UMR CNRS 5558 Laboratoire de Biométrie et Biologie Évolutive

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

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

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

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

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

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

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.

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

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.

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.

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.

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

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

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.

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

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

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

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

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

(2017)
Impact of multimorbidity on healthcare professional task shifting potential in patients with type 2 diabetes in primary care: a French cross-sectional study, BMJ Open, vol. 7 pp.e016545-e016545.

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.

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.

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

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

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

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

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

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.

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

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.

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

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.

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

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

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.

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.

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

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.

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

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.

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.

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.

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

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.

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.

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.

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

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.

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

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.

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

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

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.

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

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

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.

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.

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

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.

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.

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.

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

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.

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.

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.

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

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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, 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.

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

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

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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.

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.

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.

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

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.

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

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.

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

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.

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.

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

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.

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.

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.

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.

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.

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.

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

Fontanillas E, Hood M E, Badouin H, Petit E, Barbe V, Gouzy J, de Vienne DM, Aguileta G, Poulain J, Wincker P, Chen Z, Toh S S, Cuomo C A, Perlin M H, Gladieux P, Giraud T (2014)
Degeneration of the Nonrecombining Regions in the Mating-Type Chromosomes of the Anther-Smut Fungi, Molecular biology and evolution, vol. 32 pp.928-43.

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

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.

Murigneux V, Dufour AB, Lobry JR, Pene L (2014)
Analysis of Positive Control STR Experiments Reveals that Results Obtained for FGA D3S1358 and D13S317 Condition the Success Rate of the Analysis of Routine Reference Samples, Journal of forensic sciences, vol. 59 pp.1074-1079.

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.

Horvilleur B, Lartillot N (2014)
Monte Carlo algorithms for Brownian phylogenetic models, Bioinformatics, vol. 30 pp.3020-8.

Fraune J, Alsheimer M, Redolfi J, Brochier-Armanet C, Benavente R (2014)
Protein SYCP2 Is an Ancient Component of the Metazoan Synaptonemal Complex, Cytogenetic and genome research, vol. 144 pp.299-305.

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.

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.

Miklos I, Kiss SZ, Tannier E (2014)
Counting and sampling SCJ small parsimony solutions, Theoretical Computer Science, vol. 552 pp.83-98.

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.

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

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

Amouric A, Liebgott P P, Joseph M, Brochier-Armanet C, Lorquin J (2014)
Halomonas olivaria sp. nov. a moderately halophilic bacterium isolated from olive-processing effluents, International journal of systematic and evolutionary microbiology, vol. 64 pp.46-54.

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

Lesecque Y, Glemin S, Lartillot N, Mouchiroud D, Duret L (2014)
The red queen model of recombination hotspots evolution in the light of archaic and modern human genomes, PLoS genetics, vol. 10 pp.e1004790-e1004790.

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.

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.

Romiguier J, Gayral P, Ballenghien M, Bernard A, Cahais V, Chenuil A, Chiari Y, Dernat R, Duret L, Faivre N, Loire E, Lourenco J M, Nabholz B, Roux C, Tsagkogeorga G, Weber A A, Weinert L A, Belkhir K, Bierne N, Glemin S, Galtier N (2014)
Comparative population genomics in animals uncovers the determinants of genetic diversity, Nature, vol. 515 pp.261-3.

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.

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.

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

Höhna S, Heath TA, Boussau B (2014)
Probabilistic Graphical Model Representation in Phylogenetics, Systematic biology, vol. 63 pp.753-771.

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.

Rochette N (2014)
Étude de l’origine des eucaryotes par la phylogénie moléculaire .

Ramirez-Bahena MH, Vial L, Lassalle F, Diel B, Chapulliot D, Daubin V, Nesme X, Muller D (2014)
, Molecular phylogenetics and evolution, vol. 73 pp.202-7.

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

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

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.

Weber CC, Boussau B, Romiguier J, Jarvis ED, Ellegren H (2014)
Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition, Genome Biology, vol. 15 pp.549-549.

Vabret N, Bailly-Bechet M, Lepelley A, Najburg V, Schwartz O, Verrier B, Tangy F (2014)
Large-scale nucleotide optimization of simian immunodeficiency virus reduces its capacity to stimulate type I interferon in vitro, Journal of virology, vol. 88 pp.4161-72.

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

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

Kvikstad E M, Duret L (2014)
Strong heterogeneity in mutation rate causes misleading hallmarks of natural selection on indel mutations in the human genome, Molecular biology and evolution, vol. 31 pp.23-36.

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.

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

Jarvis DE, Mirarab S, Aberer AJ, Houde P, Cai L, Ho S, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, Da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B (2014)
Whole-genome analyses resolve early branches in the tree of life of modern birds, Science, vol. 346 pp.1230-1331.

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.

Khelifi N, Amin Ali O, Roche P, Grossi V, Brochier-Armanet C, Valette O, Ollivier B, Dolla A, Hirschler-Rea A (2014)
Anaerobic oxidation of long-chain n-alkanes by the hyperthermophilic sulfate-reducing archaeon Archaeoglobus fulgidus, ISME journal, vol. 8 pp.2153-66.

Gouyon PH, de Vienne DM, Giraud T (2014)
Sex and Evolution
in: Handbook of Evolutionary Thinking in the Sciences, Springer, pp.499-507.

Pouyet F, Jacquemetton J, Bailly-Bechet M, Guéguen L (2013)
Codon usage in E. coli: an evolutionary approach, JOBIM 2013, pp.2427-41.

Chauve C, El-Mabrouk N, Guéguen L, Semeria M, Tannier E (2013)
Duplication Rearrangement and Reconciliation: A Follow-Up 13 Years Later
in: Models and Algorithmes for Genome Evolution, Computentional BIology, pp.47-62.

Perrière G (2013)
Génomes protéomes et transcriptomes à foison, Pour la science, vol. 433 pp.38-39.

Szollosi GJ, Tannier E, Lartillot N, Daubin V (2013)
Lateral Gene Transfer from the Dead, Systematic Biology, vol. 62 pp.386-397.

Patterson M, Szollosi GJ, Daubin V, Tannier E (2013)
Lateral gene transfer rearrangement reconciliation, BMC Bioinformatics, vol. 14 pp.S4-S4.

