基本信息
肖景发  男  博导  中国科学院北京基因组研究所(国家生物信息中心)
电子邮件: xiaojingfa@big.ac.cn
通信地址: 北京市朝阳区北辰西路1-7号
邮政编码: 100101

研究领域

基因组学和生物信息学


招生信息

招收生物信息学、计算机科学、数学和生物学等相关专业背景考生

招生专业
0710J3-生物信息学
0710Z1-基因组学
招生方向
生命与健康大数据整合和挖掘

教育背景

1998-09--2003-07   吉林大学   博士学位
1991-09--1995-07   四川大学生物系   学士学位

工作经历

   
工作简历
2019-11~现在, 中国科学院北京基因组研究所(国家生物信息中心), 研究员
2012-05~现在, 中国科学院北京基因组研究所, 研究员
2007-02~2012-05,中国科学院北京基因组研究所, 副研究员
2005-11~2007-02,美国犹他大学, 博士后
2003-07~2005-08,协和医科大学药物研究所, 博士后
1995-07~1998-08,沈阳第一制药厂, 助理工程师
社会兼职
2022-08-06-今,中国医药教育协会医学基因组学与生物信息学专业委员会, 委员
2022-01-22-今,北京生物信息学研究会, 委员
2021-10-13-今,MDPI Biology, 编委
2019-09-01-今,Frontiers of Data & Computing, 编委
2018-01-01-今,科技资源导刊, 编委
2017-10-01-今,全国生物技术标准化技术委员会生物计量和质量控制分技术委员会, 委员
2016-03-19-2017-12-31,Frontiers in Plant Science, 副主编
2013-08-31-今,遗传学会基因组学专业委员会, 委员
2013-02-28-今,PLoS One 杂志, 学术编委
2012-05-01-今,Genomics, Proteomics and Bioinformatics, 学术编委
2012-04-30-今,Frontiers in Plant Science, 学术编委
2011-09-01-今,运筹学会系统生物学分会, 理事

教授课程

生命组学
大数据科学
生物信息学前沿讲座
基因组学前沿
基因组学前沿讲座
基因组信息系统与实践
基因组学
基因组学和生物技术前沿讲座
基因组学实用技术讲座

专利与奖励

   
专利成果
( 1 ) 编码蛋白质DNA序列并行比对软件, 发明, 2012, 第 2 作者, 专利号: 2012SR041110
( 2 ) RNA data anotation pipeline software 软件著作权, 发明, 2012, 第 2 作者, 专利号: 2012SR013930
( 3 ) 泛基因组自动化分析软件计算机软件著作权, 发明, 2013, 第 2 作者, 专利号: 2013SR053017
( 4 ) 人类转录组注释系统软件著作权, 发明, 2013, 第 2 作者, 专利号: 2013SR058058
( 5 ) 虚拟中国人动态基因组数据库系统软件著作权, 发明, 2014, 第 1 作者, 专利号: 2014SR113149
( 6 ) 大规模基因组数据泛基因组特征分析软件, 发明, 2014, 第 2 作者, 专利号: 2014SR113147
( 7 ) 基于RNA重亚硫酸盐测序数据的快速比对和注释软件, 发明, 2016, 第 2 作者, 专利号: 2017SR093096
( 8 ) 基于核心基因组结构框架的原核生物拼接软件, 发明, 2017, 第 2 作者, 专利号: 2017SR714259
( 9 ) 哺乳动物转录组数据库, 发明, 2017, 第 1 作者, 专利号: 2017SR714249
( 10 ) 泛基因组深度分析和可视化软件, 发明, 2019, 第 1 作者, 专利号: 2019SR0347218
( 11 ) 多物种全基因组核小体定位图谱数据库系统, 发明, 2019, 第 1 作者, 专利号: 2019SR0347246

