Publications

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# Co-first authors; * Co-corresponding authors

2025

• Yuan Li, Zewei Cheng, Shengli Li*, and Jiwei Zhang*. Immunotherapy in colorectal cancer: status and strategies. Heliyon. Volume 11, Issue 1, 15 January 2025, e41354.
• Libin Song#, Yu Zeng#, Chuanfang Pan, Jing Xie, Xiumei Zhang, Jiling Feng*, and Shengli Li*. Qingyihuaji Formula Prolongs Overall Survival Time in Patients with Pancreatic Cancer: A Retrospective Analysis. Pharmacological Research Modern Chinese Medicine. Volume 14, March 2025, 100588.
• Yangjun Wu#, Yu Zeng#, Yong Wu#, Xinyu Ha, Zheng Feng, Chaohua Liu, Ziqi Liu, Jiajia Wang, Xingzhu Ju, Shenglin Huang, Linhui Liang, Bin Zheng, Lulu Yang, Jun Wang, Xiaohua Wu*, Shengli Li*, and Hao Wen*. HIF-1α-induced long noncoding RNA LINC02776 promotes drug resistance of ovarian cancer by increasing polyADP-ribosylation. Clinical and Translational Medicine. 2025 Mar;15(3):e70244.
• Tian Liao#, Yu Zeng#, Weibo Xu#, Xiao Shi, Cenkai Shen, Yuxin Du, Meng Zhang, Yan Zhang, Ling Li, Peipei Ding, Weiguo Hu, Qinghai Ji*, Yu Wang*, Shengli Li*, and Wenjun Wei*. A spatially resolved transcriptome landscape during thyroid cancer progression. Cell Reports Medicine. 2025 Apr 15;6(4):102043.
• Qili Shi#, Haochen Li#, Junjiao Song#, Hao Wu#, Yu Zeng, Jiawen Jiang, Shengli Li*, Zhiao Chen*, and Xianghuo He*.Human Messenger RNA Harbors Widespread Noncoding Splice Isoforms. bioRxiv. Posted May 10, 2025.
• Jiling Feng#, Yu Zeng#, and Shengli Li*. Illuminating cancer therapy via cryptic antigens. Trends in Cancer. Online. July 24, 2025.

2024

• Zhiqiang Zhang, Shan Wang, Lulu Jiang, Jianwen Wei, Chang Lu, Shengli Li, Yizhu Diao, Zhongcheng Feng, Shuo He, Tingting Tan, Yisheng Yang, Kexin Zou, Jiantao Shi, James Lin, Liye Chen*, Chaohui Bao*, Jian Fei*, and Hai Fang*. Priority index for critical Covid-19 identifies clinically actionable targets and drugs. Communications Biology. 2024 Feb 16;7(1):189.
• Jiling Feng#, Hao Wu#, and Shengli Li*. Noncanonical translation of circRNAs drive antitumor immunity. Trends in Cancer. 2024 Feb;10(2):100-102.
• Yaoming Liu#, Wei Hu#, Yanjie Xie#, Junjie Tang, Huan Ma, Jinmiao Li, Jiahe Nie, Yinghao Wang, Yang Gao, Chao Cheng, Cheng Li, Yujun Ma, Shicai Su, Zhihui Zhang, Yuekun Bao, Yi Ren, Xinyue Wang, Fengyu Sun, Shengli Li*, and Rong Lu*. Single-cell transcriptomics enable the characterization of local extension in retinoblastoma. Communications Biology. 2024 Jan 3;7(1):11.
• Yueqi Wang#, Shengli Li#*, Xiaobo Bo#, Yuan Li#, Changcheng Wang#, Lingxi Nan, Dexiang Zhang, Houbao Liu*, Jiwei Zhang*. CircRNome-wide characterization reveals the promoting role of circAATF in anti-PD-L1 immunotherapy of gallbladder carcinoma. Clinical and Translational Medicine. 2024 Oct;14(10):e70060.

