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  Shunmin He, Ph.D, Prof.

  Principal Investigator

  Executive Deputy Director, Center for Big Data Research in Health,

  Key laboratory of RNA Biology, IBP, CAS 

  Professor, University of Chinese Academy of Sciences

  Bioinformatics, non-coding RNA and epigenetics

  E-mail:heshunmin(AT)ibp.ac.cn

  Tel: +861064887032

  Chinese personal homepage  

Biography & Introduction

2017 - present  Principal Investigator, Institute of Biophysics, Chinese Academy of Sciences;

                         Executive Deputy Director, Center for Big Data Research in Health;

                         Professor, University of Chinese Academy of Sciences

2016/04 - 2016/07  Visiting scholar, Cellular & Molecular Medicine, University of California San Diego: La Jolla, CA, US

2010 - 2011  Postdoctoral Fellow in Department of Biostatistics and Computational Biology, Harvard Medical School/Dana-Farber Cancer Institute and School of Public Health, Boston, MA.

2009 - 2017  Associate Investigator, and then Investigator, Key Laboratory of Zoological Systematics and Evolution, Chinese Academy of Sciences.

2004 - 2009  Ph.D. in Bioinformatics, Institute of Biophysics, Chinese Academy of Sciences;

                     Thesis: Function Research on Non-coding RNAs: From Transcriptome to Interaction Network

                     Advisor: Chen Runsheng

2001 - 2004  Software Engineer, Beijing NEC IC Design Co. Ltd.

1997 - 2001  B.S. in Electronic Engineering, Nanjin University of Science and Technology.

Research Interests:

1. Based on large-scale population cohort genome-wide data to construct of a big data multi-omics integration analysis platform.

2. Based on single-cell multi-omics to study the occurrence, development and metastasis of tumors.

3. Integration and association analysis of genomics data and clinical information, focused on variation in non-coding and regulatory regions.

Selected Publication

1. Xueye Teng#, Xiaomin Chen#, Hua Xue#, Yiheng Tang, Peng Zhang, Quan Kang, Yajing Hao, Runsheng Chen*, Yi Zhao*, Shunmin He*. (2019). NPInter v4.0: An integrated database of ncRNA interactions. Nucleic Acids Res
DOI:
https://doi.org/10.1093/nar/gkz969
 

2. Shunmin He#, Guoqiang Zhang#, Jiajia Wang#, Yaji Gao#, Ruidi sun, Zhijie Cao, Zhenping Chen, Xiudeng Zheng, Jiao Yuan, Yuewan Luo, Xiaona Wang, Wenxin Zhang, Peng Zhang, Yi Zhao, Chuan He, Yi Tao*, Qinmiao Sun*, Dahua Chen*. (2019). 6mA-DNA-binding factor Jumu controls maternal-to-zygotic transition upstream of Zelda. Nature Communication. 10(1). 2219.
DOI:
https://doi.org/10.1038/s41467-019-10202-3

3. The RNAcentral Consortium. (2019). RNAcentral: a hub of information for non-coding RNA sequences. Nucleic Acids Res.
DOI:
https://doi.org/10.1093/nar/gky1034

4. Jiajia Wang#, Peng Zhang#, Yiping Lu#, Yanyan Li, Yu Zheng, Yunchao Kan, Runsheng Chen*, Shunmin He*. (2019). piRBase: a comprehensive database of piRNA sequences. Nucleic Acids Res.
DOI:
https://doi.org/10.1093/nar/gky1043

5. Liang Chen#, Jia-Yu Chen#, Yi-Jou Huang#, Ying Gu, Jinsong Qiu, Hao Qian, Changwei Shao, Xuan Zhang, Jing Hu, Hairi Li, Shunmin He, Yu Zhou, Omar Abdel-Wahab, Dong-Er Zhang*, Xiang-Dong Fu*. (2018). The Augmented R-Loop Is a Unifying Mechanism for Myelodysplastic Syndromes Induced by High-Risk Splicing Factor Mutations. Molecular Cell. 69(3), 412-425
DOI:
https://doi.org/10.1016/j.molcel.2017.12.029

6. Xiaowei Chen, Yajing Hao, Ya Cui, Zhen Fan, Shunmin He, Jianjun Luo, Runsheng Chen. (2017). LncVar: a database of genetic variation associated with long non-coding genes. Bioinformatics. 33(1), 112-118
DOI:
https://doi.org/10.1093/bioinformatics/btw581

7. Jiao Yuan#, Peng Zhang#, Ya Cui, Jiajia Wang, Geir Skogerbo, Da-Wei Huang, Runsheng Chen*, Shunmin He*. (2016). Computational identification of piRNA targets on mouse mRNAs. Bioinformatics. 32,1170-1177
DOI:
https://doi.org/10.1093/bioinformatics/btv729