Groussin M, Boussau B, Gouy M (2013)
A branch-heterogeneous model of protein evolution for efficient inference of ancestral sequences, Systematic biology, vol. 62 pp.523-38.

Chauve C, El-Mabrouk N, Tannier E (2013) Models and Algorithms for Genome Evolution, Springer, 2013

.

Szollosi GJ, Rosikiewicz W, Boussau B, Tannier E, Daubin V (2013)
Efficient exploration of the space of reconciled gene trees, Systematic biology, vol. 62 pp.901-12.

Junillon T, Flandrois JP (2013)
Diminution of 2 3 5-triphenyltetrazolium chloride toxicity on Listeria monocytogenes growth by iron source addition to the culture medium, Food Microbiology, vol. 38 pp.1-5.

Ben Hania W, Postec A, Aullo T, Ranchou-Peyruse A, Erauso G, Brochier-Armanet C, Hamdi M, Ollivier B, Saint-Laurent S, Magot M, Fardeau ML (2013)
Mesotoga infera sp. nov. a mesophilic member of the order Thermotogales isolated from an underground gas storage aquifer, International Journal of Systematic and Evolutionary Microbiology, vol. 63 pp.3003-8.

Gueguen L, Gaillard S, Boussau B, Gouy M, Groussin M, Rochette N, Bigot T, Fournier D, Pouyet F, Cahais V, Bernard A, Scornavacca C, Nabholz B, Haudry A, Dachary L, Galtier N, Belkhir K, Dutheil J Y (2013)
Bio++: Efficient Extensible Libraries and Tools for Computational Molecular Evolution, Molecular Biology and Evolution, vol. 30 pp.1745-1750.

Lartillot N (2013)
HDR - Inférence probabiliste pour la phylogénie la génomique comparative et les sciences de la macro-évolution .

Cariou M, Duret L, Charlat S (2013)
Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization, Ecology and Evolution, vol. 3 pp.846-852.

Andres J, Arsene-Ploetze F, Barbe V, Brochier-Armanet C, Cleiss-Arnold J, Coppee J Y, Dillies M A, Geist L, Joublin A, Koechler S, Lassalle F, Marchal M, Medigue C, Muller D, Nesme X, Plewniak F, Proux C, Ramirez-Bahena M H, Schenowitz C, Sismeiro O, Vallenet D, Santini J M, Bertin P N (2013)
Life in an Arsenic-Containing Gold Mine: Genome and Physiology of the Autotrophic Arsenite-Oxidizing Bacterium Rhizobium sp. NT-26, Genome Biology and Evolution, vol. 5 pp.934-53.

Bourquard T, de Vienne D M, Azé J (2013)
Identification de complexes protéine-protéine par combinaison de classifieurs. Application à Escherichia Coli, EGC 2013 13e Conférence Francophone sur l`Extraction et la Gestion des Connaissances, pp.1-12.

Vallot C, Huret C, Lesecque Y, Resch A, Oudrhiri N, Bennaceur-Griscelli A, Duret L, Rougeulle C (2013)
XACT a long noncoding transcript coating the active X chromosome in human pluripotent cells, Nature Genetics, vol. 45 pp.239-41.

Kafer J, Talianova M, Bigot T, Michu E, Guéguen L, Widmer A, Zluvova J, Glemin S, Marais GA (2013)
Patterns of molecular evolution in dioecious and non-dioecious Silene, Journal of Evolutionary Biology, vol. 26 pp.335-46.

Guerin-Faublee V, Flandrois JP, Pichat C, Boschiroli M L, Lamy B (2013)
Mycobacterium bourgelatii sp. nov. a rapidly growing non-chromogenic species isolated from the lymph nodes of cattle, International journal of systematic and evolutionary microbiology, vol. 63 pp.4669-74.

Fraune J, Brochier-Armanet C, Alsheimer M, Benavente R (2013)
Phylogenies of Central Element Proteins Reveal the Dynamic Evolutionary History of the Mammalian Synaptonemal Complex: Ancient and Recent Components, Genetics, vol. 195 pp.781-793.

Gladieux P, Ropars J, Badouin H, Branca A, Aguileta G, de Vienne D M, Rodriguez de la Vega R C, Branco S, Giraud T (2013)
Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes, Molecular Ecology, vol. 23 pp.753-773.

Bigot T, Daubin V, Lassalle F, Perrière G (2013)
TPMS: a set of utilities for querying collections of gene trees, BMC Bioinformatics, vol. 14 pp.109-109.

Nabholz B, Uwimana N, Lartillot N (2013)
Reconstructing the phylogenetic history of long-term effective population size and life-history traits using patterns of amino acid replacement in mitochondrial genomes of mammals and birds, Genome Biology and Evolution, vol. 5 pp.1273-90.

Lartillot N, Rodrigue N, Stubbs D, Richer J (2013)
PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment, Systematic Biology, vol. 62 pp.611-615.

de Vienne DM, Giraud T, Gouyon PH (2013)
Lineage Selection and the Maintenance of Sex, PLoS one, vol. 8 pp.e66906-e66906.

Duret L, Charlat S (2013)
Eloge de l’ADN poubelle, Pour la science, vol. 81 pp.10-17.

Boussau B, Szollosi GJ, Duret L, Gouy M, Tannier E, Daubin V (2013)
Genome-scale coestimation of species and gene trees, Genome Research, vol. 23 pp.323-30.

Schumer M, Cui R, Boussau B, Walter R, Rosenthal G, Andolfatto P (2013)
An evaluation of the hybrid speciation hypothesis for Xiphophorus clemenciae based on whole genome sequences, Evolution, vol. 67 pp.1155-1168.

Berthoumieux S, Brilli M, Kahn D, de Jong H, Cinquemani E (2013)
On the identifiability of metabolic network models, Journal of mathematical biology, vol. 67 pp.1795-832.

Lesecque Y, Mouchiroud D, Duret L (2013)
GC-Biased Gene Conversion in Yeast Is Specifically Associated with Crossovers: Molecular Mechanisms and Evolutionary Significance, Molecular biology and evolution, vol. 30 pp.1409-19.

Deléage G, Gouy M (2013) Bioinformatique cours et cas pratique, Dunod, 2013

.

