Junfeng Xia

90 papers B 1Journal 68Unranked 20
YearRankTypeTitle / Venue / Authors
2026 J jnl
Omni-fMRI: A Universal Atlas-Free fMRI Foundation Model.
CoRR
Mo Wang, Wenhao Ye, Junfeng Xia, Junxiang Zhang, Xuanye Pan, Minghao Xu, Haotian Deng, Hongkai Wen, Quanying Liu
2026 J jnl
scSCCNIA: similarity matrix based contrastive clustering with neighbor information aggregation for single-cell RNA sequencing data.
Briefings Bioinform.
Jing Wang, Junfeng Xia, Yansen Su, Chun-Hou Zheng
2025 J jnl
An Enhanced Pyramid Feature Network Based on Long-Range Dependencies for Multi-Organ Medical Image Segmentation.
CoRR
Dayu Tan, Cheng Kong, Yansen Su, Hai Chen, Dongliang Yang, Junfeng Xia, Chun-Hou Zheng
2025 J jnl
DRExplainer: Quantifiable interpretability in drug response prediction with directed graph convolutional network.
Artif. Intell. Medicine
Haoyuan Shi, Tao Xu, Xiaodi Li, Qian Gao, Zhiwei Xiong, Junfeng Xia, Zhenyu Yue
2025 J jnl
Ensemble learning-based predictor for driver synonymous mutation with sequence representation.
PLoS Comput. Biol.
Chuanmei Bi, Yong Shi, Junfeng Xia, Zhen Liang, Zhiqiang Wu, Kai Xu, Na Cheng
2025 J jnl
ExplainMIX: Explaining Drug Response Prediction in Directed Graph Neural Networks With Multi-Omics Fusion.
IEEE J. Biomed. Health Informatics
Ying Xiang, Xiaodi Li, Qian Gao, Junfeng Xia, Zhenyu Yue
2025 J jnl
FDPSM: Feature-Driven Prediction Modeling of Pathogenic Synonymous Mutations.
J. Chem. Inf. Model.
Fangfang Jin, Na Cheng, Lihua Wang, Bin Ye, Junfeng Xia
2025 J jnl
MCMFPP: A Multifunctional Peptides Prediction Method Based on Class Feature Enhancement and Classifier Fusion.
J. Chem. Inf. Model.
Jintao Zhao, Henghui Fan, Jiwei Fang, Jianping Zhao, Junfeng Xia
2025 J jnl
MFDSMC: Accurate Identification of Cancer-Driver Synonymous Mutations Using Multiperspective Feature Representation Learning.
J. Chem. Inf. Model.
Lihua Wang, Chen Ye, Na Cheng, Junfeng Xia
2025 J jnl
Multi-view clustering for single-cell RNA-seq data based on graph fusion.
Briefings Bioinform.
Jing Wang, Junfeng Xia, Dayu Tan, Yunjie Ma, Yansen Su, Chun-Hou Zheng
2025 J jnl
MultiPep-DLCL: recognition of multifunctional therapeutic peptides through deep learning with label-sequence contrastive learning.
Briefings Bioinform.
Ting Li, Henghui Fan, Jianping Zhao, Xiaomei Yang, Junfeng Xia
2025 J jnl
Prediction of Human Pathogenic Start Loss Variants Based on Multi-channel Features.
J. Chem. Inf. Model.
Jie Liu, Lihua Wang, Yansen Su, Bin Ye, Junfeng Xia
2025 J jnl
Protein language model-based prediction for plant miRNA encoded peptides.
PeerJ Comput. Sci.
Yishan Yue, Henghui Fan, Jianping Zhao, Junfeng Xia
2025 J jnl
SLIM-Brain: A Data- and Training-Efficient Foundation Model for fMRI Data Analysis.
CoRR
Mo Wang, Junfeng Xia, Wenhao Ye, Enyu Liu, Kaining Peng, Jianfeng Feng, Quanying Liu, Hongkai Wen
2025 J jnl
scDMSC: Deep Multi-View Subspace Clustering for Single-Cell Multi-Omics Data.
