{"id":"https://openalex.org/W4221048327","doi":"https://doi.org/10.1371/journal.pcbi.1009909","title":"Causal reasoning over knowledge graphs leveraging drug-perturbed and disease-specific transcriptomic signatures for drug discovery","display_name":"Causal reasoning over knowledge graphs leveraging drug-perturbed and disease-specific transcriptomic signatures for drug discovery","publication_year":2022,"publication_date":"2022-02-25","ids":{"openalex":"https://openalex.org/W4221048327","doi":"https://doi.org/10.1371/journal.pcbi.1009909","pmid":"https://pubmed.ncbi.nlm.nih.gov/35213534"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1009909","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009909","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1009909","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5043459521","display_name":"Daniel Domingo\u2010Fern\u00e1nd\u00e9z","orcid":"https://orcid.org/0000-0002-2046-6145"},"institutions":[{"id":"https://openalex.org/I4210137457","display_name":"Enveda Therapeutics (United States)","ror":"https://ror.org/04p6vt455","country_code":"US","type":"company","lineage":["https://openalex.org/I4210137457"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Daniel Domingo-Fern\u00e1ndez","raw_affiliation_strings":["Enveda Biosciences, Boulder, Colorado, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-2046-6145","affiliations":[{"raw_affiliation_string":"Enveda Biosciences, Boulder, Colorado, United States of America","institution_ids":["https://openalex.org/I4210137457"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004719764","display_name":"Yojana Gadiya","orcid":"https://orcid.org/0000-0002-7683-0452"},"institutions":[{"id":"https://openalex.org/I4210137457","display_name":"Enveda Therapeutics (United States)","ror":"https://ror.org/04p6vt455","country_code":"US","type":"company","lineage":["https://openalex.org/I4210137457"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yojana Gadiya","raw_affiliation_strings":["Enveda Biosciences, Boulder, Colorado, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-7683-0452","affiliations":[{"raw_affiliation_string":"Enveda Biosciences, Boulder, Colorado, United States of America","institution_ids":["https://openalex.org/I4210137457"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028919382","display_name":"Abhishek Patel","orcid":"https://orcid.org/0000-0002-1265-7945"},"institutions":[{"id":"https://openalex.org/I4210137457","display_name":"Enveda Therapeutics (United States)","ror":"https://ror.org/04p6vt455","country_code":"US","type":"company","lineage":["https://openalex.org/I4210137457"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Abhishek Patel","raw_affiliation_strings":["Enveda Biosciences, Boulder, Colorado, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Enveda Biosciences, Boulder, Colorado, United States of America","institution_ids":["https://openalex.org/I4210137457"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012235619","display_name":"Sarah Mubeen","orcid":"https://orcid.org/0000-0002-9858-3755"},"institutions":[{"id":"https://openalex.org/I135140700","display_name":"University of Bonn","ror":"https://ror.org/041nas322","country_code":"DE","type":"education","lineage":["https://openalex.org/I135140700"]},{"id":"https://openalex.org/I4210164149","display_name":"Bonn Aachen International Center for Information Technology","ror":"https://ror.org/054zhq066","country_code":"DE","type":"facility","lineage":["https://openalex.org/I135140700","https://openalex.org/I155417937","https://openalex.org/I4210164149","https://openalex.org/I4923324"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Sarah Mubeen","raw_affiliation_strings":["Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universit\u00e4t Bonn, Bonn, Germany"],"raw_orcid":"https://orcid.org/0000-0002-9858-3755","affiliations":[{"raw_affiliation_string":"Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universit\u00e4t Bonn, Bonn, Germany","institution_ids":["https://openalex.org/I4210164149","https://openalex.org/I135140700"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073216957","display_name":"Daniel Rivas-Barragan","orcid":"https://orcid.org/0000-0003-0163-7890"},"institutions":[{"id":"https://openalex.org/I2799803557","display_name":"Barcelona Supercomputing Center","ror":"https://ror.org/05sd8tv96","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2799803557","https://openalex.org/I9617848"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Daniel Rivas-Barragan","raw_affiliation_strings":["Barcelona Supercomputing Center, Barcelona, Spain"],"raw_orcid":"https://orcid.org/0000-0003-0163-7890","affiliations":[{"raw_affiliation_string":"Barcelona Supercomputing