Publications of RE Ley

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)

Kuczynski , J.; Costello, E.; Nemergut, D.; Zaneveld, J.; Lauber, C.; Knights, D.; Koren, O.; Fierer, N.; Kelley, S.; Ley, R. et al.; Gordon, J.; Knight, R.: Direct sequencing of the human microbiome readily reveals community differences. Genome Biology 11 (5), 210 (2010)

Vijay-Kumar, M.; Aitken, J.; Carvalho, F.; Cullender, T.; Mwangi , S.; Srinivasan, S.; Sitaraman, S.; Knight, R.; Ley, R.; Gewirtz, A.: Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. Science 328 (5975), pp. 228 - 231 (2010)

Ley, R.: Obesity and the human microbiome. Current Opinion in Gastroenterology 26 (1), pp. 5 - 11 (2010)

Turnbaugh, P.; Hamady, M.; Yatsunenko, T.; Cantarel, B.; Duncan, A.; Ley, R.; Sogin, M.; Jones, W.; Roe, B.; Affourtit, J. et al.; Egholm, M.; Henrissat, B.; Heath, A.; Knight, R.; Gordon, J.: A core gut microbiome in obese and lean twins. Nature 457 (7228), pp. 480 - 484 (2009)

Godoy-Vitorino, F.; Ley, R.; Gao, Z.; Pei, Z.; Ortiz-Zuazaga, H.; Pericchi, L.; Garcia-Amado, M.; Michelangeli, F.; Blaser, M.; Gordon, J. et al.; Domínguez-Bello, M.: The crop bacterial community of the hoatzin, a neotropical folivorous flying bird. Applied and Environmental Microbiology 74 (19), pp. 5905 - 5912 (2008)

Ley, R.; Lozupone, C.; Hamady, M.; Knight, R.; Gordon, J.: Worlds within worlds: evolution of the vertebrate gut microbiota. Nature Reviews Microbiology 6 (10), pp. 776 - 788 (2008)

Wen, L.; Ley, R.; Volchkov, P.; Stranges, B.; Avanesyan, L.; Stonebraker, A.; Hu, C.; Wong, S.; Szot, G.; Bluestone, J. et al.; Gordon, J.; Chervonsky, A.: Innate immunity and intestinal microbiota in the development of Type 1 diabetes. Nature 455 (7216), pp. 1109 - 1113 (2008)

Ley, R.; Hamady, M.; Lozupone, C.; Turnbaugh, P.; Ramey, R.; Bircher, J.; Schlegel, M.; Tucker, T.; Schrenzel, M.; Knight, R. et al.; Gordon, J.: Evolution of mammals and their gut microbes. Nature 320 (5883), pp. 1647 - 1651 (2008)

Zaneveld, J.; Turnbaugh, P.; Lozupone, C.; Ley, R.; Hamady, M.; Gordon, J.; Knight, R.: Host-bacterial coevolution and the search for new drug targets. Current Opinion in Chemical Biology 12 (1), pp. 109 - 114 (2008)

Feazel, L.; Spear, J.; Berger, A.; Harris, J.; Frank, D.; Ley, R.; Pace, N.: Eucaryotic diversity in a hypersaline microbial mat. Applied and Environmental Microbiology 74 (1), pp. 329 - 332 (2008)

Turnbaugh, P.; Ley, R.; Hamady, M.; Fraser-Liggett, C.; Knight, R.; Gordon, J.: The human microbiome project. Nature 449 (7164), pp. 804 - 810 (2007)