Publications
^{_{Microbiome Science}}

de la Cuesta Zuluaga, J.; Huus, K.; Youngblut, N.; Escobar, J.; Ley, R.: Obesity is the main driver of altered gut microbiome functions in the metabolically unhealthy. Gut Microbes 15 (2), 2246634 (2023)

Casini, I.; McCubbin, T.; Esquivel-Elizondo, S.; Luque, G.; Evseeva, D.; Fink, C.; Beblawy, S.; Youngblut, N.; Aristilde, L.; Huson, D. et al.; Dräger, A.; Ley, R.; Marcellin, E.; Angenent, L.; Molitor, B.: An integrated systems-biology approach reveals differences in formate metabolism in the genus Methanothermobacter. iScience 26 (10), 108016 (2023)

Clasen, S.; Ley, R.: Wie der Toll-like-Rezeptor 5 die Immunantwort umgeht. Biospektrum 29 (6), pp. 637 - 639 (2023)

Marsh, J.; Kirk, C.; Ley, R.: Toward Microbiome Engineering: Expanding the Repertoire of Genetically Tractable Members of the Human Gut Microbiome. Annual Review of Microbiology 77, pp. 427 - 449 (2023)

Clasen, S.: The sound of silence. Science 381 (6653), pp. 37 - 38 (2023)

Bretin, A.; Zou, J.; Yeoh, V.; Ngo, V.; Winer, S.; Winer, D.; Reddivari, L.; Pellizzon, M.; Walters, W.; Patterson, A. et al.; Ley, R.; Chassaing, B.; Vijay-Kumar, M.; Gewirtz, A.: Psyllium Fiber Protects Against Colitis Via Activation of Bile Acid Sensor Farnesoid X Receptor. Cellular and Molecular Gastroenterology and Hepatology 15 (6), pp. 1421 - 1442 (2023)

Mineeva, O.; Danciu, D.; Schölkopf, B.; Ley, R.; Rätsch, G.; Youngblut, N.: ResMiCo: increasing the quality of metagenome-assembled genomes with deep learning. PLoS Computational Biology 19 (5), e1011001 (2023)

Pinto, Y.; Frishman, S.; Turjeman, S.; Eshel, A.; Nuriel-Ohayon, M.; Shrossel, O.; Ziv, O.; Walters, W.; Parsonnet, J.; Ley, C. et al.; Johnson, E.; Kumar, K.; Schweitzer, R.; Khatib, S.; Magzal, F.; Muller, E.; Tamir, S.; Tenenbaum-Gavish, K.; Rautava, S.; Salminen, S.; Isolauri, E.; Yariv, O.; Peled, Y.; Poran, E.; Chen, R.; Hod, M.; Borenstein, E.; Ley, R.; Schwartz, B.; Louzoun, Y.; Hadar, E.; Koren, O.: Gestational diabetes is driven by microbiota-induced inflammation months before diagnosis. Gut 72 (5), gutjnl-2022-328406, pp. 918 - 928 (2023)

Kleiner, M.; Kouris, A.; Violette, M.; D’Angelo, G.; Liu, Y.; Korenek, A.; Tolić, N.; Sachsenberg, T.; McCalder, J.; Lipton, M. et al.; Strous, M.: Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes. Microbiome 11 (1), 24 (2023)

Walters, W.; Granados, A.; Ley, C.; Federman, S.; Stryke, D.; Santos, Y.; Haggerty, T.; Sotomayor-Gonzalez, A.; Servellita, V.; Ley, R. et al.; Parsonnet, J.; Chiu, C.: Longitudinal comparison of the developing gut virome in infants and their mothers. Cell Host & Microbe 31 (2), pp. 187 - 198 (2023)

