基本信息
张勇男博导中国科学院动物研究所
电子邮件： zhangyong@ioz.ac.cn
通信地址： 北京市朝阳区北辰西路1号院5号动物所A220
邮政编码： 100101

研究领域?张勇课题组主要是通过对二代及三代测序技术所产生的大量果蝇和人的基因组及转录组数据的挖掘，研究物种内及物种间基因数目改变的进化过程及其对种群差异和物种分歧的贡献，进而建立支配基因产生和衰亡的理论。在理论层面，课题组紧扣突变和选择等根本问题，从基因起源和丢失这个独特的视角开展各项工作。在应用层面，研究内容将有助于理解物种乃至群体在基因组成上的差异，对于探索动物的表型差异、实现人类的个体化医疗有着重要意义。研究组依托自有小型计算机服务器和动物所所级大型计算平台，进行生物信息学方面的计算工作，同时以功能基因组学、分子生物学实验为辅，进行相关的模型构建和实验验证等工作。简言之，课题组通过对公共及自产基因组、转录组数据的分析，完善或建立新的理论，并为下游实验提供指导。



招生信息1． 有着强烈的好奇心：面对一个问题，追寻答案，并且问为什么是这样的一个答案。
2． 本科专业为生物学相关专业。
3． 获得本科所在学校的校外推荐免试生名额。
4. 具有较强的动手能力和执行力，善于实验室工作。
5. 具有良好的英语能力。
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招生专业071022-基因组学
071023-计算生物学
071021-生物信息学

招生方向进化基因组学
计算基因组学
比较基因组学


教育背景2001-09--2006-06北京大学生物信息中心博士
1997-09--2001-06北京大学生物化学和分子生物学系学士


教授课程群体遗传与分子进化
进化生物学
群体遗传及分子进化
基因组学和生物信息学前沿系列讲座
生物信息学应用
生物信息学
生物信息学之计算进化基因组学


指导学生已指导学生
黄家蔚硕士研究生0710Z1-基因组学
现指导学生
马慧静博士研究生071002-动物学
马辰宇博士研究生071002-动物学
贾行星博士研究生0710Z1-基因组学
张丹博士研究生0710Z1-基因组学
陈春燕博士研究生0710Z1-基因组学
邵毅博士研究生0710Z1-基因组学
毛亚男硕士研究生0710Z1-基因组学
余大奇博士研究生0710Z1-基因组学
王梦霞博士研究生0710Z1-基因组学
来兴欢博士研究生0710Z1-基因组学
袁昊硕士研究生0710Z1-基因组学

工作经历
中国科学院动物研究所，动物进化与系统学院重点实验室
02/2012至今

研究员，中国科学院动物研究所，动物进化与系统学院重点实验室
09/2011-02/2012

生物信息资深研究人员，美国芝加哥大学，分子遗传学和细胞生物学系
04/2009-08/2011

博士后，美国芝加哥大学，分子遗传学和细胞生物学系
07/2007-03/2009

研究人员，北京大学，生命科学学院
07/2006-05/2007





发表文章
*: co-first authors; #: co-corresponding authors
2019Yi Shao^*, Chunyan Chen^*, Hao Shen,Bin Z. He,Daqi Yu,Shuai Jiang,Shilei Zhao, Zhiqiang Gao, Zhenglin Zhu,Xi Chen,Yan Fu,Hua Chen,Ge Gao,Manyuan Long, and Yong E. Zhang. (2019) GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes. Genome Research, 29:1–15,download
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*. (2019) Adaptation and Phenotypic Diversification in Arabidopsis through Loss-of-function Mutations in Protein-coding Genes. Plant Cell, Published on 18 March 2019. download
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^#. (2019) Evolutionarily significant A-to-I RNA editing events originated through G-to-A mutations in primates.Genome Biology, 20:24.download
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^#. (2019) Rapid evolution of protein diversity by de novo origination in Oryza. Nature Ecology & Evolution , Published on 11 March 2019. download
2018FuqiangMa,PeiLin,QingjianChen,XuemeiLu,Yong E.Zhang^#,Chung-I Wu^#.(2018)Direct measurement of pervasive weak repression by microRNAs and their role at the network level. BMC Genomics,19:362,download
2017Zhen-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, 9:981-992, download
Daqi Yu*, Wenwen Shi*^#,Yong E Zhang^#.. (2017) Underrepresentation of active histone modification marks in evolutionarily young genes.Insect science, 00:1–13,download
2016Shengjun 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. download
Media report by Genomeweb

