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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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. pp.e1452-e1459.

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.

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

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.

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.

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. pp.1-20.

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

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

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.

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.

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.

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. pp.1-13.

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.

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

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.

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.

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.

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

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.

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

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

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

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.

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.

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.

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

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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.

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.

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.

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.

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.

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.

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.

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 S Y, Bateman A, Punta M, Attwood T K, Sigrist C J, Redaschi N, Rivoire C, Xenarios I, Kahn D, Guyot D, Bork P, Letunic I, Gough J, Oates M, Haft D, Huang H, Natale D A, Wu C H, Orengo C, Sillitoe I, Mi H, Thomas P D, Finn R D (2015)
The InterPro protein families database: the classification resource after 15 years, Nucleic Acids Research, vol. 43 pp.D213-21.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

Sjöstrand J, Tofigh A, Daubin V, Arvestad L, Sennblad B, Lagersen J (2014)
A Bayesian Method for Analyzing Lateral Gene Transfer, Systematic Biology, vol. 63 pp.409-420.

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.

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

Junillon T, Mosticon D, Mallen B, Baril F, Morand L, Michel D, Flandrois JP (2014)
Optimization of the reactional medium and a food impact study for a colorimetric in situ Salmonella spp. detection method, International journal of food microbiology, vol. 181 pp.48-52.

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.

Lartillot N (2014)
A phylogenetic Kalman filter for ancestral trait reconstruction using molecular data, Bioinformatics, vol. 30 pp.488-96.

Pin D, Guerin-Faublee V, Garreau V, Breysse F, Dumitrescu O, Flandrois JP, Lina G (2014)
Mycobacterium Species Related to M. leprae and M. lepromatosis from Cows with Bovine Nodular Thelitis, Emerging infectious diseases, vol. 20 pp.2111-4.

Picard F, Cadoret J C, Audit B, Arneodo A, Alberti A, Battail C, Duret L, Prioleau M N (2014)
The spatiotemporal program of DNA replication is associated with specific combinations of chromatin marks in human cells, PLoS genetics, vol. 10 pp.e1004282-e1004282.

Rochette NC, Brochier-Armanet C, Gouy M (2014)
Phylogenomic test of the hypotheses for the evolutionary origin of eukaryotes, Molecular biology and evolution, vol. 31 pp.832-45.

Singh D P, Saudemont B, Guglielmi G, Arnaiz O, Gout J F, Prajer M, Potekhin A, Przybos E, Aubusson-Fleury A, Bhullar S, Bouhouche K, Lhuillier-Akakpo M, Tanty V, Blugeon C, Alberti A, Labadie K, Aury J M, Sperling L, Duharcourt S, Meyer E (2014)
Genome-defence small RNAs exapted for epigenetic mating-type inheritance, Nature, vol. 509 pp.447-52.

Raymann K, Forterre P, Brochier-Armanet C, Gribaldo S (2014)
Global Phylogenomic Analysis Disentangles the Complex Evolutionary History of DNA Replication in Archaea, Genome biology and evolution, vol. 6 pp.192-212.

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

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.

Boussau B, Walton Z, Delgado JA, Collantes F, Beani L, Stewart IJ, Cameron SA, Whitfield JB, Johnston JS, Holland P, Bachtrog D, Kathirithamby J, Huelsenbeck JP (2014)
Strepsiptera Phylogenomics and the Long Branch Attraction Problem, PLoS one, vol. 9 pp.e107709-e107709.

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.

Lebrette H, Brochier-Armanet C, Zambelli B, de Reuse H, Borezee-Durant E, Ciurli S, Cavazza C (2014)
Promiscuous nickel import in human pathogens: structure thermodynamics and evolution of extracytoplasmic nickel-binding proteins, Structure, vol. 22 pp.1421-32.

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.

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.

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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.

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

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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

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

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

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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.

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.

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

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.

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.

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.

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

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.

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.

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

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

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.

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

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.

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.

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

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.

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.

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.

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

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.

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.

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

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

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.

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

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.

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.

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

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.

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.

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

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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.

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.

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.

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.

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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Tannier E (2010) Comparative Genomics, Springer, 2010

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

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.

