Research Areas
1. Key Technologies R & D for Biomedical Big Data Governance
2. Construction and Standardization of High-Quality Biomedical Datasets and Corpora
3. Application of Intelligent Agents and Biomedical Large Language Models

Brief Biography
2017-Present: Professor, Principal Investigator, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences
2016-2017: Professor, Principal Investigator, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
2007-2016: Leader, Life Science Center, Shanghai Center for Bioinformation Technology

Selected Publications (*Corresponding Author)

1. Yujie Chen, Mengyao Han, Jiayue Meng, Dongjian Cao, Nianhao Cheng, Qingming Luo, Jie Yang, Guoqing Zhang*. Mouse Forebrain Region Features and Cholinergic Neurons Subtyping: Integrated Analysis with Spatial Multi-omics. Genomics Proteomics Bioinformatics 2025 Nov 20:qzaf110. doi: 10.1093/gpbjnl/qzaf110.
2. Wei Chen, Yanpeng An, Ziru Chen, Ruijin Luo, Qinwei Lu, Cong Li, Chenhan Zhang, Qingxia Huang, Qinsheng Chen, Lianglong Zhang, Xiaoxuan Yi, Yixue Li*, Huiru Tang*, Guoqing Zhang*. TraceMetrix: a traceable metabolomics interactive analysis platform. Journal of Cheminformatics 17, 148 (2025).
3. Hanwen Zhou#, Yue Hu#*, Yulong Zheng, Jiefu Li, Jielong Peng, Jiang Hu, Yun Yang, Wei Chen, Guoqing Zhang*, Zefeng Wang*. A foundation language model to decipher diverse regulation of RNAs. Genome Biology 26, 301 (2025).
4. Jiayue Meng#, Mengyao Han#, Yuwei Huang#, Liang Li, Yuanhu Ju, Daqing Lv, Xiaoyi Chen, Liyun Yuan*, Guoqing Zhang*. PreDigs: A Database of Context-specific Cell Type Markers and Precise Cell Subtypes for Digestive Cell Annotation. Genomics Proteomics Bioinformatics 2025 Sep 22;23(4):qzaf066. doi: 10.1093/gpbjnl/qzaf066.
5. Wan Liu#, Pingping Wang#, Xinhao Zhuang#, Yunchao Ling, Haiyan Liu, Sheng Wang, Haihan Yu, Liangxiao Ma, Yuguo Jiang, Guoping Zhao, Xing Yan*, Zhihua Zhou*, Guoqing Zhang*. RDBSB: a database for catalytic bioparts with experimental evidence. Nucleic Acids Res 2025 Jan 6;53(D1):D709-D716.
6. Wenxing Gao#, Weili Lin#, Qiang Li#, Wanning Chen, Wenjing Yin, Xinyue Zhu, Sheng Gao, Lei Liu, Wenjie Li, Dingfeng Wu, Guoqing Zhang*, Ruixin Zhu*, Na Jiao*. Identification and validation of microbial biomarkers from cross-cohort datasets using xMarkerFinder. Nat Protoc 2024 Sep;19(9):2803-2830.
7. Yinzhao Wang#*, Liuyang Li#, Qiang Li#, Yaoxun Hu, Wenjie Li, Zhile Wu, Hungchia Huang, Zhenbo Lv, Wan Liu, Ruifang Cao, Guoping Zhao*, Fengping Wang*, Guoqing Zhang*. MASH-Ocean 1.0: Interactive platform for investigating microbial diversity, function, and biogeography with marine metagenomic data. iMeta 2024 May 19;3(3):e201.
8. Hanwen Zhou#, Liyun Yuan#, Yuanhu Ju, Yue Hu, Siqi Wang, Ruifang Cao, Zefeng Wang*, Guoqing Zhang*. IDeAS: an interactive database for dysregulated alternative splicing in cancers across Chinese and western patients. J Mol Cell Biol 2024 Apr 10;15(11):mjad074.
9. Ruifang Cao, Yunchao Ling, Jiayue Meng, Ao Jiang, Ruijin Luo, Qinwen He, Anan Li, Yujie Chen, Zoutao Zhang, Feng Liu*, Yixue Li*, Guoqing Zhang*. SMDB: a Spatial Multimodal Data Browser. Nucleic Acids Res 2023 Jul 5;51(W1):W553-W559.
10. Yimin Wang#, Yunchao Ling#, Jiao Gong#, Xiaohan Zhao, Hanwen Zhou, Bo Xie, Haiyi Lou, Xinhao Zhuang, Li Jin, The Han100K Initiative§, Shaohua Fan*, Guoqing Zhang*, Shuhua Xu*. PGG.SV: a whole-genome-sequencing-based structural variant resource and data analysis platform. Nucleic Acids Res 2023 Jan 6;51(D1):D1109-D1116.
11. Ling Wang#, Wan Liu#, Jieliang Liang#, Linna Zhao, Qiang Li, Chenfen Zhou, Hui Cen, Qingbei Weng*, Guoqing Zhang*. Mining of novel secondary metabolite biosynthetic gene clusters from acid mine drainage. Sci Data 2022 Dec 9;9(1):760.
12. Yunchao Ling#, Ruifang Cao#, Jiaqiang Qian#, Jiefu Li, Haokui Zhou, Liyun Yuan, Zhen Wang, Liangxiao Ma, Guangyong Zheng, Guoping Zhao, Zefeng Wang*, Guoqing Zhang*, Yixue Li*. An interactive viral genome evolution network analysis system enabling rapid large-scale molecular tracing of SARS-CoV-2. Sci Bull (Beijing) 2022 Apr 15;67(7):665-669.
13. Ning-ning Liu, Na Jiao, Jing-Cong Tan, Ziliang Wang, Dingfeng Wu, An-Jun Wang, Jie Chen, Liwen Tao, Chenfen Zhou, Wenjie Fang, Lo Hong Cheong, Weihua Pan, Wanqing Liao, Zisis Kozlakidis, Christopher Heeschen, Geromy G. Moore, Lixin Zhu*, Xingdong Chen*, Guoqing Zhang*, Ruixin Zhu*, Hui Wang*. Multi-kingdom microbiota analyses identify bacterial-fungal interactions and biomarkers of colorectal cancer across cohorts. Nat Microbiol 2022 Feb;7(2):238-250.
14. Weidi Huang#, Yunchao Ling#, Sirui Zhang, Qiguang Xia, Ruifang Cao, Xiaojuan Fan, Zhaoyuan Fang, Zefeng Wang*, Guoqing Zhang*. TransCirc: an interactive database for translatable circular RNAs based on multi-omics evidence. Nucleic Acids Res 2021 Jan 8;49(D1):D236-D242.
15. Yang Gao#, Chao Zhang#, Liyun Yuan#, YunChao Ling, Xiaoji Wang, Chang Liu,Yuwen Pan, Xiaoxi Zhang, Xixian Ma, Yuchen Wang, Yan Lu,Kai Yuan, Wei Ye,Jiaqiang Qian, Huidan Chang, Ruifang Cao, Xiao Yang, Ling Ma, Yuanhu Ju,Long Dai, Yuanyuan Tang, The Han100K Initiative§, Guoqing Zhang, Shuhua Xu*. PGG.Han: the Han Chinese genome database and analysis platform. Nucleic Acids Res 2020 Jan 8;48(D1):D971-D976.