Publications
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# First authors; * Corresponding authors
2024
- 61. Priority index for critical Covid-19 identifies clinically actionable targets and drugs.
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. Communications Biology. 2024 Feb 16;7(1):189.
- 60. Noncanonical translation of circRNAs drive antitumor immunity.
Jiling Feng#, Hao Wu#, and Shengli Li*. Trends in Cancer. 2024 Feb;10(2):100-102.
- 59. Single-cell transcriptomics enable the characterization of local extension in retinoblastoma.
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*. Communications Biology. 2024 Jan 3;7(1):11.
2023
- 58. Nanopore long-read RNA sequencing reveals functional alternative splicing variants in human vascular smooth muscle cells.
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*. Communications Biology. 2023 Oct 31;6(1):1104.
- 57. Cisplatin-induced PANDAR-Chemo-EVs contribute to a more aggressive and chemoresistant ovarian cancer phenotype through the SRSF9-SIRT4/SIRT6 axis.
Hao Wang, Yinuo Li, Yanan Wang, Xiumin Shang, Zhongxin Yan, Shengli Li, and Wei Bao. Journal of Gynecologic Oncology. 2023 Oct 18.
- 56. AUF1-induced circular RNA hsa_circ_0010467 promotes platinum resistance of ovarian cancer through miR-637/LIF/STAT3 axis.
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*. Cellular and Molecular Life Sciences. 2023 Aug 17;80(9):256.
- 55. Single-cell characterization of tumor evolution from precursor diseases.
Jiling Feng#, Yu Zeng#, and Shengli Li*. Trends in Cancer. 2023 Aug 4;S2405-8033(23)00139-5.
- 54. Comprehensive transcript-level analysis reveals transcriptional reprogramming during the progression of Alzheimer's disease.
Hao Wu#, Jiao Wang#, Xiaoyuan Hu, Zhuang Cheng, Jianxin Zhou, Peiru Wu, Shengli Li*, and Robert Chunhua Zhao*. Frontiers in Aging Neuroscience. 2023 Jun 15;15:1191680.
- 53. Identification of circRNA signature associated with tumor immune infiltration to predict therapeutic efficacy of immunotherapy.
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*. Nature Communications. 2023 May 3;14(1):2540.
- 52. Integrative proteomic characterization of adenocarcinoma of esophagogastric junction.
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*. Nature Communications. 2023 Feb 11;14(1):778.
2022
- 51. Single-cell transcriptomics reveals cellular heterogeneity and molecular stratification of cervical cancer.
Chunbo Li#, Hao Wu#, Luopei Guo, Danyang Liu, Shimin Yang, Shengli Li*, and Keqin Hua*. Communications Biology. 2022 Nov 10;5(1):1208.
- 50. Systematic characterization of cancer transcriptome at transcript resolution.
Wei Hu#, Yangjun Wu#, Qili Shi#, Jingni Wu, Deping Kong, Xiaohua Wu, Xianghuo He*, Teng Liu*, and Shengli Li*. Nature Communications. 2022 Nov 10;13(1):6803.
- 49. Multi-omics characterization of autophagy-related molecular features for therapeutic targeting of autophagy.
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*. Nature Communications. 2022 Oct 26;13(1):6345.
- 48. Long-read transcriptome sequencing reveals allele-specific variants at high-resolution.
Jingni Wu#, Wei Hu#, and Shengli Li*. Trends in Genetics. 2022 Oct 4;S0168-9525(22)00229-3.
- 47. Docetaxel resistance-derived LINC01085 contributes to the immunotherapy of hormone-independent prostate cancer via modulating the TBK1-Ser172 phosphorylation level.
Jiwei Zhang#*, Shengli Li#, Jianian Zhang#, Jiawen Jiang, Wen Zhang, Hao Wu, Enjiang Wu, Mu Chen, Yutao Feng, Li Yang*, and Zhe Li*. Cancer Letters. 2022 Oct 1;545:215829.
- 46. Hepatic ARID3A facilitates liver cancer malignancy by cooperating with CEP131 to regulate an embryonic stem cell-like gene signature.
