{"id":"https://openalex.org/W2952118391","doi":"https://doi.org/10.1093/bioinformatics/bty004","title":"Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer","display_name":"Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer","publication_year":2018,"publication_date":"2018-01-11","ids":{"openalex":"https://openalex.org/W2952118391","doi":"https://doi.org/10.1093/bioinformatics/bty004","mag":"2952118391","pmid":"https://pubmed.ncbi.nlm.nih.gov/29342249"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty004","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty004","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/11/1859/25171337/bty004.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/34/11/1859/25171337/bty004.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5001164623","display_name":"Bahman Afsari","orcid":"https://orcid.org/0000-0001-8717-7199"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]},{"id":"https://openalex.org/I4210164401","display_name":"Sidney Kimmel Comprehensive Cancer Center","ror":"https://ror.org/05m5b8x20","country_code":"US","type":"facility","lineage":["https://openalex.org/I2799853436","https://openalex.org/I4210164401"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Bahman Afsari","raw_affiliation_strings":["Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I4210164401","https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022815817","display_name":"Theresa Guo","orcid":"https://orcid.org/0000-0002-1689-3275"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Theresa Guo","raw_affiliation_strings":["Department of Otolaryngology\u2014Head and Neck Surgery, Johns Hopkins University, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Otolaryngology\u2014Head and Neck Surgery, Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023086953","display_name":"Michael Considine","orcid":"https://orcid.org/0000-0002-8666-4857"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]},{"id":"https://openalex.org/I4210164401","display_name":"Sidney Kimmel Comprehensive Cancer Center","ror":"https://ror.org/05m5b8x20","country_code":"US","type":"facility","lineage":["https://openalex.org/I2799853436","https://openalex.org/I4210164401"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael Considine","raw_affiliation_strings":["Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I4210164401","https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065946017","display_name":"Liliana Florea","orcid":"https://orcid.org/0000-0001-8124-2324"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Liliana Florea","raw_affiliation_strings":["McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083237199","display_name":"Luciane T. Kagohara","orcid":"https://orcid.org/0000-0003-1706-0950"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]},{"id":"https://openalex.org/I4210164401","display_name":"Sidney Kimmel Comprehensive Cancer Center","ror":"https://ror.org/05m5b8x20","country_code":"US","type":"facility","lineage":["https://openalex.org/I2799853436","https://openalex.org/I4210164401"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Luciane T Kagohara","raw_affiliation_strings":["Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I4210164401","https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069366529","display_name":"Genevieve Stein-O\u2019Brien","orcid":"https://orcid.org/0000-0001-8681-9110"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]},{"id":"https://openalex.org/I4210164401","display_name":"Sidney Kimmel Comprehensive Cancer Center","ror":"https://ror.org/05m5b8x20","country_code":"US","type":"facility","lineage":["https://openalex.org/I2799853436","https://openalex.org/I4210164401"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Genevieve L Stein-O\u2019Brien","raw_affiliation_strings":["Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I4210164401","https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004177700","display_name":"Dylan Z. Kelley","orcid":null},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dylan Kelley","raw_affiliation_strings":["Department of Otolaryngology\u2014Head and Neck Surgery, Johns Hopkins University, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Otolaryngology\u2014Head and Neck Surgery, Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033962716","display_name":"Emily Flam","orcid":"https://orcid.org/0000-0001-6262-1126"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Emily Flam","raw_affiliation_strings":["Department of Otolaryngology\u2014Head and Neck Surgery, Johns Hopkins University, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Otolaryngology\u2014Head and Neck Surgery, Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035249389","display_name":"Kristina Diana A. Zambo","orcid":"https://orcid.org/0000-0003-2247-8104"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kristina D Zambo","raw_affiliation_strings":["Department of Otolaryngology\u2014Head and Neck Surgery, Johns Hopkins University, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Otolaryngology\u2014Head and Neck Surgery, Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072610753","display_name":"Patrick K. Ha","orcid":"https://orcid.org/0000-0003-0306-6147"},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Patrick K Ha","raw_affiliation_strings":["Department of