Works by Ley, Ruth E.

Results: 52

Strain tracking in complex microbiomes using synteny analysis reveals per-species modes of evolution.

Published in:

Nature Biotechnology, 2025, v. 43, n. 5, p. 773, doi. 10.1038/s41587-024-02276-2

By:

Enav, Hagay;
Paz, Inbal;
Ley, Ruth E.

Publication type:

Article

Host genetic variation impacts microbiome composition across human body sites.

Published in:

Genome Biology, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s13059-015-0759-1

By:

Blekhman, Ran;
Goodrich, Julia K.;
Huang, Katherine;
Qi Sun;
Bukowski, Robert;
Bell, Jordana T.;
Spector, Timothy D.;
Keinan, Alon;
Ley, Ruth E.;
Gevers, Dirk;
Clark, Andrew G.

Publication type:

Article

A modified Michaelis-Menten equation estimates growth from birth to 3 years in healthy babies in the USA.

Published in:

BMC Medical Research Methodology, 2024, v. 24, n. 1, p. 1, doi. 10.1186/s12874-024-02145-1

By:

Walters, William A.;
Ley, Catherine;
Hastie, Trevor;
Ley, Ruth E.;
Parsonnet, Julie

Publication type:

Article

A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 1, p. 1, doi. 10.1371/journal.pcbi.1002863

By:

Koren, Omry;
Knights, Dan;
Gonzalez, Antonio;
Waldron, Levi;
Segata, Nicola;
Knight, Rob;
Huttenhower, Curtis;
Ley, Ruth E.

Publication type:

Article

Nutrition: When guests turn hostile.

Published in:

Nature, 2013, v. 494, n. 7438, p. 437, doi. 10.1038/494437a

By:

Ley, Ruth E.

Publication type:

Article

Defining the core Arabidopsis thaliana root microbiome.

Published in:

Nature, 2012, v. 488, n. 7409, p. 86, doi. 10.1038/nature11237

By:

Lundberg, Derek S.;
Lebeis, Sarah L.;
Paredes, Sur Herrera;
Yourstone, Scott;
Gehring, Jase;
Malfatti, Stephanie;
Tremblay, Julien;
Engelbrektson, Anna;
Kunin, Victor;
Rio, Tijana Glavina del;
Edgar, Robert C.;
Eickhorst, Thilo;
Ley, Ruth E.;
Hugenholtz, Philip;
Tringe, Susannah Green;
Dangl, Jeffery L.

Publication type:

Article

A core gut microbiome in obese and lean twins.

Published in:

2009

By:

Turnbaugh, Peter J.;
Hamady, Micah;
Yatsunenko, Tanya;
Cantarel, Brandi L.;
Duncan, Alexis;
Ley, Ruth E.;
Sogin, Mitchell L.;
Jones, William J.;
Roe, Bruce A.;
Affourtit, Jason P.;
Egholm, Michael;
Henrissat, Bernard;
Heath, Andrew C.;
Knight, Rob;
Gordon, Jeffrey I.

Publication type:

Letter

Innate immunity and intestinal microbiota in the development of Type 1 diabetes.

Published in:

Nature, 2008, v. 455, n. 7216, p. 1109, doi. 10.1038/nature07336

By:

Li Wen;
Ley, Ruth E.;
Volchkov, Pavel Yu.;
Stranges, Peter B.;
Avanesyan, Lia;
Stonebraker, Austin C.;
Changyun Hu;
Wong, F. Susan;
Szot, Gregory L.;
Bluestone, Jeffrey A.;
Gordon, Jeffrey I.;
Chervonsky, Alexander V.

Publication type:

Article

Heritable components of the human fecal microbiome are associated with visceral fat.

Published in:

Genome Biology, 2016, v. 17, p. 1, doi. 10.1186/s13059-016-1052-7

By:

Beaumont, Michelle;
Goodrich, Julia K.;
Jackson, Matthew A.;
Yet, Idil;
Davenport, Emily R.;
Vieira-Silva, Sara;
Debelius, Justine;
Pallister, Tess;
Mangino, Massimo;
Raes, Jeroen;
Knight, Rob;
Clark, Andrew G.;
Ley, Ruth E.;
Spector, Tim D.;
Bell, Jordana T.

