Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE). - Evan O. Paull; Daniel E. Carlin; Mario Niepel; Peter K. Sorger; David Haussler; Joshua M. Stuart (Bioinform., 2013)

One-Class Detection of Cell States in Tumor Subtypes. - Artem Sokolov; Evan O. Paull; Joshua M. Stuart (PSB, 2016)

Pathway-Based Genomics Prediction using Generalized Elastic Net. - Artem Sokolov; Daniel E. Carlin; Evan O. Paull; Robert Baertsch; Joshua M. Stuart (PLoS Comput. Biol., 2016)

SJARACNe: a scalable software tool for gene network reverse engineering from big data. - Alireza Khatamian; Evan O. Paull; Andrea Califano; Jiyang Yu (Bioinform., 2019)