{"id":"https://openalex.org/W2994165170","doi":"https://doi.org/10.1093/bib/bbz126","title":"Systematic evaluation of differential splicing tools for RNA-seq studies","display_name":"Systematic evaluation of differential splicing tools for RNA-seq studies","publication_year":2019,"publication_date":"2019-09-04","ids":{"openalex":"https://openalex.org/W2994165170","doi":"https://doi.org/10.1093/bib/bbz126","mag":"2994165170","pmid":"https://pubmed.ncbi.nlm.nih.gov/31802105"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbz126","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbz126","pdf_url":"https://academic.oup.com/bib/article-pdf/21/6/2052/34672001/bbz126.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bib/article-pdf/21/6/2052/34672001/bbz126.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5043404151","display_name":"Arfa Mehmood","orcid":"https://orcid.org/0000-0002-3874-2259"},"institutions":[{"id":"https://openalex.org/I183173800","display_name":"Turku Centre for Computer Science","ror":"https://ror.org/00vy7ed73","country_code":"FI","type":"facility","lineage":["https://openalex.org/I130217899","https://openalex.org/I155660961","https://openalex.org/I183173800"]},{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]},{"id":"https://openalex.org/I130217899","display_name":"\u00c5bo Akademi University","ror":"https://ror.org/029pk6x14","country_code":"FI","type":"education","lineage":["https://openalex.org/I130217899"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Arfa Mehmood","raw_affiliation_strings":["Department of Physiology, University of Turku, Turku, Finland","Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physiology, University of Turku, Turku, Finland","institution_ids":["https://openalex.org/I155660961"]},{"raw_affiliation_string":"Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland","institution_ids":["https://openalex.org/I183173800","https://openalex.org/I155660961","https://openalex.org/I130217899"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024804309","display_name":"Asta Laiho","orcid":"https://orcid.org/0000-0001-6217-6659"},"institutions":[{"id":"https://openalex.org/I130217899","display_name":"\u00c5bo Akademi University","ror":"https://ror.org/029pk6x14","country_code":"FI","type":"education","lineage":["https://openalex.org/I130217899"]},{"id":"https://openalex.org/I183173800","display_name":"Turku Centre for Computer Science","ror":"https://ror.org/00vy7ed73","country_code":"FI","type":"facility","lineage":["https://openalex.org/I130217899","https://openalex.org/I155660961","https://openalex.org/I183173800"]},{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Asta Laiho","raw_affiliation_strings":["Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland","institution_ids":["https://openalex.org/I183173800","https://openalex.org/I155660961","https://openalex.org/I130217899"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005848551","display_name":"Mikko S. Ven\u00e4l\u00e4inen","orcid":"https://orcid.org/0000-0003-1777-4259"},"institutions":[{"id":"https://openalex.org/I130217899","display_name":"\u00c5bo Akademi University","ror":"https://ror.org/029pk6x14","country_code":"FI","type":"education","lineage":["https://openalex.org/I130217899"]},{"id":"https://openalex.org/I183173800","display_name":"Turku Centre for Computer Science","ror":"https://ror.org/00vy7ed73","country_code":"FI","type":"facility","lineage":["https://openalex.org/I130217899","https://openalex.org/I155660961","https://openalex.org/I183173800"]},{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Mikko S Ven\u00e4l\u00e4inen","raw_affiliation_strings":["Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland","institution_ids":["https://openalex.org/I183173800","https://openalex.org/I155660961","https://openalex.org/I130217899"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078886010","display_name":"Aidan McGlinchey","orcid":"https://orcid.org/0000-0001-6682-6030"},"institutions":[{"id":"https://openalex.org/I183173800","display_name":"Turku Centre for Computer Science","ror":"https://ror.org/00vy7ed73","country_code":"FI","type":"facility","lineage":["https://openalex.org/I130217899","https://openalex.org/I155660961","https://openalex.org/I183173800"]},{"id":"https://openalex.org/I130217899","display_name":"\u00c5bo Akademi University","ror":"https://ror.org/029pk6x14","country_code":"FI","type":"education","lineage":["https://openalex.org/I130217899"]},{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]},{"id":"https://openalex.org/I26437253","display_name":"\u00d6rebro University","ror":"https://ror.org/05kytsw45","country_code":"SE","type":"education","lineage":["https://openalex.org/I26437253"]}],"countries":["FI","SE"],"is_corresponding":false,"raw_author_name":"Aidan J McGlinchey","raw_affiliation_strings":["School