Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

Graph-Theoretical Analysis of Biological Networks

Version 1 : Received: 13 July 2023 / Approved: 13 July 2023 / Online: 14 July 2023 (13:22:33 CEST)

A peer-reviewed article of this Preprint also exists.

Erciyes, K. Graph-Theoretical Analysis of Biological Networks: A Survey. Computation 2023, 11, 188. Erciyes, K. Graph-Theoretical Analysis of Biological Networks: A Survey. Computation 2023, 11, 188.


: Biological networks such as protein interaction networks, gene regulation networks and metabolic pathways are examples of complex networks which are large graphs with small-world and scale-free properties. Analysis of these networks has a profound effect on our understanding the origins of life, health and disease states of organisms, and diagnose diseases to aid the search for remedial processes. In this review, we describe main analysis methods of biological networks using graph theory by first defining main parameters such as clustering coefficient, modularity and centrality. We then survey fundamental graph clustering methods and algorithms followed by the network motif search algorithms with the aim of finding repeating subgraphs in a biological network graph. A frequently appearing subgraph usually conveys a basic function carried out by that small network and discovering such a function provides an insight to the overall function of the organism. Lastly, we review network alignment algorithms that achieve to find similarities between two or more graphs representing biological networks. A conserved subgraph between the biological networks of organisms may mean a common ancestor and finding such relationship may help researchers derive ancestral relationships and predict the future evolution of organisms to enable designing new drugs. We conclude by the current challenging areas of biological network analysis using graph theory and parallel processing for high performance analysis


biological network; graph analysis; clustering; network motif; network alignment


Computer Science and Mathematics, Mathematical and Computational Biology

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