CHM_cover_bigPubmed List

Google Scholar list

McGavigan A.K., Henseler Z.M., Garibay D., Butler S.D., Jayasinghe S., Ley R.E., Davisson RL, Cummings B.P. Vertical sleeve gastrectomy reduces blood pressure and hypothalamic endoplasmic reticulum stress in mice. Dis Model Mech doi: 10.1242/dmm.027474. [Epub ahead of print] (2017)

Johnson E. L., Heaver S. L., Walters W. A. and Ley, R. E. Microbiome and metabolic disease: revisiting the bacterial phylum Bacteroidetes. Journal of Molecular Medicine doi: 10.1007/s00109-016-1492-2. (2017).

Davenport E. R., Goodrich J. K., Bell J. T., Spector T. D., Ley R. E. and Clark A. G. ABO antigen and secretor statuses are not associated with gut microbiota composition in 1,500 twins. BMC Genomics. 17:941. (2016).

Beaumont M, Goodrich J.K., Jackson M.A., Yet I., Davenport E.R., Vieira-Silva S., Debelius J., Pallister T., Mangino M., Raes J., Knight R., Clark A.G., Ley R.E., Spector T.D., Bell J.T. Heritable components of the human fecal microbiome are associated with visceral fat. Genome Biology 17: 189 (2016)

Giloteaux L., Goodrich J. K., Walters W. A., Levine S. M., Ley R. E. and Hanson M. R. Reduced diversity and altered composition of the gut microbiome in individuals with myalgic encephalomyelitis/chronic fatigue syndrome . Microbiome: 30. doi: 10.1186/s40168-016-0171-4. (2016).

Ley, R. E. and A. T. Gewirzt. Corralling flagellated bacteria. New England Journal of Medicine. 375:85-7. (2016)

Beaumont M., Goodrich J. K., Jackson M. A., Yet I., Davenport E. R., Vieira-Silva S., Debelius J., Pallister T., Mangino M., Raes J., Knight R., Clark A. G., Ley R. E., Spector T. D. and Bell J. T. Heritbale components of the human fecal microbiome are associated with visceral fat. Genome Biol. 17:189. (2016).

Poole, A. C., L. Pischel, C. Ley, G. Suh, J. K. Goodrich, T. D. Haggerty, R. E. Ley, J. Parsonnet. Crossover control study of the effect of personal care products containing Triclosan on the microbiome. mSphere.00056-15 (2016)

Goodrich, J. K. , E. R. Davenport, M. A. Jackson, M. Beaumont, R. Knight, T. D. Spector, J. T. Bell, A. G. Clark, R. E. Ley. Genetic determinants of the gut microbiome assessed in UK Twins. Cell Host & Microbe. 19:731-43 (2016)

Goodrich, J. K., E. R. Davenport, J. L. Waters, A. G. Clark and R. E. Ley. Cross-species comparisons of host genetic associations with the microbiome. Science 352: 532-535. (2016)

Ley, R. E. Gut microbiota in 2015: Prevotella in the gut: Choose carefully. Nat. Rev. Gastroenterol. Hepatol. 13 (2): 69-70. (2016)

Jackson M., Jeffrey IB, Beaumont M, Bell JT, Clark AG, Ley RE, O’Toole PW, Spector TD, CJ Steves. Signatures of early frailty in the gut microbiota. Genome Med. 8:8. (2016)

Jackson MA, Goodrich JK, Maxan ME, Freedberg DE, Abrams JA, Poole AC, Sutter JL, Welter D, Ley RE, Bell JT, Spector TD, Steves CJ. Proton pump inhibitors alter the composition of the gut microbiota. Gut Dec 30. pii: gutjnl-2015-310861 (2015)

Friedman ES, McPhillips LE, Werner JJ, Poole AC, Ley R, Walter MT and Angenent L. Methane emission in a specific riparian-zone sediment decreased with bioelectrochemical manipulation and corresponded to the microbial community dynamics. Front. Microbiol. :1523. doi: 10.3389/fmicb.2015.01523 (2015)

Jin* Z., *Di Rienzi S. C., Janzon A., Werner J. J., Angenent L. T., Fowler D. M., Dangl J. L. and Ley R. E. Novel Rhizosphere Soil Alleles for the Enzyme 1-Aminocyclopropane-1-Carboxylate Deaminase Queried for Function with an In Vivo Competition Assay. Applied and Environmental Microbiology:  Dec 4. online first 03074-15 (2015)

