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Identification of TAZ as the essential molecular switch in orchestrating SCLC phenotypic transition and metastasis 期刊论文
NATIONAL SCIENCE REVIEW, 2022, 卷号: 9, 期号: 7, 页码: 15
Authors:  Jin, Yujuan;  Zhao, Qiqi;  Zhu, Weikang;  Feng, Yan;  Xiao, Tian;  Zhang, Peng;  Jiang, Liyan;  Hou, Yingyong;  Guo, Chenchen;  Huang, Hsinyi;  Chen, Yabin;  Tong, Xinyuan;  Cao, Jiayu;  Li, Fei;  Zhu, Xueliang;  Qin, Jun;  Gao, Dong;  Liu, Xin-Yuan;  Zhang, Hua;  Chen, Luonan;  Thomas, Roman K.;  Wong, Kwok-Kin;  Zhang, Lei;  Wang, Yong;  Hu, Liang;  Ji, Hongbin
Favorite  |  View/Download:123/0  |  Submit date:2023/02/07
small cell lung cancer  SWI  SNF complex  TAZ  phenotypic transition  metastasis  
Deciphering the Spatial Modular Patterns of Tissues by Integrating Spatial and Single-Cell Transcriptomic Data 期刊论文
JOURNAL OF COMPUTATIONAL BIOLOGY, 2022, 页码: 14
Authors:  Shan, Xu;  Chen, Jinyu;  Dong, Kangning;  Zhou, Wei;  Zhang, Shihua
Favorite  |  View/Download:104/0  |  Submit date:2023/02/07
data integration  single-cell transcriptomics  spatial modular patterns  spatial transcriptomics  
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:170/0  |  Submit date:2022/06/21
hDirect-MAP: projection-free single-cell modeling of response to checkpoint immunotherapy 期刊论文
BRIEFINGS IN BIOINFORMATICS, 2022, 卷号: 23, 期号: 2, 页码: 16
Authors:  Lu, Yong;  Xue, Gang;  Zheng, Ningbo;  Han, Kun;  Yang, Wenzhong;  Wang, Rui-Sheng;  Wu, Lingyun;  Miller, Lance D.;  Pardee, Timothy;  Triozzi, Pierre L.;  Lo, Hui-Wen;  Watabe, Kounosuke;  Wong, Stephen T. C.;  Pasche, Boris C.;  Zhang, Wei;  Jin, Guangxu
Favorite  |  View/Download:160/0  |  Submit date:2023/02/07
single-cell RNA sequencing (scRNA-seq)  single-cell mass cytometry (CyTOF)  Pareto optimization  projection-free single-cell modeling  response to immune checkpoint blockade  
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:175/0  |  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
Favorite  |  View/Download:143/0  |  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:148/0  |  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:212/0  |  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:185/0  |  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:215/0  |  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