Eme L, Reigstad LJ, Spang A, Lanzen A, Weinmaier T, Rattei T, Schleper C, Brochier-Armanet C (2013)
Metagenomics of Kamchatkan hot spring filaments reveal two new major (hyper)thermophilic lineages related to Thaumarchaeota, Research in Microbiology, vol. 164 pp.425-38.

Lecroisey C, Brouilly N, Qadota H, Mariol M C, Rochette NC, Martin E, Benian G M, Segalat L, Mounier N, Gieseler K (2013)
ZYX-1 the unique zyxin protein of Caenorhabditis elegans is involved in dystrophin-dependent muscle degeneration, Molecular biology of the cell, vol. 24 pp.1232-49.

Rajaraman A, Tannier E, Chauve C (2013)
The genome of the medieval Black Death agent (extended abstract), JOBIM 2013, pp.47-54.

Thakur S, Normand P, Daubin V, Tisa L S, Sen A (2013)
Contrasted evolutionary constraints on secreted and non-secreted proteomes of selected Actinobacteria, BMC Genomics, vol. 14 pp.474-474.

Rajaraman A, Tannier E, Chauve C (2013)
FPSAC: fast phylogenetic scaffolding of ancient contigs, Bioinformatics, vol. 29 pp.2987-2994.

Touzeau A, Blichert-Toft J, Amiot R, Fourel F, Martineau F, Cockitt J, Hall K, Flandrois JP, Lécuyer C (2013)
Egyptian mummies record increasing aridity in the Nile valley from 5500 to 1500yr before present, Earth and Planetary Science Letters, vol. 375 pp.92-100.

Lartillot N (2013)
Phylogenetic patterns of GC-biased gene conversion in placental mammals and the evolutionary dynamics of recombination landscapes, Molecular biology and evolution, vol. 30 pp.489-502.

de Vienne D M, Refregier G, Lopez-Villavicencio M, Tellier A, Hood M E, Giraud T (2013)
Cospeciation vs host-shift speciation: methods for testing evidence from natural associations and relation to coevolution, New phytologist, vol. 198 pp.347-385.

Rota Stabelli O, Lartillot N, Philippe H, Pisani D (2013)
Serine codon usage bias in deep phylogenomics: pancrustacean relationships as a case study, Systematic Biology, vol. 62 pp.121-133.

Gribaldo S, Brochier-Armanet C (2013)
LUCA ancêtre de tous les êtres vivants, Les dossiers de la recherche, vol. 2 pp.29-31.

Lassalle F (2013)
Les génomes bactériens une histoire de transfert de gènes de recombinaison et de cladogénèse. .

Groussin M, Boussau B, Charles S, Blanquart S, Gouy M (2013)
The molecular signal for the adaptation to cold temperature during early life on Earth, Biology Letters, vol. 9 pp.20130608-20130608.

Danchin E G, Arguel M J, Campan-Fournier A, Perfus-Barbeoch L, Magliano M, Rosso M N, Da Rocha M, Da Silva C, Nottet N, Labadie K, Guy J, Artiguenave F, Abad P (2013)
Identification of novel target genes for safer and more specific control of root-knot nematodes from a pan-genome mining, PLoS pathogens, vol. 9 pp.e1003745-e1003745.

Lafond M, Semeria M, Swenson KM, Tannier E, El-Mabrouk N (2013)
Gene tree correction guided by orthology, BMC Bioinformatics, vol. 14 pp.S5-S5.

Bigot T (2013)
Recherche automatisée de motifs dans les arbres phylogénétiques .

Montgomery S B, Goode D L, Kvikstad E, Albers C A, Zhang Z D, Mu X J, Ananda G, Howie B, Karczewski K J, Smith K S, Anaya V, Richardson R, Davis J, MacArthur D G, Sidow A, Duret L, Gerstein M, Makova K D, Marchini J, McVean G, Lunter G (2013)
The origin evolution and functional impact of short insertion-deletion variants identified in 179 human genomes, Genome Research, vol. 23 pp.749-61.

Dumas JG, Roch JL, Tannier E, Varrette S (2013) Théorie des codes, Dunod, 2013

.

Lartillot N (2013)
Interaction between selection and biased gene conversion in mammalian protein-coding sequence evolution revealed by a phylogenetic covariance analysis, Molecular biology and evolution, vol. 30 pp.356-68.

Daubin V, Penel S, Tannier E (2013)
L`ADN mémoire numérique du vivant, Pour la science, vol. 433 pp.103-108.

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

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

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

Arnaiz O, Mathy N, Baudry C, Malinsky S, Aury JM, Denby Wilkes C, Garnier O, Labadie K, Lauderdale BE, Le Mouël A, Marmignon A, Nowacki M, Poulain J, Prajer M, Wincker P, Meyer E, Duharcourt S, Duret L, Bétermier M, Sperling L (2012)
The Paramecium Germline Genome Provides a Niche for Intragenic Parasitic DNA: Evolutionary Dynamics of Internal Eliminated Sequences, PLoS Genetics, vol. 8 pp.e1002984-e1002984.

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

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

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

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

Baldazzi V, Ropers D, Geiselmann J, Kahn D, de Jong H (2012)
Importance of metabolic coupling for the dynamics of gene expression following a diauxic shift in Escherichia coli, Journal of Theoretical Biology, vol. 295 pp.100-115.

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

Abby S S, Tannier E, Gouy M, Daubin V (2012)
Lateral gene transfer as a support for the tree of life, Proceedings of the National Academy of Sciences of The United States of America, vol. 109 pp.4962-4967.

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

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

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

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

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

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

Bertrand J C, Brochier C, Gouy M, Westall F (2012)
Pendant trois milliards d`années les micro-organismes sont les seuls habitants de la terre
in: Ecologie Microbienne : Microbiologie des Milieux Naturels et Anthropisés, , pp.81-117.

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

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

Brochier-Armanet C, Moreira D (2012)
Transferts horizontaux de gènes dans les écosystèmes microbiens
in: Ecologie Microbienne : Microbiologie des Milieux Naturels et Anthropisés, , pp.471-512.

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

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

Benayoun BA, Anttonen M, L`hôte D, Bailly-Bechet M, Andersson N, Heikinheimo M, Veita RA (2012)
Adult ovarian granulosa cell tumor transcriptomics: prevalence of FOXL2 target genes misregulation gives insights into the pathogenic mechanism of the p.Cys134Trp somatic mutation, Oncogene, vol. 32 pp.2739-2746.

