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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:102/0  |  提交时间:2022/06/21
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:127/0  |  提交时间:2021/04/26
Single cell RNA-sequencing  Kernel non-negative matrix factorization  Cellular heterogeneity  
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:164/0  |  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  
Large-scale determination and characterization of cell type-specific regulatory elements in the human genome 期刊论文
Journal of Molecular Cell Biology, 2017, 卷号: 9, 期号: 6, 页码: 463
作者:  Wang Can;  Zhang Shihua
收藏  |  浏览/下载:143/0  |  提交时间:2018/07/30
Local community extraction in directed networks 期刊论文
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS, 2016, 卷号: 452, 页码: 258-265
作者:  Ning, Xuemei;  Liu, Zhaoqi;  Zhang, Shihua
收藏  |  浏览/下载:135/0  |  提交时间:2018/07/30
Complex network  Community structure  Clustering  Optimization  
High-dimensional genomic data bias correction and data integration using MANCIE 期刊论文
NATURE COMMUNICATIONS, 2016, 卷号: 7, 页码: 8
作者:  Zang, Chongzhi;  Wang, Tao;  Deng, Ke;  Li, Bo;  Hu, Sheng'en;  Qin, Qian;  Xiao, Tengfei;  Zhang, Shihua;  Meyer, Clifford A.;  He, Housheng Hansen;  Brown, Myles;  Liu, Jun S.;  Xie, Yang;  Liu, X. Shirley
收藏  |  浏览/下载:159/0  |  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:142/0  |  提交时间:2018/07/30
A hybrid graph-theoretic method for mining overlapping functional modules in large sparse protein interaction networks 期刊论文
INTERNATIONAL JOURNAL OF DATA MINING AND BIOINFORMATICS, 2009, 卷号: 3, 期号: 1, 页码: 68-84
作者:  Zhang, Shihua;  Liu, Hong-Wei;  Ning, Xue-Mei;  Zhang, Xiang-Sun
收藏  |  浏览/下载:207/0  |  提交时间:2018/07/30
PPI  protein-protein interaction network  network clustering  LGT  line graph transformation  protein complexes  functional modules  data mining  bioinformatics  
Clustering complex networks and biological networks by nonnegative matrix factorization with various similarity measures 期刊论文
NEUROCOMPUTING, 2008, 卷号: 72, 期号: 1-3, 页码: 134-141
作者:  Wang, Rui-Sheng;  Zhang, Shihua;  Wang, Yong;  Zhang, Xiang-Sun;  Chen, Luonan
收藏  |  浏览/下载:135/0  |  提交时间:2018/07/30
Complex networks  Biological networks  Community structure  Nonnegative matrix factorization  Similarity measure  
Identification of overlapping community structure in complex networks using fuzzy c-means clustering 期刊论文
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS, 2007, 卷号: 374, 期号: 1, 页码: 483-490
作者:  Zhang, Shihua;  Wang, Rui-Sheng;  Zhang, Xiang-Sun
收藏  |  浏览/下载:133/0  |  提交时间:2018/07/30
overlapping community structure  modular function  spectral mapping  fuzzy c-means clustering  complex network