowacki M, Serrano S, Gout J-F, Guglielmi G, Duharcourt S, Meyer E (2009)
Silencing-associated and meiosis-specific small RNA pathways in TextitParamecium tetraurelia, Nucleic Acids Research, vol. 37(3) pp.903-915.

Boussau B, Daubin V (2009)
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Gribaldo S, Brochier C (2009)
Phylogeny of prokaryotes: does it exist and why should we care?, Res Microbiol, vol. 160 pp.513-21.

de Vienne D M, Refregier G, Hood M E, Guigue A, Devier B, Vercken E, Smadja C, Deseille A, Giraud T (2009)
Hybrid sterility and inviability in the parasitic fungal species complex Microbotryum, Journal of evolutionary biology, vol. 22 pp.683-698.

Guillet C (2009)
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de Vienne D M, Hood M E, Giraud T (2009)
Phylogenetic determinants of potential host shifts in fungal pathogens, Journal of evolutionary biology, vol. 22 pp.2532-2541.

Fertin G, Labarre A, Rusu I, Tannier E, Vialette S (2009) Combinatorics of Genome Rearrangements, MIT press, 2009

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Galtier N, Duret L, Glémin S, Ranwez V (2009)
GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates, Trends in Genetics, vol. 25(1) pp.1-5.

Duret L, Galtier N (2009)
Comment on “Human-Specific Gain of Function in a Developmental Enhancer”, Science, vol. 323(5915) pp.714-715.

Gout J-F (2009)
Les singularités du génome de la paramécie : un bon révélateur des mécanismes évolutifs à l`oeuvre chez les êtres vivants .

Barabote RD, Xie G, Leu DH, Normand P, Necsulea A, Daubin V, Médigue C, Adney WS, Xu XC, Lapidus A, Paralez RE, Detter C, Pujic P, Bruce D, Lavire C, Challacombe JF, Brettin TS, Berry AM (2009)
Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations, Genome Research, vol. 19(6) pp.1033-1043.

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.s3-s3.

Boussau B (2009)
Phylogenetic Relationships Deduced from Whole Genome Comparisons, Encyclopedia of Life Sciences, vol. pp.1-8.

Brochier-Armanet C, Talla E, Gribaldo S (2009)
The multiple evolutionary histories of dioxygen reductases: implications for the origin and evolution of aerobic respiration, Molecular Biology and Evolution, vol. 26 pp.285-97.

Ouangraoua A, Boyer F, McPherson A, Tannier E, Chauve C (2009)
Prediction of Contiguous Regions in the Amniote Ancestral Genome, Proceedings of ISBRA`09, Springer, Lecture Notes in Bioinformatics, vol. 5542 pp.173-185.

Duret L, Galtier N (2009)
Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes, Annual Review of Genomics and Human Genetics, vol. 10 pp.285-311.

Tannier E, Zheng C, Sankoff D (2009)
Multichromosomal median and halving problems under different genomic distances, BMC Bioinformatics, vol. 10 pp.120-120.

de Vienne DM, Giraud T, Martin OC (2009)
In response to comment on ‘A congruence index for testing topological similarity between trees’, Bioinformatics, vol. 25 pp.150-151.

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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.

Khelifi A, Duret L, Mouchiroud D (2005)
HOPPSIGEN: a database of human and mouse processed pseudogenes, Nucleic Acids Research, vol. 33 pp.59-66.

Kersey P, Bower L, Morris L, Horne A, Petryszak R, Kanz C, Kanapin A, Das U, Michoud K, Phan I, Gattiker A, Kulikova T, Faruque N, Duggan K, McLaren P, Reimholz B, Duret L, Penel S, Reuter I, Apweiler R (2005)
Integr8 and Genome Reviews: integrated views of complete genomes and proteomes, Nucleic Acids Research, vol. 33 pp.297-302.

Hurst LD, Duret L (2005)
Bioinformatics with a French accent, Genome Biology, vol. 6 pp.349.1-349.3.

Calteau A, Gouy M, Perrière G (2005)
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Molecular phylogeny of Myricaceae: a reexamination of host-symbiont specificity, Molecular Phylogenetics and Evolution, vol. 34 pp.557-568.

