{"id":"https://openalex.org/W4303411653","doi":"https://doi.org/10.1186/s12859-022-04923-4","title":"Detecting protein complexes with multiple properties by an adaptive harmony search algorithm","display_name":"Detecting protein complexes with multiple properties by an adaptive harmony search algorithm","publication_year":2022,"publication_date":"2022-10-07","ids":{"openalex":"https://openalex.org/W4303411653","doi":"https://doi.org/10.1186/s12859-022-04923-4","pmid":"https://pubmed.ncbi.nlm.nih.gov/36207692"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-022-04923-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04923-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-04923-4","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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 Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-04923-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101850312","display_name":"Rongquan Wang","orcid":"https://orcid.org/0000-0002-3375-9561"},"institutions":[{"id":"https://openalex.org/I92403157","display_name":"University of Science and Technology Beijing","ror":"https://ror.org/02egmk993","country_code":"CN","type":"education","lineage":["https://openalex.org/I92403157"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Rongquan Wang","raw_affiliation_strings":["School of Computer and Communication Engineering, University of Science and Technology Beijing, No. 30 Xueyuan Road, Haidian District, Beijing, 100083, China","School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer and Communication Engineering, University of Science and Technology Beijing, No. 30 Xueyuan Road, Haidian District, Beijing, 100083, China","institution_ids":["https://openalex.org/I92403157"]},{"raw_affiliation_string":"School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing, China","institution_ids":["https://openalex.org/I92403157"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100412525","display_name":"Caixia Wang","orcid":"https://orcid.org/0000-0002-3338-2354"},"institutions":[{"id":"https://openalex.org/I195846302","display_name":"China Foreign Affairs University","ror":"https://ror.org/00kxb1h72","country_code":"CN","type":"education","lineage":["https://openalex.org/I195846302"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Caixia Wang","raw_affiliation_strings":["School of International Economics, China Foreign Affairs University, 24 Zhanlanguan Road, Xicheng District, Beijing, 100037, China","School of International Economics, China Foreign Affairs University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of International Economics, China Foreign Affairs University, 24 Zhanlanguan Road, Xicheng District, Beijing, 100037, China","institution_ids":["https://openalex.org/I195846302"]},{"raw_affiliation_string":"School of International Economics, China Foreign Affairs University, Beijing, China","institution_ids":["https://openalex.org/I195846302"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006236325","display_name":"Huimin Ma","orcid":"https://orcid.org/0000-0001-5383-5667"},"institutions":[{"id":"https://openalex.org/I92403157","display_name":"University of Science and Technology Beijing","ror":"https://ror.org/02egmk993","country_code":"CN","type":"education","lineage":["https://openalex.org/I92403157"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Huimin Ma","raw_affiliation_strings":["School of Computer and Communication Engineering, University of Science and Technology Beijing, No. 30 Xueyuan Road, Haidian District, Beijing, 100083, China. mhmpub@ustb.edu.cn","School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer and Communication Engineering, University of Science and Technology Beijing, No. 30 Xueyuan Road, Haidian District, Beijing, 100083, China. mhmpub@ustb.edu.cn","institution_ids":["https://openalex.org/I92403157"]},{"raw_affiliation_string":"School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing, China","institution_ids":["https://openalex.org/I92403157"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5006236325"],"corresponding_institution_ids":["https://openalex.org/I92403157"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.5484,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.60967735,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"23","issue":"1","first_page":"414","last_page":"414"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.980400025844574,"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":0.980400025844574,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.010700000450015068,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.0013000000035390258,"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/harmony-search","display_name":"Harmony search","score":0.7681249380111694},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6380997896194458},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5277120471000671},{"id":"https://openalex.org/keywords/filter","display_name":"Filter (signal processing)","score":0.4177483320236206},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33040517568588257},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3079615533351898}],"concepts":[{"id":"https://openalex.org/C33099171","wikidata":"https://www.wikidata.org/wiki/Q26208718","display_name":"Harmony search","level":2,"score":0.7681249380111694},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6380997896194458},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5277120471000671},{"id":"https://openalex.org/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"score":0.4177483320236206},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33040517568588257},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3079615533351898},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-022-04923-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04923-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-04923-4","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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 Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36207692","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36207692","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:18b95378fe1740d1a3b739c43bc0d1f5","is_oa":true,"landing_page_url":"https://doaj.org/article/18b95378fe1740d1a3b739c43bc0d1f5","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,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 23, Iss 1, Pp 1-32 