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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
作者:  Zhang, Lihua;  Zhang, Shihua
收藏  |  浏览/下载：161/0  |  提交时间：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  
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
作者:  Wang, Can;  Zhang, Shihua
收藏  |  浏览/下载：244/0  |  提交时间：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
作者:  Min, Wenwen;  Liu, Juan;  Zhang, Shihua
收藏  |  浏览/下载：187/0  |  提交时间：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
作者:  Chen, Jinyu;  Zhang, Shihua
收藏  |  浏览/下载：175/0  |  提交时间：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
作者:  Min, Wenwen;  Liu, Juan;  Zhang, Shihua
收藏  |  浏览/下载：248/0  |  提交时间：2018/07/30
Sparse logistic regression  network-regularized penalty  survival risk prediction  feature selection  
MSIQ: JOINT MODELING OF MULTIPLE RNA-SEQ SAMPLES FOR ACCURATE ISOFORM QUANTIFICATION 期刊论文
ANNALS OF APPLIED STATISTICS, 2018, 卷号: 12, 期号: 1, 页码: 510-539
作者:  Li, Wei Vivian;  Zhao, Anqi;  Zhang, Shihua;  Li, Jingyi Jessica
收藏  |  浏览/下载：191/0  |  提交时间：2018/07/30
Isoform abundance estimation  joint inference from multiple samples  RNA sequencing  Bayesian hierarchical models  Gibbs sampling  data heterogeneity  
Comparative DNA methylation analysis to decipher common and cell type-specific patterns among multiple cell types 期刊论文
BRIEFINGS IN FUNCTIONAL GENOMICS, 2016, 卷号: 15, 期号: 6, 页码: 399-407
作者:  Yang, Xiaofei;  Shao, Xiaojian;  Gao, Lin;  Zhang, Shihua
收藏  |  浏览/下载：158/0  |  提交时间：2018/07/30
DNA methylation patterns  differentially methylation regions  comparative studies  tissue-specific methylation  cancer epigenomics  
Integrative analysis for identifying joint modular patterns of gene-expression and drug-response data 期刊论文
BIOINFORMATICS, 2016, 卷号: 32, 期号: 11, 页码: 1724-1732
作者:  Chen, Jinyu;  Zhang, Shihua
收藏  |  浏览/下载：139/0  |  提交时间：2018/07/30