8. Guoqiang Zhang#, Hua Huang#, Di Liu#, Ying Cheng, Xiaoling Liu, Wenxin Zhang, Ruichuan Yin, Dapeng Zhang, Peng Zhang, Jianzhao Liu, Chaoyi Li, Baodong Liu, Yuewan Luo, Yuanxiang Zhu, Ning Zhang, Shunmin He, Chuan He, Hailin Wang*, Dahua Chen*. (2015). N(6)-methyladenine DNA modification in Drosophila. Cell. 161(4): 893-906.
DOI:
https://doi.org/10.1016/j.cell.2015.04.018

9. Peng Zhang#, Jun-Yan Kang#, Lan-Tao Gou#, Jiajia Wang, Yuanchao Xue, Geir Skogerboe, Peng Dai, Da-Wei Huang, Runsheng Chen, Xiang-Dong Fu*, Mo-Fang Liu*, Shunmin He*. (2015) MIWI and piRNA-mediated cleavage of messenger RNAs in mouse testes. Cell Research. 25(2): 193-207.
DOI:
https://doi.org/10.1038/cr.2015.4

10. Peng Zhang#, Xiaohui Si#, Geir Skogerbo, Jiajia Wang, Dongya Cui, Yongxing Li, Xubin Sun, Li Liu, Baofa Sun, Runsheng Chen*, Shunmin He*, Da-wei Huang*. (2014) piRBase: a web resource assisting piRNA functional study. Database (Oxford). 2014, bau110.
DOI:
https://doi.org/10.1093/database/bau110

11. JiaJia Wang#, Dongya Cui#, Tengfei Xiao#, Xubing Sun, Peng Zhang, Runsheng Chen*, Shunmin He*, Da-Wei Huang*. (2014) The influences of PRG-1 on the expression of small RNAs and mRNAs. BMC Genomics. 15:321.
DOI:
https://doi.org/10.1186/1471-2164-15-321

12. Jin-Hua Xiao#, Zhen Yue#, Ling-Yi Jia#, Xin-Hua Yang#, Li-Hua Niu#, Zhuo Wang#, Peng Zhang#, Bao-Fa Sun, Shunmin He,…James M Cook*, JunWang* and Da-Wei Huang*. (2013). Obligate Mutualism within a Host Drives the Extreme Specialization of a Fig Wasp Genome. Genome Biology. 14, no. 12: R141.
DOI:
https://doi.org/10.1186/gb-2013-14-12-r141

13. Li Liu#, Xiaowei Chen#, Geir Skogerb?, Peng Zhang, Runsheng Chen*, Shunmin He*, Da-wei Huang*. (2012). The human microbiome: A hot spot of microbial horizontal gene transfer. Genomics. 100(5):265-270.
DOI:
https://doi.org/10.1016/j.ygeno.2012.07.012

14. Dongsheng Yan#, Dandan He#, Shunmin He#, Xiaoyan Chen, Zhen Fan and Runsheng Chen. (2011). Identification and analysis of intermediate size noncoding RNAs in the human fetal brain. PLoS One. 6(7): e21652.
DOI:
https://doi.org/10.1371/journal.pone.0021652

15. Shunmin He#, Hua Su#, Changning Liu#, Geir Skogerbo, Housheng He, Dandan He, Xiaopeng Zhu, Tao Liu, Yi Zhao*, Runsheng Chen* (2008). MicroRNA-encoding long non-coding RNAs. BMC Genomics. vol. 9 pp. 236;
DOI:
https://doi.org/10.1186/1471-2164-9-236

16. Yi Zhao#, Shunmin He#, Changning Liu#, Songwei Ru, Haitao Zhao, Zhen Yang, Pengcheng Yang, Xiongyin Yuan, Shiwei Sun, Dongbo Bu, Jiefu Huang, Geir Skogerbo*, Runsheng Chen*. (2008). MicroRNA regulation of messenger-like noncoding RNAs: a network of mutual microRNA control. Trends Genet. vol. 24 (7) pp. 323-7;
DOI:
https://doi.org/10.1016/j.tig.2008.04.004

17. Shunmin He#, Zhen Yang#, Geir Skogerbo, Fei Ren, Hongliang Cui, Haitao Zhao, Runsheng Chen, Yi Zhao. (2008). The properties and functions of virus encoded microRNA, siRNA, and other small noncoding RNAs. Critical Revs. in Microbiology. vol. 34 (3-4) pp. 175-88.
DOI:
https://doi.org/10.1080/10408410802482008

18. Shunmin He#, Changning Liu#, Geir Skogerbo, Haitao Zhao, Jie Wang, Tao Liu, Baoyan Bai, Yi Zhao*, Runsheng Chen*. (2008). NONCODE v2.0: decoding the non-coding. Nucleic Acids Res.
DOI:
https://doi.org/10.1093/nar/gkm1011

 

 

From Shunmin He, 2019-11-26 update

 

 

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