基本信息

赵屹  男  研究员 博导  中国科学院计算技术研究所
电子邮件: biozy@ict.ac.cn
通信地址: 北京市海淀区中关村科学院南路6号
邮政编码: 100190

研究领域

健康医疗大数据挖掘 生物信息学

招生信息

   
招生专业
081203-计算机应用技术
招生方向
生物信息学,人工智能,
健康医学大数据挖掘

教育背景

2013-09--2016-07   清华大学   博士
1997-09--2000-07   北京大学   硕士学位
1990-09--1995-07   北京中医药大学   学士学位

出版信息

   
发表论文
[1] Guo, Duancheng, Wang, Yuan, Cheng, Yan, Liao, Shengyou, Hu, Jian, Du, Fang, Xu, Gang, Liu, Yongqiang, Cai, Kathy Q, Cheung, Martin, Wainwright, Brandon J, Lu, Q Richard, Zhao, Yi, Yang, Zengjie. Tumor cells generate astrocyte-like cells that contribute to SHH-driven medulloblastoma relapse. JOURNAL OF EXPERIMENTAL MEDICINE[J]. 2021, 218(9): http://dx.doi.org/10.1084/jem.20202350.
[2] Junya Ning, Yingnan Ye, Dechao Bu, Gang Zhao, Tianqiang Song, Pengpeng Liu, Wenwen Yu, Hailong Wang, Hui Li, Xiubao Ren, Guoguang Ying, Yi Zhao, Jinpu Yu. Imbalance of TGF-β1/BMP-7 pathways induced by M2-polarized macrophages promotes hepatocellular carcinoma aggressiveness. Molecular Therapy. 2021, 29(6): 2067-2087, http://dx.doi.org/10.1016/j.ymthe.2021.02.016.
[3] Fang, ShuangSang, Dong, Lei, Liu, Liu, Guo, JinCheng, Zhao, LianHe, Zhang, JiaYuan, Bu, DeChao, Liu, XinKui, Huo, PeiPei, Cao, WanChen, Dong, QiongYe, Wu, JiaRui, Zeng, Xiaoxi, Wu, Yang, Zhao, Yi. HERB: a high-throughput experiment- and reference-guided database of traditional Chinese medicine. NUCLEIC ACIDS RESEARCH[J]. 2021, 49(D1): D1197-D1206, http://dx.doi.org/10.1093/nar/gkaa1063.
[4] Guo, JinCheng, Wei, QingShuang, Dong, Lei, Fang, ShuangSang, Li, Feng, Zhao, Yi. Prognostic Value of an Autophagy-Related Five-Gene Signature for Lower-Grade Glioma Patients. FRONTIERS IN ONCOLOGY[J]. 2021, 11: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7985555/.
[5] Zhang, Yuwei, Bu, Dechao, Huo, Peipei, Wang, Zhihao, Rong, Hao, Li, Yanguo, Liu, Jingjia, Ye, Meng, Wu, Yang, Jiang, Zheng, Liao, Qi, Zhao, Yi. ncFANs v2.0: an integrative platform for functional annotation of non-coding RNAs. NUCLEIC ACIDS RESEARCH[J]. 2021, 49(W1): W459-W468, http://dx.doi.org/10.1093/nar/gkab435.
[6] Zhao, Lianhe, Dong, Qiongye, Luo, Chunlong, Wu, Yang, Bu, Dechao, Qi, Xiaoning, Luo, Yufan, Zhao, Yi. DeepOmix: A scalable and interpretable multi-omics deep learning framework and application in cancer survival analysis. COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL[J]. 2021, 19: 2719-2725, http://dx.doi.org/10.1016/j.csbj.2021.04.067.
[7] Bu, Dechao, Luo, Haitao, Huo, Peipei, Wang, Zhihao, Zhang, Shan, He, Zihao, Wu, Yang, Zhao, Lianhe, Liu, Jingjia, Guo, Jincheng, Fang, Shuangsang, Cao, Wanchen, Yi, Lan, Zhao, Yi, Kong, Lei. KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis. NUCLEIC ACIDS RESEARCH[J]. 2021, 49(W1): W317-W325, http://dx.doi.org/10.1093/nar/gkab447.
