{"id":"https://openalex.org/W3181448263","doi":"https://doi.org/10.1093/bioinformatics/btab288","title":"JEDI: circular RNA prediction based on junction encoders and deep interaction among splice sites","display_name":"JEDI: circular RNA prediction based on junction encoders and deep interaction among splice sites","publication_year":2021,"publication_date":"2021-04-27","ids":{"openalex":"https://openalex.org/W3181448263","doi":"https://doi.org/10.1093/bioinformatics/btab288","mag":"3181448263","pmid":"https://pubmed.ncbi.nlm.nih.gov/34252942"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab288","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab288","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/Supplement_1/i289/39620239/btab288.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/37/Supplement_1/i289/39620239/btab288.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5048749901","display_name":"Jyun\u2010Yu Jiang","orcid":"https://orcid.org/0000-0002-1753-8099"},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jyun-Yu Jiang","raw_affiliation_strings":["Department of Computer Science, University of California , Los Angeles, CA 90024, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of California , Los Angeles, CA 90024, USA","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073504925","display_name":"Chelsea J.\u2010T. Ju","orcid":"https://orcid.org/0000-0001-8674-5318"},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chelsea J -T Ju","raw_affiliation_strings":["Department of Computer Science, University of California , Los Angeles, CA 90024, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of California , Los Angeles, CA 90024, USA","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013699528","display_name":"Junheng Hao","orcid":"https://orcid.org/0000-0001-5292-9389"},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Junheng Hao","raw_affiliation_strings":["Department of Computer Science, University of California , Los Angeles, CA 90024, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of California , Los Angeles, CA 90024, USA","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102861481","display_name":"Muhao Chen","orcid":"https://orcid.org/0000-0003-0118-3147"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Muhao Chen","raw_affiliation_strings":["Department of Computer Science, University of Southern California , Los Angeles, CA 90007, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Southern California , Los Angeles, CA 90007, USA","institution_ids":["https://openalex.org/I1174212"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100392089","display_name":"Wei Wang","orcid":"https://orcid.org/0000-0002-8180-2886"},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Wei Wang","raw_affiliation_strings":["Department of Computer Science, University of California , Los Angeles, CA 90024, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of California , Los Angeles, CA 90024, USA","institution_ids":["https://openalex.org/I161318765"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5048749901","https://openalex.org/A5100392089"],"corresponding_institution_ids":["https://openalex.org/I161318765"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.6286,"has_fulltext":true,"cited_by_count":23,"citation_normalized_percentile":{"value":0.84069786,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"37","issue":"Supplement_1","first_page":"i289","last_page":"i298"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.9057999849319458,"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/T10604","display_name":"RNA Research and Splicing","score":0.9057999849319458,"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.02669999934732914,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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":0.017899999395012856,"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/splice","display_name":"splice","score":0.8035277128219604},{"id":"https://openalex.org/keywords/circular-rna","display_name":"Circular RNA","score":0.6517093181610107},{"id":"https://openalex.org/keywords/encoder","display_name":"Encoder","score":0.605088472366333},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.534514307975769},{"id":"https://openalex.org/keywords/rna-splicing","display_name":"RNA splicing","score":0.5306146740913391},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4842362105846405},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.46457231044769287},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.33395063877105713},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.29628986120224},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.25282084941864014},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.16820791363716125},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.09328877925872803}],"concepts":[{"id":"https://openalex.org/C2780989783","wikidata":"https://www.wikidata.org/wiki/Q7578557","display_name":"splice","level":3,"score":0.8035277128219604},{"id":"https://openalex.org/C2775893923","wikidata":"https://www.wikidata.org/wiki/Q17113455","display_name":"Circular