Postdoctoral researcher in the Schmitz Lab, University of Georgia, working at the intersection of AI for Science and plant biology. I build deep-learning and epigenome-informed foundation models to decode how plant genomes encode cell-type-specific regulation. Ph.D. in Bioinformatics, Zhejiang University.
佐治亚大学 Schmitz 实验室博士后。用深度学习 × 单细胞/空间多组学，解码植物基因组的细胞类型特异性调控逻辑。浙江大学生物信息学博士。
|
🤖 AI for Plant Genomics |
🔬 Single-cell & Spatial Multi-omics |
🌱 Plant Epigenetics |
|
Python package for the PEAgent models — predict single-cell chromatin accessibility from DNA sequence · Docs PEAgent 推理包：从 DNA 序列预测单细胞染色质可及性 |
Analysis code for the PEAgent manuscript — training, motif lexicon, synergy, cross-species, variant effects PEAgent 论文分析代码：训练、motif 词典、协同、跨物种、变异效应 |
|
JBrowse 2 plugin rendering base-resolution attribution maps (scBasset / BPNet) as sequence logos JBrowse 2 插件：以序列 logo 形式展示碱基级模型归因图 |
R package to quantify protoplasting-induced artifacts in plant scRNA-seq R 包：系统评估原生质体化对植物单细胞转录组的影响 |
|
Cell-wall segmentation → single-cell-resolution spatial transcriptomics for plant tissue (Stereo-seq) 植物组织细胞壁分割 → 单细胞分辨率空间转录组流程 |
A practical guide to plant spatial multi-omics analysis (companion to the Trends Plant Sci review) · Site 植物空间多组学分析实践指南 |
† co-first author · Full list on my homepage / Google Scholar
 |
Yao J, Li J, Zhang X, Li X, Marand AP, Pickering E, Schmitz RJ. Sequence-based modeling of plant epigenomes reveals cell-type-specific cis-regulatory grammar. DOI · peagent.org |
 |
Yao J, Marand AP, Bai Y, Schmitz RJ, Fan L. Advances in plant spatial multi-omics data analysis. DOI |
 |
Yao J†, Chu Q†, Guo X†, Shao W†, et al., Liu H, Fan L. Spatiotemporal transcriptomic landscape of rice embryonic cells during seed germination. DOI |
 |
Yao J, Shang N, Chen H, et al., Chu Q. Sub-clustering, marker identification and multi-omics integration influenced by protoplasting in plant scRNA-seq data analysis. DOI |
 |
Zheng Y†, Yao J†, et al., Fan L. A manually curated database and analysis platform of cell markers of scars. DOI |
Also contributed to: The Plant Cell 2026 · Nature Plants 2026 (scPlantReg) · Molecular Plant 2025 ×2 · Briefings in Bioinformatics 2025 · Molecular Plant 2021 (PlantscRNAdb)