Mengting Shen#, Shengli Li#, Yiming Zhao#, Yizhe Liu, Zhen Liu, Lin Huan, Yejun Qiao, Lu Wang*, Leng Han*, Zhiao Chen*, and Xianghuo He*. Cell Death & Disease. 2022 Aug 25;13(8):732.
- 45. Editorial: DNA Methylation Dynamics and Human Diseases.
Chunjie Jiang*, and Shengli Li*. Frontiers in Cell and Developmental Biology. 23 Jun, 2022.
- 44. SRTdb: an omnibus for human tissue and cancer-specific RNA transcripts.
Qili Shi#, Teng Liu#, Wei Hu, Zhiao Chen, Xianghuo He*, and Shengli Li*. Biomarker Research. 2022 Apr 26;10(1):27.
- 43. Special Issue on Bioinformatics and Machine Learning for Cancer Biology.
Shibio Wan*, Chunjie Jiang, Shengli Li, and Yiping Fan. Biology. 2022, 11(3), 361.
- 42. Editorial: Transcriptional Regulation in Metabolism and Immunology.
Chunjie Jiang,Shibiao Wan, Peng Hu, Yongsheng Li, and Shengli Li*. Frontiers in Genetics. 2022 Feb 2;13:845697.
- 41. LncPep: a resource of translational evidences for lncRNA.
Teng Liu#, Jingni Wu#, Yangjun Wu#, Wei Hu, Zhixiao Fang, Zishan Wang, Chunjie Jiang, and Shengli Li*. Frontiers in Cell and Developmental Biology. 2022 Jan 24;10:795084.
- 40. Dominant mutations in the severe acute respiratory syndrome coronavirus-2 genome challenge polymerase chain reaction detection.
Teng Liu, Leshan Xiu, Kun Yin, and Shengli Li*. Clinical and Translational Discovery. 2022 Mar;2(1):e23.
2021
- 39. Dissecting the single-cell transcriptome underlying chronic liver injury.
Junjun Wang#,Wei Hu#,Zhenyang Shen#,Teng Liu,Weiming Dai,Bo Shen, Xiaoman Li, Jingni Wu, Lungen Lu*, Shengli Li*, and Xiaobo Cai*. Molecular Therapy - Nucleic Acids. 2021 Dec 3;26:1364-1373.
- 38. Maximizing the Utility of Transcriptomics Data in Inflammatory Skin Diseases.
Jingni Wu#,Zhixiao Fang#,Teng Liu,Wei Hu,Yangjun Wu,and Shengli Li*. Frontiers in Immunology. 2021 Oct 29;12:761890
- 37. Alternative polyadenylation-associated loci interpret human traits and diseases.
Zhixiao Fang and Shengli Li*. Trends in Genetics. 2021 Sep;37(9):773-775.
- 36. Integrative analysis reveals clinically relevant molecular fingerprints in pancreatic cancer.
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*. Molecular Therapy - Nucleic Acids. 2021 Jul 2;26:11-21.
- 35. Retrotransposons: Jump to Cancer?
Yangjun Wu,Xiaohua Wu,and Shengli Li*. Trends in Cancer. 2021 Jul;7(7):577-579.
- 34. Single-cell transcriptomics reveals the landscape of intra-tumoral heterogeneity and transcriptional activities of ECs in CC.
Chunbo Li, Luopei Guo,Shengli Li*,and Keqin Hua*. Molecular Therapy - Nucleic Acids. 2021 June 4;24:682-694.
- 33. Optimized protocol for an inducible rat model of liver tumor with chronic hepatocellular injury, inflammation, fibrosis, and cirrhosis.
Zhiao Chen, Shengli Li*, Leng Han, and Xianghuo He*. STAR Protocols.2021 Mar;2(1):100353. -
- 32. Integrated characterization of lncRNA-immune interactions in prostate cancer.
Wei Hu#, Yanru Wang#, Zhixiao Fang, Wei He*, and Shengli Li*. Frontiers in Cell and Developmental Biology.2021 Feb;9:641891.
- 31. The potential regulatory roles of circular RNAs in tumor immunology and immunotherapy.
Zhixiao Fang, Chunjie Jiang* and Shengli Li*. Frontiers in Immunology. 2021 Feb;11:617583.
- 30. 3D spheroids propel tumor characterization.
