UMR CNRS 5558 Laboratoire de Biométrie et Biologie Évolutive

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, DOI.

Cariou M, Duret L, Charlat S (2013)
Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization, Ecology and Evolution, vol. pp.1-7, DOI.

Diagne N, Thioulouse J, Sanguin H, Prin Y, Krasova-Wade T, Sylla S, Galiana A, Baudoin E, Neyra M, Svistoonoff S, Lebrun M, Duponnois R (2013)
Ectomycorrhizal diversity enhances growth and nitrogen fixation of Acacia mangium seedlings, Soil Biology and Biochemistry, vol. 57 pp.468-476, DOI.

Giacofci M, Lambert-Lacroix S, Marot G, Picard F (2013)
Wavelet-based clustering for mixed-effects functional models in high dimension, Biometrics, vol. 69 pp.31-40, DOI.

Hafidi M, Ouahmane L, Thioulouse J, Sanguin H, Boumezzough A, Prin Y, Baudoin E, Galiana A, Duponnois R (2013)
Managing Mediterranean nurse plants-mediated effects on soil microbial functions to improve rock phosphate solubilization processes and early growth of Cupressus atlantica G, Ecological Engineering, vol. 57 pp.57-64, DOI.

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, DOI.

Ndoye L, Soumaré A, Agbangba EC, Thioulouse J, Galiana A, Prin Y, Duponnois R (2013)
A new process to promote the use of controlled mycorrhization practice in forest nurseries, African Journal of Agricultural Research, vol. 8 pp.308-316, DOI.

Ranjard L, Dequiedt S, Chemidlin Prevost-Boure N, Thioulouse J, Saby NP, Lelievre M, Maron PA, Morin FE, Bispo A, Jolivet C, Arrouays D, Lemanceau P (2013)
Turnover of soil bacterial diversity driven by wide-scale environmental heterogeneity, Nature communications, vol. 4 pp.1434-1434, DOI.

Szollosi GJ, Tannier E, Lartillot N, Daubin V (2013)
Lateral Gene Transfer from the Dead, Systematic Biology Advance Access, vol. pp.29-51, DOI.

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, DOI.

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

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, DOI.

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.

Baohanta R, Thioulouse J, Ramanankierana H, Prin Y, Rasolomampianina R, Baudoin E, Rakotoarimanga N, Galiana A, Randriambanona H, Lebrun M, Duponnois R (2012)
Restoring native forest ecosystems after exotic tree plantation in Madagascar: combination of the local ectotrophic species Leptolena bojeriana and Uapaca bojeri mitigates the negative influence of the exotic species Eucalyptus camaldulensis and Pinus patula, Biological Invasions, vol. 14 pp.2407-2421, DOI.

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. pp.1-8.

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, Chateau A, Chauve C, Paul C, Tannier E (2012)
Perfect DCJ Rearrangement, Proceedings of RECOMB-CG` 2008, Springer-Verlag, Lecture Notes in Bioinformatics, vol. 5267 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.382-388.

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, , vol. pp.81-117.

Bilgo A, Sangare SK, Thioulouse J, Prin Y, Hien V, Galiana A, Baudoin E, Hafidi M, Bâ AM, Duponnois R (2012)
Response of native soil microbial functions to the controlled mycorrhization of an exotic tree legume Acacia holosericea in a Sahelian ecosystem, Mycorrhiza, vol. 22 pp.175-187.

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

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

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

Brochier-Armanet C, Moreira D (2012)
Transferts horizontaux de gènes dans les écosystèmes microbiens, , vol. pp.471-512.

Caumette P, Brochier C, Normand P (2012)
Taxonomie et phylogénie des procaryotes, , vol. pp.159-202.

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

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

Dray S, Pélissier R, Couteron P, Fortin M-J, Legendre P, Peres-Neto P-R, Bellier E, Bivand R, Blanchet F-G, De Caceres M, Dufour A-B, Heegaard E, Jombart T, Munoz F, Oksanen J, Thioulouse J, Wagner H-H (2012)
Community ecology in the age of multivariate multiscale spatial analysis, Ecological Monographs, vol. 82 pp.257-275.

Dubruille R, Marais GAB, Loppin B (2012)
Repeated Evolution of Testis-Specific New Genes: TheCase of Telomere-Capping Genes in Drosophila, International Journal of Evolutionnary Biology, vol. 2012 pp.1-11.

Duponnois R, Baudoin E, Thioulouse J, Hafiidi M, Galiana A, Lebrun M, Prin Y (2012)
The Impact of Mycorrhizosphere Bacterial Communities on Soil Biofunctioning in Tropical and Mediterranean Forest Ecosystems, , vol. pp.292-303.

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 Evolution, vol. pp.1-14.

Frezal L, Meli F, Mousset S, Mona S, Veuille M (2012)
Geographical delimitation of a partial selective sweep in African Drosophila melanogaster, Molecular Ecology, vol. 21 pp.5702-14, DOI.

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

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

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

Lenne R, Solnon C, Stützle T, Tannier E, Birattari M (2012)
Reactive Stochastic Local Search Algorithms for the Genomic Median Problem, EvoCOP 2008, Springer Verlag, Lecture Notes in Computer Science, vol. 4972 pp.266-276.

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

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

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

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

Muyle A, Zemp N, Deschamps C, Mousset S, Wildmer A, Marais G (2012)
Rapid De Novo Evolution of X Chromosome Dosage Compensation in Silene latifolia a Plant with Young Sex Chromosomes, PLOS Biology, vol. 10 pp.1-8.

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, vol. 6 pp.81-93.

Parage C, Tavares R, Rety S, Baltenweck-Guyot R, Poutaraud A, Renault L, Heintz D, Lugan R, Marais GA, Aubourg S, Hugueney P (2012)
Structural functional and evolutionary analysis of the unusually large stilbene synthase gene family in grapevine, Plant Physiol, vol. 160 pp.1407-19, DOI.

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, PNAS, vol. 109 pp.5346-5351.

Pessia E, Popa A, Mousset S, Rezvoy C, Duret L, Marais G (2012)
Evidence for Widespread GC-biased Gene Conversion in Eukaryotes, Genome Biol. Evol, vol. 4 pp.675-682.

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, DOI.

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, Mol Microbiol, vol. 86 pp.155-71, DOI.

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.1-10.

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, Proc Natl Acad Sci U S A, vol. 109 pp.17513-8, DOI.

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

Thioulouse J, Prin Y, Duponnois R (2012)
Multivariate analyses in soil microbial ecology: a new paradigm, Environmental and Ecological Statistics, vol. 19 pp.499-520, DOI.

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.1-7.

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.

Arrouays D, Saby NPA, Thioulouse J, Jolivet C, Boulonne L, Ratié C (2011)
Large trends in French topsoil characteristics are revealed by spatially constrained multivariate analysis, Geoderma, vol. 161 pp.107-114.

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(1) pp.45-53.

Bailly-Bechet M, Benecke A, Hardt WD, Lanza V, Sturm A, Zecchina R (2011)
An externally modulated noise-driven switch for the regulation of SPI1 in Salmonella enterica serovar Typhimurium, Journal of Mathematical Biology, vol. pp.1-26.

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

Ben Hania W, Ghodbane R, Postec A, Brochier-Armanet C, Hamdi M, Fardeau M-L, Ollivier B (2011)
Cultivation of the first mesophilic representative ("mesotoga") within the order Thermotogales, Systematic and Applied Microbiology, vol. 34 pp.581-5.

