FL-QSAR: a federated learning-based QSAR prototype for collaborative drug discovery. - Shaoqi Chen; Dongyu Xue; Guohui Chuai; Qiang Yang 001; Qi Liu 019 (Bioinform., 2021)

Structure-informed Language Models Are Protein Designers. - Zaixiang Zheng; Yifan Deng; Dongyu Xue; Yi Zhou 018; Fei Ye; Quanquan Gu (ICML, 2023)

Systematic Exploration of Optimized Base Editing gRNA Design and Pleiotropic Effects with BExplorer. - Gongchen Zhang; Chenyu Zhu; Xiaohan Chen; Jifang Yan; Dongyu Xue; Zixuan Wei; Guohui Chuai; Qi Liu 019 (Genom. Proteom. Bioinform., 2023)

Diffusion Language Models Are Versatile Protein Learners. - Xinyou Wang; Zaixiang Zheng; Fei Ye; Dongyu Xue; Shujian Huang; Quanquan Gu (ICML, 2024)

Antigen-Specific Antibody Design via Direct Energy-based Preference Optimization. - Xiangxin Zhou; Dongyu Xue; Ruizhe Chen; Zaixiang Zheng; Liang Wang 001; Quanquan Gu (NeurIPS, 2024)

ProteinWeaver: A Divide-and-Assembly Approach for Protein Backbone Design. - Yiming Ma; Fei Ye; Yi Zhou 018; Zaixiang Zheng; Dongyu Xue; Quanquan Gu (CoRR, 2024)

DPLM-2: A Multimodal Diffusion Protein Language Model. - Xinyou Wang; Zaixiang Zheng; Fei Ye; Dongyu Xue; Shujian Huang; Quanquan Gu (ICLR, 2025)

ProteinBench: A Holistic Evaluation of Protein Foundation Models. - Fei Ye; Zaixiang Zheng; Dongyu Xue; Yuning Shen; Lihao Wang; Yiming Ma; Yan Wang; Xinyou Wang; Xiangxin Zhou; Quanquan Gu (ICLR, 2025)

Elucidating the Design Space of Multimodal Protein Language Models. - Cheng-Yen Hsieh; Xinyou Wang; Daiheng Zhang; Dongyu Xue; Fei Ye; Shujian Huang; Zaixiang Zheng; Quanquan Gu (CoRR, 2025)

An All-Atom Generative Model for Designing Protein Complexes. - Ruizhe Chen; Dongyu Xue; Xiangxin Zhou; Zaixiang Zheng; Xiangxiang Zeng; Quanquan Gu (CoRR, 2025)

Designing Cyclic Peptides via Harmonic SDE with Atom-Bond Modeling. - Xiangxin Zhou; Mingyu Li; Yi Xiao; Jiahan Li; Dongyu Xue; Zaixiang Zheng; Jianzhu Ma; Quanquan Gu (CoRR, 2025)

AMix-1: A Pathway to Test-Time Scalable Protein Foundation Model. - Changze Lv; Jiang Zhou; Siyu Long; Lihao Wang; Jiangtao Feng; Dongyu Xue; Yu Pei; Hao Wang; Zherui Zhang; Yuchen Cai; Zhiqiang Gao; Ziyuan Ma; et al. (CoRR, 2025)