Our research group focuses on key scientific problems in the detection, processing, and recognition of biomedical signals. We conduct research in machine learning, spatial multi-omics, computational mass spectrometry, mass spectrometry imaging, molecular network modeling, and healthcare big data analysis. The main goal is to develop computational methods and analytical tools for complex biomedical data, with an emphasis on improving the interpretation of metabolomics, mass spectrometry imaging, and multimodal spatial omics data.

In methodological research, the group focuses on mass spectrometry data preprocessing, feature extraction, molecular annotation, spatial signal reconstruction, and multimodal data integration. By combining machine learning, statistical modeling, and network analysis, we aim to establish computational models that can characterize molecular spatial distributions, metabolic regulatory relationships, and disease-associated changes. In application-oriented research, the group studies diseases such as Alzheimer’s disease, hepatocellular carcinoma, diabetic kidney disease, and nasopharyngeal carcinoma, with the aim of discovering disease-related molecular markers, analyzing spatial metabolic abnormalities, and investigating disease mechanisms through multi-omics data.

Through interdisciplinary collaboration among electronic information, artificial intelligence, analytical chemistry, life sciences, and medicine, the group seeks to advance computational mass spectrometry and spatial omics analysis methods, and to provide new data analysis technologies for disease mechanism research, early diagnosis, and precision medicine.

Government-Funded Research Projects：

15. National Natural Science Foundation of China. Development of a new method for multiscale metabolic interaction network analysis and its application to spatial metabolomics research in Alzheimer's disease. 2024.01–2027.12. Principal Investigator, ongoing.

14. National Natural Science Foundation of China. A new entropy-based network analysis method and its application to metabolomics research in hepatocellular carcinoma. 2019.01–2022.12. Principal Investigator, completed.

13. National Natural Science Foundation of China. Investigation of the mechanism by which Qingluo Yin treats heat bi syndrome from the perspective of dampness based on the regulatory role of NAMPT/SIRT1 in lipid metabolism. 2020.01–2023.12. Co-Principal Investigator, completed.

12. National Natural Science Foundation of China. New methods for metabolomics data fusion and modeling and their application to diabetic nephropathy research. 2014.01–2017.12. Principal Investigator, completed.

11. National Major Scientific Research Instrument Development Program. Development of an in situ potential-controlled electrochemistry-nuclear magnetic resonance combined system for liquid-phase and solid-phase studies. 2014.01–2017.12. Participant, completed.

10. Social Development Guiding Project (Key Project) of Fujian Provincial Science and Technology Plan. Multimodal and cross-scale metabolic intelligent subtyping of nasopharyngeal carcinoma and its application in individualized diagnosis and treatment decision-making. 2026.03–2029.02. Principal Investigator, ongoing.

9. Social Development Guiding Project (Key Project) of Fujian Provincial Science and Technology Plan. Early diagnosis and molecular mechanism study of Alzheimer’s disease based on multiscale spatial metabolomics. 2022.03–2025.02. Principal Investigator, completed.

8. Social Development Guiding Project (Key Project) of Fujian Provincial Science and Technology Plan. New nuclear magnetic resonance metabolic profiling techniques and their application to gestational diabetes mellitus research. 2015.04–2018.03. Principal Investigator, completed.

7.  Natural Science Foundation of Fujian Province. Development of new nuclear magnetic resonance metabolomics methods and their application to early diagnosis of diabetic nephropathy. 2009.03–2011.09. Principal Investigator, completed.

6. Natural Science Foundation of Fujian Province. Physics-informed magnetic resonance imaging and its applications. 2023.08–2026.08. Participant, ongoing.

5. Natural Science Foundation of Fujian Province. Development of parahydrogen-hyperpolarized 19F NMR technology and its application to high-sensitivity detection of N-heterocyclic drugs. 2025.09–2028.08. Participant, ongoing.

4. Natural Science Foundation of Fujian Province. A new metabolic phenotype-based network analysis method and its application to evaluation of acupoint compatibility effects. 2020.11–2023.10. Participant, completed.

3. Natural Science Foundation of Fujian Province. High-resolution one-dimensional and two-dimensional localized magnetic resonance spectroscopy techniques for living biological tissues. 2010.01–2012.12. Participant, completed.

2. Natural Science Foundation of Fujian Province. Solid-state spin quantum computer based on endohedral fullerene nanostructures. 2008.05–2009.04. Participant, completed.

1. Fujian Provincial Health and Education Joint Research Program. New nuclear magnetic resonance metabolomics techniques and their application to diabetes research. 2008.10–2011.06. Participant, completed.

Peer-reviewed papers

Year 2026

1. Genjin Lin, Shitao Li, Kian-Kai Cheng, Zhaodong Fei, Lingli Deng*, Jiyang Dong*, Daniel Raftery. ssNetShift: Single-Sample Metabolic Network Rewiring Reveals Hidden Prognostic Subtypes Beyond Clinical Staging in Gastric Cancer. Briefings in Bioinformatics. 2026, DOI:10.1093/bib/bbag264.