Bergeron M, Dauwalder O, Gouy M, Freydiere A-M, Bes M, Meugnier H, Benito Y, Etienne J, Lina G, Vandenesch F, Boisset S (2011)
Species identification of staphylococci by amplification and sequencing of the tuf gene compared to the gap gene and by matrix-assisted laser desorption ionization time-of-flight mass spectrometry, European Journal of Clinical Microbiology & Infectious Diseases, vol. 30(3) pp.343-354.

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.

Blavet N, Charif D, Oger-Desfeux C, Marais G, Widmer A (2011)
Comparative high-throughput transcriptome sequencing and development of SiESTa the Silene EST annotation database, BMC Genomics, vol. 12 pp.1-11.

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 phytol., vol. 191(4) pp.1108-18.

Boussau B, Brown J M, Fujita M K (2011)
NONADAPTIVE EVOLUTION OF MITOCHONDRIAL GENOME SIZE, Evolution, vol. 65 pp.2706-2711.

Brochier-Armanet C, Deschamps P, Lopez-Garcia P, Zivanovic Y, Rodriguez-Valera F, Moreira D (2011)
Complete-fosmid and fosmid-end sequences reveal frequent horizontal gene transfers in marine uncultured planktonic Thaumarchaeota and Euryarchaeota, ISME, vol. 5(8) pp.1291-302.

Brochier-Armanet C, Forterre P, Gribaldo S (2011)
Phylogeny and Evolution of the Archaea: one Hundred Genomes Later, Current opinion in microbiology, vol. 14 pp.274-81.

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(4) pp.705-718.

Coumes-Florens S, Brochier-Armanet C, Guiseppi A, Denizot F, Foglino M (2011)
A New Highly Conserved Antibiotic Sensing/Resistance Pathway in Firmicutes Involves an ABC Transporter Interplaying with a Signal Transduction System, PLOS one, vol. 6 pp.789-801.

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.1-13.

de Boer H J, Vongsombath C, Käfer J (2011)
A Fly in the Ointment: Evaluation of Traditional Use of Plants to Repel and Kill Blowfly Larvae in Fermented Fish, PLoS one, vol. 6 pp.1-6.

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

Denoeud F, Roussel, Noel B, Wawrzyniak I, Da Silva C, Diogon M, Viscogliosi E, Brochier-Armanet C, Couloux A, Poulain J, Segurens B, Anthouard V, Texier C, Blot N, Poirier P, Choo Ng G, Tan K S W, Artiguenave F, Jaillon O, Aury J-M, Delbac F, Wincker P, Vivarès C P, El Alaoui H (2011)
Genome sequence of the stramenopile Blastocystis a human anaerobic parasite, Genome Biology, vol. 12 pp.94-101.

Dequiedt S, Saby NPA, Lelievre M, Jolivet C, Thioulouse J, Toutain B, Arrouays D, Bispo A, Lemanceau P, Ranjard L (2011)
Biogeographical patterns of soil molecular microbial biomass as influenced by soil characteristics and management, Global Ecology and Biogeography, vol. 20 pp.641-652.

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, Res Microbiol, vol. 162 pp.53-70.

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

Duponnois R, Ouahmane L, Kane A, Thioulouse J, Hafidi M, Boumezzough A, Prin Y, Baudoin E, Galiana A, Dreyfus B (2011)
Nurse shrubs increased the early growth of Cupressus seedling by enhancing belowground mutualism ans doil microbial activity, Soil Biology & Biochemistry, vol. 43 pp.2160-2168.

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, J Biol Chem, vol. 286 pp.24407-16.

Durand M, Käfer J, Quilliet C, Cox S, Ataei-Talebi S, Graner F (2011)
Statistical Mechanics of Two-Dimensional Shuffled Foams: Prediction of the Correlation between Geometry and Topology, Physical review letters, vol. 107 pp.1-5.

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 Evol Biol, vol. 57(11) pp.923-33.

Gavranovic H, Chauve C, Salse J, Tannier E (2011)
Mapping ancestral genomes with massive gene loss: A matrix sandwich problem, Bioinformatics, vol. 27(13) pp.i257-i265.

Gavranovic H, Tannier E (2011)
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.

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.

Groussin M, Pawlowski J, Ziheng Y (2011)
Bayesian relaxed clock estimation of divergence times in foraminifera, Molecular Phylogenetics and Evolution, vol. 61 pp.157-166.

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(1) pp.23-28.

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

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

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

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(9) pp.1409-1418.

Marais G, Forrest A, Kamau E, Käfer 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.1-10.

Miele V, Penel S, Duret L (2011)
Ultra-fast sequence clustering from similarity networks with SiLiX, BMC Bioinformatics, vol. 12(116) pp.1-9.

Muyle A, Serres-Giardi L, Ressayre A, Escobar J, Glemin S (2011)
GC-biased gene conversion and selection affect GC content in the Oryza genus (rice), Mol Biol Evol, vol. 28 pp.2695-2706, DOI.

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

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

Picard F, Lebarbier E, Budinska E, Robin S (2011)
Joint segmentation of multivariate Gaussian processes using mixed linear models, Computational Statistics and Data Analysis, vol. 55 pp.1160-1170.

Picard F, Lebarbier E, Hoebeke M, Rigaill G, Thiam B, Robin S (2011)
Joint segmentation calling and normalization of multiple CGH profiles, Biostatistics Advance Access, vol. 12 pp.413-428.

Picard F, Schbath S, Lebarbier E, Neuvial P, Chiquet J (2011)
Statistiques et Génome, La gazette des mathématiciens, vol. 130 pp.1-32.

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, J Mol Microbiol Biotechnol, vol. 20 pp.156-67.

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

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

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., Arch Microbiol, vol. 193(6) pp.439-49.

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

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

.

Tannier E (2011)
Preface : Satellite Workshop on Comparative Genomics Research in Computational Molecular Biology (RECOMB-CG 2010), Journal of Computational Biology, vol. 18(9) pp.1-3.

Thioulouse J (2011)
SIMULTANEOUS ANALYSIS OF A SEQUENCE OF PAIRED ECOLOGICAL TABLES: A COMPARISON OF SEVERAL METHODS, The Annals of Applied Statistics, vol. 5 pp.2300-2325.

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(3) pp.347-58.

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, Int J Microbiol, vol. pp.347-58.

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, Can J Microbiol, vol. 57(11) pp.923-33.

Valiente-Moro C, Thioulouse J, Chauve C, Zenner L (2011)
Diversity Geographic Distribution and Habitat-Specific Variations of Microbiota in Natural Populations of the Chicken Mite Dermanyssus gallinae, Journal of Medical Entomology, vol. 48 pp.788-796.

Van de Wiel MA, Picard F, Van Wieringen WN, Ylstra B (2011)
Preprocessing and downstream analysis of microarray DNA copy number profiles, Briefings in Bioinformatics, vol. 12 pp.10-21.

Vergnes M, Ginevra C, Kay E, Normand P, Thioulouse J, Jarraud S, Maurin M, Schneider D (2011)
Insertion Sequences as Highly Resolutive Genomic Markers for Sequence Type 1 Legionella pneumophila Paris, Journal of Clinical Microbiology, vol. 49(1) pp.315-324.

Vernoux T, Brunoud G, Farcot E, Morin V, Van den Daele H, Legrand J, Oliva M, Das P, Larrieu A, Wells D, Guédon Y, Armitage L, Picard F, Guyomarc`h S, Cellier C, Parry G, Koumproglou R, Doonan JH, Estelle M, Godin C, Kepinski S, Bennett M, de Veylder L, Traas J (2011)
The auxin signalling network translates dynamic input into robust pattening at the shoot apex, Molecular Systems Biology, vol. 7(508) pp.1-15.

