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Samuel CHAFFRON

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Equipe : COMBI.

: Samuel.Chaffronatls2n.fr

: +33 (0)2 51 12 58 48

Page pro : https://pagespersowp.ls2n.fr/samuelchaffron

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Université de Nantes - faculté des Sciences et Techniques ( FST )
Petit Port
2 Chemin de la Houssinière
BP 92208
44322 Nantes Cedex 3

Batiment 34, étage 3, bureau 310



Publications référencées sur HAL

Revues internationales avec comité de lecture (ART_INT)

    • [1] S. Chaffron, E. Delage, M. Budinich, D. Vintache, N. Henry, C. Nef, M. Ardyna, A. Zayed, P. Junger, P. Galand, C. Lovejoy, A. Murray, H. Sarmento, S. Acinas, M. Babin, D. Iudicone, O. Jaillon, E. Karsenti, P. Wincker, L. Karp-Boss, M. Sullivan, C. Bowler, C. de Vargas, D. Eveillard. Environmental vulnerability of the global ocean epipelagic plankton community interactome. In Science Advances ; éd. American Association for the Advancement of Science (AAAS), 2021, vol. 7, num. 35.
      https://hal.archives-ouvertes.fr/hal-03329022
    • [2] S. Chaffron, E. Delage, M. Budinich, D. Vintache, N. Henry, C. Nef, M. Ardyna, A. Zayed, P. Junger, P. Galand, P. Galand, C. Lovejoy, A. Murray, H. Sarmento, S. Acinas, M. Babin, D. Iudicone, O. Jaillon, E. Karsenti, P. Wincker, L. Karp-Boss, M. Sullivan, C. Bowler, C. de Vargas, D. Eveillard. Environmental vulnerability of the global ocean epipelagic plankton community interactome. In Science Advances ; éd. American Association for the Advancement of Science (AAAS), 2021, vol. 7, num. 35.
      https://hal.archives-ouvertes.fr/hal-03443359
    • [3] Y. Lin, C. Moreno, A. Marchetti, H. Ducklow, O. Schofield, E. Delage, M. Meredith, Z. Li, D. Eveillard, S. Chaffron, N. Cassar. Decline in plankton diversity and carbon flux with reduced sea ice extent along the Western Antarctic Peninsula. In Nature Communications ; éd. Nature Publishing Group, 2021, vol. 12.
      https://hal.archives-ouvertes.fr/hal-03389081
    • [4] H. Kaneko, R. Blanc-Mathieu, H. Endo, S. Chaffron, T. Delmont, M. Gaia, N. Henry, R. Hernández-Velázquez, C. Nguyen, H. Mamitsuka, P. Forterre, O. Jaillon, C. de Vargas, M. Sullivan, C. Suttle, L. Guidi, H. Ogata. Eukaryotic virus composition can predict the efficiency of carbon export in the global ocean. In iScience ; éd. Elsevier, 2021, vol. 24, num. 1.
      https://hal.archives-ouvertes.fr/hal-03097258v2
    • [5] L. Meng, H. Endo, R. Blanc-Mathieu, S. Chaffron, R. Hernández-Velázquez, H. Kaneko, H. Ogata. Quantitative Assessment of Nucleocytoplasmic Large DNA Virus and Host Interactions Predicted by Co-occurrence Analyses. In MSphere ; éd. American Society for Microbiology., 2021, vol. 6, num. 2.
      https://hal.archives-ouvertes.fr/hal-03214058
    • [6] M. Fouesnard, J. Zoppi, M. Pétéra, L. Le Gleau, C. Migné, F. Devime, S. Durand, A. Benani, S. Chaffron, V. Douard, G. Boudry. Dietary switch to Western diet induces hypothalamic adaptation associated with gut microbiota dysbiosis in rats. In International Journal of Obesity ; éd. Nature Publishing Group, 2021, vol. 45, num. 6.
      https://hal.archives-ouvertes.fr/hal-03171983
