1. 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.（独立第一/共通讯，IF：15.7， Featured article in data integration collection）
2. 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. （独立第一/共通讯，IF：15.7）
3. 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. （独立第一/共通讯，IF：15.7）
4. 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.（共一第二/共通讯，AI for medicine，IF：52.7）
5. 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. （共一第二，主要生物信息学方法开发和计算，IF：30.083）
6. 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（共通讯，IF：14.3）
7. 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.（独立通讯，娄是本科生）
8. 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)（独立通讯，IF：7.7，严是本科生）
9. 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. （独立第一/共通讯，IF：7.9）