Shengli Li#,*, Zhao Zhang# and Leng Han*. Trends in Cancer.2020 Aug;6(8):622-624.
Before 2021
- 29. Systematic characterization of the dual functional effects of heat shock proteins (HSPs) in cancer hallmarks to aid development of HSP inhibitors.
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*. Genome Medicine.2020 Nov 23;12(1):101.
- 28. The mutational and transcriptional landscape of hepatocarcinogenesis in a rat model.
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*. iScience.2020 Oct 15;23(11):101690.
- 27. 3D spheroids propel tumor characterization.
Shengli Li#,*, Zhao Zhang# and Leng Han*. Trends in Cancer.2020 Aug;6(8):622-624.
- 26. Splicing Regulator p54nrb/NONO Enhances Carcinogenesis via Oncogenic Isoform Switch of BIN1 in Hepatocellular Carcinoma.
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*. Hepatology.2020 Aug;72(2):548-568.
- 25. RBP EIF2S2 promotes tumorigenesis and progression by regulating MYC-mediated inhibition via FHIT-related enhancers.
Jiwei Zhang#,*, Shengli Li#, Ling Zhang#, Juan Xu, Mingxu Song, Tingting Shao, Zhaohui Huang*, and Yongsheng Li*. Molecular Therapy.2020 Apr 8;28(4):1105-1118.
- 24. Resolving spliceosomal malfunctions advances RNA-based therapeutics.
Zhao Zhang#,*, Shengli Li#, and Leng Han*. Trends in Molecular Medicine.2020 Feb;26(2):135-137.
- 23. The genetic and pharmacogenomic landscape of snoRNAs in human cancer.
Yaoming Liu#, Hang Ruan#, Shengli Li, Youqiong Ye, Wei Hong, Jing Gong, Zhao Zhang, Ying Jing, Xiulan Zhang*, Lixia Diao* and Leng Han*. Molecular Cancer.2020 Jun 23;19(1):108.
- 22. APAatlas: decoding alternative polyadenylation across human tissues.
Wei Hong#, Hang Ruan#, Zhao Zhang, Youqiong Ye, Yaoming Liu, Shengli Li, Ying Jing, Huiwen Zhang, Lixia Diao, Han Liang and Leng Han. Nucleic Acids Research. 2020 Jan 8;48(D1):D34-D39.
- 21. Single-cell reconstruction of differentiation trajectory reveals a critical role of ETS1 in human cardiac lineage commitment.
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*. BMC Biology.2019 Nov 13;17:89.
- 20. Molecular treasures of cancer cell lines.
Shengli Li#, Zhao Zhang#, and Leng Han. Trends in Molecular Medicine.2019 Aug;25(8):657-659.
- 19. Comprehensive characterization of circular RNAs in~ 1000 human cancer cell lines.
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. Genome Medicine. 2019 Aug 26;11(1):55.
- 18. Circular RNAs as promising biomarkers in cancer: detection, function, and beyond.
Shengli Li and Leng Han. Genome Medicine.2019 Mar 20;11(1):15.
- 17. Transcriptome-wide analysis reveals the landscape of aberrant alternative splicing events in liver cancer.
Shengli Li, Zhixiang Hu, Yingjun Zhao, Shenglin Huang, and Xianghuo He. Hepatology. 2019 Jan;69(1):359-375.
- 16. Genome-wide analysis reveals that exon methylation facilitates its selective usage in the human transcriptome.
Shengli Li, Jiwei Zhang, Shenglin Huang*, and Xianghuo He*. Briefings in Bioinformatics.2018 Sep 28;19(5):754-764.
- 15. MicroRNA-129-5p regulates glycolysis and cell proliferation by targeting the glucose transporter SLC2A3 in gastric cancer cells.
Di Chen#, Hui Wang#, Jie Chen, Zhe Li, Shengli Li, Zhixiang Hu, Shenglin Huang, Yingjun Zhao*, Xianghuo He*. Frontiers in Pharmacology.2018 May 15;9:502.
- 14. The LINC01138 Drives Malignancies via Activating Arginine Methyltransferase 5 in Hepatocellular Carcinoma.
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*. Nature Communications.2018 Apr 20;9(1):1572.
- 13. A novel LIN28B tumor-specific transcript in cancer.
