Journal

(# equal contribution, * corresponding author)

2023

1. 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 (IF: 14.919)
   In press.


2. 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 (IF: 6.615)
   In press.


3. 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 (IF: 14.919)
   DOI: 10.1038/s41467-023-37168-7
   Access: online, pdf


4. 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 (IF: 9.438)
   DOI: 10.1101/gr.277177.122
   Access: online, pdf


5. 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

6. 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 (IF: 6.615)
   DOI: 10.1016/j.gpb.2022.11.010
   Access: online, pdf


7. SD2: Spatially resolved transcriptomics deconvolution through integration of spatial and dropout information.
   Haoyang Li, Hanmin Li, Juexiao Zhou, Xin Gao*.
   Bioinformatics (IF: 6.931)
   DOI: 10.1093/bioinformatics/btac605
   Access: online, pdf


8. 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 (IF: 25.9)
   DOI: 10.1038/s42256-022-00483-7
   Access: online, pdf

2021

9. 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 (IF: 4.755)
   DOI: 10.3389/fphys.2021.655556.
   Access: online, pdf

2020

10. 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 (IF: 6.615)
    DOI: 10.1016/j.gpb.2020.05.004.
    Access: online, pdf


11. A Rapid, Accurate and Machine-agnostic Segmentation and Quantification Method for CT-based COVID-19 Diagnosis.
    Liongxi 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 (IF: 11.037)
    DOI: 10.1109/TMI.2020.3001810.
    Access: online, pdf


12. CaMeRe: A novel tool for inference of cancer metabolic reprogramming.
    Haoyang Li, Juexiao Zhou, Huiyan Sun, Zhaowen Qiu, Xin Gao* and Ying Xu*.
    Front. Oncol. (IF: 6.244)
    DOI: 10.3389/fonc.2020.00207.
    Access: online, pdf


13. 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 (IF: 12.744)
    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. SkinGPT: A Dermatology Diagnostic System with Vision Large Language Model.
   Juexiao Zhou , Xin Gao*
   under review.
   Access: arXiv


2. 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*
   under review.


3. Audit to Forget: A Unified Method to Revoke Patients’ Private Data in Intelligent Healthcare.
   Juexiao Zhou#, Haoyang Li#, Xingyu Liao, Bin Zhang, Wenjia He, Zhongxiao Li, Longxi Zhou, Xin Gao*
   under review.
   Access: arXiv


4. GPT generates more diverse scaffolds than GRU in exploring the chemical space.
   Xiaopeng Xu, Juexiao Zhou, Chen Zhu, Qing Zhan, Zhongxiao Li, Ruochi Zhang, Xingyu Liao, Xin Gao*
   under review.


5. 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.


6. 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*
   under review.
   Access: medRxiv


7. PPML-Omics: a Privacy-Preserving federated Machine Learning system protects patients’ privacy from 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*.
   under review.
   Access: bioRxiv


8. A Workflow for Automatic, Accurate and Robust Breast Tumor Segmentation on Multi-Database 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.