{"id":"https://openalex.org/W7161998668","doi":"https://doi.org/10.1093/bioinformatics/btag252","title":"Detecting unannotated splicing events in short-read RNA-seq with SAMI, a UMI-aware Nextflow pipeline","display_name":"Detecting unannotated splicing events in short-read RNA-seq with SAMI, a UMI-aware Nextflow pipeline","publication_year":2026,"publication_date":"2026-05-18","ids":{"openalex":"https://openalex.org/W7161998668","doi":"https://doi.org/10.1093/bioinformatics/btag252","pmid":"https://pubmed.ncbi.nlm.nih.gov/42166739"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btag252","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag252","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btag252","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5071739469","display_name":"Sylvain Mareschal","orcid":"https://orcid.org/0000-0001-7492-7528"},"institutions":[{"id":"https://openalex.org/I4210100596","display_name":"Hospices Civils de Lyon","ror":"https://ror.org/01502ca60","country_code":"FR","type":"healthcare","lineage":["https://openalex.org/I4210100596"]},{"id":"https://openalex.org/I96211989","display_name":"HCL Technologies (India)","ror":"https://ror.org/02nbb5780","country_code":"IN","type":"company","lineage":["https://openalex.org/I96211989"]}],"countries":["FR","IN"],"is_corresponding":true,"raw_author_name":"Sylvain Mareschal","raw_affiliation_strings":["Hospices Civils de Lyon, NGS-HCL plateform, Bioinformatics group , Lyon F-69000,"],"raw_orcid":"https://orcid.org/0000-0001-7492-7528","affiliations":[{"raw_affiliation_string":"Hospices Civils de Lyon, NGS-HCL plateform, Bioinformatics group , Lyon F-69000,","institution_ids":["https://openalex.org/I4210100596","https://openalex.org/I96211989"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022764519","display_name":"Valentin Wucher","orcid":"https://orcid.org/0000-0002-1331-4549"},"institutions":[{"id":"https://openalex.org/I100532134","display_name":"Lyon 1 Universit\u00e9","ror":"https://ror.org/029brtt94","country_code":"FR","type":"education","lineage":["https://openalex.org/I100532134","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I4210100596","display_name":"Hospices Civils de Lyon","ror":"https://ror.org/01502ca60","country_code":"FR","type":"healthcare","lineage":["https://openalex.org/I4210100596"]},{"id":"https://openalex.org/I4405258652","display_name":"M\u00e9canismes en sciences int\u00e9gratives du vivant","ror":"https://ror.org/01138xk88","country_code":"FR","type":"facility","lineage":["https://openalex.org/I100532134","https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I203339264","https://openalex.org/I4405258652"]},{"id":"https://openalex.org/I96211989","display_name":"HCL Technologies (India)","ror":"https://ror.org/02nbb5780","country_code":"IN","type":"company","lineage":["https://openalex.org/I96211989"]}],"countries":["FR","IN"],"is_corresponding":false,"raw_author_name":"Valentin Wucher","raw_affiliation_strings":["Hospices Civils de Lyon, French Reference Center of Paraneoplastic Neurological Syndromes and Autoimmune Encephalitis , Lyon F-69000,","Hospices Civils de Lyon, NGS-HCL plateform, Bioinformatics group , Lyon F-69000,","Universit\u00e9 Claude Bernard Lyon 1, Mechanisms in integrated life sciences Institute (MeLiS), INSERM U1314, CNRS UMR 5284 , Lyon F-69008,"],"raw_orcid":"https://orcid.org/0000-0002-1331-4549","affiliations":[{"raw_affiliation_string":"Hospices Civils de Lyon, French Reference Center of Paraneoplastic Neurological Syndromes and Autoimmune Encephalitis , Lyon F-69000,","institution_ids":["https://openalex.org/I4210100596"]},{"raw_affiliation_string":"Hospices Civils de Lyon, NGS-HCL plateform, Bioinformatics group , Lyon F-69000,","institution_ids":["https://openalex.org/I4210100596","https://openalex.org/I96211989"]},{"raw_affiliation_string":"Universit\u00e9 Claude Bernard Lyon 1, Mechanisms in integrated life sciences Institute (MeLiS), INSERM U1314, CNRS UMR 5284 , Lyon F-69008,","institution_ids":["https://openalex.org/I100532134","https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I4405258652"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082659815","display_name":"Sarah Huet","orcid":"https://orcid.org/0000-0002-3408-2783"},"institutions":[{"id":"https://openalex.org/I100532134","display_name":"Lyon 1 