Publications
Since 2020, I have worked on plant genomics bioinformatics. Below are the results achieved with my collaborators.
T2T-Hub: A central platform for analyzing plant and animal telomere-to-telomere genomes
Haoyu Chao, Zhonghao Ruan, Zhuojin Li, Xinkai Zhou, Shilong Zhang, Xingxing Shen, Cong Feng†, Dijun Chen†, Ming Chen†
WebserverNucleic Acids Research, 2026
T2T-Hub is a free, web-based platform that integrates automated annotation, visualization, and comparative analysis tools for telomere-to-telomere (T2T) genomes, supports user uploads and unified analysis of 270 pre-analyzed plant and animal T2T genomes, and is freely accessible without login at two mirror sites.
A single-cell atlas of pan-cancer liver metastasis reveals dynamic cellular programs driving metastatic progression and immune modulation
Xinyu Tong, Haoyu Chao, Chenlu Zhang, Zhuojin Li, Quan Han, Lishan Wang, Nuo Wu, Ruidong Chen, Jian Gao, Shu Zhang, Lei Xu, Ming Chen†, Hui Zhao†, Lei Wang†, Dijun Chen†
ArticleResearch, 2026
This study presents a single-cell transcriptomic atlas of liver metastases across multiple cancer types, identifying four core cellular programs that drive the transition from immune-active to immunosuppressive microenvironments, thereby offering a high-resolution framework for understanding metastatic progression and guiding therapeutic strategies.
Cross-species prediction of histone modifications in plants via deep learning
Tongxuan Lv, Quan Han, Yilin Li, Chen Liang, Zhonghao Ruan, Haoyu Chao, Ming Chen, Dijun Chen†
SoftwareGenome Biology, 2026
This study demonstrates that phylogenetically informed model training significantly improves cross-species epigenomic prediction, offering a scalable computational strategy for functional annotation in non-model and agriculturally important plants.
scPlantLLM: A foundation model for exploring single-cell expression atlases in plants
Guangshuo Cao, Haoyu Chao, Wenqi Zheng, Yangming Lan, Kaiyan Lu, Yueyi Wang, Ming Chen, He Zhang†, Dijun Chen†
SoftwareGenomics, Proteomics & Bioinformatics, 2025
scPlantLLM is a Transformer-based foundation model trained on millions of plant single-cell data points that excels in clustering, cell type annotation, batch integration (0.91 zero-shot accuracy), and gene regulatory network inference, offering a powerful tool for resolving cellular heterogeneity in plant systems.
Genomic insights into drought adaptation of the forage shrub Caragana korshinskii (Fabaceae) widely planted in drylands
Fengyuan Mei, Tianrui Yang, Haoyu Chao, Xiaohui Ma, Jingjing Wu, Qi Yang, Guangpeng Ren, Li Song, Qian Wang, Liwang Qi, Xinxing Fu, Gegentu, Cuiping Gao, Ruigang Wang, Ming Chen, Xiangwen Fang, Jianquan Liu†, Guojing Li†, Shengdan Wu†
ArticleThe Plant Journal, 2025
The chromosomal-scale genome of drought-tolerant Korshinsk peashrub reveals that tandem duplications of stress-related gene families (e.g., Dehydrin) drive its adaptation to desert environments, providing a valuable genetic resource for breeding drought-resistant crops.
Integration of metabolome and transcriptome reveals flavonoid metabolic network during the developmental stage of flower buds in Cornus wilsoniana
Jiaqi Cai, Haoyu Chao, Ming Chen†, Dijun Chen†
ArticleMedicinal Plant Biology, 2025
This study integrates transcriptomic, metabolomic, and comparative genomic analyses to reveal the coordinated regulatory landscape of flavonoid biosynthesis during flower bud development in Cornus wilsoniana, identifying key genes and co-expression modules linked to hormone signaling, redox homeostasis, and light perception.
ncPlantDB: a plant ncRNA database with potential ncPEP information and cell type-specific interaction
Liya Liu, Enyan Liu, Yueming Hu, Sida Li, Shilong Zhang, Haoyu Chao, Yanshi Hu, Yanyan Zhu, Yifan Chen, Luyao Xie, Yi Shen, Liangwei Wu, Ming Chen†
DatabaseNucleic Acids Research, 2024
ncPlantDB is a comprehensive database integrating ncRNAs, ncRNA-encoded peptides (ncPEPs), and cell-specific interaction networks across 43 plant species, offering unique features such as translational potential data and single-cell expression visualization to advance plant ncRNA biology.
A chromosome-level genome assembly provides insights into Cornus wilsoniana evolution, oil biosynthesis, and floral bud development
Zhenxiang He, Haoyu Chao, Xinkai Zhou, Qingyang Ni, Yueming Hu, Ranran Yu, Minghuai Wang, Changzhu Li, Jingzhen Chen, Yunzhu Chen, Yong Chen, Chunyi Cui, Liangbo Zhang†, Ming Chen†, Dijun Chen†
ArticleHorticulture Research, 2023
This study presents a chromosome-level genome assembly of Cornus wilsoniana, revealing its evolutionary history, whole-genome duplication events, and key genes regulating fatty acid composition and flower morphology.
Integrating omics databases for enhanced crop breeding
Haoyu Chao, Shilong Zhang, Yueming Hu, Qingyang Ni, Saige Xin, Liang Zhao, Vladimir A. Ivanisenko, Yuriy L. Orlov, Ming Chen†
ReviewJournal of Integrative Bioinformatics, 2023
This review emphasizes that integrating multi-omics databases is essential for advancing crop plant breeding to enhance global food security.
CropGF: a comprehensive visual platform for crop gene family mining and analysis
Jingtian Xu, Can Zhu, Minzeng Su, Sida Li, Haoyu Chao†, Ming Chen†
DatabaseDatabase, 2023
CropGF is a comprehensive multi-omics visual platform covering seven plant species that enables flexible gene family mining, cross-species analysis, and downstream tools such as phylogenetic tree construction and ka/ks analysis.
Biogenesis, functions, interactions, and resources of Non-coding RNAs in plants
Haoyu Chao, Yueming Hu, Liang Zhao, Saige Xin, Qingyang Ni, Peijing Zhang†, Ming Chen†
ReviewInternational Journal of Molecular Sciences, 2022
This review systematically summarizes the biogenesis, functions, and interactions of five major regulatory non-coding RNAs (miRNA, siRNA, tsRNA, circRNA, lncRNA) in plants, along with bioinformatics tools, databases, and a step-by-step computational analysis protocol.
BrassicaEDB: A gene expression database for Brassica crops
Haoyu Chao, Tian Li, Chaoyu Luo, Hualei Huang, Yingfei Ruan, Xiaodong Li, Yue Niu, Yonghai Fan, Wei Sun, Kai Zhang, Jiana Li, Cunmin Qu, Kun Lu†
DatabaseInternational Journal of Molecular Sciences, 2020
The Brassica Expression Database (BrassicaEDB) provides comprehensive, user-friendly access to transcriptome expression profiles (FPKM, TPM, read counts) across 103 tissues and 70 SRA projects in rapeseed, facilitating rapid gene function elucidation and biological exploration.