{"id":"https://openalex.org/W2000503761","doi":"https://doi.org/10.1186/1752-0509-4-129","title":"Protein complex prediction based on k-connected subgraphs in protein interaction network","display_name":"Protein complex prediction based on k-connected subgraphs in protein interaction network","publication_year":2010,"publication_date":"2010-09-16","ids":{"openalex":"https://openalex.org/W2000503761","doi":"https://doi.org/10.1186/1752-0509-4-129","mag":"2000503761","pmid":"https://pubmed.ncbi.nlm.nih.gov/20846398","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/2949670"},"language":"en","primary_location":{"id":"doi:10.1186/1752-0509-4-129","doi":"https://doi.org/10.1186/1752-0509-4-129","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-4-129","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-4-129","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","jufo-1","poland-70","vabb-shw"],"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-4-129","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5055320656","display_name":"Mahnaz Habibi","orcid":"https://orcid.org/0000-0002-8969-2706","observed_orcids":["https://orcid.org/0000-0002-8969-2706","https://orcid.org/0000-0002-5240-5910"]},"institutions":[{"id":"https://openalex.org/I48379061","display_name":"Shahid Beheshti University","ror":"https://ror.org/0091vmj44","country_code":"IR","type":"education","lineage":["https://openalex.org/I48379061"]}],"countries":["IR"],"is_corresponding":false,"raw_author_name":"Mahnaz Habibi","raw_affiliation_strings":["Faculty of Mathematics, Shahid-Beheshti University, gc, Tehran, Iran","Faculty of Mathematics, Shahid Beheshti University, Tehran, Iran#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Mathematics, Shahid-Beheshti University, gc, Tehran, Iran","institution_ids":["https://openalex.org/I48379061"]},{"raw_affiliation_string":"Faculty of Mathematics, Shahid Beheshti University, Tehran, Iran#TAB#","institution_ids":["https://openalex.org/I48379061"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035605233","display_name":"Changiz Eslahchi","orcid":"https://orcid.org/0000-0002-8913-3904","observed_orcids":["https://orcid.org/0000-0002-8913-3904"]},"institutions":[{"id":"https://openalex.org/I48379061","display_name":"Shahid Beheshti University","ror":"https://ror.org/0091vmj44","country_code":"IR","type":"education","lineage":["https://openalex.org/I48379061"]}],"countries":["IR"],"is_corresponding":true,"raw_author_name":"Changiz Eslahchi","raw_affiliation_strings":["Faculty of Mathematics, Shahid-Beheshti University, g.c., Tehran, Iran","Faculty of Mathematics, Shahid Beheshti University, Tehran, Iran#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Mathematics, Shahid-Beheshti University, g.c., Tehran, Iran","institution_ids":["https://openalex.org/I48379061"]},{"raw_affiliation_string":"Faculty of Mathematics, Shahid Beheshti University, Tehran, Iran#TAB#","institution_ids":["https://openalex.org/I48379061"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012381970","display_name":"Limsoon Wong","orcid":"https://orcid.org/0000-0003-1241-5441","observed_orcids":["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":true,"raw_author_name":"Limsoon Wong","raw_affiliation_strings":["School of Computing, National University of Singapore, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing, National University of Singapore, Singapore","institution_ids":["https://openalex.org/I165932596"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5012381970","https://openalex.org/A5035605233"],"corresponding_institution_ids":["https://openalex.org/I165932596","https://openalex.org/I48379061"],"apc_list":{"value":2290,"currency":"USD","value_usd":2290},"apc_paid":{"value":2290,"currency":"USD","value_usd":2290},"fwci":1.507,"has_fulltext":true,"cited_by_count":43,"citation_normalized_percentile":{"value":0.80399763,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":99},"biblio":{"volume":"4","issue":"1","first_page":"129","last_page":"129"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9994999766349792,"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":0.9994999766349792,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":9.999999747378752e-05,"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/T10064","display_name":"Complex Network Analysis Techniques","score":0.0,"subfield":{"id":"https://openalex.org/subfields/3109","display_name":"Statistical and Nonlinear Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/protein-complex-prediction","display_name":"protein complex prediction","score":0.9990000128746033},{"id":"https://openalex.org/keywords/protein-protein-interaction-network","display_name":"protein-protein interaction network","score":0.9369999766349792},{"id":"https://openalex.org/keywords/dense-subgraphs","display_name":"dense subgraphs","score":0.5619999766349792}],"concepts":[{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.7450389266014099},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5619741678237915},{"id":"https://openalex.org/C2909613950","wikidata":"https://www.wikidata.org/wiki/Q158695","display_name":"Protein Interaction Networks","level":3,"score":0.5563145875930786},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5221817493438721},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.5043824911117554},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.45978832244873047},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.37705090641975403},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1828051507472992}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D021381","descriptor_name":"Protein