2. Lei Guo, Zeyu Zhu, Thomas Ka-Yam Lam, Yanhui Zhong, Jiacheng Fang, Xiaoxiao Wang, Jiyang Dong*, Weiji Chen*. MEMpre: Enhanced Membrane Protein Type Prediction via AlphaFold-Driven Protein Large Language Models. Chemometrics and Intelligent Laboratory Systems. 2026, 269: 105738.

3. Jiajin Yi, Yuan Wu, Dandan Zhang, Tian Lin, Shiquan Zhou, Caixia Yuan, Hairong Zhang, Chunyan Zhu, Liuxin Dong, Hanwen Bai, Yulin Hu, Alweali Yousif, Jiyang Dong*, Dunming Xu*, Caisheng Wu*. Nontargeted screening of carbonyl-containing hormonal residues in meat products for food safety by using intelligent high-resolution mass spectrometry-based workflow. Food Chemistry, 2026, 513: 149006.

4. Shuxian Niu#, Jianming Ding#, Hanshen Chen, Zeyu Zhu, Xiyi Liao, Huiling Hong, Chuanben Chen, Jiyang Dong*, Zhaodong Fei*. Positron Emission Tomography-based Intratumoral Spatial Diversity for Prognosis in Nasopharyngeal Carcinoma. Oral Oncology. 2026, 173:107845

5. Lei Guo, Jiyang Dong, Zongwei Cai*. Artificial Intelligence-based Approaches for Missing Values Imputation in Mass Spectrometry Imaging Data. Journal of Instrumental Analysis. 2026, 45:1-7. (In Chinese)

6. Linlin Wang, Chengyi Xie, Lei Guo*, Thomas Ka Yam Lam, Chris Kong Chu Wong, Mudassir Shah, Xiangnan Xu, Jianing Wang, Jingjing Xu*, Jiyang Dong, Zongwei Cai. prepIMS: a Robust Data Preprocessing Workflow for Ion Mobility Mass Spectrometry Imaging. Analytica Chimica Acta. 2026, 1384:344951.

7. Juehong Dai, Liheng Dong, Jingjing Xu, Lingli Deng, Lei Guo*, Jiyang Dong*. Explainable Machine Learning Enables Robust Evaluation of Extracted Ion Chromatograms in LC–MS Metabolomics. Chemometrics and Intelligent Laboratory System. 2026, 269: 105591.

8. Yongpei Wang, Xingxing Liu, Shuhai Lin, Kian-Kai Cheng, Lingli Deng*, Zhigang Luo*, Jiyang Dong*. Density-based Resampling Strategy Unveils Metabolic Heterogeneity and Subtypes in Liver Diseases Progression. Journal of Analysis and Testing. 2026. DOI:10.1007/s41664-026-00427-9.

9. Fanjing Guo, Lingli Deng, Kian-Kai Cheng, Keyi Lu, Yongpei Wang, Lei Guo, Daniel Raftery*, Jiyang Dong*. Local Sample Cohesion Normalization: Preserving Inherent Biological Heterogeneity in Metabolomics Data. Analytical Chemistry. 2026, 98(1):343–353.

Year 2025

1. Hairong Zhang, Dandan Zhang, Jin Li, Yi Wei, Yijie He, Yue Yuan, Aoxue Ding, Junyu Zhang, Yuhong Zhou*, Jiyang Dong*, Caisheng Wu*. MS-DDF: An intelligent high-resolution mass spectrometry data-processing tool for deciphering bioactive small molecules in animal-derived medicines. Acta Pharmaceutica Sinica B. 2025. DOI: 10.1016/j.apsb.2025.12.033.

2. Mudassir Shah, Lei Guo, Yusong Zhang, Lingli Deng, Xiangnan Xu, Zhaodong Fei, Jingjing Xu*, Jiyang Dong*. MSInet: A Self-Supervised CNN Framework Integrating Global and Local Context for Robust Mass Spectrometry Imaging Segmentation. Analytical Chemistry. 2025, 97, 44:24697–24705.

3. Zeyu Zhu, Chengyi Xie, Shaojie Lin, Xiangnan Xu, Shuxian Niu, Lei Guo*, Jiyang Dong*. Large Language Model Empowered Compound Collision Cross Section Prediction. Analytical Chemistry. 2025, 97, 36:19791–19800.

4. Wei Li, Ziwen Ren, Tong Wang, Xiaoxia Wei, Hui Wei, Houjun Tian, Ruibin Xu, Jiyang Dong*, Liangquan Wu*, Biao Huang*. Cultivar-specific volatile profiles in Passiflora edulis determine thrips (Frankliniella intonsa) feeding preferences. Frontiers in Plant Science. 2025, 16:1667805.

5. Keyi Lu, Yaru Liu, Kian-Kai Cheng, Fanjing Guo, Lingli Deng*, Jiyang Dong*. Local Neighbor Normalization: Reconciling Accurate Normalization and Heterogeneity Recovery in Large-Scale Metabolomics. Analytica Chimica Acta. 2025, 1372, 344440.

6. Lei Guo, Chengyi Xie, Xin Diao, Thomas Ka Yam Lam, Yanhui Zhong, Yanyan Chen, Jingjing Xu, Xiangnan Xu, Xiangyu Zhu, Zhuang Xiong, Shangyi Luo, Jianing Wang, Jiyang Dong*, Zongwei Cai*. De-MSI: a Deep Learning-based Data Denoising Method to Enhance Mass Spectrometry Imaging by Leveraging the Chemical Prior Knowledge. Analytical Chemistry. 2025. 97 (37): 20201–20208.

