全体研究组长

李亦学
博士 研究员 博士生导师

上海市科教兴市领军人才,上海市劳动模范,全国五一国际劳动奖章获得者

中科院计算生物学重点实验室,副主任,计算基因组学和大数据课题组组长

生物医学大数据中心,主任

研究方向:生物信息学、系统生物学、基因组学、精准医学、复杂生物系统及其临界现象

电子邮件(E-mail):yxli@sibs.ac.cn

电话(Tel):021-54920089

邮政编码:200031

课题组网站:http://picb.ac.cn/yxlilab/

简历 & 研究方向
2016-至     今  中国科学院-马普学会计算生物学伙伴研究所,研究员
2002-2015年  中国科学院上海生命科学研究院,研究员
2000-2002年  中国科学院上海生命科学研究院,副研究员
1997-2000年  欧洲分子生物学实验室,EMBL,博士后
1996-1997年  德国斯图加特大学,计算机研究所,博士后
1992-1996年  德国海德堡大学, 理论物理, 博士
1987-1992年  新疆大学,物理系,讲师
1984-1987年  新疆大学, 物理系, 硕士

研究方向
(1)生物信息学和系统生物学。
基因组结构分析,基因调控网络分析,蛋白质组学和蛋白质相互作用分析,复杂系统体系建模和动态性质模拟,组学数据整合分析,生物学系统的涨落平衡、临界现象与生物学功能的关系研究。
(2)肿瘤基因组学。
运用生物信息学和计算生物学的方法建立统计和计算模型, 整合分析多组学数据,寻找肿瘤疾病分子标志物和药物作用靶点,探求肿瘤发生发展的机制,为肿瘤的精准治疗提供线索。
(3)生物医学数据库构建和数据分析算法。
生物医学知识发现、数据挖掘和数据库构建,针对特定科学问题的大数据分析流程构建、算法研究和工具开发。
(4)疾病动物模型基因组学。
利用比较基因组学、群体遗传和功能基因组学等生物信息方法,分析研究特定动物模型的遗传和调控机制。
(5)精准医学。
整合大数据产出的前沿实验技术体系与大数据分析体系,开展基于生物医学大数据的重大疾病分子分型研究,研究建立临床用药的精准化分析与咨询系统。

代表性论文(* 通讯作者)

