Predicting antimicrobial mechanism-of-action from transcriptomes: A generalizable explainable artificial intelligence approach. - Josh L. Espinoza; Chris L. Dupont; Aubrie O'Rourke; Sinem Beyhan; Pavel Morales; Amy Spoering; Kirsten J. Meyer; Agnes P. Chan; Yongwook Choi; William C. Nierman; Kim Lewis; Karen E. Nelson (PLoS Comput. Biol., 2021)

VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes. - Josh L. Espinoza; Chris L. Dupont (BMC Bioinform., 2022)