{"id":"https://openalex.org/W4414003105","doi":"https://doi.org/10.1093/bib/bbaf437","title":"SLRanger: an integrated approach for spliced leader detection and operon prediction using long RNA reads","display_name":"SLRanger: an integrated approach for spliced leader detection and operon prediction using long RNA reads","publication_year":2025,"publication_date":"2025-08-15","ids":{"openalex":"https://openalex.org/W4414003105","doi":"https://doi.org/10.1093/bib/bbaf437","pmid":"https://pubmed.ncbi.nlm.nih.gov/40905790"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf437","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf437","pdf_url":"https://academic.oup.com/bib/article-pdf/26/5/bbaf437/64209409/bbaf437.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/26/5/bbaf437/64209409/bbaf437.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101745441","display_name":"Yanwen Shao","orcid":"https://orcid.org/0009-0002-4863-3504"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":true,"raw_author_name":"Yanwen Shao","raw_affiliation_strings":["Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong , Tat Chee Avenue, Kowloon, Hong Kong ,","Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China"],"affiliations":[{"raw_affiliation_string":"Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong , Tat Chee Avenue, Kowloon, Hong Kong ,","institution_ids":["https://openalex.org/I168719708"]},{"raw_affiliation_string":"Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025698469","display_name":"Zhihao Guo","orcid":"https://orcid.org/0000-0001-8315-5152"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Zhihao Guo","raw_affiliation_strings":["Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong , Tat Chee Avenue, Kowloon, Hong Kong ,","Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China"],"affiliations":[{"raw_affiliation_string":"Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong , Tat Chee Avenue, Kowloon, Hong Kong ,","institution_ids":["https://openalex.org/I168719708"]},{"raw_affiliation_string":"Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084535846","display_name":"J.R. Chen","orcid":"https://orcid.org/0000-0002-0469-4463"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Jinpeng Chen","raw_affiliation_strings":["Department of Computer Science, College of Computing, City University of Hong Kong , Tat Chee Avenue, Kowloon, Hong Kong ,","Department of Computer Science, College of Computing, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, College of Computing, City University of Hong Kong , Tat Chee Avenue, Kowloon, Hong Kong ,","institution_ids":["https://openalex.org/I168719708"]},{"raw_affiliation_string":"Department of Computer Science, College of Computing, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003632285","display_name":"Runsheng Li","orcid":"https://orcid.org/0000-0003-1563-1844"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]},{"id":"https://openalex.org/I4210105229","display_name":"City University of Hong Kong, Shenzhen Research Institute","ror":"https://ror.org/00xc0ma20","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210105229"]}],"countries":["CN","HK"],"is_corresponding":false,"raw_author_name":"Runsheng Li","raw_affiliation_strings":["Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong , Tat Chee Avenue, Kowloon, Hong Kong ,","Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Matter Science Research Institute (Futian) Shenzhen , 3 Binglang Road, Fubao Street, Futian District, Shenzhen, Guangdong, 518045 ,","Tung Biomedical Sciences Centre, City University of Hong Kong , Tat Chee Avenue, Kowloon, Hong Kong ,","Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Matter Science Research Institute (Futian) Shenzhen, 3 Binglang Road, Fubao Street, Futian District, Shenzhen, Guangdong, 518045, China","Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China","Tung Biomedical Sciences Centre, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China"],"affiliations":[{"raw_affiliation_string":"Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong , Tat Chee Avenue, Kowloon, Hong Kong ,","institution_ids":["https://openalex.org/I168719708"]},{"raw_affiliation_string":"Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Matter Science Research Institute (Futian) Shenzhen , 3 Binglang Road, Fubao Street, Futian District, Shenzhen, Guangdong, 518045 ,","institution_ids":["https://openalex.org/I168719708","https://openalex.org/I4210105229"]},{"raw_affiliation_string":"Tung Biomedical Sciences Centre, City University of Hong Kong , Tat Chee Avenue, Kowloon, Hong Kong ,","institution_ids":["https://openalex.org/I168719708"]},{"raw_affiliation_string":"Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Matter Science Research Institute (Futian) Shenzhen, 3 Binglang Road, Fubao Street, Futian District, Shenzhen, Guangdong, 518045, China","institution_ids":[]},{"raw_affiliation_string":"Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China","institution_ids":[]},{"raw_affiliation_string":"Tung Biomedical Sciences Centre, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5101745441"],"corresponding_institution_ids":["https://openalex.org/I168719708"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.21291898,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"26","issue":"5","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9958000183105469,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9958000183105469,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9950000047683716,"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/T11482","display_name":"RNA