2026:

1.     Sun D#, Zhang L#, Han T, Wu Q, Zhang P, Wang C*. Accurate, Scalable and Cross-platform Cell Identification for High-resolution Spatial Transcriptomics. Nat. Genet. 2026; In press.

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; 6 (11), 1880-1898

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;17 (1), 150.

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. 2025;13 (11), e012630

6.     Wang C, Zhou J, Zhang H, Zhuang Z, Bai G, Tang M, Liu S*, Liu T*. Computational analyses and challenges of single-cell ATAC-seq. Genom. Proteom. Bioinform. 2025; 23 (6), qzaf115

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.