Detangling PPI Networks to Uncover Functionally Meaningful Clusters. - Sarah Hall-Swan; Jake Crawford; Rebecca Newman; Lenore J. Cowen (BCB, 2017)

MONET: a toolbox integrating top-performing methods for network modularization. - Mattia Tomasoni; Sergio Gómez; Jake Crawford; Weijia Zhang 001; Sarvenaz Choobdar; Daniel Marbach; Sven Bergmann (Bioinform., 2020)

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)

wenda_gpu: fast domain adaptation for genomic data. - Ariel A. Hippen; Jake Crawford; Jacob R. Gardner; Casey S. Greene (Bioinform., 2022)

The effect of non-linear signal in classification problems using gene expression. - Benjamin J. Heil; Jake Crawford; Casey S. Greene (PLoS Comput. Biol., 2023)

Best holdout assessment is sufficient for cancer transcriptomic model selection. - Jake Crawford; Maria Chikina; Casey S. Greene (Patterns, 2024)