modifications and cancer","score":0.9950000047683716,"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/operon","display_name":"Operon","score":0.748476505279541},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5675948858261108},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5504400730133057},{"id":"https://openalex.org/keywords/rna-splicing","display_name":"RNA splicing","score":0.5083176493644714},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.5028738379478455},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.42796605825424194},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.327554851770401},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.32054978609085083},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.31507354974746704},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.29864996671676636},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.20759567618370056},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.11516845226287842}],"concepts":[{"id":"https://openalex.org/C203075996","wikidata":"https://www.wikidata.org/wiki/Q139677","display_name":"Operon","level":4,"score":0.748476505279541},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5675948858261108},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5504400730133057},{"id":"https://openalex.org/C54458228","wikidata":"https://www.wikidata.org/wiki/Q237218","display_name":"RNA splicing","level":4,"score":0.5083176493644714},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.5028738379478455},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.42796605825424194},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.327554851770401},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.32054978609085083},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.31507354974746704},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.29864996671676636},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.20759567618370056},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.11516845226287842},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009876","descriptor_name":"Operon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009876","descriptor_name":"Operon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009876","descriptor_name":"Operon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009876","descriptor_name":"Operon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017173","descriptor_name":"Caenorhabditis elegans","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017173","descriptor_name":"Caenorhabditis elegans","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017173","descriptor_name":"Caenorhabditis elegans","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017173","descriptor_name":"Caenorhabditis elegans","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"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":"D020038","descriptor_name":"RNA, Spliced Leader","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D020038","descriptor_name":"RNA, Spliced Leader","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D020038","descriptor_name":"RNA, Spliced Leader","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D020038","descriptor_name":"RNA, Spliced Leader","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D020040","descriptor_name":"Trans-Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020040","descriptor_name":"Trans-Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020040","descriptor_name":"Trans-Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020040","descriptor_name":"Trans-Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bib/bbaf437","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf437","pdf_url":"https://academic.oup.com/bib/article-pdf/26/5/bbaf437/64209409/bbaf437.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:40905790","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40905790","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:pure.atira.dk:publications/4f9d842d-768a-4ac5-813e-0a7ae3aa22a6","is_oa":true,"landing_page_url":"https://hdl.handle.net/2031/4f9d842d-768a-4ac5-813e-0a7ae3aa22a6","pdf_url":"https://scholars.cityu.edu.hk/files/322740630/308500127.pdf","source":{"id":"https://openalex.org/S7407055387","display_name":"CityU Scholars","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Shao, Y, Guo, Z, Chen, J & Li, R 2025, 'SLRanger : an integrated approach for spliced leader detection and operon prediction using long RNA reads', Briefings in Bioinformatics, vol. 26, no. 5, bbaf437. https://doi.org/10.1093/bib/bbaf437","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12410068","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12410068/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"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/bbaf437","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf437","pdf_url":"https://academic.oup.com/bib/article-pdf/26/5/bbaf437/64209409/bbaf437.