Works by Sunagawa, Shinichi

Results: 72
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    Sublethal systemic LPS in mice enables gut-luminal pathogens to bloom through oxygen species-mediated microbiota inhibition.

    Published in:
    Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-57979-0
    By:
    • Kroon, Sanne;
    • Malcic, Dejan;
    • Weidert, Lena;
    • Bircher, Lea;
    • Boldt, Leonardo;
    • Christen, Philipp;
    • Kiefer, Patrick;
    • Sintsova, Anna;
    • Nguyen, Bidong D.;
    • Barthel, Manja;
    • Steiger, Yves;
    • Clerc, Melanie;
    • Herzog, Mathias K.-M.;
    • Chen, Carmen;
    • Gül, Ersin;
    • Guery, Benoit;
    • Slack, Emma;
    • Sunagawa, Shinichi;
    • Vorholt, Julia A.;
    • Maier, Lisa
    Publication type:
    Article
    3

    Sublethal systemic LPS in mice enables gut-luminal pathogens to bloom through oxygen species-mediated microbiota inhibition.

    Published in:
    Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-57979-0
    By:
    • Kroon, Sanne;
    • Malcic, Dejan;
    • Weidert, Lena;
    • Bircher, Lea;
    • Boldt, Leonardo;
    • Christen, Philipp;
    • Kiefer, Patrick;
    • Sintsova, Anna;
    • Nguyen, Bidong D.;
    • Barthel, Manja;
    • Steiger, Yves;
    • Clerc, Melanie;
    • Herzog, Mathias K.-M.;
    • Chen, Carmen;
    • Gül, Ersin;
    • Guery, Benoit;
    • Slack, Emma;
    • Sunagawa, Shinichi;
    • Vorholt, Julia A.;
    • Maier, Lisa
    Publication type:
    Article
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    Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities.

    Published in:
    Communications Biology, 2021, v. 4, n. 1, p. 1, doi. 10.1038/s42003-021-02112-2
    By:
    • Acinas, Silvia G.;
    • Sánchez, Pablo;
    • Salazar, Guillem;
    • Cornejo-Castillo, Francisco M.;
    • Sebastián, Marta;
    • Logares, Ramiro;
    • Royo-Llonch, Marta;
    • Paoli, Lucas;
    • Sunagawa, Shinichi;
    • Hingamp, Pascal;
    • Ogata, Hiroyuki;
    • Lima-Mendez, Gipsi;
    • Roux, Simon;
    • González, José M.;
    • Arrieta, Jesús M.;
    • Alam, Intikhab S.;
    • Kamau, Allan;
    • Bowler, Chris;
    • Raes, Jeroen;
    • Pesant, Stéphane
    Publication type:
    Article
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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
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    MOCAT2: a metagenomic assembly, annotation and profiling framework.

    Published in:
    Bioinformatics, 2016, v. 32, n. 16, p. 2520, doi. 10.1093/bioinformatics/btw183
    By:
    • Kultima, Jens Roat;
    • Coelho, Luis Pedro;
    • Forslund, Kristoffer;
    • Huerta-Cepas, Jaime;
    • Li, Simone S.;
    • Driessen, Marja;
    • Voigt, Anita Yvonne;
    • Zeller, Georg;
    • Sunagawa, Shinichi;
    • Bork, Peer
    Publication type:
    Article
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    Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity.

    Published in:
    ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2020, v. 14, n. 5, p. 1247, doi. 10.1038/s41396-020-0600-z
    By:
    • Maistrenko, Oleksandr M.;
    • Mende, Daniel R.;
    • Luetge, Mechthild;
    • Hildebrand, Falk;
    • Schmidt, Thomas S. B.;
    • Li, Simone S.;
    • Rodrigues, João F. Matias;
    • von Mering, Christian;
    • Pedro Coelho, Luis;
    • Huerta-Cepas, Jaime;
    • Sunagawa, Shinichi;
    • Bork, Peer
    Publication type:
    Article
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    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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    Phenology and ecological role of aerobic anoxygenic phototrophs in freshwaters.

    Published in:
    Microbiome, 2024, v. 12, n. 1, p. 1, doi. 10.1186/s40168-024-01786-0
    By:
    • Villena-Alemany, Cristian;
    • Mujakić, Izabela;
    • Fecskeová, Livia K.;
    • Woodhouse, Jason;
    • Auladell, Adrià;
    • Dean, Jason;
    • Hanusová, Martina;
    • Socha, Magdalena;
    • Gazulla, Carlota R.;
    • Ruscheweyh, Hans-Joachim;
    • Sunagawa, Shinichi;
    • Silva Kavagutti, Vinicius;
    • Andrei, Adrian-Ştefan;
    • Grossart, Hans-Peter;
    • Ghai, Rohit;
    • Koblížek, Michal;
    • Piwosz, Kasia
    Publication type:
    Article
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    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
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    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
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    SPIRE: a Searchable, Planetary-scale mIcrobiome REsource.