Publication type:

Article

Host genetic variation impacts microbiome composition across human body sites.

Published in:

Genome Biology, 2015, v. 18, p. 1, doi. 10.1186/s13059-015-0759-1

By:

Blekhman, Ran;
Goodrich, Julia K.;
Katherine Huang;
Qi Sun;
Bukowski, Robert;
Bell, Jordana T.;
Spector, Timothy D.;
Keinan, Alon;
Ley, Ruth E.;
Gevers, Dirk;
Clark, Andrew G.

Publication type:

Article

Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys.

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2012, v. 6, n. 1, p. 94, doi. 10.1038/ismej.2011.82

By:

Werner, Jeffrey J;
Koren, Omry;
Hugenholtz, Philip;
DeSantis, Todd Z;
Walters, William A;
Caporaso, J Gregory;
Angenent, Largus T;
Knight, Rob;
Ley, Ruth E

Publication type:

Article

Supervised classification of microbiota mitigates mislabeling errors.

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2011, v. 5, n. 4, p. 570, doi. 10.1038/ismej.2010.148

By:

Knights, Dan;
Kuczynski, Justin;
Koren, Omry;
Ley, Ruth E;
Field, Dawn;
Knight, Rob;
DeSantis, Todd Z;
Kelley, Scott T

Publication type:

Article

Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades.

Published in:

Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-019-10191-3

By:

Youngblut, Nicholas D.;
Reischer, Georg H.;
Walters, William;
Schuster, Nathalie;
Walzer, Chris;
Stalder, Gabrielle;
Ley, Ruth E.;
Farnleitner, Andreas H.

Publication type:

Article

Harnessing Microbiota to Kill a Pathogen: The sweet tooth of Clostridium difficile.

Published in:

Nature Medicine, 2014, v. 20, n. 3, p. 248, doi. 10.1038/nm.3494

By:

Ley, Ruth E

Publication type:

Article

Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome.

Published in:

Nature, 2015, v. 519, n. 7541, p. 92, doi. 10.1038/nature14232

By:

Chassaing, Benoit;
Koren, Omry;
Goodrich, Julia K.;
Poole, Angela C.;
Srinivasan, Shanthi;
Ley, Ruth E.;
Gewirtz, Andrew T.

Publication type:

Article

The Gene-Microbe Link.

Published in:

Nature, 2015, v. 518, n. s7540, p. S7, doi. 10.1038/518S7a

By:

Ley, Ruth E.

Publication type:

Article

The Gene–Microbe Link.

Published in:

Nature, 2015, v. 518, n. 7540, p. S7, doi. 10.1038/518S7a

By:

Ley, Ruth E.

Publication type:

Article

Murine Methyl Donor Deficiency Impairs Early Growth in Association with Dysmorphic Small Intestinal Crypts and Reduced Gut Microbial Community Diversity.

Published in:

Current Developments in Nutrition, 2019, v. 3, n. 1, p. N.PAG, doi. 10.1093/cdn/nzy070

By:

Silva, Antonio V Alves da;
Oliveira, Stephanie B de Castro;
Rienzi, Sara C Di;
Brown-Steinke, Kathleen;
Dehan, Lauren M;
Rood, Jill K;
Carreira, Vinicius S;
Le, Hung;
Maier, Elizabeth A;
Betz, Kristina J;
Aihara, Eitaro;
Ley, Ruth E;
Preidis, Geoffrey A;
Shen, Lanlan;
Moore, Sean R

Publication type:

Article

Microbial population dynamics in an extreme environment: controlling factors in talus soils at 3750 m in the Colorado Rocky Mountains.

Published in:

Biogeochemistry, 2004, v. 68, n. 3, p. 297, doi. 10.1023/B:BIOG.0000031032.58611.d0

By:

Ley, Ruth E.;
Williams, Mark W.;
Schmidt, Steven K.

Publication type:

Article

Responses of Gut Microbiota to Diet Composition and Weight Loss in Lean and Obese Mice.

