Journal

(# equal contribution, * corresponding author)

2025

1. Evaluating and Mitigating Bias in AI-Driven Medical Text Generation.
   Xiuying Chen, Tairan Wang, Juexiao Zhou, Xin Gao, Xiangliang Zhang
   Nature Computational Science
   

   Accepted

2. Deep learning-driven pulmonary artery and vein segmentation reveals demography-associated vasculature anatomical differences.
   Yuetan Chu#, Gongning Luo#, Longxi Zhou, Shaodong Cao, Guolin Ma, Xianglin Meng, Changchun Yang, Dan Mu, Juexiao Zhou, Dexuan Xie, Ricardo Henao, Xigang Xiao, Lianming Wu, Zhaowen Qiu, Gianluca Setti, Xin Gao*
   

   Nature Communications
   

   DOI: https://doi.org/s41467-025-56505-6
   Access: online, pdf

   2024

3. AggNet: Advancing Protein Aggregation Analysis Through Deep Learning and Protein Language Model.
   Wenjia He, Xiaopeng Xu, Haoyang Li, Juexiao Zhou, Xin Gao
   Protein Science
   DOI: https://doi.org/10.1002/pro.70031
   

   Access: online, pdf

4. Unveiling the Power of Language Models in Chemical Research Question Answering. 
   

   Xiuying Chen, Tairan Wang, Taicheng Guo, Kehan Guo, Juexiao Zhou, Haoyang Li, Zirui Song, Xin Gao, Xiangliang Zhang.
   Communications Chemistry
   

   DOI: https://doi.org/10.1038/s42004-024-01394-x
   

   Access: online, pdf

5. Global, regional, and national burden of upper respiratory infections and otitis media, 1990–2021: a systematic analysis from the Global Burden of Disease Study 2021.

   GBD 2021 Upper Respiratory Infections Otitis Media Collaborators* (Authors listed alphabetically)
   The Lancet Infectious Diseases
   DOI: https://doi.org/10.1016/S1473-3099(24)00430-4
   Access: online, pdf

6. An AI Agent for Fully Automated Multi-omic Analyses.
   Juexiao Zhou#, Bin Zhang#, Guowei Li, Xiuying Chen, Haoyang Li, Xiaopeng Xu, Siyuan Chen, Liwei Liu, Xin Gao*
   Advanced Science
   DOI: https://doi.org/10.1002/advs.202407094
   Access: online, pdf
   Press: CBIRT news, Medium

7. Pre-trained Multimodal Large Language Model Enhances Dermatological Diagnosis using SkinGPT-4.
   Juexiao Zhou#, Xiaonan He#, Liyuan Sun#, Jiannan Xu, Xiuying Chen, Yuetan Chu, Longxi Zhou, Xingyu Liao, Bin Zhang, Shawn Afvari, Xin Gao*
   Nature Communications
   DOI: https://doi.org/10.1038/s41467-024-50043-3
   Access: online, pdf

8. 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
   DOI: https://doi.org/10.1093/bioinformatics/btae364
   Access: online, pdf

9. Burden of disease scenarios for 204 countries and territories, 2022–2050: a forecasting analysis for the Global Burden of Disease Study 2021.
   GBD 2021 Forecasting Collaborators* (Authors listed alphabetically)
   The Lancet
   DOI: https://doi.org/10.1016/S0140-6736(24)00685-8
   Access: online, pdf

10. Global burden and strength of evidence for 88 risk factors in 204 countries and 811 subnational locations, 1990–2021: a systematic analysis for the Global Burden of Disease Study 2021.
    GBD 2021 Risk Factors Collaborators* (Authors listed alphabetically)
    The Lancet
    DOI: https://doi.org/10.1016/S0140-6736(24)00933-4
    Access: online, pdf

