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Equipe Bioinformatique, Phylogénie et Génomique Evolutive

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Méthodes pour la génomique et la phylogénétique -Méthodes pour la génomique et la phylogénétique Nous développons de nouveaux modèles d’évolution des séquences, des méthodes pour l’inférence d’arbres de gènes et d’espèces, des méthodes pour reconstruire des génomes ancestraux, ou pour reconstruire des traits d’histoire de vie d’espèces disparues.
- Développements méthodologiques pour la phylogénétique
- Les modèles d’évolution des séquences que nous développons incluent des modèles hétérogènes entre branches (Manolo Gouy, Bastien Boussau), ou entre sites (Nicolas Lartillot, Laurent Guéguen). Nous développons également de nouveaux modèles d’évolution des codons (Marc Bailly-Béchet, Laurent Guéguen, Nicolas Lartillot), ainsi que des modèles à dépendance de voisinage (Laurent Guéguen).
- Les méthodes que nous développons pour reconstruire des génomes ancestraux sont basées sur des arbres de gènes et les cartes génomiques d’espèces actuelles (Eric Tannier, Laurent Guéguen)
- Les méthodes que nous développons pour l’inférence d’arbres de gènes et d’espèces incluent des modèles de duplication, perte et transfer de gènes (Vincent Daubin, Bastien Boussau, Eric Tannier, Nicolas Lartillot).
- Les méthodes que nous développons pour reconstruire des traits d’histoire de vie ancestraux sont basées sur des corrélations entre évolution des séquences et évolution des traits d’histoire de vie (Nicolas Lartillot)
- Développements méthodologiques pour la génomique
- nous développons des méthodes pour grouper les séquences homologues (Laurent Duret)
- nous développons des méthodes pour construire des bases de données pour la phylogénétique et la génomique (Laurent Duret, Manolo Gouy, Vincent Daubin).
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Paléogénomique et arbre de la vie -Paléogénomique et arbre de la vie Nous utilisons les bases de données et les méthodes que nous développons pour reconstruire des arbres phylogénétiques et pour reconstruire l’évolution des génomes dans des clades d’intérêt.
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Fonctionnement des systèmes biologiques complexes -Fonctionnement des systèmes biologiques complexes Nous maintenons une base de données d’annotations fonctionnelles de domaines protéiques, que nous utilisons pour étudier le fonctionnement des cellules actuelles et de leurs ancêtres le long de l’arbre de la vie.
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Evolution des génomes -Evolution des génomes Nous étudions l’impact des processus neutres sur l’évolution des génomes, chez l’homme et dans d’autres espèces.
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Enseignement -Enseignement Les membres de l’équipe BPGE enseignent à :
et participent à des ateliers de formation en biologie de l’évolution, génomique, bioinformatique et phylogénétique, en France ainsi qu’à l’étranger.
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Communication externe -Communication externe Nous accordons beaucoup d’importance à la vulgarisation et aimons partager nos découvertes ou commenter l’actualité scientifique.
En 2009, nous avons organisé une exposition à Lyon pour célébrer l’anniversaire de Charles Darwin et de sa théorie. Nous avons alors présenté la théorie de l’évolution ainsi que ses plus récents développements. une statue construite pour l’occasion et représentant l’arbre de la vie est désormais exposée dans un hall de l’université Claude Bernard Lyon 1.
Nous avons également écrit plusieurs articles pour des journaux de vulgarisation scientifique (Pour la Science, La Recherche, Biofutur...), et nous organisons des ateliers de formation pour les professeurs de Biologie du secondaire.
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Nous rejoindre -Nous rejoindre Il existe de nombreuses opportunités pour vous joindre a nous : pour un stage d’étude (BTS, IUT, INSA, Licence, Master, Doctorat) ou pour un travail de postdoctorant. Nous vous encourageons a nous joindre pour discuter des possibilités de sujets et de financement. L’équipe est variée et cosmopolite, nous accueillons régulièrement des étudiants de plusieurs nationalités.
Membres
Responsable : | Brochier-Armanet Céline PU UCBL | Duret Laurent DR CNRS |
- Aouad Monique doctorant UCBL
- Barreto Samuel doctorant UCBL
- Boussau Bastien CR CNRS
- Carrillo Guillaume doctorant UCBL
- Cuzin Pierre stagiaire UCBL
- Daubin Vincent DR CNRS
- Denier Elisa M2 UCBL
- de Vienne Damien CR CNRS
- Flandrois Jean-Pierre PU émérite UCBL
- Ganivet Quentin stagiaire autre
- Gautier Maud doctorant UCBL
- Gouy Manolo DR CNRS
- Guéguen Laurent MCU UCBL
- Hartasanchez Frenk Diego post-doc CNRS
- Jauffrit Frédéric doctorant UCBL
- Kobert Kassian post-doc autre
- Lafay Bénédicte CR CNRS
- Lanore Vincent post-doc CNRS
- Lartillot Nicolas DR CNRS
- Latrille Thibault doctorant UCBL
- Laverré Alexandre M2 CNRS
- Lobry Jean PU UCBL
- Mouchiroud Dominique PU UCBL
- Necsulea Anamaria CR CNRS
- Nguyen Trung Alexia M2 CNRS
- Oudart Anne doctorant UCBL
- Perrière Guy DR CNRS
- Philippon Héloise CDD CNRS
- Stoneking Mark chercheur invité autre
- Tannier Eric CR INRIA
- Tricou Théo M2 UCBL
+Anciens membres -Anciens membres
- Abby Sophie post-doc UCBL
- Aouad Monique M2 UCBL
- Arellano Davin Adrian doctorant UCBL
- Arigon Anne-Muriel doctorant UCBL
- Arnaiz Olivier CDD EZUS
- Auffret Pauline M2 UCBL
- Bailly-Bechet Marc MCU UCBL
- Barba Matthieu post-doc CNRS
- Bardet Ivan M2 UCBL
- Bartolo François CDD CNRS
- Bastien Sylvere M2 UCBL
- Bazin Adelme stagiaire UCBL
- Bechy Anne-Laure doctorant UCBL
- Bernard Thomas post-doc INRIA
- Bickerstaffe Lily stagiaire UCBL
- Bigot Thomas CDD UCBL
- Boher Elsa stagiaire UCBL
- Boniface Adrien M2 autre
- Boyer Roxane stagiaire UCBL
- Brevet Mathieu M2 CNRS
- Charret Quentin stagiaire UCBL
- Clément Yves M2 UCBL
- Clerc Olivier CDD CNRS
- Collet Marie stagiaire UCBL
- Comte Aurore M2 UCBL
- Dalino Jordi M2 UCBL
- Devillers Hugo M2 UCBL
- Duchemin Wandrille doctorant UCBL
- Duchemin Wandrille stagiaire UCBL
- Dupouy MArion stagiaire UCBL
- Dupuis Pierre CDD UCBL
- Faubladier Michael CDD CNRS
- Fey Jonathan CDD CNRS
- Fournier Cyril CDD CNRS
- Fournier Amandine CDD CNRS
- Galbert Idris M2 UCBL
- Gence Guillaume CDD UCBL
- Gence Guillaume M2 UCBL
- Gout Jean-François doctorant UCBL
- Guillet Claire doctorant UCBL
- Guyot Dominique CDD CNRS
- Ho-Huu Joan doctorant UCBL
- Horvilleur Benjamin M2 UCBL
- Jacquemetton Julien M2 UCBL
- Jouffret Virginie M2 UCBL
- Kahn Daniel DR INRA
- Keri Zsofia stagiaire UCBL
- Kobert Kassian post-doc autre
- Kvikstad Erika post-doc UCBL
- Lafay Benedicte chercheur invité CNRS
- Lassalle Florent doctorant UCBL
- Latrille Thibault stagiaire CNRS
- Latrille Thibault doctorant UCBL
- Latrille Thibault M2 ENS
- Lecocq Michel doctorant UCBL
- Le Poidevin Joachim stagiaire UCBL
- Lesecque Yann doctorant UCBL
- Letcher Brice stagiaire UCBL
- Lombard Vincent CDD UCBL
- Makova Kateryna chercheur invité UCBL
- Markov Peter CDD CNRS
- Michalik Juraj stagiaire UCBL
- Michon Lucas stagiaire CNRS
- Mifsud François stagiaire UCBL
- Morin Lise M2 UCBL
- Murray Dan Patterson post-doc INRIA
- Nekrutenko Anton chercheur invité UCBL
- Parmley Joanna post-doc UCBL
- Patterson Murray Dan post-doc UCBL
- Patterson Murray Dan post-doc INRIA
- Perin Charlotte stagiaire UCBL
- Pett Walker post-doc UCBL
- Philippon Héloise doctorant UCBL
- Picarle Justine M2 CNRS
- Planel Rémi CDD UCBL
- Ponce Rafael M2 UCBL
- Popa Alexandra CDD UCBL
- Pouyet Fanny doctorant UCBL
- Remy Robert stagiaire UCBL
- Rey Carine M2 UCBL
- Rey Carine stagiaire UCBL
- Rey Carine stagiaire ENS
- Rezvoy Clément doctorant ENS
- Roatta Adeline stagiaire UCBL
- Rocher Vincent stagiaire UCBL
- Rochette Nicolas doctorant UCBL
- Rodehenko Natalia M2 UCBL
- Ruaudel Florence CDD UCBL
- Sellis Diamantis post-doc UCBL
- Sellis Diamantis post-doc UCBL
- Semeria Magali doctorant UCBL
- Sertier Anne Sophie doctorant UCBL
- Soubrier Julien M2 UCBL
- Szollosi Gergely Janos post-doc UCBL
- Taib Najwa post-doc CNRS
- Taib Najwa post-doc CNRS
- Taib Najwa post-doc UCBL
- Taly Jean-Francois CDD CNRS
- Vassilev Ivaylo M2 UCBL
+Publications -Publications
Davin AA, Tannier E, Williams TA, Boussau B, Daubin V, Szollosi GJ (2018)
Gene transfers can date the tree of life, Nature ecology & evolution, vol. pp.1-8.
