Publications
Electronic versions of the publications listed below are available at Google scholar.
Tito R.Y., Chaffron S.*, Caenepeel C., Lima-Mendez G., Wang J., Vieira-Silva S., Falony G., et al. Population-level analysis of Blastocystis subtype prevalence and variation in the human gut microbiota. Gut, 2018. Europe PMC
Poling H.M., Wu D., Brown N., Baker M., Hausfeld T.A., Huynh N., Chaffron S. et al. Mechanically induced development and maturation of human intestinal organoids in vivo. Nature Biomedical Engineering, 2018. Europe PMC
Stec K.F., Caputi L., Buttigieg P.L., D'Alelio D., Ibarbalz F.M., Sullivan M.B., Chaffron S. et al. Modelling plankton ecosystems in the meta-omics era. Are we ready? Marine genomics, 2017. Europe PMC
Vieira-Silva S., Falony G., Darzi Y., Lima-Mendez G., Garcia Yunta R., Okuda S., Vandeputte D., Valles-Colomer M., Hildebrand F., Chaffron S. and Raes J.. Species–function relationships shape ecological properties of the human gut microbiome. Nature Microbiology, 2016. Europe PMC
Falony G.*, Joossens M.*, Vieira-Silva S.*, Wang J.* et al. Population-level analysis of gut microbiome variation. Science, 2016. Europe PMC
Guidi L.*, Chaffron S.*, Bittner L.*, Eveillard D.*, Larhlimi A., Roux S., Darzi Y. et al. Plankton networks driving carbon export in the oligotrophic ocean. Nature, 2016. Europe PMC
Takeuchi Y., Chaffron S.*, Salcher M.M., Shimizu-Inatsugi R., Kobayashi M.J., Diway B., von Mering C., Pernthaler J. and Shimizu K.K. Bacterial diversity and composition in the fluid of pitcher plants of the genus Nepenthes. Syst Appl Microbiol, 2015. Europe PMC
Sunagawa S.*, Coelho L.P.*, Chaffron S.*, Jens Roat Kultima, Karine Labadie, Guillem Salazar, Bardya Djahanschiri et al. Structure and Function of the Global Ocean Microbiome. Science, 2015. Europe PMC
Brum* J.R., Ignacio-Espinoza J.C.*, Roux S.*, Doulcier G., Acinas S., Alberti A., Chaffron S. et al. Patterns and ecological drivers of ocean viral communities. Science, 2015. Europe PMC
Lima-Mendez G.*, Faust K.*, Henry N.*, Decelle J., Colin S., Carcillo F., Chaffron S. et al. Determinants of community structure in the global plankton interactome. Science, 2015. Europe PMC
de Vargas C.*, Audic S.*, Henry N.*, Decelle J.*, Mahé F.*, Logares R., Lara E., Berney C., Le Bescot N., Probert I., Carmichael M., Poulain J., Romac S., Colin S., Aury J-M., Bittner L., Chaffron S. et al. Eukaryotic plankton diversity in the sunlit global ocean. Science, 2015. Europe PMC
Knief C., Delmotte N., Chaffron S., Stark M., Innerebner G., Wassmann R., von Mering C., and Vorholt J.A.. Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice. ISME J, 2012. Europe PMC
Endt K.*, Stecher B.*, Chaffron S., Slack E., Tchitchek N., Benecke A., Van Maele L., Sirard J.C., Mueller A.J., Heikenwalder M. et al. The microbiota mediates pathogen clearance from the gut lumen after non-typhoidal Salmonella diarrhea. PLoS Pathog 6: e1001097, 2010. Europe PMC
Chaffron S., Rehrauer H., Pernthaler J., and von Mering C. A global network of coexisting microbes from environmental and whole-genome sequence data. Genome Res 20: 947-59, 2010. Europe PMC
Chaffron S.*, Stecher B.*, Kappeli R.*, Hapfelmeier S., Freedrich S., Weber T.C., Kirundi J., Suar M., McCoy K.D., von Mering C. et al. Like will to like: abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria. PLoS Pathog 6: e1000711, 2010. Europe PMC
Delmotte N.*, Knief C.*, Chaffron S., Innerebner G., Roschitzki B., Schlapbach R., von Mering C., and Vorholt J.A. Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proc Natl Acad Sci U S A 106: 16428- 16433, 2009. Europe PMC
Jensen L.J., Kuhn M., Stark M., Chaffron S., Creevey C., Muller J., Doerks T., Julien P., Roth A., Simonovic M. et al. STRING 8–a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res 37: D412-416, 2009. Europe PMC
Stecher B., Robbiani R., Walker A.W., Westendorf A.M., Barthel M., Kremer M., Chaffron S., Macpherson A.J., Buer J., Parkhill J. et al. Salmonella enterica serovar typhimurium exploits inflammation to compete with the intestinal microbiota. PLoS Biol 5: 2177-2189, 2007. Europe PMC
Chaffron S. and von Mering C. Termites in the woodwork. Genome Biol 8: 229, 2007. Europe PMC
von Mering C., Jensen L., Kuhn M., Chaffron S., Doerks T., Kruger B., Snel B., and Bork P. STRING 7–recent developments in the integration and prediction of protein interactions. 10.1093/nar/gkh084 35: 358-362, 2007. Europe PMC