姓  名: 张 勇
学  科: 计算进化基因组学
电话/传真: +86-10-64806339 / +86-10-64806339
电子邮件: zhangyong@ioz.ac.cn
通讯地址: 北京市朝阳区北辰西路1号院5号中国科学院动物研究所A627 100101
更多信息: 计算进化基因组学研究组     

简历介绍:

张勇于2006年获北京大学生物信息学博士学位,2007年至2011年于芝加哥大学从事研究,2011年通过国家高层次人才计划(青年)加入中国科学院动物所任研究员。他长期聚焦物种特异重复基因的功能、介导基因重复的突变机制及突变机制的转化研究,在前沿基础研究和国家战略需求两方面获得系列成果。包含Cell (In press)、Nature Ecology Evolution (2022/2024)、Nature Biotechnology(2023)等论文在内,张勇共发表论文70余篇,总引用达8100次(Google Scholar);获批国内专利一项,申请国际专利两项;主持国家杰出青年科学基金、优秀青年科学基金、中国科学院从0到1原始创新等项目。更多信息请访问http://zhanglab.ioz.ac.cn ;动物所内部请访问http://10.0.60.55/

研究领域:

1)基础研究:刻画新基因起源机制,揭示新基因对表型进化的意义。

研究组开发基于从头拼接的新方法,在果蝇与人类群体中鉴定串联重复,发现与传统假定不同,串联重复多不能产生完整基因拷贝,但仍可通过基因融合等机制产生新基因结构,具有较大功能后果。该工作发表于Nature Ecology Evolution(2022)。研究组也在多种动物基因组中发现基因/转座子嵌合现象并解析其机制,即微相似序列在复制中介导模板跳转。这些工作发表于Genome Research(2016)、Nature Communications(2021)。

不仅如此,研究组开发了基因年龄推断方法,产生了高质量新基因数据集,发现其在人大脑等快速演化的器官中上调。这些工作发表于Genome Research(2019)、Developmental Cell(2021)等。研究组也解析了脊椎动物早期的进化,揭示早期产生的重复基因推动了脊椎动物祖先的发育进化;该工作发表于Nature Ecology Evolution(2024)。

2)应用研究:从基因起源演化的概念和方法出发,开发具备自主知识产权的新技术。

由于转座子编码的TnpB与基因编辑器Cas12源自同一基因家族,研究组开发新方法从原核基因组中基于进化信息预测活跃的TnpB,结合实验鉴定了目前最小的基因编辑器,方便了体内递送。这一工作发表于Nature Biotechnology(2023)。类似的,研究组从动物基因组中挖掘了40个新的转座子载体,使其数量从20上升到60;其中活性最高的新载体性能在CAR-T免疫治疗中优于常用的慢病毒。该工作发表于Cell(In press)。研究组也开发了基于转座子的非扩增三代测序微量建库技术,方便了小动物或珍惜样品的测序组装,投稿至Nature Communications(Accepted in principle)。

社会任职:

获奖及荣誉:

承担科研项目情况:

代表论著:

(*: co-first authors; #: co-corresponding authors)