Diagouraga B, Clement JAJ, Duret L, Kadlec J, De Massy B, Baudat F (2018)
PRDM9 Methyltransferase Activity Is Essential for Meiotic DNA Double-Strand Break Formation at Its Binding Sites, Molecular cell, vol. 69 pp.853-865.
Parto S, Lartillot N (2018)
Molecular adaptation in Rubisco: Discriminating between convergent evolution and positive selection using mechanistic and classical codon models, PLoS one, vol. 13 pp.e0192697-e0192697.
Anselmetti Y, Luhmann N, Bérard S, Tannier E, Chauve C (2018)
Comparative Methods for Reconstructing Ancient Genome Organization
in: Methods in Molecular Biology, , pp.343-362.
Collet M, Amat I, Sauzet S, Auguste A, Fauvergue X, Mouton L, Desouhant E (2018)
Insects and incest: sib-mating tolerance in natural populations of a parasitoid wasp, Peer Community in Evolutionary Biology, vol. pp.1-19.
Guéguen L, Duret L (2018)
Unbiased estimate of synonymous and non-synonymous substitution rates with non-stationary base composition, Molecular biology and evolution, vol. 35 pp.734-742.
Siberchicot A, Bessy A, Gueguen L, Marais GAB (2017)
MareyMap Online: A User-Friendly Web Application and Database Service for Estimating Recombination Rates Using Physical and Genetic Maps, Genome biology and evolution, vol. 9 pp.2506-2509.
Pantalacci S, Guéguen L, Petit C, Lambert A, Peterkova R, Sémon M (2017)
Transcriptomic signatures shaped by cell proportions shed light on comparative developmental biology, Genome biology, vol. 18 pp.29-29.
Philippe H, de Vienne DM, Ranwez V, Roure B, Baurain D, Delsuc F (2017)
Pitfalls in supermatrix phylogenomics, European Journal of Taxonomy, vol. 283 pp.1-25.
Williams TA, Szollosi GJ, Spang A, Foster PG, Heaps SE, Boussau B, Ettema TJG, Embley MT (2017)
Integrative modeling of gene and genome evolution roots the archaeal tree of life, Proceedings of the National Academy of Sciences of the United States of America, vol. 114 pp.E4602-E4602.
Boldanova T, Suslov A, Heim MH, Necsulea A (2017)
Transcriptional response to hepatitis C virus infection and interferon-alpha treatment in the human liver, EMBO Molecular Medicine, vol. 9 pp.816-834.
Latrille T, Duret L, Lartillot N (2017)
The Red Queen model of recombination hot-spot evolution: a theoretical investigation, Philosophical transactions of the Royal Society B Biological sciences, vol. 372 pp.20160463-20160463.
Schlapfer P, Zhang P, Wang C, Kim T, Banf M, Chae L, Dreher K, Chavali AK, Nilo-Poyanco R, Bernard T, Kahn D, Rhee SY (2017)
Genome-Wide Prediction of Metabolic Enzymes Pathways and Gene Clusters in Plants, Plant physiology, vol. 173 pp.2041-2059.
Jacox E, Weller M, Tannier E, Scornavacca C (2017)
Resolution and reconciliation of non-binary gene trees with transfers duplications and losses, Bioinformatics, vol. 33 pp.980-987.
Feuda R, Dohrmann M, Pett W, Philippe H, Rota-Stabelli O, Lartillot N, Worheide G, Pisani D (2017)
Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals, Current biology, vol. 27 pp.3864-3870 e4.
Cariou M, Duret L, Charlat S (2017)
The global impact of Wolbachia on mitochondrial diversity and evolution, Journal of Evolutionary Biology, vol. 30 pp.2204-2210.
Chauve C, Rafiey A, Davin AA, Scornavacca C, Veber P, Boussau B, Szollosi G, Daubin V, Tannier E (2017)
MaxTiC: Fast ranking of a phylogenetic tree by Maximum Time Consistency with lateral gene transfers, Peer Community In Evolutionary Biology, vol. pp.1-18.
Grey C, Clement JA, Buard J, Leblanc B, Gut I, Gut M, Duret L, de Massy B (2017)
In vivo binding of PRDM9 reveals interactions with noncanonical genomic sites, Genome research, vol. 27 pp.580-590.
Pouyet F, Mouchiroud D, Duret L, Sémon M (2017)
Recombination meiotic expression and human codon usage, eLife, vol. 6 pp.e27344-e27344.
Saudemont B, Popa A, Parmley JL, Rocher V, Blugeon C, Necsulea A, Meyer E, Duret L (2017)
The fitness cost of mis-splicing is the main determinant of alternative splicing patterns, Genome biology, vol. 18 pp.208-208.
Venner S, Miele V, Terzian C, Biemont C, Daubin V, Feschotte C, Pontier D (2017)
Ecological networks to unravel the routes to horizontal transposon transfers, PLoS Biology, vol. 15 pp.e2001536-e2001536.
Philippon H, Souvane A, Brochier-Armanet C, Perriere G (2017)
IsoSel: Protein Isoform Selector for phylogenetic reconstructions, PLoS One, vol. 12 pp.e0174250-e0174250.
Rodrigue N, Lartillot N (2017)
Detecting Adaptation in Protein-Coding Genes Using a Bayesian Site-Heterogeneous Mutation-Selection Codon Substitution Model, Molecular biology and evolution, vol. 34 pp.204-214.
Duchemin W, Anselmetti Y, Patterson M, Ponty Y, Berard S, Chauve C, Scornavacca C, Daubin V, Tannier E (2017)
DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies, Genome Biology and Evolution, vol. 9 pp.1312-1319.
Parto S, Lartillot N (2017)
Detecting consistent patterns of directional adaptation using differential selection codon models, BMC evolutionary biology, vol. 17 pp.147-147.
Elsensohn MH, Leblay N, Dimassi S, Campan-Fournier A, Labalme A, Roucher-Boulez F, Sanlaville D, Lesca G, Bardel C, Roy P (2017)
Statistical method to compare massive parallel sequencing pipelines, BMC Bioinformatics, vol. 18 pp.139-139.