7. Xiaoxu Zheng, Wen Zhu, Xiaoqi Shi, Xinjing Gao, Yao Luo, Qing Zeng, Jiyang Dong, Zhong Chen, Yanqin Lin*. Sensitivity-Enhanced Pure Shift Spectroscopy Empowered by Deep Learning and PSYCHE. Analytical Chemistry. 2025, 97 (25): 13480–13486.

8. Xiaoyan Zhang, Chao Han, Jingbo Xia, Lingli Deng, Jiyang Dong*. Dynamic Synergy Network Analysis Reveals Stage-Specific Regional Dysfunction in Alzheimer's Disease. Brain Science. 2025, 15, 636.

9. Jian Cao, Chen Qian, Yihui Huang, Dicheng Chen, Yuncheng Gao, Jiyang Dong, Di Guo, Xiaobo Qu*. A Dynamics Theory of RMSProp-based Implicit Regularization in Deep Low-Rank Matrix Factorization. IEEE Transactions on Neural Networks and Learning Systems. 2025, 36 (6): 2162-2388.

10. Xiaodong Wang, Zhaokai Zhang, Lingli Deng, Jiyang Dong*. Co-community Network Analysis Reveals Alterations of Brain Networks in Alzheimer's Disease. Brain Science. 2025, 15 (5), 517.

11. Mudassir Shah, Linlin Wang, Lei Guo, Chengyi Xie, Thomas Ka-Yam Lam, Lingli Deng, Xiangnan Xu, Jingjing Xu*, Jiyang Dong*, Zongwei Cai. SagMSI: A Graph Convolutional Network framework for Precise Spatial Segmentation in Mass Spectrometry Imaging. Analytica Chemica Acta. 2025, 1358: 344098.

12. Kui Yang#, Xia-Qing Zhou#, Kai Guo, Ling Liu, Jiyang Dong, Opeyemi Joshua Olatunji, Yong-Sheng Han*, Jian Zuo*. Diosgenin in Dioscorea spongiosa suppresses glycolysis-driven angiogenesis as a ROCK1 inhibitor. Journal of Agricultural and Food Chemistry. 2025, 73 (17): 10214-10229. 

13. Yikun Zhou, Shuang Gao, Lingli Deng*, Genjin Lin, Jiyang Dong*. A Group based Network Analysis for Alzheimer’s Disease fMRI Data. Scientific Reports. 2025.

14. Yongpei Wang, Zeyu Zhu, Lingli Deng, Kian-Kai Cheng, Fanjing Guo, Genjin Lin, Daniel Raftery*, Jiyang Dong*, Multiscale Synergy Networks Offer Insights into Diseases and Comorbidity Mechanisms. Analytical Chemistry. 2025, 97 (6): 3633–3642.

15. Caixia Yuan#, Dandan Zhang#, Hairong Zhang, Jiyang Dong*, Caisheng Wu*. Breaking barriers: MS-BDF tools in the quality control of insect-derived traditional Chinese medicine. Journal of Pharmaceutical Analysis, 2025.

16. Jie Yang, Shuang Gao, X. Yin, J. Ding, X. Qiu, Zhaodong Fei, Jiyang Dong. Metabolomics and Machine Learning Identify Novel Serum Biomarkers for Nasopharyngeal Carcinoma Diagnosis. International Journal of Radiation Oncology, Biology, Physics. 2025:, 123(1, supplement 1): e334.

17. Lei Guo, Peisi Xie, Xionghui Shen, Ka Yam Lam, Lingli Deng, Chengyi Xie, Xiangnan Xu, Chris Kong Chu Wong, Jingjing Xu, Jiacheng Fang, Xiaoxiao Wang, Zhuang Xiong, Shangyi Luo, Jianing Wang, Jiyang Dong*, Zongwei Cai*. Unraveling Spatial Heterogeneity in Mass Spectrometry Imaging Data with GraphMSI. Advance Science. 2025, 12, 2410840.

18. Zhouao Zhou, Xinli Liao, Xu Qiu, Yue Zhang, Jiyang Dong, Xiaobo Qu, Donghai Lin*. NMRformer: A Transformer-based Deep Learning Framework for Peak Assignment in 1D 1H NMR Spectroscopy. Analytical Chemistry. 2025, 97 (1): 904–911.

19. Yufei Huang, Feifei Lu, Yang Guo, Kian-Kai Cheng, Zijian Wang, Wei Li, Jiyang Dong, Biao Huang*, Xiaohong Cui*. Solvent Selection in the Quality Analysis of White Tea by Nuclear Magnetic Resonance Spectroscopy. LWT-- Food Science and Technology. 2025, 215, 117155. 

