{"id":"https://openalex.org/W2276235820","doi":"https://doi.org/10.1186/s13637-016-0040-2","title":"Inference of protein-protein interaction networks from multiple heterogeneous data","display_name":"Inference of protein-protein interaction networks from multiple heterogeneous data","publication_year":2016,"publication_date":"2016-02-19","ids":{"openalex":"https://openalex.org/W2276235820","doi":"https://doi.org/10.1186/s13637-016-0040-2","mag":"2276235820","pmid":"https://pubmed.ncbi.nlm.nih.gov/26941784"},"language":"en","primary_location":{"id":"doi:10.1186/s13637-016-0040-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13637-016-0040-2","pdf_url":"https://bsb-eurasipjournals.springeropen.com/track/pdf/10.1186/s13637-016-0040-2","source":{"id":"https://openalex.org/S22696228","display_name":"EURASIP Journal on Bioinformatics and Systems Biology","issn_l":"1687-4145","issn":["1687-4145","1687-4153"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"EURASIP Journal on Bioinformatics and Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://bsb-eurasipjournals.springeropen.com/track/pdf/10.1186/s13637-016-0040-2","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101670805","display_name":"Lei Huang","orcid":"https://orcid.org/0000-0002-3131-6417"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Lei Huang","raw_affiliation_strings":["Department of Computer and Information Sciences, University of Delaware, 18 Amstel Avenue, Newark, 19716 DE USA","Department of Computer and Information Sciences, University of Delaware, 18 Amstel Avenue, Newark, 19716, DE, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer and Information Sciences, University of Delaware, 18 Amstel Avenue, Newark, 19716 DE USA","institution_ids":[]},{"raw_affiliation_string":"Department of Computer and Information Sciences, University of Delaware, 18 Amstel Avenue, Newark, 19716, DE, USA","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101595032","display_name":"Li Liao","orcid":"https://orcid.org/0000-0002-1197-1879"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Li Liao","raw_affiliation_strings":["Department of Computer and Information Sciences, University of Delaware, 18 Amstel Avenue, Newark, 19716 DE USA","Department of Computer and Information Sciences, University of Delaware, 18 Amstel Avenue, Newark, 19716, DE, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer and Information Sciences, University of Delaware, 18 Amstel Avenue, Newark, 19716 DE USA","institution_ids":[]},{"raw_affiliation_string":"Department of Computer and Information Sciences, University of Delaware, 18 Amstel Avenue, Newark, 19716, DE, USA","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5053761444","display_name":"Cathy Wu","orcid":"https://orcid.org/0000-0001-6379-8601"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cathy H. Wu","raw_affiliation_strings":["Department of Computer and Information Sciences, University of Delaware, 18 Amstel Avenue, Newark, 19716 DE USA ; Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, 19711 DE USA","Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, 19711, DE, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer and Information Sciences, University of Delaware, 18 Amstel Avenue, Newark, 19716 DE USA ; Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, 19711 DE USA","institution_ids":[]},{"raw_affiliation_string":"Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, 19711, DE, USA","institution_ids":["https://openalex.org/I86501945"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5101670805"],"corresponding_institution_ids":["https://openalex.org/I86501945"],"apc_list":null,"apc_paid":null,"fwci":1.3945,"has_fulltext":true,"cited_by_count":16,"citation_normalized_percentile":{"value":0.81423877,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"2016","issue":"1","first_page":"8","last_page":"8"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9962999820709229,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9944999814033508,"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":0.7843448519706726},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.7196569442749023},{"id":"https://openalex.org/keywords/kernel","display_name":"Kernel (algebra)","score":0.5787358283996582},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5294746160507202},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.4260081648826599},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.4157218933105469},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.41446876525878906},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.38967764377593994},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.357998788356781},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.12358799576759338}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7843448519706726},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.7196569442749023},{"id":"https://openalex.org/C74193536","wikidata":"https://www.wikidata.org/wiki/Q574844","display_name":"Kernel (algebra)","level":2,"score":0.5787358283996582},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5294746160507202},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.4260081648826599},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.4157218933105469},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.41446876525878906},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.38967764377593994},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.357998788356781},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.12358799576759338},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/s13637-016-0040-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13637-016-0040-2","pdf_url":"https://bsb-eurasipjournals.springeropen.com/track/pdf/10.1186/s13637-016-0040-2","source":{"id":"https://openalex.org/S22696228","display_name":"EURASIP Journal on Bioinformatics and Systems Biology","issn_l":"1687-4145","issn":["1687-4145","1687-4153"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"EURASIP Journal on Bioinformatics and Systems Biology","raw_type":"journal-article"},{"id":"pmid:26941784","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26941784","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":"EURASIP journal on bioinformatics & systems biology","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:4761017","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4761017","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"EURASIP J Bioinform