Shinichi Sunagawa

ResearcherID ORCID

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 63

Top Venues

Nature communications

Nature

eLife

Nature microbiology

ETH Zurich

University of California Merced (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

ETH Zurich Jul 01 2016

Switzerland

Assistant Professor of Microbiome Research :: Department of Biology, Institute of Microbiology

Education History

University of California Merced

United States

PHD :: Quantitative and Systems Biology

Universität Bremen

Germany

MSC :: Aquatic Ecology

Publications

Lucia Campese, Luca Russo, Maria Abagnale, Adriana Alberti, Giancarlo Bachi, Cecilia Balestra, Daniele Bellardini, Angela Buondonno, Ulisse Cardini, Ylenia Carotenuto, Giovanni Checcucci, Maria Luisa Chiusano, Isabella D'Ambra, Giuliana d'Ippolito, Iole Di Capua, Vincenzo Donnarumma, Angelo Fontana, Marta Furia, Denisse Galarza-Verkovitch, Roberto Gallia, Karine Labadie, Serena Leone, Priscilla Licandro, Antonio Longo, Maira Maselli, Louise Merquiol, Carola Murano, Pedro H Oliveira, Augusto Passarelli, Isabella Percopo, Aude Perdereau, Roberta Piredda, Francesca Raffini, Vittoria Roncalli, Hans-Joachim Ruscheweyh, Ennio Russo, Maria Saggiomo, Chiara Santinelli, Diana Sarno, Shinichi Sunagawa, Ferdinando Tramontano, Anna Chiara Trano, Marco Uttieri, Patrick Wincker, Gianpaolo Zampicinini, Raffaella Casotti, Fabio Conversano, Domenico D'Alelio, Daniele Iudicone, Francesca Margiotta, Marina Montresor
The NEREA Augmented Observatory: an integrative approach to marine coastal ecology. Scientific data 11 (1) (2024)
Senka Causevic, Manupriyam Dubey, Marian Morales, Guillem Salazar, Vladimir Sentchilo, Nicolas Carraro, Hans-Joachim Ruscheweyh, Shinichi Sunagawa, Jan Roelof Van der Meer
Niche availability and competitive loss by facilitation control proliferation of bacterial strains intended for soil microbiome interventions. Nature communications 15 (1) (2024)
Anna Sintsova, Hans-Joachim Ruscheweyh, Christopher M Field, Lilith Feer, Bidong D Nguyen, Benjamin Daniel, Wolf-Dietrich Hardt, Julia A Vorholt, Shinichi Sunagawa
mBARq: a versatile and user-friendly framework for the analysis of DNA barcodes from transposon insertion libraries, knockout mutants, and isogenic strain populations. Bioinformatics (Oxford, England) 40 (2) (2024)
Senka Causevic, Manupriyam Dubey, Marian Morales, Guillem Salazar, Vladimir Sentchilo, Nicolas Carraro, Hans-Joachim Ruscheweyh, Shinichi Sunagawa, Jan Roelof Van der Meer
Niche availability and competitive loss by facilitation control proliferation of bacterial strains intended for soil microbiome interventions. Nature communications 15 (1) (2024)
Anna Sintsova, Hans-Joachim Ruscheweyh, Christopher M Field, Lilith Feer, Bidong D Nguyen, Benjamin Daniel, Wolf-Dietrich Hardt, Julia A Vorholt, Shinichi Sunagawa
mBARq: a versatile and user-friendly framework for the analysis of DNA barcodes from transposon insertion libraries, knockout mutants, and isogenic strain populations. Bioinformatics (Oxford, England) 40 (2) (2024)
Alice Rouan, Melanie Pousse, Nadir Djerbi, Barbara Porro, Guillaume Bourdin, Quentin Carradec, Benjamin Cc Hume, Julie Poulain, Julie Lê-Hoang, Eric Armstrong, Sylvain Agostini, Guillem Salazar, Hans-Joachim Ruscheweyh, Jean-Marc Aury, David A Paz-García, Ryan McMinds, Marie-Josèphe Giraud-Panis, Romane Deshuraud, Alexandre Ottaviani, Lycia Die Morini, Camille Leone, Lia Wurzer, Jessica Tran, Didier Zoccola, Alexis Pey, Clémentine Moulin, Emilie Boissin, Guillaume Iwankow, Sarah Romac, Colomban de Vargas, Bernard Banaigs, Emmanuel S Boss, Chris Bowler, Eric Douville, J Michel Flores, Stéphanie Reynaud, Olivier P Thomas, Romain Troublé, Rebecca Vega Thurber, Serge Planes, Denis Allemand, Stephane Pesant, Pierre E Galand, Patrick Wincker, Shinichi Sunagawa, Eric Röttinger, Paola Furla, Christian R Voolstra, Didier Forcioli, Fabien Lombard, Eric Gilson
Telomere DNA length regulation is influenced by seasonal temperature differences in short-lived but not in long-lived reef-building corals. Nature communications 14 (1) (2023)