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

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

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

Daubin V (2012)
HDR - Phylogénie Moléculaire 2.0 .

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

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

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

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

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

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

Caumette P, Brochier C, Normand P (2012)
Taxonomie et phylogénie des procaryotes
in: Ecologie Microbienne : Microbiologie des Milieux Naturels et Anthropisés, , pp.159-202.

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

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

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

Bérard J, Guéguen L (2012)
Accurate Estimation of Substitution Rates with Neighbor-Dependent Modelsina Phylogenetic Context, Systematic Biology, vol. 61 pp.510-521.

Bérard S, Gallien C, Boussau B, Szollosi GJ, Daubin V, Tannier E (2012)
Evolution of gene neighborhoods within reconciled phylogenies, Bioinformatics, vol. 28 pp.I382-I388.

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

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

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

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.

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.

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.

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.

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.

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

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

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.

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.

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.

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

.

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.

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.

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

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.

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.

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.

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.

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.

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.

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

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

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.

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

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.

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

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.

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.

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

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

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.

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

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.

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.

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.

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

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.

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.

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.

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.

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

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.

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

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.

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.

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.

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

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

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.

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.

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

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

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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

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.

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
in: Biologie Evolutive, de Boeck, pp.114-173.

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.

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

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.

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.

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

.

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.

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.

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.

Tannier E (2010) Comparative Genomics, Springer, 2010

.

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.

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.

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.

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.

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.

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.

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.

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

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.

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

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

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.

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.

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.

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.

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.

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.

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.

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.

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

.

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.

Penel S, Arigon A-M, Dufayard J-F, Sertier A-S, Daubin V, Duret L, Gouy M, Perrière G (2009)
Databases of homologous gene families for comparative genomics, BMC Bioinformatics, vol. 10 pp.s3-s3.

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

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

Boussau B, 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.

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.

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.

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

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.

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

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

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.

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

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.

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

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

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

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.

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.

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.

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.

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

Tannier E, Zheng C, Sankoff D (2008)
Multichromosomal Genome Median and Halving Problems, Proceedings of WABI`08, Springer-Verlag, Lecture notes in Bioinformatics, vol. 5251 pp.1-13.

Duret L (2008)
Neutral Theory: The Null Hypothesis of Molecular Evolution, Nature Education, vol. 1 pp.803-806.

Galtier N, Duret L (2008)
Biased Gene Conversion and its Impact on Human Genome Evolution
in: Encyclopedia of life sciences, , pp.273-277.

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

Handorf T, Christian N, Ebenhöh O, Kahn D (2008)
An environmental perspective on metabolism, Journal of Theoretical Biology, vol. 252 pp.530-537.

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

Bérard S, Chateau A, Chauve C, Paul C, Tannier E (2008)
Perfect DCJ Rearrangement, Proceedings of RECOMB-CG` 2008, Springer-Verlag, Lecture Notes in Bioinformatics, vol. 5267 pp.510-521.

Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist C, Thimma M, Thomas P, Valentin F, Wilson D, Wu C, Yeats C (2008)
InterPro: the integrative protein signature database, Nucleic Acids Research, vol. 37 pp.D211-D215.

Bailly-Bechet M, Kerszberg M, Gaill F, Pradillon F (2008)
A modeling approach of the influence of local hydrodynamic conditions on larval dispersal at hydrothermal vents, Journal of Theoretical Biology, vol. 255 pp.320-331.

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

Dutheil J, Boussau B (2008)
Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs, BMC Evolutionary Biology, vol. 8:255 pp.e1004892-e1004892.

Mugnier N, Gueguen L, Vieira C, Biémont C (2008)
The heterochromatic copies of the LTR retrotransposons as a record of the genomic events that have shaped the Drosophila melanogaster genome, Gene, vol. 411 pp.87-93.

Studer A, Penel S, Duret L, Robinson-Rechavi M (2008)
Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes, Genome Research, vol. 18 pp.1393-1402.

Lenne R, Solnon C, Stützle T, Tannier E, Birattari M (2008)
Reactive Stochastic Local Search Algorithms for the Genomic Median Problem, EvoCOP 2008, Springer Verlag, Lecture Notes in Computer Science, vol. 4972 pp.266-276.

Kahn D, Rezvoy C, Vivien F (2008)
Parallel large scale inference of protein domain families, , vol. pp.3011-3018.

Boyer F, Chauve C, Tannier E (2008)
Prédiction de synténies dans le génome ancestral des amniotes, Actes des Journée Ouvertes de Biologie Informatique et Mathématiques JOBIM 2008, pp.141-148.

Cadoret J-C, Meisch F, Hassan-Zadeh V, Luyten I, Guillet C, Duret L, Quesneville Q, Prioleau M-N (2008)
Genome-wide studies highlight indirect links between human replication origins and gene regulation, Proceedings of The National Academy of Sciences of The United States of America, vol. 105-41 pp.15837-15842.

Dumitrescu O, Tristan A, Meugnier H, Bes M, Gouy M, Etienne J, Lina G (2008)
Polymorphism of the Staphylococcus aureus Panton-Valentine LeukocidinGenes and Its Possible Link with the Fitness of Community-Associated Methicillin-Resistant S. aureus, Journal of infectious diseases, vol. 198(5) pp.792-794.

Brochier-Armanet C, Gribaldo S, Forterre P (2008)
DNA Topoisomerase IB in Thaumarchaeota testifies for the presence of this enzyme in the last common ancestor of Archaea and Eucarya, Biol Direct, vol. 3 pp.49-52.

Mignard S, Flandrois J-P (2008)
A seven-gene multilocus genus-wide approach to the phylogeny of mycobacteria using supertrees, International Journal of Systematic and Evolutionary Microbiology, vol. 58(part 6) pp.1432-1441.

Duret L, Cohen J, Jubin C, Dessen P, Gout J-F, Mousset S, Aury J-M, Jaillon O, Noël B, Arnaiz O, Bétermier M, Wincker P, Meyer E, Sperling L (2008)
Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia: A somatic view of the germline, Genome Research, vol. 18 pp.585-596.

