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Prediction of the transcription factor binding sites with meta-learning 期刊论文
METHODS, 2022, 卷号: 203, 页码: 207-213
作者:  Jing, Fang;  Zhang, Shao-Wu;  Zhang, Shihua
收藏  |  浏览/下载：162/0  |  提交时间：2023/02/07
Convolution neural network  Transcription factor binding sites  Meta learning  Noisy labels data  
Annotating regulatory elements by heterogeneous network embedding 期刊论文
BIOINFORMATICS, 2022, 页码: 13
作者:  Lu, Yurun;  Feng, Zhanying;  Zhang, Songmao;  Wang, Yong
收藏  |  浏览/下载：135/0  |  提交时间：2022/06/21
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：109/0  |  提交时间：2022/06/21
complex disease  disease category  functional annotation  non-coding variant  ensemble learning  
MIMIC: an optimization method to identify cell type-specific marker panel for cell sorting 期刊论文
BRIEFINGS IN BIOINFORMATICS, 2021, 卷号: 22, 期号: 6, 页码: 14
作者:  Zou, Meng;  Duren, Zhana;  Yuan, Qiuyue;  Li, Henry;  Hutchins, Andrew Paul;  Wong, Wing Hung;  Wang, Yong
收藏  |  浏览/下载：136/0  |  提交时间：2022/04/02
cell type-specific marker  TFs  surface markers  dimension reduction  hierarchical topology  
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  
Determination and estimation of optimal quarantine duration for infectious diseases with application to data analysis of COVID-19 期刊论文
BIOMETRICS, 2021, 页码: 10
作者:  Wang, Ruoyu;  Wang, Qihua
收藏  |  浏览/下载：159/0  |  提交时间：2021/04/26
incubation period  kernel estimation  maximum likelihood  optimal solution  probability constraint  statistical modeling  
3D Genome of macaque fetal brain reveals evolutionary innovations during primate corticogenesis 期刊论文
CELL, 2021, 卷号: 184, 期号: 3, 页码: 723-+
作者:  Luo, Xin;  Liu, Yuting;  Dang, Dachang;  Hu, Ting;  Hou, Yingping;  Meng, Xiaoyu;  Zhang, Fengyun;  Li, Tingting;  Wang, Can;  Li, Min;  Wu, Haixu;  Shen, Qiushuo;  Hu, Yan;  Zeng, Xuerui;  He, Xiechao;  Yan, Lanzhen;  Zhang, Shihua;  Li, Cheng;  Su, Bing
收藏  |  浏览/下载：160/0  |  提交时间：2021/06/01
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