Works by Vargas, Colomban

Results: 79
    1

    A Holistic Approach to Marine Eco-Systems Biology.

    Published in:
    PLoS Biology, 2011, v. 9, n. 10, p. 1, doi. 10.1371/journal.pbio.1001177
    By:
    • Karsenti, Eric;
    • Acinas, Silvia G.;
    • Bork, Peer;
    • Bowler, Chris;
    • De Vargas, Colomban;
    • Raes, Jeroen;
    • Sullivan, Matthew;
    • Arendt, Detlev;
    • Benzoni, Francesca;
    • Claverie, Jean-Michel;
    • Follows, Mick;
    • Gorsky, Gaby;
    • Hingamp, Pascal;
    • Iudicone, Daniele;
    • Jaillon, Olivier;
    • Kandels-Lewis, Stefanie;
    • Krzic, Uros;
    • Not, Fabrice;
    • Ogata, Hiroyuki;
    • Pesant, Stéphane
    Publication type:
    Article
    2

    Swarm v3: towards tera-scale amplicon clustering.

    Published in:
    Bioinformatics, 2022, v. 38, n. 1, p. 267, doi. 10.1093/bioinformatics/btab493
    By:
    • Mahé, Frédéric;
    • Czech, Lucas;
    • Stamatakis, Alexandros;
    • Quince, Christopher;
    • Vargas, Colomban de;
    • Dunthorn, Micah;
    • Rognes, Torbjørn
    Publication type:
    Article
    3
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    The Protist Ribosomal Reference database (PR<sup>2</sup>): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy.

    Published in:
    Nucleic Acids Research, 2013, v. 41, p. D597, doi. 10.1093/nar/gks1160
    By:
    • Guillou, Laure;
    • Bachar, Dipankar;
    • Audic, Stéphane;
    • Bass, David;
    • Berney, Cédric;
    • Bittner, Lucie;
    • Boutte, Christophe;
    • Burgaud, Gaétan;
    • de Vargas, Colomban;
    • Decelle, Johan;
    • del Campo, Javier;
    • Dolan, John R.;
    • Dunthorn, Micah;
    • Edvardsen, Bente;
    • Holzmann, Maria;
    • Kooistra, Wiebe H. C. F.;
    • Lara, Enrique;
    • Le Bescot, Noan;
    • Logares, Ramiro;
    • Mahé, Frédéric
    Publication type:
    Article
    5

    Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods.

    Published in:
    Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-24299-y
    By:
    • Pierella Karlusich, Juan José;
    • Pelletier, Eric;
    • Lombard, Fabien;
    • Carsique, Madeline;
    • Dvorak, Etienne;
    • Colin, Sébastien;
    • Picheral, Marc;
    • Cornejo-Castillo, Francisco M.;
    • Acinas, Silvia G.;
    • Pepperkok, Rainer;
    • Karsenti, Eric;
    • de Vargas, Colomban;
    • Wincker, Patrick;
    • Bowler, Chris;
    • Foster, Rachel A.
    Publication type:
    Article
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    Disentangling the mechanisms shaping the surface ocean microbiota.

    Published in:
    Microbiome, 2020, v. 8, n. 1, p. 1, doi. 10.1186/s40168-020-00827-8
    By:
    • Logares, Ramiro;
    • Deutschmann, Ina M.;
    • Junger, Pedro C.;
    • Giner, Caterina R.;
    • Krabberød, Anders K.;
    • Schmidt, Thomas S. B.;
    • Rubinat-Ripoll, Laura;
    • Mestre, Mireia;
    • Salazar, Guillem;
    • Ruiz-González, Clara;
    • Sebastián, Marta;
    • de Vargas, Colomban;
    • Acinas, Silvia G.;
    • Duarte, Carlos M.;
    • Gasol, Josep M.;
    • Massana, Ramon
    Publication type:
    Article
    10
    11

    Neobodonids are dominant kinetoplastids in the global ocean.

