scholarly journals Inference of gene regulatory networks from genome-wide knockout fitness data

2012 ◽  
Vol 29 (3) ◽  
pp. 338-346 ◽  
Author(s):  
L. Wang ◽  
X. Wang ◽  
A. P. Arkin ◽  
M. S. Samoilov
Keyword(s):  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Genome Wide ◽  
Gene Regulatory

Genome-wide RNA structure changes during human neurogenesis modulate gene regulatory networks

2021 ◽  
Author(s):  
Jiaxu Wang ◽  
Tong Zhang ◽  
Zhang Yu ◽  
Wen Ting Tan ◽  
Ming Wen ◽  
...  
Keyword(s):  
Gene Regulatory Networks ◽  
Rna Structure ◽  
Regulatory Networks ◽  
Structure Changes ◽  
Genome Wide ◽  
Gene Regulatory

scholarly journals Genome-wide RNAi screen for genes regulating glycolytic response to vemurafenib in BRAFV600 melanoma cells

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Lorey K. Smith ◽  
Tiffany Parmenter ◽  
Cathryn M. Gould ◽  
Piyush B. Madhamshettiwar ◽  
Karen E. Sheppard ◽  
...  
Keyword(s):  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Metabolic Response ◽  
Braf Inhibitor ◽  
Melanoma Cells ◽  
Genome Wide ◽  
Braf Inhibition ◽  
Mediate Response ◽  
Melanoma Patients ◽  
Gene Regulatory

Abstract Identification of mechanisms underlying sensitivity and response to targeted therapies, such as the BRAF inhibitor vemurafenib, is critical in order to improve efficacy of these therapies in the clinic and delay onset of resistance. Glycolysis has emerged as a key feature of the BRAF inhibitor response in melanoma cells, and importantly, the metabolic response to vemurafenib in melanoma patients can predict patient outcome. Here, we present a multiparameter genome-wide siRNA screening dataset of genes that when depleted improve the viability and glycolytic response to vemurafenib in BRAFV600 mutated melanoma cells. These datasets are suitable for analysis of genes involved in cell viability and glycolysis in steady state conditions and following treatment with vemurafenib, as well as computational approaches to identify gene regulatory networks that mediate response to BRAF inhibition in melanoma.

Condensing Biochemistry into Gene Regulatory Networks

2014 ◽  
Vol 4 (3) ◽  
pp. 1-25
Author(s):  
Alberto de la Fuente
Keyword(s):  
Gene Regulation ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Network Models ◽  
Transcriptional Regulatory Networks ◽  
Modern Biology ◽  
Genome Wide ◽  
Transcriptional Regulatory ◽  
Biochemical Systems ◽  
Gene Regulatory

Gene Regulatory Networks are models of gene regulation. Inferring such model from genome-wide gene-expression measurements is one of the key challenges in modern biology, and a large number of algorithms have been proposed for this task. As there is still much confusion in the current literature as to what precisely Gene Regulatory Networks are, it is important to provide a definition that is as unambiguous as possible. In this paper the author provides such a definition and explain what Gene Regulatory Networks are in terms of the underlying biochemical processes. The author will use a linear approximation to the in general non-linear kinetics underlying interactions in biochemical systems and show how a biochemical system can be ‘condensed' into a more compact description, i.e. Gene Regulatory Networks. Important differences between the defined Gene Regulatory Networks and other network models for gene regulation, i.e. Transcriptional Regulatory Networks and Co-Expression Networks, are also discussed.

scholarly journals Gene regulatory networks in neural cell fate acquisition from genome-wide chromatin association of Geminin and Zic1

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Savita Sankar ◽  
Dhananjay Yellajoshyula ◽  
Bo Zhang ◽  
Bryan Teets ◽  
Nicole Rockweiler ◽  
...  
Keyword(s):  
Cell Fate ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Neural Cell ◽  
Genome Wide ◽  
Gene Regulatory ◽  
Neural Cell Fate
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