Universit\u00e9","ror":"https://ror.org/029brtt94","country_code":"FR","type":"education","lineage":["https://openalex.org/I100532134","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I178906410","display_name":"Lyon College","ror":"https://ror.org/03c4kec23","country_code":"US","type":"education","lineage":["https://openalex.org/I178906410"]},{"id":"https://openalex.org/I4210100596","display_name":"Hospices Civils de Lyon","ror":"https://ror.org/01502ca60","country_code":"FR","type":"healthcare","lineage":["https://openalex.org/I4210100596"]},{"id":"https://openalex.org/I4210161906","display_name":"Centre International de Recherche en Infectiologie","ror":"https://ror.org/059sz6q14","country_code":"FR","type":"facility","lineage":["https://openalex.org/I100532134","https://openalex.org/I113428412","https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I203339264","https://openalex.org/I203339264","https://openalex.org/I203339264","https://openalex.org/I4210100596","https://openalex.org/I4210161906","https://openalex.org/I4405259976"]}],"countries":["FR","US"],"is_corresponding":false,"raw_author_name":"Sarah Huet","raw_affiliation_strings":["Hospices Civils de Lyon, Hematology Department , Lyon F-69000,","Universit\u00e9 Claude Bernard Lyon 1, Centre International de Recherche en Infectiologie, INSERM U1111 / CNRS UMR5308, Team Lymphoma Immuno-Biology , Lyon F-69007,","Universit\u00e9 Claude Bernard Lyon 1, Institut des Sciences Pharmaceutiques et Biologiques , Lyon F-69008,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hospices Civils de Lyon, Hematology Department , Lyon F-69000,","institution_ids":["https://openalex.org/I4210100596"]},{"raw_affiliation_string":"Universit\u00e9 Claude Bernard Lyon 1, Centre International de Recherche en Infectiologie, INSERM U1111 / CNRS UMR5308, Team Lymphoma Immuno-Biology , Lyon F-69007,","institution_ids":["https://openalex.org/I100532134","https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I4210161906"]},{"raw_affiliation_string":"Universit\u00e9 Claude Bernard Lyon 1, Institut des Sciences Pharmaceutiques et Biologiques , Lyon F-69008,","institution_ids":["https://openalex.org/I100532134","https://openalex.org/I178906410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055848697","display_name":"Camille L\u00e9once","orcid":"https://orcid.org/0000-0002-7171-0427"},"institutions":[{"id":"https://openalex.org/I4210100596","display_name":"Hospices Civils de Lyon","ror":"https://ror.org/01502ca60","country_code":"FR","type":"healthcare","lineage":["https://openalex.org/I4210100596"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Camille L\u00e9once","raw_affiliation_strings":["Hospices Civils de Lyon, Department of Pathology , Lyon F-69000,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hospices Civils de Lyon, Department of Pathology , Lyon F-69000,","institution_ids":["https://openalex.org/I4210100596"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010797184","display_name":"Kaddour Chabane","orcid":"https://orcid.org/0000-0002-6715-5133"},"institutions":[{"id":"https://openalex.org/I4210100596","display_name":"Hospices Civils de Lyon","ror":"https://ror.org/01502ca60","country_code":"FR","type":"healthcare","lineage":["https://openalex.org/I4210100596"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Kaddour Chabane","raw_affiliation_strings":["Hospices Civils de Lyon, Hematology Department , Lyon F-69000,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hospices Civils de Lyon, Hematology Department , Lyon F-69000,","institution_ids":["https://openalex.org/I4210100596"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110966466","display_name":"Sandrine Hayette","orcid":null},"institutions":[{"id":"https://openalex.org/I4210100596","display_name":"Hospices Civils de Lyon","ror":"https://ror.org/01502ca60","country_code":"FR","type":"healthcare","lineage":["https://openalex.org/I4210100596"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Sandrine Hayette","raw_affiliation_strings":["Hospices Civils de Lyon, Hematology Department , Lyon F-69000,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hospices Civils de Lyon, Hematology Department , Lyon F-69000,","institution_ids":["https://openalex.org/I4210100596"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112739237","display_name":"Pierre\u2010Paul Bringuier","orcid":null},"institutions":[{"id":"https://openalex.org/I100532134","display_name":"Lyon 1 