Detecting temporal protein complexes from dynamic protein-protein interaction networks. - Le Ou-Yang; Dao-Qing Dai; Xiaoli Li 001; Min Wu 008; Xiao-Fei Zhang; Peng Yang (BMC Bioinform., 2014)

Detecting overlapping protein complexes based on a generative model with functional and topological properties. - Xiao-Fei Zhang; Dao-Qing Dai; Le Ou-Yang; Hong Yan 001 (BMC Bioinform., 2014)

Microbial community pattern detection in human body habitats via ensemble clustering framework. - Peng Yang; Xiaoquan Su; Le Ou-Yang; Hon Nian Chua; Xiaoli Li 001; Kang Ning 001 (BMC Syst. Biol., 2014)

Determining minimum set of driver nodes in protein-protein interaction networks. - Xiao-Fei Zhang; Le Ou-Yang; Yuan Zhu; Meng-Yun Wu; Dao-Qing Dai (BMC Bioinform., 2015)

Detecting Protein Complexes from Signed Protein-Protein Interaction Networks. - Le Ou-Yang; Dao-Qing Dai; Xiao-Fei Zhang (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

Identifying protein complexes via multi-network clustering. - Le Ou-Yang; Hong Yan 001; Xiao-Fei Zhang (BIBM, 2016)

A two-layer integration framework for protein complex detection. - Le Ou-Yang; Min Wu 008; Xiao-Fei Zhang; Dao-Qing Dai; Xiaoli Li 001; Hong Yan 001 (BMC Bioinform., 2016)

Protein complex detection based on partially shared multi-view clustering. - Le Ou-Yang; Xiao-Fei Zhang; Dao-Qing Dai; Meng-Yun Wu; Yuan Zhu; Zhiyong Liu; Hong Yan 001 (BMC Bioinform., 2016)

Regularized logistic regression with network-based pairwise interaction for biomarker identification in breast cancer. - Meng-Yun Wu; Xiao-Fei Zhang; Dao-Qing Dai; Le Ou-Yang; Yuan Zhu; Hong Yan 001 (BMC Bioinform., 2016)

Comparative analysis of housekeeping and tissue-specific driver nodes in human protein interaction networks. - Xiao-Fei Zhang; Le Ou-Yang; Dao-Qing Dai; Meng-Yun Wu; Yuan Zhu; Hong Yan 001 (BMC Bioinform., 2016)

Incorporating prior information into differential network analysis using non-paranormal graphical models. - Xiao-Fei Zhang; Le Ou-Yang; Hong Yan 001 (Bioinform., 2017)

A multi-network clustering method for detecting protein complexes from multiple heterogeneous networks. - Le Ou-Yang; Hong Yan 001; Xiao-Fei Zhang (BMC Bioinform., 2017)

Node-based differential network analysis in genomics. - Xiao-Fei Zhang; Le Ou-Yang; Hong Yan 001 (Comput. Biol. Chem., 2017)

Protein Complex Detection via Effective Integration of Base Clustering Solutions and Co-Complex Affinity Scores. - Min Wu 008; Le Ou-Yang; Xiaoli Li 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

RepLong: de novo repeat identification using long read sequencing data. - Rui Guo; Yan-Ran Li 001; Shan He 001; Le Ou-Yang; Yiwen Sun; Zexuan Zhu (Bioinform., 2018)

DiffGraph: an R package for identifying gene network rewiring using differential graphical models. - Xiao-Fei Zhang; Le Ou-Yang; Shuo Yang; Xiaohua Hu 001; Hong Yan 001 (Bioinform., 2018)

Identifying Gene Network Rewiring by Integrating Gene Expression and Gene Network Data. - Ting Xu; Le Ou-Yang; Xiaohua Hu 001; Xiao-Fei Zhang (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

Improve L2-normalized Softmax with Exponential Moving Average. - Xuefei Zhe; Le Ou-Yang; Hong Yan 001 (IJCNN, 2019)

