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Publications 2015

Publié le 12 avril 2017

Comparative genomic analysis of Ralstonia solanacearum reveals candidate genes for host specificity
Ailloud F, Lowe T, Cellier G, Roche D, Allen C, Prior P
Non-invasive prenatal testing for trisomy 21 based on analysis of cell-free fetal DNA circulating in the maternal plasma
Alberti A, Salomon LJ, Le Lorc'h M, Couloux A, Bussieres L, Goupil S, Malan V, Pelletier E, Hyon C, Vialard F, Rozenberg P, Bouhanna P, Oury JF, Schmitz T, Romana S, Weissenbach J, Vekemans M, Ville Y
A population genomics insight into the Mediterranean origins of wine yeast domestication
Almeida P, Barbosa R, Zalar P, Imanishi Y, Shimizu K, Turchetti B, Legras JL, Serra M, Dequin S, Couloux A, Guy J, Bensasson D, Goncalves P, Sampaio JP
Transcriptome analyses to investigate symbiotic relationships between marine protists
Balzano S, Corre E, Decelle J, Sierra R, Wincker P, Da Silva C, Poulain J, Pawlowski J, Not F
Isoguanine and 5-Methyl-Isocytosine Bases, In Vitro and In Vivo
Bande O, Abu El Asrar R, Braddick D, Dumbre S, Pezo V, Schepers G, Pinheiro VB, Lescrinier E, Holliger P, Marliere P, Herdewijn P
The Genome of the Nucleopolyhedrosis-Causing Virus from Tipula oleracea Sheds New Light on the Nudiviridae Family
Bezier A, Theze J, Gavory F, Gaillard J, Poulain J, Drezen JM, Herniou EA
Tara Oceans studies plankton at PLANETARY SCALE
Bork P, Bowler C, de Vargas C, Gorsky G, Karsenti E, Wincker P
Patterns and ecological drivers of ocean viral communities
Brum JR, Ignacio-Espinoza JC, Roux S, Doulcier G, Acinas SG, Alberti A, Chaffron S, Cruaud C, de Vargas C, Gasol JM, Gorsky G, Gregory AC, Guidi L, Hingamp P, Iudicone D, Not F, Ogata H, Pesant S, Poulos BT, Schwenck SM, Speich S, Dimier C, Kandels-Lewis S, Picheral M, Searson S, Bork P, Bowler C, Sunagawa S, Wincker P, Karsenti E, Sullivan MB
Community assembly on remote islands: a comparison of Hawaiian and Mascarene spiders
Casquet J, Bourgeois YXC, Cruaud C, Gavory F, Gillespie RG, Thebaud C
Ultra Deep Sequencing of a Baculovirus Population Reveals Widespread Genomic Variations
Chateigner A, Bezier A, Labrousse C, Jiolle D, Barbe V, Herniou EA
Characterizing neutral genomic diversity and selection signatures in indigenous populations of Moroccan goats (Capra hircus) using WGS data.
Chentouf M, Bechchari A, Leempoel K, Alberti A, Engelen S, Chikhi A, Clarke L, Flicek P, Joost S, Taberlet P, Pompanon F, NextGen Consortium
Microbial Analysis and Efficiency of Biofiltration Packing Systems for Hydrogen Sulfide Removal from Wastewater Off Gas
Chouari R, Dardouri W, Sallami F, Ben Rais M, Le Paslier D, Sghir A
Co-occurence of Crenarchaeota, Thermoplasmata and methanogens in anaerobic sludge digesters
Chouari R, Guermazi S, Sghir A
Deep sequencing of amplified Prasinovirus and host green algal genes from an Indian Ocean transect reveals interacting trophic dependencies and new genotypes
Clerissi C, Desdevises Y, Romac S, Audic S, de Vargas C, Acinas SG, Casotti R, Poulain J, Wincker P, Hingamp P, Ogata H, Grimsley N
Towards an universal genome-based DNA barcode-The PhyloAlps project
Coissac E, Taberlet P, Roquet C, Boleda M, Gielly L, Alberti A, Wincker P, Alsos I, Boyer F, Lavergne S
Genome 58 (5), 206-206, 2015
Convergent Evolution of Endosymbiont Differentiation in Dalbergioid and Inverted Repeat-Lacking Clade Legumes Mediated by Nodule-Specific Cysteine-Rich Peptides
Czernic P, Gully D, Cartieaux F, Moulin L, Guefrachi I, Patrel D, Pierre O, Fardoux J, Chaintreuil C, Nguyen P, Gressent F, Da Silva C, Poulain J, Wincker P, Rofidal V, Hem S, Barriere Q, Arrighi JF, Mergaert P, Giraud E