[8] Ziyang Li, Shuangsang Fang, Rui Zhang, Lijia Yu, Jiawei Zhang, Dechao Bu, Liang Sun, Yi Zhao, Jinming Li. VarBen: Generating in Silico Reference Data Sets for Clinical Next-Generation Sequencing Bioinformatics Pipeline Evaluation. The Journal of Molecular Diagnostics. 2021, 23(3): 285-299, http://dx.doi.org/10.1016/j.jmoldx.2020.11.010.
[9] Zhao, Lianhe, Wang, Jiajia, Li, Yanyan, Song, Tingrui, Wu, Yang, Fang, Shuangsang, Bu, Dechao, Li, Hui, Sun, Liang, Pei, Dong, Zheng, Yu, Huang, Jianqin, Xu, Mingqing, Chen, Runsheng, Zhao, Yi, He, Shunmin. NONCODEV6: an updated database dedicated to long non-coding RNA annotation in both animals and plants. NUCLEIC ACIDS RESEARCH[J]. 2021, 49(D1): D165-D171, http://dx.doi.org/10.1093/nar/gkaa1046.
[10] Dechao Bu, Yan Xia, JiaYuan Zhang, Wanchen Cao, Peipei Huo, Zhihao Wang, Zihao He, Linyi Ding, Yang Wu, Shan Zhang, Kai Gao, He Yu, Tiegang Liu, Xia Ding, Xiaohong Gu, Yi Zhao. FangNet: Mining herb hidden knowledge from TCM clinical effective formulas using structure network algorithm. Computational and Structural Biotechnology Journal[J]. 2021, 19: 62-71, [11] Xue, Yongbiao, Bao, Yiming, Zhang, Zhang, Zhao, Wenming, Xiao, Jingfa, He, Shunmin, Zhang, Guoqing, Li, Yixue, Zhao, Guoping, Chen, Runsheng, Song, Shuhui, Ma, Lina, Zou, Dong, Tian, Dongmei, Li, Cuiping, Zhu, Junwei, Gong, Zheng, Chen, Meili, Wang, Anke, Ma, Yingke, Li, Mengwei, Teng, Xufei, Cui, Ying, Duan, Guangya, Zhang, Mochen, Jin, Tong, Shi, Chengmin, Du, Zhenglin, Zhang, Yadong, Liu, Chuandong, Li, Rujiao, Zeng, Jingyao, Hao, Lili, Jiang, Shuai, Chen, Hua, Han, Dali, Yongbiao, Xue, Zhang, Tao, Kang, Wang, Qu, Jing, Zhang, Weiqi, Liu, GuangHui, Liu, Lin, Zhang, Yang, Niu, Guangyi, Zhu, Tongtong, Feng, Changrui, Liu, Xiaonan, Zhang, Yuansheng, Li, Zhao, Chen, Ruru, Li, Qianpeng, Hua, Zhongyi, Jiang, Chao, Chen, Ziyuan, He, Fangshu, Zhao, Yuyang, Jin, Yan, Huang, Luqi, Yuan, Yuan, Zhou, Chenfen, Xu, Qingwei, He, Sheng, Ye, Wei, Cao, Ruifang, Wang, Pengyu, Ling, Yunchao, Yan, Xing, Wang, Qingzhong, Du, Qiang, Zong, Wenting, Kang, Hongen, Xiong, Zhuang, Huan, Wendi, Zhang, Sirui, Xia, Qiguang, Fan, Xiaojuan, Wang, Zefeng, Chen, Xu, Chen, Tingting, Zhang, Sisi, Tang, Bixia, Dong, Lili, Zhang, Zhewen, Wang, Zhonghuang, Kang, Hailong, Wang, Yanqing, Wu, Song, Wang, Honggen, Chen, Ming, Liu, Chang, Xiong, Yujia, Shao, Xueying, Li, Yanyan, Zhou, Honghong, Chen, Xiaomin, Zheng, Yu, Kang, Quan, Hao, Di, Zhang, Lili, Luo, Huaxia, Hao, Yajing, Zhang, Peng, Nie, Zhi, Yu, Shuhuan, Yang, Fei, Sang, Jian, Li, Zhaohua, Zhang, Xiangquan, Zhou, Qing, Zhai, Shuang, Zhang, Yaping, Wang, Guodong, Zhu, Qianghui, Li, Xin, Li, Menghua, Yan, Jun, Li, Chen, Wang, Zhennan, Wang, Xiangfeng, Liu, Yuanming, Luo, Hong, Wu, Xiaoyuan, Jing, HaiChun, Song, Tinrui, Zhao, Yi, Mehmood, Furrukh, Ali, Shahid, Ali, Amjad, Saleem, Shoaib, Hussain, Irfan, Abbasi, Amir A, Zuo, Zhixiang, Ren, Jian, Zhang, Xinxin, Xiao, Yun, Li, Xia, Tu, Yiran, Xue, Yu, Wu, Wanying, Ji, Peifeng, Zhao, Fangqing, Meng, Xianwen, Peng, Di, Luo, Hao, Gao, Feng, Ning, Wanshan, Lin, Shaofeng, Liu, Teng, Guo, AnYuan, Yuan, Hao, Zhang, Yong E, Tan, Xiaodan, Zhang, Weizhi, Xie, Yubin, Wang, Chenwei, Liu, ChunJie, Yang, DeChang, Tian, Feng, Gao, Ge, Tang, Dachao, Yao, Lan, Cui, Qinghua, An, Ni A, Li, ChuanYun, Luo, XiaoTong. Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021. Nucleic Acids Research[J]. 2021, 49(D1): D18-D28, http://dx.doi.org/10.1093/nar/gkaa1022.
[12] Teng, Xueyi, Chen, Xiaomin, Xue, Hua, Tang, Yiheng, Zhang, Peng, Kang, Quan, Hao, Yajing, Chen, Runsheng, Zhao, Yi, He, Shunmin. NPInter v4.0: an integrated database of ncRNA interactions. NUCLEIC ACIDS RESEARCH[J]. 2020, 48(D1): D160-D165, http://dx.doi.org/10.1093/nar/gkz969.
[13] Fang, ShuangSang, Guo, JinCheng, Zhang, JianHua, Liu, JinNa, Hong, Shuai, Yu, Bo, Gao, Yuhan, Hu, SuPei, Liu, HaiZhong, Sun, Liang, Zhao, Yi. A P53-related microRNA model for predicting the prognosis of hepatocellular carcinoma patients. JOURNAL OF CELLULAR PHYSIOLOGY[J]. 2020, 235(4): 3569-3578, https://www.webofscience.com/wos/woscc/full-record/WOS:000488008700001.
[14] Ye, Yingnan, Guo, Jincheng, Xiao, Pei, Ning, Junya, Zhang, Rui, Liu, Pengpeng, Yu, Wenwen, Xu, Liyan, Zhao, Yi, Yu, Jinpu. Macrophages-induced long noncoding RNA H19 up-regulation triggers and activates the miR-193b/MAPK1 axis and promotes cell aggressiveness in hepatocellular carcinoma. CANCER LETTERS[J]. 2020, 469: 310-322, http://dx.doi.org/10.1016/j.canlet.2019.11.001.
[15] Wu, Yang, Zhang, Feilong, Yang, Kuo, Fang, Shuangsang, Bu, Dechao, Li, Hui, Sun, Liang, Hu, Hairuo, Gao, Kuo, Wang, Wei, Zhou, Xuezhong, Zhao, Yi, Chen, Jianxin. SymMap: an integrative database of traditional Chinese medicine enhanced by symptom mapping. NUCLEIC ACIDS RESEARCH[J]. 2019, 47(D1): D1110-D1117, https://www.webofscience.com/wos/woscc/full-record/WOS:000462587400152.
[16] He, Shunmin, Zhang, Guoqiang, Wang, Jiajia, Gao, Yajie, Sun, Ruidi, Cao, Zhijie, Chen, Zhenping, Zheng, Xiudeng, Yuan, Jiao, Luo, Yuewan, Wang, Xiaona, Zhang, Wenxin, Zhang, Peng, Zhao, Yi, He, Chuan, Tao, Yi, Sun, Qinmiao, Chen, Dahua. 6mA-DNA-binding factor Jumu controls maternal-to-zygotic transition upstream of Zelda. NATURE COMMUNICATIONS[J]. 2019, 10(1): http://dx.doi.org/10.1038/s41467-019-10202-3.
[17] Zhang, Zhiqiang, Zhao, Yi, Liao, Xiangke, Shi, Wenqiang, Li, Kenli, Zou, Quan, Peng, Shaoliang. Deep learning in omics: a survey and guideline. BRIEFINGS IN FUNCTIONAL GENOMICS[J]. 2019, 18(1): 41-57, http://dx.doi.org/10.1093/bfgp/ely030.
[18] Li, Hui, Xiao, Li, Zhang, Lili, Wu, Jiarui, Wei, Bin, Sun, Ninghui, Zhao, Yi. FSPP: A Tool for Genome-Wide Prediction of smORF-Encoded Peptides and Their Functions. FRONTIERS IN GENETICS[J]. 2018, 9: https://doaj.org/article/2c7668c444d94897b40856e6418ebaea.