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Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bradley P, Bork P, Bucher P, Cerutti L, Copley R, Courcelle E, Das U, Durbin R, Fleischmann W, Gough J, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McDowall J, Mitchell A, Nikolskaya AN, Orchard S, Pagni M, Ponting CP, Quevillon E, Selengut J, Sigrist CJ, Silventoinen V, Studholme DJ, Vaughan R, Wu CH (2005)
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Charif D, Thioulouse J, Lobry JR, Perrière G (2005)
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Bapteste E, Brochier C, Boucher Y (2005)
Higher-level classification of the Archaea: on methanogenesis and methanogens, Archaea, vol. 1 pp.353-63.

Bonnaud B, Beliaeff J, Bouton O, Oriol G, Duret L, Mallet F (2005)
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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.

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.

Lerat E, Daubin V, Ochman H, Moran NA (2005)
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Meunier J, Khelifi A, Navratil V, Duret L (2005)
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Bazin E, Duret L, Penel S, Galtier N (2005)
Polymorphix: a sequence polymorphism database, Nucleic Acids Research, vol. 33 pp.481-484.

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.

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.

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Phylogenetic study and identification of Vibrio splendidus-related strains based on gyrB gene sequences, Diseases of Aquatic Organisms, vol. 58 pp.143-150.

Becker A, Bergès H, Krol E, Bruand C, Ruberg S, Capela D, Lauber E, Meilhoc E, Ampe F, De Bruijn FJ, Fourment J, Francez-Charlot A, Kahn D, Kuster H, Liebe C, Pühler A, Weidner S, Batut J (2004)
Global changes in gene expression in Sinorhizobium meliloti 1021 under microoxic and symbiotic conditions, Molecular plant-microbe interactions, vol. 17 pp.292-303.

Jacq N, Blanchet C, Combet C, Cornillot E, Duret L, Kurata K, Nakamura H, Silvestre T, Breton V (2004)
Grid as a bioinformatic tool, Parallel Computing, vol. 30 pp.1093-1107.

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.

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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.

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.

Brochier C, Forterre P, Gribaldo S (2004)
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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Comparative analysis of a genome fragment of an uncultivated mesopelagic crenarchaeote reveals multiple horizontal gene transfers, Environ Microbiol, vol. 6 pp.19-34.

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

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

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.

Dixon R, Kahn D (2004)
Genetic regulation of biological nitrogen fixation, Nature Reviews Microbiology, vol. 2 pp.621-631.

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.

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.

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

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How does susceptibility prevalence impact on the performance of disk diffusion susceptibility testing?, Diagnostic Microbiology and Infectious Disease, vol. 49 pp.131-139.

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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.

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FixJ-regulated genes evolved through promoter duplication in Sinorhizobium meliloti, Microbiology, vol. 150 pp.2335-2345.

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

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

Belle E, Duret L, Galtier N, Eyre-Walker A (2004)
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.

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.

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.

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.

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Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype, Nature, vol. 431 pp.946-957.

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

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.

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

Bapteste E, Brochier C (2004)
On the conceptual difficulties in rooting the tree of life, Trends Microbiol, vol. 12 pp.9-13.

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.

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.

Gravier S, Mhalla M, Tannier E (2003)
On a modular domination game, Theoretical Computer Science, vol. 306 pp.291-303.

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.

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.

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.

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.

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)
The InterPro Database 2003 brings increased coverage and new features, Nucleic Acids Research, vol. 31 pp.315-318.

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.

Marais GAB, Mouchiroud D, Duret L (2003)
Neutral effect of recombination on base composition in Drosophila, Genetical Research, vol. 81 pp.79-89.

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.

Lerat E, Daubin V, Moran NA (2003)
From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria, PLoS Biology, vol. 1 pp.101-109.

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..

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.

Lobry JR, Louarn JM (2003)
Polarisation of prokaryotic chromosomes, Current Opinion in Microbiology, vol. 6 pp.101-108.

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

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

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.

Lobry JR, Chessel D (2003)
Internal correspondence analysis of codon and amino-acid usage in thermophilic bacteria, Journal of Applied Genetics, vol. 44 pp.235-261.

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..

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)
The EMBL Nucleotide Sequence Database: major new developments, Nucleic Acids Research, vol. 31 pp.17-22.

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.

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

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.

Daubin V, Perrière G (2003)
G+C3 structuring along the genome: a common feature in prokaryotes, Molecular Biology and Evolution, vol. 20 pp.471-483.

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.

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..

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

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.

Brochier C, Bapteste E, Moreira D, Philippe H (2002)
Eubacterial phylogeny based on translational apparatus proteins, Trends Genet, vol. 18 pp.1-5.

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

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.