    • [7] J. Gonzales, J. Marchix, L. Aymeric, C. Le Berre-Scoul, J. Zoppi, P. Bordron, M. Burel, L. Davidovic, J. Richard, A. Gaman, F. Lejuste, J. Brouillet, F. Le Vacon, S. Chaffron, M. Leboyer, H. Boudin, M. Neunlist. Fecal Supernatant from Adult with Autism Spectrum Disorder Alters Digestive Functions, Intestinal Epithelial Barrier, and Enteric Nervous System. In Microorganisms ; éd. MDPI, 2021, vol. 9, num. 8.
      https://hal.archives-ouvertes.fr/hal-03637249
    • [8] S. Chaffron, E. Delage, M. Budinich, D. Vintache, N. Henry, C. Nef, M. Ardyna, A. Zayed, P. Junger, P. Galand, C. Lovejoy, A. Murray, H. Sarmento, S. Acinas, M. Babin, D. Iudicone, O. Jaillon, E. Karsenti, P. Wincker, L. Karp-Boss, M. Sullivan, C. Bowler, C. de Vargas, D. Eveillard. Environmental vulnerability of the global ocean epipelagic plankton community interactome. In Science Advances ; éd. American Association for the Advancement of Science (AAAS), 2021, vol. 7, num. 35.
      https://hal.archives-ouvertes.fr/hal-03458184
    • [9] J. Zoppi, J. Guillaume, M. Neunlist, S. Chaffron. MiBiOmics: an interactive web application for multi-omics data exploration and integration. In BMC Bioinformatics ; éd. BioMed Central, 2021, vol. 22, num. 1.
      https://hal.archives-ouvertes.fr/hal-03101013
    • [10] A. Capotondi, M. Jacox, C. Bowler, M. Kavanaugh, P. Lehodey, D. Barrie, S. Brodie, S. Chaffron, W. Cheng, D. Dias, D. Eveillard, L. Guidi, D. Iudicone, N. Lovenduski, J. Nye, I. Ortiz, D. Pirhalla, M. Pozo Buil, V. Saba, S. Sheridan, S. Siedlecki, A. Subramanian, C. de Vargas, E. Di Lorenzo, S. Doney, A. Hermann, T. Joyce, M. Merrifield, A. Miller, F. Not, S. Pesant. Observational Needs Supporting Marine Ecosystems Modeling and Forecasting: From the Global Ocean to Regional and Coastal Systems. In Frontiers in Marine Science ; éd. Frontiers Media, 2019, vol. 6.
      https://hal.archives-ouvertes.fr/hal-02316446
    • [11] L. Arsenieff, N. Simon, F. Rigaut-Jalabert, F. Le Gall, S. Chaffron, E. Corre, E. Com, E. Bigeard, A. Baudoux. First Viruses Infecting the Marine Diatom Guinardia delicatula. In Frontiers in Microbiology ; éd. Frontiers Media, 2019, vol. 9.
      https://hal.sorbonne-universite.fr/hal-01994588
    • [12] L. Caputi, Q. Carradec, D. Eveillard, A. Kirilovsky, E. Pelletier, J. Pierella Karlusich, F. Rocha Jimenez Vieira, E. Villar, S. Chaffron, S. Malviya, E. Scalco, S. Acinas, A. Alberti, J. Aury, A. Benoiston, A. Bertrand, T. Biard, L. Bittner, M. Boccara, J. Brum, C. Brunet, G. Busseni, A. Carratalà, H. Claustre, L. Coelho, S. Colin, S. d'Aniello, C. da Silva, M. del Core, H. Doré, S. Gasparini, F. Kokoszka, J. Jamet, C. Lejeusne, C. Lepoivre, M. Lescot, G. Lima-Mendez, F. Lombard, J. Lukeš, N. Maillet, M. Madoui, E. Martinez, M. Mazzocchi, M. Néou, J. Paz-Yepes, J. Poulain, S. Ramondenc, J. Romagnan, S. Roux, D. Salvagio Manta, R. Sanges, S. Speich, M. Sprovieri, S. Sunagawa, V. Taillandier, A. Tanaka, L. Tirichine, C. Trottier, J. Uitz, A. Veluchamy, J. Veselá, F. Vincent, S. Yau, S. Kandels-Lewis, S. Searson, C. Dimier, M. Picheral, P. Bork, E. Boss, C. de Vargas, M. Follows, N. Grimsley, L. Guidi, P. Hingamp, E. Karsenti, P. Sordino, L. Stemmann, M. Sullivan, A. Tagliabue, A. Zingone, L. Garczarek, F. d'Ortenzio, P. Testor, F. Not, M. d'Alcalà, P. Wincker, C. Bowler, D. Iudicone, G. Gorsky, O. Jaillon, L. Karp-Boss, U. Krzic, H. Ogata, S. Pesant, J. Raes, E. Reynaud, C. Sardet, M. Sieracki, D. Velayoudon, J. Weissenbach. Community‐Level Responses to Iron Availability in Open Ocean Plankton Ecosystems. In Global Biogeochemical Cycles ; éd. American Geophysical Union, 2019, vol. 33, num. 3.