出版信息

   
发表论文
[1] Jialin Mai, Mingming Lu, Qianwen Gao, Jingyao Zeng, Jingfa Xiao. Transcriptome-wide association studies: recent advances in methods, applications and available databases. Communications Biology[J]. 2023, 第 5 作者  通讯作者  6(1): 1-10, http://dx.doi.org/10.1038/s42003-023-05279-y.
[2] Jingfa Xiao, Jun Yu. T2T-YAO, T2T-SHUN, and more. Genomics, Proteomics & Bioinformatics[J]. 2023, 第 1 作者http://dx.doi.org/10.1016/j.gpb.2023.09.002.
[3] Cuidan Li, Qiheng Qian, Chenghao Yan, Mingming Lu, Lin Li, Pan Li, Zhuojing Fan, Wenyan Lei, Kang Shang, Peihan Wang, Jie Wang, Tianyi Lu, Yuting Huang, Hongwei Yang, Haobin Wei, Jingwan Han, Jingfa Xiao, Fei Chen. HervD Atlas: A Curated Knowledgebase of Associations Between Human Endogenous Retroviruses and Diseases. Nucleic Acids Research[J]. 2023, 第 17 作者  通讯作者  https://doi.org/10.1093/nar/gkad904.
[4] Yadong Zhang, Hao Zhang, Zaichao Zhang, Qiheng Qian, Zhewen Zhang, Jingfa Xiao. ProPan: a comprehensive database for profiling prokaryotic pan-genome dynamics. Nucleic Acids Research[J]. 2023, 第 6 作者  通讯作者  51: D767-D776, 
[5] Shuai Jiang, Qiheng Qian, Tongtong Zhu, Wenting Zong, Yunfei Shang, Tong Jin, Yuansheng Zhang, Ming Chen, Zishan Wu, Yuan Chu, Rongqin Zhang, Sicheng Luo, Wei Jing, Dong Zou, Yiming Bao, Jingfa Xiao, Zhang Zhang. Cell Taxonomy: a curated repository of cell types with multifaceted characterization. Nucleic Acids Research[J]. 2023, 第 16 作者  通讯作者  51: D853-D860, 
[6] Congfan Bu, Xinchang Zheng, Jialin Mai, Zhi Nie, Jingyao Zeng, Qiheng Qian, Tianyi Xu, Yanling Sun, Yiming Bao, Jingfa Xiao. CCLHunter: An efficient toolkit for cancer cell line authentication. Computational and Structural Biotechnology Journal[J]. 2023, 第 10 作者  通讯作者  21: 4675-4682, http://dx.doi.org/10.1016/j.csbj.2023.09.040.
[7] Zeming Wu, Mingming Lu, Di Liu, Yue Shi, Jie Ren, Si Wang, Ying Jing, Sheng Zhang, Qian Zhao, Hongyu Li, Zhihui Yu, Zunpeng Liu, Shijia Bi, Tuo Wei, YunGui Yang, Jingfa Xiao, Juan Carlos Izpisua Belmonte, Jing Qu, Weiqi Zhang, Weimin Ci, GuangHui Liu. m6A epitranscriptomic regulation of tissue homeostasis during primate aging.. Nature Aging[J]. 2023, 第 16 作者3: 705-721, 
[8] Mingming Lu, Yadong Zhang, Fengchun Yang, Jialin Mai, Qianwen Gao, Xiaowei Xu, Hongyu Kang, Li Hou, Yunfei Shang, Qiheng Qian, Jie Liu, Meiye Jiang, Hao Zhang, Congfan Bu, Jingyue Wang, Zaichao Zhang, Jingyao Zeng, Jiao Li, Jingfa Xiao. TWAS Atlas: a curated knowledgebase of transcriptome-wide association studies. Nucleic Acids Research[J]. 2023, 第 19 作者  通讯作者  51: D1179-D1187, 
[9] Chao Wu, Zhewen Zhang, Chao Kang, Qiang Zhang, Weifeng Zhu, Yadong Zhang, Hao Zhang, Jingfa Xiao, Meilin Jin. The C-Terminal Repeat Units of SpaA Mediate Adhesion of Erysipelothrix rhusiopathiae to Host Cells and Regulate Its Virulence. BIOLOGY[J]. 2022, 第 8 作者11: https://doaj.org/article/180333c923824b4b82b512ad26b88ca0.
[10] Xue, Yongbiao, Bao, Yiming, Zhang Zhang, Zhao, Wenming, Xiao, Jingfa, He, Shunmin, Zhang, Guoqing, Li, Yixue, Guoping, Zhao, Chen, Runsheng, Zeng, Jingyao, Zhang, Yadong, Shang, Yunfei, Mai, Jialin, Shi, Shuo, Lu, Mingming, Bu, Congfan, Zhang, Zhewen, Du, Zhenglin, Wang, Yinying, Kang, Hongen, Xu, Tianyi, Hao, Lili, Jia, Peilin, Jiang, Shuai, Qian, Qiheng, Zhu, Tongtong, Shang, Yunfei, Zong, Wenting, Jin, Tong, Zhang, Yuansheng, Zou, Dong, Zhang, Zhang, Du, Qiang, Feng, Changrui, Ma, Lina, Zhang, Sisi, Wang, Anke, Dong, Lili, Wang, Yanqing, Liu, Wan, Yan, Xing, Ling, Yunchao, Zhao, Guoping, Zhou, Zhihua, Kang, Wang, Zhang, Tao, Ma, Shuai, Yan, Haoteng, Liu, Zunpeng, Ji, Zejun, Cai, Yusheng, Wang, Si, Song, Moshi, Ren, Jie, Zhou, Qi, Qu, Jing, Zhang, Weiqi, Liu, Guanghui, Chen, Xu, Chen, Tingting, Sisi, Zhang, Sun, Yanling, Yu, Caixia, Tang, Bixia, Zhu, Junwei, Zhai, Shuang, Sun, Yubin, Chen, Qiancheng, Yang, Xiaoyu, Zhang, Xin, Sang, Zhengqi, Wang, Yonggang, Zhao, Yilin, Chen