of Medical Sciences, \u00d6rebro University, \u00d6rebro, Sweden","Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Medical Sciences, \u00d6rebro University, \u00d6rebro, Sweden","institution_ids":["https://openalex.org/I26437253"]},{"raw_affiliation_string":"Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland","institution_ids":["https://openalex.org/I183173800","https://openalex.org/I155660961","https://openalex.org/I130217899"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100387113","display_name":"Ning Wang","orcid":"https://orcid.org/0000-0002-1275-4710"},"institutions":[{"id":"https://openalex.org/I183173800","display_name":"Turku Centre for Computer Science","ror":"https://ror.org/00vy7ed73","country_code":"FI","type":"facility","lineage":["https://openalex.org/I130217899","https://openalex.org/I155660961","https://openalex.org/I183173800"]},{"id":"https://openalex.org/I130217899","display_name":"\u00c5bo Akademi University","ror":"https://ror.org/029pk6x14","country_code":"FI","type":"education","lineage":["https://openalex.org/I130217899"]},{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Ning Wang","raw_affiliation_strings":["Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland","institution_ids":["https://openalex.org/I183173800","https://openalex.org/I155660961","https://openalex.org/I130217899"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062339398","display_name":"Laura L. Elo","orcid":"https://orcid.org/0000-0001-5648-4532"},"institutions":[{"id":"https://openalex.org/I183173800","display_name":"Turku Centre for Computer Science","ror":"https://ror.org/00vy7ed73","country_code":"FI","type":"facility","lineage":["https://openalex.org/I130217899","https://openalex.org/I155660961","https://openalex.org/I183173800"]},{"id":"https://openalex.org/I130217899","display_name":"\u00c5bo Akademi University","ror":"https://ror.org/029pk6x14","country_code":"FI","type":"education","lineage":["https://openalex.org/I130217899"]},{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Laura L Elo","raw_affiliation_strings":["Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, Turku, Finland","institution_ids":["https://openalex.org/I183173800","https://openalex.org/I155660961","https://openalex.org/I130217899"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5062339398"],"corresponding_institution_ids":["https://openalex.org/I130217899","https://openalex.org/I155660961","https://openalex.org/I183173800"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":2702,"currency":"EUR","value_usd":2914},"fwci":6.4421,"has_fulltext":true,"cited_by_count":183,"citation_normalized_percentile":{"value":0.97594521,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"21","issue":"6","first_page":"2052","last_page":"2065"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.7877764701843262},{"id":"https://openalex.org/keywords/rna-splicing","display_name":"RNA splicing","score":0.671222448348999},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6225873231887817},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5059921145439148},{"id":"https://openalex.org/keywords/differential","display_name":"Differential (mechanical device)","score":0.4828779995441437},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.46205344796180725},{"id":"https://openalex.org/keywords/alternative-splicing","display_name":"Alternative splicing","score":0.4280734658241272},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.28564727306365967},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.21994885802268982},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.19789499044418335},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.15987160801887512},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.08703452348709106},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.08096808195114136},{"id":"https://openalex.org/keywords/messenger-rna","display_name":"Messenger RNA","score":0.08039629459381104}],"concepts":[{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.7877764701843262},{"id":"https://openalex.org/C54458228","wikidata":"https://www.wikidata.org/wiki/Q237218","display_name":"RNA splicing","level":4,"score":0.671222448348999},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6225873231887817},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5059921145439148},{"id":"https://openalex.org/C93226319","wikidata":"https://www.wikidata.org/wiki/Q193137","display_name":"Differential (mechanical device)","level":2,"score":0.4828779995441437},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.46205344796180725},{"id":"https://openalex.org/C194583182","wikidata":"https://www.wikidata.org/wiki/Q21114084","display_name":"Alternative