Yi Xiong

33 papers Journal 31Unranked 2
YearRankTypeTitle / Venue / Authors
2025 J jnl
GRATCR: Epitope-Specific T Cell Receptor Sequence Generation With Data-Efficient Pre-Trained Models.
IEEE J. Biomed. Health Informatics
Zhenghong Zhou, Junwei Chen, Shenggeng Lin, Liang Hong, Dong-Qing Wei, Yi Xiong
2024 J jnl
ReHoGCNES-MDA: prediction of miRNA-disease associations using homogenous graph convolutional networks based on regular graph with random edge sampler.
Briefings Bioinform.
Yufang Zhang, Yanyi Chu, Shenggeng Lin, Yi Xiong, Dong-Qing Wei
2023 J jnl
A Multimodal Deep Learning Framework for Predicting PPI-Modulator Interactions.
J. Chem. Inf. Model.
Heqi Sun, Jianmin Wang, Hongyan Wu, Shenggeng Lin, Junwei Chen, Jinghua Wei, Shuai Lv, Yi Xiong, Dong-Qing Wei
2023 J jnl
LS-MolGen: Ligand-and-Structure Dual-Driven Deep Reinforcement Learning for Target-Specific Molecular Generation Improves Binding Affinity and Novelty.
J. Chem. Inf. Model.
Song Li, Chao Hu, Song Ke, Chenxing Yang, Jun Chen, Yi Xiong, Hao Liu, Liang Hong
2023 J jnl
NetGO 3.0: Protein Language Model Improves Large-scale Functional Annotations.
Genom. Proteom. Bioinform.
Shaojun Wang, Ronghui You, Yunjia Liu, Yi Xiong, Shanfeng Zhu
2023 J jnl
SAM-DTA: a sequence-agnostic model for drug-target binding affinity prediction.
Briefings Bioinform.
Zhiqiang Hu, Wenfeng Liu, Chenbin Zhang, Jiawen Huang, Shaoting Zhang, Huiqun Yu, Yi Xiong, Hao Liu, Song Ke, Liang Hong
2023 J jnl
Subtype-DCC: decoupled contrastive clustering method for cancer subtype identification based on multi-omics data.
Briefings Bioinform.
Jing Zhao, Bowen Zhao, Xiaotong Song, Chujun Lyu, Weizhi Chen, Yi Xiong, Dong-Qing Wei
2022 J jnl
A transformer-based model to predict peptide-HLA class I binding and optimize mutated peptides for vaccine design.
Nat. Mach. Intell.
Yanyi Chu, Yan Zhang, Qiankun Wang, Lingfeng Zhang, Xuhong Wang, Yanjing Wang, Dennis Russell Salahub, Qin Xu, Jianmin Wang, Xue Jiang, Yi Xiong, Dong-Qing Wei
2022 J jnl
DeepPSE: Prediction of polypharmacy side effects by fusing deep representation of drug pairs and attention mechanism.
Comput. Biol. Medicine
Shenggeng Lin, Guangwei Zhang, Dong-Qing Wei, Yi Xiong
2022 J jnl
MDF-SA-DDI: predicting drug-drug interaction events based on multi-source drug fusion, multi-source feature fusion and transformer self-attention mechanism.
Briefings Bioinform.
Shenggeng Lin, Yanjing Wang, Lingfeng Zhang, Yanyi Chu, Yatong Liu, Yitian Fang, Mingming Jiang, Qiankun Wang, Bowen Zhao, Yi Xiong, Dong-Qing Wei
2022 J jnl
T4SEfinder: a bioinformatics tool for genome-scale prediction of bacterial type IV secreted effectors using pre-trained protein language model.
Briefings Bioinform.
Yumeng Zhang, Yangming Zhang, Yi Xiong, Hui Wang, Zixin Deng, Jiangning Song, Hong-Yu Ou
2022 J jnl
scHiCStackL: a stacking ensemble learning-based method for single-cell Hi-C classification using cell embedding.
Briefings Bioinform.
Hao Wu, Yingfu Wu, Yuhong Jiang, Bing Zhou, Haoru Zhou, Zhongli Chen, Yi Xiong, Quanzhong Liu, Hongming Zhang
2021 J jnl
DTI-CDF: a cascade deep forest model towards the prediction of drug-target interactions based on hybrid features.
Briefings Bioinform.
Yanyi Chu, Aman Chandra Kaushik, Xiangeng Wang, Wei Wang, Yufang Zhang, Xiaoqi Shan, Dennis Russell Salahub, Yi Xiong, Dong-Qing Wei
2021 J jnl
DTI-MLCD: predicting drug-target interactions using multi-label learning with community detection method.
Briefings Bioinform.
Yanyi Chu, Xiaoqi Shan, Tianhang Chen, Mingming Jiang, Yanjing Wang, Qiankun Wang, Dennis Russell Salahub, Yi Xiong, Dong-Qing Wei
2021 J jnl
MDA-CF: Predicting MiRNA-Disease associations based on a cascade forest model by fusing multi-source information.