Center, Barcelona, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I2799803557"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087434251","display_name":"Chris W. Diana","orcid":"https://orcid.org/0000-0002-1864-8150"},"institutions":[{"id":"https://openalex.org/I4210137457","display_name":"Enveda Therapeutics (United States)","ror":"https://ror.org/04p6vt455","country_code":"US","type":"company","lineage":["https://openalex.org/I4210137457"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chris W. Diana","raw_affiliation_strings":["Enveda Biosciences, Boulder, Colorado, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-1864-8150","affiliations":[{"raw_affiliation_string":"Enveda Biosciences, Boulder, Colorado, United States of America","institution_ids":["https://openalex.org/I4210137457"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011582725","display_name":"Biswapriya B. Misra","orcid":"https://orcid.org/0000-0003-2589-6539"},"institutions":[{"id":"https://openalex.org/I4210137457","display_name":"Enveda Therapeutics (United States)","ror":"https://ror.org/04p6vt455","country_code":"US","type":"company","lineage":["https://openalex.org/I4210137457"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Biswapriya B. Misra","raw_affiliation_strings":["Enveda Biosciences, Boulder, Colorado, United States of America"],"raw_orcid":"https://orcid.org/0000-0003-2589-6539","affiliations":[{"raw_affiliation_string":"Enveda Biosciences, Boulder, Colorado, United States of America","institution_ids":["https://openalex.org/I4210137457"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089107006","display_name":"David Healey","orcid":"https://orcid.org/0000-0002-9584-9757"},"institutions":[{"id":"https://openalex.org/I4210137457","display_name":"Enveda Therapeutics (United States)","ror":"https://ror.org/04p6vt455","country_code":"US","type":"company","lineage":["https://openalex.org/I4210137457"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David Healey","raw_affiliation_strings":["Enveda Biosciences, Boulder, Colorado, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-9584-9757","affiliations":[{"raw_affiliation_string":"Enveda Biosciences, Boulder, Colorado, United States of America","institution_ids":["https://openalex.org/I4210137457"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033032303","display_name":"Joe Rokicki","orcid":"https://orcid.org/0000-0002-8255-0828"},"institutions":[{"id":"https://openalex.org/I4210137457","display_name":"Enveda Therapeutics (United States)","ror":"https://ror.org/04p6vt455","country_code":"US","type":"company","lineage":["https://openalex.org/I4210137457"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joe Rokicki","raw_affiliation_strings":["Enveda Biosciences, Boulder, Colorado, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-8255-0828","affiliations":[{"raw_affiliation_string":"Enveda Biosciences, Boulder, Colorado, United States of America","institution_ids":["https://openalex.org/I4210137457"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003250302","display_name":"Viswa Colluru","orcid":"https://orcid.org/0000-0002-6208-9288"},"institutions":[{"id":"https://openalex.org/I4210137457","display_name":"Enveda Therapeutics (United States)","ror":"https://ror.org/04p6vt455","country_code":"US","type":"company","lineage":["https://openalex.org/I4210137457"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Viswa Colluru","raw_affiliation_strings":["Enveda Biosciences, Boulder, Colorado, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-6208-9288","affiliations":[{"raw_affiliation_string":"Enveda Biosciences, Boulder, Colorado, United States of America","institution_ids":["https://openalex.org/I4210137457"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5003250302","https://openalex.org/A5043459521"],"corresponding_institution_ids":["https://openalex.org/I4210137457"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.3887,"has_fulltext":false,"cited_by_count":17,"citation_normalized_percentile":{"value":0.80263615,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"18","issue":"2","first_page":"e1009909","last_page":"e1009909"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9995999932289124,"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":0.9995999932289124,"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":0.9994999766349792,"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":0.9847999811172485,"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/drug-repositioning","display_name":"Drug