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Eukaryotic virus composition can predict the efficiency of carbon export in the global ocean

 Hiroto Kaneko , Romain Blanc-Mathieu , Hisashi Endo , Samuel Chaffron , Tom Delmont , et al.
iScience, 2021, 24 (1), pp.102002. ⟨10.1016/j.isci.2020.102002⟩
Article dans une revue hal-03097258v3
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Quantitative Assessment of Nucleocytoplasmic Large DNA Virus and Host Interactions Predicted by Co-occurrence Analyses

 Lingjie Meng , Hisashi Endo , Romain Blanc-Mathieu , Samuel Chaffron , Rodrigo Hernández-Velázquez , et al.
MSphere, 2021, 6 (2), ⟨10.1128/mSphere.01298-20⟩
Article dans une revue hal-03214058v1

Like will to like: abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria

 B. Stecher , Samuel Chaffron , R. Kappeli , S. Hapfelmeier , S. Freedrich , et al.
PLoS Pathogens, 2010, 6 (1), pp.e1000711. ⟨10.1371/journal.ppat.1000711⟩
Article dans une revue hal-01518388v1
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The Use of Next Generation Sequencing for Improving Food Safety: Translation into practice

 Balamurugan Jagadeesan , Peter Gerner-Smidt , Marc Allard , Sébastien Leuillet , Anett Winkler , et al.
Food Microbiology, 2018, ⟨10.1016/j.fm.2018.11.005⟩
Article dans une revue hal-01934206v1
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The microbiota mediates pathogen clearance from the gut lumen after non-typhoidal salmonella diarrhea.

 Kathrin Endt , Bärbel Stecher , Samuel Chaffron , Emma Slack , Nicolas Tchitchek , et al.
PLoS Pathogens, 2010, 6 (9), pp.e1001097. ⟨10.1371/journal.ppat.1001097⟩
Article dans une revue inserm-00520162v1

Environmental vulnerability of the global ocean plankton community interactome

 S. Chaffron , E. Delage , M. Budinich , D. Vintache , N. Henry , et al.
2020
Pré-publication, Document de travail hal-03971893v1

Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice

 C. Knief , N. Delmotte , Samuel Chaffron , M. Stark , G. Innerebner , et al.
The International Society of Microbiologial Ecology Journal, 2012, 6 (7), pp.1378-90. ⟨10.1038/ismej.2011.192⟩
Article dans une revue hal-01518387v1
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Population-level analysis of Blastocystis subtype prevalence and variation in the human gut microbiota

 Raul Tito , Samuel Chaffron , Clara Caenepeel , Gipsi Lima-Mendez , Jun Wang , et al.
Gut, 2018, ⟨10.1136/gutjnl-2018-316106⟩
Article dans une revue hal-01893208v1
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MiBiOmics: an interactive web application for multi-omics data exploration and integration

 Johanna Zoppi , Jean-François Guillaume , Michel Neunlist , Samuel Chaffron
BMC Bioinformatics, 2021, 22 (1), ⟨10.1186/s12859-020-03921-8⟩
Article dans une revue hal-03101013v1
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Microbial community functioning during plant litter decomposition

 Simon Schroeter , Damien Eveillard , Samuel Chaffron , Johanna Zoppi , Bernd Kampe , et al.
Scientific Reports, 2022, 12 (1), pp.7451. ⟨10.1038/s41598-022-11485-1⟩
Article dans une revue hal-03781927v1
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Structure and function of the global ocean microbiome

 Shinichi Sunagawa , Luis Pedro Coelho , Samuel Chaffron , Jens Roat Kultima , Karine Labadie , et al.
Science, 2015, 348 (6237), pp.1261359. ⟨10.1126/science.1261359⟩
Article dans une revue hal-01233742v1
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MiBiOmics: An interactive web application for multi-omics data exploration and integration

 Johanna Zoppi , Jean-François Guillaume , Michel Neunlist , Samuel Chaffron
2020
Pré-publication, Document de travail hal-02946891v1

Bacterial diversity and composition in the fluid of pitcher plants of the genus Nepenthes

 Y. Takeuchi , Samuel Chaffron , M. M. Salcher , R. Shimizu-Inatsugi , M. J. Kobayashi , et al.
Syst Appl Microbiol, 2015, 38 (5), pp.330-9. ⟨10.1016/j.syapm.2015.05.006⟩
Article dans une revue hal-01518386v1
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Community‐Level Responses to Iron Availability in Open Ocean Plankton Ecosystems

 Luigi Caputi , Quentin Carradec , Damien Eveillard , Amos Kirilovsky , Eric Pelletier , et al.
Global Biogeochemical Cycles, 2019, 33 (3), pp.391-419. ⟨10.1029/2018GB006022⟩
Article dans une revue hal-02999805v1
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Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean

 Marta Royo-Llonch , Pablo Sánchez , Clara Ruiz-González , Guillem Salazar , Carlos Pedrós-Alió , et al.
Nature Microbiology, 2021, 6 (12), pp.1561-1574. ⟨10.1038/s41564-021-00979-9⟩
Article dans une revue hal-03781908v1
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Global observation of plankton communities from space

