{"id":"https://openalex.org/W2155806289","doi":"https://doi.org/10.1093/bioinformatics/btv034","title":"Quantitative visualization of alternative exon expression from RNA-seq data","display_name":"Quantitative visualization of alternative exon expression from RNA-seq data","publication_year":2015,"publication_date":"2015-01-22","ids":{"openalex":"https://openalex.org/W2155806289","doi":"https://doi.org/10.1093/bioinformatics/btv034","mag":"2155806289","pmid":"https://pubmed.ncbi.nlm.nih.gov/25617416","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/4542614"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv034","doi":"https://doi.org/10.1093/bioinformatics/btv034","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv034","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/14/2400/17086562/btv034.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,"listed_in":["abdc-a","anvur-class-a","anvur-scientific","ccf-a","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"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"},"volume":null,"type":"article","indexed_in":["arxiv","crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/31/14/2400/17086562/btv034.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5091284431","display_name":"Yarden Katz A","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yarden Katz","raw_affiliation_strings":["1 Department of Brain and Cognitive Sciences, MIT, Cambridge, MA,","2 Department of Biology, MIT, Cambridge, MA,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Brain and Cognitive Sciences, MIT, Cambridge, MA,","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"2 Department of Biology, MIT, Cambridge, MA,","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003957317","display_name":"Eric T. Wang","orcid":"https://orcid.org/0000-0003-2655-5525","observed_orcids":["https://orcid.org/0000-0003-2655-5525"]},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eric T. Wang","raw_affiliation_strings":["2 Department of Biology, MIT, Cambridge, MA,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"2 Department of Biology, MIT, Cambridge, MA,","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000413092","display_name":"Jacob Silterra","orcid":"https://orcid.org/0000-0001-9159-5836","observed_orcids":["https://orcid.org/0000-0001-9159-5836"]},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jacob Silterra","raw_affiliation_strings":["3 The Broad Institute of Harvard, MIT, Cambridge, MA, USA,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"3 The Broad Institute of Harvard, MIT, Cambridge, MA, USA,","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044700675","display_name":"Schraga Schwartz","orcid":"https://orcid.org/0000-0002-3671-9709","observed_orcids":["https://orcid.org/0000-0002-3671-9709"]},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Schraga Schwartz","raw_affiliation_strings":["3 The Broad Institute of Harvard, MIT, Cambridge, MA, USA,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"3 The Broad Institute of Harvard, MIT, Cambridge, MA, USA,","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057814101","display_name":"Bang Wong","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bang Wong","raw_affiliation_strings":["3 The Broad Institute of Harvard, MIT, Cambridge, MA, USA,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"3 The Broad Institute of Harvard, MIT, Cambridge, MA, USA,","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033125816","display_name":"Helga Thorvaldsd\u00f3ttir","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Helga Thorvaldsd\u00f3ttir","raw_affiliation_strings":["3 The Broad Institute of Harvard, MIT, Cambridge, MA, USA,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"3 The Broad Institute of Harvard, MIT, Cambridge, MA, USA,","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":null,"display_name":"James T. Robinson","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James T. Robinson","raw_affiliation_strings":["3 The Broad Institute of Harvard, MIT, Cambridge, MA, USA,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"3 The Broad Institute of Harvard, MIT, Cambridge, MA, USA,","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077622597","display_name":"Jill P. Mesirov","orcid":"https://orcid.org/0000-0002-9755-2818","observed_orcids":["https://orcid.org/0000-0002-9755-2818"]},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jill P. Mesirov","raw_affiliation_strings":["3 The Broad Institute of Harvard, MIT, Cambridge, MA, USA,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"3 The Broad Institute of Harvard, MIT, Cambridge, MA, USA,","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035398709","display_name":"Edoardo M. Airoldi","orcid":"https://orcid.org/0000-0002-3512-0542","observed_orcids":["https://orcid.org/0000-0002-3512-0542"]},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Edoardo M. Airoldi","raw_affiliation_strings":["3 The Broad Institute of Harvard, MIT, Cambridge, MA, USA,","4 Department of Statistics, Harvard University, Cambridge, MA, USA and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"3 The Broad Institute of Harvard, MIT, Cambridge, MA, USA,","institution_ids":["https://openalex.org/I107606265"]},{"raw_affiliation_string":"4 Department of Statistics, Harvard University, Cambridge, MA, USA and","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5048799588","display_name":"Christopher B. Burge","orcid":"https://orcid.org/0000-0001-9047-5648","observed_orcids":["https://orcid.org/0000-0001-9047-5648"]},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Christopher