IEEE J. Biomed. Health Informatics
Zile Wang, Fengyu Lei, Xiaoping Shi, Jianping Zhao, Junfeng Xia
2025 J jnl
scSDNE: A semi-supervised method for inferring cell-cell interactions based on graph embedding.
PLoS Comput. Biol.
Chenchen Jia, Haiyun Wang, Jianping Zhao, Junfeng Xia, Chun-Hou Zheng
2024 J jnl
A Novel Skip-Connection Strategy by Fusing Spatial and Channel Wise Features for Multi-Region Medical Image Segmentation.
IEEE J. Biomed. Health Informatics
Dayu Tan, Rui Hao, Xiaoping Zhou, Junfeng Xia, Yansen Su, Chun-Hou Zheng
2024 J jnl
DRExplainer: Quantifiable Interpretability in Drug Response Prediction with Directed Graph Convolutional Network.
CoRR
Haoyuan Shi, Tao Xu, Xiaodi Li, Qian Gao, Junfeng Xia, Zhenyu Yue
2024 J jnl
DeepFGRN: inference of gene regulatory network with regulation type based on directed graph embedding.
Briefings Bioinform.
Zhen Gao, Yansen Su, Junfeng Xia, Rui-Fen Cao, Yun Ding, Chun-Hou Zheng, Pi-Jing Wei
2024 J jnl
Effect Predictor of Driver Synonymous Mutations Based on Multi-Feature Fusion and Iterative Feature Representation Learning.
IEEE J. Biomed. Health Informatics
Na Cheng, Chuanmei Bi, Yong Shi, Mengya Liu, Anqi Cao, Mengkun Ren, Junfeng Xia, Zhen Liang
2024 J jnl
Evaluation of Time-Varying Stress in Prestressed Tendons Based on the Resonance-Enhanced Magnetoelastic Method.
IEEE Trans. Instrum. Meas.
Senhua Zhang, Jianting Zhou, Junfeng Xia, Hong Zhang, Zhenfeng He, Kemeng Hu, Leng Liao
2024 J jnl
Uncovering cognitive taskonomy through transfer learning in masked autoencoder-based fMRI reconstruction.
CoRR
Youzhi Qu, Junfeng Xia, Xinyao Jian, Wendu Li, Kaining Peng, Zhichao Liang, Haiyan Wu, Quanying Liu
2024 J jnl
scHyper: reconstructing cell-cell communication through hypergraph neural networks.
Briefings Bioinform.
Wenying Li, Haiyun Wang, Jianping Zhao, Junfeng Xia, Xiaoqiang Sun
2024 J jnl
scVSC: Deep Variational Subspace Clustering for Single-Cell Transcriptome Data.
IEEE ACM Trans. Comput. Biol. Bioinform.
Zile Wang, Haiyun Wang, Jianping Zhao, Junfeng Xia, Chun-Hou Zheng
2023 J jnl
CNNGRN: A Convolutional Neural Network-Based Method for Gene Regulatory Network Inference From Bulk Time-Series Expression Data.
IEEE ACM Trans. Comput. Biol. Bioinform.
Zhen Gao, Jin Tang, Junfeng Xia, Chun-Hou Zheng, Pi-Jing Wei
2023 J jnl
Deep learning-based multi-functional therapeutic peptides prediction with a multi-label focal dice loss function.
Bioinform.
Henghui Fan, Wenhui Yan, Lihua Wang, Jie Liu, Yannan Bin, Junfeng Xia
2023 J jnl
Deleterious synonymous mutation identification based on selective ensemble strategy.
Briefings Bioinform.
Lihua Wang, Tao Zhang, Lihong Yu, Chun-Hou Zheng, Wenguang Yin, Junfeng Xia, Tiejun Zhang
2023 J jnl
PhaGAA: an integrated web server platform for phage genome annotation and analysis.
Bioinform.