Published in:

Obesity (19307381), 2012, v. 20, n. 4, p. 738, doi. 10.1038/oby.2011.111

By:

Ravussin, Yann;
Koren, Omry;
Spor, Ayme;
LeDuc, Charles;
Gutman, Roee;
Stombaugh, Jesse;
Knight, Rob;
Ley, Ruth E.;
Leibel, Rudolph L.

Publication type:

Article

Obesity is the main driver of altered gut microbiome functions in the metabolically unhealthy.

Published in:

Gut Microbes, 2023, v. 15, n. 2, p. 1, doi. 10.1080/19490976.2023.2246634

By:

de la Cuesta-Zuluaga, Jacobo;
Huus, Kelsey E.;
Youngblut, Nicholas D.;
Escobar, Juan S.;
Ley, Ruth E.

Publication type:

Article

Exploring the maize rhizosphere microbiome in the field.

Published in:

Communicative & Integrative Biology, 2013, v. 6, n. 5, p. 1, doi. 10.4161/cib.25177

By:

Peiffer, Jason A.;
Ley, Ruth E.

Publication type:

Article

Signatures of early frailty in the gut microbiota.

Published in:

Genome Medicine, 2016, v. 8, p. 1, doi. 10.1186/s13073-016-0262-7

By:

Jackson, Matt;
Jeffery, Ian B.;
Beaumont, Michelle;
Bell, Jordana T.;
Clark, Andrew G.;
Ley, Ruth E.;
O'Toole, Paul W.;
Spector, Tim D.;
Steves, Claire J.

Publication type:

Article

Silent recognition of flagellins from human gut commensal bacteria by Toll-like receptor 5.

Published in:

Science Immunology, 2023, v. 8, n. 79, p. 1, doi. 10.1126/sciimmunol.abq7001

By:

Clasen, Sara J.;
Bell, Michael E. W.;
Borbón, Andrea;
Lee, Du-Hwa;
Henseler, Zachariah M.;
de la Cuesta-Zuluaga, Jacobo;
Parys, Katarzyna;
Zou, Jun;
Wang, Yanling;
Altmannova, Veronika;
Youngblut, Nicholas D.;
Weir, John R.;
Gewirtz, Andrew T.;
Belkhadir, Youssef;
Ley, Ruth E.

Publication type:

Article

Methane Emission in a Specific Riparian-Zone Sediment Decreased with Bioelectrochemical Manipulation and Corresponded to the Microbial Community Dynamics.

Published in:

Frontiers in Microbiology, 2016, p. 1, doi. 10.3389/fmicb.2015.01523

By:

Friedman, Elliot S.;
McPhillips, Lauren E.;
Werner, Jeffrey J.;
Poole, Angela C.;
Ley, Ruth E.;
Walter, M. Todd;
Angenent, Largus T.

Publication type:

Article

Incorporating genome‐based phylogeny and functional similarity into diversity assessments helps to resolve a global collection of human gut metagenomes.

Published in:

Environmental Microbiology, 2022, v. 24, n. 9, p. 3966, doi. 10.1111/1462-2920.15910

By:

Youngblut, Nicholas D.;
de la Cuesta‐Zuluaga, Jacobo;
Ley, Ruth E.

Publication type:

Article

The human microbiome: eliminating the biomedical/environmental dichotomy in microbial ecology.

Published in:

2007

By:

Ley, Ruth E.;
Knight, Rob;
Gordon, Jeffrey I.

Publication type:

Other

Soil Microbial Dynamics in Costa Rica: Seasonal and Biogeochemical Constraints.

Published in:

Biotropica, 2004, v. 36, n. 2, p. 184, doi. 10.1111/j.1744-7429.2004.tb00311.x

By:

Cleveland, Cory C.;
Townsend, Alan R.;
Constance, Briana C.;
Ley, Ruth E.;
Schmidt, Steven K.

Publication type:

Article

Worlds within worlds: evolution of the vertebrate gut microbiota.

Published in:

Nature Reviews Microbiology, 2008, v. 6, n. 10, p. 776, doi. 10.1038/nrmicro1978

By:

Ley, Ruth E.;
Lozupone, Catherine A.;
Hamady, Micah;
Knight, Rob;
Gordon, Jeffrey I.

