Xiao-Fei Zhang

Publication Activity (10 Years)

Years Active: 2011-2023
Publications (10 Years): 33

Top Topics

Ensemble Learning

Network Analysis

Protein Interaction

Gene Expression

Top Venues

IEEE ACM Trans. Comput. Biol. Bioinform.

IEEE Trans. Cybern.

Publications

Jia-Juan Tu, Hui-Sheng Li, Hong Yan, Xiao-Fei Zhang
EnDecon: cell type deconvolution of spatially resolved transcriptomics data via ensemble learning. Bioinform. 39 (1) (2023)
Bo Li, Ke Jin, Le Ou-Yang, Hong Yan, Xiao-Fei Zhang
scTSSR2: Imputing Dropout Events for Single-Cell RNA Sequencing Using Fast Two-Side Self-Representation. IEEE ACM Trans. Comput. Biol. Bioinform. 20 (2) (2023)
Yi-Xuan Xiong, Meng-Guo Wang, Luonan Chen, Xiao-Fei Zhang
Cell-type annotation with accurate unseen cell-type identification using multiple references. PLoS Comput. Biol. 19 (6) (2023)
Hui-Sheng Li, Le Ou-Yang, Yuan Zhu, Hong Yan, Xiao-Fei Zhang
scDEA: differential expression analysis in single-cell RNA-sequencing data via ensemble learning. Briefings Bioinform. 23 (1) (2022)
Yu-Ting Tan, Le Ou-Yang, Xingpeng Jiang, Hong Yan, Xiao-Fei Zhang
Identifying Gene Network Rewiring Based on Partial Correlation. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (1) (2022)
Ke Jin, Bo Li, Hong Yan, Xiao-Fei Zhang
Imputing dropouts for single-cell RNA sequencing based on multi-objective optimization. Bioinform. 38 (12) (2022)
Meng-Guo Wang, Le Ou-Yang, Hong Yan, Xiao-Fei Zhang
Inferring Gene Co-Expression Networks by Incorporating Prior Protein-Protein Interaction Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (5) (2022)
Ting Xu, Le Ou-Yang, Hong Yan, Xiao-Fei Zhang
Time-Varying Differential Network Analysis for Revealing Network Rewiring over Cancer Progression. IEEE ACM Trans. Comput. Biol. Bioinform. 18 (4) (2021)
Jia-Juan Tu, Le Ou-Yang, Yuan Zhu, Hong Yan, Hong Qin, Xiao-Fei Zhang
Differential network analysis by simultaneously considering changes in gene interactions and gene expression. Bioinform. 37 (23) (2021)
Fan Lu, Yilong Lin, Chongbin Yuan, Xiao-Fei Zhang, Le Ou-Yang
EnTSSR: A Weighted Ensemble Learning Method to Impute Single-Cell RNA Sequencing Data. IEEE ACM Trans. Comput. Biol. Bioinform. 18 (6) (2021)
Xiao-Fei Zhang, Le Ou-Yang, Ting Yan, Xiaohua Tony Hu, Hong Yan
A Joint Graphical Model for Inferring Gene Networks Across Multiple Subpopulations and Data Types. IEEE Trans. Cybern. 51 (2) (2021)
Le Ou-Yang, Dehan Cai, Xiao-Fei Zhang, Hong Yan
WDNE: an integrative graphical model for inferring differential networks from multi-platform gene expression data with missing values. Briefings Bioinform. 22 (6) (2021)
Le Ou-Yang, Xiao-Fei Zhang, Xiaohua Hu, Hong Yan
Differential Network Analysis via Weighted Fused Conditional Gaussian Graphical Model. IEEE ACM Trans. Comput. Biol. Bioinform. 17 (6) (2020)
Ke Jin, Le Ou-Yang, Xing-Ming Zhao, Hong Yan, Xiao-Fei Zhang
scTSSR: gene expression recovery for single-cell RNA sequencing using two-side sparse self-representation. Bioinform. 36 (10) (2020)
Zi-Chao Zhang, Xiao-Fei Zhang, Min Wu, Le Ou-Yang, Xing-Ming Zhao, Xiaoli Li
A graph regularized generalized matrix factorization model for predicting links in biomedical bipartite networks. Bioinform. 36 (11) (2020)
Le Ou-Yang, Xiao-Fei Zhang, Hong Yan
Sparse regularized low-rank tensor regression with applications in genomic data analysis. Pattern Recognit. 107 (2020)
Rui Yuan, Le Ou-Yang, Xiaohua Hu, Xiao-Fei Zhang
Identifying Gene Network Rewiring Using Robust Differential Graphical Model with Multivariate $t$t-Distribution. IEEE ACM Trans. Comput. Biol. Bioinform. 17 (2) (2020)
Jia-Juan Tu, Le Ou-Yang, Hong Yan, Xiao-Fei Zhang, Hong Qin
Joint reconstruction of multiple gene networks by simultaneously capturing inter-tumor and intra-tumor heterogeneity. Bioinform. 36 (9) (2020)
Xiao-Fei Zhang, Le Ou-Yang, Shuo Yang, Xiaohua Hu, Hong Yan
DiffNetFDR: differential network analysis with false discovery rate control. Bioinform. 35 (17) (2019)
Xiao-Fei Zhang, Le Ou-Yang, Shuo Yang, Xing-Ming Zhao, Xiaohua Hu, Hong Yan
EnImpute: imputing dropout events in single-cell RNA-sequencing data via ensemble learning. Bioinform. 35 (22) (2019)
Jia-Juan Tu, Le Ou-Yang, Xiaohua Hu, Xiao-Fei Zhang
Inferring Gene Network Rewiring by Combining Gene Expression and Gene Mutation Data. IEEE ACM Trans. Comput. Biol. Bioinform. 16 (3) (2019)
