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Journal Articles
- 2023
[j42]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)- [j41]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) - [j40]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): 1445-1456 (2023) - 2022
- [j39]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) - [j38]Ke Jin, Bo Li, Hong Yan, Xiao-Fei Zhang:
Imputing dropouts for single-cell RNA sequencing based on multi-objective optimization. Bioinform. 38(12): 3222-3230 (2022) - [j37]Yuting 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): 513-521 (2022) - [j36]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): 2894-2906 (2022) - 2021
- [j35]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) - [j34]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): 4414-4423 (2021) - [j33]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): 1632-1642 (2021) - [j32]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): 2781-2787 (2021) - [j31]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): 1043-1055 (2021) - 2020
- [j30]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): 2755-2762 (2020) - [j29]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): 3131-3138 (2020) - [j28]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): 3474-3481 (2020) - [j27]Le Ou-Yang, Xiao-Fei Zhang, Hong Yan:
Sparse regularized low-rank tensor regression with applications in genomic data analysis. Pattern Recognit. 107: 107516 (2020) - [j26]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): 712-718 (2020) - [j25]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): 2162-2169 (2020) - 2019
- [j24]Xiao-Fei Zhang, Le Ou-Yang, Shuo Yang, Xiaohua Hu, Hong Yan:
DiffNetFDR: differential network analysis with false discovery rate control. Bioinform. 35(17): 3184-3186 (2019) - [j23]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): 4827-4829 (2019) - [j22]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): 1042-1048 (2019) - [j21]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): 3494-3506 (2019) - 2018
- [j20]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): 1571-1573 (2018) - [j19]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): 2079-2085 (2018) - 2017
- [j18]Xiao-Fei Zhang, Le Ou-Yang, Hong Yan:
Incorporating prior information into differential network analysis using non-paranormal graphical models. Bioinform. 33(16): 2436-2445 (2017) - [j17]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): 23-34 (2017) - [j16]Xiao-Fei Zhang, Le Ou-Yang, Hong Yan:
Node-based differential network analysis in genomics. Comput. Biol. Chem. 69: 194-201 (2017) - [j15]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: 239-250 (2017) - 2016
- [j14]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: 100 (2016) - [j13]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: 108 (2016) - [j12]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: 358 (2016) - [j11]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: 371 (2016) - 2015
- [j10]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: 146:1-146:13 (2015) - [j9]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): 1333-1344 (2015) - 2014
- [j8]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: 186 (2014) - [j7]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: 335 (2014) - [j6]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): 965-975 (2014) - 2013
- [j5]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): 219-225 (2013) - [j4]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): 1889-1900 (2013) - 2012
- [j3]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): 740-753 (2012) - [j2]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): 857-870 (2012) - [j1]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): 1649-1662 (2012)
Conference and Workshop Papers
- 2016
- [c2]Le Ou-Yang, Hong Yan, Xiao-Fei Zhang:
Identifying protein complexes via multi-network clustering. BIBM 2016: 645-650 - 2011
- [c1]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: 293-297
Coauthor Index
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