Introduction
The sncRNAomics Group is at the forefront of the exploration into small noncoding RNA (sncRNA) omics. Through a synergy of molecular biology and advanced bioinformatics, we delve into the intricate world of epigenetic regulatory mechanisms governing sncRNA molecules and their modifications. Our research is firmly rooted in three primary directions:
Innovative sncRNA sequencing techniques, analysis Tools, and databases: We are pioneers in developing cutting-edge sncRNA sequencing methods, sophisticated analysis tools, and comprehensive databases. Our commitment to refining these essential aspects underscores our pursuit of deeper insights into sncRNA-related phenomena.
Unveiling sncRNA biogenesis and mechanisms of action: At the core of our work lies an ardent curiosity about the biogenesis and mechanisms underlying the actions of sncRNAs. Through meticulous investigation, we unravel the intricacies of how these small but potent molecules shape cellular processes.
Advancing clinical applications through the discovery of diagnostic biomarkers and small molecule drugs: Our dedication extends beyond the laboratory, as we actively seek to translate our findings into tangible clinical benefits. By identifying diagnostic biomarkers and uncovering potential small molecule drugs rooted in sncRNAs and their modification profiles, we aspire to contribute to the advancement of medical practices.
At the SncRNAomics Group, our journey bridges the realms of discovery, innovation, and application, paving the way for a deeper understanding of sncRNA and its far-reaching implications.
Group leader
Dr. SHI Junchao is a Principal Investigator of the sncRNAomics group in CAS Key Laboratory of Genome Sciences & Information in Beijing Institute of Genomics, Chinese Academy of Sciences (China National Center for Bioinformation). Dr. Shi obtained his Ph.D. in Genetics, Genomics & Bioinformatics at University of California, Riverside (advisors: Dr. Qi Chen and Dr. Tong Zhou). He also received his M.S. (summa cum laude) in Developmental Biology at University of Chinese academy of Sciences, China, and his B.S. (summa cum laude) in Biotechnology (animal) at Jilin University, China.
Learn more about SHI Junchao's lab
Selected Publications
(* indicates equal contributions, # indicates corresponding author)
1. Ying Zhang#, Junchao Shi#, Qi Chen, Towards the understanding of "Herbal RNA Code" for traditional medicine, Cell Research 2023 Jul 21. doi: 10.1038/s41422-023-00851-x.
2. Rebecca Hernandez*, Junchao Shi*, Jingwei Liu, Xiuchun Li, Jake Wu, Linlin Zhao, Tong Zhou, Qi Chen, Changcheng Zhou#, PANDORA-Seq unveils the hidden small noncoding RNA landscape in atherosclerosis of LDL receptor-deficient mice, Journal of Lipid Research 2023 Apr;64(4):100352. doi: 10.1016/j.jlr.2023.100352. (Cover Story)
3. Junchao Shi, Tong Zhou#, Qi Chen#, Exploring the expanding universe of small RNAs, Nature Cell Biology. 2022 Apr;24(4):415-423. doi: 10.1038/s41556-022-00880-5. (Cover Story)
4. Junchao Shi*, Yunfang Zhang*, Dongmei Tan*, Xudong Zhang*, Menghong Yan*, Ying Zhang*, Reuben Franklin*, Marta Shahbazi, Kirsty Mackinlay, Shichao Liu, Bernhard 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, Yinsheng Wang, Xuemei Chen, Bradley R Cairns, Xiang-lei Yang, Paul Schimmel, 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. doi: 10.1038/s41556-021-00652-7.
5. Wanjun Gu*, Junchao Shi*, Hui Liu*, Xudong Zhang*, Jin J Zhou, Musheng Li, Dandan Zhou, Rui Li, Jingzhu Lv, Guoxia Wen, Shanshan Zhu, Ting Qi, Wei Li, Xiaojing Wang, Zhaohua Wang, Hua Zhu, Changcheng Zhou, Kenneth S Knox, Ting Wang, Qi Chen#, Zhongqing Qian#, Tong Zhou#, Peripheral blood non-canonical small non-coding RNAs as novel biomarkers in lung cancer, Molecular Cancer. 2020 Nov 12;19(1):159. doi: 10.1186/s12943-020-01280-9.