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

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)
InterPro: an integrated documentation resource for protein families domains and functional sites, Briefings in Bioinformatics, vol. 3 pp.225-235.

Servant F, Bru C, Carrere S, Courcelle E, Gouzy J, Peyruc D, Kahn D (2002)
ProDom: automated clustering of homologous domains, Briefings in Bioinformatics, vol. 3 pp.246-251.

Lobry JR, Sueoka N (2002)
Asymmetric directional mutation pressures in bacteria, Genome Biology, vol. 26 pp.1-14.

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Sur quelques problèmes de recouvrement et empilement dans les graphes et les matroïdes .

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A non-hyperthermophilic ancestor for Bacteria, Nature, vol. 417 pp.50-53.

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

Duret L (2002)
Detecting genomic features under weak selective pressure: the example of codon usage in animals and plants, Bioinformatics, vol. 18 pp.S91-S91.

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.

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.

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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.

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.

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EMBL-Align: a new public nucleotide and amino acid multiple sequence alignment database, Bioinformatics, vol. 18 pp.763-764.

Perrière G, Thioulouse J (2002)
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Modeling the Lag Time of Listeria monocytogenes from Viable Count Enumeration and Optical Density Data, Applied and environmental microbiology, vol. 68 pp.5816-5825.

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.

Matte-Tailliez O, Brochier C, Forterre P, Philippe H (2002)
Archaeal phylogeny based on ribosomal proteins, Mol Biol Evol, vol. 19 pp.631-639.

Mougel C, Thioulouse J, Perrière G, Nesme X (2002)
A mathematical method for determining genome divergence and species delineation using AFLP, International Journal of Systematic and Evolutionary Microbiology, vol. 52 pp.573-586.

Forterre P, Brochier C, Philippe H (2002)
Evolution of the Archaea, Theor Popul Biol, vol. 61 pp.409-422.

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.

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.

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..

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.

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.

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.

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.

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.

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.

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.

Duret L (2001)
Why do genes have introns? Recombination might add a new piece to the puzzle, Trends in Genetics, vol. 17 pp.172-175.

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.

Capela D, Barloy-Hubler F, Gouzy J, Bothe G, Ampe F, Batut J, Boistard P, Becker A, Boutry M, Cadieu E, Dreano S, Gloux S, Godrie T, Goffeau A, Kahn D, Kiss E, Lelaure V, Masuy D, Pohl T, Portetelle D, Pühler A, Purnelle B, Ramsperger U, Renard C, Thébault P, Vandenbol M, Weidner S, Galibert F (2001)
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.

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.

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.

Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning M D, 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 N J, Oinn T M, Pagni M, Servant F, Sigrist C J, Zdobnov EM (2001)
The InterPro database an integrated documentation resource for protein families domains and functional sites, Nucleic Acids Research, vol. 29 pp.37-40.

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.

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.

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

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.

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.

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.

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.

Barnett MJ, Fisher RF, Jones T, Komp C, Abola AP, Barloy-Hubler F, Bowser L, Capela D, Galibert F, Gouzy J, Gurjal M, Hong A, Huizar L, Hyman RW, Kahn D, Kahn ML, Kalman S, Keating DH, Palm C, Peck MC, Surzycki R, Wells DH, Yeh KC, Davis RW, Federspiel NA, Long SR (2001)
Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid, Proceedings of The National Academy of Sciences of The United States of America, vol. 98 pp.9883-9888.

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.

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.

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

Duret L (2001)
HDR - Organisation Fonctionnement et Evolution des Génomes de Métazoaires : Mais où est donc passée la sélection naturelle ? .

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.

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.

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

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.

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.

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

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

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

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.

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

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.

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.

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.

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.

Brochier C, Philippe H (2000)
Phylogénies moléculaires et génomes
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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.

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

Duret L, Abdeddaim S (2000)
Multiple alignments for structural functional or phylogenetic analyses of homologous sequences
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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.

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

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.

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.

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

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.

Da Re S, Schumacher J, Rousseau P, Fourment J, Ebel C, Kahn D (1999)
Phosphorylation-induced dimerization of the FixJ receiver domain, Molecular Microbiology, vol. 34 pp.504-511.

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.

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.

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

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.

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.

Duret L, Perrière G, Gouy M (1999)
HOVERGEN: comparative analysis of homologous vertebrate genes
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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.

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.

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.

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

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.

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

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.

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.

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.

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.

