Inferring Strengths of Protein-Protein Interaction Using Artificial Neural Network. - Junfeng Xia; Bing Wang 004; De-Shuang Huang (IJCNN, 2007)

A New Source and Receiver Localization Method with Erroneous Receiver Positions. - Ying-Ke Lei; Junfeng Xia (ICIC (2), 2009)

Prediction of Protein-Protein Interaction Sites by Using Autocorrelation Descriptor and Support Vector Machine. - Xiao-Ming Ren; Jun-Feng Xia (ICIC (2), 2010)

APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility. - Junfeng Xia; Xing-Ming Zhao; Jiangning Song; De-Shuang Huang (BMC Bioinform., 2010)

Weighted Neighborhood Classifier for the Classification of Imbalanced Tumor Dataset. - Shulin Wang; Xueling Li; Junfeng Xia; Xiao-Ping Zhang 002 (J. Circuits Syst. Comput., 2010)

Do MicroRNAs Preferentially Target the Genes with Low DNA Methylation Level at the Promoter Region? - Zhixi Su; Junfeng Xia; Zhongming Zhao (ICIC (3), 2011)

Do cancer proteins really interact strongly in the human protein-protein interaction network? - Junfeng Xia; Jingchun Sun; Peilin Jia; Zhongming Zhao (Comput. Biol. Chem., 2011)

Virus interactions with human signal transduction pathways. - Zhongming Zhao; Junfeng Xia; Öznur Tastan; Irtisha Singh; Meghana Kshirsagar 001; Jaime G. Carbonell; Judith Klein-Seetharaman (Int. J. Comput. Biol. Drug Des., 2011)

Prediction of cytochrome P450 inhibition using ensemble of extreme learning machine. - Huan Wu; Yun-Qiang Di; Chun-Hou Zheng 001; Junfeng Xia (BIBM, 2013)

Differential coexpression analysis in gene modules level and its application to type 2 diabetes. - Lin Yuan 001; Wen Sha; Jun Zhang 011; Chun-Hou Zheng 001; Junfeng Xia (BIBM, 2013)

Application of next generation sequencing to human gene fusion detection: computational tools, features and perspectives. - Qingguo Wang; Junfeng Xia; Peilin Jia; William Pao; Zhongming Zhao (Briefings Bioinform., 2013)

Network analysis of gene fusions in human cancer. - Morgan Harrell; Junfeng Xia; Zhongming Zhao (BMC Bioinform., 2013)

Prediction of protein-protein interactions from amino acid sequences with ensemble extreme learning machines and principal component analysis. - Zhu-Hong You; Ying-Ke Lei; Lin Zhu 008; Junfeng Xia; Bing Wang 004 (BMC Bioinform., 2013)

Comparative Assessment of Data Sets of Protein Interaction Hot Spots Used in the Computational Method. - Yun-Qiang Di; Changchang Wang; Huan Wu; Xinxin Yu; Junfeng Xia (ICIC (3), 2014)

Tumor Clustering Using Independent Component Analysis and Adaptive Affinity Propagation. - Fen Ye; Junfeng Xia; Yanwen Chong; Yan Zhang 106; Chun-Hou Zheng 001 (ICIC (3), 2014)

Potential Driver Genes Regulated by OncomiRNA Are Associated with Druggability in Pan-Negative Melanoma. - Di Zhang 006; Junfeng Xia (ICIC (3), 2014)

Identification of Colorectal Cancer Candidate Genes Based on Subnetwork Extraction Algorithm. - Ran Wei; Haitao Li 004; Yanjun Wang; Chun-Hou Zheng 001; Junfeng Xia (ICIC (3), 2015)

Multi-objective Optimization Method for Identifying Mutated Driver Pathways in Cancer. - Wu Yang; Junfeng Xia; Yan Zhang 106; Chun-Hou Zheng 001 (ICIC (2), 2015)

Prediction of Clinical Drug Response Based on Differential Gene Expression Levels. - Zhenyu Yue; Yan Chen; Junfeng Xia (ICIC (2), 2015)

Discovery of Ovarian Cancer Candidate Genes Using Protein Interaction Information. - Di Zhang 006; Qingbao Wang; Rongrong Zhu; Haitao Li 004; Chun-Hou Zheng 001; Junfeng Xia (ICIC (2), 2015)

MGDB: a comprehensive database of genes involved in melanoma. - Di Zhang 006; Rongrong Zhu; Hanqian Zhang; Chun-Hou Zheng 001; Junfeng Xia (Database J. Biol. Databases Curation, 2015)

