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2019
Xiaocui Xu, Guoqiang Li, Congru Li, Jing Zhang, ..., Yong E Zhang, Mark Q Martindale, Jiang Liu. Evolutionary transition between invertebrates and vertebrates via methylation reprogramming in embryogenesis. National Science Review 6 (5), 993-1003
Margarida Cardoso-Moreira, Jean Halbert, Delphine Valloton, Britta Velten, Chunyan Chen, Yi Shao, ..., Yong E Zhang, Henrik Kaessmann. Gene expression across mammalian organ development. Nature 571 (7766), 505-509
L Chen, Q Qiu, Y Jiang, K Wang, Z Lin, Z Li, F Bibi, Y Yang, J Wang,... YE Zhang,... (2019) Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits. Science 364 (6446), eaav6202
J Zu, Y Gu, Y Li, C Li, W Zhang, YE Zhang, UJ Lee, L Zhang, M Long. (2019) Topological evolution of coexpression networks by new gene integration maintains the hierarchical and modular structures in human ancestors. Science China Life Sciences 62 (4), 594-608。
Yi 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
2018
Fuqiang Ma,Pei Lin,Qingjian Chen,Xuemei Lu,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
2017
Zhen-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
2016
Shengjun 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
2015
Zaixuan 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.
2014
Yong 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
2013
Qu Y, ..., Zhang YE, ... (2013) Ground tit genome reveals avian adaptation to living at high altitudes in the Tibetan plateau. Nature Comm. 4 download
2012
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). 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:e1001420.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
2011
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.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:e1001179 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 before
Chen 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: e1000494. download
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. 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
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