Research Report

Modeling Biological Networks: A Systematic Review of Computational Approaches to Network Dynamics  

Minghua Li , Guoliang Chen
Biotechnology Research Center, Cuixi Academy of Biotechnology, Zhuji, 311800, Zhejiang, China
Author    Correspondence author
Computational Molecular Biology, 2024, Vol. 14, No. 2   doi: 10.5376/cmb.2024.14.0006
Received: 28 Jan., 2024    Accepted: 11 Mar., 2024    Published: 29 Mar., 2024
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This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Preferred citation for this article:

Chen G.L., and Li M.H., 2024, Modeling biological networks: computational approaches to network dynamics, Computational Molecular Biology, 14(2): 45-53 (doi: 10.5376/cmb.2024.14.0006)

Abstract

Biological networks are important tools for understanding the complexity and functionality of biological systems, and their dynamic analysis can reveal the dynamic behavior of biological processes. However, the high complexity and diversity of biological networks pose urgent challenges for research, requiring the development and application of advanced computational methods. This study reviews the different types of biological networks and their functional roles in biology, and explores in detail network dynamics calculation methods including graph theory, agent-based modeling, differential equations, etc. In addition, we also focus on dynamic modeling of gene regulatory networks, protein-protein interaction networks, and metabolic networks, analyzing the applications and limitations of these methods in practical biological systems. In order to provide a comprehensive reference for researchers in the field of biological network dynamics.

Keywords
Biological networks; Network dynamics; Computational methods; Gene regulatory networks; Protein-protein interaction networks
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