Journal

(# equal contribution, * corresponding author)

    2023
  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 2022
  12. 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

  13. 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

  14. 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

  15. 2021
  16. 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

  17. 2020
  18. 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

  19. 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

  20. 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

  21. 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

  2. 2020
  3. 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

  4. 2019
  5. 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.

  6. 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.

  7. 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.

  8. 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. ScholarChemQA: Unveiling the Power of Language Models in Chemical Research Question Answering.
    Xiuying Chen, Tairan Wang, Taicheng Guo, Kehan Guo, Juexiao Zhou, Haoyang Li, Mingchen Zhuge, Jürgen Schmidhuber, Xin Gao, Xiangliang Zhang
    under review.

  2. HELM-GPT: de novo macrocyclic peptide design using generative pre-trained transformer.
    Xiaopeng Xu, Chencheng Xu, Wenjia He, Lesong Wei, Haoyang Li, Juexiao Zhou, Xin Gao
    under review.

  3. KaryoXpert: An Accurate Chromosome Segmentation and Classification Framework for Karyotyping Analysis without Training with Metaphase-Image Mask Annotations.
    Siyuan Chen, Kaichuang Zhang, Bing Niu, Na Li, Qiuye Jin, Haoyang Li, Juexiao Zhou, Yongguo Yu, and Xin Gao
    under review.

  4. Automated Bioinformatics Analysis via AutoBA.
    Juexiao Zhou#, Bin Zhang#, Xiuying Chen, Haoyang Li, Xiaopeng Xu, Siyuan Chen, Xin Gao*
    under review.
    Access: arXiv
    Press: CBIRT news, Medium

  5. 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

  6. 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

  7. Path to Medical AGI: Unify Domain-specific Medical LLMs with the Lowest Cost.
    Juexiao Zhou#, Xiuying Chen#, Xin Gao*
    under review.
    Access: arXiv

  8. SkinGPT-4: An Interactive Dermatology Diagnostic System with Visual Large Language Model.
    Juexiao Zhou#, Xiaonan He#, Liyuan Sun#, Jiannan Xu, Xiuying Chen, Yuetan Chu, Longxi Zhou, Xingyu Liao, Bin Zhang, Xin Gao*
    under review.
    Access: arXiv

  9. An end-to-end workflow for robust pulmonary artery-vein segmentation on thick-slice chest CT.
    Yuetan Chu#, Longxi Zhou#, Juexiao Zhou, Yuxin Huang, Tianyi Xing, Dexuan Xie, Xigang Xiao, Zhaowen Qiu, Xin Gao*
    under review.

  10. 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.