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BioinformatiqueBiologie des SystèmesMétagénomiqueModélisation Biologique

Samuel Chaffron

Chercheur.euse – Chargé / chargée de recherche

Equipe :

Employeur : Centre National de la Recherche Scientifique

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BioinformatiqueBiologie des systèmesMétagénomique / MicrobiomesIntégration multi-omiquesÉcologie et évolution

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Publications déposées sur HAL

Nombre de publications retournées : 101

Revues internationales avec comité de lecture

[1] 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, vol. 5, no. 10, pp. 2177-89, DOI

[2] 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, vol. 35, no. Database issue, pp. D358-62, DOI

[3] S. Chaffron, C. Mering. Termites in the woodwork, in Genome Biology, vol. 8, no. 11, pp. 229, DOI

[4] 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, vol. 37, no. Database issue, pp. D412-6, DOI

[5] 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, vol. 106, no. 38, pp. 16428-33, DOI

[6] 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, vol. 6, no. 1, pp. e1000711, DOI

[7] 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, vol. 6, no. 9, pp. e1001097, DOI

[8] 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, no. 7, pp. 947-59, DOI

[9] 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, vol. 6, no. 7, pp. 1378-90, DOI

[10] 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, vol. 348, no. 6237, pp. 1262073, DOI

[11] 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, vol. 348, no. 6237, pp. 1261605, DOI

[12] 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, no. 5, pp. 330-9, DOI

[13] 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, vol. 348, no. 6237, pp. 1261359, DOI

[14] 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, vol. 348, no. 6237, pp. 1261498, DOI

[15] 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, vol. 352, no. 6285, pp. 560-4, DOI

[16] 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, no. 8, pp. 16088, DOI

[17] 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, vol. 532, pp. 465–470, DOI

[18] 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, vol. 32, pp. 1-17, DOI

[19] 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, DOI

[20] 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, vol. 2, no. 6, pp. 429 – 442, DOI

[21] 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, DOI

[22] 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, vol. 6, pp. 623, DOI

[23] 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, vol. 9, pp. 3235, DOI

[24] L. Caputi, Q. Carradec, D. Eveillard, A. Kirilovsky, É. 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, vol. 33, no. 3, pp. 391-419, DOI

[25] C. Belkhou, R. Tadeo, R. Bacigalupe, M. Valles-Colomer, S. Chaffron, M. Joossens, A. Obregon, L. Marín Reyes, O. Trujillo, G. Huys, J. Raes. Treponema peruense sp. nov., a commensal spirochaete isolated from human faeces, in International Journal of Systematic and Evolutionary Microbiology, vol. 71, no. 10, DOI

[26] 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, vol. 7, no. 35, pp. eabg1921, DOI

[27] 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, vol. 12, pp. 4948, DOI

[28] 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, vol. 24, no. 1, pp. 102002, DOI

[29] 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, vol. 6, no. 2, DOI

[30] 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, vol. 45, no. 6, pp. 1271-1283, DOI

[31] 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, vol. 9, no. 8, pp. 1723, DOI

[32] J. Zoppi, J. Guillaume, M. Neunlist, S. Chaffron. MiBiOmics: an interactive web application for multi-omics data exploration and integration, in BMC Bioinformatics, vol. 22, no. 1, DOI

[33] 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, vol. 6, no. 12, pp. 1561-1574, DOI

[34] 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, vol. 376, no. 6589, pp. 156-162, DOI

[35] 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, vol. 12, no. 1, pp. 7451, DOI

[36] 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, vol. 31, no. 14, pp. 3761-3783, DOI

[37] 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, vol. 376, no. 6598, pp. 1202-1208, DOI

[38] B. Churcheward, M. Millet, A. Bihouée, G. Fertin, S. Chaffron. MAGNETO: An Automated Workflow for Genome-Resolved Metagenomics, in mSystems, vol. 7, no. 4, DOI

[39] 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, vol. 7, no. 7, pp. 937-947, DOI

