研究性论文（Research article）：

1. 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 Apr 3. doi: 10.1038/s41596-025-01158-4.

2. Liwen Zhang*, Xinxin Liu*, Yu Zhang*, Lang Qin*, Shijia Pan, Xueqi Yan, Sen Dong, Zerong Feng, Song-jia Fan, Rusong Zhao, Xueying Gao, Shigang Zhao^#, Junchao Shi^#, Han Zhao^#, Ying Zhang^#, Zi-Jiang Chen. Peripheral Blood RNA Modifications as a Novel Diagnostic Signature for Polycystic Ovary Syndrome. Science China Life Sciences, 2025, in press.

3. Yan J, Li S^#, Zhang Y^#, Hao A, Zhao Q. ZetaDesign: an end-to-end deep learning method for protein sequence design and side-chain packing. Briefings in Bioinformatics 2023 Jul 20;24(4):bbad257.

4. Qu Y, Zhang J, Guo S, Zhang L, Qian J, Zhu X, Duan E, Zhang Y. Three-Dimensional Visualization of Mouse Endometrial Remodeling After Superovulation. Frontiers in Cell and Development Biology, 2022, Jun 29;10:933852

5. Zhang L, Li Y, Wang J, Hong C, Lu W, Qu Y, Black S, Chen Q, Zhou Z, Jin W, Duan E, Tang H, Zhang Y. RNA Modification Signature of Peripheral Blood as a Potential Diagnostic Marker for Pulmonary Hypertension. Hypertension. 2022 Mar;79(3):e67-e69.

6. Junchao Shi^*, Yunfang Zhang^*, Dongmei Tan^*, Xudong Zhang^*, Menghong Yan^*, Ying Zhang^*, Reuben Franklin^*, Marta Shahbazi, Kirsty Mackinlay, Reuben Franklin, Shichao Liu, Bernhard Kuhle, Emma R. James, Liwen Zhang, Yongchun Qu, Qiwei Zhai, Wenxin Zhao, Linlin Zhao, Changcheng Zhou, Weifeng Gu, Jernej Murn, Jingtao Guo, Douglas T. Carrell, Yinsheng Wang, Xuemei Chen, Bradley R. Cairns, Xiang-lei Yang, Paul Schimmel, Sihem Cheloufi, Magdalena Zernicka-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;23(4):424-436

7. Yongcun Qu^*, Qi Chen^*, Shanshan Guo^*, Chiyuan Ma, Yonggang Lu, Junchao Shi, Shichao Liu, Tong Zhou, Taichi Noda, Jingjing Qian, Liwen Zhang, Xili Zhu, Xiaohua Lei, Yujing Cao, Wei Li, Wei Li, Nicolas Plachta, Martin M. Matzuk, Masahito Ikawa, Enkui Duan^#, Ying Zhang^#, Hongmei Wang^#. Cooperation-based sperm clusters mediate sperm oviduct entry and fertilization. Protein & Cell. 2021, 2021 Oct;12(10):810-817.

8. Lei X^#, Cao Y, Ma B, Zhang Y, Ning L, Qian J, Zhang L, Qu Y, Zhang T, Li D, Chen Q, Shi J, Zhang X, Ma C, Zhang Y^#, Duan E^#. Development of mouse preimplantation embryos in space. National Science Review. 2020 doi.org/10.1093/nsr/nwaa062

9. Zhang Y, Qian J, Oren Z, Mustafa B, Ariel J.J, Dan G, Duan E, David E^#. Analysis of in vivo uterine peristalsis in the non-pregnant female mouse. Interface Focus. 2019 Aug 6;9(4):20180082.

10. Qian J, Zhang Y, Qu Y, Zhang L, Shi J, Zhang X, Liu S, Kim BH, Hwang SJ, Zhou T, Chen Q, Ward SM, Duan E^#, Zhang Y^#. Caffeine consumption during early pregnancy impairs oviductal embryo transport, embryonic development and uterine receptivity in mice. Biology of Reproduction 2018; Dec 1;99(6):1266-1275

11. Zhang Y^*, Zhang X^*, Shi J^*, Tuorto F^*, Li X^*, Liu Y, Liebers R, Zhang L, Qu Y, Qian J, Pahima M, Liu Y, Yan M, Cao z, Cao Y, Peng H, Liu S, Wang Y, Zheng H, Woolsey R, Zhai Q, Li L, Zhou T, Yan W, Lyko F, Zhang Y^#, Zhou Q^#, Duan E^#, Chen Q^#. Dnmt2 mediates intergenerational transmission of paternally acquired metabolic disorders through sperm small non-coding RNAs. Nature Cell Biology 2018; 20:535-540. (获Nature Reviews Endocrinology专题点评)

12. Zhang Y^*, Chen Q^*, Zhang H^*, Wang Q^*, Li R, Jin Y, Wang H, Ma T^#, Qiao J^#, Duan E^#. Aquaporin-dependent excessive intrauterine fluid accumulation is a major contributor in hyper-estrogen induced aberrant embryo implantation. Cell Research. 2015 Jan;25(1):139-42. (SMPC新闻采访/报道)

13. Zhang Y^*, Zhang Y^*, Shi J^*, Zhang H, Cao Z, Gao X, Ren W, Ning Y, Ning L, Cao Y, Chen Y, Ji W, Chen ZJ^#, Chen Q^#, Duan E^#. Identification and characterization of an ancient class of small RNAs enriched in serum associating with active infection. Journal of Molecular Cell Biology, 2014, 6 (2): 172-174. (封面故事 & 编辑推荐)

14. Chen Q^*, Zhang Y^*, Peng H, Lei L, Kuang H, Zhang L, Ning L, Cao Y, Duan E. Transient {beta}2-adrenoceptor activation confers pregnancy loss by disrupting embryo spacing at implantation. Journal of Biological Chemistry 2011, 286: 4349-4356.

综述（Reviews）:

1. Qian J, Chen Q, Sean M. Ward, Duan E^#, Zhang Y^#. Impacts of caffeine during pregnancy. Trends in Endocrinology & Metabolism. 2020 Mar;31(3):218-227. (封面故事)

2. Zhang Y, Chen Q^#. The expanding repertoire of hereditary information carriers. Development. 2019 Mar 15;146(6). pii: dev170902

3. Zhang Y*, Wang Q*, Wang H, Duan E. Uterine Fluid in Pregnancy: A Biological and Clinical Outlook. Trends in Molecular Medicine. 2017 Jul;23(7):604-614. (封面故事 & Cell Press点评 &入选F1000)

4. Chen Q*, Zhang Y*, Elad D, Jaffa AJ, Cao Y, Ye X, Duan E. Navigating the site for embryo implantation: biomechanical and molecular regulation of intrauterine embryo distribution. Molecular Aspects of Medicine, 2013, Oct;34(5):1024-42.

观点（Comments）

1. Zhang Y^#, Shi J, Chen Q#. Towards the understanding of "Herbal RNA Code" for traditional medicine. Cell Research, 2023, Dec;33(12):900-901.

2. Zhang Y^#, Chen Q^#. Human sperm RNA code senses dietary sugar. Nature Reviews Endocrinology. 2020 Apr;16(4):200-201.

3. Zhang Y, Duan E^#. LncRNAs and paraspeckles predict cell fate in early mouse embryo. Biology of Reproduction. 2019 May 1;100(5):1129-1131.