2024 年

1. Junpeng Tian, Yongjie Zheng, Jiayang Zhang, Feng Tong*, Jiyang Dong. Design of smart dual-microphone front-end system for speech interaction of portable field medical equipment. Chines Medical Equipment Journal. 2024, 45(11): 39-43. (In Chinese)

2. Caixia Yuan#, Ying Jin#, Hairong Zhang, Simian Chen, Jiajin Yi, Qiang Xie*, Jiyang Dong*, Caisheng Wu*. An efficient and affordable strategy to empower nontargeted metabolomics combining three-dimensional combinatorial derivatization with MS-TDF software. Analytical Chemistry, 2024, 96 (19): 7634-7642(1区top)

3. Mudassir Shah, Lei Guo, Xiangnan Xu, Lingli Deng, Keyi Lu, Jiyang Dong, Chao Zhao*, Jingjing Xu*. eLIMS: Ensemble Learning-Based Spatial Segmentation of Mass Spectrometry Imaging to Explore Metabolic Heterogeneity. Journal of Proteome Research. 2024, 23. (2区)

4. Yirong Zhou, Chen Qian, Jiayu Li, Zi Wang, Yu Hu, Biao Qu, Liuhong Zhu, Jianjun Zhou, Taishan Kang, Jianzhong Lin, Qing Hong, Jiyang Dong, Di Guo, Xiaobo Qu. CloudBrain-ReconAI: A Cloud Computing Platform for MRI Reconstruction and Radiologists' Image Quality Evaluation. IEEE Transactions on Cloud Computing. 2024, 12(4): 1359-1371 (2区)

5. Shiting Qian, Qinqin Yang, Congbo Cai, Jiyang Dong, Shuhui Cai*. A study of spatial-temporal characteristics of autism fMRI by combining hidden Markov model and dynamic graph theory. Brain Science. 2024 (3区)

6. Yinghe Zhao, Qinqin Yang, Shiting Qian, Jiyang Dong, Shuhui Cai, Zhong Chen, Congbo Cai*. Improving the sensitivity of task-based multi-echo functional magnetic resonance imaging via T2* mapping using synthetic data-driven deep learning. Brain Science. 2024, 14: 828. (3区)

7. Lei Guo#, Chengyi Xie#, Rui Miao, Jingjing Xu, Xiangnan Xu, Jiacheng Fang, Xiaoxiao Wang, Wuping Liu, Xiangwen Liao*, Jianing Wang*, Jiyang Dong*, Zongwei Cai*. DeepION: a deep learning-based low-dimensional representation model of ion images for mass spectrometry imaging. Analytical Chemistry, 2024, 96 (9): 3829–3836. (1区top)

8. Xiaodie Chen, Jiayu Li, Dicheng Chen, Zhangren Tu, Meijin Lin, Taishan Kang, Jianzhong Lin, Tao Gong, Liuhong Zhu, Jianjun Zhou, Lin Ou-yang, Jiefeng Guo, Jiyang Dong, Di Guo, Xiaobo Qu*. CloudBrain-MRS: An Intelligent Cloud Computing Platform for in vivo Magnetic Resonance Spectroscopy Preprocessing, Quantification, and Analysis. Journal of Magnetic Resonance. 2024, 358, 107601 (3区)

2023 年

1. Xingxing Liu, Yifan Wu, Lei Guo, Xiaoyu Wang, Changkai Shan, Yaru Liu, Hanxiang An, Xinmei Kang, Rong Ding, Zongwei Cai, Jiyang Dong*, Yufen Zhao*, Xiang Gao*. Comprehensive Profiling of Amine-Containing Metabolite Isomers with Chiral Phosphorus Reagents. Analytical Chemistry, 2023, 95 (46):16830–16839 (1区top)

2. Biao Qu, Xiaoyuan Li, Min Xiao, Runhan Chen, Hejuan Tan, Hongwei Sun, Rushuai Li, Jingjing Xu, Jiyang Dong, Gaofeng Zheng, Shuyue Ai*, Xiaobo Qu*. Comparative study of bilateral putamen for patients with severe Parkinson’s disease detected by 1H magnetic resonance spectroscopy. Quantitative Imaging in Medicine and Surgery. 2023. doi: 10.21037/qims-23-231 (3区)

3. Xue Bai#, Caixia Yuan#, Jiyang Dong, Xiaojun Jiang, Xiaoyu Qian, Shaogui He, Xiaodan Guo, Tie Cai*, Dunming Xu*, Caisheng Wu*. Rapid and accurate identification of adulterated ingredients in lotus root powder based on liquid chromatography-high resolution mass spectrometry and MS-IDF. Journal of Food Composition and Analysis, 2023, 123:105576. (2区)

4. Genjin Lin, Liheng Dong, Kian-Kai Cheng, Xiangnan Xu, Yongpei Wang, Lingli Deng*, Daniel Raftery, Jiyang Dong*. Differential Correlations Informed Metabolite Set Enrichment Analysis to Decipher Metabolic Heterogeneity of Disease. Analytical Chemistry, 2023, 95 (33): 12505-12513 (1区top)

5. Lei Guo, Jinyu Zhu, Keqi Wang, Kian-Kai Cheng, Jingjing Xu, Liheng Dong, Xiangnan Xu, Can Chen, Mudassir Shah, Zhangxiao Peng, Jianing Wang, Zongwei Cai, Jiyang Dong*. Multimodal Image Fusion Offer Better Spatial Resolution for Mass Spectrometry Imaging. Analytical Chemistry, 2023, 95(25): 9714–9721 (1区top)

