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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A220 100101
更多信息:
计算进化基因组学研究组     
简历:

  张勇,男,1979年8月出生于山东省日照市,博士,研究员,博士生导师;中国科学院动物研究所计算进化基因组学研究组组长。
  “青年千人计划”引进海外杰出人才。2001 年毕业于北京大学,获生物信息学博士学位。2007-2011年在美国芝加哥大学进修,在Science, PLoS BiologyGenome Research等杂志上发表了多篇SCI收录论文。张勇在基因组水平雄性基因的动态进化、新基因在早期发育中的作用以及新基因对于人类大脑进化的作用等方面都取得了具有突破意义的成果,刷新了学术界的认识,代表着最前沿的水平;因此,他的工作引起了学术界的极大关注。他的工作多次被Nature Reviews Genetics 、Trends in Genetics等著名刊物的关于新基因进化的最新进展的综述所引用。 更多的信息,请访问http://zhanglab.ioz.ac.cn ;北京动物所内部请访问http://10.0.60.55/

研究领域:
  主要从事演化基因组领域的研究,在新基因起源方面取得了突出进展。长期以来,学术圈普遍接受雄性相关的基因倾向于逃离X染色体。通过比较基因组学的分析,推测出果蝇和哺乳动物(人与小鼠)基因组中90%以上基因的演化年龄。通过比较年轻基因和年老基因的染色体分布,发现年轻的雄性基因富集于X染色体;随着基因逐渐变老,老的雄性基因往往集中于常染色体。这种动态分布暗示着新老基因可能在不同的演化压力之下。不仅如此,研究组的工作将新基因的功能研究推向基因组时代。研究组在果蝇中的大规模RNAi试验证明新基因可以和老基因一样重要。一旦它们的表达被抑制,果蝇同样可能发育到成虫。这一系列的论文发表于国际知名期刊如Science,PLOS BioGenome Res
  今后将在脊椎动物系统里继续新基因的基因组学研究。此前的工作暗示新基因起源不受负向多效性的影响。换言之,对于复杂的发育网络而言,相关老基因的蛋白序列其演化空间非常局限;但是新基因则有着广泛的演化可能。从这点出发,可以预测新基因产生对于复杂的生物系统(例如人类大脑或者脊椎动物早期发育)可能非常普遍。另外,人类基因组中存在数以万计的假基因。最近的研究进展显示假基因可以发挥调节功能,甚至参与疾病发生。假基因的年龄往往比较年轻,它们其实同样可以被当作新的非编码基因进行比较分析。因为人和小鼠的有效群体数目差别很大,假基因的演化可能差别很大;可以预言假基因的生物学功能在两者之间可能也不同。
  芝加哥大学的Przworski教授说目前是研究人类群体遗传的黄金时代。实际上,目前也是研究分子演化或者计算基因组学的黄金时代。迅速积累的功能基因组学数据,物种内和物种间的序列数据允许测试上述两方面的假说。考虑到演化领域乃至整个的分子生物学领域往往倾向于研究老基因,研究组的工作将填补这个空白。另一方面,研究组将会发现新基因是如何影响物种(尤其是人类)的性状的。由于相对其它模式生物可以选择的试验操作有限,人类或者灵长类的生物学研究尤其需要我们的演化和计算生物学分析。
社会任职:
获奖及荣誉:
承担科研项目情况:
  中国科学院动物研究所青年千人计划 2011-2013 
代表论著:
  1. Gao G, Vibranovski MD, Zhang L, Li Z, Liu M, Zhang YE,Xinmin Li, Wenxia Zhang, Qichang Fan, Nicholas W VanKuren, Manyuan Long, and Liping Wei (2014) A long term demasculinization of X-linked intergenic noncoding RNAs in Drosophila melanogaster .Genome Res.Published in Advance January 9, 2014, doi:10.1101/gr.165837.113
  2. Qu Y, ..., Zhang YE, ... (2013) Ground tit genome reveals avian adaptation to living at high altitudes in the Tibetan plateau. Nature Communications 4, Article number: 2071 doi:10.1038/ncomms3071.
  3. Xie 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).
  4. Zhang YE, Landback P, Vibranovski M, Long M. (2012) New genes expressed in human brains: implications for annotating evolving genomes. Bioessays, 34(11): 982-991.
  5. Ni X, Zhang YE, Negre N, Chen S, Long M, White KP (2012) Adaptive evolution and the birth of CTCF binding sites in the Drosophila genome. PLoS Biol., 10(11): e1001420.
  6. Vibranovski MD, Zhang YE, Kemkemer C, Lopes HF, Karr TL, Long M (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.
  7. Vibranovski MD, Zhang YE, Kemkemer C, VanKuren NW, Lopes HF, Karr TL, Long MY. (2012) Segmental dataset and whole body expression data do not support the hypothesis that non-random movement is an intrinsic property of Drosophilaretrogenes. BMC Evol Biol., 12.
  8. Chen S, Ni X, Krinsky BH, Zhang YE, Vibranovski MD, White KP, Long M. 2012. Reshaping of global gene expression networks and sex-biased gene expression by integration of a young gene. EMBO J. 31(12): 2798-2809.
  9. Guisbert KS, Zhang YE, Flatow J, Hurtado S, Staley JP, Lin S, and Sontheimer EJ (2012) Meiosis-induced Alterations in Transcript Architecture and Noncoding RNA Expression in S. cerevisiaeRNA, 18(6): 1142-1153.
  10. Airavaara 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, 45093-45102.
  11. Zhang YE, Landback, P., Vibranovski, M.D. and Long, M. (2011) Accelerated recruitment of new brain development genes into the human genome. PLoS Biol., 9(10): e1001179.
  12. Zhang YE#, 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(13): 1749-1753.
  13. Chen Z, Zhang YE, 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., 28(10): 2823-2832.
  14. Chen S, Zhang YE, Long M. (2010) New genes in Drosophila quickly become essential. Science, 2010, 330:1682-1685
  15. Zhang YE, Vibranovski MD, Krinsky BH, Long M (2010) Age-dependent chromosomal distribution of male-biased genes in Drosophila. Genome Res., 20: 1526-1533.
  16. Zhang YE, 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: e1000494.
  17. Li CY, Zhang Y, Wang Z, Cao C, Zhang PW, et al. (2010) A human-specific de novo protein-coding gene associated with human brain functions. PLoSComput. Biol., 6: e1000734.
  18. 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.
  19. 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.
  20. Zhu Z, Zhang Y, Long M (2009) Extensive structural renovation of retrogenes in the evolution of the Populus genome. Plant Physiol., 151: 1943-1951.
  21. Vibranovski MD, Zhang Y, Long M (2009) General gene movement off the X chromosome in the Drosophila genus. Genome Res., 19: 897-903.
  22. 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.
  23. 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.
  24. 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–W349
  25. 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.
  26. 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.
  27. 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.
  28. Qian Z, Yin Y, Zhang Y, Lu L, Li Y, Jiang Y. 2006. Genomic characterization of ribitolteichoic acid synthesis in Staphylococcus aureus: genes, genomic organization and gene duplication. BMC Genomics7: 74.
  29. 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.
  30. 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. ActaBiochimBiophys Sin (Shanghai), 37, 341-348.
  31. 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.
  32. Ghen 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. ActageneticaSinica, 30, 509-514.
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