Location: Home > Scientists
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Name:
 ZHANG Yong
Subject:
 Computational Evolutionary Genomics
Tel/Fax:
 +86-10-64806339  /  +86-10-64806339
E-mail:
 zhangyong@ioz.ac.cn
Address:
 Room A220, Institute of Zoology, Chinese Academy of Science, 1 Beichen West Road, Chaoyang District, Beijing 100101, P.R.China
More:
 Group of Computational Evolutionary Genomics      
Resume:
2009.4-2011.8 Bioinformatics Scientist, Department of Molecular Genetics and Cell Biology, University of Chicago
2007.7-2009.3 Postdoc Scholar, Department of Ecology and Evolution, University of Chicago
2006.7-2007.5 Research Scientist, College of Life Sciences, Peking University
2006.12-2007.3 Teaching Assistant for Evolutionary Genomics, Peking University
2003.7-2004.1 Teaching Assistant for Biostatistics, Peking University
2001.9-2006.7 Ph.D. in Bioinformatics, Center for Bioinformatics, Peking University
1997.9-2001.7 B.S. in Biochemistry and Molecular Biology, Peking University

Research Interests:
Computational Genomics, Molecular Evolution.

Awards and Honors:
2013, Excellent Young Scientists Fund by National Natural Science Fund of China

Professional Activities:
2013-present, Editor, Journal of Systematics and Evolution
2013-present, Editor,Hereditas（Beijing)
2008-present, Reviewer, PLoS Genetics, Nucleic Acids Research, Molecular Biology and Evolution, Genome Biology and Evolution, BMC Evoltionary Biology, BMC Genomics, PLoS ONE, Development, Genes and Evolution, Journal of Molecular Evolution and Journal of Biomedical Informatics
2010-present, Member, The Society for Molecular Biology & Evolution

Research Grants:
2014-present, The Strategic Priority Research Program of the Chinese Academy of Sciences (XDB13010400)
2014-2016 Excellent Young Scientists Fund by National Natural Science Fund of China
2014-2016 Training Program of MicroEvolution Fund by National Natural Science Fund of China
2013-2017 Group coordinator for Functional genomics of mitocondria in the project entitled with Disfunction of mitocondria in heart failure supported by National Basic Research Program (973), 2013CB531200

Selected Publications:

  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.