2023

• Hao Wu#, Yicheng Lu#, Zhenzhen Duan#, Jingni Wu, Minghui Lin, Yangjun Wu, Siyang Han, Tongqi Li, Yuqi Fan, Xiaoyuan Hu, Hongyan Xiao, Jiaxuan Feng, Zhiqian Lu*, Deping Kong*, Shengli Li*. Nanopore long-read RNA sequencing reveals functional alternative splicing variants in human vascular smooth muscle cells. Communications Biology. 2023 Oct 31;6(1):1104.
• Hao Wang, Yinuo Li, Yanan Wang, Xiumin Shang, Zhongxin Yan, Shengli Li, and Wei Bao*. Cisplatin-induced PANDAR-Chemo-EVs contribute to a more aggressive and chemoresistant ovarian cancer phenotype through the SRSF9-SIRT4/SIRT6 axis. Journal of Gynecologic Oncology. 2023 Oct 18.
• Yangjun Wu#, Miao Xu#, Zheng Feng#, Hao Wu, Jingni Wu, Xinyu Ha, Yong Wu, Siyu Chen, Fei Xu, Hao Wen, Shengli Li*, and Xiaohua Wu*. AUF1-induced circular RNA hsa_circ_0010467 promotes platinum resistance of ovarian cancer through miR-637/LIF/STAT3 axis. Cellular and Molecular Life Sciences. 2023 Aug 17;80(9):256.
• Jiling Feng#, Yu Zeng#, and Shengli Li*. Single-cell characterization of tumor evolution from precursor diseases. Trends in Cancer. 2023 Aug 4;S2405-8033(23)00139-5.
• Hao Wu#, Jiao Wang#, Xiaoyuan Hu, Zhuang Cheng, Jianxin Zhou, Peiru Wu, Shengli Li*, and Robert Chunhua Zhao*. Comprehensive transcript-level analysis reveals transcriptional reprogramming during the progression of Alzheimer’s disease. Frontiers in Aging Neuroscience. 2023 Jun 15;15:1191680.
• Yu Dong#, Qian Gao#, Yong Chen#, Zhao Zhang#, Yanhua Du#, Yuan Liu, Guangxiong Zhang, Shengli Li, Gaoyang Wang, Xiang Chen*, Hong Liu*, Leng Han*, and Youqiong Ye*. Identification of circRNA signature associated with tumor immune infiltration to predict therapeutic efficacy of immunotherapy. Nature Communications. 2023 May 3;14(1):2540.
• Shengli Li#, Li Yuan#, Zhi-Yuan Xu, Jing-Li Xu, Gui-Ping Chen, Xiaoqing Guan, Guang-Zhao Pan, Can Hu, Jinyun Dong, Yi-An Du, Li-Tao Yang, Mao-Wei Ni, Rui-Bin Jiang, Xiu Zhu, Hang Lv, Han-Dong Xu, Sheng-Jie Zhang, Jiang-Jiang Qin*, and Xiang-Dong Cheng*. Integrative proteomic characterization of adenocarcinoma of esophagogastric junction. Nature Communications. 2023 Feb 11;14(1):778.

