{"id":"https://openalex.org/W2119359534","doi":"https://doi.org/10.1142/s0219720008003497","title":"USING INDIRECT PROTEIN\u2013PROTEIN INTERACTIONS FOR PROTEIN COMPLEX PREDICTION","display_name":"USING INDIRECT PROTEIN\u2013PROTEIN INTERACTIONS FOR PROTEIN COMPLEX PREDICTION","publication_year":2008,"publication_date":"2008-06-01","ids":{"openalex":"https://openalex.org/W2119359534","doi":"https://doi.org/10.1142/s0219720008003497","mag":"2119359534","pmid":"https://pubmed.ncbi.nlm.nih.gov/18574858"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720008003497","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720008003497","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5056590153","display_name":"Hon Nian Chua","orcid":null},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]}],"countries":["SG"],"is_corresponding":true,"raw_author_name":"HON NIAN CHUA","raw_affiliation_strings":["Graduate School of Integrated Sciences, National University of Singapore, Singapore"],"affiliations":[{"raw_affiliation_string":"Graduate School of Integrated Sciences, National University of Singapore, Singapore","institution_ids":["https://openalex.org/I165932596"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076346443","display_name":"Kang Ning","orcid":"https://orcid.org/0000-0003-3325-5387"},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"KANG NING","raw_affiliation_strings":["Department of Computer Science, National University of Singapore, Singapore","Department of Computer Science, National University of Singapore, Singapore,"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, National University of Singapore, Singapore","institution_ids":["https://openalex.org/I165932596"]},{"raw_affiliation_string":"Department of Computer Science, National University of Singapore, Singapore,","institution_ids":["https://openalex.org/I165932596"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012563463","display_name":"Wing\u2010Kin Sung","orcid":"https://orcid.org/0000-0001-7806-7086"},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"WING-KIN SUNG","raw_affiliation_strings":["Department of Computer Science, National University of Singapore, Singapore","Department of Computer Science, National University of Singapore, Singapore,"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, National University of Singapore, Singapore","institution_ids":["https://openalex.org/I165932596"]},{"raw_affiliation_string":"Department of Computer Science, National University of Singapore, Singapore,","institution_ids":["https://openalex.org/I165932596"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037482622","display_name":"Wai Yie Leong","orcid":"https://orcid.org/0000-0002-5389-1121"},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"HON WAI LEONG","raw_affiliation_strings":["Department of Computer Science, National University of Singapore, Singapore","Department of Computer Science, National University of Singapore, Singapore,"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, National University of Singapore, Singapore","institution_ids":["https://openalex.org/I165932596"]},{"raw_affiliation_string":"Department of Computer Science, National University of Singapore, Singapore,","institution_ids":["https://openalex.org/I165932596"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012381970","display_name":"Limsoon Wong","orcid":"https://orcid.org/0000-0003-1241-5441"},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"LIMSOON WONG","raw_affiliation_strings":["Department of Computer Science, National University of Singapore, Singapore","Department of Computer Science, National University of Singapore, Singapore,"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, National University of Singapore, Singapore","institution_ids":["https://openalex.org/I165932596"]},{"raw_affiliation_string":"Department of Computer Science, National University of Singapore, Singapore,","institution_ids":["https://openalex.org/I165932596"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5056590153"],"corresponding_institution_ids":["https://openalex.org/I165932596"],"apc_list":null,"apc_paid":null,"fwci":5.8088,"has_fulltext":false,"cited_by_count":150,"citation_normalized_percentile":{"value":0.96936296,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"06","issue":"03","first_page":"435","last_page":"466"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9951000213623047,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9835000038146973,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/merge","display_name":"Merge (version control)","score":0.6495916247367859},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6265895366668701},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.601116418838501},{"id":"https://openalex.org/keywords/clique","display_name":"Clique","score":0.5150906443595886},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.4785659611225128},{"id":"https://openalex.org/keywords/complex-network","display_name":"Complex network","score":0.47053441405296326},{"id":"https://openalex.org/keywords/interaction-network","display_name":"Interaction network","score":0.4673972725868225},{"id":"https://openalex.org/keywords/network-motif","display_name":"Network motif","score":0.42334604263305664},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.39862772822380066},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3759171962738037},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3509408235549927},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.22206783294677734},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16828271746635437},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.0832790732383728},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08118662238121033}],"concepts":[{"id":"https://openalex.org/C197129107","wikidata":"https://www.wikidata.org/wiki/Q1921621","display_name":"Merge (version control)","level":2,"score":0.6495916247367859},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6265895366668701},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.601116418838501},{"id":"https://openalex.org/C2777035058","wikidata":"https://www.wikidata.org/wiki/Q1662634","display_name":"Clique","level":2,"score":0.5150906443595886},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.4785659611225128},{"id":"https://openalex.org/C34947359","wikidata":"https://www.wikidata.org/wiki/Q665189","display_name":"Complex network","level":2,"score":0.47053441405296326},{"id":"https://openalex.org/C55105296","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interaction network","level":3,"score":0.4673972725868225},{"id":"https://openalex.org/C60723933","wikidata":"https://www.wikidata.org/wiki/Q7001080","display_name":"Network motif","level":3,"score":0.42334604263305664},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.39862772822380066},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3759171962738037},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3509408235549927},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.22206783294677734},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16828271746635437},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0832790732383728},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08118662238121033},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.0},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1142/s0219720008003497","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720008003497","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:18574858","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18574858","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of bioinformatics and computational biology","raw_type":null},{"id":"pmh:oai:scholarbank.nus.edu.sg:10635/40060","is_oa":false,"landing_page_url":"http://scholarbank.nus.edu.sg/handle/10635/40060","pdf_url":null,"source":{"id":"https://openalex.org/S7407052290","display_name":"National University of Singapore","issn_l":null,"issn":[],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Scopus","raw_type":"Conference Paper"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.122.4068","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.122.4068","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.comp.nus.edu.sg/~wongls/psZ/PCP_v18-submitted.pdf","raw_type":"text"},{"id":"pmh:oai:ir.qibebt.ac.cn:337004/976","is_oa":false,"landing_page_url":"http://124.16.151.184:8080/handle/337004/976","pdf_url":null,"source":{"id":"https://openalex.org/S4306400842","display_name":"Institutional knowledge base (Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I19820366","host_organization_name":"Chinese Academy of Sciences","host_organization_lineage":["https://openalex.org/I19820366"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Hon Nian Chua; Kang Ning; Wing-Kin Sung; Hon Wai Leong ;Limsoon Wong.Using Indirect Protein-Protein Interactions for Protein Complex Prediction.Journal of Bioinformatics and Computational