研究介绍
一、单细胞空间多组学增强、生成和网络解析智能算法
单细胞和空间多组学技术已经彻底改变了我们对复杂生物系统中细胞异质性的认识。然而，相应的分析目前面临着各种挑战，包括分辨率不足、基因覆盖范围有限，以及难以整合和生成异质性的多模态数据。为了解决这些问题，课题组开发了一系列智能算法。STRIDE（Nucleic Acids Res. 2022）和Cellist（Nat. Genet. 2025）能够分别增强低分辨率和高分辨率的空间转录组数据信号，将其提升至单细胞精度。SCRIP（Nucleic Acids Res. 2022）和SCRIPro（Bioinform. 2024）利用单细胞和空间多组学数据构建基因调控网络。EvaCCI用于评估细胞间相互作用（Genome Biol. 2022），SCREE可分析多模态单细胞CRISPR筛选数据（Brief. Bioinformatics 2023）。这些算法提高了单细胞空间组学数据的可用性，并为单细胞时空多模态数据整合分析以及生理、病理状态的细胞计算拟合奠定了基础。
二、基于人工智能和大规模时空组学数据的虚拟细胞、器官及个体构建
多细胞系统中的细胞表型受到内在因素（如基因表达调控）和外在因素（如细胞间相互作用）的调控。课题组前期在小鼠及人类胚胎发育中的工作已经证明了内在表观遗传调控可以用来准确的预测细胞命运（Nature 2016; Nat. Cell Biol. 2018; Cell Stem Cell 2018, 2022; Cell Res. 2022）。目前，课题组正在开发基于大规模单细胞多模态数据预训练的生成式虚拟细胞及组织模型。这些模型旨在揭示基因调控、细胞间相互作用以及代谢物和机械影响等环境因素的协同效应，以预测细胞和组织表型。课题组开发了基于多对抗领域自适应网络的SELINA算法（Cell Rep. Methods., 2023），使用大规模预训练的人类单细胞RNA测序参考数据集自动注释细胞类型。我们希望利用生成式人工智能模型，深入了解驱动细胞表型的分子机制，并进一步指导和重塑这一转变过程。
三、疾病及衰老微环境中细胞生态位多样性、可塑性及表型关联
癌症和与衰老相关的疾病源于细胞和组织生态的失衡，偏离了健康状态。课题组目前正结合人工智能驱动的虚拟细胞、器官及个体模型与实验验证，以识别肿瘤和衰老相关疾病中与疾病相关的细胞类型、组织生态位与多器官协作。课题组已经开发了一个全面的单细胞RNA测序数据资源TISCH （Nucleic Acids Res. 2021, 2023），用于分析肿瘤微环境中的基因表达和细胞类型组成。课题组也构建了全癌种的细胞表型图谱TabulaTIME（Nat. Cancer 2025），并发现广泛存在的调节肿瘤免疫的纤维化生态型。目前，课题组正在与肿瘤学家和免疫学家紧密合作，研究不同类型癌症中肿瘤微环境演变和免疫治疗耐药性的机制（Cell 2024; Nat. Genet. 2024; Cancer Immunol. Res. 2023; Genome Med. 2023; EMBO J. 2023）。
团队成员
王晨飞
Principal Investigator
吴秋
研究员
孙冬青
研究员
董鑫
研究员
韩雅
博士后
季鲁章
博士后
董中华
2025级博士研究生
李梓嘉
2025级博士研究生
张乐熠
2025级博士研究生
李亚子
2025级博士研究生
王永焰
2024级博士研究生
郑欣崴
2024级博士研究生
周天瑞
2023级博士研究生
邹启航
2022级博士研究生
刘朝阳
2021级博士研究生
王玉婷
2021级博士研究生
唐珂
2020级博士研究生
魏海霖
2020级博士研究生
江贤桐
2025级硕士研究生
武鹏鹏
2024级硕士研究生
丁炫鑫
2024级硕士研究生
邵文文
2023级硕士研究生
发表论文
2025
Reference-guided computational framework identifies microenvironment metabolic subtypes and targets using pan-cancer single-cell datasets
Ke Tang, Ya Han, Dongqing Sun, Xin Dong, Tong Han, Hailin Wei, Wenwen Shao, Junjie Hu, Zhaoyang Liu, Lele Zhang, Taiwen Li, Peng Zhang, Qiu Wu, Chenfei Wang
Genome Medicine
DOI
2025
Oligoclonal tumor-specific CD8 T-cell revival and IRE1α/XBP1-GDF15-mediated immunosuppressive niches determine neoadjuvant chemoimmunotherapy efficacy in cervical cancer
Guangxu Cao, Yuhan Wang, Huimin Zeng, Yong Zhi, Yi Guo, Mengting Xu, Yetian Ruan, Ying Wang, Yuhang Xiao, Jianqiao Lu, Ka Yu Tse, Jinli Gao, Qingfeng Zhang, Chenfei Wang, Zhiqiang Han, Fang Li
Journal for ImmunoTherapy of Cancer
DOI
2025
Cisformer: a scalable cross-modality generation framework for decoding transcriptional regulation at single-cell resolution
