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Circular Trajectory Reconstruction Uncovers Cell-Cycle Progression and Regulatory Dynamics from Single-Cell Hi-C Maps 期刊论文
ADVANCED SCIENCE, 2019, 页码: 13
Authors:  Ye, Yusen;  Gao, Lin;  Zhang, Shihua
Favorite  |  View/Download:23/0  |  Submit date:2020/01/10
cell cycle  chromosomal architectures  circular trajectory  dynamic structures  single-cell Hi-C maps  
Learning common and specific patterns from data of multiple interrelated biological scenarios with matrix factorization 期刊论文
NUCLEIC ACIDS RESEARCH, 2019, 卷号: 47, 期号: 13, 页码: 6606-6617
Authors:  Zhang, Lihua;  Zhang, Shihua
Favorite  |  View/Download:17/0  |  Submit date:2020/01/10
MSTD: an efficient method for detecting multi-scale topological domains from symmetric and asymmetric 3D genomic maps 期刊论文
NUCLEIC ACIDS RESEARCH, 2019, 卷号: 47, 期号: 11, 页码: 11
Authors:  Ye, Yusen;  Gao, Lin;  Zhang, Shihua
Favorite  |  View/Download:15/0  |  Submit date:2020/01/10
Simple tricks of convolutional neural network architectures improve DNA-protein binding prediction 期刊论文
BIOINFORMATICS, 2019, 卷号: 35, 期号: 11, 页码: 1837-1843
Authors:  Cao, Zhen;  Zhang, Shihua
Favorite  |  View/Download:15/0  |  Submit date:2020/01/10
Brief Survey of Biological Network Alignment and a Variant with Incorporation of Functional Annotations 期刊论文
CURRENT BIOINFORMATICS, 2019, 卷号: 14, 期号: 1, 页码: 4-10
Authors:  Jing, Fang;  Zhang, Shao-Wu;  Zhang, Shihua
Favorite  |  View/Download:19/0  |  Submit date:2019/04/02
Biological network  network alignment  gene ontology  alignment graph  optimization  
Reveal cell type-specific regulatory elements and their characterized histone code classes via a hidden Markov model 期刊论文
BMC GENOMICS, 2018, 卷号: 19, 页码: 13
Authors:  Wang, Can;  Zhang, Shihua
Favorite  |  View/Download:20/0  |  Submit date:2019/01/11
Epigenomics  Cell type-specific regulatory elements  Hidden Markov model  Histone modification  
Edge-group sparse PCA for network-guided high dimensional data analysis 期刊论文
BIOINFORMATICS, 2018, 卷号: 34, 期号: 20, 页码: 3479-3487
Authors:  Min, Wenwen;  Liu, Juan;  Zhang, Shihua
Favorite  |  View/Download:20/0  |  Submit date:2019/01/11
Omics tools for the needle out of haystack? 期刊论文
JOURNAL OF GENETICS AND GENOMICS, 2018, 卷号: 45, 期号: 7, 页码: 343-344
Authors:  Cao, Zhiwei;  Wang, Xiu-Jie;  Zhang, Shihua
Favorite  |  View/Download:19/0  |  Submit date:2018/10/07
Matrix Integrative Analysis (MIA) of Multiple Genomic Data for Modular Patterns 期刊论文
FRONTIERS IN GENETICS, 2018, 卷号: 9, 页码: 12
Authors:  Chen, Jinyu;  Zhang, Shihua
Favorite  |  View/Download:20/0  |  Submit date:2018/07/30
bioinformatics  multi-dimensional genomics  matrix integrative analysis  data integration  module discovery  non-negative matrix factorization (NMF)  partial least squares (PLS)  
Network-Regularized Sparse Logistic Regression Models for Clinical Risk Prediction and Biomarker Discovery 期刊论文
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 2018, 卷号: 15, 期号: 3, 页码: 944-953
Authors:  Min, Wenwen;  Liu, Juan;  Zhang, Shihua
Favorite  |  View/Download:23/0  |  Submit date:2018/07/30
Sparse logistic regression  network-regularized penalty  survival risk prediction  feature selection