Lefebure T, Morvan C, Malard F, Francois C, Konecny-Dupre L, Gueguen L, Weiss-Gayet M, Seguin-Orlando A, Ermini L, Sarkissian C, Charrier N P, Eme D, Mermillod-Blondin F, Duret L, Vieira C, Orlando L, Douady CJ (2017)
Less effective selection leads to larger genomes, Genome research, vol. 27 pp.1016-1028.
Bailly-Bechet M, Martins-Simoes P, Szollosi GJ, Mialdea G, Sagot MF, Charlat S (2017)
How Long Does Wolbachia Remain on Board?, Molecular Biology and Evolution, vol. 34 pp.1183-1193.
Boutin H, de Vienne DM (2017)
Sonification of phylogenetic trees: listening to evolution, Journées d`Informatique Musicale 2017, pp.1-4.
Fertin G, Jean G, Tannier E (2017)
Algorithms for computing the double cut and join distance on both gene order and intergenic sizes, Algorithms for Molecular Biology, vol. 12 pp.16-16.
Bulteau L, Fertin G, Tannier E (2016)
Genome rearrangements with indels in intergenes restrict the scenario space, BMC Bioinformatics, vol. 17 pp.225-231.
Philippon H (2016)
Étude de l`histoire évolutive des PI3K et des voies de signalisation associées .
Biller P, Knibbe C, Beslon G, Tannier E (2016)
Comparative Genomics on Artifical Life, Computability in Europe, pp.1-10.
Schep R, Necsulea A, Rodriguez-Carballo E, Guerreiro I, Andrey G, Nguyen Huynh TH, Marcet V, Zakany J, Duboule D, Beccari L (2016)
Control of Hoxd gene transcription in the mammary bud by hijacking a preexisting regulatory landscape, Proceedings of the National Academy of Sciences of the United States of America, vol. 113 pp.e7720-e7729.
Beccari L, Yakushiji-Kaminatsui N, Woltering J M, Necsulea A, Lonfat N, Rodriguez-Carballo E, Mascrez B, Yamamoto S, Kuroiwa A, Duboule D (2016)
A role for HOX13 proteins in the regulatory switch between TADs at the HoxD locus, Genes & development, vol. 30 pp.1172-86.
Cariou M, Duret L, Charlat S (2016)
How and how much does RAD-seq bias genetic diversity estimates?, BMC evolutionary biology, vol. 16 pp.240-240.
Thiaville JJ, Kellner SM, Yuan Y, Hutinet G, Thiaville PC, Jumpathong W, Mohapatra S, Brochier-Armanet C, Letarov AV, Hillebrand R, Malik CK, Rizzo CJ, Dedon PC, de Crécy-Lagard V (2016)
Novel genomic island modifies DNA with 7-deazaguanine derivatives, Proceedings of the National Academy of Sciences of the United States of America, vol. 113 pp.e1452-e1459.
Boccara M, Fedala Y, Bryan Venien C, Bailly-Bechet M, Bowler C, Boccara AC (2016)
Full-field interferometry for counting and differentiating aquatic biotic nanoparticles: from laboratory to Tara Oceans, Biomedical Optics Express, vol. 7 pp.3736-3736.
Ronquist F, Lartillot N, Phillips MJ (2016)
Closing the gap between rocks and clocks using total-evidence dating, Philosophical transactions of the Royal Society B-Biological sciences, vol. 371 pp.20150136-20150136.
Fertin G, Jean G, Tannier E (2016)
Genome Rearrangements on Both Gene Order and Intergenic Regions, WABI, , vol. 9838 pp.162-173.
Noutahi E, Semeria M, Lafond M, Seguin J, Boussau B, Gueguen L, El-Mabrouk N, Tannier E (2016)
Efficient Gene Tree Correction Guided by Genome Evolution, PLoS One, vol. 11 pp.e0159559-e0159559.
Groussin M, Boussau B, Szollosi G, Eme L, Gouy M, Brochier-Armanet C, Daubin V (2016)
Gene Acquisitions from Bacteria at the Origins of Major Archaeal Clades Are Vastly Overestimated, Molecular Biology and Evolution, vol. 33 pp.305-10.
Lazzerini N, Lecuyer C, Amiot R, Angst D, Buffetaut E, Fourel F, Daux V, Betancort JF, Flandrois JP, Marco AS, Lomoschitz A (2016)
Oxygen isotope fractionation between bird eggshell calcite and body water: application to fossil eggs from Lanzarote (Canary Islands), Naturwissenschaften, vol. 103 pp.81-81.
Collet M, Vayssade C, Auguste A, Mouton L, Desouhant E, Malausa T, Fauvergue X (2016)
Diploid male production correlates with genetic diversity in the parasitoid wasp Venturia canescens : a genetic approach with new microsatellite markers, Ecology and Evolution, vol. 6 pp.6721-6734.
Pichat C, Couvin D, Carret G, Fredenucci I, Jacomo V, Carricajo A, Boisset S, Dumitrescu O, Flandrois JP, Lina G, Rastogi N (2016)
Combined Genotypic Phylogenetic and Epidemiologic Analyses of Mycobacterium tuberculosis Genetic Diversity in the Rhone Alpes Region France, PLoS One, vol. 11 pp.e0153580-e0153580.
Freyermuth F, Rau F, Kokunai Y, Linke T, Sellier C, Nakamori M, Kino Y, Arandel L, Jollet A, Thibault C, Philipps M, Vicaire S, Jost B, Udd B, Day JW, Duboc D, Wahbi K, Matsumura T, Fujimura H, Mochizuki H, Deryckere F, Kimura T, Nukina N, Ishiura S, Lacroix V, Campan-Fournier A, Navratil V, Chautard E, Auboeuf D, Horie M, Imoto K, Lee KY, Swanson MS, Lopez de Munain A, Inada S, Itoh H, Nakazawa K, Ashihara T, Wang E, Zimmer T, Furling D, Takahashi MP, Charlet-Berguerand N (2016)
Splicing misregulation of SCN5A contributes to cardiac-conduction delay and heart arrhythmia in myotonic dystrophy, Nature communications, vol. 7 pp.11067-11067.
Biller P, Gueguen L, Knibbe C, Tannier E (2016)
Breaking Good: Accounting for Fragility of Genomic Regions in Rearrangement Distance Estimation, Genome Biology and Evolution, vol. 8 pp.1427-39.
Pisani D, Pett W, Dohrmann M, Feuda R, Rota-Stabelli O, Philippe H, Lartillot N, Worheide G (2016)
Reply to Halanych et al.: Ctenophore misplacement is corroborated by independent datasets, Proceedings of the National Academy of Sciences of the United States of America, vol. 113 pp.E948-9.
Duprey A, Nasser W, Leonard S, Brochier-Armanet C, Reverchon S (2016)
Transcriptional start site turnover in the evolution of bacterial paralogous genes - the pelE-pelD virulence genes in Dickeya, FEBS journal, vol. 283 pp.4192-4207.
Antunes LC, Poppleton D, Klingl A, Criscuolo A, Dupuy B, Brochier-Armanet C, Beloin C, Gribaldo S (2016)
Phylogenomic analysis supports the ancestral presence of LPS-outer membranes in the Firmicutes, eLife, vol. 5 pp.e14589-e14589.
Martin C, Maureille B, Amiot R, Touzeau A, Royer A, Fourel F, Panczer G, Flandrois JP, Lécuyer C (2016)
Record of Nile seasonality in Nubian neonates, Isotopes in Environmental and Health Studies, vol. 53 pp.223-242.
Jauffrit F, Penel S, Delmotte S, Rey C, De Vienne DM, Gouy M, Charrier JP, Flandrois JP, Brochier-Armanet C (2016)
RiboDB Database: A Comprehensive Resource for Prokaryotic Systematics, Molecular Biology and Evolution, vol. 33 pp.2170-2172.
Fraune J, Brochier-Armanet C, Alsheimer M, Volff J N, Schucker K, Benavente R (2016)
Evolutionary history of the mammalian synaptonemal complex, Chromosoma, vol. 125 pp.355-60.
Pouyet F, Bailly-Bechet M, Mouchiroud D, Gueguen L (2016)
SENCA: A Multilayered Codon Model to Study the Origins and Dynamics of Codon Usage, Genome Biology and Evolution, vol. 8 pp.2427-41.
