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Zhang Yong

Yong's CV

Yong Zhang, PhD
Email: ZhangLabIOZ@gmail.com
Address: Institute of Zoology, Chinese Academy of Sciences, Datun Road, Chaoyang District, Beijing 100101
Motto
1. Research is largely driven by interest and curiosity.
2. Tax payers pays us to play and let’s play well.

Education

2006 Ph.D. in Bioinformatics, Center for Bioinformatics, Peking University
2001 B.S. in Biochemistry and Molecular Biology, Peking University

Experience

Working Experience
2012.2-Present Principle Investigator supported by One Thousand Young Talents Program, Institute of Zoology, CAS
2011.9-2012.1 Principle Investigator supported by 100 Talents Program, Institute of Zoology, CAS
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

Teaching Experience
2006.12-2007.3 Teaching Assistant for Evolutionary Genomics, Peking University
2003.7-2004.1 Teaching Assistant for Biostatistics, Peking University

Academic Services

Reviewers for 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.

Honors & Distinctions

2004-2005 DongGang Scholarship
2003-2004 DongGang Scholarship
2002-2003 5•4 Scholarship
2001-2002 GangSong Scholarship

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

  1. H-W Yang*, B He*, H-J Ma, S-C Tsaur, C-Y Ma, Y Wu, C-T Ting, YE Zhang#. (2014) Expression profile  and gene age jointly shaped the genome-wide distribution of premature termination codons in Drosophila population. Molecular Biology and Evolution.
  2. YE Zhang# & M-Y Long#. (2014) New genes contribute to genetic and phenotypic novelties in human evolution. Current Opinion in Genetics and Development, 29:90-96.
  3. S-J Tan, Z-L Zhu, T Zhu, R-G Te, YE Zhang#. (2014) Chance and necessity: Emerging introns in intronless retrogenes. Encyclopedia of Life Sciences.
  4. 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
  5. Qu Y, ..., Zhang YE, ... (2013) Ground tit genome reveals avian adaptation to living at high altitudes in the Tibetan plateau. Nature Comm. 4
  6. 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:e1001420.
  7. Zhang YE, Patrick Landback, Maria Vibranovski#and Manyuan Long#. (2012) New genes expressed in human brains: Implications for annotating evolving genomes. Bioessays 34: 982–991.
  8. Xie C*, Zhang YE*, Chen J*, Liu C, Zhou W and others. (2012) Hominoid-specific de novo protein-coding genes originating from long non-coding RNAs. PLoS Genet. Accepted
  9. 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.
  10. 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.
  11. 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.
  12. 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, 286:45093-102.
  13. 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(10): e1001179.
  14. 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(13): 1749-1753.
  15. 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., 28(10): 2823-2832.
  16. Chen S, Zhang Y.E., Long M. (2010) New genes in Drosophila quickly become essential. Science, 2010, 330:1682-1685 (Highlighted in Nature Review Genetics of February 2011).
  17. 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.
  18. 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: e1000494.
  19. 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. PLoS Comput. Biol., 6: e1000734.
  20. 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.
  21. 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.
  22. Zhu Z, Zhang Y, Long M (2009) Extensive structural renovation of retrogenes in the evolution of the Populus genome. Plant Physiol., 151: 1943-1951.
  23. Vibranovski MD, Zhang Y, Long M (2009) General gene movement off the X chromosome in the Drosophila genus. Genome Res., 19: 897-903.
  24. 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.
  25. 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.
  26. 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
  27. 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.
  28. 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.
  29. 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.
  30. 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.
  31. 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.
  32. 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 Biochim Biophys Sin (Shanghai), 37, 341-348.
  33. 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.
  34. 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. Acta genetica Sinica, 30, 509-514.


Invited Talks

2012.8 The 2nd Genetics, Development and Evolution International Symposium, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS)
2012.7 the 10th International Bioinformatics Workshop, Jilin University
2012.6  Institute of Biotechnology, University of Helsinki
2011.11 Beijing Institutes of Life Science, CAS
2010.12 Chicagoland RNA club, Northwestern University