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Disease category-specific annotation of variants using an ensemble learning framework 期刊论文
BRIEFINGS IN BIOINFORMATICS, 2022, 卷号: 23, 期号: 1, 页码: 15
作者:  Cao, Zhen;  Huang, Yanting;  Duan, Ran;  Jin, Peng;  Qin, Zhaohui S.;  Zhang, Shihua
收藏  |  浏览/下载：108/0  |  提交时间：2022/06/21
complex disease  disease category  functional annotation  non-coding variant  ensemble learning  
Network diffusion for scalable embedding of massive single-cell ATAC-seq data 期刊论文
SCIENCE BULLETIN, 2021, 卷号: 66, 期号: 22, 页码: 2271-2276
作者:  Dong, Kangning;  Zhang, Shihua
收藏  |  浏览/下载：113/0  |  提交时间：2022/04/02
Approximate distance correlation for selecting highly interrelated genes across datasets 期刊论文
PLOS COMPUTATIONAL BIOLOGY, 2021, 卷号: 17, 期号: 11, 页码: 18
作者:  Shen, Qunlun;  Zhang, Shihua
收藏  |  浏览/下载：114/0  |  提交时间：2022/04/02
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：111/0  |  提交时间：2022/04/02
cis-regulatory interaction networks  single-cell ATAC-seq  Gaussian graphical LASSO  
Bayesian Joint Matrix Decomposition for Data Integration with Heterogeneous Noise 期刊论文
IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE, 2021, 卷号: 43, 期号: 4, 页码: 1184-1196
作者:  Zhang, Chihao;  Zhang, Shihua
收藏  |  浏览/下载：174/0  |  提交时间：2021/04/26
Matrix decomposition  Bayes methods  Data integration  Inference algorithms  Data models  Data mining  Gaussian distribution  Bayesian methods  matrix decomposition  data integration  variational Bayesian inference  maximum a posterior  
Imputing single-cell RNA-seq data by considering cell heterogeneity and prior expression of dropouts 期刊论文
JOURNAL OF MOLECULAR CELL BIOLOGY, 2021, 卷号: 13, 期号: 1, 页码: 29-40
作者:  Zhang, Lihua;  Zhang, Shihua
收藏  |  浏览/下载：125/0  |  提交时间：2021/10/26
single-cell RNA-seq  dropout  imputation  low-rank  systems biology  
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：160/0  |  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：137/0  |  提交时间：2021/01/14
Enhancer–  promoter interactions  Cell line  Convolutional neural network  Transfer learning  Gradient reversal layer  
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：160/0  |  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  
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：179/0  |  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