Le Ou-Yang, Xiao-Fei Zhang, Xing-Ming Zhao, Debby Dan Wang, Fu Lee Wang, Baiying Lei, Hong Yan
Joint Learning of Multiple Differential Networks With Latent Variables. IEEE Trans. Cybern. 49 (9) (2019)
Xiao-Fei Zhang, Le Ou-Yang, Shuo Yang, Xiaohua Hu, Hong Yan
DiffGraph: an R package for identifying gene network rewiring using differential graphical models. Bioinform. 34 (9) (2018)
Ting Xu, Le Ou-Yang, Xiaohua Hu, Xiao-Fei Zhang
Identifying Gene Network Rewiring by Integrating Gene Expression and Gene Network Data. IEEE ACM Trans. Comput. Biol. Bioinform. 15 (6) (2018)
Xiao-Fei Zhang, Le Ou-Yang, Hong Yan
Node-based differential network analysis in genomics. Comput. Biol. Chem. 69 (2017)
Le Ou-Yang, Hong Yan, Xiao-Fei Zhang
A multi-network clustering method for detecting protein complexes from multiple heterogeneous networks. BMC Bioinform. 18 (S-13) (2017)
Xiao-Fei Zhang, Le Ou-Yang, Hong Yan
Incorporating prior information into differential network analysis using non-paranormal graphical models. Bioinform. 33 (16) (2017)
Chao-Qing Dai, Xiao-Fei Zhang, Yan Fan, Liang Chen
Localized modes of the (n+1)-dimensional Schrödinger equation with power-law nonlinearities in PT-symmetric potentials. Commun. Nonlinear Sci. Numer. Simul. 43 (2017)
Le Ou-Yang, Min Wu, Xiao-Fei Zhang, Dao-Qing Dai, Xiaoli Li, Hong Yan
A two-layer integration framework for protein complex detection. BMC Bioinform. 17 (2016)
Meng-Yun Wu, Xiao-Fei Zhang, Dao-Qing Dai, Le Ou-Yang, Yuan Zhu, Hong Yan
Regularized logistic regression with network-based pairwise interaction for biomarker identification in breast cancer. BMC Bioinform. 17 (2016)
Xiao-Fei Zhang, Le Ou-Yang, Dao-Qing Dai, Meng-Yun Wu, Yuan Zhu, Hong Yan
Comparative analysis of housekeeping and tissue-specific driver nodes in human protein interaction networks. BMC Bioinform. 17 (2016)
Le Ou-Yang, Hong Yan, Xiao-Fei Zhang
Identifying protein complexes via multi-network clustering. BIBM (2016)
Le Ou-Yang, Xiao-Fei Zhang, Dao-Qing Dai, Meng-Yun Wu, Yuan Zhu, Zhiyong Liu, Hong Yan
Protein complex detection based on partially shared multi-view clustering. BMC Bioinform. 17 (2016)
Le Ou-Yang, Dao-Qing Dai, Xiao-Fei Zhang
Detecting Protein Complexes from Signed Protein-Protein Interaction Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 12 (6) (2015)
Xiao-Fei Zhang, Le Ou-Yang, Yuan Zhu, Meng-Yun Wu, Dao-Qing Dai
Determining minimum set of driver nodes in protein-protein interaction networks. BMC Bioinform. 16 (2015)
Le Ou-Yang, Dao-Qing Dai, Xiaoli Li, Min Wu, Xiao-Fei Zhang, Peng Yang
Detecting temporal protein complexes from dynamic protein-protein interaction networks. BMC Bioinform. 15 (2014)
Xiao-Fei Zhang, Dao-Qing Dai, Le Ou-Yang, Hong Yan
Detecting overlapping protein complexes based on a generative model with functional and topological properties. BMC Bioinform. 15 (2014)
Xiaoli Li, Xiao-Fei Zhang, Chao Jia, De-Xin Liu
Multi-model adaptive control based on fuzzy neural networks. J. Intell. Fuzzy Syst. 27 (2) (2014)
Yuan Zhu, Xiao-Fei Zhang, Dao-Qing Dai, Meng-Yun Wu
Identifying Spurious Interactions and Predicting Missing Interactions in the Protein-Protein Interaction Networks via a Generative Network Model. IEEE ACM Trans. Comput. Biol. Bioinform. 10 (1) (2013)
Xiao-Xin Li, Dao-Qing Dai, Xiao-Fei Zhang, Chuan-Xian Ren
Structured Sparse Error Coding for Face Recognition With Occlusion. IEEE Trans. Image Process. 22 (5) (2013)
Xiao-Fei Zhang, Dao-Qing Dai
A Framework for Incorporating Functional Interrelationships into Protein Function Prediction Algorithms. IEEE ACM Trans. Comput. Biol. Bioinform. 9 (3) (2012)
Xiao-Fei Zhang, Dao-Qing Dai, Xiao-Xin Li
Protein Complexes Discovery Based on Protein-Protein Interaction Data via a Regularized Sparse Generative Network Model. IEEE ACM Trans. Comput. Biol. Bioinform. 9 (3) (2012)
Meng-Yun Wu, Dao-Qing Dai, Yu Shi, Hong Yan, Xiao-Fei Zhang
Biomarker Identification and Cancer Classification Based on Microarray Data Using Laplace Naive Bayes Model with Mean Shrinkage. IEEE ACM Trans. Comput. Biol. Bioinform. 9 (6) (2012)
Xiao-Xin Li, Dao-Qing Dai, Xiao-Fei Zhang, Chuan-Xian Ren
Face recognition with continuous occlusion using partially iteratively reweighted sparse coding. ACPR (2011)