(#) 共同第一作者; (*) 通讯作者
[1] Hua Yu#*, Jing Zhao#, Yuxuan Shen, Qiao Lu, Yuheng Liu, Guanglei Xie, Shuhui Chang, Tingying Ge, Nan Li, Ming Chen, Hu Li, Jin Zhang*, Xi Wang*. The dynamic landscape of enhancer-derived RNA during mammalian early embryo development. Cell Reports, 2024, 43(4):114077. https://doi.org/10.1016/j.celrep.2024.114077.
[2] Hua Yu#, Zhen Sun#, Tianyu Tan#, Hongru Pan#, Jing Zhao, Ling Zhang, Jiayu Chen, Yuqing Zhu, Lang Chen, Yuyan Xu, Shaorong Gao, George Q. Daley, Jin Zhang*. rRNA Biogenesis Regulates Mouse 2C-like State by 3D Structure Reorganization of Peri-Nucleolar Heterochromatin. Nature Communications, 2021, 12(1):6365. https://doi.org/10.1038/s41467-021-26576-2.
[3] Anhua Lei#, Hua Yu#, Shan Lu, Hengxing Lu, Xizhong Ding, Tianyu Tan, Hailing Zhang, Mengmeng Zhu, Lin Tian, Xudong Wang, Siyu Su, Dixuan Xue, Shaolong Zhang, Wei Zhao, Yuge Chen, Wanrun Xie, Li Zhang, Yuqing Zhu, Jing Zhao, Wenhong Jiang, George Church, Francis Ka-Ming Chan, Zhihua Gao, Jin Zhang*. A second generation M1-polarized CAR macrophage with antitumor efficacy. Nature Immunology, 2023, 25(1):102-116. https://doi.org/10.1038/s41590-023-01687-8.
[4] Zhen Sun#, Hua Yu#, Jing Zhao#, Tianyu Tan, Hongru Pan, Bo Gao, Yuqing Zhu, Lang Chen, Cheng Zhang, Li Zhang, Anhua Lei, Yuyan Xu, Xianju Bi, Xin Huang, Cristina Correia, Ming Chen, Qiming Sun, Li Shen, Longfei Wang, Yu Feng, Jianlong Wang, Xiaohua Shen, Hu Li, Hao Wu, George Q. Daley, Jin Zhang*. LIN28 coordinately promotes nucleolar/ribosomal functions and represses the 2C-like transcriptional program in pluripotent stem cells. Protein & Cell, 2021, 13(7):490-512. https://doi.org/10.1007/s13238-021-00864-5.
[5] Jing Zhao#, Ke Yao#, Hua Yu#, Ling Zhang, Yuyan Xu, Lang Chen1, Zhen Sun, Yuqing Zhu, Chen Zhang, Yuli Qian, Zhuyan Ji, Min Zhang, Jie Chen, Cristina Correia, Taylor Weiskittel, Dan Zhang, Hu Li, Wei Xie, Zeping Hu*, Jin Zhang*. Metabolic reprogramming during mouse early embryo development. Nature Metabolism，2021, 3(10):1372-1384. https://doi.org/10.1038/s42255-021-00464-x.
[6] Lin Yang, Yuqing Zhu#, Hua Yu#, Xiaolong Cheng, Sitong Chen, Yulan Chu, He Huang, Jin Zhang*, Wei Li*. scMAGeCK links genotypes with multiple phenotypes in single-cell CRISPR screens. Genome Biology, 2020 21(1):19. https://doi.org/10.1186/s13059-020-1928-4.
[7] Li Zhang#, Lin Tian#, Xiaoyang Dai#, Hua Yu#, Jiajia Wang#, Anhua Lei, Mengmeng Zhu, Jianpo Xu, Wei Zhao, Yuqing Zhu, Zhen Sun, Hao Zhang, Yongxian Hu, Yanlin Wang, Yuming Xu, George M. Church, He Huang, Qinjie Weng*, Jin Zhang*. Pluripotent stem cell-derived CAR-macrophage cells with antigen-dependent anti-cancer cell functions. Journal of Hematology and Oncology, 2020 13(1):153. https://doi.org/10.1186/s13045-020-00983-2.
[8] Hua Yu#*, Lu Lu#, Bingke Jiao, Chengzhi Liang*. Systematic discovery of novel and valuable plant gene modules by large-scale RNA-seq samples. Bioinformatics, 2019, 35(3):361-364. https://doi.org/10.1093/bioinformatics/bty642.
[9] Hua Yu*, Biaoke Jiao, Lu Lu, Pengfei Wang, Shuangcheng Chen, Chengzhi Liang*, Wei Liu*, NetMiner-an ensemble pipeline for building genome-wide and high-quality gene co-expression network using massive-scale RNA-seq samples. PLoS ONE, 2018, 13(2): e019261. https://doi.org/10.1371/journal.pone.0192613.
[10] Hua Yu#*, Lu Lu#, Ming Chen, Chen Li*, Jin Zhang*, Genome-wide discovery of hidden genes mediating known drug-disease association using KDDANet. npj Genomic Medicine, 2021 6(1):50. https://doi.org/10.1038/s41525-021-00216-6.
[11] Hua Yu#, Jianxin Chen#, Xue Xu, Yan Li, Huihui Zhao, Xiuxiu Li, Wei Zhou, Wei Wang* and Yonghua Wang*. A systematic prediction of multiple drug-target interactions from chemical, genomic and pharmacological data. PLoS ONE, 2012, 7(5): e37608. https://doi.org/10.1371/journal.pone.0037608.
[12] Hua Yu#*, Xiaojun Chen#*, Lu Lu. Large-scale prediction of microRNA-disease associations by combinatorial prioritization algorithm. Scientific Reports, 2017, 7(1):43792. https://doi.org/10.1038/srep43792.