Luzhang Ji, Qihang Zou, Ke Tang, Chenfei Wang
Genome Biology
DOI
2025
Spatiotemporal analyses of the pan-cancer single-cell landscape reveal widespread profibrotic ecotypes associated with tumor immunity
Ya Han, Lele Zhang, Dongqing Sun, Guangxu Cao, Yuting Wang, Jiali Yue, Junjie Hu, Zhonghua Dong, Fang Li, Taiwen Li, Peng Zhang, Qiu Wu, Chenfei Wang
Nature Cancer
DOI
2025
Multi-omic profiling highlights factors associated with resistance to immuno-chemotherapy in non-small-cell lung cancer
Yilv Yan, Dongqing Sun, Junjie Hu, Yue Chen, Liangdong Sun, Huansha Yu, Yicheng Xiong, Zhida Huang, Haoran Xia, Xinsheng Zhu, Dongliang Bian, Fenghuan Sun, Likun Hou, Chunyan Wu, Orion R. Fan, Haiyang Hu, An Zeng, Lele Zhang, Yi Eve Sun, Chenfei Wang, Peng Zhang
Nature Genetics
DOI
2025
Single-cell omics: experimental workflow, data analyses and applications
Fengying Sun, Haoyan Li, Dongqing Sun, Shaliu Fu, Lei Gu, Xin Shao, Qinqin Wang, Xin Dong, Bin Duan, Feiyang Xing, Jun Wu, Minmin Xiao, Fangqing Zhao, Jing-Dong J. Han, Qi Liu, Xiaohui Fan, Chen Li, Chenfei Wang, Tieliu Shi
Science China Life Sciences
DOI
2024
Single-cell dissection of multifocal bladder cancer reveals malignant and immune cells variation between primary and recurrent tumor lesions
Shenghua Liu, Chenchen Feng, Linyi Tan, Dengwei Zhang, Yong-xin Li, Ya Han, Chenfei Wang
Communications Biology
DOI
2024
Single-cell and spatial multiomic inference of gene regulatory networks using SCRIPro
Zhanhe Chang, Yunfan Xu, Xin Dong, Yawei Gao, Chenfei Wang
Bioinformatics
DOI
2024
Proteogenomic characterization of small cell lung cancer identifies biological insights and subtype-specific therapeutic strategies
Qian Liu, Jing Zhang, Chenchen Guo, Mengcheng Wang, Chenfei Wang, Yilv Yan, Liangdong Sun, Di Wang, Lele Zhang, Huansha Yu, Likun Hou, Chunyan Wu, Yuming Zhu, Gening Jiang, Hongwen Zhu, Yanting Zhou, Shanhua Fang, Tengfei Zhang, Liang Hu, Junqiang Li, Yansheng Liu, Hui Zhang, Bing Zhang, Li Ding, Ana I. Robles, Henry Rodriguez, Daming Gao, Hongbin Ji, Hu Zhou, Peng Zhang
Cell
DOI
2023
Single-cell assignment using multiple-adversarial domain adaptation network with large-scale references
Pengfei Ren, Xiaoying Shi, Zhiguang Yu, Xin Dong, Xuanxin Ding, Jin Wang, Liangdong Sun, Yilv Yan, Junjie Hu, Peng Zhang, Qianming Chen, Jing Zhang, Taiwen Li, Chenfei Wang
Cell Reports Methods
DOI
2023
