I am a Postdoctoral Researcher in the Schmitz Lab at the University of Georgia, where I specialize in plant epigenetics and bioinformatics. I earned my Ph.D. in Bioinformatics from Zhejiang University.
My research integrates plant epigenetics with computational biology, with a particular focus on harnessing single-cell/spatial multi-omics and deep learning to decode the complexities of plant systems. My work has been featured in leading journals, including Developmental Cell, Molecular Plant, and Trends in Plant Science.
🧬 Research Interests
- Plant epigenetics
- Single-cell and spatial multi-omics
- Deep learning and epigenome-informed foundation models for plant systems biology
🎓 Educations
- 2025 - Present, University of Georgia, Genetics department, Schmitz Lab, Postdoctoral Researcher
- 2024 - 2025, University of Michigan, LSA/MCDB, Marand Lab, Research Scholar
- 2020 - 2025, Zhejiang University, Bioinformatics, Ph.D
- 2016 - 2020, Zhejiang University, College of Agriculture and Biotechnology, Bachelor Degree （top 1%）
📝 Publications
11. The plant ontology of cell types.
- Hongyu Chen, Pu Liang, Xiaolin Lu, Shuai Jiang, Jingjing Jin, Jiaqi Cai, Yaqian Lu, Dihuai Zheng, Jie Yao, Qinjie Chu, Huixia Shou, Chengxin Fu, Tingting Lu, Yi Jing, Yinqi Bai, Ning Yang, Silin Zhong, Jun Xiao, Fang Yang, Xing Guo, Jixian Zhai, Alexandre P. Marand, Zhixi Tian, Fan Chen, Jian Xu, Yuling Jiao, Dijun Chen, Peijian Cao, Xiaofeng Cui, Dave Jackson, Tatsuya Nobori, Xiaofeng Gu, Jiawei Wang, James Whelan, Jianbing Yan, Robert J. Schmitz, Zhang Zhang, Longjiang Fan, POCT Consortium. (2025). DOI: 10.1016/j.molp.2025.12.025
Molecular Plant (JCR=Q1, IF=24.1)
10. PlantscRNAdb 4.0: Improved marker identification and annotation under a cell type uniformity for plants.
- Dihuai Zheng, Xiaolin Lu, Yaqian Lu, Pu Liang, Nianmin Shang, Jiwei Xu, Jie Yao, Fangyu Mo, Qinjie Chu, Longjiang Fan, Hongyu Chen. (2025). DOI: 10.1016/j.molp.2025.12.026
Molecular Plant (JCR=Q1, IF=24.1)
9. Advances in plant spatial multi-omics data analysis.
- Jie Yao, Alexandre P. Marand, Yinqi Bai, Robert J. Schmitz, Longjiang Fan*. (2025). DOI: 10.1016/j.tplants.2025.10.005
Trends in Plant Science (JCR=Q1, IF=20.8)
- Plant spatial omics is advancing from transcriptomics to multi-omics, with subcellular resolution enabling studies in non-model species and mature tissues.
- A step-by-step workflow is presented for spatial multi-omics data analysis in plants.
- Key computational tools and plant-specific analytical considerations are summarized.
- Spatial multi-omics reveals regulatory mechanisms of cell development, stress response, plant–microbe interaction, and cross-species evolution.
8. mKmer: An unbiased K-mer embedding of microbiomic single-microbe RNA sequencing data.
- Fangyu Mo, Qinghong Qian, Dihuai Zheng, Wenjie Cai, Xiaolin Lu, Jie Yao, Hongyu Chen, Yujie Huang, Xiang Zhang, Sanling Wu, Yifei Shen, Yingqi Bai, Yongcheng Wang, Weiqin Jiang, Longjiang Fan*. (2025). DOI: 10.1093/bib/bbaf227
Briefings in Bioinformatics (JCR=Q1, IF=6.8)