Automatic classification for field crop insects via multiple-task sparse representation and multiple-kernel learning. - Chengjun Xie; Jie Zhang 033; Rui Li 027; Jinyan Li 001; Peilin Hong; Junfeng Xia; Peng Chen 001 (Comput. Electron. Agric., 2015)

Cancer genes discovery based on integtating transcriptomic data and the impact of gene length. - Pi-Jing Wei; Di Zhang 006; Chun-Hou Zheng 001; Junfeng Xia (BIBM, 2016)

Srrr-cluster: Using Sparse Reduced-Rank Regression to Optimize iCluster. - Shu-Guang Ge; Junfeng Xia; Pi-Jing Wei; Chun-Hou Zheng 001 (ICIC (3), 2016)

dbDSM: a manually curated database for deleterious synonymous mutations. - Pengbo Wen; Peng Xiao; Junfeng Xia (Bioinform., 2016)

CINOEDV: a co-information based method for detecting and visualizing n-order epistatic interactions. - Junliang Shang; Yingxia Sun; Jin-Xing Liu 001; Junfeng Xia; Junying Zhang; Chun-Hou Zheng 001 (BMC Bioinform., 2016)

LNDriver: identifying driver genes by integrating mutation and expression data based on gene-gene interaction network. - Pi-Jing Wei; Di Zhang 006; Junfeng Xia; Chun-Hou Zheng 001 (BMC Bioinform., 2016)

Identification of mutated driver pathways in cancer using a multi-objective optimization model. - Chun-Hou Zheng 001; Wu Yang; Yanwen Chong; Junfeng Xia (Comput. Biol. Medicine, 2016)

A Sequence-Based Dynamic Ensemble Learning System for Protein Ligand-Binding Site Prediction. - Peng Chen 001; ShanShan Hu; Jun Zhang 011; Xin Gao 001; Jinyan Li 001; Junfeng Xia; Bing Wang 004 (IEEE ACM Trans. Comput. Biol. Bioinform., 2016)

Investigating Alzheimer's Disease Candidate Genes Based on Combined Network Using Subnetwork Extraction Algorithms. - Xiaojuan Wang; Hua Yan; Di Zhang 006; Le Zhao; Yannan Bin; Junfeng Xia (ICIC (2), 2017)

DriverFinder: A Gene Length-Based Network Method to Identify Cancer Driver Genes. - Pi-Jing Wei; Di Zhang 006; Haitao Li 004; Junfeng Xia; Chun-Hou Zheng 001 (Complex., 2017)

Cancer Subtype Discovery Based on Integrative Model of Multigenomic Data. - Shu-Guang Ge; Junfeng Xia; Wen Sha; Chun-Hou Zheng 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

Further Evidence for Role of Promoter Polymorphisms in TNF Gene in Alzheimer's Disease. - Yannan Bin; Ling Shu; Qizhi Zhu; Huanhuan Zhu; Junfeng Xia (ICIC (2), 2018)

Nucleotide-Based Significance of Somatic Synonymous Mutations for Pan-Cancer. - Yannan Bin; Xiaojuan Wang; Qizhi Zhu; Pengbo Wen; Junfeng Xia (ICIC (2), 2018)

Computational Prediction of Driver Missense Mutations in Melanoma. - Haiyang Sun; Zhenyu Yue; Le Zhao; Junfeng Xia; Yannan Bin; Di Zhang 006 (ICIC (2), 2018)

dbCRSR: a manually curated database for regulation of cancer radiosensitivity. - Pengbo Wen; Junfeng Xia; Xianbin Cao 002; Bin Chen; Yinping Tao; Lijun Wu; An Xu; Guoping Zhao (Database J. Biol. Databases Curation, 2018)

Improved Inductive Matrix Completion Method for Predicting MicroRNA-Disease Associations. - Xin Ding; Jun-Feng Xia; Yutian Wang; Jing Wang 057; Chun-Hou Zheng 001 (ICIC (2), 2019)

Discovering Driver Mutation Profiles in Cancer with a Local Centrality Score. - Ying Hui; Pi-Jing Wei; Jun-Feng Xia; Hong-Bo Wang; Jing Wang 057; Chun-Hou Zheng 001 (ICIC (2), 2019)

Sequence-Based Prediction of Hot Spots in Protein-RNA Complexes Using an Ensemble Approach. - Le Zhao; Sijia Zhang; Junfeng Xia (ICIC (1), 2019)