      https://hal.archives-ouvertes.fr/hal-02999805
    • [13] R. Tito, S. Chaffron, C. Caenepeel, G. Lima-Mendez, J. Wang, S. Vieira-Silva, G. Falony, F. Hildebrand, Y. Darzi, L. Rymenans, C. Verspecht, P. Bork, S. Vermeire, M. Joossens, J. Raes. Population-level analysis of Blastocystis subtype prevalence and variation in the human gut microbiota. In Gut ; éd. BMJ Publishing Group, 2018.
      https://hal.archives-ouvertes.fr/hal-01893208
    • [14] H. Poling, D. Wu, N. Brown, M. Baker, T. Hausfeld, N. Huynh, S. Chaffron, J. Dunn, S. Hogan, J. Wells, M. Helmrath, M. Mahé. Mechanically induced development and maturation of human intestinal organoids in vivo. In Nature Biomedical Engineering ; éd. Nature Publishing Group, 2018, vol. 2, num. 6.
      https://hal.archives-ouvertes.fr/hal-01816387
    • [15] B. Jagadeesan, P. Gerner-Smidt, M. Allard, S. Leuillet, A. Winkler, Y. Xiao, S. Chaffron, J. Vossen, S. Tang, M. Katase, P. Mcclure, B. Kimura, L. Ching Chai, J. Chapman, K. Grant. The Use of Next Generation Sequencing for Improving Food Safety: Translation into practice. In Food Microbiology ; éd. Elsevier, 2018.
      https://hal.archives-ouvertes.fr/hal-01934206
    • [16] K. Stec, L. Caputi, P. Buttigieg, D. d'Alelio, F. Ibarbalz, M. Sullivan, S. Chaffron, C. Bowler, M. Ribera d'Alcalà, D. Iudicone. Modelling plankton ecosystems in the meta-omics era. Are we ready?. In Marine Genomics ; éd. Elsevier, 2017, vol. 32.
      https://hal.archives-ouvertes.fr/hal-01584309
    • [17] G. Falony, M. Joossens, S. Vieira-Silva, J. Wang, Y. Darzi, K. Faust, A. Kurilshikov, M. Bonder, M. Valles-Colomer, D. Vandeputte, R. Tito, S. Chaffron, L. Rymenans, C. Verspecht, L. de Sutter, G. Lima-Mendez, K. d'Hoe, K. Jonckheere, D. Homola, R. Garcia, E. Tigchelaar, L. Eeckhaudt, J. Fu, L. Henckaerts, A. Zhernakova, C. Wijmenga, J. Raes. Population-level analysis of gut microbiome variation. In Science ; éd. American Association for the Advancement of Science (AAAS), 2016, vol. 352, num. 6285.
      https://hal.archives-ouvertes.fr/hal-01518384
    • [18] S. Vieira-Silva, G. Falony, Y. Darzi, G. Lima-Mendez, R. Garcia Yunta, S. Okuda, D. Vandeputte, M. Valles-Colomer, F. Hildebrand, S. Chaffron, J. Raes. Species-function relationships shape ecological properties of the human gut microbiome. In Nat Microbiol, vol. 1, num. 8. 2016
      https://hal.archives-ouvertes.fr/hal-01518385
    • [19] L. Guidi, S. Chaffron, L. Bittner, D. Eveillard, A. Larhlimi, S. Roux, Y. Darzi, S. Audic, L. Berline, J. Brum, L. Coelho, J. Espinoza, S. Malviya, S. Sunagawa, C. Dimier, S. Kandels-Lewis, M. Picheral, J. Poulain, S. Searson, L. Stemmann, F. Not, P. Hingamp, S. Speich, M. Follows, L. Karp-Boss, E. Boss, H. Ogata, S. Pesant, J. Weissenbach, P. Wincker, S. Acinas, P. Bork, D. Iudicone, M. Sullivan, J. Raes, E. Karsenti, C. Bowler, G. Gorsky. Plankton networks driving carbon export in the oligotrophic ocean. In Nature ; éd. Nature Publishing Group, 2016, vol. 532.
