{"id":"https://openalex.org/W4283811348","doi":"https://doi.org/10.1093/bib/bbac270","title":"Deep generative model for therapeutic targets using transcriptomic disease-associated data\u2014USP7 case study","display_name":"Deep generative model for therapeutic targets using transcriptomic disease-associated data\u2014USP7 case study","publication_year":2022,"publication_date":"2022-07-05","ids":{"openalex":"https://openalex.org/W4283811348","doi":"https://doi.org/10.1093/bib/bbac270","pmid":"https://pubmed.ncbi.nlm.nih.gov/35789255"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac270","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac270","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","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/A5020082077","display_name":"Tiago Pereira","orcid":"https://orcid.org/0000-0003-2487-0097"},"institutions":[{"id":"https://openalex.org/I76903346","display_name":"University of Coimbra","ror":"https://ror.org/04z8k9a98","country_code":"PT","type":"education","lineage":["https://openalex.org/I76903346"]}],"countries":["PT"],"is_corresponding":true,"raw_author_name":"Tiago Pereira","raw_affiliation_strings":["Centre for Informatics and Systems of the University of Coimbra, Department of Informatics Engineering , Univ Coimbra, Coimbra, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Informatics and Systems of the University of Coimbra, Department of Informatics Engineering , Univ Coimbra, Coimbra, Portugal","institution_ids":["https://openalex.org/I76903346"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064251517","display_name":"Maryam Abbasi","orcid":"https://orcid.org/0000-0002-9011-0734"},"institutions":[{"id":"https://openalex.org/I76903346","display_name":"University of Coimbra","ror":"https://ror.org/04z8k9a98","country_code":"PT","type":"education","lineage":["https://openalex.org/I76903346"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Maryam Abbasi","raw_affiliation_strings":["Centre for Informatics and Systems of the University of Coimbra, Department of Informatics Engineering , Univ Coimbra, Coimbra, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Informatics and Systems of the University of Coimbra, Department of Informatics Engineering , Univ Coimbra, Coimbra, Portugal","institution_ids":["https://openalex.org/I76903346"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063602589","display_name":"Rita I. Oliveira","orcid":"https://orcid.org/0000-0002-1511-4364"},"institutions":[{"id":"https://openalex.org/I4394709155","display_name":"Centro de Neuroci\u00eancias e Biologia Celular","ror":"https://ror.org/01nzkd566","country_code":"PT","type":"facility","lineage":["https://openalex.org/I4394709155","https://openalex.org/I76903346"]},{"id":"https://openalex.org/I76903346","display_name":"University of Coimbra","ror":"https://ror.org/04z8k9a98","country_code":"PT","type":"education","lineage":["https://openalex.org/I76903346"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Rita I Oliveira","raw_affiliation_strings":["Center for Neuroscience and Cell Biology Center for Innovative Biomedicine and Biotechnology, Univ Coimbra , Coimbra, Portugal","Laboratory of Pharmaceutical Chemistry Faculty of Pharmacy, Univ Coimbra , Coimbra, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Neuroscience and Cell Biology Center for Innovative Biomedicine and Biotechnology, Univ Coimbra , Coimbra, Portugal","institution_ids":["https://openalex.org/I4394709155","https://openalex.org/I76903346"]},{"raw_affiliation_string":"Laboratory of Pharmaceutical Chemistry Faculty of Pharmacy, Univ Coimbra , Coimbra, Portugal","institution_ids":["https://openalex.org/I76903346"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101517328","display_name":"Romina A. Guedes","orcid":"https://orcid.org/0000-0002-4397-7968"},"institutions":[{"id":"https://openalex.org/I4394709155","display_name":"Centro de Neuroci\u00eancias e Biologia Celular","ror":"https://ror.org/01nzkd566","country_code":"PT","type":"facility","lineage":["https://openalex.org/I4394709155","https://openalex.org/I76903346"]},{"id":"https://openalex.org/I76903346","display_name":"University of Coimbra","ror":"https://ror.org/04z8k9a98","country_code":"PT","type":"education","lineage":["https://openalex.org/I76903346"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Romina A Guedes","raw_affiliation_strings":["Center for Neuroscience and Cell Biology Center for Innovative Biomedicine and Biotechnology, Univ Coimbra , Coimbra, Portugal","Laboratory of Pharmaceutical Chemistry Faculty of Pharmacy, Univ Coimbra , Coimbra, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Neuroscience and Cell Biology Center for Innovative Biomedicine and Biotechnology, Univ Coimbra , Coimbra, Portugal","institution_ids":["https://openalex.org/I4394709155","https://openalex.org/I76903346"]},{"raw_affiliation_string":"Laboratory of Pharmaceutical Chemistry Faculty of Pharmacy, Univ Coimbra , Coimbra, Portugal","institution_ids":["https://openalex.org/I76903346"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060222682","display_name":"Jorge A. R. Salvador","orcid":"https://orcid.org/0000-0003-0779-6083"},"institutions":[{"id":"https://openalex.org/I4394709155","display_name":"Centro de Neuroci\u00eancias e Biologia Celular","ror":"https://ror.org/01nzkd566","country_code":"PT","type":"facility","lineage":["https://openalex.org/I4394709155","https://openalex.org/I76903346"]},{"id":"https://openalex.org/I76903346","display_name":"University of Coimbra","ror":"https://ror.org/04z8k9a98","country_code":"PT","type":"education","lineage":["https://openalex.org/I76903346"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Jorge A R Salvador","raw_affiliation_strings":["Center for Neuroscience and Cell Biology Center for Innovative Biomedicine and Biotechnology, Univ Coimbra , Coimbra, Portugal","Laboratory of Pharmaceutical Chemistry Faculty of Pharmacy, Univ Coimbra , Coimbra, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Neuroscience and Cell Biology Center for Innovative Biomedicine and Biotechnology, Univ Coimbra , Coimbra, Portugal","institution_ids":["https://openalex.org/I4394709155","https://openalex.org/I76903346"]},{"raw_affiliation_string":"Laboratory of Pharmaceutical Chemistry Faculty of Pharmacy, Univ Coimbra , Coimbra, Portugal","institution_ids":["https://openalex.org/I76903346"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5043572862","display_name":"Joel P. Arrais","orcid":"https://orcid.org/0000-0003-4937-2334"},"institutions":[{"id":"https://openalex.org/I76903346","display_name":"University of Coimbra","ror":"https://ror.org/04z8k9a98","country_code":"PT","type":"education","lineage":["https://openalex.org/I76903346"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Joel P Arrais","raw_affiliation_strings":["Centre for Informatics and Systems of the University of Coimbra, Department of Informatics Engineering , Univ Coimbra, Coimbra, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Informatics and Systems of the University of Coimbra, Department of Informatics Engineering , Univ Coimbra, Coimbra, Portugal","institution_ids":["https://openalex.org/I76903346"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5020082077"],"corresponding_institution_ids":["https://openalex.org/I76903346"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":1.8592,"has_fulltext":false,"cited_by_count":16,"citation_normalized_percentile":{"value":0.87030746,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"23","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.996999979019165,"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":0.996999979019165,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.982699990272522,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9696000218391418,"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/in-silico","display_name":"In silico","score":0.7020132541656494},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7005496025085449},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6981835961341858},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.5102486610412598},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5074002146720886},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.4800192415714264},{"id":"https://openalex.org/keywords/drug-repositioning","display_name":"Drug repositioning","score":0.4619178771972656},{"id":"https://openalex.org/keywords/generative-grammar","display_name":"Generative grammar","score":0.4399047791957855},{"id":"https://openalex.org/keywords/drug-target","display_name":"Drug target","score":0.4348355531692505},{"id":"https://openalex.org/keywords/biological-data","display_name":"Biological data","score":0.4299834966659546},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3879566192626953},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3851761221885681},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.34837400913238525},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.26343727111816406},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.177729994058609},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1675562560558319},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.08669117093086243}],"concepts":[{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.7020132541656494},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7005496025085449},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6981835961341858},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.5102486610412598},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5074002146720886},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4800192415714264},{"id":"https://openalex.org/C103637391","wikidata":"https://www.wikidata.org/wiki/Q5308921","display_name":"Drug repositioning","level":3,"score":0.4619178771972656},{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.4399047791957855},{"id":"https://openalex.org/C2989108626","wikidata":"https://www.wikidata.org/wiki/Q904407","display_name":"Drug