By hybrid neural networks for prediction and interpretation of transcription factor binding sites based on multi-omics. - Yongqing Zhang; Zixuan Wang 025; Yuhang Liu; Libo Lu; Xiaoyao Tan; Quan Zou 001 (BIBM, 2021)

High-resolution transcription factor binding sites prediction improved performance and interpretability by deep learning method. - Yongqing Zhang; Zixuan Wang 025; Yuanqi Zeng; Jiliu Zhou; Quan Zou 001 (Briefings Bioinform., 2021)

Single-cell TF-DNA binding prediction and analysis based on transfer learning framework. - Zixuan Wang 025; Yongqing Zhang; Yun Yu; Maocheng Wang; Yuhang Liu; Quan Zou 001 (BIBM, 2022)

Predicting cell type-specific effects of variants on TF-DNA binding by meta-learning. - Yongqing Zhang; Yuhang Liu; Zixuan Wang 025; Maocheng Wang; Shuwen Xiong; Quan Zou 001 (BIBM, 2022)

A novel convolution attention model for predicting transcription factor binding sites by combination of sequence and shape. - Yongqing Zhang; Zixuan Wang 025; Yuanqi Zeng; Yuhang Liu; Shuwen Xiong; Maocheng Wang; Jiliu Zhou; Quan Zou 001 (Briefings Bioinform., 2022)

Exploring Parameter-Efficient Fine-Tuning of a Large-Scale Pre-Trained Model for scRNA-seq Cell Type Annotation. - Yuhang Liu; Tianhao Li; Zixuan Wang 025; Guiquan Zhu; Yongqing Zhang; Quan Zou 001 (BIBM, 2023)

KDProg: A Knowledge distillation graph neural network for cancer prognosis prediction and analysis. - Shuwen Xiong; Zixuan Wang 025; Junming Zhang; Hong Luo; Yongqing Zhang; Quan Zou 001 (BIBM, 2023)

HGTDG: An Interpretable Heterogeneous Graph Transformer Framework for Cancer Driver Gene Prediction. - Shuwen Xiong; Zixuan Wang 025; Junming Zhang; Guiquan Zhu; Yongqing Zhang; Quan Zou 001 (BIBM, 2023)

Cell-Specific Highly Correlated Network for Self-Supervised Distillation in Cell Type Annotation. - Tianhao Li; Yugui Xu; Sihan He; Yuhang Liu; Zixuan Wang 025; Zhigan Zhou; Yongqing Zhang; Quan Zou 001 (BIBM, 2024)

Supervised pre-training for feature extraction in cell type annotation of single-cell multi-omics data. - Yongqing Zhang; Tianhao Li; Yuhang Liu; Hong Luo; Yugui Xu; Zixuan Wang 025; Quan Zou 001 (Appl. Soft Comput., 2025)

An overview of computational methods in single-cell transcriptomic cell type annotation. - Tianhao Li; Zixuan Wang 025; Yuhang Liu; Sihan He; Quan Zou 001; Yongqing Zhang (Briefings Bioinform., 2025)