Sparse Low-rank Constrained Adaptive Structure Learning using Multi-template for Autism Spectrum Disorder Diagnosis. - Fanglin Huang; Ahmed El-Azab; Le Ou-Yang; Joseph Tan; Tianfu Wang 001; Baiying Lei (ISBI, 2019)

Graph Convolutional Network Analysis for Mild Cognitive Impairment Prediction. - Xin Zhao 029; Feng Zhou 003; Le Ou-Yang; Tianfu Wang 001; Baiying Lei (ISBI, 2019)

Multi-template Based Auto-Weighted Adaptive Structural Learning for ASD Diagnosis. - Fanglin Huang; Peng Yang 011; Shan Huang; Le Ou-Yang; Tianfu Wang 001; Baiying Lei (MLMI@MICCAI, 2019)

DiffNetFDR: differential network analysis with false discovery rate control. - Xiao-Fei Zhang; Le Ou-Yang; Shuo Yang; Xiaohua Hu 001; Hong Yan 001 (Bioinform., 2019)

EnImpute: imputing dropout events in single-cell RNA-sequencing data via ensemble learning. - Xiao-Fei Zhang; Le Ou-Yang; Shuo Yang; Xing-Ming Zhao; Xiaohua Hu 001; Hong Yan 001 (Bioinform., 2019)

Predicting synthetic lethal interactions in human cancers using graph regularized self-representative matrix factorization. - Jiang Huang; Min Wu 008; Fan Lu; Le Ou-Yang; Zexuan Zhu (BMC Bioinform., 2019)

Semantic Hierarchy Preserving Deep Hashing for Large-scale Image Retrieval. - Xuefei Zhe; Le Ou-Yang; Shifeng Chen; Hong Yan 001 (CoRR, 2019)

Inferring Gene Network Rewiring by Combining Gene Expression and Gene Mutation Data. - Jia-Juan Tu; Le Ou-Yang; Xiaohua Hu 001; Xiao-Fei Zhang (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Joint Learning of Multiple Differential Networks With Latent Variables. - Le Ou-Yang; Xiao-Fei Zhang; Xing-Ming Zhao; Debby Dan Wang; Fu Lee Wang; Baiying Lei; Hong Yan 001 (IEEE Trans. Cybern., 2019)

scTSSR: gene expression recovery for single-cell RNA sequencing using two-side sparse self-representation. - Ke Jin; Le Ou-Yang; Xing-Ming Zhao; Hong Yan 001; Xiao-Fei Zhang (Bioinform., 2020)

Joint reconstruction of multiple gene networks by simultaneously capturing inter-tumor and intra-tumor heterogeneity. - Jia-Juan Tu; Le Ou-Yang; Hong Yan 001; Xiao-Fei Zhang; Hong Qin 008 (Bioinform., 2020)

A graph regularized generalized matrix factorization model for predicting links in biomedical bipartite networks. - Zi-Chao Zhang 001; Xiao-Fei Zhang; Min Wu 008; Le Ou-Yang; Xing-Ming Zhao; Xiaoli Li 001 (Bioinform., 2020)

Self-weighted adaptive structure learning for ASD diagnosis via multi-template multi-center representation. - Fanglin Huang; Ee-Leng Tan; Peng Yang 011; Shan Huang; Le Ou-Yang; Jiuwen Cao; Tianfu Wang 001; Baiying Lei (Medical Image Anal., 2020)

Sparse regularized low-rank tensor regression with applications in genomic data analysis. - Le Ou-Yang; Xiao-Fei Zhang; Hong Yan 001 (Pattern Recognit., 2020)

Differential Network Analysis via Weighted Fused Conditional Gaussian Graphical Model. - Le Ou-Yang; Xiao-Fei Zhang; Xiaohua Hu 001; Hong Yan 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

Identifying Gene Network Rewiring Using Robust Differential Graphical Model with Multivariate $t$t-Distribution. - Rui Yuan; Le Ou-Yang; Xiaohua Hu 001; Xiao-Fei Zhang (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

A Machine Learning Approach to Phase Reference Estimation With Noise. - Ning Xie 007; Le Ou-Yang; Alex X. Liu (IEEE Trans. Commun., 2020)

