{"id":"https://openalex.org/W4413658080","doi":"https://doi.org/10.1007/s41109-025-00727-6","title":"Positive impact of structural asymmetries in PPI networks on protein complex detection","display_name":"Positive impact of structural asymmetries in PPI networks on protein complex detection","publication_year":2025,"publication_date":"2025-08-26","ids":{"openalex":"https://openalex.org/W4413658080","doi":"https://doi.org/10.1007/s41109-025-00727-6"},"language":"en","primary_location":{"id":"doi:10.1007/s41109-025-00727-6","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s41109-025-00727-6","pdf_url":"https://appliednetsci.springeropen.com/counter/pdf/10.1007/s41109-025-00727-6","source":{"id":"https://openalex.org/S3035517252","display_name":"Applied Network Science","issn_l":"2364-8228","issn":["2364-8228"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319965","host_organization_name":"Springer Nature","host_organization_lineage":["https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Applied Network Science","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://appliednetsci.springeropen.com/counter/pdf/10.1007/s41109-025-00727-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5094024191","display_name":"Lukas Papik","orcid":null},"institutions":[{"id":"https://openalex.org/I142208455","display_name":"VSB - Technical University of Ostrava","ror":"https://ror.org/05x8mcb75","country_code":"CZ","type":"education","lineage":["https://openalex.org/I142208455"]}],"countries":["CZ"],"is_corresponding":true,"raw_author_name":"Lukas Papik","raw_affiliation_strings":["Department of Computer Science, VSB - Technical University Ostrava, 17. listopadu 15/2172, 708 00, Ostrava, Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, VSB - Technical University Ostrava, 17. listopadu 15/2172, 708 00, Ostrava, Czech Republic","institution_ids":["https://openalex.org/I142208455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054972868","display_name":"Eli\u0161ka Ochodkov\u00e1","orcid":"https://orcid.org/0000-0001-8892-8900"},"institutions":[{"id":"https://openalex.org/I142208455","display_name":"VSB - Technical University of Ostrava","ror":"https://ror.org/05x8mcb75","country_code":"CZ","type":"education","lineage":["https://openalex.org/I142208455"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Eliska Ochodkova","raw_affiliation_strings":["Department of Computer Science, VSB - Technical University Ostrava, 17. listopadu 15/2172, 708 00, Ostrava, Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, VSB - Technical University Ostrava, 17. listopadu 15/2172, 708 00, Ostrava, Czech Republic","institution_ids":["https://openalex.org/I142208455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016480427","display_name":"Eva Kriegov\u00e1","orcid":"https://orcid.org/0000-0002-8969-4197"},"institutions":[{"id":"https://openalex.org/I70703428","display_name":"Palack\u00fd University Olomouc","ror":"https://ror.org/04qxnmv42","country_code":"CZ","type":"education","lineage":["https://openalex.org/I70703428"]},{"id":"https://openalex.org/I4210107161","display_name":"University Hospital Olomouc","ror":"https://ror.org/01jxtne23","country_code":"CZ","type":"healthcare","lineage":["https://openalex.org/I4210107161"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Eva Kriegova","raw_affiliation_strings":["Department of Immunology, Palacky University Olomouc and University Hospital Olomouc, Krizkovskeho, 779 00, Olomouc, Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Immunology, Palacky University Olomouc and University Hospital Olomouc, Krizkovskeho, 779 00, Olomouc, Czech Republic","institution_ids":["https://openalex.org/I4210107161","https://openalex.org/I70703428"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054131585","display_name":"Milo\u0161 Kud\u011blka","orcid":"https://orcid.org/0000-0002-7219-1008"},"institutions":[{"id":"https://openalex.org/I142208455","display_name":"VSB - Technical University of Ostrava","ror":"https://ror.org/05x8mcb75","country_code":"CZ","type":"education","lineage":["https://openalex.org/I142208455"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Milos