Identifying modifications on DNA-bound histones with joint deep learning of multiple binding sites in DNA sequence. - Yan Li; Lijun Quan; Yiting Zhou; Yelu Jiang; Kailong Li; Tingfang Wu; Qiang Lyu (Bioinform., 2022)

SemanticCAP: Chromatin Accessibility Prediction Enhanced by Features Learning from a Language Model. - Yikang Zhang; Xiaomin Chu; Yelu Jiang; Hongjie Wu; Lijun Quan (CoRR, 2022)

DGCddG: Deep Graph Convolution for Predicting Protein-Protein Binding Affinity Changes Upon Mutations. - Yelu Jiang; Lijun Quan; Kailong Li; Yan Li; Yiting Zhou; Tingfang Wu; Qiang Lyu (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

ctP2ISP: Protein-Protein Interaction Sites Prediction Using Convolution and Transformer With Data Augmentation. - Kailong Li; Lijun Quan; Yelu Jiang; Yan Li; Yiting Zhou; Tingfang Wu; Qiang Lyu (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

Simultaneous Prediction of Interaction Sites on the Protein and Peptide Sides of Complexes through Multilayer Graph Convolutional Networks. - Kailong Li; Lijun Quan; Yelu Jiang; Hongjie Wu; Jian Wu; Yan Li; Yiting Zhou; Tingfang Wu; Qiang Lyu (J. Chem. Inf. Model., 2023)

RPEMHC: improved prediction of MHC-peptide binding affinity by a deep learning approach based on residue-residue pair encoding. - Xuejiao Wang; Tingfang Wu; Yelu Jiang; Taoning Chen; Deng Pan; Zhi Jin; Jingxin Xie; Lijun Quan; Qiang Lyu (Bioinform., 2024)

DS-MVP: identifying disease-specific pathogenicity of missense variants by pre-training representation. - Qiufeng Chen; Lijun Quan; Lexin Cao; Bei Zhang; Zhijun Zhang; Liangchen Peng; Junkai Wang; Yelu Jiang; Liangpeng Nie; Geng Li; Tingfang Wu; Qiang Lyu (Briefings Bioinform., 2025)

A lightweight visualization tool for protein unfolding by collision detection and elimination. - Hua Qian; Yu Chen; Yelu Jiang (Frontiers Comput. Sci., 2025)

AffiGrapher: Contrastive Heterogeneous Graph Learning with Aromatic Virtual Nodes for RNA-Small Molecule Binding Affinity Prediction. - Junkai Wang; Jian Wu; Zhijun Zhang; Yelu Jiang; Liangchen Peng; Bei Zhang; Qiufeng Chen; Lexin Cao; Lijun Quan; Qiang Lyu (J. Chem. Inf. Model., 2025)

MMSol: Predicting Protein Solubility with an Antinoise Multimodal Deep Model. - Jia Xu; Tingfang Wu; Yelu Jiang; Liangpeng Nie; Geng Li; Yi Zhang; Zhenglong Zhou; Yiwei Chen; Lijun Quan; Qiang Lyu (J. Chem. Inf. Model., 2025)

MVCL-DTI: Predicting Drug-Target Interactions Using a Multiview Contrastive Learning Model on a Heterogeneous Graph. - Bei Zhang; Lijun Quan; Zhijun Zhang; Lexin Cao; Qiufeng Chen; Liangchen Peng; Junkai Wang; Yelu Jiang; Liangpeng Nie; Geng Li; Tingfang Wu; Qiang Lyu (J. Chem. Inf. Model., 2025)