  2022

• Chunbo Li#, Hao Wu#, Luopei Guo, Danyang Liu, Shimin Yang, Shengli Li*, and Keqin Hua*. Single-cell transcriptomics reveals cellular heterogeneity and molecular stratification of cervical cancer.Communications Biology. 2022 Nov 10;5(1):1208.
• Wei Hu#, Yangjun Wu#, Qili Shi#, Jingni Wu, Deping Kong, Xiaohua Wu, Xianghuo He*, Teng Liu*, and Shengli Li*. Systematic characterization of cancer transcriptome at transcript resolution. Nature Communications. 2022 Nov 10;13(1):6803.
• Mei Luo#, Lin Ye#, Ruimin Chang#, Youqiong Ye, Zhao Zhang, Chunjie Liu, Shengli Li, Ying Jing, Hang Ruan, Guanxiong Zhang, Yi He, Yaoming Liu, Yu Xue, Xiang Chen*, An-Yuan Guo*, Hong Liu*, and Leng Han*. Multi-omics characterization of autophagy-related molecular features for therapeutic targeting of autophagy. Nature Communications. 2022 Oct 26;13(1):6345.
• Jingni Wu#, Wei Hu#, and Shengli Li*. Long-read transcriptome sequencing reveals allele-specific variants at high-resolution. Trends in Genetics. 2022 Oct 4;S0168-9525(22)00229-3.
• Jiwei Zhang#*, Shengli Li#, Jianian Zhang#, Jiawen Jiang, Wen Zhang, Hao Wu, Enjiang Wu, Mu Chen, Yutao Feng, Li Yang*, and Zhe Li*. Docetaxel resistance-derived LINC01085 contributes to the immunotherapy of hormone-independent prostate cancer via modulating the TBK1-Ser172 phosphorylation level. Cancer Letters. 2022 Oct 1;545:215829.
• Mengting Shen#, Shengli Li#, Yiming Zhao#, Yizhe Liu, Zhen Liu, Lin Huan, Yejun Qiao, Lu Wang*, Leng Han*, Zhiao Chen*, and Xianghuo He*. Hepatic ARID3A facilitates liver cancer malignancy by cooperating with CEP131 to regulate an embryonic stem cell-like gene signature. Cell Death & Disease. 2022 Aug 25;13(8):732.
• Chunjie Jiang*, and Shengli Li*. Editorial: DNA Methylation Dynamics and Human Diseases. Frontiers in Cell and Developmental Biology. 23 Jun, 2022.
• Qili Shi#, Teng Liu#, Wei Hu, Zhiao Chen, Xianghuo He*, and Shengli Li*. SRTdb: an omnibus for human tissue and cancer-specific RNA transcripts. Biomarker Research. 2022 Apr 26;10(1):27.
• Shibio Wan*, Chunjie Jiang, Shengli Li, and Yiping Fan. Special Issue on Bioinformatics and Machine Learning for Cancer Biology. Biology. 2022, 11(3), 361.
• Chunjie Jiang,Shibiao Wan, Peng Hu, Yongsheng Li, and Shengli Li*. Editorial: Transcriptional Regulation in Metabolism and Immunology. Frontiers in Genetics. 2022 Feb 2;13:845697.
• Teng Liu#, Jingni Wu#, Yangjun Wu#, Wei Hu, Zhixiao Fang, Zishan Wang, Chunjie Jiang, and Shengli Li*. LncPep: a resource of translational evidences for lncRNA. Frontiers in Cell and Developmental Biology. 2022 Jan 24;10:795084.
• Teng Liu, Leshan Xiu, Kun Yin, and Shengli Li*. Dominant mutations in the severe acute respiratory syndrome coronavirus-2 genome challenge polymerase chain reaction detection. Clinical and Translational Discovery. 2022 Mar;2(1):e23.

2021

• Junjun Wang#,Wei Hu#,Zhenyang Shen#,Teng Liu,Weiming Dai,Bo Shen, Xiaoman Li, Jingni Wu, Lungen Lu*, Shengli Li*, and Xiaobo Cai*. Dissecting the single-cell transcriptome underlying chronic liver injury. Molecular Therapy - Nucleic Acids. 2021 Dec 3;26:1364-1373.
• Jingni Wu#,Zhixiao Fang#,Teng Liu,Wei Hu,Yangjun Wu,and Shengli Li*. Maximizing the Utility of Transcriptomics Data in Inflammatory Skin Diseases. Frontiers in Immunology. 2021 Oct 29;12:761890
• Zhixiao Fang and Shengli Li*. Alternative polyadenylation-associated loci interpret human traits and diseases. Trends in Genetics. 2021 Sep;37(9):773-775.
• Libin Song#,Simin Qi#,Wei Hu#,Zhixiao Fang#,Dehua Yu,Teng Liu,Jingni Wu,Yangjun Wu,Aiwei Wu,Lanyun Feng,Jing Xie,Bo Zhang,Wenguang He,Zhouyu Ning,Luming Liu*,Jiangjiang Qin*,and Shengli Li*. Integrative analysis reveals clinically relevant molecular fingerprints in pancreatic cancer. Molecular Therapy - Nucleic Acids. 2021 Jul 2;26:11-21.
• Yangjun Wu,Xiaohua Wu,and Shengli Li*. Retrotransposons: Jump to Cancer? Trends in Cancer. 2021 Jul;7(7):577-579.
• Chunbo Li, Luopei Guo,Shengli Li*,and Keqin Hua*. Single-cell transcriptomics reveals the landscape of intra-tumoral heterogeneity and transcriptional activities of ECs in CC. Molecular Therapy - Nucleic Acids. 2021 June 4;24:682-694.
• Zhiao Chen, Shengli Li*, Leng Han, and Xianghuo He*. Optimized protocol for an inducible rat model of liver tumor with chronic hepatocellular injury, inflammation, fibrosis, and cirrhosis. STAR Protocols.2021 Mar;2(1):100353.
• Wei Hu#, Yanru Wang#, Zhixiao Fang, Wei He*, and Shengli Li*. Integrated characterization of lncRNA-immune interactions in prostate cancer. Frontiers in Cell and Developmental Biology.2021 Feb;9:641891.
• Zhixiao Fang, Chunjie Jiang* and Shengli Li*. The potential regulatory roles of circular RNAs in tumor immunology and immunotherapy. Frontiers in Immunology. 2021 Feb;11:617583.

