Aether: leveraging linear programming for optimal cloud computing in genomics. - Jacob M. Luber; Braden T. Tierney; Evan M. Cofer; Chirag J. Patel; Aleksandar D. Kostic (Bioinform., 2018)

A systematic machine learning and data type comparison yields metagenomic predictors of infant age, sex, breastfeeding, antibiotic usage, country of origin, and delivery type. - Alan Le Goallec; Braden T. Tierney; Jacob M. Luber; Evan M. Cofer; Aleksandar D. Kostic; Chirag J. Patel (PLoS Comput. Biol., 2020)

Ten Quick Tips for Deep Learning in Biology. - Benjamin D. Lee; Anthony Gitter; Casey S. Greene; Sebastian Raschka; Finlay Maguire; Alexander J. Titus; Michael D. Kessler; Alexandra J. Lee; Marc G. Chevrette; Paul Allen Stewart; Thiago Britto-Borges; Evan M. Cofer; et al. (CoRR, 2021)

Ten quick tips for deep learning in biology. - Benjamin D. Lee; Anthony Gitter; Casey S. Greene; Sebastian Raschka; Finlay Maguire; Alexander J. Titus; Michael D. Kessler; Alexandra J. Lee; Marc G. Chevrette; Paul Allen Stewart; Thiago Britto-Borges; Evan M. Cofer; et al. (PLoS Comput. Biol., 2022)

A Computational Approach to the Study of Regulatory Genomics - Evan M. Cofer (2023)

Self-supervised learning predicts plant growth trajectories from multi-modal industrial greenhouse data. - Adam J. Riesselman; Evan M. Cofer; Therese LaRue; Wim Meeussen (CoRR, 2025)