splicing","level":4,"score":0.4280734658241272},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.28564727306365967},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.21994885802268982},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19789499044418335},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.15987160801887512},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.08703452348709106},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.08096808195114136},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.08039629459381104},{"id":"https://openalex.org/C146978453","wikidata":"https://www.wikidata.org/wiki/Q3798668","display_name":"Aerospace engineering","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D005091","descriptor_name":"Exons","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":true},{"descriptor_ui":"D012326","descriptor_name":"RNA Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012326","descriptor_name":"RNA Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012326","descriptor_name":"RNA Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","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":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":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bib/bbz126","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbz126","pdf_url":"https://academic.oup.com/bib/article-pdf/21/6/2052/34672001/bbz126.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31802105","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31802105","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:www.utupub.fi:10024/188770","is_oa":true,"landing_page_url":"https://www.utupub.fi/handle/10024/188770","pdf_url":"https://www.utupub.fi/bitstream/10024/188770/1/bbz126.pdf","source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:7711265","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7711265","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"},{"id":"pmh:oai:www.utupub.fi:10024/156867","is_oa":false,"landing_page_url":"https://www.utupub.fi/handle/10024/156867","pdf_url":null,"source":{"id":"https://openalex.org/S4306402470","display_name":"UTUPub (University of Turku)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I155660961","host_organization_name":"University of Turku","host_organization_lineage":["https://openalex.org/I155660961"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""}],"best_oa_location":{"id":"doi:10.1093/bib/bbz126","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbz126","pdf_url":"https://academic.oup.com/bib/article-pdf/21/6/2052/34672001/bbz126.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1310452693","display_name":null,"funder_award_id":"296801","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G1956569869","display_name":null,"funder_award_id":"677943","funder_id":"https://openalex.org/F4320334678","funder_display_name":"European Research Council"},{"id":"https://openalex.org/G3060148298","display_name":null,"funder_award_id":"310561","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G4039138905","display_name":null,"funder_award_id":"310561","funder_id":"https://openalex.org/F4320323313","funder_display_name":"Turun Yliopisto"},{"id":"https://openalex.org/G4428230132","display_name":"Tools to translate proteomes to human health and diagnostics","funder_award_id":"310561","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G5084329356","display_name":null,"funder_award_id":"314443","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G5970345159","display_name":null,"funder_award_id":"1877/31/2016","funder_id":"https://openalex.org/F4320321855","funder_display_name":"Tekes"},{"id":"https://openalex.org/G6521496116","display_name":null,"funder_award_id":"2-2013-32","funder_id":"https://openalex.org/F4320310820","funder_display_name":"Juvenile Diabetes Research Foundation United States of America"},{"id":"https://openalex.org/G872430211","display_name":null,"funder_award_id":"304995","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"}],"funders":[{"id":"https://openalex.org/F4320310820","display_name":"Juvenile Diabetes Research Foundation United States of America","ror":"https://ror.org/00vqxjy61"},{"id":"https://openalex.org/F4320321108","display_name":"Academy of Finland","ror":"https://ror.org/05k73zm37"},{"id":"https://openalex.org/F4320321855","display_name":"Tekes","ror":"https://ror.org/02ag8cq23"},{"id":"https://openalex.org/F4320322725","display_name":"China Scholarship Council","ror":"https://ror.org/04atp4p48"},{"id":"https://openalex.org/F4320323313","display_name":"Turun Yliopisto","ror":"https://ror.org/05vghhr25"},{"id":"https://openalex.org/F4320324828","display_name":"\u00c5bo Akademi","ror":null},{"id":"https://openalex.org/F4320328139","display_name":"Biocenter Finland","ror":"https://ror.org/03aay6c48"},{"id":"https://openalex.org/F4320334678","display_name":"European Research