scPreGAN, a deep generative model for predicting the response of single-cell expression to perturbation. - Xiajie Wei; Jiayi Dong; Fei Wang 017 (Bioinform., 2022)

scSemiAE: a deep model with semi-supervised learning for single-cell transcriptomics. - Jiayi Dong; Yin Zhang; Fei Wang 017 (BMC Bioinform., 2022)

GROD: Joint Inference of Gene Regulatory Networks and Data Imputation in Single-Cell RNA Sequencing with Temporal Consideration. - Jiayi Dong; Fei Wang 017 (BIBM, 2023)

Deep Learning in Gene Regulatory Network Inference: A Survey. - Jiayi Dong; Jiahao Li; Fei Wang 017 (IEEE ACM Trans. Comput. Biol. Bioinform., 2024)

Conditional Causal Representation Learning for Heterogeneous Single-cell RNA Data Integration and Prediction. - Jiayi Dong; Jiahao Li; Fei Wang (IJCAI, 2025)

Roundtable Policy: Improving Scientific Reasoning and Narratives through Confidence-Weighted Consensus of LLMs. - Yu Yao; Jiayi Dong; Ju Li; Yang Yang; Yilun Du (CoRR, 2025)