Biology,2008(6)","raw_type":"\u671f\u520a\u8bba\u6587"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320698","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49"},{"id":"https://openalex.org/F4320321026","display_name":"Ministry of Earth Sciences","ror":"https://ror.org/013cf5k59"},{"id":"https://openalex.org/F4320322724","display_name":"Ministry of Education, India","ror":"https://ror.org/048xjjh50"},{"id":"https://openalex.org/F4320325599","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":19,"referenced_works":["https://openalex.org/W1783384641","https://openalex.org/W1847661395","https://openalex.org/W2037036397","https://openalex.org/W2050721857","https://openalex.org/W2065304353","https://openalex.org/W2079007492","https://openalex.org/W2084619201","https://openalex.org/W2104080300","https://openalex.org/W2107710781","https://openalex.org/W2116117181","https://openalex.org/W2118446779","https://openalex.org/W2136850043","https://openalex.org/W2137786672","https://openalex.org/W2138003801","https://openalex.org/W2152495216","https://openalex.org/W2160429376","https://openalex.org/W2163485494","https://openalex.org/W2167869241","https://openalex.org/W4246925013"],"related_works":["https://openalex.org/W2369673098","https://openalex.org/W4310014943","https://openalex.org/W19833001","https://openalex.org/W2020319151","https://openalex.org/W2057065397","https://openalex.org/W2045843285","https://openalex.org/W1517695644","https://openalex.org/W1486498127","https://openalex.org/W2119359534","https://openalex.org/W2318401729"],"abstract_inverted_index":{"Protein":[0],"complexes":[1,51],"are":[2,18,117,135,146],"fundamental":[3],"for":[4,35,80,172,253,258],"understanding":[5],"principles":[6],"of":[7,13,72,128,196,213,260],"cellular":[8],"organizations.":[9],"As":[10],"the":[11,59,70,126,138,149,175,194,211,241],"sizes":[12],"protein-protein":[14,204],"interaction":[15,97,150,230],"(PPI)":[16],"networks":[17,29,231],"increasing,":[19],"accurate":[20],"and":[21,64,114,178,199,221],"fast":[22],"protein":[23,41,50,81,254,262],"complex":[24,82,255],"prediction":[25,259],"from":[26,52,86,137],"these":[27],"PPI":[28,53,60,243],"can":[30,155,206],"serve":[31],"as":[32],"a":[33,108,167,185],"guide":[34],"biological":[36,103],"experiments":[37],"to":[38,48,159,181,202,209],"discover":[39],"novel":[40,168,261],"complexes.":[42,263],"However,":[43],"it":[44],"is":[45,62,245],"not":[46,93],"easy":[47],"predict":[49],"networks,":[54],"especially":[55,257],"in":[56,110,174,233],"situations":[57],"where":[58],"network":[61,244],"noisy":[63],"still":[65],"incomplete.":[66],"Here,":[67],"we":[68],"study":[69],"use":[71,195],"indirect":[73,115,197],"interactions":[74,116,142,198,205],"between":[75],"level-2":[76,141],"neighbors":[77],"(level-2":[78,99],"interactions)":[79],"prediction.":[83],"We":[84,105,163],"know":[85],"previous":[87],"work":[88],"that":[89,170,192],"proteins":[90],"which":[91,111,124],"do":[92],"interact":[94],"but":[95],"share":[96,102],"partners":[98],"neighbors)":[100],"often":[101],"functions.":[104],"have":[106,164],"proposed":[107,166],"method":[109],"all":[112],"direct":[113],"first":[118],"weighted":[119],"using":[120,184],"topological":[121,200],"weight":[122,134,145,201],"(FS-Weight),":[123],"estimates":[125],"strength":[127],"functional":[129],"association.":[130],"Interactions":[131],"with":[132,143],"low":[133],"removed":[136],"network,":[139,177],"while":[140],"high":[144],"introduced":[147],"into":[148],"network.":[151,162],"Existing":[152],"clustering":[153,219],"algorithms":[154],"then":[156],"be":[157,207,250],"applied":[158],"this":[160,234],"modified":[161,176,232],"also":[165],"algorithm":[169,225],"searches":[171],"cliques":[173,180],"merge":[179],"form":[182],"clusters":[183,214],"\"partial":[186],"clique":[187],"merging\"":[188],"method.":[189],"Experiments":[190],"show":[191],"(1)":[193],"augment":[203],"used":[208],"improve":[210],"precision":[212],"predicted":[215],"by":[216],"various":[217],"existing":[218],"algorithms;":[220],"(2)":[222],"our":[223,247],"complex-finding":[224],"performs":[226],"very":[227,251],"well":[228],"on":[229],"way.":[235],"Since":[236],"no":[237],"other":[238],"information":[239],"except":[240],"original":[242],"used,":[246],"approach":[248],"would":[249],"useful":[252],"prediction,":[256]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":8},{"year":2018,"cited_by_count":10},{"year":2017,"cited_by_count":10},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":13},{"year":2013,"cited_by_count":19},{"year":2012,"cited_by_count":18}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}