Whitney K D, Boussau B, Baack J E, Garland T Jr (2011)
Drift and Genome Complexity Revisited, PLoS GENETICS, vol. 7 pp.1-5.

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

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(9) pp.479-487.

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

Arnaiz O, Gout J-F, Betermier M, Bouhouche K, Cohen J, Duret L, Kapusta A, Meyer E, Sperling L (2010)
Gene expression in a paleopolyploid: a transcriptome resource for the ciliate Paramecium tetraurelia, BMC Genomics, vol. 11(547) pp.1-13.

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.107-114.

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(355) pp.1-12.

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(6) pp.1-12.

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

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

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

Cegan R, Marais GAB, Kubekova H, Blavet N, Widmer A, Vyskot B, Dolezel J, Safar J, Hobza R (2010)
Structure and evolution of Apetala3 a sex-linked gene in Silene latifolia, BMC Plant Biology, vol. 10(180) pp.1-10.

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.

Chenuil A, Hoareau TB, Egea E, Penant G, Rocher C, Aurelle D, Mokhtar-Jamai K, Bishop JDD, Boissin E, Diaz A, Krakau M, Luttikhuizen PC, Patti F P, Blavet N, Mousset S (2010)
An efficient method to find potentially universal population genetic markers applied to metazoans, BMC Evolutionary Biology, vol. 10(276) pp.1-17.

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, Mol Biol Evol, vol. 27 pp.2062-77.

Dubruille R, Orsi GA, Delabaere L, Cortier E, Couble P, Marais GAB, Loppin B (2010)
Specialization of a Drosophila Capping Protein Essential for the Protection of Sperm Telomeres, Current Biology, vol. 20 pp.1-10.

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

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 Genetic, vol. 6 pp.e1000944-e1000944, DOI.

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, DOI.

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 Reviews Microbiology, vol. 8 pp.743-752.

Hochwagen A, Marais G (2010)
Meiosis: A PRDM9 Guide to the Hotspots of Recombination, Current Biology, vol. 20(6) pp.R271-R274, DOI.

Marais GAB, Campos PRA, Gordo I (2010)
Can Intra-Y Gene Conversion Oppose the Degeneration of the Human Y Chromosome? A Simulation Study, Genome Biology and Evolution, vol. 2 pp.347-357, DOI.

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

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, DOI.

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

.

Ranjard L, Dequiedt S, Jolivet C, Saby NPA, Thioulouse J, Harmand J, Loisel P, Rapaport A, Fall S, Simonet P, Joffre R, Chemidlin Prévost-Bouré N, Maron P-A, Mougel C, Martin MP, Toutain B, Arrouays D, Lemanceau P (2010)
Biogeography of soil microbial communities: a review and a description of the ongoing french national initiative, Agronomy for Sustainable Development, vol. 30(2) pp.359-365.

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(1552) 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, Environ Microbiol, vol. 12 pp.1498-512.

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 Microbiol, vol. 18(8) pp.331-40.

Tannier E (2010) Comparative Genomics, Springer, 2010

.

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

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(240) pp.1-7.

Thioulouse J, Valiente Moro C, Zenner L (2010)
Online Reproducible Research: An Application to Multivariate Analysis of Bacterial DNA Fingerprint Data, The R Journal, vol. 2(1) pp.44-52.

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, Proc Natl acad, vol. 107 pp.8818-23.

Zanghi H, Picard F, Miele V, Ambroise C (2010)
Strategies for online inference of model-based clustering in large and growing networks, The annals of Applied Statistics, vol. 4(2) pp.687-714.

Zhang YE, Vibranovski MD, Landback P, Marais GAB, Long M (2010)
Chromosomal Redistribution of Male-Biased Genes in Mammalian Evolution with Two Bursts of Gene Gain on the X Chromosome, PLoS Biology, vol. 8(10) pp.1-13.

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.1-17, DOI.

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

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.

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, DOI.

Bernasconi G, Antonovics J, Biere A, Charlesworth D, Delph LF, Filatov D, Giraud T, Hood ME, Marais GAB, McCauley D, Pannell JR, Shykoff JA, Vyskot B, Wolfe LM, Widmer A (2009)
Silene as a model system in ecology and evolution, Heredity, vol. pp.583-589.

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

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

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.

Braga MDV, Sagot M-F, Scornavacca C, Tannier E (2009)
The solution space of sorting by reversals, Proceedings of ISBRA`07, Lecture Notes in Bioinformatics, vol. 4463 pp.293-304.

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

Dequiedt S, Lelièvre M, Jolivet C, Saby NPA, Martin M, Thioulouse J, Maron P-A, Mougel C, Chemidlin Prévost-Bouré N, Arrouays D, Lemanceau P, Ranjard L (2009)
ECOMIC-RMQS: biogéographie microbienne à l`échelle de la France, Etude et Gestion des Sols, vol. 16(3) pp.219-231.

Dequiedt S, Thioulouse J, Jolivet C, Savy NPA, Lelievre M, Maron P-A, Martin M, Chemidlin Prévost-Bouré N, Toutain B, Arrouays D, Lemanceau P, Ranjard L (2009)
Biogeographical patterns of soil bacterial communities, Environmental Microbiology Reports, vol. 1(4) pp.251-255, DOI.

Duponnois R, Hafidi M, Thioulouse J, Galiana A, Ouahmane L, Dreyfus B, Prin Y (2009)
Monitoring the Development of Nurse Plant Species to Improve the Performances of Reforestation Programs in Mediterranean Areas, , vol. pp.255-265.

Duponnois R, Hafidi M, Thioulouse J, Galiana A, Ouahmane L, Dreyfus B, Prin Y (2009)
Monitoring the Development of Nurse Plant Species to Improve the Performances of Reforestation Programs in Mediterranean Areas, , vol. pp.255-265.

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

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.

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

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.235-239.

Faye A, Krasova-Wabe T, Thiao M, Thioulouse J, Neyra M, Prin Y, Galiana A, Ndoye I, Dreyfus B, Duponnois R (2009)
Controlled ectomycorrhization of an exotic legume tree species Acacia holosericea affects the structure of root nodule bacteria community and their symbiotic effectiveness on Faidherbia albida a native Sahelian Acacia, Soil Biology & Biochemistry, vol. 41(6) pp.1245-1252.

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

.

Forterre P, Gribaldo S, Brochier-Armanet C (2009)
, Biol, vol. 8 pp.16-32.

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, DOI.

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

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, DOI.

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

Gribaldo S, Talla E, Brochier-Armanet C (2009)
Evolution of the haem copper oxidases superfamily: a rooting tale, Trends Biochem Sci, vol. 34 pp.375-81.

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

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.

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, DOI.

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.

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, DOI.

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

Markov GV, Tavares R, Dauphin-Villemante C, Demeneix BA, Bakerf ME, Laudet V (2009)
Independent elaboration of steroid hormone signaling pathways in metazoans, Proceedings of the national academy of sciences of the United States of America, vol. 106(29) pp.11913-11918.

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, DOI.

Moccia MD, Oger-Desfeux C, Marais GAB, Widmer A (2009)
A White Campion textit(Silene latifolia) floral expressed sequence tag (EST) library: annotation EST-SSR characterization transferability and utility for comparative mapping, BMC Genomics, vol. 10(243) pp.1-14, DOI.

