{"id":"https://openalex.org/W2892346327","doi":"https://doi.org/10.1093/bioinformatics/bty785","title":"Ambiguous splice sites distinguish circRNA and linear splicing in the human genome","display_name":"Ambiguous splice sites distinguish circRNA and linear splicing in the human genome","publication_year":2018,"publication_date":"2018-09-04","ids":{"openalex":"https://openalex.org/W2892346327","doi":"https://doi.org/10.1093/bioinformatics/bty785","mag":"2892346327","pmid":"https://pubmed.ncbi.nlm.nih.gov/30192918"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty785","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty785","pdf_url":"https://watermark.silverchair.com/bty785.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAr4wggK6BgkqhkiG9w0BBwagggKrMIICpwIBADCCAqAGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMTEb7IQTTD7QdadTSAgEQgIICcXddOoBC8lEmjZX1YtEI-EEDvIMjhZhaoDgT6sKaVD1vM_n_2H52ejRle9UWngAGJGyAZ_5WWuaFHG8yp9Y_xJYJESYlKKktlmsQ0lK2neW5UrZQb3hWVDC85ongn5cxSRjsAgZEWIXmV0GoJLPO6eiELbHdWe_x1Azcqk8f1zTiffDUad3RzKaCoXKh4q04ivGEF1etsKh33JcqG8_iOrkg1mdVMf0Qpt3F49czOi0at7FxMcXx2ZxMOUtyrG1ZinHkdF1PQGe4VwXU9U4Xyek_jwa2jS0cJGO45OebmHvj8BqEvfNtDNnhudoUnrAnFG-B6fqgoEDNUdPtB-vzon1RzRjmi-z5KAFz0Zx28HpIcCpEjFEHX50n5WPYvN-83yREG6Q7avUdN9UioPwhI8HO5BbNTDwwG7AKddqZBZ-bmML-QZD_4LKqeuxvtFZblqh14h3Ph5qxw6IReUG_0_4qxNBuCw5zRkSI497iN3hDwLHLGwZGAv5lKbqWrYcXcKD9soszHn2RQIs7YrDYjetl64QIDASUJmcLs2sJerAAagd1fa6pEriuv-_6TtlJH1YPkuXFu2cs20IvFiSK8iUxebfhnvFWLa0cWKw7RR4s0TGbfhKYlNwbIIg624l7qHKhOfKZyZn4XzXnVZyDMBRIZrBuqIgaX-pCI9R1oZgMlg-A7GYLEaSTTEQmaEX6nlNZ2ybBFhG0ejfXxVpUlfkBkmru_5B9EJB9vWhPeQjD3MP3kwzXCuV6kWKR7vRHHhkDVaTJJ1kVqiA_FA-Fb-o11LGRnGgm5kRRe4qVKsYx8vnnfbzzhgBRhh_5TBHhX4k","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":null,"license_id":null,"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":"bronze","oa_url":"https://watermark.silverchair.com/bty785.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAr4wggK6BgkqhkiG9w0BBwagggKrMIICpwIBADCCAqAGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMTEb7IQTTD7QdadTSAgEQgIICcXddOoBC8lEmjZX1YtEI-EEDvIMjhZhaoDgT6sKaVD1vM_n_2H52ejRle9UWngAGJGyAZ_5WWuaFHG8yp9Y_xJYJESYlKKktlmsQ0lK2neW5UrZQb3hWVDC85ongn5cxSRjsAgZEWIXmV0GoJLPO6eiELbHdWe_x1Azcqk8f1zTiffDUad3RzKaCoXKh4q04ivGEF1etsKh33JcqG8_iOrkg1mdVMf0Qpt3F49czOi0at7FxMcXx2ZxMOUtyrG1ZinHkdF1PQGe4VwXU9U4Xyek_jwa2jS0cJGO45OebmHvj8BqEvfNtDNnhudoUnrAnFG-B6fqgoEDNUdPtB-vzon1RzRjmi-z5KAFz0Zx28HpIcCpEjFEHX50n5WPYvN-83yREG6Q7avUdN9UioPwhI8HO5BbNTDwwG7AKddqZBZ-bmML-QZD_4LKqeuxvtFZblqh14h3Ph5qxw6IReUG_0_4qxNBuCw5zRkSI497iN3hDwLHLGwZGAv5lKbqWrYcXcKD9soszHn2RQIs7YrDYjetl64QIDASUJmcLs2sJerAAagd1fa6pEriuv-_6TtlJH1YPkuXFu2cs20IvFiSK8iUxebfhnvFWLa0cWKw7RR4s0TGbfhKYlNwbIIg624l7qHKhOfKZyZn4XzXnVZyDMBRIZrBuqIgaX-pCI9R1oZgMlg-A7GYLEaSTTEQmaEX6nlNZ2ybBFhG0ejfXxVpUlfkBkmru_5B9EJB9vWhPeQjD3MP3kwzXCuV6kWKR7vRHHhkDVaTJJ1kVqiA_FA-Fb-o11LGRnGgm5kRRe4qVKsYx8vnnfbzzhgBRhh_5TBHhX4k","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053317035","display_name":"Roozbeh Dehghannasiri","orcid":"https://orcid.org/0000-0001-7413-3437"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Roozbeh Dehghannasiri","raw_affiliation_strings":["Department of Biochemistry, Stanford University, Stanford, CA, USA"],"raw_orcid":"https://orcid.org/0000-0001-7413-3437","affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Stanford University, Stanford, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030114257","display_name":"Linda Szabo","orcid":null},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Linda Szabo","raw_affiliation_strings":["Department of Biomedical Data Science, Stanford University, Stanford, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Data Science, Stanford University, Stanford, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080771167","display_name":"Julia Salzman","orcid":"https://orcid.org/0000-0002-7397-4354"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Julia Salzman","raw_affiliation_strings":["Department of Biochemistry, Stanford University, Stanford, CA, USA","Department of Biomedical Data Science, Stanford University, Stanford, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Stanford