{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,17]],"date-time":"2025-10-17T13:45:17Z","timestamp":1760708717641},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"18","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Given the growth of large-scale protein\u2013protein interaction (PPI) networks obtained across multiple species and conditions, network alignment is now an important research problem. Network alignment performs comparative analysis across multiple PPI networks to understand their connections and relationships. However, PPI data in high-throughput experiments still suffer from significant false-positive and false-negatives rates. Consequently, high-confidence network alignment across entire PPI networks is not possible. At best, local network alignment attempts to alleviate this problem by completely ignoring low-confidence mappings; global network alignment, on the other hand, pairs all proteins regardless. To this end, we propose an alternative strategy: instead of full alignment across the entire network or completely ignoring low-confidence regions, we aim to perform highly specific protein-to-protein alignments where data confidence is high, and fall back on broader functional region-to-region alignment where detailed protein\u2013protein alignment cannot be ascertained. The basic idea is to provide an alignment of multiple granularities to allow biological predictions at varying specificity.<\/jats:p>\n               <jats:p>Results: \u00a0DualAligner performs dual network alignment , in which both region-to-region alignment, where whole subgraph of one network is aligned to subgraph of another, and protein-to-protein alignment, where individual proteins in networks are aligned to one another, are performed to achieve higher accuracy network alignments. Dual network alignment is achieved in DualAligner via background information provided by a combination of Gene Ontology annotation information and protein interaction network data. We tested DualAligner on the global networks from IntAct and demonstrated the superiority of our approach compared with state-of-the-art network alignment methods. We studied the effects of parameters in DualAligner in controlling the quality of the alignment. We also performed a case study that illustrates the utility of our approach.<\/jats:p>\n               <jats:p>Availability and implementation: \u00a0http:\/\/www.cais.ntu.edu.sg\/\u223cassourav\/DualAligner\/<\/jats:p>\n               <jats:p>Contact: \u00a0seah0097@ntu.edu.sg or assourav@ntu.edu.sg<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu358","type":"journal-article","created":{"date-parts":[[2014,5,29]],"date-time":"2014-05-29T03:33:46Z","timestamp":1401334426000},"page":"2619-2626","source":"Crossref","is-referenced-by-count":16,"title":["<tt>DualAligner<\/tt>\n            : a dual alignment-based strategy to align protein interaction networks"],"prefix":"10.1093","volume":"30","author":[{"given":"Boon-Siew","family":"Seah","sequence":"first","affiliation":[{"name":"1 Division of Software and Information Systems, School of Computer Engineering, Nanyang Technological University, 2 Singapore-MIT Alliance, Nanyang Technological University, Singapore 639798 and 3 Biological Engineering Department, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA"},{"name":"1 Division of Software and Information Systems, School of Computer Engineering, Nanyang Technological University, 2 Singapore-MIT Alliance, Nanyang Technological University, Singapore 639798 and 3 Biological Engineering Department, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA"}]},{"given":"Sourav S.","family":"Bhowmick","sequence":"additional","affiliation":[{"name":"1 Division of Software and Information Systems, School of Computer Engineering, Nanyang Technological University, 2 Singapore-MIT Alliance, Nanyang Technological University, Singapore 639798 and 3 Biological Engineering Department, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA"},{"name":"1 Division of Software and Information Systems, School of Computer Engineering, Nanyang Technological University, 2 Singapore-MIT Alliance, Nanyang Technological University, Singapore 639798 and 3 Biological Engineering Department, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA"}]},{"suffix":"Jr","given":"C. Forbes","family":"Dewey","sequence":"additional","affiliation":[{"name":"1 Division of Software and Information Systems, School of Computer Engineering, Nanyang Technological University, 2 Singapore-MIT Alliance, Nanyang Technological University, Singapore 639798 and 3 Biological Engineering Department, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA"},{"name":"1 Division of Software and Information Systems, School of Computer Engineering, Nanyang Technological University, 2 Singapore-MIT Alliance, Nanyang Technological University, Singapore 639798 and 3 Biological Engineering Department, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA"}]}],"member":"286","published-online":{"date-parts":[[2014,5,28]]},"reference":[{"key":"2023012711553073100_btu358-B1","doi-asserted-by":"crossref","first-page":"2765","DOI":"10.1093\/bioinformatics\/btt486","article-title":"Optimizing a global alignment of protein interaction networks","volume":"29","author":"Chindelevitch","year":"2013","journal-title":"Bioinformatics"},{"key":"2023012711553073100_btu358-B2","doi-asserted-by":"crossref","first-page":"1169","DOI":"10.1101\/gr.5235706","article-title":"Graemlin: general and robust alignment of multiple large interaction networks","volume":"16","author":"Flannick","year":"2006","journal-title":"Genome Res."