Large-Scale Cell Representation Learning via Divide-and-Conquer Contrastive Learning. - Suyuan Zhao; Jiahuan Zhang; Zaiqing Nie (CoRR, 2023)

LangCell: Language-Cell Pre-training for Cell Identity Understanding. - Suyuan Zhao; Jiahuan Zhang; Yushuai Wu; Yizhen Luo; Zaiqing Nie (ICML, 2024)

MutaPLM: Protein Language Modeling for Mutation Explanation and Engineering. - Yizhen Luo; Zikun Nie; Massimo Hong; Suyuan Zhao; Hao Zhou 012; Zaiqing Nie (NeurIPS, 2024)

DeepCRE: Transforming Drug R&D via AI-Driven Cross-drug Response Evaluation. - Yushuai Wu; Ting Zhang; Hao Zhou 012; Hainan Wu; Hanwen Sunchu; Lei Hu; Xiaofang Chen; Suyuan Zhao; Gaochao Liu; Chao Sun; Jiahuan Zhang; Yizhen Luo; et al. (CoRR, 2024)

SToFM: a Multi-scale Foundation Model for Spatial Transcriptomics. - Suyuan Zhao; Yizhen Luo; Ganbo Yang; Yan Zhong; Hao Zhou 012; Zaiqing Nie (CoRR, 2025)