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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：143/0  |  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)  
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：169/0  |  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  
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
作者:  An, Shaokun;  Ma, Liang;  Wan, Lin
收藏  |  浏览/下载：208/0  |  提交时间：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  
Multi-Level Comparative Framework Based on Gene Pair-Wise Expression Across Three Insulin Target Tissues for Type 2 Diabetes 期刊论文
FRONTIERS IN GENETICS, 2019, 卷号: 10, 页码: 16
作者:  Sun, Shaoyan;  Sung, Fengnan;  Wang, Yong
收藏  |  浏览/下载：202/0  |  提交时间：2020/01/10
type 2 diabetes  gene pairwise expression  dysfunctional interactions  multi-level analysis  random walk with restart  
Discovering cooperative biomarkers for heterogeneous complex disease diagnoses 期刊论文
BRIEFINGS IN BIOINFORMATICS, 2019, 卷号: 20, 期号: 1, 页码: 89-101
作者:  Sun, Duanchen;  Ren, Xianwen;  Ari, Eszter;  Korcsmaros, Tamas;  Csermely, Peter;  Wu, Ling-Yun
收藏  |  浏览/下载：305/0  |  提交时间：2019/03/05
heterogeneous diseases  cancer biomarker  network-based  cooperative biomarker  gene expression  
Substrate concentration effect on gene expression in genetic circuits with additional positive feedback 期刊论文
SCIENCE CHINA-TECHNOLOGICAL SCIENCES, 2018, 卷号: 61, 期号: 8, 页码: 1175-1183
作者:  Wu, LuLu;  Wang, Pei;  Lu, JinHu
收藏  |  浏览/下载：156/0  |  提交时间：2018/10/07
substrate concentration  additional positive feedback loop  stochastic switch behavior  gene expression  gene differentiation  
A linear programming model based on network flow for pathway inference 期刊论文
JOURNAL OF SYSTEMS SCIENCE & COMPLEXITY, 2010, 卷号: 23, 期号: 5, 页码: 971-977
作者:  Ren, Xianwen;  Zhang, Xiang-Sun
收藏  |  浏览/下载：104/0  |  提交时间：2018/07/30
Gene expression  linear programming  network flow  pathway inference  protein interaction network  
Assessment of cell number for a multinomial distribution with application to genomic data 期刊论文
METRIKA, 2010, 卷号: 71, 期号: 2, 页码: 151-164
作者:  Li, Qizhai;  Li, Guoying;  Xiong, Shifeng
收藏  |  浏览/下载：97/0  |  提交时间：2018/07/30
Multinomial distribution  Quadratic programming  Gene expression  Expression abundance  Expression sequence tags