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A Machine Learning Approach to Simulate Gene Expression and Infer Gene Regulatory Networks †

The ability to simulate gene expression and infer gene regulatory networks has vast potential applications in various fields, including medicine, agriculture, and environmental science. In recent years, machine learning approaches to simulate gene expression and infer gene regulatory networks have g...

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Detalles Bibliográficos
Autores principales: Zito, Francesco, Cutello, Vincenzo, Pavone, Mario
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10453511/
https://www.ncbi.nlm.nih.gov/pubmed/37628244
http://dx.doi.org/10.3390/e25081214
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author Zito, Francesco
Cutello, Vincenzo
Pavone, Mario
author_facet Zito, Francesco
Cutello, Vincenzo
Pavone, Mario
author_sort Zito, Francesco
collection PubMed
description The ability to simulate gene expression and infer gene regulatory networks has vast potential applications in various fields, including medicine, agriculture, and environmental science. In recent years, machine learning approaches to simulate gene expression and infer gene regulatory networks have gained significant attention as a promising area of research. By simulating gene expression, we can gain insights into the complex mechanisms that control gene expression and how they are affected by various environmental factors. This knowledge can be used to develop new treatments for genetic diseases, improve crop yields, and better understand the evolution of species. In this article, we address this issue by focusing on a novel method capable of simulating the gene expression regulation of a group of genes and their mutual interactions. Our framework enables us to simulate the regulation of gene expression in response to alterations or perturbations that can affect the expression of a gene. We use both artificial and real benchmarks to empirically evaluate the effectiveness of our methodology. Furthermore, we compare our method with existing ones to understand its advantages and disadvantages. We also present future ideas for improvement to enhance the effectiveness of our method. Overall, our approach has the potential to greatly improve the field of gene expression simulation and gene regulatory network inference, possibly leading to significant advancements in genetics.
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spelling pubmed-104535112023-08-26 A Machine Learning Approach to Simulate Gene Expression and Infer Gene Regulatory Networks † Zito, Francesco Cutello, Vincenzo Pavone, Mario Entropy (Basel) Article The ability to simulate gene expression and infer gene regulatory networks has vast potential applications in various fields, including medicine, agriculture, and environmental science. In recent years, machine learning approaches to simulate gene expression and infer gene regulatory networks have gained significant attention as a promising area of research. By simulating gene expression, we can gain insights into the complex mechanisms that control gene expression and how they are affected by various environmental factors. This knowledge can be used to develop new treatments for genetic diseases, improve crop yields, and better understand the evolution of species. In this article, we address this issue by focusing on a novel method capable of simulating the gene expression regulation of a group of genes and their mutual interactions. Our framework enables us to simulate the regulation of gene expression in response to alterations or perturbations that can affect the expression of a gene. We use both artificial and real benchmarks to empirically evaluate the effectiveness of our methodology. Furthermore, we compare our method with existing ones to understand its advantages and disadvantages. We also present future ideas for improvement to enhance the effectiveness of our method. Overall, our approach has the potential to greatly improve the field of gene expression simulation and gene regulatory network inference, possibly leading to significant advancements in genetics. MDPI 2023-08-15 /pmc/articles/PMC10453511/ /pubmed/37628244 http://dx.doi.org/10.3390/e25081214 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Zito, Francesco
Cutello, Vincenzo
Pavone, Mario
A Machine Learning Approach to Simulate Gene Expression and Infer Gene Regulatory Networks †
title A Machine Learning Approach to Simulate Gene Expression and Infer Gene Regulatory Networks †
title_full A Machine Learning Approach to Simulate Gene Expression and Infer Gene Regulatory Networks †
title_fullStr A Machine Learning Approach to Simulate Gene Expression and Infer Gene Regulatory Networks †
title_full_unstemmed A Machine Learning Approach to Simulate Gene Expression and Infer Gene Regulatory Networks †
title_short A Machine Learning Approach to Simulate Gene Expression and Infer Gene Regulatory Networks †
title_sort machine learning approach to simulate gene expression and infer gene regulatory networks †
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10453511/
https://www.ncbi.nlm.nih.gov/pubmed/37628244
http://dx.doi.org/10.3390/e25081214
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