论文
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| • Zhu, W.#*, Meng, J.#, Li, Y.#, Gu, L.#, Liu, W., Li, Z., Shen, Y., Shen, X., Wang, Z., Wu, Y., Wang, G., Zhang, J., Zhang, H., Yang, H., Dong, X., Wang, H., Huang, X., Sun,Y.*, Li, C.*, Mu, L.*, Liu, Z*. (2025) Comparative proteomic landscapes elucidate human preimplantation development and failure. Cell. 188(3): 814-831 |
| • Cheng, Y.#, Chen, X.#, Feng, L.#, Yang, Z.#, Xiao, L.#, Xiang, B., Wang, X., Liu, D., Lin, P., Shi, J., Song, G., Qian, W., Zhang, B., Xu, Y., Gao, Z., Chen, L., Wu, Y., Ma, J., Lin, Y., Zhao, H., Peng, L., Mao, X., Liu, Y., Hou, H., Yang, M., Ji, Y., Wang, X., Zhou, J., Xu, X., Liu, X., Wei, W., Zhang, X., Gao, Q.*, Zhou, H.*, Sun,Y.*, Wu, K.*, Fan, J*. (2025) Stromal architecture and fibroblast subpopulations with opposing effects on outcomes in hepatocellular carcinoma. Cell Discov. 11(1): 1 |
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| • Ma F#, Wang S#, Xu L#, Huang W#, Shi G, Sun Z, Cai W, Wu Z, Huang Y, Meng J, Sun Y, Fang M, Cheng M, Ji Y, Hu T, Zhang Y, Gu B, Zhang J*, Song S*, Sun,Y.*, Yan W*. (2024) Single-cell profiling of the microenvironment in human bone metastatic renal cell carcinoma. Commun Biol. 7(1): 91 |
| • Lu JC#, Wu LL#, Sun YN#, Huang XY#, Gao C#, Guo XJ, Zeng HY, Qu XD, Chen Y, Wu D, Pei YZ, Meng XL, Zheng YM, Liang C, Zhang PF, Cai JB, Ding ZB, Yang GH, Ren N, Huang C, Wang XY, Gao Q, Sun QM, Shi YH, Qiu SJ, Ke AW, Shi GM*, Zhou J*, Sun,YD.*, Fan J*. (2024) Macro CD5L(+) deteriorates CD8(+)T cells exhaustion and impairs combination of Gemcitabine-Oxaliplatin-Lenvatinib-anti-PD1 therapy in intrahepatic cholangiocarcinoma. Nat Commun. 15(1): 621 |
| • Qiu S#, Hu Y#, Huang Y#, Gao T#, Wang X, Wang D, Ren B, Shi X, Chen Y, Wang X, Wang D, Han L, Liang Y, Liu D, Liu Q, Deng L, Chen Z, Zhan L, Chen T, Huang Y, Wu Q, Xie T, Qian L, Jin C, Huang J, Deng W, Jiang T, Li X, Jia X, Yuan J, Li A, Yan J, Xu N, Xu L, Luo Q, Poo MM, Sun,Y.*, Li CT*, Yao H*, Gong H*, Sun YG*, Xu C*. (2024) Whole-brain spatial organization of hippocampal single-neuron projectomes. Science. 383(6682): eadj9198. |
| • Hao S#, Zhu X#, Huang Z#, Yang Q#, Liu H#, Wu Y#, Zhan Y#, Dong Y#, Li C#, Wang H, Haasdijk E, Wu Z, Li S, Yan H, Zhu L, Guo S, Wang Z, Ye A, Lin Y, Cui L, Tan X, Liu H, Wang M, Chen J, Zhong Y, Du W, Wang G, Lai T, Cao M, Yang T, Xu Y, Li L, Yu Q, Zhuang Z, Xia Y, Lei Y, An Y, Cheng M, Zhao Y, Han L, Yuan Y, Song X, Song Y, Gu L, Liu C, Lin X, Wang R, Wang Z, Wang Y, Li S, Li H, Song J, Chen M, Zhou W, Yuan N, Sun S, Wang S, Chen Y, Zheng M, Fang J, Zhang R, Zhang S, Chai Q, Liu J, Wei W, He J, Zhou H, Sun Y, Liu Z, Liu C, Yao J, Liang Z, Xu X, Poo M, Li C, De Zeeuw CI, Shen Z, Liu Z, Liu L, Liu S, Sun,Y.*, Liu C*. (2024) Cross-species single-cell spatial transcriptomic atlases of the cerebellar cortex. Science. 385(6716): eado3927 |
