论文涉及的代码及软件可以从以下网址获取：https://github.com/Zhangxf-ccnu

选择的代表作(#共同第一作者，*通讯作者)

[10] 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 in Bioinformatics, 2021, 10.1093/bib/bbab086.

[9] Zi-Chao Zhang#, Xiao-Fei Zhang#, Min Wu, Le Ou-Yang*, Xing-Ming Zhao, Xiao-Li Li, A graph regularized generalized matrix factorization model for predicting links in biomedical bipartite networks, Bioinformatics, 2020, 36(11), 3474–3481.

[8] 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, Bioinformatics, 2020, 36(10), 3131–3138.

[7] 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，Bioinformatics, 2020, 36(9), 2755–2762.

[6] Xiao-Fei Zhang, Le Ou-Yang*, Ting Yan, Xiaohua Hu, Hong Yan, A joint graphical model for inferring gene networks across multiple subpopulations and data types，IEEE Transactions on Cybernetics, 2019, DOI: 10.1109/TCYB.2019.2952711.

[5] 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, Bioinformatics, 2019, 35(22), 4827–4829.

[4] Le Ou-Yang, Xiao-Fei Zhang*, Xing-Ming Zhao, Debby D Wang, Fu Lee Wang, Baiying Lei, Hong Yan, Joint learning of multiple differential networks with latent variables, IEEE Transactions on Cybernetics, 2019, 49(9): 3494 - 3506.

[3] Xiao-Fei Zhang, Le Ou-Yang*, Shuo Yang, Xiaohua Hu, Hong Yan, DiffNetFDR: differential network analysis with false discovery rate control, Bioinformatics, 2019, 35(17), 3184–3186.

[2] 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, Bioinformatics, 2018,34(9): 1571-1573.

[1] Xiao-Fei Zhang#, Le Ou-Yang#*, Hong Yan, Incorporating prior information into differential network analysis using non-paranormal graphical models, Bioinformatics, 2017, 33(16): 2436–2445.

2021

[1] Xiao-Fei Zhang, Le Ou-Yang*, Ting Yan, Xiaohua Hu, Hong Yan, A joint graphical model for inferring gene networks across multiple subpopulations and data types，IEEE Transactions on Cybernetics, 2021, 51(2): 1043 - 1055

[2] Le Ou-Yang, Dehan Ca, Xiao-Fei Zhang*, Hong Yan, WDNE: an integrative graphical model for inferring differential networks from multi-platform gene expression data with missing values, Briefings in Bioinformatics, 2021, 10.1093/bib/bbab086.

2020年

[1] 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, Bioinformatics, 2020, 36(10), 3131–3138.

[2] 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，Bioinformatics, 2020, 36(9), 2755–2762.

[3] Zi-Chao Zhang#, Xiao-Fei Zhang#, Min Wu, Le Ou-Yang*, Xing-Ming Zhao, Xiao-Li Li, A graph regularized generalized matrix factorization model for predicting links in biomedical bipartite networks, Bioinformatics, 2020, 36(11), 3474–3481.

[4] Le Ou-Yang, Xiao-Fei Zhang*, Hong Yan, Sparse regularized low-rank tensor regression with applications in genomic data analysis, Pattern Recognition, 2020, 107, 107516.

[5] Le Ou-Yang, Xiao-Fei Zhang*, Xiaohua Hu, Hong Yan, Differential network analysis via weighted fused conditional Gaussian graphical model, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2020, 17(6): 2162 - 2169

[6] Rui Yuan, Le Ou-Yang, Xiaohua Hu, Xiao-Fei Zhang*, Identifying gene network rewiring using robust differential graphical model with multivariate t-distribution, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2020, 17(2): 712 - 718

[7] Yu-Ting Tan, Le Ou-Yang, Xingpeng Jiang, Hong Yan, Xiao-Fei Zhang*, Identifying gene network rewiring based on partial correlation, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2020, DOI: 10.1109/TCBB.2020.3002906.

2019年

[1] 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, Bioinformatics, 2019, 35(22), 4827–4829.

[2] Xiao-Fei Zhang, Le Ou-Yang*, Shuo Yang, Xiaohua Hu, Hong Yan, DiffNetFDR: Differential network analysis with false discovery rate control, Bioinformatics, 2019, 35(17), 3184–3186.

[3] Le Ou-Yang, Xiao-Fei Zhang*, Xing-Ming Zhao, Debby D Wang, Fu Lee Wang, Baiying Lei, Hong Yan, Joint learning of multiple differential networks with latent variables, IEEE Transactions on Cybernetics, 2019, 49(9): 3494 - 3506.

[4] Jia-Juan Tu, Le Ou-Yang, Xiaohua Hu, Xiao-Fei Zhang*, Identifying gene network rewiring by combining gene expression and gene mutation data, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2019, 16(3): 1042 - 1048.

[5] Nuosi Wu, Jiang Huang, Xiao-Fei Zhang, Le Ou-Yang*, Shan He, Zexuan Zhu, Weixin Xie, Weighted fused pathway graphical lasso for joint estimation of multiple gene networks, Frontiers in Genetics, 2019, 10: 623.