  1. Tongtong Zhang*, Shengjun Tan*, Na Tang*, Yuanqing Li*, Jing Sun, Yanyan Guo, Hui Gao, Chenze Zhang, Yujia Cai, Wen Sun, Xiaoxuan Hu, Xuechun Zhang, Liangzheng Fu, Yachao Wu, Peter Gee, Weihua Yan, Yahui Zhao, Qiang Chen, Baocheng Guo, Haoyi Wang# and Yong E. Zhang#. A large-scale heterologous survey of 130 DNA transposons in human cells highlights their functional divergence and expands genome engineering toolbox. Cell, In press.
  2. Hangxing Jia*#, Shengjun Tan*#, Yingao Cai*, Yanyan Guo, Jieyu Shen, Yaqiong Zhang, Jinfeng Chen, Gexia Qiao, Jue Ruan#, Yong E. Zhang#. Low-input long-read sequencing generates high-quality individual fly genomes and characterizes mutational processes. Nature Communications, Accepted in principle.
  3. Daqi Yu*, Yandong Ren*, Masahiro Uesaka*, Alan J. S. Beavan*, Matthieu Muffato#, Jieyu Shen, Yongxin Li, Iori Sato, Wenting Wan, James W. Clark, Joseph N. Keating, Emily M. Carlisle, Richard P. Dearden, Sam Giles, Emma Randle, Robert S. Sansom, ..., Fergal J. Martin#, Wen Wang#, Philip C. J. Donoghue#, Yong E. Zhang# & Juan Pascual-Anaya#. Hagfish genome illuminates vertebrate whole genome duplications and their evolutionary consequences. Nature Ecology and Evolution, 2024, 8(3):519-535.
  4. Guanghai Xiang*#, Yuanqing Li*, Jing Sun*, Yongyuan Huo*, Shiwei Cao, Yuanwei Cao, Yanyan Guo, Ling Yang, Yujia Cai, Yong E. Zhang# & Haoyi Wang#. Evolutionary mining and functional characterization of TnpB nucleases identify efficient miniature genome editors, Nature Biotechnology, 2023,29:1-3.
  5. Huijing Ma*, Mengxia Wang*, Yong E. Zhang#, Shengjun Tan#, The power of “controllers”: Transposon-mediated duplicated genes evolve towards neofunctionalization. Journal of Genetics and Genomics, 2023,50(7):462-472.
  6. Chenyu Ma*; Chunyan Li*; Huijing Ma*; Daqi Yu; Yufei Zhang; Dan Zhang; Tianhan Su; Jianmin Wu; Xiaoyue Wang; Li Zhang; ChunLong Chen; Yong E. Zhang. Pan-cancer surveys indicate cell cycle related roles of primate-specific genes in tumors and embryonic cerebrum. Genome Biology, 2022, 23(1):251.
  7. Dan Zhang*, Liang Leng*, Chunyan Chen, Jiawei Huang, Yaqiong Zhang, Hao Yuan, Chenyu Ma, Hua Chen and Yong E. Zhang. Dosage sensitivity and exon shuffling shape the landscape of polymorphic duplicates in Drosophila and humans. Nature Ecology and Evolution. 2022, 6:273-287.
  8. Shengjun Tan*, Huijing Ma*, Jinbo Wang*, Man Wang*, Mengxia Wang,Haodong Yin, Yaqiong Zhang, Xinying Zhang,Jieyu Shen, Danyang Wang,Graham L. Banes,Zhihua Zhang,Jianmin Wu,Xun Huang, Hua Chen, Siqin Ge, Chun-Long Chen#, Yong E. Zhang#. DNA transposons mediate duplications via transposition-independent and -dependent mechanisms in metazoans. Nature Communications, 2021, 12: 4280.
  9. Yanni Ma#, Siqi Liu,Jie Gao, Chunyan Chen, Xin Zhang,Hao Yuan,4,5 Zhongyang Chen,..., James Douglas Engel, Lihong Shi#, Yong E. Zhang# and Jia Yu#. G enome-wide analysis of pseudogenes reveals HBBP1’s human-specific essentiality in erythropoiesis and implication in b-thalassemia. Developmental Cell, 2021, 56(4), 478-493.e11.
  10. Yi Shao*, Chunyan Chen*, Hao Shen, Bin Z. He, Daqi Yu,S huai Jiang, Shilei Zhao, Zhiqiang Gao, Zhenglin Zhu, Xi Chen, Yan Fu, Hua Chen, Ge Gao, Manyuan Long, and Yong E. Zhang. GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes. Genome Research, 2019, 29:1–15.