, Huanxin, Lan, Li, Wang, Yanqing, Ma, Yingke, Jia, Yaokai, Zheng, Xinchang, Chen, Meili, Dong, Zou, Zhu, Tongtong, Ming, Chen, Niu, Guangyi, Pan, Rong, Jing, Wei, Sang, Jian, Liu, Chang, Xiong, Yujia, Lili, Hao, Zhang, Mochen, Wang, Guoliang, Yi, Lizhi, Wei, Zhao, Zong, Wenting, Wu, Song, Xiong, Zhuang, Rujiao, Li, Zheng, Gong, Li, Rujiao, Liu, Lin, Li, Zhao, Li, Qianpeng, Wei, Jing, Luo, Sicheng, Wang, Jiajia, Shi, Yirong, Zhou, Honghong, Zhang, Peng, Song, Tingrui, Li, Yanyan, Yang, Fei, Li, Mengwei, Li, Zhaohua, Kang, Hongen, Zheng, Xinchang, Li, Rujiao, Tian, Dongmei, Liu, Xiaonan, Li, Cuiping, Teng, Xufei, Song, Shuhui, Zhang, Yang, Niu, Guangyi, Zhu, Tongtong, Zhang, Yuansheng, Chen, Ruru, Zhang, Rongqin, Xu, Feng, Wang, Yifan, Ling, Yunchao, Zhou, Chenfen, Wang, Haizhou, Teschendorff, Andrew E, He, Yungang, Zhen, Yang, Li, Cuiping, Zhu, Junwei, Li, Lun, Li, Na, Gong, Zheng, Chen, Meili, Ying Cui, Duan, Guangya, Tong, Jin, Wu, Gangao, Huang, Tianhao, Jin, Enhui, Zhao, Wei, Kang, Hailong, Wang, Zhonghuang, Zeng, Jingyao, Chen, Hua, Li, Mingkun, Zhao, Wenming, Ning, Wanshan, Xue, Yu, Liu, Yanhu, Cui, Ying, Zhou, Qijun, Liu, Xingyan, Zhang, Longlong, Mao, Bingyu, Zhang, Shihua, Zhang, Yaping, Wang, Guodong, Zhu, Qianghui, Li, Xin, Li, Menghua, Liu, Yuanming, Luo, Hong, Wu, Xiaoyuan, Jing, Haichun, Pan, Yitong, Chen, Ming, Ma, Lina, Shi, Leisheng, Li, Mingkun, Lan, Li, Bao, Yiming, Zhao, Wenming, Zuo, Zhixiang, Ren, Jian, Zhang, Xinxin, Xiao, Yun, Li, Xia, Liu, Dan, Zhang, Chi, Xue, Yu, Zhao, Zheng, Jiang, Tao, Wu, Wanying, Zhao, Fangqing, Meng, Xianwen, Peng, Di, Luo, Hao, Gao, Feng, Lin, Shaofeng, Liu, Chuijie, Guo, Anyuan, Yuan, Hao, Su, Tianhan, Zhang, Yong E, Zhou, Yincong, Zhang, Weizhi, Fu, Shanshan, Tan, Xiaodan, Xie, Yubin, Guo, Guoji, Wang, Chenwei, Liao, Xingyu, Gao, Xin, Wang, Jianxin, Xie, Guiyan, Yuan, Chunhui, Tian, Feng, Yang, Dechang, Tang, Dachao, Wu, Wenyi, Gou, Yujie, Han, Cheng, Cui, Qinghua, Li, Xiang Shang, Li, ChuanYun, Luo, XiaoTong, Ren, Jia, Li, Xia, CNCBNGDC Members Partners. Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022. Nucleic Acids Research[J]. 2022, 第 5 作者  通讯作者  50(D1): D27-D38, http://dx.doi.org/10.1093/nar/gkab951.
[11] Shuo Shi, Qi Wang, Yunfei Shang, Congfan Bu, Mingming Lu, Meiye Jiang, Hao Zhang, Shuhuan Yu, Jingyao Zeng, Zaichao Zhang, Zhenglin Du, Jingfa Xiao. TSomVar: a tumor-only somatic and germline variant identification method with random forest. Briefings in Bioinformatics[J]. 2022, 第 12 作者  通讯作者  23(5): 1-10, 
[12] Xinchang Zheng, Wenting Zong, Zhaohua Li, Yingke Ma, Yanling Sun, Zhuang Xiong, Song Wu, Fei Yang, Wei Zhao, Congfan Bu, Zhenglin Du, Jingfa Xiao, Yiming Bao. CCAS: One-stop and comprehensive annotation system for individual cancer genome at multi-omics level. Frontiers in Genetics[J]. 2022, 第 12 作者  通讯作者  13: https://doaj.org/article/a9039c0ef81f42969902478e74ac9958.
[13] Shuo Shi, Qiheng Qian, Shuhuan Yu, Qi Wang, Jinyue Wang, Jingyao Zeng, Zhenglin Du, Jingfa Xiao. RefRGim: an intelligent reference panel reconstruction method for genotype imputation with convolutional neural networks. BRIEFINGS IN BIOINFORMATICS[J]. 2021, 第 8 作者  通讯作者  22(6): 
[14] Jiang, Meiye, Bu, Congfan, Zeng, Jingyao, Du, Zhenglin, Xiao, Jingfa. Applications and challenges of high performance computing in genomics. CCF TRANSACTIONS ON HIGH PERFORMANCE COMPUTING. 2021, 第 5 作者  通讯作者  3(4): 344-352, 
[15] Zhang, Yuansheng, Zou, Dong, Zhu, Tongtong, Xu, Tianyi, Chen, Ming, Niu, Guangyi, Zong, Wenting, Pan, Rong, Jing, Wei, Sang, Jian, Liu, Chang, Xiong, Yujia, Sun, Yubin, Zhai, Shuang, Chen, Huanxin, Zhao, Wenming, Xiao, Jingfa, Bao, Yiming, Hao, Lili, Zhang, Zhang. Gene Expression Nebulas (GEN): a comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels. NUCLEIC ACIDS RESEARCH[J]. 2021, 第 17 作者50(D1): D1016-D1024, http://dx.doi.org/10.1093/nar/gkab878.
