1.   Ruifeng Li*, Kun Wei*, Qinli Sun, Bowen Xie, Peng Wei, Tian Xie, Xinyi, Yongzhen Chen, Birui Pan, Zixuan Zhao, Ling Ni, Chen Dong^# (2025). "Analysis of three-dimensional genome of exhausted CD8⁺ T cells reveals a critical role of IRF8 in their differentiation and functions in cancer." Nature Immunology, 2025: 1-16.

2.   Kun Wei*, Ruifeng Li*, Xiaohong Zhao, Bowen Xie, Tian Xie, Qinli Sun, Yongzhen Chen, Peng Wei, Wei Xu, Xinyi Guo, Zixuan Zhao, Han Feng, Ling Ni, Chen Dong^# (2025). "TRIM28 is an essential regulator of three- dimensional chromatin state underpinning CD8⁺ T cell activation." Nature Communications, 2025, 16(1): 750.

3.   Huidong Guo*, Ruifeng Li*, Ming Wang, Yingping Hou, Shuoshuo Liu, Ting Peng, Xiang-Yu Zhao, Liming Lu, Yali Han, Yiming Shao, Ying-Jun Chang, ^# Cheng Li,^# and Xiao-Jun Huang^#. "Multiomics Analysis Identifies SOCS1 as Restraining T Cell Activation and Preventing Graft-Versus-Host Disease." Advanced Science, 2022, 9(21): 2200978.

4.   Pengze Wu*, Tingting Li*, Ruifeng Li*, Lumeng Jia, Ping Zhu, Yifang Liu, Qing Chen, Daiwei Tang, Yuezhou Yu and Cheng Li^# (2017). "3D genome of multiple myeloma reveals spatial genome disorganization associated with copy number variations." Nature Communications, 2017, 8(1): 1937.

5.   Tingting Li*, Ruifeng Li*, Xuan Dong*, Lin Shi*, Miao Lin*, Ting Peng*, Pengze Wu, Yuting Liu, Xiaoting Li, Xuheng He, Xu Han, Bin Kang, Yinan Wang, Zhiheng Liu, Qing Chen, Yue Shen, Mingxiang Feng, Xiangdong Wang, Duojiao Wu, Jian Wang, Cheng Li^# (2021). “Integrative analysis of genome, 3D genome, and transcriptome alterations of clinical lung cancer samples.” Genomics, Proteomics & Bioinformatics, 2021, 19(5): 741-753.

6.   Xiang Xu*, Jingbo Gan*, Zhaoya Gao*, Ruifeng Li*, Dandan Huang*, Lin Lin, Yawen Luo, Qian Yang, Jingxuan Xu, Yaru Li, Qing Fang, Ting Peng, Yaqi Wang, Zihan Xu, An Huang, Haopeng Hong, Fuming Lei, Wensheng Huang, Jianjun Leng, Tingting Li, Xiaochen Bo, Hebing Chen^#, Cheng Li^#, Jin Gu^# (2025) “3D genome landscape of primary and metastatic colorectal carcinoma reveals the regulatory mechanism of tumorigenic and metastatic gene expression.” Communications Biology, 2025, 8(1): 365.

7.   Ruifeng Li*^{, #}, Yuting Liu*, Yingping Hou*, Jingbo Gan*, Pengze Wu and Cheng Li^# (2018). "3D genome and its disorganization in diseases." Cell Biology and Toxicology, 2018, 34(5): 351-365.

8.   Ruifeng Li*, Yifang Liu*, Tingting Li and Cheng Li^# (2016). "3Disease Browser: A Web server for integrating 3D genome and disease-associated chromosome rearrangement data." Scientific Reports, 2016, 6(1): 34651.

9.   Bowen Xie*, Bowen Yuan, Xiaohong Zhao, Tian Xie, Ruifeng Li, Peng Wei, Qinli Sun, Wenbo Hu, Birui Pan, Yongzhen Chen, Kun Wei, Zixuan Zhao, Lei Yuan, Xuan Zhong, Xue Bai, Qiuyan Lan, Lei Qin, Ling Ni, Chen Dong^#. (2025) “Ms4a7 expression in cDC1s determines cross-presentation and antitumor immunity.” Science, 2025, 390(6774): eady5362.

10.  Jing Hao*, Ruifeng Li, Xiaohong Zhao, Xinwei Liu, Xiang Chen, Tian Xie, Xiaoli Li, Chenjun Yao, Qinli Sun, Kun Wei, Mengting Gou, Xinxin Chi, Wei Xu, Ling Ni and Chen Dong^#. (2024) “NR4A1 transcriptionally regulates the differentiation of stem-like CD8⁺ T cells in the tumor microenvironment.” Cell Reports, 2024, 43(6).

11.  Qinli Sun*, Xiaohong Zhao, Ruifeng Li, Dingfeng Liu, Birui Pan1, Bowen Xie, Xinxin Chi, Dongli Cai, Peng Wei, Wei Xu, Kun Wei, Zixuan Zhao, Yujie Fu, Ling Ni, and Chen Dong^#. (2023) “STAT3 regulates CD8⁺ T cell differentiation and functions in cancer and acute infection.” Journal of Experimental Medicine, 2023, 220(4): e20220686.

12.  Qinli Sun*, Dongli Cai, Dingfeng Liu, Xiaohong Zhao, Ruifeng Li, Wei Xu, Bowen Xie, Mengting Gou, Kun Wei, Yuling Li, Jinling Huang, Xinxin Chi, Peng Wei, Jing Hao, Xinyi Guo, Birui Pan ,Yujie Fu, Ling Ni and Chen Dong^#. (2023) “BCL6 promotes a stem-like CD8⁺ T cell program in cancer via antagonizing BLIMP1.” Science Immunology, 2023, 8(88): eadh1306.

13.  Mian Wei*, Xiaoying Fan, Miao Ding, Ruifeng Li, Shipeng Shao, Yingping Hou, Shaoshuai Meng, Fuchou Tang, Cheng Li, Yujie Sun^#.  (2020) “Nuclear actin regulates inducible transcription by enhancing RNA polymerase II clustering.” Science Advances, 2020, 6(16): eaay6515.

14.  Lei Chang*, Mengfan Li*, Shipeng Shao*, Chen Li, Shanshan Ai, Boxin Xue, Yingping Hou, Yiwen Zhang, Ruifeng Li, Xiaoying Fan, Aibin He, Cheng Li and Yujie Sun^#. (2022) “Nuclear peripheral chromatin-lamin B1 interaction is required for global integrity of chromatin architecture and dynamics in human cells.” Protein &Cell, 2022, 13(4): 258-280.

    (*co-first author, ^# corresponding author)