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- 2026
[j9]Aoyun Geng
, Jinwei Wang, Yanfei Qu, Junlin Xu, Yajie Meng, Quan Zou, Zilong Zhang, Feifei Cui:
AdaptIPs: A dual-channel deep learning framework integrating protein language model representations and transfer learning for phosphorylation-site prediction. Eng. Appl. Artif. Intell. 182: 115882 (2026)- [j8]Guanjie Song, Zhenjie Luo, Aoyun Geng, Junlin Xu, Yajie Meng, Feifei Cui, Leyi Wei, Quan Zou, Zilong Zhang:
Protein Solubility Prediction Using Fused Graph Convolutional Networks and Improved Attention Networks with AlphaFold3-Derived Features. J. Chem. Inf. Model. 66(2): 894-909 (2026) - [j7]Ziyuan Yan, Aoyun Geng, Yazi Li, Jiajing Wang, Junlin Xu, Yajie Meng, Leyi Wei, Quan Zou, Zilong Zhang, Feifei Cui:
CNNCaps-DBP: Leveraging protein language models with attention-augmented convolution for DNA-binding protein prediction. Neural Networks 195: 108261 (2026) - [j6]Jinwei Wang, Zhenjie Luo, Aoyun Geng, Junlin Xu, Yajie Meng, Shankai Yan, Leyi Wei, Zilong Zhang, Qingchen Zhang, Quan Zou, Feifei Cui:
DeepNhKcr: Explainable Deep Learning Framework for the Prediction of Crotonylation Sites of Non-Histone Lysine in Plants Based on Pre-Trained Protein Language Model. IEEE Trans. Comput. Biol. Bioinform. 23(1): 326-340 (2026) - [c2]Aoyun Geng, Chunyan Cui, Yunyun Su, Zhenjie Luo, Feifei Cui, Zilong Zhang:
TLAGC: Taylor Linear Attention-Guided Graph Convolutions for Revealing Spatial Domains in Spatial Multi-Omics Data. AAAI 2026: 21269-21277 - 2025
- [j5]Aoyun Geng, Zhenjie Luo, Aohan Li, Zilong Zhang, Quan Zou, Leyi Wei, Feifei Cui:
ACP-CLB: An Anticancer Peptide Prediction Model Based on Multichannel Discriminative Processing and Integration of Large Pretrained Protein Language Models. J. Chem. Inf. Model. 65(5): 2336-2349 (2025) - [j4]Yuanhao Li, Aoyun Geng, Zheyu Zhou, Feifei Cui, Junlin Xu, Yajie Meng, Leyi Wei, Quan Zou, Qingchen Zhang, Zilong Zhang:
AVP-HNCL: Innovative Contrastive Learning with a Queue-Based Negative Sampling Strategy for Dual-Phase Antiviral Peptide Prediction. J. Chem. Inf. Model. 65(12): 5868-5886 (2025) - [j3]Qianmao Wen, Aoyun Geng, Junlin Xu, Yajie Meng, Leyi Wei, Zilong Zhang, Quan Zou, Feifei Cui:
DeepMaT: Prediction of Target Peptide Classification and Cleavage Site by Combining Mamba2 and Multiple Attention Mechanisms. J. Chem. Inf. Model. 65(19): 10011-10024 (2025) - [j2]Jiaxing Song, Aoyun Geng, Qianmao Wen, Junlin Xu, Yajie Meng, Feifei Cui, Quan Zou, Leyi Wei, Zilong Zhang:
AcidProNet: Acidophilic Protein Classification via DCGAN-GP-Based Data Augmentation and Parameter-Shared Mixture-of-Experts Transformer. J. Chem. Inf. Model. 65(24): 13145-13162 (2025) - [c1]Yunyun Su, Binlu Yang, Aoyun Geng, Yuxuan Chen, Zilong Zhang, Feifei Cui:
RTCDB: A Multi-Omics Database Supporting Research and Discovery in Rare Tumor Oncology. BIBM 2025: 556-561 - 2024
- [j1]Chaorui Yan, Aoyun Geng, Zhuoyu Pan, Zilong Zhang, Feifei Cui:
MultiFeatVotPIP: a voting-based ensemble learning framework for predicting proinflammatory peptides. Briefings Bioinform. 25(6) (2024)
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