[19] JianYi Wu, Yang Wu, EnMin Li, ZhiYong Wu, LiYan Xu, XiuE Xu, Yang Chen, Feng Pan, JiaSheng Zhang, JianMei Zhao, Yi Zhao, JinCheng Guo. Protein-coding genes combined with long noncoding RNA as a novel transcriptome molecular staging model to predict the survival of patients with esophageal squamous cell carcinoma. Springer. 2018, http://oa.las.ac.cn/oainone/service/browseall/read1?ptype=JA&workid=JA201904021619400ZK.
[20] Fang, ShuangSang, Zhang, LiLi, Guo, JinCheng, Niu, YiWei, Wu, Yang, Li, Hui, Zhao, Lian He, Li, Xi Yuan, Teng, Xue Yi, Sun, XianHui, Sun, Liang, Zhang, Michael Q, Chen, RunSheng, Zhao, Yi. NONCODEV5: a comprehensive annotation database for long non-coding RNAs. NUCLEIC ACIDS RESEARCH[J]. 2018, 46(D1): D308-D314, https://www.webofscience.com/wos/woscc/full-record/WOS:000419550700047.
[21] Luo, Haitao, Fang, Shuangsang, Sun, Liang, Liu, Zhiyong, Zhao, Yi. Comprehensive Characterization of the RNA Editomes in Cancer Development and Progression. FRONTIERS IN GENETICS[J]. 2018, 8: https://doaj.org/article/f2597ce71a244b80abc2aac0c6ef38d7.
[22] Wang, Binbin, Xiao, Li, Liu, Yang, Wang, Jing, Liu, Beihong, Li, Tengyan, Ma, Xu, Zhao, Yi. Application of a deep convolutional neural network in the diagnosis of neonatal ocular fundus hemorrhage. BIOSCIENCE REPORTS[J]. 2018, 38(6): https://www.webofscience.com/wos/woscc/full-record/WOS:000454266100019.
[23] Yang, Zhen, Wu, Liangcai, Wang, Anqiang, Tang, Wei, Zhao, Yi, Zhao, Haitao, Teschendorff, Andrew E. dbDEMC 2.0: updated database of differentially expressed miRNAs in human cancers. NUCLEIC ACIDS RESEARCH[J]. 2017, 45(D1): D812-D818, https://www.webofscience.com/wos/woscc/full-record/WOS:000396575500113.
[24] Ye Zhen, Zhao Xinghui, Wu Chao, Zhao Yi, Chen Jinwen, Gao Ruifang, Zhang Chao, Zhao Min, Guo Chunlei, Fang Yan, Du Lingfang, Shen Long, Shen Wenzhi, Luo Xiaohe, Xiang Rong. Several microRNAs could predict survival in patients with hepatitis B-related liver cancer. SCIENTIFIC REPORTS[J]. 2017, 7: https://www.webofscience.com/wos/woscc/full-record/WOS:000396852900001.
[25] Luo, Haitao, Bu, Dechao, Sun, Liang, Fang, Shuangsang, Liu, Zhiyong, Zhao, Yi. Identification and function annotation of long intervening noncoding RNAs. BRIEFINGS IN BIOINFORMATICS[J]. 2017, 18(5): 789-797, https://www.webofscience.com/wos/woscc/full-record/WOS:000411516400008.
[26] Zhao, Yi, Li, Hui, Fang, Shuangsang, Kang, Yue, Wu, Wei, Hao, Yajing, Li, Ziyang, Bu, Dechao, Sun, Ninghui, Zhang, Michael Q, Chen, Runsheng. NONCODE 2016: an informative and valuable data source of long non-coding RNAs. NUCLEIC ACIDS RESEARCH[J]. 2016, 44(D1): D203-D208, https://www.webofscience.com/wos/woscc/full-record/WOS:000371261700027.