Transport","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/1752-0509-4-129","doi":"https://doi.org/10.1186/1752-0509-4-129","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-4-129","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-4-129","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","jufo-1","poland-70","vabb-shw"],"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2949670","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2949670","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Syst Biol","raw_type":"Text"},{"id":"pmid:20846398","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20846398","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,"listed_in":[],"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":"BMC systems biology","raw_type":"Journal Article"},{"id":"pmh:oai:scholarbank.nus.edu.sg:10635/38978","doi":null,"is_oa":false,"landing_page_url":"http://scholarbank.nus.edu.sg/handle/10635/38978","pdf_url":null,"source":{"id":"https://openalex.org/S7407052290","display_name":"National University of Singapore","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":"Article"},{"id":"pmh:oai:doaj.org/article:61898f466c854dea9e838d68223c1c01","doi":null,"is_oa":false,"landing_page_url":"https://doaj.org/article/61898f466c854dea9e838d68223c1c01","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":"BMC Systems Biology, Vol 4, Iss 1, p 129 (2010)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/1752-0509-4-129","doi":"https://doi.org/10.1186/1752-0509-4-129","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-4-129","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-4-129","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","jufo-1","poland-70","vabb-shw"],"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320671","display_name":"National Research Foundation","ror":"https://ror.org/05s0g1g46"},{"id":"https://openalex.org/F4320323645","display_name":"Institute for Research in Fundamental Sciences","ror":"https://ror.org/04xreqs31"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2000503761.pdf","grobid_xml":"https://content.openalex.org/works/W2000503761.grobid-xml"},"referenced_works_count":44,"referenced_works":["https://openalex.org/W1485582261","https://openalex.org/W1569275112","https://openalex.org/W1783384641","https://openalex.org/W1956694423","https://openalex.org/W1993229737","https://openalex.org/W2005422315","https://openalex.org/W2011986160","https://openalex.org/W2036826052","https://openalex.org/W2037036397","https://openalex.org/W2050721857","https://openalex.org/W2057885377","https://openalex.org/W2065304353","https://openalex.org/W2071753136","https://openalex.org/W2084619201","https://openalex.org/W2095780712","https://openalex.org/W2100371004","https://openalex.org/W2100585269","https://openalex.org/W2103017472","https://openalex.org/W2107424557","https://openalex.org/W2107710781","https://openalex.org/W2116117181","https://openalex.org/W2117412805","https://openalex.org/W2119359534","https://openalex.org/W2121564430","https://openalex.org/W2124166542","https://openalex.org/W2126760155","https://openalex.org/W2131984349","https://openalex.org/W2136850043","https://openalex.org/W2137786672","https://openalex.org/W2138003801","https://openalex.org/W2138582694","https://openalex.org/W2140280811","https://openalex.org/W2142798246","https://openalex.org/W2151875636","https://openalex.org/W2152495216","https://openalex.org/W2160042914","https://openalex.org/W2163485494","https://openalex.org/W2163899891","https://openalex.org/W2167869241","https://openalex.org/W2171430493","https://openalex.org/W2395595192","https://openalex.org/W2798588639","https://openalex.org/W4246925013","https://openalex.org/W4252706339"],"related_works":["https://openalex.org/W2757624129","https://openalex.org/W2403079677","https://openalex.org/W7098045801","https://openalex.org/W2046656611","https://openalex.org/W2030750186","https://openalex.org/W1977065177","https://openalex.org/W2623199466","https://openalex.org/W2752886248","https://openalex.org/W2151432137","https://openalex.org/W7096026534"],"abstract_inverted_index":{"BACKGROUND:":[0],"Protein":[1],"complexes":[2,19,89,103,132,143],"play":[3],"an":[4],"important":[5],"role":[6],"in":[7,20,90,120,148],"cellular":[8],"mechanisms.":[9],"Recently,":[10],"several":[11,82],"methods":[12,114],"have":[13,51],"been":[14],"presented":[15],"to":[16,52,108],"predict":[17],"protein":[18,22,29,38,47,65,83,88,111,149],"a":[21,28,34,46,54,62,135],"interaction":[23,84,150],"network.":[24],"In":[25],"these":[26],"methods,":[27],"complex":[30,48,66,112],"is":[31,71],"predicted":[32,154],"as":[33],"dense":[35,57],"subgraph":[36],"of":[37,122,138],"interactions.":[39],"However,":[40],"interactions":[41],"data":[42,93],"are":[43,164],"incomplete":[44],"and":[45,96,100,118,124,162],"does":[49],"not":[50],"be":[53,153],"complete":[55],"or":[56],"subgraph.":[58],"RESULTS:":[59],"We":[60,78,105,126],"propose":[61],"more":[63,131],"appropriate":[64],"prediction":[67,113],"method,":[68],"CFA,":[69],"that":[70,128],"based":[72,155],"on":[73,76,86,156],"connectivity":[74,146,157],"number":[75],"subgraphs.":[77],"evaluate":[79],"CFA":[80,107,129,160],"using":[81],"networks":[85],"reference":[87],"two":[91],"benchmark":[92],"sets":[94],"(MIPS":[95],"Aloy),":[97],"containing":[98],"1142":[99],"61":[101],"known":[102],"respectively.":[104],"compare":[106],"some":[109],"existing":[110],"(CMC,":[115],"MCL,":[116],"PCP":[117],"RNSC)":[119],"terms":[121],"recall":[123],"precision.":[125,139],"show":[127],"predicts":[130],"correctly":[133],"at":[134],"competitive":[136],"level":[137,147],"CONCLUSIONS:":[140],"Many":[141],"real":[142],"with":[144],"different":[145],"network":[151],"can":[152],"number.":[158],"Our":[159],"program":[161],"results":[163],"freely":[165],"available":[166],"from":[167],"http://www.bioinf.cs.ipm.ir/softwares/cfa/CFA.rar.":[168]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":12},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":6}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}