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A Novel Sparse Graph-Regularized Singular Value Decomposition Model and Its Application to Genomic Data Analysis 期刊论文
IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS, 2021, 页码: 15
作者:  Min, Wenwen;  Wan, Xiang;  Chang, Tsung-Hui;  Zhang, Shihua
收藏  |  浏览/下载：168/0  |  提交时间：2022/04/02
Gene expression  Biology  Biological system modeling  Principal component analysis  Mathematical model  Data models  Big Data  Absolute-valued graph regularization  graph regularization  sparse learning  structured sparse singular value decomposition (SVD)  
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
作者:  Zhang, Lihua;  Zhang, Shihua
收藏  |  浏览/下载：158/0  |  提交时间：2021/10/26
single-cell RNA-seq  dropout  imputation  low-rank  systems biology  
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：200/0  |  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  
Systems biology intertwines with single cell and AI 期刊论文
BMC BIOINFORMATICS, 2019, 卷号: 20, 页码: 3
作者:  Wang, Yong;  Zhang, Xiang-Sun;  Chen, Luonan
收藏  |  浏览/下载：221/0  |  提交时间：2019/10/28
Systems biology  Network  Data integration  
Integrative cancer genomics: models, algorithms and analysis 期刊论文
FRONTIERS OF COMPUTER SCIENCE, 2017, 卷号: 11, 期号: 3, 页码: 392-406
作者:  Chen, Jinyu;  Zhang, Shihua
收藏  |  浏览/下载：162/0  |  提交时间：2018/07/30
cancer genomics  model  algorithm  data integration  bioinformatics  computational biology  
The knowledge-integrated network biomarkers discovery for Major Adverse Cardiac Events 期刊论文
JOURNAL OF PROTEOME RESEARCH, 2008, 卷号: 7, 期号: 9, 页码: 4013-4021
作者:  Jin, Guangxu;  Zhou, Xiaobo;  Wang, Honghui;  Zhao, Hong;  Cui, Kemi;  Zhang, Xiang-Sun;  Chen, Luonan;  Hazen, Stanley L.;  Li, King;  Wong, Stephen T. C.
收藏  |  浏览/下载：119/0  |  提交时间：2018/07/30
proteomics  mass spectrometry  MACE  network biomarker  cross validation  systems biology  
Analysis of protein surface patterns by pocket similarity network 期刊论文
PROTEIN AND PEPTIDE LETTERS, 2008, 卷号: 15, 期号: 5, 页码: 448-455
作者:  Liu, Zhi-Ping;  Wu, Ling-Yun;  Wang, Yong;  Zhang, Xiang-Sun;  Chen, Luonan
收藏  |  浏览/下载：183/0  |  提交时间：2018/07/30
protein surface pattern  pocket similarity  complex network  functional genomics  systems biology  
Supervised inference of gene regulatory networks by linear programming 期刊论文
COMPUTATIONAL INTELLIGENCE AND BIOINFORMATICS, PT 3, PROCEEDINGS, 2006, 卷号: 4115, 页码: 551-561
作者:  Wang, Yong;  Joshi, Trupti;  Xu, Dong;  Zhang, Xiang-Sun;  Chen, Luonan
收藏  |  浏览/下载：122/0  |  提交时间：2018/07/30
systems biology  gene regulatory network  linear programming