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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  
Integrated profiling of human pancreatic cancer organoids reveals chromatin accessibility features associated with drug sensitivity 期刊论文
NATURE COMMUNICATIONS, 2022, 卷号: 13, 期号: 1, 页码: 16
作者:  Shi, Xiaohan;  Li, Yunguang;  Yuan, Qiuyue;  Tang, Shijie;  Guo, Shiwei;  Zhang, Yehan;  He, Juan;  Zhang, Xiaoyu;  Han, Ming;  Liu, Zhuang;  Zhu, Yiqin;  Gao, Suizhi;  Wang, Huan;  Xu, Xiongfei;  Zheng, Kailian;  Jing, Wei;  Chen, Luonan;  Wang, Yong;  Jin, Gang;  Gao, Dong
收藏  |  浏览/下载：127/0  |  提交时间：2022/06/21
Deciphering spatial domains from spatially resolved transcriptomics with an adaptive graph attention auto-encoder 期刊论文
NATURE COMMUNICATIONS, 2022, 卷号: 13, 期号: 1, 页码: 12
作者:  Dong, Kangning;  Zhang, Shihua
收藏  |  浏览/下载：99/0  |  提交时间：2022/06/21
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：136/0  |  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  
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：115/0  |  提交时间：2022/04/02
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：175/0  |  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  
Group-Sparse SVD Models via L-1- and L-0-norm Penalties and their Applications in Biological Data 期刊论文
IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING, 2021, 卷号: 33, 期号: 2, 页码: 536-550
作者:  Min, Wenwen;  Liu, Juan;  Zhang, Shihua
收藏  |  浏览/下载：152/0  |  提交时间：2021/04/26
Sparse SVD  low-rank matrix decomposition  group-sparse penalty  overlapping group-sparse penalty  coordinate descent method  alternating direction method of multipliers (ADMM)  data mining  
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  
A General Joint Matrix Factorization Framework for Data Integration and Its Systematic Algorithmic Exploration 期刊论文
IEEE TRANSACTIONS ON FUZZY SYSTEMS, 2020, 卷号: 28, 期号: 9, 页码: 1971-1983
作者:  Zhang, Lihua;  Zhang, Shihua
收藏  |  浏览/下载：144/0  |  提交时间：2021/01/14
Sparse matrices  Pattern recognition  Data integration  Prediction algorithms  Data models  Matrix decomposition  Signal processing algorithms  Bioinformatics  data integration  network-regularized constraint  nonnegative matrix factorization (NMF)  pattern recognition