Xiao-Fei Zhang

发表

Identifying Gene Network Rewiring Using Robust Differential Graphical Model with Multivariate

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Xiaohua Hu, Rui Yuan, Le Ou-Yang, 2020, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Identifying binary protein-protein interactions from affinity purification mass spectrometry data

Xiaohua Hu, Dao-Qing Dai, Le Ou-Yang, 2015, BMC Genomics.

Cancer Subtype Discovery and Biomarker Identification via a New Robust Network Clustering Algorithm

D. Dai, Yuan Zhu, Meng-Yun Wu, 2013, PloS one.

Identifying differential networks based on multi-platform gene expression data.

Le Ou-Yang, Hong Yan, Xiao-Fei Zhang, 2016, Molecular bioSystems.

Determining minimum set of driver nodes in protein-protein interaction networks

Xiao-Fei Zhang, Le Ou-Yang, Yuan Zhu, 2015, BMC Bioinformatics.

Incorporating prior information into differential network analysis using nonparanormal graphical models : supplementary data

Le Ou-Yang, Xiao-Fei Zhang, Hong Yan, 2017 .

Weighted Fused Pathway Graphical Lasso for Joint Estimation of Multiple Gene Networks

Weixin Xie, Zexuan Zhu, Xiao-Fei Zhang, 2019, Front. Genet..

Node-based learning of differential networks from multi-platform gene expression data.

Min Wu, Xiao-Li Li, Xiao-Fei Zhang, 2017, Methods.

Inferring Gene Co-Expression Networks by Incorporating Prior Protein-Protein Interaction Networks

Le Ou-Yang, Xiao-Fei Zhang, Hong Yan, 2021, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Editorial: Machine Learning and Mathematical Models for Single-Cell Data Analysis

Le Ou-Yang, Xiao-Fei Zhang, Jiajun Zhang, 2022, Frontiers in Genetics.

WDNE: an integrative graphical model for inferring differential networks from multi-platform gene expression data with missing values

Le Ou-Yang, Xiao-Fei Zhang, Dehan Cai, 2021, Briefings Bioinform..

scDEA: differential expression analysis in single-cell RNA-sequencing data via ensemble learning

Yuan Zhu, Le Ou-Yang, Xiao-Fei Zhang, 2021, Briefings Bioinform..

A Joint Graphical Model for Inferring Gene Networks Across Multiple Subpopulations and Data Types

Hong Yan, Ting Yan, Le Ou-Yang, 2019, IEEE Transactions on Cybernetics.

DiffGraph: an R package for identifying gene network rewiring using differential graphical models

Hong Yan, Xiao-Fei Zhang, Le Ou-Yang, 2018, Bioinform..

Detecting overlapping protein complexes based on a generative model with functional and topological properties

D. Dai, Le Ou-Yang, Xiao-Fei Zhang, 2014, BMC Bioinformatics.

Detecting overlapping protein complexes based on a generative model with functional and topological properties

Dao-Qing Dai, Hong Yan, Le Ou-Yang, 2014, BMC Bioinformatics.

Protein Complexes Discovery Based on Protein-Protein Interaction Data via a Regularized Sparse Generative Network Model

Dao-Qing Dai, Xiao-Fei Zhang, Xiao-Xin Li, 2012, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Exploring Overlapping Functional Units with Various Structure in Protein Interaction Networks

Dao-Qing Dai, Le Ou-Yang, Meng-Yun Wu, 2012, PloS one.

A two-layer integration framework for protein complex detection

Min Wu, Xiaoli Li, Hong Yan, 2016, BMC Bioinformatics.

Detecting temporal protein complexes from dynamic protein-protein interaction networks

Peng Yang, Xiaoli Li, Dao-Qing Dai, 2014, BMC Bioinformatics.

Protein Complex Detection via Weighted Ensemble Clustering Based on Bayesian Nonnegative Matrix Factorization

Le Ou-Yang, Xiao-Fei Zhang, Dao-Qing Dai, 2013, PloS one.