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. download
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. download
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. download
2015Zaixuan 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. download
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. download
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). download
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. download
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 download
Highlighted by F1000 Faculty.
2014Yong E Zhang^# and Manyuan Long^#. . (2014) New genes contribute to genetic and phenotypic novelties in human evolution. Current Opinion in Genetics and Development, 29:90-96. download
Shengjun Tan, Zhenglin Zhu, Tao Zhu, Rigen Te and Yong E. Zhang^#. (2014) Chance and necessity: Emerging introns in intronless retrogenes. Encyclopedia of Life Sciences. download Invited review
Gao G, Vibranovski MD, Zhang L, Li Z, Liu M, Zhang YE, ... (2014) A long term demasculinization of X-linked intergenic noncoding RNAs in Drosophila melanogaster Genome Res. 165837.113 download
2013Qu Y, ..., Zhang YE, ... (2013) Ground tit genome reveals avian adaptation to living at high altitudes in the Tibetan plateau. Nature Comm. 4 download
2012Xie C*, Zhang YE*, Chen JY*, Liu CJ, Zhou WZ, Li Y, Zhang M, Zhang RL, Wei LP, Li CY. (2012) Hominoid-Specific De Novo Protein-Coding Genes Originating from Long Non-Coding RNAs. PLoS Genet 8(9). download
Highlighted by F1000 Faculty.
Ni X, Zhang YE, Ne`gre N, Chen S, Long M, White KP. (2012)Adaptive Evolution and the Birth of CTCF Binding Sites in the Drosophila Genome.PLoS Biol.10:e**.download
With Synopsis of PLoS Bio.; Highlighted by Nature Rev. Genet.
Maria D Vibranovski#, Yong E Zhang, Claus Kemkemer, Nicholas W VanKuren, Hedibert F Lopes, Timothy L Karr, Manyuan Long#. （2012) Segmental dataset and whole body expression data do not support the hypothesis that non-random movement is an intrinsic property of Drosophila retrogenes. BMC Evol Bio 12:169. download
Vibranovski MD, Zhang YE, Kemkemer C, Lopes HF, Karr TL and others. (2012) Re-analysis of the larval testis data on meiotic sex chromosome inactivation revealed evidence for tissue-specific gene expression related to the drosophila X chromosome. BMC Biol 10:49.download
Chen S, Ni X, Krinsky BH, Zhang YE, Vibranovski MD and others. (2012) Reshaping of global gene expression networks and sex-biased gene expression by integration of a young gene. The EMBO journal 31:2798-809.download
Kim Guisbert KS, Zhang YE, Flatow J, Hurtado S, Staley JP and others. (2012) Meiosis-induced alterations in transcript architecture and noncoding RNA expression in S. cerevisiae. RNA 18:1142-53.download
2011Airavaara M, Pletnikova O, Doyle ME, Zhang YE, Troncoso JC, Liu QR. (2011) Identification of novel GDNF isoforms and cis-antisense GDNFOS gene and their regulation in human middle temporal gyrus of Alzheimer disease. JBC, 286:45093-102.download
Zhang Y.E., Landback P., Vibranovski M.D. and Long M. (2011) Accelerated recruitment of new brain development genes into the human genome, PLoS Biol. 9:e** download
With Perspectives by Jose M. Ranz and John Parsch in BioEssays, and by Genevieve Konopka in Brain Behav. Evol.
Highlighted by Science and Nature Rev. Genet
Media report by The Scientist, UChicago Press, etc.
Chen Z, Zhang Y.E., Vibranovski MD, Wei L, Luo J, Gao G, Long M. (2011) Deficiency of the X-linked inverted duplicates with male-biased expression and the underlying evolutionary mechanisms in the Drosophila genome. Mol. Biol. Evol. In Print. download
Zhang Y.E.#, Vibranovski MD, Krinsky BH, Long M#. (2011) A cautionary note for the retrocopy identification: DNA-based duplication of intron-containing genes significantly contributes to the origination of single exon genes. Bioinformatics, 27: 1749-1753. download
2010 and beforeChen S, Zhang Y.E., Long M. (2010) New genes in Drosophila quickly become essential. Science, 2010, 330:1682-1685
Highlighted by Nature Rev. Genet
Media report by ScienceDaily, UChicago Press, etc.

