1.Zhou, Y., ..., Chen L.*, Zuo, C.*, Reconstructing tissue dynamics and enabling in silico perturbation from spatial omics through niche-driven multi-agent learning, 2026, under review.
2.Ren, L#; Yang, Q.#; Sun, D.; Liu, Z., …, Zuo, C.*, Mao, Y. *, Hu, H. *, ORVI-HCR-guided organoid drug screening identifies panobinostat as a repurposed therapeutic candidate for liver cancer. 2026, In submission.
3.Zhang, W.#, Wang, Y.,# Zuo, C.#, …, Liu, Y.*, Sun, L.*, Long-term confinement triggers RIPK3-independent necroptosis in amoeboid cancer cells to shape tumor evolution. 2026, Development Cell, Under review.
4.Yang, Q., Wang Y.*, Chen L.*, Zuo, C.*, stMixer for scalable mosaic integration and label transfer in spatial histology and multi-omics. Advanced Science, 2026 (接收).
5.Yang, Q.#, Zhou, Y.#, Zhang, H.#, Cai, M., Hong, J., Li, K., Xie, X., Chu, C., Zuo, C.*, A User's Roadmap to Foundation Models on Single-Cell and Spatial-Omics - Cell Type and Lineage applications. National Science Review, 2026 (接收)
6.Zuo, C.*, Xia, J., Xu, Y., Xu, Y., Gao, P., Zhang, J., Wang, Y., Chen, L.*, stClinic dissects clinically relevant niches by integrating spatial multi-slice multi-omics data in dynamic graphs. Nature Communications, 2025. 16, 5317.
7.Gao, P.#, Zuo, C.#*, Yuan, W., Cai, J., Chai, X., Gong, R., Yu, J., Yao, L., Su, W., Liu, Z., Lin, S., Wang, Y., Dai, M., Ma, L., Li, Q.*, Zhou, P.*. Spatiotemporal multi-omics analysis uncovers NAD-dependent immunosuppressive niche triggering early gastric cancer. Signal Transduction and Targeted Therapy, 2025. 10: 313.
8.Jiao, M.#, Li, J.#, Zhang, M., Du, S., Zhong B., Li, S., Zhang, B., Liu, F.*, Zuo, C.*, Wang, S.*, Chen, L.*, De novo reconstruction of 3D human facial images from DNA sequence. Advanced Science, 2025. doi: 10.1002/advs.202414507.
9.Lou, Y.#, Li, X.#, Yang, Q., Dai, H., Ma K., Zuo, C.*, Vector-guided graph learning for spatial multi-slice multi-omics alignment. Cell Reports Methods, 2025, 101241.
10.Yan, Q.#, Li, X.#, Cui, J., Rong, J., Zhang J., Gao, P., Xu, Y., Qiu, F., Zuo, C.*, Spatial histology and gene-expression representation and generative learning via online self-distillation contrastive learning. Briefings in Bioinformatics, 2025. 26(4).
11.Zuo, C.*, Zhu, J., Zou, J., Chen, L.*, Unraveling tumour spatiotemporal heterogeneity using spatial multimodal data. Clinical and Translational Medicine, 2025. doi: 10.1002/ctm2.70331.
12.Wang, Y., Xie, X., Wang, Y., Sheng, N., Huang, L.*, Zuo, C.*, Supervised contrastive knowledge graph learning for ncRNA-disease association prediction. Expert Systems with Applications, 2025. 269: p. 126257.
13.Shi, M.#, Yan, Q.#, Zhao, W.#, Tang, C,#. Han, F., Chen, H., Li, Y., Xu, L., Yang, F., Yan, Z., Ren, Y., Jin, G.*, Bao, Y.*, Zuo, C.*, Li, J.*, NeoAtlas-Tumor and NeoBert: A database and A predictive Model for Canonical and Noncanonical Tumor Neoantigens. Genomics, Proteomics & Bioinformatics, 2025, qzaf105.
14.Cui, J., Gao, Y., Wang, Q., Li, X., Xu, K., Huang, Z., Zhang, J., Zuo, C.*. Advanced Cross-Graph Cycle Attention Model for Dissecting Complex Structures in Mass Spectrometry Imaging. Journal of Computer Science and Technology, 2025, doi: 10.1007/s11390-025-4342-2.
15.Rong, J.#, Zhong, H.#, Meng, Y., Jin, Q., Zhang, Y., Zuo, C.*, HLIP: A pan-cancer model for histological image analysis in clinical research using TCGA. Computational Biology and Chemistry, 2025, 108589.
16.Xu, Y., Dai, H., Feng, J., Xu, K., Wang, Q., Gao, P.*, Zuo, C.*, stGuide advances label transfer in spatial transcriptomics through attention-based supervised graph representation learning. Frontiers in Genetics, 2025, 16, 1566675.
17.Zuo, C.*, Xia, J., Chen, L.*, Dissecting tumor microenvironment from spatially resolved transcriptomics data by heterogeneous graph learning. Nature Communications, 2024. 15(1): p. 5057.
18.Zhang, Y.#, Zuo, C.#*, Li, Y., Liu, L., Yang, B., Xia, J., Cui, J., Xu, K., Wu, X.*, Gong, W.*, Liu, Y.*, Single-cell characterization of infiltrating T cells identifies novel targets for gallbladder cancer immunotherapy. Cancer Letters, 2024. 586: p. 216675.