Kudelka","raw_affiliation_strings":["Department of Computer Science, VSB - Technical University Ostrava, 17. listopadu 15/2172, 708 00, Ostrava, Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, VSB - Technical University Ostrava, 17. listopadu 15/2172, 708 00, Ostrava, Czech Republic","institution_ids":["https://openalex.org/I142208455"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5094024191"],"corresponding_institution_ids":["https://openalex.org/I142208455"],"apc_list":{"value":790,"currency":"GBP","value_usd":969},"apc_paid":{"value":790,"currency":"GBP","value_usd":969},"fwci":0.6802,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.72563021,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"10","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9976999759674072,"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":0.9933000206947327,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3674156665802002},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3539845943450928},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.33820968866348267},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2580972909927368}],"concepts":[{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3674156665802002},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3539845943450928},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.33820968866348267},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2580972909927368}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1007/s41109-025-00727-6","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s41109-025-00727-6","pdf_url":"https://appliednetsci.springeropen.com/counter/pdf/10.1007/s41109-025-00727-6","source":{"id":"https://openalex.org/S3035517252","display_name":"Applied Network Science","issn_l":"2364-8228","issn":["2364-8228"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319965","host_organization_name":"Springer Nature","host_organization_lineage":["https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Applied Network Science","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:31fdc9dc76424b4baeee13ecaace0fb0","is_oa":true,"landing_page_url":"https://doaj.org/article/31fdc9dc76424b4baeee13ecaace0fb0","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":"Applied Network Science, Vol 10, Iss 1, Pp 1-29 (2025)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1007/s41109-025-00727-6","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s41109-025-00727-6","pdf_url":"https://appliednetsci.springeropen.com/counter/pdf/10.1007/s41109-025-00727-6","source":{"id":"https://openalex.org/S3035517252","display_name":"Applied Network Science","issn_l":"2364-8228","issn":["2364-8228"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319965","host_organization_name":"Springer Nature","host_organization_lineage":["https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Applied Network Science","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3487419101","display_name":null,"funder_award_id":"FNOl 0098892","funder_id":"https://openalex.org/F4320321798","funder_display_name":"Ministerstvo Zdravotnictv\u00ed Cesk\u00e9 Republiky"},{"id":"https://openalex.org/G3974059543","display_name":null,"funder_award_id":"0098892","funder_id":"https://openalex.org/F4320321798","funder_display_name":"Ministerstvo Zdravotnictv\u00ed Cesk\u00e9 Republiky"}],"funders":[{"id":"https://openalex.org/F4320321798","display_name":"Ministerstvo Zdravotnictv\u00ed Cesk\u00e9 Republiky","ror":"https://ror.org/00y6khe77"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4413658080.pdf","grobid_xml":"https://content.openalex.org/works/W4413658080.grobid-xml"},"referenced_works_count":42,"referenced_works":["https://openalex.org/W1570643690","https://openalex.org/W1998586430","https://openalex.org/W2006961239","https://openalex.org/W2082565035","https://openalex.org/W2084168100","https://openalex.org/W2096173332","https://openalex.org/W2097923880","https://openalex.org/W2100761975","https://openalex.org/W2107067224","https://openalex.org/W2116117181","https://openalex.org/W2116447934","https://