Before 2021

• Zhao Zhang#, Ji Jing#, Youqiong Ye, Zhiao Chen, Ying Jing, Shengli Li, Wei Hong, Hang Ruan, Yaoming Liu, Qingsong Hu, Yun Huang, Wenbo Li, Chunru Lin, Lixia Diao*, Yubin Zhou*, and Leng Han*. Systematic characterization of the dual functional effects of heat shock proteins (HSPs) in cancer hallmarks to aid development of HSP inhibitors. Genome Medicine.2020 Nov 23;12(1):101.
• Zhiao Chen#, Shengli Li#, Mengting Shen#, Xinyuan Lu, Chunyang Bao, Di Chen, Jie Ding, Qifeng Wang, Shenglin Huang, Wenming Cong, Leng Han*, and Xianghuo He*. The mutational and transcriptional landscape of hepatocarcinogenesis in a rat model. iScience.2020 Oct 15;23(11):101690.
• Shengli Li#,*, Zhao Zhang# and Leng Han*. 3D spheroids propel tumor characterization. Trends in Cancer.2020 Aug;6(8):622-624.
• Zhixiang Hu#, Liangqing Dong#, Shengli Li, Zhe Li, Yejun Qiao, Yuchen Li, Jie Ding, Zhiao Chen, Yangjun Wu, Zhen Wang, Shenglin Huang, Qiang Gao*, Yingjun Zhao*, and Xianghuo He*. Splicing Regulator p54nrb/NONO Enhances Carcinogenesis via Oncogenic Isoform Switch of BIN1 in Hepatocellular Carcinoma. Hepatology.2020 Aug;72(2):548-568.
• Jiwei Zhang#,*, Shengli Li#, Ling Zhang#, Juan Xu, Mingxu Song, Tingting Shao, Zhaohui Huang*, and Yongsheng Li*. RBP EIF2S2 promotes tumorigenesis and progression by regulating MYC-mediated inhibition via FHIT-related enhancers. Molecular Therapy.2020 Apr 8;28(4):1105-1118.
• Zhao Zhang#,*, Shengli Li#, and Leng Han*. Resolving spliceosomal malfunctions advances RNA-based therapeutics. Trends in Molecular Medicine.2020 Feb;26(2):135-137.
• Yaoming Liu#, Hang Ruan#, Shengli Li, Youqiong Ye, Wei Hong, Jing Gong, Zhao Zhang, Ying Jing, Xiulan Zhang*, Lixia Diao* and Leng Han*. The genetic and pharmacogenomic landscape of snoRNAs in human cancer. Molecular Cancer.2020 Jun 23;19(1):108.
• Wei Hong#, Hang Ruan#, Zhao Zhang, Youqiong Ye, Yaoming Liu, Shengli Li, Ying Jing, Huiwen Zhang, Lixia Diao, Han Liang and Leng Han*. APAatlas: decoding alternative polyadenylation across human tissues. Nucleic Acids Research. 2020 Jan 8;48(D1):D34-D39.
• Hang Ruan#, Yingnan Liao#, Zongna Ren, Lin Mao, Fang Yao, Peng Yu, Youqiong Ye, Zhao Zhang, Shengli Li, Hanshi Xu, Jiewei Liu, Lixia Diao, Bingying Zhou, Leng Han* and Li Wang*. Single-cell reconstruction of differentiation trajectory reveals a critical role of ETS1 in human cardiac lineage commitment. BMC Biology.2019 Nov 13;17:89.
• Shengli Li#, Zhao Zhang#, and Leng Han*. Molecular treasures of cancer cell lines. Trends in Molecular Medicine.2019 Aug;25(8):657-659.