19.Xia, J., Cui, J., Huang, Z., Zhang, S., Yao, F., Zhang, Y., Zuo, C.*, CellMirror: deciphering cell populations from spatial transcriptomics data by interpretable contrastive learning. IEEE International Conference on Medical Artificial Intelligence. 2023, 165-176.
20.Cui, J., Xia, J., Li, X., Wang, Y., Qiu, F., Xu, Y., Xu, K., Zuo, C.*, Elucidating Spatial Complex Structures from Mass Spectrometry Imaging with Deep Multimodal Model. IEEE International Conference on Medical Artificial Intelligence. 2023, 110-121.
21.Zuo, C.*, Zhang, Y., Cao, C., Feng, J., Jiao, M., Chen, L.*, Elucidating tumor heterogeneity from spatially resolved transcriptomics data by multi-view graph collaborative learning. Nature Communications, 2022. 13(1): p. 5962.
22.Zhang, Y.#, Zuo, C.#, Liu, L.#, Hu, Y.#, Yang, B.#, Qiu, S., Li, Y., Cao, D., Ju, Z., Ge, J., Wang, Q., Wang, T., Bai, L., Yang, Y., Li, G., Shao, Z., Gao, Y., Li, Y., Bian, R., Miao, H., Li, L., Li, X., Jiang, C., Yan, S., Wang, Z., Wang, Z., Cui, X., Huang, W., Xiang, D., Wang, C., Li, Q., Wu, X., Gong, W., Liu, Y., Shao, R.*, Liu, F.*, Li, M.*, Chen, L.*, Liu, Y.*, Single-cell RNA-sequencing atlas reveals an MDK-dependent immunosuppressive environment in ErbB pathway-mutated gallbladder cancer. Journal of Hepatology, 2021. 75(5): p. 1128-1141.
23.Xia, J., Wang, L., Zhang, G.*, Zuo, C.*, Chen, L., RDAClone: deciphering tumor heterozygosity through single-cell genomics data analysis with robust deep autoencoder. Genes, 2021, 12(12): 1847.
24.Zuo, C., and Chen, L.*, Deep-joint-learning analysis model of single cell transcriptome and open chromatin accessibility data. Briefings in Bioinformatics, 2021. 22(4): p. bbaa287.
25.Zuo, C., Dai, H. and Chen, L.*, Deep cross-omics cycle attention model for joint analysis of single-cell multi-omics data. Bioinformatics, 2021. 37(22): p. 4091-4099.
26.Zuo, C., Tang, Y., Fu, H., Liu, Y., Zhang, X., Zhao, B., Xu, Y.*, Elucidation and analyses of the regulatory networks of upland and lowland ecotypes of switchgrass in response to drought and salt stresses. Plos one, 2018, 13(9): e0204426.
27.Zuo, C., Blow, M., Sreedasyam, A., Kuo, A., Ramamoorthy, G., Torres-Jerez. I., Li, G., Wang, M., Dilworth, D., Barry, K., Udvardi, M., Schmutz, J., Tang, Y., Xu, Y.*, Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing. Biotechnology for biofuels, 2018, 11(1): 170.
28.Jiao M., Li J., Zuo C., Wang S., Chen L., Reply to “Comment on ‘De Novo Reconstruction of 3D Human Facial Images From DNA Sequence’”. Advanced Science 2026, e73979.
29.Huang, Z., Mu, X., Chen, Q., Zhong, L., Xiao, J., Zuo, C., Zhang, Y., Shi, B., Qu, Y., Tan, R., Xu, L., Guan, R., Xu, Y.*, A Model for the Development of Alzheimer’s Disease. Genomics, Proteomics & Bioinformatics, 2025, qzaf087.
30.Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2025. Nucleic Acids Research, 2025, 53(D1): D30-D44.
31.Zhang, S., Wu, X., Lian, Z., Zuo, C., Wang, Y.*, GNNMF: a multi-view graph neural network for ATAC-seq motif finding. BMC genomics, 2025, 25(1): 300.
32.Hong, J., Hou, W., Sheng, N., Zuo, C., Wang, Y. *, HATZFS predicts pancreatic cancer driver biomarkers by hierarchical reinforcement learning and zero-forcing set. Expert Systems with Applications, 2025, 260: 125435.
33.Cao, C., Shao, M., Zuo, C., Kwok, D., Liu, L., Ge, Y., Zhang, Z., Cui, F., Chen, M., Fan, R., Ding, Y., Jiang, H., Wang, G., Zou, Q. *, AVAR: a curated repository for rare variant–trait associations. Nucleic Acids Research, 2024, 52(D1): D990-D997.
34.Feng, J., Zhang, S.*, Chen, L.*, Zuo, C., Alzheimer’s Disease Neuroimaging Initiative, Detection of Alzheimer’s disease using features of brain region-of-interest-based individual network constructed with the sMRI image. Computerized Medical Imaging and Graphics, 2022, 98:102057.
35.Jin, Q., Zuo, C., Cui, H., Li, L., Yang, Y., Dai, H.*, Chen, L.*, Single-cell entropy network detects the activity of immune cells based on ribosomal protein genes. Computational and Structural Biotechnology Journal, 2022, 20: 3556-3566.