repositioning","score":0.8015533685684204},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.7249398827552795},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.6068266034126282},{"id":"https://openalex.org/keywords/disease","display_name":"Disease","score":0.5883184671401978},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5709412097930908},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.48358601331710815},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.44450920820236206},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.4374195635318756},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.43275880813598633},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.37078970670700073},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3349050283432007},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.32880932092666626},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2543327808380127},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.2233368456363678},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.15029755234718323}],"concepts":[{"id":"https://openalex.org/C103637391","wikidata":"https://www.wikidata.org/wiki/Q5308921","display_name":"Drug repositioning","level":3,"score":0.8015533685684204},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.7249398827552795},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.6068266034126282},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.5883184671401978},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5709412097930908},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.48358601331710815},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.44450920820236206},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.4374195635318756},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.43275880813598633},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.37078970670700073},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3349050283432007},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.32880932092666626},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2543327808380127},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.2233368456363678},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.15029755234718323},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"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":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058492","descriptor_name":"Drug Repositioning","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058492","descriptor_name":"Drug Repositioning","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058492","descriptor_name":"Drug Repositioning","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1009909","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009909","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:35213534","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35213534","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:b49c0101aa904aeab86986c60f4f3dca","is_oa":true,"landing_page_url":"https://doaj.org/article/b49c0101aa904aeab86986c60f4f3dca","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 18, Iss 2, p e1009909 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8906585","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8906585","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,"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":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:upcommons.upc.edu:2117/364531","is_oa":true,"landing_page_url":"http://hdl.handle.net/2117/364531","pdf_url":null,"source":{"id":"https://openalex.org/S4210207057","display_name":"QRU Quaderns de Recerca en Urbanisme","issn_l":"2014-9689","issn":["2014-9689","2385-6777"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/P4310322448","host_organization_name":"Q71272178","host_organization_lineage":["https://openalex.org/P4310322448"],"host_organization_lineage_names":["Q71272178"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"},{"id":"pmh:oai:upcommons.upc.edu:2117/367390","is_oa":true,"landing_page_url":"http://hdl.handle.net/2117/367390","pdf_url":null,"source":{"id":"https://openalex.org/S4210207057","display_name":"QRU Quaderns de Recerca en Urbanisme","issn_l":"2014-9689","issn":["2014-9689","2385-6777"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/P4310322448","host_organization_name":"Q71272178","host_organization_lineage":["https://openalex.org/P4310322448"],"host_organization_lineage_names":["Q71272178"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1009909","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009909","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.6899999976158142,"display_name":"Good health and