Publication type:

Article

Microbial Biomass Levels in Barren and Vegetated High Altitude Talus Soils.

Published in:

Soil Science Society of America Journal, 2001, v. 65, n. 1, p. 111, doi. 10.2136/sssaj2001.651111x

By:

Ley, Ruth E.;
Lipson, David A.

Publication type:

Article

DeepMAsED: evaluating the quality of metagenomic assemblies.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3011, doi. 10.1093/bioinformatics/btaa124

By:

Mineeva, Olga;
Rojas-Carulla, Mateo;
Ley, Ruth E;
Schölkopf, Bernhard;
Youngblut, Nicholas D

Publication type:

Article

Struo: a pipeline for building custom databases for common metagenome profilers.

Published in:

Bioinformatics, 2020, v. 36, n. 7, p. 2314, doi. 10.1093/bioinformatics/btz899

By:

de la Cuesta-Zuluaga, Jacobo;
Ley, Ruth E;
Youngblut, Nicholas D

Publication type:

Article

Alterations to the Gut Microbiome Impair Bone Strength and Tissue Material Properties.

Published in:

Journal of Bone & Mineral Research, 2017, v. 32, n. 6, p. 1343, doi. 10.1002/jbmr.3114

By:

Guss, Jason D;
Horsfield, Michael W;
Fontenele, Fernanda F;
Sandoval, Taylor N;
Luna, Marysol;
Apoorva, Fnu;
Lima, Svetlana F;
Bicalho, Rodrigo C;
Singh, Ankur;
Ley, Ruth E;
van der Meulen, Marjolein CH;
Goldring, Steven R;
Hernandez, Christopher J

Publication type:

Article

The Human Microbiome Project.

Published in:

Nature, 2007, v. 449, n. 7164, p. 804, doi. 10.1038/nature06244

By:

Turnbaugh, Peter J.;
Ley, Ruth E.;
Hamady, Micah;
Fraser-Liggett, Claire M.;
Knight, Rob;
Gordon, Jeffrey I.

Publication type:

Article

Microbial ecology: Human gut microbes associated with obesity.

Published in:

Nature, 2006, v. 444, n. 7122, p. 1022, doi. 10.1038/4441022a

By:

Ley, Ruth E.;
Turnbaugh, Peter J.;
Klein, Samuel;
Gordon, Jeffrey I.

Publication type:

Article

An obesity-associated gut microbiome with increased capacity for energy harvest.

Published in:

Nature, 2006, v. 444, n. 7122, p. 1027, doi. 10.1038/nature05414

By:

Turnbaugh, Peter J.;
Ley, Ruth E.;
Mahowald, Michael A.;
Magrini, Vincent;
Mardis, Elaine R.;
Gordon, Jeffrey I.

Publication type:

Article

Sphingolipids produced by gut bacteria enter host metabolic pathways impacting ceramide levels.

Published in:

Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-16274-w

By:

Johnson, Elizabeth L.;
Heaver, Stacey L.;
Waters, Jillian L.;
Kim, Benjamin I.;
Bretin, Alexis;
Goodman, Andrew L.;
Gewirtz, Andrew T.;
Worgall, Tilla S.;
Ley, Ruth E.

Publication type:

Article

Flagellin-elicited adaptive immunity suppresses flagellated microbiota and vaccinates against chronic inflammatory diseases.

Published in:

Nature Communications, 2019, v. 10, n. 1, p. 1, doi. 10.1038/s41467-019-13538-y

By:

Tran, Hao Q.;
Ley, Ruth E.;
Gewirtz, Andrew T.;
Chassaing, Benoit

Publication type:

Article

Gut-Microbiota-Metabolite Axis in Early Renal Function Decline.

Published in:

PLoS ONE, 2015, v. 10, n. 8, p. 1, doi. 10.1371/journal.pone.0134311

By:

Barrios, Clara;
Beaumont, Michelle;
Pallister, Tess;
Villar, Judith;
Goodrich, Julia K.;
Clark, Andrew;
Pascual, Julio;
Ley, Ruth E.;
Spector, Tim D.;
Bell, Jordana T.;
Menni, Cristina

Publication type:

Article

Branched Chain Fatty Acids Reduce the Incidence of Necrotizing Enterocolitis and Alter Gastrointestinal Microbial Ecology in a Neonatal Rat Model.