其他工作(2015年以后):

  1. Hangxing Jia#*, Shengjun Tan*, Yong E. Zhang#. Chasing Sequencing Perfection: Marching Toward Higher Accuracy and Lower Costs. Genomics, Proteomics & Bioinformatics. 2024. qzae024.
  2. Ruoyang Hu*, Xuedong Li*, Yong Hu, Runjie Zhang, Qiang Lv, Min Zhang, Xianyong Sheng, Feng Zhao, Zhijia Chen, Yuhan Ding, Huan Yuan, Xiaofeng Wu, Shuang Xing, Xiaoyu Yan, Fang Bao, Ping Wan, Lihong Xiao, Xiaoqin Wang, Wei Xiao, Eva L. Decker, Nico van Gessel, Hugues Renault, Gertrud Wiedemann, Nelly A. Horst, Fabian B. Haas, Per K.I. Wilhelmsson, Kristian K. Ullrich, Eva Neumann, Bin Lv, Chengzhi Liang, Huilong Du, Hongwei Lu…Yong E. Zhang…. Ralf Reski# and Yikun He#. Adaptive evolution of the enigmatic Takakia now facing climate change in Tibet. Cell, 2023, 186, 3558–3576.
  3. Xiaoqian Liu*, Zunpeng Liu*, Zeming Wu*, Jie Ren*, Yanling Fan, Liang Sun, Gang Cao, Yuyu Niu, Baohu Zhang, Qianzhao Ji, Xiaoyu Jiang, Cui Wang, Qiaoran Wang, Zhejun Ji, Lanzhu Li, Concepcion Rodriguez Esteban, Kaowen Yan, Wei Li, Yusheng Cai, Si Wang, Aihua Zheng, Yong E. Zhang, Shengjun Tan, Yingao Cai, Moshi Song, Falong Lu, Fuchou Tang, Weizhi Ji, Qi Zhou, Juan Carlos Izpisua Belmonte, Weiqi Zhang#, Jing Qu# and Guang-Hui Liu2#.Resurrection of endogenous retroviruses during aging reinforces senescence. Cell, 2023, 186, 287–304.
  4. Chunyan Chen*; Yuan Yin*; Haorong Li*; Botong Zhou; Jiong Zhou; Xiaofang Zhou; Zhipeng Li; Guichun Liu; Xiangyu Pan; Ru Zhang; Zeshan Lin; Lei Chen#; Qiang Qiu#; Yong E. Zhang#; Wen Wang# ; Ruminant-specific genes identified using high-quality genome data and their roles in rumen evolution, Science Bulletin, 2022, 67(8):825.
  5. Limin S. Ding*, Yuhang Zhang*, Dan Wen, Jianbo Ma, Hao Yuan, Hongyue Li, Shuguang Duo, Fei Yuan, Yong E. Zhang, and Aihua Zheng. Growth, Antigenicity, and Immunogenicity of SARS-CoV-2 Spike Variants Revealed by a Live rVSV-SARS-CoV-2 Virus. Front Med (Lausanne), 2022, 8, e793437.
  6. Shengqian Xia*, Nicholas W*, VanKuren*, Chunyan Chen, Li Zhang, Clause Kemkemer, Yi Shao, Hangxing Jia, UnJin Lee, Alexander S. Advani, Andrea Gschwend, Maria D. Vibranovski, Sidi Chen, Yong E. Zhang#, Manyuan Long#. Genomic analyses of new genes and their phenotypic effects reveal rapid evolution of essential functions in Drosophila development. PLOS Genetics, 2021, 17(7): e1009654.
  7. Yanhua Qu#*; Chunhai Chen*; Xiumin Chen*; Yan Hao*; Huishang She; Mengxia Wang; Per G.P. Ericson; Haiyan Lin; Tianlong Cai; Gang Song; Chenxi Jia; Chunyan Chen; Hailin Zhang; Jiang Li; Liping Liang; Tianyu Wu; Jinyang Zhao; Qiang Gao; Guojie Zhang; Weiwei Zhai; Chi Zhang#; Yong E. Zhang#; Fumin Lei#; The evolution of ancestral and species-specific adaptations in snowfinches at the Qinghai-Tibet Plateau, PNAS, 2021, 18(13), e2012398118.
  8. Xupeng Bi*,Kun Wang*, Liandong Yang*, Hailin Pan*, Haifeng Jiang*,Qiwei Wei*,..., Yong E. Zhang,Wen Wang#, Min Zhu#,Shunping He#, and Guojie Zhang#. Tracing the genetic footprints of vertebrate landing in non-teleost ray-finned fishes.Cell, 2021, 184(5):1377-1391.
