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Samuel CHAFFRON

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: Samuel.Chaffronatls2n.fr

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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] I. Deutschmann, E. Delage, C. Giner, M. Sebastián, J. Poulain, J. Arístegui, C. Duarte, S. Acinas, R. Massana, J. Gasol, D. Eveillard, S. Chaffron, R. Logares. Disentangling microbial networks across pelagic zones in the tropical and subtropical global ocean. In Nature Communications ; éd. Nature Publishing Group, 2024, vol. 15, num. 1.
      https://hal.science/hal-04407573v1
    • [2] J. Jacquin, M. Budinich, S. Chaffron, V. Barbe, F. Lombard, M. Pedrotti, G. Gorsky, A. ter Halle, S. Bruzaud, M. Kedzierski, J. Ghiglione. Niche partitioning and plastisphere core microbiomes in the two most plastic polluted zones of the world ocean. In Environmental Science and Pollution Research ; éd. Springer Verlag, 2024, vol. 31, num. 28.
      https://hal.science/hal-04625794v1
    • [3] N. Giordano, M. Gaudin, C. Trottier, E. Delage, C. Nef, C. Bowler, S. Chaffron. Genome-scale community modelling reveals conserved metabolic cross-feedings in epipelagic bacterioplankton communities. In Nature Communications ; éd. Nature Publishing Group, 2024, vol. 15.
      https://hal.science/hal-04682542v1
    • [4] A. Lambert, M. Budinich, M. Mahé, D. Eveillard, S. Chaffron. Community metabolic modeling of host-microbiota interactions through multi-objective optimization. In iScience ; éd. Elsevier, 2024, vol. 27, num. 6.
      https://hal.science/hal-04674843v1
    • [5] M. Gaudin, D. Eveillard, S. Chaffron. Ecological associations distribution modelling of marine plankton at a global scale. In Philosophical Transactions of the Royal Society B: Biological Sciences ; éd. Royal Society, The, 2024, vol. 379.
      https://hal.science/hal-04674860v1
    • [6] H. Kaneko, H. Endo, N. Henry, C. Berney, F. Mahé, J. Poulain, K. Labadie, O. Beluche, R. El Hourany, S. Acinas, M. Babin, P. Bork, C. Bowler, G. Cochrane, C. de Vargas, G. Gorsky, L. Guidi, N. Grimsley, P. Hingamp, D. Iudicone, O. Jaillon, S. Kandels, E. Karsenti, F. Not, N. Poulton, S. Pesant, C. Sardet, S. Speich, L. Stemmann, M. Sullivan, S. Sunagawa, P. Wincker, R. Nakamura, L. Karp-Boss, E. Boss, C. Bowler, C. de Vargas, K. Tomii, H. Ogata, S. Chaffron. Predicting global distributions of eukaryotic plankton communities from satellite data. In ISME Communications ; éd. Springer Nature, 2023, vol. 3, num. 1.
      https://hal.science/hal-04394784v1
    • [7] I. Deutschmann, A. Krabberød, F. Latorre, E. Delage, C. Marrasé, V. Balagué, J. Gasol, R. Massana, D. Eveillard, S. Chaffron, R. Logares. Disentangling temporal associations in marine microbial networks. In Microbiome ; éd. BioMed Central, 2023, vol. 11, num. 83.
      https://hal.science/hal-03781901v2
    • [8] A. Lê, A. Selle, P. Aubert, T. Durand, C. Brosseau, P. Bordron, E. Delage, S. Chaffron, C. Petitfils, N. Cenac, M. Neunlist, M. Bodinier, M. Rolli-Derkinderen. Maternal prebiotic supplementation impacts colitis development in offspring mice. In Frontiers in Nutrition ; éd. Frontiers Media S.A., 2023, vol. 9.
      https://hal.science/hal-03930453v1
    • [9] L. Fizanne, A. Villard, N. Benabbou, S. Recoquillon, R. Soleti, E. Delage, M. Wertheimer, X. Vidal‐gómez, T. Oullier, M. Martínez, M. Neunlist, J. Boursier, R. Andriantsitohaina, S. Chaffron. Faeces‐derived extracellular vesicles participate in the onset of barrier dysfunction leading to liver diseases. In Journal of Extracellular Vesicles ; éd. Taylor & Francis, 2023, vol. 12, num. 2.
      https://hal.science/hal-04118139v1
    • [10] J. Marchix, L. Quénéhervé, P. Bordron, P. Aubert, T. Durand, T. Oullier, C. Blondeau, S. Ait Abdellah, S. Bruley Des Varannes, E. Coron, M. Neunlist, S. Chaffron. Could the Microbiota Be a Predictive Factor for the Clinical Response to Probiotic Supplementation in IBS-D? A Cohort Study. In Microorganisms ; éd. MDPI, 2023, vol. 11, num. 2.
      https://nantes-universite.hal.science/hal-04163623v1
    • [11] P. Rubbens, S. Brodie, T. Cordier, D. Destro Barcellos, P. Devos, J. Fernandes-Salvador, J. Fincham, A. Gomes, N. Handegard, K. Howell, C. Jamet, K. Kartveit, H. Moustahfid, C. Parcerisas, D. Politikos, R. Sauzède, M. Sokolova, L. Uusitalo, L. van den Bulcke, A. van Helmond, J. Watson, H. Welch, O. Beltran-Perez, S. Chaffron, D. Greenberg, B. Kühn, R. Kiko, M. Lo, R. Lopes, K. Möller, W. Michaels, A. Pala, J. Romagnan, P. Schuchert, V. Seydi, S. Villasante, K. Malde, J. Irisson. Machine learning in marine ecology: an overview of techniques and applications. In ICES Journal of Marine Science ; éd. Oxford University Press, 2023, vol. 80, num. 7.