S. Sun, R. Lourie, S. B. Cohen, Y. Ji, J. K. Goodrich, A. C. Poole, R. E. Ley, E. Y. Denkers, M. A. McGuckin, Q. Long, G. E. Duhamel, K. W. Simpson, L. Qi. Epithelial Sel1L is required for the maintenance of intestinal homeostasis. Molecular Biology of the Cell: E15-10-0724 (2015)

McGavigan AK, Garibay D, Henseler ZM, Chen J, Bettaieb A, Haj FG, Ley RE, Chouinard ML, Cummings BP. TGR5 contributes to glucoregulatory improvements after vertical sleeve gastrectomy in mice. Gut Oct 28. pii: gutjnl-2015-30987. (2015)

Blekhman R, Goodrich JK, Huang K, Sun Q, Bukowski R, Bell JT, Spector TD, Keinan A, Ley RE, Gevers D, Clark AG. Host genetic variation impacts microbiome composition across body sites. Genome Biol. 2015 Sep 15;16:191. doi: 10.1186/s13059-015-0759-1. (2015)

Barrios, C., M. Beaumont, T. Pallister, J. Villar, J. K Goodrich, A. Clark, J. Pascual, R. E. Ley, T. D. Spector, J. T. Bell, C. Menni. Gut-microbiota-metabolite axis in early renal function decline. PloS One 10 e0134311 (2015)

Hacquard, S., R. Garrido-Oter, A. González, S. Spaepen, G. Ackermann, S. Lebeis, A. C. McHardy, J. L. Dangl, Rob Knight, R. E. Ley, P. Schulze-Lefert. Microbiota and host nutrition across plant and animal kingdoms. Cell Host and Microbe 17: 603-616. (2015)

Ley, R. E. The Gene-Microbe link. Nature 518: S7, doi:10.1038/518S7a (2015).

Chassaing, B., O. Koren, J. Goodrich, A. Poole, S. Srinivasan, R. E. Ley and Andrew T. Gewirtz. Dietary emulsifiers alter gut microbiota-intestinal interactions promoting colitis and metabolic syndrome. Nature. DOI: 10.1038/nature14232 (2015)

Kumar H, R. Lund, A. Laiho, K. Lundelin, R. E. Ley, E. Isolauri, and S. Salminen. Gut microbiota as an epigenetic regulator: pilot study based on whole-genome methylation analysis. MBio 16;5(6). pii: e02113-14. (2014)

Goodrich, J. K., J. L. Waters, A. C. Poole, J. L. Sutter, O. Koren, R. Blekhman, M. Beaumont, W. Van Treuren, R. Knight, J. T. Bell, T. D. Spector, A. G. Clark,and R. E. Ley.. Human genetics shape the gut microbiome. Cell 159: 789-799. (2014)

K. Panke-Buisse, A. C. Poole, J. K. Goodrich, R. E. Ley and J. Kao-Kniffin. Selection on plant microbiomes reveals reproducible impacts on plant function. The ISME Journal. Oct 28, Epub ahead of print. (2014)

Huttenhower, C., R. Knight, C. T. Brown, J. G. Caporaso, J. C. Clemente, D. Gevers, E. A. Franzosa, S. T. Kelley, D. Knights, R. E. Ley, A. Marhurkar, J. Ravel, Scientists for Advancement of Microbiome Research, O. White. Advancing the Microbiome Research Community. Cell 159: 227-230 (2014)

Goodrich, J. K., S. C. Di Rienzi, A. C. Poole, O. Koren, W. A. Walters, G. Caporaso, R. Knight and R. E. Ley. Conducting a Microbiome Study. Cell 17: 250-262. (2014).

Leifer, C. A., C. McConkey, S. Li, B. Chassaing, A. T. Gewirtz and R. E. Ley. Linking genetic variation in Toll-like Receptor 5 genes to the gut microbiome’s potential to cause inflammation. Immunology Letters DOI: 10.1016/j.imlet.2014.07.017 (2014)

Chassaign, B., R. E. Ley and A. T. Gewirtz. Intestinal epithelial cell Toll-like Receptor 5 regulates the intestinal microbiota to prevent low-grade inflammation and metabolic syndrome in mice. Gastroenterology 147: 1363-1377 (2014).

Ji, Yewei, S. Sun, J. K. Goodrich, H. Kim, A. C. Poole, G. E. Duhamel, R. E. Ley and L. Qi. Diet-induced alterations in gut microflora contribute to lethal pulmonary damage in TLR2/TLR4-deficient mice. Cell Reports 10: 137-149 (2014).

