Publications

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* Co-first authors; # Co-corresponding authors

2026

• Yan Zhu, Xin Wang, Yun Li, Wenlin Jiang, Zheng Wu, San Xu, Zixin Tan, Aike Wu, Yisheng Cai, Yandi Yang, Xin Xiao, Xinwei Kuang, Guangtong Deng, Yiya Zhang, Mengting Chen, Ji Li#, Yunfang Zhang#, Zhili Deng#. Dynamic tRNA modification landscapes reveal METTL1 in fibroblasts as a central regulator of aging. Science China Life Sciences. (2026). [HTML] [PDF]

• Cao Zheng*, Zongyu Yu*, Xin Wang*, Dongqi Jiang, Yafei Yuan, Ze Shu, Yiting Yang#, Yunfang Zhang#. Deciphering RNA modification dynamics during spermatogenesis and sperm maturation. Science China Life Sciences. (2026). [HTML] [PDF]

• Yun Li*, Xin Wang*, Ruofan Huang*, Haoquan Yu, You Wu, Ze Shu, Wenlin Jiang, Zheng Cao, Zongyu Yu, Hongyan Li, Rushuang Yan, Yawei Gao#, Xiao-Ou Zhang#, Yunfang Zhang#. Deciphering tRNA Repertoires and Translation Coordination during Mouse Early Embryogenesis by ORACLE-tRNAseq. Nature Communications. (2026) 17(1):5893. [HTML] [PDF]

• Shijia Pan, Liwen Zhang, Yunfang Zhang#, Junchao Shi#, Ying Zhang#. RNA modifications: disease biomarkers and signaling molecules. Trends in Endocrinology & Metabolism. (2026) Apr; 37(4):297–300. doi: 10.1016/j.tem.2026.01.004. [HTML] [PDF]

2025

• Xiaoli Zhu*, Caoling Xu*, Xue Jiang, Jiaqi Zou, Wenqing Li, Xuemei Xing, Xiaoxiao Gao, Jiao Lei, Fei Meng, Xin Wang, Yuzhang Zhu, Yu Cheng, Muhammad Azhar, Wenjie Han, Ge Lin, Yunfang Zhang#, Ge Shan#, Shen Zhang#, Jianqiang Bao#. NAT10 primes a posttranscriptional repertoire essential for the maintenance of spermatogonial homeostasis. Science Bulletin. (2025) 70(6):842–846. [HTML] [PDF]

• Junchao Shi#, Yunfang Zhang#, Yun Li, Liwen Zhang, Xudong Zhang, Menghong Yan, Qi Chen, Ying Zhang#. Optimized identification and characterization of small RNAs with PANDORA-seq. Nature Protocols. (2025) 20(11):3314–3338. [HTML] [PDF]

• Zhibin Li*, Shuying Li*, Yufeng Xiao*, Junfeng Guo*, Jianchun Zhou, Yang Chen, Juan Yang, Chunli Gong, Bing He, Yuyun Wu, Nannan Gao, Huan Yang, Limin Gao, Hua Hu#, Yunfang Zhang#, Shiming Yang#. Hypoxia exposure impairs male fertility via inhibiting Septin2-mediated spermatogonial proliferation. Human Reproduction Open. (2025) 2025(3):hoaf027. [HTML] [PDF]

• Ruofan Huang*, Yiting Yang*, Wenlin Jiang, Zheng Cao, Junchao Shi#, Xiao-Ou Zhang#, Yunfang Zhang#. PANDORA-seq reveals human sperm sncRNA signature endowed with sperm quality assessment. Genes & Diseases. (2025) 101807. [HTML] [PDF]

2024

• Yun Li*, Zongyu Yu*, Wenlin Jiang, Xinyi Lyu, Ailian Guo, Xiaorui Sun, Yiting Yang#, Yunfang Zhang#. tRNA and tsRNA: From Heterogeneity to Multifaceted Regulators. Biomolecules. (2024) 14(10):1340. [HTML] [PDF]

• Yiting Yang*, Yun Li*, Ailian Guo, Xinyi Lv, Xin Wang, Zheng Cao, Ze Shu, Yunfang Zhang#​. Advances in the Biogenesis and Functional Research of tRNA-Derived Small Non-Coding RNA. Chinese Journal of Cell Biology. (2024), 46(2): 201–213. [HTML] [PDF]

• Xin Wang, Zheng Cao, Yiting Yang, Yun Li, Yunfang Zhang#​. Progress in RNA mediated intergenerational / transgenerational epigenetic inheritance of acquired traits. Science China - Life sciences. (2024), Accepted. [HTML] [PDF]

