Struo2: efficient metagenome profiling database construction for ever-expanding microbial genome datasets by Nicholas D. Youngblut, Ruth E. Ley

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HTSSIP: An R package for analysis of high throughput sequencing data from nucleic acid stable isotope probing (SIP) experiments. by Nicholas D Youngblut, Samuel E Barnett, Daniel H Buckley

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SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments by Nicholas D. Youngblut, Samuel E. Barnett, Daniel H. Buckley

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Interpreting tree ensemble machine learning models with endoR. by Albane Ruaud, Niklas Pfister, Ruth E Ley, Nicholas D Youngblut

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Plant Phylogeny and Life History Shape Rhizosphere Bacterial Microbiome of Summer Annuals in an Agricultural Field by Bryan D. Emmett, Nicholas D. Youngblut, Daniel H. Buckley, Laurie E. Drinkwater

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Differentiation and Structure in Sulfolobus islandicus Rod-Shaped Virus Populations by Maria A. Bautista, Jesse A. Black, Nicholas D. Youngblut, Rachel J. Whitaker

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Strain-Level Analysis of <italic toggle="yes">Bifidobacterium</italic> spp. from Gut Microbiomes of Adults with Differing Lactase Persistence Genotypes by Victor Schmidt, Hagay Enav, Timothy D. Spector, Nicholas D. Youngblut, Ruth E. Ley

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ResMiCo: Increasing the quality of metagenome-assembled genomes with deep learning. by Olga Mineeva, Daniel Danciu, Bernhard Schölkopf, Ruth E Ley, Gunnar Rätsch, Nicholas D Youngblut

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Genomic Insights into Adaptations of Trimethylamine-Utilizing Methanogens to Diverse Habitats, Including the Human Gut by Jacobo de la Cuesta-Zuluaga, Tim D. Spector, Nicholas D. Youngblut, Ruth E. Ley

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Millimeter-scale patterns of phylogenetic and trait diversity in a salt marsh microbial mat by David W. Armitage, Kimberley L. Gallagher, Nicholas D. Youngblut, Daniel H. Buckley, Stephen H. Zinder

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Obesity is the main driver of altered gut microbiome functions in the metabolically unhealthy by Jacobo de la Cuesta-Zuluaga, Kelsey E. Huus, Nicholas D. Youngblut, Juan S. Escobar, Ruth E. Ley

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Syntrophy via Interspecies H₂ Transfer between <italic toggle="yes">Christensenella</italic> and <italic toggle="yes">Methanobrevibacter</italic> Underlies Their Global... by Albane Ruaud, Sofia Esquivel-Elizondo, Jacobo de la Cuesta-Zuluaga, Jillian L. Waters, Largus T. Angenent, Nicholas D. Youngblut, Ruth E. Ley

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Large-Scale Metagenome Assembly Reveals Novel Animal-Associated Microbial Genomes, Biosynthetic Gene Clusters, and Other Genetic Diversity by Nicholas D. Youngblut, Jacobo de la Cuesta-Zuluaga, Georg H. Reischer, Silke Dauser, Nathalie Schuster, Chris Walzer, Gabrielle Stalder, Andreas H. Farnleitner, Ruth E. Ley

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Metagenomic evidence for reciprocal particle exchange between the mainstem estuary and lateral bay sediments of the lower Columbia River by Mariya W Smith, Richard E Davis, Nicholas D Youngblut, Tuomas eKärnä, Lydie eHerfort, Rachel J Whitaker, William W Metcalf, Bradley M. Tebo, Antonio M Baptista, Holly M Simon

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Free-Living, Psychrotrophic Bacteria of the Genus Psychrobacter Are Descendants of Pathobionts by Daphne K. Welter, Albane Ruaud, Zachariah M. Henseler, Hannah N. De Jong, Peter van Coeverden de Groot, Johan Michaux, Linda Gormezano, Jillian L. Waters, Nicholas D. Youngblut, Ruth E. Ley

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Free-Living, Psychrotrophic Bacteria of the Genus <italic toggle="yes">Psychrobacter</italic> Are Descendants of Pathobionts by Daphne K. Welter, Albane Ruaud, Zachariah M. Henseler, Hannah N. De Jong, Peter van Coeverden de Groot, Johan Michaux, Linda Gormezano, Jillian L. Waters, Nicholas D. Youngblut, Ruth E. Ley

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An integrated systems biology approach reveals differences in formate metabolism in the genus Methanothermobacter by Isabella Casini, Tim McCubbin, Sofia Esquivel-Elizondo, Guillermo G. Luque, Daria Evseeva, Christian Fink, Sebastian Beblawy, Nicholas D. Youngblut, Ludmilla Aristilde, Daniel H. Huson, Andreas Dräger, Ruth E. Ley, Esteban Marcellin, Largus T. Angenent, Bastian Molitor

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