Otolaryngology\u2014Head and Neck Surgery, University of California, San Francisco, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Otolaryngology\u2014Head and Neck Surgery, University of California, San Francisco, CA, USA","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013551450","display_name":"Donald Geman","orcid":null},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Donald Geman","raw_affiliation_strings":["Department of Applied Mathematics & Statistics, Johns Hopkins University, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Applied Mathematics & Statistics, Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014591184","display_name":"Michael F. Ochs","orcid":null},"institutions":[{"id":"https://openalex.org/I64281891","display_name":"College of New Jersey","ror":"https://ror.org/02nx5r318","country_code":"US","type":"education","lineage":["https://openalex.org/I64281891"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael F Ochs","raw_affiliation_strings":["Department of Mathematics & Statistics, The College of New Jersey, Ewing, NJ, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics & Statistics, The College of New Jersey, Ewing, NJ, USA","institution_ids":["https://openalex.org/I64281891"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017600358","display_name":"Joseph A. Califano","orcid":"https://orcid.org/0000-0002-4715-6761"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joseph A Califano","raw_affiliation_strings":["Division of Otolaryngology, Department of Surgery, University of California, San Diego, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Otolaryngology, Department of Surgery, University of California, San Diego, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052817116","display_name":"Daria A. Gaykalova","orcid":"https://orcid.org/0000-0001-5037-0147"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daria A Gaykalova","raw_affiliation_strings":["Department of Otolaryngology\u2014Head and Neck Surgery, Johns Hopkins University, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Otolaryngology\u2014Head and Neck Surgery, Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080546333","display_name":"Alexander V. Favorov","orcid":"https://orcid.org/0000-0003-2595-1091"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]},{"id":"https://openalex.org/I4210148309","display_name":"Vavilov Institute of General Genetics","ror":"https://ror.org/05ermrg42","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210129690","https://openalex.org/I4210148309"]},{"id":"https://openalex.org/I4210164401","display_name":"Sidney Kimmel Comprehensive Cancer Center","ror":"https://ror.org/05m5b8x20","country_code":"US","type":"facility","lineage":["https://openalex.org/I2799853436","https://openalex.org/I4210164401"]}],"countries":["RU","US"],"is_corresponding":true,"raw_author_name":"Alexander V Favorov","raw_affiliation_strings":["Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA","Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, RAS, Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I4210164401","https://openalex.org/I145311948"]},{"raw_affiliation_string":"Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, RAS, Moscow, Russia","institution_ids":["https://openalex.org/I4210148309"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027701541","display_name":"Elana J. Fertig","orcid":"https://orcid.org/0000-0003-3204-342X"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]},{"id":"https://openalex.org/I4210164401","display_name":"Sidney Kimmel Comprehensive Cancer Center","ror":"https://ror.org/05m5b8x20","country_code":"US","type":"facility","lineage":["https://openalex.org/I2799853436","https://openalex.org/I4210164401"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Elana J Fertig","raw_affiliation_strings":["Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA"],"raw_orcid":"https://orcid.org/0000-0003-3204-342X","affiliations":[{"raw_affiliation_string":"Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I4210164401","https://openalex.org/I145311948"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":16,"corresponding_author_ids":["https://openalex.org/A5001164623","https://openalex.org/A5027701541","https://openalex.org/A5080546333"],"corresponding_institution_ids":["https://openalex.org/I145311948","https://openalex.org/I4210148309","https://openalex.org/I4210164401"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.7423,"has_fulltext":false,"cited_by_count":18,"citation_normalized_percentile":{"value":0.71461159,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"34","issue":"11","first_page":"1859","last_page":"1867"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.4537000060081482,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.4537000060081482,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.22939999401569366,"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/T10885","display_name":"Gene expression and cancer classification","score":0.061900001019239426,"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/alternative-splicing","display_name":"Alternative splicing","score":0.7630870938301086},{"id":"https://openalex.org/keywords/splice","display_name":"splice","score":0.6945329308509827},{"id":"https://openalex.org/keywords/gene-isoform","display_name":"Gene