Journal & Conference

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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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, 2020.
    DOI: 10.1109/TMI.2020.3001810.
    Access: online, pdf

  7. 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., 2020.
    DOI: 10.3389/fonc.2020.00207.
    Access: online, pdf

  8. 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, 2020.
    DOI: 10.15252/msb.20199367.
    Access: online, pdf

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. 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 or under review

  1. 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.

  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
    under review.

  3. Benchmarking and guidelines of cellular deconvolution for spatial transcriptomics.
    Haoyang Li*, Juexiao Zhou*, Zhongxiao Li, Hanmin Li, Siyuan Chen, Xin Gao
    under review.

  4. Application of Deep Learning in Understanding Gene Expression Regulation.
    Zhongxiao Li, Elva Gao, Juexiao Zhou, Wenkai Han, Xiaopeng Xu, and Xin Gao
    under review.

  5. Antibody library design with transformer and deep reinforcement learning.
    Xiaopeng Xu, Tiantian Xu, Juexiao Zhou, Xingyu Liao, Lu Zhang and Xin Gao
    under review.

  6. 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.

  7. DeeReCT-TSS: A novel meta-learning-based method annotates TSS in multiple cell types based on DNA sequences and RNA-seq data.
    Juexiao Zhou*, Bin Zhang*, Haoyang Li, Longxi Zhou, Zhongxiao Li, Yongkang Long, Wenkai Han, Mengran Wang, Huanhuan Cui, Wei Chen, Xin Gao.
    under review.

  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.

  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
    under review.