Prediction of Heme Binding Sites in Heme Proteins Using an Integrative Sequence Profile Coupling Evolutionary Information with Physicochemical Properties. - Yi Xiong 002; Wen Zhang 008; Tao Zeng 003; Juan Liu 007 (BIBM, 2011)

Prediction of conformational B-cell epitopes from 3D structures by random forest with a distance-based feature. - Wen Zhang 008; Yi Xiong 002; Meng Zhao; Hua Zou; Xinghuo Ye; Juan Liu 007 (BMC Bioinform., 2011)

Predicting immunogenic T-cell epitopes by combining various sequence-derived features. - Wen Zhang 008; Juan Liu 007; Yi Xiong 002; Meng Ke; Ke Zhang (BIBM, 2013)

Large-scale binding ligand prediction by improved patch-based method Patch-Surfer2.0. - Xiaolei Zhu 001; Yi Xiong 002; Daisuke Kihara (Bioinform., 2015)

Navigating 3D electron microscopy maps with EM-SURFER. - Juan Esquivel-Rodríguez; Yi Xiong 002; Xusi Han; Shuomeng Guang; Charles Christoffer; Daisuke Kihara (BMC Bioinform., 2015)

dbAMEPNI: a database of alanine mutagenic effects for protein-nucleic acid interactions. - Ling Liu; Yi Xiong 002; Hongyun Gao; Dong-Qing Wei; Julie C. Mitchell; Xiaolei Zhu 001 (Database J. Biol. Databases Curation, 2018)

GOLabeler: improving sequence-based large-scale protein function prediction by learning to rank. - Ronghui You; Zihan Zhang; Yi Xiong 002; Fengzhu Sun; Hiroshi Mamitsuka; Shanfeng Zhu (Bioinform., 2018)

PseUI: Pseudouridine sites identification based on RNA sequence information. - Jingjing He; Ting Fang; Zizheng Zhang; Bei Huang; Xiaolei Zhu 001; Yi Xiong 002 (BMC Bioinform., 2018)

Protein-protein interface hot spots prediction based on a hybrid feature selection strategy. - Yanhua Qiao; Yi Xiong 002; Hongyun Gao; Xiaolei Zhu 001; Peng Chen 001 (BMC Bioinform., 2018)

Prediction of CYP450 Enzyme-Substrate Selectivity Based on the Network-Based Label Space Division Method. - Xiaoqi Shan; Xiangeng Wang; Cheng-Dong Li; Yanyi Chu; Yufang Zhang; Yi Xiong 002; Dong-Qing Wei (J. Chem. Inf. Model., 2019)

NetGO: improving large-scale protein function prediction with massive network information. - Ronghui You; Shuwei Yao; Yi Xiong 002; Xiaodi Huang; Fengzhu Sun; Hiroshi Mamitsuka; Shanfeng Zhu (Nucleic Acids Res., 2019)

m5CPred-SVM: a novel method for predicting m5C sites of RNA. - Xiao Chen; Yi Xiong 002; Yinbo Liu; Yuqing Chen; Shoudong Bi; Xiaolei Zhu 001 (BMC Bioinform., 2020)

iPNHOT: a knowledge-based approach for identifying protein-nucleic acid interaction hot spots. - Xiaolei Zhu 001; Ling Liu; Jingjing He; Ting Fang; Yi Xiong 002; Julie C. Mitchell (BMC Bioinform., 2020)

LMI-DForest: A deep forest model towards the prediction of lncRNA-miRNA interactions. - Wei Wang 309; Xiaoqing Guan; Muhammad Tahir Khan; Yi Xiong 002; Dong-Qing Wei (Comput. Biol. Chem., 2020)

DTI-CDF: a cascade deep forest model towards the prediction of drug-target interactions based on hybrid features. - Yanyi Chu; Aman Chandra Kaushik; Xiangeng Wang; Wei Wang 309; Yufang Zhang; Xiaoqi Shan; Dennis Russell Salahub; Yi Xiong 002; Dong-Qing Wei (Briefings Bioinform., 2021)

DTI-MLCD: predicting drug-target interactions using multi-label learning with community detection method. - Yanyi Chu; Xiaoqi Shan; Tianhang Chen; Mingming Jiang; Yanjing Wang 003; Qiankun Wang; Dennis Russell Salahub; Yi Xiong 002; Dong-Qing Wei (Briefings Bioinform., 2021)

MDA-GCNFTG: identifying miRNA-disease associations based on graph convolutional networks via graph sampling through the feature and topology graph. - Yanyi Chu; Xuhong Wang; Qiuying Dai; Yanjing Wang 003; Qiankun Wang; Shaoliang Peng; Xiaoyong Wei; Jingfei Qiu; Dennis Russell Salahub; Yi Xiong 002; Dong-Qing Wei (Briefings Bioinform., 2021)

NeuroPpred-Fuse: an interpretable stacking model for prediction of neuropeptides by fusing sequence information and feature selection methods. - Mingming Jiang; Bowen Zhao; Shenggan Luo; Qiankun Wang; Yanyi Chu; Tianhang Chen; Xueying Mao; Yatong Liu; Yanjing Wang 003; Xue Jiang; Dong-Qing Wei; Yi Xiong 002 (Briefings Bioinform., 2021)