6. Congcong Guo#, Jiyang Dong#, lingli Deng, Kian-Kai Cheng, Yue Xu, Haowen Zhu, Anjun Deng, Qinhai Lin*, Yinghong Wang*. Application of bs-HSQC-NMR in Species identification and Adulteration behavior analysis of Panax Linn. Molecules, 2023, 28, 4332 (2区top)

7. Fanjing Guo, Genjin Lin, Liheng Dong, Kian-Kai Cheng, Lingli Deng, Xiangnan Xu, Daniel Raftery*, Jiyang Dong*. Conccordance-Based Batch Effect Correction Method for Large-Scale Metabolomics. Analytical Chemistry. 2023, 95(18): 7220-7228 (1区top)

8. Xiaoyu Wang#, Chunjing Chen#, Yaohui He#, Lianshuai Ding, Yifan Wu, Chengting Huang, Jun Wu, Rong Ding, Yuhua Xue, Zhiwei Lin, Pengxiang Xu, Yile Wu, Wen Liu, Jijun Li, Zongwei Cai, Yufen Zhao, Jiyang Dong*, Qiang Zhou*, Xiang Gao*. Isobaric stable isotope N-Phosphorylation labeling (iSIPL) for accurate and sensitive proteome quantification. Angewandte Chemie International Edition. 2023, 62: e202303656. (1区top)

9. Yongpei Wang#, Xingxing Liu#, Liheng Dong, Kian-Kai Cheng, Caigui Lin, Xiaomin Wang, Jiyang Dong*, Lingli Deng*, Daniel Raftery. iMSEA: A Novel Metabolite Set Enrichment Analysis Strategy to Decipher Drug Interactions. Analytical Chemistry. 2023, 95(15): 6203-6211 (1区top)

10. G. A. Nagana Gowda*, Vadim Pascua, John A. Lusk, Natali N. Hong, Lin Guo, Jiyang Dong, Ian R. Sweet, Daniel Raftery*. Monitoring Live Mitochondrial Metabolism in Real-Time Using NMR Spectroscopy. Magnetic Resonance in Chemistry. 2023,61:718-727(3区)

11. Jiyang Dong, Qianwen Peng, Lingli Deng, Chao Zhao*, Zongwei Cai*. Protocol for metabolic synergy analysis of multi-organs in mice using iMS2Net. STAR Protocols, 2023, 4: 102159. (4区)

12. Lei Guo#, Jiyang Dong^#,*, Xiangnan Xu, Zhichao Wu, Yinbin Zhang, Yongwei Wang, Pengfei Li, Chao Zhao*, Zongwei Cai*. Divide-and-conquer: a flexible deep learning strategy for exploring metabolic heterogeneity from mass spectrometry imaging data. Analytical Chemistry, 2023, 95 (3): 1924-1932 (1区top)

2022 年

1. Caigui Lin#, Qing Hu#, Jiyang Dong, Zhiliang Wei, Jie Li*, Zhong Chen*. Serum metabolic signatures of schizophrenia patients complicated with hepatitis B virus infection: A 1H NMR-based metabolomics study. Frontiers in Psychiatry, 2022, 13: 998709 (3区)

2. Xin Liu, Yue Li, Chunjing Chen, Jiyang Dong, Jie Zhou, Lei Wang, Xiang Gao, Xinmei Kang*. Exosomal EphA2 Promotes Tumor Metastasis of Triple-Negative Breast Cancer by Destroying Endothelial Barrier. Clinical & Experimental Metastasis, 2022, 40(1): 105-116 (3区)

3. Lei Guo#, Xingxing Liu#, Chao Zhao, Zhenxing Hu, Xiangnan Xu, Kian-Kai Cheng, Mudassir Shah, Jingjing Xu*, Jiyang Dong *, Zongwei Cai. iSegMSI: An Interactive Strategy to Improve Spatial Segmentation of Mass Spectrometry Imaging Data. Analytical Chemistry. 2022, 94 (42): 14522-14529. (1区top)

4. Jiyang Dong, Qianwen Peng, Lingli Deng, Jianjun Liu, Wei Huang, Xin Zhou, Chao Zhao*, Zongwei Cai*. iMS2Net: A Multiscale Networking Methodology to Decipher Metabolic Synergy of Organism. iScience. 2022, 25(9): 104896 (2区)

5. Chao Zhao, Jiyang Dong, Lingli Deng, Yawen Tan, Wei Jiang, Zongwei Cai*. Molecular Network Strategy in Metabolomics and Mass Spectrometry Imaging. Current Opinion in Chemical Biology, 2022, 70:102199 (2区)

6. Qinqin Yang, Jiechao Wang, Jianfeng Bao, Xiaoyin Wang, Lingceng Ma, Qizhi Yang, Shuhui Cai, Hongjian He, Congbo Cai*, Jiyang Dong*, Zhong Chen, Jianhui Zhong. MOdel-based SyntheTic Data-driven Learning (MOST-DL): Application in Single-shot T2 Mapping with Severe Head Motion Using Overlapping-echo Acquisition. IEEE Transactions on Medical Imaging. 2022, 41 (11): 3167-3181. (1区top)