    Published in:
    Environmental Microbiology, 2018, v. 20, n. 2, p. 878, doi. 10.1111/1462-2920.14034
    By:
    • Flegontova, Olga;
    • Flegontov, Pavel;
    • Malviya, Shruti;
    • Poulain, Julie;
    • de Vargas, Colomban;
    • Bowler, Chris;
    • Lukeš, Julius;
    • Horák, Aleš
    Publication type:
    Article
    12
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    Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities.

    Published in:
    Environmental Microbiology, 2014, v. 16, n. 9, p. 2659, doi. 10.1111/1462-2920.12250
    By:
    • Logares, Ramiro;
    • Sunagawa, Shinichi;
    • Salazar, Guillem;
    • Cornejo ‐ Castillo, Francisco M.;
    • Ferrera, Isabel;
    • Sarmento, Hugo;
    • Hingamp, Pascal;
    • Ogata, Hiroyuki;
    • Vargas, Colomban;
    • Lima ‐ Mendez, Gipsi;
    • Raes, Jeroen;
    • Poulain, Julie;
    • Jaillon, Olivier;
    • Wincker, Patrick;
    • Kandels ‐ Lewis, Stefanie;
    • Karsenti, Eric;
    • Bork, Peer;
    • Acinas, Silvia G.
    Publication type:
    Article
    15
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    Seasonal dynamics of marine protist communities in tidally mixed coastal waters.

    Published in:
    Molecular Ecology, 2022, v. 31, n. 14, p. 3761, doi. 10.1111/mec.16539
    By:
    • Caracciolo, Mariarita;
    • Rigaut‐Jalabert, Fabienne;
    • Romac, Sarah;
    • Mahé, Frédéric;
    • Forsans, Samuel;
    • Gac, Jean‐Philippe;
    • Arsenieff, Laure;
    • Manno, Maxime;
    • Chaffron, Samuel;
    • Cariou, Thierry;
    • Hoebeke, Mark;
    • Bozec, Yann;
    • Goberville, Eric;
    • Le Gall, Florence;
    • Guilloux, Loïc;
    • Baudoux, Anne‐Claire;
    • de Vargas, Colomban;
    • Not, Fabrice;
    • Thiébaut, Eric;
    • Henry, Nicolas
    Publication type:
    Article
    19
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    The global genetic diversity of planktonic foraminifera reveals the structure of cryptic speciation in plankton.

    Published in:
    Biological Reviews, 2024, v. 99, n. 4, p. 1218, doi. 10.1111/brv.13065
    By:
    • Morard, Raphaël;
    • Darling, Kate F.;
    • Weiner, Agnes K. M.;
    • Hassenrück, Christiane;
    • Vanni, Chiara;
    • Cordier, Tristan;
    • Henry, Nicolas;
    • Greco, Mattia;
    • Vollmar, Nele M.;
    • Milivojevic, Tamara;
    • Rahman, Shirin Nurshan;
    • Siccha, Michael;
    • Meilland, Julie;
    • Jonkers, Lukas;
    • Quillévéré, Frédéric;
    • Escarguel, Gilles;
    • Douady, Christophe J.;
    • de Garidel‐Thoron, Thibault;
    • de Vargas, Colomban;
    • Kucera, Michal
    Publication type:
    Article
    22

    The Evolution of Silicon Transport in Eukaryotes.

    Published in:
    Molecular Biology & Evolution, 2016, v. 33, n. 12, p. 3226, doi. 10.1093/molbev/msw209
    By:
    • Marron, Alan O.;
    • Ratcliffe, Sarah;
    • Wheeler, Glen L.;
    • Goldstein, Raymond E.;
    • King, Nicole;
    • Not, Fabrice;
    • de Vargas, Colomban;
    • Richter, Daniel J.
    Publication type:
    Article
    23
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    Pan-Arctic plankton community structure and its global connectivity.

