{"id":"https://openalex.org/W4406271258","doi":"https://doi.org/10.1109/bibm62325.2024.10822065","title":"Unveiling drug-induced side effects through network-based analysis: an update","display_name":"Unveiling drug-induced side effects through network-based analysis: an update","publication_year":2024,"publication_date":"2024-12-03","ids":{"openalex":"https://openalex.org/W4406271258","doi":"https://doi.org/10.1109/bibm62325.2024.10822065"},"language":"en","primary_location":{"id":"doi:10.1109/bibm62325.2024.10822065","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822065","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5017183612","display_name":"Alessio Funari","orcid":"https://orcid.org/0000-0002-1132-4719"},"institutions":[{"id":"https://openalex.org/I4210155236","display_name":"National Research Council","ror":"https://ror.org/04zaypm56","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I4210155236"]},{"id":"https://openalex.org/I4210162062","display_name":"Istituto di Analisi dei Sistemi ed Informatica Antonio Ruberti","ror":"https://ror.org/054ye0e45","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210155236","https://openalex.org/I4210162062"]},{"id":"https://openalex.org/I861853513","display_name":"Sapienza University of Rome","ror":"https://ror.org/02be6w209","country_code":"IT","type":"education","lineage":["https://openalex.org/I861853513"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Alessio Funari","raw_affiliation_strings":["Sapienza University of Rome Institute for Systems Analysis and Computer Science &#x201C;Antonio Ruberti&#x201D;, National Research Council,Department of Translational and Precision Medicine,Rome,Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Sapienza University of Rome Institute for Systems Analysis and Computer Science &#x201C;Antonio Ruberti&#x201D;, National Research Council,Department of Translational and Precision Medicine,Rome,Italy","institution_ids":["https://openalex.org/I4210162062","https://openalex.org/I861853513","https://openalex.org/I4210155236"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023495931","display_name":"Federica Conte","orcid":"https://orcid.org/0000-0003-0427-1476"},"institutions":[{"id":"https://openalex.org/I4210155236","display_name":"National Research Council","ror":"https://ror.org/04zaypm56","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I4210155236"]},{"id":"https://openalex.org/I4210162062","display_name":"Istituto di Analisi dei Sistemi ed Informatica Antonio Ruberti","ror":"https://ror.org/054ye0e45","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210155236","https://openalex.org/I4210162062"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Federica Conte","raw_affiliation_strings":["National Research Council,Institute for Systems Analysis and Computer Science &#x201C;Antonio Ruberti&#x201D;,Rome,Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Research Council,Institute for Systems Analysis and Computer Science &#x201C;Antonio Ruberti&#x201D;,Rome,Italy","institution_ids":["https://openalex.org/I4210162062","https://openalex.org/I4210155236"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5043250067","display_name":"Paola Paci","orcid":"https://orcid.org/0000-0002-9393-2047"},"institutions":[{"id":"https://openalex.org/I861853513","display_name":"Sapienza University of Rome","ror":"https://ror.org/02be6w209","country_code":"IT","type":"education","lineage":["https://openalex.org/I861853513"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Paola Paci","raw_affiliation_strings":["Sapienza University of Rome,Department of Computer, Control and Management Engineering,Rome,Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Sapienza University of Rome,Department of Computer, Control and Management Engineering,Rome,Italy","institution_ids":["https://openalex.org/I861853513"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.28357976,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"6091","last_page":"6098"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9983999729156494,"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"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9983999729156494,"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/T10375","display_name":"Pharmacogenetics and Drug Metabolism","score":0.9832000136375427,"subfield":{"id":"https://openalex.org/subfields/3004","display_name":"Pharmacology"},"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9758999943733215,"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":0.6043514609336853},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.5586827993392944},{"id":"https://openalex.org/keywords/side-effect","display_name":"Side effect (computer science)","score":0.4349942207336426},{"id":"https://openalex.org/keywords/side-channel-attack","display_name":"Side channel attack","score":0.42859724164009094},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.21864822506904602},{"id":"https://openalex.org/keywords/computer-security","display_name":"Computer