openalex.org/W2128049108","https://openalex.org/W2131323902","https://openalex.org/W2131615228","https://openalex.org/W2136850043","https://openalex.org/W2154600255","https://openalex.org/W2165533101","https://openalex.org/W2168316093","https://openalex.org/W2409496124","https://openalex.org/W2439325218","https://openalex.org/W2908670560","https://openalex.org/W2910124299","https://openalex.org/W2917858269","https://openalex.org/W2950742983","https://openalex.org/W2980341789","https://openalex.org/W3023677370","https://openalex.org/W3036675046","https://openalex.org/W3121027314","https://openalex.org/W3201074858","https://openalex.org/W4212817532","https://openalex.org/W4225725885","https://openalex.org/W4281676089","https://openalex.org/W4291021611","https://openalex.org/W4298144280","https://openalex.org/W4308834893","https://openalex.org/W4309161067","https://openalex.org/W4384303408","https://openalex.org/W4393222396","https://openalex.org/W4400241564","https://openalex.org/W4400726535","https://openalex.org/W4403468966","https://openalex.org/W4409166938"],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2899084033","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W4391375266","https://openalex.org/W2078814861","https://openalex.org/W2527526854","https://openalex.org/W1976181487"],"abstract_inverted_index":{"Groups":[0],"of":[1,21,43,49,59,79,93,112,133,168,171,211],"two":[2,77,136,169],"or":[3],"more":[4,197],"proteins":[5,94],"interacting":[6],"to":[7,95,119],"form":[8],"protein":[9,60,97,103,203],"complexes":[10,23,39,98],"are":[11],"essential":[12],"for":[13,29,145,202,230],"cellular":[14],"activity.":[15],"Despite":[16],"their":[17,216],"importance,":[18],"our":[19,185,209],"knowledge":[20],"these":[22,38],"remains":[24],"limited,":[25],"underscoring":[26],"the":[27,44,56,80,113,117,121,125,131,151,212,223],"demand":[28],"robust":[30],"detection":[31,232],"methods":[32],"in":[33,67],"bioinformatics.":[34],"However,":[35],"accurately":[36],"identifying":[37,219],"is":[40,64],"challenging":[41],"because":[42],"complex":[45,204],"and":[46,140,148,153,175,199],"dynamic":[47],"structure":[48],"protein\u2013protein":[50],"interaction":[51],"(PPI)":[52],"networks,":[53],"compounded":[54],"by":[55,178],"asymmetric":[57,89],"nature":[58],"interactions;":[61],"this":[62,73],"feature":[63],"often":[65],"overlooked":[66],"conventional":[68],"PPI":[69,138],"network":[70,127],"analyses.":[71],"In":[72,156],"article,":[74],"we":[75,158,214],"present":[76],"variants":[78],"(Mutually":[81],"Dependent":[82],"Star":[83],"(mDepStar)":[84],"method.":[85],"The":[86,108],"method":[87,115],"uses":[88],"relationships":[90],"between":[91],"pairs":[92],"detect":[96],"around":[99],"a":[100,166,196],"single":[101],"(core)":[102],"from":[104,124],"its":[105],"local":[106,110],"interactions.":[107],"modified":[109],"variant":[111],"mDepStar":[114,134,189],"eliminates":[116],"need":[118],"use":[120],"information":[122],"obtained":[123],"whole":[126],"analysis.":[128],"We":[129],"evaluated":[130],"performance":[132],"on":[135],"established":[137],"networks":[139,144],"three":[141],"newly":[142],"constructed":[143],"Saccharomyces":[146],"cerevisiae":[147],"humans":[149],"using":[150],"BioGRID":[152],"STRING":[154],"databases.":[155],"addition,":[157],"created":[159],"new":[160],"Gene":[161],"Ontology":[162],"(GO)-based":[163],"references.":[164],"Using":[165],"combination":[167],"sets":[170],"measures,":[172],"mostly":[173],"known":[174],"partly":[176],"proposed":[177],"us,":[179],"together":[180],"with":[181],"GO":[182],"pair":[183],"similarity,":[184],"results":[186],"show":[187],"that":[188,221],"consistently":[190],"outperforms":[191],"seven":[192],"state-of-the-art":[193],"methods,":[194,213],"providing":[195],"accurate":[198],"reliable":[200],"tool":[201],"detection.":[205],"To":[206],"further":[207],"refine":[208],"understanding":[210],"examined":[215],"key":[217],"features,":[218],"those":[220],"yielded":[222],"best":[224],"results.":[225],"These":[226],"insights":[227],"provide":[228],"guidance":[229],"improving":[231],"methods.":[233]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