isoform","score":0.6899797916412354},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.637491762638092},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5675696134567261},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5603417158126831},{"id":"https://openalex.org/keywords/phenotype","display_name":"Phenotype","score":0.5309801697731018},{"id":"https://openalex.org/keywords/genetic-heterogeneity","display_name":"Genetic heterogeneity","score":0.48564258217811584},{"id":"https://openalex.org/keywords/rna-splicing","display_name":"RNA splicing","score":0.4715804159641266},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4629908800125122},{"id":"https://openalex.org/keywords/bioconductor","display_name":"Bioconductor","score":0.4534693658351898},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.1774628758430481}],"concepts":[{"id":"https://openalex.org/C194583182","wikidata":"https://www.wikidata.org/wiki/Q21114084","display_name":"Alternative splicing","level":4,"score":0.7630870938301086},{"id":"https://openalex.org/C2780989783","wikidata":"https://www.wikidata.org/wiki/Q7578557","display_name":"splice","level":3,"score":0.6945329308509827},{"id":"https://openalex.org/C53345823","wikidata":"https://www.wikidata.org/wiki/Q5531554","display_name":"Gene isoform","level":3,"score":0.6899797916412354},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.637491762638092},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5675696134567261},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5603417158126831},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.5309801697731018},{"id":"https://openalex.org/C64618202","wikidata":"https://www.wikidata.org/wiki/Q3733697","display_name":"Genetic heterogeneity","level":4,"score":0.48564258217811584},{"id":"https://openalex.org/C54458228","wikidata":"https://www.wikidata.org/wiki/Q237218","display_name":"RNA splicing","level":4,"score":0.4715804159641266},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4629908800125122},{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.4534693658351898},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.1774628758430481}],"mesh":[{"descriptor_ui":"D006258","descriptor_name":"Head and Neck Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006258","descriptor_name":"Head and Neck Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006258","descriptor_name":"Head and Neck Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015972","descriptor_name":"Gene Expression Regulation, Neoplastic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015972","descriptor_name":"Gene Expression Regulation, Neoplastic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015972","descriptor_name":"Gene Expression Regulation, Neoplastic","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":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/bty004","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty004","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/11/1859/25171337/bty004.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29342249","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29342249","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:escholarship.org:ark:/13030/qt6kg1f5br","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/6kg1f5br","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, vol 34, iss 11","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5511600","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5972655","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty004","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty004","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/11/1859/25171337/bty004.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4399999976158142,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G1570158730","display_name":null,"funder_award_id":"17-00-00208","funder_id":"https://openalex.org/F4320321079","funder_display_name":"Russian Foundation for Basic Research"},{"id":"https://openalex.org/G290554522","display_name":null,"funder_award_id":"ABI-1356078","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3603597131","display_name":null,"funder_award_id":"R21 DE025398","funder_id":"https://openalex.org/F4320337365","funder_display_name":"National Institute of Dental and Craniofacial Research"},{"id":"https://openalex.org/G4822803319","display_name":null,"funder_award_id":"P50 DE019032","funder_id":"https://openalex.org/F4320337365","funder_display_name":"National Institute of Dental and Craniofacial Research"},{"id":"https://openalex.org/G6325397735","display_name":null,"funder_award_id":"R01 CA177669","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G7745404508","display_name":null,"funder_award_id":"T32DC000027-26","funder_id":"https://openalex.org/F4320337352","funder_display_name":"National Institute on Deafness and Other Communication Disorders"},{"id":"https://openalex.org/G7842274340","display_name":null,"funder_award_id":"R01 DE023227","funder_id":"https://openalex.org/F4320337365","funder_display_name":"National Institute of Dental and Craniofacial Research"},{"id":"https://openalex.org/G8154960712","display_name":null,"funder_award_id":"R01 DE023347","funder_id":"https://openalex.org/F4320337365","funder_display_name":"National Institute of Dental and Craniofacial