Caroline Belser, Julie Poulain, Karine Labadie, Frederick Gavory, Adriana Alberti, Julie Guy, Quentin Carradec, Corinne Cruaud, Corinne Da Silva, Stefan Engelen, Paul Mielle, Aude Perdereau, Gaelle Samson, Shahinaz Gas, null null, Christian R Voolstra, Pierre E Galand, J Michel Flores, Benjamin C C Hume, Gabriela Perna, Maren Ziegler, Hans-Joachim Ruscheweyh, Emilie Boissin, Sarah Romac, Guillaume Bourdin, Guillaume Iwankow, Clémentine Moulin, David A Paz García, Sylvain Agostini, Bernard Banaigs, Emmanuel S Boss, Chris Bowler, Colomban de Vargas, Eric Douville, Didier Forcioli, Paola Furla, Eric Gilson, Fabien Lombard, Stéphanie Reynaud, Stéphanie Reynaud, Shinichi Sunagawa, Olivier P Thomas, Romain Troublé, Rebecca Vega Thurber, Didier Zoccola, Claude Scarpelli, E' Krame Jacoby, Pedro H Oliveira, Jean-Marc Aury, Denis Allemand, Serge Planes, Patrick Wincker
Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition. Scientific data 10 (1) (2023)
Corentin Hochart, Lucas Paoli, Hans-Joachim Ruscheweyh, Guillem Salazar, Emilie Boissin, Sarah Romac, Julie Poulain, Guillaume Bourdin, Guillaume Iwankow, Clémentine Moulin, Maren Ziegler, Barbara Porro, Eric J Armstrong, Benjamin C C Hume, Jean-Marc Aury, Claudia Pogoreutz, David A Paz-García, Maggy M Nugues, Sylvain Agostini, Bernard Banaigs, Emmanuel S Boss, Chris Bowler, Colomban de Vargas, Eric Douville, J Michel Flores, Didier Forcioli, Paola Furla, Eric Gilson, Fabien Lombard, Stéphane Pesant, Stéphanie Reynaud, Olivier P Thomas, Romain Troublé, Patrick Wincker, Didier Zoccola, Denis Allemand, Serge Planes, Rebecca L Vega Thurber, Christian R Voolstra, Shinichi Sunagawa, Pierre E Galand
Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean. Nature communications 14 (1) (2023)
Daniel Hoces, Giorgia Greter, Markus Arnoldini, Melanie L Stäubli, Claudia Moresi, Anna Sintsova, Sara Berent, Isabel Kolinko, Florence Bansept, Aurore Woller, Janine Häfliger, Eric Martens, Wolf-Dietrich Hardt, Shinichi Sunagawa, Claude Loverdo, Emma M C Slack
Fitness advantage of Bacteroides thetaiotaomicron capsular polysaccharide in the mouse gut depends on the resident microbiota. eLife 12 (2023)
Janaina Rigonato, Marko Budinich, Alejandro A Murillo, Manoela C Brandão, Juan J Pierella Karlusich, Yawouvi Dodji Soviadan, Ann C Gregory, Hisashi Endo, Florian Kokoszka, Dean Vik, Nicolas Henry, Paul Frémont, Karine Labadie, Ahmed A Zayed, Céline Dimier, Marc Picheral, Sarah Searson, Julie Poulain, Stefanie Kandels, Stéphane Pesant, Eric Karsenti, null null, Peer Bork, Chris Bowler, Colomban de Vargas, Damien Eveillard, Marion Gehlen, Daniele Iudicone, Fabien Lombard, Hiroyuki Ogata, Lars Stemmann, Matthew B Sullivan, Shinichi Sunagawa, Patrick Wincker, Samuel Chaffron, Olivier Jaillon
Ocean-wide comparisons of mesopelagic planktonic community structures. ISME communications 3 (1) (2023)
Fabien Lombard, Guillaume Bourdin, Stéphane Pesant, Sylvain Agostini, Alberto Baudena, Emilie Boissin, Nicolas Cassar, Megan Clampitt, Pascal Conan, Ophélie Da Silva, Céline Dimier, Eric Douville, Amanda Elineau, Jonathan Fin, J Michel Flores, Jean François Ghiglione, Benjamin C C Hume, Laetitia Jalabert, Seth G John, Rachel L Kelly, Ilan Koren, Yajuan Lin, Dominique Marie, Ryan McMinds, Zoé Mériguet, Nicolas Metzl, David A Paz García, Maria Luiza Pedrotti, Julie Poulain, Mireille Pujo-Pay, Joséphine Ras, Gilles Reverdin, Sarah Romac, Alice Rouan, Eric Röttinger, Assaf Vardi, Christian R Voolstra, Clémentine Moulin, Guillaume Iwankow, Bernard Banaigs, Chris Bowler, Colomban de Vargas, Didier Forcioli, Paola Furla, Pierre E Galand, Eric Gilson, Stéphanie Reynaud, Shinichi Sunagawa, Matthew B Sullivan, Olivier P Thomas, Romain Troublé, Rebecca Vega Thurber, Patrick Wincker, Didier Zoccola, Denis Allemand, Serge Planes, Emmanuel S Boss, Gaby Gorsky
Open science resources from the Tara Pacific expedition across coral reef and surface ocean ecosystems. Scientific data 10 (1) (2023)
Álvaro Rodríguez Del Río, Joaquín Giner-Lamia, Carlos P Cantalapiedra, Jorge Botas, Ziqi Deng, Ana Hernández-Plaza, Martí Munar-Palmer, Saray Santamaría-Hernando, José J Rodríguez-Herva, Hans-Joachim Ruscheweyh, Lucas Paoli, Thomas Sebastian Benedikt Schmidt, Shinichi Sunagawa, Peer Bork, Emilia López-Solanilla, Luis Pedro Coelho, Huerta-Cepas Jaime
Functional and evolutionary significance of unknown genes from uncultivated taxa. Nature (2023)
Álvaro Rodríguez Del Río, Joaquín Giner-Lamia, Carlos P Cantalapiedra, Jorge Botas, Ziqi Deng, Ana Hernández-Plaza, Martí Munar-Palmer, Saray Santamaría-Hernando, José J Rodríguez-Herva, Hans-Joachim Ruscheweyh, Lucas Paoli, Thomas Sebastian Benedikt Schmidt, Shinichi Sunagawa, Peer Bork, Emilia López-Solanilla, Luis Pedro Coelho, Huerta-Cepas Jaime
