{"id":"https://openalex.org/W3181822107","doi":"https://doi.org/10.1186/s12859-021-04282-6","title":"SPLICE-q: a Python tool for genome-wide quantification of splicing efficiency","display_name":"SPLICE-q: a Python tool for genome-wide quantification of splicing efficiency","publication_year":2021,"publication_date":"2021-07-15","ids":{"openalex":"https://openalex.org/W3181822107","doi":"https://doi.org/10.1186/s12859-021-04282-6","mag":"3181822107","pmid":"https://pubmed.ncbi.nlm.nih.gov/34266387"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-021-04282-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04282-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04282-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04282-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5031926283","display_name":"Veronica Costa","orcid":null},"institutions":[{"id":"https://openalex.org/I4210142260","display_name":"Max Planck Institute for Molecular Genetics","ror":"https://ror.org/03ate3e03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210142260"]},{"id":"https://openalex.org/I75951250","display_name":"Freie Universit\u00e4t Berlin","ror":"https://ror.org/046ak2485","country_code":"DE","type":"education","lineage":["https://openalex.org/I75951250"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Ver\u00f4nica R. de Melo Costa","raw_affiliation_strings":["Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany. veronica.melocosta@gmail.com","Institute of Computer Science and Institute of Bioinformatics, Freie Universit\u00e4t Berlin, Berlin, Germany. veronica.melocosta@gmail.com","Institute of Computer Science and Institute of Bioinformatics, Freie Universit\u00e4t Berlin, Berlin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany. veronica.melocosta@gmail.com","institution_ids":["https://openalex.org/I4210142260"]},{"raw_affiliation_string":"Institute of Computer Science and Institute of Bioinformatics, Freie Universit\u00e4t Berlin, Berlin, Germany. veronica.melocosta@gmail.com","institution_ids":["https://openalex.org/I75951250"]},{"raw_affiliation_string":"Institute of Computer Science and Institute of Bioinformatics, Freie Universit\u00e4t Berlin, Berlin, Germany","institution_ids":["https://openalex.org/I75951250"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038875783","display_name":"Julianus Pfeuffer","orcid":"https://orcid.org/0000-0001-8948-9209"},"institutions":[{"id":"https://openalex.org/I75951250","display_name":"Freie Universit\u00e4t Berlin","ror":"https://ror.org/046ak2485","country_code":"DE","type":"education","lineage":["https://openalex.org/I75951250"]},{"id":"https://openalex.org/I8087733","display_name":"University of T\u00fcbingen","ror":"https://ror.org/03a1kwz48","country_code":"DE","type":"education","lineage":["https://openalex.org/I8087733"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Julianus Pfeuffer","raw_affiliation_strings":["Department of Computer Science, Eberhard Karls Universit\u00e4t T\u00fcbingen, T\u00fcbingen, Germany","Institute for Bioinformatics and Medical Informatics T\u00fcbingen, Eberhard Karls Universit\u00e4t T\u00fcbingen, T\u00fcbingen, Germany","Institute of Computer Science and Institute of Bioinformatics, Freie Universit\u00e4t Berlin, Berlin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Eberhard Karls Universit\u00e4t T\u00fcbingen, T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733"]},{"raw_affiliation_string":"Institute for Bioinformatics and Medical Informatics T\u00fcbingen, Eberhard Karls Universit\u00e4t T\u00fcbingen, T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733"]},{"raw_affiliation_string":"Institute of Computer Science and Institute of Bioinformatics, Freie Universit\u00e4t Berlin, Berlin, Germany","institution_ids":["https://openalex.org/I75951250"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090995335","display_name":"Annita Louloupi","orcid":"https://orcid.org/0000-0003-3729-9002"},"institutions":[{"id":"https://openalex.org/I205582932","display_name":"Max Delbr\u00fcck Center","ror":"https://ror.org/04p5ggc03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I205582932"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Annita Louloupi","raw_affiliation_strings":["Max Delbr\u00fcck Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, Berlin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Max Delbr\u00fcck Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, Berlin, Germany","institution_ids":["https://openalex.org/I205582932"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053637737","display_name":"Ulf Andersson \u00d8rom","orcid":"https://orcid.org/0000-0002-0643-0592"},"institutions":[{"id":"https://openalex.org/I204337017","display_name":"Aarhus University","ror":"https://ror.org/01aj84f44","country_code":"DK","type":"education","lineage":["https://openalex.org/I204337017"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Ulf A. V. \u00d8rom","raw_affiliation_strings":["Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark","institution_ids":["https://openalex.org/I204337017"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5060099317","display_name":"Rosario M. Piro","orcid":"https://orcid.org/0000-0002-3066-7397"},"institutions":[{"id":"https://openalex.org/I93860229","display_name":"Politecnico di Milano","ror":"https://ror.org/01nffqt88","country_code":"IT","type":"education","lineage":["https://openalex.org/I93860229"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Rosario