1. Rui Zou1# Zhihui Lu1#,*, Armin Djamei2, Friedrich Kragler3, Hon-Ming Lam4, Shoudong Zhang1* (2025) The Roles of Epigenetics in the Interplay between beneficial rhizobacteria and Plants. Modern Agriculture
2. Shoudong Zhang1,2,3#, *，Zhixia Xiao2,3,#, Ailin Liu2,3,#, Dongpeng Ren1, #, Shengjie Chen2,3, , Hanxue Zhang1, Li Zhang2,3, Zhili Wang2,3, Jun Yang4, Hon-Ming Lam2,3* （2025）salt stress adaptations in soybean involve alterations in pre-mRNA processing. Plant, cell & environment (in press)
3. Ming Luo, Tomasz Jacek Sarnowski, Marc Libault, Gabino Ríos, Jean-Benoit Charron, Nitin Mantri, Shoudong Zhang (2023) Editorial: New insights into mechanisms of epigenetic modifiers in plant growth and development, volume II. Front Plant Sci. 14:1213511. doi: 10.3389/fpls.2023.1213511
2. Hafiz Mamoon Rehman , Shengjie Chen, Shoudong Zhang , Memoona Khalid , Muhammad Uzair , Phillip A. Wilmarth, Shakeel Ahmad and Hon-Ming Lam (2022) Membrane Proteomic Profiling of Soybean Leaf and Root Tissues Uncovers Salt-Stress-Responsive Membrane Proteins. Int. J. Mol. Sci. 23(21), 13270; https://doi.org/10.3390/ijms232113270
3. Yiping Wang, Hailei Zhang, Pengxi Wang, Huan Zhong, Wuzhen Liu, Shoudong Zhang, Liming Xiong, Yingying Wu, Yiji Xia (2022) ArabidopsisEXTRA-LARGE G PROTEIN 1 (XLG1) functions together with XLG2 and XLG3 in PAMP-triggered MAPK activationand immunity. J. Integr. Plant Biology DOI:10.1111/jipb.13391
4. Qianwen Wang1,2†, Xiucong Bao3†, Shengjie Chen1,2†, Huan Zhong4†, Yaqin Liu1,2, Li Zhang1,2, Yiji Xia2,4,5, Friedrich Kragler6, Ming Luo7*, David Xiang Li4*, Hon-Ming Lam1,2*, Shoudong Zhang1,2* (2021) AtHDA6 functions as an H3K18ac eraser to maintain pericentromeric CHG methylation in Arabidopsis thaliana. Nucleic Acids Research, 49(17): 9755-9767
5. Shangqian Xie 1, #, Amy Wing-Sze Leung2,#, Zhenxian Zheng2, Dake Zhang3, Chuanle Xiao4,*, Ruibang Luo2,*, Ming Luo5,*, Shoudong Zhang6,7,* (2021) Applications and potentials of nanopore sequencing in the (epi)genome and (epi)transcriptome era. The innovation, 2(4):100153
6. Zhaogeng Lu , Jiawen Cui , Li Wang , Nianjun Teng , Shoudong Zhang , Hon-Ming Lam , Yingfang Zhu , Siwei Xiao , Wensi Ke , Jinxing Lin , Chenwu Xu , Biao Jin (2021) Genome-wide DNA mutations in Arabidopsis plants after multigenerational exposure to high temperatures. Genome Biology 22(1):160. doi: 10.1186/s13059-021-02381-4.
7. Hailei Zhang, Huan Zhong, Xufeng Wang, Shoudong Zhang, Xiaojian Shao, Hao Hu, Zhiling Yu, Zongwei Cai, Xuemei Chen, and Yiji Xia (2021) Use of NAD tagSeq II to identify growth phase-dependent alterations in E. coli RNA NAD+ capping PNAS, 118 (14) e2026183118
8. Shoudong Zhang, †,*, Runsheng Li, †, Li Zhang, Shengjie Chen, Min Xie, Liu Yang, Yiji Xia, Christine H. Foyer, Zhongying Zhao, *, Hon-Ming Lam, * (2020) New insights into Arabidopsis transcriptome complexity revealed by direct sequencing of native RNAs, Nucleic Acids Research, 48(14):7700-7711
9. Ming Luo, Gabino Ríos, Tomasz Jacek Sarnowski, Shoudong Zhang, Nitin Mantri, Jean-Benoit Charron and Marc Libault (2020) Editorial: New Insights Into Mechanisms of Epigenetic Modifiers in Plant Growth and Development. Front. Plant Sci. 10:1661. doi: 10.3389/fpls.2019.01661
10. Hailei Zhang, Huan Zhong, Shoudong Zhang, Xiaojian Shao, Min Ni, Zongwei Cai, Xuemei Chen, and Yiji Xia (2019) NAD tagSeq reveals that NAD+-capped RNAs are mostly produced from a large number of protein-coding genes in Arabidopsis. PNAS, 116 (24) 12072-12077
11. Daogang Guan, Yiji Xia, Shoudong Zhang* (2019) Analyzing and Predicting Phloem Mobility of Macromolecules with an Online Database. In Phloem pp 433-438 edited by Johannes Leische, Springer Nature publisher.
