{"id":"https://openalex.org/W2795829718","doi":"https://doi.org/10.1109/tcbb.2018.2822709","title":"Measuring Boundedness for Protein Complex Identification in PPI Networks","display_name":"Measuring Boundedness for Protein Complex Identification in PPI Networks","publication_year":2018,"publication_date":"2018-04-03","ids":{"openalex":"https://openalex.org/W2795829718","doi":"https://doi.org/10.1109/tcbb.2018.2822709","mag":"2795829718","pmid":"https://pubmed.ncbi.nlm.nih.gov/29993661"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2018.2822709","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2018.2822709","pdf_url":null,"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":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":"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/A5024619357","display_name":"Tiantian He","orcid":"https://orcid.org/0000-0003-4839-681X"},"institutions":[{"id":"https://openalex.org/I14243506","display_name":"Hong Kong Polytechnic University","ror":"https://ror.org/0030zas98","country_code":"HK","type":"education","lineage":["https://openalex.org/I14243506"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Tiantian He","raw_affiliation_strings":["Department of Computing, The Hong Kong Polytechnic University, Hung Hom, Hong Kong SAR, China"],"raw_orcid":"https://orcid.org/0000-0003-4839-681X","affiliations":[{"raw_affiliation_string":"Department of Computing, The Hong Kong Polytechnic University, Hung Hom, Hong Kong SAR, China","institution_ids":["https://openalex.org/I14243506"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5107049960","display_name":"Keith C. C. Chan","orcid":"https://orcid.org/0000-0001-7962-6564"},"institutions":[{"id":"https://openalex.org/I14243506","display_name":"Hong Kong Polytechnic University","ror":"https://ror.org/0030zas98","country_code":"HK","type":"education","lineage":["https://openalex.org/I14243506"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Keith C. C. Chan","raw_affiliation_strings":["Department of Computing, The Hong Kong Polytechnic University, Hung Hom, Hong Kong SAR, China"],"raw_orcid":"https://orcid.org/0000-0001-7962-6564","affiliations":[{"raw_affiliation_string":"Department of Computing, The Hong Kong Polytechnic University, Hung Hom, Hong Kong SAR, China","institution_ids":["https://openalex.org/I14243506"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I14243506"],"apc_list":null,"apc_paid":null,"fwci":0.5772,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.63746946,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"16","issue":"3","first_page":"967","last_page":"979"},"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":0.9857000112533569,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9768000245094299,"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/jaccard-index","display_name":"Jaccard index","score":0.8882283568382263},{"id":"https://openalex.org/keywords/social-connectedness","display_name":"Social connectedness","score":0.7719812393188477},{"id":"https://openalex.org/keywords/measure","display_name":"Measure (data warehouse)","score":0.6889178156852722},{"id":"https://openalex.org/keywords/protein-function-prediction","display_name":"Protein function prediction","score":0.6388352513313293},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.5976234674453735},{"id":"https://openalex.org/keywords/bounded-function","display_name":"Bounded function","score":0.5929591655731201},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.563168466091156},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5456947684288025},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.5273352861404419},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4672541320323944},{"id":"https://openalex.org/keywords/degree","display_name":"Degree (music)","score":0.4660875201225281},{"id":"https://openalex.org/keywords/similarity-measure","display_name":"Similarity measure","score":0.4557982087135315},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.36750346422195435},{"id":"https://openalex.org/keywords/protein-function","display_name":"Protein function","score":0.3038270175457001},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.22908270359039307},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1776529848575592},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.16615426540374756},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11897912621498108},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09087231755256653}],"concepts":[{"id":"https://openalex.org/C203519979","wikidata":"https://www.wikidata.org/wiki/Q865360","display_name":"Jaccard index","level":3,"score":0.8882283568382263},{"id":"https://openalex.org/C201943243","wikidata":"https://www.wikidata.org/wiki/Q7551008","display_name":"Social connectedness","level":2,"score":0.7719812393188477},{"id":"https://openalex.org/C2780009758","wikidata":"https://www.wikidata.org/wiki/Q6804172","display_name":"Measure (data warehouse)","level":2,"score":0.6889178156852722},{"id":"https://openalex.org/C207060522","wikidata":"https://www.wikidata.org/wiki/Q7251473","display_name":"Protein function prediction","level":4,"score":0.6388352513313293},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.5976234674453735},{"id":"https://openalex.org/C34388435","wikidata":"https://www.wikidata.org/wiki/Q2267362","display_name":"Bounded function","level":2,"score":0.5929591655731201},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.563168466091156},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5456947684288025},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5273352861404419},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4672541320323944},{"id":"https://openalex.org/C2775997480","wikidata":"https://www.wikidata.org/wiki/Q586277","display_name":"Degree (music)","level":2,"score":0.4660875201225281},{"id":"https://openalex.org/C2776517306","wikidata":"https://www.wikidata.org/wiki/Q29017317","display_name":"Similarity measure","level":2,"score":0.4557982087135315},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.36750346422195435},{"id":"https://openalex.org/C2986374874","wikidata":"https://www.wikidata.org/wiki/Q8054","display_name":"Protein function","level":3,"score":0.3038270175457001},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.22908270359039307},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1776529848575592},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.16615426540374756},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11897912621498108},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09087231755256653},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C542102704","wikidata":"https://www.wikidata.org/wiki/Q183257","display_name":"Psychotherapist","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","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":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":2,"locations":[{"id":"doi:10.1109/tcbb.2018.2822709","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2018.2822709","pdf_url":null,"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":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":"journal-article"},{"id":"pmid:29993661","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29993661","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}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":49,"referenced_works":["https://openalex.org/W177104057","https://openalex.org/W585702508","https://openalex.org/W1485582261","https://openalex.org/W1513501940","https://openalex.org/W1552669063","https://openalex.org/W1958717431","https://openalex.org/W1971013885","https://openalex.org/W1974515660","https://openalex.org/W1980860611","https://openalex.org/W1986214964","https://openalex.org/W1990567865","https://openalex.org/W1991008210","https://openalex.org/W2007448777","https://openalex.org/W2010793412","https://openalex.org/W2037036397","https://openalex.org/W2050721857","https://openalex.org/W2060948468","https://openalex.org/W2079665010","https://openalex.org/W2082565035","https://openalex.org/W2084619201","https://openalex.org/W2090422756","https://openalex.org/W2099982459","https://openalex.org/W2103017472","https://openalex.org/W2107067224","https://openalex.org/W2108491719","https://openalex.org/W2116117181","https://openalex.org/W2116447934","https://openalex.org/W2121564430","https://openalex.org/W2132290594","https://openalex.org/W2132582966","https://openalex.org/W2136850043","https://openalex.org/W2137786672","https://openalex.org/W2138003801","https://openalex.org/W2140280811","https://openalex.org/W2144393227","https://openalex.org/W2148043260","https://openalex.org/W2152495216","https://openalex.org/W2162038040","https://openalex.org/W2162891889","https://openalex.org/W2163485494","https://openalex.org/W2165533101","https://openalex.org/W2166557397","https://openalex.org/W2166574880","https://openalex.org/W2325276118","https://openalex.org/W2513497485","https://openalex.org/W2886992141","https://openalex.org/W4233437719","https://openalex.org/W4236956086","https://openalex.org/W6670200328"],"related_works":["https://openalex.org/W2084099224","https://openalex.org/W2612383974","https://openalex.org/W3123940961","https://openalex.org/W2151474089","https://openalex.org/W2171272270","https://openalex.org/W4285136945","https://openalex.org/W2094822546","https://openalex.org/W4388708026","https://openalex.org/W1969080446","https://openalex.org/W3108941781"],"abstract_inverted_index":{"The":[0],"problem":[1,16],"of":[2,17,43,46,57,138,148],"identifying":[3,18,193],"protein":[4,36,142,194],"complexes":[5,37,195],"in":[6,21,99,196],"Protein-Protein":[7],"Interaction":[8],"(PPI)":[9],"networks":[10],"is":[11,51,113,131,188],"usually":[12],"formulated":[13],"as":[14,53,124,134],"the":[15,41,100,106,110,119,128,135,146,170,183],"dense":[19],"regions":[20],"such":[22],"networks.":[23,198],"In":[24],"this":[25],"paper,":[26],"we":[27],"present":[28],"a":[29,44,49,58,72,158,164],"novel":[30],"approach,":[31],"called":[32],"TBPCI,":[33],"to":[34,76,115,161],"identify":[35,141],"based":[38,94],"instead":[39],"on":[40,95,105],"concept":[42],"measure":[45,50,62,82],"boundedness.":[47,139],"Such":[48],"defined":[52],"an":[54,80,189],"objective":[55,111,129],"function":[56,112],"Jaccard":[59],"Index-based":[60],"connectedness":[61],"which":[63,83],"takes":[64,84],"into":[65,85,169],"consideration":[66,86],"how":[67,87,117],"much":[68,88],"two":[69,89,108],"proteins":[70,91,120],"within":[71],"network":[73],"are":[74,92],"connected":[75],"each":[77],"other,":[78],"and":[79,127,182],"association":[81],"connecting":[90],"associated":[93],"their":[96],"attributes":[97],"found":[98],"Gene":[101],"Ontology":[102],"database.":[103],"Based":[104],"above":[107],"measures,":[109],"derived":[114],"capture":[116],"strong":[118],"can":[121],"be":[122,167],"considered":[123],"bounded":[125],"together":[126],"value":[130],"therefore":[132],"referred":[133],"aggregated":[136],"degree":[137,147],"To":[140],"complexes,":[143],"TBPCI":[144,156,173],"computes":[145],"boundedness":[149],"between":[150],"all":[151],"possible":[152],"pairwise":[153],"proteins.":[154],"Then,":[155],"uses":[157],"Breadth-First-Search":[159],"method":[160],"determine":[162],"whether":[163],"protein-pair":[165],"should":[166],"incorporated":[168],"same":[171],"complex.":[172],"has":[174],"been":[175],"tested":[176],"with":[177],"several":[178],"real":[179],"data":[180],"sets":[181],"experimental":[184],"results":[185],"show":[186],"it":[187],"effective":[190],"approach":[191],"for":[192],"PPI":[197]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":3}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}