 Hiroto Kaneko , Hisashi Endo , Nicolas Henry , Cédric Berney , Frédéric Mahé , et al.
2022
Pré-publication, Document de travail hal-03855690v1
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Disentangling temporal associations in marine microbial networks

 Ina Maria Deutschmann , Anders Krabberød , Francisco Latorre , Erwan Delage , Cèlia Marrasé , et al.
Microbiome, 2023, 11 (83), https://doi.org/10.1186/s40168-023-01523-z. ⟨10.1101/2021.07.13.452187⟩
Article dans une revue hal-03781901v2

Species-function relationships shape ecological properties of the human gut microbiome

 S. Vieira-Silva , G. Falony , Y. Darzi , G. Lima-Mendez , R. Garcia Yunta , et al.
Nat Microbiol, 2016, 1 (8), pp.16088. ⟨10.1038/nmicrobiol.2016.88⟩
Article dans une revue hal-01518385v1

Community proteogenomics reveals insights into the physiology of phyllosphere bacteria

 N. Delmotte , C. Knief , Samuel Chaffron , G. Innerebner , B. Roschitzki , et al.
Proceedings of the National Academy of Sciences of the United States of America, 2009, 106 (38), pp.16428-33. ⟨10.1073/pnas.0905240106⟩
Article dans une revue hal-01518391v1
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Plankton networks driving carbon export in the oligotrophic ocean

 Lionel Guidi , Samuel Chaffron , Lucie Bittner , Damien Eveillard , Abdelhalim Larhlimi , et al.
Nature, 2016, 532, pp.465-470. ⟨10.1038/nature16942⟩
Article dans une revue hal-01275276v1
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MAGNETO: An Automated Workflow for Genome-Resolved Metagenomics

 Benjamin Churcheward , Maxime Millet , Audrey Bihouée , Guillaume Fertin , Samuel Chaffron
mSystems, 2022, 7 (4), ⟨10.1128/msystems.00432-22⟩
Article dans une revue hal-03781944v1

Salmonella enterica serovar typhimurium exploits inflammation to compete with the intestinal microbiota

 B. Stecher , R. Robbiani , A. W. Walker , A. M. Westendorf , M. Barthel , et al.
PLoS Biology, 2007, 5 (10), pp.2177-89. ⟨10.1371/journal.pbio.0050244⟩
Article dans une revue hal-01518394v1
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Decline in plankton diversity and carbon flux with reduced sea ice extent along the Western Antarctic Peninsula

 Yajuan Lin , Carly Moreno , Adrian Marchetti , Hugh Ducklow , Oscar Schofield , et al.
Nature Communications, 2021, 12, pp.4948. ⟨10.1038/s41467-021-25235-w⟩
Article dans une revue hal-03389081v1
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Mechanically induced development and maturation of human intestinal organoids in vivo

 Holly Poling , David Wu , Nicole Brown , Michael Baker , Taylor Hausfeld , et al.
Nature Biomedical Engineering, 2018, 2 (6), pp.429 - 442. ⟨10.1038/s41551-018-0243-9⟩
Article dans une revue hal-01816387v1
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Maternal prebiotic supplementation impacts colitis development in offspring mice

 Amélie Lê , Amandine Selle , Philippe Aubert , Tony Durand , Carole Brosseau , et al.
Frontiers in Nutrition, 2023, 9, pp.988529. ⟨10.3389/fnut.2022.988529⟩
Article dans une revue hal-03930453v1

STRING 7―recent developments in the integration and prediction of protein interactions

 C. Von Mering , L. J. Jensen , M. Kuhn , Samuel Chaffron , T. Doerks , et al.
Nucleic Acids Research, 2007, 35 (Database issue), pp.D358-62. ⟨10.1093/nar/gkl825⟩
Article dans une revue hal-01518392v1
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Machine learning in marine ecology: an overview of techniques and applications

 Peter Rubbens , Stephanie Brodie , Tristan Cordier , Diogo Destro Barcellos , Paul Devos , et al.
ICES Journal of Marine Science, 2023, 80 (7), pp.1829-1853. ⟨10.1093/icesjms/fsad100⟩
Article dans une revue hal-04284704v1

STRING 8―a global view on proteins and their functional interactions in 630 organisms

 L. J. Jensen , M. Kuhn , M. Stark , Samuel Chaffron , C. Creevey , et al.
Nucleic Acids Research, 2009, 37 (Database issue), pp.D412-6. ⟨10.1093/nar/gkn760⟩
Article dans une revue hal-01518390v1
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Patterns and ecological drivers of ocean viral communities

 Jennifer Brum , J Cesar Ignacio-Espinoza , Simon Roux , Guilhem Doulcier , Silvia G. Acinas , et al.
Science, 2015, 348 (6237), pp.1261498. ⟨10.1126/science.1261498⟩
Article dans une revue hal-01768331v1
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Priorities for ocean microbiome research

 Andre Abreu , Etienne Bourgois , Adam Gristwood , Romain Troublé , Silvia Acinas , et al.
Nature Microbiology, 2022, 7 (7), pp.937-947. ⟨10.1038/s41564-022-01145-5⟩
Article dans une revue hal-03781942v1
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