Functional and evolutionary significance of unknown genes from uncultivated taxa. Nature 626 (7998) (2023)
Álvaro Rodríguez Del Río, Joaquín Giner-Lamia, Carlos P Cantalapiedra, Jorge Botas, Ziqi Deng, Ana Hernández-Plaza, Martí Munar-Palmer, Saray Santamaría-Hernando, José J Rodríguez-Herva, Hans-Joachim Ruscheweyh, Lucas Paoli, Thomas Sebastian Benedikt Schmidt, Shinichi Sunagawa, Peer Bork, Emilia López-Solanilla, Luis Pedro Coelho, Huerta-Cepas Jaime
Functional and evolutionary significance of unknown genes from uncultivated taxa. Nature 626 (7998) (2023)
Pierre E Galand, Hans-Joachim Ruscheweyh, Guillem Salazar, Corentin Hochart, Nicolas Henry, Benjamin C C Hume, Pedro H Oliveira, Aude Perdereau, Karine Labadie, Caroline Belser, Emilie Boissin, Sarah Romac, Julie Poulain, Guillaume Bourdin, Guillaume Iwankow, Clémentine Moulin, Eric J Armstrong, David A Paz-García, Maren Ziegler, Sylvain Agostini, Bernard Banaigs, Emmanuel S Boss, Chris Bowler, Colomban de Vargas, Eric Douville, J Michel Flores, Didier Forcioli, Paola Furla, Eric Gilson, Fabien Lombard, Stéphane Pesant, Stéphanie Reynaud, Olivier P Thomas, Romain Troublé, Didier Zoccola, Christian R Voolstra, Rebecca L Vega Thurber, Shinichi Sunagawa, Patrick Wincker, Denis Allemand, Serge Planes
Diversity of the Pacific Ocean coral reef microbiome. Nature communications 14 (1) (2023)
Daniel Hoces, Giorgia Greter, Markus Arnoldini, Melanie L Stäubli, Claudia Moresi, Anna Sintsova, Sara Berent, Isabel Kolinko, Florence Bansept, Aurore Woller, Janine Häfliger, Eric Martens, Wolf-Dietrich Hardt, Shinichi Sunagawa, Claude Loverdo, Emma M C Slack
Fitness advantage of Bacteroides thetaiotaomicron capsular polysaccharide in the mouse gut depends on the resident microbiota. eLife 12 (2023)
Daniel Hoces, Giorgia Greter, Markus Arnoldini, Melanie L Stäubli, Claudia Moresi, Anna Sintsova, Sara Berent, Isabel Kolinko, Florence Bansept, Aurore Woller, Janine Häfliger, Eric Martens, Wolf-Dietrich Hardt, Shinichi Sunagawa, Claude Loverdo, Emma M C Slack
Fitness advantage of Bacteroides thetaiotaomicron capsular polysaccharide in the mouse gut depends on the resident microbiota. eLife 12 (2023)
Eric J Armstrong, Julie Lê-Hoang, Quentin Carradec, Jean-Marc Aury, Benjamin Noel, Benjamin C C Hume, Christian R Voolstra, Julie Poulain, Caroline Belser, David A Paz García, Corinne Cruaud, Karine Labadie, Corinne Da Silva, Clémentine Moulin, Emilie Boissin, Guillaume Bourdin, Guillaume Iwankow, Sarah Romac, Sylvain Agostini, Bernard Banaigs, Emmanuel S Boss, Chris Bowler, Colomban de Vargas, Eric Douville, J Michel Flores, Didier Forcioli, Paola Furla, Pierre E Galand, Eric Gilson, Fabien Lombard, Stéphane Pesant, Stéphanie Reynaud, Matthew B Sullivan, Shinichi Sunagawa, Olivier P Thomas, Romain Troublé, Rebecca L Vega Thurber, Didier Zoccola, Serge Planes, Denis Allemand, Patrick Wincker
Host transcriptomic plasticity and photosymbiotic fidelity underpin Pocillopora acclimatization across thermal regimes in the Pacific Ocean. Nature communications 14 (1) (2023)
Alex J Veglia, Kalia S I Bistolas, Christian R Voolstra, Benjamin C C Hume, Hans-Joachim Ruscheweyh, Serge Planes, Denis Allemand, Emilie Boissin, Patrick Wincker, Julie Poulain, Clémentine Moulin, Guillaume Bourdin, Guillaume Iwankow, Sarah Romac, Sylvain Agostini, Bernard Banaigs, Emmanuel S Boss, Chris Bowler, Colomban de Vargas, Eric Douville, J Michel Flores, Didier Forcioli, Paola Furla, Pierre E Galand, Eric Gilson, Fabien Lombard, Stéphane Pesant, Stéphanie Reynaud, Shinichi Sunagawa, Olivier P Thomas, Romain Troublé, Didier Zoccola, Adrienne M S Correa, Rebecca L Vega Thurber
Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes. Communications biology 6 (1) (2023)
Daniel Hoces, Giorgia Greter, Markus Arnoldini, Melanie L Stäubli, Claudia Moresi, Anna Sintsova, Sara Berent, Isabel Kolinko, Florence Bansept, Aurore Woller, Janine Häfliger, Eric Martens, Wolf-Dietrich Hardt, Shinichi Sunagawa, Claude Loverdo, Emma M C Slack
Fitness advantage of Bacteroides thetaiotaomicron capsular polysaccharide in the mouse gut depends on the resident microbiota. eLife 12 (2023)
Álvaro Rodríguez Del Río, Joaquín Giner-Lamia, Carlos P Cantalapiedra, Jorge Botas, Ziqi Deng, Ana Hernández-Plaza, Martí Munar-Palmer, Saray Santamaría-Hernando, José J Rodríguez-Herva, Hans-Joachim Ruscheweyh, Lucas Paoli, Thomas Sebastian Benedikt Schmidt, Shinichi Sunagawa, Peer Bork, Emilia López-Solanilla, Luis Pedro Coelho, Huerta-Cepas Jaime