• Hang Ruan#, Yu Xiang#, Junsuk Ko#, Shengli Li#, Ying Jing, Xiaoyu Zhu, Youqiong Ye, Zhao Zhang, Tingting Mills, Jing Feng, Chun-Jie Liu, Ji Jing, Jin Cao, Bingying Zhou, Li Wang, Yubin Zhou, Chunru Lin, An-Yuan Guo, Xi Chen, Lixia Diao, Wenbo Li, Zhiao Chen, Xianghuo He, Gordon B. Mills, Michael R. Blackburn, and Leng Han*. Comprehensive characterization of circular RNAs in~ 1000 human cancer cell lines. Genome Medicine. 2019 Aug 26;11(1):55.
• Shengli Li and Leng Han*. Circular RNAs as promising biomarkers in cancer: detection, function, and beyond. Genome Medicine.2019 Mar 20;11(1):15.
• Shengli Li, Zhixiang Hu, Yingjun Zhao, Shenglin Huang, and Xianghuo He*. Transcriptome-wide analysis reveals the landscape of aberrant alternative splicing events in liver cancer. Hepatology. 2019 Jan;69(1):359-375.
• Shengli Li, Jiwei Zhang, Shenglin Huang*, and Xianghuo He*. Genome-wide analysis reveals that exon methylation facilitates its selective usage in the human transcriptome. Briefings in Bioinformatics.2018 Sep 28;19(5):754-764.
• Di Chen#, Hui Wang#, Jie Chen, Zhe Li, Shengli Li, Zhixiang Hu, Shenglin Huang, Yingjun Zhao*, Xianghuo He*. MicroRNA-129-5p regulates glycolysis and cell proliferation by targeting the glucose transporter SLC2A3 in gastric cancer cells. Frontiers in Pharmacology.2018 May 15;9:502.
• Zhe Li#, Jiwei Zhang#, Xinyang Liu#, Shengli Li, Qifeng Wang, Di Chen, Zhixiang Hu, Tao Yu, Jie Ding, Jinjun Li, Ming Yao, Jia Fan, Shenglin Huang, Qiang Gao*, Yingjun Zhao*, and Xianghuo He*. The LINC01138 Drives Malignancies via Activating Arginine Methyltransferase 5 in Hepatocellular Carcinoma. Nature Communications.2018 Apr 20;9(1):1572.
• Weijie Guo#, Zhixiang Hu#, Yichao Bao, Shengli Li, Qiupeng Zheng, Dongbin Lyu, Di Chen, Tao Yu, Yuchen Li, Yan Li, Jie Ding, Yingjun Zhao, Xianghuo He* and Shenglin Huang*. A novel LIN28B tumor-specific transcript in cancer. Cell Reports. 2018 Feb 20;22(8):2016-2025.
• Jiwei Zhang#, Zhe Li#, Longzi Liu#, Qifeng Wang, Shengli Li, Di Chen, Zhixiang Hu, Tao Yu, Jie Ding, Jinjun Li, Ming Yao, Shenglin Huang, Yingjun Zhao* and Xianghuo He*. Long noncoding RNA TSLNC8 is a tumor suppressor that inactivates the interleukin-6/STAT3 signaling pathway. Hepatology.2018 Jan;67(1):171-187.
• Juan Xu#, Zishan Wang#, Shengli Li#, Juan Chen, Jinwen Zhang, Chunjie Jiang, Zheng Zhao, Jing Li, Yongsheng Li* and Xia Li*. Combinatorial epigenetic regulation of non-coding RNAs has profound effects on oncogenic pathways in breast cancer subtypes. *Briefings in Bioinformatics.2018 Jan 1;19(1):52-64.
• Shengli Li, Yuchen Li, Bing Chen, Jingjing Zhao, Shulin Yu, Yan Tang, Qiupeng Zheng, Yan Li, Peng Wang, Xianghuo He, and Shenglin Huang*. exoRBase: a database of circRNA, lncRNA and mRNA in human blood exosomes. Nucleic Acids Research.2018 Jan 4;46(D1):D106-D112.
