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中国科学院数学与系统科学研究院机构知识库
KMS Of Academy of mathematics and systems sciences, CAS
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Identifying phenotype-associated subpopulations by integrating bulk and single-cell sequencing data
期刊论文
NATURE BIOTECHNOLOGY, 2021, 页码: 18
Authors:
Sun, Duanchen
;
Guan, Xiangnan
;
Moran, Amy E.
;
Wu, Ling-Yun
;
Qian, David Z.
;
Schedin, Pepper
;
Dai, Mu-Shui
;
Danilov, Alexey, V
;
Alumkal, Joshi J.
;
Adey, Andrew C.
;
Spellman, Paul T.
;
Xia, Zheng
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View/Download:18/0
  |  
Submit date:2022/04/02
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
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View/Download:39/0
  |  
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
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View/Download:26/0
  |  
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
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View/Download:46/0
  |  
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
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View/Download:65/0
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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
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View/Download:74/0
  |  
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
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View/Download:75/0
  |  
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
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View/Download:68/0
  |  
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
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View/Download:73/0
  |  
Submit date:2019/12/13
coupled clustering
NMF
single-cell genomic data