代表著作
2026
[19] Mingke Wei†, Jo-Wei Allison Hsieh†, Jr-Fong Dang†, Botong Tong, Hui Li, Ronald Sederoff, Ying-Chung Jimmy Lin* and Quanzi Li* (2026) Thick walls, hidden stories: integrating scRNA-seq and snRNA-seq with spatial transcriptomics to complete the xylem puzzle. Genome Biology (Accepted) †co-first authors; *co-corresponding authors
[18] Fei-Man Hsu†, Jo-Wei Allison Hsieh†, Shiang-Chin Huang and Pao-Yang Chen (2026) Genome-wide DNA methylation in rice regeneration and transformation. The International Symposium on Rice Functional Genomics 2024. ISBN 978-1-80631-418-8. (Accepted) †co-first authors
[17] Kyungyong Seong, Rakesh Kumar, Daniil M Prigozhin, China Lunde, Thales Henrique Cherubino Ribeiro, Sébastien Bélanger, Jo-Wei Allison Hsieh, McCree Tang, Blake C. Meyers and Ksenia V Krasileva (2026) The Annotated Blueprint: Integrated Functional Genomic Resources for a model Tetraploid Wheat Triticum turgidum cv. Kronos. New Phytologist (Accepted)
[16] Jo-Wei Allison Hsieh†, Fu-Hui Wu†, Dian-Xuan Yang†, Ai-En Wu†, Ching-Ann Liu†, Chang-Hung Chen, Shinn-Zong Lin*, Ying-Chung Jimmy Lin* and Choun-Sea Lin* (2026) Protoplast-Based Functional Genomics and Genome Editing: Progress, Challenges and Applications. Plant, Cell & Environment https://doi.org/10.1111/pce.70375 †co-first authors; *co-corresponding authors
2025
[15] Peng Shuai†, Jo-Wei Allison Hsieh†, Chung-Ting Kao†, Chen-Wei Hu, Ray Wang, Shang-Che Kuo, Ming-Ren Yen, Pin-Chien Liou, Yi-Chi Ho, Chia-Chen Chu, Shuotian Huang, Jiao Liu, Lixia Zhang, Chia-Chen Wu, Yi-Jyun Luo, Quanzi Li, Chuan-Chih Hsu, Chao-Li Huang, Jung‐Chen Su, Mei-Chun Tseng, Ying-Lan Chen*, Te-Lun Mai* and Ying-Chung Jimmy Lin* (2025) Single-cell and spatial omics reveal progressive loss of xylem developmental complexity across seed plants. The Plant Cell 37(11):koaf253 †co-first authors; *co-corresponding authors
[14] Jhong-He Yu, Jo-Wei Allison Hsieh, Zhifeng Wang, Jia Wei, Quanzi Li, Ying-Lan Chen*, Ying-Chung Jimmy Lin* (2025) Decoding Xylem Development in Flowering Plants: Insights from Single-Cell Transcriptomics. Plant, Cell & Environment 48:8756–8770
[13] Jo-Wei Allison Hsieh†, Pin-Chien Liou†, Chia-Chang Lin†, Xiufang Dai†, Chen-Wei Hu†, I-Fan Wang, Jr-Fong Dang, Yi-Chi Ho, Kai-Wen Cheng, Wenjing Xu, Shang-Che Kuo, Chung-Ting Kao, Dian-Xuan Yang, Ray Wang, Ke Xiao, Jeng-Shane Lin, Cheng-Chih Hsu, Chuan-Chih Hsu, Te-Lun Mai, Yuxiang Cheng, Mei-Chun Tseng, Wei Li*, Ying-Lan Chen* and Ying-Chung Jimmy Lin* (2025) Single-cell and spatial multiomics identifies heterogeneous xylem development driven by mechanical stress in Populus. Developmental Cell 60(22):17 †co-first authors; *co-corresponding authors
[12] Chun-Che Huang†, Han-Wei Chen†, Jo-Wei Allison Hsieh†, Yen-Chun Lin, Yi-Pei Li, Chunxian Chen, Te-Lun Mai, Ying-Chung Jimmy Lin* and Yuan-Kai Tu* (2025) Transcriptomic analysis of peaches and nectarines reveals alternative mechanism for trichome formation. BMC Plant Biology 25:620 †co-first authors; *co-corresponding authors