[16] Zeng, Jingyao, Zhang, Yadong, Shang, Yunfei, Mai, Jialin, Shi, Shuo, Lu, Mingming, Bu, Congfan, Zhang, Zhewen, Zhang, Zaichao, Li, Yang, Du, Zhenglin, Xiao, Jingfa. CancerSCEM: a database of single-cell expression map across various human cancers. NUCLEIC ACIDS RESEARCH[J]. 2021, 第 12 作者  通讯作者  50(D1): D1147-D1155, http://dx.doi.org/10.1093/nar/gkab905.
[17] 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, 第 5 作者  通讯作者  49(D1): D18-D28, http://dx.doi.org/10.1093/nar/gkaa1022.
[18] Zhang, Zhang, Song, Shuhui, Yu, Jun, Zhao, Wenming, Xiao, Jingfa, Bao, Yiming. The Elements of Data Sharing. GENOMICS PROTEOMICS & BIOINFORMATICS[J]. 2020, 第 5 作者18(1): 1-4, http://lib.cqvip.com/Qikan/Article/Detail?id=00002HUHLL7G7JP0MPDO8JP1MNR.
[19] Zhang, Zhang, Zhao, Wenming, Xiao, Jingfa, Bao, Yiming, He, Shunmin, Zhang, Guoqing, Li, Yixue, Zhao, Guoping, Chen, Runsheng, Gao, Yang, Zhang, Chao, Yuan, Liyun, Xu, Shuhua, Ning, Zhilin, Lu, Yan, Zeng, Jingyao, Yuan, Na, Zhu, Junwei, Pan, Mengyu, Zhang, Hao, Wang, Qi, Shi, Shuo, Jiang, Meiye, Lu, Mingming, Qian, Qiheng, Gao, Qianwen, Shang, Yunfei, Wang, Jinyue, Du, Zhenglin, Tian, Dongmei, Wang, Pei, Tang, Bixia, Li, Cuiping, Teng, Xufei, Liu, Xiaonan, Zou, Dong, Song, Shuhui, Xiong, Zhuang, Li, Mengwei, Yang, Fei, Ma, Yingke, Sang, Jian, Li, Zhaohua, Li, Rujiao, Wang, Zhonghuang, Zhu, Qianghui, Li, Xin, Zhang, Sisi, Kang, Hailong, Dong, Lili, Ying, Cui, Duan, Guangya, Li, Menghua, Zhi, Xiaoyang, Ling, Yunchao, Cao, Ruifang, Jiang, Zhao, Zhou, Haokui, Lv, Daqing, Liu, Wan, Klenk, HansPeter, Zhang, Yadong, Zhang, Zhewen, Chen, Tingting, Chen, Xu, Wang, Yanqing, Wu, Song, Gong, Zheng, Chen, Meili, Fang, Shuangsang, Zhang, Lili, Guo, Jincheng, Niu, Yiwei, Wu, Yang, Li, Hui, Zhao, Lianhe, Li, Xiyuan, Teng, Xueyi, Sun, Xianhui, Sun, Liang, Zhao, Yi, Wang, Jiajia, Zhang, Peng, Li, Yanyan, Zheng, Yu, Chen, Xiaomin, Xue, Hua, Teng, Yiheng, Kang, Quan, Hao, Yajing, Cao, Jiabao, Liu, Lin, Li, Zhao, Li, Qianpeng, Du, Qiang, Abbasi, Amir A, Shireen, Huma, Pervaiz, Nashaiman, Batool, Fatima, Raza, Rabail Z, Ma, Lina, Niu, Guangyi, Zhang, Yuansheng, Zhu, Tongtong, Hao, Lili, Wang, Guoliang, Yan, Jun, Li, Chen, Wang, Zhennan, Wang, Xiangfeng, Li, Zhonghai, Zhang, Yang, Wang, Houling, Zhang, Yi, Xia, Xinli, Guo, Hongwei, Zhu, Junwen, Zhou, Qing, Kang, Hongen, Lan, Li, Zhang, Xin, Xue, Yongbiao, Sun, Yubin, Zhai, Shuang, Yu, Lei, Sun, Mingyuan, Chen, Huanxin, Hu, Hui, Guo, AnYuan, Lin, Shaofeng, Xue, Yu, Wang, Chenwei, Ning, Wanshan, Zhang, Xinxin, Xiao, Yun, Li, Xia, Tu, Yiran, Wu, Wanying, Ji, Peifeng, Zhao, Fangqing, Luo, Hao, Gao, Feng, Guo, Yaping, Yuan, Hao, Zhang, Yong E, Zhang, Qiong, Zhou, Jiaqi, Huang, Zhou, Cui, Qinghua, Miao, YaRu, Ruan, Chen, Yuan, Chunhui, Chen, Ming, Jin, JinPu, Tian, Feng, Gao, Ge, Shi, Ying, Yao, Lan, Li, Xiangshang, Li, ChuanYun, Tang, Qing, Peng, Di. Database Resources of the National Genomics Data Center in 2020. NUCLEIC ACIDS RESEARCH[J]. 2020, 第 3 作者  通讯作者  48(D1): D24-D33, https://www.webofscience.com/wos/woscc/full-record/WOS:000525956700004.
[20] Zhang, Yadong, Zhang, Zhewen, Zhang, Hao, Zhao, Yongbing, Zhang, Zaichao, Xiao, Jingfa. PADS Arsenal: a database of prokaryotic defense systems related genes. NUCLEICACIDSRESEARCH[J]. 2020, 第 6 作者  通讯作者  48(D1): D590-D598, http://dx.doi.org/10.1093/nar/gkz916.
[21] Song, Shuhui, Ma, Lina, Zou, Dong, Tian, Dongmei, Li, Cuiping, Zhu, Junwei, 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, Xiao, Jingfa, Zhang, Zhang, Zhao, Wenming, Xue, Yongbiao, Bao, Yiming. The Global Landscape of SARS-CoV-2 Genomes, Variants, and Haplotypes in 2019nCoVR. GENOMICS PROTEOMICS & BIOINFORMATICS[J]. 2020, 第 26 作者18(6): 749-759, http://dx.doi.org/10.1016/j.gpb.2020.09.001.
