Publications

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

Journal Articles

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Patent

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

Thesis

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

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