Council","ror":"https://ror.org/0472cxd90"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2994165170.pdf","grobid_xml":"https://content.openalex.org/works/W2994165170.grobid-xml"},"referenced_works_count":58,"referenced_works":["https://openalex.org/W785925703","https://openalex.org/W1883773314","https://openalex.org/W1960424936","https://openalex.org/W1963918734","https://openalex.org/W1984965281","https://openalex.org/W1990210083","https://openalex.org/W1999574084","https://openalex.org/W2006368030","https://openalex.org/W2011920499","https://openalex.org/W2018608365","https://openalex.org/W2030828197","https://openalex.org/W2036913140","https://openalex.org/W2037429868","https://openalex.org/W2046233258","https://openalex.org/W2046583421","https://openalex.org/W2047452386","https://openalex.org/W2050814645","https://openalex.org/W2066141805","https://openalex.org/W2066231767","https://openalex.org/W2097065948","https://openalex.org/W2103017472","https://openalex.org/W2103823493","https://openalex.org/W2107018762","https://openalex.org/W2108234281","https://openalex.org/W2109322710","https://openalex.org/W2114104545","https://openalex.org/W2117787165","https://openalex.org/W2118874738","https://openalex.org/W2119204091","https://openalex.org/W2120599553","https://openalex.org/W2123402634","https://openalex.org/W2123579165","https://openalex.org/W2133237718","https://openalex.org/W2138207763","https://openalex.org/W2141458291","https://openalex.org/W2146512944","https://openalex.org/W2155804510","https://openalex.org/W2159730169","https://openalex.org/W2160164696","https://openalex.org/W2166820820","https://openalex.org/W2168175751","https://openalex.org/W2169456326","https://openalex.org/W2170551349","https://openalex.org/W2176968637","https://openalex.org/W2255131131","https://openalex.org/W2268486506","https://openalex.org/W2336198110","https://openalex.org/W2395491655","https://openalex.org/W2566567183","https://openalex.org/W2774883395","https://openalex.org/W2793520807","https://openalex.org/W2902200003","https://openalex.org/W2949317881","https://openalex.org/W2950254282","https://openalex.org/W4233279703","https://openalex.org/W6640968788","https://openalex.org/W6663386463","https://openalex.org/W6712067400"],"related_works":["https://openalex.org/W2321791250","https://openalex.org/W4213427798","https://openalex.org/W2564462691","https://openalex.org/W2023199111","https://openalex.org/W2065030615","https://openalex.org/W2885403345","https://openalex.org/W2052498125","https://openalex.org/W2094867951","https://openalex.org/W1535548930","https://openalex.org/W2426516634"],"abstract_inverted_index":{"Differential":[0],"splicing":[1],"(DS)":[2],"is":[3,50],"a":[4,13,23,42],"post-transcriptional":[5],"biological":[6],"process":[7],"with":[8],"critical,":[9],"wide-ranging":[10],"effects":[11],"on":[12,122],"plethora":[14],"of":[15,25,47,159],"cellular":[16],"activities":[17],"and":[18,33,45,65,69,79,101,113,118,140],"disease":[19],"processes.":[20],"To":[21],"date,":[22],"number":[24],"computational":[26],"approaches":[27,49],"have":[28],"been":[29],"developed":[30],"to":[31,86],"identify":[32],"quantify":[34],"differentially":[35,76],"spliced":[36,77],"genes":[37,78],"from":[38],"RNA-seq":[39],"data,":[40],"but":[41],"comprehensive":[43],"intercomparison":[44],"appraisal":[46],"these":[48],"currently":[51],"lacking.":[52],"In":[53],"this":[54],"study,":[55],"we":[56],"systematically":[57],"evaluated":[58],"10":[59,128],"DS":[60],"analysis":[61,148],"tools":[62,83,129,149],"for":[63],"consistency":[64],"reproducibility,":[66],"precision,":[67],"recall":[68],"false":[70],"discovery":[71],"rate,":[72],"agreement":[73],"upon":[74],"reported":[75],"functional":[80],"enrichment.":[81],"The":[82],"were":[84],"selected":[85,124],"represent":[87],"the":[88,110,123,127,131,138,145],"three":[89],"different":[90,146,154],"methodological":[91],"categories:":[92],"exon-based":[93,111,132],"(DEXSeq,":[94],"edgeR,":[95],"JunctionSeq,":[96],"limma),":[97],"isoform-based":[98,139],"(cuffdiff2,":[99],"DiffSplice)":[100],"event-based":[102,115,141],"methods":[103,112,116,133],"(dSpliceType,":[104],"MAJIQ,":[105],"rMATS,":[106],"SUPPA).":[107],"Overall,":[108],"all":[109],"two":[114],"(MAJIQ":[117],"rMATS)":[119],"scored":[120],"well":[121],"measures.":[125],"Of":[126],"tested,":[130],"performed":[134,150],"generally":[135],"better":[136],"than":[137],"methods.":[142],"However,":[143],"overall,":[144],"data":[147,155],"strikingly":[151],"differently":[152],"across":[153],"sets":[156],"or":[157],"numbers":[158],"samples.":[160]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":22},{"year":2024,"cited_by_count":37},{"year":2023,"cited_by_count":43},{"year":2022,"cited_by_count":30},{"year":2021,"cited_by_count":31},{"year":2020,"cited_by_count":14}],"updated_date":"2026-04-25T08:17:42.794288","created_date":"2025-10-10T00:00:00"}