  1. Zuo EW*, Sun YD, Yuan TL, He BB, Zhou CY, Ying WQ, Liu J, Wei W, Zeng R, Li YX*, Yang H*. A rationally engineered cytosine base editor retains high on-target activity while reducing both DNA and RNA off-target effects. Nat Methods 2020;17(6):600-604
  2. Li CY, Lu WL, Yang LG, Li ZW, Zhou XY, Guo R, Wang JQ, Wu ZB, Dong ZY, Ning G, Shi YJ, Gu YM, Chen P, Hao ZJ, Han TT, Yang MQ, Wang W, Huang XH, Li YX*, Gao S*, Hu RG*. MKRN3 regulates the epigenetic switch of mammalian puberty via ubiquitination of MBD3. National Science Review 2020;7:671-685
  3. Zuo E, Sun Y, Wei W, Yuan T, Ying W, Sun H, Yuan L, Steinmetz LM*, Li Y*, Yang H*. Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos. Science 2019;364(6437):289-292
  4. Zhou C, Sun Y, Yan R, Liu Y, Zuo E, Gu C, Han L, Wei Y, Hu X, Zeng R, Li Y*, Zhou H*, Guo F*, Yang H*. Off-target RNA mutation induced by DNA base editing and its elimination by mutagenesis. Nature 2019;571(7764):275-278
  5. Qiu Z, Li H, Zhang Z, Zhu Z, He S, Wang X, Wang P, Qin J, Zhuang L, Wang W, Xie F, Gu Y, Zou K, Li C, Li C, Wang C, Cen J, Chen X, Shu Y, Zhang Z, Sun L, Min L, Fu Y, Huang X, Lv H, Zhou H, Ji Y, Zhang Z, Meng Z, Shi X*, Zhang H*, Li Y*, Hui L*. A Pharmacogenomic Landscape in Human Liver Cancers. Cancer Cell 2019;36(2):179-193
  6. Li W, Yang L, He Q, Hu C, Zhu L, Ma X, Ma X, Bao S, Li L, Chen Y, Deng X, Zhang X, Cen J, Zhang L, Wang Z, Xie WF, Li H*, Li Y*, Hui L*. A Homeostatic Arid1a-Dependent Permissive Chromatin State Licenses Hepatocyte Responsiveness to Liver-Injury-Associated YAP Signaling. Cell Stem Cell 2019;25(1):54-68.e5
  7. Benpeng Miao, Zhen Wang*, Yixue Li*. Genomic Analysis Reveals Hypoxia Adaptation in the Tibetan Mastiff by Introgression of the Gray Wolf from the Tibetan Plateau, Mol Biol Evol 2017;34(3):734-743
  8. Li Mao#, Chenglin Liu#, Zhen Wang, Xiaofeng Niu, Liang Xue, Zhilei Zhou, Zhenying Cai, Meng Yu, Yixue Li*, Dianqing Wu*, Lin Li*. A genome-wide loss-of-function screening method for minimizing false-negatives caused by functional redundancy. Cell research 2016;26(9):1067-1070
  9. Xiao Gou#, Zhen Wang#, Ning Li#, Feng Qiu#, Ze Xu, Dawei Yan, Shuli Yang, Jia Jia, Xiaoyan Kong, Zehui Wei, Shaoxiong Lu, Linsheng Lian, Changxin Wu, Xueyan Wang, Guozhi Li, Teng Ma, Qiang Jiang, Xue Zhao, Jiaqiang Yang, Baohong Liu, Dongkai Wei, Hong Li, Jianfa Yang, Yulin Yan, Guiying Zhao, Xinxing Dong, Mingli Li, Weidong Deng, Jing Leng, Chaochun Wei, Chuan Wang, Huaming Mao*, Hao Zhang*, Guohui Ding*, Yixue Li*. Whole-genome sequencing of six dog breeds from continuous altitudes reveals adaptation to high-altitude hypoxia. Genome Res 2014;24(8):1308-1315
  10. Zhijian Cao#, Yao Yu#, Yingliang Wu#, Pei Hao#, Zhiyong Di#, Yawen He#, Zongyun Chen, Weishan Yang, Zhiyong Shen, Xiaohua He, Jia Sheng, Xiaobo Xu, Bohu Pan, Jing Feng, Xiaojuan Yang, Wei Hong, Wenjuan Zhao, Zhongjie Li, Kai Huang, Tian Li, Yimeng Kong, Hui Liu, Dahe Jiang, Binyan Zhang, Jun Hu, Youtian Hu, Bin Wang, Jianliang Dai, Bifeng Yuan, Yuqi Feng, Wei Huang, Xiaojing Xing, Guoping Zhao, Xuan Li*, Yixue Li*, Wenxin Li*. The genome of Mesobuthus martensii reveals a unique adaptation model of arthropods, Nat Commun 2013;4:2602