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.

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.

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.

Brochier-Armanet C (2010)
Minimal cell: the biologist point of view
in: Origin of life, , pp.26-46.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

Oberto J, Breuil N, Hecker A, Farina F, Brochier-Armanet C, Culetto E, Forterre P (2009)
Qri7/OSGEPL the mitochondrial version of the universal Kae1/YgjD protein is essential for mitochondrial genome maintenance, Nucleic Acids Research, vol. 37 pp.5343-52.

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.

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.

Necşulea A, Sémon M, Duret L, Hurst LD (2009)
Monoallelic expression and tissue specificity are associated with high crossover rates, Trends in Genetics, vol. 25(12) pp.519-522.

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

Tannier E (2009)
Yeast Ancestral Genome Reconstructions: The Possibilities of Computational Methods, Proceedings of RECOMB Comparative Genomics, Springer, Lecture notes in Bioinformatics, vol. 5817 pp.1-12.

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.

Bailly-Bechet M, Bradde S, Braunstein A, Flaxman A, Foini L, Zecchina R (2009)
Clustering with shallow trees, Journal of Statistical Mechanics: Theory and Experiment, vol. pp.p12010-p12010.

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.

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.

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.

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.

Bailly-Bechet M, Braunstein A, Zecchina R (2009)
A Prize-Collecting Steiner Tree Approach for Transduction Network Inference, CMSB 2009, Springer-Verlag pp.83-95.

Lemaitre C, Braga Marilia D V , Gautier C, Sagot M-F, Tannier E, Marais GAB (2009)
Footprints of Inversions at Present and Past Pseudoautosomal Boundaries in Human Sex Chromosomes, Genome Biology and Evolution, vol. 1(1) pp.56-66.

Masson J-B, Bailly-Bechet M, Vergassola M (2009)
Chasing information to search in random environments, Journal of physics A: Mathematical and Theoretical, vol. 42(43) pp.1-14.

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.

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.

Guillet C (2009)
Evolution des Ilots CpG chez les Primates .

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

Billy F, Ribba B, Saut O, Morre-Trouilhet H, Colin T, Bresch D, Boissel J-P, Grenier E, Flandrois J-P (2009)
A pharmacologically based multiscale mathematical model of angiogenesis and its use in investigating the efficacy of a new cancer treatment strategy, Journal of Theoretical Biology, vol. 260 pp.545-562.

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.

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.

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

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.

Teillier A, de Vienne DM, Giraud T, Hood M E, Refrégier G (2009)
Theory and examples of reciprocal influence between hosts and pathogens from short-term to long term interactions: coevolution cospeciation and pathogen speciation following host shifts.
in: Host-Pathogen Interactions: Genetics Immunology and Physiology., , pp.161-161.

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.

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

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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.

Gout J-F, Duret L, Kahn D (2009)
Differential Retention of Metabolic Genes Following Whole-Genome Duplication, Molecular Biology and Evolution, vol. 26(5) pp.1067-1072.

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

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.

Boussau B, Daubin V (2009)
Genomes as documents of evolutionary history, Trends in Ecology & Evolution, vol. 1192 pp.1-9.

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

Penel S, Arigon A-M, Dufayard J-F, Sertier A-S, Daubin V, Duret L, Gouy M, Perrière G (2009)
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Nicolas M, Marais GAB, Hykelova V, Janousek B, Laporte V, Vyskot B, Mouchiroud D, Negrutiu I, Charlesworth D, Moneger F (2005)
A gradual process of recombination restriction in the evolutionary history of the sex chromosomes in dioecious plants, PLoS Biology, vol. 3 pp.0047-0056.

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Molecular phylogeny of Myricaceae: a reexamination of host-symbiont specificity, Molecular Phylogenetics and Evolution, vol. 34 pp.557-568.

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.

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.

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

Ginolhac A, Jarrin C, Robe P, Perrière G, Vogel TM, Simonet P, Nalin R (2005)
Type I polyketide synthases may have evolved through horizontal gene transfer, Journal of Molecular Evolution, vol. 60 pp.716-725.