Garcia PS, Simorre JP, Brochier-Armanet C, Grangeasse C (2016)
Cell division of Streptococcus pneumoniae: think positive!, Current opinion in microbiology, vol. 34 pp.18-23.
Lopez-Maestre H, Brinza L, Marchet C, Kielbassa J, Bastien S, Boutigny M, Monnin D, El Filali A, Carareto CM, Vieira C, Picard F, Kremer N, Vavre F, Sagot MF, Lacroix V (2016)
SNP calling from RNA-seq data without a reference genome: identification quantification differential analysis and impact on the protein sequence, Nucleic Acids Research, vol. 44 pp.e148-e148.
de Vienne DM (2016)
Lifemap: Exploring the Entire Tree of Life, PLoS Biology, vol. 14 pp.e2001624-e2001624.
Groussin M, Daubin V, Gouy M, Tannier E (2016)
Ancestral Reconstruction: Theory and Practice
in: The Encyclopedia of Evolutionary Biology, , pp.70-77.
Lays C, Tannier E, Henry T (2016)
Francisella IglG protein and the DUF4280 proteins: PAAR-like proteins in non-canonical Type VI secretion systems?, Microbial Cell, vol. 3 pp.445-447.
Pouyet F (2016)
Etude bioinformatique de l`evolution de l`usage du code génétique .
Hohna S, Landis MJ, Heath T A, Boussau B, Lartillot N, Moore BR, Huelsenbeck JP, Ronquist F (2016)
RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language, Systematic biology, vol. 65 pp.726-36.
Karaki L, Da Silva P, Rizk F, Chouabe C, Chantret N, Eyraud V, Gressent F, Sivignon C, Rahioui I, Kahn D, Brochier-Armanet C, Rahbe Y, Royer C (2016)
Genome-wide analysis identifies gain and loss/change of function within the small multigenic insecticidal Albumin 1 family of Medicago truncatula, BMC plant biology, vol. 16 pp.63-63.
Sellis D, Kvitek D J, Dunn B, Sherlock G, Petrov DA (2016)
Heterozygote Advantage Is a Common Outcome of Adaptation in Saccharomyces cerevisiae, Genetics, vol. 203 pp.1401-1413.
Francois CM, Duret L, Simon L, Mermillod-Blondin F, Malard F, Konecny-Dupre L, Planel R, Penel S, Douady CJ, Lefebure T (2016)
No Evidence That Nitrogen Limitation Influences the Elemental Composition of Isopod Transcriptomes and Proteomes, Molecular Biology and Evolution, vol. 33 pp.2605-20.
Dacks JB, Field MC, Buick R, Eme L, Gribaldo S, Roger AJ, Brochier-Armanet C, Devos DP (2016)
The changing view of eukaryogenesis - fossils cells lineages and how they all come together, Journal of Cell Science, vol. 129 pp.3695-3703.
Amandio AR, Necsulea A, Joye E, Mascrez B, Duboule D (2016)
Hotair Is Dispensible for Mouse Development, PLoS Genetics, vol. 12 pp.e1006232-e1006232.
Attaiech L, Boughammoura A, Brochier-Armanet C, Allatif O, Peillard-Fiorente F, Edwards RA, Omar AR, MacMillan AM, Glover M, Charpentier X (2016)
Silencing of natural transformation by an RNA chaperone and a multitarget small RNA, Proceedings of the National Academy of Sciences of the United States of America, vol. 113 pp.8813-8818.
Lartillot N, Phillips M J, Ronquist F (2016)
A mixed relaxed clock model, Philosophical transactions of the Royal Society B-Biological sciences, vol. 371 pp.20150132-20150132.
Safa E, Barreau JB, Gaugne R, Duchemin W, Talma JD, Arnaldi B, Dumont G, Gouranton V (2016)
Digital and Handcrafting Processes Applied to Sound-Studies of Archaeological Bone Flutes, International conference on digital heritage EUROMED 2016, pp.184-195.
Flandrois JP, Perrière G, Gouy M (2015)
leBIBIQBPP: a set of databases and a webtool for automatic phylogenetic analysis of prokaryotic sequences, BMC Bioinformatics, vol. 16 pp.251-251.
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Lesecque Y, Mouchiroud D, Duret L (2013)
GC-Biased Gene Conversion in Yeast Is Specifically Associated with Crossovers: Molecular Mechanisms and Evolutionary Significance, Molecular biology and evolution, vol. 30 pp.1409-19.
Schumer M, Cui R, Boussau B, Walter R, Rosenthal G, Andolfatto P (2013)
An evaluation of the hybrid speciation hypothesis for Xiphophorus clemenciae based on whole genome sequences, Evolution, vol. 67 pp.1155-1168.
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.
Danchin E G, Arguel M J, Campan-Fournier A, Perfus-Barbeoch L, Magliano M, Rosso M N, Da Rocha M, Da Silva C, Nottet N, Labadie K, Guy J, Artiguenave F, Abad P (2013)
Identification of novel target genes for safer and more specific control of root-knot nematodes from a pan-genome mining, PLoS pathogens, vol. 9 pp.e1003745-e1003745.
Lartillot N, Rodrigue N, Stubbs D, Richer J (2013)
PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment, Systematic Biology, vol. 62 pp.611-615.
de Vienne D M, Refregier G, Lopez-Villavicencio M, Tellier A, Hood M E, Giraud T (2013)
Cospeciation vs host-shift speciation: methods for testing evidence from natural associations and relation to coevolution, New phytologist, vol. 198 pp.347-385.
Fraune J, Brochier-Armanet C, Alsheimer M, Benavente R (2013)
Phylogenies of Central Element Proteins Reveal the Dynamic Evolutionary History of the Mammalian Synaptonemal Complex: Ancient and Recent Components, Genetics, vol. 195 pp.781-793.
Lartillot N (2013)
Phylogenetic patterns of GC-biased gene conversion in placental mammals and the evolutionary dynamics of recombination landscapes, Molecular biology and evolution, vol. 30 pp.489-502.
Gladieux P, Ropars J, Badouin H, Branca A, Aguileta G, de Vienne D M, Rodriguez de la Vega R C, Branco S, Giraud T (2013)
Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes, Molecular Ecology, vol. 23 pp.753-773.
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Gribaldo S, Brochier-Armanet C (2013)
LUCA ancêtre de tous les êtres vivants, Les dossiers de la recherche, vol. 2 pp.29-31.
Lartillot N (2013)
HDR - Inférence probabiliste pour la phylogénie la génomique comparative et les sciences de la macro-évolution .
Lassalle F (2013)
Les génomes bactériens une histoire de transfert de gènes de recombinaison et de cladogénèse. .
Cariou M, Duret L, Charlat S (2013)
Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization, Ecology and Evolution, vol. 3 pp.846-852.
Rajaraman A, Tannier E, Chauve C (2013)
The genome of the medieval Black Death agent (extended abstract), JOBIM 2013, pp.47-54.
Szollosi GJ, Rosikiewicz W, Boussau B, Tannier E, Daubin V (2013)
Efficient exploration of the space of reconciled gene trees, Systematic biology, vol. 62 pp.901-12.
Gueguen L, Gaillard S, Boussau B, Gouy M, Groussin M, Rochette N, Bigot T, Fournier D, Pouyet F, Cahais V, Bernard A, Scornavacca C, Nabholz B, Haudry A, Dachary L, Galtier N, Belkhir K, Dutheil J Y (2013)
Bio++: Efficient Extensible Libraries and Tools for Computational Molecular Evolution, Molecular Biology and Evolution, vol. 30 pp.1745-1750.
Patterson M, Szollosi GJ, Daubin V, Tannier E (2013)
Lateral gene transfer rearrangement reconciliation, BMC Bioinformatics, vol. 14 pp.S4-S4.
Guerin-Faublee V, Flandrois JP, Pichat C, Boschiroli M L, Lamy B (2013)
Mycobacterium bourgelatii sp. nov. a rapidly growing non-chromogenic species isolated from the lymph nodes of cattle, International journal of systematic and evolutionary microbiology, vol. 63 pp.4669-74.
