{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T15:38:38Z","timestamp":1740152318965,"version":"3.37.3"},"reference-count":22,"publisher":"Wiley","license":[{"start":{"date-parts":[[2009,2,23]],"date-time":"2009-02-23T00:00:00Z","timestamp":1235347200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Advances in Bioinformatics"],"published-print":{"date-parts":[[2009,2,23]]},"abstract":"<jats:p>A protein network shows physical interactions as well as functional associations. An important\nusage of such networks is to discover unknown members of partially known complexes and\npathways. A number of methods exist for such analyses, and they can be divided into two main\ncategories based on their treatment of highly connected proteins. In this paper, we show that\nmethods that are not affected by the degree (number of linkages) of a protein give more accurate\npredictions for certain complexes and pathways. We propose a network flow-based technique\nto compute the association probability of a pair of proteins. We extend the proposed technique\nusing hierarchical clustering in order to scale well with the size of proteome. We also show that\ntop-k queries are not suitable for a large number of cases, and threshold queries are more meaningful\nin these cases. Network flow technique with clustering is able to optimize meaningful\nthreshold queries and answer them with high efficiency compared to a similar method that uses\nMonte Carlo simulation.<\/jats:p>","DOI":"10.1155\/2009\/787128","type":"journal-article","created":{"date-parts":[[2010,2,24]],"date-time":"2010-02-24T07:02:04Z","timestamp":1266994924000},"page":"1-9","source":"Crossref","is-referenced-by-count":1,"title":["Accurate and Scalable Techniques for the Complex\/Pathway Membership Problem in Protein Networks"],"prefix":"10.1155","volume":"2009","author":[{"given":"Orhan","family":"\u00c7amo\u011flu","sequence":"first","affiliation":[{"name":"Department of Computer Science, University of California, Santa Barbara, CA 93106, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5532-0154","authenticated-orcid":true,"given":"Tolga","family":"Can","sequence":"additional","affiliation":[{"name":"Department of Computer Engineering, Middle East Technical University, 06531 Ankara, Turkey"}]},{"given":"Ambuj K.","family":"Singh","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of California, Santa Barbara, CA 93106, USA"}]}],"member":"311","reference":[{"volume":"2","volume-title":"Random walks on graphs: a survey","year":"1996","key":"1"},{"year":"2004","key":"2"},{"key":"3","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btg1026"},{"key":"4","doi-asserted-by":"publisher","DOI":"10.1101\/gr.2203804"},{"key":"5","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bti1054"},{"key":"6","doi-asserted-by":"crossref","first-page":"410","DOI":"10.1137\/0208032","volume":"8","year":"1979","journal-title":"SIAM Journal on Computing"},{"key":"7","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btn161"},{"key":"8","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btn164"},{"key":"9","doi-asserted-by":"publisher","DOI":"10.1021\/pr900073d"},{"key":"10","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.0030025"},{"key":"11","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btm194"},{"key":"12","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1000132"},{"key":"13","doi-asserted-by":"publisher","DOI":"10.1038\/35075138"},{"issue":"1","key":"14","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1093\/nar\/30.1.42","volume":"30","year":"2002","journal-title":"Nucleic Acids Research"},{"issue":"3","key":"15","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1016\/0166-218X(88)90065-0","volume":"21","year":"1988","journal-title":"Discrete Applied Mathematics"},{"year":"1969","key":"16"},{"volume-title":"On spectral clustering: analysis and an algorithm","year":"2002","key":"18"},{"issue":"4","key":"19","first-page":"406","volume":"4","year":"1987","journal-title":"Molecular Biology and Evolution"},{"key":"21","doi-asserted-by":"publisher","DOI":"10.1038\/35001009"},{"key":"22","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.061034498"},{"key":"23","doi-asserted-by":"publisher","DOI":"10.1038\/415141a"},{"key":"24","doi-asserted-by":"publisher","DOI":"10.1038\/415180a"}],"container-title":["Advances in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/downloads.hindawi.com\/archive\/2009\/787128.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/downloads.hindawi.com\/archive\/2009\/787128.xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/downloads.hindawi.com\/archive\/2009\/787128.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,12,8]],"date-time":"2020-12-08T17:13:44Z","timestamp":1607447624000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.hindawi.com\/journals\/abi\/2009\/787128\/"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,2,23]]},"references-count":22,"alternative-id":["787128","787128"],"URL":"https:\/\/doi.org\/10.1155\/2009\/787128","relation":{},"ISSN":["1687-8027","1687-8035"],"issn-type":[{"type":"print","value":"1687-8027"},{"type":"electronic","value":"1687-8035"}],"subject":[],"published":{"date-parts":[[2009,2,23]]}}}