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

Galtier N, Daubin V (2008)
Dealing with incongruence in phylogenomic analyses, Philosophical transactions of the royal society B-Biological Sciences, vol. pp.1233-1241.

Elkins J G, Podar M, Graham D E, Makarova K S, Wolf Y, Randau L, Hedlund B P, Brochier-Armanet C, Kunin V, Anderson I, Lapidus A, Goltsman E, Barry K, Koonin E V, Hugenholtz P, Kyrpides N, Wanner G, Richardson P, Keller M, Stetter K O (2008)
A korarchaeal genome reveals insights into the evolution of the Archaea, Proc Natl Acad Sci USA, vol. 105 pp.8102-7.

Braga MDV, Sagot M-F, Scornavacca C, Tannier E (2008)
Exploring the Solution Space of Sorting by Reversals with Experiments and an Application to Evolution, IEEE-ACM Transactions on Computational Biology and Bioinformatics, vol. 5 - n°3 pp.348-356.

Benayoun B-A, Caburet S, Dipietromaria A, Bailly-Bechet M, Batista F, Fellous M, Vaiman D, Veitia R-A (2008)
The identification and characterization of a FOXL2 response element provides insights into the pathogenesis of mutant alleles, Human Molecular Genetics, vol. 17 pp.3118-3127.

Boussau B (2008)
Early Evolution and Phylogeny .

Giraud T, Refregier G, Le Gac M, de Vienne D M, Hood M E (2008)
Speciation in fungi, Fungal genetics and biology, vol. 45 pp.791-802.

Tannier E (2008)
Sorting Signed Permutations by Reversal (Reversal Sequence) 2004; Tannier Sagot
in: Encyclopedia of algorithms, Springer, pp.860-863.

Urbonavicius J, Auxilien S, Walbott H, Trachana K, Golinelli-Pimpaneau B, Brochier-Armanet C, Grosjean H (2008)
Acquisition of a bacterial RumA-type tRNA(uracil-54 C5)methyltransferase by Archaea through an ancient horizontal gene transfer, Mol Microbiol, vol. 67 pp.323-335.

Lemaitre C, Tannier E, Gautier C, Sagot M-F (2008)
Precise detection of rearrangement breakpoints in mammalian chromosomes, BMC Bioinformatics, vol. 9 pp.286-322.

Navratil V, Penel S, Delmotte S , Mouchiroud D, Gautier C, Aouacheria A (2008)
DigiPINS: A database for vertebrate exonic single nucleotide polymorphisms and its application to cancer association studies, Biochimie, vol. 90 pp.563-569.

Duret L, Arndt PF (2008)
The Impact of Recombination on Nucleotide Substitutions in the Human Genome, PLoS Genetics, vol. 4 pp.1-19.

Giraud T, Yockteng R, Marthey S, Chiapello H, Jonot O, Lopez-Villavicencio M, de Vienne D M, Hood M E, Refregier G, Gendrault-Jacquemard A, Wincker P, Dossat C (2008)
Isolation of 60 polymorphic microsatellite loci in EST libraries of four sibling species of the phytopathogenic fungal complex Microbotryum, Molecular ecology resources, vol. 8 pp.387-392.

Brochier-Armanet C, Boussau B, Gribaldo S, Forterre P (2008)
Mesophilic crenarchaeota: proposal for a third archaeal phylum the Thaumarchaeota, Nature Reviews Microbiology, vol. 6 pp.245-252.

Morisset S, Peyron F, Lobry JR, Garweg J, Ferrandiz J, Musset K, Gomez-Marin JE, de la Torre A, Demar M, Carme B, Mercier Co, Garin JF, Cesbron-Delauw MF (2008)
Serotyping of Toxoplasma gondii: striking homogeneous pattern between symptomatic and asymptomatic infections within Europe and South America, Microbes and Infection, vol. 10 pp.742-747.

Gribaldo S, Forterre P, Brochier-Armanet C (2008)
Les Archaea : évolution et diversité du troisième domaine du vivant
in: , , pp.137-145.

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

Perrière G (2008)
Bioinformatics in the complete genome sequence era, Biochimie, vol. 90 pp.553-554.

Jaillon O, Bouhouche K, Gout J-F, Aury J-M, Noel B, Saudemont B, Nowacki M, Serrano V, Porcel BM, Ségurens B, Le Mouël A , Lepère G, Schächter V, Bétermier M, Cohen J, Wincker P, Sperling L, Duret L , Meyer E (2008)
Translational control of intron splicing in eukaryotes, Nature, vol. 451 pp.359-362.

Moreira D, Brochier-Armanet C (2008)
Giant viruses giant chimeras: The multiple evolutionary histories of Mimivirus genes, BMC Evol Biol, vol. 8 pp.259-287.

Devillers H, Lobry JR, Menu F (2008)
An agent-based model for predicting the prevalence of Trypanosoma cruzi I and II in their host and vector populations, Journal of Theoretical Biology, vol. 255 pp.307-315.

Couté Y, Kindbeiter K, Belin S, Dieckmann R, Duret L, Bezin L, Sanchez J-C, Diaz J-J (2008)
ISG20L2 a novel vertebrate nucleolar exoribonuclease involved in ribosome biogenesis, Molecular & cellular proteomics, vol. 7 pp.546-559.

Chauve C, Tannier E (2008)
A Methodological Framework for the Reconstruction of Contiguous Regions of Ancestral Genomes and Its Application to Mammalian Genomes, PLoS Computational Biology, vol. 4 pp.1-18.

Dufour A-B, Lobry JR (2008)
From W.S. Gosset`s pieces of card (1908) to R software : analysing Macdonell`s dataset of 3000 criminals, Biométrie Humaine et Anthropologie, vol. 26 pp.33-39.

Hingamp P, Brochier C, Talla E, Gautheret D, Thieffry D, Herrmann C (2008)
Metagenome Annotation Using a Distributed Grid of Undergraduate Students, PLOS Biology, vol. 6 pp.239-241.

Brochier-Armanet C (2008)
Origine et évolution des microorganismes
in: , , pp.529-33.

Urbonavicius J, Brochier-Armanet C, Skouloubris S, Myllykallio H, Grosjean H (2007)
In vitro detection of the enzymatic activity of folate-dependent tRNA(U54 C5)methyltransferase, Methods Enzymol, vol. 25 pp.103-19.