6. Yunfang Zhang*, Junchao Shi*, Minoo Rassoulzadegan, Francesca Tuorto, Qi Chen#, Sperm RNA code programmes the metabolic health of offspring, Nature Reviews Endocrinology. 2019 Aug;15(8):489-498. doi: 10.1038/s41574-019-0226-2.
7. Junchao 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. doi: 10.1016/j.tibs.2018.09.007
8. Junchao Shi#, Eun-A Ko, Kenton M. Sanders, Qi Chen#, Tong Zhou#, SPORTS1.0: a tool for annotating and profiling non-coding RNAs optimized for rRNA- and tRNA- derived small RNAs, Genomics Proteomics & Bioinformatics. 2018 Apr;16(2):144-151.
9. Qi Chen*, Junchao Shi*, Yi Tao, Magdalena Zernicka-Goetz#, Tracing the origin of heterogeneity and symmetry breaking in the early mammalian embryo, Nature Communications. 2018 May 8;9(1):1819.
10. Yunfang Zhang*, Xudong Zhang*, Junchao Shi*, Francesca Tuorto*, Xin Li*, Yusheng Liu, Reinhard Liebers, Liwen Zhang, Yongcun Qu, Jingjing Qian, Maya Pahima, Ying Liu, Menghong Yan, Zhonghong Cao, Xiaohua Lei, Yujing Cao, Hongying Peng, Shichao Liu, Yue Wang, Huili Zheng, Rebekah Woolsey, David Quilici, Qiwei Zhai, Lei Li, Tong Zhou, Wei Yan, Frank Lyko, Ying Zhang#, Qi Zhou#, Enkui Duan#, Qi Chen#, Dnmt2-dependent intergenerational transmission of paternally acquired metabolic disorders via sperm RNAs. Nature Cell Biology. 2018 May;20(5):535-540. (Highlighted in Nature Reviews Endocrinology. 2018 14, 446-447)
11. Junchao Shi, Xudong Zhang, Ying Liu, Qi Chen#, Epigenetic information in gametes: Gaming from before fertilization, Physics of Life Review. 2017 Mar;20:146-149.
12. Junchao Shi, Qi Chen, Enkui Duan#, Mammalian transgenerational inheritance of acquired traits via germline transmission, Chinese Bulletin of Life Sciences. 2017 29(1).
13. Junchao Shi*, Yunfang Zhang*, Qi Chen#, Molecular carriers of acquired inheritance: absence of evidence is not evidence of absence, Environmental Epigenetics. 2016 Aug 3;2(2):dvw014.
14. 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#, Qi Zhou#, Sperm tsRNAs contribute to intergenerational inheritance of an acquired metabolic disorder, Science. 2016 Jan 22;351(6271):397-400. (Highlighted in Science. 2016 351:13; Highlighted in Nature Reviews Genetics. 2016 doi:10.1038/nrg.2016.1)
15. Junchao Shi*, Qi Chen*#, Xin Li*, Xiudeng Zheng*, Ying Zhang, Jie Qiao, Fuchou Tang, Yi Tao#, Qi Zhou#, Enkui Duan#, Dynamic transcriptional symmetry-breaking in pre-implantation mammalian embryo development revealed by single-cell RNA-seq, Development. 2015 Oct 15;142(20):3468-77. (Highlighted in Development. 142: e2OO2)
16. 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#, 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 Apr;6(2):172-4. (Editor’s Recommendation & Cover Story)
17. Hongying Peng*, Junchao Shi*, Ying Zhang, He Zhang, Shangying Liao, Wei Li, Li Lei, Chunsheng Han, Lina Ning, Yujing Cao, Qi Zhou, Qi Chen#, Enkui Duan#, A novel class of tRNA-derived small RNAs extremely enriched in mature mouse sperm, Cell Research. 2012 Nov;22(11):1609-12. (Highlighted in Cell Research. 2013 23:18-19)
Group Members
Staff:
Dr. WANG fang (Assistant Researcher)
Graduate Students：
FENG zerong (PhD student, 2023)
HUANG Ao (Master student, 2023)
Contact：
Email: shijc[at]big.ac.cn