7. Suping Wang#, Xiaojuan Jiang#, Rong Ding, Binbin Chen, Haiyan Lyu, Junyang Liu, Chunyan Zhu, Rong Shen, Jiayun Chen, Yun Hong, Yun-long Wu, Jiyang Dong*, Caisheng Wu*. MS-IDF: A Software Tool for Nontargeted Identification of Endogenous Metabolites after Chemical Isotope Labeling Based on a Narrow Mass Defect Filter. Analytical Chemistry. 2022, 94 (7): 3194-3202 (1区top)

8. Yuhan Hu, Xinlin Zhang, Dicheng Chen, Zhiping Yan, Xiaoyong Shen, Gen Yan, Lin Ou-yang, Jianzhong Lin, Jiyang Dong, Xiaobo Qu*. Spatiotemporal Flexible Sparse Reconstruction for Rapid Dynamic Contrast-enhanced MRI. IEEE Transactions on Biomedical Engineering, 2022, 69(1):229-243. (2区)

2021 年

1. Dandan Wang#, Xinyue Wu#, Jiyang Dong, Xiuping Cheng, Shaofei Gu,Opeyemi Joshua Olatunji, Yan Li*, Jian Zuo*. Qing-Luo-Yin alleviated experimental arthritis in rats by disrupting immune feedback between inflammatory T cells and monocytes: Key evidences from its effects on immune cell phenotypes. Journal of Inflammation Research, 2021, 14: 7467-7486. (2区)

2. Jingjing Xu, Yuanshan Wang, Xiangnan Xu, Kian-Kai Cheng, Daniel Raftery, Jiyang Dong*. NMF-based approach for missing values imputation of mass spectrometry metabolomics data. Molecules, 2021, 26(19): 5787. (2区)

3. Chao Zhao, Lei Guo, Jiyang Dong*, Zongwei Cai*. Mass spectrometry imaging-based multi-modal technique: The next-generation of biochemical analysis strategy. The Innovation, 2021, 2(4): 100151. (1区top)

4. Lingli Deng, Lei Ma, Kian-Kai Cheng, Xiangnan Xu, Daniel Raftery, Jiyang Dong*. A Sparse PLS-based Method for Overlapping Metabolite Set Enrichment Analysis. Journal of Proteome Research. 2021, 20(6): 3204–3213. (2区)

5. Lei Guo#, Zhenxing Hu#, Chao Zhao*, Xiangnan Xu, Shujuan Wang, Jingjing Xu, Jiyang Dong, Zongwei Cai. Data filtering and its prioritization in pipelines for spatial segmentation of mass spectrometry imaging. Analytical Chemistry. 2021, 93(11): 4788–4793. (1区top)

6. Dongbao Liu, Yonggui Yang, Dicheng Chen, Zi Wang, Di Guo, Lijun Bao, Jiyang Dong, Xiaobo Qu*. Brain metabolic differences between temporal lobe epileptic seizures and organic non-epileptic seizures in postictal phase: A retrospective study with magnetic resonance spectroscopy. Quantitative Imaging in Medicine and Surgery, 2021, 11(8):3781-3791 (2区)

7. Jian Zuo#, Mengqing Tao#, Xinyue Wu, Tiantian Jiang, Opeyemi Joshua Olatunji, Jiyang Dong, Jun Han*, Cong-Lan Ji*. Securidaca inappendiculata-Derived Xanthones Protected Joints from Degradation in Male Rats with Collagen-Induced Arthritis by Regulating PPAR-γ Signaling. Journal of Inflammation Research, 2021, 14: 395 – 411. (2区)

8. Lei Guo, Yongpei Wang, Xiangnan Xu, Kian-Kai Cheng, Yichi Long, Jingjing Xu, Sanshu Li, Jiyang Dong*. DeepPSP: A global-local information based deep neural network for prediction of protein phosphorylation site. Journal of Proteome Research. 2021, 20(1): 346–356 (2区)

9. Guiping Shen*, Zenan Ding, Tao Dai, Jianghua Feng, Jiyang Dong, Feng Xia, Jingjing Xu, Jidan Ye. Effect of dietary taurine supplementation on metabolome variation in plasma of Nile tilapia (Oreochromis niloticus). Animal. 2021, 15(3):100167. (2区)

10. Conglan Ji, Sheng Dai, Hong Liu, Jiyang Dong, Chunsheng Liu, Jian Zuo. Polyphenols from Securidaca inappendiculata alleviated acute lung injury in rats by inhibiting oxidative stress sensitive pathways. Chinese Herbal Medicines. 2021, 13 (2):381-388. (4区)

2020年

1. Xinyu Zhang, Jiyang Dong, Daniel Raftery*. Five Easy Metrics of Data Quality for LC-MS based Global Metabolite Profiling. Analytical Chemistry. 2020, 92,12925-12933. https://doi.org/10.1021/acs.analchem.0c01493 (1区top)

2. Shi Yan Lee, Won Fen Wong, Jiyang Dong, Kian-Kai Cheng*. Momordica charantia suppresses inflammation and glycolysis in lipopolysaccharide-activated RAW264.7 macrophages. Molecules. 2020. 25, 3783. https://doi.org/10.3390/molecules25173783. (2区)

