GeNet: Deep Representations for Metagenomics. - Mateo Rojas-Carulla; Ilya O. Tolstikhin; Guillermo Luque; Nicholas D. Youngblut; Ruth E. Ley; Bernhard Schölkopf (CoRR, 2019)

Struo: a pipeline for building custom databases for common metagenome profilers. - Jacobo de la Cuesta-Zuluaga; Ruth E. Ley; Nicholas D. Youngblut (Bioinform., 2020)

DeepMAsED: evaluating the quality of metagenomic assemblies. - Olga Mineeva; Mateo Rojas-Carulla; Ruth E. Ley; Bernhard Schölkopf; Nicholas D. Youngblut (Bioinform., 2020)

Interpreting tree ensemble machine learning models with endoR. - Albane Ruaud; Niklas Pfister; Ruth E. Ley; Nicholas D. Youngblut (PLoS Comput. Biol., 2022)

ResMiCo: Increasing the quality of metagenome-assembled genomes with deep learning. - Olga Mineeva; Daniel Danciu; Bernhard Schölkopf; Ruth E. Ley; Gunnar Rätsch; Nicholas D. Youngblut (PLoS Comput. Biol., 2023)

Whole Genome Transformer for Gene Interaction Effects in Microbiome Habitat Specificity. - Zhufeng Li; Sandeep Suresh Cranganore; Nicholas D. Youngblut; Niki Kilbertus (AAAI, 2025)