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*. Cell Reports. 2018 Feb 20;22(8):2016-2025.
- 12. Long noncoding RNA TSLNC8 is a tumor suppressor that inactivates the interleukin-6/STAT3 signaling pathway.
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*. Hepatology.2018 Jan;67(1):171-187.
- 11. Combinatorial epigenetic regulation of non-coding RNAs has profound effects on oncogenic pathways in breast cancer subtypes.
Juan Xu#, Zishan Wang#, Shengli Li#, Juan Chen, Jinwen Zhang, Chunjie Jiang, Zheng Zhao, Jing Li*, Yongsheng Li* and Xia Li*. Briefings in Bioinformatics.2018 Jan 1;19(1):52-64.
- 10. exoRBase: a database of circRNA, lncRNA and mRNA in human blood exosomes.
Shengli Li, Yuchen Li, Bing Chen, Jingjing Zhao, Shulin Yu, Yan Tang, Qiupeng Zheng, Yan Li, Peng Wang, Xianghuo He, and Shenglin Huang. Nucleic Acids Research.2018 Jan 4;46(D1):D106-D112.
- 9. Profiling and co-expression network analysis of learned helplessness regulated mRNAs and lncRNAs in the mouse hippocampus.
Chaoqun Li, Feifei Cao, Shengli Li, Shenglin Huang, Wei Li*, Nashat Abumaria*. Frontiers in Molecular Neuroscience. 2018 Jan 11;10:454.
- 8. MetaLnc9 facilitates lung cancer metastasis via a PGK1-activated AKT/mTOR pathway.
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*. Cancer Research.2017 Nov 1;77(21):5782-5794.
- 7. Transcriptomic analyses of RNA-binding proteins reveal eIF3c promotes cell proliferation in hepatocellular carcinoma.
Tangjian Li#, Shengli Li#, Di Chen, Bing Chen, Tao Yu, Fangyu Zhao, Qifeng Wang, Ming Yao, Shenglin Huang, Zhiao Chen*, and Xianghuo He*. Cancer Science.2017 May;108(5):877-885.
- 6. Functional dissection of virus-human crosstalk mediated by miRNAs based on the VmiReg database.
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*. Molecular BioSystems.2015 May;11(5):1319-28.
- 5. Genome-wide DNA methylome analysis reveals epigenetically dysregulated non-coding RNAs in human breast cancer.
Yongsheng Li#, Yunpeng Zhang#, Shengli Li#, Jianping Lu, Juan Chen, Yuan Wang, Yixue Li*, Juan Xu*, and Xia Li*. Scientific Reports.2015 Mar 5;5:8790.
- 4. Comparative epigenetic analyses reveal distinct patterns of oncogenic pathways activation in breast cancer subtypes.
Yongsheng Li#, Shengli Li#, Juan Chen, Tingting Shao, Chunjie Jiang, Yuan Wang, Hong Chen, Juan Xu* and Xia Li*. Human Molecular Genetics.2014 Oct 15;23(20):5378-93.
- 3. Integrating analysis reveals microRNA-mediated pathway crosstalk among Crohn's disease, ulcerative colitis and colorectal cancer.
Jing Bai#, Yongsheng Li#, Tingting shao, Zheng Zhao, Yuan Wang, Aiwei Wu, Hong Chen, Shengli Li, Chunjie Jiang, Juan Xu* , and Xia Li*. Molecular BioSystems.2014 Jul 29;10(9):2317-28.
- 2. Comprehensive analysis of the functional microRNA-mRNA regulatory network identifies miRNA signatures associated with glioma malignant progression.
Yongsheng Li, Juan Xu, Hong Chen, Jing Bai, Shengli Li, Zheng Zhao, Tingting Shao, Tao Jiang, Huan Ren*, Chunsheng Kang* and Xia Li*. Nucleic Acids Research.2013 Dec;41(22):e203.
- 1. Characterizing genes with distinct methylation patterns in the context of protein-protein interaction network: application to human brain tissues.
Yongsheng Li#, Juan Xu#, Hong Chen#, Zheng Zhao, Shengli Li, Jing Bai, Aiwei Wu, Chunjie Jiang, Yuan Wang, Bin Su, and Xia Li. PLOS ONE.2013 Jun 12;8(6):e65871.