Comput. Biol. Medicine
Qiuying Dai, Yanyi Chu, Zhiqi Li, Yusong Zhao, Xueying Mao, Yanjing Wang, Yi Xiong, Dong-Qing Wei
2021 J jnl
MDA-GCNFTG: identifying miRNA-disease associations based on graph convolutional networks via graph sampling through the feature and topology graph.
Briefings Bioinform.
Yanyi Chu, Xuhong Wang, Qiuying Dai, Yanjing Wang, Qiankun Wang, Shaoliang Peng, Xiaoyong Wei, Jingfei Qiu, Dennis Russell Salahub, Yi Xiong, Dong-Qing Wei
2021 J jnl
MLCDForest: multi-label classification with deep forest in disease prediction for long non-coding RNAs.
Briefings Bioinform.
Wei Wang, Qiuying Dai, Fang Li, Yi Xiong, Dong-Qing Wei
2021 J jnl
NetGO 2.0: improving large-scale protein function prediction with massive sequence, text, domain, family and network information.
Nucleic Acids Res.
Shuwei Yao, Ronghui You, Shaojun Wang, Yi Xiong, Xiaodi Huang, Shanfeng Zhu
2021 J jnl
NeuroPpred-Fuse: an interpretable stacking model for prediction of neuropeptides by fusing sequence information and feature selection methods.
Briefings Bioinform.
Mingming Jiang, Bowen Zhao, Shenggan Luo, Qiankun Wang, Yanyi Chu, Tianhang Chen, Xueying Mao, Yatong Liu, Yanjing Wang, Xue Jiang, Dong-Qing Wei, Yi Xiong
2020 J jnl
LMI-DForest: A deep forest model towards the prediction of lncRNA-miRNA interactions.
Comput. Biol. Chem.
Wei Wang, Xiaoqing Guan, Muhammad Tahir Khan, Yi Xiong, Dong-Qing Wei
2020 J jnl
iPNHOT: a knowledge-based approach for identifying protein-nucleic acid interaction hot spots.
BMC Bioinform.
Xiaolei Zhu, Ling Liu, Jingjing He, Ting Fang, Yi Xiong, Julie C. Mitchell
2020 J jnl
m5CPred-SVM: a novel method for predicting m5C sites of RNA.
BMC Bioinform.
Xiao Chen, Yi Xiong, Yinbo Liu, Yuqing Chen, Shoudong Bi, Xiaolei Zhu
2019 J jnl
NetGO: improving large-scale protein function prediction with massive network information.
Nucleic Acids Res.
Ronghui You, Shuwei Yao, Yi Xiong, Xiaodi Huang, Fengzhu Sun, Hiroshi Mamitsuka, Shanfeng Zhu
2019 J jnl
Prediction of CYP450 Enzyme-Substrate Selectivity Based on the Network-Based Label Space Division Method.
J. Chem. Inf. Model.
Xiaoqi Shan, Xiangeng Wang, Cheng-Dong Li, Yanyi Chu, Yufang Zhang, Yi Xiong, Dong-Qing Wei
2018 J jnl
GOLabeler: improving sequence-based large-scale protein function prediction by learning to rank.
Bioinform.
Ronghui You, Zihan Zhang, Yi Xiong, Fengzhu Sun, Hiroshi Mamitsuka, Shanfeng Zhu
2018 J jnl
Protein-protein interface hot spots prediction based on a hybrid feature selection strategy.
BMC Bioinform.
Yanhua Qiao, Yi Xiong, Hongyun Gao, Xiaolei Zhu, Peng Chen
2018 J jnl
PseUI: Pseudouridine sites identification based on RNA sequence information.
BMC Bioinform.
Jingjing He, Ting Fang, Zizheng Zhang, Bei Huang, Xiaolei Zhu, Yi Xiong
2018 J jnl
dbAMEPNI: a database of alanine mutagenic effects for protein-nucleic acid interactions.
Database J. Biol. Databases Curation
Ling Liu, Yi Xiong, Hongyun Gao, Dong-Qing Wei, Julie C. Mitchell, Xiaolei Zhu
2015 J jnl
Large-scale binding ligand prediction by improved patch-based method Patch-Surfer2.0.
Bioinform.
Xiaolei Zhu, Yi Xiong, Daisuke Kihara
2015 J jnl
Navigating 3D electron microscopy maps with EM-SURFER.
BMC Bioinform.
Juan Esquivel-Rodríguez, Yi Xiong, Xusi Han, Shuomeng Guang, Charles Christoffer, Daisuke Kihara
2013 — conf
Predicting immunogenic T-cell epitopes by combining various sequence-derived features.
BIBM
Wen Zhang, Juan Liu, Yi Xiong, Meng Ke, Ke Zhang
2011 — conf
Prediction of Heme Binding Sites in Heme Proteins Using an Integrative Sequence Profile Coupling Evolutionary Information with Physicochemical Properties.
BIBM
Yi Xiong, Wen Zhang, Tao Zeng, Juan Liu
2011 J jnl
Prediction of conformational B-cell epitopes from 3D structures by random forest with a distance-based feature.
BMC Bioinform.
Wen Zhang, Yi Xiong, Meng Zhao, Hua Zou, Xinghuo Ye, Juan Liu