Functional network community detection can disaggregate and filter multiple underlying pathways in enrichment analyses. - Lia X. Harrington; Gregory P. Way; Jennifer A. Doherty; Casey S. Greene (PSB, 2018)

Extracting a biologically relevant latent space from cancer transcriptomes with variational autoencoders. - Gregory P. Way; Casey S. Greene (PSB, 2018)

PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia. - Kathleen M. Chen; Jie Tan; Gregory P. Way; Georgia Doing; Deborah A. Hogan; Casey S. Greene (BioData Min., 2018)

A field guide to cultivating computational biology. - Anne E. Carpenter; Casey S. Greene; Piero Carnici; Benilton S. Carvalho; Michiel de Hoon; Stacey D. Finley; Kim-Anh Lê Cao; Jerry S. H. Lee; Luigi Marchionni; Suzanne Sindi; Fabian J. Theis; Gregory P. Way; et al. (CoRR, 2021)

Predicting drug polypharmacology from cell morphology readouts using variational autoencoder latent space arithmetic. - Yuen Ler Chow; Shantanu Singh; Anne E. Carpenter; Gregory P. Way (PLoS Comput. Biol., 2022)