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ACS Omega|March 17, 2025
DeepEpiIL13: Deep Learning for Rapid and Accurate Prediction of IL-13-Inducing Epitopes Using Pretrained Language Models and Multiwindow Convolutional Neural NetworksCheng-Che Chuang, Yu-Chen Liu, Yu-Yen OuInternational Journal of Biological Macromolecules|October 4, 2024
DeepNeoAG: Neoantigen epitope prediction from melanoma antigens using a synergistic deep learning model combining protein language models and multi-window scanning convolutional neural networksCheng-Che Chuang, Yu-Chen Liu, Yu-Yen OuJournal of Chemical Information and Modeling|February 19, 2025
RAG_MCNNIL6: A Retrieval-Augmented Multi-Window Convolutional Network for Accurate Prediction of IL-6 Inducing EpitopesCheng-Che Chuang, Yu-Chen Liu, Wei-En Jhang, et al.Journal of Molecular Biology|August 30, 2024
Deciphering the Language of Protein-DNA Interactions: A Deep Learning Approach Combining Contextual Embeddings and Multi-Scale Sequence ModelingYu-Chen Liu, Yi-Jing Lin, Yan-Yun Chang, et al.Journal of Chemical Information and Modeling|June 18, 2025
RTK_RAG: Leveraging Retrieval Augmented Generation with Multi-Window Convolutional Neural Networks for Superior ATP Binding Site Prediction in Receptor Tyrosine KinasesSin-Siang Wei, Wei-En Jhang, Yu-Chen Liu, et al.Journal of Chemical Information and Modeling|August 12, 2024
MCNN_MC: Computational Prediction of Mitochondrial Carriers and Investigation of Bongkrekic Acid Toxicity Using Protein Language Models and Convolutional Neural NetworksMuhammad Shahid Malik, Yan-Yun Chang, Yu-Chen Liu, et al.International Journal of Biological Macromolecules|September 27, 2024
VesiMCNN: Using pre-trained protein language models and multiple window scanning convolutional neural networks to identify vesicular transport proteinsVan The Le, Yi-Hsuan Tseng, Yu-Chen Liu, et al.Journal of Chemical Information and Modeling|February 7, 2025
CaBind_MCNN: Identifying Potential Calcium Channel Blocker Targets by Predicting Calcium-Binding Sites in Ion Channels and Ion Transporters Using Protein Language Models and Multiscale Feature ExtractionYan-Yun Chang, Yu-Chen Liu, Wei-En Jhang, et al.Computers in Biology and Medicine|December 9, 2024
ATP_mCNN: Predicting ATP binding sites through pretrained language models and multi-window neural networksVan-The Le, Muhammad-Shahid Malik, Yi-Jing Lin, et al.Briefings in Bioinformatics|March 26, 2013
Bioinformatics approaches for functional annotation of membrane proteinsM Michael Gromiha, Yu-Yen OuPageof 29