Functional and evolutionary significance of unknown genes from uncultivated taxa. Nature 626 (7998) (2023)
Álvaro Rodríguez Del Río, Joaquín Giner-Lamia, Carlos P Cantalapiedra, Jorge Botas, Ziqi Deng, Ana Hernández-Plaza, Martí Munar-Palmer, Saray Santamaría-Hernando, José J Rodríguez-Herva, Hans-Joachim Ruscheweyh, Lucas Paoli, Thomas Sebastian Benedikt Schmidt, Shinichi Sunagawa, Peer Bork, Emilia López-Solanilla, Luis Pedro Coelho, Huerta-Cepas Jaime
Functional and evolutionary significance of unknown genes from uncultivated taxa. Nature 626 (7998) (2023)
Thomas Sebastian Benedikt Schmidt, Anthony Fullam, Pamela Ferretti, Askarbek Orakov, Oleksandr M Maistrenko, Hans-Joachim Ruscheweyh, Ivica Letunic, Yiqian Duan, Thea Van Rossum, Shinichi Sunagawa, Daniel R Mende, Robert D Finn, Michael Kuhn, Luis Pedro Coelho, Peer Bork
SPIRE: a Searchable, Planetary-scale mIcrobiome REsource. Nucleic acids research (2023)
Álvaro Rodríguez Del Río, Joaquín Giner-Lamia, Carlos P Cantalapiedra, Jorge Botas, Ziqi Deng, Ana Hernández-Plaza, Martí Munar-Palmer, Saray Santamaría-Hernando, José J Rodríguez-Herva, Hans-Joachim Ruscheweyh, Lucas Paoli, Thomas Sebastian Benedikt Schmidt, Shinichi Sunagawa, Peer Bork, Emilia López-Solanilla, Luis Pedro Coelho, Huerta-Cepas Jaime
Functional and evolutionary significance of unknown genes from uncultivated taxa. Nature 626 (7998) (2023)
Álvaro Rodríguez Del Río, Joaquín Giner-Lamia, Carlos P Cantalapiedra, Jorge Botas, Ziqi Deng, Ana Hernández-Plaza, Martí Munar-Palmer, Saray Santamaría-Hernando, José J Rodríguez-Herva, Hans-Joachim Ruscheweyh, Lucas Paoli, Thomas Sebastian Benedikt Schmidt, Shinichi Sunagawa, Peer Bork, Emilia López-Solanilla, Luis Pedro Coelho, Huerta-Cepas Jaime
Functional and evolutionary significance of unknown genes from uncultivated taxa. Nature (2023)
Karin H U Meier, Julian Trouillon, Hai Li, Melanie Lang, Tobias Fuhrer, Nicola Zamboni, Shinichi Sunagawa, Andrew J Macpherson, Uwe Sauer
Metabolic landscape of the male mouse gut identifies different niches determined by microbial activities. Nature metabolism (2023)
Isabel Sanz-Sáez, Pablo Sánchez, Guillem Salazar, Shinichi Sunagawa, Colomban de Vargas, Chris Bowler, Matthew B Sullivan, Patrick Wincker, Eric Karsenti, Carlos Pedrós-Alió, Susana Agustí, Takashi Gojobori, Carlos M Duarte, Josep M Gasol, Olga Sánchez, Silvia G Acinas
Top abundant deep ocean heterotrophic bacteria can be retrieved by cultivation. ISME communications 3 (1) (2023)
Álvaro Rodríguez Del Río, Joaquín Giner-Lamia, Carlos P Cantalapiedra, Jorge Botas, Ziqi Deng, Ana Hernández-Plaza, Martí Munar-Palmer, Saray Santamaría-Hernando, José J Rodríguez-Herva, Hans-Joachim Ruscheweyh, Lucas Paoli, Thomas Sebastian Benedikt Schmidt, Shinichi Sunagawa, Peer Bork, Emilia López-Solanilla, Luis Pedro Coelho, Huerta-Cepas Jaime
Functional and evolutionary significance of unknown genes from uncultivated taxa. Nature (2023)
Benjamin Noel, France Denoeud, Alice Rouan, Carol Buitrago-López, Laura Capasso, Julie Poulain, Emilie Boissin, Mélanie Pousse, Corinne Da Silva, Arnaud Couloux, Eric J Armstrong, Quentin Carradec, Corinne Cruaud, Karine Labadie, Julie Lê-Hoang, Sylvie Tambutté, Valérie Barbe, Clémentine Moulin, Guillaume Bourdin, Guillaume Iwankow, Sarah Romac, Sylvain Agostini, Bernard Banaigs, Emmanuel S Boss, Chris Bowler, Colomban de Vargas, Eric Douville, J Michel Flores, Didier Forcioli, Paola Furla, Pierre E Galand, Fabien Lombard, Stéphane Pesant, Stéphanie Reynaud, Matthew B Sullivan, Shinichi Sunagawa, Olivier P Thomas, Romain Troublé, Rebecca L Vega Thurber, Denis Allemand, Serge Planes, Eric Gilson, Didier Zoccola, Patrick Wincker, Christian R Voolstra, Jean-Marc Aury
Pervasive tandem duplications and convergent evolution shape coral genomes. Genome biology 24 (1) (2023)