Clasen, S.; Bell, M.; Borbón, A.; Lee, D.-H.; Henseler, Z.; de la Cuesta-Zuluaga, J.; Parys, K.; Zou, J.; Wang, Y.; Altmannova, V. et al.; Youngblut, N.; Weir, J.; Gewirtz, A.; Belkhadir, Y.; Ley, R.: Silent recognition of flagellins from human gut commensal bacteria by Toll-like receptor 5. Science Immunology 8 (79), eabq7001 (2023)

Kennedy, K.; de Goffau, M.; Perez-Muñoz, M.; Arrieta, M.-C.; Bäckhed, F.; Bork, P.; Braun, T.; Bushman, F.; Dore, J.; de Vos, W. et al.; Earl, A.; Eisen, J.; Elovitz, M.; Ganal-Vonarburg, S.; Gänzle, M.; Garrett, W.; Hall, L.; Hornef, M.; Huttenhower, C.; Konnikova, L.; Lebeer, S.; Macpherson, A.; Massey, R.; McHardy, A.; Koren, O.; Lawley, T.; Ley, R.; O'Mahony, L.; O'Toole, P.; Pamer, E.; Parkhill, J.; Raes, J.; Rattei, T.; Salonen, A.; Segal, E.; Segata, N.; Shanahan, F.; Sloboda, D.; Smith, D.; Sokol, H.; Spector, T.; Surette, M.; Tannock, G.; Walker, A.; Yassour, M.; Walter, J.: Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature 613 (7945), pp. 639 - 649 (2023)

Enav, H.; Ley, R.: SynTracker differentiates evolution via mutation or recombination on a per-species basis in complex microbiomes. In The Local Pangenome, 8, p. 55. The Local Pangenome, Alicante, Spain, October 25, 2023 - October 28, 2023. (2023)

Huus, K.; Esen, M.; μ. Study Group; Dauser, S.; Loum, S.; Youngblut, N.; Tyakht, A.; Ley, R.: Vaccine-induced fevers are associated with diet and the gut microbiome. In 3rd International Conference Controlling Microbes to Fight Infections (CMFI 2023), FT 14, p. 21. 3rd International Conference Controlling Microbes to Fight Infections (CMFI 2023), Tübingen, Germany, October 11, 2023 - October 13, 2023. (2023)

Clasen, S.; Bell, M.; Borbón, A.; Lee, D.-H.; Henseler, Z.; de la Cuesta-Zuluaga, J.; Parys, K.; Zou, J.; Wang, Y.; Altmannova, V. et al.; Youngblut, N.; Weir, J.; Gewirtz, A.; Belkhadir, Y.; Ley, R.: Silent recognition of flagellins from human gut commensal bacteria by Toll-like receptor 5. In Cell Symposia: Infection Biology in the Age of the Microbiome, ST.01. Cell Symposia: Infection Biology in the Age of the Microbiome, Paris, France, June 07, 2023 - June 09, 2023. (2023)

Suzuki, T.; Schön, T.; Waters, J.; Ballinger, M.; Ley, R.: Artificial selection experiment on the mammalian microbiome. In Evolution 2023, 321. Evolution 2023: Joint Annual Meeting of the American Society of Naturalists, the Society for the Study of Evolution, and the Society of Systematic Biologists, Albuquerque, NM, USA, June 21, 2023 - June 25, 2023. (2023)

Huus, K.: Evolutionary histories and adaptations of human gut microbiota. 3rd International Conference Controlling Microbes to Fight Infections (CMFI 2023), Tübingen, Germany (2023)

Ley, R.: Evolutionary histories and adaptations of human gut microbiota. 3rd International Conference Controlling Microbes to Fight Infections (CMFI 2023), Tübingen, Germany (2023)

Maier, L.: The consequences of drugging the gut microbiome: from the individual microbe to the host. 3rd International Conference Controlling Microbes to Fight Infections (CMFI 2023), Tübingen, Germany (2023)

Ley, R.: Silent flagellins, or how the gut immune system turns a blind eye. EMBO EMBL Symposium: The Human Microbiome , Heidelberg, Germany (2023)