| • Ji, S.#, Feng, L.#, Fu, Z.#, Wu, G.#, Wu, Y.#, Lin, Y., Lu, D., Song, Y., Cui, P., Yang, Z., Sang, C., Song, G., Cai, S., Li, Y., Lin, H., Zhang, S., Wang, X., Qiu, S., Zhang, X., Hua, G., Li, J., Zhou, J., Dai, Z., Wang, X., Ding, L., Wang, P., Gao, D., Zhang, B., Rodriguez, H., Fan, J., Clevers, H., Zhou, H.*,.Sun,Y.*, Gao, Q.* (2023) Pharmaco-proteogenomic characterization of liver cancer organoids for precision oncology Sci Transl Med 15(706): eadg3358. |
| • Chen, A.#, Sun,Y.#*, Lei, Y.#, Li, C.#, Liao, S.#, Meng, J.#, Bai, Y.#, Liu, Z.#, Liang, Z.#, Zhu, Z.#, Yuan, N.#, Yang, H.#, Wu, Z.#, …… , Yao, J*., Wei, W.*, Li, Y.*, Shen, Z.*, Liu, L.*, Liu, Z.*, Xu, X.*, Li, C.* (2023) Single-cell spatial transcriptome reveals cell-type organization in the macaque cortex. Cell. 186(17): 3726-3743. |
| • Yan, N.,#, Feng, H.#, Sun, y.#, Xin, Y. #, Zhang, H.#, Lu, H., Zheng, J., He, C., Zuo,Z., Yuan,T., Li,N., Xie,L., Wei,W.*,Sun,Y.* ,Zuo,E.* (2023) Cytosine base editors induce off-target mutations and adverse phenotypic effects in transgenic mice. Nature Communications 14: 1784 |
| • Zhu,W.#, Ding,Y.#,Meng,J.#,Gu,L.#,Liu,W.#,Li,L. , Chen,H.,Wang,Y.,Li,Z.,Li,C.,Sun,Y.* Liu,Z.* (2023) Reading and writing of mRNA m6A modification orchestrate maternal-to-zygotic transition in mice. Genome Biology 24: 67 |
| • Yang,Q.,Wu,L.,Meng,J.,Ma,L.,Zuo,E.*,Sun,Y.* (2022) EpiCas-DL: Predicting sgRNA activity for CRISPR-mediated epigenome editing by deep learning. Computational and Structural Biotechnology Journal 21: 202-211 |
| • Li,Z .#, Huang,Y.#, Li,Q.,Sun,Y. ,Li,C., Wu,J.,Zheng,H.*Zeng,R.* (2022) TreeQNet: a webserver for Treatment evaluation with Quantified Network. BMC Bioinformatics 23(1): 473 |
| • Gao, N.#, Hu, J.#, He, B.#, Ji, Z.#, Hu, X.#, Huang, J., Wei, Y., Peng, J., Wei, Y., Zhou, Y., Shen, X., Li, H., Feng, X., Xiao, Q., Shi, L.,Sun,Y. ,Zhou, C., Zhou, H.*, Yang, H.* (2021) Endogenous promoter-driven sgRNA for monitoring the expression of low-abundance transcripts and lncRNAs Nature cell biology 23(1): 99-108 |
| • Zhang,H.# ,Li,T.# ,Sun,Y. ,Yang,H.* (2021) Perfecting Targeting in CRISPR. Annual Review of Genetics 55: 453-477 |