  9. Wenyu Zhanga, Chen Xiea, Kristian Ullricha, Yong E. Zhang, and Diethard Tautza.The mutational load in natural populations is significantly affected by high primary rates of retroposition. PNAS, 2021, 118(6), e2013043118.
  10. Yanhua Qu#, Chunhai Chen, Ying Xiong, Huishang She, Yong E. Zhang, Yalin Cheng, Shane DuBay, ... , Fumin Lei#. Rapid phenotypic evolution with shallow genomic differentiation during early stages of high elevation adaptation in Eurasian Tree Sparrows.National Science Review, 2020, 7(1),113-127.
  11. Yuting Wang, Guangyi Dai, Zhili Gu, Guopeng Liu, ..., Yong E. Zhang, ...,Chun Xu , Naihe Jing  and Haipeng Li. Accelerated evolution of an Lhx2 enhancer shapes mammalian social hierarchies.Cell Res, 2020, 30(5),408-420.
  12. Xiaocui Xu, Guoqiang Li, Congru Li, Jing Zhang, ..., Yong E. Zhang, Mark Q Martindale, Jiang Liu. Evolutionary transition between invertebrates and vertebrates via methylation reprogramming in embryogenesis. National Science Review, 2019, 6 (5), 993-1003.
  13. Margarida Cardoso-Moreira, Jean Halbert, Delphine Valloton, Britta Velten, Chunyan Chen, Yi Shao, ..., Yong E. Zhang, Henrik Kaessmann. Gene expression across mammalian organ development. Nature, 2019, 571 (7766), 505-509.
  14. L Chen, Q Qiu, Y Jiang, K Wang, Z Lin, Z Li, F Bibi, Y Yang, J Wang,... YE Zhang,... uojie Zhang#, Rasmus Heller#, Wen Wang#. Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits. Science, 2019, 364 (6446), eaav6202.
  15. J Zu, Y Gu, Y Li, C Li, W Zhang, YE Zhang, UJ Lee, L Zhang, M Long. Topological evolution of coexpression networks by new gene integration maintains the hierarchical and modular structures in human ancestors. Science China Life Sciences, 2019, 62 (4), 594-608.
  16. Yong-Chao Xu, Xiao-Min Niu, Xin-Xin Li, Wenrong He, Jia-Fu Chen, Yu-Pan Zou, Qiong Wu, Yong E. Zhang, Wolfgang Busch, Ya-Long Guo*. Adaptation and Phenotypic Diversification in Arabidopsis through Loss-of-function Mutations in Protein-coding Genes. Plant Cell, 2019, 31(5):1012-1025.
  17. Ni A. An*, Wanqiu Ding*, Xin-Zhuang Yang*, Jiguang Peng, Bin Z. He, Qing Sunny Shen, Fujian Lu, Aibin He, Yong E. Zhang, Bertrand Chin-Ming Tan, Jia-Yu Chen# and Chuan-Yun Li#. Evolutionarily significant A-to-I RNA editing events originated through G-to-A mutations in primates.Genome Biology, 2019, 20:24.
  18. Li Zhang, Yan Ren, Tao Yang, Guangwei Li, Jianhai Chen, Andrea R. Gschwend, Yeisoo Yu, Guixue Hou, Jin Zi, Ruo Zhou, Bo Wen, Jianwei Zhang, Kapeel Chougule, Muhua Wang, Dario Copetti, Zhiyu Peng, Chengjun Zhang, Yong Zhang, Yidan Ouyang, Rod A. Wing#, Siqi Liu# and Manyuan Long#. Rapid evolution of protein diversity by de novo origination in Oryza. Nature Ecology & Evolution, 2019, 3(4):679-690.
  19. Fuqiang Ma, Pei Lin, Qingjian Chen, Xuemei Lu, Yong E. Zhang#, Chung-I Wu#. Direct measurement of pervasive weak repression by microRNAs and their role at the network level. BMC Genomics, 2018, 19:362.
