2024
29. Yueying Zhang, Qianli Dong, Zhen Wang, Qinzhe Liu, Haopeng Yu, Wenqing Sun, Jitender Cheema, Qiancheng You, Ling Ding, Xiaofeng Cao, Chuan He, Yiliang Ding, Huakun Zhang. A fine-scale Arabidopsis chromatin landscape reveals chromatin conformation-associated transcriptional dynamics. Nature Communications, 2024, DOI: 10.1038/s41467-024-47678-7
2023
28. Huakun Zhang, Betty Y.-W. Chung, Zhiye Wang, Yiliang Ding. Editorial: Plant RNA structure. Frontiers in Plant Science, 2023, DOI: 10.3389/fpls.2023.1204600
27. Ruili Lv, Xiaowan Gou, Ning Li, Zhibin Zhang, Changyi Wang, Ruisi Wang, Bin Wang, Chunwu Yang, Lei Gong, Huakun Zhang, Bao Liu. Chromosome translocation affects multiple phenotypes, causes genome-wide dysregulation of gene expression, and remodels metabolome in hexaploid wheat. The Plant Journal, 2023, DOI: 10.1111/tpj.16338
2022
26. Xiaofei Yang, Haopeng Yu, Susan Duncan, Yueying Zhang, Jitender Cheema, Haifeng Liu, J. Benjamin Miller, Jie Zhang, Chun Kit Kwok, Huakun Zhang & Yiliang Ding. RNA G-quadruplex structure contributes to cold adaptation in plants. Nature Communication, 2022, 13, 6224. DOI: 10.1038/s41467-022-34040-y
25. Wenqing Sun ,Ling Ding, and Huakun Zhang. The Potential Rule of RNA Structure in Crop Molecular Breeding[J]. Frontiers in Plant Science, 2022, 13. DOI: 10.3389/fpls.2022.868771
24. Bingbing Xu, Yanda Zhu, Changchang Cao, Hao Chen, Qiongli Jin, Guangnan Li, Junfeng Ma, Jieyu Zhao, Jianghui Zhu, Yiliang Ding, Xianyang Fang, Yongfeng Jin, Chun Kit Kwok, Aiming Ren, Yue Wan, Zhiye Wang, Yuanchao Xue, Huakun Zhang, Qiangfeng Cliff Zhang, and Yu Zhou. Recent advances in RNA structurome[J]. SCIENCE CHINA Life Sciences, 2022,65(7):1285-1324. DOI: 10.1007/s11427-021-2116-2
2021
23. Xiaofei Yang, Haopeng Yu, Wenqing Sun, Ling Ding, Ji Li, Jitender Cheema, Ricardo Ramirez-Gonzalez, Xuebo Zhao, Azahara C. Martín, Fei Lu, Bao Liu, Cristobal Uauy, Yiliang Ding, and Huakun Zhang. Wheat in vivo RNA structure landscape reveals a prevalent rule of RNA structure in modulating translational subgenome expression asymmetry[J]. Genome biology, 2021, 22(1): 1-26. DOI: 10.1186/s13059-021-02549-y
22. Huakun Zhang, and Yiliang Ding. Novel insights into the pervasive rule of RNA structure in post-transcriptional regulation of gene expression in plants[J]. Biochemical Society Transactions, 2021, 49(4): 1829-1839. DOI: 10.1042/BST20210318
21. Zhenshan Liu, Qi Liu, Xiaofei Yang, Yueying Zhang, Matthew Norris, Xiaoxi Chen, Jitender Cheema, Huakun Zhang, and Yiliang Ding. In vivo nuclear RNA structurome reveals RNA-structure regulation of mRNA processing in plants[J]. Genome biology, 2021, 22(1): 1-22. DOI: 10.1186/s13059-020-02236-4
2020
20. Chris Morgana, Huakun Zhang, Clare E. Henrya, F. Chris H. Franklinc, and Kirsten Bombliesa. Derived alleles of two axis proteins affect meiotic traits in autotetraploid Arabidopsis arenosa[J]. Proceedings of the National Academy of Sciences, 2020, 117(16): 8980-8988. DOI: 10.1073/pnas.1919459117
