Computational Approaches to Study Microbes and Microbiomes. - Casey S. Greene; James A. Foster; Bruce A. Stanton; Deborah A. Hogan; Yana Bromberg (PSB, 2016)

ADAGE signature analysis: differential expression analysis with data-defined gene sets. - Jie Tan; Matt Huyck; Dongbo Hu; René A. Zelaya; Deborah A. Hogan; Casey S. Greene (BMC Bioinform., 2017)

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)

SOPHIE: Generative Neural Networks Separate Common and Specific Transcriptional Responses. - Alexandra J. Lee; Dallas L. Mould; Jake Crawford; Dongbo Hu; Rani K. Powers; Georgia Doing; James C. Costello; Deborah A. Hogan; Casey S. Greene (Genom. Proteom. Bioinform., 2022)