{"id":"https://openalex.org/W3216227965","doi":"https://doi.org/10.1109/tcbb.2022.3231489","title":"Parallel Exchange of Randomized SubGraphs for Optimization of Network Alignment: PERSONA","display_name":"Parallel Exchange of Randomized SubGraphs for Optimization of Network Alignment: PERSONA","publication_year":2022,"publication_date":"2022-12-22","ids":{"openalex":"https://openalex.org/W3216227965","doi":"https://doi.org/10.1109/tcbb.2022.3231489","mag":"3216227965","pmid":"https://pubmed.ncbi.nlm.nih.gov/37015402"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2022.3231489","is_oa":true,"landing_page_url":"https://doi.org/10.1109/tcbb.2022.3231489","pdf_url":"https://ieeexplore.ieee.org/ielx7/8857/10144451/09996385.pdf","source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","datacite","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://ieeexplore.ieee.org/ielx7/8857/10144451/09996385.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5067492217","display_name":"Erhun Giray Tuncay","orcid":"https://orcid.org/0000-0002-1407-7362"},"institutions":[{"id":"https://openalex.org/I2802635041","display_name":"Technische Informationsbibliothek (TIB)","ror":"https://ror.org/04aj4c181","country_code":"DE","type":"archive","lineage":["https://openalex.org/I2802635041","https://openalex.org/I315704651"]},{"id":"https://openalex.org/I75951250","display_name":"Freie Universit\u00e4t Berlin","ror":"https://ror.org/046ak2485","country_code":"DE","type":"education","lineage":["https://openalex.org/I75951250"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Erhun Giray Tuncay","raw_affiliation_strings":["Freie Universit&#x00E4;t Berlin, Berlin, Germany","TIB - Leibniz Information Centre for Science & Technology, Hannover, Germany"],"raw_orcid":"https://orcid.org/0000-0002-1407-7362","affiliations":[{"raw_affiliation_string":"Freie Universit&#x00E4;t Berlin, Berlin, Germany","institution_ids":["https://openalex.org/I75951250"]},{"raw_affiliation_string":"TIB - Leibniz Information Centre for Science & Technology, Hannover, Germany","institution_ids":["https://openalex.org/I2802635041"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076719875","display_name":"R\u0131za Cenk Erdur","orcid":"https://orcid.org/0000-0001-6124-6352"},"institutions":[{"id":"https://openalex.org/I41641357","display_name":"Ege University","ror":"https://ror.org/02eaafc18","country_code":"TR","type":"education","lineage":["https://openalex.org/I41641357"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"R\u0131za Cenk Erdur","raw_affiliation_strings":["Ege University, &#x0130;zmir, Turkey"],"raw_orcid":"https://orcid.org/0000-0001-6124-6352","affiliations":[{"raw_affiliation_string":"Ege University, &#x0130;zmir, Turkey","institution_ids":["https://openalex.org/I41641357"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012229905","display_name":"Tim Conrad","orcid":"https://orcid.org/0000-0002-5590-5726"},"institutions":[{"id":"https://openalex.org/I195893171","display_name":"Zuse Institute Berlin","ror":"https://ror.org/02eva5865","country_code":"DE","type":"facility","lineage":["https://openalex.org/I195893171"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Tim Conrad","raw_affiliation_strings":["Zuse Institute Berlin, Berlin, Germany"],"raw_orcid":"https://orcid.org/0000-0002-5590-5726","affiliations":[{"raw_affiliation_string":"Zuse Institute Berlin, Berlin, Germany","institution_ids":["https://openalex.org/I195893171"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0784,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.35044944,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"20","issue":"3","first_page":"2064","last_page":"2077"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9991000294685364,"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":0.9991000294685364,"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":0.953000009059906,"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":0.9430999755859375,"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/heuristics","display_name":"Heuristics","score":0.7655024528503418},{"id":"https://openalex.org/keywords/persona","display_name":"Persona","score":0.6838200092315674},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6606420278549194},{"id":"https://openalex.org/keywords/relevance","display_name":"Relevance (law)","score":0.6439763307571411},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.6250584125518799},{"id":"https://openalex.org/keywords/node","display_name":"Node (physics)","score":0.5482568740844727},{"id":"https://openalex.org/keywords/particle-swarm-optimization","display_name":"Particle swarm optimization","score":0.4551141858100891},{"id":"https://openalex.org/keywords/space","display_name":"Space (punctuation)","score":0.4267596900463104},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.37978288531303406},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3797251582145691},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.34271180629730225},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.2625143527984619},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.21323120594024658},{"id":"https://openalex.org/keywords/human\u2013computer-interaction","display_name":"Human\u2013computer interaction","score":0.17929914593696594},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.08191227912902832}],"concepts":[{"id":"https://openalex.org/C127705205","wikidata":"https://www.wikidata.org/wiki/Q5748245","display_name":"Heuristics","level":2,"score":0.7655024528503418},{"id":"https://openalex.org/C313442","wikidata":"https://www.wikidata.org/wiki/Q778556","display_name":"Persona","level":2,"score":0.6838200092315674},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6606420278549194},{"id":"https://openalex.org/C158154518","wikidata":"https://www.wikidata.org/wiki/Q7310970","display_name":"Relevance (law)","level":2,"score":0.6439763307571411},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.6250584125518799},{"id":"https://openalex.org/C62611344","wikidata":"https://www.wikidata.org/wiki/Q1062658","display_name":"Node (physics)","level":2,"score":0.5482568740844727},{"id":"https://openalex.org/C85617194","wikidata":"https://www.wikidata.org/wiki/Q2072794","display_name":"Particle swarm optimization","level":2,"score":0.4551141858100891},{"id":"https://openalex.org/C2778572836","wikidata":"https://www.wikidata.org/wiki/Q380933","display_name":"Space (punctuation)","level":2,"score":0.4267596900463104},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.37978288531303406},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3797251582145691},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.34271180629730225},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2625143527984619},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.21323120594024658},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.17929914593696594},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.08191227912902832},{"id":"https://openalex.org/C66938386","wikidata":"https://www.wikidata.org/wiki/Q633538","display_name":"Structural engineering","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000066506","descriptor_name":"Heuristics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000066506","descriptor_name":"Heuristics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000066506","descriptor_name":"Heuristics","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":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":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1109/tcbb.2022.3231489","is_oa":true,"landing_page_url":"https://doi.org/10.1109/tcbb.2022.3231489","pdf_url":"https://ieeexplore.ieee.org/ielx7/8857/10144451/09996385.pdf","source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37015402","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37015402","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null},{"id":"pmh:oai:refubium.fu-berlin.de:fub188/40417","is_oa":true,"landing_page_url":"https://refubium.fu-berlin.de/handle/fub188/40417","pdf_url":"https://refubium.fu-berlin.de/bitstream/fub188/40417/1/Parallel_Exchange_of_Randomized_SubGraphs_for_Optimization_of_Network_Alignment_PERSONA.pdf","source":{"id":"https://openalex.org/S4306402444","display_name":"Refubium (Universit\u00e4tsbibliothek der Freien Universit\u00e4t Berlin)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I75951250","host_organization_name":"Freie Universit\u00e4t Berlin","host_organization_lineage":["https://openalex.org/I75951250"],"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":"","raw_type":"doc-type:article"},{"id":"doi:10.17169/refubium-40138","is_oa":true,"landing_page_url":"https://doi.org/10.17169/refubium-40138","pdf_url":null,"source":{"id":"https://openalex.org/S7407052913","display_name":"Universit\u00e4tsbibliothek der FU Berlin Hochschulschriftenstelle u. Dokumentenserver","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","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.1109/tcbb.2022.3231489","is_oa":true,"landing_page_url":"https://doi.org/10.1109/tcbb.2022.3231489","pdf_url":"https://ieeexplore.ieee.org/ielx7/8857/10144451/09996385.pdf","source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320310862","display_name":"Colorado School of