BatmanNet: bi-branch masked graph transformer autoencoder for molecular representation. - Zhen Wang 056; Zheng Feng; Yanjun Li 005; Bowen Li; Yongrui Wang; Chulin Sha; Min He; Xiaolin Li 001 (Briefings Bioinform., 2023)

DrugMetric: quantitative drug-likeness scoring based on chemical space distance. - Bowen Li; Zhen Wang 056; Ziqi Liu; Yanxin Tao; Chulin Sha; Min He; Xiaolin Li 001 (Briefings Bioinform., 2024)

RNADiffFold: generative RNA secondary structure prediction using discrete diffusion models. - Zhen Wang 056; Yizhen Feng; Qingwen Tian; Ziqi Liu; Pengju Yan; Xiaolin Li 001 (Briefings Bioinform., 2024)

AptaDiff: de novo design and optimization of aptamers based on diffusion models. - Zhen Wang 056; Ziqi Liu; Wei Zhang; Yanjun Li 005; Yizhen Feng; Shaokang Lv; Han Diao; Zhaofeng Luo; Pengju Yan; Min He; Xiaolin Li 001 (Briefings Bioinform., 2024)

Improving Covalent and Noncovalent Molecule Generation via Reinforcement Learning with Functional Fragments. - Yongrui Wang; Zhen Wang 056; Yanjun Li 005; Pengju Yan; Xiaolin Li 001 (J. Chem. Inf. Model., 2025)