Jie Tan

PathCORE-T identifies and visualizes globally co-occurring pathways across transcriptomic datasets by analyzing features from machine learning models.

ADAGE signature analysis identifies perturbed biological processes by learning gene signatures from public data, outperforming curated gene sets in revealing novel processes in Pseudomonas aeruginosa.

The paper introduces eADAGE, an ensemble method to extract stable expression signatures from public data, revealing a phosphate starvation response in Pseudomonas aeruginosa controlled by PhoB and requiring KinB.