Eukaryotic plankton diversity in the sunlit ocean
de Vargas C, Audic S, Henry N, Decelle J, Mahe F, Logares R, Lara E, Berney C, Le Bescot N, Probert I, Carmichael M, Poulain J, Romac S, Colin S, Aury JM, Bittner L, Chaffron S, Dunthorn M, Engelen S, Flegontova O, Guidi L, Horak A, Jaillon O, Lima-Mendez G, Lukes J, Malviya S, Morard R, Mulot M, Scalco E, Siano R, Vincent F, Zingone A, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Acinas SG, Bork P, Bowler C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Not F, Ogata H, Pesant S, Raes J, Sieracki ME, Speich S, Stemmann L, Sunagawa S, Weissenbach J, Wincker P, Karsenti E
Reconstructing Rare Soil Microbial Genomes using in situ Enrichments and Metagenomics
Delmont TO, Eren AM, Maccario L, Prestat E, Esen O, Pelletier E, LePaslier D, Simonet P, Vogel TM
Mitochondrial DNA Intraspecific Variability in Sergentomyia minuta (Diptera: Psychodidae)
Depaquit J, Hadj-Henni L, Bounamous A, Strutz S, Boussaa S, Morillas-Marquez F, Pesson B, Gallego M, Delecolle JC, Afonso MO, Alves-Pires C, Capela RA, Couloux A, Leger N
Small RNA Deep-Sequencing Analyses Reveal a New Regulator of Virulence in Agrobacterium fabrum C58
Dequivre M, Diel B, Villard C, Sismeiro O, Durot M, Coppee JY, Nesme X, Vial L, Hommais F
Spodoptera frugiperda (Lepidoptera: Noctuidae) host-plant variants: two host strains or two distinct species?
Dumas P, Legeai F, Lemaitre C, Scaon E, Orsucci M, Labadie K, Gimenez S, Clamens AL, Henri H, Vavre F, Aury JM, Fournier P, Kergoat GJ, d'Alencon E
Detecting natural hybridization between two vulnerable Andean pupfishes (Orestias agassizii and O-luteus) representative of the Altiplano endemic fisheries
Esquer-Garrigos Y, Hugueny B, Ibanez C, Zepita C, Koerner K, Lambourdiere J, Couloux A, Gaubert P
16S rRNA and As-Related Functional Diversity: Contrasting Fingerprints in Arsenic-Rich Sediments from an Acid Mine Drainage
Fahy A, Giloteaux L, Bertin P, Le Paslier D, Medigue C, Weissenbach J, Duran R, Lauga B
Thiomonas sp CB2 is able to degrade urea and promote toxic metal precipitation in acid mine drainage waters supplemented with urea
Farasin J, Andres J, Casiot C, Barbe V, Faerber J, Halter D, Heintz D, Koechler S, Lievremont D, Ugan R, Marchal M, Plewniak F, Seby F, Bertin PN, Arsene-Ploetze F
Degeneration of the Nonrecombining Regions in the Mating-Type Chromosomes of the Anther-Smut Fungi
Fontanillas E, Hood ME, Badouin H, Petit E, Barbe V, Gouzy J, de Vienne DM, Aguileta G, Poulain J, Wincker P, Chen ZH, Toh SS, Cuomo CA, Perlin MH, Gladieux P, Giraud T
Towards the Rose Genome Sequence and Its Use in Research and Breeding
Foucher F, Hibrand-Saint Oyant L, Hamama L, Sakr S, Nybom H, Baudino S, Caissard JP, Hokanson SC, Byrne DM, Smulder JMS, Desnoye B, Debener T, Bruneau A, De Riek J, Matsumoto S, Torres A, Millan T, Amaya I, Yamada K, Wincker P, Zamir D, Gouzy J, Sargent D, Bendahmane M, Raymond O, Vergne P, Dubois A, Just J
Adaptation in Toxic Environments: Arsenic Genomic Islands in the Bacterial Genus Thiomonas
Freel KC, Krueger MC, Farasin J, Brochier-Armanet C, Barbe V, Andres J, Cholley PE, Dillies MA, Jagla B, Koechler S, Leva Y, Magdelenat G, Plewniak F, Proux C, Coppee JY, Bertin PN, Heipieper HJ, Arsene-Ploetze F
The complex phylogeography of the Indo-Malayan Alophoixus bulbuls with the description of a putative new ring species complex
Fuchs J, Ericson PGP, Bonillo C, Couloux A, Pasquet E
AAC(3)-XI, a New Aminoglycoside 3-N-Acetyltransferase from Corynebacterium striatum
Galimand M, Fishovitz J, Lambert T, Barbe V, Zajicek J, Mobashery S, Courvalin P
Recurrent Domestication by Lepidoptera of Genes from Their Parasites Mediated by Bracoviruses
