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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.Pageof 1