19. Xiaowan Gou, Ruili Lv, Changyi Wang, Tiansi Fu, Yan Sha, Lei Gong, Huakun Zhang, and Bao Liu. Balanced Genome Triplication in Wheat Causes Premature Growth Arrest and an Upheaval of Genome-Wide Gene Regulation[J]. Frontiers in genetics, 2020, 11: 687. DOI: 10.3389/fgene.2020.00687
2019
18. Yueying Zhang, Minglei Yang, Susan Duncan, Xiaofei Yang, Mahmoud A.S. Abdelhamid, Lin Huang, Huakun Zhang, Philip N. Benfey, Zoe A.E. Waller, and Yiliang Ding. G-quadruplex structures trigger RNA phase separation[J]. Nucleic Acids Research, 2019, 47(22): 11746-11754. DOI: 10.1093/nar/gkz978
2018
17. Xiaowan Gou, Yao Bian, Ai Zhang, Huakun Zhang, Bin Wang, Ruili Lv, Juzuo Li, Bo Zhu, Lei Gong, and Bao Liu. Transgenerationally precipitated meiotic chromosome instability fuels rapid karyotypic evolution and phenotypic diversity in an artificially constructed allotetraploid wheat (AADD)[J]. Molecular biology and evolution, 2018, 35(5): 1078-1091. DOI: 10.1093/molbev/msy009
16. Yao Bian, Chunwu Yang, Xiufang Ou, Zhibin Zhang, Bin Wang, Weiwei Ma, Lei Gong, Huakun Zhang, and Bao Liu. Meiotic chromosome stability of a newly formed allohexaploid wheat is facilitated by selection under abiotic stress as a spandrel[J]. New phytologist, 2018, 220(1): 262-277. DOI: 10.1111/nph.15267
2017
15. Ai Zhang, Ning Li, Lei Gong, Xiaowan Gou, Bin Wang, Xin Deng, Changping Li, Qianli Dong, Huakun Zhang, and Bao Liu. Global analysis of gene expression in response to whole-chromosome aneuploidy in hexaploid wheat[J]. Plant Physiology, 2017, 175(2): 828-847. DOI: 10.1104/pp.17.0081
14. Christopher H. Morgan, Huakun Zhang, and Kirsten Bomblies. Are the effects of elevated temperature on meiotic recombination and thermotolerance linked via the axis and synaptonemal complex?[J]. Philosophical Transactions of the Royal Society B: Biological Sciences, 2017, 372(1736): 20160470. DOI: 10.1098/rstb.2016.0470
2016
13. Xutong Wang, Huakun Zhang, Yaling Li, Zhibin Zhang, Linfeng Li, and Bao Liu. Transcriptome asymmetry in synthetic and natural allotetraploid wheats, revealed by RNA‐sequencing[J]. New Phytologist, 2016, 209(3): 1264-1277. DOI: 10.1111/nph.13678
12. Huakun Zhang, Xiaowan Gou, Ai Zhang, XutongWang, Na Zhao, Yuzhu Dong, Linfeng Li, and Bao Liu. Transcriptome shock invokes disruption of parental expression-conserved genes in tetraploid wheat[J]. Scientific reports2016, 6(1): 1-11. DOI: 10.1038/srep26363
11. Meishan Zhang, Ning Li, Wenan He, Huakun Zhang, Wei Yang, and Bao Liu. Genome‐wide screen of genes imprinted in sorghum endosperm, and the rules of allelic differential cytosine methylation[J]. The Plant Journal, 2016, 85(3): 424-436. DOI: 10.1111/tpj.13116
10. Lihong Gao, Moussa Diarso, Ai Zhang, Huakun Zhang, Yuzhu Dong, Lixia Liu, Zhenling Lv, and Bao Liu. Heritable alteration of DNA methylation induced by whole‐chromosome aneuploidy in wheat[J]. New Phytologist, 2016, 209(1): 364-375. DOI: 10.1111/nph.13595
2015