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

Frank AC, Lobry JR (1999)
Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms, Gene, vol. 238 pp.65-77.

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.

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

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.

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.

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

Galtier N, Mouchiroud D (1998)
Isochore evolution in mammals: a human-like ancestral structure, Genetics, vol. 150 pp.1577-1584.

Duret L, Guex N, Peitsch M C, Bairoch A (1998)
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.

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.

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.

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.

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

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.

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.

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

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.

Spicher A, Guicherit O M, Duret L, Aslanian A, Sanjines E M, Denko N C, Giaccia A J, Blau H M (1998)
Highly conserved RNA sequences that are sensors of environmental stress, Molecular and Cellular Biology, vol. 18 pp.7371-7382.

Guehenneux F, Duret L, Callanan M B, Bouhas R, Hayette S, Berthet C, Samarut C, Rimokh R, Birot A M, Wang Q, Magaud J P, Rouault J P (1997)
Cloning of the mouse BTG3 gene and definition of a new gene family (the BTG family) involved in the negative control of the cell cycle, Leukemia, vol. 11 pp.370-375.

Perrière G, Moszer I, Gojobori T (1997)
The NRSub database: update 1997, Nucleic Acids Research, vol. 25 pp.53-56.

Robinson M, Catzeflis F, Briolay J, Mouchiroud D (1997)
Molecular phylogeny of rodents with special emphasis on murids: evidence from nuclear gene LCAT, Molecular Phylogenetics and Evolution, vol. 8 pp.423-434.

Breand S, Fardel G , Flandrois J-P, Rosso L, Tomassone R (1997)
A model describing the relationship between lag time and mild temperature increase duration, International Journal of Food Microbiology, vol. 38 pp.157-167.

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.

Lesenechal M, Duret L, Cano M I, Mortara R A, Jolivet M, Camargo M E, da Silveira J F, Paranhos-Baccala G (1997)
Cloning and characterization of a gene encoding a novel immunodominant antigen of Trypanosoma cruzi, Molecular and Biochemical Parasitology, vol. 87 pp.193-204.

Arcondéguy T, Huez I, Tillard P, Gangneux C, de Billy F, Gojon A, Truchet G, Kahn D (1997)
The Rhizobium meliloti PII protein which controls bacterial nitrogen metabolism affects alfalfa nodule development, Genes and Development, vol. 11 pp.1194-1206.

Mouchiroud D, Robinson M, Gautier C (1997)
Impact of changes in GC content on the silent molecular clock in murids, Gene, vol. 205 pp.317-322.

Bernardi G, Hughes S, Mouchiroud D (1997)
The major compositional transitions in the vertebrate genome, Journal of Molecular Evolution, vol. 44 Suppl 1 pp.S44-S51.

Robinson M, Gautier C, Mouchiroud D (1997)
Evolution of isochores in rodents, Molecular Biology and Evolution, vol. 14 pp.823-828.

Guérin-Faublée V, Charles S, Chomarat M, Flandrois J-P (1997)
Reappraisal of the effect of temperature on the growth kinetics of Aeromonas salmonicida, Letters in Applied Microbiology, vol. 25 pp.363-366.

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.

Duret L, Bucher P (1997)
Searching for regulatory elements in human noncoding sequences, Current Opinion in Structural Biology, vol. 7 pp.399-406.

Lobry JR (1997)
Influence of genomic G+C content on average amino-acid composition of proteins from 59 bacterial species, Gene, vol. 205 pp.309-316.

Galtier N, Lobry JR (1997)
Relationships between genomic G+C content RNA secondary structures and optimal growth temperature in prokaryotes, Journal of Molecular Evolution, vol. 44 pp.632-636.

Gouzy J, Eugene P, Greene EA, Kahn D, Corpet F (1997)
XDOM a graphical tool to analyse domain arrangements in any set of protein sequences, Computer Applications in the Biosciences, vol. 13 pp.601-608.

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.

Bajard S, Rosso L, Fardel G, Flandrois J-P (1996)
The particular behaviour of Listeria monocytogenes under sub-optimal conditions, International Journal of Food Microbiology, vol. 29 pp.201-211.

Rosso L, Bajard S, Flandrois J-P, Lahellec C, Fournaud J, Veit P (1996)
Differential growth of Listeria monocytogenes at 4° and 8° C. Consequences on self-life of chilled products, Journal of Food Protection, vol. 59 pp.944-949.

