Publications of RE Ley

de la Cuesta-Zuluaga, J.; Spector, T.; Youngblut, N.; Ley, R.: Genomic Insights into Adaptations of Trimethylamine-Utilizing Methanogens to Diverse Habitats, Including the Human Gut. mSystems 6 (1), e00939-20 (2021)

Suzuki, T.; Ley, R.: The role of the microbiota in human genetic adaptation. Science 370 (6521), eaaz6827, p. 9 (2020)

Youngblut, N.; de la Cuesta-Zuluaga, J.; Reischer, G.; Dauser, S.; Schuster, N.; Walzer, C.; Stalder, G.; Farnleitner, A.; Ley, R.: Large-Scale Metagenome Assembly Reveals Novel Animal-Associated Microbial Genomes, Biosynthetic Gene Clusters, and Other Genetic Diversity. mSystems 5 (6), e01045-20 (2020)

Schmidt, V.; Enav, H.; Enav, H.; Spector, T.; Youngblut, N.; Ley, R.: Strain-Level Analysis of Bifidobacterium spp. from Gut Microbiomes of Adults with Differing Lactase Persistence Genotypes. mSystems 5 (5), e00911-20 (2020)

Walters, W.; Reyes, F.; Soto, G.; Reynolds, N.; Fraser, J.; Aviles, R.; Tribble, D.; Irvin, A.; Kelley-Loughnane, N.; Gutierrez, R. et al.; Riddle, M.; Ley, R.; Goodson, M.; Simons, M.: Epidemiology and associated microbiota changes in deployed military personnel at high risk of traveler's diarrhea. PLoS One 15 (8), e0236703 (2020)

Johnson, E.; Heaver, S.; Waters, J.; Kim, B.; Bretin, A.; Goodman, A.; Gewirtz, A.; Worgall, T.; Ley, R.: Sphingolipids produced by gut bacteria enter host metabolic pathways impacting ceramide levels. Nature Communications 11, 2471 (2020)

Mineeva, O.; Rojas-Carulla, M.; Ley, R.; Schölkopf, B.; Youngblut, N.: DeepMAsED: evaluating the quality of metagenomic assemblies. Bioinformatics 36 (10), pp. 3011 - 3017 (2020)

de la Cuesta-Zuluaga, J.; Ley, R.; Youngblut, N.: Struo: a pipeline for building custom databases for common metagenome profilers. Bioinformatics 36 (7), pp. 2314 - 2315 (2020)

Ruaud, A.; Esquivel-Elizondo, S.; de la Cuesta-Zuluaga, J.; Waters, J.; Angenent, L.; Youngblut, N.; Ley, R.: Syntrophy via Interspecies H2 Transfer between Christensenella and Methanobrevibacter Underlies Their Global Cooccurrence in the Human Gut. mBio 11 (1), e03235-19 (2020)

Clasen, S.; Ley, R.: Iron Deficiency Causes Wrinkles in Host-Commensal Relationships. Cell Metabolism 31 (1), pp. 8 - 10 (2020)

Tran, H.; Ley, R.; Gewirtz, A.; Chassaing, B.: Flagellin-elicited adaptive immunity suppresses flagellated microbiota and vaccinates against chronic inflammatory diseases. Nature Communications 10, 5650 (2019)

Janzon, A.; Goodrich, J.; Koren, O.; TEDDY Study Group; Waters, J.; Ley, R.: Interactions between the Gut Microbiome and Mucosal Immunoglobulins A, M, and G in the Developing Infant Gut. mSystems 4 (6), e00612-19 (2019)

Waters, J.; Ley, R.: The human gut bacteria Christensenellaceae are widespread, heritable, and associated with health. BMC Biology 17, 83 (2019)

Bolyen, E.; Rideout, J.; Dillon, M.; Bokulich, N.; Abnet, C.; Al-Ghalith, G.; Alexander, H.; Alm, E.; Arumugam, M.; Asnicar, F. et al.; Bai, Y.; Bisanz, J.; Bittinger, K.; Brejnrod, A.; Brislawn, C.; Brown, C.; Callahan, B.; Caraballo-Rodríguez, A.; Chase, J.; Cope, E.; Da Silva, R.; Diener, C.; Dorrestein, P.; Douglas, G.; Durall, D.; Duvallet, C.; Edwardson, C.; Ernst, M.; Estaki, M.; Fouquier, J.; Gauglitz, J.; Gibbons, S.; Gibson, D.; Gonzalez, A.; Gorlick, K.; Guo, J.; Hillmann, B.; Holmes, S.; Holste, H.; Huttenhower, C.; Huttley, G.; Janssen, S.; Jarmusch, A.; Jiang, L.; Kaehler, B.; Kang, K.; Keefe, C.; Keim, P.; Kelley, S.; Knights, D.; Koester, I.; Kosciolek, T.; Kreps, J.; Langille, M.; Lee, J.; Ley, R.; Liu, Y.-X.; Loftfield, E.; Lozupone, C.; Maher, M.; Marotz, C.; Martin, B.; McDonald, D.; McIver, L.; Melnik, A.; Metcalf, J.; Morgan, S.; Morton, J.; Naimey, A.; Navas-Molina, J.; Nothias, L.; Orchanian, S.; Pearson, T.; Peoples, S.; Petras, D.; Preuss, M.; Pruesse, E.; Rasmussen, L.; Rivers, A.; Robeson 2nd, M.; Rosenthal, P.; Segata, N.; Shaffer , M.; Shiffer , A.; Sinha, R.; Song, S.; Spear, J.; Swafford, A.; Thompson, L.; Torres, P.; Trinh, P.; Tripathi, A.; Turnbaugh, P.; Ul-Hasan, S.; van der Hooft, J.; Vargas, F.; Vázquez-Baeza, Y.; Vogtmann, E.; von Hippel, M.; Walters, W.; Wan, Y.; Wang, M.; Warren, J.; Weber, K.; Williamson, C.; Willis, A.; Xu, Z.; Zaneveld, J.; Zhang, Y.; Zhu, Q.; Knight, R.; Caporaso, J.: Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology 37 (9), p. 1091 (2019)

