姓  名: 張 勇
學  科: 計算進化基因組學
電話/傳真: +86-10-64806339 / +86-10-64806339
電子郵件: zhangyong@ioz.ac.cn
通訊地址: 北京市朝陽區北辰西路1號院5號必威精装版app西汉姆联 A627 100101
更多信息: 計算進化基因組學研究組     

簡曆介紹:

張勇於2006年獲北京大學生物信息學博士學位,2007年至2011年於芝加哥大學從事研究,2011年通過國家高層次人才計劃(青年)加入中國科學院動物所任研究員。他長期聚焦物種特異重複基因的功能、介導基因重複的突變機製及突變機製的轉化研究,在前沿基礎研究和國家戰略需求兩方麵獲得係列成果。包含Cell (In press)、Nature Ecology Evolution (2022/2024)、Nature Biotechnology(2023)等論文在內,張勇共發表論文70餘篇,總引用達8100次(Google Scholar);獲批國內專利一項,申請國際專利兩項;主持國家傑出青年科學基金、優秀青年科學基金、中國科學院從0到1原始創新等項目。更多信息請訪問http://zhanglab.ioz.ac.cn ;動物所內部請訪問http://10.0.60.55/

研究領域:

1)基礎研究:刻畫新基因起源機製,揭示新基因對表型進化的意義。

研究組開發基於從頭拚接的新方法,在果蠅與人類群體中鑒定串聯重複,發現與傳統假定不同,串聯重複多不能產生完整基因拷貝,但仍可通過基因融合等機製產生新基因結構,具有較大功能後果。該工作發表於Nature Ecology Evolution(2022)。研究組也在多種動物基因組中發現基因/轉座子嵌合現象並解析其機製,即微相似序列在複製中介導模板跳轉。這些工作發表於Genome Research(2016)、Nature Communications(2021)。

不僅如此,研究組開發了基因年齡推斷方法,產生了高質量新基因數據集,發現其在人大腦等快速演化的器官中上調。這些工作發表於Genome Research(2019)、Developmental Cell(2021)等。研究組也解析了脊椎動物早期的進化,揭示早期產生的重複基因推動了脊椎動物祖先的發育進化;該工作發表於Nature Ecology Evolution(2024)。

2)應用研究:從基因起源演化的概念和方法出發,開發具備自主知識產權的新技術。

由於轉座子編碼的TnpB與基因編輯器Cas12源自同一基因家族,研究組開發新方法從原核基因組中基於進化信息預測活躍的TnpB,結合實驗鑒定了目前最小的基因編輯器,方便了體內遞送。這一工作發表於Nature Biotechnology(2023)。類似的,研究組從動物基因組中挖掘了40個新的轉座子載體,使其數量從20上升到60;其中活性最高的新載體性能在CAR-T免疫治療中優於常用的慢病毒。該工作發表於Cell(In press)。研究組也開發了基於轉座子的非擴增三代測序微量建庫技術,方便了小動物或珍惜樣品的測序組裝,投稿至Nature Communications(Accepted in principle)。

社會任職:

獲獎及榮譽:

承擔科研項目情況:

代表論著:

(*: 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年以後):

  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.

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