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2020 – today
- 2024
[j15]Yuchuan Zhang
, Zhikang Wang, Fang Ge, Xiaoyu Wang, Yiwen Zhang, Shanshan Li, Yuming Guo, Jiangning Song, Dong-Jun Yu:
MLSNet: a deep learning model for predicting transcription factor binding sites. Briefings Bioinform. 25(6) (2024)- [j14]Ming Zhang, Jianren Zhou, Xiaohua Wang, Xun Wang, Fang Ge:
DeepBP: Ensemble deep learning strategy for bioactive peptide prediction. BMC Bioinform. 25(1): 352 (2024) - [j13]Jia-Shun Wu, Yan Liu, Fang Ge, Dong-Jun Yu:
Prediction of protein-ATP binding residues using multi-view feature learning via contextual-based co-attention network. Comput. Biol. Medicine 172: 108227 (2024) - [j12]Ming Zhang, Chao Gong, Fang Ge, Dong-Jun Yu:
FCMSTrans: Accurate Prediction of Disease-Associated nsSNPs by Utilizing Multiscale Convolution and Deep Feature Combination within a Transformer Framework. J. Chem. Inf. Model. 64(4): 1394-1406 (2024) - [j11]Zihao Yan, Fang Ge, Yan Liu, Yumeng Zhang, Fuyi Li, Jiangning Song, Dong-Jun Yu:
TransEFVP: A Two-Stage Approach for the Prediction of Human Pathogenic Variants Based on Protein Sequence Embedding Fusion. J. Chem. Inf. Model. 64(4): 1407-1418 (2024) - [j10]Ming Zhang, Xiaohua Wang, Shanruo Xu, Fang Ge, Ian Costa Paixao, Jiangning Song, Dong-Jun Yu:
MetalTrans: A Biological Language Model-Based Approach for Predicting Disease-Associated Mutations in Protein Metal-Binding Sites. J. Chem. Inf. Model. 64(15): 6216-6229 (2024) - 2023
- [j9]Fang Ge, Chen Li, Shahid Iqbal, Muhammad Arif, Fuyi Li, Maha A. Thafar, Zihao Yan, Apilak Worachartcheewan, Xiaofeng Xu, Jiangning Song, Dong-Jun Yu:
VPatho: a deep learning-based two-stage approach for accurate prediction of gain-of-function and loss-of-function variants. Briefings Bioinform. 24(1) (2023) - [j8]Fang Ge, Muhammad Arif, Zihao Yan, Hanin H. Alahmadi, Apilak Worachartcheewan, Dong-Jun Yu, Watshara Shoombuatong:
MMPatho: Leveraging Multilevel Consensus and Evolutionary Information for Enhanced Missense Mutation Pathogenic Prediction. J. Chem. Inf. Model. 63(22): 7239-7257 (2023) - [j7]Ying Zhang, Fang Ge, Fuyi Li, Xibei Yang, Jiangning Song, Dong-Jun Yu:
Prediction of Multiple Types of RNA Modifications via Biological Language Model. IEEE ACM Trans. Comput. Biol. Bioinform. 20(5): 3205-3214 (2023) - 2022
- [j6]Fang Ge, Ying Zhang, Jian Xu, Muhammad Arif, Jiangning Song, Dong-Jun Yu:
Prediction of disease-associated nsSNPs by integrating multi-scale ResNet models with deep feature fusion. Briefings Bioinform. 23(1) (2022) - [j5]Meng Zhang, Jian Zhao, Chen Li, Fang Ge, Jing Wu, Bin Jiang, Jiangning Song, Xiaofeng Song:
csORF-finder: an effective ensemble learning framework for accurate identification of multi-species coding short open reading frames. Briefings Bioinform. 23(6) (2022) - [j4]Shahid Iqbal, Fang Ge, Fuyi Li, Tatsuya Akutsu, Yuanting Zheng, Robin B. Gasser, Dong-Jun Yu, Geoffrey I. Webb, Jiangning Song:
PROST: AlphaFold2-aware Sequence-Based Predictor to Estimate Protein Stability Changes upon Missense Mutations. J. Chem. Inf. Model. 62(17): 4270-4282 (2022) - [j3]Muhammad Arif, Muhammad Kabir, Saeed Ahmed, Abid Khan, Fang Ge, Adel Khelifi, Dong-Jun Yu:
DeepCPPred: A Deep Learning Framework for the Discrimination of Cell-Penetrating Peptides and Their Uptake Efficiencies. IEEE ACM Trans. Comput. Biol. Bioinform. 19(5): 2749-2759 (2022) - 2021
- [j2]Yi-Heng Zhu, Jun Hu, Fang Ge, Fuyi Li, Jiangning Song, Yang Zhang, Dong-Jun Yu:
Accurate multistage prediction of protein crystallization propensity using deep-cascade forest with sequence-based features. Briefings Bioinform. 22(3) (2021) - 2020
- [j1]Ming-Cai Chen, Yang Li, Yi-Heng Zhu, Fang Ge, Dong-Jun Yu:
SSCpred: Single-Sequence-Based Protein Contact Prediction Using Deep Fully Convolutional Network. J. Chem. Inf. Model. 60(6): 3295-3303 (2020)
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