[22] Li, Zhao, Liu, Lin, Jiang, Shuai, Li, Qianpeng, Feng, Changrui, Du, Qiang, Zou, Dong, Xiao, Jingfa, Zhang, Zhang, Ma, Lina. LncExpDB: an expression database of human long non-coding RNAs. NUCLEIC ACIDS RESEARCH[J]. 2020, 第 8 作者49(D1): D962-D968, http://dx.doi.org/10.1093/nar/gkaa850.
[23] Teng, Xufei, Li, Qianpeng, Li, Zhao, Zhang, Yuansheng, Niu, Guangyi, Xiao, Jingfa, Yu, Jun, Zhang, Zhang, Song, Shuhui. Compositional Variability and Mutation Spectra of Monophyletic SARS-CoV-2 Clades. GENOMICS PROTEOMICS & BIOINFORMATICS[J]. 2020, 第 6 作者18(6): 648-663, http://dx.doi.org/10.1016/j.gpb.2020.10.003.
[24] Zhao, Yongbing, Wang, Jinyue, Liang, Fang, Liu, Yanxia, Wang, Qi, Zhang, Hao, Jiang, Meiye, Zhang, Zhewen, Zhao, Wenming, Bao, Yiming, Zhang, Zhang, Wu, Jiayan, Asmann, Yan W, Li, Rujiao, Xiao, Jingfa. NucMap: a database of genome-wide nucleosome positioning map across species. NUCLEIC ACIDS RESEARCH[J]. 2019, 第 15 作者  通讯作者  47(D1): D163-D169, 
[25] Zhang, Zhang, Zhao, Wenming, Xiao, Jingfa, Bao, Yiming, Wang, Fan, Hao, Lili, Zhu, Junwei, Chen, Tingting, Zhang, Sisi, Chen, Xu, Tang, Bixia, Zhou, Qing, Wang, Zhonghuang, Dong, Lili, Wang, Yanqing, Ma, Yingke, Zhang, Zhewen, Wang, Zhonghuang, Chen, Meili, Tian, Dongmei, Li, Cuiping, Teng, Xufei, Du, Zhenglin, Yuan, Na, Zeng, Jingyao, Wang, Jinyue, Shi, Shuo, Zhang, Yadong, Wang, Qi, Pan, Mengyu, Qian, Qiheng, Song, Shuhui, Niu, Guangyi, Li, Man, Xia, Lin, Zou, Dong, Zhang, Yuansheng, Sang, Jian, Li, Mengwei, Zhang, Yang, Wang, Pei, Gao, Qianwen, Liang, Fang, Li, Rujiao, Liu, Lin, Cao, Jiabao, abbasi, Amir A, Shireen, Huma, Li, Zhao, Xiong, Zhuang, Jiang, Meiye, Guo, Tongkun, Li, Zhaohua, Zhang, Hao, Ma, Lina, Gao, Ran, Zhang, Tao, Li, Wulue, Zhang, Xiangquan, Lan, Li, Zhai, Shuang, Zhang, Yaping, Wang, Guodong, Wang, Zhennan, Xue, Yongbiao, Sun, Yubin, Yu, Lei, Sun, Mingyuan, Chen, Huanxin, Hu, Hui, Guo, AnYuan, Lin, Shaofeng, Xue, Yu, Wang, Chenwei, Ning, Wanshan, Zhang, Ying, Luo, Hao, Gao, Feng, Guo, Yaping, Zhang, Qiong, Zhou, Jiaqi, Huang, Zhou, Cui, Qinghua, Miao, YaRu, Ruan, Chen, Yuan, Chunhui, Chen, Ming, Jinpu, Jin, Gao, Ge, Xu, Haodong, Li, Yumei, Li, ChuanYun, Tang, Qing, Peng, Di, Deng, Wankun, Big Data Ctr Members. Database Resources of the BIG Data Center in 2019. NUCLEIC ACIDS RESEARCH[J]. 2019, 第 3 作者  通讯作者  47(D1): D8-D14, http://dx.doi.org/10.1093/nar/gky993.
[26] Du, Zhenglin, Ma, Liang, Qu, Hongzhu, Chen, Wei, Zhang, Bing, Lu, Xi, Zhai, Weibo, Sheng, Xin, Sun, Yongqiao, Li, Wenjie, Lei, Meng, Qi, Qiuhui, Yuan, Na, Shi, Shuo, Zeng, Jingyao, Wang, Jinyue, Yang, Yadong, Liu, Qi, Hong, Yaqiang, Dong, Lili, Zhang, Zhewen, Zou, Dong, Wang, Yanqing, Song, Shuhui, Liu, Fan, Fang, Xiangdong, Chen, Hua, Liu, Xin, Xiao, Jingfa, Zeng, Changqing. Whole Genome Analyses of Chinese Population and De Novo Assembly of A Northern Han Genome. GENOMICS PROTEOMICS & BIOINFORMATICS[J]. 2019, 第 29 作者  通讯作者  17(3): 229-247, http://lib.cqvip.com/Qikan/Article/Detail?id=71806673504849574851484851.
[27] Chen, Xinyu, Zhang, Yadong, Zhang, Zhewen, Zhao, Yongbing, Sun, Chen, Yang, Ming, Wang, Jinyue, Liu, Qian, Zhang, Baohua, Chen, Meili, Yu, Jun, Wu, Jiayan, Jin, Zhong, Xiao, Jingfa. PGAweb: A Web Server for Bacterial Pan-Genome Analysis. FRONTIERS IN MICROBIOLOGY[J]. 2018, 第 14 作者  通讯作者  9: http://www.corc.org.cn/handle/1471x/2374278.
[28] Li, Rujiao, Liang, Fang, Li, Mengwei, Zou, Dong, Sun, Shixiang, Zhao, Yongbing, Zhao, Wenming, Bao, Yiming, Xiao, Jingfa, Zhang, Zhang. MethBank 3.0: a database of DNA methylomes across a variety of species. NUCLEIC ACIDS RESEARCH[J]. 2018, 第 9 作者46(D1): D288-D295, https://www.webofscience.com/wos/woscc/full-record/WOS:000419550700044.
