姓名：王晨飞

学位：博士

导师情况：博士生导师

研究领域：生物信息学与人工智能、微环境失调与疾病发生

E-mail：08chenfeiwang at tongji.edu.cn

联系电话：021-65981195

通讯地址：上海市四平路1239号，同济大学生命科学与技术学院（200092）

实验室主页：https://wanglabtongji.github.io/

个人简介：

王晨飞，博士生导师，同济大学生命科学与技术学院生物信息系长聘教授，上海市自主智能无人系统科学中心PI，梧桐岛生命科学研究院客座研究员。研究方向为生物信息学与人工智能，微环境失调与疾病发生。近年来发展了一系列单细胞时空多组学数据增强、生成和功能解析智能算法，揭示了复杂微环境中多细胞调控、互作失调与疾病发生的关联机制。以通讯作者（含共同）身份在Nat. Genet.、Nat. Cancer. 、Cell Stem Cell、Genome Biol.、Nucleic Acids Res.等杂志发表二十余篇论文。担任Nat. Rev. Genet.、Nat. Methods、Nat. Cell Biol., Nat. Commun.等杂志审稿人，BMC Bioinfor.杂志编委。主持和参与多个国家级科研项目，包括科技部重点研发青年项目、国家优青、面上、青年基金等。获得吴瑞奖学金、博新计划、上海市科技启明星等荣誉。担任上海市生物信息学会理事，青年委员会主任委员。

研究方向为：

一、单细胞时空组学数据增强、跨模态生成及网络解析AI算法

二、基于AI和大规模时空组学数据的虚拟细胞、器官及个体构建

三、疾病及衰老环境中细胞细胞调控与互作多样性、可塑性及表型关联

代表文章：

#:第一作者 *:通讯作者

2025：

^{1. Han Y, Zhang L, Sun D, Cao G, Wang Y, Yue J, Hu J, Dong Z, Li F, Li T, Zhang P, Wu Q*, Wang C*. Spatiotemporal analyses of the pan-cancer single-cell landscape reveal widespread profibrotic ecotypes associated with tumor immunity. Nat. Cancer. 2025; 1-19}

^{2. Ji L#, Zou Q#, Tang K, Wang C*. Cisformer: a scalable cross-modality generation framework for decoding transcriptional regulation at single-cell resolution. Genome Biol. 2025; 26 (1), 340}

^{3. Tang K#, Han Y#, Sun D, Dong X, Han T, Wei H, Shao W, Hu J, Liu Z, Zhang L, Li T, Zhang P, Wu Q*, Wang C*. Reference-guided computational framework identifies microenvironment metabolic subtypes and targets using pan-cancer single-cell datasets. Genome Med. 2025; In press.}

^{4. Yan Y#, Sun D#, Hu J#, Sun L, Yu H, Xiong Y, Huang Z, Xia H, Zhu X, Bian D, Sun F, Chen Y, Hou L, Wu C, Fan R, Zeng A*, Zhang L*, Sun Y*, Wang C*, Zhang P*. Multi-omic profiling highlights factors associated with resistance to immuno-chemotherapy in non-small cell lung cancer. Nat. Genet. 2025; 57(1), 126-139}

^{5. Cao G#, Wang Y#, Zeng H#, Zhi Y#, Guo Y, Xu M, Ruan Y, Wang Y, Xiao Y, Lu J, Tse K, Gao J, Zhang Q, Wang C*, Han Z* and Li F*. Oligoclonal tumor specific CD8 T-cell Revival and IRE1α/XBP1-GDF15 Mediated Immunosuppressive Niches Determine Neoadjuvant Chemoimmunotherapy Efficacy in Cervical Cancer. J. Immunother. Cancer.13 (11), e012630}

2024:

^{1. Liu S#*, Feng C#, Tan L#, Zhang D, Li Y, Han Y*, Wang C*. Single-cell dissection of multifocal bladder cancer reveals malignant and immune cells variation between primary and recurrent tumor lesions. Commu. Biol. 2024; 7 (1), 1659}

