单细胞测序数据分析

成员

  • 邹    权   教    授 （电子科技大学）
  • 张永清   教    授 （成都信息工程大学）
  • 张子龙   副教授 （海南大学）
  • 张    杨   副教授 （成都中医药大学）
  • 齐    忍   副研究员 （北京理工大学）
  • 王嘉程   博士后 （KAUST）
  • 李鸿飞   博士后 （电子科技大学）
  • 刘    怡   博士生 （电子科技大学）
  • 钱昱罄   博士生 （电子科技大学）
  • 孙一迪   博士生 （海南大学）
  • 高鹏飞   博士生 （海南师范大学）
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    项目

  • 国家自然科学基金重点项目：面向单细胞RNA测序数据的深度迁移模型与细胞通信网络研究（62131004）
  • 国家自然科学基金面上项目：基于植物单细胞转录组和多组学数据分析及基因调控网络构建方法的研究（62272321）
  • 国家自然科学基金面上项目：基于单细胞多组学数据的细胞-药物反应预测深度强化学习模型的构建与研究（62372332）
  • 国家自然科学基金青年基金项目：大型单细胞转录组数据降维与可视化（62102064）
  • 国家自然科学基金青年基金项目：基于单细胞测序数据的药物反应预测研究（62201129）
  • 国家自然科学基金青年基金项目：面向单细胞多组学数据的癌症基因调控网络预测（62301369）
  • 国家自然科学基金地区基金项目：单细胞转录组与空间转录组数据整合方法研究（62261018）
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    获奖

  • 2023年度海南省自然科学奖三等奖（题目：人工智能在单细胞组学数据的应用研究，所有获奖人：张子龙、齐忍、邹权、王紫薇、齐琦）
    •

    网站

  • webSCST: an interactive web application for single-cell RNA-seq data and spatial transcriptome data integration
  • scIMC: a platform for benchmarking comparison and visualization analysis of scRNA-seq data imputation methods
    •

    专刊

  • Machine Learning Methods in Single-Cell Immune and Drug Response Prediction in Frontiers of Genetics
    •

