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Annotating regulatory elements by heterogeneous network embedding 期刊论文
BIOINFORMATICS, 2022, 页码: 13
Authors:  Lu, Yurun;  Feng, Zhanying;  Zhang, Songmao;  Wang, Yong
Favorite  |  View/Download:53/0  |  Submit date:2022/06/21
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
Favorite  |  View/Download:65/0  |  Submit date:2022/04/02
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
Authors:  Shen, Qunlun;  Zhang, Shihua
Favorite  |  View/Download:47/0  |  Submit date:2022/04/02
MIMIC: an optimization method to identify cell type-specific marker panel for cell sorting 期刊论文
BRIEFINGS IN BIOINFORMATICS, 2021, 卷号: 22, 期号: 6, 页码: 14
Authors:  Zou, Meng;  Duren, Zhana;  Yuan, Qiuyue;  Li, Henry;  Hutchins, Andrew Paul;  Wong, Wing Hung;  Wang, Yong
Favorite  |  View/Download:58/0  |  Submit date:2022/04/02
cell type-specific marker  TFs  surface markers  dimension reduction  hierarchical topology  
MUREN: a robust and multi-reference approach of RNA-seq transcript normalization 期刊论文
BMC Bioinformatics, 2021, 卷号: 22, 期号: 1
Authors:  Feng,Yance;  Li,Lei M.
Favorite  |  View/Download:57/0  |  Submit date:2021/10/26
RNA-seq  Normalization  Asymmetrically regulated transcription profiles (ART)  Skewness  Mode  Multi-reference  
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:70/0  |  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:62/0  |  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:84/0  |  Submit date:2021/01/14
single-cell RNA sequencing  elastic embedding  neural networks  large-scale  stochastic optimization  parametric models  generalizable models  
Chromatin accessibility landscape and regulatory network of high-altitude hypoxia adaptation 期刊论文
NATURE COMMUNICATIONS, 2020, 卷号: 11, 期号: 1, 页码: 20
Authors:  Xin, Jingxue;  Zhang, Hui;  He, Yaoxi;  Duren, Zhana;  Bai, Caijuan;  Chen, Lang;  Luo, Xin;  Yan, Dong-Sheng;  Zhang, Chaoyu;  Zhu, Xiang;  Yuan, Qiuyue;  Feng, Zhanying;  Cui, Chaoying;  Qi, Xuebin;  Ouzhuluobu;  Wong, Wing Hung;  Wang, Yong;  Su, Bing
Favorite  |  View/Download:84/0  |  Submit date:2021/01/14
scTIM: seeking cell-type-indicative marker from single cell RNA-seq data by consensus optimization 期刊论文
BIOINFORMATICS, 2020, 卷号: 36, 期号: 8, 页码: 2474-2485
Authors:  Feng, Zhanying;  Ren, Xianwen;  Fang, Yuan;  Yin, Yining;  Huang, Chutian;  Zhao, Yimin;  Wang, Yong
Favorite  |  View/Download:102/0  |  Submit date:2020/06/30