M. Piro","raw_affiliation_strings":["Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, Italy. rosariomichael.piro@polimi.it","Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, Italy"],"raw_orcid":"https://orcid.org/0000-0002-3066-7397","affiliations":[{"raw_affiliation_string":"Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, Italy. rosariomichael.piro@polimi.it","institution_ids":["https://openalex.org/I93860229"]},{"raw_affiliation_string":"Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, Italy","institution_ids":["https://openalex.org/I93860229"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5060099317"],"corresponding_institution_ids":["https://openalex.org/I93860229"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.2212,"has_fulltext":true,"cited_by_count":21,"citation_normalized_percentile":{"value":0.78731085,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"22","issue":"1","first_page":"368","last_page":"368"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.9811999797821045,"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":0.9811999797821045,"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":0.004600000102072954,"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"}},{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":0.0032999999821186066,"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/python","display_name":"Python (programming language)","score":0.8088730573654175},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6493953466415405},{"id":"https://openalex.org/keywords/splice","display_name":"splice","score":0.555971622467041},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5371554493904114},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.49412086606025696},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.48124003410339355},{"id":"https://openalex.org/keywords/rna-splicing","display_name":"RNA splicing","score":0.47099655866622925},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.39342713356018066},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.38835906982421875},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.22162777185440063},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.18939924240112305},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.08716699481010437},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.07825645804405212}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8088730573654175},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6493953466415405},{"id":"https://openalex.org/C2780989783","wikidata":"https://www.wikidata.org/wiki/Q7578557","display_name":"splice","level":3,"score":0.555971622467041},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5371554493904114},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.49412086606025696},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.48124003410339355},{"id":"https://openalex.org/C54458228","wikidata":"https://www.wikidata.org/wiki/Q237218","display_name":"RNA splicing","level":4,"score":0.47099655866622925},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.39342713356018066},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.38835906982421875},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.22162777185440063},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.18939924240112305},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.08716699481010437},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.07825645804405212}],"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007438","descriptor_name":"Introns","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007438","descriptor_name":"Introns","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007438","descriptor_name":"Introns","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007438","descriptor_name":"Introns","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012326","descriptor_name":"RNA Splicing","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012326","descriptor_name":"RNA Splicing","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012326","descriptor_name":"RNA Splicing","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012326","descriptor_name":"RNA Splicing","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","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":true},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D022821","descriptor_name":"RNA Splice Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D022821","descriptor_name":"RNA Splice Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D022821","descriptor_name":"RNA Splice Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D022821","descriptor_name":"RNA Splice Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":7,"locations":[{"id":"doi:10.1186/s12859-021-04282-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04282-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04282-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34266387","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34266387","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pure.atira.dk:publications/ff251d65-56f8-4b43-8b2c-7c7a91174ac9","is_oa":true,"landing_page_url":"https://pure.au.dk/portal/en/publications/ff251d65-56f8-4b43-8b2c-7c7a91174ac9","pdf_url":null,"source":null,"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"de Melo Costa, V R, Pfeuffer, J, Louloupi, A, \u00d8rom, U A V & Piro, R M 2021, 'SPLICE-q : a Python tool for genome-wide quantification of splicing efficiency', BMC Bioinformatics, vol. 22, no. 1, 368. https://doi.org/10.1186/s12859-021-04282-6","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:edoc.mdc-berlin.de:20481","is_oa":true,"landing_page_url":"http://edoc.mdc-berlin.de/20481/2/20481suppl.zip","pdf_url":"http://edoc.mdc-berlin.de/20481/1/20481oa.pdf","source":{"id":"https://openalex.org/S4306400224","display_name":"MDC Repository (Max-Delbrueck-Center for Molecular Medicine)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I149899117","host_organization_name":"Max Planck Society","host_organization_lineage":["https://openalex.org/I149899117"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:doaj.org/article:82a272f99e1d4d96a0d1c1fa080632fc","is_oa":true,"landing_page_url":"https://doaj.org/article/82a272f99e1d4d96a0d1c1fa080632fc","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 22, Iss 1, Pp 1-14 (2021)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8281633","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8281633","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":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:re.public.polimi.it:11311/1186428","is_oa":true,"landing_page_url":"http://hdl.handle.net/11311/1186428","pdf_url":null,"source":{"id":"https://openalex.org/S4306400312","display_name":"Virtual