q2-sample-classifier: machine-learning tools for microbiome classification and regression. - Nicholas A. Bokulich; Matthew R. Dillon; Evan Bolyen; Benjamin D. Kaehler; Gavin A. Huttley; J. Gregory Caporaso (J. Open Source Softw., 2018)

Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops. - Matthew R. Dillon; Evan Bolyen; Anja Adamov; Aeriel Belk; Emily Borsom; Zachary Burcham; Justine W. Debelius; Heather Deel; Alex Emmons; Mehrbod Estaki; Chloe Herman; Christopher R. Keefe; et al. (PLoS Comput. Biol., 2021)

RESCRIPt: Reproducible sequence taxonomy reference database management. - Michael S. Robeson II; Devon R. O'Rourke; Benjamin D. Kaehler; Michal Ziemski; Matthew R. Dillon; Jeffrey T. Foster; Nicholas A. Bokulich (PLoS Comput. Biol., 2021)

Facilitating bioinformatics reproducibility with QIIME 2 Provenance Replay. - Christopher R. Keefe; Matthew R. Dillon; Elizabeth Gehret; Chloe Herman; Mary Jewell; Colin V. Wood; Evan Bolyen; J. Gregory Caporaso (PLoS Comput. Biol., 2023)