{"id":"https://openalex.org/W2058722111","doi":"https://doi.org/10.1109/tcbb.2014.2355216","title":"P-Finder: Reconstruction of Signaling Networks from Protein-Protein Interactions and GO Annotations","display_name":"P-Finder: Reconstruction of Signaling Networks from Protein-Protein Interactions and GO Annotations","publication_year":2014,"publication_date":"2014-09-17","ids":{"openalex":"https://openalex.org/W2058722111","doi":"https://doi.org/10.1109/tcbb.2014.2355216","mag":"2058722111","pmid":"https://pubmed.ncbi.nlm.nih.gov/26357219"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2014.2355216","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2014.2355216","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/A5013149893","display_name":"Young\u2010Rae Cho","orcid":"https://orcid.org/0000-0002-4645-2542"},"institutions":[{"id":"https://openalex.org/I157394403","display_name":"Baylor University","ror":"https://ror.org/005781934","country_code":"US","type":"education","lineage":["https://openalex.org/I157394403"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Young-Rae Cho","raw_affiliation_strings":["Department of Computer Science, Baylor University, Waco, TX"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Baylor University, Waco, TX","institution_ids":["https://openalex.org/I157394403"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101641867","display_name":"Yanan Xin","orcid":"https://orcid.org/0000-0003-3866-821X"},"institutions":[{"id":"https://openalex.org/I157394403","display_name":"Baylor University","ror":"https://ror.org/005781934","country_code":"US","type":"education","lineage":["https://openalex.org/I157394403"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yanan Xin","raw_affiliation_strings":["Department of Computer Science, Baylor University, Waco, TX"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Baylor University, Waco, TX","institution_ids":["https://openalex.org/I157394403"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5112286821","display_name":"Greg Speegle","orcid":"https://orcid.org/0000-0003-1739-0271"},"institutions":[{"id":"https://openalex.org/I157394403","display_name":"Baylor University","ror":"https://ror.org/005781934","country_code":"US","type":"education","lineage":["https://openalex.org/I157394403"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Greg Speegle","raw_affiliation_strings":["Department of Computer Science, Baylor University, Waco, TX"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Baylor University, Waco, TX","institution_ids":["https://openalex.org/I157394403"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I157394403"],"apc_list":{"value":2645,"currency":"USD","value_usd":2645},"apc_paid":null,"fwci":0.3896,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":{"value":0.60548892,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"12","issue":"2","first_page":"309","last_page":"321"},"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9968000054359436,"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/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.9919000267982483,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6805463433265686},{"id":"https://openalex.org/keywords/preprocessor","display_name":"Preprocessor","score":0.5285849571228027},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5151354074478149},{"id":"https://openalex.org/keywords/path","display_name":"Path (computing)","score":0.4618021845817566},{"id":"https://openalex.org/keywords/weighting","display_name":"Weighting","score":0.4501148462295532},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4447256326675415},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.43034395575523376},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4194737672805786},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.35847610235214233},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.32561439275741577},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3164534568786621},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18849343061447144}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6805463433265686},{"id":"https://openalex.org/C34736171","wikidata":"https://www.wikidata.org/wiki/Q918333","display_name":"Preprocessor","level":2,"score":0.5285849571228027},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5151354074478149},{"id":"https://openalex.org/C2777735758","wikidata":"https://www.wikidata.org/wiki/Q817765","display_name":"Path (computing)","level":2,"score":0.4618021845817566},{"id":"https://openalex.org/C183115368","wikidata":"https://www.wikidata.org/wiki/Q856577","display_name":"Weighting","level":2,"score":0.4501148462295532},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4447256326675415},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.43034395575523376},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4194737672805786},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.35847610235214233},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.32561439275741577},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3164534568786621},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18849343061447144},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C126838900","wikidata":"https://www.wikidata.org/wiki/Q77604","display_name":"Radiology","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":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2014.2355216","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2014.2355216","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:26357219","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26357219","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":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320309840","display_name":"Baylor University","ror":"https://ror.org/005781934"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":45,"referenced_works":["https://openalex.org/W1529730227","https://openalex.org/W1647729745","https://openalex.org/W1806630989","https://openalex.org/W1970095512","https://openalex.org/W1976722121","https://openalex.org/W1980948656","https://openalex.org/W1998767819","https://openalex.org/W2003652380","https://openalex.org/W2010134474","https://openalex.org/W2042301222","https://openalex.org/W2043364653","https://openalex.org/W2057545775","https://openalex.org/W2060351001","https://openalex.org/W2066235893","https://openalex.org/W2066580949","https://openalex.org/W2084168100","https://openalex.org/W2099364528","https://openalex.org/W2105302963","https://openalex.org/W2107249189","https://openalex.org/W2110095004","https://openalex.org/W2110699703","https://openalex.org/W2112262143","https://openalex.org/W2112580417","https://openalex.org/W2113642685","https://openalex.org/W2117805756","https://openalex.org/W2117960318","https://openalex.org/W2124533460","https://openalex.org/W2127563440","https://openalex.org/W2128049108","https://openalex.org/W2131397861","https://openalex.org/W2131532450","https://openalex.org/W2136345497","https://openalex.org/W2136940180","https://openalex.org/W2137804845","https://openalex.org/W2141914340","https://openalex.org/W2144636447","https://openalex.org/W2153624566","https://openalex.org/W2159348493","https://openalex.org/W2161358836","https://openalex.org/W2169896388","https://openalex.org/W2915108429","https://openalex.org/W2917375902","https://openalex.org/W2950225692","https://openalex.org/W6636975626","https://openalex.org/W6677712588"],"related_works":["https://openalex.org/W2180954594","https://openalex.org/W2361861616","https://openalex.org/W2052835778","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2049003611","https://openalex.org/W2127804977","https://openalex.org/W2108418243","https://openalex.org/W2218034408","https://openalex.org/W2392921965"],"abstract_inverted_index":{"Because":[0],"most":[1],"complex":[2],"genetic":[3],"diseases":[4],"are":[5,174],"caused":[6],"by":[7],"defects":[8],"of":[9,66,83,94,114,179],"cell":[10],"signaling,":[11],"illuminating":[12],"a":[13,33,58,63,126,131],"signaling":[14,30,53,195],"cascade":[15],"is":[16,55,75],"essential":[17],"for":[18,77],"understanding":[19],"their":[20],"mechanisms.":[21],"We":[22],"present":[23],"three":[24,85],"novel":[25],"computational":[26],"algorithms":[27,165],"to":[28,192],"reconstruct":[29],"networks":[31,45],"between":[32],"starting":[34],"protein":[35,39],"and":[36,46,152],"an":[37,101,185],"ending":[38,102],"using":[40],"genome-wide":[41],"protein-protein":[42],"interaction":[43],"(PPI)":[44],"gene":[47],"ontology":[48],"(GO)":[49],"annotation":[50],"data.":[51],"A":[52],"network":[54,115,128],"represented":[56],"as":[57,80],"directed":[59,156],"acyclic":[60],"graph":[61],"in":[62,125,130],"merged":[64],"form":[65],"multiple":[67],"linear":[68],"pathways.":[69],"An":[70],"advanced":[71],"semantic":[72],"similarity":[73],"metric":[74],"applied":[76],"weighting":[78],"PPIs":[79],"the":[81,92,112,119,138,149,154,163],"preprocessing":[82],"all":[84],"methods.":[86],"The":[87,104,134],"first":[88],"algorithm":[89,106,136],"repeatedly":[90,107],"extends":[91],"list":[93],"nodes":[95],"based":[96,110,147],"on":[97,111,148,176],"path":[98,150],"frequency":[99],"towards":[100],"protein.":[103],"second":[105],"appends":[108],"edges":[109],"occurrence":[113],"motifs":[116],"which":[117,142],"indicate":[118],"link":[120],"patterns":[121],"more":[122],"frequently":[123],"appearing":[124],"PPI":[127],"than":[129,169],"random":[132],"graph.":[133],"last":[135],"uses":[137],"information":[139],"propagation":[140],"technique":[141],"iteratively":[143],"updates":[144],"edge":[145],"orientations":[146],"strength":[151],"merges":[153],"selected":[155],"edges.":[157],"Our":[158],"experimental":[159],"results":[160],"demonstrate":[161],"that":[162],"proposed":[164],"achieve":[166],"higher":[167],"accuracy":[168],"previous":[170],"methods":[171],"when":[172],"they":[173],"tested":[175],"well-studied":[177],"pathways":[178],"S.":[180],"cerevisiae.":[181],"Furthermore,":[182],"we":[183],"introduce":[184],"interactive":[186],"web":[187],"application":[188],"tool,":[189],"called":[190],"P-Finder,":[191],"visualize":[193],"reconstructed":[194],"networks.":[196]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