7. Fundamentals of single-cell omics (1st ed.)
- Longjiang Fan, Yongcheng Wang, Qinjie Chu, Yinqi Bai, Tingting Lu, Xing Guo, Jie Yao, Hongyu Chen, Lu Chen, Hongshan Guo, Yifei Shen, Shiping Liu, Shenyu Ni, Binnan He, Wenwen Shao, Nianmin Shang (2024). Science Press. ISBN 978-7-03-079344-7
6. Sub-clustering, marker identification and multi-omics integration influenced by protoplasting in plant scRNA-seq data analysis
- Jie Yao, Nianmin Shang, Hongyu Chen, Yurong Hu, Qian-Hao Zhu, Longjiang Fan, Chuyu Ye, Qinjie Chu*. (2024). DOI: 10.1101/2024.12.14.628512
bioRxiv
5. Spatiotemporal transcriptomic landscape of rice embryonic cells during seed germination
- Jie Yao+, Qinjie Chu+, Xing Guo+, Wenwen Shao+, Nianmin Shang, Kang Luo, Xiaohan Li, Hongyu Chen, Qing Cheng, Fangyu Mo, Fan Xu, Fu Guo, Qian-Hao Zhu, Shuiguang Deng, Chengcai Chu, Xun Xu, Huan liu* and Longjiang Fan*. (2024). DOI: 10.1016/j.devcel.2024.05.016
Developmental Cell (JCR=Q1, IF=11.5)
- Establish a rice embryo germination spatiotemporal transcriptomic census
- Develop AI-based plant cell wall segmentation for precise cell-type identification
- Identify scutellum cell subtypes and cell-type-specific gene expression pattern
- OsMFT2 specifically expressed in SCL2, with decreasing trends during seed germination
4. A Manually curated database and analysis platform of cell markers of scars.
- Yan Zheng+, Jie Yao+, Xiner Shen, Haijun Cheng, Yinbo Peng, Weiqiang Tan, Michael P. Timko, Longjiang Fan*. (2022). DOI: 10.1016/j.jid.2022.10.008
Journal of Investigative Dermatology (JCR=Q1, IF=8.3)
3. PlantscRNAdb: A Database for Plant Single-cell RNA Analysis.
- Hongyu Chen, Xinxin Yin, Longbiao Guo, Jie Yao, Yuwen Ding, Xiaoxu Xu, Lu Liu, Zhu Qian-Hao, Qinjie Chu, Longjiang Fan. (2021). DOI: 10.1016/j.molp.2021.05.002
Molecular Plant (JCR=Q1, IF=21.4)
2. Signaling pathway perturbation analysis for assessment of biological impact of cigarette smoke on lung cells.
- Hongyu Chen, Fangjie Liu, Lu Liu, Jie Yao, Qinjie Chu, Yaqin Wang, Hongyan Qi, Michael P. Timko, Weijia Fang, Longjiang Fan*. (2021). DOI: 10.1038/s41598-021-95938-z
Scientific Reports (JCR=Q1, IF=5.5)
📰 1. Isolation endophytic microorganisms from different tea cultivars
- Xin-Qiang Zheng, Jie Yao, Si-Li Huang, Kai Zhao, Zi-Yi Chen, Dong Zhao*. (2019). ISSN 1314-8591, Volume 7, 2019
Journal of International Scientific Publications
🏅 Honors and Awards
- 2024 National Scholarship (top 1%)
- 2024 Outstanding Interdisciplinary Academic Achievement Award, Zhejiang University (Limited to 5 Recipients)
- 2023 Doctoral Academic Rising Star, Zhejiang University
- 2021-2024 Outstanding Graduate Student (4 times), Zhejiang University`
- 2019 National Scholarship (top 1%)
- 2018 National Scholarship (top 1%)
🏛️ Acedemic Reports
-
2025.12 Poster Presentation, Plant Center Retreat, Atlanta, USA.
PEAgent: sequence-based modeling for plant epigenomics reveals cell-type–specific regulatory grammar - 2024.06, Poster Presentation, International Conference on Plant Spatial Omics, Shenzhen
- 2024.04, Oral Presentation, Crop Design Editorial Board Meeting
- 2023.06, Oral Presentation, 1st Yangtze River Delta Bioinformatics Conference, Zhejiang Province
💻 Work Experience and Internships
- 2023.06 - 2024.06, BioLinkX (Bioinformatics Association)，Chairman
- 2023.09 - 2024.05, WinX Capital (FA), Life Science Group, Investment Researcher
- 2022.05 - 2022.11, Linear Capital (VC) , Health Care Group, Intern