Universit\u00e9","ror":"https://ror.org/029brtt94","country_code":"FR","type":"education","lineage":["https://openalex.org/I100532134","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I4210100596","display_name":"Hospices Civils de Lyon","ror":"https://ror.org/01502ca60","country_code":"FR","type":"healthcare","lineage":["https://openalex.org/I4210100596"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Pierre-Paul Bringuier","raw_affiliation_strings":["Hospices Civils de Lyon, Department of Pathology , Lyon F-69000,","Universit\u00e9 Claude Bernard Lyon 1 , Villeurbanne F-69100,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hospices Civils de Lyon, Department of Pathology , Lyon F-69000,","institution_ids":["https://openalex.org/I4210100596"]},{"raw_affiliation_string":"Universit\u00e9 Claude Bernard Lyon 1 , Villeurbanne F-69100,","institution_ids":["https://openalex.org/I100532134"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011707982","display_name":"S. Pinson","orcid":"https://orcid.org/0000-0002-6804-4021"},"institutions":[{"id":"https://openalex.org/I4210100596","display_name":"Hospices Civils de Lyon","ror":"https://ror.org/01502ca60","country_code":"FR","type":"healthcare","lineage":["https://openalex.org/I4210100596"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"St\u00e9phane Pinson","raw_affiliation_strings":["Hospices Civils de Lyon, Genetics department , Lyon F-69000,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hospices Civils de Lyon, Genetics department , Lyon F-69000,","institution_ids":["https://openalex.org/I4210100596"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018902791","display_name":"Marc Barritault","orcid":"https://orcid.org/0000-0003-3311-4058"},"institutions":[{"id":"https://openalex.org/I100532134","display_name":"Lyon 1 Universit\u00e9","ror":"https://ror.org/029brtt94","country_code":"FR","type":"education","lineage":["https://openalex.org/I100532134","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I4210100596","display_name":"Hospices Civils de Lyon","ror":"https://ror.org/01502ca60","country_code":"FR","type":"healthcare","lineage":["https://openalex.org/I4210100596"]},{"id":"https://openalex.org/I4210125048","display_name":"Centre de Recherche en Canc\u00e9rologie de Lyon","ror":"https://ror.org/02mgw3155","country_code":"FR","type":"facility","lineage":["https://openalex.org/I100532134","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I203339264","https://openalex.org/I4210096427","https://openalex.org/I4210105738","https://openalex.org/I4210125048"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Marc Barritault","raw_affiliation_strings":["Hospices Civils de Lyon, Department of Pathology , Lyon F-69000,","Universit\u00e9 Claude Bernard Lyon 1, Cancer Research Centre of Lyon (CRCL), INSERM 1052, CNRS 5286, Cancer Initiation and Tumoral Cell Identity Department , Lyon F-69008,"],"raw_orcid":"https://orcid.org/0000-0003-3311-4058","affiliations":[{"raw_affiliation_string":"Hospices Civils de Lyon, Department of Pathology , Lyon F-69000,","institution_ids":["https://openalex.org/I4210100596"]},{"raw_affiliation_string":"Universit\u00e9 Claude Bernard Lyon 1, Cancer Research Centre of Lyon (CRCL), INSERM 1052, CNRS 5286, Cancer Initiation and Tumoral Cell Identity Department , Lyon F-69008,","institution_ids":["https://openalex.org/I100532134","https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I4210125048"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5136669791","display_name":"Claire Bardel","orcid":null},"institutions":[{"id":"https://openalex.org/I100532134","display_name":"Lyon 1 Universit\u00e9","ror":"https://ror.org/029brtt94","country_code":"FR","type":"education","lineage":["https://openalex.org/I100532134","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I178906410","display_name":"Lyon College","ror":"https://ror.org/03c4kec23","country_code":"US","type":"education","lineage":["https://openalex.org/I178906410"]},{"id":"https://openalex.org/I4210100596","display_name":"Hospices Civils de Lyon","ror":"https://ror.org/01502ca60","country_code":"FR","type":"healthcare","lineage":["https://openalex.org/I4210100596"]},{"id":"https://openalex.org/I4210135640","display_name":"Laboratoire de Biom\u00e9trie et Biologie