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Items: 1 to 50 of 79

1.

Insights into the harmful algal flora in northwestern Mediterranean coastal lagoons revealed by pyrosequencing metabarcodes of the 28S rRNA gene.

Grzebyk D, Audic S, Lasserre B, Abadie E, de Vargas C, Bec B.

Harmful Algae. 2017 Sep;68:1-16. doi: 10.1016/j.hal.2017.06.003. Epub 2017 Jul 24.

PMID:
28962972
2.

Biogeography and diversity of Collodaria (Radiolaria) in the global ocean.

Biard T, Bigeard E, Audic S, Poulain J, Gutierrez-Rodriguez A, Pesant S, Stemmann L, Not F.

ISME J. 2017 Jun;11(6):1331-1344. doi: 10.1038/ismej.2017.12. Epub 2017 Mar 24.

PMID:
28338675
3.

UniEuk: Time to Speak a Common Language in Protistology!

Berney C, Ciuprina A, Bender S, Brodie J, Edgcomb V, Kim E, Rajan J, Parfrey LW, Adl S, Audic S, Bass D, Caron DA, Cochrane G, Czech L, Dunthorn M, Geisen S, Glöckner FO, Mahé F, Quast C, Kaye JZ, Simpson AGB, Stamatakis A, Del Campo J, Yilmaz P, de Vargas C.

J Eukaryot Microbiol. 2017 May;64(3):407-411. doi: 10.1111/jeu.12414. Epub 2017 Apr 21. Review.

4.

Extreme Diversity of Diplonemid Eukaryotes in the Ocean.

Flegontova O, Flegontov P, Malviya S, Audic S, Wincker P, de Vargas C, Bowler C, Lukeš J, Horák A.

Curr Biol. 2016 Nov 21;26(22):3060-3065. doi: 10.1016/j.cub.2016.09.031.

5.

The Tara Oceans voyage reveals global diversity and distribution patterns of marine planktonic ciliates.

Gimmler A, Korn R, de Vargas C, Audic S, Stoeck T.

Sci Rep. 2016 Sep 16;6:33555. doi: 10.1038/srep33555.

6.

Benthic protists: the under-charted majority.

Forster D, Dunthorn M, Mahé 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 WH, 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, Stoeck T.

FEMS Microbiol Ecol. 2016 Aug;92(8). pii: fiw120. doi: 10.1093/femsec/fiw120. Epub 2016 Jun 5.

PMID:
27267932
7.

Diversity and oceanic distribution of the Parmales (Bolidophyceae), a picoplanktonic group closely related to diatoms.

Ichinomiya M, Dos Santos AL, Gourvil P, Yoshikawa S, Kamiya M, Ohki K, Audic S, de Vargas C, Noël MH, Vaulot D, Kuwata A.

ISME J. 2016 Oct;10(10):2419-34. doi: 10.1038/ismej.2016.38. Epub 2016 Mar 22.

8.

Insights into global diatom distribution and diversity in the world's ocean.

Malviya S, Scalco E, Audic S, Vincent F, Veluchamy A, Poulain J, Wincker P, Iudicone D, de Vargas C, Bittner L, Zingone A, Bowler C.

Proc Natl Acad Sci U S A. 2016 Mar 15;113(11):E1516-25. doi: 10.1073/pnas.1509523113. Epub 2016 Feb 29.

9.

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, Coelho LP, Espinoza JCI, Malviya S, Sunagawa S, Dimier C, Kandels-Lewis S, Picheral M, Poulain J, Searson S; Tara Oceans coordinators, 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.

Nature. 2016 Apr 28;532(7600):465-470. doi: 10.1038/nature16942. Epub 2016 Feb 10.

10.

A role for diatom-like silicon transporters in calcifying coccolithophores.

Durak GM, Taylor AR, Walker CE, Probert I, de Vargas C, Audic S, Schroeder D, Brownlee C, Wheeler GL.

Nat Commun. 2016 Feb 4;7:10543. doi: 10.1038/ncomms10543.

11.

The symbiotic life of Symbiodinium in the open ocean within a new species of calcifying ciliate (Tiarina sp.).

Mordret S, Romac S, Henry N, Colin S, Carmichael M, Berney C, Audic S, Richter DJ, Pochon X, de Vargas C, Decelle J.

ISME J. 2016 Jun;10(6):1424-36. doi: 10.1038/ismej.2015.211. Epub 2015 Dec 18.

12.

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.

Environ Microbiol Rep. 2015 Dec;7(6):979-89. doi: 10.1111/1758-2229.12345.

PMID:
26472079
13.

Global distribution and vertical patterns of a prymnesiophyte-cyanobacteria obligate symbiosis.

