The art of modeling gene regulatory circuits

There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

Abstract

The amazing complexity of gene regulatory circuits, and biological systems in general, makes mathematical modeling an essential tool to frame and develop our understanding of their properties. Here, we present some fundamental considerations to develop and analyze a model of a gene regulatory circuit of interest, either representing a natural, synthetic, or theoretical system. A mathematical model allows us to effectively evaluate the logical implications of our hypotheses. Using our models to systematically perform in silico experiments, we can then propose specific follow-up assessments of the biological system as well as to reformulate the original assumptions, enriching both our knowledge and our understanding of the system. We want to invite the community working on different aspects of gene regulatory circuits to explore the power and benefits of mathematical modeling in their system.

Related collections

Most cited references 38

Record: found
Abstract: found
Article: not found

Nature, nurture, or chance: stochastic gene expression and its consequences.

Arjun Raj, Alexander van Oudenaarden (2008)

Gene expression is a fundamentally stochastic process, with randomness in transcription and translation leading to cell-to-cell variations in mRNA and protein levels. This variation appears in organisms ranging from microbes to metazoans, and its characteristics depend both on the biophysical parameters governing gene expression and on gene network structure. Stochastic gene expression has important consequences for cellular function, being beneficial in some contexts and harmful in others. These situations include the stress response, metabolism, development, the cell cycle, circadian rhythms, and aging.

0 comments Cited 978 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: not found

The second wave of synthetic biology: from modules to systems.

Priscilla E M Purnick, Ron Weiss (2009)

Synthetic biology is a research field that combines the investigative nature of biology with the constructive nature of engineering. Efforts in synthetic biology have largely focused on the creation and perfection of genetic devices and small modules that are constructed from these devices. But to view cells as true 'programmable' entities, it is now essential to develop effective strategies for assembling devices and modules into intricate, customizable larger scale systems. The ability to create such systems will result in innovative approaches to a wide range of applications, such as bioremediation, sustainable energy production and biomedical therapies.

0 comments Cited 326 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: not found

Network motifs: theory and experimental approaches.

Uri Alon (2007)

Transcription regulation networks control the expression of genes. The transcription networks of well-studied microorganisms appear to be made up of a small set of recurring regulation patterns, called network motifs. The same network motifs have recently been found in diverse organisms from bacteria to humans, suggesting that they serve as basic building blocks of transcription networks. Here I review network motifs and their functions, with an emphasis on experimental studies. Network motifs in other biological networks are also mentioned, including signalling and neuronal networks.

0 comments Cited 284 times – based on 0 reviews      Review now

Bookmark

All references

Author and article information

Contributors

Mariana Gómez-Schiavon:

ORCID: http://orcid.org/0000-0002-0955-7257

MGSchiavon@liigh.unam.mx

Journal

Journal ID (nlm-ta): NPJ Syst Biol Appl

Journal ID (iso-abbrev): NPJ Syst Biol Appl

Title: NPJ Systems Biology and Applications

Publisher: Nature Publishing Group UK (London )

ISSN (Electronic): 2056-7189

Publication date (Electronic): 29 May 2024

Publication date PMC-release: 29 May 2024

Publication date Collection: 2024

Volume: 10

Electronic Location Identifier: 60

Affiliations

[1 ]International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México, ( https://ror.org/01tmp8f25) Queretaro, 76230 Mexico

[2 ]ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), ( https://ror.org/05xcmte05) Santiago, 8331150 Chile

Author information

Mariana Gómez-Schiavon http://orcid.org/0000-0002-0955-7257

Cristina Sotomayor-Vivas http://orcid.org/0000-0001-8228-477X

Article

Publisher ID: 380

DOI: 10.1038/s41540-024-00380-2

PMC ID: 11137155

PubMed ID: 38811585

SO-VID: b289000d-7273-453d-9c7c-207ffb7fa803

License:

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

History

Date received : 16 November 2023

Date accepted : 8 May 2024

Funding

Funded by: Programa de Apoyo a Proyectos de Investigación e Innovación Tecnológica (PAPIIT UNAM; IA204022). ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio; ICN17_022).

Funded by: Programa de Apoyo a Proyectos de Investigación e Innovación Tecnológica (PAPIIT UNAM; IA204022).