B. Burge","raw_affiliation_strings":["2 Department of Biology, MIT, Cambridge, MA,","5 Department of Biological Engineering, MIT, Cambridge, MA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"2 Department of Biology, MIT, Cambridge, MA,","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"5 Department of Biological Engineering, MIT, Cambridge, MA","institution_ids":["https://openalex.org/I63966007"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5035398709","https://openalex.org/A5048799588","https://openalex.org/A5077622597"],"corresponding_institution_ids":["https://openalex.org/I107606265","https://openalex.org/I136199984","https://openalex.org/I63966007"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":6.1329,"has_fulltext":true,"cited_by_count":220,"citation_normalized_percentile":{"value":0.97667424,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"31","issue":"14","first_page":"2400","last_page":"2402"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.9365000128746033,"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":0.9365000128746033,"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":0.05820000171661377,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.0015999999595806003,"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":0.7149999737739563},{"id":"https://openalex.org/keywords/isoform-expression","display_name":"isoform expression","score":0.6100000143051147},{"id":"https://openalex.org/keywords/exon-usage","display_name":"exon usage","score":0.6990000009536743},{"id":"https://openalex.org/keywords/miso","display_name":"miso","score":0.5450000166893005},{"id":"https://openalex.org/keywords/read-mapping","display_name":"read mapping","score":0.3630000054836273},{"id":"https://openalex.org/keywords/tissue-specific-expression","display_name":"tissue-specific gene expression","score":0.5460000038146973}],"concepts":[{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.648985743522644},{"id":"https://openalex.org/C194583182","wikidata":"https://www.wikidata.org/wiki/Q21114084","display_name":"Alternative splicing","level":4,"score":0.6182243824005127},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.6056170463562012},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5574164390563965},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5522680878639221},{"id":"https://openalex.org/C36823959","wikidata":"https://www.wikidata.org/wiki/Q373027","display_name":"Exon","level":3,"score":0.5299590229988098},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5148910284042358},{"id":"https://openalex.org/C53345823","wikidata":"https://www.wikidata.org/wiki/Q5531554","display_name":"Gene isoform","level":3,"score":0.4887056350708008},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.45327651500701904},{"id":"https://openalex.org/C54458228","wikidata":"https://www.wikidata.org/wiki/Q237218","display_name":"RNA splicing","level":4,"score":0.4406145215034485},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.4277433454990387},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.403919517993927},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.3525822162628174},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.341043084859848},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.339652419090271},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.30780142545700073},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.21274033188819885},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005091","descriptor_name":"Exons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059368","descriptor_name":"RNA Isoforms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D059368","descriptor_name":"RNA Isoforms","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":8,"locations":[{"id":"doi:10.1093/bioinformatics/btv034","doi":"https://doi.org/10.1093/bioinformatics/btv034","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv034","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/14/2400/17086562/btv034.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,"listed_in":["abdc-a","anvur-class-a","anvur-scientific","ccf-a","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"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":"doi:10.1101/002576","doi":"https://doi.org/10.1101/002576","is_oa":true,"landing_page_url":"https://doi.org/10.1101/002576","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2014/02/11/002576.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmh:oai:europepmc.org:3910512","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4542614","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,"listed_in":[],"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:4542614","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4542614","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,"listed_in":[],"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","raw_type":"Text"},{"id":"pmid:25617416","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25617416","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,"listed_in":[],"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:arXiv.org:1306.3466","doi":null,"is_oa":true,"landing_page_url":"http://arxiv.org/abs/1306.3466","pdf_url":"https://arxiv.org/pdf/1306.3466","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:31/14/2400","doi":null,"is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/31/14/2400","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"},{"id":"pmh:oai:scholarshare.temple.edu:20.500.12613/5822","doi":null,"is_oa":false,"landing_page_url":"http://hdl.handle.net/20.500.12613/5822","pdf_url":null,"source":{"id":"https://openalex.org/S4306402624","display_name":"TUScholarShare (Temple University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I84392919","host_organization_name":"Temple University","host_organization_lineage":["https://openalex.org/I84392919"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv034","doi":"https://doi.org/10.1093/bioinformatics/btv034","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv034","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/14/2400/17086562/btv034.