Single‐cell dissection of cervical cancer reveals key subsets of the tumor immune microenvironment
Guangxu Cao, Jiali Yue, Yetian Ruan, Ya Han, Yong Zhi, Jianqiao Lu, Min Liu, Xinxin Xu, Jin Wang, Quan Gu, Xuejun Wen, Jinli Gao, Qingfeng Zhang, Jiuhong Kang, Chenfei Wang, Fang Li
The EMBO Journal
DOI
2023
SCREE: a comprehensive pipeline for single-cell multi-modal CRISPR screen data processing and analysis
Hailin Wei, Tong Han, Taiwen Li, Qiu Wu, Chenfei Wang
Briefings in Bioinformatics
DOI
2023
Tumor microenvironment remodeling after neoadjuvant immunotherapy in non-small cell lung cancer revealed by single-cell RNA sequencing
Junjie Hu, Lele Zhang, Haoran Xia, Yilv Yan, Xinsheng Zhu, Fenghuan Sun, Liangdong Sun, Shuangyi Li, Dianke Li, Jin Wang, Ya Han, Jing Zhang, Dongliang Bian, Huansha Yu, Yan Chen, Pengyu Fan, Qiang Ma, Gening Jiang, Chenfei Wang, Peng Zhang
Genome Medicine
DOI
2023
Cancer Cell Resistance to IFNγ Can Occur via Enhanced Double-Strand Break Repair Pathway Activity
Tong Han, Xujun Wang, Sailing Shi, Wubing Zhang, Jue Wang, Qiu Wu, Ziyi Li, Jingxin Fu, Rongbin Zheng, Jiamin Zhang, Qin Tang, Peng Zhang, Chenfei Wang
Cancer Immunology Research
DOI
2023
TISCH2: expanded datasets and new tools for single-cell transcriptome analyses of the tumor microenvironment
Ya Han, Yuting Wang, Xin Dong, Dongqing Sun, Zhaoyang Liu, Jiali Yue, Haiyun Wang, Taiwen Li, Chenfei Wang
Nucleic Acids Research
DOI
2023
HUSCH: an integrated single-cell transcriptome atlas for human tissue gene expression visualization and analyses
Xiaoying Shi, Zhiguang Yu, Pengfei Ren, Xin Dong, Xuanxin Ding, Jiaming Song, Jing Zhang, Taiwen Li, Chenfei Wang
Nucleic Acids Research
DOI
2022
Single-cell gene regulation network inference by large-scale data integration
Xin Dong, Ke Tang, Yunfan Xu, Hailin Wei, Tong Han, Chenfei Wang
Nucleic Acids Research
DOI
2022
Evaluation of cell-cell interaction methods by integrating single-cell RNA sequencing data with spatial information
Zhaoyang Liu, Dongqing Sun, Chenfei Wang
Genome Biology
DOI
2022
Stage-specific H3K9me3 occupancy ensures retrotransposon silencing in human pre-implantation embryos
Ruimin Xu, Sen Li, Qiu Wu, Chong Li, Manxi Jiang, Lei Guo, Mo Chen, Lingyue Yang, Xin Dong, Hong Wang, Chenfei Wang, Xiaoyu Liu, Xianghong Ou, Shaorong Gao
Cell Stem Cell
DOI
2022
STRIDE: accurately decomposing and integrating spatial transcriptomics using single-cell RNA sequencing
Dongqing Sun, Zhaoyang Liu, Taiwen Li, Qiu Wu, Chenfei Wang