Ahmed A Zayed, James M Wainaina, Guillermo Dominguez-Huerta, Eric Pelletier, Jiarong Guo, Mohamed Mohssen, Funing Tian, Akbar Adjie Pratama, Benjamin Bolduc, Olivier Zablocki, Dylan Cronin, Lindsey Solden, Erwan Delage, Adriana Alberti, Jean-Marc Aury, Quentin Carradec, Corinne Da Silva, Karine Labadie, Julie Poulain, Hans-Joachim Ruscheweyh, Guillem Salazar, Elan Shatoff, null null, Ralf Bundschuh, Kurt Fredrick, Laura S Kubatko, Samuel Chaffron, Alexander I Culley, Shinichi Sunagawa, J Thomas Beatty, Patrick Wincker, Matthew B Sullivan, Silvia G Acinas, Marcel Babin, Peer Bork, Emmanuel Boss, Chris Bowler, Guy Cochrane, Colomban de Vargas, Gabriel Gorsky, Lionel Guidi, Nigel Grimsley, Pascal Hingamp, Daniele Iudicone, Olivier Jaillon, Stefanie Kandels, Lee Karp-Boss, Eric Karsenti, Fabrice Not, Hiroyuki Ogata, Nicole Poulton, Stéphane Pesant, Christian Sardet, Sabrinia Speich, Lars Stemmann, Matthew B Sullivan, Shinichi Sungawa, Patrick Wincker
Cryptic and abundant marine viruses at the evolutionary origins of Earth's RNA virome. Science (New York, N.Y.) 376 (6589) (2022)
Lucas Paoli, Hans-Joachim Ruscheweyh, Clarissa C Forneris, Florian Hubrich, Satria Kautsar, Agneya Bhushan, Alessandro Lotti, Quentin Clayssen, Guillem Salazar, Alessio Milanese, Charlotte I Carlström, Chrysa Papadopoulou, Daniel Gehrig, Mikhail Karasikov, Harun Mustafa, Martin Larralde, Laura M Carroll, Pablo Sánchez, Ahmed A Zayed, Dylan R Cronin, Silvia G Acinas, Peer Bork, Chris Bowler, Tom O Delmont, Josep M Gasol, Alvar D Gossert, André Kahles, Matthew B Sullivan, Patrick Wincker, Georg Zeller, Serina L Robinson, Jörn Piel, Shinichi Sunagawa
Biosynthetic potential of the global ocean microbiome. Nature 607 (7917) (2022)
Daniel J Richter, Romain Watteaux, Thomas Vannier, Jade Leconte, Paul Frémont, Gabriel Reygondeau, Nicolas Maillet, Nicolas Henry, Gaëtan Benoit, Ophélie Da Silva, Tom O Delmont, Antonio Fernandez-Guerra, Samir Suweis, Romain Narci, Cédric Berney, Damien Eveillard, Frederick Gavory, Lionel Guidi, Karine Labadie, Eric Mahieu, Julie Poulain, Sarah Romac, Simon Roux, Céline Dimier, Stefanie Kandels, Marc Picheral, Sarah Searson, null null, Stéphane Pesant, Jean-Marc Aury, Jennifer R Brum, Claire Lemaitre, Eric Pelletier, Peer Bork, Shinichi Sunagawa, Fabien Lombard, Lee Karp-Boss, Chris Bowler, Matthew B Sullivan, Eric Karsenti, Mahendra Mariadassou, Ian Probert, Pierre Peterlongo, Patrick Wincker, Colomban de Vargas, Maurizio Ribera d'Alcalà, Daniele Iudicone, Olivier Jaillon
Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems. eLife 11 (2022)
Anthony Fullam, Ivica Letunic, Thomas Sebastian Benedikt Schmidt, Quinten R Ducarmon, Nicolai Karcher, Supriya Khedkar, Michael Kuhn, Martin Larralde, Oleksandr M Maistrenko, Lukas Malfertheiner, Alessio Milanese, Joao Frederico Matias Rodrigues, Claudia Sanchis-López, Christian Schudoma, Damian Szklarczyk, Shinichi Sunagawa, Georg Zeller, Huerta-Cepas Jaime, Christian von Mering, Peer Bork, Daniel R Mende
proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes. Nucleic acids research (2022)
Caroline Vernette, Julien Lecubin, Pablo Sánchez, null null, Shinichi Sunagawa, Tom O Delmont, Silvia G Acinas, Eric Pelletier, Pascal Hingamp, Magali Lescot
The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes. Nucleic acids research (2022)
Fernando Meyer, Adrian Fritz, Zhi-Luo Deng, David Koslicki, Till Robin Lesker, Alexey Gurevich, Gary Robertson, Mohammed Alser, Dmitry Antipov, Francesco Beghini, Denis Bertrand, Jaqueline J Brito, C Titus Brown, Jan P Buchmann, Aydin Buluç, Bo Chen, Rayan Chikhi, Philip Thomas Lanken Conradsen Clausen, Alexandru Cristian, Piotr Wojciech Dabrowski, Aaron E Darling, Rob Egan, Eleazar Eskin, Evangelos Georganas, Eugene Goltsman, Melissa A Gray, Lars Hestbjerg Hansen, Steven Hofmeyr, Pingqin Huang, Luiz Irber, Huijue Jia, Tue Sparholt Jørgensen, Silas D Kieser, Terje Klemetsen, Axel Kola, Mikhail Kolmogorov, Anton Korobeynikov, Jason Kwan, Nathan LaPierre, Claire Lemaitre, Chenhao Li, Antoine Limasset, Fábio Malcher Miranda, Serghei Mangul, Vanessa R Marcelino, Camille Marchet, Pierre Marijon, Dmitry Meleshko, Daniel R Mende, Alessio Milanese, Niranjan Nagarajan, Jakob Nissen, Sergey Nurk, Leonid Oliker, Lucas Paoli, Pierre Peterlongo, Vitor C Piro, Jacob S Porter, Simon Rasmussen, Evan R Rees, Knut Reinert, Bernhard Y Renard, Espen Mikal Robertsen, Gail L Rosen, Hans-Joachim Ruscheweyh, Varuni Sarwal, Nicola Segata, Enrico Seiler, Lizhen Shi, Fengzhu Sun, Shinichi Sunagawa, Søren Johannes Sørensen, Ashleigh Thomas, Chengxuan Tong, Mirko Trajkovski, Julien Tremblay, Gherman Uritskiy, Riccardo Vicedomini, Zhengyang Wang, Ziye Wang, Zhong Wang, Andrew Warren, Nils Peder Willassen, Katherine Yelick, Ronghui You, Georg Zeller, Zhengqiao Zhao, Shanfeng Zhu, Jie Zhu, Ruben Garrido-Oter, Petra Gastmeier, Stéphane Hacquard, Susanne Häußler, Ariane Khaledi, Friederike Maechler, Fantin Mesny, Simona Radutoiu, Paul Schulze-Lefert, Nathiana Smit, Till Strowig, Andreas Bremges, Alexander Sczyrba, Alice Carolyn McHardy