^{2. Chang Z#, Xu Y#, Dong X#, Gao Y, Wang C*. Single-cell and spatial multiomic inference of gene regulatory networks using SCRIPro. Bioinform. 2024; 40 (7)}

^{3. Sun F#, Li H#, Sun D#, Fu S#, Gu L#, Shao X#, Wang Q#, Dong X#, Duan B#, Xing F#, Wu J#, Xiao M*, Zhao F*, Han J*, Liu Q*, Fan X*, Li C*, Wang C*, Shi T*. Single-Cell Omics: experimental workflow, data analyses and applications. Sci. China Life Sci. 2024; 1-98.}

^{4. Liu Q#, Zhang J#, Guo C#, Wang M#, Wang C#, Yan Y, Sun L, Wang D, Zhang L, Yu H, Hou L, Wu C, Zhu Y, Jiang G, Zhu H, Zhou Y, Fang S, Zhang T, Hu L, Li J, Liu Y, Zhang H, Zhang B, Ding L, Robles A, Rodriguez H, Gao D*, Ji H*, Zhou H*, Zhang P*. Proteogenomic characterization of small cell lung cancer identifies biological insights and subtype-specific therapeutic strategies. Cell 2024; 187 (1), 184-203.} 

^2023：

^{1. Han T#, Wang X#, Shi S, Zhang W, Wang J, Wu Q, Li Z, Fu J, Zheng R, Zhang J, Tang Q, Zhang P*, Wang C*. Cancer Cells Resistance to IFN-γ via Enhanced Double-Strand Break Repair Pathway. Cancer Immunol. Res. 2023; 11(3), 381–398.}

^{2. Wei H#, Han T, Li T, Wu Q*, Wang C*. SCREE: a comprehensive pipeline for single-cell multi-modal CRISPR screen data processing and analysis. Brief. Bioinformatics 2023; 24 (3), bbad123.}

^{3. Ren P#, Shi X#, Dong X, Yu Z, Ding X, Wang J, Sun L, Yan Y, Hu J, Zhang P, Chen Q, Zhang J*, Li T*, Wang C*. SELINA: Single-cell Assignment using Multiple-Adversarial Domain Adaptation Network with Large-scale References. Cell Rep. Methods 2023; 3 (9).}

^{4. Hu J#, Zhang L#, Xia H#, Yan Y#, Zhu X, Sun F, Sun L, Li S, Li D, Wang J, Han Y, Zhang J, Bian D, Yu H, Chen Y, Fan P, Ma Q, Jiang G, Wang C*, Zhang P*. Tumor microenvironment remodeling after neoadjuvant immunotherapy in non-small cell lung cancer revealed by single-cell RNA sequencing. Genome Med. 2023; 15(1), 1-14.}

^{5. Cao G#, Yue J#, Ruan Y#, Han Y, Zhi Y, Lu J, Liu M, Xu X, Wang J, Gu Q, Wen X, Gao J, Kang J, Zhang Q, Wang C*, Li F*. Single-cell Dissection of Cervical Cancer Reveals Key Subsets of the Tumor Immune Microenvironment. EMBO J. 2023; 42 (16), e110757.}

^{6. Han Y#, Wang Y#, Dong X#, Sun D, Liu Z, Yue J, Wang H, Li T*, Wang C*. TISCH2: expanded datasets and new tools for single-cell transcriptome analyses of the tumor microenvironment. Nucleic Acids Res. 2023; 51 (D1), D1425-D1431.}

^{7. Shi X#, Yu Z#, Ren P, Dong X, Ding X, Song J, Zhang J, Li T*, Wang C*. HUSCH: an integrated single-cell transcriptome atlas for human tissue gene expression visualization and analyses. Nucleic Acids Res. 2023; 51 (D1), D1029-D1037.}

