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Biology
Special Issues
From Basics to Applications of Gene Regulatory Networks
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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 4405

Special Issue Editor

Dr. Thomas Ulas

E-Mail Website
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
Special Issues, Collections and Topics in MDPI journals

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

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biology is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

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

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Published Papers (3 papers)

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13 pages, 1784 KiB  
Article
Identification of DNA Methylation Differences in Pituitary Tissues of Sichuan White Geese Using Whole-Genome Bisulfite Sequencing (WGBS)
by Lin Ma, Xianzhi Zhao, Guoda A, Tongtong Song, Meng Wu, Zhihao Yan, Min Xiao, Wenbo Jiang, Yixiao Gao, Haiwei Wang, Zhuping Chen, Keshan Zhang, Jiajia Xue, Yi Luo, Chao Wang, Youhui Xie, Ying Chen, Guangliang Gao and Qigui Wang
Biology 2025, 14(2), 154; https://doi.org/10.3390/biology14020154 - 3 Feb 2025
Cited by 1 | Viewed by 809
Abstract
To explore the impact of epigenetic modifications on egg-laying traits in geese, we employed genome-wide bisulfite sequencing (WGBS) to analyze DNA methylation patterns in pituitary tissues of high-(HYP) and low-yield (LYP) Sichuan White geese. We achieved high-quality sequencing data (mean 19.09 Gb raw [...] Read more.
To explore the impact of epigenetic modifications on egg-laying traits in geese, we employed genome-wide bisulfite sequencing (WGBS) to analyze DNA methylation patterns in pituitary tissues of high-(HYP) and low-yield (LYP) Sichuan White geese. We achieved high-quality sequencing data (mean 19.09 Gb raw reads, 15.49 Gb clean reads, 79.1% unique mapping rate) with a bisulfite conversion efficiency of 99.88%. Comparative analysis revealed 2394 differentially methylated regions (DMRs) and 422 differentially methylated genes (DMGs) between HYP and LYP groups. We identified five key differentially methylated candidate genes (BMPER, INHA, NMBR, NK3R, and DSG2) linked to egg-laying traits in Sichuan White geese. Integrated GO and KEGG enrichment analysis conducted to explore the role of regulatory networks of epigenetic modification on egg-laying traits in Sichuan White geese identified multiple metabolic pathways associated with egg-laying traits (promoting egg transport, ovulation, and yolk protein synthesis and secretion), thus providing a basis for subsequent functional verification. Full article
(This article belongs to the Special Issue From Basics to Applications of Gene Regulatory Networks)
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20 pages, 4425 KiB  
Article
Investigating the Activities of CAF20 and ECM32 in the Regulation of PGM2 mRNA Translation
by Mustafa Al-gafari, Sasi Kumar Jagadeesan, Thomas David Daniel Kazmirchuk, Sarah Takallou, Jiashu Wang, Maryam Hajikarimlou, Nishka Beersing Ramessur, Waleed Darwish, Calvin Bradbury-Jost, Houman Moteshareie, Kamaledin B. Said, Bahram Samanfar and Ashkan Golshani
Biology 2024, 13(11), 884; https://doi.org/10.3390/biology13110884 - 30 Oct 2024
Viewed by 1059
Abstract
Translation is a fundamental process in biology, and understanding its mechanisms is crucial to comprehending cellular functions and diseases. The regulation of this process is closely linked to the structure of mRNA, as these regions prove vital to modulating translation efficiency and control. [...] Read more.
Translation is a fundamental process in biology, and understanding its mechanisms is crucial to comprehending cellular functions and diseases. The regulation of this process is closely linked to the structure of mRNA, as these regions prove vital to modulating translation efficiency and control. Thus, identifying and investigating these fundamental factors that influence the processing and unwinding of structured mRNAs would be of interest due to the widespread impact in various fields of biology. To this end, we employed a computational approach and identified genes that may be involved in the translation of structured mRNAs. The approach is based on the enrichment of interactions and co-expression of genes with those that are known to influence translation and helicase activity. The in silico prediction found CAF20 and ECM32 to be highly ranked candidates that may play a role in unwinding mRNA. The activities of neither CAF20 nor ECM32 have previously been linked to the translation of PGM2 mRNA or other structured mRNAs. Our follow-up investigations with these two genes provided evidence of their participation in the translation of PGM2 mRNA and several other synthetic structured mRNAs. Full article
(This article belongs to the Special Issue From Basics to Applications of Gene Regulatory Networks)
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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
Cited by 1 | Viewed by 1915
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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