Spectrum Sharing in mmWave Cellular Networks Using Clustering Algorithms. - Ning Xie 007; Le Ou-Yang; Alex X. Liu (IEEE/ACM Trans. Netw., 2020)

A Machine Learning Approach to Blind Multi-Path Classification for Massive MIMO Systems. - Ning Xie 007; Le Ou-Yang; Alex X. Liu (IEEE/ACM Trans. Netw., 2020)

Semantic Hierarchy Preserving Deep Hashing for Large-Scale Image Retrieval. - Ming Zhang 023; Xuefei Zhe; Le Ou-Yang; Shifeng Chen; Hong Yan 001 (MVA, 2021)

Recent advances in network-based methods for disease gene prediction. - Sezin Kircali Ata; Min Wu 008; Yuan Fang 001; Le Ou-Yang; Chee Keong Kwoh 001; Xiaoli Li 001 (Briefings Bioinform., 2021)

WDNE: an integrative graphical model for inferring differential networks from multi-platform gene expression data with missing values. - Le Ou-Yang; Dehan Cai; Xiao-Fei Zhang; Hong Yan 001 (Briefings Bioinform., 2021)

Differential network analysis by simultaneously considering changes in gene interactions and gene expression. - Jia-Juan Tu; Le Ou-Yang; Yuan Zhu; Hong Yan 001; Hong Qin 008; Xiao-Fei Zhang (Bioinform., 2021)

The selection of the optimal parameter in the modulus-based matrix splitting algorithm for linear complementarity problems. - Zhizhi Li; Huai Zhang; Le Ou-Yang (Comput. Optim. Appl., 2021)

EnTSSR: A Weighted Ensemble Learning Method to Impute Single-Cell RNA Sequencing Data. - Fan Lu; Yilong Lin; Chongbin Yuan; Xiao-Fei Zhang; Le Ou-Yang (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

WMLRR: A Weighted Multi-View Low Rank Representation to Identify Cancer Subtypes From Multiple Types of Omics Data. - Yesen Sun; Le Ou-Yang; Dao-Qing Dai (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

Time-Varying Differential Network Analysis for Revealing Network Rewiring over Cancer Progression. - Ting Xu; Le Ou-Yang; Hong Yan 001; Xiao-Fei Zhang (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

A Joint Graphical Model for Inferring Gene Networks Across Multiple Subpopulations and Data Types. - Xiao-Fei Zhang; Le Ou-Yang; Ting Yan; Xiaohua Tony Hu; Hong Yan 001 (IEEE Trans. Cybern., 2021)

scDEA: differential expression analysis in single-cell RNA-sequencing data via ensemble learning. - Hui-Sheng Li; Le Ou-Yang; Yuan Zhu; Hong Yan 001; Xiao-Fei Zhang (Briefings Bioinform., 2022)

Matrix factorization for biomedical link prediction and scRNA-seq data imputation: an empirical survey. - Le Ou-Yang; Fan Lu; Zi-Chao Zhang 001; Min Wu 008 (Briefings Bioinform., 2022)

DEMOC: a deep embedded multi-omics learning approach for clustering single-cell CITE-seq data. - Guanhua Zou; Yilong Lin; Tianyang Han; Le Ou-Yang (Briefings Bioinform., 2022)

MARS: A Motif-based Autoregressive Model for Retrosynthesis Prediction. - Jiahan Liu; Chaochao Yan; Yang Yu 010; Chan Lu; Junzhou Huang; Le Ou-Yang; Peilin Zhao (CoRR, 2022)

Predicting Protein-Ligand Binding Affinity with Equivariant Line Graph Network. - Yiqiang Yi; Xu Wan; Kangfei Zhao; Le Ou-Yang; Peilin Zhao (CoRR, 2022)

Anderson accelerating the preconditioned modulus approach for linear complementarity problems on second-order cones. - Zhizhi Li; Huai Zhang; Yimin Jin; Le Ou-Yang (Numer. Algorithms, 2022)

