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Genoscope

Publications 2016

Publié le 12 avril 2017

  
A single three-dimensional chromatin compartment in amphioxus indicates a stepwise evolution of vertebrate Hox bimodal regulation
Acemel RD, Tena JJ, Irastorza-Azcarate I, Marletaz F, Gomez-Marin C, de la Calle-Mustienes E, Bertrand S, Diaz SG, Aldea D, Aury JM, Mangenot S, Holland PWH, Devos DP, Maeso I, Escriva H, Gomez-Skarmeta JL
In planta comparative transcriptomics of host-adapted strains of Ralstonia solanacearum
Ailloud F, Lowe TM, Robene I, Cruveiller S, Allen C, Prior P
Molecular phylogenetics of Sarcolaenaceae (Malvales), Madagascar's largest endemic plant family
Aubriot X, Soulebeau A, Haevermans T, Schatz GE, Cruaud C, Lowry PP
Habitat and taxon as driving forces of carbohydrate catabolism in marine heterotrophic bacteria: example of the model algae-associated bacterium Zobellia galactanivorans Dsij(T)
Barbeyron T, Thomas F, Barbe V, Teeling H, Schenowitz C, Dossat C, Goesmann A, Leblanc C, Glockner FO, Czjzek M, Amann R, Michel G
The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis
Belda E, van Heck RGA, Lopez-Sanchez MJ, Cruveiller S, Barbe V, Fraser C, Klenk HP, Petersen J, Morgat A, Nikel PI, Vallenet D, Rouy Z, Sekowska A, dos Santos VAPM, de Lorenzo V, Danchin A, Medigue C
Polysaccharide utilisation loci of Bacteroidetes from two contrasting open ocean sites in the North Atlantic
Bennke CM, Kruger K, Kappelmann L, Huang SX, Gobet A, Schuler M, Barbe VE, Fuchs BM, Michel G, Teeling H, Amann RI
Global repositioning of transcription start sites in a plant-fermenting bacterium
Boutard M, Ettwiller L, Cerisy T, Alberti A, Labadie K, Salanoubat M, Schildkraut I, Tolonen AC
Reference Transcriptomes and Detection of Duplicated Copies in Hexaploid and Allododecaploid Spartina Species (Poaceae)
Boutte J, de Carvalho JF, Rousseau-Gueutin M, Poulain J, Da Silva C, Wincker P, Ainouche M, Salmon A
Draft Genome Sequence of Campylobacter jejuni Bf, an Atypical Strain Able To Grow under Aerobiosis.
Bronnec V, Haddad N, Cruveiller S, Hernould M, Tresse O, Zagorec M
Adhesion, Biofilm Formation, and Genomic Features of Campylobacter jejuni Bf, an Atypical Strain Able to Grow under Aerobic Conditions
Bronnec V, Turonova H, Bouju A, Cruveiller S, Rodrigues R, Demnerova K, Tresse O, Haddad N, Zagorec M
Microbial Degradation of a Recalcitrant Pesticide: Chlordecone
Chaussonnerie S, Saaidi PL, Ugarte E, Barbance A, Fossey A, Barbe V, Gyapay G, Bruls T, Chevalier M, Couturat L, Fouteau S, Muselet D, Pateau E, Cohen GN, Fonknechten N, Weissenbach J, Le Paslier D
Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton
Cornejo-Castillo FM, Cabello AM, Salazar G, Sanchez-Baracaldo P, Lima-Mendez G, Hingamp P, Alberti A, Sunagawa S, Bork P, de Vargas C, Raes J, Bowler C, Wincker P, Zehr JP, Gasol JM, Massana R, Acinas SG
Permanent draft genome sequence of the probiotic strain Propionibacterium freudenreichii CIRM-BIA 129 (ITG P20)
Falentin H, Deutsch SM, Loux V, Hammani A, Buratti J, Parayre S, Chuat V, Barbe V, Aury JM, Jan G, Le Loir Y
Delineating ecologically significant taxonomic units from global patterns of marine picocyanobacteria
Farrant GK, Dore H, Cornejo-Castillo FM, Partensky F, Ratin M, Ostrowski M, Pitt FD, Wincker P, Scanlan DJ, Iudicone D, Acinas SG, Garczarek L
Extreme Diversity of Diplonemid Eukaryotes in the Ocean
Flegontova O, Flegontov P, Malviya S, Audic S, Wincker P, de Vargas C, Bowler C, Lukes J, Horak A
Complete Genome Sequence of Bacillus methylotrophicus Strain B25, a Potential Plant Growth-Promoting Rhizobacterium.