Published in:

PLoS ONE, 2011, v. 6, n. 12, p. 1, doi. 10.1371/journal.pone.0029032

By:

Ran-Ressler, Rinat R.;
Khailova, Ludmila;
Arganbright, Kelly M.;
Adkins-Rieck, Camille K.;
Jouni, Zeina E.;
Koren, Omry;
Ley, Ruth E.;
Brenna, J. Thomas;
Dvorak, Bohuslav

Publication type:

Article

ABO antigen and secretor statuses are not associated with gut microbiota composition in 1,500 twins.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-3290-1

By:

Davenport, Emily R.;
Goodrich, Julia K.;
Bell, Jordana T.;
Spector, Tim D.;
Ley, Ruth E.;
Clark, Andrew G.

Publication type:

Article

The human gut bacteria Christensenellaceae are widespread, heritable, and associated with health.

Published in:

BMC Biology, 2019, v. 17, n. 1, p. 1, doi. 10.1186/s12915-019-0699-4

By:

Waters, Jillian L.;
Ley, Ruth E.

Publication type:

Article

Struo2: efficient metagenome profiling database construction for ever-expanding microbial genome datasets.

Published in:

PeerJ, 2021, p. 1, doi. 10.7717/peerj.12198

By:

Youngblut, Nicholas D.;
Ley, Ruth E.

Publication type:

Article

Reduced diversity and altered composition of the gut microbiome in individuals with myalgic encephalomyelitis/chronic fatigue syndrome.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0171-4

By:

Giloteaux, Ludovic;
Goodrich, Julia K.;
Walters, William A.;
Levine, Susan M.;
Ley, Ruth E.;
Hanson, Maureen R.

Publication type:

Article

ALTERATION OF ECOSYSTEM NITROGEN DYNAMICS BY EXOTIC PLANTS: A CASE STUDY OF C<sub>4</sub> GRASSES IN HAWAII.

Published in:

Ecological Applications, 2001, v. 11, n. 5, p. 1323, doi. 10.1890/1051-0761(2001)011[1323:AOENDB]2.0.CO;2

By:

Mack, Michelle C.;
D'Antonio, Carla M.;
Ley, Ruth E.

Publication type:

Article

Epidemiology and associated microbiota changes in deployed military personnel at high risk of traveler's diarrhea.

Published in:

PLoS ONE, 2020, v. 15, n. 8, p. 1, doi. 10.1371/journal.pone.0236703

By:

Walters, William A.;
Reyes, Faviola;
Soto, Giselle M.;
Reynolds, Nathanael D.;
Fraser, Jamie A.;
Aviles, Ricardo;
Tribble, David R.;
Irvin, Adam P.;
Kelley-Loughnane, Nancy;
Gutierrez, Ramiro L.;
Riddle, Mark S.;
Ley, Ruth E.;
Goodson, Michael S.;
Simons, Mark P.

Publication type:

Article

ResMiCo: Increasing the quality of metagenome-assembled genomes with deep learning.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011001

By:

Mineeva, Olga;
Danciu, Daniel;
Schölkopf, Bernhard;
Ley, Ruth E.;
Rätsch, Gunnar;
Youngblut, Nicholas D.

Publication type:

Article

Interpreting tree ensemble machine learning models with endoR.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 12, p. 1, doi. 10.1371/journal.pcbi.1010714

By:

Ruaud, Albane;
Pfister, Niklas;
Ley, Ruth E.;
Youngblut, Nicholas D.

Publication type:

Article

Soil ecological interactions: comparisons between tropical and subalpine forests.

Published in:

Oecologia, 2001, v. 128, n. 4, p. 549, doi. 10.1007/s004420100685

By:

González, Grizelle;
Ley, Ruth E.;
Schmidt, Steven K.;
Xiaoming Zou;
Seastedt, Timothy R.

Publication type:

Article

Expanding the scope and scale of microbiome research.

Published in:

2019

By:

Knight, Rob;
Ley, Ruth E.;
Raes, Jeroen;
Grice, Elizabeth A.

Publication type:

Editorial