Bailly-Bechet M, Vergassola M, Rocha E (2007)
Causes for the intriguing presence of tRNAs in phages, Genome Research, vol. 17 pp.1486-1495.

Braga MDV, Sagot M-F, Scornavacca C, Tannier E (2007)
The solution space of sorting by reversals, Proceedings of ISBRA`07, Lecture Notes in Bioinformatics, vol. 4463 pp.293-304.

Abby S, Daubin V (2007)
Comparative genomics and the evolution of prokaryotes, Trends in Microbiology, vol. 15 pp.135-141.

Necşulea A, Lobry JR (2007)
A New Method for Assessing the Effect of Replication on DNA Base Composition Asymmetry, Molecular Biology and Evolution, vol. 24 pp.2169-2179.

Rezvoy C, Charif D, Guéguen L , Marais GAB (2007)
MareyMap: an R-based tool with graphical interface for estimating recombination rates, Bioinformatics, vol. 23 pp.2188-2189.

Dumas J-G, Roch J-L, Tannier E, Varrette S (2007) Théorie des codes: compression cryptage correction, Dunod, 2007

.

Kulikova T, Akhtar R, Aldebert P, Althorpe N, Andersson M, Baldwin A, Bates K, Bhattacharyya S, Bower L, Browne P, Castro M, Cochrane G, Duggan K, Eberhardt R, Faruque N, Hoad G, Kanz C, Lee C, Leinonen R, Lin Q, Lombard V, Lopez R, Lorenc D, McWilliam H, Mukherjee G, Nardone F, Pastor M P, Plaister S, Sobhany S, Stoehr P, Vaughan R, Wu D, Zhu W, Apweiler R (2007)
EMBL Nucleotide Sequence Database in 2006, Nucleic Acids Research, vol. 35 pp.D16-D20.

Aouacheria A, Navratil V, Lopez-Perez R, Gutierrez N C, Churkin A, Barash D, Mouchiroud D, Gautier C (2007)
In silico whole-genome screening for cancer-related single-nucleotide polymorphisms located in human mRNA untranslated regions, BMC Genomics, vol. 8 pp.2-2.

Tannier E, Bergeron A, Sagot M-F (2007)
Advances on sorting by reversals, Discrete Applied Mathematics, vol. 155 pp.881-888.

Galtier N, Duret L (2007)
Adaptation or biased gene conversion? Extending the null hypothesis of molecular evolution, Trends in Genetics, vol. 23 pp.273-277.

Brochier-Armanet C, Forterre P (2007)
Widespread distribution of archaeal reverse gyrase in thermophilic bacteria suggests a complex history of vertical inheritance and lateral gene transfers, Archaea, vol. 2 pp.83-93.

Jeffery IB, Madden SF, McGettigan PA, Perrière G, Culhane AC, Higgins DG (2007)
Integrating transcription factor binding site information with gene expression datasets, Bioinformatics, vol. 23 pp.298-305.

De Crécy-Lagard V, Marck C, Brochier-Armanet C, Grosjean H (2007)
Comparative RNomics and modomics in mollicutes: prediction of gene function and evolutionary implications, IUBMB Life, vol. 59 pp.634-58.

Diekmann Y, Sagot M-F, Tannier E (2007)
Evolution under Reversals: Parsimony and Conservation of Common Intervals, IEEE-ACM Transactions on Computational Biology and Bioinformatics, vol. 4 pp.301-309.

Keime C, Sémon M, Mouchiroud D, Duret L, Gandrillon O (2007)
Unexpected observations after mapping LongSAGE tags to the human genome, BMC Bioinformatics, vol. 8 pp.1-11.

Chomont N, Hocini H, Gresenguet G, Brochier C, Bouhlal H, Andreoletti L, Becquart P, Charpentier C, de Dieu Longo J, Si-Mohamed A, Kazatchkine M D, Belec L (2007)
Early archives of genetically-restricted proviral DNA in the female genital tract after heterosexual transmission of HIV-1, AIDS, vol. 21 pp.153-162.

de Vienne D M, Giraud T, Shykoff J A (2007)
When can host shifts produce congruent host and parasite phylogenies? A simulation approach, Journal of evolutionary biology, vol. 20 pp.1428-38.

Fall S, Mercier A, Bertolla F, Calteau A, Gueguen L, Perrière G, Vogel TM , Simonet P (2007)
Horizontal Gene Transfer Regulation in Bacteria as a "Spandrel" of DNA Repair Mechanisms, PLoS One, vol. 2 pp.e1055-e1055.

Necşulea A, Lobry JR (2007)
A New Method for Assessing the Effect of Replication on DNA Base Composition Asymmetry, , vol. pp.379-381.

Hecker A, Leulliot N, Gadelle D, Graille M, Justome A, Dorlet P, Brochier C, Quevillon-Cheruel S, Le Cam E, van Tilbeurgh H, Forterre P (2007)
An archaeal orthologue of the universal protein Kae1 is an iron metalloprotein which exhibits atypical DNA-binding properties and apurinic-endonuclease activity in vitro, Nucleic Acids Research, vol. 35 pp.6042-51.

Normand P, Lapierre P, Tisa LS, Gogarten JP, Alloisio N, Bagnarol E, Bassi CA, Berry AM, Bickhart DM, Choisne N, Couloux A, Cournoyer B, Cruveiller S, Daubin V, Demange N, Francino MP, Goltsman E, Huang Y, Kopp OR, Labarre L, Lapidus A, Lavire C, Marechal J, Martinez M, Mastronunzio JE, Mullin BC, Niemann J, Pujic P, Rawnsley T, Rouy Z, Schenowitz C, Sellstedt A, Tavares F, Tomkins JP, Vallenet D, Valverde C, Wall LG, Wang Y, Medigue C, Benson DR (2007)
Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography, Genome Research, vol. pp.7-15.

Desmond E, Brochier-Armanet C, Gribaldo S (2007)
Phylogenomics of the archaeal flagellum: rare horizontal gene transfer in a unique motility structure, BMC Evol Biol, vol. 7 pp.53-70.