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, DOI.

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.

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.

Ouahmane L, Revel JC, Hafidi M, Thioulouse J, Prin Y, Galiana A, Dreyfus B, Duponnois R (2009)
Responses of Pinus halepensis growth soil microbial catabolic functions and phosphate-solubilizing bacteria after rock phosphate amendment and ectomycorrhizal inoculation, Plant Soil, vol. 320 (1-2) pp.169-179, DOI.

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

Picard F, Miele V, Daudin JJ, Cottret L, Robin S (2009)
Deciphering the connectivity structure of biological networks using MixNet, BMC Bioinformatics, vol. 10 pp.1-11.

Saby NPA, Thioulouse J, Jolivet C, Ratié C, Boulonne L, Bispo A, Arrouays D (2009)
Multivariate analysis of the spatial patterns of 8 trace elements using the French soil monitoring network data, Science of the Total Environment, vol. 407 pp.5644-5652.

Sanon A, Andrianjaka ZN, Prin Y, Bally R, Thioulouse J, Comte G, Duponnois R (2009)
Rhizosphere microbiota interfers with plant-plant interactions, Plant Soil, vol. 321(1-2) pp.259-278.

Santos CL, Tavares F, Thioulouse J, Normand P (2009)
Aphylogenomic analysis of bacterial helix^turn^helix transcription factors, FEMS Microbiology Reviews, vol. 33 pp.411-429, DOI.

Tannier E, Zheng C, Sankoff D (2009)
Multichromosomal median and halving problems under different genomic distances, BMC Bioinformatics, vol. 10(120) pp.1-15, DOI.

Valiente Moro C, Thioulouse J, Chauve C, Normand P, Zenner L (2009)
Bacterial taxa associated with the hematophagous mite Dermanyssus gallinae detected by 16S rRNA PCR amplification and TTGE fingerprinting, Research in Microbiology, vol. 160 pp.63-70, DOI.

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.261-268.

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.

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, DOI.

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, DOI.

Bernt M, Chao K-M, Kao J-W, Middendorf M, Tannier E (2008)
Preserving Inversion Phylogeny Reconstruction, WABI 2012, Springer-Verlag, vol. 7534 pp.1-13.

Boussau B (2008)
Early Evolution and Phylogeny .

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, DOI.

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, DOI.

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.

Brochier-Armanet C (2008)
Origine et évolution des microorganismes, , vol. 22(4) pp.529-33.

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.

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.

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.

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.1097-1112, DOI.

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.

Daudin J-J, Picard F, Robin S (2008)
A mixture model for random graphs, Statistics and Computing, vol. 18 pp.173-183.

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, DOI.

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.

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.

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

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

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.

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.31-42, DOI.

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.

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

Galtier N, Duret L (2008)
Biased Gene Conversion and its Impact on Human Genome Evolution, , vol. pp.273-277.

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

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

Gribaldo S, Forterre P, Brochier-Armanet C (2008)
Les Archaea : évolution et diversité du troisième domaine du vivant, , vol. 23 pp.137-145.

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

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.

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, DOI.

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.

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

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.

Marais GAB, Nicolas M, Bergero R, Chambrier P, Kejnovsky E, Monéger F, Hobza R, Widmer A, Charlesworth D (2008)
Evidence for Degeneration of the Y Chromosome in the Dioecious Plant Silene latifolia, Current biology, vol. 18 pp.545-549.

Moreira D, Brochier-Armanet C (2008)
Giant viruses giant chimeras: The multiple evolutionary histories of Mimivirus genes, BMC Evol Biol, vol. 8 pp.1-7.

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.

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.

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.

Picard F, Daudin J -J, Koskas M, Schbath S, Robin S (2008)
Assessing the exceptionality of network motifs, Journal of Computational Biology, vol. 15 pp.1-20.

Remigi P, Faye A, Kane A, Deruaz M, Thioulouse J, Cissoko M, Prin Y, Galiana A, Dreyfus B, Duponnois R (2008)
The exotic legume tree species Acacia holosericea alters microbial soil functionalities and the structure of the arbuscular mycorrhizal community, Applied and Environmental Microbiology, vol. 74 pp.1485-1493.

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, DOI.

Tannier E (2008)
Sorting Signed Permutations by Reversal (Reversal Sequence) 2004; Tannier Sagot, , vol. pp.860-863.

Tannier E (2008)
Yeast Ancestral Genome Reconstructions: The Possibilities of Computational Methods, Proceedings of RECOMB Comparative Genomics, Springer, Lecture notes in Bioinformatics, vol. 5817 pp.1-12.

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.

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

Andrianjaka Z, Bally R, Lepage M, Thioulouse J, Comte G, Duponnois R (2007)
Biological control of Striga hermonthica by Cubitermes termite mound powder amendment in sorghum culture, Applied Soil Ecology, vol. 37 pp.175-183.

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.1-13.

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

Bertrand S, Thisse B, Tavares R, Sachs L, Chaumot A, Bardet P-L, Escrivà H, Duffraisse M, Marchand O, Safi R, Thisse C, Laudet V (2007)
Unexpected Novel Relational Links Uncovered by Extensive Developmental Profiling of Nuclear Receptor Expression, PLoS Genetics, vol. 3 pp.e188-e188.

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.

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, , vol. pp.207-232.

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 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.

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.

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.

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

.

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-e1066.

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.

Guedj M, Della-Chiesa E, Picard F, Nuel G (2007)
Computing power in case-control association studies through the use of quadratic approximations: application to meat-statistics, Annals of Human genetics, vol. pp.57-62.

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.

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.

Kejnovsky E, Hobza R, Kubat Z, Widmer A, Marais GAB, Vyskot B (2007)
High intrachromosomal similarity of retrotransposon long terminal repeats: Evidence for homogenization by gene conversion on plant sex chromosomes?, Gene, vol. 390 pp.92-97.

Kisa M, Sanon A, Thioulouse J, Assigbetse K, Sylla S, Dieng L, Berthelin J, Prin Y, Galiana A , Lepage M, Duponnois R (2007)
Arbuscular mycorrhizal symbiosis can counterbalance the negative influence of the exotic tree species Eucalyptus camaldulensis on the structure and functioning of soil microbial communities in a sahelian soil, FEMS Microbiology Ecology, vol. 62 pp.32-44.

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.

Lasne F, Thioulouse J, Martin L, de Ceaurriz J (2007)
Detection of recombinant human erythropoietin in urine for doping analysis: interpretation of isoelectric profiles by discriminant analysis, Electrophoresis, vol. 28 pp.1875-1881.

Marais GAB (2007)
Sex chromosomes and mitochondrial DNA polymorphism in birds: The Hill–Robertson effects extend from nucleus to mitochondria, Heredity, vol. 99 pp.357-358.

Marais GAB, Calteau A, Tenaillon O (2007)
Mutation rate and genome reduction in endosymbiotic and free-living bacteria, Genetica, vol. DOI 10.1007/s10709-007-9226-6 pp.357-358.

Melodelima C, Guéguen L, Gautier C, Piau D (2007)
A Markovian Approach for the Analysis of the Gene Structure, Proceedings of the Prague Stringology Conference, , vol. 19(1) pp.19-35.

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.

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.

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

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.

Ouahmane L, Hafidi M, Thioulouse J, Ducousso M, Kisa M, Prin Y, Galiana A, Boumezzough A, Duponnois R (2007)
Improvement of Cupressus atlantica Gaussen growth by inoculation with native arbuscular mycorrhizal fungi, Journal of Applied Ecology, vol. 103 pp.683-690.