9. Chang Liu, Xuejiao Yang, Huakun Zhang, Xutong Wang, Zhibin Zhang, Yao Bian, Bo Zhu, Yuzhu Dong, and Bao Liu. Genetic and epigenetic modifications to the BBAA component of common wheat during its evolutionary history at the hexaploid level[J]. Plant Molecular Biology, 2015, 88(1): 53-64. DOI: 10.1007/s11103-015-0307-0
2014
8. Huakun Zhang, Bo Zhu, Bao Qi, Xiaowan Gou, Yuzhu Dong, Chunming Xu, Bangjiao Zhang, Wei Huang, Chang Liu, Xutong Wang, Chunwu Yang, Hao Zhou, Khalil Kashkush, Moshe Feldman, Jonathan F. Wendel, and Bao Liu. Evolution of the BBAA component of bread wheat during its history at the allohexaploid level[J]. The Plant Cell, 2014, 26(7): 2761-2776. DOI: 10.1105/tpc.114.128439
7. Chunwu Yang, Long Zhao, Huakun Zhang, Zongze Yang, Huan Wang, Shanshan Wen, Chunyu Zhang, Sachin Rustgi, Diter von Wettstein, and Bao Liu. Evolution of physiological responses to salt stress in hexaploid wheat[J]. Proceedings of the National Academy of Sciences, 2014, 111(32): 11882-11887. DOI: 10.1073/pnas.1412839111
2013
6. Huakun Zhang, Yao Bian, Xiaowan Gou, Bo Zhu, Chunming Xu, Bao Qi, Ning Li, Sachin Rustgi, Hao Zhou, Fangpu Han, Jiming Jiang, Diter von Wettstein, and Bao Liu. Persistent whole-chromosome aneuploidy is generally associated with nascent allohexaploid wheat[J]. Proceedings of the National Academy of Sciences, 2013, 110(9): 3447-3452. DOI: 10.1073/pnas.1300153110
5. Huakun Zhang, Yao Bian, Xiaowan Gou, Yuzhu Dong, Sachin Rustgi, Bangjiao Zhang, Chunming Xu, Ning Li, Bao Qi, Fangpu Han, Diter von Wettstein, and Bao Liu. Intrinsic karyotype stability and gene copy number variations may have laid the foundation for tetraploid wheat formation[J]. Proceedings of the National Academy of Sciences, 2013, 110(48): 19466-19471. DOI: 10.1073/pnas.1319598110
2012
4. Bao Qi, Wei Huang, Bo Zhu, Xiaofang Zhong, Jianhua Guo , Na Zhao, Chunming Xu, Huakun Zhang, Jinsong Pang , Fangpu Han, and Bao Liu. Global transgenerational gene expression dynamics in two newly synthesized allohexaploid wheat (Triticum aestivum) lines[J]. BMC biology, 2012, 10(1): 1-18. DOI: 10.1186/1741-7007-10-3
2011
3. Na Zhao, Bo Zhu, Mingjiu Li, Li Wang, Liying Xu, Huakun Zhang, Shuangshuang Zheng, Bao Qi, Fangpu Han, and Bao Liu. Extensive and heritable epigenetic remodeling and genetic stability accompany allohexaploidization of wheat[J]. Genetics, 2011, 188(3): 499-510. DOI: 10.1534/genetics.111.127688
2. Na Zhao, Liying Xu, Bo Zhu, Mingjiu Li, Huakun Zhang, Bao Qi, Chunming Xu, Fangpu Han, and Bao Liu. Chromosomal and genome-wide molecular changes associated with initial stages of allohexaploidization in wheat can be transit and incidental[J]. Genome, 2011, 54(8): 692-699. DOI: 10.1139/g11-028
2010
1. Bao Qi, Xiaofang Zhong, Bo Zhu, Na Zhao, Liying Xu, Huakun Zhang, Xiaoming Yu, and Bao Liu. Generality and characteristics of genetic and epigenetic changes in newly synthesized allotetraploid wheat lines[J]. Journal of Genetics and Genomics, 2010, 37(11): 737-748. DOI: 110.1016/S1673-8527(09)60091-6