well-being"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":63,"referenced_works":["https://openalex.org/W1559830894","https://openalex.org/W1972853281","https://openalex.org/W1980242148","https://openalex.org/W1984209370","https://openalex.org/W1989842786","https://openalex.org/W1991874467","https://openalex.org/W1996816252","https://openalex.org/W1997707189","https://openalex.org/W2094791588","https://openalex.org/W2118258530","https://openalex.org/W2120890012","https://openalex.org/W2122264952","https://openalex.org/W2122671437","https://openalex.org/W2137632714","https://openalex.org/W2146038288","https://openalex.org/W2150196286","https://openalex.org/W2153660769","https://openalex.org/W2162143298","https://openalex.org/W2162825929","https://openalex.org/W2163411228","https://openalex.org/W2301957251","https://openalex.org/W2320234496","https://openalex.org/W2417048285","https://openalex.org/W2524066112","https://openalex.org/W2581030038","https://openalex.org/W2603532979","https://openalex.org/W2612467560","https://openalex.org/W2656695974","https://openalex.org/W2767301558","https://openalex.org/W2776484474","https://openalex.org/W2778765825","https://openalex.org/W2786016794","https://openalex.org/W2794313083","https://openalex.org/W2801069509","https://openalex.org/W2884131479","https://openalex.org/W2899760200","https://openalex.org/W2905315292","https://openalex.org/W2914553756","https://openalex.org/W2937762029","https://openalex.org/W2939519112","https://openalex.org/W2982659388","https://openalex.org/W2986455832","https://openalex.org/W3017271475","https://openalex.org/W3020759564","https://openalex.org/W3032892710","https://openalex.org/W3032982805","https://openalex.org/W3093271628","https://openalex.org/W3106143834","https://openalex.org/W3106972347","https://openalex.org/W3132273599","https://openalex.org/W3132689447","https://openalex.org/W3138273194","https://openalex.org/W3153939186","https://openalex.org/W3156260318","https://openalex.org/W3158868742","https://openalex.org/W3161748363","https://openalex.org/W3163233738","https://openalex.org/W3163501683","https://openalex.org/W3163873945","https://openalex.org/W3174753721","https://openalex.org/W4206681098","https://openalex.org/W4225690840","https://openalex.org/W4254765330"],"related_works":["https://openalex.org/W2951512731","https://openalex.org/W4312078611","https://openalex.org/W2158714033","https://openalex.org/W1977623644","https://openalex.org/W4386628104","https://openalex.org/W78967844","https://openalex.org/W3213185671","https://openalex.org/W4206945140","https://openalex.org/W2509687359","https://openalex.org/W4212865750"],"abstract_inverted_index":{"Network-based":[0],"approaches":[1],"are":[2,154],"becoming":[3],"increasingly":[4],"popular":[5],"for":[6,52,65,78],"drug":[7,43,112],"discovery":[8],"as":[9,35,96,98,204,206],"they":[10],"provide":[11],"a":[12,72,79,88,111,114,134],"systems-level":[13],"overview":[14],"of":[15,30,49,56,63,145,161,163],"the":[16,53,106,129,143,159,164,199],"mechanisms":[17],"underlying":[18],"disease":[19,64,81,144],"pathophysiology.":[20],"They":[21],"have":[22],"demonstrated":[23],"significant":[24],"early":[25],"promise":[26],"over":[27,84,120,184],"other":[28,185],"methods":[29],"biological":[31,57],"data":[32,51],"representation,":[33],"such":[34],"in":[36,87,133,142],"target":[37],"discovery,":[38],"side":[39],"effect":[40],"prediction":[41],"and":[42,137,179],"repurposing.":[44],"In":[45],"parallel,":[46],"an":[47],"explosion":[48],"-omics":[50],"deep":[54],"characterization":[55],"systems":[58],"routinely":[59],"uncovers":[60],"molecular":[61],"signatures":[62,131,140],"similar":[66,186],"applications.":[67],"Here,":[68],"we":[69,189],"present":[70,190],"RPath,":[71],"novel":[73,208],"algorithm":[74],"that":[75,109,126],"prioritizes":[76,171],"drugs":[77],"given":[80],"by":[82,93,202],"reasoning":[83],"causal":[85,107],"paths":[86,108,122,148],"knowledge":[89],"graph":[90],"(KG),":[91],"guided":[92],"both":[94],"drug-perturbed":[95],"well":[97,205],"disease-specific":[99],"transcriptomic":[100],"signatures.":[101],"First,":[102],"our":[103],"approach":[104],"identifies":[105],"connect":[110],"to":[113,123,139,157],"particular":[115],"disease.":[116],"Next,":[117],"it":[118],"reasons":[119],"these":[121],"identify":[124],"those":[125],"correlate":[127],"with":[128],"transcriptional":[130],"observed":[132,141],"drug-perturbation":[135],"experiment,":[136],"anti-correlate":[138],"interest.":[146],"The":[147],"which":[149],"match":[150],"this":[151],"signature":[152],"profile":[153],"then":[155],"proposed":[156],"represent":[158],"mechanism":[160],"action":[162],"drug.":[165],"We":[166],"demonstrate":[167],"how":[168,195],"RPath":[169,203],"consistently":[170],"clinically":[172],"investigated":[173],"drug-disease":[174],"pairs":[175],"on":[176],"multiple":[177],"datasets":[178],"KGs,":[180],"achieving":[181],"better":[182],"performance":[183],"methodologies.":[187],"Furthermore,":[188],"two":[191],"case":[192],"studies":[193],"showing":[194],"one":[196],"can":[197],"deconvolute":[198],"predictions":[200],"made":[201],"predict":[207],"targets.":[209]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":3}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}