Cabello AM, Cornejo-Castillo FM, Raho N, Blasco D, Vidal M, Audic S, de Vargas C, Latasa M, Acinas SG, Massana R.

ISME J. 2016 Mar;10(3):693-706. doi: 10.1038/ismej.2015.147. Epub 2015 Sep 25.

14.

Global patterns of pelagic dinoflagellate diversity across protist size classes unveiled by metabarcoding.

Le Bescot N, Mahé F, Audic S, Dimier C, Garet MJ, Poulain J, Wincker P, de Vargas C, Siano R.

Environ Microbiol. 2016 Feb;18(2):609-26. doi: 10.1111/1462-2920.13039. Epub 2015 Oct 26.

PMID:
26337598
15.

MicRhoDE: a curated database for the analysis of microbial rhodopsin diversity and evolution.

Boeuf D, Audic S, Brillet-Guéguen L, Caron C, Jeanthon C.

Database (Oxford). 2015 Aug 18;2015. pii: bav080. doi: 10.1093/database/bav080. Print 2015.

16.

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 WH, Logares R, Mahé 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.

Environ Microbiol. 2015 Oct;17(10):4035-49. doi: 10.1111/1462-2920.12955. Epub 2015 Aug 4.

PMID:
26119494
17.

Ocean plankton. 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, Sánchez P, Sebastian M, Souffreau C, Dimier C, Picheral M, Searson S, Kandels-Lewis S; Tara Oceans coordinators, 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.

Science. 2015 May 22;348(6237):1262073. doi: 10.1126/science.1262073.

18.

Ocean plankton. Eukaryotic plankton diversity in the sunlit ocean.

de Vargas C, Audic S, Henry N, Decelle J, Mahé 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, Horák A, Jaillon O, Lima-Mendez G, Lukeš J, Malviya S, Morard R, Mulot M, Scalco E, Siano R, Vincent F, Zingone A, Dimier C, Picheral M, Searson S, Kandels-Lewis S; Tara Oceans Coordinators, 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.

Science. 2015 May 22;348(6237):1261605. doi: 10.1126/science.1261605.

19.

Ocean plankton. 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; Tara Oceans Coordinators, 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.

Science. 2015 May 22;348(6237):1261447. doi: 10.1126/science.1261447.

20.

PFR²: a curated database of planktonic foraminifera 18S ribosomal DNA as a resource for studies of plankton ecology, biogeography and evolution.

Morard R, Darling KF, Mahé F, Audic S, Ujiié Y, Weiner AK, André A, Seears HA, Wade CM, Quillévéré F, Douady CJ, Escarguel G, de Garidel-Thoron T, Siccha M, Kucera M, de Vargas C.

Mol Ecol Resour. 2015 Nov;15(6):1472-85. doi: 10.1111/1755-0998.12410. Epub 2015 Apr 15.

PMID:
25828689
21.

Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms.

Forster D, Bittner L, Karkar S, Dunthorn M, Romac S, Audic S, Lopez P, Stoeck T, Bapteste E.

BMC Biol. 2015 Feb 24;13:16. doi: 10.1186/s12915-015-0125-5.

22.

PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy.

Decelle J, Romac S, Stern RF, Bendif el M, Zingone A, Audic S, Guiry MD, Guillou L, Tessier D, Le Gall F, Gourvil P, Dos Santos AL, Probert I, Vaulot D, de Vargas C, Christen R.

Mol Ecol Resour. 2015 Nov;15(6):1435-45. doi: 10.1111/1755-0998.12401. Epub 2015 Apr 6.

PMID:
25740460
23.

Life-cycle modification in open oceans accounts for genome variability in a cosmopolitan phytoplankton.

von Dassow P, John U, Ogata H, Probert I, Bendif el M, 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.

ISME J. 2015 Jun;9(6):1365-77. doi: 10.1038/ismej.2014.221. Epub 2014 Dec 2.

24.

Assessment of species diversity and distribution of an ancient diatom lineage using a DNA metabarcoding approach.

Nanjappa D, Audic S, Romac S, Kooistra WH, Zingone A.

PLoS One. 2014 Aug 18;9(8):e103810. doi: 10.1371/journal.pone.0103810. eCollection 2014.

25.

Diverse molecular signatures for ribosomally 'active' Perkinsea in marine sediments.

Chambouvet A, Berney C, Romac S, Audic S, Maguire F, De Vargas C, Richards TA.

BMC Microbiol. 2014 Apr 29;14:110. doi: 10.1186/1471-2180-14-110.

26.

Patterns of rare and abundant marine microbial eukaryotes.