Critical Assessment of Metagenome Interpretation: the second round of challenges. Nature methods 19 (4) (2022)
Jakob Wirbel, Konrad Zych, Morgan Essex, Nicolai Karcher, Ece Kartal, Guillem Salazar, Peer Bork, Shinichi Sunagawa, Georg Zeller
Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox. Genome biology 22 (1) (2021)
Luis Pedro Coelho, Renato Jc Alves, Rodríguez Del Río Álvaro, Pernille Neve Myers, Carlos P Cantalapiedra, Joaquín Giner-Lamia, Thomas Sebastian Schmidt, Daniel R Mende, Askarbek Orakov, Ivica Letunic, Falk Hildebrand, Thea Van Rossum, Sofia Kirke Forslund-Startceva, Supriya Khedkar, Oleksandr M Maistrenko, Shaojun Pan, Longhao Jia, Pamela Ferretti, Shinichi Sunagawa, Xing-Ming Zhao, Henrik Bjørn Nielsen, Huerta-Cepas Jaime, Peer Bork
Towards the biogeography of prokaryotic genes. Nature 601 (7892) (2021)
Serina L Robinson, Jörn Piel, Shinichi Sunagawa
A roadmap for metagenomic enzyme discovery. Natural product reports 38 (11) (2021)
Marta Royo-Llonch, Pablo Sánchez, Clara Ruiz-González, Guillem Salazar, Carlos Pedrós-Alió, Marta Sebastián, Karine Labadie, Lucas Paoli, Federico M Ibarbalz, Lucie Zinger, Benjamin Churcheward, null null, Samuel Chaffron, Damien Eveillard, Eric Karsenti, Shinichi Sunagawa, Patrick Wincker, Lee Karp-Boss, Chris Bowler, Silvia G Acinas
Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean. Nature microbiology 6 (12) (2021)
Algera Goga, Büsra Yagabasan, Karolin Herrmanns, Svenja Godbersen, Pamuditha N Silva, Remy Denzler, Mirjam Zünd, Markus Furter, Gerald Schwank, Shinichi Sunagawa, Wolf-Dietrich Hardt, Markus Stoffel
miR-802 regulates Paneth cell function and enterocyte differentiation in the mouse small intestine. Nature communications 12 (1) (2021)
Benjamin A Maier, Patrick Kiefer, Christopher M Field, Lucas Hemmerle, Miriam Bortfeld-Miller, Barbara Emmenegger, Martin Schäfer, Sebastian Pfeilmeier, Shinichi Sunagawa, Christine M Vogel, Julia A Vorholt
A general non-self response as part of plant immunity. Nature plants 7 (5) (2021)
Silvia G Acinas, Pablo Sánchez, Guillem Salazar, Francisco Miguel Cornejo-Castillo, Marta Sebastián, Ramiro Logares, Marta Royo-Llonch, Lucas Paoli, Shinichi Sunagawa, Pascal Hingamp, Hiroyuki Ogata, Gipsi Lima-Mendez, Simon Roux, José M González, Jesús Maria Arrieta, Intikhab S Alam, Allan Kamau, Chris Bowler, Jeroen Raes, Stéphane Pesant, Peer Bork, Susana Agustí, Takashi Gojobori, Dolors Vaqué, Matthew B Sullivan, Carlos Pedrós-Alió, Ramon Massana, Carlos M Duarte, Josep M Gasol
Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities. Communications biology 4 (1) (2021)
Sebastian Pfeilmeier, Gabriella C Petti, Miriam Bortfeld-Miller, Benjamin Daniel, Christopher M Field, Shinichi Sunagawa, Julia A Vorholt
The plant NADPH oxidase RBOHD is required for microbiota homeostasis in leaves. Nature microbiology 6 (7) (2021)
Mirjam Zünd, Hans-Joachim Ruscheweyh, Christopher M Field, Natalie Meyer, Miguelangel Cuenca, Daniel Hoces, Wolf-Dietrich Hardt, Shinichi Sunagawa
High throughput sequencing provides exact genomic locations of inducible prophages and accurate phage-to-host ratios in gut microbial strains. Microbiome 9 (1) (2021)
Michael Rust, Eric J N Helfrich, Michael F Freeman, Pakjira Nanudorn, Christopher M Field, Christian Rückert, Tomas Kündig, Michael J Page, Victoria L Webb, Jörn Kalinowski, Shinichi Sunagawa, Jörn Piel
A multiproducer microbiome generates chemical diversity in the marine sponge Mycale hentscheli. Proceedings of the National Academy of Sciences of the United States of America 117 (17) (2020)
Lucas Paoli, Shinichi Sunagawa
Space, time and microdiversity: towards a resolution revolution in microbiomics. Environmental microbiology reports 13 (1) (2020)
Hisashi Endo, Romain Blanc-Mathieu, Yanze Li, Guillem Salazar, Nicolas Henry, Karine Labadie, Colomban de Vargas, Matthew B Sullivan, Chris Bowler, Patrick Wincker, Lee Karp-Boss, Shinichi Sunagawa, Hiroyuki Ogata
Biogeography of marine giant viruses reveals their interplay with eukaryotes and ecological functions. Nature ecology & evolution 4 (12) (2020)
