Publications of RE Ley

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)

Ran-Ressler, R.; Khailova, L.; Arganbright, K.; Adkins-Rieck, C.; Jouni, Z.; Koren, O.; Ley, R.; Brenna, J.; Dvorak, B.: Branched chain fatty acids reduce the incidence of necrotizing enterocolitis and alter gastrointestinal microbial ecology in a neonatal rat model. PLoS One 6 (12), e29032 (2011)

Vaishnava, S.; Yamamoto, M.; Severson, K.; Ruhn, K.; Yu, X.; Koren, O.; Ley, R.; Wakeland, E.; Hooper, L.: The antibacterial lectin RegIIIgamma promotes the spatial segregation of microbiota and host in the intestine. Science 334 (6053), pp. 255 - 258 (2011)

Dominguez-Bello, M.; Blaser, M.; Ley, R.; Knight, R.: Development of the human gastrointestinal microbiota and insights from high-throughput sequencing. Gastroenterology 140 (6), pp. 1713 - 1719 (2011)

Yilmaz, P.; Kottmann, R.; Field, D.; Knight, R.; Cole, J. R.; Amaral-Zettler, L.; Gilbert, J. A.; Karsch-Mizrachi, I.; Johnston, A.; Cochrane, G. et al.; Vaughan, R.; Hunter, C.; Park, J.; Morrison, N.; Rocca-Serra, P.; Sterk, P.; Arumugam, M.; Bailey, M.; Baumgartner, L.; Birren, B. W.; Blaser, M. J.; Bonazzi, V.; Booth, T.; Bork, P.; Bushman, F. D.; Buttigieg, P.; Chain, P. S. G.; Charlson, E.; Costello, E. K.; Huot-Creasy, H.; Dawyndt, P.; DeSantis, T.; Fierer, N.; Fuhrman, J. A.; Gallery, R. E.; Gevers, D.; Gibbs, R. A.; Gil, I. S.; Gonzalez, A.; Gordon, J. I.; Guralnick, R.; Hankeln, W.; Highlander, S.; Hugenholtz, P.; Jansson, J.; Kau, A. L.; Kelley, S. T.; Kennedy, J.; Knights, D.; Koren, O.; Kuczynski, J.; Kyrpides, N.; Larsen, R.; Lauber, C. L.; Legg, T.; Ley, R.; Lozupone, C. A.; Ludwig, W.; Lyons, D.; Maguire, E.; Methe, B. A.; Meyer, F.; Muegge, B.; Nakielny, S.; Nelson, K. E.; Nemergut, D.; Neufeld, J. D.; Newbold, L. K.; Oliver, A. E.; Pace, N. R.; Palanisamy, G.; Peplies, J.; Proctor, L.; Pruesse, E.; Quast, C.; Raes, J.; Ratnasingham, S.; Ravel, J.; Relman, D. A.; Assunta-Sansone, S.; Schloss, P. D.; Schriml, L.; Sinha, R.; Smith, M. I.; Sodergren, E.; Spor, A.; Stombaugh, J.; Tiedje, J. M.; Ward, D. V.; Weinstock, G. M.; Wendel, D.; White, O.; Whiteley, A.; Wilke, A.; Wortman, J. R.; Yatsunenko, T.; Glöckner, F.: Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nature Biotechnology 29 (5), pp. 415 - 420 (2011)

Yilmaz, P.; Kottmann, R.; Field, D.; Knight, R.; Cole, J.; Amaral-Zettler, L.; Gilbert, J.; Karsch-Mizrachi, I.; Johnston, A.; Cochrane, G. et al.; Vaughan, R.; Hunter, C.; Park, J.; Morrison, N.; Rocca-Serra, P.; Sterk, P.; Arumugam, M.; Bailey, M.; Baumgartner, L.; Birren, B.; Blaser, M.; Bonazzi, V.; Booth, T.; Bork, P.; Bushman, F.; Buttigieg, P.; Chain, P.; Charlson, E.; Costello, E.; Huot-Creasy, H.; Dawyndt, P.; DeSantis, T.; Fierer, N.; Fuhrman, J.; Gallery, R.; Gevers, D.; Gibbs, R.; San Gil, I.; Gonzalez, A.; Gordon, J.; Guralnick, R.; Hankeln, W.; Highlander, S.; Hugenholtz, P.; Jansson, J.; Kau, A.; Kelley, S.; Kennedy, J.; Knights, D.; Koren, O.; Kuczynski, J.; Kyrpides, N.; Larsen, R.; Lauber, C.; Legg, T.; Ley, R.; Lozupone, C.; Ludwig, W.; Lyons, D.; Maguire, E.; Methé, B.; Meyer, F.; Muegge, B.; Nakielny, S.; Nelson, K.; Nemergut, D.; Neufeld, J.; Newbold, L.; Oliver, A.; Pace, N.; Palanisamy, G.; Peplies, J.; Petrosino, J.; Proctor, L.; Pruesse, E.; Quast, C.; Raes, J.; Ratnasingham, S.; Ravel, J.; Relman, D.; Assunta-Sansone, S.; Schloss, P.; Schriml, L.; Sinha, R.; Smith, M.; Sodergren, E.; Spo, A.; Stombaugh, J.; Tiedje, J.; Ward, D.; Weinstock, G.; Wendel, D.; White, O.; Whiteley, A.; Wilke, A.; Wortman, J.; Yatsunenko, T.; Glöckner, F.: Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nature Biotechnology 29 (5), pp. 415 - 420 (2011)

Knights, D.; Kuczynski, J.; Koren, O.; Ley, R.; Field, D.; Knight, R.; DeSantis, T.; Kelley, S.: Supervised classification of microbiota mitigates mislabeling errors. The ISME Journal 5 (4), pp. 570 - 573 (2011)

Spor, A.; Koren, O.; Ley, R.: Unravelling the effects of the environment and host genotype on the gut microbiome. Nature Reviews Microbiology 9 (4), pp. 279 - 290 (2011)

Koenig, J.; Spor, A.; Scalfone, N.; Fricker, A.; Stombaugh, J.; Knight, R.; Angenent, L.; Ley, R.: Succession of microbial consortia in the developing infant gut microbiome. Proceedings of the National Academy of Sciences of the United States of America 108 (Supplement 1), pp. 4578 - 4585 (2011)

Koren, O.; Spor, A.; Felin, J.; Fåk, F.; Stombaugh, J.; Tremaroli, V.; Behre, J.; Knight, R.; Fagerberg, B.; Ley, R. et al.; Bäckhed, F.: Human oral, gut, and plaque microbiota in patients with atherosclerosis. Proceedings of the National Academy of Sciences of the United States of America 108 (Supplement 1), pp. 4592 - 4598 (2011)

Walter, J.; Ley, R.: The human gut microbiome: ecology and recent evolutionary changes. Annual Review of Microbiology 65, pp. 411 - 429 (2011)

Caporaso, J.; Kuczynski, J.; Stombaugh, J.; Bittinger, K.; Bushman, F.; Costello, E.; Fierer, N.; Gonzalez Peña, A.; Goodrich, J.; Gordon, J. et al.; Huttley, G.; Kelley, S.; Knights, D.; Koenig, J.; Ley, R.; Lozupone, C.; McDonald, D.; Muegge, B.; Pirrung, M.; Reeder, J.; Sevinsky, J.; Turnbaugh, P.; Walters, W.; Widmann, J.; Yatsunenko, T.; Zaneveld, J.; Knight, R.: QIIME allows analysis of high-throughput community sequencing data. Nature Methods 7 (5), pp. 335 - 336 (2010)