University, Stanford, CA, USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Department of Biomedical Data Science, Stanford University, Stanford, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5080771167"],"corresponding_institution_ids":["https://openalex.org/I97018004"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.7423,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.70864268,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"35","issue":"8","first_page":"1263","last_page":"1268"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.947700023651123,"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":0.947700023651123,"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":0.015200000256299973,"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/T11765","display_name":"Circular RNAs in diseases","score":0.010599999688565731,"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/computational-biology","display_name":"Computational biology","score":0.6268757581710815},{"id":"https://openalex.org/keywords/intron","display_name":"Intron","score":0.6018548011779785},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5643927454948425},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5567276477813721},{"id":"https://openalex.org/keywords/rna-splicing","display_name":"RNA splicing","score":0.5462992191314697},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5095282196998596},{"id":"https://openalex.org/keywords/splice","display_name":"splice","score":0.4866827130317688},{"id":"https://openalex.org/keywords/exon","display_name":"Exon","score":0.4534395933151245},{"id":"https://openalex.org/keywords/gene-annotation","display_name":"Gene Annotation","score":0.4486885964870453},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3353474736213684},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.3161739706993103}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6268757581710815},{"id":"https://openalex.org/C94671646","wikidata":"https://www.wikidata.org/wiki/Q207551","display_name":"Intron","level":3,"score":0.6018548011779785},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5643927454948425},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5567276477813721},{"id":"https://openalex.org/C54458228","wikidata":"https://www.wikidata.org/wiki/Q237218","display_name":"RNA splicing","level":4,"score":0.5462992191314697},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5095282196998596},{"id":"https://openalex.org/C2780989783","wikidata":"https://www.wikidata.org/wiki/Q7578557","display_name":"splice","level":3,"score":0.4866827130317688},{"id":"https://openalex.org/C36823959","wikidata":"https://www.wikidata.org/wiki/Q373027","display_name":"Exon","level":3,"score":0.4534395933151245},{"id":"https://openalex.org/C2908923196","wikidata":"https://www.wikidata.org/wiki/Q5205742","display_name":"Gene Annotation","level":4,"score":0.4486885964870453},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3353474736213684},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.3161739706993103}],"mesh":[{"descriptor_ui":"D000079962","descriptor_name":"RNA, Circular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000079962","descriptor_name":"RNA, Circular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000079962","descriptor_name":"RNA, Circular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005091","descriptor_name":"Exons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005091","descriptor_name":"Exons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005091","descriptor_name":"Exons","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":"D007438","descriptor_name":"Introns","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007438","descriptor_name":"Introns","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007438","descriptor_name":"Introns","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":"D012326","descriptor_name":"RNA Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D022821","descriptor_name":"RNA Splice Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D022821","descriptor_name":"RNA Splice Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D022821","descriptor_name":"RNA Splice Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bty785","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty785","pdf_url":"https://watermark.silverchair.com/bty785.