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Probe Efficient Feature Representation of Gapped K-mer Frequency Vectors from Sequences Using Deep Neural Networks 期刊论文
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 2020, 卷号: 17, 期号: 2, 页码: 657-667
Authors:  Cao, Zhen;  Zhang, Shihua
Favorite  |  View/Download:6/0  |  Submit date:2020/05/24
DNA  Bioinformatics  Kernel  Feature extraction  Support vector machines  Genomics  Task analysis  Bioinformatics  machine learning  gapped k-mer  deep neural network  transcription factor binding site prediction  
Comparison of Computational Methods for Imputing Single-Cell RNA-Sequencing Data 期刊论文
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 2020, 卷号: 17, 期号: 2, 页码: 376-389
Authors:  Zhang, Lihua;  Zhang, Shihua
Favorite  |  View/Download:6/0  |  Submit date:2020/05/24
Gene expression  Sequential analysis  Bioinformatics  RNA  Matrix converters  Computational biology  Bayes methods  Single-cell RNA-sequencing technique  dropout event  imputation  algorithm  bioinformatics  
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
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)