[40] F. Ibarbalz, N. Henry, F. Mahé, M. Ardyna, A. Zingone, E. Scalco, C. Lovejoy, F. Lombard, O. Jaillon, D. Iudicone, S. Malviya, M. Sullivan, S. Chaffron, E. Karsenti, M. Babin, E. Boss, P. Wincker, L. Zinger, C. de Vargas, C. Bowler, L. Karp-Boss. Pan-Arctic plankton community structure and its global connectivity, in Elementa: Science of the Anthropocene, vol. 11, no. 1, pp. 00060, DOI

[41] 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, vol. 11, no. 83, pp. https://doi.org/10.1186/s40168-023-01523-z, DOI

[42] 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, vol. 9, pp. 988529, DOI

[43] L. Fizanne, A. Villard, N. Benabbou, S. Recoquillon, R. Soleti, E. Delage, M. Wertheimer, X. Vidal-Gomez, 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, vol. 12, no. 2, pp. 12303, DOI

[44] J. Marchix, L. Quénéhervé, P. Bordron, P. Aubert, T. Durand, T. Oullier, C. Blondeau, S. Ait Abdellah, S. Bruley Des Varannes, S. Chaffron, E. Coron, M. Neunlist. Could the Microbiota Be a Predictive Factor for the Clinical : Response to Probiotic Supplementation in IBS-D? A Cohort Study, in Microorganisms, vol. 11, no. 2, pp. 277, DOI

[45] 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, vol. 80, no. 7, pp. 1829-1853, DOI

[46] 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, vol. 14, no. 1, pp. 6233, DOI

[47] 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, vol. 3, no. 1, pp. 101, DOI

[48] 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, vol. 3, no. 1, pp. 83, DOI

[49] 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, vol. 15, no. 1, pp. 126, DOI

[50] 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, vol. 31, no. 28, pp. 41118-41136, DOI

[51] 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, vol. 15, pp. 2721, DOI

[52] A. Lambert, M. Budinich, M. Mahé, S. Chaffron, D. Eveillard. Community metabolic modeling of host-microbiota interactions through multi-objective optimization, in iScience, vol. 27, no. 6, pp. 110092, DOI

[53] 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, vol. 379, DOI

[54] C. Cardaillac, C. Trottier, C. Brochard, P. Aubert, P. Bordron, M. Perrouin-Verbe, T. Thubert, S. Chaffron, A. Levesque, S. Ploteau, J. Marchix, M. Neunlist. Gut, vaginal, and urinary microbiota as potential biomarkers of sensitization in women with chronic pelvic pain, in American Journal of Obstetrics and Gynecology, DOI

[55] U. Chandola, M. Gaudin, C. Trottier, L. Lavier-Aydat, E. Manirakiza, S. Menicot, E. Fischer, I. Louvet, T. Lacour, T. Chaumier, A. Tanaka, G. Pohnert, S. Chaffron, L. Tirichine. Non-cyanobacterial diazotrophs support the survival of marine microalgae in nitrogen-depleted environment, in Genome Biology, vol. 26, no. 1, pp. 146, DOI

[56] J. Pierella Karlusich, K. Cosnier, L. Zinger, N. Henry, C. Nef, G. Bernard, E. Scalco, E. Dvorak, S. Acinas, M. Babin, P. Bork, E. Boss, C. Bowler, G. Cochrane, C. de Vargas, G. Gorsky, N. Grimsley, L. Guidi, D. Iudicone, O. Jaillon, S. Kandels, L. Karp-Boss, E. Karsenti, F. Not, H. Ogata, S. Pesant, N. Poulton, C. Sardet, S. Speich, L. Stemmann, M. Sullivan, S. Sunagawa, P. Wincker, F. Rocha Jimenez Vieira, E. Delage, S. Chaffron, S. Ovchinnikov, A. Zingone, C. Bowler. Patterns and drivers of diatom diversity and abundance in the global ocean, in Nature Communications, vol. 16, no. 1, pp. 3452, DOI

