{"id":"https://openalex.org/W2113768712","doi":"https://doi.org/10.1093/bioinformatics/btt591","title":"ORMAN: Optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms","display_name":"ORMAN: Optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms","publication_year":2013,"publication_date":"2013-10-15","ids":{"openalex":"https://openalex.org/W2113768712","doi":"https://doi.org/10.1093/bioinformatics/btt591","mag":"2113768712","pmid":"https://pubmed.ncbi.nlm.nih.gov/24130305"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt591","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt591","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/5/644/48919013/bioinformatics_30_5_644.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":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://academic.oup.com/bioinformatics/article-pdf/30/5/644/48919013/bioinformatics_30_5_644.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022850021","display_name":"Phuong Dao","orcid":"https://orcid.org/0000-0001-5285-6271"},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]},{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]},{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["CA","US"],"is_corresponding":false,"raw_author_name":"Phuong Dao","raw_affiliation_strings":["1 School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 2Department of Genome Sciences, University of Washington, Seattle, WA, USA, 3Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada and 4Division of Computer Science, School of Informatics and Computing, Indiana University, Bloomington, IN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 2Department of Genome Sciences, University of Washington, Seattle, WA, USA, 3Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada and 4Division of Computer Science, School of Informatics and Computing, Indiana University, Bloomington, IN, USA","institution_ids":["https://openalex.org/I141945490","https://openalex.org/I18014758","https://openalex.org/I201448701","https://openalex.org/I4210119109"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060847860","display_name":"Ibrahim Numanagi\u0107","orcid":"https://orcid.org/0000-0002-2970-7937"},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]},{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]},{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["CA","US"],"is_corresponding":true,"raw_author_name":"Ibrahim Numanagi\u0107","raw_affiliation_strings":["1 School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 2Department of Genome Sciences, University of Washington, Seattle, WA, USA, 3Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada and 4Division of Computer Science, School of Informatics and Computing, Indiana University, Bloomington, IN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 2Department of Genome Sciences, University of Washington, Seattle, WA, USA, 3Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada and 4Division of Computer Science, School of Informatics and Computing, Indiana University, Bloomington, IN, USA","institution_ids":["https://openalex.org/I141945490","https://openalex.org/I18014758","https://openalex.org/I201448701","https://openalex.org/I4210119109"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048247983","display_name":"Yen\u2010Yi Lin","orcid":"https://orcid.org/0000-0002-4379-1231"},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]},{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]},{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["CA","US"],"is_corresponding":false,"raw_author_name":"Yen-Yi Lin","raw_affiliation_strings":["1 School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 2Department of Genome Sciences, University of Washington, Seattle, WA, USA, 3Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada and 4Division of Computer Science, School of Informatics and Computing, Indiana University, Bloomington, IN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 2Department of Genome Sciences, University of Washington, Seattle, WA, USA, 3Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada and 4Division of Computer Science, School of Informatics and Computing, Indiana University, Bloomington, IN, USA","institution_ids":["https://openalex.org/I141945490","https://openalex.org/I18014758","https://openalex.org/I201448701","https://openalex.org/I4210119109"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006644128","display_name":"Faraz Hach","orcid":"https://orcid.org/0000-0003-1143-0172"},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]},{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]},{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["CA","US"],"is_corresponding":false,"raw_author_name":"Faraz Hach","raw_affiliation_strings":["1 School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 2Department of Genome Sciences, University of Washington, Seattle, WA, USA, 3Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada and 4Division of Computer Science, School of Informatics and Computing, Indiana University, Bloomington, IN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 2Department of Genome Sciences, University of Washington, Seattle, WA, USA, 3Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada and 4Division of Computer Science, School of Informatics and Computing, Indiana University, Bloomington, IN, USA","institution_ids":["https://openalex.org/I141945490","https://openalex.org/I18014758","https://openalex.org/I201448701","https://openalex.org/I4210119109"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027896699","display_name":"Emre Karako\u00e7","orcid":"https://orcid.org/0000-0002-2324-8127"},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]},{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]},{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["CA","US"],"is_corresponding":false,"raw_author_name":"Emre Karakoc","raw_affiliation_strings":["1 School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 2Department of Genome Sciences, University of Washington, Seattle, WA, USA, 3Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada and 4Division of Computer Science, School of Informatics and Computing, Indiana University, Bloomington, IN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 2Department of Genome Sciences, University of Washington, Seattle, WA, USA, 3Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada and 4Division of Computer Science, School of Informatics and Computing, Indiana University, Bloomington, IN, USA","institution_ids":["https://openalex.org/I141945490","https://openalex.org/I18014758","https://openalex.org/I201448701","https://openalex.org/I4210119109"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053611147","display_name":"Nilgun