Gasmi L, Boulain H, Gauthier J, Hua-Van A, Musset K, Jakubowska AK, Aury JM, Volkoff AN, Huguet E, Herrero S, Drezen JM
Comparative genomics of 43 strains of Xanthomonas citri pv. citri reveals the evolutionary events giving rise to pathotypes with different host ranges
Gordon JL, Lefeuvre P, Escalon A, Barbe V, Cruveiller S, Gagnevin L, Pruvost O
Improving biodiversity assessment of anuran amphibians using DNA barcoding of tadpoles. Case studies from Southeast Asia
Grosjean S, Ohler A, Chuaynkern Y, Cruaud C, Hassanin A
Genome Mining for Innovative Biocatalysts: New Dihydroxyacetone Aldolases for the Chemist's Toolbox
Guerard-Helaine C, de Berardinis V, Besnard-Gonnet M, Darii E, Debacker M, Debard A, Fernandes C, Helaine V, Mariage A, Pellouin V, Perret A, Petit JL, Sancelme M, Lemaire M, Salanoubat M
Arsenic hypertolerance in the protist Euglena mutabilis is mediated by specific transporters and functional integrity maintenance mechanisms
Halter D, Andres J, Plewniak F, Poulain J, Da Silva C, Arsene-Ploetze F, Bertin PN
Straightforward Synthesis of Terminally Phosphorylated L-Sugars via Multienzymatic Cascade Reactions
Helaine V, Mahdi R, Babu GVS, de Berardinis V, Wohlgemuth R, Lemaire M, Guerard-Helaine C
Against All Odds: Trehalose-6-Phosphate Synthase and Trehalase Genes in the Bdelloid Rotifer Adineta vaga Were Acquired by Horizontal Gene Transfer and Are Upregulated during Desiccation
Hespeels B, Li X, Flot JF, Pigneur LM, Malaisse J, Da Silva C, Van Doninck K
Phylogeography and evolutionary history of the Crocidura olivieri complex (Mammalia, Soricomorpha): from a forest origin to broad ecological expansion across Africa
Jacquet F, Denys C, Verheyen E, Bryja J, Hutterer R, Peterhans JCK, Stanley WT, Goodman SM, Couloux A, Colyn M, Nicolas V
Deciphering metatranscriptomic data
Kopylova E, Noé L, Da Silva C, Berthelot JF, Alberti A, Aury JM, Touzet H
Populations, not clones, are the unit of vibrio pathogenesis in naturally infected oysters
Lemire A, Goudenège D, Versigny T, Petton B, Calteau A, Labreuche Y, Le Roux F
The Conserved nhaAR Operon Is Drastically Divergent between B2 and Non-B2 Escherichia coli and Is Involved in Extra-Intestinal Virulence (vol 9, e108738, 2014)
Lescat M, Reibel F, Pintard C, Dion S, Glodt J, Gateu C, Cruveiller S
The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release
Lesur I, Le Provost G, Bento P, Da Silva C, Leple JC, Murat F, Ueno S, Bartholome J, Lalanne C, Ehrenmann F, Noirot C, Burban C, Leger V, Amselem J, Belser C, Quesneville H, Stierschneider M, Fluch S, Feldhahn L, Tarkka M, Herrmann S, Buscot F, Klopp C, Kremer A, Salse J, Aury JM, Plomion C
Characterization of functional communities and metabolic pathways during methanogenesis in wastewater sludge by isotopic and molecular analysis
Limam RD, Grossin-Debattista J, Chouari R, Landoulsi A, Sghir A
Biotechnol. Agron. Soc. 19 (4), 338-345, 2015
Determinants of community structure in the global plankton interactome
Lima-Mendez G, Faust K, Henry N, Decelle J, Colin S, Carcillo F, Chaffron S, Ignacio-Espinosa JC, Roux S, Vincent F, Bittner L, Darzi Y, Wang J, Audic S, Berline L, Bontempi G, Cabello AM, Coppola L, Cornejo-Castillo FM, d'Ovidio F, De Meester L, Ferrera I, Garet-Delmas MJ, Guidi L, Lara E, Pesant S, Royo-Llonch M, Salazar G, Sanchez P, Sebastian M, Souffreau C, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Gorsky G, Not F, Ogata H, Speich S, Stemmann L, Weissenbach J, Wincker P, Acinas SG, Sunagawa S, Bork P, Sullivan MB, Karsenti E, Bowler C, de Vargas C, Raes J
Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of Propionibacterium freudenreichii