[27] Zhang, Haohai, Zhu, Chengpei, Zhao, Yi, Li, Ming, Wu, Liangcai, Yang, Xiaobo, Wan, Xueshuai, Wang, Anqiang, Zhang, Michael Q, Sang, Xinting, Zhao, Haitao. Long non-coding RNA expression profiles of hepatitis C virus-related dysplasia and hepatocellular carcinoma. ONCOTARGET[J]. 2015, 6(41): 43770-43778, https://www.webofscience.com/wos/woscc/full-record/WOS:000369908400045.
[28] Yang, Xiaobo, Li, Ming, Liu, Qi, Zhang, Yabing, Qian, Junyan, Wan, Xueshuai, Wang, Anqiang, Zhang, Haohai, Zhu, Chengpei, Lu, Xin, Mao, Yilei, Sang, Xinting, Zhao, Haitao, Zhao, Yi, Zhang, Xiaoyan. Dr.VIS v2.0: an updated database of human disease-related viral integration sites in the era of high-throughput deep sequencing. NUCLEIC ACIDS RESEARCH[J]. 2015, 43(D1): D887-D892, https://www.webofscience.com/wos/woscc/full-record/WOS:000350210400130.
[29] 陈润生. NONCODEv4: exploring the world of long non-coding RNA genes. NUCLEIC ACIDS RESEARCH[J]. 2014, 42(30): D98-D103, https://www.webofscience.com/wos/woscc/full-record/WOS:000331139800016.
[30] Miao, Ruoyu, Luo, Haitao, Zhou, Huandi, Li, Guangbing, Bu, Dechao, Yang, Xiaobo, Zhao, Xue, Zhang, Haohai, Liu, Song, Zhong, Ying, Zou, Zhen, Zhao, Yan, Yu, Kuntao, He, Lian, Sang, Xinting, Zhong, Shouxian, Huang, Jiefu, Wu, Yan, Miksad, Rebecca A, Robson, Simon C, Jiang, Chengyu, Zhao, Yi, Zhao, Haitao. Identification of prognostic biomarkers in hepatitis B virus-related hepatocellular carcinoma and stratification by integrative multi-omics analysis. JOURNAL OF HEPATOLOGY[J]. 2014, 61(4): 840-849, http://dx.doi.org/10.1016/j.jhep.2014.05.025.
[31] 赵屹. Computational Methods To Predict Long Non-Coding RNA Functions Based On Co-Expression Network. Methods In Molecular Biology. 2014, [32] 赵屹. De novo approach to classify protein-coding and non-coding transcripts by utilizing sequence intrinsic composition. 2014, [33] 陈润生. Long non-coding RNAs function annotation: a global prediction method based on bi-colored networks. NUCLEIC ACIDS RESEARCH[J]. 2013, 41(41): http://www.irgrid.ac.cn/handle/1471x/756478.
[34] 陈润生. Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts. NUCLEIC ACIDS RESEARCH[J]. 2013, 41(17): e166-e166, [35] 陈润生. NONCODE v3.0: integrative annotation of long noncoding RNAs. NUCLEIC ACIDS RESEARCH[J]. 2012, 40(51): D210-D215, http://www.irgrid.ac.cn/handle/1471x/756876.
[36] 陈润生. ncFANs: a web server for functional annotation of long non-coding RNAs. NUCLEIC ACIDS RESEARCH[J]. 2011, 39(54): W118-W124, http://www.irgrid.ac.cn/handle/1471x/757406.
[37] Liao, Qi, Liu, Changning, Yuan, Xiongying, Kang, Shuli, Miao, Ruoyu, Xiao, Hui, Zhao, Guoguang, Luo, Haitao, Bu, Dechao, Zhao, Haitao, Skogerbo, Geir, Wu, Zhongdao, Zhao, Yi. Large-scale prediction of long non-coding RNA functions in a coding-non-coding gene co-expression network. NUCLEIC ACIDS RESEARCH[J]. 2011, 39(9): 3864-3878, https://www.webofscience.com/wos/woscc/full-record/WOS:000290589500037.