      https://hal.science/hal-04284704v1
    • [12] L. Meng, T. Delmont, M. Gaïa, E. Pelletier, A. Fernàndez-Guerra, R. Neches, J. Wu, H. Kaneko, H. Endo, H. Ogata, S. Chaffron. Genomic adaptation of giant viruses in polar oceans. In Nature Communications ; éd. Nature Publishing Group, 2023, vol. 14, num. 1.
      https://hal.science/hal-04385851v1
    • [13] J. Rigonato, M. Budinich, A. Murillo, M. Brandão, J. Pierella Karlusich, Y. Soviadan, A. Gregory, H. Endo, F. Kokoszka, D. Vik, N. Henry, P. Frémont, K. Labadie, A. Zayed, C. Dimier, M. Picheral, S. Searson, J. Poulain, S. Kandels, S. Pesant, E. Karsenti, C. Bowler, C. de Vargas, D. Eveillard, M. Gehlen, D. Iudicone, F. Lombard, H. Ogata, L. Stemmann, M. Sullivan, S. Sunagawa, P. Wincker, S. Chaffron, O. Jaillon. Ocean-wide comparisons of mesopelagic planktonic community structures. In ISME Communications ; éd. Springer Nature, 2023, vol. 3, num. 1.
      https://hal.science/hal-04184772v1
    • [14] A. Zayed, J. Wainaina, G. Dominguez-Huerta, E. Pelletier, J. Guo, M. Mohssen, F. Tian, A. Pratama, B. Bolduc, O. Zablocki, D. Cronin, L. Solden, E. Delage, A. Alberti, J. Aury, Q. Carradec, C. da Silva, K. Labadie, J. Poulain, H. Ruscheweyh, G. Salazar, E. Shatoff, R. Bundschuh, K. Fredrick, L. Kubatko, S. Chaffron, A. Culley, S. Sunagawa, J. Kuhn, P. Wincker, M. Sullivan, S. Acinas, M. Babin, P. Bork, E. Boss, C. Bowler, G. Cochrane, C. de Vargas, G. Gorsky, L. Guidi, N. Grimsley, P. Hingamp, D. Iudicone, O. Jaillon, S. Kandels, L. Karp-Boss, E. Karsenti, F. Not, H. Ogata, N. Poulton, S. Pesant, C. Sardet, S. Speich, L. Stemmann, M. Sullivan, S. Sungawa, P. Wincker. Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome. In Science ; éd. American Association for the Advancement of Science (AAAS), 2022, vol. 376, num. 6589.
      https://hal.science/hal-03872940v1
    • [15] A. Zayed, J. Wainaina, G. Dominguez-Huerta, E. Pelletier, J. Guo, M. Mohssen, F. Tian, A. Pratama, B. Bolduc, O. Zablocki, D. Cronin, L. Solden, E. Delage, A. Alberti, J. Aury, Q. Carradec, C. da Silva, K. Labadie, J. Poulain, H. Ruscheweyh, G. Salazar, E. Shatoff, R. Bundschuh, K. Fredrick, L. Kubatko, S. Chaffron, A. Culley, S. Sunagawa, J. Kuhn, P. Wincker, M. Sullivan. Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome. In Science ; éd. American Association for the Advancement of Science (AAAS), 2022, vol. 376, num. 6589.
      https://hal.science/hal-03781924v1
    • [16] S. Schroeter, D. Eveillard, S. Chaffron, J. Zoppi, B. Kampe, P. Lohmann, N. Jehmlich, M. von Bergen, C. Sanchez-Arcos, G. Pohnert, M. Taubert, K. Küsel, G. Gleixner. Microbial community functioning during plant litter decomposition. In Scientific Reports ; éd. Nature Publishing Group, 2022, vol. 12, num. 1.
      https://hal.science/hal-03781927v1
    • [17] M. Caracciolo, F. Rigaut-Jalabert, S. Romac, F. Mahé, S. Forsans, J. Gac, L. Arsenieff, M. Manno, S. Chaffron, T. Cariou, M. Hoebeke, Y. Bozec, E. Goberville, F. Le Gall, L. Guilloux, A. Baudoux, C. de Vargas, F. Not, E. Thiébaut, N. Henry, N. Simon. Seasonal dynamics of marine protist communities in tidally mixed coastal waters. In Molecular Ecology ; éd. Wiley, 2022, vol. 31, num. 14.
      https://hal.science/hal-03781932v1
    • [18] G. Dominguez-Huerta, A. Zayed, J. Wainaina, J. Guo, F. Tian, A. Pratama, B. Bolduc, M. Mohssen, O. Zablocki, E. Pelletier, E. Delage, A. Alberti, J. Aury, Q. Carradec, C. da Silva, K. Labadie, J. Poulain, C. Bowler, D. Eveillard, L. Guidi, E. Karsenti, J. Kuhn, H. Ogata, P. Wincker, A. Culley, S. Chaffron, M. Sullivan. Diversity and ecological footprint of Global Ocean RNA viruses. In Science ; éd. American Association for the Advancement of Science (AAAS), 2022, vol. 376, num. 6598.
      https://hal.science/hal-03781935v1
    • [19] B. Churcheward, M. Millet, A. Bihouée, G. Fertin, S. Chaffron. MAGNETO: An Automated Workflow for Genome-Resolved Metagenomics. In mSystems, vol. 7, num. 4. 15-06-2022
      https://hal.science/hal-03781944v1