Clay O, Caccio S, Zoubak S, Mouchiroud D, Bernardi G (1996)
Human coding and noncoding DNA: compositional correlations, Molecular Phylogenetics and Evolution, vol. 5 pp.2-12.

Perrière G, Moszer I, Gojobori T (1996)
NRSub: a non-redundant database for Bacillus subtilis, Nucleic Acids Research, vol. 24 pp.41-45.

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

Duret L, Gasteiger E, Perrière G (1996)
LALNVIEW: a graphical viewer for pairwise sequence alignments, Computer Applications in the Biosciences, vol. 12 pp.507-510.

Lobry JR (1996)
Origin of replication of Mycoplasma genitalium, Science, vol. 272 pp.745-746.

Gouzy J, Corpet F, Kahn D (1996)
Graphical interface for ProDom domain families, Trends in Biochemical Sciences, vol. 21 pp.499-507.

van Heeswijk WC, Hoving S, Molenaar D, Stegeman B, Kahn D, Westerhoff HV (1996)
An alternative PII protein in the regulation of glutamine synthetase in Escherichia coli, Molecular Microbiology, vol. 21 pp.133-146.

Guérin-Faublée V, Delignette-Muller M-L, Vigneulle M, Flandrois J-P (1996)
Application of a modified disc diffusion technique to antimicrobial susceptibility testing of Vibrio anguillarum and Aeromonas salmonicida clinical isolates, Veterinary Microbiology, vol. 51 pp.137-149.

Perrière G, Lobry JR, Thioulouse J (1996)
Correspondence discriminant analysis: a multivariate method for comparing classes of protein and nucleic acid sequences, Computer Applications in the Biosciences, vol. 12 pp.519-524.

Perrière G, Thioulouse J (1996)
On-line tools for sequence retrieval and multivariate statistics in molecular biology, Computer Applications in the Biosciences, vol. 12 pp.63-69.

Lobry JR (1996)
A simple vectorial representation of DNA sequences for the detection of replication origins in bacteria, Biochimie, vol. 78 pp.323-326.

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

Lobry JR (1996)
Asymmetric substitution patterns in the two DNA strands of bacteria, Molecular Biology and Evolution, vol. 13 pp.660-665.

Arcondéguy T, Huez I, Fourment J, Kahn D (1996)
Symbiotic nitrogen fixation does not require adenylylation of glutamine synthetase I in Rhizobium meliloti, FEMS Microbiology Letters, vol. 145 pp.33-40.

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.

Rosso L, Lobry JR, Bajard S, Flandrois J-P (1995)
Convenient Model To Describe the Combined Effects of Temperature and pH on Microbial Growth, Applied and Environmental Microbiology, vol. 61 pp.610-616.

Thioulouse J, Lobry JR (1995)
Co-inertia analysis of amino-acid physico-chemical properties and protein composition with the ADE package, Bioinformatics, vol. 11 pp.321-329.

Mouchiroud D, Gautier C, Bernardi G (1995)
Frequencies of synonymous substitutions in mammals are gene-specific and correlated with frequencies of nonsynonymous substitutions, Journal of Molecular Evolution, vol. 40 pp.107-113.

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.

van Heeswijk WC, Stegeman B, Hoving S, Molenaar D, Kahn D, Westerhoff HV (1995)
An additional PII in Escherichia coli: a new regulatory protein in the glutamine synthetase cascade, FEMS Microbiology Letters, vol. 132 pp.153-157.

Duret L, Mouchiroud D, Gautier C (1995)
Statistical analysis of vertebrate sequences reveals that long genes are scarce in GC-rich isochores, Journal of Molecular Evolution, vol. 40 pp.308-317.

Schuster S, Kahn D, Westerhoff HV (1995)
Control analysis of metabolic systems consisting of uni- and/or multifunctional units. Application to modular systems and slipping enzymes, Journal of Biological Systems, vol. 3 pp.217-230.

Lobry JR (1995)
Properties of a general model of DNA evolution under no-strand-bias conditions, Journal of Molecular Evolution, vol. 40 pp.326-330.

Da Re S, Bertagnoli S, Fourment J, Reyrat JM, Kahn D (1994)
Intramolecular signal transduction within the FixJ transcriptional activator: in vitro evidence for the inhibitory effect of the phosphorylatable regulatory domain, Nucleic Acids Research, vol. 22 pp.1555-1561.

Sonnhammer ELL, Kahn D (1994)
Modular arrangement of proteins as inferred from analysis of homology, Protein Science, vol. 3 pp.482-492.