• Pan Zhao*, Lin Xia*, Dan Chen*, Wei Xu*, Huanping Guo, Yinying Xu, Bingbing Yan, Xiao Wu, Yuxia Li, Yunfang Zhang#​, Xi Zhang#. METTL1 mediated tRNA m7G modification promotes leukaemogenesis of AML via tRNA regulated translational control. Experimental Hematology & Oncology. (2024) 13:8. [HTML] [PDF]

2023

• Huanping Guo*, Lin Xia* , Wei Wang*, Wei Xu*, Xipeng Shen, Xiao Wu, Tong He, Xuelin Jiang, Yinying Xu, Pan Zhao, Dongmei Tan, Xi Zhang#, Yunfang Zhang#. Hypoxia induces alterations in tRNA modifications involved in translational control. BMC Biology. (2023) Feb 21;21(1):39. [HTML] [PDF]

• Lin Xia*, Huanping Guo*, Xiao Wu*, Yinying Xu*, Pan Zhao*, Bingbing Yan, Yunjing Zeng, Yundi He, Dan Chen, Robert Peter Gale, Yunfang Zhang#​, Xi Zhang# . Human circulating small non-coding RNA signature as a non-invasive biomarker in clinical diagnosis of acute myeloid leukaemia. Theranostics. (2023) Feb 13;13(4):1289-1301. [HTML] [PDF]

2022

• Huanping Guo*, Xipeng Shen*, Hua Hu*, Peng Zhou, Tong He, Lin Xia, Dongmei Tan，Xi Zhang#, and Yunfang Zhang # . Alteration of RNA modification signature in human sperm correlates with sperm motility. Molecular Human Reproduction. (2022) Aug 12; 28(9):gaac031. [HTML] [PDF]

• Tong He*, Huanping Guo*, Lin Xia*, Xipeng Shen, Yun Huang, Xiao Wu, Xuelin Jiang, Yinying Xu, Yi Tan, Yunfang Zhang#, Dongmei Tan#. Alterations of RNA Modification in Mouse Germ Cell-2 Spermatids Under Hypoxic Stress. Frontiers in Molecular Biosciences. (2022) Jun 14; 9:871737. [HTML] [PDF]

• Bin Wang, Lin Xia, Dan Zhu, Hongtao Zeng, Bin Wei, Likui Lu, Weisheng Li, Yajun Shi, Jingliu Liu, Yunfang Zhang# & Mao Sun#. Paternal High-Fat Diet Altered Sperm 5‘tsRNA-Gly-GCC Is Associated with Enhanced Gluconeogenesis in the Offspring. Frontiers in Molecular Biosciences. (2022) Apr 11;9:857875. [HTML] [PDF]

2021

• Junchao Shi*, Yunfang Zhang*, Dongmei Tan*, Xudong Zhang*, Menghong Yan*, Ying Zhang*, Marta Shahbazi, Kirsty Mackinlay, Reuben Franklin, Shichao Liu, Bemhard Kuhle, Emma R, James, Liwen Zhang, Yongcun Qu, Qiwei Zhai, Wenxin Zhao, Linlin Zhao, Changcheng Zhou, Weifeng Gu, Jernej Murn, Jingtao Guo, Douglas T. Carrell, Yingsheng Wang, Xuemei Chen, Bradley R. Cairms, Xianglei Yang, Paul Schimmel, Magdalena Zemicka-Goetz, Sihem Cheloufi#, Ying Zhang#, Tong Zhou#, Qi Chen#. PANDORA-Seq expands the repertoire of regulatory small RNAs by overcoming RNA modifications. Nature Cell Biology. (2021) Apr 05; 23(4), 424-436. [HTML] [PDF]

• Tong He*, Huanping Guo*, Xipeng Shen*, Xiao Wu, Lin Xia, Xuelin Jiang, Yinying Xu, Dan Chen, Yunfang Zhang# , Dongmei Tan#, Yi Tan#. Hypoxia-induced alteration of RNA modifications in the mouse testis and sperm. Biology of Reproduction. (2021) Nov 15;105(5):1171-1178. [HTML] [PDF]

• Zheng Wang*, Chengyan Chai*, Rui Wang, Yimei Feng, Lei Huang, Yiming Zhang, Xia Xiao, Shijie Yang, Yunfang Zhang, Xi Zhang#. Single-cell transcriptome atlas of human mesenchymal stem cells exploring cellular heterogeneity. Clinical and Translational Medicine. (2021);11:e650. [HTML] [PDF]

2020

• 杨程*；夏琳*；赫童；苟阳；唐永杰；彭贤贵；张曦#；张云芳#​。表观遗传学修饰在血液肿瘤中的研究进展。 《生物化学与生物物理进展》. (2020) 年第 05 期。[HTML] [PDF]