    • [20] A. Abreu, E. Bourgois, A. Gristwood, R. Troublé, S. Acinas, P. Bork, E. Boss, C. Bowler, M. Budinich, S. Chaffron, C. de Vargas, T. Delmont, D. Eveillard, L. Guidi, D. Iudicone, S. Kandels, H. Morlon, F. Lombard, R. Pepperkok, J. Karlusich, G. Piganeau, A. Régimbeau, G. Sommeria-Klein, L. Stemmann, M. Sullivan, S. Sunagawa, P. Wincker, O. Zablocki, D. Arendt, J. Bilic, R. Finn, E. Heard, B. Rouse, J. Vamathevan, R. Casotti, I. Cancio, M. Cunliffe, A. Kervella, W. Kooistra, M. Obst, N. Pade, D. Power, I. Santi, T. Tsagaraki, J. Vanaverbeke. Priorities for ocean microbiome research. In Nature Microbiology ; éd. Nature Publishing Group, 2022, vol. 7, num. 7.
      https://hal.science/hal-03781942v1
    • [21] 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.science/hal-03443359v2
    • [22] 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.science/hal-03389081v1
    • [23] 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.science/hal-03097258v3
    • [24] 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.science/hal-03214058v1
    • [25] 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.science/hal-03171983v1
    • [26] 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.science/hal-03637249v1
    • [27] 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.science/hal-03101013v1
    • [28] M. Royo-Llonch, P. Sánchez, C. Ruiz-González, G. Salazar, C. Pedrós-Alió, M. Sebastián, K. Labadie, L. Paoli, F. M. Ibarbalz, L. Zinger, B. Churcheward, S. Chaffron, D. Eveillard, E. Karsenti, S. Sunagawa, P. Wincker, L. Karp-Boss, C. Bowler, S. Acinas. Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean. In Nature Microbiology ; éd. Nature Publishing Group, 2021, vol. 6, num. 12.
      https://hal.science/hal-03781908v1
    • [29] 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.science/hal-02316446v1
    • [30] 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-01994588v1
    • [31] 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, 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, C. Bowler, D. Iudicone. 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.science/hal-02999805v1
    • [32] 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.science/hal-01893208v1
    • [33] 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.science/hal-01816387v1
    • [34] 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.science/hal-01934206v1
    • [35] 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.science/hal-01584309v1
    • [36] 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.science/hal-01518384v1
    • [37] 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.science/hal-01518385v1
    • [38] 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-01275276v1
    • [39] 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.science/hal-01234200v1
    • [40] 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.science/hal-01253979v1
    • [41] 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.science/hal-01518386v1
    • [42] 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.science/hal-01233742v1
    • [43] J. Brum, J. Ignacio-Espinoza, S. Roux, G. Doulcier, S. Acinas, A. Alberti, S. Chaffron, C. Cruaud, C. de Vargas, J. Gasol, G. Gorsky, A. Gregory, L. Guidi, P. Hingamp, D. Iudicone, F. Not, H. Ogata, S. Pesant, B. Poulos, S. Schwenck, S. Speich, C. Dimier, S. Kandels-Lewis, M. Picheral, S. Searson, P. Bork, C. Bowler, S. Sunagawa, P. Wincker, E. Karsenti, M. Sullivan, C. Ignacio-Espinoza, M. Gasol, C. Gregory, M. Schwenck. Patterns and ecological drivers of ocean viral communities. In Science ; éd. American Association for the Advancement of Science (AAAS), 2015, vol. 348, num. 6237.
      https://amu.hal.science/hal-01768331v1
    • [44] 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 The International Society of Microbiologial Ecology Journal ; éd. Nature Publishing Group, 2012, vol. 6, num. 7.
      https://hal.science/hal-01518387v1
    • [45] 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.science/hal-01518388v1
    • [46] 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://inserm.hal.science/inserm-00520162v1
    • [47] 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.science/hal-01518389v1
    • [48] 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.science/hal-01518390v1
    • [49] 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.science/hal-01518391v1
    • [50] 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.science/hal-01518394v1
    • [51] 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.science/hal-01518392v1

