{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,11]],"date-time":"2025-09-11T17:53:31Z","timestamp":1757613211425,"version":"3.44.0"},"reference-count":38,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2025,9,4]],"date-time":"2025-09-04T00:00:00Z","timestamp":1756944000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>Network alignment (NA) is a computational methodology employed to compare biological networks across different species or conditions. By identifying conserved structures, functions, and interactions, NA provides invaluable insights into shared biological processes, evolutionary relationships, and system-level behaviors. This manuscript presents a comprehensive overview of NA methodologies, including the importance of preprocessing network data, selecting suitable input formats, and understanding diverse network types such as attributed, temporal, and multilayer networks. Additionally, it explores key challenges such as seed nodes selection, algorithm configuration, and cross-species alignment, emphasizing the necessity of integrating functional annotations, sequence similarity, and network topology for biologically meaningful results. Various NA strategies, including Local and Global Network Alignment, are discussed alongside their respective advantages and limitations. Practical recommendations for effectively documenting and visualizing NA experiments are also provided, ensuring reproducibility and clarity in research. By leveraging diverse alignment tools and adopting best practices, researchers can unlock the potential of NA to advance our understanding of complex biological systems.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1013386","type":"journal-article","created":{"date-parts":[[2025,9,4]],"date-time":"2025-09-04T17:54:11Z","timestamp":1757008451000},"page":"e1013386","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Ten practical tips and tricks to improve the effectiveness of biological network 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Mamano","year":"2017","journal-title":"Bioinformatics."},{"issue":"14","key":"pcbi.1013386.ref017","first-page":"2151","article-title":"On the current failure\u2014but bright future\u2014of biological network alignment","volume":"33","author":"l Mamano N i","year":"2017","journal-title":"Bioinformatics."},{"issue":"43","key":"pcbi.1013386.ref018","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"A Subramanian","year":"2005","journal-title":"Proc Natl Acad Sci."},{"key":"pcbi.1013386.ref019","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkad1027","article-title":"PathDIP 5: improving coverage and making enrichment analysis more biologically meaningful","volume":"52","author":"C Pastrello","year":"2024","journal-title":"Nucleic Acids 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In: 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops. 2012. p. 174\u201381.","DOI":"10.1109\/BIBMW.2012.6470300"},{"issue":"17","key":"pcbi.1013386.ref029","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btu450","article-title":"HubAlign: an accurate and efficient method for global alignment of protein-protein interaction networks","volume":"30","author":"S Hashemifar","year":"2014","journal-title":"Bioinformatics."},{"issue":"13","key":"pcbi.1013386.ref030","doi-asserted-by":"crossref","first-page":"1654","DOI":"10.1093\/bioinformatics\/btt202","article-title":"NETAL: a new graph-based method for global alignment of protein\u2013protein interaction networks","volume":"29","author":"B Neyshabur","year":"2013","journal-title":"Bioinformatics."},{"issue":"14","key":"pcbi.1013386.ref031","doi-asserted-by":"crossref","first-page":"2409","DOI":"10.1093\/bioinformatics\/btv161","article-title":"MAGNA: maximizing accuracy in global network alignment via both node and edge conservation","volume":"31","author":"V Vijayan","year":"2015","journal-title":"Bioinformatics."},{"issue":"12","key":"pcbi.1013386.ref032","article-title":"IsoRankN: spectral methods for global alignment of multiple protein networks","volume":"25","author":"C-S Liao","year":"2009","journal-title":"Bioinformatics."},{"issue":"50","key":"pcbi.1013386.ref033","doi-asserted-by":"crossref","first-page":"1341","DOI":"10.1098\/rsif.2010.0063","article-title":"Topological network alignment uncovers biological function and phylogeny","volume":"7","author":"O Kuchaiev","year":"2010","journal-title":"J R Soc Interface."},{"issue":"3","key":"pcbi.1013386.ref034","first-page":"472","article-title":"Survey of local and global biological network alignment: the need to reconcile the two sides of the same coin","volume":"19","author":"PH Guzzi","year":"2018","journal-title":"Brief Bioinform."},{"key":"pcbi.1013386.ref035","first-page":"1","article-title":"The post-genomic era of biological network alignment","author":"FE Faisal","year":"2015","journal-title":"EURASIP Journal on Bioinformatics and Systems Biology."},{"key":"pcbi.1013386.ref036","doi-asserted-by":"crossref","unstructured":"Mohammadi S, Grama A. 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