3. Mengqing Tao, Cong-Lan Ji, Yijin Wu, Jiyang Dong, Opeyemi J Olatunji, Yan Li, Jian Zuo*. 1,7-Dihydroxy-3,4-Dimethoxyxanthone Inhibits Lipopolysaccharide-Induced Inflammation in RAW264.7 Macrophages by Suppressing TLR4/NF-κB Signaling Cascades. Inflammation. 2020. 43 (5):1821-1831. https://doi.org/10.1007/s10753-020-01256-3. (2区)

4. Jingjing Xu, Yijia Liu, Xiangnan Xu, Kian-Kai Cheng, Zongbao Yang, Jiyang Dong*. Selection of acupoints combination based on pseudo mutual information maximization. IEEE Access, 2020, 8: 153707-153718. https://doi.org/10.1109/ACCESS.2020.3018504. (2区) 

5. Yueyue Liu#, Xiangnan Xu#, Lingli Deng, Kian-Kai Cheng, Jingjing Xu, Daniel Raftery, Jiyang Dong*. A Novel Network Modelling for Metabolite Set Analysis: A Case Study on CRC Metabolomics. IEEE Access, 2020, 8: 106425-106436. https://doi.org/10.1109/ACCESS.2020.3000432. (2区) 

6. Lingli Deng, Fanjing Guo, Kian-Kai Cheng, Jiangjiang Zhu, Haiwei Gu, Daniel Raftery*, Jiyang Dong*. Identifying Significant Metabolic Pathways Using Multi-Block Partial Least Squares Analysis. Journal of Proteome Research. 2020, 19 (5): 1965-1974. https://doi.org/10.1021/acs.jproteome.9b00793. (2区)

7. Jian Zuo, Cong-Lan Ji, Olatunji Opeyemi, Zhe Yang, Hui-Fang Xu, Jun Han*, Jiyang Dong*. Bioactive fractions from Securidaca inappendiculata alleviated collagen induced arthritis in rats by regulating metabolism related signaling. The Kaohsiung Journal of Medical Sciences. 2020, 36:523–534. https://doi.org/10.1002/kjm2.12205 (4区)

8. Caigui Lin, Jiyang Dong, Zhiliang Wei, Kian-Kai Cheng, Jie Li, Song You, Yueyue Liu, Xiaomin Wang*, Zhong Chen*. 1H-NMR based metabolic profiles delineate the anticancer effect of vitamin C and oxaliplatin on hepatocellular carcinoma cells. Journal of Proteome Research. 2020, 19(2): 781-793. https://doi.org/10.1021/acs.jproteome.9b00635. (2区)

9. Qinqin Yang, Zhexin Xu, Chenxi Liao, Jianyong Cai, Ying Huang, Hong Chen, Xuan Tao, Zheng Huang, Jianxin Chen, Jiyang Dong*, Xiaoqin Zhu*. Epithelium segmentation and automated Gleason grading of prostate cancer via deep learning in label-free multiphoton microscopic images. Journal of Biophotonics, 2020, 13: e201900203. https://doi.org/10.1002/jbio.201900203. (2区)

10. Mi Liu, Jiacheng Shen, Caichun Liu, Huan Zhong, Qing Yang, Wenna Shu, Mingzhu Ma, Jiyang Dong, Zongbao Yang, Xiaorong Chang, Chang She*, Shu Yu*. Effect of moxibustion and acupuncture at Zusanli (ST36) and Zhongwan (CV12) on chronic atrophic gastritis rats. Journal of Traditional Chinese Medicine. 2020, 40(5):827-835. https://doi.org/10.19852/j.cnki.jtcm.2020.05.013 (4区)

Granted Invention Patent

18. 董继扬，韩超，郭凡靖，邓伶莉. 基于局部空间结构的质谱成像数据归一化方法及系统, 发明专利, ZL2025 1 0069576.1 (2026.03.27)

17. 许晶晶, 张沁池, 董继扬. 基于边信息熵有偏游走的异构网络节点表示方法及系统. 发明专利, ZL 2023 1 0807159.3 (2025.12.12)

16. 董继扬, 沈雄辉, 郭磊, 徐向南. 一种用于识别质谱成像数据中空间群聚离子的方法及系统. 发明专利, ZL 2024 1 1538584.8 (2025.11.07)

15. 董继扬, 陆可懿, 郭凡靖, 邓伶莉. 一种基于局部相似性的代谢组学样本归一化方法及系统。发明专利, ZL 2024 1 1681323.1 (2025.11.07)

14. 董继扬, 朱宇涛, 先后松, 郭磊, 许晶晶. 基于标签传播网络的质谱成像空间超分辨重构方法及系统. 发明专利, ZL 2024 1 1349381.4 (2025.10.21)

13. 董继扬, 先后松, 郭磊, 朱晋宇. 一种H&E染色显微图像驱动的质谱成像超分辨重构方法. 发明专利, ZL 2022 1 0729711.7 (2025.10.21)

12. 董继扬, 张钊恺, 高爽, 邓伶莉. 一种用于fMRI脑功能连接分析的单样本网络方法与系统. 发明专利, ZL 2024 1 1877040.4 (2025.10.10)

11. 董继扬, 苗瑞, 郭磊, 许晶晶. 基于质谱成像数据的同位素峰识别方法、装置及可读介质. 发明专利, ZL 2023 1 1030777.8 (2025.08.12)

