Introduction
Dr. XIAO’s research focuses on bioinformatics algorithms and pipeline development, as well as high-throughput omics data integration and mining, particularly in cancer single-cell transcriptome data and multi-omics association studies. These studies will drive the transformation of big data into big discoveries, enable the development of novel tools for high-efficiency data mining, and provide further insight into knowledge networks for precision medicine. He has published in peer-reviewed journals, including Nature Communications, Science Bulletin, and Nucleic Acids Research.
Group leader
XIAO Jingfa
Biography
2019-Present, Professor, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, China
2012−2019, Professor, Beijing Institute of Genomics, Chinese Academy of Sciences, China
2007−2012, Associate Professor, Beijing Institute of Genomics, Chinese Academy of Sciences, China
2005−2007, Postdoctoral Fellow, Department of Chemistry, Utah University, United States of America
2003−2005, Postdoctoral Fellow, Institute of Materia Medica, Chinese Academy of Medical Sciences, China
1998−2003, Ph.D. in Computational Chemistry and Biology, State Key Laboratory of Theoretical and Computational Chemistry, Jilin University, China
1995−1998, Assistant Engineer, Shenyang First Pharmaceutical Co., Ltd., China
1991−1995, B.S. in Biology, Department of Biology, Sichuan University, China
Research Fields
1. Integrated analysis of cancer single-cell transcriptome data and resource construction
2. Construction of a knowledge graph for multi-omics association studies
3. Establish the microbial pan-genome annotation and data analysis platform
Selected Publications
1. Congfan Bu#, Hao Zhang#, Fengnian Zhang#, Wenhao Liang, Hao Gao, Jing Zhao, Fangming Lv, Ruikun Xue, Qian Liu, Zhewen Zhang, Zhong Jin*, Jingfa Xiao*, PGAP2: A Comprehensive Toolkit for Prokaryotic Pan-Genome Analysis Based on Fine-grained Feature Networks. Nature Communications. 16:9865 (2025).
2. Meiye Jiang#, Qiheng Qian#, Mingming Lu, Meili Chen, Zhuojing Fan, Yunfei Shang, Congfan Bu, Zhenglin Du, Shuhui Song, Jingyao Zeng*, Jingfa Xiao*, PlantPan: A comprehensive multi-species plant pan-genome database. The Plant Journal. 122, e70144 (2025).
3. Yunfei Shang#, Jingyao Zeng#,*, Jialin Mai, Jingfa Xiao*, Metabolic reprogramming landscape of pan-cancer by single-cell transcriptome data integration. Science Bulletin. 70:852-855 (2025).
4. Jingyao Zeng#, Zhi Nie#, Yunfei Shang#, Jialin Mai#, Yadong Zhang, Yuntian Yang, Chenle Xu, Jing Zhao, Zhuojing Fan, Jingfa Xiao*, CancerSCEM 2.0: an updated data resource of single-cell expression map across various human cancers. Nucleic Acids Research. 53:D1278-D12286 (2025).
5. Jialin Mai#, Qiheng Qian#, Hao Gao#, Zhuojing Fan, Jingyao Zeng*, Jingfa Xiao*, scTWAS Atlas: an integrative knowledgebase of single-cell transcriptome-wide association studies. Nucleic Acids Research. 53:D1195-D1204 (2025).
6. Qiheng Qian#, Ruikun Xue#, Chenle Xu, Fengyu Wang, Jingyao Zeng, Jingfa Xiao*, CVD Atlas: a multi-omics database of cardiovascular disease. Nucleic Acids Research. 53:D1348-D1355 (2025).
7. Jialin Mai#, Mingming Lu#, Qianwen Gao, Jingyao Zeng*, Jingfa Xiao*, Transcriptome-wide association studies: recent advances in methods, applications and available databases. Communications Biology. 6:899 (2023).
8. Yadong Zhang#, Hao Zhang#, Zaichao Zhang, Qiheng Qian, Zhewen Zhang*, Jingfa Xiao*, ProPan: A comprehensive database for profiling prokaryotic pan-genome dynamics. Nucleic Acids Research. 51:D767-D776 (2023).
9. Mingming Lu#, Yadong Zhang#, Fengchun Yang#, Jialin Mai#, Qianwen Gao, Yunfei Shang, Qiheng Qian, Meiye Jiang, Hao Zhang, Jie Liu, Jinyue Wang, Zhewen Zhang, Zaichao Zhang, Jingyao Zeng*, Jiao Li*, Jingfa Xiao*, TWAS Atlas: a curated knowledgebase of transcriptome-wide association studies. Nucleic Acids Research. 51:D1179-D1187 (2023).