[29] Xu, Xingjian, Hao, Lili, Zhu, Junwei, Zhou, Qing, Song, Fuhai, Chen, Tingting, Zhang, Sisi, Dong, Lili, Lan, Li, Wang, Yanqing, Liang, Fang, Cao, Jiabao, Liu, Fang, Liu, Lin, Wang, Fan, Ma, Yingke, Zhang, Lijuan, Chen, Meili, Tian, Dongmei, Li, Cuiping, Du, Zhenglin, Yuan, Na, Zeng, Jingyao, Zhang, Zhewen, Wang, Jinyue, Shi, Shuo, Zhang, Yadong, Pan, Mengyu, Tang, Bixia, Zou, Dong, Song, Shuhui, Sang, Jian, Xia, Lin, Wang, Zhennan, Li, Man, Niu, Guangyi, Zhang, Yang, Sheng, Xin, Lu, Mingming, Wang, Qi, Liang, Fang, Li, Mengwei, Sun, Shixiang, Li, Rujiao, Yu, Chunlei, Wang, Guangyu, Li, Man, Yin, Hongyan, Ma, Lina, Chen, Huanxin, Sun, Yubin, Yu, Lei, Zhai, Shuang, Sun, Mingyuan, Zhang, Zhang, Zhao, Wenming, Xiao, Jingfa, Bao, Yiming, Song, Shuhui, Miao, YaRu, Guo, AnYuan, Lin, Shaofeng, Xue, Yu, Luo, Hao, Gao, Feng, Ma, Wei, Cui, Qinghua, Xu, Haodong, BIG Data Ctr, BioCode Team, BioProject BioSample GSA Team, GWH Team, GVM Team, GEN Team, MethBank Team, Science Wikis Team, Hardware System Administration, Writing Grp, AnimalTFDB lncRNASNP Team, dbPAF Team, DEG DoriC Team, LncRNADis Team, PLMD Team. Database Resources of the BIG Data Center in 2018. NUCLEIC ACIDS RESEARCH[J]. 2018, 第 57 作者  通讯作者  46(D1): D14-D20, http://dx.doi.org/10.1093/nar/gkx897.
[30] Zhao, Yongbing, Sun, Chen, Zhao, Dongyu, Zhang, Yadong, You, Yang, Jia, Xinmiao, Yang, Junhui, Wang, Lingping, Wang, Jinyue, Fu, Haohuan, Kang, Yu, Chen, Fei, Yu, Jun, Wu, Jiayan, Xiao, Jingfa. PGAP-X: extension on pan-genome analysis pipeline. BMC Genomics[J]. 2018, 第 15 作者  通讯作者  19(S1): https://doaj.org/article/778dfe46a6174e30abed0aee35dafbc8.
[31] Jin, Jun, Li, Rujiao, Jiang, Chunlai, Zhang, Ruosi, Ge, Xiaomeng, Liang, Fang, Sheng, Xin, Dai, Wenwen, Chen, Meili, Wu, Jiayan, Xiao, Jingfa, Su, Weiheng. Transcriptome analysis reveals dynamic changes in coxsackievirus A16 infected HEK 293T cells. BMC GENOMICS[J]. 2017, 第 11 作者  通讯作者  18(Suppl 1): http://dx.doi.org/10.1186/s12864-016-3253-6.
[32] Zhang, Zhang, Zhao, Wenming, Xiao, Jingfa, Song, Shuhui, Hao, Lili, Li, Rujiao, Ma, Lina, Sheng, Xin, Sang, Jian, Wang, Yanqing, Tang, Bixia, Zhang, Zhewen, BIG Data Ctr Members. The BIG Data Center: from deposition to integration to translation. NUCLEIC ACIDS RESEARCH[J]. 2017, 第 3 作者  通讯作者  45(D1): D18-D24, http://dx.doi.org/10.1093/nar/gkw1060.
[33] Yuan, Lina, Yu, Yang, Zhu, Yanmin, Li, Yulai, Li, Changqing, Li, Rujiao, Ma, Qin, Siu, Gilman KitHang, Yu, Jun, Jiang, Taijiao, Xiao, Jingfa, Kang, Yu. GAAP: Genome-organization-framework-Assisted Assembly Pipeline for prokaryotic genomes. BMC GENOMICS[J]. 2017, 第 11 作者  通讯作者  18(Suppl 1): http://dx.doi.org/10.1186/s12864-016-3267-0.
[34] Shi, Shuo, Yuan, Na, Yang, Ming, Du, Zhenglin, Wang, Jinyue, Sheng, Xin, Wu, Jiayan, Xiao, Jingfa. Comprehensive Assessment of Genotype Imputation Performance. HUMAN HEREDITY[J]. 2017, 第 8 作者  通讯作者  83(3): 107-116, http://dx.doi.org/10.1159/000489758.
[35] Sheng, Xin, Wu, Jiayan, Sun, Qianqian, Li, Xue, Xian, Feng, Sun, Manman, Fang, Wan, Chen, Meili, Yu, Jun, Xiao, Jingfa. MTD: a mammalian transcriptomic database to explore gene expression and regulation. BRIEFINGS IN BIOINFORMATICS[J]. 2017, 第 11 作者18(1): 28-36, https://www.webofscience.com/wos/woscc/full-record/WOS:000397059700003.
[36] Sun, Shixiang, Xiao, Jingfa, Zhang, Huiyong, Zhang, Zhang. Pangenome Evidence for Higher Codon Usage Bias and Stronger Translational Selection in Core Genes of Escherichia coli. FRONTIERS IN MICROBIOLOGY[J]. 2016, 第 2 作者7: http://www.corc.org.cn/handle/1471x/2374454.
[37] Tian, Xinpeng, Zhang, Zhewen, Yang, Tingting, Chen, Meili, Li, Jie, Chen, Fei, Yang, Jin, Li, Wenjie, Zhang, Bing, Zhang, Zhang, Wu, Jiayan, Zhang, Changsheng, Long, Lijuan, Xiao, Jingfa. Comparative Genomics Analysis of Streptomyces Species Reveals Their Adaptation to the Marine Environment and Their Diversity at the Genomic Level. Frontiers in Microbiology[J]. 2016, 第 14 作者  通讯作者  7: http://ir.scsio.ac.cn/handle/344004/15393.
[38] Zhao, Yongbing, Yin, Jinlong, Guo, Haiyan, Zhang, Yuyu, Xiao, Wen, Sun, Chen, Wu, Jiayan, Qu, Xiaobo, Yu, Jun, Wang, Xumin, Xiao, Jingfa. The complete chloroplast genome provides insight into the evolution and polymorphism of Panax ginseng. FRONTIERS IN PLANT SCIENCE[J]. 2015, 第 11 作者  通讯作者  5: https://doaj.org/article/40897713878a43e591df7acdedbb8b99.