Comprehensive Analysis of Alzheimer's Disease Biologically Candidate Causal Genes Revealed by Function Association Study With GWAS. - Yannan Bin; Qizhi Zhu; Menglu Li; Junfeng Xia (IEEE Access, 2019)

SPHot: Prediction of Hot Spots in Protein-RNA Complexes by Protein Sequence Information and Ensemble Classifier. - Sijia Zhang; Le Zhao; Junfeng Xia (IEEE Access, 2019)

dbCID: a manually curated resource for exploring the driver indels in human cancer. - Zhenyu Yue; Le Zhao; Na Cheng; Hua Yan; Junfeng Xia (Briefings Bioinform., 2019)

The 2017 Network Tools and Applications in Biology (NETTAB) workshop: aims, topics and outcomes. - Paolo Romano 001; Arnaud Céol; Andreas Dräger; Antonino Fiannaca; Rosalba Giugno; Massimo La Rosa; Luciano Milanesi; Ulrich Pfeffer; Riccardo Rizzo; Soo-Yong Shin; Junfeng Xia; Alfonso Urso (BMC Bioinform., 2019)

Computational Approaches for Modeling Signal Transduction Networks. - Zhongming Zhao; Junfeng Xia (Encyclopedia of Bioinformatics and Computational Biology (2), 2019)

Predicting lncRNA-disease Association based on Extreme Gradient Boosting. - Xi Tang; Menglu Li; Wei Zhang; Junfeng Xia (ICBBB, 2020)

Comparison and integration of computational methods for deleterious synonymous mutation prediction. - Na Cheng; Menglu Li; Le Zhao; Bo Zhang 001; Yuhua Yang; Chun-Hou Zheng 001; Junfeng Xia (Briefings Bioinform., 2020)

dbCPM: a manually curated database for exploring the cancer passenger mutations. - Zhenyu Yue; Le Zhao; Junfeng Xia (Briefings Bioinform., 2020)

A feature-based approach to predict hot spots in protein-DNA binding interfaces. - Sijia Zhang; Le Zhao; Chun-Hou Zheng 001; Junfeng Xia (Briefings Bioinform., 2020)

Prediction of hot spots in protein-DNA binding interfaces based on supervised isometric feature mapping and extreme gradient boosting. - Ke Li; Sijia Zhang; Di Yan; Yannan Bin; Junfeng Xia (BMC Bioinform., 2020)

usDSM: a novel method for deleterious synonymous mutation prediction using undersampling scheme. - Xi Tang; Tao Zhang; Na Cheng; Huadong Wang; Chun-Hou Zheng 001; Junfeng Xia; Tiejun Zhang (Briefings Bioinform., 2021)

Erratum: usDSM: a novel method for deleterious synonymous mutation prediction using undersampling scheme. - Xi Tang; Tao Zhang; Na Cheng; Huadong Wang; Chun-Hou Zheng 001; Junfeng Xia; Tiejun Zhang (Briefings Bioinform., 2021)

GAERF: predicting lncRNA-disease associations by graph auto-encoder and random forest. - Qing-Wen Wu; Jun-Feng Xia; Jian-Cheng Ni 001; Chun-Hou Zheng 001 (Briefings Bioinform., 2021)

PredCID: prediction of driver frameshift indels in human cancer. - Zhenyu Yue; Xinlu Chu; Junfeng Xia (Briefings Bioinform., 2021)

Identification of driver genes based on gene mutational effects and network centrality. - Yun-Yun Tang; Pi-Jing Wei; Jian-ping Zhao 001; Junfeng Xia; Rui-Fen Cao; Chun-Hou Zheng 001 (BMC Bioinform., 2021)

An improved DNA-binding hot spot residues prediction method by exploring interfacial neighbor properties. - Sijia Zhang; Lihua Wang; Le Zhao; Menglu Li; Mengya Liu; Ke Li; Yannan Bin; Junfeng Xia (BMC Bioinform., 2021)

Double matrix completion for circRNA-disease association prediction. - Zong-Lan Zuo; Rui-Fen Cao; Pi-Jing Wei; Jun-Feng Xia; Chun-Hou Zheng 001 (BMC Bioinform., 2021)

BBPpred: Sequence-Based Prediction of Blood-Brain Barrier Peptides with Feature Representation Learning and Logistic Regression. - Ruyu Dai; Wei Zhang; Wending Tang; Evelien Wynendaele; Qizhi Zhu; Yannan Bin; Bart De Spiegeleer; Junfeng Xia (J. Chem. Inf. Model., 2021)

