{"id":"https://openalex.org/W4404112173","doi":"https://doi.org/10.1093/bib/bbae563","title":"siRNADiscovery: a graph neural network for siRNA efficacy prediction via deep RNA sequence analysis","display_name":"siRNADiscovery: a graph neural network for siRNA efficacy prediction via deep RNA sequence analysis","publication_year":2024,"publication_date":"2024-09-23","ids":{"openalex":"https://openalex.org/W4404112173","doi":"https://doi.org/10.1093/bib/bbae563","pmid":"https://pubmed.ncbi.nlm.nih.gov/39503523"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae563","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae563","pdf_url":"https://academic.oup.com/bib/article-pdf/25/6/bbae563/60441414/bbae563.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bib/article-pdf/25/6/bbae563/60441414/bbae563.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101445103","display_name":"Rongzhuo Long","orcid":"https://orcid.org/0000-0003-3755-5491"},"institutions":[{"id":"https://openalex.org/I161716053","display_name":"China Pharmaceutical University","ror":"https://ror.org/01sfm2718","country_code":"CN","type":"education","lineage":["https://openalex.org/I161716053"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Rongzhuo Long","raw_affiliation_strings":["School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University , 211198, Nanjing ,"],"raw_orcid":"https://orcid.org/0000-0003-3755-5491","affiliations":[{"raw_affiliation_string":"School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University , 211198, Nanjing ,","institution_ids":["https://openalex.org/I161716053"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114400807","display_name":"Ziyu Guo","orcid":"https://orcid.org/0000-0001-9606-9691"},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"HK","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Ziyu Guo","raw_affiliation_strings":["Department of Computer Science and Engineering, The Chinese University of Hong Kong , Central Ave, Hong Kong SAR ,"],"raw_orcid":"https://orcid.org/0000-0001-9606-9691","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, The Chinese University of Hong Kong , Central Ave, Hong Kong SAR ,","institution_ids":["https://openalex.org/I177725633"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000249616","display_name":"Da Han","orcid":"https://orcid.org/0000-0002-0804-2964"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I2800570007","display_name":"Renji Hospital","ror":"https://ror.org/03ypbx660","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I2800570007"]},{"id":"https://openalex.org/I4210146488","display_name":"Institute of Molecular Medicine","ror":"https://ror.org/04eb14s37","country_code":"IN","type":"facility","lineage":["https://openalex.org/I4210146488"]}],"countries":["CN","IN"],"is_corresponding":false,"raw_author_name":"Da Han","raw_affiliation_strings":["Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences , 310022, Hangzhou, Zhejiang ,","Institute of Molecular Medicine (IMM) and Department of Laboratory Medicine , Renji Hospital, School of Medicine, , 200240, Shanghai ,","Shanghai Jiao Tong University , Renji Hospital, School of Medicine, , 200240, Shanghai ,"],"raw_orcid":"https://orcid.org/0000-0002-0804-2964","affiliations":[{"raw_affiliation_string":"Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences , 310022, Hangzhou, Zhejiang ,","institution_ids":["https://openalex.org/I19820366"]},{"raw_affiliation_string":"Institute of Molecular Medicine (IMM) and Department of Laboratory Medicine , Renji Hospital, School of Medicine, , 200240, Shanghai ,","institution_ids":["https://openalex.org/I2800570007","https://openalex.org/I4210146488"]},{"raw_affiliation_string":"Shanghai Jiao Tong University , Renji Hospital, School of Medicine, , 200240, Shanghai ,","institution_ids":["https://openalex.org/I2800570007","https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052636953","display_name":"Boxiang Liu","orcid":"https://orcid.org/0000-0002-2595-4463"},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Boxiang Liu","raw_affiliation_strings":["Department of Pharmacy , Faculty of Science, , Singapore, 117543 ,","National University of Singapore , Faculty of Science, , Singapore, 117543 ,"],"raw_orcid":"https://orcid.org/0000-0002-2595-4463","affiliations":[{"raw_affiliation_string":"Department of Pharmacy , Faculty of Science, , Singapore, 117543 ,","institution_ids":["https://openalex.org/I165932596"]},{"raw_affiliation_string":"National University of Singapore , Faculty of Science, , Singapore, 117543 ,","institution_ids":["https://openalex.org/I165932596"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101468229","display_name":"Xudong Yuan","orcid":"https://orcid.org/0000-0002-8683-4297"},"institutions":[{"id":"https://openalex.org/I4210134296","display_name":"Edison Pharmaceuticals (United States)","ror":"https://ror.org/048fxk571","country_code":"US","type":"company","lineage":["https://openalex.org/I4210134296"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xudong Yuan","raw_affiliation_strings":["ACON Pharmaceuticals , 2557 Route 130 S, Ste 3, Cranbury, NJ 08512 ,"],"raw_orcid":"https://orcid.org/0000-0002-8683-4297","affiliations":[{"raw_affiliation_string":"ACON Pharmaceuticals , 2557 Route 130 S, Ste 3, Cranbury, NJ 08512 ,","institution_ids":["https://openalex.org/I4210134296"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101415870","display_name":"Guangyong Chen","orcid":"https://orcid.org/0000-0002-5892-8608"},"institutions":[{"id":"https://openalex.org/I4210123185","display_name":"Zhejiang Lab","ror":"https://ror.org/02m2h7991","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210123185"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guangyong Chen","raw_affiliation_strings":["Zhejiang Lab , Ke Chuang Avenue, 311121, Zhejiang ,"],"raw_orcid":"https://orcid.org/0000-0002-5892-8608","affiliations":[{"raw_affiliation_string":"Zhejiang Lab , Ke Chuang Avenue, 311121, Zhejiang ,","institution_ids":["https://openalex.org/I4210123185"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032708386","display_name":"Pheng\u2010Ann Heng","orcid":"https://orcid.org/0000-0003-3055-5034"},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"HK","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Pheng-Ann Heng","raw_affiliation_strings":["Department of Computer Science and Engineering, The Chinese University of Hong Kong , Central Ave, Hong Kong SAR ,"],"raw_orcid":"https://orcid.org/0000-0003-3055-5034","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, The Chinese University of Hong Kong , Central Ave, Hong Kong SAR ,","institution_ids":["https://openalex.org/I177725633"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100425266","display_name":"Liang Zhang","orcid":"https://orcid.org/0000-0003-1146-7848"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Liang Zhang","raw_affiliation_strings":["Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences , 310022, Hangzhou, Zhejiang ,"],"raw_orcid":"https://orcid.org/0000-0003-1146-7848","affiliations":[{"raw_affiliation_string":"Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences , 310022, Hangzhou, Zhejiang ,","institution_ids":["https://openalex.org/I19820366"]}]}],"institutions":[],"countries_distinct_count":5,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5101445103"],"corresponding_institution_ids":["https://openalex.org/I161716053"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":3.1173,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.92397746,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"25","issue":"6","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10725","display_name":"RNA Interference and Gene Delivery","score":0.9998999834060669,"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/T10725","display_name":"RNA Interference and Gene Delivery","score":0.9998999834060669,"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/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.998199999332428,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.996999979019165,"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":0.6853198409080505},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.6802316904067993},{"id":"https://openalex.org/keywords/gene-silencing","display_name":"Gene silencing","score":0.6632709503173828},{"id":"https://openalex.org/keywords/small-interfering-rna","display_name":"Small interfering RNA","score":0.5649961829185486},{"id":"https://openalex.org/keywords/limiting","display_name":"Limiting","score":0.5065628290176392},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4447399973869324},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.442596971988678},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.42239925265312195},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3982919454574585},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.39814817905426025},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.34500807523727417},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21482959389686584},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.18914684653282166},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.1268669068813324},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.0819263756275177}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6853198409080505},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.6802316904067993},{"id":"https://openalex.org/C119056186","wikidata":"https://www.wikidata.org/wiki/Q1431332","display_name":"Gene