Evolutive","ror":"https://ror.org/03skt0t88","country_code":"FR","type":"facility","lineage":["https://openalex.org/I100532134","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I203339264","https://openalex.org/I4210100596","https://openalex.org/I4210104684","https://openalex.org/I4210107625","https://openalex.org/I4210135640"]},{"id":"https://openalex.org/I96211989","display_name":"HCL Technologies (India)","ror":"https://ror.org/02nbb5780","country_code":"IN","type":"company","lineage":["https://openalex.org/I96211989"]}],"countries":["FR","IN","US"],"is_corresponding":false,"raw_author_name":"Claire Bardel","raw_affiliation_strings":["Hospices Civils de Lyon, Genetics department , Lyon F-69000,","Hospices Civils de Lyon, NGS-HCL plateform, Bioinformatics group , Lyon F-69000,","Universit\u00e9 Claude Bernard Lyon 1, Institut des Sciences Pharmaceutiques et Biologiques , Lyon F-69008,","Universit\u00e9 Claude Bernard Lyon 1, LBBE, CNRS UMR 5558 , Villeurbanne F-69100,"],"raw_orcid":"https://orcid.org/0009-0001-7197-8730","affiliations":[{"raw_affiliation_string":"Hospices Civils de Lyon, Genetics department , Lyon F-69000,","institution_ids":["https://openalex.org/I4210100596"]},{"raw_affiliation_string":"Hospices Civils de Lyon, NGS-HCL plateform, Bioinformatics group , Lyon F-69000,","institution_ids":["https://openalex.org/I4210100596","https://openalex.org/I96211989"]},{"raw_affiliation_string":"Universit\u00e9 Claude Bernard Lyon 1, Institut des Sciences Pharmaceutiques et Biologiques , Lyon F-69008,","institution_ids":["https://openalex.org/I100532134","https://openalex.org/I178906410"]},{"raw_affiliation_string":"Universit\u00e9 Claude Bernard Lyon 1, LBBE, CNRS UMR 5558 , Villeurbanne F-69100,","institution_ids":["https://openalex.org/I100532134","https://openalex.org/I1294671590","https://openalex.org/I4210135640"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5071739469"],"corresponding_institution_ids":["https://openalex.org/I4210100596","https://openalex.org/I96211989"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.49576679,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"42","issue":"6","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.8493000268936157,"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":0.8493000268936157,"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/T12610","display_name":"RNA regulation and disease","score":0.029200000688433647,"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":0.021800000220537186,"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/pipeline","display_name":"Pipeline (software)","score":0.7401000261306763},{"id":"https://openalex.org/keywords/rna-splicing","display_name":"RNA splicing","score":0.717199981212616},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5582000017166138},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5144000053405762},{"id":"https://openalex.org/keywords/splice","display_name":"splice","score":0.5038999915122986},{"id":"https://openalex.org/keywords/intron","display_name":"Intron","score":0.49790000915527344},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4361000061035156}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7401000261306763},{"id":"https://openalex.org/C54458228","wikidata":"https://www.wikidata.org/wiki/Q237218","display_name":"RNA splicing","level":4,"score":0.717199981212616},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6000999808311462},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5582000017166138},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.548799991607666},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5144000053405762},{"id":"https://openalex.org/C2780989783","wikidata":"https://www.wikidata.org/wiki/Q7578557","display_name":"splice","level":3,"score":0.5038999915122986},{"id":"https://openalex.org/C94671646","wikidata":"https://www.wikidata.org/wiki/Q207551","display_name":"Intron","level":3,"score":0.49790000915527344},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4361000061035156},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4325999915599823},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4223000109195709},{"id":"https://openalex.org/C188198153","wikidata":"https://www.wikidata.org/wiki/Q1613840","display_name":"Limiting","level":2,"score":0.4133000075817108},{"id":"https://openalex.org/C194583182","wikidata":"https://www.wikidata.org/wiki/Q21114084","display_name":"Alternative