Vabret N, Bailly-Bechet M, Najburg V, Müller-Trutwin M, Verrier B, Tangy F (2012)
The Biased Nucleotide Composition of HIV-1 Triggers Type I Interferon Response and Correlates with Subtype D Increased Pathogenicity, PLoS one, vol. 7 pp.e33502-e33502.
De Crécy-Lagard V, Forouhar F, Brochier-Armanet C, Tong L, Hunt JF (2012)
Comparative genomic analysis of the DUF71/COG2102 family predicts roles in diphthamide biosynthesis and B12 salvage, Biology Direct, vol. 7 pp.1-13.
Popa A, Samollow P, Gautier C, Mouchiroud D (2012)
The sex-specific impact of meiotic recombination on nucleotide composition, Genome Biology and Evolution, vol. 4 pp.412-422.
Brochier-Armanet C, Gribaldo S (2012)
Les défis de la systématique face au monde microbien, Biofutur, vol. 328 pp.49-52.
Boussau B, Gouy M (2012)
What genomes have to say about the evolution of the Earth, Gondwana Research, vol. 21 pp.483-494.
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Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations, Proceedings of the National Academy of Sciences of The United States of America, vol. 109 pp.17513-17518.
Benayoun BA, Anttonen M, L`hôte D, Bailly-Bechet M, Andersson N, Heikinheimo M, Veita RA (2012)
Adult ovarian granulosa cell tumor transcriptomics: prevalence of FOXL2 target genes misregulation gives insights into the pathogenic mechanism of the p.Cys134Trp somatic mutation, Oncogene, vol. 32 pp.2739-2746.
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ReNaBi-IFB : The French Bioinformatics Infrastructure, EMBNet.journal, vol. 18 pp.12-13.
Bernt M, Chao K-M, Kao J-W, Middendorf M, Tannier E (2012)
Preserving Inversion Phylogeny Reconstruction, WABI 2012, Springer-Verlag, vol. 7534 pp.1-13.
Brochier-Armanet C, Moreira D (2012)
Transferts horizontaux de gènes dans les écosystèmes microbiens
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Morin L, Lobry JR, Peyron F, Wallon M (2012)
Seasonal variations in acute toxoplasmosis in pregnant women in the Rhône-Alpes region (France), Clinical Microbiology and Infection, vol. 18 pp.E401-E403.
Daubin V, Abby S (2012)
Les transferts horizontaux de gènes et l’arbre de la vie, M S-Médecine Sciences, vol. 28 pp.695-698.
Paganini J, Campan-Fournier A, Da Rocha M, Gouret P, Pontarotti P, Wajnberg E, Abad P, Danchin E G (2012)
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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.
Brochier-Armanet C, Gribaldo S, Forterre P (2012)
Spotlight on the Thaumarchaeota, Isme Journal, vol. 6 pp.227-230.
Caumette P, Brochier C, Normand P (2012)
Taxonomie et phylogénie des procaryotes
in: Ecologie Microbienne : Microbiologie des Milieux Naturels et Anthropisés, , pp.159-202.
Manuch J, Patterson M, Wittler R, Chauve C, Tannier E (2012)
Linearization of ancestral multichromosomal genomes, BMC Bioinformatics, vol. 13 pp.11-11.
Daubin V (2012)
HDR - Phylogénie Moléculaire 2.0 .
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
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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.
Junillon T, Vimont A, Mosticone D, Mallen B, Baril F, Rozand C, Flandrois JP (2012)
Simplified detection of food-borne pathogens: An in situ high affinity capture and staining concept, Journal of Microbiological Methods, vol. 91 pp.501-505.
Fong JJ, Brown JM, Fujita MK, Boussau B (2012)
A Phylogenomic Approach to Vertebrate Phylogeny Supports a Turtle-Archosaur Affinity and a Possible Paraphyletic Lissamphibia, PLoS one, vol. 7 pp.e48990-e48990.
Petit E, Giraud T, de Vienne D M, Coelho M A, Aguileta G, Amselem J, Kreplak J, Poulain J, Gavory F, Wincker P, Young S K, Cuomo C, Perlin M H, Hood M E (2012)
Linkage to the mating-type locus across the genus Microbotryum: insights into nonrecombining chromosomes, Evolution, vol. 66 pp.3519-3533.
Szollosi GJ, Daubin V (2012)
Modeling Gene Family Evolution and Reconciling Phylogenetic Discord, Methods in Molecular Biology, vol. 856 pp.29-51.
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.
Gribaldo S, Brochier-Armanet C (2012)
Time for order in microbial systematics, Trends in Microbiology, vol. 20 pp.209-210.
Dutheil J Y, Galtier N, Romiguier J, Douzery E J P, Ranwez V, Boussau B (2012)
Efficient Selection of Branch-Specific Models of Sequence Evolution, Molecular Biology and Evolution, vol. 29 pp.1861-1874.
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.
Lesecque Y, Keightley PD, Eyre-Walker A (2012)
A Resolution of the Mutation Load Paradox in Humans, Genetics, vol. 191 pp.1321-1330.
Py B, Gerez C, Angelini S, Planel R, Vinella D, Loiseau L, Talla E, Brochier-Armanet C, Garcia Serres R, Latour J M, Ollagnier-de Choudens S, Fontecave M, Barras F (2012)
Molecular organization biochemical function cellular role and evolution of NfuA an atypical Fe-S carrier, Molecular microbiology, vol. 86 pp.155-71.
de Vienne D M, Azé J (2012)
Efficient Prediction of Co-Complexed Proteins Based on Coevolution, PLoS one, vol. 7 pp.e48728-e48728.
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.
Pessia E, Popa A, Mousset S, Rezvoy C, Duret L, Marais G (2012)
Evidence for Widespread GC-biased Gene Conversion in Eukaryotes, Genome Biology and Evolution, vol. 4 pp.787-794.
Bérard S, Gallien C, Boussau B, Szollosi GJ, Daubin V, Tannier E (2012)
Evolution of gene neighborhoods within reconciled phylogenies, Bioinformatics, vol. 28 pp.I382-I388.
Bérard J, Guéguen L (2012)
Accurate Estimation of Substitution Rates with Neighbor-Dependent Modelsina Phylogenetic Context, Systematic Biology, vol. 61 pp.510-521.
Jones BR, Rajaraman A, Tannier E, Chauve C (2012)
ANGES: reconstructing ANcestral GEnomeS maps, Bioinformatics, vol. 28 pp.2388-90.
Romiguier J, Figuet E, Galtier N, Douzery E J P, Boussau B, Dutheil J Y, Ranwez V (2012)
Fast and Robust Characterization of Time Heterogeneous Sequence Evolutionary Processes Using Substitution Mapping, PLos One, vol. 7 pp.e33852-e33852.
Lartillot N, Delsuc F (2012)
Joint reconstruction of divergence times and life-history evolution in placental mammals using a phylogenetic covariance model, Evolution, vol. 66 pp.1773-1787.
Miklos I, Tannier E (2012)
Approximating the number of Double Cut-and-Join scenarios, Theoretical Computer Science, vol. 439 pp.30-40.
de Vienne D M, Ollier S, Aguileta G (2012)
Phylo-MCOA: a fast and efficient method to detect outlier genes and species in phylogenomics using multiple co-inertia analysis, Molecular biology and evolution, vol. 29 pp.1587-1598.
Narasingarao P, Podell S, Ugalde J A, Brochier-Armanet C, B Emerson J, Brocks J J, Heidelberg K B, Banfield J F, Allen E E (2012)
De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities, ISME Journal, vol. 6 pp.81-93.
Pessia E, Makino T, Bailly-Bechet M, McLysaght A, Marais GAB (2012)
Mammalian X chromosome inactivation evolved as a dosage-compensation mechanism for dosage-sensitive genes on the X chromosome, Proceedings of the National Academy of Sciences of the United States of America, vol. 109 pp.5346-5351.
Abby S S, Tannier E, Gouy M, Daubin V (2012)
Lateral gene transfer as a support for the tree of life, Proceedings of the National Academy of Sciences of The United States of America, vol. 109 pp.4962-4967.
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.
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.
