Xiaopeng Xu
About Research Publications Awards Notes
Xiaopeng Xu

Publications

For the most up-to-date list, see my Google Scholar profile. (* denotes equal contribution.)

Journal Articles

  1. Xiaopeng Xu, Chenjie Feng, Chao Zha, Wenjia He, Maolin He, Bin Xiao, Xin Gao. “ProteinMCP: An agentic AI framework for autonomous protein engineering.” Protein Science 35.4 (2026): e70547. Paper

  2. Chenjie Feng, Junbo Yin, Chao Zha, Mohammed Saif, Xiaopeng Xu, Xin Gao, Wenjia He. “SegDesign: A modular framework for controllable protein segment engineering.” Protein Science 35.4 (2026): e70542. Paper

  3. Wenjia He, Xiaopeng Xu, Haoyang Li, Juexiao Zhou, Xin Gao. “AggNet: Advancing Protein Aggregation Analysis Through Deep Learning and Protein Language Model.” Protein Science. Paper

  4. Haoyang Li, Yingxin Lin, Wenjia He, Wenkai Han, Xiaopeng Xu, Chencheng Xu, Elva Gao, Hongyu Zhao, Xin Gao. “SANTO: a coarse-to-fine alignment and stitching method for spatial omics.” Nature Communications 15.1 (2024): 6048. Paper

  5. Juexiao Zhou, Bin Zhang, Guowei Li, Xiuying Chen, Haoyang Li, Xiaopeng Xu, Siyuan Chen, Wenjia He, Chencheng Xu, Liwei Liu, Xin Gao. “An AI Agent for Fully Automated Multi-Omic Analyses.” Advanced Science (2024): 2407094. Paper

  6. Xiaopeng Xu, Chencheng Xu, Wenjia He, Lesong Wei, Haoyang Li, Juexiao Zhou, Ruochi Zhang, Yu Wang, Yuanpeng Xiong, Xin Gao. “HELM-GPT: de novo macrocyclic peptide design using generative pre-trained transformer.” Bioinformatics 40.6 (2024): btae364. Paper

  7. Xingyu Liao, Juexiao Zhou, Bin Zhang, Xiaopeng Xu, Haoyang Li, Xin Gao. “Deep Learning Enhanced Tandem Repeat Variation Identification via Multi-Modal Conversion of Nanopore Reads Alignment.” bioRxiv (2023): 2023-08. Preprint · PDF

  8. Xingyu Liao, Wufei Zhu, Juexiao Zhou, Haoyang Li, Xiaopeng Xu, Bin Zhang, Xin Gao. “Repetitive DNA sequence detection and its role in the human genome.” Communications Biology (2023). Paper

  9. Xiaopeng Xu, Juexiao Zhou, Chen Zhu, Qing Zhan, Zhongxiao Li, Ruochi Zhang, Yu Wang, Xingyu Liao, Xin Gao. “Optimization of binding affinities in chemical space with generative pretrained transformer and deep reinforcement learning” (SGPT-RL). F1000Research (2023): 12-757. Paper · PDF

  10. Xiaopeng Xu, Tiantian Xu, Juexiao Zhou, Xingyu Liao, Ruochi Zhang, Yu Wang, Lu Zhang, Xin Gao. “AB-Gen: Antibody Library Design with Generative Pre-trained Transformer and Deep Reinforcement Learning.” Genomics, Proteomics & Bioinformatics (2023). Paper · PDF

  11. Juexiao Zhou, Longxi Zhou, Di Wang, Xiaopeng Xu, Haoyang Li, Yuetan Chu, Wenkai Han, Xin Gao. “Personalized and privacy-preserving federated heterogeneous medical image analysis with PPPML-HMI.” Computers in Biology and Medicine (2023). Paper

  12. Zhongxiao Li, Elva Gao, Juexiao Zhou, Wenkai Han, Xiaopeng Xu, Xin Gao. “Applications of deep learning in understanding gene regulation.” Cell Reports Methods (2023). Paper

  13. Cheng Chi, Xiaopeng Xu, Dominique Thévenin. “Efficient premixed turbulent combustion simulations using flamelet manifold neural networks: A priori and a posteriori assessment.” Combustion and Flame 245 (2022): 112325. Paper · PDF

  14. Francesco Napolitano*, Xiaopeng Xu*, Xin Gao. “Impact of computational approaches in the fight against COVID-19: an AI guided review of 17 000 studies.” Briefings in Bioinformatics (2022). Paper · Poster

  15. Qianqian Zhang, Li Zhang, Yaohua Tang, Xiarong Li, Xiaopeng Xu, Ming Qi, Xiangmin Xu. “A comprehensive repository of mutation data and a clinical assistant decision system for hemoglobinopathy in the Chinese population.” Yi Chuan = Hereditas 41.8 (2019): 746-753. Paper · PDF

  16. Jun Yan, Zhaowu Ma, Xiaopeng Xu, An-Yuan Guo. “Evolution, functional divergence and conserved exon–intron structure of bHLH/PAS gene family.” Molecular Genetics and Genomics 289.1 (2014): 25-36. Paper · PDF

Patent

  1. Xin Gao, Xiaopeng Xu, Xiao Zhang, Yu Wang. “Reinforcement learning (RL) for protein design.” World Intellectual Property Organization WO2023246834A1, filed June 21, 2023. Patent

Thesis

  1. Xiaopeng Xu (2024). “A ChatGPT-like solution for protein design: combining generative and predictive AI to design functional proteins.” PhD dissertation, KAUST Research Repository. Link

  2. Xiaopeng Xu (2015). “Flux Balance Analysis of Escherichia coli under Temperature and pH Stress Conditions.” Master thesis, KAUST Research Repository. Link