[39] Ling, Yunchao, Jin, Zhong, Su, Mingming, Zhong, Jun, Zhao, Yongbing, Yu, Jun, Wu, Jiayan, Xiao, Jingfa. VCGDB: a dynamic genome database of the Chinese population. BMC GENOMICS[J]. 2014, 第 8 作者  通讯作者  15(1): http://www.corc.org.cn/handle/1471x/2374155.
[40] Wang, Wenquan, Feng, Binxiao, Xiao, Jingfa, Xia, Zhiqiang, Zhou, Xincheng, Li, Pinghua, Zhang, Weixiong, Wang, Ying, Moller, Birger Lindberg, Zhang, Peng, Luo, MingCheng, Xiao, Gong, Liu, Jingxing, Yang, Jun, Chen, Songbi, Rabinowicz, Pablo D, Chen, Xin, Zhang, HongBin, Ceballos, Henan, Lou, Qunfeng, Zou, Meiling, Carvalho, Luiz J C B, Zeng, Changying, Xia, Jing, Sun, Shixiang, Fu, Yuhua, Wang, Haiyan, Lu, Cheng, Ruan, Mengbin, Zhou, Shuigeng, Wu, Zhicheng, Liu, Hui, Kannangara, Rubini Maya, Jorgensen, Kirsten, Neale, Rebecca Louise, Bonde, Maya, Heinz, Nanna, Zhu, Wenli, Wang, Shujuan, Zhang, Yang, Pan, Kun, Wen, Mingfu, Ma, PingAn, Li, Zhengxu, Hu, Meizhen, Liao, Wenbin, Hu, Wenbin, Zhang, Shengkui, Pei, Jinli, Guo, Anping, Guo, Jianchun, Zhang, Jiaming, Zhang, Zhengwen, Ye, Jianqiu, Ou, Wenjun, Ma, Yaqin, Liu, Xinyue, Tallon, Luke J, Galens, Kevin, Ott, Sandra, Huang, Jie, Xue, Jingjing, An, Feifei, Yao, Qingqun, Lu, Xiaojing, Fregene, Martin, Augusto Becerra LopezLavalle, L, Wu, Jiajie, You, Frank M, Chen, Meili, Hu, Songnian, Wu, Guojiang, Zhong, Silin, Ling, Peng, Chen, Yeyuan, Wang, Qinghuang, Liu, Guodao, Liu, Bin, Li, Kaimian, Peng, Ming. Cassava genome from a wild ancestor to cultivated varieties. NATURE COMMUNICATIONS[J]. 2014, 第 3 作者5: http://ir.scbg.ac.cn/handle/344003/17978.
[41] Zhao, Dongyu, Wu, Jiayan, Zhou, Yuanyuan, Gong, Wei, Xiao, Jingfa, Yu, Jun. WikiCell: A Unified Resource Platform for Human Transcriptomics Research. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY[J]. 2012, 第 5 作者  通讯作者  16(6): 357-362, http://dx.doi.org/10.1089/omi.2011.0139.
[42] Zhao Qian, Xiao JingFa, Yu Jun. An Integrated Analysis of Lineage-specific Small Proteins Across Eight Eukaryotes Reveals Functional and Evolutionary Significance. PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS[J]. 2012, 第 2 作者  通讯作者  39(4): 359-367, https://www.webofscience.com/wos/woscc/full-record/WOS:000303278200009.
[43] Ming Yang, Yan Ge, Jiayan Wu, Jingfa Xiao, Jun Yu. Coevolution study of mitochondria respiratory chain proteins: Toward the understanding of protein-protein interaction. 遗传学报[J]. 2011, 第 4 作者  通讯作者  38(5): 201-207, http://lib.cqvip.com/Qikan/Article/Detail?id=38016235.
[44] Zhao, Yongbing, Xiao, Jingfa. Homology Modeling and Molecular Dynamics Simulation Studies of Human Type 1 3 beta-Hydroxysteroid Dehydrogenase: Toward the Understanding of Cofactor Specificity. JOURNAL OF COMPUTATIONAL CHEMISTRY[J]. 2011, 第 2 作者  通讯作者  32(1): 33-42, http://dx.doi.org/10.1002/jcc.21595.
[45] Zhang, Anding, Yang, Ming, Hu, Pan, Wu, Jiayan, Chen, Bo, Hua, Yafeng, Yu, Jun, Chen, Huanchun, Xiao, Jingfa, Jin, Meilin. Comparative genomic analysis of Streptococcus suis reveals significant genomic diversity among different serotypes. BMC GENOMICS[J]. 2011, 第 9 作者  通讯作者  12(1): 523-523, http://dx.doi.org/10.1186/1471-2164-12-523.
[46] Hu, Pan, Yang, Ming, Zhang, Anding, Wu, Jiayan, Chen, Bo, Hua, Yafeng, Yu, Jun, Xiao, Jingfa, Jin, Meilin. Complete Genome Sequence of Streptococcus suis Serotype 14 Strain JS14. JOURNAL OF BACTERIOLOGY[J]. 2011, 第 8 作者  通讯作者  193(9): 2375-2376, https://www.webofscience.com/wos/woscc/full-record/WOS:000289670000044.
发表著作
(1) 基因组学核心实验方法, Genomics:essential methods, 科学出版社, 2012-03, 第 3 作者
(2) 第二代测序信息处理, next-generation DNA sequencing informatics, 科学出版社, 2014-06, 第 2 作者
(3) 基因组学与精准医学, Genomics and Precision Medicine, 上海交通大学出版社, 2017-12, 第 3 作者
(4) 系统生物学, Systems Biology, 重庆出版社, 2018-09, 第 5 作者

