Incorporating deep learning with convolutional neural networks and position specific scoring matrices for identifying electron transport proteins. - Nguyen-Quoc-Khanh Le; Quang-Thai Ho; Yu-Yen Ou (J. Comput. Chem., 2017)

Using two-dimensional convolutional neural networks for identifying GTP binding sites in Rab proteins. - Nguyen-Quoc-Khanh Le; Quang-Thai Ho; Yu-Yen Ou (J. Bioinform. Comput. Biol., 2019)

DeepETC: A deep convolutional neural network architecture for investigating and classifying electron transport chain's complexes. - Nguyen-Quoc-Khanh Le; Quang-Thai Ho; Edward Kien Yee Yapp; Yu-Yen Ou; Hui-Yuan Yeh (Neurocomputing, 2020)

A transformer architecture based on BERT and 2D convolutional neural network to identify DNA enhancers from sequence information. - Nguyen-Quoc-Khanh Le; Quang-Thai Ho; Trinh-Trung-Duong Nguyen; Yu-Yen Ou (Briefings Bioinform., 2021)

FAD-BERT: Improved prediction of FAD binding sites using pre-training of deep bidirectional transformers. - Quang-Thai Ho; Trinh-Trung-Duong Nguyen; Nguyen-Quoc-Khanh Le; Yu-Yen Ou (Comput. Biol. Medicine, 2021)

GT-Finder: Classify the family of glucose transporters with pre-trained BERT language models. - Syed Muazzam Ali Shah; Semmy Wellem Taju; Quang-Thai Ho; Trinh-Trung-Duong Nguyen; Yu-Yen Ou (Comput. Biol. Medicine, 2021)

mCNN-ETC: identifying electron transporters and their functional families by using multiple windows scanning techniques in convolutional neural networks with evolutionary information of protein sequences. - Quang-Thai Ho; Nguyen-Quoc-Khanh Le; Yu-Yen Ou (Briefings Bioinform., 2022)

BERT-Promoter: An improved sequence-based predictor of DNA promoter using BERT pre-trained model and SHAP feature selection. - Nguyen-Quoc-Khanh Le; Quang-Thai Ho; Van-Nui Nguyen; Jung-Su Chang (Comput. Biol. Chem., 2022)

Identifying SNARE Proteins Using an Alignment-Free Method Based on Multiscan Convolutional Neural Network and PSSM Profiles. - Quang-Hien Kha; Quang-Thai Ho; Nguyen-Quoc-Khanh Le (J. Chem. Inf. Model., 2022)

Use Chou's 5-Steps Rule With Different Word Embedding Types to Boost Performance of Electron Transport Protein Prediction Model. - Trinh-Trung-Duong Nguyen; Quang-Thai Ho; Nguyen-Quoc-Khanh Le; Van-Dinh Phan; Yu-Yen Ou (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

mCNN-GenEfflux: enhanced predicting Efflux protein and their super families by using generative proteins combined with multiple windows convolution neural networks. - Muhammad Hussain; Yu-Yen Ou; Quang-Thai Ho (Comput. Biol. Chem., 2025)