[57] M. Boosten, C. Sant, O. da Silva, S. Chaffron, L. Guidi, L. Leclère. Independent transitions to fully planktonic life cycles shaped the global distribution of medusozoans in the epipelagic zone, in Proceedings of the National Academy of Sciences of the United States of America, vol. 122, no. 22, pp. e2415979122, DOI

[58] H. Sarmento, P. Huber, C. Santos-Júnior, A. Abreu, T. Makhalanyane, N. Karenyi, E. Rocke, S. Acinas, L. Amaral-Zettler, M. Araujo, C. Arboleda-Baena, G. Bachi, D. Bănaru, É. Becker, M. Bellacicco, F. Benedetti, C. Bowler, B. Buongiorno Nardelli, L. Campese, D. Canu, U. Cardini, R. Casotti, S. Chaffron, D. Couet, H. Cruz de Carvalho, D. D’alelio, G. Dall’olmo, N. Dames, C. de Vargas, C. Delgado, C. Dimier, D. Eveillard, S. Faye, M. Flores, P. Galand, L. Gammage, J. Gasol, M. Gehlen, A. Green Koettker, V. Guinder, T. Heggeset, L. Heimbürger-Boavida, A. Hidas, C. Hörstmann, F. Ibarbalz, O. Jaillon, D. Johns, F. Jordán, P. Junger, K. Labadie, R. Laxenaire, S. Libralato, C. Longo, R. Lopes, M. Loschi, S. Mafwila, L. Maiorano, M. Meredith, E. Muxagata, G. Nguyen, S. Nicolau, P. Oliveira, L. Olivier, R. Palmela de Oliveira, N. Patin, P. Pita, G. Pohnert, A. Ruggiero, A. S. Freire, M. Saraceno, R. Schwamborn, A. Soccodato, C. Solidoro, D. Sousa, S. Speich, S. Sunagawa, A. Tagliabue, L. Thompson, R. Troublé, L. Veado, F. Vincent, M. Vogt, S. Zunino, S. Pesant, D. Iudicone. The southern gap in ocean microbiome science, in Ocean Microbiology, vol. 1, no. 1, pp. 6, DOI

[59] M. Beauvais, P. Schatt, T. Soulié, S. Lambert, L. Montiel, M. Gaudin, S. Chaffron, R. Logares, F. Bouget, P. Galand. Functional complementarity between vitamin B1 and B12 metabolisms shapes seasonal marine microbial communities, in The International Society of Microbiologial Ecology Journal, vol. 20, no. 1, pp. wrag029, DOI

[60] P. Junger, V. Kavagutti, I. Deutschmann, C. Gazulla, P. Huber, M. Menezes, R. Paranhos, A. Amado, I. Ferrera, J. Rigonato, S. Chaffron, J. Gasol, R. Logares, H. Sarmento. Ecological Processes Shaping Marine Microbial Assemblages Diverge Between Equatorial and Temperate Time‐Series, in Molecular Ecology, vol. 35, no. 2, pp. e70241, DOI

[61] G. Douglas, N. Tromas, M. Gaudin, P. Lypaczewski, L. Bobay, B. Shapiro, S. Chaffron. Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny, in The International Society of Microbiologial Ecology Journal, vol. 20, no. 1, pp. wraf275, DOI

[62] J. Dias, V. Pochic, S. Chaffron, P. Gernez. Diatoms vs dinoflagellates: a temporal network analysis of bloom impacts on phytoplankton diversity and community structure in French coastal waters, in ISME Communications, vol. 6, no. 1, DOI

Conférences internationales avec comité de lecture et actes

[63] 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, Roscoff, France,

[64] 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 réseaux, GDR génomique environnementale, Nantes, France,

[65] 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, Nancy, France,

[66] 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, La Rochelle, France,

[67] 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, Paris, France,

[68] O. El Khettari, S. Chaffron, S. Quiniou. Building a Corpus for Biomedical Relation Extraction of Species Mentions, in The 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks, Toronto, Canada, DOI

