Ø 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）
Ø 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）
Ø 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）
Ø 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）
Ø 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）
Ø 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）
Ø 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）
Ø 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）
邹权 （教授，电子科大）
魏乐义（教授，山东大学）
张子龙
（副教授，海南大学）
张永清
（副教授，成都信息工程大学）
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，电子科大）
刘怡（博士生，电子科大）
钱昱罄（博士生，电子科大）
孙一迪（博士生，海南大学）
高鹏飞（博士生，海南师范大学）
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
Machine
Learning Methods in Single-Cell Immune and Drug Response Prediction in
Frontiers of Genetics
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Ziwei Wang, Hui Ding, Quan Zou*. Identifying Cell Types to
Interpret scRNA-seq Data: How, Why, and More Possibilities. Briefings in Functional Genomics. 2020,
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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.
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
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. (Codes)
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Zilong Zhang, Feifei Cui, Chunyu
Wang, Lingling Zhao*, Quan Zou*.
Goals and Approaches for Each Processing Step for Single-Cell RNA Sequencing
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2021, 22(4): bbaa314. (codes)
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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. (codes)
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
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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
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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
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
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
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. (web server)
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. (web server)
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
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. (codes)
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
18.
Zixuan Wang, Yongqing Zhang, Yun Yu, Junming Zhang, Yuhang
Liu, Quan Zou*. Single-cell ATAC-seq analysis by Transformer-based
cell embedding. International Journal of Molecular Sciences. 2023, 24(5): 4784
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 (codes)
20.
Ren Qi, Quan Zou*. Editorial: Machine Learning
Methods in Single-Cell Immune and Drug Response Prediction. Frontiers in
Genetics. 2023, 19: 1233078
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
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 (codes)
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. (codes)
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 (web site)
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
26.
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
27.
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. Doi: 10.1093/bfgp/elae023