Trigui H, Masmoudi S, Brochier-Armanet C, Barani A, Grégori G, Denis M, Dukan S, Maalej S (2011)
Characterization of heterotrophic prokaryote subgroups in the Sfax coastal solar salterns by combining flow cytometry cell sorting and phylogenetic analysis., Extremophiles, vol. 15 pp.347-358.
Slyemi D, Moinier D, Brochier-Armanet C, Bonnefoy V, Johnson D B (2011)
Characteristics of a phylogenetically ambiguous arsenic-oxidizing Thiomonas sp. Thiomonas arsenitoxydans strain 3As(T) sp. nov., Archives of Microbiology, vol. 193 pp.439-449.
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Picard F, Perrière G (2011)
Bioinformatics developments for NGS data analysis at PRABI, EMBnet.journal, vol. 17 pp.12-12.
Bergeron M, Dauwalder O, Gouy M, Freydiere A-M, Bes M, Meugnier H, Benito Y, Etienne J, Lina G, Vandenesch F, Boisset S (2011)
Species identification of staphylococci by amplification and sequencing of the tuf gene compared to the gap gene and by matrix-assisted laser desorption ionization time-of-flight mass spectrometry, European Journal of Clinical Microbiology & Infectious Diseases, vol. 30 pp.343-354.
Trigui H, Masmoudi S, Brochier-Armanet C, Maalej S, Dukan S (2011)
Survival of extremely and moderately halophilic isolates of Tunisian solar salterns after UV-B or oxidative stress, Canadian Journal of Microbiology, vol. 57 pp.923-33.
Whitney K D, Boussau B, Baack J E, Garland T Jr (2011)
Drift and Genome Complexity Revisited, PLoS Genetics, vol. 7 pp.e1002092-e1002092.
Sertier AS (2011)
L’évolution modulaire des protéines : un point de vue phylogénétique .
Rouxel T, Grandaubert J, Hane JK, Hoede C, Van de Wouw AP, Couloux A, Dominguez V, Antouhard V, Bally P, Bourras S, Cozijnsen AJ, Ciuffetti LM, Degrave A, Dilmaghani A, Duret L, Fudal I, Goodwin SB, Gout L, Glaser N, Linglin J, GH Keman, Lapalu N, Lawrence CB, May K, Meyer M, Ollivier B, Poulain J, Schoch CL, Simon A, Spatafora JW, Stachoviak A, Turgeon BG, Tyler BM, Vincent D, Weissenbach J, Amselem J, Quesneville H, Oliver RP, Wincker P, Balesdent MH, Howlett BJ (2011)
Effector diversification with in compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations, Nature communications, vol. 2 pp.1-10.
Trigui H, Masmoudi S, Brochier-Armanet C, Maalej S, Dukan S (2011)
Characterization of Halorubrum sfaxense sp. nov. a New Halophilic Archaeon Isolated from the Solar Saltern of Sfax in Tunisia, International Journal of Microbiology, vol. 2011 pp.240191-240191.
Tannier E (2011)
HDR - Evolution combinatoire Algorithmique des chromosomes .
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.
Eme L, Trilles A, Moreira D, Brochier-Armanet C (2011)
The phylogenomic analysis of the anaphase promoting complex and its targets points to complex and modern-like control of the cell cycle in the last common ancestor of eukaryotes, BMC Evolutionary Biology, vol. 11 pp.923-33.
Luciano J, Agrebi R, Le Gall AV, Wartel M, Fiegna F, Ducret A, Brochier-Armanet C, Mignot T (2011)
Emergence and Modular Evolution of a Novel Motility Machinery in Bacteria, PLoS Genetics, vol. 7 pp.e1002268-e1002268.
Gribaldo S, Forterre P, Brochier-Armanet C (2011)
Archaea and the tree of life, Research in microbiology, vol. 162 pp.1-4.
Durand E, Alphonse S, Brochier-Armanet C, Ball G, Douzi B, Filloux A, Bernard C, Voulhoux R (2011)
The Assembly Mode of the Pseudopilus: a hallmark to distinguish a novel secretion system subtype, Journal of Biological Chemistry, vol. 286 pp.24407-24416.
Leyssene D, Gardes S, Vilquin P, Flandrois JP, Carret G, Lamy B (2011)
Species-driven interpretation guidelines in case of a single-sampling strategy for blood culture, European Journal of Clinical Microbiology & Infectious Diseases, vol. 30 pp.1537-1541.
Chureau C, Chantalat S, Romito A, Galvani A, Duret L, Avner P, Rougeulle C (2011)
Ftx is a non-coding RNA which affects Xist expression and chromatin structure within the X-inactivation center region, Human Molecular Genetics, vol. 20 pp.705-718.
Gavranovic H, Chauve C, Salse J, Tannier E (2011)
Mapping ancestral genomes with massive gene loss: A matrix sandwich problem, Bioinformatics, vol. 27 pp.i257-i265.
Le Fourn C, Brasseur G, Brochier-Armanet C, Pieulle L, Brioukhanov A, Ollivier B, Dolla A (2011)
An oxygen reduction chain in the hyperthermophilic anaerobe Thermotoga maritima highlights horizontal gene transfer between Thermococcales and Thermotogales, Environmental Microbiology, vol. 13 pp.2132-45.
Miele V, Penel S, Duret L (2011)
Ultra-fast sequence clustering from similarity networks with SiLiX, BMC Bioinformatics, vol. 12 pp.116-116.
Bigot T, Daubin V, Perrière G (2011)
Tpms: a Tree Pattern-matching Utility for Querying Gene Trees Collections, Journées Ouvertes Biologie Informatique Mathématiques (JOBIM), pp.111-112.
Bailly-Bechet M, Benecke A, Hardt WD, Lanza V, Sturm A, Zecchina R (2011)
An externally modulated noise-driven switch for the regulation of SPI1 in Salmonella enterica serovar Typhimurium, Journal of Mathematical Biology, vol. 63 pp.637-662.
Campan-Fournier A, Perfus-Barbeoch L, Rosso MN, Arguel MJ, Da Silva C, Vens C, Marteu N, Labadie K, Artiguenave F, Abad P, Danchin EG (2011)
Identification of Putative Parasitism Genes in Plant-Parasitic Nematodes - In silico Screening of Whole Genomes and Transcriptomes, Journées Ouvertes en Biologie Informatique et Mathématiques (JOBIM), pp.1-8.
Arguel MJ, Campan-Fournier A, Perfus-Barbeoch L, Danchin EG, Rosso MN, Da Silva C, Labadie K, Marteu N, Artiguenave F, Abad P (2011)
Identification of plant-parasitism genes in nematodes in silico screening and in vivo validation in Meloidogyne incognita., Communications in agricultural and applied biological sciences, vol. 76 pp.409-412.
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.
Denoeud F, Roussel, Noel B, Wawrzyniak I, Da Silva C, Diogon M, Viscogliosi E, Brochier-Armanet C, Couloux A, Poulain J, Segurens B, Anthouard V, Texier C, Blot N, Poirier P, Choo Ng G, Tan K S W, Artiguenave F, Jaillon O, Aury J-M, Delbac F, Wincker P, Vivarès C P, El Alaoui H (2011)
Genome sequence of the stramenopile Blastocystis a human anaerobic parasite, Genome Biology, vol. 12 pp.R29-R29.
Marais G, Forrest A, Kamau E, Kafer J, Daubin V, Charlesworth D (2011)
Multiple Nuclear Gene Phylogenetic Analysis of the Evolution of Dioecy and Sex Chromosomes in the Genus Silene, PLoS One, vol. 6 pp.e21915-e21915.
Cusack BP, Arndt PF, Duret L, Roest Crollius H (2011)
Preventing Dangerous Nonsense: Selection for Robustness to Transcriptional Error in Human Genes, PLoS Genetics, vol. 7 pp.e1002276-e1002276.
Brochier-Armanet C, Forterre P, Gribaldo S (2011)
Phylogeny and Evolution of the Archaea: one Hundred Genomes Later, Current opinion in microbiology, vol. 14 pp.274-281.