Perez-Munoz, M., K. Bergstrom, V. Peng, R. Schmaltz, R. Jimenez-Cardona, N. Marsteller, S. McGee, T. Clavel, R. Ley, L. Xia and D. Peterson. Discordance between changes in the microbiota and pathogenicity in a mouse model of spontaneous colitis. Gut Microbes Mar 24; 5(3) Epub ahead of Print. (2014).

Ley, R. E. Harnessing microbiota to kill a pathogen: The sweet tooth of Clostridium difficile. Nature Medicine 4: 248-249. (2014)

Petschow B, Doré J, Hibberd P, Dinan T, Reid G, Blaser M, Cani PD, Degnan FH, Foster J, Gibson G, Hutton J, Klaenhammer TR, Ley R, Nieuwdorp M, Pot B, Relman D, Serazin A, Sanders ME. Probiotics, prebiotics, and the host microbiome: the science of translation. Ann NY Acad Sci 1306: 1-17. (2013)

Peiffer, J.A. and R. E. Ley. Exploring the maize rhizosphere microbiome in the field: A glimpse into a highly complex system. Commun Integra Bio 6: e25177. (2013).

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

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

Chassaing, B., O. Koren, F. A. Carvalho, R. E. Ley and A. T. Gewirtz. AIEC pathobiont instigates chronic colitis in susceptible hosts by altering microbiota composition. Gut Online Jul. 29. (2013)

Peiffer*, J., A. Spor*, Z. Jin, O. Koren, S. G. Tringe, J. L. Dangl, E. S. Buckler, and R. E. Ley. Diversity and heritability of the Maize rhizosphere microbiome under field conditions. Proceedings of the National Academy of Sciences USA 5: 570-573. (2013)

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

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

Koren, O., J. K. Goodrich, T. C. Cullender, A. Spor, K. Laitinen, H. Backhed, A. Gonzalez, J. J. Werner, L. T. Angenent, R. Knight, F. Backhed, E. Isolauri, S. Salminen and R. E. Ley. Remodeling of the gut microbiome and metabolic changes during pregnancy. Cell 150: 1-11 (2012).

Carvalho, F. A., O. Koren, M. Johansson, I. Nalbantoglu, J. D. Aitken, Y. Su, W. A. Walters, A. González Peña, J. C. Clemente, N. Barnich, A. Darfeuille-Michaud, M.Vijay-Kumar, R. Knight, R. E. Ley, and A. T. Gewirtz. Transient inability to manage Proteobacteria promotes chronic gut inflammation in TLR5-deficient mice. Cell Host & Microbe 12: 139-152 (2012).

Lundberg, D. S., S. L. Lebeis, S. H. Paredes, S. Yourstone, J. Gehring, S. Malfatti, J. Tremblay, A. Engelbrekston, V. Kunin, T. G. del Rio, R. Edgar, T. Eickhorst, R. E. Ley, P. Hugenholtz, S. G. Tringe, J. L. Dangl. Defining the core Arabidopsis thaliana root microbiome. Nature 486: 207-214. (2012).

The Human Microbiome Consortium. Structure, function and diversity of the healthy human microbiome.  Nature 486: 207-214. (2012)

The Human Microbiome Consortium. A framework for human microbiome research. Nature 486: 215-221. (2012)

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

Larsson, E., V. Tremaroli, Y. S. Lee, O. Koren, A. Fricker, I. Nookaew, J. Nielsen, R. E. Ley and F. Bäckhed. 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: 1124-1131 (2012)

Werner*, J. J., O. Koren*, P. Hugenholtz, T. Z. DeSantis, W. A. Walters, J. G. Caporaso, L. T. Angenent, R. Knight, R. E. Ley.  Impact of training sets on classification of high-throughput bacterial 16S rRNA gene surveys.  ISME Journal 6: 94-103 (2012)

Carvalho, F. A., I. Nalbantoglu, S. Ortega-Fernandez, J. D. Aitken, Y. Su, O. Koren, W. A. Walters, R. Knight, R. E. Ley, M. Vijay-Kumar, and A. T. Gewirtz. IL-1β promotes susceptibility of Toll-like receptor 5 KO mice to colitis. Gut 61: 373-384. (2012)

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

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

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

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

*Spor, A, O. *Koren, and R. Ley.  Unraveling the effects of environment and host genotype on the gut microbiome. Nature Reviews Microbiology 9:279-90. (2011)