  20. Zhen-Xia Chen, Brian Oliver, Yong E. Zhang, Ge Gao, Manyuan Long. (2017) Expressed Structurally Stable Inverted Duplicates in Mammalian Genomes as Functional Noncoding Elements. Genome Biology and Evolution, 2017, 9:981-992
  21. Daqi Yu*, Wenwen Shi*#, Yong E. Zhang#. Underrepresentation of active histone modification marks in evolutionarily young genes. Insect science, 2017,00:1–13.
  22. Shengjun Tan, Margarida Cardoso-Moreira, Wenwen Shi, Dan Zhang, Jiawei Huang, Yanan Mao, Hangxing Jia, Yaqiong Zhang, Chunyan Chen, Yi Shao, Liang Leng, Zhonghua Liu, Xun Huang, Manyuan Long, Yong E. Zhang. (2016) LTR-mediated retroposition as a mechanism of RNA-based duplication in metazoans. Genome Research, 26: 1663-1675.
  23. Zaixuan Zhong, Kang Du, Qian Yu, Yong E. Zhang, Shunping He. (2016) Divergent DNA Methylation Provides Insights into the Evolution of Duplicate Genes in Zebrafish. G3: Genes| Genomes| Genetics,vol.6 no.11:3581-3591.
  24. Sai Luo, J Yuyang Lu, Lichao Liu, Yafei Yin, Chunyan Chen, Xue Han, Bohou Wu, Ronggang Xu, Wei Liu, Pixi Yan, Wen Shao, Zhi Lu, Haitao Li, Jie Na, Fuchou Tang, Jianlong Wang, Yong E. Zhang, Xiaohua Shen. (2016) Divergent lncRNAs Regulate Gene Expression and Lineage Differentiation in Pluripotent Cells. Cell Stem Cell,18(5):637–652.
  25. Zhenglin Zhu, Shengjun Tan, Yaqiong Zhang, Yong E. Zhang#. (2016) LINE-1-like retrotransposons contribute to RNA-based gene duplication in dicots. Scientific Reports,6:24755.
  26. Zaixuan Zhong, Liandong Yang, Yong E. Zhang, Yu Xue, Shunping He. (2015) Correlated expression of retrocopies and parental genes in zebrafish. Molecular Genetics and Genomics,291(2):723-37.
  27. Dong-Dong Wu, Ling-Qun Ye, Yan Li, Yan-Bo Sun, Yi Shao, Chunyan Chen, Zhu Zhu, Li Zhong, Lu Wang, David M Irwin, Yong E. Zhang, Ya-Ping Zhang. (2015) Integrative analyses of RNA-editing, alternative splicing, and expression of young genes in human brain transcriptome by deep RNA-sequencing. Journal of Molecular Cell Biology, 6:24755.
  28. Jia-Yu Chen, Qing Sunny Shen, Wei-Zhen Zhou, Jiguang Peng, Bin Z He, Yumei Li, Chu-Jun Liu, Xuke Luan, Wanqiu Ding, Shuxian Li, Chunyan Chen, Bertrand Chin-Ming Tan, Yong E. Zhang, Aibin He, Chuan-Yun Li. (2015) Emergence, Retention and Selection: A Trilogy of Origination for Functional De Novo Proteins from Ancestral LncRNAs in Primates. PLoS Genet. 2015 Jul;11(7).
  29. Yanhua Qu, Shilin Tian, Naijian Han, Hongwei Zhao, Bin Gao, Jun Fu, Yalin Cheng, Gang Song, Per GP Ericson, Yong E. Zhang, Dawei Wang, Qing Quan, Zhi Jiang, Ruiqiang Li, Fumin Lei. (2015) Genetic responses to seasonal variation in altitudinal stress: whole-genome resequencing of great tit in eastern Himalayas. Sci Rep.2015;5:14256.
  30. Haiwang Yang*, Bin Z. He*, Huijing Ma, Shun-Chern Tsaur, Chenyu Ma, Ying Wu, Chau-Ti Ting and Yong E. Zhang#. (2015) Expression profile and gene age jointly shaped the genome-wide distribution of premature termination codons in Drosophila population. Molecular Biology and Evolution.32(1):216–228.

写给考生的话:

关于我们
联系我们
地  址:北京市朝阳区北辰西路1号院5号
邮  编:100101
电子邮件:ioz@ioz.ac.cn
电  话:+86-10-64807098
传  真:+86-10-64807099
友情链接