  11. Yunwen Hu#, Shuihua Lu, Zhigang Song#, Wei Wang#, Pei Hao#, Jianhua Li#, Xiaonan Zhang#, Huiling Yen, Bisheng Shi, Tao Li, Wencai Guan, Lei Xu, Yi Liu, Sen Wang, Xiaoling Zhang, Di Tian, Zhaoqin Zhu, Jing He, Kai Huang, Huijie Chen, Lulu Zheng, Xuan Li, Jie Ping, Bin Kang, Xiuhong Xi, Lijun Zha, Yixue Li, Zhiyong Zhang, Malik Peirisx*, Zhenghong Yuan*. Association between adverse clinical outcome in human disease caused by novel influenza A H7N9 virus and sustained viral shedding and emergence of antiviral resistance. Lancet 2013;381(9885):2273-2279
  12. Huaixing Li#, Wei Gan#, Ling Lu#, Xiao Dong#, Xueyao Han#, Cheng Hu#, Zhen Yang#, Liang Sun#, Wei Bao#, Pengtao Li#, Meian He, Liangdan Sun, Yiqin Wang, Jingwen Zhu, Qianqian Ning, Yong Tang, Rong Zhang, Jie Wen, Di Wang, Xilin Zhu, Kunquan Guo, Xianbo Zuo, Xiaohui Guo, Handong Yang, Xianghai Zhou, DIAGRAM Consortium, AGEN-T2D Consortium, Xuejun Zhang, Lu Qi, Ruth J.F. Loos, Frank B. Hu, Tangchun Wu, Ying Liu, Liegang Liu, Ze Yang, Renming Hu, Weiping Jia, Linong Ji, Yixue Li*, Xu Lin*. A genome-wide association study identifies GRK5 and RASGRP1 as type 2 diabetes loci in Chinese Hans. Diabetes 2013;62(1):291-298
  13. Jirimutu#, Zhen Wang#, Guohui Ding#, Gangliang Chen#, Yamin Sun#, Zhihong Sun#, Heping Zhang, Lei Wang, Surong Hasi, Yan Zhang, Jianmei Li, Yixiang Shi, ZeXu, Chuan He, Siriguleng Yu, Shengdi Li, Wenbin Zhang, Mijiddorj Batmunkh, Batsukh Ts, Narenbatu, Unierhu, Shirzana Bat-Ireedui, Hongwei Gao, Banzragch Baysgalan, Qing Li, Zhiling Jia, Turigenbayila,Subudenggerile, Narenmanduhu, Zhaoxia Wang, Juan Wang, Lei Pan, Yongcan Chen, Yaichil Ganerdene, Dabxilt, Erdemt, Altansha, Altansukh, Tuya Liu, Minhui Cao, Aruuntsever, Bayart, Hosblig, Fei He, A Zha-ti, Guangyong Zheng, Feng Qiu, Zikui Sun, Lele Zhao,Wenjing Zhao, Baohong Liu, Chao Li, Yunqin Chen, Xiaoyan Tang, Chunyan Guo, Wei Liu, Liang Ming, Temuulen, Aiying Cui, YiLi, Junhui Gao, Jing Li, Wurentaodi, Shen Niu, Tao Sun, Zhengxiao Zhai, Min Zhang, Chen Chen, Tunteg Baldan, Tuman Bayaer, Yixue Li*, He Meng*. Genome sequences of wild and domestic bactrian camels. Nature communications 2012;3:1202
  14. Zhen Wang#, Guohui Ding#, Ludwig Geistlinger, Hong Li, Lei Liu, Rong Zeng*, Yoshio Tateno*, Yixue Li*. Evolution of protein phosphorylation for distinct functional modules in vertebrate genomes. Molecular biology and evolution 2011;28(3):1131-1140
  15. Shimin Zhao, Wei Xu,Wenqing Jiang, Wei Yu, Yan Lin, Tengfei Zhang, Jun Yao, Li Zhou, Yaxue Zeng, Hong Li, Yixue Li, Jiong Shi, Wenlin An, Susan M. Hancock, Fuchu He, Lunxiu Qin, Jason Chin, Pengyuan Yang, Xian Chen, Qunying Lei, Yue Xiong*, Kunliang Guan*. Regulation of cellular metabolism by protein lysine acetylation. Science 2010;327(5968):1000-1004
  16. Ruoyu Luo#, Haibin Wei#, Lin Ye, Kankan Wang, Fan Chen, Lijun Luo, Lei Liu, Yuanyuan Li, M. James C. Crabbe, Li Jin, Yixue Li*, Yang Zhong*. Photosynthetic metabolism of C3 plants shows highly cooperative regulation under changing environments: a systems biological analysis. Proceedings of the National Academy of Sciences of the United States of America 2009;106(3):847-852