Auxilien S, Rasmussen A, Rose S, Brochier-Armanet C, Husson C, Fourmy D, Grosjean H, Douthwaite S (2011)
Specificity shifts in the rRNA and tRNA nucleotide targets of archaeal and bacterial m5U methyltransferases, RNA, vol. 17 pp.45-53.
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.
Boileau C, Eme L, Brochier-Armanet C, Janicki A, Zhang C-C, Latifi A (2011)
A eukaryotic-like sulfiredoxin involved in oxidative stress responses and in the reduction of the sulfinic form of 2 Cys-peroxiredoxin in the cyanobacterium Anabaena PCC 7120, New phytologist, vol. 191 pp.1108-1118.
Boussau B, Brown J M, Fujita M K (2011)
Nonadaptive evolution of mitochondrial genome size, Evolution, vol. 65 pp.2706-2711.
de Vienne D M, Aguileta G, Ollier S (2011)
Euclidean Nature of Phylogenetic Distance Matrices, Systematic Biology, vol. 60 pp.826-832.
Pompeo F, Luciano J, Brochier-Armanet C, Galinier A (2011)
The GTPase Function of YvcJ and Its Subcellular Relocalization Are Dependent on Growth Conditions in Bacillus subtilis, Journal of Molecular Microbiology and Biotechnology, vol. 20 pp.156-167.
Lartillot N, Poujol R (2011)
A phylogenetic model for investigating correlated evolution of substitution rates and continuous phenotypic characters, Molecular biology and evolution, vol. 28 pp.729-44.
Bailly-Bechet M, Borgs C, Braunstein A, Chayes J, Dagkessamanskaia A, François JM, Zecchina R (2011)
Finding undetected protein associations in cell signaling by belief propagation, Proceedings of The National Academy of Sciences of The United States of America, vol. 108 pp.882-887.
Ben Hania W, Ghodbane R, Postec A, Brochier-Armanet C, Hamdi M, Fardeau M-L, Ollivier B (2011)
Cultivation of the first mesophilic representative ("mesotoga") within the order Thermotogales, Systematic and Applied Microbiology, vol. 34 pp.581-585.
Desmond E, Brochier-Armanet C, Forterre P, Gribaldo S (2011)
On the last common ancestor and early evolution of eukaryotes: Reconstructing the history of mitochondrial ribosomes, Research in Microbiology, vol. 162 pp.53-70.
Ouangraoua A, Tannier E, Chauve C (2011)
Reconstructing the architecture of the ancestral amniote genome, Bioinformatics, vol. 27 pp.2664-2671.
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.
Haned H, Pène L, Lobry JR, Dufour A-B, Pontier D (2011)
Estimating the Number of Contributors to Forensic DNA Mixtures: Does Maximum Likelihood Perform Better Than Maximum Allele Count?, Journal of Forensic Sciences, vol. 56 pp.23-28.
Heinrich-Salmeron A, Cordi A, Brochier-Armanet C, Halter D, Pagnout C, Abbaszadeh-Fard E, Montaut D, Seby F, Bertin P N, Bauda P, Arsène-Ploetze F (2011)
Unsuspected Diversity of Arsenite-Oxidizing Bacteria Revealed by a Widespread Distribution of the aoxB Gene in Prokaryotes, Applied and Environmental Microbiology, vol. 77 pp.4685-92.
Brochier-Armanet C, Deschamps P, Lopez-Garcia P, Zivanovic Y, Rodriguez-Valera F, Moreira D (2011)
Complete-fosmid and fosmid-end sequences reveal frequent horizontal gene transfers in marine uncultured planktonic Thaumarchaeota and Euryarchaeota, ISME, vol. 5 pp.1291-302.
Doyon J-P, Ranwez V, Daubin V, Berry V (2011)
Models algorithms and programs for phylogeny reconciliation, Briefings in Bioinformatics, vol. 12 pp.392-400.
Popa A (2011)
The evolution of recombintion and genomic structures: a modeling approach .
Coumes-Florens S, Brochier-Armanet C, Guiseppi A, Denizot F, Foglino M (2011)
A New Highly Conserved Antibiotic Sensing/Resistance Pathway in Firmicutes Involves an ABC Transporter Interplaying with a Signal Transduction System, PLoS one, vol. 6 pp.e15951-e15951.
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Paramecium tetraurelia: The Renaissance of an Early Unicellular Model, Emerging Model Organisms, vol. 2010 pp.1-55.
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The Relationship among Gene Expression the Evolution of Gene Dosage and the Rate of Protein Evolution, PLoS Genetics, vol. 6 pp.e1000944-e1000944.
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Arnaiz O, Gout J-F, Betermier M, Bouhouche K, Cohen J, Duret L, Kapusta A, Meyer E, Sperling L (2010)
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The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse?, Nature Rewiews Microbiology, vol. 8 pp.743-752.
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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.
Abby S, Tannier E, Gouy M, Daubin V (2010)
Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests, BMC Bioinformatics, vol. 11 pp.324-324.
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Spang A, Hatzenpichler R, Brochier-Armanet C, Rattei T, Tischler P, Spieck E, Streit W, Stahl D A, Wagner M, Schleper C (2010)
Distinct gene set in two different lineages of ammoniaoxidizing archaea supports the phylum Thaumarchaeota, Trends in Microbiology, vol. 18 pp.331-340.
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Proposals for classification methods dedicated to biological data, International Journal of Biomedical Engineering and Technology, vol. 3(1) pp.4-21.
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Abrouk M, Murat F, Pont C, Messing J, Jackson S, Faraut T, Tannier E, Plomion C, Cooke R, Feuillet C, Salse J (2010)
Palaeogenomics of plants: syntenybased modelling of extinct ancestors, Trends in Plant Science, vol. 15 pp.479-487.
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SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building, Molecular Biology and Evolution, vol. 27 pp.221-224.
Miklos I, Tannier E (2010)
Bayesian sampling of genomic rearrangement scenarios via double cut and join, Bioinformatics, vol. 26 pp.3012-3019.
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Le génome aux ordres des mathématiciens, La Recherche, vol. 439 pp.54-56.
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Biosynthesis of wyosine derivatives in tRNA: an ancient and highly diverse pathway in Archaea, Molecular Biology and Evolution, vol. 27 pp.2062-77.
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Evolution Moléculaire
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Salacha R, Kovacic F, Brochier-Armanet C, Wilhelm S, Tommassen J, Filloux A, Voulhoux R, Bleves S (2010)
The Pseudomonas aeruginosa patatin-like protein PlpD is the archetype of a novel Type V secretion system, Environmental Microbiology, vol. 12 pp.1498-512.
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Testing the recent theories for the origin of the hermaphrodite flower by comparison of the transcriptomes of gymnosperms and angiosperms, BMC Evolutionary Biology, vol. 10 pp.1-7.
Baldazzi V, Ropers D, Markowicz Y, Kahn D, Geiselmann J, de Jong H (2010)
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Yeast Ancestral Genome Reconstructions: The Possibilities of Computational Methods II, Journal of Computational Biology, vol. 17(9) pp.1097-1112.
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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.
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Billy F, Ribba B, Saut O, Morre-Trouilhet H, Colin T, Bresch D, Boissel J-P, Grenier E, Flandrois J-P (2009)
A pharmacologically based multiscale mathematical model of angiogenesis and its use in investigating the efficacy of a new cancer treatment strategy, Journal of Theoretical Biology, vol. 260 pp.545-562.
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Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes, Annual Review of Genomics and Human Genetics, vol. 10 pp.285-311.
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Iron-sulfur (Fe/S) protein biogenesis: phylogenomic and genetic studies of A-type carriers, PLoS Genetics, vol. 5 pp.e1000497-e1000497.
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Chasing information to search in random environments, Journal of physics A: Mathematical and Theoretical, vol. 42(43) pp.1-14.
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Les singularités du génome de la paramécie : un bon révélateur des mécanismes évolutifs à l`oeuvre chez les êtres vivants .
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The multiple evolutionary histories of dioxygen reductases: implications for the origin and evolution of aerobic respiration, Molecular Biology and Evolution, vol. 26 pp.285-97.
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A korarchaeal genome reveals insights into the evolution of the Archaea, Proc Natl Acad Sci USA, vol. 105 pp.8102-7.