[13] Lu Lu#, Jiale Qin#, Jiandong Chen, Hao Wu, Qiang Zhao, Satoru Miyano, Yaozhong Zhang*, Hua Yu* and Chen Li*. DDIT: An Online Predictor for Multiple Clinical Phenotypic Drug-Disease Associations. Frontier in Pharmacology, 2022, 12(1):772026. https://doi.org/10.3389/fphar.2021.772026
[14] Lu Lu*, Hua Yu*. DR2DI: a powerful computational tool for predicting novel drug-disease associations. Journal of Computer-Aided Molecular Design, 2018, 32(5):633-642. https://doi.org/10.1007/s10822-018-0117-y.
[15] Lingtong Liu#, Yunlong Lu#, Liqin Wei#, Hua Yu#, Yinghao Cao, Yan Li, Ning Yang, Yunyun Song, Chengzhi Liang*, Tai Wang*, Transcriptomics analyses reveal the molecular roadmap and long noncoding RNA landscape of sperm cell lineage development. The Plant Journal, 2018, 96(2):421-437. https://doi.org/10.1111/tpj.14041.
[16] Chengzhen Liang#, Aifu Li#, Hua Yu#, Wenzhen Li, Chengzhi Liang, Sandui Guo, Rui Zhang, Chengcai Chu. Melatonin Regulates Root Architecture by Modulating Auxin Response in Rice. Frontier in Plant Science, 2017, 8(1):134. https://doi.org/10.3389/fpls.2017.00134.
[17] Hong-Qing Ling#*, Bin Ma#, Xiaoli Shi#, Hui Liu#, Lingli Dong#, Hua Sun#, Yinghao Cao, Qiang Gao, Shusong Zheng, Ye Li, Ying Yu, Huilong Du, Ming Qi, Yan Li, Hongwei Lu, Hua Yu, Yan Cui, Ning Wang, Chunlin Chen, Huilan Wu, Yan Zhao, Juncheng Zhang, Yiwen Li, Wenjuan Zhou, Bairu Zhang, Weijuan Hu, Michiel J. T. van Eijk, Jifeng Tang, Hanneke M. A. Witsenboer, Shancen Zhao, Zhensheng Li, Aimin Zhang*, Daowen Wang*, Chengzhi Liang*. Genome sequence of the progenitor of wheat A subgenome Triticum Urartu. Nature, 2018, 557(7705):424-428. https://doi.org/10.1038/s41586-018-0108-0.
[18] Ling Zhang#, Jing Zhao#, Sin Man Lam#, Lang Chen#, Yingzhuo Gao#, Wenjie Wang#, Yuyan Xu, Tianyu Tan, Hua Yu, Min Zhang, Xufeng Liao, Mengchen Wu, Tianyun Zhang, Jie Huang, Bowen Li, Quan D. Zhou, Ning Shen, Hyeon Jeong Lee, Cunqi Ye, Da Li*, Guanghou Shui*, Jin Zhang*. Low input lipidomics reveals lipid metabolism remodeling during early mammalian embryo development. Nature Cell Biology, 2024, 26(1): 278–293. https://doi: 10.1038/s41556-023-01341-3
(19) Tianyu Tan, Bo Gao, Hua Yu, Hongru Pan, Zhen Sun, Anhua Lei, Li Zhang, Hengxing Lu, Hao Wu, George Q. Daley, Yu Feng, Jin Zhang. Dynamic Nucleolar Phase Separation Influenced by Non-canonical Function of LIN28A Instructs Pluripotent Stem Cell Fate Decisions. Nature Communications, 2024, 15(1):1256. https://doi.org/10.1038/s41467-024-45451-4.
[20] Li Chen#, Qiaoqiao Tong#, Xiaowen Chen#, Penglei Jiang, Hua Yu, Qianbing Zhao, Lingang Sun, Chao Liu, Bin Gu, Yuping Zheng, Lijiang Fei, Xiao Jiang, Wenjuan Li, Giacomo Volpe, Mazid MD. Abdul, Guoji Guo, Jin Zhang, Pengxu Qian, Qiming Sun, Dante Neculai, Miguel A. Esteban, Chen Li, Feiqiu Wen, Junfeng Ji. PHC1 maintains pluripotency by organizing genome-wide chromatin interactions of the Nanog locus. Nature Communications, 2021, 12(1): 2829. https://doi.org/10.1038/s41467-021-22871-0.
[21] Lu Su#, Linkang Zhou#, Feng-Jung Chen, Huimin Wang, Hui Qian, Yuanyuan Sheng, Yuangang Zhu, Hua Yu, Xinqi Gong, Lie Cai, Xuerui Yang, Li Xu, Tong-Jin Zhao, John Zhong Li, Xiao-Wei Chen*, Peng Li*. Cideb controls sterol-regulated ER export of SREBP/ SCAP by promoting cargo loading at ER exit sites. The EMBO Journal, 2019, 38(8):e100156. https://doi.org/10.15252/embj.2018100156.
[22] Xue Li#, Xin Guo#, Yuqing Zhu#, Guoqing Wei, Yanlei Zhang, Xia Li, Huijun Xu, Jiazhen Cui, Wenjun Wu, Jingsong He, Matthew E.Ritchie, M.Weiskittel, Hu Li, Hua Yu, Lijuan Ding, Mi Shao, Qian Luo, XiaoxiaoXu, Xinyi Teng, Alex H.Chang, Jin Zhang*, He Huang*, Yongxian Hu*, Single cell transcriptomic analysis reveals BCMA CAR-T cell dynamics in a patient with refractory primary plasma cell leukemia. Molecular Therapy, 2021, 29(2):645-657. https://doi.org/10.1016/j.ymthe.2020.11.028.