Buchet-Poyau K, Courchet J, Hir H L, Seraphin B, Scoazec J Y, Duret L, Domon-Dell C, Freund J N, Billaud M (2007)
Identification and characterization of human Mex-3 proteins a novel family of evolutionarily conserved RNA-binding proteins differentially localized to processing bodies, Nucleic Acids Research, vol. 35 pp.1289-1300.

Charif D, Lobry JR (2007)
SeqinR 1.0-2: a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis
in: Structural approaches to sequence evolution: Molecules networks populations, Springer Verlag, pp.207-232.

de Vienne D M, Giraud T, Martin O C (2007)
A congruence index for testing topological similarity between trees, Bioinformatics, vol. 23 pp.3119-24.

Mulder N J, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Buillard V, Cerutti L, Copley R, Courcelle E, Das U, Daugherty L, Dibley M, Finn R, Fleischmann W, Gough J, Haft D, Hulo N, Hunter S, Kahn D, Kanapin A, Kejariwal A, Labarga A, Langendijk-Genevaux P S, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Nikolskaya A N, Orchard S, Orengo C, Petryszak R, Selengut J D, Sigrist C J, Thomas P D, Valentin F, Wilson D, Wu C H, Yeats C (2007)
New developments in the InterPro database, Nucleic Acids Research, vol. 35 pp.D224-D228.

Duret L (2006)
The GC Content of Primates and Rodents Genomes Is Not at Equilibrium : a Reply to Antezana, Journal of Molecular Evolution, vol. pp.803-806.

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

Sémon M, Duret L (2006)
Evolutionary origin and maintenance of coexpressed gene clusters in mammals., Molecular Biology and Evolution, vol. 23 pp.1715-1723.

Duret L, Eyre-Walker A, Galtier N (2006)
A new perspective on isochore evolution, Gene, vol. pp.71-74.

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

De Laplanche E, Gouget K, Cleris G, Dragounoff F, Demont J, Morales A, Bezin L, Godinot C, Perrière G, Mouchiroud D, Simonnet H (2006)
Physiological oxygenation status is required for fully differentiated phenotype in kidney cortex proximal tubules, American Journal of Physiology - Renal Physiology, vol. 291 pp.F750-F760.

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

Aouacheria A, Navratil V, Barthelaix A, Mouchiroud D, Gautier C (2006)
Bioinformatic sreening of human ESTs for differentially expressed genes in normal and tumor tissues, BMC Genomics, vol. 7 pp.94-94.

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

Melodelima C, Guéguen L, Gautier C, Piau D (2006)
A Markovian Approach for the Analysis of the Gene Structure, Proceedings of the Prague Stringology Conference, , vol. 19(1) pp.19-35.

Bailly-Bechet M, Danchin A, Iqbal M, Marsili M, Vergassola M (2006)
Codon Usage Domains over Bacterial Chromosomes, PLos Computational Biology, vol. 2(4) pp.83-95.

Melodelima C, Guéguen L, Piau D, Gautier C (2006)
A computational prediction of isochores based on hidden Markov models, Gene, vol. 385 pp.41-49.

Peyron F, Lobry JR, Musset K, Ferrandiz J, Gómez-Marín J E, Petersen E, Meroni V, Rausher B, Mercier CO, Picot S, Cesbron-Delauw MF (2006)
Serotyping of Toxoplasma gondii in chronically infected pregnant women : predominance of type II in Europe and types I and III in Colombia (South America), Microbes and Infection, vol. 8 pp.2333-2340.

Forterre P, Gribaldo S, Brochier-Armanet C (2006)
Natural history of the archaeal domain
in: , , pp.16-32.

Duret L, Chureau C, Samain S, Weissenbach J, Avner P (2006)
The Xist RNA Gene Evolved in Eutherians by Pseudogenization of a Protein-Coding Gene, Science, vol. 312 pp.1653-1655.

Gribaldo S, Brochier-Armanet C (2006)
The origin and evolution of Archaea: a state of the art, Philos Trans R Soc Lond B Biol Sci, vol. 361 pp.1007-22.

Sémon M, Lobry JR, Duret L (2006)
No Evidence for Tissue-Specific Adaptation of Synonymous Codon Usage in Humans, Molecular Biology and Evolution, vol. 23 pp.523-529.

Arigon A-M, Tchounikine A, Miquel M (2006)
Handling Multiple Points of View in a Multimedia Data Warehouse, ACM Transactions on Multimedia Computing Communications and Applications, vol. 2 pp.199-218.

Khelifi A, Meunier J, Duret L, Mouchiroud D (2006)
GC Content Evolution of the Human and Mouse Genomes : Insights from the Study of Processed Pseudogenes in Regions of Different Recombination Rates., Journal of Molecular Evolution, vol. 62 pp.745-752.

Rodriguez-Nava V, Couble A, Devulder G, Flandrois J-P, Boiron P, Laurent F (2006)
Use of PCR-Restriction Enzyme Pattern Analysis and Sequencing Database for hsp65 Gene-Based Identification of Nocardia Species, Journal of Clinical Microbiology, vol. 44 pp.536-546.

Aury J-M, Jaillon O, Duret L, Noel B, Jubin C, Porcel BM, Segurens B, Daubin V, Anthouard V, Aiach N, Arnaiz O, Billaut A, Beisson J, Blanc I, Bouhouche K, Camara F, Duharcourt S, Guigo R, Gogendeau D, Katinka M, Keller AM, Kissmehl R, Klotz C, Koll F, Le Mouel A, Lepere G, Malinsky S, Nowacki M, Nowak JK, Plattner H, Poulain J, Ruiz F, Serrano V, Zagulski M, Dessen P, Betermier M, Weissenbach J, Scarpelli C, Schachter V, Sperling L, Meyer E, Cohen J, Wincker P (2006)
Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia, Nature, vol. 444 pp.171-178.

Palmeira L, Guéguen L, Lobry JR (2006)
UV-Targeted Dinucleotides Are Not Depleted in Light-Exposed Prokaryotic Genomes, Molecular Biology and Evolution, vol. 23 pp.2214-2219.

Mignard S, Flandrois J-P (2006)
16S rRNA sequencing in routine bacterial identification : A 30-month experiment, Journal of Microbiological Methods, vol. 67 pp.574-581.

Necşulea A, Lobry JR (2006)
Revisiting the directionnal mutation pressure theory : The analysis of a particular genomic structure in Leishmania major, Gene, vol. 385 pp.28-40.