Gerbore J, Brutel A, Lemainque A, Mairey B, Medigue C, Vallenet D, Lefort F, Grizard D
A scalable assembly-free variable selection algorithm for biomarker discovery from metagenomes
Gkanogiannis A, Gazut S, Salanoubat M, Kanj S, Bruls T
Plankton networks driving carbon export in the oligotrophic ocean.
Guidi L, Chaffron S, Bittner L, Eveillard D, Larhlimi A, Roux S, Darzi Y, Audic S, Berline L, Brum J R, Coelho L P, Espinoza J C, Malviya S, Sunagawa S, Dimier C, Kandels-Lewis S, Picheral M, Poulain J, Searson S, Stemmann L, Not F, Hingamp P, Speich S, Follows M, Karp-Boss L, Boss E, Ogata H, Pesant S, Weissenbach J, Wincker P, Acinas S G, Bork P, de Vargas C, Iudicone D, Sullivan M B, Raes J, Karsenti E, Bowler C, Gorsky G
Continuous colorimetric screening assays for the detection of specific l- or d-alpha-amino acid transaminases in enzyme libraries
Heuson E, Petit JL, Debard A, Job A, Charmantray F, de Berardinis V, Gefflaut T
Identification of an Alternative Splicing Product of the Otx2 Gene Expressed in the Neural Retina and Retinal Pigmented Epithelial Cells
Kole C, Berdugo N, Da Silva C, Ait-Ali N, Millet-Puel G, Pagan D, Blond F, Poidevin L, Ripp R, Fontaine V, Wincker P, Zack DJ, Sahel JA, Poch O, Leveillard T
Global patterns of pelagic dinoflagellate diversity across protist size classes unveiled by metabarcoding
Le Bescot N, Mahe F, Audic S, Dimier C, Garet MJ, Poulain J, Wincker P, de Vargas C, Siano R
Implication of the suberin pathway in adaptation to waterlogging and hypertrophied lenticels formation in pedunculate oak (Quercus robur L.)
Le Provost G, Lesur I, Lalanne C, Da Silva C, Labadie K, Aury JM, Leple JC, Plomion C
Comparative Genomic Analysis of Drechmeria coniospora Reveals Core and Specific Genetic Requirements for Fungal Endoparasitism of Nematodes
Lebrigand K, He LD, Thakur N, Arguel MJ, Polanowska J, Henrissat B, Record E, Magdelenat G, Barbe V, Raffaele S, Barbry P, Ewbank JJ
Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages
Lescot M, Hingamp P, Kojima KK, Villar E, Romac S, Veluchamy A, Boccara M, Jaillon O, Iudicone D, Bowler C, Wincker P, Claverie JM, Ogata H
MaGuS: a tool for quality assessment and scaffolding of genome assemblies with Whole Genome Profiling (TM) Data
Madoui MA, Dossat C, d'Agata L, van Oeveren J, van der Vossen E, Aury JM
Insights into global diatom distribution and diversity in the world's ocean
Malviya S, Scalco E, Audic S, Vincenta F, Veluchamy A, Poulain J, Wincker P, Iudicone D, de Vargas C, Bittner L, Zingone A, Bowler C
Comparative venomics of Psyttalia lounsburyi and P-concolor, two olive fruit fly parasitoids: a hypothetical role for a GH1 beta-glucosidase
Mathe-Hubert H, Colinet D, Deleury E, Belghazi M, Ravallec M, Poulain J, Dossat C, Poirie M, Gatti JL
Asymmetric reductive amination by a wild-type amine dehydrogenase from the thermophilic bacteria Petrotoga mobilis
Mayol O, David S, Darii E, Debard A, Mariage A, Pellouin V, Petit JL, Salanoubat M, de Berardinis V, Zaparucha A, Vergne-Vaxelaire C
The Arabidopsis hnRNP-Q Protein LIF2 and the PRC1 Subunit LHP1 Function in Concert to Regulate the Transcription of Stress-Responsive Genes
