基本信息

何顺民 ,理学博士,博士生导师

中国科学院生物物理研究所,研究员

健康大数据研究中心,常务副主任

中国科学院大学生命科学学院,教授

电子邮件: heshunmin@ibp.ac.cn
通信地址: 北京市朝阳区大屯路15号

中科院生物物理所个人主页

ORCID

简历

何顺民毕业于中科院生物物理所,获得中科院院长优秀奖,并在哈佛大学医学院完成博士后研究。现任中科院生物物理所研究员,健康大数据研究中心常务副主任,首席技术专家,中国科学院大学教授,博士生导师。从2004年开始从事生物大数据的分析,开发相关算法、软件和数据库20多个,发表SCI论文30多篇,总影响因子超过200,被引次数超过2000。其中以第一作者/通讯作者在Cell Research、Genome Research、Nature CommunicationTrends in Genetics、Nucleic Acids Research、Bioinformatics、Scientific Reports、Database(Oxford)等国际期刊上发表论文20多篇。有PB量级大数据处理分析的经验和能力;擅长大规模队列人群的多组学和大数据分析;擅长基因组变异位点的分析和解读,尤其是针对基因组中97%的非编码区域的变异位点的分析和解读;擅长不同来源数据和多组学数据的整合分析。作为课题负责人承担过国家重点基础研发计划(973计划)、国家高技术研究发展计划(863计划)、精准医学重点研发专项、中国科学院战略先导专项(B类)、国家自然科学基金和中科院知识创新工程等项目。

招生信息

招生专业:

071021,生物信息学

招生方向:

生物信息学

学习和工作经历

2017/05 - 至今 : 中国科学院生物物理研究所,研究员;健康大数据研究中心,常务副主任。

2009/07-2017/04 :中国科学院动物研究所,先后担任副研究员,创新研究员岗位。

                              研究方向:生物信息学、组学大数据整合分析和精准医学。

2016/04-2016/07 :美国加州大学圣地亚哥分校,细胞与分子医学系,访问学者;

                              合作教授:付向东教授 

2010/09-2011/09 :哈佛大学Dana-farber癌症研究所 & 哈佛大学公共卫生学院生物统计系,博士后;

                              研究方向:癌症和表观遗传学;

                              合作教授:Xiaole Shirley Liu教授 

2004/09-2009/07 :中国科学院生物物理研究所,生物信息学,硕博连读。

                               导师:陈润生院士

                               毕业论文:非编码RNA的功能研究——从转录组到相互作用网络。

2001/08-2004/08 :北京NEC电子有限公司,软件工程师。

1997/09-2001/07 :南京理工大学,电子工程专业,学士。

代表性论文

一共发表SCI论文30多篇,完整列表和更多信息参考 Publons 


(#第一/并列第一作者, *通讯/共同通讯作者)

1.  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

2.  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

3.  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

4.  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

5.  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

6. 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

7.  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

8.  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

9.  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

10.  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

11.  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

12.  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

13.  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

14.  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

15.  Li Liu#, Xiaowei Chen#, Geir Skogerbø, 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

16.  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

17.  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

18.  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

19.  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

20.  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

21.  吴涛,何顺民,陈润生(2007). 非编码基因的功能、调控与双色网络.2007科学发展报告》