Jiejun Shi

TEDDY reconstructs and characterizes TE-dependent isoforms across biological contexts, revealing regulatory networks and identifying novel regulators like Arid3a with clinical relevance in cancer.

The paper introduces cFOOT-seq, a method for high-resolution, quantitative detection of TF occupancy across the genome, and demonstrates its application in analyzing TF dynamics and dependencies.

The paper introduces CHALM, a methylation quantification method that accounts for cellular heterogeneity, improving the correlation between methylation and gene expression.