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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
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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.
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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).
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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Chen S, Zhang YE, Long M. (2010) New genes in Drosophila quickly become essential. Science, 2010, 330:1682-1685
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Zhang YE, Vibranovski MD, Krinsky BH, Long M (2010) Age-dependent chromosomal distribution of male-biased genes in Drosophila. Genome Res., 20: 1526-1533.
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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.
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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.
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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.
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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.
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Zhu Z, Zhang Y, Long M (2009) Extensive structural renovation of retrogenes in the evolution of the Populus genome. Plant Physiol., 151: 1943-1951.
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Vibranovski MD, Zhang Y, Long M (2009) General gene movement off the X chromosome in the Drosophila genus. Genome Res., 19: 897-903.
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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.
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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.
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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
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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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