Jiawei Wu, Qingrui Liu, Min Li, Jiliang Xu, Chen Wang, Junyin Zhang, Minfeng Xiao, Yannan Bin, Junfeng Xia
2023 J jnl
frDSM: An Ensemble Predictor With Effective Feature Representation for Deleterious Synonymous Mutation in Human Genome.
IEEE ACM Trans. Comput. Biol. Bioinform.
Huadong Wang, Jianhui Sun, Mengya Liu, Chun-Hou Zheng, Junfeng Xia, Na Cheng
2023 J jnl
scDCCA: deep contrastive clustering for single-cell RNA-seq data based on auto-encoder network.
Briefings Bioinform.
Jing Wang, Junfeng Xia, Haiyun Wang, Yansen Su, Chun-Hou Zheng
2022 — conf
An Ensemble Framework Integrating Whole Slide Pathological Images and miRNA Data to Predict Radiosensitivity of Breast Cancer Patients.
ICIC (2)
Chao Dong, Jie Liu, Wenhui Yan, Mengmeng Han, Lijun Wu, Junfeng Xia, Yannan Bin
2022 J jnl
An Ensemble Framework for Improving the Prediction of Deleterious Synonymous Mutation.
IEEE Trans. Circuits Syst. Video Technol.
Na Cheng, Huadong Wang, Xi Tang, Tao Zhang, Jie Gui, Chun-Hou Zheng, Junfeng Xia
2022 J jnl
DPProm: A Two-Layer Predictor for Identifying Promoters and Their Types on Phage Genome Using Deep Learning.
IEEE J. Biomed. Health Informatics
Chen Wang, Junyin Zhang, Li Cheng, Jiawei Wu, Minfeng Xiao, Junfeng Xia, Yannan Bin
2022 J jnl
Identifying multi-functional bioactive peptide functions using multi-label deep learning.
Briefings Bioinform.
Wending Tang, Ruyu Dai, Wenhui Yan, Wei Zhang, Yannan Bin, En-Hua Xia, Junfeng Xia
2022 J jnl
PrMFTP: Multi-functional therapeutic peptides prediction based on multi-head self-attention mechanism and class weight optimization.
PLoS Comput. Biol.
Wenhui Yan, Wending Tang, Lihua Wang, Yannan Bin, Junfeng Xia
2022 J jnl
dbBIP: a comprehensive bipolar disorder database for genetic research.
Database J. Biol. Databases Curation
Xiaoyan Li, Shunshuai Ma, Wenhui Yan, Yong Wu, Hui Kong, Mingshan Zhang, Xiongjian Luo, Junfeng Xia
2022 J jnl
scHFC: a hybrid fuzzy clustering method for single-cell RNA-seq data optimized by natural computation.
Briefings Bioinform.
Jing Wang, Junfeng Xia, Dayu Tan, Rongxin Lin, Yansen Su, Chun-Hou Zheng
2021 J jnl
A Deep Learning-Based Method for Identification of Bacteriophage-Host Interaction.
IEEE ACM Trans. Comput. Biol. Bioinform.
Menglu Li, Yanan Wang, Fuyi Li, Yun Zhao, Mengya Liu, Sijia Zhang, Yannan Bin, Alexander Ian Smith, Geoffrey I. Webb, Jian Li, Jiangning Song, Junfeng Xia
2021 J jnl
An improved DNA-binding hot spot residues prediction method by exploring interfacial neighbor properties.
BMC Bioinform.
Sijia Zhang, Lihua Wang, Le Zhao, Menglu Li, Mengya Liu, Ke Li, Yannan Bin, Junfeng Xia
2021 J jnl
BBPpred: Sequence-Based Prediction of Blood-Brain Barrier Peptides with Feature Representation Learning and Logistic Regression.
J. Chem. Inf. Model.
Ruyu Dai, Wei Zhang, Wending Tang, Evelien Wynendaele, Qizhi Zhu, Yannan Bin, Bart De Spiegeleer, Junfeng Xia
2021 J jnl
Erratum: usDSM: a novel method for deleterious synonymous mutation prediction using undersampling scheme.