A Deep Learning-Based Method for Identification of Bacteriophage-Host Interaction. - Menglu Li; Yanan Wang 003; Fuyi Li; Yun Zhao 004; Mengya Liu; Sijia Zhang; Yannan Bin; Alexander Ian Smith; Geoffrey I. Webb; Jian Li 052; Jiangning Song; Junfeng Xia (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

An Ensemble Framework Integrating Whole Slide Pathological Images and miRNA Data to Predict Radiosensitivity of Breast Cancer Patients. - Chao Dong; Jie Liu; Wenhui Yan; Mengmeng Han; Lijun Wu; Junfeng Xia; Yannan Bin (ICIC (2), 2022)

Identifying multi-functional bioactive peptide functions using multi-label deep learning. - Wending Tang; Ruyu Dai; Wenhui Yan; Wei Zhang; Yannan Bin; En-Hua Xia; Junfeng Xia (Briefings Bioinform., 2022)

scHFC: a hybrid fuzzy clustering method for single-cell RNA-seq data optimized by natural computation. - Jing Wang 057; Junfeng Xia; Dayu Tan; Rongxin Lin; Yansen Su; Chun-Hou Zheng 001 (Briefings Bioinform., 2022)

dbBIP: a comprehensive bipolar disorder database for genetic research. - Xiaoyan Li; Shunshuai Ma; Wenhui Yan; Yong Wu; Hui Kong; Mingshan Zhang; Xiongjian Luo; Junfeng Xia (Database J. Biol. Databases Curation, 2022)

Extra Trees Method for Predicting LncRNA-Disease Association Based On Multi-Layer Graph Embedding Aggregation. - Qing-Wen Wu; Rui-Fen Cao; Jun-Feng Xia; Jian-Cheng Ni 001; Chunhou Zheng 001; Yan-Sen Su (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

An Ensemble Framework for Improving the Prediction of Deleterious Synonymous Mutation. - Na Cheng; Huadong Wang; Xi Tang; Tao Zhang; Jie Gui; Chun-Hou Zheng 001; Junfeng Xia (IEEE Trans. Circuits Syst. Video Technol., 2022)

DPProm: A Two-Layer Predictor for Identifying Promoters and Their Types on Phage Genome Using Deep Learning. - Chen Wang; Junyin Zhang; Li Cheng; Jiawei Wu; Minfeng Xiao; Junfeng Xia; Yannan Bin (IEEE J. Biomed. Health Informatics, 2022)

PrMFTP: Multi-functional therapeutic peptides prediction based on multi-head self-attention mechanism and class weight optimization. - Wenhui Yan; Wending Tang; Lihua Wang; Yannan Bin; Junfeng Xia (PLoS Comput. Biol., 2022)

CNNGRN: A Convolutional Neural Network-Based Method for Gene Regulatory Network Inference From Bulk Time-Series Expression Data. - Zhen Gao; Jin Tang 001; Junfeng Xia; Chun-Hou Zheng 001; Pi-Jing Wei (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

frDSM: An Ensemble Predictor With Effective Feature Representation for Deleterious Synonymous Mutation in Human Genome. - Huadong Wang; Jianhui Sun; Mengya Liu; Chun-Hou Zheng 001; Junfeng Xia; Na Cheng (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

scDCCA: deep contrastive clustering for single-cell RNA-seq data based on auto-encoder network. - Jing Wang 057; Junfeng Xia; Haiyun Wang; Yansen Su; Chun-Hou Zheng 001 (Briefings Bioinform., 2023)

Deleterious synonymous mutation identification based on selective ensemble strategy. - Lihua Wang; Tao Zhang; Lihong Yu; Chun-Hou Zheng 001; Wenguang Yin; Junfeng Xia; Tiejun Zhang (Briefings Bioinform., 2023)

PhaGAA: an integrated web server platform for phage genome annotation and analysis. - Jiawei Wu; Qingrui Liu; Min Li; Jiliang Xu; Chen Wang; Junyin Zhang; Minfeng Xiao; Yannan Bin; Junfeng Xia (Bioinform., 2023)