Ouahmane L, Thioulouse J, Hafidi M, Prin Y, Galiana A, Plenchette C, Kisa M, R Duponnois (2007)
Soil functional diversity and P solubilization from rock phosphate after inoculation with native or allochtonous arbuscular mycorrhizal fungi, Forest Ecology and Management, vol. 241 pp.200-208.

Ouangraoua A, Boyer F, McPherson A, Tannier E, Chauve C (2007)
Prediction of Contiguous Regions in the Amniote Ancestral Genome, Proceedings of ISBRA`09, Springer, Lecture Notes in Bioinformatics, vol. 5542 pp.173-185.

Picard F, Robin S, Lebarbier E, Daudin J -J (2007)
A segmentation/clustering model for the analysis of array CGH data, Biometrics, vol. 63 pp.758-766.

Ramanankierana N, Ducousso M, Rakotoarimanga N, Prin Y, Thioulouse J, Randrianjohany E, Ramaroson L, Kisa M, Galiana A, Duponnois R (2007)
Arbuscular mycorrhizas and ectomycorrhizas of Uapaca bojeri L. (Euphorbiaceae): sporophore diversity patterns of root colonization and effects on seedling growth and soil microbial catabolic diversity, Mycorrhiza, vol. 17 pp.195-208.

Ramos-Onsins SE, Mousset S, Mitchell-Olds T, Stephan W (2007)
Population genetic inference using a fixed number of segregating sites : a reassessment, Genetical Research, vol. 89 pp.231-244.

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.

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

Tannier E, Sagot M-F (2007)
Sorting by reversals in subquadratic time, Proceedings of CPM`04, Springer Verlag, Lecture Notes in Computer Science, vol. 3109 pp.1-13.

Tannier E, Zheng C, Sankoff D (2007)
Multichromosomal Genome Median and Halving Problems, Proceedings of WABI`08, Springer-Verlag, Lecture notes in Bioinformatics, vol. 5251 pp.1-13.

Thioulouse J, Dray S (2007)
Interactive Multivariate Data Analysis in R with the ade4 and ade4TkGUI Packages, Journal of Statistical Software, vol. 22 pp.1-14.

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.

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.1-11.

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

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.

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.

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, DOI.

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

Boyer F, Chauve C, Tannier E (2006)
Prédiction de synténies dans le génome ancestral des amniotes, Actes des Journée Ouvertes de Biologie Informatique et Mathématiques JOBIM 2008, pp.141-148.

Clement Y, Tavares R, Marais GAB (2006)
Does lack of recombination enhance asymmetric evolution among duplicate genes? Insights from the Drosophila melanogaster genome, Gene, vol. 385 pp.89-95.

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.

Culhane AC, Thioulouse J (2006)
A multivariate approach to integrating Datasets using made4 and ade4, R News, vol. pp.1-15.

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.

Diallo MD, Duponnois R, Guisse A, Sall S, Chotte J-L, Thioulouse J (2006)
Biological effects of native and exotic plant residues on plant growth microbial biomass and N availability under controlled conditions, European Journal of Soil Biology, vol. 42 pp.238-246.

Duponnois R, Assikbetse K, Ramanankierana H, Kisa M, Thioulouse J, Lepage M (2006)
Litter-forager termite mounds enhance the ectomycorrhizal symbiosis between Acacia holosericea A. Cunn. Ex G. Don and Scleroderma dictyosporum isolates, FEMS Microbiology Ecology, vol. 56 pp.292-303.

Duponnois R, Kisa M, Assigbetse K, Prin Y, Thioulouse J, Issartel M, Moulin P, Lepage M (2006)
Fluorescent pseudomonads occurring in Macrotermes subhyalinus mound structures decrease Cd toxicity and improve its accumulation in sorghum plants, Science of the Total Environment, vol. 370 pp.391-400.

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.

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.

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

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.

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

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.

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.

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.

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.

Le Hesran JY, Fievet N, Thioulouse J, Personne P, Maubert B, M`bidias S, Etye`ale D, Cot M, Deloron P (2006)
Development of cellular immune responses to Plasmodium falciparum blood stage antigens from birth to 36 months of age in Cameroon, Acta Tropica, vol. 98 pp.261-269.

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

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

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

Lubrano-Berthelier C, Dubern B, Lacorte J-M, Picard F, Shapiro A, Zhang S, Bertrais S, Hercberg S, Basdevant A, Clement K, Vaisse C (2006)
Melanocortin-4 receptor mutations in a large cohort of severely obese adults: prevalence functional classification genotype-phenotype relationship and lack of association with binge eating, Journal of Clinical Endocrinology and Metabolism, vol. 91 pp.1811-1818.

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.

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.

Ouahmane L, Duponnois R, Hafidi M, Kisa M, Boumezzough A, Thioulouse J, Plenchette C (2006)
Some Mediterranean plant species (Lavandula spp. and Thymus satureioides) act as potential `plant nurses` for the early growth of Cupressus atlantica, Plant Ecology, vol. 185 pp.123-134.

Ouahmane L, Hafidi M, Plenchette C, Kisa M, Boumezzough A, Thioulouse J, Duponnois R (2006)
Lavandula species as accompanying plants in Cupressus replanting strategies : Effect on plant growth mycorrhizal soil infectivity and soil microbial catabolic diversity, Applied Soil Ecology, vol. pp.190-199.

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.

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.

Portier P, Fischer-Le Saux M, Mougel C, Lerondelle C, Chapulliot D, Thioulouse J, Nesme X (2006)
Identification of genomic species in Agrobacterium biovar 1 by AFLP genomic markers., Applied and Environmental Microbiology, vol. 72 pp.7123-7131.

Ramanankierana N, Rakotoarimanga N, Thioulouse J, Marija K, Randrianjohany E, Ramaroson L, Duponnois R (2006)
The Ectomycorrhizosphere Effect Influences Functional Diversity of Soil Microflora, International Journal of Soil Sciences, vol. 1 pp.8-19.

Sanguin H, Remenat B, Dechesne A, Thioulouse J, Vogel TM, Nesme X, Moënne-Loccoz Y, Grundmann GL (2006)
Potential of 16S rRNA-Based Taxonomic Microarray for Analyzing the Rhizosphere Effects of Maize on Agrobacterium spp. and Bacterial Communities, Applied and Environmental Microbiology, vol. 72 pp.4302-4312.

Sanon A, Martin P, Thioulouse J, Plenchette C, Spichiger R, Lepage M, Duponnois R (2006)
Displacement of an herbaceous plant species community by mycorrhizal and non-mycorrhizal Gmelina arborea an exotic tree grown in a microcosm experiment, Mycorrhiza, vol. 16 pp.125-132.

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

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.

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

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

Assigbetse K, Gueye M, Thioulouse J, Duponnois R (2005)
Soil bacterial diversity responses to root colonization by an ectomycorrhizal fungus are not root-growth dependent, Microbial Ecology, vol. 50 pp.350-359.

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.

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

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.

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

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.1-7.

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.

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.

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.

Cadet P, Masse D, Thioulouse J (2005)
Relationships between plant-parasitic nematode community fallow duration and soil factors in the Sudano-Sahelian area of Senegal, Agriculture Ecosystems & Environment, vol. 108 pp.302-317.

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.

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.

