研究方向

计算生物学、生物信息学。主要包括单细胞与时空多组学建模分析、人工智能的生物信息学应用等研究领域。发表相关SCI论文30余篇，包括Briefings in Bioinformatics, Bioinformatics, PLOS Computational Biology等生物信息顶级期刊。参与、主持多项省市国家级科研项目，包括主持国家基金委项目1项，参与国家基金委重点支持项目和面上项目各1项。目前担任多个国际学术刊物的审稿人，包括Genome Biology，Briefings in Bioinformatics, IEEE/ACM Transactions on Computational Biology and Bioinformatics, BMC bioinformatic等。

代表性成果(*通讯作者)

[1] Xiaosheng Bai, Xinyu Bao, Chuanchao Zhang*, Qianqian Shi*, Luonan Chen*. SpaDCN: Deciphering spatial functional landscape from spatially resolved transcriptomics by aligning cell–cell communications. Small Methods (2025): 2402111. (SCI二区，影响因子：10.55)

[2] Wendong Huang, Yaofeng Hu, Lequn Wang, Guangsheng Wu, Chuanchao Zhang*, Qianqian Shi*. Spatially aligned graph transfer learning for characterizing spatial regulatory heterogeneity. Briefings in Bioinformatics (2024) 26: bbaf021. (CCF生物信息类TOP期刊，CCF B类，SCI一区，影响因子：6.82)

[3] Lequn Wang, Xiaosheng Bai, Chuanchao Zhang*, Qianqian Shi*, Luonan Chen*. Spatially aware domain adaptation enables cell type deconvolution from multi‐modal spatially resolved transcriptomics. Small Methods (2024): 2401163. (SCI二区，影响因子：10.55)

[4] Yaofeng Hu, Kai Xiao, Hengyu Yang, Xiaoping Liu*, Chuanchao Zhang*, Qianqian Shi*. Spatially contrastive variational autoencoder for deciphering tissue heterogeneity from spatially resolved transcriptomics. Briefings in Bioinformatics (2024) 25: bbae016. (CCF生物信息类TOP期刊，CCF B类，SCI一区，影响因子：6.82)

[5] Chuanchao Zhang*, Lequn Wang, Qianqian Shi*. Computational modeling for deciphering tissue microenvironment heterogeneity from spatially resolved transcriptomics. Computational and Structural Biotechnology Journal (2024) 23: 2109-2115. (SCI二区，影响因子：4.21）

[6] Chuanchao Zhang, Xinxing Li, Wendong Huang, Lequn Wang*, Qianqian Shi*. Spatially aware self-representation learning for tissue structure characterization and spatial functional genes identification. Briefings in Bioinformatics (2023) 24: bbad197. (CCF生物信息类TOP期刊，CCF B类，SCI一区，影响因子：13.99)

[7] Xinxing Li, Wendong Huang, Xuan Xu, Hong-Yu Zhang, Qianqian Shi*. Deciphering tissue heterogeneity from spatially resolved transcriptomics by the autoencoder-assisted graph convolutional neural network. Frontiers in Genetics (2023) 14: 1202409. (SCI三区，影响因子：4.77)

[8] Qianqian Shi, Xinxing Li, Qirui Peng, Chuanchao Zhang*, Luonan Chen*. scDA: Single cell discriminant analysis for single-cell RNA sequencing data. Computational and Structural Biotechnology Journal (2021) 19: 3234-3244. (SCI二区，影响因子：7.27）

[9]  Qianqian Shi*, Bin Hu, Tao Zeng, Chuanchao Zhang*. Multi-view subspace clustering analysis for aggregating multiple heterogeneous omics data. Frontiers in Genetics (2019) 10: 744. （SCI三区，影响因子：4.77）

[10]  Qianqian Shi, Chuanchao Zhang, Minrui Peng, Xiangtian Yu, Tao Zeng*, Juan Liu* and Luonan Chen*. Pattern fusion analysis by adaptive alignment of multiple heterogeneous omics data. Bioinformatics, 2017, 33: 2706-2714. (CCF生物信息类TOP期刊，CCF B类，SCI二区，影响因子：7.31)