[69] O. El Khettari, N. Nishida, S. Liu, R. Munne, Y. Yamagata, S. Chaffron, Y. Matsumoto, S. Quiniou. Mention-Agnostic Information Extraction for Ontological Annotation of Biomedical Articles, in Proceedings of the 23rd Workshop on Biomedical Natural Language Processing, Bangkok, Thaïlande, DOI

[70] B. Quemeneur, A. Bihouée, S. Chaffron, C. Médigue, H. Ménager, A. Gaignard. A multi-modal and temporal antibiotic resistance knowledge graph, in SWAT4HCLS 2025 – 16th International SWAT4HCLS conference : Semantic Web Applications and Tools for Health Care and Life Sciences, Barcelone, Espagne,

[71] U. Le Clanche, M. Atay, É. Bannier, A. Baudot, L. Bellenger, A. Bodrug-Schepers, S. Chaffron, E. Charpentier, E. Corre, C. Frioux, A. Lardenois, F. Lemoine, C. Maumet, C. Noel, P. Paul-Gilloteaux, P. Simion, M. Térézol, O. Dameron, A. Gaignard. Ground-truth Construction and Evaluation of LLM Contribution to Life Sciences Tool Annotation, in LLM4KGOE 2026 – Workshop on LLM-driven Knowledge Graph and Ontology Engineering, Co-located with ESWC 2026, Dubrovnik, Croatie,

[72] J. Lao, R. Tackx, A. Dieuaide, T. Mignon, C. Siguret, H. Lefeuvre, B. Quemeneur, P. Marin, B. Batut, N. Goué, E. Ruppe, G. Le Corguillé, A. Consortium, A. Bihouée, S. Chaffron, A. Gaignard, P. Glaser, C. Medigue, F. Mareuil. ABRomics: a platform for antibiotic resistance research and public health using an integrated "One Health" approach, in ECCB 2026 – 25th European Conference on Computational Biology, Geneva, Suisse,

Conférences nationales avec comité de lecture et actes

[73] O. El Khettari, S. Quiniou, S. Chaffron. Summarization for Generative Relation Extraction in the Microbiome Domain, in 20e Conférence en Recherche d’Information et Applications (CORIA) 32ème Conférence sur le Traitement Automatique des Langues Naturelles (TALN) 27ème Rencontre des Étudiants Chercheurs en Informatique pour le Traitement Automatique des Langues (RECITAL) Les 18e Rencontres Jeunes Chercheurs en RI (RJCRI), Marseille, France,

Ouvrages – Chapitres d'ouvrages et directions d'ouvrages

[74] L. Bittner, L. Guidi, S. Chaffron, D. Eveillard. Les microbiomes de l'océan : une démarche à haut débit pour une compréhension globale et systémique,

Autres publications

[75] 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, Clermont-Ferrand, France,

[76] 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, Leipzig, Allemagne,

[77] 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 plankton community interactome, DOI

[78] M. Royo-Llonch, P. Sánchez, C. Ruiz-González, G. Salazar, C. Pedrós-Alió, K. Labadie, L. Paoli, S. Chaffron, D. Eveillard, E. Karsenti, S. Sunagawa, P. Wincker, L. Karp-Boss, C. Bowler, S. Acinas. Ecogenomics of key prokaryotes in the arctic ocean, DOI

[79] S. de Scally, S. Chaffron, T. Makhalanyane. Polar opposites; bacterioplankton susceptibility and mycoplankton resistance to ocean acidification, DOI

[80] J. Zoppi, J. Guillaume, M. Neunlist, S. Chaffron. MiBiOmics: An interactive web application for multi-omics data exploration and integration, DOI

[81] 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 global ocean, DOI

[82] 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. Gall, L. Guilloux, A. Baudoux, C. de Vargas, F. Not, E. Thiébaut, N. Henry, N. Simon. Seasonal temporal dynamics of marine protists communities in tidally mixed coastal waters, DOI