Donmez","orcid":null},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]},{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]},{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["CA","US"],"is_corresponding":false,"raw_author_name":"Nilgun Donmez","raw_affiliation_strings":["1 School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 2Department of Genome Sciences, University of Washington, Seattle, WA, USA, 3Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada and 4Division of Computer Science, School of Informatics and Computing, Indiana University, Bloomington, IN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 2Department of Genome Sciences, University of Washington, Seattle, WA, USA, 3Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada and 4Division of Computer Science, School of Informatics and Computing, Indiana University, Bloomington, IN, USA","institution_ids":["https://openalex.org/I141945490","https://openalex.org/I18014758","https://openalex.org/I201448701","https://openalex.org/I4210119109"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050325886","display_name":"Colin C. Collins","orcid":"https://orcid.org/0000-0001-6148-6110"},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]},{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]},{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["CA","US"],"is_corresponding":false,"raw_author_name":"Colin Collins","raw_affiliation_strings":["1 School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 2Department of Genome Sciences, University of Washington, Seattle, WA, USA, 3Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada and 4Division of Computer Science, School of Informatics and Computing, Indiana University, Bloomington, IN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 2Department of Genome Sciences, University of Washington, Seattle, WA, USA, 3Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada and 4Division of Computer Science, School of Informatics and Computing, Indiana University, Bloomington, IN, USA","institution_ids":["https://openalex.org/I141945490","https://openalex.org/I18014758","https://openalex.org/I201448701","https://openalex.org/I4210119109"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014870107","display_name":"Evan E. Eichler","orcid":"https://orcid.org/0000-0002-8246-4014"},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]},{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]},{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["CA","US"],"is_corresponding":false,"raw_author_name":"Evan E. Eichler","raw_affiliation_strings":["1 School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 2Department of Genome Sciences, University of Washington, Seattle, WA, USA, 3Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada and 4Division of Computer Science, School of Informatics and Computing, Indiana University, Bloomington, IN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 2Department of Genome Sciences, University of Washington, Seattle, WA, USA, 3Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada and 4Division of Computer Science, School of Informatics and Computing, Indiana University, Bloomington, IN, USA","institution_ids":["https://openalex.org/I141945490","https://openalex.org/I18014758","https://openalex.org/I201448701","https://openalex.org/I4210119109"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5102972238","display_name":"S. Cenk \u015eahinalp","orcid":"https://orcid.org/0000-0002-2170-2808"},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]},{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]},{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["CA","US"],"is_corresponding":true,"raw_author_name":"S. Cenk Sahinalp","raw_affiliation_strings":["1 School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 2Department of Genome Sciences, University of Washington, Seattle, WA, USA, 3Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada and 4Division of Computer Science, School of Informatics and Computing, Indiana University, Bloomington, IN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 2Department of Genome Sciences, University of Washington, Seattle, WA, USA, 3Vancouver Prostate Centre & Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada and 4Division of Computer Science, School of Informatics and Computing, Indiana University, Bloomington, IN, USA","institution_ids":["https://openalex.org/I141945490","https://openalex.org/I18014758","https://openalex.org/I201448701","https://openalex.org/I4210119109"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5060847860","https://openalex.org/A5102972238"],"corresponding_institution_ids":["https://openalex.org/I141945490","https://openalex.org/I18014758","https://openalex.org/I201448701","https://openalex.org/I4210119109"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.8255,"has_fulltext":true,"cited_by_count":18,"citation_normalized_percentile":{"value":0.72478342,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"30","issue":"5","first_page":"644","last_page":"651"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.5620999932289124,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.5620999932289124,"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/T10604","display_name":"RNA Research and Splicing","score":0.2037000060081482,"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":0.06700000166893005,"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/rna-seq","display_name":"RNA-Seq","score":0.7543744444847107},{"id":"https://openalex.org/keywords/focus","display_name":"Focus (optics)","score":0.6505680680274963},{"id":"https://openalex.org/keywords/gene-isoform","display_name":"Gene isoform","score":0.6268713474273682},{"id":"https://openalex.org/keywords/resolution","display_name":"Resolution (logic)","score":0.5525163412094116},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5318583846092224},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.48236650228500366},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.4133458137512207},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3115931749343872},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.28849196434020996},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1813451647758484},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.14584994316101074},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.14481425285339355},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.09868770837783813},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.07048299908638}],"concepts":[{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.7543744444847107},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.6505680680274963},{"id":"https://openalex.org/C53345823","wikidata":"https://www.wikidata.org/wiki/Q5531554","display_name":"Gene