Publications of RE Ley

Huttenhower, C.; Knight, R.; Brown, C.; Caporaso, J.; Clemente, J.; Gevers, D.; Franzosa, E.; Kelley, S.; Knights, D.; Ley, R. et al.; Mahurkar, A.; Ravel, J.; Scientists for Advancement of Microbiome Research; White, O.: Advancing the microbiome research community. Cell 159 (2), pp. 227 - 230 (2014)

Goodrich, J.; Di Rienzi, S.; Poole, A.; Koren, O.; Walters, W.; Caporaso, J.; Knight, R.; Ley, R.: Conducting a microbiome study. Cell 158 (2), pp. 250 - 262 (2014)

Ji, Y.; Sun, S.; Goodrich, J.; Kim, H.; Poole, A.; Duhamel, G.; Ley, R.; Qi, L.: Diet-induced alterations in gut microflora contribute to lethal pulmonary damage in TLR2/TLR4-deficient mice. Cell Reports 8 (1), pp. 137 - 149 (2014)

Perez-Muñoz, M.; Bergstrom, K.; Peng, V.; Schmaltz, R.; Jimenez-Cardona, R.; Marsteller, N.; McGee, S.; Clavel, T.; Ley, R.; Fu, X. et al.; Xia, L.; Peterson, D.: Discordance between changes in the gut microbiota and pathogenicity in a mouse model of spontaneous colitis. Gut Microbes 5 (3), pp. 286 - 295 (2014)

Ley, R.: Harnessing microbiota to kill a pathogen: the sweet tooth of Clostridium difficile. Nature Medicine 20 (3), pp. 248 - 249 (2014)

Petschow, B.; Doré, J.; Hibberd, P.; Dinan, T.; Reid, G.; Blaser, M.; Cani, P.; Degnan, F.; Foster, J.; Gibson, G. et al.; Hutton, J.; Klaenhammer, T.; Ley, R.; Nieuwdorp, M.; Pot, B.; Relman, D.; Serazin, A.; Sanders, M.: Probiotics, prebiotics, and the host microbiome: the science of translation. Annals of the New York Academy of Sciences 1306 (1), pp. 1 - 17 (2013)

Cullender, T.; Chassaing, B.; Janzong, A.; Kumar, K.; Muller, C.; Werner, J.; Angenent, L.; Bell, M.; Hay, A.; Peterson, D. et al.; Walter, J.; Vijay-Kumar, M.; Gewirtz, A.; Ley, R.: Innate and adaptive immunity interact to quench microbiome flagellar motility in the gut. Cell Host & Microbe 14 (5), pp. 571 - 581 (2013)

Di Rienzi, S.; Sharon, I.; Wrighton, K.; Koren, O.; Hug, L.; Thomas, B.; Goodrich, J.; Bell, J.; Spector, T.; Banfield, J. et al.; Ley, R.: The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria. eLife 2, e01102 (2013)

Pfeiffer, J.; Ley, R.: Exploring the maize rhizosphere microbiome in the field: A glimpse into a highly complex system. Communicative & Integrative Biology 6 (5), e25177 (2013)

Pfeiffer, J.; Spor, A.; Koren, O.; Jin, Z.; Green Tringe, S.; Dangl, J.; Buckler, E.; Ley, R.: Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proceedings of the National Academy of Sciences of the United States of America 110 (16), pp. 6548 - 6553 (2013)

Ley, R.: Nutrition: When guests turn hostile. Nature 494 (7438), pp. 437 - 438 (2013)

Koren, O.; Knights, D.; Gonzalez , A.; Waldron, L.; Segata, N.; Knight, R.; Huttenhower, C.; Ley, R.: A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets. PLoS Computational Biology 9 (1), e1002863 (2013)

Brook, S.; van Coeverden de Groot, P.; Scott, C.; Boag, P.; Long, B.; Ley, R.; Reischer, G.; Williams, A.; Mahood, S.; Hien, T. et al.; Polet, G.; Cox, N.; Hai, B.: Integrated and novel survey methods for rhinoceros populations confirm the extinction of Rhinoceros sondaicus annamiticus from Vietnam. Biological Conservation 155, pp. 59 - 67 (2012)

Carvalho, F.; Koren, O.; Goodrich, J.; Johansson, M.; Nalbantoglu, I.; Aitken, J.; Su, Y.; Chassaing, B.; Walters, W.; González, A. et al.; Clemente, J.; Cullender, T.; Barnich, N.; Darfeuille-Michaud, A.; Vijay-Kumar, M.; Knight, R.; Ley, R.; Gewirtz, A.: Transient inability to manage proteobacteria promotes chronic gut inflammation in TLR5-deficient mice. Cell Host & Microbe 12 (2), pp. 139 - 152 (2012)

Koren, O.; Goodrich, J.; Cullender, T.; Spor, A.; Laitinen, K.; Kling Bäckhed, H.; Gonzalez, A.; Werner, J.; Angenent, L.; Knight, R. et al.; Bäckhed, F.; Salminen, S.; Ley, R.: Host remodeling of the gut microbiome and metabolic changes during pregnancy. Cell 150 (3), pp. 470 - 480 (2012)

Larsson, E.; Tremaroli, V.; Lee, Y.; Koren, O.; Nookaew, I.; Fricker, A.; Nielsen, J.; Ley, R.; Bäckhead, F.: Analysis of gut microbial regulation of host gene expression along the length of the gut and regulation of gut microbial ecology through MyD88. Gut 61 (8), pp. 1124 - 1131 (2012)

Lundberg, D.; Lebeis, S.; Paredes, S.; Yourstone, S.; Gehring, J.; Malfatti, S.; Tremblay, J.; Engelbrektson , A.; Kunin, V.; Del Rio, T. et al.; Edgar, R.; Eickhorst, T.; Ley, R.; Hugenholtz, P.; Tringe, S.; Dangl, J.: Defining the core Arabidopsis thaliana root microbiome. Nature 488 (7409), pp. 86 - 90 (2012)

Ravussin, Y.; Koren, O.; Spor, A.; LeDuc, C.; Gutman, R.; Stombaugh, J.; Knight, R.; Ley, R.; Leibel, R.: Responses of gut microbiota to diet composition and weight loss in lean and obese mice. Obesity 20 (4), pp. 738 - 747 (2012)

Carvalho, F.; Nalbantoglu, I.; Ortega-Fernandez, S.; Aitken, J.; Su, Y.; Koren, O.; Walters, W.; Ley, R.; Vijay-Kumar, M.; Gewirtz, A.: Interleukin-1β (IL-1β) promotes susceptibility of Toll-like receptor 5 (TLR5) deficient mice to colitis. Gut 61 (3), pp. 373 - 384 (2012)

Werner, J.; Koren, O.; Hugenholtz, P.; DeSantis, T.; Walters, W.; Caporaso, J.; Angenent, L.; Knight, R.; Ley, R.: Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys. The ISME Journal 6 (1), pp. 94 - 103 (2012)