[83] U. Chandola, C. Trottier, M. Gaudin, E. Manirakiza, S. Menicot, I. Louvet, T. Lacour, T. Chaumier, A. Tanaka, S. Chaffron, L. Tirichine. Combined in vivo and in situ genome-resolved metagenomics reveals novel symbiotic nitrogen fixing interactions between non-cyanobacterial diazotrophs and microalgae, DOI

[84] H. Kaneko, H. Endo, N. Henry, C. Berney, F. Mahé, J. Poulain, K. Labadie, O. Beluche, R. El Hourany, S. Chaffron, P. Wincker, R. Nakamura, L. Karp-Boss, E. Boss, C. Bowler, C. de Vargas, K. Tomii, H. Ogata. Global observation of plankton communities from space, DOI

[85] J. Rigonato, M. Budinich, A. Murillo, M. Brandão, J. 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, P. Bork, C. Bowler, S. Chaffron, C. de Vargas, D. Eveillard, M. Gehlen, D. Iudicone, F. Lombard, H. Ogata, L. Stemmann, M. Sullivan, S. Sunagawa, P. Wincker, O. Jaillon. Insights into biotic and abiotic modulation of ocean mesopelagic communities, DOI

[86] C. Guieu, S. Bonnet, F. Abadou, S. Alliouane, S. Arnaud-Haond, V. Arnone, A. Baudoux, C. Baumas, L. Beillard, M. Benavides, I. Berman-Frank, N. Bhairy, E. Bigeard, C. Boulart, P. Bouruet-Aubertot, P. Boyd, M. Bressac, M. Camps, S. Chaffron, V. Chavagnac, S. Chevaillier, J. Collot, Y. Cuypers, G. de Liège, E. de Saint Léger, C. de Vargas, K. Desboeufs, M. Desgranges, C. Destrigneville, C. Dimier, W. Diruit, D. Dissard, J. Doussin, A. Dufour, G. Dulaquais, J. Fernandez, A. Feron, M. Ferrieux, A. Filella, H. Forrer, P. Fourrier, J. Gac, M. Gachenot, C. Gaimoz, L. Garczarek, F. Gazeau, A. González, D. González‐Santana, T. Gorgues, N. Grima, J. Grisoni, O. Grosso, C. Guigue, J. Habasque, L. Heimbürger-Boavida, C. Jeandel, C. Jeanthon, E. Journet, A. Knapp, F. Lacan, F. Le Gall, F. Le Moigne, P. Le Moal, K. Leblanc, N. Leblond, A. Lebourges-Dhaussy, J. Leconte, D. Lefèvre, F. Lombard, A. Lorrain, C. Lory, C. Maes, L. Mahieu, D. Marie, C. Mazoyer, C. Menkes, V. Michoud, M. Montanes, F. Not, S. Nunige, F. Paparella, M. Patriat, B. Pelletier, A. Petrenko, H. Planquette, D. Point, G. Portlock, I. Probert, E. Pulido-Villena, M. Ratin, L. Ratnarajah, R. Riso, A. Rizzo, P. Salaun, G. Sarthou, C. Schmechtig, K. Sellegri, N. Simon, A. Tagliabue, V. Taillandier, C. Tamburini, M. Tedetti, F. Thibon, C. Tilliette, N. Torres-Rodríguez, S. Triquet, J. Uitz, F. van Wambeke, D. Vaulot, N. Vigier, M. Vilain, M. Vorrath, L. Weppe, H. Whitby. BIOGEOCHEMICAL dataset collected during the TONGA cruise, DOI

[87] 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, DOI

[88] M. Boosten, C. Sant, O. da Silva, S. Chaffron, L. Guidi, L. Leclère. Loss of the benthic life stage in Medusozoa and colonization of the open ocean, DOI

[89] A. Lambert, M. Budinich, M. Mahé, S. Chaffron, D. Eveillard. Community metabolic modeling of host-microbiota interactions through multi-objective optimization, DOI