Conférences internationales avec comité de lecture et actes (COMM_INT)

    • [53] O. El Khettari, S. Quiniou, S. Chaffron. Annotation d'interactions hôte-microbiote dans des articles scientifiques par similarité sémantique avec une ontologie. In 18e Conférence en Recherche d'Information et Applications -- 16e Rencontres Jeunes Chercheurs en RI -- 30e Conférence sur le Traitement Automatique des Langues Naturelles -- 25e Rencontre des Étudiants Chercheurs en Informatique pour le Traitement Automatique des Langues, 2023, Paris, France.
      https://hal.science/hal-04309357v1
    • [54] O. El Khettari, S. Quiniou, S. Chaffron. Building a Corpus for Biomedical Relation Extraction of Species Mentions. In The 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks, juillet 2023, Toronto, Canada.
      https://hal.science/hal-04309226v1
    • [55] R. Blan-Mathieu, H. Kaneko, H. Endo, S. Chaffron, L. Guidi, H. Ogata. Large DNA viruses of microalgae are predicted to enhance carbon export efficiency in the global sunlit ocean. In 5e Colloque de Génomique Environnementale, 2019, La Rochelle, France.
      https://hal.science/hal-04024043v1
    • [56] S. Ayata, E. Faure, A. Benoiston, F. Not, O. Aumont, L. Guidi, S. Chaffron, D. Eveillard, L. Bittner. From plankton functional traits to marine ecosystem functions: Assessing functional diversity of plankton communities from high throughput -omics data and its impact on oceanic biogeochemical cycles. In Functional Ecology Conference, 2018, Nancy, France.
      https://hal.science/hal-04024046v1
    • [57] A. Benoiston, L. Bittner, L. Guidi, S. Chaffron, D. Eveillard, S. Ayata, G. Jean, E. Pelletier, S. Pesant, C. de Vargas, E. Karsenti, C. Bowler, G. Gorsky, T. Consortium. Plankton networks correlated to the biological carbon pump in the global ocean. In Journée analyse des réseau, GDR génomique environnementale, 2017, Nantes, France.
      https://hal.science/hal-04024048v1
    • [58] 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.science/hal-01176727v1

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

    • [59] 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.science/hal-01996304v1

Autres publications (AUTRES)

    • [60] S. Ayata, E. Faure, A. Benoiston, O. Silva, V. Sonnet, F. Benedetti, F. Not, O. Aumont, L. Guidi, S. Chaffron, D. Eveillard, L. Bittner. Assessing functional diversity of plankton communities from high throughput –omics data. In Colloque de Bilan et de Prospective du programme LEFE, mars 2018, Clermont-Ferrand, France.
      https://hal.science/hal-04021818v1
    • [61] A. Benoiston, E. Eveillard, S. Chaffron, S. Ayata, C. Bowler, L. Guidi, E. Delage, G. Jean, L. Bittner, T. Corrdinators. Biological pump processes are driven by microbial networks in the global oligotrophic ocean. In ISME17, août 2018, Leipzig, Allemagne.
      https://hal.science/hal-04021817v1
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