• Chaoqun Li, Feifei Cao, Shengli Li, Shenglin Huang, Wei Li*, Nashat Abumaria*. Profiling and co-expression network analysis of learned helplessness regulated mRNAs and lncRNAs in the mouse hippocampus. Frontiers in Molecular Neuroscience. 2018 Jan 11;10:454.
• Tao Yu#, Yingjun Zhao#, Zhixiang Hu, Jing Li, Dandan Chu, Jiwei Zhang, Zhe Li, Bing Chen, Xiao Zhang, Hongyu Pan, Shengli Li, Hechun Lin, Lei Liu, Ming xia Yan, Xianghuo He*, and Ming Yao*. MetaLnc9 facilitates lung cancer metastasis via a PGK1-activated AKT/mTOR pathway. Cancer Research.2017 Nov 1;77(21):5782-5794.
• Tangjian Li#, Shengli Li#, Di Chen, Bing Chen, Tao Yu, Fangyu Zhao, Qifeng Wang, Ming Yao, Shenglin Huang, Zhiao Chen*, and Xianghuo He*. Transcriptomic analyses of RNA-binding proteins reveal eIF3c promotes cell proliferation in hepatocellular carcinoma. Cancer Science.2017 May;108(5):877-885.
• Tingting Shao, Zheng Zhao, Aiwei Wu, Jing Bai, Yongsheng Li, Hong Chen, Chunjie Jiang, Yuan Wang, Shengli Li, Letian Wang, Fengmin Zhang*,Juan Xu*, and Xia Li*. Functional dissection of virus-human crosstalk mediated by miRNAs based on the VmiReg database. Molecular BioSystems.2015 May;11(5):1319-28.
• Yongsheng Li#, Yunpeng Zhang#, Shengli Li#, Jianping Lu, Juan Chen, Yuan Wang, Yixue Li*, Juan Xu*, and Xia Li*. Genome-wide DNA methylome analysis reveals epigenetically dysregulated non-coding RNAs in human breast cancer. Scientific Reports.2015 Mar 5;5:8790.
• Yongsheng Li#, Shengli Li#, Juan Chen, Tingting Shao, Chunjie Jiang, Yuan Wang, Hong Chen, Juan Xu*, and Xia Li*. Comparative epigenetic analyses reveal distinct patterns of oncogenic pathways activation in breast cancer subtypes. Human Molecular Genetics.2014 Oct 15;23(20):5378-93.
• Jing Bai#, Yongsheng Li#, Tingting shao, Zheng Zhao, Yuan Wang, Aiwei Wu, Hong Chen, Shengli Li, Chunjie Jiang, Juan Xu*, and Xia Li*. Integrating analysis reveals microRNA-mediated pathway crosstalk among Crohn’s disease, ulcerative colitis and colorectal cancer. Molecular BioSystems.2014 Jul 29;10(9):2317-28.
• Yongsheng Li, Juan Xu, Hong Chen, Jing Bai, Shengli Li, Zheng Zhao, Tingting Shao, Tao Jiang, Huan Ren, Chunsheng Kang*, and Xia Li*. Comprehensive analysis of the functional microRNA-mRNA regulatory network identifies miRNA signatures associated with glioma malignant progression. *Nucleic Acids Research.2013 Dec;41(22):e203.
• Yongsheng Li#, Juan Xu#, Hong Chen#, Zheng Zhao, Shengli Li, Jing Bai, Aiwei Wu, Chunjie Jiang, Yuan Wang, Bin Su, and Xia Li*. Characterizing genes with distinct methylation patterns in the context of protein-protein interaction network: application to human brain tissues. PLOS ONE.2013 Jun 12;8(6):e65871.