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

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

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

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

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

2016.4 - 2016.7 Visiting scholar, Cellular & Molecular Medicine, University of California San Diego: La Jolla, CA, US

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

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.

1. Shuai Liu^#, Huaxia Luo^#, Peng Zhang, Yanyan Li, Di Hao, Sijia Zhang, Tingrui Song, Tao Xu*, Shunmin He*. (2024). Adaptive Selection of Cis-regulatory Elements in the Han Chinese. Mol. Biol. Evol.

DOI: https://doi.org/10.1093/molbev/msae034

2. Huaxia Luo^#, Peng Zhang^#, Wanyu Zhang, Yu Zheng, Di Hao, Yirong Shi, Yiwei Niu, Tingrui Song, Yanyan Li, Shilei Zhao, Hua Chen*, Tao Xu*, Shunmin He*. (2023). Recent positive selection signatures reveal phenotypic evolution in the Han Chinese population. Science Bulletin.

DOI: https://doi.org/10.1016/j.scib.2023.08.027

3. Honghong Zhou^#, Xinpei Hao^#, Peng Zhang, Shunmin He*. (2023). Noncoding RNA mutations in cancer. Wiley Interdisciplinary Reviews: RNA.

DOI: https://doi.org/10.1002/wrna.1812

4. Yirong Shi^#, Yiwei Niu^#, Peng Zhang, Huaxia Luo, Shuai Liu, Sijia Zhang, Jiajia Wang, Yanyan Li, Xinyue Liu, Tingrui Song, Tao Xu*, Shunmin He*. (2023). Characterization of genome-wide STR variation in 6,487 human genomes. Nature Communication.

DOI: https://doi.org/10.1038/s41467-023-37690-8

5. Yu Zheng^#, Huaxia Luo^#, Xueyi Teng^#, Xinpei Hao, Xiaoyu Yan, Yiheng Tang, Wanyu Zhang, Yuanxin Wang, Peng Zhang, Yanyan Li, Yi Zhao, Runsheng Chen*, Shunmin He*. (2023). NPInter v5.0: ncRNA interaction database in a new era. Nucleic Acids Res.

DOI: https://doi.org/10.1093/nar/gkac1002

6. Yiwei Niu^#, Xueyi Teng^#, Honghong Zhou^#, Yirong Shi, Yanyan Li, Yiheng Tang, Peng Zhang, Huaxia Luo, Quan Kang, Tao Xu*, Shunmin He*. (2022). Characterizing mobile element insertions in 5675 genomes. Nucleic Acids Res.

DOI: https://doi.org/10.1093/nar/gkac128

7. Peng Zhang^#, Huaxia Luo^#, Yanyan Li^#, You Wang^#, Jiajia Wang^#, Yu Zheng^#, Yiwei Niu, Yirong Shi, Honghong Zhou, Tingrui Song, Quan Kang, Han100K Initiative; Tao Xu*, Shunmin He*.(2021). NyuWa Genome resource: A deep whole-genome sequencing-based variation profile and reference panel for the Chinese population. Cell Rep 37, 110017.

DOI: https://doi.org/10.1016/j.celrep.2021.110017

8. Jiajia Wang^#, Yirong Shi^#, Honghong Zhou^#, Peng Zhang, Tingrui Song, Zhiye Ying, Haopeng Yu, Yanyan Li, Yi Zhao , Xiaoxi Zeng*, Shunmin He*, Runsheng Chen*.(2021). piRBase: integrating piRNA annotation in all aspects. Nucleic Acids Res.

DOI: https://doi.org/10.1093/nar/gkab1012

9.  Yanyan Li^#, Honghong Zhou^#, Xiaomin Chen^#, Yu Zheng, Quan Kang, Di Hao, Lili Zhang, Tingrui Song, Huaxia Luo, Yajing Hao, Runsheng Chen*, Peng Zhang*, Shunmin He*.(2021). SmProt: A Reliable Repository with Comprehensive Annotation of Small Proteins Identified from Ribosome Profiling. Genomics Proteomics Bioinformatics.

DOI: https://doi.org/10.1016/j.gpb.2021.09.002

10.  Ruibao Su^#, Li-Hua Fan^#, Changchang Cao^#, Lei Wang, Zongchang Du, Zhaokui Cai, Ying-Chun Ouyang, Yue Wang , Qian Zhou, Ligang Wu, Nan Zhang, Xiaoxiao Zhu, Wen-Long Lei, Hailian Zhao, Yong Tian, Shunmin He, Catherine C L Wong*, Qing-Yuan Sun*, Yuanchao Xue*.(2021). Global profiling of RNA-binding  protein target sites by LACE-seq. Nat Cell Biol 23, 664-675.

DOI: https://doi.org/10.1038/s41556-021-00696-9

11.  CNCB-NGDC Members and Partners. (2021). Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022. Nucleic Acids Res.

DOI: https://doi.org/10.1093/nar/gkab951

12.  Yajing Hao^#, Dongpeng Wang^#, Shuheng Wu, Xiao Li, Changwei Shao, Peng Zhang, Jia-Yu Chen, Do-Hwan Lim, Xiang-Dong Fu*, Runsheng Chen*, Shunmin He*. (2020). Active retrotransposons help maintain pericentromeric heterochromatin required for faithful cell division. Genome Research.

DOI: https://doi.org/10.1101/gr.256131.119

13.  Lianhe Zhao^#, Jiajia Wang^#, Yanyan Li^#,, Tingrui Song, Yang Wu, Shuangsang Fang, Dechao Bu, Hui Li, Liang Sun, Dong Pei, Yu Zheng, Jianqin Huang, Mingqing Xu, Runsheng Chen*, Yi Zhao*, Shunmin He*. (2020). NONCODEV6: an updated database dedicated to long non-coding RNA annotation in both animals and plants. Nucleic Acids Res.

DOI: https://doi.org/10.1093/nar/gkaa1046

14.  Zhaokui Cai^#, Changchang Cao^#, Lei Ji^#, Rong Ye, Di Wang, Cong Xia, Sui Wang, Zongchang Du, Naijing Hu, Xiaohua Yu, Juan Chen, Lei Wang, Xianguang Yang, Shunmin He, Yuanchao Xue*. (2020). RIC-seq for global in situ profiling of RNA-RNA spatial interactions. Nature.

DOI: https://doi.org/10.1038/s41586-020-2249-1

15.  Xueye Teng^#, Xiaomin Chen^#, Hua Xue^#, Yiheng Tang, Peng Zhang, Quan Kang, Yajing Hao, Runsheng Chen*, Yi Zhao*, Shunmin He*. (2020). NPInter v4.0: An integrated database of ncRNA interactions. Nucleic Acids Res.

DOI: https://doi.org/10.1093/nar/gkz969

16.  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

17. 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

18.  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

19.  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

(From Shunmin He, September 12, 2024)