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Prédiction de synténies dans le génome ancestral des amniotes, Actes des Journée Ouvertes de Biologie Informatique et Mathématiques JOBIM 2008, pp.141-148.
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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.
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A seven-gene multilocus genus-wide approach to the phylogeny of mycobacteria using supertrees, International Journal of Systematic and Evolutionary Microbiology, vol. 58(part 6) pp.1432-1441.
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Giant viruses giant chimeras: The multiple evolutionary histories of Mimivirus genes, BMC Evol Biol, vol. 8 pp.259-287.
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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.
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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.
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Warm-blooded isochore structure in Nile crocodile and turtle, Molecular Biology and Evolution, vol. 16 pp.1521-1527.
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Physical mapping of an origin of bidirectional replication at the centre of the Borrelia burgdorferi linear chromosome, Molecular Microbiology, vol. 32 pp.437-445.
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Human and nematode orthologs--lessons from the analysis of 1800 human genes and the proteome of Caenorhabditis elegans, Gene, vol. 238 pp.163-170.
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A model describing the relationship between regrowth lag time and mild temperature increase for Listeria monocytogenes, International Journal of Food Microbiology, vol. 46 pp.251-261.
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Characterization of Unexpected Growth of Escherichia coli O157:H7 by Modeling, Applied and environmental microbiology, vol. 65 pp.5322-5327.
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Recent improvements of the ProDom database of protein domain families., Nucleic Acids Research, vol. 27 pp.263-267.
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Whole genome protein domain analysis using a new method for domain clustering, Journal of Computational Chemistry, vol. 23 pp.333-340.
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Molecular characterization and placental expression of HERV-W a new human endogenous retrovirus family, Journal of Virology, vol. 73 pp.1175-1185.
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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.
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Isochore evolution in mammals: a human-like ancestral structure, Genetics, vol. 150 pp.1577-1584.
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New insulin-like proteins with atypical disulfide bond pattern characterized in Caenorhabditis elegans by comparative sequence analysis and homology modeling, Genome Research, vol. 8 pp.348-353.
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Phylogenetic analysis and genome size of Ostreococcus tauri (Chlorophyta Prasinophyceae), Journal of Phycology, vol. 34 pp.844-849.
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Model of the influence of time and mild temperature on Listeria monocytogenes nonlinear survival curves, International Journal of Food Microbiology, vol. 40 pp.185-195.
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Cloning and characterization of a gene encoding a novel immunodominant antigen of Trypanosoma cruzi, Molecular and Biochemical Parasitology, vol. 87 pp.193-204.
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Searching for regulatory elements in human noncoding sequences, Current Opinion in Structural Biology, vol. 7 pp.399-406.
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Convenient Model To Describe the Combined Effects of Temperature and pH on Microbial Growth, Applied and Environmental Microbiology, vol. 61 pp.610-616.
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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.
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Molecular phylogeny of the symbiotic actinomycetes of the genus Frankia matches host-plant infection processes, Molecular Biology and Evolution, vol. 10 pp.1303-1316.
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The regulatory strength: how to be precise about regulation and homeostasis, Acta Biotheoretica, vol. 41 pp.85-96.
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An unexpected correlation between cardinal temperatures of microbial growth highlighted by a new model, Journal of Theoretical Biology, vol. 162 pp.447-463.
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Insect muscle actins differ distinctly from invertebrate and vertebrate cytoplasmic actins, Journal of Molecular Evolution, vol. 34 pp.406-415.
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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.
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, Bernardi G (1988)
The compositional distribution of coding sequences and DNA molecules in humans and murids, Journal of Molecular Evolution, vol. 27 pp.311-320.
Flandrois J-P, Fardel G, Carret G (1988)
Early stages of in vitro killing curve of LY146032 and vancomycin for Staphylococcus aureus, Antimicrobial Agents and Chemotherapy, vol. 32 pp.454-457.
Flandrois J-P, Carret G, Fardel G (1988)
A mathematical study of the mortality curve of Escherichia coli exposed to aminoglycosides, Pathologie Biologie (Paris), vol. 36 pp.446-451.
Bernardi G, Mouchiroud D, Gautier C (1988)
Compositional patterns in vertebrate genomes: conservation and change in evolution, Journal of Molecular Evolution, vol. 28 pp.7-18.
Mouchiroud D, Gautier C (1988)
High codon-usage changes in mammalian genes, Molecular Biology and Evolution, vol. 5 pp.192-194.
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.
Mouchiroud D, Fichant G, Bernardi G (1987)
Compositional compartmentalization and gene composition in the genome of vertebrates, Journal of Molecular Evolution, vol. 26 pp.198-204.
Higgins DG, Gouy M (1987)
Interfacing similarity search software with the sequence retrieval system ACNUC, Bioinformatics, vol. 3 pp.239-241.
Mouchiroud D (1986)
[Relationship between base composition in non-coding DNA of genes and codon composition], Comptes Rendus de l`Académie des Sciences - Séries III - Sciences de la Vie, vol. 303 pp.743-748.
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.
Carret G, Emonard H, Fardel G, Druguet M, Herbage D, Flandrois J-P (1985)
Gelatin and collagen binding to Staphylococcus aureus strains, Annales de l`Institut Pasteur-Microbiologie, vol. 136A pp.241-245.
Gouy M, Gautier C, Milleret F (1985)
System analysis and nucleic acid sequence banks, Biochimie, vol. 67 pp.433-436.
Savatier P, Trabuchet G, Faure C, Chebloune Y, Gouy M, Verdier G, Nigon V M (1985)
Evolution of the primate beta-globin gene region. High rate of variation in CpG dinucleotides and in short repeated sequences between man and chimpanzee, Journal of Molecular Biology, vol. 182 pp.21-29.
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.
Gautier C, Gouy M, Louail S (1985)
Non-parametric statistics for nucleic acid sequence study, Biochimie, vol. 67 pp.449-453.
Eloy C, Fardel G, Flandrois J-P (1985)
Fast protein liquid chromatography for the isolation of Clostridium perfringens type A alpha-toxin, Journal of Chromatography, vol. 321 pp.235-239.
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.
Blanquet S, Dessen P, Kahn D (1984)
Properties and specificity of methionyl-tRNAfMet formyltransferase from Escherichia coli, Methods in Enzymology, vol. 106 pp.141-152.
Papanicolaou C, Gouy M, Ninio J (1984)
An energy model that predicts the correct folding of both the tRNA and the 5S RNA molecules, Nucleic Acids Research, vol. 12 pp.31-44.
Gouy M, Milleret F, Mugnier C, Jacobzone M, Gautier C (1984)
ACNUC: a nucleic acid sequence data base and analysis system, Nucleic Acids Research, vol. 12 pp.121-127.
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.
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.
![]() | Gautier C, Gouy M, Jacobzone M, Grantham R (1981) Nucleic acid sequences handbook, Praeger, 1981 |
Kahn D, Fromant M, Fayat G, Dessen P, Blanquet S (1980)
Methionyl-transfer-RNA transformylase from Escherichia coli. Purification and characterisation, European Journal of Biochemistry, vol. 105 pp.489-497.
Dixon R, Eady RR, Espin G, Hill S, Iaccarino M, Kahn D, Merrick M (1980)
Analysis of regulation of Klebsiella pneumoniae nitrogen fixation (nif) gene cluster with gene fusions, Nature, vol. 286 pp.128-132.
Gouy M, Grantham R (1980)
Polypeptide elongation and tRNA cycling in Escherichia coli: a dynamic approach, FEBS Letters, vol. 115 pp.151-155.
Grantham R, Gautier C, Gouy M, Mercier R, Pave A (1980)
Codon catalog usage and the genome hypothesis, Nucleic Acids Research, vol. 8 pp.R49-R62.
Grantham R, Gautier C, Gouy M (1980)
Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type, Nucleic Acids Research, vol. 8 pp.1893-1912.
Fayat G, Fromant M, Kahn D, Blanquet S (1977)
Affinity chromatography on agarose-hexyl-adenosine-5`-phosphate of methionyl-tRNA synthetase from Escherichia coli. Application of the couplings between the methionine and ATP sites, European Journal of Biochemistry, vol. 78 pp.333-336.