Oleksandr M Maistrenko, Daniel R Mende, Mechthild Luetge, Falk Hildebrand, Thomas S B Schmidt, Simone S Li, Joao Frederico Matias Rodrigues, Christian von Mering, Luis Pedro Coelho, Jaime Huerta-Cepas, Shinichi Sunagawa, Peer Bork
Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity. The ISME journal 14 (5) (2020)
Shinichi Sunagawa, Silvia G Acinas, Peer Bork, Chris Bowler, null null, Damien Eveillard, Gabriel Gorsky, Lionel Guidi, Daniele Iudicone, Eric Karsenti, Fabien Lombard, Hiroyuki Ogata, Stephane Pesant, Matthew B Sullivan, Patrick Wincker, Colomban de Vargas
Tara Oceans: towards global ocean ecosystems biology. Nature reviews. Microbiology 18 (8) (2020)
Alessio Milanese, Daniel R Mende, Lucas Paoli, Guillem Salazar, Hans-Joachim Ruscheweyh, Miguelangel Cuenca, Pascal Hingamp, Renato Jc Alves, Paul Igor Costea, Luis Pedro Coelho, Thomas Sebastian Benedikt Schmidt, Alexandre Almeida, Alex L Mitchell, Robert D Finn, Jaime Huerta-Cepas, Peer Bork, Georg Zeller, Shinichi Sunagawa
Microbial abundance, activity and population genomic profiling with mOTUs2. Nature communications 10 (1) (2019)
Serge Planes, Denis Allemand, Sylvain Agostini, Bernard Banaigs, Emilie Boissin, Emmanuel S Boss, Guillaume Bourdin, Chris Bowler, Eric Douville, J Michel Flores, Didier Forcioli, Paola Furla, Pierre E Galand, Jean-François Ghiglione, Eric Gilson, Fabien Lombard, Clémentine Moulin, Stéphane Pesant, Julie Poulain, Stéphanie Reynaud, Sarah Romac, Matthew B Sullivan, Shinichi Sunagawa, Olivier P Thomas, Romain Troublé, Colomban de Vargas, Rebecca L Vega Thurber, Christian R Voolstra, Patrick Wincker, Didier Zoccola, null null
The Tara Pacific expedition-A pan-ecosystemic approach of the "-omics" complexity of coral reef holobionts across the Pacific Ocean. PLoS biology 17 (9) (2019)
Jakob Wirbel, Paul-Theodor Pyl, Ece Kartal, Konrad Zych, Alireza Kashani, Alessio Milanese, Jonas S Fleck, Anita Y Voigt, Albert Palleja, Ruby Ponnudurai, Shinichi Sunagawa, Luis Pedro Coelho, Petra Schrotz-King, Emily Vogtmann, Nina Habermann, Emma Niméus, Andrew Maltez Thomas, Paolo Manghi, Sara Gandini, Davide Serrano, Sayaka Mizutani, Hirotsugu Shiroma, Satoshi Shiba, Tatsuhiro Shibata, Shinichi Yachida, Takuji Yamada, Levi Waldron, Alessio Naccarati, Nicola Segata, Rashmi Sinha, Cornelia M Ulrich, Hermann Brenner, Manimozhiyan Arumugam, Peer Bork, Georg Zeller
Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer. Nature medicine 25 (4) (2019)
Sandra Y Wotzka, Markus Kreuzer, Lisa Maier, Markus Arnoldini, Bidong D Nguyen, Alexander O Brachmann, Dorothée Lisa Berthold, Mirjam Zünd, Annika Hausmann, Erik Bakkeren, Daniel Hoces, Ersin Gül, Markus Beutler, Tamas Dolowschiak, Michael Zimmermann, Tobias Fuhrer, Kathrin Moor, Uwe Sauer, Athanasios Typas, Jörn Piel, Médéric Diard, Andrew J Macpherson, Bärbel Stecher, Shinichi Sunagawa, Emma Slack, Wolf-Dietrich Hardt
Escherichia coli limits Salmonella Typhimurium infections after diet shifts and fat-mediated microbiota perturbation in mice. Nature microbiology 4 (12) (2019)
Julien Massoni, Miriam Bortfeld-Miller, Ludwig Jardillier, Guillem Salazar, Shinichi Sunagawa, Julia A Vorholt
Consistent host and organ occupancy of phyllosphere bacteria in a community of wild herbaceous plant species. The ISME journal 14 (1) (2019)
Víctor M Eguíluz, Guillem Salazar, Juan Fernández-Gracia, John K Pearman, Josep M Gasol, Silvia G Acinas, Shinichi Sunagawa, Xabier Irigoien, Carlos M Duarte
Scaling of species distribution explains the vast potential marine prokaryote diversity. Scientific reports 9 (1) (2019)
Charlotte I Carlström, Christopher M Field, Miriam Bortfeld-Miller, Barbara Müller, Shinichi Sunagawa, Julia A Vorholt
Synthetic microbiota reveal priority effects and keystone strains in the Arabidopsis phyllosphere. Nature ecology & evolution 3 (10) (2019)
Simon Roux, Evelien M Adriaenssens, Bas E Dutilh, Eugene V Koonin, Andrew M Kropinski, Mart Krupovic, Jens H Kuhn, Rob Lavigne, J Rodney Brister, Darren P Martin, Clara Amid, Ramy K Aziz, Seth R Bordenstein, Peer Bork, Mya Breitbart, Guy R Cochrane, Rebecca A Daly, Christelle Desnues, Melissa B Duhaime, Joanne B Emerson, François Enault, Jed A Fuhrman, Pascal Hingamp, Philip Hugenholtz, Bonnie L Hurwitz, Natalia N Ivanova, Jessica M Labonté, Kyung-Bum Lee, Rex R Malmstrom, Manuel Martinez-Garcia, Ilene Karsch Mizrachi, Hiroyuki Ogata, A David Páez-Espino, Marie-Agnès Petit, Catherine Putonti, Thomas Rattei, Alejandro Reyes, Francisco Rodriguez-Valera, Karyna Rosario, Lynn Schriml, Frederik Schulz, Grieg F Steward, Matthew B Sullivan, Shinichi Sunagawa, Curtis A Suttle, Ben Temperton, Susannah G Tringe, Rebecca Vega Thurber, Nicole Suzanne Webster, Katrine L Whiteson, Steven W Wilhelm, K Eric Wommack, Tanja Woyke, Kelly C Wrighton, Pelin Yilmaz, Takashi Yoshida, Mark J Young, Natalya Yutin, Lisa Zeigler Allen, Nikos C Kyrpides, Emiley A Eloe-Fadrosh