Loux V, Mariadassou M, Almeida S, Chiapello H, Hammani A, Buratti J, Gendrault A, Barbe V, Aury JM, Deutsch SM, Parayre S, Madec MN, Chuat V, Jan G, Peterlongo P, Azevedo V, Le Loir Y, Falentin H
Synonymous Genetic Variation in Natural Isolates of Escherichia coli Does Not Predict Where Synonymous Substitutions Occur in a Long-Term Experiment
Maddamsetti R, Hatcher PJ, Cruveiller S, Medigue C, Barrick JE, Lenski RE
Genome assembly using Nanopore-guided long and error-free DNA reads
Madoui MA, Engelen S, Cruaud C, Belser C, Bertrand L, Alberti A, Lemainque A, Wincker P, Aury JM
Design of Artificial Metabolisms in Layered Nanomaterials for the Enzymatic Synthesis of Phosphorylated Sugars
Mahdi R, Guerard-Helaine C, Prevot V, de Berardinis V, Forano C, Lemaire M
Evolutionary Advantage Conferred by an Eukaryote-to-Eukaryote Gene Transfer Event in Wine Yeasts
Marsit S, Mena A, Bigey F, Sauvage FX, Couloux A, Guy J, Legras JL, Barrio E, Dequin S, Galeote V
Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing
Massana R, Gobet A, Audic S, Bass D, Bittner L, Boutte C, Chambouvet A, Christen R, Claverie JM, Decelle J, Dolan JR, Dunthorn M, Edvardsen B, Forn I, Forster D, Guillou L, Jaillon O, Kooistra WHCF, Logares R, Mahe F, Not F, Ogata H, Pawlowski J, Pernice MC, Probert I, Romac S, Richards T, Santini S, Shalchian-Tabrizi K, Siano R, Simon N, Stoeck T, Vaulot D, Zingone A, de Vargas C
Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts
Morel G, Sterck L, Swennen D, Marcet-Houben M, Onesime D, Levasseur A, Jacques N, Mallet S, Couloux A, Labadie K, Amselem J, Beckerich JM, Henrissat B, Van de Peer Y, Wincker P, Souciet JL, Gabaldon T, Tinsley CR, Casaregola S
Updates in Rhea-a manually curated resource of biochemical reactions
Morgat A, Axelsen KB, Lombardot T, Alcantara R, Aimo L, Zerara M, Niknejad A, Belda E, Hyka-Nouspikel N, Coudert E, Redaschi N, Bougueleret L, Steinbeck C, Xenarios I, Bridge A
Recent species in old Islands: the origin of introduced populations of Litoria aurea (Anura: Hylidae) in New Caledonia and Wallis
Nicolas V, Grandcolas P, Braux F, Jourdan H, Malau A, Couloux A, Ohler A
Expanding the Mutation Spectrum Affecting alpha IIb beta 3 Integrin in Glanzmann Thrombasthenia: Screening of the ITGA2B and ITGB3 Genes in a Large International Cohort
Nurden AT, Pillois X, Fiore M, Alessi MC, Bonduel M, Dreyfus M, Goudemand J, Gruel Y, Benabdallah-Guerida S, Latger-Cannard V, Negrier C, Nugent D, Oiron RD, Rand ML, Sie P, Trossaert M, Alberio L, Martins N, Sirvain-Trukniewicz P, Couloux A, Canault M, Fronthroth JP, Fretigny M, Nurden P, Heilig R, Vinciguerra C
An inter-ocean comparison of coral endemism on seamounts: the case of Chrysogorgia
Pante E, France SC, Gey D, Cruaud C, Samadi S
Candidatus Frankia Datiscae Dg1, the Actinobacterial Microsymbiont of Datisca glomerata, Expresses the Canonical nod Genes nodABC in Symbiosis with Its Host Plant
Persson T, Battenberg K, Demina IV, Vigil-Stenman T, Heuvel BV, Pujic P, Facciotti MT, Wilbanks EG, O'Brien A, Fournier P, Hernandez MAC, Herrera AM, Medigue C, Normand P, Pawlowski K, Berry AM
Genome and Transcriptome of Clostridium phytofermentans, Catalyst for the Direct Conversion of Plant Feedstocks to Fuels
Petit E, Coppi MV, Hayes JC, Tolonen AC, Warnick T, Latouf WG, Amisano D, Biddle A, Mukherjee S, Ivanova N, Lykidis A, Land M, Hauser L, Kyrpides N, Henrissat B, Lau J, Schnell DJ, Church GM, Leschine SB, Blanchard JL
A nonsense loss-of-function mutation in PCSK1 contributes to dominantly inherited human obesity
Philippe J, Stijnen P, Meyre D, De Graeve F, Thuillier D, Delplanque J, Gyapay G, Sand O, Creemers JW, Froguel P, Bonnefond A
Draft Genome Sequence of Xanthomonas sacchari Strain LMG 476.
