Mengting Niu

• software
• Deep learning
• classification of unbalanced data

• circRNA identification
• circRNA-disease association prediction
• circRNA&RBP interaction sites predication

Papers:

1. circRNA idenPredicting circRNA¨Cdisease associations with shared units and multi-channel attention mechanisms.
Xue Zhang,Quan ZouMengting Niu*, Chunyu Wang*
Bioinformatics 2025 (code&data))
Xue Zhang, Quan Zou, Mengting Niu, Chunyu Wang, Predicting circRNA-disease associations with shared units and multi-channel attention mechanisms, Bioinformatics, Volume 41, Issue 3, March 2025, btaf088, https://doi.org/10.1093/bioinformatics/btaf088. (cite)
2. Interpretable Multi-Instance Heterogeneous Graph Network Learning Modeling circRNA-Drug Sensitivity Association Prediction.
Mengting Niu,Quan Zou, Lei Xu,Ximei Luo
BMC Biology(under review)

3. circRNA identification and feature interpretability analysis.
Mengting Niu, Chunyu Wang, Yaojia Chen, Quan Zou, Ren Qi, Lei Xu
BMC Biology 2024 (code&data))
Mengting Niu, Chunyu Wang, Yaojia Chen, Quan Zou, Ren Qi, Lei Xu. CircRNA identification and feature interpretability analysis[J]. BMC Biology, 2024, 22(1):44. Doi: 10.1186/s12915-023-01804-x. (cite)
4. A computational model of circRNA-associated diseases based on a graph neural network: prediction, and case studies for follow-up experimental validation.
Mengting Niu,Chunyu Wang, Zhanguo Zhang,Quan Zou
BMC Biology 2024 (code&data))
Mengting Niu, Chunyu Wang, Zhanguo Zhang, Quan Zou. A computational model of circRNA-associated diseases based on a graph neural network: prediction and case studies for follow-up experimental validation[J]. BMC Biology, 2024, 22(1): 24. Doi.org/10.1186/s12915-024-01826-z. (cite)
5. Identification, characterization and expression analysis of circRNA encoded by SARS-CoV-1 and SARS-CoV-2.
Mengting Niu, Chunyu Wang, Yaojia Chen, Quan Zou, Lei Xu
Briefings in Bioinformatics 2024
Mengting Niu, Chunyu Wang, Yaojia Chen, Quan Zou, Lei Xu. Identification, characterization and expression analysis of circRNA encoded by SARS-CoV-1 and SARS-CoV-2[J]. Briefings in Bioinformatics, 2024, 25(2): bbad537. (cite)
6. Interpretable prediction and generation of ASC-speck aptamers using multiscale deep biological learning models .
Mengting Niu,Quan Zou, Lei Xu
IEEE/ACM Transactions on Computational Biology and Bioinformatics(under review)