Briefings Bioinform.
Xi Tang, Tao Zhang, Na Cheng, Huadong Wang, Chun-Hou Zheng, Junfeng Xia, Tiejun Zhang
2021 J jnl
Identification of driver genes based on gene mutational effects and network centrality.
BMC Bioinform.
Yun-Yun Tang, Pi-Jing Wei, Jian-ping Zhao, Junfeng Xia, Rui-Fen Cao, Chun-Hou Zheng
2021 J jnl
PredCID: prediction of driver frameshift indels in human cancer.
Briefings Bioinform.
Zhenyu Yue, Xinlu Chu, Junfeng Xia
2021 J jnl
usDSM: a novel method for deleterious synonymous mutation prediction using undersampling scheme.
Briefings Bioinform.
Xi Tang, Tao Zhang, Na Cheng, Huadong Wang, Chun-Hou Zheng, Junfeng Xia, Tiejun Zhang
2020 J jnl
A feature-based approach to predict hot spots in protein-DNA binding interfaces.
Briefings Bioinform.
Sijia Zhang, Le Zhao, Chun-Hou Zheng, Junfeng Xia
2020 J jnl
Comparison and integration of computational methods for deleterious synonymous mutation prediction.
Briefings Bioinform.
Na Cheng, Menglu Li, Le Zhao, Bo Zhang, Yuhua Yang, Chun-Hou Zheng, Junfeng Xia
2020 — conf
Predicting lncRNA-disease Association based on Extreme Gradient Boosting.
ICBBB
Xi Tang, Menglu Li, Wei Zhang, Junfeng Xia
2020 J jnl
Prediction of hot spots in protein-DNA binding interfaces based on supervised isometric feature mapping and extreme gradient boosting.
BMC Bioinform.
Ke Li, Sijia Zhang, Di Yan, Yannan Bin, Junfeng Xia
2020 J jnl
dbCPM: a manually curated database for exploring the cancer passenger mutations.
Briefings Bioinform.
Zhenyu Yue, Le Zhao, Junfeng Xia
2019 J jnl
Comprehensive Analysis of Alzheimer's Disease Biologically Candidate Causal Genes Revealed by Function Association Study With GWAS.
IEEE Access
Yannan Bin, Qizhi Zhu, Menglu Li, Junfeng Xia
2019 — ch.
Computational Approaches for Modeling Signal Transduction Networks.
Encyclopedia of Bioinformatics and Computational Biology (2)
Zhongming Zhao, Junfeng Xia
2019 J jnl
SPHot: Prediction of Hot Spots in Protein-RNA Complexes by Protein Sequence Information and Ensemble Classifier.
IEEE Access
Sijia Zhang, Le Zhao, Junfeng Xia
2019 — conf
Sequence-Based Prediction of Hot Spots in Protein-RNA Complexes Using an Ensemble Approach.
ICIC (1)
Le Zhao, Sijia Zhang, Junfeng Xia
2019 J jnl
The 2017 Network Tools and Applications in Biology (NETTAB) workshop: aims, topics and outcomes.
BMC Bioinform.
Paolo Romano, Arnaud Céol, Andreas Dräger, Antonino Fiannaca, Rosalba Giugno, Massimo La Rosa, Luciano Milanesi, Ulrich Pfeffer, Riccardo Rizzo, Soo-Yong Shin, Junfeng Xia, Alfonso Urso
2019 J jnl
dbCID: a manually curated resource for exploring the driver indels in human cancer.
Briefings Bioinform.
Zhenyu Yue, Le Zhao, Na Cheng, Hua Yan, Junfeng Xia
2018 — conf
Computational Prediction of Driver Missense Mutations in Melanoma.
ICIC (2)
Haiyang Sun, Zhenyu Yue, Le Zhao, Junfeng Xia, Yannan Bin, Di Zhang
2018 — conf
Further Evidence for Role of Promoter Polymorphisms in TNF Gene in Alzheimer's Disease.
