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Shunmin He, Ph.D, Prof.
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Principal Investigator
Executive Deputy Director, Center for Big Data Research in Health
Chinese Academy of Sciences Key Laboratory of Nucleic Acid Biology, IBP
Research Interests: Bioinformatics, non-coding RNA and epigenetics
Email: heshunmin@ibp.ac.cn
Tel: 010-64887032
Address: 15 Datun Road, Chaoyang District, Beijing, 100101, China
Chinese personal homepage
- Biography
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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
- Awards
- Membership in Academies & Societies
- Research Interests
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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.
- Grants
- Selected Publications
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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 Rep37, 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 Biol23, 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)