microRNA-disease relationship prediction

Objective

The identification of disease-related microRNAs (miRNAs) is an essential but challenging task in bioinformatics research. We have developed several related methods on this problem.

1. Friendly web servers were developed and maintained.
2. We try our best to avoid overfitting problems.
3. We have proposed and improved several novel techniques,including random walks, miRNA-miRNA similarity computation, etc.

People

• Xiangxiang Zeng (Associated Professor, XMU, China)
• Quan Zou (Professor, UESTC, China)
• Alfonso Rodriguez-Paton (Professor, UPM, Spain)

Web Servers

• MDPredict (Disease-microRNA associations Prediction)
• IMDS (Infer microRNA-disease association)
• MMCOP (miRNA and Methylation CUP Origin Predictor)

Publications

microRNA-disease relationship

• Xiangxiang Zeng, Wen Wang, Gaoshan Deng, Jiaxin Bing, Quan Zou*. Prediction of potential disease-associated microRNAs by using neural network. Molecular Therapy-Nucleic Acids. 2019, 16: 566-575. (SCI, IF2017=5.66, PMID: 31077936)
• Xiangxiang Zeng, Li Liu, Linyuan Lu*, Quan Zou*. Prediction of potential disease-associated microRNAs using structural perturbation method. Bioinformatics. 2018, 34(14): 2425-2432.(SCI, IF2016=7.307, PMID:29490018)(codes)(BibTeX, EndNote)
• Wei Tang, Shixiang Wan, Zhen Yang, Andrew E. Teschendorff*, Quan Zou*. Tumor Origin Detection with Tissue-Specific miRNA and DNA methylation Markers. Bioinformatics. 2018, 34(3): 398-406. (SCI, IF2016=7.307, PMID:29028927) (web server)(BibTeX, EndNote)
• Xiangxiang Zeng, Xuan Zhang, Quan Zou*. Integrative approaches for predicting microRNA function and prioritizing disease-related microRNA using biological interaction networks. Briefings in Bioinformatics. 2016,17(2):193-203.(SCI, IF2016=5.134, PMID:26059461)(BibTeX, EndNote)
• Yuansheng Liu, Xiangxiang Zeng, Zengyou He*, Quan Zou*. Inferring microRNA-disease associations by random walk on a heterogeneous network with multiple data sources. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2017, 14(4): 905-915.(Web Server)(SCI, IF2015=1.609, PMID:27076459)(BibTeX, EndNote)
• Quan Zou, Jinjin Li, Li Song, Xiangxiang Zeng, Guohua Wang. Similarity computation strategies in the microRNA-disease network: A Survey. Briefings in Functional Genomics. 2016, 15(1): 55-64. (SCI, IF2017=3.783,PMID: 26134276)most cited articles in this journal(BibTeX, EndNote)
• Xuan Zhang, Quan Zou, Alfonso Rodriguez-Paton, Xiangxiang Zeng*. Meta-path methods for prioritizing candidate disease miRNAs. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2019, 16(1): 283-291. (web server) (PMID: 29990255)
• Xiangxiang Zeng, Xuan Zhang,Yuanlu Liao, Linqiang Pan. Prediction and validation of association between microRNAs and diseases by multipath methods. BBA - General Subjects. 2016, 1860(11): 2735-2739
• Xiangxiang Zeng, Ningxiang Ding, Alfonso Rodriguez-Paton, Ziyu Lin, Ying Ju. Prediction of MicroRNA disease Associations by Matrix Completion. Current Proteomics. 2016, 13(2): 151-157
• Wei Tang, Zhijun Liao, Quan Zou*. Which statistical significance test best detects oncomiRNAs in cancer tissues? An exploratory analysis. Oncotarget. 2016, 7(51):85613-85623. (PMID: 27784000)
• Quan Zou, Jinjin Li, Qingqi Hong, Ziyu Lin, Hua Shi, Yun Wu, Ying Ju. Prediction of microRNA-disease associations based on social network analysis methods. BioMed Research International. 2015, 2015: 810514. (SCI, IF2012=2.88, PMID: 26273645)
• Hua Shi, Yun Wu, Zhiqiang Zeng, Quan Zou*. A Discussion of MicroRNAs in Cancers. Current Bioinformatics. 2014, 9(5):453-462.
• Zhijun Liao, Dapeng Li, Xinrui Wang, Lisheng Li, Quan Zou*. Cancer diagnosis from isomiR expression with machine learning method. Current Bioinformatics. 2018, 13(1): 57-63
• Qicong Wang, Leyi Wei, Xinjun Guan, Yunfeng Wu, Quan Zou, Zhiliang Ji. Briefing in family characteristics of microRNAs and their applications in cancer research. BBA - Proteins and Proteomics. 2014, 1844:191-197. (PMID: 23954304)
• Haochen Zhao, Linai Kuang, Xiang Feng, Quan Zou, Lei Wang. A Novel Approach based on Weighted Interactive Network to Predict Associations of MiRNAs and Diseases. International Journal of Molecular Sciences. 2019, 20: 110(PMID: 30597923)
• Hailin Feng, Dongdong Jin, Jian Li, Yane Li, Quan Zou, Tongcun Liu. Matrix Reconstruction with Reliable Neighbors for Predicting Potential MiRNA-Disease Association. Briefings in Bioinformatics. 2023, 24(1): bbac571.
• Yizheng Wang, Xin Zhang, Ying Ju, Qing Liu, Quan Zou, Yazhou Zhang, Yijie Ding*, Ying Zhang*. Identification of human microRNA-disease association via low-rank approximation-based link propagation and multiple kernel learning. Frontiers of Computer Science. 2024, 18(2): 182903
• Hailin Feng, Chenchen Ke, Quan Zou, Zhechen Zhu, Tongcun Liu*. Prediction of potential miRNA-disease associations based on a masked graph autoencoder. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2024, 21(6): 1874-1885

