何顺民

中国科学院生物物理研究所研究员
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。
个人简介
何顺民，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。何顺民博士从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，其中以第一作者/通讯作者在Cell Research、Trends in Genetics、Nucleic Acids Research、Bioinformatics、Scientific Reports、Database(Oxford)等国际期刊上发表论文16篇。有PB量级大数据处理分析的经验和能力；擅长基因组数据的分析和变异位点的解读，尤其是针对基因组中97%的非编码区域的变异位点的解读；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“973”、 “863”、精准医学重点研发专项和国家自然科学基金面上等项目。
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，更多信息参考 ORCID，ResearcherID，Publons或 Research Gate。
(*第一/并列第一作者, #通讯/共同通讯作者)
1.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》
2.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. vol. 36 (Database issue) pp. D170-2.
3.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.
4.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;
5.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;
6.Yuliang Tan, Bo Zhang, Tao Wu, Geir Skogerbo, Xiaopeng Zhu, Xiangqian Guo,Shunmin He, Runsheng Chen (2009). Transcriptional inhibiton of Hoxd4 expression by miRNA-10a in human breast cancer cells.BMC Molecular Biology. 10:12
7.Xiongying yuan, Changning Liu, Pengcheng Yang,Shunmin He, Qi Liao, Shuli Kang andYi Zhao (2009). Clustered microRNAs' coordination in regulating protein-protein interaction network.BMC systems biology. vol. 3 pp. 65
8.Zhen Yang, Fei Ren, Changning Liu,Shunmin He, Gang Sun, Qian Gao, Lei Yao, Yangde Zhang, Ruoyu Miao, Ying Cao, Yi Zhao, Yang Zhong and Haitao Zhao. (2010) dbDEMC: a database of differentially expressed miRNAs in human cancers.BMC Genomics.vol. 11 Suppl 4 pp. S5
9.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 One6(7): e21652.
10.Yunfei Wang, Jingjing Chen, Guifeng Wei, Housheng He, Xiaopeng Zhu, Tengfei Xiao, Jiao Yuan, Bo Dong,Shunmin He, Geir Skogerbø and Runsheng Chen. (2011)The Caenorhabditis elegans intermediate-size transcriptome shows high degree of stage-specific expression.Nucleic acids research.39(12):5203-5214.
11.Bo Dong*, Peng Zhang*, Xiaowei Chen, Li Liu, Yunfei Wang,Shunmin He#, Runsheng Chen#. (2011) Predicting Housekeeping Genes Based on Fourier Analysis.PLoS One6(6): e21012.
12.Xiuqin Liu*,Shunmin He*, Geir Skogerbø, Fuzhou Gong#, Runsheng Chen#. (2012)Integrated Sequence-Structure Motifs Suffice toIdentify microRNA Precursors.PloS one7(3):e32797
13.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.Genomics100(5):265-270.
14.Dapeng Xiong, Fen Xiao, Li Liu, Kai Hu, Yanping Tan,Shunmin He#, Xieping Gao#. (2012) Towards a better detection of horizontally transferred genes by combining unusual properties effectively.PloS one7(8):e43126
15.Baofa Sun, Jinhua Xiao,Shunmin He, Li Liu, RW Murphy, Da-wei Huang. (2013)Multiple ancient horizontal gene transfers and duplications in lepidopteran species.Insect molecular biology.22(1):72-87.
16.Bao-Fa Sun, Jin-Hua Xiao,Shunmin He, Li Liu, Robert W. Murphy, Da-Wei Huang. (2013)Multiple Interkingdom Horizontal Gene Transfers in Pyrenophora and Closely Related Species andTheir Contributions to Phytopathogenic Lifestyles.PloS one8(3):e60029.
17.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 Biol14, no. 12: R141.
18.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 genomics15:321.
19.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.
20.Dongya Cui, Jiajia Wang, Xubin Sun, Peng Zhang,Shunmin He#,Da-wei Huang#. (2014) The Research ofCaenorhabditis elegansNew piRNAs.Prog. Biochem. Biophys.41(12).
21.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 Research25(2): 193-207.
22.Li-Hua Niu*, Xiu-Feng Song*,Shun-Min He, Peng Zhang, Ning-Xin Wang, Yi Li, Da-Wei Huang. (2015) New insights into the fungal community from the raw genomic sequence data of fig wasp Ceratosolen solmsi.BMC microbiology15(1): 27.
23.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.Cell161(4): 893-906.
24.Bao-fa Sun*, Yong-Xing Li*, Ling-Yi Jia, Li-Hua Niu, Robert W. Murphy, Peng Zhang,Shunmin He#, Da-Wei Huang#(2015). Regulation of transcription factors on sexual dimorphism of fig wasps.Scientific reports5: 10696.
25.Dongya Cui, Xubin Sun, Jiajia Wang, Peng Zhang, Baofa Sun, Xiaowei Chen, Robert W.Murphy.Shunmin He #, Da-Wei Huang#(2016) Research on Co-expression Genes of a Fig Wasp.Prog. Biochem. Biophys.43(1).
26.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
27.Da-wei Huang*#, Dongya Cui, Jiajia Wang,Shunmin He, Peng Zhang. (2016). The Effect ofprg-1on Small RNAs Expression ofCaenorhabditis elegans.Prog. Biochem. Biophys.43(3).
28.Ya Cui*, Xiaowei Chen*, Huaxia Luo, Zhen Fan, Jianjun Luo,ShunminHe, Haiyan Yue, Peng Zhang, Runsheng Chen. (2016). BioCircos.js: an interactive Circos JavaScript library for biological data visualization on web applications.Bioinformatics32(8), 1740-1742.
29.Baofa Sun, Tong Li, Jinhua Xiao, Li Liu, Peng Zhang, Robert W. Murphy,Shunmin He, Da-Wei Huang (2016). Contribution of Multiple Inter-Kingdom Horizontal Gene Transfers to Evolution and Adaptation of Amphibian-Killing Chytrid, Batrachochytrium dendrobatidis.Frontiers in microbiology7, 1360.
30.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
31.Yajing Hao*, Lili Zhang*, Yiwei Niu, Tanxi Cai, Jianjun Luo,Shunmin He, Bao Zhang, Dejiu Zhang, Yan Qin, Fuquan Yang, Runsheng Chen (2017). SmProt: a database of small proteins encoded by annotated coding and non-coding RNA loci.Briefings in Bioinformatics.bbx005
32.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
33.Jiajia Wang*, Peng Zhang*, Yiping Lu*, Yanyan Li, Yu Zheng, Yunchao Kan, Runsheng Chen#,Shunmin He#.(2018). piRBase: a comprehensive database of piRNA sequences.Nucleic acids research.pii: 5146202. doi: 10.1093/nar/gky1043.
34.The RNAcentral Consortium (2018). RNAcentral: a hub of information for non-coding RNA sequences.Nucleic acids research.Doi:10.1093/nar/gky1034