    Published in:
    Elementa: Science of the Anthropocene, 2023, v. 11, n. 1, p. 1, doi. 10.1525/elementa.2022.00060
    By:
    • Ibarbalz, Federico M.;
    • Henry, Nicolas;
    • Mahé, Frédéric;
    • Ardyna, Mathieu;
    • Zingone, Adriana;
    • Scalco, Eleonora;
    • Lovejoy, Connie;
    • Lombard, Fabien;
    • Jaillon, Olivier;
    • Iudicone, Daniele;
    • Malviya, Shruti;
    • Sullivan, Matthew B.;
    • Chaffron, Samuel;
    • Karsenti, Eric;
    • Babin, Marcel;
    • Boss, Emmanuel;
    • Wincker, Patrick;
    • Zinger, Lucie;
    • de Vargas, Colomban;
    • Bowler, Chris
    Publication type:
    Article
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    Life-cycle modification in open oceans accounts for genome variability in a cosmopolitan phytoplankton.

    Published in:
    ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2015, v. 9, n. 6, p. 1365, doi. 10.1038/ismej.2014.221
    By:
    • von Dassow, Peter;
    • John, Uwe;
    • Ogata, Hiroyuki;
    • Probert, Ian;
    • Bendif, El Mahdi;
    • Kegel, Jessica U;
    • Audic, Stéphane;
    • Wincker, Patrick;
    • Da Silva, Corinne;
    • Claverie, Jean-Michel;
    • Doney, Scott;
    • Glover, David M;
    • Flores, Daniella Mella;
    • Herrera, Yeritza;
    • Lescot, Magali;
    • Garet-Delmas, Marie-José;
    • de Vargas, Colomban
    Publication type:
    Article
    33

    Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes.

    Published in:
    ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2013, v. 7, n. 9, p. 1678, doi. 10.1038/ismej.2013.59
    By:
    • Hingamp, Pascal;
    • Grimsley, Nigel;
    • Acinas, Silvia G;
    • Clerissi, Camille;
    • Subirana, Lucie;
    • Poulain, Julie;
    • Ferrera, Isabel;
    • Sarmento, Hugo;
    • Villar, Emilie;
    • Lima-Mendez, Gipsi;
    • Faust, Karoline;
    • Sunagawa, Shinichi;
    • Claverie, Jean-Michel;
    • Moreau, Hervé;
    • Desdevises, Yves;
    • Bork, Peer;
    • Raes, Jeroen;
    • de Vargas, Colomban;
    • Karsenti, Eric;
    • Kandels-Lewis, Stefanie
    Publication type:
    Article
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    Diatom diversity through HTS-metabarcoding in coastal European seas.

    Published in:
    Scientific Reports, 2018, v. 8, n. 1, p. 1, doi. 10.1038/s41598-018-36345-9
    By:
    • Piredda, Roberta;
    • Claverie, Jean-Michel;
    • Decelle, Johan;
    • de Vargas, Colomban;
    • Dunthorn, Micah;
    • Edvardsen, Bente;
    • Eikrem, Wenche;
    • Forster, Dominik;
    • Kooistra, Wiebe H. C. F.;
    • Logares, Ramiro;
    • Massana, Ramon;
    • Montresor, Marina;
    • Not, Fabrice;
    • Ogata, Hiroyuki;
    • Pawlowski, Jan;
    • Romac, Sarah;
    • Sarno, Diana;
    • Stoeck, Thorsten;
    • Zingone, Adriana
    Publication type:
    Article
    40

    Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton.

    Published in:
    Nature Communications, 2016, v. 7, n. 3, p. 11071, doi. 10.1038/ncomms11071
    By:
    • Cornejo-Castillo, Francisco M.;
    • Cabello, Ana M.;
    • Salazar, Guillem;
    • Sánchez-Baracaldo, Patricia;
    • Lima-Mendez, Gipsi;
    • Hingamp, Pascal;
    • Alberti, Adriana;
    • Sunagawa, Shinichi;
    • Bork, Peer;
    • de Vargas, Colomban;
    • Raes, Jeroen;
    • Bowler, Chris;
    • Wincker, Patrick;
    • Zehr, Jonathan P.;
    • Gasol, Josep M.;
    • Massana, Ramon;
    • Acinas, Silvia G.
    Publication type:
    Article
    41
    42

    A robust approach to estimate relative phytoplankton cell abundances from metagenomes.