      https://hal.sorbonne-universite.fr/hal-01275276
    • [20] G. Lima-Mendez, K. Faust, N. Henry, J. Decelle, S. Colin, F. Carcillo, S. Chaffron, J. Ignacio-Espinosa, S. Roux, F. Vincent, L. Bittner, Y. Darzi, J. Wang, S. Audic, L. Berline, G. Bontempi, A. Cabello, L. Coppola, F. Cornejo-Castillo, F. d'Ovidio, L. Meester, I. Ferrera, M. Garet-Delmas, L. Guidi, E. Lara, S. Pesant, M. Royo-Llonch, G. Salazar, P. Sánchez, M. Sebastian, C. Souffreau, C. Dimier, M. Picheral, S. Searson, S. Kandels-Lewis, T. Coordinators, G. Gorsky, F. Not, H. Ogata, S. Speich, L. Stemmann, J. Weissenbach, P. Wincker, S. Acinas, S. Sunagawa, P. Bork, M. Sullivan, E. Karsenti, C. Bowler, C. de Vargas, J. Raes. Determinants of community structure in the global plankton interactome. In Science ; éd. American Association for the Advancement of Science (AAAS), 2015, vol. 348, num. 6237.
      https://hal.archives-ouvertes.fr/hal-01234200
    • [21] N. Le Bescot, I. Probert, M. Carmichael, J. Poulain, S. Romac, S. Colin, J. Aury, L. Bittner, S. Chaffron, M. Dunthorn, S. Engelen, O. Flegontova, L. Guidi, A. Horák, O. Jaillon, G. Lima-Mendez, J. Lukes, S. Malviya, R. Morard, M. Mulot, E. Scalco, R. Siano, F. Vincent, A. Zingone, C. Dimier, M. Picheral, S. Searson, S. Kandels-Lewis, S. Acinas, P. Bork, C. Bowler, G. Gorsky, N. Grimsley, P. Hingamp, D. Iudicone, F. Not, H. Ogata, S. Pesant, J. Raes, M. Sieracki, S. Speich, L. Stemmann, S. Sunagawa, J. Weissenbach, P. Wincker, E. Karsenti, T. Coordinators, S. Audic, N. Henry, J. Decelle, F. Mahé, R. Logares, E. Lara, C. Berney. Eukaryotic plankton diversity in the sunlit ocean. In Science ; éd. American Association for the Advancement of Science (AAAS), 2015, vol. 348, num. 6237.
      https://hal.archives-ouvertes.fr/hal-01253979
    • [22] Y. Takeuchi, S. Chaffron, M. Salcher, R. Shimizu-Inatsugi, M. Kobayashi, B. Diway, C. Mering, J. Pernthaler, K. Shimizu. Bacterial diversity and composition in the fluid of pitcher plants of the genus Nepenthes. In Syst Appl Microbiol, vol. 38, num. 5. 2015
      https://hal.archives-ouvertes.fr/hal-01518386
    • [23] S. Sunagawa, L. Coelho, S. Chaffron, J. Kultima, K. Labadie, G. Salazar, B. Djahanschiri, G. Zeller, D. Mende, A. Alberti, F. Cornejo-Castillo, P. Costea, C. Cruaud, F. d'Ovidio, S. Engelen, I. Ferrera, J. Gasol, L. Guidi, F. Hildebrand, F. Kokoszka, C. Lepoivre, G. Lima-Mendez, J. Poulain, B. Poulos, M. Royo-Llonch, H. Sarmento, S. Vieira-Silva, C. Dimier, M. Picheral, S. Searson, S. Kandels-Lewis, (. Tara Oceans Coordinators, C. Bowler, C. de Vargas, G. Gorsky, N. Grimsley, P. Hingamp, D. Iudicone, O. Jaillon, F. Not, H. Ogata, S. Pesant, S. Speich, L. Stemmann, M. Sullivan, J. Weissenbach, P. Wincker, E. Karsenti, J. Raes, S. Acinas, P. Bork. Structure and function of the global ocean microbiome. In Science ; éd. American Association for the Advancement of Science (AAAS), 2015, vol. 348, num. 6237.
      https://hal.archives-ouvertes.fr/hal-01233742
    • [24] C. Knief, N. Delmotte, S. Chaffron, M. Stark, G. Innerebner, R. Wassmann, C. Mering, J. Vorholt. Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice. In ISME Journal ; éd. Nature Publishing Group, 2012, vol. 6, num. 7.