12. Lei Yang, Valentina Perrera, Eleftheria Saplaoura, Federico Apelt, Mathieu Bahin, Amira Kramdi, Justyna Olas, Bernd Mueller-Roeber, Ewelina Sokolowska, Wenna Zhang, Runsheng Li, Nicolas Pitzalis, Manfred Heinlein, Shoudong Zhang, Auguste Genovesio, Vincent Colot, Friedrich Kragler (2019) m5C Methylation Guides Systemic Transport of Messenger RNA over Graft Junctions in Plants. Current Biology. 29(15): 2465-2476.e5
13. Wei Huang, Chao Zhao, Huan Zhong, Shoudong Zhang, Yiji Xia, Zongwei Cai (2019) Bisphenol S induced epigenetic and transcriptional changes in human breast cancer cell line MCF-7. Environ Pollut 246:697-703.
14. Shoudong Zhang*, Huoming ZHANG, Yiji XIA*, Liming Xiong*. (2018) The caseinolytic protease complex component CLPC1 in Arabidopsis maintains proteome and RNA homeostasis in chloroplasts. BMC Plant Biology. 18:192 (doi.org/10.1186/s12870-018-1396-0)
15. Daogang Guan, Bin Yan, Jianmin Hua, Christopher Thieme, Hailong Zhu, Zhongying Zhao, Friedrich Kragler *, Yiji Xia*, Shoudong Zhang*. (2017) PlaMoM: A comprehensive database compiles plant mobile macromolecules. NUCLEIC ACIDS RESEARCH （NAR） 45(Database issue): D1021–D1028.
16. Shoudong Zhang, Xiangqiang Zhan, Xiaoming Xu, Peng Cui, Jian-Kang Zhu, Yiji Xia and Liming Xiong（2015）Two domain-disrupted hda6 alleles have opposite epigenetic effects on transgenes and some endogenous targets Scientific Reports 5:17832.
17. Peng Cui†, Shoudong Zhang†, Feng Ding, Shajahan Ali and Liming Xiong (2014) Dynamic Regulation of Genome-wide Alternative Splicing and Stress Tolerance by the Sm-like Protein SAD1 in Arabidopsis. Genome Biology, 15:R1 (#, co-first author).
18. Feng Ding, Peng Cui, Zhenyu Wang, Shoudong Zhang, Shajahan Ali and Liming Xiong (2014) Genome-wide analysis of alternative splicing of pre-mRNA under salt stress in Arabidopsis. BMC Genomics. 15:431
19. Tao Chen, Peng Cui, Hao Chen, Shajahan Ali, Shoudong Zhang, Liming Xiong (2013) A KH-Domain RNA-Binding Protein Interacts with FIERY2/CTD Phosphatase-Like 1 and Splicing Factors and Is Important for Pre-mRNA Splicing in Arabidopsis. Plos genetics 9(10): e1003875.
20. Zhihuan Gao, Hai-Liang Liu, Lucia Daxinger, Olga Pontes, Xinjian He, Weiqiang Qian, Huixin Lin, Mingtang Xie, Zdravko J. Lorkovic, Shoudong Zhang, Daisuke Miki, Xianqiang Zhan, Dominique Pontier, Thierry Lagrange, Hailing Jin, Antonius J. Matzke, Marjori Matzke, Craig S. Pikaard, and Jian-Kang Zhu, (2010) An RNA polymerase II- and AGO4-associated protein acts in RNA-directed DNA methylation. Nature. May 6; 465(7294): 106–109
21. Na You, Gabriel Murillo, Xiaoquan Su, Xiaowei Zeng, Jian Xu, Kang Ning, Shoudong Zhang, Jiankang Zhu, and Xinping Cui (2012) SNP calling using genotype model selection on high-throughput sequencing data. Bioinformatics. 28(5): 643-650
22. Shoudong Zhang, Li Sun and Friedrich Kragler (2009) The Phloem-Delivered RNA Pool Contains Small Noncoding RNAs and Interferes with Translation. Plant Physiology 150:378-387
23. Nikola Winter, Gregor Kollwig, Shoudong Zhang and Friedrich Kragler (2007) MPB2C, a Microtubule-Associated Protein, Regulates Non-Cell-Autonomy of the Homeodomain Protein KNOTTED. The Plant Cell 19:3001-3018