10. 刘雅茹，陆可懿，徐向南，董继扬. 基于微生物组分层特征自适应融合的疾病预测方法及系统. 发明专利, ZL 2025 1 0361147.1 (2025.07.01)

9. 陈祥, 董继扬, 张晓燕, 石浩, 罗攀, 韩超, 廖加铭. 基于自适应学习和聚合的多视图立体重建方法. 发明专利, ZL 2022 1 1183328.2 (2025.09.19)

8. 董继扬, 吴昕玥, 邓伶莉. 一种基于代谢物关联网络的受扰动通路分析方法. 发明专利, ZL 2021 1 1301560.7 (2024.06.28)

7. 许晶晶, 黄自鑫, 郭磊, 董继扬. 用于预测蛋白质翻译后修饰位点的深度学习方法. 发明专利, ZL 2022 1 0406078.8 (2024.05.31)

6. 董继扬, 郭磊, 胡振兴, 徐向南, 许晶晶. 一种用于质谱成像数据的交互式空间分割方法. 发明专利, ZL 2022 1 0072775.4 (2024.05.03)

5. 董继扬, 张璇, 邓伶莉, 许晶晶. 一种受扰动代谢通路确定方法及系统. 发明专利, ZL 2020 1 0008409.3 (2023.03.14)

4. 许晶晶，王远山，董继扬. 一种基于非负矩阵分解的质谱数据缺失值填补方法及系统. 发明专利, ZL 2020 1 0701528.7 (2022.08.12)

3. 董继扬, 龙怡驰, 邓伶莉. 一种基于圆弧切线模型的核磁共振波谱基线校正方法. 发明专利, ZL 2020 1 1594412.4 (2021.10.29)

2. 秦家辉, 徐向南, 董继扬, 许晶晶. 基于核磁共振和质谱的代谢组学数据融合方法及其应用. 发明专利, ZL 2018 1 1130259.2 (2020.03.06)

1. 董继扬, 邓伶莉. 一种模型自适应的NMR代谢组学数据归一化方法. 发明专利, ZL 2015 1 0084309.8 (2017.05.03)

软件版权：

14. 董继扬, 吴彩胜, 易佳缙, 袁彩霞, 钱小雨, 林田, 张丹丹, 周世权, 胡仰旺，董留鑫. 用于聚糖识别的高分辨质谱数据处理软件(MS-GDF). 计算机软件著作登记证书. 2026SR0632452, 2026.06.01

13. 吴彩胜, 董继扬, 周煦婷, 钟毓婧, 关垭迪, 李锦轩. 基于双重衍生化的脂肪酸精准鉴定质谱数据处理软件(MS-FDF). 计算机软件著作登记证书. 2026SR0497052, 2026.03.27

12. 董继扬, 吴彩胜, 史景景. 氢氘交换质谱数据解析软件(HDXF). 计算机软件著作登记证书. 2026SR0386330, 2026.03.05

11. 吴彩胜, 董继扬, 史景景. 质谱数据驱动的小分子自组装筛选软件(SADF). 计算机软件著作登记证书. 2026SR0386329, 2026.03.05

10. 吴彩胜, 董继扬, 张海容, 张丹丹, 林田, 胡仰旺, 张倩. 基于多重去噪和智能匹配的衍生化质谱数据集处理软件(简称：MS-DDF). 计算机软件著作登记证书. 2025SR2225193, 2025.11.19

9. 吴彩胜, 袁彩霞, 董继扬, 蒋福全, 林田. 基于三维组合衍生化的质谱数据处理软件(简称：MS-TDF). 计算机软件著作登记证书. 2023SR1410351, 2023.11.09

8. 黄自鑫，许晶晶，董继扬. 扰动代谢子网分析与可视化软件. 计算机软件著作登记证书. 2022SR1397000, 2022.11.10.

7. 董继扬，刘星星，高祥. 基于同位素标记质谱的同分异构体分析软件. 计算机软件著作权登记证书. 2020SR1034701, 2020.09.03

6. 秦家辉, 夏金梅, 许晶晶, 杨献文, 董继扬. 生物样品出入库管理系统(简称: 样品管理系统 Ver 1.0). 计算机软件著作权登记证书. 2019SR0204569, 2019.03.04

5. 董继扬. 一维核磁共振波谱数据处理软件(NMReditor Ver.1.0). 计算机软件著作权登记证书. 2018SR843992, 2018.10.23

4. 徐向南, 董继扬. 核磁共振氢谱定量分析软件(NMR SpectFitting Ver.1.0). 计算机软件著作权登记证书. 2017SR158343, 2017.05.04

3. 郑旭娟, 董继扬. 核磁共振谱峰可视化归属软件 (NMR Assignment Ver.1.0). 计算机软件著作权登记证书. 2016SR178801, 2016.7.22

2. 董继扬, 周玲, 邓伶莉. 代谢组学数据挖掘软件(简称: MetaboMinerV1.0). 计算机软件著作权登记证书. 2013SR060215, 2013.06.21

1. 董继扬. 核磁共振代谢组学数据处理软件(MetPro Ver.1.0). 计算机软件著作权登记证书. 2009SR054958, 2009.11.26