Molitor AM, Latrasse D, Zytnicki M, Andrey P, Houba-Herin N, Hachet M, Battail C, Del Prete S, Alberti A, Quesneville E, Gaudin V
Dual RNA-seq reveals Meloidogyne graminicola transcriptome and candidate effectors during the interaction with rice plants
Petitot AS, Dereeper A, Agbessi M, Da Silva C, Guy J, Ardisson M, Fernandez D
Parasitic wasps have domesticated viruses repeatedly during their evolution
Pichon A, Bezier A, Barbe V, Drezen JM, Volkoff AN
Contrasting effects of historical contingency on phenotypic and genomic trajectories during a two-step evolution experiment with bacteria
Plucain J, Suau A, Cruveiller S, Medigue C, Schneider D, Le Gac M
RNase J depletion leads to massive changes in mRNA abundance in Helicobacter pylori
Redko Y, Galtier E, Arnion H, Darfeuille F, Sismeiro O, Coppee JY, Medigue C, Weiman M, Cruveiller S, De Reuse H
Toolbox for Protein Structure Prediction.
Roche D B, McGuffin L J
Understanding the evolution of holoparasitic plants: the complete plastid genome of the holoparasite Cytinus hypocistis (Cytinaceae)
Roquet C, Coissac E, Cruaud C, Boleda M, Boyer F, Alberti A, Gielly L, Taberlet P, Thuiller W, Van Es J, Lavergne S
Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses
Roux S, Brum JR, Dutilh BE, Sunagawa S, Duhaime MB, Loy A, Poulos BT, Solonenko N, Lara E, Poulain J, Pesant S, Kandels-Lewis S, Dimier C, Picheral M, Searson S, Cruaud C, Alberti A, Duarte CM, Gasol JM, Vaque D, Bork P, Acinas SG, Wincker P, Sullivan MB
Osmotic stress response in Acinetobacter baylyi: identification of a glycine-betaine biosynthesis pathway and regulation of osmoadaptive choline uptake and glycine-betaine synthesis through a choline-responsive BetI repressor
Scholz A, Stahl J, de Berardinis V, Muller V, Averhoff B
Tempo and mode of genome evolution in a 50,000-generation experiment
Tenaillon O, Barrick JE, Ribeck N, Deatherage DE, Blanchard JL, Dasgupta A, Wu GC, Wielgoss S, Cruveiller S, Medigue C, Schneider D, Lenski RE
Copper homeostasis at the host vibrio interface: lessons from intracellular vibrio transcriptomics
Vanhove AS, Rubio TP, Nguyen AN, Lemire A, Roche D, Nicod J, Vergnes A, Poirier AC, Disconzi E, Bachere E, Le Roux F, Jacq A, Charriere GM, Destoumieux-Garzon D
Survey of the green picoalga Bathycoccus genomes in the global ocean
Vannier T, Leconte J, Seeleuthner Y, Mondy S, Pelletier E, Aury JM, de Vargas C, Sieracki M, Iudicone D, Vaulot D, Wincker P, Jaillon O
Genetic Dissection of the Type VI Secretion System in Acinetobacter and Identification of a Novel Peptidoglycan Hydrolase, TagX, Required for Its Biogenesis
Weber BS, Hennon SW, Wright MS, Scott NE, de Berardinis V, Foster LJ, Ayala JA, Adams MD, Feldman MF
The rise of genomics
Weissenbach J
Microbiotes and metagenomics
Weissenbach J, Sghir A
Genomic and physiological analysis reveals versatile metabolic capacity of deep-sea Photobacterium phosphoreum ANT-2200
Zhang SD, Santini CL, Zhang WJ, Barbe V, Mangenot S, Guyomar C, Garel M, Chen HT, Li XG, Yin QJ, Zhao Y, Armengaud J, Gaillard JC, Martini S, Pradel N, Vidaud C, Alberto F, Medigue C, Tamburini C, Wu LF