silencing","level":3,"score":0.6632709503173828},{"id":"https://openalex.org/C22615655","wikidata":"https://www.wikidata.org/wiki/Q203221","display_name":"Small interfering RNA","level":4,"score":0.5649961829185486},{"id":"https://openalex.org/C188198153","wikidata":"https://www.wikidata.org/wiki/Q1613840","display_name":"Limiting","level":2,"score":0.5065628290176392},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4447399973869324},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.442596971988678},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.42239925265312195},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3982919454574585},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.39814817905426025},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.34500807523727417},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21482959389686584},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.18914684653282166},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.1268669068813324},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0819263756275177},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","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":"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","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":"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":"D020868","descriptor_name":"Gene Silencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020868","descriptor_name":"Gene Silencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020868","descriptor_name":"Gene Silencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020868","descriptor_name":"Gene Silencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020868","descriptor_name":"Gene Silencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D034622","descriptor_name":"RNA Interference","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D034622","descriptor_name":"RNA Interference","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D034622","descriptor_name":"RNA Interference","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D034622","descriptor_name":"RNA Interference","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D034622","descriptor_name":"RNA Interference","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbae563","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae563","pdf_url":"https://academic.oup.com/bib/article-pdf/25/6/bbae563/60441414/bbae563.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39503523","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39503523","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},{"id":"pmh:oai:pubmedcentral.nih.gov:11539000","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11539000","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11539000/pdf/bbae563.pdf","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":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbae563","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae563","pdf_url":"https://academic.oup.com/bib/article-pdf/25/6/bbae563/60441414/bbae563.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4087520510","display_name":null,"funder_award_id":"ITS/241/21","funder_id":"https://openalex.org/F4320324196","funder_display_name":"Innovation and Technology Commission - Hong Kong"},{"id":"https://openalex.org/G455209869","display_name":null,"funder_award_id":"62376254","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6691289981","display_name":null,"funder_award_id":"32341018","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8618925650","display_name":null,"funder_award_id":"32470995\uff0c62376254","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G955589337","display_name":null,"funder_award_id":"ITS/241/21","funder_id":"https://openalex.org/F4320326427","funder_display_name":"Innovation and Technology Fund"}],"funders":[{"id":"https://openalex.org/F4320306137","display_name":"Bill and Melinda Gates Foundation","ror":"https://ror.org/0456r8d26"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320324196","display_name":"Innovation and Technology Commission - Hong Kong","ror":"https://ror.org/04vf9tr09"},{"id":"https://openalex.org/F4320326427","display_name":"Innovation and Technology