11. KaryoXpert: An Accurate Chromosome Segmentation and Classification Framework for Karyotyping Analysis without Training with Manually Labeled Metaphase-Image Mask Annotations.
    Siyuan Chen, Kaichuang Zhang, Jingdong Hu, Na Li, Ao Xu, Haoyang Li, Juexiao Zhou, Chao Huang, Yongguo Yu, and Xin Gao
    Computers in Biology and Medicine
    DOI: https://doi.org/10.1016/j.compbiomed.2024.108601
    Access: online, pdf

12. Global incidence, prevalence, years lived with disability (YLDs), disability-adjusted life-years (DALYs), and healthy life expectancy (HALE) for 371 diseases and injuries in 204 countries and territories and 811 subnational locations, 1990–2021: a systematic analysis for the Global Burden of Disease Study 2021.
    GBD 2021 Diseases and Injuries Collaborators* (Authors listed alphabetically)
    The Lancet
    DOI: https://doi.org/10.1016/S0140-6736(24)00757-8
    Access: online, pdf

13. Global burden of 288 causes of death and life expectancy decomposition in 204 countries and territories and 811 subnational locations, 1990–2021: a systematic analysis for the Global Burden of Disease Study 2021.
    GBD 2021 Causes of Death Collaborators* (Authors listed alphabetically)
    The Lancet
    DOI: https://doi.org/10.1016/S0140-6736(24)00367-2
    Access: online, pdf

14. Global fertility in 204 countries and territories, 1950–2021, with forecasts to 2100: a comprehensive demographic analysis for the Global Burden of Disease Study 2021.
    GBD 2021 Fertility and Forecasting Collaborators* (Authors listed alphabetically)
    The Lancet
    DOI: https://doi.org/10.1016/S0140-6736(24)00550-6
    Access: online, pdf

15. Patient privacy in AI-driven omics methods.
    Juexiao Zhou, Chao Huang, Xin Gao
    Trends in Genetics
    DOI: https://doi.org/10.1016/j.tig.2024.03.004
    Access: online, pdf

16. Global age-sex-specific mortality, life expectancy, and population estimates in 204 countries and territories and 811 subnational locations, 1950–2021, and the impact of the COVID-19 pandemic: a comprehensive demographic analysis for the Global Burden of Disease Study 2021.
    GBD 2021 Demographics Collaborators* (Authors listed alphabetically)
    The Lancet
    DOI: https://doi.org/10.1016/S0140-6736(24)00476-8
    Access: online, pdf

    2023

17. PPML-Omics: A privacy-preserving federated machine learning method protects patients’ privacy in omic data.
    Juexiao Zhou#, Siyuan Chen#, Yulian Wu#, Haoyang Li, Bin Zhang, Longxi Zhou, Yan Hu, Zihang Xiang, Zhongxiao Li, Ningning Chen, Wenkai Han, Di Wang and Xin Gao*.
    Science Advances
    DOI: 10.1126/sciadv.adh8601
    Access: online, pdf
    Press: Inside Precision Medicine, Today Headline, Tech Xplore, ScienMag, Bioengineer.org,Newswise, EurekAlert, Biocompare, nabd.ws

18. 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
    DOI: 10.1016/j.compbiomed.2023.107861
    Access: online, pdf

19. 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
    DOI: 10.1038/s42003-023-05322-y
    Access: online, pdf

20. A unified method to revoke the private data of patients in intelligent healthcare with audit to forget.
    Juexiao Zhou#, Haoyang Li#, Xingyu Liao, Bin Zhang, Wenjia He, Zhongxiao Li, Longxi Zhou, Xin Gao*
    Nature Communications
    DOI: 10.1038/s41467-023-41703-x
    Access: online, pdf
    Press: KAUST Discovery, Enerzine

21. Optimization of binding affinities in chemical space with generative pre-trained transformer and deep reinforcement learning.  
    Xiaopeng Xu, Juexiao Zhou, Chen Zhu, Qing Zhan, Zhongxiao Li, Ruochi Zhang, Yu Wang, Xingyu Liao, Xin Gao*
    F1000 Research
    DOI: 10.12688/f1000research.130936.1
    Access: online, pdf