Nucleic Acids Research
DOI
2022
Dynamic nucleosome organization after fertilization reveals regulatory factors for mouse zygotic genome activation
Chenfei Wang, Chuan Chen, Xiaoyu Liu, Chong Li, Qiu Wu, Xiaolan Chen, Lingyue Yang, Xiaochen Kou, Yanhong Zhao, Hong Wang, Yawei Gao, Yong Zhang, Shaorong Gao
Cell Research
DOI
2021
TISCH: a comprehensive web resource enabling interactive single-cell transcriptome visualization of tumor microenvironment
Dongqing Sun, Jin Wang, Ya Han, Xin Dong, Jun Ge, Rongbin Zheng, Xiaoying Shi, Binbin Wang, Ziyi Li, Pengfei Ren, Liangdong Sun, Yilv Yan, Peng Zhang, Fan Zhang, Taiwen Li, Chenfei Wang
Nucleic Acids Research
DOI
2020
Integrative analyses of single-cell transcriptome and regulome using MAESTRO
Chenfei Wang, Dongqing Sun, Xin Huang, Changxin Wan, Ziyi Li, Ya Han, Qian Qin, Jingyu Fan, Xintao Qiu, Yingtian Xie, Clifford A. Meyer, Myles Brown, Ming Tang, Henry Long, Tao Liu, X. Shirley Liu
Genome Biology
DOI
2018
Inhibition of Aberrant DNA Re-methylation Improves Post-implantation Development of Somatic Cell Nuclear Transfer Embryos
Rui Gao, Chenfei Wang, Yawei Gao, Wenchao Xiu, Jiayu Chen, Xiaochen Kou, Yanhong Zhao, Yuhan Liao, Dandan Bai, Zhibin Qiao, Lei Yang, Mingzhu Wang, Ruge Zang, Xiaoyu Liu, Yanping Jia, Yanhe Li, Yalin Zhang, Jiqing Yin, Hong Wang, Xiaoping Wan, Wenqiang Liu, Yong Zhang, Shaorong Gao
Cell Stem Cell
DOI
2018
Reprogramming of H3K9me3-dependent heterochromatin during mammalian embryo development
Chenfei Wang, Xiaoyu Liu, Yawei Gao, Lei Yang, Chong Li, Wenqiang Liu, Chuan Chen, Xiaochen Kou, Yanhong Zhao, Jiayu Chen, Yixuan Wang, Rongrong Le, Hong Wang, Tao Duan, Yong Zhang, Shaorong Gao
Nature Cell Biology
DOI
2016
Distinct features of H3K4me3 and H3K27me3 chromatin domains in pre-implantation embryos
Xiaoyu Liu, Chenfei Wang, Wenqiang Liu, Jingyi Li, Chong Li, Xiaochen Kou, Jiayu Chen, Yanhong Zhao, Haibo Gao, Hong Wang, Yong Zhang, Yawei Gao, Shaorong Gao
Nature
DOI
2016
Identification of key factors conquering developmental arrest of somatic cell cloned embryos by combining embryo biopsy and single-cell sequencing
Wenqiang Liu, Xiaoyu Liu, Chenfei Wang, Yawei Gao, Rui Gao, Xiaochen Kou, Yanhong Zhao, Jingyi Li, You Wu, Wenchao Xiu, Su Wang, Jiqing Yin, Wei Liu, Tao Cai, Hong Wang, Yong Zhang, Shaorong Gao
Cell Discovery
DOI
研究动态
联系方式
王晨飞 Lab
Sycamore Research Institute of Life Sciences
上海市浦东新区张江路88号
上海梧桐岛生命科学研究院