{"id":"https://openalex.org/W2016914833","doi":"https://doi.org/10.1186/1471-2105-14-s16-s3","title":"Pathway-based drug repositioning using causal inference","display_name":"Pathway-based drug repositioning using causal inference","publication_year":2013,"publication_date":"2013-10-01","ids":{"openalex":"https://openalex.org/W2016914833","doi":"https://doi.org/10.1186/1471-2105-14-s16-s3","mag":"2016914833","pmid":"https://pubmed.ncbi.nlm.nih.gov/24564553","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/3853312"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-14-s16-s3","doi":"https://doi.org/10.1186/1471-2105-14-s16-s3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-s16-s3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-S16-S3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","ccf-c","cwts-core","doaj","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-2","oarl","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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":"BMC Bioinformatics","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-S16-S3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074284592","display_name":"Jiao Li","orcid":"https://orcid.org/0000-0001-6391-8343","observed_orcids":["https://orcid.org/0000-0001-6391-8343","https://orcid.org/0000-0002-8876-3728"]},"institutions":[{"id":"https://openalex.org/I200296433","display_name":"Chinese Academy of Medical Sciences & Peking Union Medical College","ror":"https://ror.org/02drdmm93","country_code":"CN","type":"education","lineage":["https://openalex.org/I200296433"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiao Li","raw_affiliation_strings":["Institute of Medical Information, Chinese Academy of Medical Sciences, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Medical Information, Chinese Academy of Medical Sciences, Beijing, China","institution_ids":["https://openalex.org/I200296433"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083081872","display_name":"Zhiyong Lu","orcid":"https://orcid.org/0000-0001-9998-916X","observed_orcids":["https://orcid.org/0000-0001-9998-916X","https://orcid.org/0000-0002-8301-9553"]},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Zhiyong Lu","raw_affiliation_strings":["National Center for Biotechnology Information (NCBI), National Institutes of Health, Bethesda, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information (NCBI), National Institutes of Health, Bethesda, USA","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210109390"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5083081872"],"corresponding_institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210109390"],"apc_list":{"value":2990,"currency":"USD","value_usd":2990},"apc_paid":{"value":2990,"currency":"USD","value_usd":2990},"fwci":4.2212,"has_fulltext":true,"cited_by_count":95,"citation_normalized_percentile":{"value":0.95787089,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":88,"max":100},"biblio":{"volume":"14","issue":"S16","first_page":"S3","last_page":"S3"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9653000235557556,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9653000235557556,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.024800000712275505,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.006200000178068876,"subfield":{"id":"https://openalex.org/subfields/2718","display_name":"Health Informatics"},"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/drug-repurposing","display_name":"drug repurposing","score":0.9919999837875366},{"id":"https://openalex.org/keywords/causal-inference","display_name":"causal inference","score":0.9160000085830688},{"id":"https://openalex.org/keywords/causal-chains","display_name":"causal chains","score":0.6330000162124634},{"id":"https://openalex.org/keywords/crohn-s-disease","display_name":"Crohn's disease","score":0.8259999752044678},{"id":"https://openalex.org/keywords/hypothesis-generation","display_name":"hypothesis generation","score":0.6340000033378601},{"id":"https://openalex.org/keywords/knowledge-base","display_name":"knowledge base","score":0.6290000081062317}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.709186315536499},{"id":"https://openalex.org/C103637391","wikidata":"https://www.wikidata.org/wiki/Q5308921","display_name":"Drug repositioning","level":3,"score":0.6898263692855835},{"id":"https://openalex.org/C158600405","wikidata":"https://www.wikidata.org/wiki/Q5054566","display_name":"Causal inference","level":2,"score":0.6865994930267334},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.5991984009742737},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5669457316398621},{"id":"https://openalex.org/C64357122","wikidata":"https://www.wikidata.org/wiki/Q1149766","display_name":"Causality (physics)","level":2,"score":0.5487285256385803},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5450671911239624},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.5060743689537048},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.49086886644363403},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4779151380062103},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.4622490406036377},{"id":"https://openalex.org/C64903051","wikidata":"https://www.wikidata.org/wiki/Q2198549","display_name":"Drug development","level":3,"score":0.4433871805667877},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.2509579658508301},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2076537311077118},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.17952561378479004},{"id":"https://openalex.org/C149782125","wikidata":"https://www.wikidata.org/wiki/Q160039","display_name":"Econometrics","level":1,"score":0.14555802941322327},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.124712735414505},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.11102917790412903},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003424","descriptor_name":"Crohn Disease","qualifier_ui":"Q000188","qualifier_name":"drug therapy","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","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":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058492","descriptor_name":"Drug