From Basics to Applications of Gene Regulatory Networks

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Genetics and Genomics".

Deadline for manuscript submissions: 15 June 2025 | Viewed by 471

Special Issue Editor


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Guest Editor
Platform for Single Cell Genomics and Epigenomics (PRECISE), University of Bonn and Deutsches Zentrum für Neurodegenerative Erkrankungen e.V., 53127 Bonn, Germany
Interests: computational biology; bioinformatics; innate immunity; neonate immunity; R; bulk and single-cell transcriptomics co-expression network analysis; data integration
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Special Issue Information

Dear Colleagues,

Understanding how genes are regulated within cells is crucial in the field of cell biology. Gene regulatory networks play a central role in this process, dictating when and how genes are expressed, which in turn affects cellular functions and overall development. Investigating these networks has become essential for uncovering basic biological processes and their relevance to health and disease.

We are pleased to invite you to contribute to a Special Issue delving into the depths of gene regulatory networks and their applications. This Special Issue aims to explore the complexity of gene regulatory networks and investigate their role in various biological systems. Our goal is to provide insights on the complex structure of gene regulation in order to uncover new information about how cells operate and the processes underlying disease.

The goal of this Special Issue is to showcase the latest research on gene regulatory networks and their diverse applications in the field of transcriptomics. We are looking for innovative studies and methodologies that enhance our understanding of gene regulation and its real-world applications. By featuring a wide range of contributions, we hope to encourage collaboration across different fields and inspire future research directions.

This Special Issue aims to explore key aspects of gene regulatory networks, encompassing computational methods for inferring these networks, modeling and simulation studies aimed at understanding regulatory mechanisms, and applications of gene regulatory networks in understanding disease mechanisms. Additionally, we seek contributions focusing on therapeutic targeting strategies directed towards gene regulatory networks, as well as technological advancements facilitating their study.

Dr. Thomas Ulas
Guest Editor

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Keywords

  • gene regulatory networks
  • computational methods
  • modeling and simulation
  • disease mechanisms
  • therapeutic targeting
  • transcriptomics

Published Papers (1 paper)

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Research

12 pages, 2128 KiB  
Article
Using a Combination of Novel Research Tools to Understand Social Interaction in the Drosophila melanogaster Model for Fragile X Syndrome
by Maja Stojkovic, Milan Petrovic, Maria Capovilla, Sara Milojevic, Vedrana Makevic, Dejan B. Budimirovic, Louise Corscadden, Shuhan He and Dragana Protic
Biology 2024, 13(6), 432; https://doi.org/10.3390/biology13060432 - 12 Jun 2024
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Abstract
Fragile X syndrome (FXS), the most common monogenic cause of inherited intellectual disability and autism spectrum disorder, is caused by a full mutation (>200 CGG repeats) in the Fragile X Messenger Ribonucleoprotein 1 (FMR1) gene. Individuals with FXS experience various challenges [...] Read more.
Fragile X syndrome (FXS), the most common monogenic cause of inherited intellectual disability and autism spectrum disorder, is caused by a full mutation (>200 CGG repeats) in the Fragile X Messenger Ribonucleoprotein 1 (FMR1) gene. Individuals with FXS experience various challenges related to social interaction (SI). Animal models, such as the Drosophila melanogaster model for FXS where the only ortholog of human FMR1 (dFMR1) is mutated, have played a crucial role in the understanding of FXS. The aim of this study was to investigate SI in the dFMR1B55 mutants (the groups of flies of both sexes simultaneously) using the novel Drosophila Shallow Chamber and a Python data processing pipeline based on social network analysis (SNA). In comparison with wild-type flies (w1118), SNA analysis in dFMR1B55 mutants revealed hypoactivity, fewer connections in their networks, longer interaction duration, a lower ability to transmit information efficiently, fewer alternative pathways for information transmission, a higher variability in the number of interactions they achieved, and flies tended to stay near the boundaries of the testing chamber. These observed alterations indicate the presence of characteristic strain-dependent social networks in dFMR1B55 flies, commonly referred to as the group phenotype. Finally, combining novel research tools is a valuable method for SI research in fruit flies. Full article
(This article belongs to the Special Issue From Basics to Applications of Gene Regulatory Networks)
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