22. Predicting the antigenic evolution of SARS-COV-2 with deep learning.  
    Wenkai Han#, NingNing Chen#, Xinzhou Xu#, Adil Salhi, Juexiao Zhou, Zhongxiao Li, Huawen Zhong, Elva Gao, Ruochi Zhang, Yu Wang, Shiwei Sun*, Peter Cheung*, Xin Gao*
    Nature Communications
    DOI: 10.1038/s41467-023-39199-6
    Access: online, pdf

23. 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
    DOI: 10.1016/j.gpb.2023.03.004
    Access: online, pdf

24. A comprehensive benchmarking with practical guidelines for cellular deconvolution of spatial transcriptomics.  
    Haoyang Li#, Juexiao Zhou#, Zhongxiao Li, Siyuan Chen, Xingyu Liao, Bin Zhang, Ruochi Zhang, Yu Wang, Shiwei Sun, Xin Gao*
    Nature Communications
    DOI: 10.1038/s41467-023-37168-7
    Access: online, pdf
    Press: BioMed, CBIRT news, KAUST news
    Chosen as Editors’ Highlights in Nature Communications

25. Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ.  
    Yongkang Long#, Bin Zhang#, Shuye Tian, Jiajia Chan, Juexiao Zhou, Zhongxiao Li, Yisheng Li, Zheng An, Xingyu Liao, Yu Wang, Shiwei Sun, Ying Xu, Yvonne Tay, Wei Chen*, Xin Gao*
    Genome Research
    DOI: 10.1101/gr.277177.122
    Access: online, pdf

26. Applications of Deep Learning in Understanding Gene Regulation.  
    Zhongxiao Li#, Elva Gao#, Juexiao Zhou, Wenkai Han, Xiaopeng Xu, and Xin Gao*
    Cell Reports Methods
    DOI: 10.1016/j.crmeth.2022.100384
    Access: online, pdf

    2022

27. Annotating TSSs in Multiple Cell Types Based on DNA Sequences and RNA-seq Data via DeeReCT-TSS.  
    Juexiao Zhou#, Bin Zhang#, Haoyang Li, Longxi Zhou, Zhongxiao Li, Yongkang Long, Wenkai Han, Mengran Wang, Huanhuan Cui, Wei Chen, Xin Gao*.
    Genomics, Proteomics & Bioinformatics
    DOI: 10.1016/j.gpb.2022.11.010
    Access: online, pdf

28. SD2: Spatially resolved transcriptomics deconvolution through integration of spatial and dropout information.
    Haoyang Li, Hanmin Li, Juexiao Zhou, Xin Gao*.
    Bioinformatics
    DOI: 10.1093/bioinformatics/btac605
    Access: online, pdf

29. An Interpretable Deep Learning Workflow for Discovering Sub-Visual Abnormalities in CT Scans of COVID-19 Inpatients and Survivors.   
    Longxi Zhou#, Xianglin Meng#, Yuxin Huang#, Kai Kang#, Juexiao Zhou, Yuetan Chu, Haoyang Li, Dexuan Xie, Jiannan Zhang, Weizhen Yang, Na Bai, Yi Zhao, Mingyan Zhao, Guohua Wang, Lawrence Carin, Xigang Xiao, Kaijiang Yu, Zhaowen Qiu, Xin Gao*.
    Nature Machine Intelligence
    DOI: 10.1038/s42256-022-00483-7
    Access: online, pdf

    2021

30. An interpretable computer-aided diagnosis method for periodontitis from panoramic radiographs.  
    Haoyang Li, Juexiao Zhou, Yi Zhou, Jieyu Chen, Feng Gao, Ying Xu, Xin Gao*.
    Frontiers in Physiology, section Computational Physiology and Medicine
    DOI: 10.3389/fphys.2021.655556.
    Access: online, pdf

