{"id":"https://openalex.org/W2023170582","doi":"https://doi.org/10.1109/tcbb.2014.2359441","title":"A Bayesian Framework for Combining Protein and Network Topology Information for Predicting Protein-Protein Interactions","display_name":"A Bayesian Framework for Combining Protein and Network Topology Information for Predicting Protein-Protein Interactions","publication_year":2014,"publication_date":"2014-11-05","ids":{"openalex":"https://openalex.org/W2023170582","doi":"https://doi.org/10.1109/tcbb.2014.2359441","mag":"2023170582","pmid":"https://pubmed.ncbi.nlm.nih.gov/26357265"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2014.2359441","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2014.2359441","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":true,"oa_status":"green","oa_url":"http://hdl.handle.net/2066/132693","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022862389","display_name":"Adriana Birlutiu","orcid":"https://orcid.org/0000-0002-7267-2530"},"institutions":[{"id":"https://openalex.org/I145872427","display_name":"Radboud University Nijmegen","ror":"https://ror.org/016xsfp80","country_code":"NL","type":"education","lineage":["https://openalex.org/I145872427"]},{"id":"https://openalex.org/I4210140223","display_name":"1 Decembrie 1918 University","ror":"https://ror.org/04577k168","country_code":"RO","type":"education","lineage":["https://openalex.org/I4210140223"]}],"countries":["NL","RO"],"is_corresponding":false,"raw_author_name":"Adriana Birlutiu","raw_affiliation_strings":["Institute for Computing and Information Sciences, \u201c1 Decembrie 1918\u201d University, Alba-Iulia, Romania","Institute for Computing and Information Sciences, Radboud University Nijmegen, The Netherlands and Faculty of Science, 1 Decembrie 1918 University, Alba-Iulia, Romania#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Computing and Information Sciences, \u201c1 Decembrie 1918\u201d University, Alba-Iulia, Romania","institution_ids":["https://openalex.org/I4210140223"]},{"raw_affiliation_string":"Institute for Computing and Information Sciences, Radboud University Nijmegen, The Netherlands and Faculty of Science, 1 Decembrie 1918 University, Alba-Iulia, Romania#TAB#","institution_ids":["https://openalex.org/I145872427"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066766964","display_name":"Florence d\u2019Alch\u00e9\u2013Buc","orcid":"https://orcid.org/0000-0002-8353-0589"},"institutions":[{"id":"https://openalex.org/I4210107733","display_name":"Informatique, BioInformatique, Syst\u00e8mes Complexes","ror":"https://ror.org/01aqxgr98","country_code":"FR","type":"facility","lineage":["https://openalex.org/I277688954","https://openalex.org/I277688954","https://openalex.org/I4210107733","https://openalex.org/I88467170"]},{"id":"https://openalex.org/I4210128926","display_name":"Genopole (France)","ror":"https://ror.org/0380k9k47","country_code":"FR","type":"company","lineage":["https://openalex.org/I4210128926"]},{"id":"https://openalex.org/I88467170","display_name":"Universit\u00e9 d'\u00c9vry Val-d'Essonne","ror":"https://ror.org/00e96v939","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954","https://openalex.org/I88467170"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Florence d'Alche-Buc","raw_affiliation_strings":["IBISC, Universit\u00e9 d\u2019Evry-Val d\u2019Essonne, Genopole, France","IBISC, Universit\u00e9 d'Evry-Val d'Essonne, Genopole, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBISC, Universit\u00e9 d\u2019Evry-Val d\u2019Essonne, Genopole, France","institution_ids":["https://openalex.org/I4210107733","https://openalex.org/I4210128926","https://openalex.org/I88467170"]},{"raw_affiliation_string":"IBISC, Universit\u00e9 d'Evry-Val d'Essonne, Genopole, France","institution_ids":["https://openalex.org/I88467170"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015444349","display_name":"Tom Heskes","orcid":"https://orcid.org/0000-0002-3398-5235"},"institutions":[{"id":"https://openalex.org/I145872427","display_name":"Radboud University Nijmegen","ror":"https://ror.org/016xsfp80","country_code":"NL","type":"education","lineage":["https://openalex.org/I145872427"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Tom Heskes","raw_affiliation_strings":["Institute for Computing and Information Sciences, Radboud University Nijmegen, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Computing and Information Sciences, Radboud University Nijmegen, The