[11] Debamalya Chatterjee, Ziru Zhang, Pei-Yu Lin, Po-Hao Wang, Gurpreet K Sidhu, Neela H Yennawar, Jo-Wei Allison Hsieh, Pao-Yang Chen, Rentao Song, Blake C Meyers and Surinder Chopra (2025) Maize unstable factor for orange1 encodes a nuclear protein that affects redox accumulation during kernel development. The Plant Cell 37(1):koae301
2024
[10] Chih-Hung Hsieh, Ya-Ting Sabrina Chang, Ming-Ren Yen, Jo-Wei Allison Hsieh and Pao-Yang Chen (2024) Predicting protein synergistic effect in Arabidopsis using epigenome profiling. Nature Communications 15:9160
[9] Jo-Wei Allison Hsieh, Ming-Ren Yen, Fu-Yu Hung, Keqiang Wu* and Pao-Yang Chen* (2024) Epigenetic factors direct synergistic and antagonistic regulation of transposable elements in Arabidopsis. Plant Physiology 196(3):1939-1952 *co-corresponding authors
[8] Jo-Wei Allison Hsieh†, Pei-Yu Lin†, Chi-Ting Wang, Yi-Jing Lee, Pearl Chang, Rita Jui-Hsien Lu, Pao-Yang Chen* and Chung-Ju Rachel Wang* (2024) Establishing an optimized ATAC-seq protocol for the maize. Frontiers in Plant Science 15:1370618 †co-first authors; *co-corresponding authors
[7] Ying-Lan Chen†*, Jo-Wei Allison Hsieh†, Shang-Che Kuo, Chung-Ting Kao, Chia-Chun Tung, Jhong-He Yu, Tien-Hsien Chang, Chuan Ku, Jianbo Xie, Deqiang Zhang, Quanzi Li and Ying-Chung Jimmy Lin* (2024) Merit of integrating in situ transcriptomics and anatomical information for cell annotation and lineage construction in single-cell analyses of Populus. Genome Biology 25:85 †co-first authors; *co-corresponding authors
2023
[6] Jo-Wei Allison Hsieh, Pearl Chang, Lin-Yun Kuang, Yue-Ie C. Hsing and Pao-Yang Chen (2023) Rice transformation treatments leave specific epigenome changes beyond tissue culture. Plant Physiology 193(2):1297-1312
Before 2023
[5] Yi-Tsung Tu, Chia-Yang Chen, Yi-Sui Huang, Chung-Han Chang, Ming-Ren Yen, Jo-Wei Allison Hsieh, Pao-Yang Chen* and Keqiang Wu* (2022) HISTONE DEACETYLASE 15 and MOS4-Associated Complex subunits 3A/3B coregulate intron retention of ABA-responsive genes. Plant Physiology 190(1):882-897; *co-corresponding authors
[4] Huei-Mien Ke*, Hsin-Han Lee, Chan-Yi Ivy Lin, Yu-Ching Liu, Min R. Lu, Jo-Wei Allison Hsieh, Chiung-Chih Chang, Pei-Hsuan Wu, Meiyeh Jade Lu, Jeng-Yi Li, Gaus Shang, Rita Jui-Hsien Lu, László G. Nagy, Pao-Yang Chen, Hsiao-Wei Kao and Isheng Jason Tsai* (2020) Mycena genomes resolve the evolution of fungal bioluminescence. Proceedings of the National Academy of Sciences 117(49):31267-31277 *co-corresponding authors
[3] Fu-Yu Hung, Chen Chen, Ming-Ren Yen, Jo-Wei Allison Hsieh, Chenlong Li, Yuan-Hsin Shih, Fang-Fang Chen, Pao-Yang Chen*, Yuhai Cui* and Keqiang Wu* (2020) The expression of long noncoding RNAs is associated with H3Ac and H3K4me2 changes regulated by the HDA6-LDL1/2 histone modification complex in Arabidopsis. NAR Genomics and Bioinformatics 2(3):lqaa066 *co-corresponding authors
[2] Jo-Wei Allison Hsieh, Ming-Ren Yen and Pao-Yang Chen (2020) Epigenomic regulation of OTU5 in Arabidopsis thaliana. Genomics 112(5):3549-3559
[1] Cheng-Ruei Lee, Jo-Wei Hsieh, M. E. Schranz and Thomas Mitchell-Olds (2018) The functional change and deletion of FLC homologs contribute to the evolution of rapid flowering in Boechera stricta. Frontiers in Plant Science 9:1078
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