    2020

31. DeeReCT-APA: Prediction of Alternative Polyadenylation Site Usage through Deep Learning.  
    Zhongxiao Li, Yisheng Li, Bin Zhang, Yu Li, Yongkang Long, Juexiao Zhou, Xudong Zou, Min Zhang, Yuhui Hu, Wei Chen, Xin Gao*.
    Genomics Proteomics and Bioinformatics
    DOI: 10.1016/j.gpb.2020.05.004.
    Access: online, pdf

32. A Rapid, Accurate and Machine-agnostic Segmentation and Quantification Method for CT-based COVID-19 Diagnosis.  
    Longxi Zhou, Zhongxiao Li, Juexiao Zhou, Haoyang Li, Yupeng Chen, Yuxin Huang, Dexuan Xie, Lintao Zhao, Ming Fan, Shahrukh Hashmi, Faisal AbdelKareem, Riham Eiada, Xigang Xiao, Lihua Li, Zhaowen Qiu, and Xin Gao*.
    Transactions on Medical Imaging
    DOI: 10.1109/TMI.2020.3001810.
    Access: online, pdf

33. CaMeRe: A novel tool for inference of cancer metabolic reprogramming.
    Haoyang Li, Juexiao Zhou, Huiyan Sun, Zhaowen Qiu, Xin Gao* and Ying Xu*.
    Frontiers in Oncology
    DOI: 10.3389/fonc.2020.00207.
    Access: online, pdf

34. Pan-tissue analysis of allelic alternative polyadenylation suggests widespread functional regulation.
    Yisheng Li#, Bernhard Schaefke#, Xudong Zou, Min Zhang, Florian Heyd, Wei Sun, Bin Zhang, Guipeng Li, Weizheng Liang, Yuhao He, Juexiao Zhou, Yunfei Li, Liang Fang, Yuhui Hu*.
    Molecular Systems Biology
    DOI: 10.15252/msb.20199367.
    Access: online, pdf

Conference

2020

1. Automatic and interpretable model for periodontitis diagnosis in panoramic radiographs.  
   Haoyang Li, Juexiao Zhou, Yi Zhou, Jieyu Chen, Feng Gao, Ying Xu, Xin Gao*.
   Medical Image Computing and Computer Assisted Interventions 2020 DOI: 10.1007/978-3-030-59713-9_44.
   Access: online, pdf

Posters

2023

1. Privacy in Bioinformatics and Intelligent Healthcare. Juexiao Zhou, Xin Gao*.  
   Poster. Smart-Health Student Research Symposium, KAUST, Saudi Arabia, November 10, 2022.
   Access: certificate

   2020

2. Deetal-Perio: DEEp denTAL Advisor for Periodontitis Diagnosis based on Two-step Segmentation of Teeth and Gingiva with Lower-dimensional Features.  
   Haoyang Li, Juexiao Zhou, Xin Gao*.
   Poster. DigitalHealth, KAUST, 2020.
   Access: online

   2019

3. CaMeRe: A novel tool for inference of cancer metabolic reprogramming.  
   Haoyang Li, Juexiao Zhou, Huiyan Sun, Zhaowen Qiu, Xin Gao* and Ying Xu*.
   Poster. Advance In Artificial Intelligence, KAUST, 2019.

4. DeeRect-PAS—A Deep-Learning based method for Transcriptome-wide PAS Identification.  
   Yongkang Long, Juexiao Zhou, Zhongxiao Li, Wei Chen, Xin Gao*.
   Poster. Advance In Artificial Intelligence, KAUST, 2019.

5. Systematical discovery of cis-elements regulating alternative polyadenylation in mammalian cells.  
   Min Zhang, Yisheng Li, Juexiao Zhou, Yuhao He, Guipeng Li, Liang Fang, Wei Chen*.
   Poster. RNA Biology, CSH Asia, 2019.

