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Identification of Biomarker in Brain-specific Gene Regulatory Network Using Structural Controllability Analysis [PDF]

Frontiers in Bioinformatics, 2022
Brain tumor research has been stapled for human health while brain network research is crucial for us to understand brain activity. Here the structural controllability theory is applied to study three human brain-specific gene regulatory networks ...
Zhihua Chen, Siyuan Chen, Xiaoli Qiang
doaj   +2 more sources

Approaches for Benchmarking Single-Cell Gene Regulatory Network Methods [PDF]

Bioinformatics and Biology Insights
Gene regulatory networks are powerful tools for modeling genetic interactions that control the expression of genes driving cell differentiation, and single-cell sequencing offers a unique opportunity to build these networks with high-resolution genomic ...
Karamveer, Yasin Uzun
doaj   +2 more sources

Survey of Research on Non-homogeneous Gene Regulatory Network Models [PDF]

Jisuanji kexue yu tansuo, 2023
In the field of bioinformatics, the construction of gene regulatory networks is crucial. In recent years, non-homogeneous dynamic Bayesian networks have become a common modeling tool for learning gene regulatory networks from gene expression time-series ...
ZHANG Qianqian, HU Chunling, ZHANG Jiayao, LI Dawei, SHAO Mingyi
doaj   +1 more source

Gat2Get: A Novel Approach to Infer Gene Regulatory Network from Gene Activity using Dynamic Bayesian Network learning [PDF]

Port Said Engineering Research Journal, 2023
Discovering Gene Regulatory Network (GRN) gives some idea about gene pathways and helps many potential applications in medicine. The essential source of data for this task is the gene expression data.
safaa saleh, Iman Alnsari, Waleed Ead, Hattem Khatter   +3 more
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A gene regulatory network for neural induction

eLife, 2023
During early vertebrate development, signals from a special region of the embryo, the organizer, can redirect the fate of non-neural ectoderm cells to form a complete, patterned nervous system.
Katherine E Trevers, Hui-Chun Lu, Youwen Yang, Alexandre P Thiery, Anna C Strobl, Claire Anderson, Božena Pálinkášová, Nidia MM de Oliveira, Irene M de Almeida, Mohsin AF Khan, Natalia Moncaut, Nicholas M Luscombe, Leslie Dale, Andrea Streit, Claudio D Stern   +14 more
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Network Inference from Gene Expression Data with Distance Correlation and Network Topology Centrality

Algorithms, 2021
The reconstruction of gene regulatory networks based on gene expression data can effectively uncover regulatory relationships between genes and provide a deeper understanding of biological control processes.
Kuan Liu, Haiyuan Liu, Dongyan Sun, Lei Zhang   +3 more
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Construction and Clarification of Dynamic Gene Regulatory Network of Cancer Cell Cycle via Microarray Data

Cancer Informatics, 2006
Background Cell cycle is an important clue to unravel the mechanism of cancer cells. Recently, expression profiles of cDNA microarray data of Cancer cell cycle are available for the information of dynamic interactions among Cancer cell cycle related ...
Cheng-Wei Li, Yung-Hsiang Chu, Bor-Sen Chen   +2 more
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Inferring gene dependency network specific to phenotypic alteration based on gene expression data and clinical information of breast cancer. [PDF]

PLoS ONE, 2014
Although many methods have been proposed to reconstruct gene regulatory network, most of them, when applied in the sample-based data, can not reveal the gene regulatory relations underlying the phenotypic change (e.g. normal versus cancer). In this paper,
Xionghui Zhou, Juan Liu
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Comprehensive information-based differential gene regulatory networks analysis (CIdrgn): Application to gastric cancer and chemotherapy-responsive gene network identification.

PLoS ONE, 2023
Biological condition-responsive gene network analysis has attracted considerable research attention because of its ability to identify pathways or gene modules involved in the underlying mechanisms of diseases.
Heewon Park, Seiya Imoto, Satoru Miyano
doaj   +2 more sources

Reconstructing genome-wide regulatory network of E. coli using transcriptome data and predicted transcription factor activities

BMC Bioinformatics, 2011
Background Gene regulatory networks play essential roles in living organisms to control growth, keep internal metabolism running and respond to external environmental changes.
Dickerson Julie A, Jarboe Laura R, Fu Yao   +2 more
doaj   +1 more source