Publications of RE Ley

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)

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)

Ruaud, A.; Pfister, N.; Ley, R.; Youngblut, N.: Interpreting tree ensemble machine learning models with endoR. PLoS Computational Biology 18 (12), e1010714 (2022)

Welter, D.; Ruaud, A.; Henseler, Z.; De Jong, H.; van Coeverden de Groot, P.; Michaux, J.; Gormezano, L.; Waters, J.; Youngblut, N.; Ley, R.: Free-living psychrophilic bacteria of the genus Psychrobacter are descendants of pathobionts. mSystems (accepted)

Suzuki, T.; Fitzstevens, J.; Schmidt, V.; Enav, H.; Huus, K.; Mbong Ngwese, M.; Grießhammer, A.; Pfleiderer, A.; Adegbite, B.; Zinsou, J. et al.; Esen, M.; Velavan, T.; Adegnika, A.; Song, L.; Spector, T.; Muehlbauer, A.; Marchi, N.; Kang, H.; Maier, L.; Blekhman, R.; Ségurel, L.; Ko, G.; Youngblut, N.; Kremsner, P.; Ley, R.: Codiversification of gut microbiota with humans. Science 377 (6612), pp. 1328 - 1332 (2022)

Youngblut, N.; de la Cuesta-Zuluaga, J.; Ley, R.: Incorporating genome-based phylogeny and functional similarity into diversity assessments helps to resolve a global collection of human gut metagenomes. Environmental Microbiology 24 (9), pp. 3966 - 3984 (2022)

Heaver, S.; He, H.; Tang, P.; Baslé, A.; Mirretta Barone, C.; Vu, D.; Waters, J.; Marles-Wright, J.; Johnson, E.; Campopiano, D. et al.; Ley, R.: Characterization of inositol lipid metabolism in gut-associated Bacteroidetes. Nature Microbiology 7 (7), pp. 986 - 1000 (2022)

Enav, H.; Bäckhed, F.; Ley, R.: The developing infant gut microbiome: A strain-level view. Cell Host & Microbe 30 (5), pp. 627 - 638 (2022)

Chassaing, B.; Compher, C.; Bonhomme, B.; Liu, Q.; Tian, Y.; Walters, W.; Nessel, L.; Delaroque, C.; Hao, F.; Gershuni, V. et al.; Chau, L.; Ni, J.; Bewtra, M.; Albenberg, L.; Bretin, A.; McKeever, L.; Ley, R.; Patterson, A.; Wu, G.; Gewirtz, A.; Lewis, J.: Randomized Controlled-Feeding Study of Dietary Emulsifier Carboxymethylcellulose Reveals Detrimental Impacts on the Gut Microbiota and Metabolome. Gastroenterology 162 (3), pp. 743 - 756 (2022)

Marsh, J.; Ley, R.: Microbiome engineering: Taming the untractable. Cell 185 (3), pp. 416 - 418 (2022)

Suzuki, T.; Ley, R.: Microbes set the (woodrat) menu: Host genetics control diet-specific gut microbes. Proceedings of the National Academy of Sciences of the United States of America 119 (2), e2120125118 (2022)

Di Rienzi, S.; Johnson, E.; Waters, J.; Kennedy, E.; Jacobson, J.; Lawrence, P.; Wang, D.; Worgall, T.; Brenna, J.; Ley, R.: The microbiome affects liver sphingolipids and plasma fatty acids in a murine model of the Western diet based on soybean oil. The Journal of Nutritional Biochemistry 97, 108808 (2021)

Youngblut, N.; Reischer, G.; Dauser, S.; Maisch, S.; Walzer, C.; Stalder, G.; Farnleitner, A.; Ley, R.: Vertebrate host phylogeny influences gut archaeal diversity. Nature Microbiology 6 (11), pp. 1443 - 1454 (2021)

Huus, K.; Ley, R.: Blowing Hot and Cold: Body Temperature and the Microbiome. mSystems 6 (5), e00707-21 (2021)

Youngblut, N.; Ley, R.: Struo2: efficient metagenome profiling database construction for ever-expanding microbial genome datasets. PeerJ 9, e12198 (2021)

Du, X.; Ley, R.; Buck, A.: MicroRNAs and extracellular vesicles in the gut: new host modulators of the microbiome? microLife 2, uqab010 (2021)

Liu, X.; Sutter, J.; de la Cuesta-Zuluaga, J.; Waters, J.; Youngblut, N.; Ley, R.: Reclassification of Catabacter hongkongensis as Christensenella hongkongensis comb. nov. based on whole genome analysis. International Journal of Systematic and Evolutionary Microbiology 71 (4), 004774 (2021)