Publications
A collection of my research work.
Spatial integration of multi-omics single-cell data with SIMO
Penghui Yang, Kaiyu Jin, Yue Yao, Lijun Jin, Xin Shao, Chengyu Li, Xiaoyan Lu, Xiaohui Fan
Nature Communications 2025
SIMO integrates spatial and multi-omics single-cell data to reveal the spatial organization of complex biological systems.
ChatCell: Facilitating Single-Cell Analysis with Natural Language
Yin Fang, Kangwei Liu, Ningyu Zhang, Xinle Deng, Penghui Yang, Zhuo Chen, Xiangru Tang, Mark Gerstein, Xiaohui Fan, Huajun Chen
arXiv preprint 2024
ChatCell leverages large language models to facilitate single-cell analysis through natural language interaction.
A Single-Cell Landscape of Human Liver Transplantation Reveals a Pathogenic Immune Niche Associated with Early Allograft Dysfunction
Xin Shao, Zheng Wang, Kai Wang, Xiaoyan Lu, Ping Zhang, Rongfang Guo, Jie Liao, Penghui Yang, Shusen Zheng, Xiao Xu, Xiaohui Fan
Engineering 2024
Single-cell transcriptomic analysis of human liver transplantation revealing immune dynamics associated with early allograft dysfunction.
Revealing spatial multimodal heterogeneity in tissues with SpaTrio
Penghui Yang†, Lijun Jin†, Jie Liao†, Kaiyu Jin, Xin Shao, Chengyu Li, Jingyang Qian, Junyun Cheng, Dingyi Yu, Rongfang Guo, Xiao Xu, Xiaoyan Lu, Xiaohui Fan
Cell Genomics 2023
SpaTrio reveals the spatial multimodal heterogeneity in tissues by integrating spatial transcriptomics with single-cell multi-omics data.
Single-cell RNA sequencing reveals enhanced antitumor immunity after combined application of PD-1 inhibitor and Shenmai injection in non-small cell lung cancer
Dingyi Yu, Penghui Yang, Xiaoyan Lu, Shaoze Huang, Li Liu, Xiaohui Fan
Cell Communication and Signaling 2023
Single-cell RNA sequencing reveals the immune landscape changes after combined PD-1 inhibitor and Shenmai injection treatment in non-small cell lung cancer.
Reconstruction of the cell pseudo-space from single-cell RNA sequencing data with scSpace
Jingyang Qian, Jie Liao, Ziqi Liu, Ying Chi, Yin Fang, Yanrong Zheng, Xin Shao, Bingqi Liu, Yongjin Cui, Wenbo Guo, Yining Hu, Hudong Bao, Penghui Yang, Qian Chen, Mingxiao Li, Bing Zhang, Xiaohui Fan
Nature Communications 2023
scSpace reconstructs the pseudo-spatial organization of cells from scRNA-seq data, bridging spatial and single-cell transcriptomics.
De novo analysis of bulk RNA-seq data at spatially resolved single-cell resolution
Jie Liao, Jingyang Qian, Yin Fang, Zhuo Chen, Xiang Zhuang, Ningyu Zhang, Xin Shao, Haihong Yang, Penghui Yang, Junyun Cheng, Yang Hu, Yining Hu, Lingqi Yu, Jinlu Zhang, Xiaoyan Lu, Li Shao, Dan Wu, Yue Gao, Huajun Chen, Xiaohui Fan
Nature Communications 2022
bulk2space deconvolves bulk RNA-seq data to single-cell and spatial resolution without paired single-cell reference.
Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data with SpaTalk
Xin Shao, Chengyu Li, Haihong Yang, Xiaoyan Lu, Jie Liao, Jingyang Qian, Kai Wang, Junyun Cheng, Penghui Yang, Huajun Chen, Xiao Xu, Xiaohui Fan
Nature Communications 2022
SpaTalk infers cell-cell communication from spatial transcriptomics data using knowledge graph-based approaches.
Single-cell RNA sequencing reveals the temporal diversity and dynamics of cardiac immunity after myocardial infarction
Kaiyu Jin†, Shan Gao†, Penghui Yang†, Rongfang Guo, Dan Li, Yunsha Zhang, Xiaoyan Lu, Guanwei Fan, Xiaohui Fan
Small Methods 2022
Single-cell RNA sequencing reveals the dynamic changes of cardiac immune cells after myocardial infarction, providing insights into cardiac immunity and potential therapeutic targets.
Revealing the Transcriptional Heterogeneity of Organ-Specific Metastasis in Human Gastric Cancer Using Single-cell RNA Sequencing
Haiping Jiang†, Dingyi Yu†, Penghui Yang†, Rongfang Guo, Mei Kong, Yuan Gao, Xiongfei Yu, Xiaoyan Lu, Xiaohui Fan
Clinical and Translational Medicine 2022
Single-cell RNA sequencing reveals transcriptional heterogeneity underlying organ-specific metastasis patterns in gastric cancer. (Open Science ExcelLent Author Program)
Modern research on Chinese medicine based on single-cell omics: technologies and strategies
Penghui Yang, Lijun Jin, Jie Liao, Xin Shao, Lu Li, Xiaoyan Lu, Xiaohui Fan
China Journal of Chinese Materia Medica 2022
A comprehensive review of single-cell omics technologies and their applications in modern Chinese medicine research. (Cover Article)
scDeepSort: a pre-trained cell-type annotation method for single-cell transcriptomics using deep learning with a weighted graph neural network
Xin Shao, Haihong Yang, Xiang Zhuang, Jie Liao, Penghui Yang, Junyun Cheng, Xiaoyan Lu, Huajun Chen, Xiaohui Fan
Nucleic Acids Research 2021
scDeepSort uses a weighted graph neural network for automated cell-type annotation in single-cell transcriptomics.