ICIC (2)
Yannan Bin, Ling Shu, Qizhi Zhu, Huanhuan Zhu, Junfeng Xia
2018 — conf
Nucleotide-Based Significance of Somatic Synonymous Mutations for Pan-Cancer.
ICIC (2)
Yannan Bin, Xiaojuan Wang, Qizhi Zhu, Pengbo Wen, Junfeng Xia
2018 J jnl
dbCRSR: a manually curated database for regulation of cancer radiosensitivity.
Database J. Biol. Databases Curation
Pengbo Wen, Junfeng Xia, Xianbin Cao, Bin Chen, Yinping Tao, Lijun Wu, An Xu, Guoping Zhao
2017 J jnl
Cancer Subtype Discovery Based on Integrative Model of Multigenomic Data.
IEEE ACM Trans. Comput. Biol. Bioinform.
Shu-Guang Ge, Junfeng Xia, Wen Sha, Chun-Hou Zheng
2017 J jnl
DriverFinder: A Gene Length-Based Network Method to Identify Cancer Driver Genes.
Complex.
Pi-Jing Wei, Di Zhang, Haitao Li, Junfeng Xia, Chun-Hou Zheng
2017 — conf
Investigating Alzheimer's Disease Candidate Genes Based on Combined Network Using Subnetwork Extraction Algorithms.
ICIC (2)
Xiaojuan Wang, Hua Yan, Di Zhang, Le Zhao, Yannan Bin, Junfeng Xia
2016 J jnl
A Sequence-Based Dynamic Ensemble Learning System for Protein Ligand-Binding Site Prediction.
IEEE ACM Trans. Comput. Biol. Bioinform.
Peng Chen, Shanshan Hu, Jun Zhang, Xin Gao, Jinyan Li, Junfeng Xia, Bing Wang
2016 J jnl
CINOEDV: a co-information based method for detecting and visualizing
BMC Bioinform.
Junliang Shang, Yingxia Sun, Jin-Xing Liu, Junfeng Xia, Junying Zhang, Chun-Hou Zheng
2016 — conf
Cancer genes discovery based on integtating transcriptomic data and the impact of gene length.
BIBM
Pi-Jing Wei, Di Zhang, Chun-Hou Zheng, Junfeng Xia
2016 J jnl
Identification of mutated driver pathways in cancer using a multi-objective optimization model.
Comput. Biol. Medicine
Chun-Hou Zheng, Wu Yang, Yanwen Chong, Junfeng Xia
2016 J jnl
LNDriver: identifying driver genes by integrating mutation and expression data based on gene-gene interaction network.
BMC Bioinform.
Pi-Jing Wei, Di Zhang, Junfeng Xia, Chun-Hou Zheng
2016 — conf
Srrr-cluster: Using Sparse Reduced-Rank Regression to Optimize iCluster.
ICIC (3)
Shu-Guang Ge, Junfeng Xia, Pi-Jing Wei, Chun-Hou Zheng
2016 J jnl
dbDSM: a manually curated database for deleterious synonymous mutations.
Bioinform.
Pengbo Wen, Peng Xiao, Junfeng Xia
2015 J jnl
Automatic classification for field crop insects via multiple-task sparse representation and multiple-kernel learning.
Comput. Electron. Agric.
Chengjun Xie, Jie Zhang, Rui Li, Jinyan Li, Peilin Hong, Junfeng Xia, Peng Chen
2015 — conf
Discovery of Ovarian Cancer Candidate Genes Using Protein Interaction Information.
ICIC (2)
Di Zhang, Qingbao Wang, Rongrong Zhu, Haitao Li, Chun-Hou Zheng, Junfeng Xia
2015 — conf
Identification of Colorectal Cancer Candidate Genes Based on Subnetwork Extraction Algorithm.