10. Shuo Shi#, Qi Wang#, Yunfei Shang#, Congfan Bu, Mingming Lu, Meiye Jiang, Hao Zhang, Shuhuan Yu, Jingyao Zeng, Zaichao Zhang, Zhenglin Du*, Jingfa Xiao*, TSomVar: a tumor-only somatic and germline variant identification method with random forest. Briefings in Bioinformatics. 23(5): bbac381 (2022).
11. Jingyao Zeng#, Yadong Zhang#, Yunfei Shang#, Jialin Mai, Shuo Shi, Mingming Lu, Congfan Bu, Zhewen Zhang, Zaichao Zhang, Yang Li, Zhenglin Du, Jingfa Xiao*, CancerSCEM: A database of single-cell expression map across various human cancers. Nucleic Acids Research. 50: D1147-D1155 (2022).
12. Shuo Shi, Qiheng Qian, Shuhuan Yu, Qi Wang, Jinyue Wang, Jingyao Zeng, Zhenglin Du*, Jingfa Xiao*, RefRGim: an intelligent reference panel reconstruction method for genotype imputation with convolutional neural networks. Briefings in Bioinformatics. 22(6):bbab326 (2021).
13. Yadong Zhang, Zhewen Zhang*, Hao Zhang, Yongbing Zhao, Zaichao Zhang, Jingfa Xiao*, PADS Arsenal: a database of prokaryotic defense systems related genes. Nucleic Acids Research. 48: D590-D598 (2020).
14. Zhang Zhang*, Wenming Zhao*, Jingfa Xiao*, Yiming Bao*, Shunmin He*, Guoqing Zhang*, Yixue Li*, Guoping Zhao*, Runsheng Chen*, in National Genomics Data Center Members and Partners, Database Resources of the National Genomics Data Center in 2020. Nucleic Acids Research. 48: D24-D33 (2020).
15. Zhenglin Du, Liang Ma, Hongzhu Qu, et al., Xin Liu, Jingfa Xiao*, Changqing Zeng*, Whole genome analyses of Chinese population and the de novo assembly of a northern Han genome. Genomics Proteomics Bioinformatics. 17:229-247 (2019).
16. Yongbing Zhao, Jinyue Wang, Fang Liang, et al., Wenming Zhao, Yiming Bao, Zhang Zhang, Jiayan Wu, Yan W. Asmann*, Rujiao Li*, Jingfa Xiao*, NucMap: a database of genome-wide nucleosome positioning map across species. Nucleic Acids Research. 47: D163-D169 (2019).
17. Zhang Zhang*, Wenming Zhao*, Jingfa Xiao*, Yiming Bao*, in BIG Data Center Members, Database Resources of the BIG Data Center in 2018. Nucleic Acids Research. 46: D14-D20 (2018).
18. Xin Sheng, Jiayan Wu, Qianqian Sun, Xue Li, Feng Xian, Manman Sun, Wan Fang, Meili Chen, Jun Yu*, Jingfa Xiao*, MTD: A mammalian transcriptomic database to explore gene expression regulation. Briefings in Bioinformatics. 18, 28-36 (2017).
19. Zhang Zhang*, Wenming Zhao*, Jingfa Xiao*, in BIG Data Center Members. The BIG Data Center: from deposition to integration to translation. Nucleic Acids Research. 45, D18-D24 (2017).
20. Wenquan Wang#, Binxiao Feng#, Jingfa Xiao#, Zhiqiang Xia, et al., Ming Peng*. Cassava Genome from a Wild Ancestor to Cultivated Varieties. Nature Communications. DOI:10.1038/ncomms6110 (2014).
Group Members
Staff:
Dr. ZENG Jingyao, Senior Engineer, zengjy@big.ac.cn
Mr. BU Congfan, Engineer, bucf@big.ac.cn
Dr. QIAN Qiheng, Research Assistant, qianqiheng2018m@big.ac.cn
Dr. SHANG Yunfei, Research Assistant, shangyunfei2019m@big.ac.cn
Graduate Students：
NIE Zhi, 2020
MAI Jialin, 2021
XUE Ruikun, 2023
GAO Hao, 2023
LIU Kaifeng, 2024
ZHAO Jing, 2024
LV Fangming, 2024
QIAN Zhiming, 2025
XIE Jiachuan, 2025
ZHANG Sheng, 2025
Contact：
xiaojingfa@big.ac.cn