RNA","level":4,"score":0.6517093181610107},{"id":"https://openalex.org/C118505674","wikidata":"https://www.wikidata.org/wiki/Q42586063","display_name":"Encoder","level":2,"score":0.605088472366333},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.534514307975769},{"id":"https://openalex.org/C54458228","wikidata":"https://www.wikidata.org/wiki/Q237218","display_name":"RNA splicing","level":4,"score":0.5306146740913391},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4842362105846405},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.46457231044769287},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33395063877105713},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.29628986120224},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.25282084941864014},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.16820791363716125},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.09328877925872803}],"mesh":[{"descriptor_ui":"D000079962","descriptor_name":"RNA, Circular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000079962","descriptor_name":"RNA, Circular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000079962","descriptor_name":"RNA, Circular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012326","descriptor_name":"RNA Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012326","descriptor_name":"RNA Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012326","descriptor_name":"RNA Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D022821","descriptor_name":"RNA Splice Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D022821","descriptor_name":"RNA Splice Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D022821","descriptor_name":"RNA Splice Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btab288","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab288","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/Supplement_1/i289/39620239/btab288.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34252942","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34252942","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:escholarship.org:ark:/13030/qt7gx7q7h0","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/7gx7q7h0","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"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":"Bioinformatics, vol 37, iss Supplement_1","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8336595","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8336595","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btab288","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab288","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/Supplement_1/i289/39620239/btab288.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15","score":0.49000000953674316}],"awards":[{"id":"https://openalex.org/G1366815325","display_name":null,"funder_award_id":"NIH-R35-HL135772","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2449105890","display_name":null,"funder_award_id":"NSF-IIS-2031187","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4777767270","display_name":null,"funder_award_id":"NSF-DGE-1829071","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7141822765","display_name":null,"funder_award_id":"R35 HL135772","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G7189626769","display_name":"NRT-HDR: Modeling and Understanding Human Behavior: Harnessing Data from Genes to Social Networks","funder_award_id":"1829071","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7517944603","display_name":null,"funder_award_id":"R35-HL135772","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8442901025","display_name":null,"funder_award_id":"DGE-1829071","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3181448263.pdf","grobid_xml":"https://content.openalex.org/works/W3181448263.grobid-xml"},"referenced_works_count":46,"referenced_works":["https://openalex.org/W1486144458","https://openalex.org/W1566841623","https://openalex.org/W1966411071","https://openalex.org/W1981726010","https://openalex.org/W2015947713","https://openalex.org/W2017919052","https://openalex.org/W2019230794","https://openalex.org/W2054891772","https://openalex.org/W2058835062","https://openalex.org/W2064165694","https://openalex.org/W2064675550","https://openalex.org/W2091161969","https://openalex.org/W2095488795","https://openalex.org/W2100495367","https://openalex.org/W2101234009