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAr4wggK6BgkqhkiG9w0BBwagggKrMIICpwIBADCCAqAGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMTEb7IQTTD7QdadTSAgEQgIICcXddOoBC8lEmjZX1YtEI-EEDvIMjhZhaoDgT6sKaVD1vM_n_2H52ejRle9UWngAGJGyAZ_5WWuaFHG8yp9Y_xJYJESYlKKktlmsQ0lK2neW5UrZQb3hWVDC85ongn5cxSRjsAgZEWIXmV0GoJLPO6eiELbHdWe_x1Azcqk8f1zTiffDUad3RzKaCoXKh4q04ivGEF1etsKh33JcqG8_iOrkg1mdVMf0Qpt3F49czOi0at7FxMcXx2ZxMOUtyrG1ZinHkdF1PQGe4VwXU9U4Xyek_jwa2jS0cJGO45OebmHvj8BqEvfNtDNnhudoUnrAnFG-B6fqgoEDNUdPtB-vzon1RzRjmi-z5KAFz0Zx28HpIcCpEjFEHX50n5WPYvN-83yREG6Q7avUdN9UioPwhI8HO5BbNTDwwG7AKddqZBZ-bmML-QZD_4LKqeuxvtFZblqh14h3Ph5qxw6IReUG_0_4qxNBuCw5zRkSI497iN3hDwLHLGwZGAv5lKbqWrYcXcKD9soszHn2RQIs7YrDYjetl64QIDASUJmcLs2sJerAAagd1fa6pEriuv-_6TtlJH1YPkuXFu2cs20IvFiSK8iUxebfhnvFWLa0cWKw7RR4s0TGbfhKYlNwbIIg624l7qHKhOfKZyZn4XzXnVZyDMBRIZrBuqIgaX-pCI9R1oZgMlg-A7GYLEaSTTEQmaEX6nlNZ2ybBFhG0ejfXxVpUlfkBkmru_5B9EJB9vWhPeQjD3MP3kwzXCuV6kWKR7vRHHhkDVaTJJ1kVqiA_FA-Fb-o11LGRnGgm5kRRe4qVKsYx8vnnfbzzhgBRhh_5TBHhX4k","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30192918","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30192918","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:europepmc.org:6103328","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6477988","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty785","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty785","pdf_url":"https://watermark.silverchair.com/bty785.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAr4wggK6BgkqhkiG9w0BBwagggKrMIICpwIBADCCAqAGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMTEb7IQTTD7QdadTSAgEQgIICcXddOoBC8lEmjZX1YtEI-EEDvIMjhZhaoDgT6sKaVD1vM_n_2H52ejRle9UWngAGJGyAZ_5WWuaFHG8yp9Y_xJYJESYlKKktlmsQ0lK2neW5UrZQb3hWVDC85ongn5cxSRjsAgZEWIXmV0GoJLPO6eiELbHdWe_x1Azcqk8f1zTiffDUad3RzKaCoXKh4q04ivGEF1etsKh33JcqG8_iOrkg1mdVMf0Qpt3F49czOi0at7FxMcXx2ZxMOUtyrG1ZinHkdF1PQGe4VwXU9U4Xyek_jwa2jS0cJGO45OebmHvj8BqEvfNtDNnhudoUnrAnFG-B6fqgoEDNUdPtB-vzon1RzRjmi-z5KAFz0Zx28HpIcCpEjFEHX50n5WPYvN-83yREG6Q7avUdN9UioPwhI8HO5BbNTDwwG7AKddqZBZ-bmML-QZD_4LKqeuxvtFZblqh14h3Ph5qxw6IReUG_0_4qxNBuCw5zRkSI497iN3hDwLHLGwZGAv5lKbqWrYcXcKD9soszHn2RQIs7YrDYjetl64QIDASUJmcLs2sJerAAagd1fa6pEriuv-_6TtlJH1YPkuXFu2cs20IvFiSK8iUxebfhnvFWLa0cWKw7RR4s0TGbfhKYlNwbIIg624l7qHKhOfKZyZn4XzXnVZyDMBRIZrBuqIgaX-pCI9R1oZgMlg-A7GYLEaSTTEQmaEX6nlNZ2ybBFhG0ejfXxVpUlfkBkmru_5B9EJB9vWhPeQjD3MP3kwzXCuV6kWKR7vRHHhkDVaTJJ1kVqiA_FA-Fb-o11LGRnGgm5kRRe4qVKsYx8vnnfbzzhgBRhh_5TBHhX4k","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3336612505","display_name":null,"funder_award_id":"R01 GM116847","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G3445278825","display_name":null,"funder_award_id":"R25 CA180993","funder_id":"https://openalex.org/F4320306151","funder_display_name":"Alfred P. Sloan Foundation"},{"id":"https://openalex.org/G4715084799","display_name":null,"funder_award_id":"R25 CA180993","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G4968224489","display_name":null,"funder_award_id":"T15 LM007033","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"},{"id":"https://openalex.org/G7835246993","display_name":null,"funder_award_id":"MCB-1552196","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8722800612","display_name":null,"funder_award_id":"R00 CA168987","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306151","display_name":"Alfred P. Sloan