Charlesworth D, Charlesworth B, Marais G (2005)
Steps in the evolution of heteromorphic sex chromosomes, Heredity, vol. 95 pp.118-128.

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.

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.

Duponnois R, Colombet A, Hien V, Thioulouse J (2005)
The mycorrhizal fungus Glomus intraradices and rock phosphate amendment influence plant growth and microbial activity in the rhizosphere of Acacia holosericea, Soil Biology and Biochemistry, vol. 37 pp.1460-1468.

Duponnois R, Paugy M, Thioulouse J, Masse D, Lepage M (2005)
Functional diversity of soil microbial community rock phosphate dissolution and growth of Acacia seyal as influenced by grass- litter- and soil-feeding termite nest structure amendments, Geoderma, vol. 124 pp.349-361.

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

Forterre P, Gribaldo S, Brochier C (2005)
LUCA: the last universal common ancestor, , vol. 21 pp.860-865.

Govaerts C, Srinivasan S , Shapiro A, Zhang S, Picard F, Clement K, Lubrano-Berthelier C, Vaisse C (2005)
Obesity-associated mutations in the melanocortin-4 receptor provide novel insights into its function, Peptides, vol. 26 pp.1909-1919.

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

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.

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

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.

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.

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

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

Marais GAB, Nouvellet P, Keightley PD, Charlesworth B (2005)
Intron size and exon evolution in Drosophila, Genetics, vol. 170 pp.481-485.

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

Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bradley P, Bork P, Bucher P, Cerutti L, Copley R, Courcelle E, Das U, Durbin R, Fleischmann W, Gough J, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McDowall J, Mitchell A, Nikolskaya AN, Orchard S, Pagni M, Ponting CP, Quevillon E, Selengut J, Sigrist CJ, Silventoinen V, Studholme DJ, Vaughan R, Wu CH (2005)
InterPro progre, Nucleic Acids Research, vol. 33 Database Issue pp.D201-D205.

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.

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.

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.

Picard F, Robin S, Lavielle M, Vaisse C, Daudin J -J (2005)
A statistical approach for array CGH data analysis, BMC Bioinformatics, vol. 6 pp.1-14.

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.

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.

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.

Baines JF, Das A, Mousset S, Stephan W (2004)
The role of natural selection in genetic differentiation of worldwide populations of Drosophila ananassae, Genetics, vol. 168 pp.1987-1998.

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

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.

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.

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.

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.

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.

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.

Chessel D, Dufour A-B, Thioulouse J (2004)
The ade4 package - I : One-table methods, R News, vol. 4 pp.5-10.

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

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

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

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

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.

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.

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.

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

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

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

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

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

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

Marais GAB, Charlesworth B, Wright SI (2004)
Recombination and base composition: the case of the highly self-fertilizing plant Arabidopsis thaliana, Genome Biology, vol. 5 pp.R45.1-R45.9.

Marais GAB, Domazet-Loso T, Tautz D, Charlesworth B (2004)
Correlated evolution of synonymous and nonsynonymous sites in Drosophila, Journal of Molecular Evolution, vol. 59 pp.771-779.

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

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

Mousset S, Derome N (2004)
Molecular polymorphism in Drosophila melanogaster and D. simulans: what have we learned from recent studies?, Genetica, vol. 120 pp.79-86.

Mousset S, Derome N, Veuille M (2004)
A test of neutrality and constant population size based on the mismatch distribution, Molecular Biology and Evolution, vol. 21 pp.724-731.

Naizot T, Auda Y, Dervieux A, Thioulouse J, Bellan MF (2004)
Une nouvelle analyse multi-temporelle d`images satellitales les residus de l`Analyse en Composantes Principales. Un cas d`etude: une serie d`images Landsat Thematic Mapper de la Camargue France., International Journal of Remote Sensing, vol. 25 pp.1925-1938.

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

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

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

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

Srinivasan S, Lubrano-Berthelier C, Govaerts C, Picard F, Santiago P, Conklin B, Vaisse C (2004)
Constitutive activity of the melanocortin-4 receptor is maintained by its N-terminal domain and plays a role in energy homeostasis in humans, Journal of Clinical Investigation, vol. 114 pp.1158-1164.

Thioulouse J, Simier M, Chessel D (2004)
Simultaneous analysis of a sequence of paired ecological tables with the STATICO method, Ecology, vol. 85 pp.272-283.

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.

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

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

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

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

Cadet P, Pate E, Thioulouse J (2003)
Relationship of nematode communities to human demographics and environment in agricultural fields and fallow lands in Senegal., Journal of Tropical Ecology, vol. 19 pp.279-290.

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.

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.

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

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

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.

Depaulis F, Mousset S, Veuille M (2003)
Power of neutrality tests to detect bottlenecks and hitchhiking, Journal of Molecular Evolution, vol. 57 pp.S190-S200.

Dray S, Chessel D, Thioulouse J (2003)
Co-inertia analysis and the linking of ecological tables, Ecology, vol. 84 pp.3078-3089.

Dray S, Chessel D, Thioulouse J (2003)
Procustean co-inertia analysis for the linking of multivariate datasets, Ecoscience, vol. 10 pp.110-119.

Glinka S, Ometto L, Mousset S, Stephan W, De Lorenzo D (2003)
Demography and natural selection have shaped genetic variation in Drosophila melanogaster: a multi-locus approach, Genetics, vol. 165 pp.1269-1278.

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

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

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

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

Lubrano-Berthelier C, Cavazos M, Dubern B, Shapiro A, Le Stunff C, Zhang SM, Picard F, Govaerts C, Froguel P, Bougneres P, Clement K, Vaisse C (2003)
Molecular genetics of human obesity-associated MC4R mutations, Annals of the New Yok Academy of Sciences, vol. 994 pp.49-57.

Marais GAB (2003)
Biased gene conversion: implications for genome and sex evolution, Trends in Genetics, vol. 19 pp.330-338.

Marais GAB, Charlesworth B (2003)
Genome evolution: recombination speeds up adaptive evolution, Current Biology, vol. 13 pp.R68-R70.

Marais GAB, Galtier N (2003)
Sex chromosomes: how X-Y recombination stops, Current Biology, vol. 13 pp.R641-R643.

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

Mousset S, Brazier L, Cariou ML, Chartois F, Depaulis F, Veuille M (2003)
Evidence of a high rate of selective sweeps in African Drosophila melanogaster, Genetics, vol. 163 pp.599-609.

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.

Ollier S, Chessel D, Couteron P, Pélissier R, Thioulouse J (2003)
Comparing and classifying one-dimensional spatial patterns: an application to laser altimeter profiles., Remote Sensing of Environment, vol. 85 pp.453-462.

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

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

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

Stoesser G, Baker W, van den Broek A, Garcia-Pastor M, Kanz C, Kulikova T, Leinonen R, Lin Q, Lombard V, Lopez R, Mancuso R, Nardone F, Stoehr P, Tuli MA, Tzouvara K, Vaughan R (2003)
The EMBL Nucleotide Sequence Database: major new developments, Nucleic Acids Research, vol. 31 pp.17-22.

Vogel J, Normand P, Thioulouse J, Nesme X, Grundmann G (2003)
Relationship between spatial and genetic distance in Agrobacterium spp. in 1 cubic centimeter of soil., Applied and Environmental Microbiology, vol. 69 pp.1482-1487.

