Method Choice, Not Biology, Determines In Silico Perturbation Results: A Systematic Evaluation of Eight Methods Across Four Datasets
Shixiang Wu, Shixiang Wu, Zhangquan Yang, Zhangquan Yang, Jianping CAI, Jianping CAI, Wenjie Ge
This paper evaluates eight in silico perturbation methods across four datasets, finding that only two consistently detect TF-to-pathway regulation, highlighting method choice's impact on results.
bioRxiv · Aug 19, 2026 · PreprintBioinformatics