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Publications 2016

Published on 13 April 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 and Gomez-Skarmeta JL
In planta comparative transcriptomics of host-adapted strains of Ralstonia solanacearum
Ailloud F, Lowe TM, Robene I, Cruveiller S, Allen C and Prior P
The complete mitochondrial genome of Acanthastrea maxima (Cnidaria, Scleractinia, Lobophylliidae)
Arrigoni R, Vacherie B, Benzoni F and Barbe V
A new sequence data set of SSU rRNA gene for Scleractinia and its phylogenetic and ecological applications
Arrigoni R, Vacherie B, Benzoni F, Stefani F, Karsenti E, Jaillon O, Not F, Nunes F, Payri C, Wincker P and Barbe V
Molecular phylogenetics of Sarcolaenaceae (Malvales), Madagascar's largest endemic plant family
Aubriot X, Soulebeau A, Haevermans T, Schatz GE, Cruaud C and 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 and 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 V, de Lorenzo V, Danchin A and 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 and Amann RI
Comparative Genomics between Two Xenorhabdus bovienii Strains Highlights Differential Evolutionary Scenarios within an Entomopathogenic Bacterial Species
Bisch G, Ogier JC, Medigue C, Rouy Z, Vincent S, Tailliez P, Givaudan A and Gaudriault S
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 and 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 and 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 and 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 and 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 and 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 and 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 and 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 and 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 and Horak A
Benthic protists: the under-charted majority
Forster D, Dunthorn M, Mahe F, Dolan JR, Audic S, Bass D, Bittner L, Boutte C, Christen R, Claverie JM, Decelle J, Edvardsen B, Egge E, Eikrem W, Gobet A, Kooistra W, Logares R, Massana R, Montresor M, Not F, Ogata H, Pawlowski J, Pernice MC, Romac S, Shalchian-Tabrizi K, Simon N, Richards TA, Santini S, Sarno D, Siano R, Vaulot D, Wincker P, Zingone A, de Vargas C and Stoeck T
Microbial community structure associated with the high loading anaerobic codigestion of olive mill and abattoir wastewaters
Gannoun H, Omri I, Chouari R, Khelifi E, Keskes S, Godon JJ, Hamdi M, Sghir A and Bouallagui H
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 and Grizard D
Genome announcements 4 (2), , 2016
A scalable assembly-free variable selection algorithm for biomarker discovery from metagenomes
Gkanogiannis A, Gazut S, Salanoubat M, Kanj S and Bruls T
Complete Genome Sequence of Mycoplasma mycoides subsp. mycoides T1/44, a Vaccine Strain against Contagious Bovine Pleuropneumonia
Gourgues G, Barre A, Beaudoing E, Weber J, Magdelenat G, Barbe V, Schieck E, Jores J, Vashee S, Blanchard A, Lartigue C and Sirand-Pugnet P
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 JR, Coelho LP, Espinoza JCI, 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 SG, Bork P, de Vargas C, Iudicone D, Sullivan MB, Raes J, Karsenti E, Bowler C, Gorsky G and Tara Oceans Consortium C
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 and 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 and 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 and 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 and 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 and 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 and 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 and 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 and Bowler C
"Improvement of the banana ""Musa acuminata"" reference sequence using NGS data and semi-automated bioinformatics methods"
Martin G, Baurens FC, Droc G, Rouard M, Cenci A, Kilian A, Hastie A, Dolezel J, Aury JM, Alberti A, Carreel F and D'Hont A
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 and 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 and 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 and Gaudin V
Back to the Future of Soil Metagenomics
Nesme J, Achouak W, Agathos SN, Bailey M, Baldrian P, Brunel D, Frostegard A, Heulin T, Jansson JK, Jurkevitch E, Kruus KL, Kowalchuk GA, Lagares A, Lappin-Scott HM, Lemanceau P, Le Paslier D, Mandic-Mulec I, Murrell JC, Myrold DD, Nalin R, Nannipieri P, Neufeld JD, O'Gara F, Parnell JJ, Puhler A, Pylro V, Ramos JL, Roesch LFW, Schloter M, Schleper C, Sczyrba A, Sessitsch A, Sjoling S, Sorensen J, Sorensen SJ, Tebbe CC, Topp E, Tsiamis G, van Elsas JD, van Keulen G, Widmer F, Wagner M, Zhang T, Zhang XJ, Zhao LP, Zhu YG, Vogel TM and Simonet P
Frontiers in Microbiology 7 (), 73, 2016
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 and Fernandez D
Parasitic wasps have domesticated viruses repeatedly during their evolution
Pichon A, Bezier A, Barbe V, Drezen JM and Volkoff AN
Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies
Plomion C, Aury JM, Amselem J, Alaeitabar T, Barbe V, Belser C, Berges H, Bodenes C, Boudet N, Boury C, Canaguier A, Couloux A, Da Silva C, Duplessis S, Ehrenmann F, Estrada-Mairey B, Fouteau S, Francillonne N, Gaspin C, Guichard C, Klopp C, Labadie K, Lalanne C, Le Clainche I, Leple JC, Le Provost G, Leroy T, Lesur I, Martin F, Mercier J, Michotey C, Murat F, Salin F, Steinbach D, Faivre-Rampant P, Wincker P, Salse J, Quesneville H and Kremer A
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 and 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 and De Reuse H
Toolbox for Protein Structure Prediction
Roche DB and McGuffin LJ
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 and 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 and Tara Oceans C
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 and 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 and 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 and 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 and 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 and Feldman MF
The rise of genomics
Weissenbach J
Microbiotes and metagenomics
Weissenbach J and 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 and Wu LF