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.

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.

Lobry JR, Gautier C (1994)
Hydrophobicity expressivity and aromaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encoded genes, Nucleic Acids Research, vol. 22 pp.3174-3180.

Galinier A, Garnerone AM, Reyrat JM, Kahn D, Batut J, Boistard P (1994)
Phosphorylation of the Rhizobium meliloti FixJ protein induces its binding to a compound regulatory region at the fixK promoter, Journal of Biological Chemistry, vol. 269 pp.23784-23789.

Rimokh R, Berger F, Bastard C, Klein B, French M, Archimbaud E, Rouault J P, Santa Lucia B, Duret L, Vuillaume M (1994)
Rearrangement of CCND1 (BCL1/PRAD1) 3` untranslated region in mantle-cell lymphomas and t(11q13)-associated leukemias, Blood, vol. 83 pp.3689-3696.

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.

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.

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.

Westerhoff HV, Kahn D (1993)
Control involving metabolism and gene expression: the square- matrix method for modular decomposition, Acta Biotheoretica, vol. 41 pp.75-83.

Mouchiroud D, Bernardi G (1993)
Compositional properties of coding sequences and mammalian phylogeny, Journal of Molecular Evolution, vol. 37 pp.109-116.

Schmeltzer O, Medigue C, Uvietta P, Rechenmann F, Dorkeld F, Perrière G, Gautier C (1993)
Building large knowledge bases in molecular biology, In Proceedings of the First International Conference on Intelligent Systems for Molecular Biology, vol. 1 pp.345-353.

Duret L, Dorkeld F, Gautier C (1993)
Strong conservation of non-coding sequences during vertebrates evolution: potential involvement in post-transcriptional regulation of gene expression, Nucleic Acids Research, vol. 21 pp.2315-2322.

Kahn D, Westerhoff HV (1993)
The regulatory strength: how to be precise about regulation and homeostasis, Acta Biotheoretica, vol. 41 pp.85-96.

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.

Kahn D (1993)
Shuffling of an oxygen sensor haem domain, Molecular Microbiology, vol. 8 pp.786-787.

Rosso L, Lobry JR, Flandrois JP (1993)
An unexpected correlation between cardinal temperatures of microbial growth highlighted by a new model, Journal of Theoretical Biology, vol. 162 pp.447-463.

Rouault JP, Samarut C, Duret L, Tessa C, Samarut J, Magaud J P (1993)
Sequence analysis reveals that the BTG1 anti-proliferative gene is conserved throughout evolution in its coding and 3` non-coding regions, Gene, vol. 129 pp.303-306.

Schuster S, Kahn D, Westerhoff HV (1993)
Modular analysis of the control of complex metabolic pathways, Biophysical Chemistry, vol. 48 pp.1-17.

Bernardi G, Mouchiroud D, Gautier C (1993)
Silent substitutions in mammalian genomes and their evolutionary implications, Journal of Molecular Evolution, vol. 37 pp.583-589.

van Heeswijk WC, Rabenberg M, Westerhoff HV, Kahn D (1993)
The genes of the glutamine synthetase adenylylation cascade are not regulated by nitrogen in Escherichia coli, Molecular Microbiology, vol. 9 pp.443-457.

Perrière G, Dorkeld F, Rechenmann F, Gautier C (1993)
Object-oriented knowledge bases for the analysis of prokaryotic and eukaryotic genomes, In Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology, vol. 1 pp.319-327.

Perrière G, Gautier C (1993)
ColiGene: object-centered representation for the study of E coli gene expressivity by sequence analysis, Biochimie, vol. 75 pp.415-422.

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.

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.

Rouault JP, Rimokh R, Tessa C, Paranhos G, Ffrench M, Duret L, Garoccio M, Germain D, Samarut J, Magaud JP (1992)
BTG1 a member of a new family of antiproliferative genes, EMBO Journal, vol. 11 pp.1663-1670.

Lobry JR, Carret G, Flandrois J-P (1992)
Maintenance requirements of Escherichia coli ATCC 25922 in the presence of sub-inhibitory concentrations of various antibiotics, Journal of Antimicrobial Chemotherapy, vol. 29 pp.121-127.

van Heeswijk W, Kuppinger O, Merrick M, Kahn D (1992)
Localization of the glnD gene on a revised map of the 200- kilobase region of the Escherichia coli chromosome, Journal of Bacteriology, vol. 174 pp.1702-1703.