7. Computational approaches for circRNA-disease association prediction: A review.
Mengting Niu,Yaojia Chen,Chunyu Wang, Quan Zou, Lei Xu
Front. Comput. Sci.
Mengting Niu,Yaojia Chen, Chunyu Wang, , Quan Zou, Lei Xu. Computational approaches for circRNA-disease association prediction: a review.Frontiers of Computer Science,2025, 19(4): 194904.
8. CRBPDL: Identification of circRNA-RBP interaction sites using an ensemble neural network approach.
Mengting Niu, Quan Zou, Chen Lin
PLOS Computational Biology 2022 (code&data))
Mengting Niu, Quan Zou, Chen Lin. CRBPDL: identification of circRNA-RBP interaction sites using an ensemble neural network approach[J]. PLoS Computational Biology, 2022, 18(1): e1009798-e1009798. (cite)
9. GMNN2CD: Identification of circRNA-disease associations based on variational inference and graph Markov neural networks.
Mengting Niu, Quan Zou, Chunyu Wang
Bioinformatics 2022 (code&data)
Mengting Niu, Quan Zou, Chunyu Wang, GMNN2CD: identification of circRNA¨Cdisease associations based on variational inference and graph markov neural networks[J]. Bioinformatics, 2022, 38(8): 2246-2253.(cite)
10. Characterizing viral circRNAs and their application in identifying circRNAs in viruses
Mengting Niu, Ying Ju, Chen Lin, Quan Zou
Briefings in Bioinformatics 2021
Mengting Ni, Ying Ju, Chen Lin, Quan Zou. Characterizing viral circRNAs and their application in identifying circRNAs in viruses[J]. Briefings in Bioinformatics, 2022, 23(1): bbab404. (cite)
11. rBPDL: Predicting RNA-binding proteins using deep learning
Mengting Niu, Jin Wu, Quan Zou, Zhendong Liu, Lei Xu
IEEE Journal of Biomedical and Health Informatics(data and codes)
Mengting Niu, Jin Wu#, Quan Zou, Zhendong Liu, Lei Xu. rBPDL: predicting RNA-binding proteins using deep learning[J]. IEEE Journal of Biomedical and Health Informatics, 2021, 25(9): 3668-3676. (cite)
12. sgRNACNN: identifying sgRNA on-target activity in four crops using ensembles of convolutional neural networks.
Mengting Niu,Yuan Lin, Quan Zou
Plant molecular biology 2021 (data and code )
Mengting Niu, Yuan Lin, Quan Zou. sgRNACNN: identifying sgRNA on-target activity in four crops using ensembles of convolutional neural networks[J]. Plant Molecular Biology, 2021, 105(4-5): 483-495. (cite)
13. SgRNA-RF: identification of SgRNA on-target activity with imbalanced datasets
Mengting Niu, Quan Zou
IEEE/ACM Transactions on Computational Biology and Bioinformatics 2021 (web)and dataset)
Mengting Niu, Quan Zou. SgRNA-RF: identification of SgRNA on-target activity with imbalanced datasets[J]. IEEE-ACM Transactions on Computational Biology and Bioinformatics, 2021, 19(4): 2442-2453. (cite)
14. CirRNAPL: a web server for the identification of circRNA based on extreme learning machine
Mengting Niu, Jun Zhang, Yanjuan Li, Cankun Wang, Zhaoqian Liu, Hui Ding, Quan Zou, Qin Ma
Computational and structural biotechnology journal 2020 (web) and dataset)
Niu M, Zhang J, Li Y, et al. CirRNAPL: a web server for the identification of circRNA based on extreme learning machine[J]. Computational and structural biotechnology journal, 2020, 18: 834-842. (cite)
15. GATSDCD: Prediction of circRNA-Disease Associations Based on Singular Value Decomposition and Graph Attention Network
Mengting Niu,Hesham A E L, Zou Quan
International Conference on Intelligent Computing 2022
Niu M, Hesham A E L, Zou Q. GATSDCD: Prediction of circRNA-Disease Associations Based on Singular Value Decomposition and Graph Attention Network[C]//International Conference on Intelligent Computing. Springer, Cham, 2022: 14-27.(cite)
16. ELM-MHC: an improved MHC identification method with extreme learning machine algorithm
Y Li,Mengting Niu, , Q Zou
Journal of proteome research 2019 (web)and dataset)
Li Y, Niu M, Zou Q. ELM-MHC: an improved MHC identification method with extreme learning machine algorithm[J]. Journal of proteome research, 2019, 18(3): 1392-1401. (cite)
17. RFAmyloid: a web server for predicting amyloid proteins.
    Mengting Niu,Yanjuan Li, Chunyu Wang, Ke Han
    International journal of molecular sciences 2019 (web)and dataset)
    Niu M, Li Y, Wang C, et al. RFAmyloid: A Web Server for Predicting Amyloid Proteins[J]. International journal of molecular sciences, 2018, 19(7): 2071. (cite)

18. Application of remote sensing image clustering based on bee colony K-means algorithm
Computer engineering and applications.2019 (Chinese)

19. Collaborative filtering recommendation algorithm based on bee colony K-means clustering model
computer engineering and science.2019(Cinese)

20. An Intelligent Recommendation Mobile Application Privacy Risk Evaluation Method Based on Optimized SVM
2020 IEEE 4th Information Technology, Networking, Electronic and Automation
21. An inductive logic programming algorithm based on artificial bee colony.
Journal of Information Technology Research (JITR)

Recent Projects

The main project involved is the related research of circular RNA. Currently, I am leading the GMNN and MSRN project, which aims to develop a series of deep learning models to solve computational problems of circRNA.

GMNN Neural Networks

MSRN

Participate in the project

Host.The Natural Science Foundation of China (No.62473268)

Host.The Natural Science Foundation of China (No.62303328)

Host.The National funded postdoctoral researcher program of China (GZC20230382)

Participate: The Natural Science Foundation of China (No.62131004,62172076)