","https://openalex.org/W2108206849","https://openalex.org/W2115662330","https://openalex.org/W2126144698","https://openalex.org/W2137691989","https://openalex.org/W2141831115","https://openalex.org/W2147625377","https://openalex.org/W2147806662","https://openalex.org/W2155158847","https://openalex.org/W2157331557","https://openalex.org/W2194134194","https://openalex.org/W2409907752","https://openalex.org/W2464424326","https://openalex.org/W2530008209","https://openalex.org/W2599812844","https://openalex.org/W2736280136","https://openalex.org/W2740619578","https://openalex.org/W2755267339","https://openalex.org/W2769047057","https://openalex.org/W2782869019","https://openalex.org/W2886900083","https://openalex.org/W2898598946","https://openalex.org/W2919115771","https://openalex.org/W2941873727","https://openalex.org/W2944735543","https://openalex.org/W2954519497","https://openalex.org/W2977553419","https://openalex.org/W2977708519","https://openalex.org/W2997580564","https://openalex.org/W3006973450","https://openalex.org/W6675354045","https://openalex.org/W6676145377"],"related_works":["https://openalex.org/W2029220916","https://openalex.org/W2274928342","https://openalex.org/W1943031701","https://openalex.org/W3129862691","https://openalex.org/W1993348797","https://openalex.org/W3006402873","https://openalex.org/W2887346131","https://openalex.org/W2008832338","https://openalex.org/W2014791263","https://openalex.org/W2024248021"],"abstract_inverted_index":{"MOTIVATION:":[0],"Circular":[1],"RNA":[2,100],"(circRNA)":[3],"is":[4,245],"a":[5,26,129,199],"novel":[6,168],"class":[7],"of":[8,119,231,242],"long":[9],"non-coding":[10],"RNAs":[11],"that":[12],"have":[13,75],"been":[14,76],"broadly":[15],"discovered":[16],"in":[17,55,209],"the":[18,31,63,80,84,96,108,149,167,232],"eukaryotic":[19],"transcriptome.":[20],"The":[21,240],"circular":[22,81],"structure":[23,82],"arises":[24],"from":[25,83,99],"non-canonical":[27],"splicing":[28],"process,":[29],"where":[30,229],"donor":[32],"site":[33,156],"backspliced":[34],"to":[35,78,94,106,114,152,171,194],"an":[36],"upstream":[37],"acceptor":[38],"site.":[39],"These":[40],"circRNA":[41,140,210],"sequences":[42,101],"are":[43,253],"conserved":[44],"across":[45],"species.":[46],"More":[47],"importantly,":[48],"rising":[49],"evidence":[50],"suggests":[51],"their":[52,68,104,123],"vital":[53],"roles":[54],"gene":[56,200,217],"regulation":[57],"and":[58,70,102,122,164,216],"association":[59],"with":[60,135],"diseases.":[61],"As":[62],"fundamental":[64],"effort":[65],"toward":[66],"elucidating":[67],"functions":[69],"mechanisms,":[71],"several":[72],"computational":[73,89],"methods":[74,90,112],"proposed":[77],"predict":[79,185],"primary":[85],"sequence.":[86],"Recently,":[87],"advanced":[88],"leverage":[91],"deep":[92,124,159,173],"learning":[93],"capture":[95],"relevant":[97],"patterns":[98],"model":[103,172],"interactions":[105],"facilitate":[107],"prediction.":[109],"However,":[110],"these":[111,176],"fail":[113],"fully":[115],"explore":[116],"positional":[117],"information":[118],"splice":[120,192],"junctions":[121],"interaction.":[125],"RESULTS:":[126],"We":[127],"present":[128],"robust":[130],"end-to-end":[131],"framework,":[132],"Junction":[133],"Encoder":[134],"Deep":[136],"Interaction":[137],"(JEDI),":[138],"for":[139,178],"prediction":[141,211],"using":[142],"only":[143,184],"nucleotide":[144],"sequences.":[145],"JEDI":[146,181,204,220],"first":[147],"leverages":[148],"attention":[150],"mechanism":[151],"encode":[153],"each":[154],"junction":[155],"based":[157],"on":[158,212,225],"bidirectional":[160],"recurrent":[161],"neural":[162],"networks":[163],"then":[165],"presents":[166],"cross-attention":[169],"layer":[170],"interaction":[174],"among":[175,191],"sites":[177,193],"backsplicing.":[179],"Finally,":[180],"can":[182,235],"not":[183],"circRNAs":[186],"but":[187],"also":[188,221],"interpret":[189],"relationships":[190],"discover":[195],"backsplicing":[196,227],"hotspots":[197],"within":[198],"region.":[201],"Experiments":[202],"demonstrate":[203],"significantly":[205],"outperforms":[206],"state-of-the-art":[207],"approaches":[208,234],"both":[213],"isoform":[214],"level":[215],"level.":[218],"Moreover,":[219],"shows":[222],"promising":[223],"results":[224],"zero-shot":[226],"discovery,":[228],"none":[230],"existing":[233],"achieve.":[236],"AVAILABILITY":[237],"AND":[238],"IMPLEMENTATION:":[239],"implementation":[241],"our":[243],"framework":[244],"available":[246,254],"at":[247,255],"https://github.com/hallogameboy/JEDI.":[248],"SUPPLEMENTARY":[249],"INFORMATION:":[250],"Supplementary":[251],"data":[252],"Bioinformatics":[256],"online.":[257]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":2}],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2025-10-10T00:00:00"}