DeepFGRN: inference of gene regulatory network with regulation type based on directed graph embedding. - Zhen Gao; Yansen Su; Junfeng Xia; Rui-Fen Cao; Yun Ding; Chun-Hou Zheng 001; Pi-Jing Wei (Briefings Bioinform., 2024)

scHyper: reconstructing cell-cell communication through hypergraph neural networks. - Wenying Li; Haiyun Wang; Jianping Zhao 001; Junfeng Xia; Xiaoqiang Sun (Briefings Bioinform., 2024)

Uncovering cognitive taskonomy through transfer learning in masked autoencoder-based fMRI reconstruction. - Youzhi Qu; Junfeng Xia; Xinyao Jian; Wendu Li; Kaining Peng; Zhichao Liang; Haiyan Wu; Quanying Liu (CoRR, 2024)

DRExplainer: Quantifiable Interpretability in Drug Response Prediction with Directed Graph Convolutional Network. - Haoyuan Shi; Tao Xu; Xiaodi Li; Qian Gao; Junfeng Xia; Zhenyu Yue (CoRR, 2024)

scVSC: Deep Variational Subspace Clustering for Single-Cell Transcriptome Data. - Zile Wang; Hai-Yun Wang; Jianping Zhao 001; Junfeng Xia; Chun-Hou Zheng 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2024)

Evaluation of Time-Varying Stress in Prestressed Tendons Based on the Resonance-Enhanced Magnetoelastic Method. - Senhua Zhang; Jianting Zhou; Junfeng Xia; Hong Zhang 002; Zhenfeng He; Kemeng Hu; Leng Liao (IEEE Trans. Instrum. Meas., 2024)

Effect Predictor of Driver Synonymous Mutations Based on Multi-Feature Fusion and Iterative Feature Representation Learning. - Na Cheng; Chuanmei Bi; Yong Shi; Mengya Liu; Anqi Cao; Mengkun Ren; Junfeng Xia; Zhen Liang (IEEE J. Biomed. Health Informatics, 2024)

A Novel Skip-Connection Strategy by Fusing Spatial and Channel Wise Features for Multi-Region Medical Image Segmentation. - Dayu Tan; Rui Hao; Xiaoping Zhou; Junfeng Xia; Yansen Su; Chun-Hou Zheng 001 (IEEE J. Biomed. Health Informatics, 2024)

DRExplainer: Quantifiable interpretability in drug response prediction with directed graph convolutional network. - Haoyuan Shi; Tao Xu; Xiaodi Li; Qian Gao; Zhiwei Xiong; Junfeng Xia; Zhenyu Yue (Artif. Intell. Medicine, 2025)

MultiPep-DLCL: recognition of multifunctional therapeutic peptides through deep learning with label-sequence contrastive learning. - Ting Li; Henghui Fan; Jianping Zhao 001; Xiaomei Yang; Junfeng Xia (Briefings Bioinform., 2025)

Multi-view clustering for single-cell RNA-seq data based on graph fusion. - Jing Wang 057; Junfeng Xia; Dayu Tan; Yunjie Ma; Yansen Su; Chun-Hou Zheng 001 (Briefings Bioinform., 2025)

FDPSM: Feature-Driven Prediction Modeling of Pathogenic Synonymous Mutations. - Fangfang Jin; Na Cheng; Lihua Wang; Bin Ye; Junfeng Xia (J. Chem. Inf. Model., 2025)

MFDSMC: Accurate Identification of Cancer-Driver Synonymous Mutations Using Multiperspective Feature Representation Learning. - Lihua Wang; Chen Ye; Na Cheng; Junfeng Xia (J. Chem. Inf. Model., 2025)

Protein language model-based prediction for plant miRNA encoded peptides. - Yishan Yue; Henghui Fan; Jianping Zhao 001; Junfeng Xia (PeerJ Comput. Sci., 2025)

Ensemble learning-based predictor for driver synonymous mutation with sequence representation. - Chuanmei Bi; Yong Shi; Junfeng Xia; Zhen Liang; Zhiqiang Wu; Kai Xu; Na Cheng (PLoS Comput. Biol., 2025)

scDMSC: Deep Multi-View Subspace Clustering for Single-Cell Multi-Omics Data. - Zile Wang; Fengyu Lei; Xiaoping Shi; Jianping Zhao 001; Junfeng Xia (IEEE J. Biomed. Health Informatics, 2025)

ExplainMIX: Explaining Drug Response Prediction in Directed Graph Neural Networks With Multi-Omics Fusion. - Ying Xiang; Xiaodi Li; Qian Gao; Junfeng Xia; Zhenyu Yue (IEEE J. Biomed. Health Informatics, 2025)