Netherlands","institution_ids":["https://openalex.org/I145872427"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.78,"has_fulltext":false,"cited_by_count":16,"citation_normalized_percentile":{"value":0.69734151,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"12","issue":"3","first_page":"538","last_page":"550"},"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":0.9979000091552734,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.991599977016449,"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/computer-science","display_name":"Computer science","score":0.5176882743835449},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.46370014548301697},{"id":"https://openalex.org/keywords/bayesian-network","display_name":"Bayesian network","score":0.45805275440216064},{"id":"https://openalex.org/keywords/network-topology","display_name":"Network topology","score":0.4239156246185303},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.32546466588974},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2959807515144348},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.16722038388252258},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16292139887809753},{"id":"https://openalex.org/keywords/computer-network","display_name":"Computer network","score":0.16181087493896484}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5176882743835449},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.46370014548301697},{"id":"https://openalex.org/C33724603","wikidata":"https://www.wikidata.org/wiki/Q812540","display_name":"Bayesian network","level":2,"score":0.45805275440216064},{"id":"https://openalex.org/C199845137","wikidata":"https://www.wikidata.org/wiki/Q145490","display_name":"Network topology","level":2,"score":0.4239156246185303},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32546466588974},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2959807515144348},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.16722038388252258},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16292139887809753},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.16181087493896484},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","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":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005656","descriptor_name":"Fungal Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005656","descriptor_name":"Fungal Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005656","descriptor_name":"Fungal Proteins","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":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","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":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":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","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":false}],"locations_count":3,"locations":[{"id":"doi:10.1109/tcbb.2014.2359441","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2014.2359441","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:26357265","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26357265","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:ru:oai:repository.ubn.ru.nl:2066/132693","is_oa":true,"landing_page_url":"http://hdl.handle.net/2066/132693","pdf_url":null,"source":{"id":"https://openalex.org/S4306401843","display_name":"Data Archiving and Networked Services (DANS)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1322597698","host_organization_name":"Royal Netherlands Academy of Arts and Sciences","host_organization_lineage":["https://openalex.org/I1322597698"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Ieee/ACM Transactions on Computational Biology and Bioinformatics, 12, 538 - 550","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"pmh:ru:oai:repository.ubn.ru.nl:2066/132693","is_oa":true,"landing_page_url":"http://hdl.handle.net/2066/132693","pdf_url":null,"source":{"id":"https://openalex.org/S4306401843","display_name":"Data Archiving and Networked Services (DANS)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1322597698","host_organization_name":"Royal Netherlands Academy of Arts and Sciences","host_organization_lineage":["https://openalex.org/I1322597698"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Ieee/ACM Transactions on Computational Biology and Bioinformatics, 12, 538 - 