Cochrane G, Aldebert P, Althorpe N, Andersson M, Baker W, Baldwin A, Bates K, Bhattacharyya S, Browne P, van den Broek A, Castro M, Duggan K, Eberhardt R, Faruque N, Gamble J, Kanz C, Kulikova T, Lee C, Leinonen R, Lin Q, Lombard V, Lopez R, McHale M, McWilliam H, Mukherjee G, Nardone F, Pastor MP, Sobhany S, Stoehr P, Tzouvara K, Vaughan R, Wu D, Zhu W, Apweiler R (2006)
EMBL Nucleotide Sequence Database: developments in 2005, Nucleic Acids Research, vol. 34 pp.D10-D15.

Handorf T, Ebenhöh O, Kahn D, Heinrich R (2006)
Hierarchy of metabolic compounds based on their synthesising capacity, IEE Proceedings Systems Biology, vol. 153 pp.359-363.

Mignard S, Flandrois J-P (2006)
Mycobacterium bovis Infection, Journal of Medical Microbiology, vol. 56 pp.1033-1041.

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

Lobry JR, Necşulea A (2006)
Synonymous codon usage and its potential link with optimal growth temperature in prokaryotes., Gene, vol. 385 pp.128-136.

Ebenhöh O, Handorf T, Kahn D (2006)
Evolutionary changes of metabolic networks and their biosynthetic capacities, IEE Proceedings Systems Biology, vol. 153 pp.354-358.

Delmas J, Breysse F, Devulder G, Flandrois J-P, Chomarat M (2006)
Rapid identification of Enterobacteriaceae by sequencing DNA gyrase subunit B encoding gene, Diagnostic Microbiology and Infectious Disease, vol. 55 pp.263-268.

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

Aouacheria A, 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.

Duret L (2005)
Les trésors cachés du génome humain, Pour la Science, vol. pp.16-21.

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)
The EMBL Nucleotide Sequence Database, Nucleic Acids Research, vol. 33 pp.D29-D33.

Zagordi O, Lobry JR (2005)
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.

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

Lamy B, Carret G, Flandrois J-P, Delignette-Muller M-L (2005)
De la prévalence aux valeurs prédictives: L`antibiogramme face à l`évolution de la résistance aux antibiotiques, Annales de Biologie Clinique (Paris), vol. 63 pp.493-502.

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.

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)
InterPro progre, Nucleic Acids Research, vol. 33 Database Issue pp.D201-D205.

Sagot MF, Tannier E (2005)
Perfect sorting by reversals, Proceedings of COCOON`05, Springer-Verlag, Lecture Notes in Computer Science, vol. 3595 pp.42-51.

Forterre P, Gribaldo S, Brochier C (2005)
LUCA: the last universal common ancestor
in: , , pp.860-865.

Baty F, Bihl MP, Perrière G, Culhane AC, Brutsche MH (2005)
Optimized between-group classification: a new jackknife-based gene selection procedure for genome-wide expression data, BMC Bioinformatics, vol. 6 pp.239-239.

Devulder G, Perouse de Montclos M, Flandrois J-P (2005)
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.

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.

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

Brochier C, Forterre P, Gribaldo S (2005)
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.

Bapteste E, Brochier C, Boucher Y (2005)
Higher-level classification of the Archaea: on methanogenesis and methanogens, Archaea, vol. 1 pp.353-63.

Guéguen L (2005)
Sarment: Python modules for HMM analysis and partitioning of sequences, Bioinformatics, vol. 21 pp.3427-3428.

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

Bru C, Courcelle E, Carrere S, Beausse Y , Dalmar S, Kahn D (2005)
The ProDom database of protein domain families : more emphasis on 3D, Nucleic Acids Research, vol. 33 pp.D212-D215.

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

Culhane AC, Thioulouse J, Perrière G, Higgins DG (2005)
MADE4: an R package for multivariate analysis of gene expression data, Bioinformatics, vol. 21 pp.2789-2790.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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

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.

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.

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.

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.

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

Ferrières L, Francez-Charlot A, Gouzy J, Rouillé S, Kahn D (2004)
FixJ-regulated genes evolved through promoter duplication in Sinorhizobium meliloti, Microbiology, vol. 150 pp.2335-2345.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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

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

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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

Dechesne A, Pallud C, Debouzie D, Flandrois J-P, 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.

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.

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.

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

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

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

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

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

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

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

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.

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.

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

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

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

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.

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.

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.

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.

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.

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

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

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.

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..

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

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.

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..

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

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.

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

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.

Perrière G, Thioulouse J (2002)
Use and misuse of correspondence analysis in codon usage studies, Nucleic Acids Research, vol. 30 pp.4548-4555.

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.

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

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

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

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.

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

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.

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.

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.

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

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.

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

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

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

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.

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

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.

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

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

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

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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, 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.

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

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.

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.

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.

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.

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

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.

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, 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.

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

Duret L, Galtier N (2000)
The covariation between TpA deficiency CpG deficiency and G+C content of human isochores is due to a mathematical artifact, Molecular Biology and Evolution, vol. 17 pp.1620-1625.

Duret L (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.

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.

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

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

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

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

Brochier C, Philippe H, 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.

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.

Brochier C, Philippe H (2000)
Phylogénies moléculaires et génomes
in: , , pp.50-53.

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

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.

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.

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.

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

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

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

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

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.

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.

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

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.

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.

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.

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

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

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

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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

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.

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.

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

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.

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.

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.

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.

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.

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.

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

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.

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.

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

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

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.

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.

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

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

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.

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.

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.

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.

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

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.

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

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

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

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.

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.

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

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.

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.

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.

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.

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.

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

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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 (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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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

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.

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

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

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

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.

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.

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.

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

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

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

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.

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.

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

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

Lobry JR, 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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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

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.

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

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

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

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.

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.

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.

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)
Phylogenetic analysis based on rRNA sequences supports the archaebacterial rather than the eocyte tree, Nature, vol. 339 pp.145-147.

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

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

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

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.

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.

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

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

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.

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, 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.

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.

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

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

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

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.

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

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.

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

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.

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

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.

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.

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.

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.

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

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

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

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

.

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.

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.

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

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.