• 作为副主编撰写了 《医话血液》 科普书籍，重庆大学出版社，2020年10月1日；获评国家精品科普书籍。

• Xiaohua Lei#*, Yujing Cao*, Baohua Ma*, Yunfang Zhang, Lina Ning, Jingjing Qian, Liwen Zhang, Yongcun Qu, Tao Zhang, Dehong Li, Qi Chen, Junchao Shi, Xudong Zhang, Chiyuan Ma, Ying Zhang#; Enkui Duan#; Development of mouse preimplantation embryos in space. National Science Reviews. (2020), nsr(nwaa062). [HTML] [PDF]

2019

• Yunfang Zhang*, Junchao Shi*, Minoo Rassoulzadegan, Francesca Tuorto and Qi Chen#. Sperm RNA code programmes the metabolic health of offspring. Nature Reviews Endocrinology. (2019) Jun 24; (15):489–498. [HTML] [PDF]

• Jun Chao Shi*, Yunfang Zhang* , Tong Zhou#, Qi Chen#. tsRNAs: The Swiss Army Knife for Translational Regulation. Trends in Biochemical Sciences. (2019) Mar;44(3):185-189. [HTML] [PDF]

2018

• Yunfang Zhang*, Xudong Zhang*, Junchao Shi*, Francesca Tuorto*, Xin Li*, Yusheng Liu, Reinhard Liebers, Tong Zhou, Wei Yan, Frank Lyko, Ying Zhang#, Qi Zhou#, Enkui Duan#, Qi Chen#. Dnmt2 mediates intergenerational transmission of paternally acquired metabolic disorders through sperm small non-coding RNAs. Nature Cell Biology. (2018) April 24(20),535-540. [HTML] [PDF]

  -Highlighted in Nature Reviews Endocrinology;

• 张云芳, 张莹, 陈琦#, 段恩奎#, 精子 RNA 及 RNA 修饰在获得性遗传中的研究进展。《生命科学》 (2018), 30(11): 1202-1209. [HTML] [PDF]

• Jingjing Qian, Yunfang Zhang, Yongcun Qu, Liwen Zhang, Junchao Shi, Xudong Zhang, Shichao Liu, Kim BH, Hwang SJ, Tong Zhou, Qi Chen, Ward SM, Enkui Duan#, Ying Zhang#, Caffeine consumption during early pregnancy impairs oviductal embryo transport, embryonic development and uterine receptivity in mice. Biology of Reproduction. (2018), 99(6): 1266-1275. [HTML] [PDF]

Before 2018

• Yunfang Zhang* Junchao Shi, Qi Chen#. tsRNAs: new players in mammalian retrotransposon control. Cell Research. (2017) Nov;27(11):1307-1308. [HTML] [PDF]

• Qi Chen*, Menghong Yan*, Zhonghong Cao*, Xin Li*, Yunfang Zhang* , Junchao Shi*, Gui-hai Feng, Hongying Peng, Xudong Zhang, Ying Zhang, Jingjing Qian, Enkui Duan#, Qiwei Zhai# and Qi Zhou#. Sperm tsRNAs contribute to intergenerational inheritance of an acquired metabolic disorder. Science. (2016) Jan 22;351(6271):397-400. [HTML] [PDF]

  -News story by Science

  -Highlighted in Nat Rev Genet, Cell Metab, Cell Res, FASEB J, Bio Reprod, and Science Bulletin.

• Junchao Shi*, Yunfang Zhang* and Qi Chen#. Molecular carriers of acquired inheritance: absence of evidence is not evidence of absence. Environmental Epigenetics. (2016) 2 (2): dvw014. [HTML] [PDF]

• Yunfang Zhang* , Ying Zhang*, Junchao Shi*, He Zhang, Zhonghong Cao, Xuan Gao, Wanhua Ren, Yunna Ning, Lina Ning, Yujing Cao, Yongchang Chen, Weizhi Ji, Zi-jiang Chen^#^, Qi Chen#, and Enkui Duan#. Identification and characterization of an ancient class of small RNAs enriched in serum associating with active infection. Journal of Molecular Cell Biology. (2014) 6:172-174. [HTML] [PDF]

  -Cover Story

  -Editor’s Recommendation

• Lina Ning*, Xiaohua Lei*, Yujing Cao, Yunfang Zhang, Zhonghong Cao, Qi Chen, Enkui Duan#. Effect of Short-Term Hypergravity Treatment on Mouse 2-Cell Embryo Development. Microgravity Sci. Technol. (2015) 27:465–471. [HTML] [PDF]

• He Zhang*, Ying Zhang*, Huashan Zhao, Yunfang Zhang, Qi Chen, Hongying Peng, Li Lei Jingqiao Qiao, Junchao Shi, Zhonghong Cao, Enkui Duan#, Yaping Jin#. Hormonal regulation of ovarian bursa fluid in mice and involvement of aquaporins. PLOS ONE. (2013) May 22;8(5):e63823. [HTML] [PDF]