Fund","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4404112173.pdf","grobid_xml":"https://content.openalex.org/works/W4404112173.grobid-xml"},"referenced_works_count":41,"referenced_works":["https://openalex.org/W1520518044","https://openalex.org/W1978209709","https://openalex.org/W1978552532","https://openalex.org/W1984006325","https://openalex.org/W1988783048","https://openalex.org/W1996164865","https://openalex.org/W2003722342","https://openalex.org/W2014165982","https://openalex.org/W2023246459","https://openalex.org/W2025150647","https://openalex.org/W2026156218","https://openalex.org/W2039633802","https://openalex.org/W2051713039","https://openalex.org/W2054757478","https://openalex.org/W2057019601","https://openalex.org/W2068725534","https://openalex.org/W2071596792","https://openalex.org/W2086561953","https://openalex.org/W2089492417","https://openalex.org/W2093605534","https://openalex.org/W2098489216","https://openalex.org/W2099915551","https://openalex.org/W2129552332","https://openalex.org/W2146341019","https://openalex.org/W2149538815","https://openalex.org/W2157962453","https://openalex.org/W2160923685","https://openalex.org/W2170918433","https://openalex.org/W2580930830","https://openalex.org/W2601708340","https://openalex.org/W2725568163","https://openalex.org/W2782412385","https://openalex.org/W2891523875","https://openalex.org/W2968492662","https://openalex.org/W3101369110","https://openalex.org/W3188579603","https://openalex.org/W4294558607","https://openalex.org/W4309604682","https://openalex.org/W4384130557","https://openalex.org/W4396986127","https://openalex.org/W6738964360"],"related_works":["https://openalex.org/W3140432620","https://openalex.org/W1978057048","https://openalex.org/W2165430941","https://openalex.org/W2105774848","https://openalex.org/W2065502723","https://openalex.org/W4388050945","https://openalex.org/W1981917339","https://openalex.org/W1649999227","https://openalex.org/W3003042077","https://openalex.org/W1492982021"],"abstract_inverted_index":{"The":[0],"clinical":[1],"adoption":[2],"of":[3,12,37,63,84,94,146,170,191],"small":[4],"interfering":[5],"RNAs":[6],"(siRNAs)":[7],"has":[8,157],"prompted":[9],"the":[10,34,38,59,91,130,142,168,189],"development":[11],"various":[13,150],"computational":[14],"strategies":[15],"for":[16,185,195],"siRNA":[17,39,47,85],"design,":[18],"from":[19],"traditional":[20],"data":[21,131],"analysis":[22],"to":[23,88,167,176,181],"advanced":[24],"machine":[25],"learning":[26],"techniques.":[27],"However,":[28],"previous":[29,139],"studies":[30,114],"have":[31],"inadequately":[32],"considered":[33],"full":[35],"complexity":[36],"silencing":[40],"mechanism,":[41],"neglecting":[42],"critical":[43],"elements":[44],"such":[45],"as":[46],"positioning":[48],"on":[49,116],"mRNA,":[50],"RNA":[51],"base-pairing":[52],"probabilities,":[53],"and":[54,61,80,86,115,144,162],"RNA-AGO2":[55],"interactions,":[56],"thereby":[57],"limiting":[58],"insight":[60],"accuracy":[62,161],"existing":[64,109],"models.":[65],"Here,":[66],"we":[67,122],"introduce":[68],"siRNADiscovery,":[69],"a":[70,124,134],"Graph":[71],"Neural":[72],"Network":[73],"(GNN)":[74],"framework":[75],"that":[76,128],"leverages":[77],"both":[78],"non-empirical":[79],"empirical":[81],"rule-based":[82],"features":[83],"mRNA":[87],"effectively":[89],"capture":[90],"complex":[92],"dynamics":[93],"gene":[95,171],"silencing.":[96,172],"On":[97],"multiple":[98],"internal":[99],"datasets,":[100],"siRNADiscovery":[101,106,156],"achieves":[102],"state-of-the-art":[103],"performance.":[104],"Significantly,":[105],"also":[107],"outperforms":[108],"methodologies":[110],"in":[111,112,138,188],"vitro":[113],"an":[117],"externally":[118],"validated":[119],"dataset.":[120],"Additionally,":[121],"develop":[123],"new":[125,183],"data-splitting":[126,178],"methodology":[127],"addresses":[129],"leakage":[132],"issue,":[133],"frequently":[135],"overlooked":[136],"problem":[137],"studies,":[140],"ensuring":[141],"robustness":[143],"stability":[145],"our":[147,174],"model":[148],"under":[149],"experimental":[151],"settings.":[152],"Through":[153],"rigorous":[154],"testing,":[155],"demonstrated":[158],"remarkable":[159],"predictive":[160,192],"robustness,":[163],"making":[164],"significant":[165],"contributions":[166],"field":[169],"Furthermore,":[173],"approach":[175],"redefining":[177],"standards":[179],"aims":[180],"set":[182],"benchmarks":[184],"future":[186],"research":[187],"domain":[190],"biological":[193],"modeling":[194],"siRNA.":[196]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":10}],"updated_date":"2026-03-12T06:13:28.667946","created_date":"2025-10-10T00:00:00"}