Gilbert JA, Meyer F, Jansson J, Gordon J, Pace N, Tiedje J, Ley R, Fierer N, Field D, Kyrpides N, Glöckner FO, Klenk HP, Wommack KE, Glass E, Docherty K, Gallery R, Stevens R, Knight R. The Earth Microbiome Project: Meeting report of the “1 EMP meeting on sample selection and acquisition” at Argonne National Laboratory October 6 2010. Standards in Genomic Sciences (3): 249-53. (2011)

Yilmaz, P., the MIMARKS consortium*.  The “Minimal Information about a MARKer gene Sequence” (MIMARKS) specification.  Nature Biotechnology 29: 415-420.  (*includes A. Spor, O. Koren and R. E. Ley)(2011)

Dominguez-Bello, M. G., M. J. Blaser, R. E. Ley and R. Knight. Development of the infant gut microbiota: insights from high-throughput sequencing.  Gastroenterology 140: 1713-1719. (2011)

Koren*, O., A. Spor*, J. Felin*, F. Fak, J. Stombaugh, V. Tremaroli, C. B. Behre, R. Knight, B. Fagerberg, R. E. Ley and F. aBackhed.  Human oral, gut , and plaque microbiota in patients with atherosclerosis.  Proceedings of the National Academy of Sciences USA 108 Suppl 1: 4592-4598. (2011)

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

Koenig, J. E., A. Spor, N. Scalfone , A. D. Fricker, J. Stombaugh, R. Knight, L. T. Angenent and R. E. Ley. 2011. Succession of microbial consortia in the developing infant gut microbiome. Proceedings of the National Academy of Sciences USA 108 Suppl1: 4578-4585. (2011)

Kuczynski, J., E. K. Costello, D. R. Nemergut, J. Zaneveld, C. L. Lauber, D. Knights, O. Koren, N. Fierer, S. Kelley, R. E. Ley, J. I. Gordon, and R. Knight. Direct sequencing of the human microbiome readily revelas community differences. Genome Biology 5: 210-219 (2010).

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

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

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

Ley, R. E. In Person: Breaking all the rules.  Science Career Magazine, May 29 (online, 2009)

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

Wen, I, P. Volchkov*, R. E. Ley*, P. Stranges, L. Avanesyan, A. Stonebraker, C. Hu, F. S. Wong, G. L. Szot, J. A. Bluestone, J. I. Gordon and A. V. Chervonsky. Innate immunity and intestinal microbiota in the development of Type 1 diabetes. Nature 455:1109-1113. (2008)

Ley, R. E.*, C. A. Lozupone*, M. Hamady, R. Knight and J. I. Gordon.  Worlds within worlds: evolution of the vertebrate gut microbiota. Nature Reviews Microbiology 6: 776-788. (2008)

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

Ley, R. E., M. Hamady, C. Lozupone, P. J. Turnbaugh, R. R. Ramey, J. S. Bircher, M. L. Schlegel, T.A. Tucker, M. D. Schrenzel, R. Knight and J. I. Gordon.  Evolution of mammals and their gut microbes. Science 320: 1647-1651. (2008)

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

Feazel, L. M., J. R. Spear, A. B. Berger, J. K. Harris, D. N. Frank, R. E. Ley and N. R. Pace.  Eucaryotes in the Guerrero Negro hypersaline microbial mat. Applied and Environmental Microbiology 74: 329-332. (2007)

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

Ley, R. E. and J. I. Gordon. The human intestinal microbiota and microbiome. Textbook of Gastroenterology, Fifth edition (Dr. Tadataka Yamada, Ed.). Blackwell Publishing.

Xu, J., M. A. Mahowald, R. E. Ley, C. A. Lozupone, M. Hamady,  E. C. Martens, B. Henrissat, P. M. Coutinho, P. Minx, P. Latreille, H. Cordum, A. Van Brunt, K. Kim, R. S. Fulton, L. A. Fulton, S. W. Clifton, R. K. Wilson, R. D. Knight, and J. I. Gordon. Evolution of symbiotic bacteria in the distal human intestine.  PLoS Biology 5: e156. (2007)

Ley, R. E., R. D. Knight and J. I. Gordon. The human microbiome: eliminating the biomedical/environmental dichotomy in microbial ecology. Environmental Microbiology 9: 3-4. (2007)

Turnbaugh, P. J., R. E. Ley, M. Mahowald, V. Magrini, E. R. Mardis, and J. I. Gordon. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444: 1027-1031. (2006)

Ley, R. E., P. Turnbaugh, S. Klein and J. I. Gordon. Human gut microbial ecology linked to obesity.  Nature 444: 1022-1023. (2006)