科研活动

   
科研项目
( 1 ) 生物信息技术共享、转化研究平台建设, 负责人, 国家任务, 2012-01--2015-12
( 2 ) 基于RNA-seq策略研究天然反义转录本的调控机制, 负责人, 国家任务, 2013-01--2016-12
( 3 ) 南海部分海区重要微生物类群基因组多样性初步研究, 负责人, 中国科学院计划, 2013-01--2015-12
( 4 ) 基于深度测序和Hi-C方法对染色体层次上基因表达调控机制的研究, 负责人, 国家任务, 2015-01--2018-12
( 5 ) 中科院人群队列建立及精准医学研究, 负责人, 中国科学院计划, 2015-10--2018-12
( 6 ) 精准医疗和个性化药物应用示范, 负责人, 国家任务, 2016-06--2020-12
( 7 ) 中国人群多组学参比数据库与分析系统建设, 参与, 国家任务, 2017-06--2020-12
( 8 ) 微生物泛基因组信息深度挖掘新方法研究, 负责人, 国家任务, 2018-01--2021-12
( 9 ) 精准医疗大数据管理平台与应用示范, 负责人, 国家任务, 2017-01--2019-12
( 10 ) 基于基因型填补的无参肿瘤基因组变异鉴定新算法研究, 负责人, 国家任务, 2020-01--2023-12
( 11 ) 中国人群多组学知识库体系研发与建设, 负责人, 中国科学院计划, 2020-01--2024-12
( 12 ) 基于多级编解码技术的 DNA 活字生成器研究, 负责人, 国家任务, 2021-01--2025-12
( 13 ) 大规模数据整合分析细菌的泛基因组形成机制, 负责人, 国家任务, 2022-01--2025-12
参与会议
(1)中科院人群队列建立和精准医学研究   第六届基因组科学与应用大会   2019-09-20
(2)NucMap: a database of genome-wide nucleosome positioning map across species   2019-04-08
(3)CASPMI project and Precision Medicine   2019-03-30
(4)CASPMI project and genetic reports study   2018-10-20
(5)Knowledge database of genome variation map for life and health   2018-07-25
(6)Comprehensive assessment of genotype imputation performance   2018-06-10
(7)De novo assembly of a northern Chinese genome.   Zhenglin Du, Na Yuan, Jingyao Zeng, Shuo Shi, Hongzhu Qu, Lili Dong, Jingfa Xiao   2018-04-08
(8)CAS precision medicine initiative   2018-03-26
(9)PGAP-X: Extension on pan-genome analysis pipeline   2017-09-20
(10)The BIG Data Center’s database resources: towards precision medicine   2017-03-29
(11)MTD: a mammalian transcriptomic database to explore gene expression and regulation   Shengxin, Jiayan Wu, Jun Yu, Jingfa Xiao   2016-10-03
(12)VCGDB: a dynamic genome database of the Chinese population   97. Yunchao Ling, Jiayan Wu, Jun Yu,    2015-04-23
(13)The complexity of mammalian transcriptomes and need for a pan-mammalian transcriptome project   JiayanWu, Lina Ma, Jingfa Xiao, Zhang Zhang, Xumin Wang, Shuangxiu Wu, Yu Kang, Songnian Hu, Jun Yu   2014-10-06
(14)Gene expression analysis of induced pluripotent stem cells from aneuploid chromosomal syndromes   Ruosi Zhang, Lili Hao, Lingping Wang, Meili Chen, Wen Li, M Esteban, Jun Yu,   2013-09-20
(15)General flow for high plant organelle genome sequence assembling and analysis    第六期木薯生物技术与功能基因组学研讨会   Yongbing Zhao, Jingfa Xiao.    2012-10-26
(16)Human cancer signatures in gene expression   Meili Chen, Jiayan Wu, Jingfa Xiao   2011-09-08
(17)Interrogating Transcriptome   第七届国际生物信息学研讨会   Jiang Zhu,Fuhong He, Jiayan Wu, Jingfa Xiao, Jun Yu   2009-06-18

指导学生

已指导学生

张再超  硕士研究生  071021-生物信息学  

孙世翔  硕士研究生  071021-生物信息学  

苏明明  硕士研究生  071021-生物信息学  

杨俊辉  硕士研究生  071021-生物信息学  

杨婷婷  硕士研究生  085211-计算机技术  

方皖  硕士研究生  085238-生物工程  

李雪  硕士研究生  085211-计算机技术  

王金月  博士研究生  0710J3-生物信息学  

张亚东  博士研究生  0710J3-生物信息学  

潘梦宇  硕士研究生  0710J3-生物信息学  

盛欣  博士研究生  0710J3-生物信息学  

高晨  硕士研究生  0710J3-生物信息学  

张莉娟  硕士研究生  0710Z1-基因组学  

王琪  硕士研究生  0710J3-生物信息学  

张好  硕士研究生  085211-计算机技术  

时硕  博士研究生  0710J3-生物信息学  

路明明  博士研究生  0710J3-生物信息学  

高千雯  硕士研究生  085238-生物工程  

现指导学生

姜美叶  博士研究生  0710J3-生物信息学  

于淑欢  硕士研究生  0710J3-生物信息学  

聂致  硕士研究生  0710Z1-基因组学  

张好  博士研究生  0710J3-生物信息学  

钱启衡  博士研究生  0710J3-生物信息学  

麦嘉琳  硕士研究生  0710J3-生物信息学  

尚云飞  博士研究生  0710J3-生物信息学  

徐晨乐  硕士研究生  0710J3-生物信息学  

方哲剑  硕士研究生  0710J3-生物信息学