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

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

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

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

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

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

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

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

Founoune H, Duponnois R, Meyer JM, Thioulouse J, Masse D, Chotte J-L, Neyra M (2002)
Interactions between ectomycorrhizal symbiosis and fluorescent pseudomonads on Acacia holosericea: isolation of mycorrhiza helper bacteria (MHB) from a Soudano-Sahelian soil, FEMS Microbiology Ecology, vol. 41 pp.37-46.

Jarraud S, Mougel C, Thioulouse J, Lina G, Meugnier H, Forey F, Nesme X, Etienne J, Vandenesch F (2002)
Relationships between Staphylococcus aureus genetic background virulence factors agr groups (alleles) and human disease., Infection and Immunity, vol. 70 pp.631-641.

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.

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

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.

Marais GAB, Piganeau G (2002)
Hill-Robertson interference is a minor determinant of variations in codon bias across Drosophila melanogaster and Caenorhabditis elegans genomes, Molecular Biology and Evolution, vol. 19 pp.1399-1406.

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

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

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.

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

Piganeau G, Mouchiroud D, Duret L, Gautier C (2002)
Expected Relationship Between the Silent Substitution Rate and the GC Content: Implications for the Evolution of Isochores, Journal of Molecular Evolution, vol. 54 pp.129-133..

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

Pontier D, Say L, Débias F, Bried J, Thioulouse J, Micol T, Natoli E (2002)
The diet of feral cats (Felis catus L.) at five sites on the Grande Terre Kerguelen archipelago., Polar Biology, vol. 25 pp.833-837.

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.

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.

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.

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.

Tavares R, Vidal J, van Lammeren A, Kreis M (2002)
AtSKtheta a plant homologue of SGG/GSK-3 marks developing tissues in Arabidopsis thaliana, Plant Molecular Biology, vol. 50 pp.261-271.

Tavares R, Vidal J, van Lammeren A, Kreis M (2002)
Non-purified anti-peptide sera generate tissue specific artefacts in immunohistochemical staining of Arabidopsis thaliana, Plant Science, vol. 162 pp.309-314.

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

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

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

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.

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.

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.

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.

Depaulis F, Mousset S, Veuille M (2001)
Haplotype tests using coalescent simulations conditional on the number of segregating sites, Molecular Biology and Evolution, vol. 18 pp.1136-1138.

Duponnois R, Plenchette C, Thioulouse J, Cadet P (2001)
Mycorrhizal soil infectivity and AM fungal spore communities of different aged fallows in Senegal, Applied Soil Ecology, vol. 17 pp.239-251.

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.

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

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

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

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

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

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

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

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

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

Mougel C, Teyssier S, d`Angelo C, Groud K, Neyra M, Sidi-Boumedine K, Cloeckaert A, Peloille M, Baucheron S, Chaslus-Dancla E, Jarraud S, Meugnier H, Forey F, Vandenesch F, Lina G, Etienne J, Thioulouse J, Manceau C, Robbe P, Nalin R, Briolay J, Nesme X (2001)
Experimental and theoretical evaluation of typing methods based upon random amplification of genomic restriction fragments (AFLP) for bacterial population genetics, Genetics Selection Evolution, vol. 33 pp.S319-S338 .

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

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

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

Ranjard L, Poly F, Lata J C, Mougel C, Thioulouse J, Nazaret S (2001)
Characterization of bacterial and fungal soil communities by automated ribosomal intergenic spacer analysis fingerprints: biological and methodological variability, Applied and Environmental Microbiology, vol. 67 pp.4479-4487.

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

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

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

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

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

Berthe FC, Le Roux F, Peyretaillade E, Peyret P, Rodriguez D, Gouy M, Vivares C P (2000)
Phylogenetic analysis of the small subunit ribosomal RNA of Marteilia refringens validates the existence of phylum Paramyxea (Desportes and Perkins 1990), Journal of Eukaryotic Microbiology, vol. 47 pp.288-293.

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

Brochier C, Philippe H (2000)
Phylogénies moléculaires et génomes, , vol. 206 pp.50-53.

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

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

Depaulis F, Brazier L, Mousset S, Turbe A, Veuille M (2000)
Selective sweep near the In(2L)t inversion breakpoint in an African population of Drosophila melanogaster, Genetical Research, vol. 76 pp.149-158.

Duponnois R, Fargette M, Fould S, Thioulouse J, Davies KG (2000)
Diversity of the bacterial hyperparasite Pasteuria penetrans in relation to the control of root-knot nematodes (Meloidogyne spp.) on Acacia holosericea, Nematology, vol. 2 pp.435-442.

Duponnois R, Founoune H, Lesueur D, Thioulouse J, Neyra M (2000)
Ectomycorrhization of six Acacia auriculiformis provenances from Australia Papua New Guinea and Senegal in glasshouse conditions: effect on the plant growth and on the multiplication of plant parasitic nematodes, Australian Journal of Experimental Agriculture, vol. 40 pp.443-450.

Durand J, Garnier L, Dajoz I, Mousset S, Veuille M (2000)
Gene flow in a facultative apomictic poacea the savanna grass Hyparrhenia diplandra, Genetics, vol. 156 pp.823-831.

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

Duret L, Abdeddaim S (2000)
Multiple alignments for structural functional or phylogenetic analyses of homologous sequences, , vol. pp.51-76.

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

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

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

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

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

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

Manlay R, Cadet P, Thioulouse J, Chotte JL (2000)
Relationships between abiotic and biotic soil properties during fallow periods in the sudanian zone of Senegal, Applied Soil Ecology, vol. 14 pp.89-101.

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.

Pate E, Ndiaye-Faye N, Thioulouse J, Villenave C, Bongers T, Cadet P, Debouzie D (2000)
Successional trends in the characteristics of soil nematodes communities in cropped and fallow lands in Senegal (Sonkorong), Applied Soil Ecology, vol. 14 pp.5-15.

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

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

Ranjard L, Nazaret S, Gourbiere F, Thioulouse J, Linet P, Richaume A (2000)
A soil microscale study to reveal the heterogeneity of Hg(II) impact on indigenous bacteria by quantification of adapted phenotypes and analysis of community DNA fingerprints, FEMS Microbiology Ecology, vol. 31 pp.107-115.

Ranjard L, Poly F, Combrisson J, Richaume A, Gourbiere F, Thioulouse J, Nazaret S (2000)
Heterogeneous Cell Density and Genetic Structure of Bacterial Pools Associated with Various Soil Microenvironments as Determined by Enumeration and DNA Fingerprinting Approach (RISA), Microbial Ecology, vol. 39 pp.263-272.

Reynaud PA, Thioulouse J (2000)
Identification of birds as biological markers along a neotropical urban-rural gradient using co-inertia analysis, Journal of Environmental Management, vol. 59 pp.121-140.

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

Tavares R, Aubourg S, Lecharny A, Kreis M (2000)
Organization and structural evolution of four multigene families in Arabidopsis thaliana: AtLCAD AtLGT AtMYST and AtHD-GL2, Plant Molecular Biology, vol. 42 pp.703-717.

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

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

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

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.

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

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

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.

Duponnois R, Senghor K, Thioulouse J, Ba A (1999)
Susceptibility of several sahelian Acacia to Meloidogyne javanica (Treub) Chitw, Agroforestry Systems, vol. 46 pp.123-130.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Cadet P, Thioulouse J (1998)
Identification of soil factors that relate to the structure of the plant parasitic nematode community, Applied Soil Ecology, vol. 8 pp.35-49.

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

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

Duret L, Guex N, Peitsch M C, Bairoch A (1998)
New insulin-like proteins with atypical disulfide bond pattern characterized in Caenorhabditis elegans by comparative sequence analysis and homology modeling, Genome Research, vol. 8 pp.348-353.