Pieretti I, Bolot S, Carrere S, Barbe V, Cociancich S, Rott P, Royer M
Deep transcriptome sequencing provides new insights into the structural and functional organization of the wheat genome
Pingault L, Choulet F, Alberti A, Glover N, Wincker P, Feuillet C, Paux E
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, Bergès H, Bodénès 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, Leplé 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, Kremer A
The enzymatic nature of an anonymous protein sequence cannot reliably be inferred from superfamily level structural information alone
Roche DB, Bruls T
An assessment of the amount of untapped fold level novelty in under-sampled areas of the tree of life
Roche DB, Bruls T
Two Host Clades, Two Bacterial Arsenals: Evolution through Gene Losses in Facultative Endosymbionts
Rollat-Farnier PA, Santos-Garcia D, Rao Q, Sagot MF, Silva FJ, Henri H, Zchori-Fein E, Latorre A, Moya A, Barbe V, Liu SS, Wang XW, Vavre F, Mouton L
Debromokeramadine from the marine sponge Agelas cf. mauritiana: isolation and short regioselective and flexible synthesis
Schroif-Gregoire C, Appenzeller J, Debitus C, Zaparucha A, Al-Mourabit A
A new network representation of the metabolism to detect chemical transformation modules
Sorokina M, Medigue C, Vallenet D
Structure and function of the global ocean microbiome
Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, Djahanschiri B, Zeller G, Mende DR, Alberti A, Cornejo-Castillo FM, Costea PI, Cruaud C, d'Ovidio F, Engelen S, Ferrera I, Gasol JM, Guidi L, Hildebrand F, Kokoszka F, Lepoivre C, Lima-Mendez G, Poulain J, Poulos BT, Royo-Llonch M, Sarmento H, Vieira-Silva S, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Bowler C, de Vargas C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Not F, Ogata H, Pesant S, Speich S, Stemmann L, Sullivan MB, Weissenbach J, Wincker P, Karsenti E, Raes J, Acinas SG, Bork P
Improving soil bacterial taxa-area relationships assessment using DNA meta-barcoding
Terrat S, Dequiedt S, Horrigue W, Lelievre M, Cruaud C, Saby NPA, Jolivet C, Arrouays D, Maron PA, Ranjard L, Prevost-Boure NC
Fungal lysis by a soil bacterium fermenting cellulose
Tolonen AC, Cerisy T, El-Sayyed H, Boutard M, Salanoubat M, Church GM
Physiology, Genomics, and Pathway Engineering of an Ethanol-Tolerant Strain of Clostridium phytofermentans
Tolonen AC, Zuroff TR, Ramya M, Boutard M, Cerisy T, Curtis WR
Systematics of the Southeast Asian mongooses (Herpestidae, Carnivora): solving the mystery of the elusive collared mongoose and Palawan mongoose
Veron G, Patou ML, Debruyne R, Couloux A, Fernandez DAP, Wong ST, Fuchs J, Jennings AP
Environmental characteristics of Agulhas rings affect interocean plankton transport
Villar E, Farrant GK, Follows M, Garczarek L, Speich S, Audic S, Bittner L, Blanke B, Brum JR, Brunet C, Casotti R, Chase A, Dolan JR, d'Ortenzio F, Gattuso JP, Grima N, Guidi L, Hill CN, Jahn O, Jamet JL, Le Goff H, Lepoivre C, Malviya S, Pelletier E, Romagnan JB, Roux S, Santini S, Scalco E, Schwenck SM, Tanaka A, Testor P, Vannier T, Vincent F, Zingone A, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Acinas SG, Bork P, Boss E, de Vargas C, Gorsky G, Ogata H, Pesant S, Sullivan MB, Sunagawa S, Wincker P, Karsenti E, Bowler C, Not F, Hingamp P, Iudicone D
Life-cycle modification in open oceans accounts for genome variability in a cosmopolitan phytoplankton
von Dassow P, John U, Ogata H, Probert I, Bendif E, Kegel JU, Audic S, Wincker P, Da Silva C, Claverie JM, Doney S, Glover DM, Flores DM, Herrera Y, Lescot M, Garet-Delmas MJ, de Vargas C