Community of Pathological Anatomy (University of Castilla La Mancha)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I79189158","host_organization_name":"University of Castilla-La Mancha","host_organization_lineage":["https://openalex.org/I79189158"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1186/s12859-021-04282-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04282-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04282-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1164920944","display_name":null,"funder_award_id":"99999","funder_id":"https://openalex.org/F4320321091","funder_display_name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior"},{"id":"https://openalex.org/G1536267163","display_name":null,"funder_award_id":"FKZ 031A535A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G4480115467","display_name":null,"funder_award_id":"031A535A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G4685373625","display_name":null,"funder_award_id":"BEX 99999.002121/2015-08","funder_id":"https://openalex.org/F4320321091","funder_display_name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior"}],"funders":[{"id":"https://openalex.org/F4320321091","display_name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior","ror":"https://ror.org/00x0ma614"},{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"},{"id":"https://openalex.org/F4320336557","display_name":"Ci\u00eancia sem Fronteiras","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3181822107.pdf","grobid_xml":"https://content.openalex.org/works/W3181822107.grobid-xml"},"referenced_works_count":43,"referenced_works":["https://openalex.org/W193423965","https://openalex.org/W1907787906","https://openalex.org/W1941193127","https://openalex.org/W1966626059","https://openalex.org/W1974272975","https://openalex.org/W1983954245","https://openalex.org/W1985975914","https://openalex.org/W1994260783","https://openalex.org/W1996955639","https://openalex.org/W2021449777","https://openalex.org/W2045131720","https://openalex.org/W2047726241","https://openalex.org/W2063550395","https://openalex.org/W2087230189","https://openalex.org/W2095998476","https://openalex.org/W2096237610","https://openalex.org/W2102979437","https://openalex.org/W2115806147","https://openalex.org/W2123123598","https://openalex.org/W2129963496","https://openalex.org/W2148393113","https://openalex.org/W2160947271","https://openalex.org/W2160955060","https://openalex.org/W2178351989","https://openalex.org/W2217310620","https://openalex.org/W2519744449","https://openalex.org/W2554008396","https://openalex.org/W2559891632","https://openalex.org/W2580302003","https://openalex.org/W2592811885","https://openalex.org/W2602408874","https://openalex.org/W2783291377","https://openalex.org/W2786478597","https://openalex.org/W2794574704","https://openalex.org/W2898598946","https://openalex.org/W2903774577","https://openalex.org/W2905646971","https://openalex.org/W2960426428","https://openalex.org/W2993557395","https://openalex.org/W3007694665","https://openalex.org/W4206037526","https://openalex.org/W4230644176","https://openalex.org/W4287541611"],"related_works":["https://openalex.org/W2029220916","https://openalex.org/W2274928342","https://openalex.org/W2341492732","https://openalex.org/W1943031701","https://openalex.org/W3129862691","https://openalex.org/W1993348797","https://openalex.org/W3006402873","https://openalex.org/W2887346131","https://openalex.org/W2008832338","https://openalex.org/W2014791263"],"abstract_inverted_index":{"BACKGROUND:":[0],"Introns":[1],"are":[2],"generally":[3],"removed":[4],"from":[5,102,162],"primary":[6,23],"transcripts":[7,24],"to":[8,37,42,64,105,117,140,176,199],"form":[9],"mature":[10],"RNA":[11],"molecules":[12],"in":[13,29,94,148],"a":[14,73,163,178,185],"post-transcriptional":[15],"process":[16,49],"called":[17],"splicing.":[18],"An":[19],"efficient":[20],"splicing":[21,66,92,107,182],"of":[22,47,91,121,134,145,181,188],"is":[25,35,62,174,209],"an":[26],"essential":[27],"step":[28],"gene":[30,205],"expression":[31,206],"and":[32,50,75,113,150,191],"its":[33,157],"misregulation":[34],"related":[36],"numerous":[38],"human":[39,151],"diseases.":[40],"Thus,":[41],"better":[43],"understand":[44],"the":[45,51,89,115,124,143],"dynamics":[46,144],"this":[48],"perturbations":[52],"that":[53,172],"might":[54,193],"be":[55,194],"caused":[56],"by":[57],"aberrant":[58],"transcript":[59,95],"processing":[60,96],"it":[61,192,197],"important":[63],"quantify":[65,106],"efficiency.":[67],"RESULTS:":[68],"Here,":[69],"we":[70],"introduce":[71],"SPLICE-q,":[72],"fast":[74],"user-friendly":[76],"Python":[77],"tool":[78],"for":[79,109],"genome-wide":[80],"SPLICing":[81],"Efficiency":[82],"quantification.":[83],"It":[84],"supports":[85],"studies":[86],"focusing":[87],"on":[88],"implications":[90],"efficiency":[93,108,183],"dynamics.":[97],"SPLICE-q":[98,139,173,208],"uses":[99],"aligned":[100],"reads":[101],"strand-specific":[103],"RNA-seq":[104,161,190],"each":[110],"intron":[111,146],"individually":[112],"allows":[114],"user":[116],"select":[118],"different":[119],"levels":[120],"restrictiveness":[122],"concerning":[123],"introns'":[125],"overlap":[126],"with":[127],"other":[128,135],"genomic":[129],"elements":[130],"such":[131],"as":[132],"exons":[133],"genes.":[136],"We":[137,154],"applied":[138],"globally":[141],"assess":[142],"excision":[147],"yeast":[149],"nascent":[152,189],"RNA-seq.":[153],"also":[155],"show":[156],"application":[158],"using":[159],"total":[160],"patient-matched":[164],"prostate":[165],"cancer":[166,201],"sample.":[167],"CONCLUSIONS:":[168],"Our":[169],"analyses":[170],"illustrate":[171],"suitable":[175],"detect":[177],"progressive":[179],"increase":[180],"throughout":[184],"time":[186],"course":[187],"useful":[195],"when":[196],"comes":[198],"understanding":[200],"progression":[202],"beyond":[203],"mere":[204],"levels.":[207],"available":[210],"at:":[211],"https://github.com/vrmelo/SPLICE-q.":[212]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":7}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}