Lobry JR, Flandrois J-P, Carret G, Pavé A (1992)
Monod`s bacterial growth model revisited, Bulletin of Mathematical Biology, vol. 54(1) pp.117-122.

Lobry JR, Rosso L, Flandrois J-P (1991)
A FORTRAN subroutine for the determination of parameter confidence limits in non-linear Models, Binary, vol. 3 pp.86-93.

Kahn D, Westerhoff HV (1991)
Control theory of regulatory cascades, Journal of Theoretical Biology, vol. 153 pp.255-285.

Aissani B, D`Onofrio G, Mouchiroud D, Gardiner K, Gautier C, Bernardi G (1991)
The compositional properties of human genes, Journal of Molecular Evolution, vol. 32 pp.493-503.

Lobry JR, Flandrois J-P (1991)
Comparison of estimates of Monod`s growth model from the same data set, Binary, vol. 3 pp.20-23.

Westerhoff HV, van Heeswijk W, Kahn D, Kell DB (1991)
Quantitative approaches to the analysis of the control and regulation of microbial metabolism, Antonie Van Leeuwenhoek, vol. 60 pp.193-207.

D`Onofrio G, Mouchiroud D, Aissani B, Gautier C, Bernardi G (1991)
Correlations between the compositional properties of human genes codon usage and amino acid composition of proteins, Journal of Molecular Evolution, vol. 32 pp.504-510.

Kahn D, Ditta G (1991)
Modular structure of FixJ: homology of the transcriptional activator domain with the -35 binding domain of sigma factors, Molecular Microbiology, vol. 5 pp.987-997.

Carret G, Flandrois J-P, Lobry JR (1991)
Biphasic kinetics of bacterial killing by quinolones, Journal of Antimicrobial Chemotherapy, vol. 27 pp.319-327.

Lobry JR (1991)
Re-Evalution du modèle de croissance de Monod. Effet des antibiotiques sur l`énergie de maintenance. .

Cortay JC, Negre D, Galinier A, Duclos B, Perrière G, Cozzone AJ (1991)
Regulation of the acetate operon in Escherichia coli: purification and functional characterization of the IclR repressor, EMBO Journal, vol. 10 pp.675-679.

Peyret M, Flandrois J-P, Fardel G (1991)
Time-killing curves of Pseudomonas aeruginosa strains exposed to polymyxin B, Pathologie Biologie (Paris), vol. 39 pp.446-450.

Mouchiroud D, D`Onofrio G, Aissani B, Macaya G, Gautier C, Bernardi G (1991)
The distribution of genes in the human genome, Gene, vol. 100 pp.181-187.

Galinier A, Bleicher F, Negre D, Perrière G, Duclos B, Cozzone A J, Cortay J C (1991)
Primary structure of the intergenic region between aceK and iclR in the Escherichia coli chromosome, Gene, vol. 97 pp.149-150.

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

Mouchiroud D, Gautier C (1990)
Codon usage changes and sequence dissimilarity between human and rat, Journal of Molecular Evolution, vol. 31 pp.81-91.

Peyret M, Flandrois J-P, Fardel G (1990)
Mathematical study of the sensitivity curves of Escherichia coli exposed to polymyxins, Pathologie Biologie (Paris), vol. 38 pp.441-445.

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.

Westerhoff HV, Aon MA, van Dam K, Cortassa S, Kahn D, van Workum M (1990)
Dynamical and hierarchical coupling, Biochimica et Biophysica Acta, vol. 1018 pp.142-146.

Cherfils J, Gibrat JF, Levin J, Batut J, Kahn D (1989)
Model-building of Fnr and FixK DNA-binding domains suggests a basis for specific DNA recognition, Journal of Molecular Recognition, vol. 2 pp.114-121.

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

Batut J, Daveran-Mingot ML, David M, Jacobs J, Garnerone AM, Kahn D (1989)
fixK a gene homologous with fnr and crp from Escherichia coli regulates nitrogen fixation genes both positively and negatively in Rhizobium meliloti, EMBO Journal, vol. 8 pp.1279-1286.

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.

Hertig C, Li RY, Louarn AM, Garnerone AM, David M, Batut J, Kahn D, Boistard P (1989)
Rhizobium meliloti regulatory gene fixJ activates transcription of R. meliloti nifA and fixK genes in Escherichia coli, Journal of Bacteriology, vol. 171 pp.1736-1738.