Syst Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13637-016-0040-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13637-016-0040-2","pdf_url":"https://bsb-eurasipjournals.springeropen.com/track/pdf/10.1186/s13637-016-0040-2","source":{"id":"https://openalex.org/S22696228","display_name":"EURASIP Journal on Bioinformatics and Systems Biology","issn_l":"1687-4145","issn":["1687-4145","1687-4153"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"EURASIP Journal on Bioinformatics and Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1284298868","display_name":null,"funder_award_id":"P20 GM10344","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G1692384024","display_name":null,"funder_award_id":"NIGMS (P20 GM103446)","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G378664609","display_name":null,"funder_award_id":"NIGMS (P20 GM103446)","funder_id":"https://openalex.org/F4320314254","funder_display_name":"Delaware IDeA Network of Biomedical Research Excellence"},{"id":"https://openalex.org/G4359693134","display_name":null,"funder_award_id":"NIGMS","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4629778535","display_name":null,"funder_award_id":"P20 GM103446","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6718912342","display_name":null,"funder_award_id":"GM103446","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6905243600","display_name":null,"funder_award_id":"P20 GM103446","funder_id":"https://openalex.org/F4320314254","funder_display_name":"Delaware IDeA Network of Biomedical Research Excellence"},{"id":"https://openalex.org/G7089253139","display_name":null,"funder_award_id":"GM103446","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8479182213","display_name":null,"funder_award_id":"P20 GM103446","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320314254","display_name":"Delaware IDeA Network of Biomedical Research Excellence","ror":null},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2276235820.pdf","grobid_xml":"https://content.openalex.org/works/W2276235820.grobid-xml"},"referenced_works_count":48,"referenced_works":["https://openalex.org/W34646664","https://openalex.org/W179694669","https://openalex.org/W1575130722","https://openalex.org/W1774304772","https://openalex.org/W1854214752","https://openalex.org/W1872375678","https://openalex.org/W1966879929","https://openalex.org/W1975414584","https://openalex.org/W1979104937","https://openalex.org/W1988469564","https://openalex.org/W1990144966","https://openalex.org/W2000265519","https://openalex.org/W2024060531","https://openalex.org/W2024883193","https://openalex.org/W2039473152","https://openalex.org/W2045131140","https://openalex.org/W2050583899","https://openalex.org/W2055043387","https://openalex.org/W2060906118","https://openalex.org/W2063049279","https://openalex.org/W2065933707","https://openalex.org/W2067799837","https://openalex.org/W2081166868","https://openalex.org/W2097706952","https://openalex.org/W2098468136","https://openalex.org/W2102957091","https://openalex.org/W2104535569","https://openalex.org/W2105295920","https://openalex.org/W2107569009","https://openalex.org/W2118169662","https://openalex.org/W2128817214","https://openalex.org/W2129448726","https://openalex.org/W2130687290","https://openalex.org/W2136116685","https://openalex.org/W2138397600","https://openalex.org/W2141914340","https://openalex.org/W2144231753","https://openalex.org/W2147330086","https://openalex.org/W2161444669","https://openalex.org/W2161811112","https://openalex.org/W2167851075","https://openalex.org/W2168999611","https://openalex.org/W2169847772","https://openalex.org/W2221073334","https://openalex.org/W2570589864","https://openalex.org/W2745750801","https://openalex.org/W2911841449","https://openalex.org/W6601364618"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W4224009465","https://openalex.org/W4286629047","https://openalex.org/W4306321456","https://openalex.org/W4285260836","https://openalex.org/W3046775127","https://openalex.org/W2081647779","https://openalex.org/W3170094116","https://openalex.org/W4205958290"],"abstract_inverted_index":{"Protein-protein":[0],"interaction":[1],"(PPI)":[2],"prediction":[3,164],"is":[4,168],"a":[5,10,63,71,178],"central":[6],"task":[7],"in":[8,111,143],"achieving":[9],"better":[11],"understanding":[12],"of":[13,31,36,49,54,94,113,162,202],"cellular":[14],"and":[15,25,27,38,79,85,100,107,123,155,194,198],"intracellular":[16],"processes.":[17],"Because":[18],"high-throughput":[19],"experimental":[20],"methods":[21,42,151],"are":[22,28,119],"both":[23],"expensive":[24],"time-consuming,":[26],"also":[29],"known":[30],"suffering":[32],"from":[33,57,97],"the":[34,52,124,144,156,160,190],"problems":[35],"incompleteness":[37],"noise,":[39],"many":[40],"computational":[41],"have":[43,152],"been":[44,153],"developed,":[45],"with":[46,149],"varied":[47],"degrees":[48],"success.":[50],"However,":[51],"inference":[53,93],"PPI":[55,95,145,163],"network":[56],"multiple":[58,101],"heterogeneous":[59,102],"data":[60],"sources":[61],"remains":[62],"great":[64],"challenge.":[65],"In":[66],"this":[67],"work,":[68],"we":[69],"developed":[70],"novel":[72],"method":[73,91,185],"based":[74,128],"on":[75,129],"approximate":[76],"Bayesian":[77],"computation":[78],"modified":[80],"differential":[81],"evolution":[82],"sampling":[83],"(ABC-DEP)":[84],"regularized":[86],"laplacian":[87],"(RL)":[88],"kernel.":[89],"The":[90,116,184],"enables":[92],"networks":[96],"topological":[98],"properties":[99],"features":[103],"including":[104],"gene":[105],"expression":[106],"Pfam":[108],"domain":[109],"profiles,":[110],"forms":[112],"weighted":[114],"kernels.":[115],"optimal":[117,130,182],"weights":[118,131],"obtained":[120],"by":[121,166,170,211],"ABC-DEP,":[122],"kernel":[125],"fusion":[126],"built":[127],"serves":[132],"as":[133,175],"input":[134],"to":[135,137,172,177],"RL":[136,213],"infer":[138],"missing":[139],"or":[140],"new":[141],"edges":[142],"network.":[146],"Detailed":[147],"comparisons":[148],"control":[150],"made,":[154],"results":[157],"show":[158],"that":[159,206],"accuracy":[161],"measured":[165],"AUC":[167],"increased":[169],"up":[171],"23":[173],"%,":[174],"compared":[176],"baseline":[179],"without":[180],"using":[181],"weights.":[183],"can":[186],"provide":[187],"insights":[188],"into":[189],"relations":[191],"between":[192],"PPIs":[193],"various":[195],"feature":[196],"kernels":[197],"demonstrates":[199],"strong":[200],"capability":[201],"predicting":[203],"faraway":[204],"interactions":[205],"cannot":[207],"be":[208],"well":[209],"detected":[210],"traditional":[212],"method.":[214]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}