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/G1223952294","display_name":null,"funder_award_id":"9610497","funder_id":"https://openalex.org/F4320309893","funder_display_name":"City University of Hong Kong"},{"id":"https://openalex.org/G4456605733","display_name":null,"funder_award_id":"08194126","funder_id":"https://openalex.org/F4320335055","funder_display_name":"Health and Medical Research Fund"}],"funders":[{"id":"https://openalex.org/F4320309893","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23"},{"id":"https://openalex.org/F4320335055","display_name":"Health and Medical Research Fund","ror":"https://ror.org/03qh32912"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4414003105.pdf","grobid_xml":"https://content.openalex.org/works/W4414003105.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W1965968267","https://openalex.org/W1977004097","https://openalex.org/W1986223165","https://openalex.org/W2000484828","https://openalex.org/W2019854397","https://openalex.org/W2025027384","https://openalex.org/W2028586967","https://openalex.org/W2036354940","https://openalex.org/W2049330983","https://openalex.org/W2063622795","https://openalex.org/W2064384066","https://openalex.org/W2090175965","https://openalex.org/W2106012325","https://openalex.org/W2106774119","https://openalex.org/W2121644981","https://openalex.org/W2124876345","https://openalex.org/W2126591934","https://openalex.org/W2127217280","https://openalex.org/W2131108757","https://openalex.org/W2142544428","https://openalex.org/W2149699485","https://openalex.org/W2158510176","https://openalex.org/W2162262271","https://openalex.org/W2170929168","https://openalex.org/W2194172909","https://openalex.org/W2593488635","https://openalex.org/W2626546666","https://openalex.org/W2807469923","https://openalex.org/W2831542631","https://openalex.org/W2883511460","https://openalex.org/W2989499631","https://openalex.org/W3004480435","https://openalex.org/W3004933912","https://openalex.org/W3041114474","https://openalex.org/W3138185021","https://openalex.org/W3202060848","https://openalex.org/W3213101281","https://openalex.org/W4210914372","https://openalex.org/W4293104998","https://openalex.org/W4313706450","https://openalex.org/W4323041688","https://openalex.org/W4389131581","https://openalex.org/W4399397507","https://openalex.org/W4406609698","https://openalex.org/W4410301909"],"related_works":["https://openalex.org/W1608194938","https://openalex.org/W2572774164","https://openalex.org/W1985756322","https://openalex.org/W2111346700","https://openalex.org/W2090900888","https://openalex.org/W1541592150","https://openalex.org/W1546742425","https://openalex.org/W2145489399","https://openalex.org/W2089533157","https://openalex.org/W3092571534"],"abstract_inverted_index":{"Spliced":[0],"leader":[1],"(SL)":[2],"trans-splicing":[3,41,198],"occurs":[4],"in":[5,16,36,86,108,153,165],"a":[6,13,60,126,134,192],"wide":[7],"range":[8],"of":[9,45,161],"eukaryotes":[10],"and":[11,82,180,215],"plays":[12],"critical":[14],"role":[15],"processing":[17],"mRNAs":[18],"derived":[19],"from":[20,123,175],"operon":[21,84,154,163,208],"structures.":[22],"However,":[23],"current":[24],"research":[25],"on":[26],"this":[27],"mechanism":[28],"remains":[29],"limited,":[30],"partly":[31],"due":[32],"to":[33,78,105,172],"the":[34,92,145],"difficulty":[35],"accurately":[37],"identifying":[38],"genuine":[39],"SL":[40,80,106,146,174,197],"events.":[42],"The":[43],"advent":[44],"long-read":[46],"RNA":[47,53,111,120,178],"sequencing":[48,54,121],"technologies,":[49],"such":[50],"as":[51,203],"direct":[52,119],"by":[55,98],"Oxford":[56],"Nanopore":[57],"Technologies,":[58],"offers":[59],"more":[61,158],"promising":[62],"avenue":[63],"for":[64,130,195,207,213],"detecting":[65],"these":[66],"events":[67,199],"with":[68],"greater":[69],"resolution.":[70],"Here,":[71],"we":[72],"present":[73],"SLRanger,":[74],"an":[75,100,204],"integrated":[76],"tool":[77],"detect":[79,173],"sequences":[81],"predict":[83],"structures":[85],"eukaryotic":[87],"transcriptomes.":[88],"SLRanger":[89,138,148,168,188],"improves":[90],"upon":[91],"traditional":[93],"Smith-Waterman":[94],"(SW)":[95],"alignment":[96],"framework":[97,206],"incorporating":[99],"optimized":[101],"scoring":[102],"scheme":[103],"tailored":[104],"detection":[107],"native":[109],"long":[110,177],"reads.":[112,143],"We":[113],"primarily":[114],"validated":[115],"our":[116],"method":[117],"using":[118],"data":[122],"Caenorhabditis":[124],"elegans,":[125],"well-established":[127],"model":[128],"organism":[129],"studying":[131],"trans-splicing.":[132],"Through":[133],"dynamic":[135],"cutoff":[136],"strategy,":[137],"robustly":[139],"identified":[140],"high-confidence":[141],"SL-carrying":[142],"Leveraging":[144],"information,":[147],"achieved":[149],"over":[150],"80%":[151],"accuracy":[152],"gene":[155],"prediction,":[156],"recovering":[157],"than":[159],"70%":[160],"known":[162],"genes":[164],"C.":[166],"elegans.":[167],"was":[169],"also":[170,201],"applied":[171],"cDNA":[176],"reads":[179],"another":[181],"trans-spliced":[182],"species.":[183],"Our":[184],"results":[185],"demonstrate":[186],"that":[187],"not":[189],"only":[190],"provides":[191],"reliable":[193],"approach":[194],"characterizing":[196],"but":[200],"serves":[202],"effective":[205],"discovery,":[209],"enabling":[210],"transcriptomic":[211],"analysis":[212],"operons":[214],"facilitating":[216],"downstream":[217],"data-mining":[218],"applications.":[219]},"counts_by_year":[],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}