    论文

    1. Ziwei Wang, Hui Ding, Quan Zou*. Identifying Cell Types to Interpret scRNA-seq Data: How, Why, and More Possibilities. Briefings in Functional Genomics. 2020, 19(4):286-291.谷歌学术引用次
    2. Ren Qi, Anjun Ma, Qin Ma*, Quan Zou*. Clustering and Classification Methods for Single-cell RNA-sequencing Data. Briefings in Bioinformatics. 2020, 21(4): 1196-1208.谷歌学术引用次
    3. Ziwei Wang, Chi-chang Chang*, Quan Zou*. COVID-19 Related Research by Data Mining in Single Cell Transcriptome Profiles. Journal of Electronic Science and Technology. 2021, 19(1):1-5.谷歌学术引用次
    4. Ren Qi, Jin Wu, Fei Guo, Lei Xu*, Quan Zou*. A Spectral Clustering with Self-weighted Multiple Kernel Learning Method for single-cell RNA-seq Data. Briefings in Bioinformatics. 2021, 22(4): bbaa216.谷歌学术引用次
    5. Zilong Zhang, Feifei Cui, Chunyu Wang, Lingling Zhao*, Quan Zou*. Goals and Approaches for Each Processing Step for Single-Cell RNA Sequencing Data. Briefings in Bioinformatics. 2021, 22(4): bbaa314.谷歌学术引用次
    6. Zilong Zhang, Feifei Cui, Chen Lin, Lingling Zhao, Chunyu Wang*, Quan Zou*. Critical downstream analysis steps for single-cell RNA sequencing data. Briefings in Bioinformatics. 2021,22(5):bbab105.谷歌学术引用次
    7. Zilong Zhang, Feifei Cui, Murong Zhou, Song Wu*, Quan Zou*, Bo Gao*. Single-cell RNA sequencing analysis identifies key genes in brain metastasis from lung adenocarcinoma. Current Gene Therapy. 2021, 21(4): 338-348.谷歌学术引用次
    8. Zilong Zhang, Feifei Cui, Chen Cao, Qingsuo Wang*, Quan Zou*. Single-cell RNA analysis reveals the potential risk of organ-specific cell types vulnerable to SARS-CoV-2 infections. Computers in Biology and Medicine. 2022, 140: 105092.谷歌学术引用次
    9. Jiacheng Wang, Quan Zou*, Chen Lin*. A comparison of deep learning-based pre-processing and clustering approaches for single-cell RNA sequencing data. Briefings in Bioinformatics. 2022, 23(1): bbab345.谷歌学术引用次
    10. Ziwei Wang, Ying Zhang, Qun Li, Quan Zou*, Qing Liu*. A road map for happiness: The psychological factors related cell types in various parts of human body from single cell RNA-seq data analysis. Computers in Biology and Medicine. 2022, 143:105286.谷歌学术引用次
    11. Mengyuan Zhao, Wenying He, Jijun Tang*, Quan Zou*, Fei Guo*. A hybrid deep learning framework for gene regulatory network inference from single-cell transcriptomic data. Briefings in Bioinformatics. 2022, 23(2): bbab568.谷歌学术引用次
    12. Zilong Zhang, Feifei Cui, Wei Su, Lijun Dou, Anqi Xu, Chen Cao, Quan Zou*. webSCST: an interactive web application for single-cell RNA-sequencing data and spatial transcriptomic data integration. Bioinformatics. 2022, 38(13):3488-3489.谷歌学术引用次
    13. Chichi Dai, Yi Jiang, Chenglin Yin, Ran Su, Xiangxiang Zeng, Quan Zou, Kenta Nakai*, Leyi Wei*. scIMC: a platform for benchmarking comparison and visualization analysis of scRNA-seq data imputation methods. Nucleic Acids Research. 2022, 50(9):4877-4899.谷歌学术引用次
    14. Yongqing Zhang, Maocheng Wang, Zixuan Wang, Yuhang Liu, Shuwen Xiong, Quan Zou*. MetaSEM: Gene regulatory network inference from single-cell RNA data by Meta-learning. International Journal of Molecular Sciences. 2023, 24: 2595.谷歌学术引用次
    15. Ren Qi, Quan Zou*. Trends and Potential of Machine Learning and Deep Learning in Drug Study at Single-cell Level. Research. 2023, 6: 0050.谷歌学术引用次
    16. Jing Jiang, Junlin Xu, Yuansheng Liu, Bosheng Song, Xiulan Guo, Xiangxiang Zeng, Quan Zou*. Dimensionality reduction and visualization of single-cell RNA-seq data with an improved deep variational autoencoder. Briefings in Bioinformatics. 2023, 24(3): bbad152.谷歌学术引用次
    17. Yushan Qiu, Chang Yan, Pu Zhao, Quan Zou*. SSNMDI: a novel joint learning model of semi-supervised non-negative matrix factorization and data imputation for clustering of single-cell RNA-seq data. Briefings in Bioinformatics. 2023, 24(3): bbad149.谷歌学术引用次
    18. Zixuan Wang, Yongqing Zhang, Yun Yu, Junming Zhang, Yuhang Liu, Quan Zou*. A Unified Deep Learning Framework for Single-Cell ATAC-Seq Analysis Based on ProdDep Transformer Encoder. International Journal of Molecular Sciences. 2023, 24(5): 4784.谷歌学术引用次
    19. Jiacheng Wang, Yaojia Chen, Quan Zou*. Inferring gene regulatory network from single-cell transcriptomes with graph autoencoder model. PLoS Genetics. 2023, 19(9): e1010942.谷歌学术引用次
    20. Ren Qi, Quan Zou*. Editorial: Machine Learning Methods in Single-Cell Immune and Drug Response Prediction. Frontiers in Genetics. 2023, 19: 1233078.谷歌学术引用次
    21. Chaorui Yan, Yanxu Zhu, Miao Chen, Kainan Yang, Feifei Cui*, Quan Zou*, Zilong Zhang*. Integration tools for scRNA-seq data and spatial transcriptomics sequencing data. Briefings in Functional Genomics. 2024, 23(4): 295-302.谷歌学术引用次
    22. Yushan Qiu, Lingfei Yang, Hao Jiang*, Quan Zou*. scTPC: a novel semi-supervised deep clustering model for scRNA-seq data. Bioinformatics. 2024, 40(5): btae293.谷歌学术引用次
    23. Yushan Qiu, Dong Guo, Pu Zhao, Quan Zou*. scMNMF: a novel method for single-cell multi-omics clustering based on matrix factorization. Briefings in Bioinformatics. 2024, 25(3): bbae228.谷歌学术引用次
    24. Yuncong Zhang, Yu Yang, Liping Ren, Meixiao Zhan, Taoping Sun*, Quan Zou*, Yang Zhang*. Predicting intercellular communication based on metabolite-related ligand-receptor interactions with MRCLinkdb. BMC Biology. 2024, 22: 152.谷歌学术引用次
    25. Yuqing Qian, Quan Zou, Mengyuan Zhao, Yi Liu, Fei Guo*, Yijie Ding*. scRNMF: an imputation method for single-cell RNA-seq data by robust and non-negative matrix factorization. PLOS Computational Biology. 2024, 20(8): e1012339.谷歌学术引用次
    26. Yidi Sun, Zhouyu Pan, Ziyi Wang, Haofei Wang, Leyi Wei, Feifei Cui*, Quan Zou*, Zilong Zhang*. Single-cell transcriptome analysis reveals immune microenvironment changes and insights into the transition from DCIS to IDC with associated prognostic genes. Journal of Translational Medicine. 2024, 22: 894. 谷歌学术引用次
    27. Jiacheng Wang, Yaojia Chen, Quan Zou*. GRACE: Unveiling Gene Regulatory Networks with Causal Mechanistic Graph Neural Networks in single-cell RNA-sequencing Data. IEEE Transactions on Neural Networks and Learning Systems. Doi: 10.1109/TNNLS.2024.3412753.
    28. Yidi Sun, Lingling Kong, Jiayi Huang, Hongyan Deng, Xinling Bian, Xingfeng Li, Feifei Cui, Lijun Dou, Chen Cao, Quan Zou*, Zilong Zhang*. A comprehensive survey of dimensionality reduction and clustering methods for single-cell and spatial transcriptomics data. Briefings in Functional Genomics. 2024, 23(6): 733-744. 谷歌学术引用次
    29. Tianxiang Liu, Cangzhi Jia*, Yue Bi, Xudong Guo, Quan Zou*, Fuyi Li*. scDFN: Enhancing single-cell RNA-seq Clustering with Deep Fusion Networks. Briefings in Bioinformatics. 2024, 25(6): bbae486. 谷歌学术引用次
    30. Runqing Wang, Qiguo Dai*, Xiaodong Duan, Quan Zou*. stHGC: A Self-Supervised Graph Representation Learning for Spatial Domain Recognition with Hybrid Graph and Spatial Regularization. Briefings in Bioinformatics. 2025, 26(1): bbae666 谷歌学术引用次
    31. Lubin Cui, Guiliang Guo, Michael K.Ng, Quan Zou, Yushan Qiu*. GSTRPCA: Irregular tensor singular value decomposition for single-cell multi-omics data clustering. Briefings in Bioinformatics. 2025, 26(1): bbae649 谷歌学术引用次

      32. 最后修改时间：2024.12.27
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