General
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.

Research Areas

  • Computational genomics
  • Population genetics
  • Molecular evolution

Education

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

Experience

   
Work Experience
  • 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

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

2019

  • 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

  • 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


Research Interests

Model organism oriented molecular biology by its nature reminds us a fact that we are all decedents of a common ancestor as described by Darwin. Thus, we can understand human biology more by studying model species. Such a way of practice often leads us to believe that biology is all about conservation. However, Darwin’s original emphasis is to provide a theory (i.e., natural selection) on how species diverges between each other. Nowadays, numerous comparative analyses in genomic era demonstrated that species can evolve by various mechanisms, such as protein substitutions, regulatory changes and gene gain. The scientific community invests extensive efforts or protein evolution and regulatory changes. By contrast, gene gain or gene origination is less touched although H. J. Muller speculated its importance as early as one century before. 

In 1993, Manyuan Long characterized the first new gene (Jingwei) in Drosophila . In the subsequent decade, the field is biased to new genes generated by retroposition, which only represents a small portion of all retrogenes. I developed a novel pipeline to analyze the syntenic genomic alignment and assigned evolutionary ages to majority (>90%) of annotated genes in both Drosophila and mammals. This unparalleled dataset of new genes enabled a large scale functional study which leads to an unexpected discovery that development frequently recruits new genes. 

In the short term, there are at least two types of questions waiting for us, which are never fully addressed previously. First, we found that an excess of new genes are transcribed in developing brain in human lineage compared to mouse. Does this pattern still hold if we compared human with other primates? How about other fast evolving brains such as that of song bird? Secondly, between-species sequence analyses often suggest that adaptive selection drives the evolution of new genes. However, we never know how new genes initially fixed in the population. The quickly accumulating resequencing data in human provided us an opportunity to tackle this question. The answer may significantly help us to understand how different human ethnic groups differentiate between each other. 

In the long term, we hope to trace how a new gene emerged mechanistically, how it get fixed in the population, what function it often plays and why, and how and why some gene gets lost from the genome. In brief, we would like to have a complete picture of the life history of genes. In this research direction, we not only build up concepts governing gene gain and loss, but understand how gene gain and loss contributes to species or population level difference. 

The development of next and next to next generation sequencing technique generates all kinds of omics data, including genomes, transcriptomes and regulatomes between and within species (especially for human). Other high-throughput functional genomic data, such as proteomic data, are also rapidly accumulating. We never had such a rich and diverse dataset to perform our computational genomic analysis previously. In this prospective, as computational biologists, we do live in a golden age.

Collaboration

  • Jon Staley, University of Chicago
  • Manyuan Long, University of Chicago
  • Erik Sontheimer, Northwestern University
  • Tim Liu, NIH
  • Liping Wei, Peking University
  • Chuanyun Li, Peking University
  • Fumin Lei, Institute of Zoology, CAS

Prospective Students

已指导学生

马慧静  博士研究生  071002-动物学  

贾行星  博士研究生  0710Z1-基因组学  

张丹  博士研究生  0710Z1-基因组学  

黄家蔚  硕士研究生  0710Z1-基因组学  

陈春燕  博士研究生  0710Z1-基因组学  

邵毅  博士研究生  0710Z1-基因组学  

毛亚男  硕士研究生  0710Z1-基因组学  

现指导学生

马辰宇  博士研究生  0710Z1-基因组学  

余大奇  博士研究生  0710Z1-基因组学  

王梦霞  博士研究生  0710Z1-基因组学  

来兴欢  博士研究生  0710Z1-基因组学  

袁昊  硕士研究生  0710Z1-基因组学  

孙玲  博士研究生  0710Z1-基因组学