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An Integrative Framework for Combining Sequence and Epigenomic Data to Predict Transcription Factor Binding Sites Using Deep Learning 期刊论文
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 2021, 卷号: 18, 期号: 1, 页码: 355-364
作者:  Jing, Fang;  Zhang, Shao-Wu;  Cao, Zhen;  Zhang, Shihua
收藏  |  浏览/下载:185/0  |  提交时间:2021/04/26
Bioinformatics  machine learning  transcription factors binding sites  convolutional neural networks  DNA accessibility  histone modification  
Prediction of enhancer-promoter interactions using the cross-cell type information and domain adversarial neural network 期刊论文
BMC BIOINFORMATICS, 2020, 卷号: 21, 期号: 1, 页码: 16
作者:  Jing, Fang;  Zhang, Shao-Wu;  Zhang, Shihua
收藏  |  浏览/下载:147/0  |  提交时间:2021/01/14
Enhancer–  promoter interactions  Cell line  Convolutional neural network  Transfer learning  Gradient reversal layer  
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
作者:  Cao, Zhen;  Zhang, Shihua
收藏  |  浏览/下载:203/0  |  提交时间: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  
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
作者:  Cao, Zhen;  Zhang, Shihua
收藏  |  浏览/下载:193/0  |  提交时间:2020/01/10
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:194/0  |  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:182/0  |  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:255/0  |  提交时间:2018/07/30
Sparse logistic regression  network-regularized penalty  survival risk prediction  feature selection  
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:147/0  |  提交时间:2018/07/30
Systematic DNA methylation analysis of multiple cell lines reveals common and specific patterns within and across tissues of origin 期刊论文
HUMAN MOLECULAR GENETICS, 2015, 卷号: 24, 期号: 15, 页码: 4374-4384
作者:  Yang, Xiaofei;  Shao, Xiaojian;  Gao, Lin;  Zhang, Shihua
收藏  |  浏览/下载:160/0  |  提交时间:2018/07/30