[6] Le Ou-Yang, Jiang Huang, Xiao-Fei Zhang, Yan-Ran Li, Yiwen Sun, Shan He, Zexuan Zhu, LncRNA-Disease Association Prediction using Two-Side Sparse Self-Representation, Frontiers in Genetics, 2019, 10: 476

[7] Ting Xu, Le Ou-Yang, Hong Yan, Xiao-Fei Zhang*, Time-varying differential network analysis for revealing network rewiring over cancer progression, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2019, DOI: 10.1109/TCBB.2019.2949039.

2018年

[1] 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, Bioinformatics, 2018,34(9): 1571-1573.

[2] Ting Xu, Le Ou-Yang, Xiaohua Hu, Xiao-Fei Zhang*, Identifying gene network rewiring by integrating gene expression and gene network data, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2018, 15(6): 2079-2085.

2017年

[1] Xiao-Fei Zhang#, Le Ou-Yang#*, Hong Yan, Incorporating prior information into differential network analysis using non-paranormal graphical models, Bioinformatics, 2017, 33(16): 2436–2445.

[2] Xiao-Fei Zhang, Le Ou-Yang*, Hong Yan, Node-based differential network analysis in genomics, Computational Biology and Chemistry, 2017, 69: 194-201.

[3] Le Ou-Yang, Hong Yan, Xiao-Fei Zhang*, A multi-network clustering method for detecting protein complexes from multiple heterogeneous networks, BMC Bioinformatics, 2017, 8(Suppl 13):46.

[4] Le Ou-Yang, Xiao-Fei Zhang*, Min Wu, Xiao-Li Li, Node-based learning of differential networks from multi-platform gene expression data, Methods, 2017, 129:41-49.

[5] Le Ou-Yang, Hong Yan, Xiao-Fei Zhang*, Identifying differential networks based on multi-platform gene expression data, Molecular Biosystems, 2017, 13(1):183~192.

2016年

[1] Xiao-Fei Zhang#, Le Ou-Yang#*, Xing-Ming Zhao, Hong Yan, Differential network analysis from cross-platform gene expression data, Scientific Reports, 2016, 6: 34112.

[2] 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 Bioinformatics, 2016, 17:371.

[3] 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 Bioinformatics, 2016, 17:358.

[4] 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 Bioinformatics, 2016, 17:108.

[5] Le Ou-Yang, Min Wu, Xiao-Fei Zhang, Dao-Qing Dai*, Xiao-Li Li*, Hong Yan, A two-layer integration framework for protein complex detection, BMC Bioinformatics, 2016.2.24, 17:100.

2015年

[1] Xiao-Fei Zhang, Le Ou-Yang, Xiaohua Hu, Dao-Qing Dai*, Identifying binary protein-protein interactions from affinity purification mass spectrometry data, BMC Genomics, 2015, 16: 745.

[2] 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 Bioinformatics, 2015, 16: 146.

[3] Le Ou-Yang, Dao-Qing Dai*, Xiao-Fei Zhang, Detecting protein complexes from signed protein-protein interaction networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2015, 12(6):1333~1344.

2014年

[1] 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 Bioinformatics, 2014, 15: 186.

[2] Le Ou-Yang, Dao-Qing Dai*, Xiao-Li Li*, Min Wu, Xiao-Fei Zhang, Peng Yang, Detecting temporal protein complexes from dynamic protein-protein interaction networks, BMC Bioinformatics, 2014, 15:335.

2013年

[1] Meng-Yun Wu, Dao-Qing Dai*, Xiao-Fei Zhang, Yuan Zhu, Cancer subtype discovery and biomarker identification via a new robust network clustering algorithm, PLos One, 2013, 8(6):e66256.

[2] Le Ou-Yang, Dao-Qing Dai*, Xiao-Fei Zhang, Protein complex detection via weighted ensemble custering based on Bayesian nonnegative matrix factorization, PLos One, 2013, 8(5):e62158.

[3] Xiao-Xin Li, Dao-Qing Dai*, Xiao-Fei Zhang, Chuan-Xian Ren, Structured sparse error coding for face recognition with occlusion, IEEE Transactions on Image Processing, 2013, 22(5):1889~1900.

[4] 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 Transactions on Computational Biology and Bioinformatics, 2013, 10(1):219~225.

2012年

[1] 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 Transactions on Computational Biology and Bioinformatics, 2012, 9(3): 857~870.

[2] Xiao-Fei Zhang, Dao-Qing Dai*, A framework for incorporating functional interrelationships into protein function prediction algorithms, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2012, 9(3): 740~753.

[3] Xiao-Fei Zhang, Dao-Qing Dai*, Le Ou-Yang, Meng-Yun Wu, Exploring overlapping functional units with various structure in protein interaction networks, Plos One, 2012.8.20, 7(8): e43092.

[4] 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 Transactions on Computational Biology and Bioinformatics, 2012, 9(6):1649~1662.