    Published in:
    Nucleic Acids Research, 2024, v. 52, n. D1, p. D777, doi. 10.1093/nar/gkad943
    By:
    • Schmidt, Thomas S B;
    • Fullam, Anthony;
    • Ferretti, Pamela;
    • Orakov, Askarbek;
    • Maistrenko, Oleksandr M;
    • Ruscheweyh, Hans-Joachim;
    • Letunic, Ivica;
    • Duan, Yiqian;
    • Van Rossum, Thea;
    • Sunagawa, Shinichi;
    • Mende, Daniel R;
    • Finn, Robert D;
    • Kuhn, Michael;
    • Pedro Coelho, Luis;
    • Bork, Peer
    Publication type:
    Article
    38

    proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes.

    Published in:
    Nucleic Acids Research, 2023, v. 51, n. D1, p. D760, doi. 10.1093/nar/gkac1078
    By:
    • Fullam, Anthony;
    • Letunic, Ivica;
    • Schmidt, Thomas S B;
    • Ducarmon, Quinten R;
    • Karcher, Nicolai;
    • Khedkar, Supriya;
    • Kuhn, Michael;
    • Larralde, Martin;
    • Maistrenko, Oleksandr M;
    • Malfertheiner, Lukas;
    • Milanese, Alessio;
    • Rodrigues, Joao Frederico Matias;
    • Sanchis-López, Claudia;
    • Schudoma, Christian;
    • Szklarczyk, Damian;
    • Sunagawa, Shinichi;
    • Zeller, Georg;
    • Huerta-Cepas, Jaime;
    • von Mering, Christian;
    • Bork, Peer
    Publication type:
    Article
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    Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans.

    Published in:
    Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-017-02235-3
    By:
    • Seeleuthner, Yoann;
    • Mondy, Samuel;
    • Lombard, Vincent;
    • Carradec, Quentin;
    • Pelletier, Eric;
    • Wessner, Marc;
    • Leconte, Jade;
    • Mangot, Jean-François;
    • Poulain, Julie;
    • Labadie, Karine;
    • Logares, Ramiro;
    • Shinichi Sunagawa;
    • de Berardinis, Véronique;
    • Salanoubat, Marcel;
    • Dimier, Céline;
    • Kandels-Lewis, Stefanie;
    • Picheral, Marc;
    • Searson, Sarah;
    • Pesant, Stephane;
    • Poulton, Nicole
    Publication type:
    Article
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    A fair comparison.

    Published in:
    Nature Methods, 2014, v. 11, n. 4, p. 359, doi. 10.1038/nmeth.2897
    By:
    • Costea, Paul I;
    • Zeller, Georg;
    • Sunagawa, Shinichi;
    • Bork, Peer
    Publication type:
    Article
    48

    Metagenomic species profiling using universal phylogenetic marker genes.

    Published in:
    Nature Methods, 2013, v. 10, n. 12, p. 1196, doi. 10.1038/nmeth.2693
    By:
    • Sunagawa, Shinichi;
    • Mende, Daniel R;
    • Zeller, Georg;
    • Izquierdo-Carrasco, Fernando;
    • Berger, Simon A;
    • Kultima, Jens Roat;
    • Coelho, Luis Pedro;
    • Arumugam, Manimozhiyan;
    • Tap, Julien;
    • Nielsen, Henrik Bjørn;
    • Rasmussen, Simon;
    • Brunak, Søren;
    • Pedersen, Oluf;
    • Guarner, Francisco;
    • de Vos, Willem M;
    • Wang, Jun;
    • Li, Junhua;
    • Doré, Joël;
    • Ehrlich, S Dusko;
    • Stamatakis, Alexandros
    Publication type:
    Article
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    Subspecies in the global human gut microbiome.

    Published in:
    Molecular Systems Biology, 2017, v. 13, n. 12, p. 1, doi. 10.15252/msb.20177589
    By:
    • Costea, Paul I;
    • Coelho, Luis Pedro;
    • Sunagawa, Shinichi;
    • Munch, Robin;
    • Huerta‐Cepas, Jaime;
    • Forslund, Kristoffer;
    • Hildebrand, Falk;
    • Kushugulova, Almagul;
    • Zeller, Georg;
    • Bork, Peer
    Publication type:
    Article