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Forcing reversibility in the no-strand-bias substitution model allows for the theoretical and practical identifiability of its 5 parameters from pairwise DNA sequence comparisons, Gene, vol. 347 pp.175-182.

Kanz C, Aldebert P, Althorpe N, Baker W, Baldwin A, Bates K, Browne P, Van den Broek A, Castro M, Cochrane G, Duggan K, Eberhardt R, Faruque N, Gamble J, Diez F G, Harte N, Kulikova T, Lin Q, Lombard V, Lopez R, Mancuso R, McHale M, Nardone F, Silventoinen V, Sobhany S, Stoehr P, Tuli MA, Tzouvara K, Vaughan R, Wu D, Zhu W, Apweiler R (2005)
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A multigene approach to phylogenetic analysis using the genus Mycobacterium as a model, International Journal of Systematic and Evolutionary Microbiology, vol. 55 pp.293-302.

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An emerging phylogenetic core of Archaea: phylogenies of transcription and translation machineries converge following addition of new genome sequences, BMC Evol Biol, vol. 5 pp.1-5.

Hurst LD, Duret L (2005)
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Ochman H, Lerat E, Daubin V (2005)
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.

Bazin E, Duret L, Penel S, Galtier N (2005)
Polymorphix: a sequence polymorphism database, Nucleic Acids Research, vol. 33 pp.481-484.

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

Charif D, Thioulouse J, Lobry JR, Perrière G (2005)
Online synonymous codon usage analyses with the ade4 and seqinR packages, Bioinformatics, vol. 21 pp.545-547.

Meunier J, Khelifi A, Navratil V, Duret L (2005)
Homology-dependent methylation in primate repetitive DNA, Proceedings of The National Academy of Sciences of The United States of America, vol. 102 pp.5471-5476.

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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Duret L (2005)
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Lerat E, Daubin V, Ochman H, Moran NA (2005)
Evolutionary origins of genomic repertoires in bacteria, PLoS Biology, vol. 3 pp.0807-0814.

Bapteste E, Charlebois R L, Macleod D, Brochier C (2005)
The two tempos of nuclear pore complex evolution: highly adapting proteins in an ancient frozen structure, Genome Biology, vol. 6 pp.353-63.

Bonnaud B, Beliaeff J, Bouton O, Oriol G, Duret L, Mallet F (2005)
Natural history of the ERVWE1 endogenous retroviral locus, Retrovirology, vol. 2 pp.57-57.

Guéguen L (2005)
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The ProDom database of protein domain families : more emphasis on 3D, Nucleic Acids Research, vol. 33 pp.D212-D215.

Ochman H, Daubin V, Lerat E (2005)
A bunch of fun-guys: the whole-genome view of yeast evolution, Trends in Genetics, vol. 21 pp.1-3.

Calteau A, Gouy M, Perrière G (2005)
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Aurell H, Farge P, Meugnier H, Gouy M, Forey F, Lina G, Vandenesch F, Etienne J, Jarraud S (2005)
Clinical and environmental isolates of Legionella pneumophila serogroup 1 cannot be distinguished by sequence analysis of two surface protein genes and three housekeeping genes, Applied and Environmental Microbiology, vol. 71 pp.282-289.

Forterre P, Gribaldo S, Brochier C (2005)
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Sémon M, Mouchiroud D, Duret L (2005)
Relationship between gene expression and GC-content in mammals: statistical significance and biological relevance, Human Molecular Genetics, vol. 14 pp.421-427.

Brochier C, Gribaldo S, Forterre P (2005)
Nanoarchaea: representatives of a novel archaeal phylum or fast-evolving euryarchaeal lineage related to Thermococcales?, Genome Biology, vol. 6 pp.1-5.

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.

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.

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

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

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.

Boussau B, Karlberg EO, Frank AC, Legault BA, Andersson SG (2004)
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.

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.

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.

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.

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

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.

Davalos M, Fourment J, Lucas A, Bergès H, Kahn D (2004)
Nitrogen regulation in Sinorhizobium meliloti probed with whole genome arrays, FEMS Microbiology Letters, vol. 241 pp.33-40.

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

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

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.

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

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

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.

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.