Repositioning","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-14-s16-s3","doi":"https://doi.org/10.1186/1471-2105-14-s16-s3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-s16-s3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-S16-S3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","ccf-c","cwts-core","doaj","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-2","oarl","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:europepmc.org:2850518","doi":null,"is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC3853312","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3853312","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3853312","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmid:24564553","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24564553","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,"listed_in":[],"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":"BMC bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.797.4532","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.797.4532","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/b3/dc/1471-2105-14-S16-S3.PMC3853312.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-14-s16-s3","doi":"https://doi.org/10.1186/1471-2105-14-s16-s3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-s16-s3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-S16-S3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","ccf-c","cwts-core","doaj","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-2","oarl","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.9537000060081482}],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320326853","display_name":"Peking Union Medical College","ror":"https://ror.org/02drdmm93"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2016914833.pdf","grobid_xml":"https://content.openalex.org/works/W2016914833.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W1969709265","https://openalex.org/W1970263201","https://openalex.org/W1979924529","https://openalex.org/W1982407085","https://openalex.org/W1984054151","https://openalex.org/W1995919293","https://openalex.org/W2009313526","https://openalex.org/W2018317955","https://openalex.org/W2028279608","https://openalex.org/W2032177802","https://openalex.org/W2036904266","https://openalex.org/W2040620807","https://openalex.org/W2044340941","https://openalex.org/W2061016350","https://openalex.org/W2062941476","https://openalex.org/W2075897300","https://openalex.org/W2081388499","https://openalex.org/W2091262011","https://openalex.org/W2094464340","https://openalex.org/W2094791588","https://openalex.org/W2096541451","https://openalex.org/W2122031852","https://openalex.org/W2123877028","https://openalex.org/W2127553917","https://openalex.org/W2128054164","https://openalex.org/W2136640051","https://openalex.org/W2137632714","https://openalex.org/W2138512826","https://openalex.org/W2138898897","https://openalex.org/W2159739075","https://openalex.org/W2164298117","https://openalex.org/W2171437346","https://openalex.org/W2528445297","https://openalex.org/W3144008936"],"related_works":["https://openalex.org/W7098926390","https://openalex.org/W2020274161","https://openalex.org/W3106972347","https://openalex.org/W2005314755","https://openalex.org/W1979488516","https://openalex.org/W2374683108","https://openalex.org/W2185855656","https://openalex.org/W2100709719","https://openalex.org/W7096968548","https://openalex.org/W7203582073"],"abstract_inverted_index":{"BACKGROUND:":[0],"Recent":[1],"in":[2,26,39,81,97,124,136,154,175],"vivo":[3],"studies":[4],"showed":[5,118,183],"new":[6,45,166],"hopes":[7],"of":[8,48,93,144,168],"drug":[9,197],"repositioning":[10],"through":[11],"causality":[12],"inference":[13,174],"from":[14,191],"drugs":[15,36,69,150,170],"to":[16,42,70],"disease.":[17],"Inspired":[18],"by":[19],"their":[20],"success,":[21],"here":[22],"we":[23,61,147],"present":[24],"an":[25,40],"silico":[27],"method":[28,89,117,163,187],"for":[29,151,164,196],"building":[30],"a":[31,142,161,176],"causal":[32,59,66,95],"network":[33,99],"(CauseNet)":[34],"between":[35],"and":[37,74,138],"diseases,":[38],"attempt":[41],"systematically":[43],"identify":[44],"therapeutic":[46],"uses":[47,167],"existing":[49,169],"drugs.":[50],"METHODS:":[51],"Unlike":[52],"the":[53,98],"traditional":[54],"'one":[55],"drug-one":[56],"target-one":[57],"disease'":[58],"model,":[60],"simultaneously":[62],"consider":[63],"all":[64],"possible":[65],"chains":[67],"connecting":[68],"diseases":[71],"via":[72],"target-":[73],"gene-involved":[75],"pathways":[76],"based":[77,100,171],"on":[78,101,172],"rich":[79],"information":[80],"several":[82,149],"expert-curated":[83],"knowledge-bases.":[84],"With":[85],"statistical":[86],"learning,":[87],"our":[88,116,128,185],"estimates":[90],"transition":[91],"likelihood":[92],"each":[94],"chain":[96],"known":[102],"drug-disease":[103],"treatment":[104],"associations":[105],"(e.g.":[106],"bexarotene":[107],"treats":[108],"skin":[109],"cancer).":[110],"RESULTS:":[111],"To":[112],"demonstrate":[113],"its":[114,145],"validity,":[115],"high":[119],"performance":[120],"(AUC":[121],"=":[122],"0.859)":[123],"cross":[125],"validation.":[126],"Moreover,":[127],"top":[129],"scored":[130],"prediction":[131],"results":[132,182],"are":[133],"highly":[134],"enriched":[135],"literature":[137],"clinical":[139],"trials.":[140],"As":[141],"showcase":[143],"utility,":[146],"show":[148],"potential":[152],"re-use":[153],"Crohn's":[155],"Disease.":[156],"CONCLUSIONS:":[157],"We":[158],"successfully":[159],"developed":[160],"computational":[162],"discovering":[165],"casual":[173],"layered":[177],"drug-target-pathway-gene-":[178],"disease":[179],"network.":[180],"The":[181],"that":[184],"proposed":[186],"enables":[188],"hypothesis":[189],"generation":[190],"public":[192],"accessible":[193],"biological":[194],"data":[195],"repositioning.":[198]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":10},{"year":2019,"cited_by_count":17},{"year":2018,"cited_by_count":12},{"year":2017,"cited_by_count":10},{"year":2016,"cited_by_count":11},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":7}],"updated_date":"2026-11-07T11:25:07.637180","created_date":"2016-06-24T00:00:00"}