Cell-type annotation with accurate unseen cell-type identification using multiple references

Xiao-Fei Zhang, Luonan Chen, Meng-Guo Wang, 2022, bioRxiv.

EnImpute: imputing dropout events in single-cell RNA-sequencing data via ensemble learning

Hong Yan, Xing-Ming Zhao, Le Ou-Yang, 2019, Bioinform..

EnTSSR: A Weighted Ensemble Learning Method to Impute Single-Cell RNA Sequencing Data

Le Ou-Yang, Fan Lu, Xiao-Fei Zhang, 2021, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

scTSSR: gene expression recovery for single-cell RNA sequencing using two-side sparse self-representation

Hong Yan, Xing-Ming Zhao, Le Ou-Yang, 2020, Bioinform..

EnDecon: cell type deconvolution of spatially resolved transcriptomics data via ensemble learning

Xiao-Fei Zhang, Hong Yan, Hui-Sheng Li, 2022, Bioinformatics.

Differential network analysis from cross-platform gene expression data

Hong Yan, Xing-Ming Zhao, Xiao-Fei Zhang, 2016, Scientific Reports.

Identifying Spurious Interactions and Predicting Missing Interactions in the Protein-Protein Interaction Networks via a Generative Network Model

Dao-Qing Dai, Yuan Zhu, Xiao-Fei Zhang, 2013, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Identifying Gene Network Rewiring by Integrating Gene Expression and Gene Network Data

Le Ou-Yang, Ting Xu, Xiaohua Hu, 2018, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Joint reconstruction of multiple gene networks by simultaneously capturing inter-tumor and intra-tumor heterogeneity

Hong Yan, Le Ou-Yang, Xiao-Fei Zhang, 2020, Bioinform..

A Framework for Incorporating Functional Interrelationships into Protein Function Prediction Algorithms

Dao-Qing Dai, Xiao-Fei Zhang, D. Dai, 2012, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Sparse regularized low-rank tensor regression with applications in genomic data analysis

Hong Yan, Le Ou-Yang, Xiao-Fei Zhang, 2020, Pattern Recognit..

Biomarker Identification and Cancer Classification Based on Microarray Data Using Laplace Naive Bayes Model with Mean Shrinkage

Hong Yan, Yu Shi, Dao-Qing Dai, 2012, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Regularized logistic regression with network-based pairwise interaction for biomarker identification in breast cancer

D. Dai, Yuan Zhu, Meng-Yun Wu, 2016, BMC Bioinformatics.

Regularized logistic regression with network-based pairwise interaction for biomarker identification in breast cancer

Dao-Qing Dai, Hong Yan, Le Ou-Yang, 2016, BMC Bioinformatics.

A multi-network clustering method for detecting protein complexes from multiple heterogeneous networks

Hong Yan, Le Ou-Yang, Xiao-Fei Zhang, 2017, BMC Bioinformatics.

Comparative analysis of housekeeping and tissue-specific driver nodes in human protein interaction networks

Hong Yan, Dao-Qing Dai, Le Ou-Yang, 2016, BMC Bioinformatics.

Detecting Protein Complexes from Signed Protein-Protein Interaction Networks

Xiao-Fei Zhang, Le Ou-Yang, Dao-Qing Dai, 2015, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Cell-type annotation with accurate unseen cell-type identification using multiple references

Xiao-Fei Zhang, Luonan Chen, Meng-Guo Wang, 2023, bioRxiv.

Identifying Gene Network Rewiring Based on Partial Correlation

Xingpeng Jiang, Hong Yan, Le Ou-Yang, 2020, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Time-Varying Differential Network Analysis for Revealing Network Rewiring over Cancer Progression

Ting Xu, Hong Yan, Le Ou-Yang, 2019, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Comparative analysis of housekeeping and tissue-specific driver nodes in human protein interaction networks

D. Dai, Yuan Zhu, Meng-Yun Wu, 2016, BMC Bioinformatics.

A graph regularized generalized matrix factorization model for predicting links in biomedical bipartite networks

Xing-Ming Zhao, Min Wu, Le Ou-Yang, 2020, Bioinform..