Kahn D, David M, Domergue O, Daveran ML, Ghai J, Hirsch PR, Batut J (1989)
Rhizobium meliloti fixGHI sequence predicts involvement of a specific cation pump in symbiotic nitrogen fixation, Journal of Bacteriology, vol. 171 pp.929-939.

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.

Mouchiroud D, Gautier C, Bernardi G (1988)
The compositional distribution of coding sequences and DNA molecules in humans and murids, Journal of Molecular Evolution, vol. 27 pp.311-320.

Flandrois J-P, Fardel G, Carret G (1988)
Early stages of in vitro killing curve of LY146032 and vancomycin for Staphylococcus aureus, Antimicrobial Agents and Chemotherapy, vol. 32 pp.454-457.

David M, Daveran ML, Batut J, Dedieu A, Domergue O, Ghai J, Hertig C, Boistard P, Kahn D (1988)
Cascade regulation of nif gene expression in Rhizobium meliloti, Cell, vol. 54 pp.671-683.

Flandrois J-P, Carret G, Fardel G (1988)
A mathematical study of the mortality curve of Escherichia coli exposed to aminoglycosides, Pathologie Biologie (Paris), vol. 36 pp.446-451.

Mouchiroud D, Gautier C (1988)
High codon-usage changes in mammalian genes, Molecular Biology and Evolution, vol. 5 pp.192-194.

Bernardi G, Mouchiroud D, Gautier C (1988)
Compositional patterns in vertebrate genomes: conservation and change in evolution, Journal of Molecular Evolution, vol. 28 pp.7-18.

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

David M, Domergue O, Pognonec P, Kahn D (1987)
Transcription patterns of Rhizobium meliloti symbiotic plasmid pSym: identification of nifA-independent fix genes, Journal of Bacteriology, vol. 169 pp.2239-2244.

Mouchiroud D, Fichant G, Bernardi G (1987)
Compositional compartmentalization and gene composition in the genome of vertebrates, Journal of Molecular Evolution, vol. 26 pp.198-204.

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

Mouchiroud D (1986)
[Relationship between base composition in non-coding DNA of genes and codon composition], Comptes Rendus de l`Académie des Sciences - Séries III - Sciences de la Vie, vol. 303 pp.743-748.

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.

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

Carret G, Emonard H, Fardel G, Druguet M, Herbage D, Flandrois J-P (1985)
Gelatin and collagen binding to Staphylococcus aureus strains, Annales de l`Institut Pasteur-Microbiologie, vol. 136A pp.241-245.

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.

Eloy C, Fardel G, Flandrois J-P (1985)
Fast protein liquid chromatography for the isolation of Clostridium perfringens type A alpha-toxin, Journal of Chromatography, vol. 321 pp.235-239.

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.

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

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.

Blanquet S, Dessen P, Kahn D (1984)
Properties and specificity of methionyl-tRNAfMet formyltransferase from Escherichia coli, Methods in Enzymology, vol. 106 pp.141-152.

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.

Eady RR, Kahn D , Buchanan-Wollaston V (1982)
The molecular enzymology of nitrogen fixation, Israel Journal of Botany, vol. 31 pp.45-60.

Kahn D, Hawkins M, Eady R (1982)
Nitrogen fixation in Klebsiella pneumoniae: nitrogenase levels and the effect of added molybdate on nitrogenase derepressed under molybdenum deprivation, Journal of General Microbiology, vol. 128 pp.779-787.

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

Kahn D, Hawkins M, Eady R R (1982)
Metabolic control of Klebsiella pneumoniae mRNA degradation by the availability of fixed nitrogen, Journal of General Microbiology, vol. 128 pp.3011-3018.

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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.

Kahn D, Fromant M, Fayat G, Dessen P, Blanquet S (1980)
Methionyl-transfer-RNA transformylase from Escherichia coli. Purification and characterisation, European Journal of Biochemistry, vol. 105 pp.489-497.

Dixon R, Eady RR, Espin G, Hill S, Iaccarino M, Kahn D, Merrick M (1980)
Analysis of regulation of Klebsiella pneumoniae nitrogen fixation (nif) gene cluster with gene fusions, Nature, vol. 286 pp.128-132.

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

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.

Fayat G, Fromant M, Kahn D, Blanquet S (1977)
Affinity chromatography on agarose-hexyl-adenosine-5`-phosphate of methionyl-tRNA synthetase from Escherichia coli. Application of the couplings between the methionine and ATP sites, European Journal of Biochemistry, vol. 78 pp.333-336.