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VP-Detector: A 3D multi-scale dense convolutional neural network for macromolecule localization and classification in cryo-electron tomograms 期刊论文
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE, 2022, 卷号: 221, 页码: 14
作者:  Hao, Yu;  Wan, Xiaohua;  Yan, Rui;  Liu, Zhiyong;  Li, Jintao;  Zhang, Shihua;  Cui, Xuefeng;  Zhang, Fa
收藏  |  浏览/下载：96/0  |  提交时间：2023/02/07
Cryo-ET  Sub-tomogram averaging  Particle localization  Particle classification  Convolutional neural networks  
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：113/0  |  提交时间：2022/04/02
cis-regulatory interaction networks  single-cell ATAC-seq  Gaussian graphical LASSO  
A kernel non-negative matrix factorization framework for single cell clustering 期刊论文
APPLIED MATHEMATICAL MODELLING, 2021, 卷号: 90, 页码: 875-888
作者:  Jiang, Hao;  Yi, Ming;  Zhang, Shihua
收藏  |  浏览/下载：124/0  |  提交时间：2021/04/26
Single cell RNA-sequencing  Kernel non-negative matrix factorization  Cellular heterogeneity  
Circular Trajectory Reconstruction Uncovers Cell-Cycle Progression and Regulatory Dynamics from Single-Cell Hi-C Maps 期刊论文
ADVANCED SCIENCE, 2019, 页码: 13
作者:  Ye, Yusen;  Gao, Lin;  Zhang, Shihua
收藏  |  浏览/下载：261/0  |  提交时间：2020/01/10
cell cycle  chromosomal architectures  circular trajectory  dynamic structures  single-cell Hi-C maps  
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：158/0  |  提交时间：2020/01/10
A fast mathematical programming procedure for simultaneous fitting of assembly components into cryoEM density maps 期刊论文
BIOINFORMATICS, 2010, 卷号: 26, 期号: 12, 页码: i261-i268
作者:  Zhang, Shihua;  Vasishtan, Daven;  Xu, Min;  Topf, Maya;  Alber, Frank
收藏  |  浏览/下载：118/0  |  提交时间：2018/07/30