6. Systematical discovery of cis-elements regulating alternative polyadenylation in mammalian cells.  
   Min Zhang, Yisheng Li, Juexiao Zhou, Yuhao He, Guipeng Li, Liang Fang, Wei Chen*.
   Poster. Regulatory RNAs, Cell Symposia, Berlin, Germany, May 12-14, 2019.

Preprint

1. Mitigating Bias Catastrophic Inheritance in Medical Large Vision-Language Models with Logit Fairness Adjustment
   under review.
2. Agentic Bioinformatics  
   Juexiao Zhou#, Jindong Jiang, Zhongyi Han, Xin Gao
   under review.
3. Adaptive Feature Unlearning for Trustworthy Healthcare Data Privacy
   Zhongyi Han#, Bin Wang#, Shenjing Wu#, Juexiao Zhou#, Wenhao Wang, Gongning Luo, Benzheng Wei, Xin Gao
   under review.
4. Large Language Models in Biomedicine and Healthcare.  
   Juexiao Zhou, Haoyang Li, Siyuan Chen, Zhongyi Han, Xin Gao
   under review.
5. SkinCAP: A Multi-modal Dermatology Dataset Annotated with Rich Medical Captions.  
   Juexiao Zhou#, Liyuan Sun#, Yan Xu#, Wenbin Liu#, Shawn Afvari#, Zhongyi Han, Jiaoyan Song, Yongzhi Ji, Xiaonan He, Xin Gao
   under review.
6. Wiskott-Aldrich Syndrome Protein Regulates Nucleolar Organization and Function in Innate Immune Response.
   Xuan Zhou#, Baolei Yuan#, Yeteng Tian, Juexiao Zhou, Mengge Wang, Ismail shakir, Yingzi Zhang, Chongwei Bi, Bayan Mohammed Aljamal, Mais Omar Hashem, Omar Imad Abuyousef, Firdous Mohammed Abdulwahab, Afshan Ali, Sarah Dunn, James Moresco, John Robert Yates III, Francesco Frassoni, Xin Gao, Fowzan Alkuraya, Juan Carlo Izpisua Belmonte, Mo Li*
   under review.
   Access: bioRxiv
7. Deep Learning Enhanced Tandem Repeat Variation Identification via Multi-Modal Conversion of Nanopore Reads Alignment.  
   Xingyu Liao#, Juexiao Zhou#, Bin Zhang#, Xingyi Li, Xiaopeng Xu, Haoyang Li, Xin Gao*
   under review.
   Access: arXiv
8. Path to Medical AGI: Unify Domain-specific Medical LLMs with the Lowest Cost.  
   Juexiao Zhou#, Xiuying Chen#, Xin Gao*
   under review.
   Access: arXiv
9. Heart Region Anchoring: a Model-Agnostic Workflow to Improve Segmentation Robustness for Breast Cancer in DCE-MRI.  
   Longxi Zhou, Yitong Ding, Jiayang Guo, Ming Fan, Juexiao Zhou, Haoyang Li, Yujiao Li, Yuxin Huang, Yi Zhao, Yuetan Chu, Kun Wang, Qiming Fang, Xin Gao, Hongxia Zhang, Lihua Li.
   under review.

Patents and Patent Applications

1. Automated Bioinformatics Analysis via AutoBA.  
   Juexiao Zhou, Xin Gao
   KAUST reference: 2024-010.
2. Personalized and privacy-preserving federated heterogeneous medical image analysis with PPPML-HMI.  
   Juexiao Zhou, Xin Gao
   KAUST reference: 2023-012.
3. A high-precision identification method of tandem repeat expansion based on refined alignment and deep learning.  
   Xingyu Liao, Juexiao Zhou, Xin Gao
   KAUST reference: 2023-054.
4. Audit to forget: a unified suite to revoke patients’ private data in intelligent healthcare.  
   Juexiao Zhou, Xin Gao
   KAUST reference: 2023-056.
5. A camera-based privacy-preserving early warning system for critical diseases.
   Juexiao Zhou, Xin Gao
   KAUST reference: 2023-074.