Galtier N, 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.

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

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

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

Peyretaillade E, Biderre C, Peyret P, Duffieux F, Metenier G, Gouy M, Michot B, Vivares C P (1998)
Microsporidian Encephalitozoon cuniculi a unicellular eukaryote with an unusual chromosomal dispersion of ribosomal genes and a LSU rRNA reduced to the universal core, Nucleic Acids Research, vol. 26 pp.3513-3520.

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

Robert V, Awono-Ambene HP, Thioulouse J (1998)
Ecology of larval mosquitoes with special reference to Anopheles arabiensis (Diptera: Culcidae) in market-garden wells in urban Dakar Senegal, Journal of Medical Entomology, vol. 35 pp.948-955.

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.

Sagot M-F, Tannier E (1998)
Perfect sorting by reversals, Proceedings of COCOON`05, Springer-Verlag, Lecture Notes in Computer Science, vol. 3595 pp.42-51.

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.

Tichtinsky G, Tavares R, Takvorian A, Schwebel-Dugué N, Twell D, Kreis M (1998)
An evolutionary conserved group of plant GSK-3/shaggy-like protein kinases preferentially expressed in developing pollen, Biochimica et Biophysica Acta, vol. 1442 pp.261-273.

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.

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.

Champely S, Guinand B, Thioulouse J, Clermidy A (1997)
Functional data analysis of curve asymmetry with application to the color pattern of Hydropsyche contubernalis head capsule, Biometrics, vol. 53 pp.294-305.

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

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.

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.

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.

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.

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.

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.

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.

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.

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

Thioulouse J , Chessel D, Dolédec S, Olivier JM (1997)
ADE-4: a multivariate analysis and graphical display software, Statistics and Computing, vol. 7 pp.75-83.

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, 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.

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.

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.

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.

Gouzy J, Corpet F, Kahn D (1996)
Graphical interface for ProDom domain families, Trends in Biochemical Sciences, vol. 21 pp.121-127.

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

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

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

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

Loustau D, Berbigier P, Roumagnac P, Arruda-Pacheco C, David JS, Ferreira MI, Pereira JS, Tavares R (1996)
Transpiration of a 64 year-old maritime pine stand in Portugal. 1. Seasonal course of water flux through maritime pine, Oecologia, vol. 107 pp.33-42.

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

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

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.

Thioulouse J (1996)
Towards Better Graphics for Multivariate Analysis: the Interactive Factor Map, Computational Statistics & Data Analysis, vol. 11 pp.11-21.

Thioulouse J, Chevenet F (1996)
NetMul a World-Wide Web user interface for multivariate analysis sofware, Computational Statistics & Data Analysis, vol. 21 pp.369-372.

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.

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.

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

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

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

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.

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.

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.

Sebo A, Tannier E (1995)
Connected Joins in Graphs, Proceedings of IPCO`01, Springer Verlag, Lecture Notes in Computer Science, vol. 2081 pp.383-391.

Thioulouse J, Chessel D, Champely S (1995)
Multivariate analysis of spatial patterns: a unified approach to local and global structures, Environmental and Ecological Statistics, vol. 2 pp.1-14.

Thioulouse J, Doledec S, Chessel D, Olivier JM (1995)
DE software: multivariate analysis and graphical display of environmental data, , vol. pp.57-62.

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.

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.

Cadet P, Thioulouse J, Albrecht A (1994)
Relationships between ferrisol properties and the structure of plant parasitic nematode communities on sugarcane in Martinique (French West Indies), Acta Oecologica, vol. 15 pp.767-780.

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.

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

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.

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.

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.

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

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

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

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

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.

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

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.

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.

Devillers J, Thioulouse J, Karcher W (1993)
Chemometrical evaluation of multispecies-multichemical data by means of graphical techniques combined with multivariate analyses, Ecotoxicology and environmental safety, vol. 26 pp.333-345.

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

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

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

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

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

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

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

Thioulouse J, Royet JP, Ploye H, Houllier F (1993)
Evaluation of the Precision of Systematic Sampling : Nugget Effect and Covariogram Modelling, Journal of Microscopy, vol. 172 pp.249-256.

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.

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.

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.

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

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

Perrin-Pecontal P, Gouy M, Nigon V M, Trabuchet G (1992)
Evolution of the primate beta-globin gene region: nucleotide sequence of the delta-beta-globin intergenic region of gorilla and phylogenetic relationships between African apes and man, Journal of Molecular Evolution, vol. 34 pp.17-30.

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.

Thioulouse J, Chessel D (1992)
A method for reciprocal scaling of species tolerance and sample diversity, Ecology, vol. 73 pp.670-680.

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.

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.

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

Chessel D, Thioulouse J (1991)
Auto-Modelisation en Analyse des Donnees, , vol. pp.71-86.

Devillers J, Thioulouse J, Domine D, Chastrette M, Karcher W (1991)
Multivariate Analysis of the Input and Output Data in the Fugacity Model Level I, , vol. pp.281-345.

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

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

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

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

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, 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.

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.

Thioulouse J, Devillers J, Chessel D, Auda Y (1991)
Graphical Techniques for Multidimensional Data Analysis, , vol. pp.153-205.

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.

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

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

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

Thioulouse J (1990)
MacMul and GraphMu :two Macintosh programs for the display and analysis of multivariate data, Computers and Geosciences UK, vol. 16 pp.1235-1240.

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.

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.

Cadet P, Thioulouse J (1989)
Traitements nematicides et peuplement de nematodes parasites de la canne a sucre au Burkina Faso. I : Repousses, Revue de Nématologie, vol. 12 pp.35-44.

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

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

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

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.

Thioulouse J (1989)
Statistical analysis and graphical display of multivariate data on the Macintosh, Computer Applications in the Biosciences, vol. 5 pp.287-292.

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.

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, 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.

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.

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

David M, 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.

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

Thioulouse J (1987)
Space-Time Structure in a Winter Rape Pest Population Psylliodes chrysocephala (Col. chrysomelidae): methodological proposals and biological interpretations, Journal of Applied Ecology, vol. 24 pp.435-450.

Thioulouse J, Chessel D (1987)
Les analyses multitableaux en ecologie factorielle. I : de la typologie d`etat a la typologie de fonctionnement par l`analyse triadique, Acta Oecologica Oecologia Generalis, vol. 8 pp.463-480.

Debouzie D, Thioulouse J (1986)
Statistics to find spatial and temporal structures in populations, , vol. G11 pp.263-282.

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.

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

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

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

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

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

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

Thioulouse J, Houllier F, Onillon JC (1985)
Variables regionalisees et denombrement d`Insectes : cas unidimensionnel, Comptes Rendus de l`Académie des Sciences - Séries III - Sciences de la Vie, vol. 301 pp.423-428.

Thioulouse J, Mathy B, Ploye H (1985)
Estimation d`un Volume a partir de Coupes Seriees : Sous-Echantillonnage Covariogramme Transitif et Calcul de Precision, Mikroskopie (Wien), vol. 42 pp.215-224.

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

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

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

Thioulouse J, Debouzie D, Ballanger Y (1984)
Structures spatiales et temporelles des populations d`un ravageur du Colza (Psylliodes chrysocephala L. (Col. Chrysomelidae)) dans plusieurs parcelles de culture, Acta Oecologica Oecologia Applicata, vol. 5 pp.335-353.

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

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

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

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.

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.

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

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

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

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

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.

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.