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,"listed_in":["abdc-a","anvur-class-a","anvur-scientific","ccf-a","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"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":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1142689760","display_name":"A next-generation Integrative Genomics Viewer for biomedical and cancer research.","funder_award_id":"R01CA157304","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G3255881711","display_name":"CAREER: Quantifying diffusion and dynamics on healthcare, innovation and communication networks","funder_award_id":"1149662","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4484814523","display_name":"Quant. methods for systems-level analyses of regulation & signaling dynamics","funder_award_id":"R01GM096193","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G4841860181","display_name":"Ppst-transcriptional regulation of gene expression in neuromuscular disease","funder_award_id":"DP5OD017865","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4993874805","display_name":"Dynamics of Gene and Isoform Regulation during EMT and tumor progression","funder_award_id":"U01CA184897","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G5113298768","display_name":"Regulation and Function of Alternative mRNA Isoform Expression in Mammals","funder_award_id":"R01HG002439","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G9000918103","display_name":"Function of Sequence-specific RNA Binding Proteins","funder_award_id":"R01GM085319","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320314070","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2155806289.pdf","grobid_xml":"https://content.openalex.org/works/W2155806289.grobid-xml"},"referenced_works_count":12,"referenced_works":["https://openalex.org/W1575879600","https://openalex.org/W2011301426","https://openalex.org/W2011920499","https://openalex.org/W2013963839","https://openalex.org/W2095998476","https://openalex.org/W2098456123","https://openalex.org/W2117131162","https://openalex.org/W2128016314","https://openalex.org/W2151462466","https://openalex.org/W2154431984","https://openalex.org/W2155804510","https://openalex.org/W6891697816"],"related_works":["https://openalex.org/W6891697816","https://openalex.org/W4396678559","https://openalex.org/W2146762043","https://openalex.org/W4386453612","https://openalex.org/W7100140913","https://openalex.org/W7096447130","https://openalex.org/W4408478911","https://openalex.org/W2086323500","https://openalex.org/W2123402634","https://openalex.org/W3157326977"],"abstract_inverted_index":{"Abstract":[0],"Motivation:":[1],"Analysis":[2],"of":[3,13,68,76],"RNA":[4],"sequencing":[5],"(RNA-Seq)":[6],"data":[7,121],"revealed":[8],"that":[9,29,72],"the":[10,90],"vast":[11],"majority":[12],"human":[14,37],"genes":[15],"express":[16],"multiple":[17,53],"mRNA":[18],"isoforms,":[19],"produced":[20],"by":[21],"alternative":[22,31],"pre-mRNA":[23],"splicing":[24],"and":[25,28,103,107],"other":[26],"mechanisms,":[27],"most":[30],"isoforms":[32],"vary":[33],"in":[34,43],"expression":[35,51],"between":[36],"tissues.":[38],"As":[39],"RNA-Seq":[40,70],"datasets":[41],"grow":[42],"size,":[44],"it":[45],"remains":[46],"challenging":[47],"to":[48],"visualize":[49],"isoform":[50],"across":[52,79],"samples.":[54],"Results:":[55],"To":[56],"help":[57],"address":[58],"this":[59],"problem,":[60],"we":[61],"present":[62],"Sashimi":[63,84],"plots,":[64],"a":[65,97],"quantitative":[66,74],"visualization":[67],"aligned":[69],"reads":[71],"enables":[73],"comparison":[75],"exon":[77],"usage":[78],"samples":[80],"or":[81,95,116],"experimental":[82],"conditions.":[83],"plots":[85],"can":[86],"be":[87],"made":[88],"using":[89],"Broad":[91],"Integrated":[92],"Genome":[93],"Viewer":[94],"with":[96],"stand-alone":[98],"command":[99],"line":[100],"program.":[101],"Availability":[102],"implementation:":[104],"Software":[105],"code":[106],"documentation":[108],"freely":[109],"available":[110,123],"here:":[111],"http://miso.readthedocs.org/en/fastmiso/sashimi.html":[112],"Contact:":[113],"mesirov@broadinstitute.org,":[114],"airoldi@fas.harvard.edu":[115],"cburge@mit.edu":[117],"Supplementary":[118,120],"information:":[119],"are":[122],"at":[124],"Bioinformatics":[125],"online.":[126]},"counts_by_year":[{"year":2026,"cited_by_count":8},{"year":2025,"cited_by_count":20},{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":14},{"year":2022,"cited_by_count":19},{"year":2021,"cited_by_count":26},{"year":2020,"cited_by_count":46},{"year":2019,"cited_by_count":21},{"year":2018,"cited_by_count":16},{"year":2017,"cited_by_count":15},{"year":2016,"cited_by_count":10},{"year":2015,"cited_by_count":11},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":1}],"updated_date":"2026-11-05T12:25:35.769452","created_date":"2016-06-24T00:00:00"}