},{"key":"2023012711553073100_btu358-B3","doi-asserted-by":"crossref","first-page":"372","DOI":"10.1093\/bioinformatics\/btn640","article-title":"Precision and recall estimates for two-hybrid screens","volume":"25","author":"Huang","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012711553073100_btu358-B4","doi-asserted-by":"crossref","first-page":"594","DOI":"10.1093\/bioinformatics\/btm630","article-title":"NetworkBLAST: comparative analysis of protein networks","volume":"24","author":"Kalaev","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012711553073100_btu358-B5","doi-asserted-by":"crossref","first-page":"989","DOI":"10.1089\/cmb.2009.0136","article-title":"Fast and accurate alignment of multiple protein networks","volume":"16","author":"Kalaev","year":"2009","journal-title":"J. Comput. Biol."},{"key":"2023012711553073100_btu358-B6","doi-asserted-by":"crossref","first-page":"W83","DOI":"10.1093\/nar\/gkh411","article-title":"PathBLAST: a tool for alignment of protein interaction networks","volume":"32","author":"Kelley","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023012711553073100_btu358-B7","doi-asserted-by":"crossref","first-page":"D561","DOI":"10.1093\/nar\/gkl958","article-title":"IntAct\u2013open source resource for molecular interaction data","volume":"35","author":"Kerrien","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2023012711553073100_btu358-B8","doi-asserted-by":"crossref","first-page":"S59","DOI":"10.1186\/1471-2105-10-S1-S59","article-title":"A new graph-based method for pairwise global network alignment","volume":"10","author":"Klau","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2023012711553073100_btu358-B9","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1089\/cmb.2006.13.182","article-title":"Pairwise alignment of protein interaction networks","volume":"13","author":"Koyut\u00fcrk","year":"2006","journal-title":"J. Comput. Biol"},{"key":"2023012711553073100_btu358-B10","doi-asserted-by":"crossref","first-page":"1390","DOI":"10.1093\/bioinformatics\/btr127","article-title":"Integrative network alignment reveals large regions of global network similarity in yeast and human","volume":"27","author":"Kuchaiev","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012711553073100_btu358-B11","doi-asserted-by":"crossref","first-page":"i253","DOI":"10.1093\/bioinformatics\/btp203","article-title":"IsoRankN: spectral methods for global alignment of multiple protein networks","volume":"25","author":"Liao","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012711553073100_btu358-B12","doi-asserted-by":"crossref","first-page":"e31220","DOI":"10.1371\/journal.pone.0031220","article-title":"A novel framework for the comparative analysis of biological networks","volume":"7","author":"Pache","year":"2012","journal-title":"PloS One"},{"key":"2023012711553073100_btu358-B13","doi-asserted-by":"crossref","first-page":"1239","DOI":"10.1093\/bioinformatics\/bts119","article-title":"PINALOG: a novel approach to align protein interaction networks\u2013implications for complex detection and function prediction","volume":"28","author":"Phan","year":"2012","journal-title":"Bioinformatics"},{"key":"2023012711553073100_btu358-B14","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1038\/nbt1196","article-title":"Modeling cellular machinery through biological network comparison","volume":"24","author":"Sharan","year":"2006","journal-title":"Nat. Biotechnol"},{"key":"2023012711553073100_btu358-B15","doi-asserted-by":"crossref","first-page":"S11","DOI":"10.1186\/1471-2105-13-S3-S11","article-title":"Scalable global alignment for multiple biological networks","volume":"13","author":"Shih","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"2023012711553073100_btu358-B16","doi-asserted-by":"crossref","first-page":"12763","DOI":"10.1073\/pnas.0806627105","article-title":"Global alignment of multiple protein interaction networks with application to functional orthology detection","volume":"105","author":"Singh","year":"2008","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012711553073100_btu358-B17","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1083\/jcb.200202016","article-title":"Characterization of a mammalian Golgi-localized protein complex, COG, that is required for normal Golgi morphology and function","volume":"157","author":"Ungar","year":"2002","journal-title":"J. Cell Biol."},{"key":"2023012711553073100_btu358-B18","doi-asserted-by":"crossref","first-page":"i259","DOI":"10.1093\/bioinformatics\/btp196","article-title":"Global alignment of protein-protein interaction networks by graph matching methods","volume":"25","author":"Zaslavskiy","year":"2009","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/18\/2619\/48929140\/bioinformatics_30_18_2619.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/18\/2619\/48929140\/bioinformatics_30_18_2619.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T12:36:19Z","timestamp":1674822979000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/18\/2619\/2475625"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,5,28]]},"references-count":18,"journal-issue":{"issue":"18","published-print":{"date-parts":[[2014,9,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu358","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2014,9,15]]},"published":{"date-parts":[[2014,5,28]]}}}