550","raw_type":"info:eu-repo/semantics/article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.4300000071525574}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":78,"referenced_works":["https://openalex.org/W120668671","https://openalex.org/W130254859","https://openalex.org/W133025315","https://openalex.org/W141326033","https://openalex.org/W1544009106","https://openalex.org/W1755826643","https://openalex.org/W1849803292","https://openalex.org/W1936662467","https://openalex.org/W1966879929","https://openalex.org/W1977876909","https://openalex.org/W1983762150","https://openalex.org/W1993803315","https://openalex.org/W1994108141","https://openalex.org/W2008620264","https://openalex.org/W2021389024","https://openalex.org/W2027377866","https://openalex.org/W2034099022","https://openalex.org/W2038854622","https://openalex.org/W2041987655","https://openalex.org/W2045131140","https://openalex.org/W2047606947","https://openalex.org/W2050583899","https://openalex.org/W2051196362","https://openalex.org/W2060246191","https://openalex.org/W2062021443","https://openalex.org/W2062533676","https://openalex.org/W2074019887","https://openalex.org/W2074888914","https://openalex.org/W2077398039","https://openalex.org/W2087064593","https://openalex.org/W2099862356","https://openalex.org/W2100827857","https://openalex.org/W2101637493","https://openalex.org/W2112090702","https://openalex.org/W2112976607","https://openalex.org/W2113654464","https://openalex.org/W2115062943","https://openalex.org/W2118009636","https://openalex.org/W2118169662","https://openalex.org/W2119561170","https://openalex.org/W2125055259","https://openalex.org/W2125631472","https://openalex.org/W2128817214","https://openalex.org/W2130790725","https://openalex.org/W2133138357","https://openalex.org/W2133990480","https://openalex.org/W2138776954","https://openalex.org/W2145268834","https://openalex.org/W2145404290","https://openalex.org/W2145427519","https://openalex.org/W2147774652","https://openalex.org/W2148762636","https://openalex.org/W2149310258","https://openalex.org/W2152991541","https://openalex.org/W2153624566","https://openalex.org/W2156269526","https://openalex.org/W2156737316","https://openalex.org/W2159944419","https://openalex.org/W2160268549","https://openalex.org/W2162422091","https://openalex.org/W2163630575","https://openalex.org/W2164353258","https://openalex.org/W2166020074","https://openalex.org/W2167785155","https://openalex.org/W2175110005","https://openalex.org/W2185993773","https://openalex.org/W2213533165","https://openalex.org/W2911964244","https://openalex.org/W4247595764","https://openalex.org/W4293282039","https://openalex.org/W6605326799","https://openalex.org/W6605742777","https://openalex.org/W6648664407","https://openalex.org/W6676987060","https://openalex.org/W6677844391","https://openalex.org/W6681755325","https://openalex.org/W6686663181","https://openalex.org/W6688285680"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2086397253","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655"],"abstract_inverted_index":{"Computational":[0],"methods":[1,65],"for":[2,62,84],"predicting":[3,126],"protein-protein":[4,71,127],"interactions":[5,26,46,102],"are":[6],"important":[7],"tools":[8],"that":[9,66,111],"can":[10,29,59,67,120],"complement":[11],"high-throughput":[12],"technologies":[13],"and":[14,24,45,94,100],"guide":[15],"biologists":[16],"in":[17,49,125],"designing":[18],"new":[19],"laboratory":[20],"experiments.":[21],"The":[22,105],"proteins":[23,44,99],"the":[25,57,101],"between":[27,47,103],"them":[28],"be":[30,60],"described":[31],"by":[32,38,112,130],"a":[33,76,122],"network":[34,91],"which":[35],"is":[36,110],"characterized":[37],"several":[39],"topological":[40,54],"properties.":[41],"Information":[42],"about":[43,53],"them,":[48],"combination":[50],"with":[51],"knowledge":[52],"properties":[55],"of":[56,88,107,117,138],"network,":[58],"used":[61],"developing":[63],"computational":[64],"accurately":[68],"predict":[69],"unknown":[70],"interactions.":[72],"This":[73],"paper":[74],"presents":[75],"supervised":[77],"learning":[78],"framework":[79],"based":[80],"on":[81],"Bayesian":[82],"inference":[83],"combining":[85,113],"two":[86,115,136],"types":[87,116,137],"information:":[89],"i)":[90],"topology":[92],"information,":[93],"ii)":[95],"information":[96,118,139],"related":[97],"to":[98],"them.":[104],"motivation":[106],"our":[108],"model":[109],"these":[114,135],"one":[119],"achieve":[121],"better":[123],"accuracy":[124],"interactions,":[128],"than":[129],"using":[131],"models":[132],"constructed":[133],"from":[134],"independently.":[140]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":1}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}