Foundation","ror":"https://ror.org/052csg198"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2892346327.pdf","grobid_xml":"https://content.openalex.org/works/W2892346327.grobid-xml"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W1536677592","https://openalex.org/W1883773314","https://openalex.org/W1991402780","https://openalex.org/W2001730018","https://openalex.org/W2011920499","https://openalex.org/W2034305079","https://openalex.org/W2047452386","https://openalex.org/W2051631967","https://openalex.org/W2058805572","https://openalex.org/W2070494252","https://openalex.org/W2080667183","https://openalex.org/W2086055453","https://openalex.org/W2097065948","https://openalex.org/W2103534177","https://openalex.org/W2115662330","https://openalex.org/W2126419817","https://openalex.org/W2127471603","https://openalex.org/W2139312181","https://openalex.org/W2159833474","https://openalex.org/W2160053034","https://openalex.org/W2166187656","https://openalex.org/W2340210804","https://openalex.org/W2521004200","https://openalex.org/W2531297636","https://openalex.org/W2902200003","https://openalex.org/W2951498553","https://openalex.org/W6665081546"],"related_works":["https://openalex.org/W2083833254","https://openalex.org/W1978448871","https://openalex.org/W2082856106","https://openalex.org/W1973164572","https://openalex.org/W1988731563","https://openalex.org/W2068962637","https://openalex.org/W3090446747","https://openalex.org/W1995725827","https://openalex.org/W2083872838","https://openalex.org/W2608025469"],"abstract_inverted_index":{"MOTIVATION:":[0],"Identification":[1],"of":[2,26,59,78,96,113,145,159,165,185,195,199,207,223],"splice":[3,82,97,148,224],"sites":[4,149,225],"is":[5,41,69,110,217],"critical":[6],"to":[7,11,43,80,101,204],"gene":[8],"annotation":[9],"and":[10,28,139,143,152,162,229],"determine":[12],"which":[13,109],"sequences":[14],"control":[15],"circRNA":[16,153],"biogenesis.":[17],"Full-length":[18],"RNA":[19,121,126,200],"transcripts":[20,201],"could":[21],"in":[22,30,56,87,118,135,141,150,219,226],"principle":[23],"complete":[24],"annotations":[25],"introns":[27],"exons":[29],"genomes":[31,138],"without":[32,202],"external":[33],"ontologies,":[34],"i.e.,":[35],"ab":[36,196,215],"initio.":[37],"However,":[38],"whether":[39],"it":[40,68],"possible":[42],"reconstruct":[44],"genomic":[45,103,115],"positions":[46,116],"where":[47],"splicing":[48],"occurs":[49],"from":[50],"full-length":[51],"transcripts,":[52],"even":[53],"if":[54],"sampled":[55],"the":[57,63,76,88,102,111,119,163,175,193,205,220],"absence":[58],"noise,":[60],"depends":[61],"on":[62,75,192],"genome":[64],"sequence":[65,104,122,242],"composition.":[66],"If":[67],"not,":[70],"there":[71],"exist":[72],"provable":[73],"limits":[74],"use":[77],"RNA-Seq":[79],"define":[81],"locations":[83],"(linear":[84],"or":[85,181],"circular)":[86],"genome.":[89],"RESULTS:":[90],"We":[91,128],"provide":[92],"a":[93,189],"formal":[94],"definition":[95],"site":[98],"ambiguity":[99],"due":[100],"by":[105],"introducing":[106],"equivalent":[107,131,160,186,240],"junction,":[108],"set":[112],"local":[114],"resulting":[117],"same":[120],"when":[123,172],"joined":[124],"through":[125],"splicing.":[127],"show":[129],"that":[130],"junctions":[132,161,187],"are":[133,169,245,253],"prevalent":[134],"diverse":[136],"eukaryotic":[137],"occur":[140],"88.64%":[142],"78.64%":[144],"annotated":[146,227],"human":[147],"linear":[151,230],"junctions,":[154],"respectively.":[155],"The":[156,183],"observed":[157],"fractions":[158],"frequency":[164,184],"many":[166],"individual":[167],"motifs":[168],"statistically":[170],"significant":[171],"compared":[173],"against":[174],"null":[176],"distribution":[177],"computed":[178],"via":[179],"simulation":[180],"closed-form.":[182],"establishes":[188],"fundamental":[190],"limit":[191],"possibility":[194],"initio":[197,216],"reconstruction":[198],"appealing":[203],"ontology":[206],"\"GT-AG\"":[208],"boundaries":[209],"defining":[210],"introns.":[211],"Said":[212],"differently,":[213],"completely":[214],"impossible":[218],"vast":[221],"majority":[222],"circRNAs":[228],"transcripts.":[231],"AVAILABILITY":[232],"AND":[233],"IMPLEMENTATION:":[234],"Two":[235],"python":[236],"scripts":[237],"generating":[238],"an":[239],"junction":[241,244],"per":[243],"available":[246,254],"at:":[247],"https://github.com/salzmanlab/Equivalent-Junctions.":[248],"SUPPLEMENTARY":[249],"INFORMATION:":[250],"Supplementary":[251],"data":[252],"at":[255],"Bioinformatics":[256],"online.":[257]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}