Zhang Y.E., Vibranovski MD, Krinsky BH, Long M (2010) Age-dependent chromosomal distribution of male-biased genes in Drosophila. Genome Res. 20: 1526-1533. download
Zhang Y.E., Vibranovski, M.D., Landback P., Marais G. and Long M. (2010) Chromosomal redistribution of male-biased genes in mammalian evolution with two bursts of gene gain on X chromosome. PLoS Biol., 8: e**. download
LiCY, Zhang Y, Wang Z, Cao C, Zhang PW, et al. (2010) A human-specific de novo protein-coding gene associated with human brain functions. PLoS Comput. Biol., 6: e**. download
Raleigh DR, Marchiando AM, Zhang Y, Shen L, Sasaki H, et al. (2010) Tight junction-associated MARVEL proteins marveld3, tricellulin, and occludin have distinct but overlapping functions. Mol. Biol. Cell, 21: 1200-1213. download
Zhang Y, Lu S, Zhao S, Zheng X, Long M, et al. (2009) Positive selection for the male functionality of a co-retroposed gene in the hominoids. BMC Evol. Biol., 9: 252. download
Zhu Z, Zhang Y, Long M (2009) Extensive structural renovation of retrogenes in the evolution of the Populus genome. Plant Physiol., 151: 1943-1951. download
Vibranovski MD, Zhang Y, Long M (2009) General gene movement off the X chromosome in the Drosophila genus. Genome Res., 19: 897-903. download
Fan C.*, Zhang Y.*, Yu Y.*, Rounsley S., Long M. and Wing R.A. (2008) The Subtelomere of Oryza sativa Chromosome 3 Short Arm as a Hot Bed of New Gene Origination in Rice. Mol. Plant, ssn050. download
Li J.-T., Zhang Y., Kong L., Liu Q.-R. and Wei L. (2008) Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation. Nucleic Acids Res., gkn470. download
Kong L., Zhang Y., Ye Z., Wei L. and Gao G. (2007) CPC: assess transcript protein-coding potential by sequence features. Nucleic Acids Res., 35, W345– 349. download
Zhang Y., Li J., Kong L., Gao G., Liu Q.R. and Wei L. (2007) NATsDB: Natural Antisense Transcripts DataBase. Nucleic Acids Res., 35, D156-161. download
Zhang W.*, Zhang Y.*, Zheng H.*, Zhang C., Xiong W., Olyarchuk J.G., Walker M., Xu W., Zhao M., Zhao S. et al. (2007) SynDB: a Synapse protein DataBase based on synapse ontology. Nucleic Acids Res., 35, D737-741. download
Zhang Y., Liu X.S., Liu Q.R. and Wei L. (2006) Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species. Nucleic Acids Res., 34, 3465-3475. download
Qian Z, Yin Y, Zhang Y, Lu L, Li Y, Jiang Y. 2006. Genomic characterization of ribitol teichoic acid synthesis in Staphylococcus aureus: genes, genomic organization and gene duplication. BMC Genomics 7: 74. download
Chen Y.*, Zhang Y.*, Yin Y., Gao G., Li S., Jiang Y., Gu X. and Luo J. (2005) SPD--a web-based secreted protein database. Nucleic Acids Res., 33, D169-173. download
Yin Y.B., Zhang Y., Yu P., Luo J.C., Jiang Y. and Li S.G. (2005) Comparative study of apoptosis-related gene loci in human, mouse and rat genomes. Acta Bochim Biophys Sin (Shanghai), 37, 341-348. download
Zhang Y., Yin Y., Chen Y., Gao G., Yu P., Luo J. and Jiang Y. (2003) PCAS--a precomputed proteome annotation database resource. BMC Genomics, 4, 42. download
Chen X., Zhang Y., Wang J.M., Huang Y., Luo J.C., Wu C.H. and Gu X.C. (2003) GPCEG-A database for genomic polymorphism of Chinese ethnic groups. Acta genetica Sinica, 30, 509-514. download





科研项目与奖励
1. 国家重点研发计划项目，2018YFC**，高质量企鹅参考基因组图谱绘制和适应性进化的基因组学基础，99.50万元，2018.08-2021.12，在研，参加
2. 国家自然科学基金常规面上项目，**，果蝇中多态新复制基因的鉴定、选择压力分析和功能研究， 69.00万元，2018/1-2021/12，在研，主持
3. 国家自然科学基金，重大研究计划集成项目，，肿瘤发生、发展和治疗过程中细胞进化模式及机制研究，200.00万元，2018/1-2019/12，在研，参加
4. 中国科学院先导B研究专项课题，XDB**，基因内容演化对动物脑演化的驱动机制，647.20万元，2014/6-2019/6，在研，主持
5. 科技部973计划子课题，2015CB943001，精子发生相关转录本的比较基因组研究，145.50万元，2015/1-2019/12，在研，参加
6. 科技部973计划课题，2013CB531202，早期心衰的线粒体遗传与功能基因组学研究，504.00万元，2013/1-2017/12，结题，主持
7. 国家自然科学基金重大研究计划培育项目，**，突变和选择压力在果蝇新复制基因起源中的作用机制解析，120万元，2014/1-2016/12，结题，主持
8. 国家自然科学基金优秀青年科学基金项目，**，动物进化/计算进化基因组学，100万元，2014/1-2016/12，结题，主持
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