A review of protein-protein interaction network alignment: From pathway comparison to global alignment

Cheng-Yu Ma; Chung-Shou Liao

doi:10.1016/j.csbj.2020.09.011

A review of protein-protein interaction network alignment: From pathway comparison to global alignment

Comput Struct Biotechnol J. 2020 Sep 18:18:2647-2656. doi: 10.1016/j.csbj.2020.09.011. eCollection 2020.

Authors

Cheng-Yu Ma¹, Chung-Shou Liao²

Affiliations

¹ Chang Gung Memorial Hospital, No. 5, Fu-Hsing St., Kuei Shan Dist., Taoyuan City 33305, Taiwan, ROC.
² National Tsing Hua University, No. 101, Section 2, Kuang-Fu Rd., Hsinchu City 30013, Taiwan, ROC.

Abstract

Network alignment provides a comprehensive way to discover the similar parts between molecular systems of different species based on topological and biological similarity. With such a strong basis, one can do comparative studies at a systems level in the field of computational biology. In this survey paper, we focus on protein-protein interaction networks and review some representative algorithms for network alignment in the past two decades as well as the state-of-the-art aligners. We also introduce the most popular evaluation measures in the literature to benchmark the performance of these approaches. Finally, we address several future challenges and the possible ways to conquer the existing problems of biological network alignment.

Keywords: Biological network; Network alignment; Protein interaction network; Systems biology.

Publication types

Review