ncRNA-disease relationship

• Hao Wu, Qi Liang, Wenxiang Zhang, Quan Zou, Abd EI-Latif Hesham, Bin Liu. iLncDA-LTR: Identification of lncRNA-disease associations by learning to rank. Computers in Biology and Medicine. 2022, 146: 105605 (web server)
• Mengting Niu, Quan Zou*, Chunyu Wang*. GMNN2CD: Identification of circRNA¨Cdisease associations based on variational inference and graph Markov neural networks. Bioinformatics. 2022, 38(8): 2246-2253. (codes and data)
• Zhongsheng Li, Junru Jin, Wenjia He, Wentao Long, Haoqing Yu, Xin Gao, Kenta Nakai, Quan Zou*, Leyi Wei*. CoraL: Interpretable contrastive meta-learning for the prediction of cancer-associated ncRNA-encoded small peptides. Briefings in Bioinformatics. 2023, 24(6): bbad352

gene-disease relationship

• Xiangxiang Zeng, Yuanlu Liao, Yuansheng Liu, Quan Zou*. Prediction and validation of disease genes using HeteSim Scores. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2017, 14(3):687-695. (SCI, IF2017=2.428, PMID:26890920)(Codes and Data)(BibTeX, EndNote)
• Xiangxiang Zeng, Ningxiang Ding, Alfonso Rodriguez-Paton, Quan Zou*. Probability-based collaborative filtering model for predicting gene-disease associations. BMC Medical Genomics. 2017,10(Suppl 5):76 (SCI, IF2016=2.848, PMID:29297351)(BibTeX, EndNote)
• Quan Zou, Jinjin Li, Chunyu Wang, Xiangxiang Zeng*. Approaches for recognizing disease genes based on Network. BioMed Research International. 2014,2014: 416323. (SCI, IF2012=2.88, PMID: 24707485)
• Shaopeng Wang, Guohua Huang, Qinghua Hu*, Quan Zou*. A network-based method for the identification of putative genes related to infertility. BBA - General Subjects. 2016, 1860(11): 2716-2724 (SCI, IF2017=3.679, PMID: 27102279)
• Liucun Zhu, Fangchu Su, YaoChen Xu, Quan Zou*. Network-based method for mining novel HPV infection related genes using random walk with restart algorithm. BBA - Molecular Basis of Disease. 2018, 1864(6): 2376-2383 (SCI, IF2017=5.108, PMID: 29197659)
• Quan Zou. Machine Learning Techniques for Protein Structure, Genomics Function Analysis and Disease Prediction. Current Proteomics. 2016, 13(2): 77-78
• Jieru Zhang, Ying Ju, Huijuan Lu, Ping Xuan*, Quan Zou*. Accurate identification of cancerlectins through hybrid machine learning technology. International Journal of Genomics. 2016, 2016: 7604641(SCI, IF2015=1.830, PMID: 27478823)
• Jun Wang, Le Zhang, Quan Zou, Jun Tan, Xiaowei Chen, Yukun Wu. Association studies on mtDNA and Parkinson¡¯s disease population discrimination using the statistical classification. Current Bioinformatics. 2014, 9(5):481-489 (SCI, IF2012=2.017)
• Xiangxiang Zeng, Ningxiang Ding, Quan Zou. Latent factor model with heterogeneous similarity regularization for predicting gene¨Cdisease associations. 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2016). 682-687.
• Xiangyi Meng, Quan Zou, Alfonso Rodriguez-Paton, Xiangxiang Zeng. Iteratively collective prediction of disease-gene associations through the incomplete network. 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2017). 1324-1330 (codes)

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Last revised 2025.6.14