Supplementary Information for the article: “Cell-type Annotation with Accurate Unseen Cell-type Identification Using Multiple References”

Xiao-Fei Zhang, Luonan Chen, Meng-Guo Wang, 2023 .

A two-layer integration framework for protein complex detection

Xiaoli Li, D. Dai, Le Ou-Yang, 2016, BMC Bioinformatics.

Identifying binary protein-protein interactions from affinity purification mass spectrometry data

Xiaohua Hu, D. Dai, Le Ou-Yang, 2015, BMC Genomics.

Identifying Gene Network Rewiring Using Robust Differential Graphical Model with Multivariate

$t$

-Distributi

Xiao-Fei Zhang, Le Ou-Yang, Xiaohua Hu, 2020, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Incorporating prior information into differential network analysis using non‐paranormal graphical models

Hong Yan, Xiao-Fei Zhang, Le Ou-Yang, 2017, Bioinform..

Inferring Gene Network Rewiring by Combining Gene Expression and Gene Mutation Data

Xiaohua Hu, Xiao-Fei Zhang, Le Ou-Yang, 2019, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

scTSSR2: Imputing Dropout Events for Single-Cell RNA Sequencing Using Fast Two-Side Self-Representation

Le Ou-Yang, Xiao-Fei Zhang, Hong Yan, 2022, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Structured Sparse Error Coding for Face Recognition With Occlusion

Dao-Qing Dai, Chuan-Xian Ren, Xiao-Fei Zhang, 2013, IEEE Transactions on Image Processing.

EC-PGMGR: Ensemble Clustering Based on Probability Graphical Model With Graph Regularization for Single-Cell RNA-seq Data

Le Ou-Yang, Ming Yi, Yuan Zhu, 2020, Frontiers in Genetics.

Differential network analysis by simultaneously considering changes in gene interactions and gene expression

Le Ou-Yang, Hong Qin, Jia-Juan Tu, 2021, Bioinform..

Inferring cancer common and specific gene networks via multi-layer joint graphical model

Le Ou-Yang, Xiao-Fei Zhang, Ou-Yang Le, 2023, Computational and structural biotechnology journal.

Protein complex detection based on partially shared multi-view clustering

D. Dai, Yuan Zhu, Meng-Yun Wu, 2016, BMC Bioinformatics.

A Framework for Incorporating Functional Interrelationships into Protein Function Prediction Algorithms

D. Dai, Xiao-Fei Zhang, 2012, IEEE/ACM Transactions on Computational Biology & Bioinformatics.

Differential Network Analysis via Weighted Fused Conditional Gaussian Graphical Model

Hong Yan, Xiao-Fei Zhang, Le Ou-Yang, 2020, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Node-based differential network analysis in genomics

Hong Yan, Xiao-Fei Zhang, Le Ou-Yang, 2017, Comput. Biol. Chem..

LncRNA-Disease Association Prediction Using Two-Side Sparse Self-Representation

Yiwen Sun, Zexuan Zhu, Le Ou-Yang, 2019, Front. Genet..

Comparative analysis of housekeeping and tissue-specific driver nodes in human protein interaction networks

D. Dai, Hong Yan, Yuan Zhu, 2016, BMC Bioinformatics.

Joint Learning of Multiple Differential Networks With Latent Variables

Hong Yan, Xing-Ming Zhao, Fu Lee Wang, 2019, IEEE Transactions on Cybernetics.

Detecting overlapping protein complexes based on a generative model with functional and topological properties : Additional file 1

D. Dai, Xiao-Fei Zhang, Ou-Yang Le, 2014 .

NJGCG: A node-based joint Gaussian copula graphical model for gene networks inference across multiple states

Xiao-Fei Zhang, Ou-Yang Le, Yun Huang, 2024, Computational and structural biotechnology journal.