target","level":2,"score":0.4348355531692505},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.4299834966659546},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3879566192626953},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3851761221885681},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.34837400913238525},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.26343727111816406},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.177729994058609},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1675562560558319},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.08669117093086243},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","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}],"mesh":[{"descriptor_ui":"D000076084","descriptor_name":"Ubiquitin-Specific Peptidase 7","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000076084","descriptor_name":"Ubiquitin-Specific Peptidase 7","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000076084","descriptor_name":"Ubiquitin-Specific Peptidase 7","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbac270","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac270","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35789255","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35789255","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.8100000023841858}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":41,"referenced_works":["https://openalex.org/W2034549041","https://openalex.org/W2064675550","https://openalex.org/W2069081118","https://openalex.org/W2095916340","https://openalex.org/W2121604817","https://openalex.org/W2145546477","https://openalex.org/W2150365399","https://openalex.org/W2160592148","https://openalex.org/W2529996553","https://openalex.org/W2587517604","https://openalex.org/W2592487518","https://openalex.org/W2610148085","https://openalex.org/W2734505834","https://openalex.org/W2736137960","https://openalex.org/W2738923789","https://openalex.org/W2753588101","https://openalex.org/W2790759781","https://openalex.org/W2883583109","https://openalex.org/W2943380091","https://openalex.org/W2948978827","https://openalex.org/W2984336612","https://openalex.org/W2998571806","https://openalex.org/W3028161460","https://openalex.org/W3033869790","https://openalex.org/W3044169888","https://openalex.org/W3049675384","https://openalex.org/W3112587790","https://openalex.org/W3133523400","https://openalex.org/W3144179941","https://openalex.org/W3177533410","https://openalex.org/W3195161349","https://openalex.org/W3196480782","https://openalex.org/W3204360269","https://openalex.org/W4287266177","https://openalex.org/W6680596189","https://openalex.org/W6683799085","https://openalex.org/W6730543993","https://openalex.org/W6737184443","https://openalex.org/W6740619299","https://openalex.org/W6761982119","https://openalex.org/W6787696101"],"related_works":["https://openalex.org/W4226161264","https://openalex.org/W3156186218","https://openalex.org/W4283722810","https://openalex.org/W4319455836","https://openalex.org/W2558461040","https://openalex.org/W2474546929","https://openalex.org/W3021212276","https://openalex.org/W4206326513","https://openalex.org/W3004450058","https://openalex.org/W2809645723"],"abstract_inverted_index":{"The":[0],"generation":[1,51,72,94],"of":[2,49,52,86,95,110,144],"candidate":[3],"hit":[4],"molecules":[5],"with":[6,106,122],"the":[7,39,46,50,55,60,84,93,99,120,123,141,145],"potential":[8],"to":[9,31,68,82,92,102],"be":[10],"used":[11],"in":[12,33],"cancer":[13],"treatment":[14],"is":[15],"a":[16,66,129],"challenging":[17],"task.":[18],"In":[19],"this":[20,126],"context,":[21],"computational":[22],"methods":[23],"based":[24],"on":[25,45,140],"deep":[26],"learning":[27],"have":[28,42],"been":[29],"employed":[30],"improve":[32],"silico":[34],"drug":[35],"design":[36],"methodologies.":[37],"Nonetheless,":[38],"applied":[40,91],"strategies":[41],"focused":[43,139],"solely":[44],"chemical":[47],"aspect":[48],"compounds,":[53,105],"disregarding":[54],"likely":[56],"biological":[57,75,142],"consequences":[58],"for":[59,119,134],"organism's":[61],"dynamics.":[62],"Herein,":[63],"we":[64],"propose":[65],"method":[67,133],"implement":[69],"targeted":[70],"molecular":[71],"that":[73],"employs":[74],"information,":[76],"namely,":[77],"disease-associated":[78],"gene":[79],"expression":[80],"data,":[81],"conduct":[83],"process":[85],"identifying":[87],"interesting":[88],"hits.":[89],"When":[90],"USP7":[96],"putative":[97],"inhibitors,":[98],"framework":[100],"managed":[101],"generate":[103],"promising":[104,137],"more":[107],"than":[108],"90%":[109],"them":[111],"containing":[112],"drug-like":[113],"properties":[114],"and":[115,131],"essential":[116],"active":[117],"groups":[118],"interaction":[121],"target.":[124],"Hence,":[125],"work":[127],"provides":[128],"novel":[130],"reliable":[132],"generating":[135],"new":[136],"compounds":[138],"context":[143],"disease.":[146]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":1}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}