Ruau D, Duarte J, Ourjdal T, Perrière G, Laudet V, Robinson-Rechavi M (2004)
Update of NUREBASE: nuclear hormone receptor functional genomics, Nucleic Acids Research, vol. 32 pp.D165-D167.

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

Thomarat F, Vivares CP, Gouy M (2004)
Phylogenetic analysis of the complete genome sequence of Encephalitozoon cuniculi supports the fungal origin of microsporidia and reveals a high frequency of fast-evolving genes, Journal of Molecular Evolution, vol. 59 pp.780-791.

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

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.

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

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.

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.

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

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.

Brochier C, Lopez-Garcia P, Moreira D (2004)
Horizontal gene transfer and archaeal origin of deoxyhypusine synthase homologous genes in bacteria, Gene, vol. 330 pp.169-76.

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.

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.

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.

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

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.

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.

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.

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..

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

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

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.

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.

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.

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.

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.

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.

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

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

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.

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

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.

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

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.

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.

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

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.

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

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.

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

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..

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.

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..

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.

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

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

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.

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.

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

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

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.

Roche P, Mouawad L, Perahia D, Samama J P, Kahn D (2002)
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.

Baty F, Flandrois J-P, Delignette-Muller M-L (2002)
Modeling the Lag Time of Listeria monocytogenes from Viable Count Enumeration and Optical Density Data, Applied and environmental microbiology, vol. 68 pp.5816-5825.

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.

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

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.

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.

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.

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.

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Archaeal phylogeny based on ribosomal proteins, Mol Biol Evol, vol. 19 pp.631-639.

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Lombard V, Camon EB, Parkinson H E, Hingamp P, Stoesser G, Redaschi N (2002)
EMBL-Align: a new public nucleotide and amino acid multiple sequence alignment database, Bioinformatics, vol. 18 pp.763-764.

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

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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

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.

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.

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

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

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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

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

Duret L, Abdeddaim S (2000)
Multiple alignments for structural functional or phylogenetic analyses of homologous sequences
in: Bioinformatics a Practical Approach, Oxford University Press, pp.51-76.

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

Duret L, 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.

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

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

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

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

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.

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

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.

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

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

Brochier C, Philippe H, 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.

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

Duret L, 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.

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

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

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.

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.

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.

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.

Duret L, Perrière G, Gouy M (1999)
HOVERGEN: comparative analysis of homologous vertebrate genes
in: Bioinformatics: databases and systems, Kluwer Academic Publishers, pp.21-35.

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.

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.

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

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

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.

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.

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.

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.

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

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

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

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

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

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.

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.

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

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

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

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

Breand S, Fardel G, Flandrois J-P, Rosso L, Tomassone R (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.

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

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

Peyretaillade E, 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.

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

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.

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.

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.

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

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

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

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.

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.

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.

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

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.

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.

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

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

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.

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.

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.

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.

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.

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

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.

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

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.

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.

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

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, 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.

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.

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

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

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.

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

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.

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.

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

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.

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.

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.

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

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

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.

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.

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.

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.

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.

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

Duret L, Mouchiroud D, 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.

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.

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.

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.

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.

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.

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.

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.

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

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

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.

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.

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

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.

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.

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.

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.

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.

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.

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

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.

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.

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

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.

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

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

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.

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, 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.

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.

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

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.

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.

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.

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.

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.

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.

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

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. .

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.

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

Li W-H, Gouy M, Sharp P M, O`Huigin C, Yang Y W (1990)
Molecular phylogeny of Rodentia Lagomorpha Primates Artiodactyla and Carnivora and molecular clocks, Proceedings of The National Academy of Sciences of The United States of America, vol. 87 pp.6703-6707.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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

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

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.

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

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.

Savatier P, Trabuchet G, Faure C, Chebloune Y, Gouy M, Verdier G, Nigon V M (1985)
Evolution of the primate beta-globin gene region. High rate of variation in CpG dinucleotides and in short repeated sequences between man and chimpanzee, Journal of Molecular Biology, vol. 182 pp.21-29.

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

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.

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.

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.

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.

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

Gouy M, 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.

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.

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

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 (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.

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

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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.

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.

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

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

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.

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.