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Joint reconstruction of cis-regulatory interaction networks across multiple tissues using single-cell chromatin accessibility data 期刊论文
BRIEFINGS IN BIOINFORMATICS, 2021, 卷号: 22, 期号: 3, 页码: 15
作者:  Dong, Kangning;  Zhang, Shihua
收藏  |  浏览/下载：115/0  |  提交时间：2022/04/02
cis-regulatory interaction networks  single-cell ATAC-seq  Gaussian graphical LASSO  
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：140/0  |  提交时间：2021/01/14
Enhancer–  promoter interactions  Cell line  Convolutional neural network  Transfer learning  Gradient reversal layer  
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
作者:  Jing,Fang;  Zhang,Shao-Wu;  Zhang,Shihua
收藏  |  浏览/下载：142/0  |  提交时间：2021/01/14
Enhancer–promoter interactions  Cell line  Convolutional neural network  Transfer learning  Gradient reversal layer  
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
作者:  Ye, Yusen;  Gao, Lin;  Zhang, Shihua
收藏  |  浏览/下载：159/0  |  提交时间：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
作者:  Jing, Fang;  Zhang, Shao-Wu;  Zhang, Shihua
收藏  |  浏览/下载：182/0  |  提交时间：2019/04/02
Biological network  network alignment  gene ontology  alignment graph  optimization  
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：250/0  |  提交时间：2018/07/30
Sparse logistic regression  network-regularized penalty  survival risk prediction  feature selection  
Integrative Analysis of Transcription Factor Combinatorial Interactions Using a Bayesian Tensor Factorization Approach 期刊论文
FRONTIERS IN GENETICS, 2017, 卷号: 8, 页码: 12
作者:  Ye, Yusen;  Gao, Lin;  Zhang, Shihua
收藏  |  浏览/下载：151/0  |  提交时间：2018/07/30
transcription regulation  TF regulatory networks  tensor factorization  integrative analysis of omics data  biological networks  
DrugE-Rank: improving drug-target interaction prediction of new candidate drugs or targets by ensemble learning to rank 期刊论文
BIOINFORMATICS, 2016, 卷号: 32, 期号: 12, 页码: 18-27
作者:  Yuan, Qingjun;  Gao, Junning;  Wu, Dongliang;  Zhang, Shihua;  Mamitsuka, Hiroshi;  Zhu, Shanfeng
收藏  |  浏览/下载：132/0  |  提交时间：2018/07/30
IIIDB: a database for isoform-isoform interactions and isoform network modules 期刊论文
BMC Genomics, 2015, 卷号: 16, 期号: Suppl 2
作者:  Tseng,Yu-Ting;  Li,Wenyuan;  Chen,Ching-Hsien;  Zhang,Shihua;  Chen,Jeremy JW;  Zhou,Xianghong Jasmine;  Liu,Chun-Chi
收藏  |  浏览/下载：141/0  |  提交时间：2018/07/30
Determining modular organization of protein interaction networks by maximizing modularity density 期刊论文
BMC SYSTEMS BIOLOGY, 2010, 卷号: 4, 页码: 12
作者:  Zhang, Shihua;  Ning, Xue-Mei;  Ding, Chris;  Zhang, Xiang-Sun
收藏  |  浏览/下载：141/0  |  提交时间：2018/07/30