      https://hal.archives-ouvertes.fr/hal-01518387
    • [25] B. Stecher, S. Chaffron, R. Kappeli, S. Hapfelmeier, S. Freedrich, T. Weber, J. Kirundi, M. Suar, K. Mccoy, C. Mering, A. Macpherson, W. Hardt. Like will to like: abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria. In PLoS Pathogens ; éd. Public Library of Science, 2010, vol. 6, num. 1.
      https://hal.archives-ouvertes.fr/hal-01518388
    • [26] K. Endt, B. Stecher, S. Chaffron, E. Slack, N. Tchitchek, A. Benecke, L. van Maele, J. Sirard, A. Mueller, M. Heikenwalder, A. Macpherson, R. Strugnell, C. von Mering, W. Hardt. The microbiota mediates pathogen clearance from the gut lumen after non-typhoidal salmonella diarrhea.. In PLoS Pathogens ; éd. Public Library of Science, 2010, vol. 6, num. 9.
      https://www.hal.inserm.fr/inserm-00520162
    • [27] S. Chaffron, H. Rehrauer, J. Pernthaler, C. Mering. A global network of coexisting microbes from environmental and whole-genome sequence data. In Genome Res, vol. 20, num. 7. 2010
      https://hal.archives-ouvertes.fr/hal-01518389
    • [28] L. Jensen, M. Kuhn, M. Stark, S. Chaffron, C. Creevey, J. Muller, T. Doerks, P. Julien, A. Roth, M. Simonovic, P. Bork, C. Mering. STRING 8―a global view on proteins and their functional interactions in 630 organisms. In Nucleic Acids Research ; éd. Oxford University Press, 2009, vol. 37, num. Database issue.
      https://hal.archives-ouvertes.fr/hal-01518390
    • [29] N. Delmotte, C. Knief, S. Chaffron, G. Innerebner, B. Roschitzki, R. Schlapbach, C. Mering, J. Vorholt. Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. In Proceedings of the National Academy of Sciences of the United States of America ; éd. National Academy of Sciences, 2009, vol. 106, num. 38.
      https://hal.archives-ouvertes.fr/hal-01518391
    • [30] B. Stecher, R. Robbiani, A. Walker, A. Westendorf, M. Barthel, M. Kremer, S. Chaffron, A. Macpherson, J. Buer, J. Parkhill, G. Dougan, C. Mering, W. Hardt. Salmonella enterica serovar typhimurium exploits inflammation to compete with the intestinal microbiota. In PLoS Biology ; éd. Public Library of Science, 2007, vol. 5, num. 10.
      https://hal.archives-ouvertes.fr/hal-01518394
    • [31] C. Mering, L. Jensen, M. Kuhn, S. Chaffron, T. Doerks, B. Kruger, B. Snel, P. Bork. STRING 7―recent developments in the integration and prediction of protein interactions. In Nucleic Acids Research ; éd. Oxford University Press, 2007, vol. 35, num. Database issue.
      https://hal.archives-ouvertes.fr/hal-01518392

Conférences internationales avec comité de lecture et actes (COMM_INT)

    • [33] D. Eveillard, L. Guidi, L. Bittner, S. Chaffron, J. Raes, E. Karsenti, C. Bowler, G. Gorsky. Revealing and analyzing networks of marine microbial ecosystems. In Conférence Jacques Monod - Marine Ecosystems Biology, 2015, Roscoff, France.
      https://hal.archives-ouvertes.fr/hal-01176727

Ouvrages - Chapitres d‘ouvrages et directions d‘ouvrages (OUV)

    • [34] L. Bittner, L. Guidi, S. Chaffron, D. Eveillard. Les microbiomes de l'océan : une démarche à haut débit pour une compréhension globale et systémique. In Microbiodiversité : un nouveau regard. 01-12-2018
      https://hal.archives-ouvertes.fr/hal-01996304
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