| • Ma,Y.#,Sun,Y.# , Sun,L.#,Liu,X.,Zeng,R.* , Lin,X.* ,Li,Y.* (2021) Effects of gut microbiota and fatty acid metabolism on dyslipidemia following weight-loss diets in women: Results from a randomized controlled trial. Clinical Nutrition 40(11): 5511-5520 |
| • Feng,L.#,Sun,Y.# ,Li,C.,Li,Y.,Chen,L.,Zeng,R.* (2021) Pan-cancer network disorders revealed by overall and local signaling entropy. Journal of Molecular Cell Biology 13(9): 622–635 |
| • Huang,X.# ,Lv,J.#,Li,Y.#,Mao,S.,Li,Z.,Jing,Z., Sun,Y. , Zhang,X.,Shen,S.,Wang,X., Di,M., Ge,J.,Huang,X.,Zuo,E.* ,Chi,T.* (2020) Programmable C-to-U RNA editing using the human APOBEC3A deaminase. The EMBO Journal 39: e104741 |
| • Yuan, T.#, Yan, N.#, Fei, T.#, Zheng, J.#, Meng, J.#, Li, N.#, Liu, J.#, Zhang, H., Xie, L., Ying, W., Li, D., Shi, L., Sun, Y., Li, Y., Li, Y., Sun, Y.* & Zuo, E.* (2021) Optimization of C-to-G base editors with sequence context preference predictable by machine learning methods Nat. Commun. 12: 4902 |
| • Zuo, E.#, Sun, Y.#, Wei, W.#, Yuan, T.#, Ying, W., Sun, H., Yuan, L., Steinmetz, L. M.*, Li, Y.*, Yang, H.* (2019) Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos Science 364: 289-292 |
| • Zhou, C.#, Sun, Y.#, Yan, R.#, Liu, Y.#, Zuo, E.#, Gu, C., Han, L., Wei, Y., Hu, X., Zeng, R., Li, Y.*, Zhou, H.*, Guo, F.*, Yang, H.* (2019) Off-target RNA mutation induced by DNA base editing and its elimination by mutagenesis Nature 571: 275-278 |
| • Zuo, E.#, Sun, Y.#, Yuan, T.#, He, B.#, Zhou, C.#, Ying, W., Liu, J., Wei, W., Zeng, R., Li, Y.*, Yang, H.* (2020) A rationally engineered cytosine base editor retains high on-target activity while reducing both DNA and RNA off-target effects Nature Methods 17: 600-604 |
| • Sun, Y., Li, C., Pang, S., Yao, Q., Chen, L.*, Li, Y.*, Zeng, R.* (2020) Kinase-substrate Edge Biomarkers Provide A More Accurate Prognostic Prediction in ER-negative Breast Cancer Genomics, Proteomics & Bioinformatics 18(5): 525-538. |
| • Zuo, E.#, Sun, Y.#, Wei, W.#, Yuan, T.#, Ying, W., Sun, H., Yuan, L., Steinmetz, L. M.*, Li, Y.*, Yang, H.* (2020) GOTI, a method to identify genome-wide off-target effects of genome editing in mouse embryos Nature Protocols 15(9): 3009-3029 |
| • Zhou, H., Su, J., Hu, X., Zhou, C., Li, H., Chen, Z., Xiao, Q., Wang, B., Wu, W., Sun, Y., Zhou, Y., Tang, C., Liu, F., Wang, L., Feng, C., Liu, M., Li, S., Zhang, Y., Xu, H., Yao, H., Shi, L., & Yang H. (2020) Glia-to-Neuron Conversion by CRISPR-CasRx Alleviates Symptoms of Neurological Disease in Mice Cell 181: 590-603 |
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