^2022：

^{1. Xu R#, Li S#, Wu Q#, Li C#, Jiang M#, Guo L, Chen M, Yang L, Dong X, Wang H, Wang C*, Liu X*, Ou X*, Gao S*. Stage-specific H3K9me3 occupancy ensures retrotransposon silencing in human preimplantation embryos. Cell Stem Cell 2022; 29 (7), 1051-1066. (Cover Story)}

^{2. Sun D, Liu Z, Li T, Wu Q*, Wang C*. STRIDE: accurately decomposing and integrating spatial transcriptomics using single-cell RNA sequencing. Nucleic Acids Res. 2022; 50 (7), e42-e42.}

^{3. Dong X#, Tang K#, Xu Y, Wei H, Han T, Wang C*. Single-cell Gene Regulation Network Inference by Large-scale Data Integration. Nucleic Acids Res. 2022; 50 (21), e-126-e126.}

^{4. Liu Z, Sun D, Wang C*. Evaluation of cell-cell interaction methods by integrating single-cell RNA sequencing data with spatial information. Genome Biol. 2022; 23 (1), 1-38.}

^{5. Wang C#, Chen C#, Liu X#, Li C#, Wu Q, Chen X, Yang L, Kou X, Zhao Y, Wang H, Gao Y*, Zhang Y*, Gao S*. Dynamic nucleosome organization after fertilization reveals regulatory factors for mouse zygotic genome activation. Cell Res. 2022; 32 (9), 801-813. (Cover Story)}

^2016-2021:

^{1. Sun D#, Wang J#, Han Y#, Dong X, Zheng R, Ge J, Shi X, Wang B, Li Z, Ren P, Sun L, Yan Y, Zhang P, Zhang F*, Li T*, Wang C*. TISCH: a comprehensive web resource enabling interactive single-cell transcriptome visualization of tumor microenvironment. Nucleic Acid Res. 2021; 49 (D1), D1420-D1430.}

^{2. Wang C#, Sun D#, Huang X, Wan C, Li Z, Han Y, Qin Q, Fan J, Qiu X, Xie Y, Meyer CA, Brown M, Tang M, Long H, Liu T*, and Liu XS*. Integrative analyses of single-cell transcriptome and regulome using MAESTRO. Genome Biol. 2020; 21(1), 1-28.}

^{3. Wang C#, Liu X#, Gao Y#*, Yang L#, Li C, Liu W, Chen C, Kou X, Zhao Y, Chen J, Wang Y, Le R, Wang H, Duan T, Zhang Y*, Gao S*. Reprogramming of H3K9me3-dependent heterochromatin during mammalian embryo development. Nat. Cell Biol. 2018; 20(5), 620-631.}

^{4. Gao R#, Wang C#, Gao Y#, Bai D, Liu X, Kou X, Zhao Y, Zang R, Liao Y, Jia Y, Chen J, Wang H, Wan X, Liu W*, Zhang Y*, Gao S*. Inhibition of aberrant DNA re-methylation improves the development of nuclear transfer embryos. Cell Stem Cell 2018; 23(3), 426-435.}

^{5. Liu X#, Wang C#, Liu W#, Li J#, Li C, Kou X, Chen J, Zhao Y, Gao H, Wang H, Zhang Y*, Gao Y*, Gao S*. Distinct features of H3K4me3 and H3K27me3 chromatin domains in pre-implantation embryos. Nature 2016; 537(7621), 558-562.}

^{6. Liu W#, Liu X#, Wang C#, Gao Y#, Gao R, Kou X, Zhao Y, Li J, Wu Y, Xiu W, Wang S, Yin J, Liu W, Cai T, Wang H, Zhang Y*, Gao S*. Identification of key factors conquering developmental arrest of somatic cell cloned embryos by combining embryo biopsy and single-cell sequencing. Cell Discov. 2016; 2(1), 1-15.}