    Published in:
    Molecular Ecology Resources, 2023, v. 23, n. 1, p. 16, doi. 10.1111/1755-0998.13592
    By:
    • Pierella Karlusich, Juan José;
    • Pelletier, Eric;
    • Zinger, Lucie;
    • Lombard, Fabien;
    • Zingone, Adriana;
    • Colin, Sébastien;
    • Gasol, Josep M.;
    • Dorrell, Richard G.;
    • Henry, Nicolas;
    • Scalco, Eleonora;
    • Acinas, Silvia G.;
    • Wincker, Patrick;
    • de Vargas, Colomban;
    • Bowler, Chris
    Publication type:
    Article
    43
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    Phyto REF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy.

    Published in:
    Molecular Ecology Resources, 2015, v. 15, n. 6, p. 1435, doi. 10.1111/1755-0998.12401
    By:
    • Decelle, Johan;
    • Romac, Sarah;
    • Stern, Rowena F.;
    • Bendif, El Mahdi;
    • Zingone, Adriana;
    • Audic, Stéphane;
    • Guiry, Michael D.;
    • Guillou, Laure;
    • Tessier, Désiré;
    • Le Gall, Florence;
    • Gourvil, Priscillia;
    • Dos Santos, Adriana L.;
    • Probert, Ian;
    • Vaulot, Daniel;
    • Vargas, Colomban;
    • Christen, Richard
    Publication type:
    Article
    45

    PFR<sup>2</sup>: a curated database of planktonic foraminifera 18S ribosomal DNA as a resource for studies of plankton ecology, biogeography and evolution.

    Published in:
    Molecular Ecology Resources, 2015, v. 15, n. 6, p. 1472, doi. 10.1111/1755-0998.12410
    By:
    • Morard, Raphaël;
    • Darling, Kate F.;
    • Mahé, Frédéric;
    • Audic, Stéphane;
    • Ujiié, Yurika;
    • Weiner, Agnes K. M.;
    • André, Aurore;
    • Seears, Heidi A.;
    • Wade, Christopher M.;
    • Quillévéré, Frédéric;
    • Douady, Christophe J.;
    • Escarguel, Gilles;
    • Garidel‐Thoron, Thibault;
    • Siccha, Michael;
    • Kucera, Michal;
    • Vargas, Colomban
    Publication type:
    Article
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    Predicting global distributions of eukaryotic plankton communities from satellite data.

    Published in:
    ISME Communications, 2023, v. 3, n. 1, p. 1, doi. 10.1038/s43705-023-00308-7
    By:
    • Kaneko, Hiroto;
    • Endo, Hisashi;
    • Henry, Nicolas;
    • Berney, Cédric;
    • Mahé, Frédéric;
    • Poulain, Julie;
    • Labadie, Karine;
    • Beluche, Odette;
    • El Hourany, Roy;
    • Tara Oceans Coordinators;
    • Acinas, Silvia G.;
    • Babin, Marcel;
    • Bork, Peer;
    • Bowler, Chris;
    • Cochrane, Guy;
    • de Vargas, Colomban;
    • Gorsky, Gabriel;
    • Guidi, Lionel;
    • Grimsley, Nigel;
    • Hingamp, Pascal
    Publication type:
    Article
    50

    Top abundant deep ocean heterotrophic bacteria can be retrieved by cultivation.

    Published in:
    ISME Communications, 2023, v. 3, n. 1, p. 1, doi. 10.1038/s43705-023-00290-0
    By:
    • Sanz-Sáez, Isabel;
    • Sánchez, Pablo;
    • Salazar, Guillem;
    • Sunagawa, Shinichi;
    • de Vargas, Colomban;
    • Bowler, Chris;
    • Sullivan, Matthew B.;
    • Wincker, Patrick;
    • Karsenti, Eric;
    • Pedrós-Alió, Carlos;
    • Agustí, Susana;
    • Gojobori, Takashi;
    • Duarte, Carlos M.;
    • Gasol, Josep M.;
    • Sánchez, Olga;
    • Acinas, Silvia G.
    Publication type:
    Article