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

por Youngblut, Nicholas D., Ley, Ruth E.
Publicado 2021

HTSSIP: An R package for analysis of high throughput sequencing data from nucleic acid stable isotope probing (SIP) experiments

por Youngblut, Nicholas D., Barnett, Samuel E., Buckley, Daniel H.
Publicado 2018

SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments

por Youngblut, Nicholas D., Barnett, Samuel E., Buckley, Daniel H.
Publicado 2018

Interpreting tree ensemble machine learning models with endoR

por Ruaud, Albane, Pfister, Niklas, Ley, Ruth E., Youngblut, Nicholas D.
Publicado 2022

Differentiation and Structure in Sulfolobus islandicus Rod-Shaped Virus Populations

por Bautista, Maria A., Black, Jesse A., Youngblut, Nicholas D., Whitaker, Rachel J.
Publicado 2017

Plant Phylogeny and Life History Shape Rhizosphere Bacterial Microbiome of Summer Annuals in an Agricultural Field

por Emmett, Bryan D., Youngblut, Nicholas D., Buckley, Daniel H., Drinkwater, Laurie E.
Publicado 2017

Strain-Level Analysis of Bifidobacterium spp. from Gut Microbiomes of Adults with Differing Lactase Persistence Genotypes

por Schmidt, Victor, Enav, Hagay, Spector, Timothy D., Youngblut, Nicholas D., Ley, Ruth E.
Publicado 2020

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

por Mineeva, Olga, Danciu, Daniel, Schölkopf, Bernhard, Ley, Ruth E., Rätsch, Gunnar, Youngblut, Nicholas D.
Publicado 2023

Genomic Insights into Adaptations of Trimethylamine-Utilizing Methanogens to Diverse Habitats, Including the Human Gut

por de la Cuesta-Zuluaga, Jacobo, Spector, Tim D., Youngblut, Nicholas D., Ley, Ruth E.
Publicado 2021

Millimeter-Scale Patterns of Phylogenetic and Trait Diversity in a Salt Marsh Microbial Mat

por Armitage, David W., Gallagher, Kimberley L., Youngblut, Nicholas D., Buckley, Daniel H., Zinder, Stephen H.
Publicado 2012

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

por de la Cuesta-Zuluaga, Jacobo, Huus, Kelsey E., Youngblut, Nicholas D., Escobar, Juan S., Ley, Ruth E.
Publicado 2023

Reclassification of Catabacter hongkongensis as Christensenella hongkongensis comb. nov. based on whole genome analysis

por Liu, Xiaoying, Sutter, Jessica L., de la Cuesta-Zuluaga, Jacobo, Waters, Jillian L., Youngblut, Nicholas D., Ley, Ruth E.
Publicado 2021

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

por Youngblut, Nicholas D., Reischer, Georg H., Walters, William, Schuster, Nathalie, Walzer, Chris, Stalder, Gabrielle, Ley, Ruth E., Farnleitner, Andreas H.
Publicado 2019

Vertebrate host phylogeny influences gut archaeal diversity

por Youngblut, Nicholas D., Reischer, Georg H., Dauser, Silke, Maisch, Sophie, Walzer, Chris, Stalder, Gabrielle, Farnleitner, Andreas H., Ley, Ruth E.
Publicado 2021

Syntrophy via Interspecies H(2) Transfer between Christensenella and Methanobrevibacter Underlies Their Global Cooccurrence in the Human Gut

por Ruaud, Albane, Esquivel-Elizondo, Sofia, de la Cuesta-Zuluaga, Jacobo, Waters, Jillian L., Angenent, Largus T., Youngblut, Nicholas D., Ley, Ruth E.
Publicado 2020

Large-Scale Metagenome Assembly Reveals Novel Animal-Associated Microbial Genomes, Biosynthetic Gene Clusters, and Other Genetic Diversity

por Youngblut, Nicholas D., de la Cuesta-Zuluaga, Jacobo, Reischer, Georg H., Dauser, Silke, Schuster, Nathalie, Walzer, Chris, Stalder, Gabrielle, Farnleitner, Andreas H., Ley, Ruth E.
Publicado 2020

Metagenomic evidence for reciprocal particle exchange between the mainstem estuary and lateral bay sediments of the lower Columbia River

por Smith, Maria W., Davis, Richard E., Youngblut, Nicholas D., Kärnä, Tuomas, Herfort, Lydie, Whitaker, Rachel J., Metcalf, William W., Tebo, Bradley M., Baptista, António M., Simon, Holly M.
Publicado 2015

Free-Living, Psychrotrophic Bacteria of the Genus Psychrobacter Are Descendants of Pathobionts

por Welter, Daphne K., Ruaud, Albane, Henseler, Zachariah M., De Jong, Hannah N., van Coeverden de Groot, Peter, Michaux, Johan, Gormezano, Linda, Waters, Jillian L., Youngblut, Nicholas D., Ley, Ruth E.
Publicado 2021

Lake microbial communities are resilient after a whole-ecosystem disturbance

por Shade, Ashley, Read, Jordan S, Youngblut, Nicholas D, Fierer, Noah, Knight, Rob, Kratz, Timothy K, Lottig, Noah R, Roden, Eric E, Stanley, Emily H, Stombaugh, Jesse, Whitaker, Rachel J, Wu, Chin H, McMahon, Katherine D
Publicado 2012

An integrated systems biology approach reveals differences in formate metabolism in the genus Methanothermobacter

por Casini, Isabella, McCubbin, Tim, Esquivel-Elizondo, Sofia, Luque, Guillermo G., Evseeva, Daria, Fink, Christian, Beblawy, Sebastian, Youngblut, Nicholas D., Aristilde, Ludmilla, Huson, Daniel H., Dräger, Andreas, Ley, Ruth E., Marcellin, Esteban, Angenent, Largus T., Molitor, Bastian
Publicado 2023