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9541083","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9541083","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,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-022-04923-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04923-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-04923-4","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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 Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2943922739","display_name":null,"funder_award_id":"No. FRF-TP-20-064A1Z","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G5356393250","display_name":null,"funder_award_id":"U20B2062","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7134410915","display_name":null,"funder_award_id":"FRF-TP-20-064A1Z","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G870904179","display_name":null,"funder_award_id":"62172036","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8844763788","display_name":null,"funder_award_id":"FRF-IDRY-21-001","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G8949608771","display_name":null,"funder_award_id":"No. U20B2062","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320324522","display_name":"Civil Aviation Administration of China","ror":"https://ror.org/05gfwht30"},{"id":"https://openalex.org/F4320325365","display_name":"University of Science and Technology Beijing","ror":"https://ror.org/02egmk993"},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4303411653.pdf"},"referenced_works_count":71,"referenced_works":["https://openalex.org/W1575542444","https://openalex.org/W1772231674","https://openalex.org/W1783384641","https://openalex.org/W1968842724","https://openalex.org/W1971227936","https://openalex.org/W1973508741","https://openalex.org/W1976937534","https://openalex.org/W1985086849","https://openalex.org/W1986214964","https://openalex.org/W1988496202","https://openalex.org/W1993885071","https://openalex.org/W2042301222","https://openalex.org/W2046656611","https://openalex.org/W2050721857","https://openalex.org/W2057793636","https://openalex.org/W2074490119","https://openalex.org/W2077386490","https://openalex.org/W2082565035","https://openalex.org/W2084619201","https://openalex.org/W2090422756","https://openalex.org/W2093446113","https://openalex.org/W2096183628","https://openalex.org/W2099521715","https://openalex.org/W2100371004","https://openalex.org/W2105249086","https://openalex.org/W2112090702","https://openalex.org/W2116117181","https://openalex.org/W2116447934","https://openalex.org/W2120423098","https://openalex.org/W2120428260","https://openalex.org/W2124166542","https://openalex.org/W2124354935","https://openalex.org/W2130687290","https://openalex.org/W2130790725","https://openalex.org/W2138003801","https://openalex.org/W2140280811","https://openalex.org/W2141144378","https://openalex.org/W2159710443","https://openalex.org/W2160313295","https://openalex.org/W2163485494","https://openalex.org/W2166574880","https://openalex.org/W2178465836","https://openalex.org/W2191274703","https://openalex.org/W2523588407","https://openalex.org/W2531496612","https://openalex.org/W2549976854","https://openalex.org/W2581439210","https://openalex.org/W2761205072","https://openalex.org/W2789631796","https://openalex.org/W2907043693","https://openalex.org/W2908670560","https://openalex.org/W2912312581","https://openalex.org/W2937420412","https://openalex.org/W2949332308","https://openalex.org/W2973129733","https://openalex.org/W2981958531","https://openalex.org/W3007888226","https://openalex.org/W3008459824","https://openalex.org/W3013264051","https://openalex.org/W3116125956","https://openalex.org/W3120506419","https://openalex.org/W3196854072","https://openalex.org/W3201074858","https://openalex.org/W4200555891","https://openalex.org/W4205118710","https://openalex.org/W4213450471","https://openalex.org/W4254808359","https://openalex.org/W4288060525","https://openalex.org/W6677090979","https://openalex.org/W6679290402","https://openalex.org/W6681254755"],"related_works":["https://openalex.org/W2372590961","https://openalex.org/W4214893532","https://openalex.org/W4294306415","https://openalex.org/W883652255","https://openalex.org/W2027176979","https://openalex.org/W2028503915","https://openalex.org/W2365965409","https://openalex.org/W2332892177","https://openalex.org/W4200117979","https://openalex.org/W2366109092"],"abstract_inverted_index":{"BACKGROUND:":[0],"Accurate":[1],"identification":[2],"of":[3,17,51,103],"protein":[4,30,85,131,142,154,158,168,200,210],"complexes":[5,86,211],"in":[6,28],"protein-protein":[7],"interaction":[8],"(PPI)":[9],"networks":[10],"is":[11,97,112,138,146,162,176],"crucial":[12],"for":[13,198],"understanding":[14],"the":[15,24,42,49,52,101,104,122,167,180,190,203,209,214],"principles":[16],"cellular":[18],"organization.":[19],"Most":[20],"computational":[21],"methods":[22,54,61,197],"ignore":[23],"fact":[25],"that":[26,189,208],"proteins":[27,151],"a":[29,33,78,108,135,141,157],"complex":[31,132,143,159],"have":[32,217],"functional":[34,115,204],"similarity":[35],"and":[36,39,45,91,117,121,140,152],"are":[37,55,127],"co-localized":[38],"co-expressed":[40],"at":[41],"same":[43],"place":[44],"time,":[46],"respectively.":[47],"Meanwhile,":[48],"parameters":[50,102,183],"current":[53],"specified":[56],"by":[57,213],"users,":[58],"so":[59],"these":[60,73],"cannot":[62],"effectively":[63],"deal":[64],"with":[65,87],"different":[66],"input":[67],"PPI":[68,110],"networks.":[69],"RESULT:":[70],"To":[71],"address":[72],"issues,":[74],"this":[75],"study":[76],"proposes":[77],"new":[79],"method":[80,193],"called":[81],"MP-AHSA":[82,192,215],"to":[83,99,129,148,164,178],"detect":[84,149],"Multiple":[88],"Properties":[89],"(MP),":[90],"an":[92,171],"Adaptation":[93],"Harmony":[94],"Search":[95],"Algorithm":[96],"developed":[98,177],"optimize":[100],"MP":[105,181],"algorithm.":[106],"First,":[107],"weighted":[109],"network":[111],"constructed":[113],"using":[114],"annotations,":[116],"multiple":[118],"biological":[119,219],"properties":[120],"Markov":[123],"cluster":[124],"algorithm":[125,175,216],"(MCL)":[126],"used":[128],"mine":[130],"cores.":[133],"Then,":[134],"fitness":[136],"function":[137],"defined,":[139],"forming":[144],"strategy":[145,161],"designed":[147],"attachment":[150],"form":[153],"complexes.":[155,169,201],"Next,":[156],"filtering":[160],"formulated":[163],"filter":[165],"out":[166],"Finally,":[170],"adaptation":[172],"harmony":[173],"search":[174],"determine":[179],"algorithm's":[182],"automatically.":[184],"CONCLUSIONS:":[185],"Experimental":[186],"results":[187],"show":[188],"proposed":[191],"outperforms":[194],"14":[195],"state-of-the-art":[196],"identifying":[199],"Also,":[202],"enrichment":[205],"analyses":[206],"reveal":[207],"identified":[212],"significant":[218],"relevance.":[220]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