Identifying Gene Network Rewiring Based on Partial Correlation. - Yuting Tan 001; Le Ou-Yang; Xingpeng Jiang; Hong Yan 001; Xiao-Fei Zhang (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Inferring Gene Co-Expression Networks by Incorporating Prior Protein-Protein Interaction Networks. - Meng-Guo Wang; Le Ou-Yang; Hong Yan 001; Xiao-Fei Zhang (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Contrastive Subspace Clustering with Dissimilarity Regularization. - Yu-Jie Chen; Wenhui Wu 001; Le Ou-Yang (ICMLC, 2023)

MoVAE: A Variational AutoEncoder for Molecular Graph Generation. - Zerun Lin; Yuhan Zhang; Lixin Duan; Le Ou-Yang; Peilin Zhao (SDM, 2023)

ETDock: A Novel Equivariant Transformer for Protein-Ligand Docking. - Yiqiang Yi; Xu Wan; Yatao Bian; Le Ou-Yang; Peilin Zhao (CoRR, 2023)

Self-representative kernel concept factorization. - Wenhui Wu 001; Yujie Chen; Ran Wang 001; Le Ou-Yang (Knowl. Based Syst., 2023)

scTSSR2: Imputing Dropout Events for Single-Cell RNA Sequencing Using Fast Two-Side Self-Representation. - Bo Li; Ke Jin; Le Ou-Yang; Hong Yan 001; Xiao-Fei Zhang (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

Inferring gene regulatory networks from single-cell gene expression data via deep multi-view contrastive learning. - Zerun Lin; Le Ou-Yang (Briefings Bioinform., 2023)

A partially shared joint clustering framework for detecting protein complexes from multiple state-specific signed interaction networks. - Youlin Zhan; Jiahan Liu; Min Wu 008; Chris Soon Heng Tan; Xiaoli Li 001; Le Ou-Yang (Comput. Biol. Medicine, 2023)

Reading Multilevel 2-D Barcodes Using a Machine Learning Approach. - Jiaheng Zhang; Junjie Chen; Le Ou-Yang; Changsheng Chen; Ning Xie 007 (IEEE Internet Things J., 2023)

scMIC: A Deep Multi-Level Information Fusion Framework for Clustering Single-Cell Multi-Omics Data. - Youlin Zhan; Jiahan Liu; Le Ou-Yang (IEEE J. Biomed. Health Informatics, 2023)

Pathway Activity Autoencoders for Enhanced Omics Analysis and Clinical Interpretability. - Pedro Henrique da Costa Avelar; Le Ou-Yang; Min Wu 008; Sophia Tsoka (BIBM, 2024)

SCDMSC: Deep Multi-View Subspace Clustering for Single-Cell Multi-Omics Data. - Ke-Pei Wen; Ying Li; Le Ou-Yang (ICMLC, 2024)

Equivariant Line Graph Neural Network for Protein-Ligand Binding Affinity Prediction. - Yiqiang Yi; Xu Wan; Kangfei Zhao; Le Ou-Yang; Peilin Zhao (IEEE J. Biomed. Health Informatics, 2024)

GeCC: Generalized Contrastive Clustering with Domain Shifts Modeling. - Yujie Chen; Wenhui Wu 001; Le Ou-Yang; Ran Wang 001; Debby D. Wang (AAAI, 2025)

SpaFusion: A multi-level fusion model for clustering spatial multi-omics data. - Fuqun Chen; Guangchang Cai; Ying Li; Le Ou-Yang (Inf. Fusion, 2025)

GRESS: Grouping Belief-Based Deep Contrastive Subspace Clustering. - Yujie Chen; Wenhui Wu 001; Le Ou-Yang; Ran Wang 001; Sam Kwong (IEEE Trans. Cybern., 2025)

Identifying spatial domains from spatial multi-omics data using consistent and specific deep subspace learning. - Guangchang Cai; Fuqun Chen; Ke-Pei Wen; Ying Li; Le Ou-Yang (Inf. Fusion, 2026)

FEQIN: A feature-enhanced query interaction network for breast ultrasound segmentation. - Xiling Luo; Le Ou-Yang (Pattern Recognit., 2026)