Logares R, Audic S, Bass D, Bittner L, Boutte C, Christen R, Claverie JM, Decelle J, Dolan JR, Dunthorn M, Edvardsen B, Gobet A, Kooistra WH, Mahé F, Not F, Ogata H, Pawlowski J, Pernice MC, Romac S, Shalchian-Tabrizi K, Simon N, Stoeck T, Santini S, Siano R, Wincker P, Zingone A, Richards TA, de Vargas C, Massana R.

Curr Biol. 2014 Apr 14;24(8):813-21. doi: 10.1016/j.cub.2014.02.050. Epub 2014 Apr 3.

27.

Placing environmental next-generation sequencing amplicons from microbial eukaryotes into a phylogenetic context.

Dunthorn M, Otto J, Berger SA, Stamatakis A, Mahé F, Romac S, de Vargas C, Audic S; Biomarks Consortium, Stock A, Kauff F, Stoeck T.

Mol Biol Evol. 2014 Apr;31(4):993-1009. doi: 10.1093/molbev/msu055. Epub 2014 Jan 27.

PMID:
24473288
28.

Exploring the uncultured microeukaryote majority in the oceans: reevaluation of ribogroups within stramenopiles.

Massana R, del Campo J, Sieracki ME, Audic S, Logares R.

ISME J. 2014 Apr;8(4):854-66. doi: 10.1038/ismej.2013.204. Epub 2013 Nov 7.

29.

454 pyrosequencing to describe microbial eukaryotic community composition, diversity and relative abundance: a test for marine haptophytes.

Egge E, Bittner L, Andersen T, Audic S, de Vargas C, Edvardsen B.

PLoS One. 2013 Sep 12;8(9):e74371. doi: 10.1371/journal.pone.0074371. eCollection 2013.

30.

The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy.

Guillou L, Bachar D, Audic S, Bass D, Berney C, Bittner L, Boutte C, Burgaud G, de Vargas C, Decelle J, Del Campo J, Dolan JR, Dunthorn M, Edvardsen B, Holzmann M, Kooistra WH, Lara E, Le Bescot N, Logares R, Mahé F, Massana R, Montresor M, Morard R, Not F, Pawlowski J, Probert I, Sauvadet AL, Siano R, Stoeck T, Vaulot D, Zimmermann P, Christen R.

Nucleic Acids Res. 2013 Jan;41(Database issue):D597-604. doi: 10.1093/nar/gks1160. Epub 2012 Nov 27.

31.

Diversity patterns of uncultured Haptophytes unravelled by pyrosequencing in Naples Bay.

Bittner L, Gobet A, Audic S, Romac S, Egge ES, Santini S, Ogata H, Probert I, Edvardsen B, de Vargas C.

Mol Ecol. 2013 Jan;22(1):87-101. doi: 10.1111/mec.12108. Epub 2012 Nov 19.

PMID:
23163508
32.

CBOL protist working group: barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms.

Pawlowski J, Audic S, Adl S, Bass D, Belbahri L, Berney C, Bowser SS, Cepicka I, Decelle J, Dunthorn M, Fiore-Donno AM, Gile GH, Holzmann M, Jahn R, Jirků M, Keeling PJ, Kostka M, Kudryavtsev A, Lara E, Lukeš J, Mann DG, Mitchell EA, Nitsche F, Romeralo M, Saunders GW, Simpson AG, Smirnov AV, Spouge JL, Stern RF, Stoeck T, Zimmermann J, Schindel D, de Vargas C.

PLoS Biol. 2012;10(11):e1001419. doi: 10.1371/journal.pbio.1001419. Epub 2012 Nov 6. No abstract available.

33.

Diversity patterns and activity of uncultured marine heterotrophic flagellates unveiled with pyrosequencing.

Logares R, Audic S, Santini S, Pernice MC, de Vargas C, Massana R.

ISME J. 2012 Oct;6(10):1823-33. doi: 10.1038/ismej.2012.36. Epub 2012 Apr 26.

34.

Genome-wide analysis of heteroduplex DNA in mismatch repair-deficient yeast cells reveals novel properties of meiotic recombination pathways.

Martini E, Borde V, Legendre M, Audic S, Regnault B, Soubigou G, Dujon B, Llorente B.

PLoS Genet. 2011 Sep;7(9):e1002305. doi: 10.1371/journal.pgen.1002305. Epub 2011 Sep 29.

35.

The genome sequence of Brucella pinnipedialis B2/94 sheds light on the evolutionary history of the genus Brucella.

Audic S, Lescot M, Claverie JM, Cloeckaert A, Zygmunt MS.

BMC Evol Biol. 2011 Jul 11;11:200. doi: 10.1186/1471-2148-11-200.

36.

Gene expression in proliferating cells of the dinoflagellate Alexandrium catenella (Dinophyceae).