security","score":0.217174232006073},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.2159293293952942},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.11141201853752136}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6043514609336853},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.5586827993392944},{"id":"https://openalex.org/C3454156","wikidata":"https://www.wikidata.org/wiki/Q1144241","display_name":"Side effect (computer science)","level":2,"score":0.4349942207336426},{"id":"https://openalex.org/C49289754","wikidata":"https://www.wikidata.org/wiki/Q2267081","display_name":"Side channel attack","level":3,"score":0.42859724164009094},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.21864822506904602},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.217174232006073},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.2159293293952942},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.11141201853752136},{"id":"https://openalex.org/C178489894","wikidata":"https://www.wikidata.org/wiki/Q8789","display_name":"Cryptography","level":2,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/bibm62325.2024.10822065","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822065","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},{"id":"pmh:oai:iris.uniroma1.it:11573/1737561","is_oa":false,"landing_page_url":"https://hdl.handle.net/11573/1737561","pdf_url":null,"source":{"id":"https://openalex.org/S4377196107","display_name":"IRIS Research product catalog (Sapienza University of Rome)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/conferenceObject"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":40,"referenced_works":["https://openalex.org/W193004981","https://openalex.org/W1160401237","https://openalex.org/W1800166884","https://openalex.org/W1966454287","https://openalex.org/W1977012853","https://openalex.org/W1982002340","https://openalex.org/W2005850081","https://openalex.org/W2006617902","https://openalex.org/W2035106953","https://openalex.org/W2046716112","https://openalex.org/W2046885214","https://openalex.org/W2048654643","https://openalex.org/W2053998276","https://openalex.org/W2057946435","https://openalex.org/W2068351636","https://openalex.org/W2071598106","https://openalex.org/W2080104628","https://openalex.org/W2082624887","https://openalex.org/W2085752173","https://openalex.org/W2111450699","https://openalex.org/W2113031313","https://openalex.org/W2116581628","https://openalex.org/W2119002393","https://openalex.org/W2121774438","https://openalex.org/W2144423360","https://openalex.org/W2345356016","https://openalex.org/W2548357532","https://openalex.org/W2789789321","https://openalex.org/W2791340464","https://openalex.org/W2897753544","https://openalex.org/W2939112498","https://openalex.org/W2944226869","https://openalex.org/W2951531839","https://openalex.org/W3016962540","https://openalex.org/W3158868742","https://openalex.org/W4224236693","https://openalex.org/W4377104366","https://openalex.org/W4390971202","https://openalex.org/W4402497081","https://openalex.org/W6661196222"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W4323824501","https://openalex.org/W2355552010","https://openalex.org/W2136687465","https://openalex.org/W2390279801","https://openalex.org/W3016859066","https://openalex.org/W4391913857","https://openalex.org/W2358668433"],"abstract_inverted_index":{"In":[0],"this":[1,50],"article,":[2],"we":[3],"propose":[4],"an":[5],"updated":[6],"version":[7],"of":[8,33,45,78,113,123,135],"our":[9],"previously":[10],"developed":[11],"model":[12,105,119,151],"for":[13,184],"predicting":[14],"drug-side":[15],"effect":[16,38],"associations,":[17],"applied":[18],"to":[19,99,110,156],"two":[20],"case":[21],"studies:":[22],"long":[23],"QT":[24],"syndrome":[25],"and":[26,41,176],"asthma.":[27],"The":[28,146],"classifier":[29,70],"accepts":[30],"the":[31,60,63,69,76,79,84,87,94,101,104,111,114,118,121,129,133,150,171],"name":[32],"a":[34,43,89],"specific":[35,144],"drug":[36,56,90],"side":[37,51,80,102,115,137,161,187],"as":[39,140,163,165],"input":[40],"outputs":[42],"list":[44],"drugs":[46,107,124,154,166],"potentially":[47,73,108],"associated":[48,74,158],"with":[49,66,75,159],"effect.":[52,81,116],"By":[53],"simulating":[54],"how":[55],"effects":[57],"propagate":[58],"within":[59],"interactome":[61],"using":[62,128],"Random":[64],"Walk":[65],"Restart":[67],"algorithm,":[68],"identifies":[71,106,152],"genes":[72],"onset":[77,112],"Based":[82],"on":[83],"rationale":[85],"that":[86,149],"more":[88,95,143],"perturbs":[91],"these":[92],"genes,":[93],"likely":[96],"it":[97],"is":[98,181],"cause":[100],"effect,":[103],"linked":[109],"Moreover,":[117],"enables":[120],"categorization":[122],"into":[125],"chemical":[126],"subclasses":[127],"ClassyFire":[130],"schema,":[131],"facilitating":[132],"analysis":[134],"complex":[136],"effects,":[138,162],"such":[139],"asthma,":[141],"through":[142],"mechanisms.":[145],"results":[147],"show":[148],"both":[153],"known":[155],"be":[157],"certain":[160],"well":[164],"not":[167],"officially":[168],"reported":[169],"by":[170],"FDA,":[172],"demonstrating":[173],"its":[174],"generalizability":[175],"practical":[177],"relevance.":[178],"This":[179],"method":[180],"also":[182],"adaptable":[183],"analyzing":[185],"other":[186],"effects.":[188]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