科研活动

   
科研项目
( 1 ) 非编码RNA调控网络及功能研究, 主持, 部委级, 2011-10--2013-10
( 2 ) 蛋白质组海量质谱数据的解析及其在人类基因组注释中的应用, 主持, 国家级, 2010-01--2014-12
( 3 ) 病毒性肝炎恶性转化的多元调控网络研究, 主持, 国家级, 2013-01--2015-12
( 4 ) 非编码RNA参与的生物网络分析, 主持, 国家级, 2011-01--2013-12
( 5 ) siRNA药物设计软件研发, 主持, 国家级, 2012-11--2015-12
( 6 ) 基于高通量测序数据的长非编码RNA调控网络及在癌症中的应用, 主持, 国家级, 2014-01--2017-12
( 7 ) 基础医学科学数据中心共建项目, 主持, 国家级, 2016-06--2017-06
( 8 ) 肝癌极高危人群队列的建立及早期诊断与预警研究, 参与, 国家级, 2015-04--2016-12
( 9 ) 基于不同测序策略的长非编码RNA拼接、鉴定算法和功能注释的系统性研究, 主持, 国家级, 2018-01--2020-12
( 10 ) 后基因组时代的高通量生命多组学 数据分析算法研究, 主持, 市地级, 2018-01--2019-12
( 11 ) 特色经济林重要性状形成与调控-NGS数据分析算法研究, 主持, 国家级, 2019-01--2021-12

指导学生

已指导学生

余鲲涛  硕士研究生  081202-计算机软件与理论  

解朝勇  硕士研究生  081203-计算机应用技术  

谭程夫  硕士研究生  081203-计算机应用技术  

李明  硕士研究生  081201-计算机系统结构  

杨瑞  硕士研究生  081203-计算机应用技术  

朱城  硕士研究生  081203-计算机应用技术  

李慧  博士研究生  081201-计算机系统结构  

现指导学生

罗纯龙  博士研究生  081203-计算机应用技术  

刘阳  硕士研究生  081203-计算机应用技术  

齐晓宁  硕士研究生  081203-计算机应用技术  

乔艺璇  博士研究生  081203-计算机应用技术  

罗宇凡  博士研究生  081203-计算机应用技术