Research"},{"id":"https://openalex.org/G8582673968","display_name":null,"funder_award_id":"P30 CA006973","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320309044","display_name":"Adenoid Cystic Carcinoma Research Foundation","ror":"https://ror.org/04fafj987"},{"id":"https://openalex.org/F4320321079","display_name":"Russian Foundation for Basic Research","ror":"https://ror.org/02mh1ke95"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337352","display_name":"National Institute on Deafness and Other Communication Disorders","ror":"https://ror.org/04mhx6838"},{"id":"https://openalex.org/F4320337365","display_name":"National Institute of Dental and Craniofacial Research","ror":"https://ror.org/004a2wv92"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2952118391.pdf","grobid_xml":"https://content.openalex.org/works/W2952118391.grobid-xml"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W1968239355","https://openalex.org/W1986241711","https://openalex.org/W1990210083","https://openalex.org/W2000875411","https://openalex.org/W2036913140","https://openalex.org/W2046583421","https://openalex.org/W2047452386","https://openalex.org/W2051019655","https://openalex.org/W2053520154","https://openalex.org/W2066231767","https://openalex.org/W2068540164","https://openalex.org/W2082773579","https://openalex.org/W2088477148","https://openalex.org/W2103823493","https://openalex.org/W2104005232","https://openalex.org/W2112876600","https://openalex.org/W2114843025","https://openalex.org/W2117787165","https://openalex.org/W2119204091","https://openalex.org/W2120865735","https://openalex.org/W2122496897","https://openalex.org/W2124097252","https://openalex.org/W2126144698","https://openalex.org/W2140729960","https://openalex.org/W2142109616","https://openalex.org/W2143513235","https://openalex.org/W2146512944","https://openalex.org/W2154954867","https://openalex.org/W2162871445","https://openalex.org/W2255292617","https://openalex.org/W2295094052","https://openalex.org/W2298558585","https://openalex.org/W2322546955","https://openalex.org/W2739132338","https://openalex.org/W3104999573","https://openalex.org/W6668007073"],"related_works":["https://openalex.org/W2001319824","https://openalex.org/W2067501355","https://openalex.org/W2008389025","https://openalex.org/W1943031701","https://openalex.org/W2136950317","https://openalex.org/W2321791250","https://openalex.org/W4213427798","https://openalex.org/W2023199111","https://openalex.org/W2564462691","https://openalex.org/W2155793948"],"abstract_inverted_index":{"Motivation:":[0],"Current":[1],"bioinformatics":[2],"methods":[3],"to":[4,82,114],"detect":[5],"changes":[6],"in":[7,11,20,26,29,66,126,156,161,198,212,242],"gene":[8,37,67,130,195,230],"isoform":[9,18,27,68,131,145,196,231],"usage":[10,19,28,69,89,146,197,232],"distinct":[12],"phenotypes":[13],"compare":[14],"the":[15,52,55,105,115,152,192,216,243],"relative":[16],"expected":[17],"phenotypes.":[21],"These":[22,220],"statistics":[23],"model":[24,83,143],"differences":[25],"normal":[30,95],"tissues,":[31],"which":[32],"have":[33,45],"stable":[34],"regulation":[35,47],"of":[36,48,54,57,86,107,129,148,154,170,177,183,194,229],"splicing.":[38],"Pathological":[39],"conditions,":[40],"such":[41,63],"as":[42],"cancer,":[43],"can":[44],"broken":[46],"splicing":[49],"that":[50,103,122,142,214,223],"increases":[51],"heterogeneity":[53,65,85,128,180,193,206,228],"expression":[56,109],"splice":[58,87,159,172,178,217],"variants.":[59,173],"Inferring":[60],"events":[61],"with":[62,210],"differential":[64,144,227],"requires":[70],"new":[71],"statistical":[72],"approaches.":[73],"Results:":[74],"We":[75,150],"introduce":[76],"Splice":[77],"Expression":[78],"Variability":[79],"Analysis":[80],"(SEVA)":[81],"increased":[84,205],"variant":[88,179,218],"between":[90,181,191],"conditions":[91],"(e.g.":[92],"tumor":[93],"and":[94,133,140,163,166,185,200,203,237],"samples).":[96],"SEVA":[97,123,155,224,239],"uses":[98],"a":[99],"rank-based":[100],"multivariate":[101],"statistic":[102],"compares":[104],"variability":[106,116],"junction":[108],"profiles":[110],"within":[111,117],"one":[112],"condition":[113],"another.":[118],"Simulated":[119],"data":[120,256],"show":[121,222],"is":[124,240],"unique":[125],"modeling":[127],"usage,":[132],"benchmark":[134],"SEVA's":[135],"performance":[136],"against":[137],"EBSeq,":[138],"DiffSplice":[139],"rMATS":[141],"instead":[147],"heterogeneity.":[149],"confirm":[151],"accuracy":[153],"identifying":[157],"known":[158],"variants":[160],"head":[162,184],"neck":[164,186],"cancer":[165,187],"perform":[167],"cross-study":[168],"validation":[169],"novel":[171,175],"A":[174],"comparison":[176],"subtypes":[182,202],"demonstrated":[188],"unanticipated":[189],"similarity":[190],"HPV-positive":[199],"HPV-negative":[201,208],"anticipated":[204],"among":[207],"samples":[209],"mutations":[211],"genes":[213],"regulate":[215],"machinery.":[219],"results":[221],"accurately":[225],"models":[226],"from":[233],"RNA-seq":[234],"data.":[235],"Availability":[236],"implementation:":[238],"implemented":[241],"R/Bioconductor":[244],"package":[245],"GSReg.":[246],"Contact:":[247],"bahman@jhu.edu":[248],"or":[249,251],"favorov@sensi.org":[250],"ejfertig@jhmi.edu.":[252],"Supplementary":[253,255],"information:":[254],"are":[257],"available":[258],"at":[259],"Bioinformatics":[260],"online.":[261]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}