[90] M. Burel, A. Régimbeau, S. Chaffron, D. Eveillard, E. Pelletier. PhotoEukStein: Towards an omics-based definition of unicellular eukaryote phototrophs functional traits via metabolic modelling, DOI

[91] G. Douglas, N. Tromas, M. Gaudin, P. Lypaczewksi, L. Bobay, B. Shapiro, S. Chaffron. Co-occurrence drives horizontal gene transfer among marine prokaryotes, DOI

[92] B. Quemeneur, A. Bihouée, S. Chaffron, C. Médigue, H. Ménager, A. Gaignard. A multi-modal and temporal antibiotic resistance knowledge graph, in JOBIM 2025, Bordeaux, France,

[93] H. Lefeuvre, A. Bihouée, B. Batut, S. Chaffron, C. Médigue, P. Glaser. ABRomics-analysis : developing Metagenomic Workflows for National Antibiotic Resistance Surveillance Platform, in JOBIM, Bordeaux, France,

[94] M. Crédeville, R. El Hourany, S. Sow, J. Poulain, M. Depaty, E. Pelletier, Z. Mériguet, M. Racault, A. Perdereau, L. Bertrand, F. Gavory, P. Gourvil, C. Orvain, M. Ratin, L. Garczarek, T. Delmont, A. Thurotte, C. Le Quéré, J. Pierella Karlusich, C. Bowler, S. Chaffron, P. Wincker, F. Lombard, O. Jaillon. Genomics-based quantitative biogeography of marine plankton, DOI

[95] G. Gautreau, E. Belda, C. Blanchet, S. Chaffron, H. Chiapello, K. Clement, A. Fraboulet, A. Gaignard, R. Patino Navarrete, D. Salgado, J. van Helden, N. Pons, C. Medigue, N. Gandon. Problématiques soulevées par l'analyse et la gestion des données du microbiome humain,

[96] O. El Khettari, D. Batteux, S. Quiniou, S. Chaffron. MicrobioRel : A Set of Datasets for Microbiome Relation Extraction, DOI

[97] A. Lambert, S. Chaffron, D. Eveillard. MIMEco: Multi-objective metabolic modeling to predict and explain pairwise interactions, DOI

[98] J. Dias, V. Pochic, S. Chaffron, P. Gernez. Diatoms vs dinoflagellates: a temporal network analysis of bloom impacts on diversity and phytoplankton community structure in French coastal waters, DOI

[99] L. Patron, F. Petrilli, A. Bout, M. Gaudin, L. Gouhier, C. Hubert, D. Réveillon, S. Chaffron, E. Briand, M. Garnier. Multi-omics uncovers nutrient stress-driven interactions in the <i>Prymnesium parvum</i> holobiont, with vitamin B12 limitation highlighting mutualism, DOI

[100] P. Barbet, E. Belda, A. Bihouee, A. Bodrug, P. Breugnot, S. Delmotte, G. Gautreau, M. Lasmenes, R. Patino Navarrete, B. Quemeneur, M. Zouari, F. Beck, C. Blanchet, S. Chaffron, H. Chiapello, K. Clement, A. Fraboulet, A. Gaignard, N. Gandon, D. Salgado, J. van Helden, C. Medigue, N. Pons. Cloud4SAMS: un environnement sécurisé de recherche pour le traitement des données de microbiome, in JOBIM 2026, Strasbourg, France,

[101] J. Lao, R. Tackx, A. Dieuaide, T. Mignon, C. Siguret, H. Lefeuvre, B. Quemeneur, P. Marin, B. Batut, N. Goué, E. Ruppe, G. Le Corguillé, A. Consortium, A. Bihouée, S. Chaffron, A. Gaignard, P. Glaser, C. Medigue, F. Mareuil. ABRomics: a platform for antibiotic resistance research and public health using an integrated "One Health" approach, in ECCB 2026 – 25th European Conference on Computational Biology, Geneva, Suisse,

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