DeepPLM_mCNN: An approach for enhancing ion channel and ion transporter recognition by multi-window CNN based on features from pre-trained language models. - Van-The Le; Muhammad-Shahid Malik; Yi-Hsuan Tseng; Yu-Cheng Lee; Cheng-I Huang; Yu-Yen Ou (Comput. Biol. Chem., 2024)

MCNN_MC: Computational Prediction of Mitochondrial Carriers and Investigation of Bongkrekic Acid Toxicity Using Protein Language Models and Convolutional Neural Networks. - Muhammad-Shahid Malik; Yan-Yun Chang; Yu-Chen Liu 009; Van-The Le; Yu-Yen Ou (J. Chem. Inf. Model., 2024)

ATP_mCNN: Predicting ATP binding sites through pretrained language models and multi-window neural networks. - Van-The Le; Muhammad-Shahid Malik; Yi-Jing Lin; Yu-Chen Liu 009; Yan-Yun Chang; Yu-Yen Ou (Comput. Biol. Medicine, 2025)