Minimum Information about an Uncultivated Virus Genome (MIUViG). Nature biotechnology 37 (1) (2018)
Quentin Carradec, Eric Pelletier, Corinne Da Silva, Adriana Alberti, Yoann Seeleuthner, Romain Blanc-Mathieu, Gipsi Lima-Mendez, Fabio Rocha, Leila Tirichine, Karine Labadie, Amos Kirilovsky, Alexis Bertrand, Stefan Engelen, Mohammed-Amin Madoui, Raphaël Méheust, Julie Poulain, Sarah Romac, Daniel J Richter, Genki Yoshikawa, Céline Dimier, Stefanie Kandels-Lewis, Marc Picheral, Sarah Searson, null null, Olivier Jaillon, Jean-Marc Aury, Eric Karsenti, Matthew B Sullivan, Shinichi Sunagawa, Peer Bork, Fabrice Not, Pascal Hingamp, Jeroen Raes, Lionel Guidi, Hiroyuki Ogata, Colomban de Vargas, Daniele Iudicone, Chris Bowler, Patrick Wincker
A global ocean atlas of eukaryotic genes. Nature communications 9 (1) (2018)
Brandon I Morinaka, Edgars Lakis, Marjan Verest, Maximilian J Helf, Thibault Scalvenzi, Anna Lisa Vagstad, James W Sims, Shinichi Sunagawa, Muriel Gugger, Jörn Piel
Natural noncanonical protein splicing yields products with diverse β-amino acid residues. Science (New York, N.Y.) 359 (6377) (2018)
Yoann Seeleuthner, Samuel Mondy, Vincent Lombard, Quentin Carradec, Eric Pelletier, Marc Wessner, Jade Leconte, Jean-François Mangot, Julie Poulain, Karine Labadie, Ramiro Logares, Shinichi Sunagawa, Véronique de Berardinis, Marcel Salanoubat, Céline Dimier, Stefanie Kandels-Lewis, Marc Picheral, Sarah Searson, null null, Stephane Pesant, Nicole Poulton, Ramunas Stepanauskas, Peer Bork, Chris Bowler, Pascal Hingamp, Matthew B Sullivan, Daniele Iudicone, Ramon Massana, Jean-Marc Aury, Bernard Henrissat, Eric Karsenti, Olivier Jaillon, Mike Sieracki, Colomban de Vargas, Patrick Wincker
Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans. Nature communications 9 (1) (2018)
Paul Igor Costea, Falk Hildebrand, Manimozhiyan Arumugam, Fredrik Bäckhed, Martin J Blaser, Frederic D Bushman, Willem Meindert de Vos, S Dusko Ehrlich, Claire M Fraser, Masahira Hattori, Curtis Huttenhower, Ian B Jeffery, Dan Knights, James D Lewis, Ruth E Ley, Howard Ochman, Paul W O'Toole, Christopher Quince, David A Relman, Fergus Shanahan, Shinichi Sunagawa, Jun Wang, George M Weinstock, Gary D Wu, Georg Zeller, Liping Zhao, Jeroen Raes, Rob Knight, Peer Bork
Enterotypes in the landscape of gut microbial community composition. Nature microbiology 3 (1) (2017)
Paul Igor Costea, Georg Zeller, Shinichi Sunagawa, Eric Pelletier, Adriana Alberti, Florence Levenez, Melanie Tramontano, Marja Driessen, Rajna Hercog, Ferris-Elias Jung, Jens Roat Kultima, Matthew R Hayward, Luis Pedro Coelho, Emma Allen-Vercoe, Laurie Bertrand, Michael Blaut, Jillian R M Brown, Thomas Carton, Stéphanie Cools-Portier, Michelle Daigneault, Muriel Derrien, Anne Druesne, Willem Meindert de Vos, B Brett Finlay, Harry J Flint, Francisco Guarner, Masahira Hattori, Hans Heilig, Ruth Ann Luna, Johan van Hylckama Vlieg, Jana Junick, Ingeborg Klymiuk, Philippe Langella, Emmanuelle Le Chatelier, Volker Mai, Chaysavanh Manichanh, Jennifer C Martin, Clémentine Mery, Hidetoshi Morita, Paul W O'Toole, Céline Orvain, Kiran Raosaheb Patil, John Penders, Søren Persson, Nicolas Pons, Milena Popova, Anne Salonen, Delphine Saulnier, Karen P Scott, Bhagirath Singh, Kathleen Slezak, Patrick Veiga, James Versalovic, Liping Zhao, Erwin G Zoetendal, S Dusko Ehrlich, Joel Dore, Peer Bork
Towards standards for human fecal sample processing in metagenomic studies. Nature biotechnology 35 (11) (2017)
Francisco M Cornejo-Castillo, Ana M Cabello, Guillem Salazar, Patricia Sánchez-Baracaldo, Gipsi Lima-Mendez, Pascal Hingamp, Adriana Alberti, Shinichi Sunagawa, Peer Bork, Colomban de Vargas, Jeroen Raes, Chris Bowler, Patrick Wincker, Jonathan P Zehr, Josep M Gasol, Ramon Massana, Silvia G Acinas
Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton. Nature communications 7 (2016)

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Shinichi Sunagawa