Toulza E, Shin MS, Blanc G, Audic S, Laabir M, Collos Y, Claverie JM, Grzebyk D.

Appl Environ Microbiol. 2010 Jul;76(13):4521-9. doi: 10.1128/AEM.02345-09. Epub 2010 Apr 30.

37.

mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus.

Legendre M, Audic S, Poirot O, Hingamp P, Seltzer V, Byrne D, Lartigue A, Lescot M, Bernadac A, Poulain J, Abergel C, Claverie JM.

Genome Res. 2010 May;20(5):664-74. doi: 10.1101/gr.102582.109. Epub 2010 Apr 1.

38.

BLAST-EXPLORER helps you building datasets for phylogenetic analysis.

Dereeper A, Audic S, Claverie JM, Blanc G.

BMC Evol Biol. 2010 Jan 12;10:8. doi: 10.1186/1471-2148-10-8.

39.

Transcriptome analysis of functional differentiation between haploid and diploid cells of Emiliania huxleyi, a globally significant photosynthetic calcifying cell.

von Dassow P, Ogata H, Probert I, Wincker P, Da Silva C, Audic S, Claverie JM, de Vargas C.

Genome Biol. 2009;10(10):R114. doi: 10.1186/gb-2009-10-10-r114. Epub 2009 Oct 15.

40.

Brucella microti: the genome sequence of an emerging pathogen.

Audic S, Lescot M, Claverie JM, Scholz HC.

BMC Genomics. 2009 Aug 4;10:352. doi: 10.1186/1471-2164-10-352.

41.

The polyadenylation site of Mimivirus transcripts obeys a stringent 'hairpin rule'.

Byrne D, Grzela R, Lartigue A, Audic S, Chenivesse S, Encinas S, Claverie JM, Abergel C.

Genome Res. 2009 Jul;19(7):1233-42. doi: 10.1101/gr.091561.109. Epub 2009 Apr 29.

42.

Analysis of the Rickettsia africae genome reveals that virulence acquisition in Rickettsia species may be explained by genome reduction.

Fournier PE, El Karkouri K, Leroy Q, Robert C, Giumelli B, Renesto P, Socolovschi C, Parola P, Audic S, Raoult D.

BMC Genomics. 2009 Apr 20;10:166. doi: 10.1186/1471-2164-10-166.

43.

The genome of Borrelia recurrentis, the agent of deadly louse-borne relapsing fever, is a degraded subset of tick-borne Borrelia duttonii.

Lescot M, Audic S, Robert C, Nguyen TT, Blanc G, Cutler SJ, Wincker P, Couloux A, Claverie JM, Raoult D, Drancourt M.

PLoS Genet. 2008 Sep 12;4(9):e1000185. doi: 10.1371/journal.pgen.1000185.

44.

Phylogeny.fr: robust phylogenetic analysis for the non-specialist.

Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, Chevenet F, Dufayard JF, Guindon S, Lefort V, Lescot M, Claverie JM, Gascuel O.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W465-9. doi: 10.1093/nar/gkn180. Epub 2008 Apr 19.

45.

Rapid comparative genomic analysis for clinical microbiology: the Francisella tularensis paradigm.

La Scola B, Elkarkouri K, Li W, Wahab T, Fournous G, Rolain JM, Biswas S, Drancourt M, Robert C, Audic S, Löfdahl S, Raoult D.

Genome Res. 2008 May;18(5):742-50. doi: 10.1101/gr.071266.107. Epub 2008 Apr 11.

46.

Lateral gene transfer between obligate intracellular bacteria: evidence from the Rickettsia massiliae genome.

Blanc G, Ogata H, Robert C, Audic S, Claverie JM, Raoult D.

Genome Res. 2007 Nov;17(11):1657-64. Epub 2007 Oct 4.

47.

Genome analysis of Minibacterium massiliensis highlights the convergent evolution of water-living bacteria.

Audic S, Robert C, Campagna B, Parinello H, Claverie JM, Raoult D, Drancourt M.

PLoS Genet. 2007 Aug;3(8):e138. Epub 2007 Jul 5.

48.

Reductive genome evolution from the mother of Rickettsia.

Blanc G, Ogata H, Robert C, Audic S, Suhre K, Vestris G, Claverie JM, Raoult D.

PLoS Genet. 2007 Jan 19;3(1):e14.

49.

Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee.

Armougom F, Moretti S, Poirot O, Audic S, Dumas P, Schaeli B, Keduas V, Notredame C.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W604-8.

50.

PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignments.

Moretti S, Reinier F, Poirot O, Armougom F, Audic S, Keduas V, Notredame C.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W600-3.

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