Rawls, J. F., M. M. Mahowald, R. E. Ley and J. I. Gordon. Reciprocal transplantation of gut microbial communities from zebrafish and mice into gnotobiotic recipients reveals host habitat selection of a microbiota. Cell 127: 423-433. (2006)

Ley, R. E., D. A. Peterson and J. I. Gordon. An extended view of ourselves: ecological and evolutionary forces that shape microbial diversity and genome content in the human intestine. Cell 124: 837-848. (2006)

Bäckhed, F. R., R. E. Ley, J. L. Sonnenburg, and J. I. Gordon. The human intestinal microbiota and its relationship to energy balance. Scandinavian Journal of Food and Nutrition 50: 121-123. (2006)

Ley, R. E., J. K. Harris, J. Wilcox, J. R. Spear, S. R. Miller, B. M. Bebout, J. A. Maresca, D. A. Bryant, M. Sogin and N. R. Pace. Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat.  Applied and Environmental Microbiology 72: 3685-3695. (2006)

Gordon, J. I, R. E. Ley, R. Wilson, E. Mardis, J. Xu, C. M. Fraser and D. A. Relman. Extending our view of self: the human gut microbiome initiative (HGMI). NHGRI White paper (prioritized), published online at (2005)

Ley, R. E., F. Bäckhed, P. Turnbaugh, C. Lozupone, R. Knight, and J. I. Gordon. Obesity alters gut microbial ecology. Proceedings of the National Academy of Sciences USA 31: 11070-11075. (2005)

Bäckhed*, F. R., R. E. Ley*, , J. L. Sonnenburg, D. A. Peterson, and J. I. Gordon. Host-bacterial mutualism in the human intestine.  Science 307: 1915-1920. (2005)

Ley, R. E., M. W. Williams, and S. K. Schmidt. Microbial population dynamics in an extreme environment: controlling factors in unvegetated talus soils at 3750m in the Colorado Rocky Mountains.  Biogeochemistry 68: 313-335. (2004)

Schmidt, S. K., D. A. Lipson, R. E. Ley, M. C. Fisk, and A. E. West. The impacts of chronic nitrogen additions vary seasonally and by microbial functional group in tundra soils.  Biogeochemistry 69: 1-17. (2004)

Cleveland, C. C, A. R. Townsend, B. C. Constance, R. E. Ley, and S. K. Schmidt. Soil microbial dynamics in Costa Rica:  seasonal and biogeochemical constraints. Biotropica 36: 184-195. (2004)

Jakosky, B. M., K. H. Nealson, C. Bakermans, R. E. Ley, and M. T. Mellon. Sub-freezing activity of microorganisms and the potential habitability of Mars’ polar regions. Astrobiology 3: 343-351. (2003)

Spear, J. S., R. E. Ley, A. B. Berger, and N. R. Pace. The complexity of the genome pool in natural microbial ecosystems:  The Guerrero Negro experience. Biological Bulletin 204: 168-173. (2003)

Ley, R. E. and S. K. Schmidt. Fungal and bacterial responses to amino acid and phenolic compound additions in high altitude barren soil.  Soil Biology and Biochemistry 34: 989-995. (2002)

Mack, M. A., C. M. D’Antonio, and R. E. Ley. Alteration of ecosystem nitrogen dynamics by exotic plants: a case study of C4 grasses in Hawai’i.  Ecological Applications 11: 1323-1335. (2002)

Gonzalez, G., R. E. Ley, S. K Schmidt, Xiaoming Zou, and T. R. Seastedt. Soil ecological interactions: comparisons between tropical and subalpine forests. Oecologia 128: 549-556. (2001)

Ley, R. E., D. A. Lipson and S. K. Schmidt. Microbial biomass levels in high elevation vegetated and barren talus soils. Soil Science Society of America Journal 65: 111-117. (2001)

Schmidt, S. K. and R. E. Ley. Microbial competition and soil structure limit the expression of allelochemicals in nature.  InAllelopathy: Procedures and Processes. (S.Inderjit, Ed.).  CRC Press, p. 339-351. (1999)

Ley, R. E. and C. M. D’Antonio. Alien plant invasions decrease potential rates of nitrogen fixation in dry tropical forests of Hawai’i. Oecologia 113: 179-18. (1998)

D’Antonio, C., J.T. Tunison, R. Ley and R. Loh. Ongoing research into revegetation of degraded dry forest in Hawai’i. Restoration and Management Notes, Winter (1994)

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