MLCDForest: multi-label classification with deep forest in disease prediction for long non-coding RNAs. - Wei Wang 309; Qiuying Dai; Fang Li; Yi Xiong 002; Dong-Qing Wei (Briefings Bioinform., 2021)

MDA-CF: Predicting MiRNA-Disease associations based on a cascade forest model by fusing multi-source information. - Qiuying Dai; Yanyi Chu; Zhiqi Li; Yusong Zhao; Xueying Mao; Yanjing Wang 003; Yi Xiong 002; Dong-Qing Wei (Comput. Biol. Medicine, 2021)

NetGO 2.0: improving large-scale protein function prediction with massive sequence, text, domain, family and network information. - Shuwei Yao; Ronghui You; Shaojun Wang; Yi Xiong 002; Xiaodi Huang; Shanfeng Zhu (Nucleic Acids Res., 2021)

MDF-SA-DDI: predicting drug-drug interaction events based on multi-source drug fusion, multi-source feature fusion and transformer self-attention mechanism. - Shenggeng Lin; Yanjing Wang 003; Lingfeng Zhang; Yanyi Chu; Yatong Liu; Yitian Fang; Mingming Jiang; Qiankun Wang; Bowen Zhao; Yi Xiong 002; Dong-Qing Wei (Briefings Bioinform., 2022)

scHiCStackL: a stacking ensemble learning-based method for single-cell Hi-C classification using cell embedding. - Hao Wu 062; Yingfu Wu; Yuhong Jiang; Bing Zhou; Haoru Zhou; Zhongli Chen; Yi Xiong 002; Quanzhong Liu; Hongming Zhang 002 (Briefings Bioinform., 2022)

T4SEfinder: a bioinformatics tool for genome-scale prediction of bacterial type IV secreted effectors using pre-trained protein language model. - Yumeng Zhang; Yangming Zhang; Yi Xiong 002; Hui Wang 126; Zixin Deng; Jiangning Song; Hong-Yu Ou (Briefings Bioinform., 2022)

DeepPSE: Prediction of polypharmacy side effects by fusing deep representation of drug pairs and attention mechanism. - Shenggeng Lin; Guangwei Zhang; Dong-Qing Wei; Yi Xiong 002 (Comput. Biol. Medicine, 2022)

A transformer-based model to predict peptide-HLA class I binding and optimize mutated peptides for vaccine design. - Yanyi Chu; Yan Zhang; Qiankun Wang; Lingfeng Zhang; Xuhong Wang; Yanjing Wang 003; Dennis Russell Salahub; Qin Xu; Jianmin Wang 016; Xue Jiang; Yi Xiong 002; Dong-Qing Wei (Nat. Mach. Intell., 2022)

SAM-DTA: a sequence-agnostic model for drug-target binding affinity prediction. - Zhiqiang Hu; Wenfeng Liu; Chenbin Zhang; Jiawen Huang; Shaoting Zhang 001; Huiqun Yu; Yi Xiong 002; Hao Liu 081; Song Ke; Liang Hong (Briefings Bioinform., 2023)

Subtype-DCC: decoupled contrastive clustering method for cancer subtype identification based on multi-omics data. - Jing Zhao; Bowen Zhao; Xiaotong Song; Chujun Lyu; Weizhi Chen; Yi Xiong 002; Dong-Qing Wei (Briefings Bioinform., 2023)

NetGO 3.0: Protein Language Model Improves Large-scale Functional Annotations. - Shaojun Wang; Ronghui You; Yunjia Liu; Yi Xiong 002; Shanfeng Zhu (Genom. Proteom. Bioinform., 2023)

LS-MolGen: Ligand-and-Structure Dual-Driven Deep Reinforcement Learning for Target-Specific Molecular Generation Improves Binding Affinity and Novelty. - Song Li; Chao Hu; Song Ke; Chenxing Yang; Jun Chen; Yi Xiong 002; Hao Liu 081; Liang Hong (J. Chem. Inf. Model., 2023)

A Multimodal Deep Learning Framework for Predicting PPI-Modulator Interactions. - Heqi Sun; Jianmin Wang 016; Hongyan Wu; Shenggeng Lin; Junwei Chen; Jinghua Wei; Shuai Lv; Yi Xiong 002; Dong-Qing Wei (J. Chem. Inf. Model., 2023)

ReHoGCNES-MDA: prediction of miRNA-disease associations using homogenous graph convolutional networks based on regular graph with random edge sampler. - Yufang Zhang; Yanyi Chu; Shenggeng Lin; Yi Xiong 002; Dong-Qing Wei (Briefings Bioinform., 2024)

GRATCR: Epitope-Specific T Cell Receptor Sequence Generation With Data-Efficient Pre-Trained Models. - Zhenghong Zhou; Junwei Chen; Shenggeng Lin; Liang Hong; Dong-Qing Wei; Yi Xiong 002 (IEEE J. Biomed. Health Informatics, 2025)