Knight, R.; Ley, R.; Raes, J.; Grice, E.: Expanding the scope and scale of microbiome research. Genome Biology 20, 191 (2019)

Bolyen, E.; Rideout, J.; Dillon, M.; Bokulich, N.; Abnet, C.; Al-Ghalith, G.; Alexander, H.; Alm, E.; Arumugam, M.; Asnicar, F. et al.; Bai, Y.; Bisanz, J.; Bittinger, K.; Brejnrod, A.; Brislawn, C.; Brown, C.; Callahan, B.; Caraballo-Rodríguez, A.; Chase, J.; Cope, E.; Da Silva, R.; Diener, C.; Dorrestein, P.; Douglas, G.; Durall, D.; Duvallet, C.; Edwardson, C.; Ernst, M.; Estaki, M.; Fouquier, J.; Gauglitz, J.; Gibbons, S.; Gibson, D.; Gonzalez, A.; Gorlick, K.; Guo, J.; Hillmann, B.; Holmes, S.; Holste, H.; Huttenhower, C.; Huttley, G.; Janssen, S.; Jarmusch, A.; Jiang, L.; Kaehler, B.; Kang, K.; Keefe, C.; Keim, P.; Kelley, S.; Knights, D.; Koester, I.; Kosciolek, T.; Kreps, J.; Langille, M.; Lee, J.; Ley, R.; Liu, Y.-X.; Loftfield, E.; Lozupone, C.; Maher, M.; Marotz, C.; Martin, B.; McDonald, D.; McIver, L.; Melnik, A.; Metcalf, J.; Morgan, S.; Morton, J.; Naimey, A.; Navas-Molina, J.; Nothias, L.; Orchanian, S.; Pearson, T.; Peoples, S.; Petras, D.; Preuss, M.; Pruesse, E.; Rasmussen, L.; Rivers, A.; Robeson 2nd, M.; Rosenthal, P.; Segata, N.; Shaffer , M.; Shiffer , A.; Sinha, R.; Song, S.; Spear, J.; Swafford, A.; Thompson, L.; Torres, P.; Trinh, P.; Tripathi, A.; Turnbaugh, P.; Ul-Hasan, S.; van der Hooft, J.; Vargas, F.; Vázquez-Baeza, Y.; Vogtmann, E.; von Hippel, M.; Walters, W.; Wan, Y.; Wang, M.; Warren, J.; Weber, K.; Williamson, C.; Willis, A.; Xu, Z.; Zaneveld, J.; Zhang, Y.; Zhu, Q.; Knight, R.; Caporaso, J.: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology 37 (8), pp. 852 - 857 (2019)

de la Cuesta-Zuluaga, J.; Kelley, S.; Chen, Y.; Escobar, J.; Mueller, N.; Ley, R.; McDonald, D.; Huang, S.; Swafford, A.; Knight, R. et al.; Thackray, V.: Age- and Sex-Dependent Patterns of Gut Microbial Diversity in Human Adults. mSystems 4 (4), e00261-19 (2019)

Youngblut, N.; Reischer, G.; Walters, W.; Schuster, N.; Walzer, C.; Stalder, G.; Ley, R.; Farnleiter, A.: Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades. Nature Communications 10, 2200 (2019)

Poole, A.; Goodrich, J.; Youngblut, N.; Luque, G.; Ruaud, A.; Sutter, J.; Waters, J.; Shi, Q.; El-Hadidi, M.; Johnson, L. et al.; Bar, H.; Huson, D.; Booth, J.; Ley, R.: Human Salivary Amylase Gene Copy Number Impacts Oral and Gut Microbiomes. Cell Host & Microbe 25 (4), pp. 553 - 564 (2019)

Moreno-Gallego, J.; Chou, S.-P.; Di Rienzi, S.; Goodrich, J.; Spector, T.; Bell, J.; Youngblut, N.; Hewson, I.; Reyes, A.; Ley, R.: Virome Diversity Correlates with Intestinal Microbiome Diversity in Adult Monozygotic Twins. Cell Host & Microbe 25 (2), pp. 261 - 272 (2019)