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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
Authors:  Jiang, Hao;  Yi, Ming;  Zhang, Shihua
Favorite  |  View/Download:9/0  |  Submit date:2021/04/26
Single cell RNA-sequencing  Kernel non-negative matrix factorization  Cellular heterogeneity  
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
Authors:  Zhang, Lihua;  Zhang, Shihua
Favorite  |  View/Download:2/0  |  Submit date:2021/10/26
single-cell RNA-seq  dropout  imputation  low-rank  systems biology  
NeuralEE: A GPU-Accelerated Elastic Embedding Dimensionality Reduction Method for Visualizing Large-Scale scRNA-Seq Data 期刊论文
FRONTIERS IN GENETICS, 2020, 卷号: 11, 页码: 8
Authors:  Xiong, Jiankang;  Gong, Fuzhou;  Wan, Lin;  Ma, Liang
Favorite  |  View/Download:13/0  |  Submit date:2021/01/14
single-cell RNA sequencing  elastic embedding  neural networks  large-scale  stochastic optimization  parametric models  generalizable models  
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
Authors:  Zhang, Lihua;  Zhang, Shihua
Favorite  |  View/Download:36/0  |  Submit date: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  
ELF: Extract Landmark Features By Optimizing Topology Maintenance, Redundancy, and Specificity 期刊论文
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 2020, 卷号: 17, 期号: 2, 页码: 411-421
Authors:  Feng, Zhan-Ying;  Wang, Yong
Favorite  |  View/Download:43/0  |  Submit date:2020/05/24
Feature extraction  Topology  Ground penetrating radar  Geophysical measurement techniques  Redundancy  Maintenance engineering  Manganese  Feature selection  topology maintenance  optimization  single cell  
DensityPath: an algorithm to visualize and reconstruct cell state-transition path on density landscape for single-cell RNA sequencing data 期刊论文
BIOINFORMATICS, 2019, 卷号: 35, 期号: 15, 页码: 2593-2601
Authors:  Chen, Ziwei;  An, Shaokun;  Bai, Xiangqi;  Gong, Fuzhou;  Ma, Liang;  Wan, Lin
Favorite  |  View/Download:47/0  |  Submit date:2020/01/10
TSEE: an elastic embedding method to visualize the dynamic gene expression patterns of time series single-cell RNA sequencing data 期刊论文
BMC GENOMICS, 2019, 卷号: 20, 页码: 16
Authors:  An, Shaokun;  Ma, Liang;  Wan, Lin
Favorite  |  View/Download:40/0  |  Submit date:2019/10/28
Nonlinear dimensionality reduction  Elastic embedding  Visualization  Single-cell RNA sequencing  Time series  Cell fate decisions  Gene expression pattern  Oscillation  In-group proportion  
Integrative analysis of single-cell genomics data by coupled nonnegative matrix factorizations 期刊论文
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2018, 卷号: 115, 期号: 30, 页码: 7723-7728
Authors:  Duren, Zhana;  Chen, Xi;  Zamanighomi, Mahdi;  Zeng, Wanwen;  Satpathy, Ansuman T.;  Chang, Howard Y.;  Wang, Yong;  Wong, Wing Hung
Favorite  |  View/Download:56/0  |  Submit date:2019/12/13
coupled clustering  NMF  single-cell genomic data