isoform","level":3,"score":0.6268713474273682},{"id":"https://openalex.org/C138268822","wikidata":"https://www.wikidata.org/wiki/Q1051925","display_name":"Resolution (logic)","level":2,"score":0.5525163412094116},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5318583846092224},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.48236650228500366},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.4133458137512207},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3115931749343872},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.28849196434020996},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1813451647758484},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.14584994316101074},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14481425285339355},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.09868770837783813},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.07048299908638},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","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":"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":"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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","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":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":null,"qualifier_name":null,"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":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059368","descriptor_name":"RNA Isoforms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D059368","descriptor_name":"RNA Isoforms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D059368","descriptor_name":"RNA Isoforms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D059368","descriptor_name":"RNA Isoforms","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D059368","descriptor_name":"RNA Isoforms","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D059368","descriptor_name":"RNA Isoforms","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btt591","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt591","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/5/644/48919013/bioinformatics_30_5_644.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:24130305","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24130305","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btt591","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt591","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/5/644/48919013/bioinformatics_30_5_644.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2113768712.pdf","grobid_xml":"https://content.openalex.org/works/W2113768712.grobid-xml"},"referenced_works_count":21,"referenced_works":["https://openalex.org/W162544871","https://openalex.org/W1988245212","https://openalex.org/W1999574084","https://openalex.org/W2001994418","https://openalex.org/W2010637767","https://openalex.org/W2030914835","https://openalex.org/W2042930277","https://openalex.org/W2049997041","https://openalex.org/W2093253451","https://openalex.org/W2097065948","https://openalex.org/W2102813686","https://openalex.org/W2105875994","https://openalex.org/W2122789575","https://openalex.org/W2126144698","https://openalex.org/W2126333123","https://openalex.org/W2131088968","https://openalex.org/W2138773756","https://openalex.org/W2141458291","https://openalex.org/W2154431984","https://openalex.org/W2157054705","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W1540936366","https://openalex.org/W2079625624","https://openalex.org/W2004254765","https://openalex.org/W2126407448","https://openalex.org/W2125691904","https://openalex.org/W200174347","https://openalex.org/W2048132363","https://openalex.org/W2953122964","https://openalex.org/W1971262350","https://openalex.org/W2507850257"],"abstract_inverted_index":{"MOTIVATION:":[0],"RNA-Seq":[1,38,53,63,177,221],"technology":[2],"is":[3,29,162,207,227,252],"promising":[4],"to":[5,31,44,75,118,131,136,229,232,239],"uncover":[6],"many":[7],"novel":[8,84,92,199],"alternative":[9],"splicing":[10],"events,":[11],"gene":[12,129],"fusions":[13],"and":[14,24,55,91,130,171,197,205],"other":[15],"variations":[16],"in":[17,80,216,244],"RNA":[18],"transcripts.":[19],"For":[20],"an":[21,217],"accurate":[22,95],"detection":[23],"quantification":[25],"of":[26,48,57,83,106,111,123,138,146,183,191,213],"transcripts,":[27,200],"it":[28],"important":[30],"resolve":[32,76,230],"the":[33,49,58,77,81,120,143,147,150,186,189,211,240],"mapping":[34,67,78],"ambiguity":[35,79],"for":[36,127,195],"those":[37],"reads":[39,50,59],"that":[40,225,236],"can":[41],"be":[42],"mapped":[43],"multiple":[45,66],"loci:":[46],">17%":[47],"from":[51,60,185],"mouse":[52],"data":[54,64],"50%":[56],"some":[61],"plant":[62],"have":[65],"loci.":[68],"In":[69],"this":[70,154],"study,":[71],"we":[72,223],"show":[73,224],"how":[74],"presence":[82],"transcriptomic":[85],"events":[86],"such":[87,201],"as":[88,202],"exon":[89],"skipping":[90],"indels":[93],"towards":[94],"downstream":[96],"analysis.":[97],"We":[98],"introduce":[99],"ORMAN":[100,152,226,251],"(":[101],"O":[102],"ptimal":[103],"R":[104,112],"esolution":[105],"M":[107],"ultimapping":[108],"A":[109],"mbiguity":[110],"N":[113],"A-Seq":[114],"Reads),":[115],"which":[116,161],"aims":[117],"compute":[119],"minimum":[121],"number":[122],"potential":[124],"transcript":[125],"products":[126],"each":[128,133],"assign":[132],"multimapping":[134,231],"read":[135],"one":[137],"these":[139],"transcripts":[140,184],"based":[141],"on":[142],"estimated":[144],"distribution":[145],"region":[148],"covering":[149],"read.":[151],"achieves":[153],"objective":[155],"through":[156,164,210],"a":[157,175,180],"combinatorial":[158],"optimization":[159],"formulation,":[160],"solved":[163],"well-known":[165],"approximation":[166],"algorithms,":[167],"integer":[168],"linear":[169],"programs":[170],"heuristics.":[172],"RESULTS:":[173],"On":[174],"simulated":[176],"dataset":[178],"including":[179],"random":[181],"subset":[182],"UCSC":[187],"database,":[188],"performance":[190],"several":[192],"state-of-the-art":[193],"methods":[194],"identifying":[196],"quantifying":[198],"Cufflinks,":[203],"IsoLasso":[204],"CLIIQ,":[206],"significantly":[208],"improved":[209],"use":[212],"ORMAN.":[214],"Furthermore,":[215],"experiment":[218],"using":[219],"real":[220],"reads,":[222],"able":[228],"produce":[233],"coverage":[234],"values":[235],"are":[237],"similar":[238],"original":[241],"distribution,":[242],"even":[243],"genes":[245],"with":[246],"highly":[247],"non-uniform":[248],"coverage.":[249],"AVAILABILITY:":[250],"available":[253],"at":[254],"http://orman.sf.net":[255]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":5},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":1}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