Mines","ror":"https://ror.org/04raf6v53"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3216227965.pdf","grobid_xml":"https://content.openalex.org/works/W3216227965.grobid-xml"},"referenced_works_count":60,"referenced_works":["https://openalex.org/W1488296747","https://openalex.org/W1583981513","https://openalex.org/W1686696692","https://openalex.org/W1779639821","https://openalex.org/W1995683190","https://openalex.org/W2043764521","https://openalex.org/W2055043387","https://openalex.org/W2092123736","https://openalex.org/W2095266828","https://openalex.org/W2099364528","https://openalex.org/W2103017472","https://openalex.org/W2108984616","https://openalex.org/W2118853019","https://openalex.org/W2119021615","https://openalex.org/W2119151462","https://openalex.org/W2125810455","https://openalex.org/W2127957894","https://openalex.org/W2128408632","https://openalex.org/W2130237248","https://openalex.org/W2130810176","https://openalex.org/W2131298592","https://openalex.org/W2136845897","https://openalex.org/W2137648512","https://openalex.org/W2140084895","https://openalex.org/W2142678478","https://openalex.org/W2155834877","https://openalex.org/W2158714788","https://openalex.org/W2163485494","https://openalex.org/W2164928285","https://openalex.org/W2170241526","https://openalex.org/W2171108134","https://openalex.org/W2222512263","https://openalex.org/W2254156100","https://openalex.org/W2306608239","https://openalex.org/W2505369411","https://openalex.org/W2524167673","https://openalex.org/W2548028586","https://openalex.org/W2564310132","https://openalex.org/W2584993989","https://openalex.org/W2587997094","https://openalex.org/W2602125535","https://openalex.org/W2607363173","https://openalex.org/W2759651139","https://openalex.org/W2778129513","https://openalex.org/W2799059383","https://openalex.org/W2890382235","https://openalex.org/W2967236170","https://openalex.org/W3100057034","https://openalex.org/W4210702584","https://openalex.org/W4231566795","https://openalex.org/W4249580866","https://openalex.org/W6654087933","https://openalex.org/W6677712588","https://openalex.org/W6678090203","https://openalex.org/W6682642761","https://openalex.org/W6690731163","https://openalex.org/W6745097058","https://openalex.org/W6773102187","https://openalex.org/W6797653620","https://openalex.org/W6801814466"],"related_works":["https://openalex.org/W2795366572","https://openalex.org/W2886588594","https://openalex.org/W3005214328","https://openalex.org/W2920961600","https://openalex.org/W3091061106","https://openalex.org/W2610743940","https://openalex.org/W4312802148","https://openalex.org/W4285553851","https://openalex.org/W2892165056","https://openalex.org/W2098964748"],"abstract_inverted_index":{"The":[0,128,188],"aim":[1],"of":[2,56,72,109,118,134,157,165,175],"Network":[3],"Alignment":[4],"in":[5,123],"Protein-Protein":[6],"Interaction":[7],"Networks":[8],"is":[9,26],"discovering":[10],"functionally":[11],"similar":[12],"regions":[13],"between":[14],"compared":[15],"organisms.":[16],"One":[17,59],"major":[18],"compromise":[19],"for":[20,62,115,198],"solving":[21,63],"a":[22,83,110,124,135,138],"network":[23],"alignment":[24,36,39,74,121],"problem":[25,122,181],"the":[27,53,69,119,131,162,180],"trade-off":[28],"among":[29],"multiple":[30],"similarity":[31,203],"objectives":[32,48],"while":[33,45,97],"applying":[34],"an":[35],"strategy.":[37],"An":[38],"may":[40,66],"lose":[41],"its":[42],"biological":[43],"relevance":[44,55],"favoring":[46],"certain":[47],"upon":[49,155],"others":[50],"due":[51],"to":[52,91],"actual":[54],"unfavored":[57],"objectives.":[58,204],"possible":[60],"solution":[61,136],"this":[64],"issue":[65],"be":[67,186],"blending":[68],"stronger":[70,132,152],"aspects":[71],"various":[73],"strategies":[75],"until":[76],"achieving":[77],"mature":[78],"solutions.":[79,160],"This":[80],"study":[81],"proposes":[82],"parallel":[84,176],"approach":[85],"called":[86],"PERSONA":[87,192],"that":[88,113,140,179],"allows":[89],"aligners":[90,102],"share":[92],"their":[93,104,150],"partial":[94,159],"solutions":[95,117],"continuously":[96],"they":[98,141],"progress.":[99],"All":[100],"these":[101],"pursue":[103],"particular":[105],"heuristics":[106,164],"as":[107,137],"part":[108],"particle":[111],"swarm":[112],"searches":[114],"multi-objective":[116],"same":[120],"reactive":[125],"actor":[126,167],"environment.":[127],"actors":[129,147],"use":[130],"portion":[133],"subgraph":[139],"receive":[142],"from":[143],"leading":[144],"or":[145],"other":[146],"and":[148,196,201],"send":[149],"own":[151],"subgraphs":[153],"back":[154],"evaluation":[156],"those":[158],"Moreover,":[161],"individual":[163],"each":[166,173],"takes":[168],"randomized":[169],"parameter":[170],"values":[171],"at":[172],"cycle":[174],"execution":[177],"so":[178],"search":[182],"space":[183],"can":[184],"thoroughly":[185],"investigated.":[187],"results":[189],"achieved":[190],"with":[191],"are":[193],"remarkably":[194],"optimized":[195],"balanced":[197],"both":[199],"topological":[200],"node":[202]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}
