Wenjia He, Xiaopeng Xu, Haoyang Li, Juexiao Zhou, and Xin Gao. AggNet: Advancing Protein Aggregation Analysis Through Deep Learning and Protein Language Model. Protein Science.
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.
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.
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 (2024): btae364.
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. [PDF]
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): 2023-09. [PDF]
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." F1000Research (2023): 2023-06. [PDF]
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): 2023-03. [PDF]
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): 2023-02. [PDF]
Zhongxiao Li, Elva Gao, Juexiao Zhou, Wenkai Han, Xiaopeng Xu, Xin Gao. "Applications of deep learning in understanding gene regulation." Cell Reports Methods (2023): 2023-01. [PDF]
Cheng Chi, Xiaopeng Xu, and Dominique Thévenin. "Efficient premixed turbulent combustion simulations using flamelet manifold neural networks: A priori and a posteriori assessment." Combustion and Flame 245 (2022): 112325. [PDF]
Francesco Napolitano*, Xiaopeng Xu*, and Xin Gao. "Impact of computational approaches in the fight against COVID-19: an AI guided review of 17 000 studies." Briefings in Bioinformatics (2022). [PDF][Poster]
Qianqian Zhang, Li Zhang, Yaohua Tang, Xiarong Li, Xiaopeng Xu, Ming Qi, and Xiangmin Xu. "A comprehensive repository of mutation data and a clinical assistant decision system for hemoglobinopathy in the Chinese population." Yi Chuan= Hereditas 41, no. 8 (2019): 746-753. [PDF]
Jun Yan, Zhaowu Ma, Xiaopeng Xu, and An-Yuan Guo. "Evolution, functional divergence and conserved exon–intron structure of bHLH/PAS gene family." Molecular genetics and genomics 289, no. 1 (2014): 25-36. [PDF]
Xin Gao, Xiaopeng Xu, Xiao Zhang, Yu Wang. "Reinforcement learning (rl) for protein design". World Intellectual Property Organization WO2023246834A1, filed June 21, 2023.
Xiaopeng Xu. (2024). "A ChatGPT-like solution for protein design: combining generative and predictive AI to design functional proteins". KAUST Research Repository. PhD dissertation.
Xiaopeng Xu. (2015). "Flux Balance Analysis of Escherichia coli under Temperature and pH Stress Conditions". KAUST Research Repository. Master thesis.