Publication

*: co-first authors; #: co-corresponding authors

Selected recent publications

• Tongtong Zhang*, Shengjun Tan*, Na Tang*, Yuanqing Li*, Jing Sun, Yanyan Guo, Hui Gao, Chenze Zhang, Yujia Cai, Wen Sun, Xiaoxuan Hu, Xuechun Zhang, Liangzheng Fu, Yachao Wu, Peter Gee, Weihua Yan, Yahui Zhao, Qiang Chen, Baocheng Guo, Haoyi Wang# and Yong E. Zhang#. A large-scale heterologous survey of 130 DNA transposons in human cells highlights their functional divergence and expands genome engineering toolbox. Cell, 2024, 187, 1–20. view
• Hangxing Jia *#, Shengjun Tan *#, Yingao Cai *, Yanyan Guo, Jieyu Shen, Yaqiong Zhang , Huijing Ma, Qingzhu Zhang, Jinfeng Chen, GexiaQiao, Jue Ruan # & Yong E. Zhang #. Low-input PacBio sequencing generates high-quality individual fly genomes and characterizes mutational processes. Nature Communications , 2024, 15: 5644. download
• Daqi Yu*, Yandong Ren*, Masahiro Uesaka*, Alan J. S. Beavan*, Matthieu Muffato#, Jieyu Shen, Yongxin Li, Iori Sato, Wenting Wan, James W. Clark, Joseph N. Keating, Emily M. Carlisle, Richard P. Dearden, Sam Giles, Emma Randle, Robert S. Sansom, ..., Fergal J. Martin#, Wen Wang#, Philip C. J. Donoghue#, Yong E. Zhang# & Juan Pascual-Anaya#. Hagfish genome illuminates vertebrate whole genome duplications and their evolutionary consequences. Nature Ecology and Evolution, 2024, 8(3):519-535.download. 22IF-16.8, 22-5IF-16.9
• Guanghai Xiang*#, Yuanqing Li*, Jing Sun*, Yongyuan Huo*, Shiwei Cao, Yuanwei Cao, Yanyan Guo, Ling Yang, Yujia Cai, Yong E. Zhang# & Haoyi Wang#. Evolutionary mining and functional characterization of TnpB nucleases identify efficient miniature genome editors, Nature Biotechnology, 2023,29:1-3. download.22IF-46.9, 22-5IF-59.1
• Dan Zhang*, Liang Leng*, Chunyan Chen, Jiawei Huang, Yaqiong Zhang, Hao Yuan, Chenyu Ma, Hua Chen and Yong E. Zhang. Dosage sensitivity and exon shuffling shape the landscape of polymorphic duplicates in Drosophila and humans. Nature Ecology and Evolution, 2022, link, 22IF-16.8, 22-5IF16.9
• Shengjun Tan*, Huijing Ma*, Jinbo Wang*, Man Wang*, Mengxia Wang,Haodong Yin,Yaqiong Zhang, Xinying Zhang,Jieyu Shen, Danyang Wang,Graham L. Banes,Zhihua Zhang,Jianmin Wu,Xun Huang, Hua Chen, Siqin Ge, Chun-Long Chen#, Yong E. Zhang#. DNA transposons mediate duplications via transposition-independent and -dependent mechanisms in metazoans. Nature Communications , 2021, 12: 4280.download
• 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. GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes. Genome Research, 2019, 29:1–15, download. 19IF-11.093, 19-5IF-12.01

2021

2020

• Yanhua Qu#, Chunhai Chen, Ying Xiong, Huishang She, Yong E. Zhang, Yalin Cheng, Shane DuBay,... , Fumin Lei#.Rapid phenotypic evolution with shallow genomic differentiation during early stages of high elevation adaptation in Eurasian Tree Sparrows.National Science Review, 2020, 7(1),113-127. download
• Yuting Wang, Guangyi Dai, Zhili Gu, Guopeng Liu, ...,Yong E. Zhang, ...,Chun Xu , Naihe Jing  and Haipeng Li. Accelerated evolution of an Lhx2 enhancer shapes mammalian social hierarchies.Cell Res, 2020, 30(5),408-420.download

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, 2019, 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, 2019, 571 (7766), 505-509
  
• L Chen, Q Qiu, Y Jiang, K Wang, Z Lin, Z Li, F Bibi, Y Yang, J Wang,... YE Zhang,...Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits. Science, 2019, 364 (6446), eaav6202
  
• J Zu, Y Gu, Y Li, C Li, W Zhang, YE Zhang, UJ Lee, L Zhang, M Long.Topological evolution of coexpression networks by new gene integration maintains the hierarchical and modular structures in human ancestors. Science China Life Sciences, 2019, 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. GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes. Genome Research,  2019, 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*. Adaptation and Phenotypic Diversification in Arabidopsis through Loss-of-function Mutations in Protein-coding Genes. Plant Cell, 2019, 31(5):1012-1025. 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^#.  Evolutionarily significant A-to-I RNA editing events originated through G-to-A mutations in primates.Genome Biology,  2019, 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^#. Rapid evolution of protein diversity by de novo origination in Oryza. Nature Ecology & Evolution , 2019,3(4):679-690. download

2018

• Fuqiang Ma,Pei Lin,Qingjian Chen,Xuemei Lu,Yong E.Zhang^#, Chung-I Wu^#.Direct measurement of pervasive weak repression by microRNAs and their role at the network level. BMC Genomics, 2018,19:362, download

2017

• Zhen-Xia Chen, Brian Oliver, Yong E. Zhang, Ge Gao, Manyuan Long. Expressed Structurally Stable Inverted Duplicates in Mammalian Genomes as Functional Noncoding Elements. Genome Biology and Evolution,,2017, 9:981-992, download
• Daqi Yu*, Wenwen Shi*^#, Yong E Zhang^#.. Underrepresentation of active histone modification marks in evolutionarily young genes. Insect science, ,2017,00:1–13, 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
  
• 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
  

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
  

• 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