DensityPath: an algorithm to visualize and reconstruct cell state-transition path on density landscape for single-cell RNA sequencing data. - Ziwei Chen; Shaokun An; Xiangqi Bai; Fuzhou Gong; Liang Ma; Lin Wan (Bioinform., 2019)

TSEE: an elastic embedding method to visualize the dynamic gene expression patterns of time series single-cell RNA sequencing data. - Shaokun An; Liang Ma; Lin Wan (BMC Genom., 2019)

A New Context Tree Inference Algorithm for Variable Length Markov Chain Model with Applications to Biological Sequence Analyses. - Shaokun An; Jie Ren 006; Fengzhu Sun; Lin Wan (J. Comput. Biol., 2022)

Causal Disentanglement of Treatment Effects in Single-Cell RNA Sequencing Through Counterfactual Inference. - Shaokun An; Jae-Won Cho; Kai Cao; Jiankang Xiong; Martin Hemberg; Lin Wan (RECOMB, 2025)