splicing","level":4,"score":0.3968999981880188},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.38100001215934753},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.31040000915527344},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.30790001153945923},{"id":"https://openalex.org/C141674004","wikidata":"https://www.wikidata.org/wiki/Q1344256","display_name":"Ensembl","level":5,"score":0.30649998784065247},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3003999888896942},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.28999999165534973},{"id":"https://openalex.org/C2908923196","wikidata":"https://www.wikidata.org/wiki/Q5205742","display_name":"Gene Annotation","level":4,"score":0.27149999141693115},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.26330000162124634}],"mesh":[{"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":"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":"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":"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":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btag252","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag252","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:42166739","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42166739","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":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:13242923","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13242923/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btag252","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag252","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W1905089044","https://openalex.org/W2036897871","https://openalex.org/W2066231767","https://openalex.org/W2138207763","https://openalex.org/W2151651283","https://openalex.org/W2169456326","https://openalex.org/W2174938954","https://openalex.org/W2263582186","https://openalex.org/W2432815617","https://openalex.org/W2605897695","https://openalex.org/W2787742192","https://openalex.org/W2949317881","https://openalex.org/W2980759299","https://openalex.org/W2981094865","https://openalex.org/W3006653136","https://openalex.org/W3017021858","https://openalex.org/W3085774086","https://openalex.org/W3118238647","https://openalex.org/W3131443014","https://openalex.org/W3134765669","https://openalex.org/W3160610114","https://openalex.org/W4323048959","https://openalex.org/W4388979986"],"related_works":[],"abstract_inverted_index":{"SUMMARY:":[0],"Although":[1],"RNA-sequencing":[2],"has":[3],"replaced":[4],"microarrays":[5],"for":[6,18,31],"gene":[7,114],"expression":[8],"profiling":[9],"over":[10],"the":[11,75],"past":[12],"15":[13],"years,":[14],"its":[15],"full":[16],"potential":[17,86],"splicing":[19,67,111],"analysis":[20],"in":[21,40,49],"clinical":[22],"settings":[23],"remains":[24],"underexploited.":[25],"Most":[26],"available":[27,143],"tools":[28],"are":[29],"tailored":[30],"large":[32],"cohorts":[33],"or":[34],"known":[35],"isoforms,":[36],"limiting":[37],"their":[38],"applicability":[39],"routine":[41],"diagnostics":[42],"where":[43],"non-recurring":[44],"events":[45,68],"must":[46],"be":[47],"identified":[48],"low-dimension":[50],"datasets.":[51],"We":[52],"present":[53],"SAMI":[54,79,104],"(Splicing":[55],"Analysis":[56],"with":[57,93,131],"Molecular":[58],"Indexes),":[59],"a":[60,123],"fully-integrated":[61],"UMI-aware":[62],"pipeline":[63,137],"designed":[64],"to":[65,89,108],"detect":[66,109],"diverging":[69],"from":[70,122],"transcript":[71],"annotations.":[72],"Building":[73],"upon":[74],"well-proven":[76],"STAR":[77],"aligner,":[78],"introduces":[80],"original":[81],"post-processing":[82],"of":[83,103],"gaps":[84],"and":[85,97,105,113,127,138],"intron":[87],"retention":[88],"maximize":[90],"accuracy,":[91],"along":[92],"clear":[94],"graphical":[95],"representations":[96],"tunable":[98],"filtering":[99],"stringency.":[100],"The":[101],"ability":[102],"concurrent":[106],"software":[107],"intragenic":[110],"aberrations":[112],"fusions":[115],"was":[116],"assessed,":[117],"both":[118],"on":[119],"real":[120],"data":[121,129],"commercial":[124],"control":[125],"sample":[126],"simulated":[128],"generated":[130],"ASimulatoR.":[132],"AVAILABILITY":[133],"AND":[134],"IMPLEMENTATION:":[135],"Nextflow":[136],"Singularity":[139],"container":[140],"recipe":[141],"freely":[142],"under":[144],"GPL":[145],"3":[146],"license":[147],"at":[148],"https://github.com/HCL-HUBL/SAMI.":[149]},"counts_by_year":[],"updated_date":"2026-08-05T07:39:15.569665","created_date":"2026-05-22T00:00:00"}