ICIC (3)
Ran Wei, Haitao Li, Yanjun Wang, Chun-Hou Zheng, Junfeng Xia
2015 J jnl
MGDB: a comprehensive database of genes involved in melanoma.
Database J. Biol. Databases Curation
Di Zhang, Rongrong Zhu, Hanqian Zhang, Chun-Hou Zheng, Junfeng Xia
2015 — conf
Multi-objective Optimization Method for Identifying Mutated Driver Pathways in Cancer.
ICIC (2)
Wu Yang, Junfeng Xia, Yan Zhang, Chun-Hou Zheng
2015 — conf
Prediction of Clinical Drug Response Based on Differential Gene Expression Levels.
ICIC (2)
Zhenyu Yue, Yan Chen, Junfeng Xia
2014 — conf
Comparative Assessment of Data Sets of Protein Interaction Hot Spots Used in the Computational Method.
ICIC (3)
Yun-Qiang Di, Changchang Wang, Huan Wu, Xinxin Yu, Junfeng Xia
2014 — conf
Potential Driver Genes Regulated by OncomiRNA Are Associated with Druggability in Pan-Negative Melanoma.
ICIC (3)
Di Zhang, Junfeng Xia
2014 — conf
Tumor Clustering Using Independent Component Analysis and Adaptive Affinity Propagation.
ICIC (3)
Fen Ye, Junfeng Xia, Yanwen Chong, Yan Zhang, Chun-Hou Zheng
2013 J jnl
Application of next generation sequencing to human gene fusion detection: computational tools, features and perspectives.
Briefings Bioinform.
Qingguo Wang, Junfeng Xia, Peilin Jia, William Pao, Zhongming Zhao
2013 — conf
Differential coexpression analysis in gene modules level and its application to type 2 diabetes.
BIBM
Lin Yuan, Wen Sha, Jun Zhang, Chun-Hou Zheng, Junfeng Xia
2013 J jnl
Network analysis of gene fusions in human cancer.
BMC Bioinform.
Morgan Harrell, Junfeng Xia, Zhongming Zhao
2013 — conf
Prediction of cytochrome P450 inhibition using ensemble of extreme learning machine.
BIBM
Huan Wu, Yun-Qiang Di, Chun-Hou Zheng, Junfeng Xia
2013 J jnl
Prediction of protein-protein interactions from amino acid sequences with ensemble extreme learning machines and principal component analysis.
BMC Bioinform.
Zhu-Hong You, Ying-Ke Lei, Lin Zhu, Junfeng Xia, Bing Wang
2011 — conf
Do MicroRNAs Preferentially Target the Genes with Low DNA Methylation Level at the Promoter Region?
ICIC (3)
Zhixi Su, Junfeng Xia, Zhongming Zhao
2011 J jnl
Do cancer proteins really interact strongly in the human protein-protein interaction network?
Comput. Biol. Chem.
Junfeng Xia, Jingchun Sun, Peilin Jia, Zhongming Zhao
2011 J jnl
Virus interactions with human signal transduction pathways.
Int. J. Comput. Biol. Drug Des.
Zhongming Zhao, Junfeng Xia, Öznur Tastan, Irtisha Singh, Meghana Kshirsagar, Jaime G. Carbonell, Judith Klein-Seetharaman
2010 J jnl
APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility.
BMC Bioinform.
Junfeng Xia, Xing-Ming Zhao, Jiangning Song, De-Shuang Huang
2010 J jnl
Weighted Neighborhood Classifier for the Classification of Imbalanced Tumor Dataset.
J. Circuits Syst. Comput.
Shulin Wang, Xueling Li, Junfeng Xia, Xiao-Ping Zhang
2009 — conf
A New Source and Receiver Localization Method with Erroneous Receiver Positions.
ICIC (2)
Ying-Ke Lei, Junfeng Xia
2007 B conf
Inferring Strengths of Protein-Protein Interaction Using Artificial Neural Network.
IJCNN
Junfeng Xia, Bing Wang, De-Shuang Huang