{"id":"https://openalex.org/W1784654175","doi":"https://doi.org/10.1371/journal.pcbi.1003314","title":"Systematically Differentiating Functions for Alternatively Spliced Isoforms through Integrating RNA-seq Data","display_name":"Systematically Differentiating Functions for Alternatively Spliced Isoforms through Integrating RNA-seq Data","publication_year":2013,"publication_date":"2013-11-07","ids":{"openalex":"https://openalex.org/W1784654175","doi":"https://doi.org/10.1371/journal.pcbi.1003314","mag":"1784654175","pmid":"https://pubmed.ncbi.nlm.nih.gov/24244129"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1003314","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003314","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003314&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003314&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5037352571","display_name":"Ridvan Eksi","orcid":"https://orcid.org/0000-0003-2757-0057"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I4210111179","display_name":"Michigan United","ror":"https://ror.org/0291ys696","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210111179"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ridvan Eksi","raw_affiliation_strings":["Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210111179"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112014086","display_name":"Hong-Dong Li","orcid":null},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I4210111179","display_name":"Michigan United","ror":"https://ror.org/0291ys696","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210111179"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hong-Dong Li","raw_affiliation_strings":["Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210111179"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078425221","display_name":"Rajasree Menon","orcid":"https://orcid.org/0000-0001-6280-9639"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I4210111179","display_name":"Michigan United","ror":"https://ror.org/0291ys696","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210111179"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rajasree Menon","raw_affiliation_strings":["Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210111179"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026794297","display_name":"Yuchen Wen","orcid":null},"institutions":[{"id":"https://openalex.org/I4210111179","display_name":"Michigan United","ror":"https://ror.org/0291ys696","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210111179"]},{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yuchen Wen","raw_affiliation_strings":["Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210111179"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008478119","display_name":"Gilbert S. Omenn","orcid":"https://orcid.org/0000-0002-8976-6074"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I4210111179","display_name":"Michigan United","ror":"https://ror.org/0291ys696","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210111179"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Gilbert S. Omenn","raw_affiliation_strings":["Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America","Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210111179"]},{"raw_affiliation_string":"Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210111179"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073141203","display_name":"Matthias Kretzler","orcid":"https://orcid.org/0000-0003-4064-0582"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I4210111179","display_name":"Michigan United","ror":"https://ror.org/0291ys696","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210111179"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Matthias Kretzler","raw_affiliation_strings":["Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America","Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210111179"]},{"raw_affiliation_string":"Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210111179"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5011032655","display_name":"Yuanfang Guan","orcid":"https://orcid.org/0000-0001-8275-2852"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I4210111179","display_name":"Michigan United","ror":"https://ror.org/0291ys696","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210111179"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yuanfang Guan","raw_affiliation_strings":["Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America","Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, Michigan, United States of America","Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210111179"]},{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, Michigan, United States of America","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210111179"]},{"raw_affiliation_string":"Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210111179"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5008478119","https://openalex.org/A5011032655","https://openalex.org/A5073141203"],"corresponding_institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210111179"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":4.3378,"has_fulltext":true,"cited_by_count":90,"citation_normalized_percentile":{"value":0.94996161,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"9","issue":"11","first_page":"e1003314","last_page":"e1003314"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":0.9995999932289124,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9994000196456909,"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/gene-isoform","display_name":"Gene isoform","score":0.9096540212631226},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6890622973442078},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.659579873085022},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6153950691223145},{"id":"https://openalex.org/keywords/alternative-splicing","display_name":"Alternative splicing","score":0.5736662745475769},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.5404804944992065},{"id":"https://openalex.org/keywords/functional-genomics","display_name":"Functional genomics","score":0.5161657929420471},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4603111743927002},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.42731714248657227},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.3534654974937439},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.2866380214691162}],"concepts":[{"id":"https://openalex.org/C53345823","wikidata":"https://www.wikidata.org/wiki/Q5531554","display_name":"Gene isoform","level":3,"score":0.9096540212631226},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6890622973442078},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.659579873085022},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6153950691223145},{"id":"https://openalex.org/C194583182","wikidata":"https://www.wikidata.org/wiki/Q21114084","display_name":"Alternative splicing","level":4,"score":0.5736662745475769},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5404804944992065},{"id":"https://openalex.org/C161078062","wikidata":"https://www.wikidata.org/wiki/Q1068690","display_name":"Functional genomics","level":5,"score":0.5161657929420471},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4603111743927002},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.42731714248657227},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.3534654974937439},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.2866380214691162}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"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},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1003314","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003314","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003314&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmid:24244129","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24244129","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:RePEc:plo:pcbi00:1003314","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003314","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"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":"article"},{"id":"pmh:oai:doaj.org/article:44d3897abd1d4400a87a1f45085e984e","is_oa":true,"landing_page_url":"https://doaj.org/article/44d3897abd1d4400a87a1f45085e984e","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":"PLoS Computational Biology, Vol 9, Iss 11, p e1003314 (2013)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2815063","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3820534","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:figshare.com:article/844487","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/_Systematically_Differentiating_Functions_for_Alternatively_Spliced_Isoforms_through_Integrating_RNA_seq_Data_/844487","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"","raw_type":"Dataset"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1003314","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003314","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003314&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4426994749","display_name":null,"funder_award_id":"1R21NS082212-01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1784654175.pdf","grobid_xml":"https://content.openalex.org/works/W1784654175.grobid-xml"},"referenced_works_count":85,"referenced_works":["https://openalex.org/W24402856","https://openalex.org/W205082804","https://openalex.org/W1492851286","https://openalex.org/W1527927437","https://openalex.org/W1544691147","https://openalex.org/W1819481941","https://openalex.org/W1963867239","https://openalex.org/W1965444063","https://openalex.org/W1968569455","https://openalex.org/W1981509058","https://openalex.org/W1986113553","https://openalex.org/W1989500357","https://openalex.org/W1995232179","https://openalex.org/W1999574084","https://openalex.org/W1999956761","https://openalex.org/W2001504871","https://openalex.org/W2003605043","https://openalex.org/W2011920499","https://openalex.org/W2012284471","https://openalex.org/W2030880783","https://openalex.org/W2031291897","https://openalex.org/W2033791476","https://openalex.org/W2037312364","https://openalex.org/W2038230536","https://openalex.org/W2042303135","https://openalex.org/W2043292259","https://openalex.org/W2050824831","https://openalex.org/W2052688256","https://openalex.org/W2066562817","https://openalex.org/W2068072987","https://openalex.org/W2071059511","https://openalex.org/W2075496125","https://openalex.org/W2086104179","https://openalex.org/W2092170757","https://openalex.org/W2095647330","https://openalex.org/W2096373458","https://openalex.org/W2096465161","https://openalex.org/W2097065948","https://openalex.org/W2098849734","https://openalex.org/W2100305481","https://openalex.org/W2100448568","https://openalex.org/W2101199302","https://openalex.org/W2102037268","https://openalex.org/W2102245393","https://openalex.org/W2103017472","https://openalex.org/W2104224685","https://openalex.org/W2106554405","https://openalex.org/W2106848050","https://openalex.org/W2109936378","https://openalex.org/W2110119381","https://openalex.org/W2112464428","https://openalex.org/W2116041602","https://openalex.org/W2118028844","https://openalex.org/W2118697091","https://openalex.org/W2121893605","https://openalex.org/W2124122363","https://openalex.org/W2124410428","https://openalex.org/W2130706354","https://openalex.org/W2131456688","https://openalex.org/W2132023322","https://openalex.org/W2133279561","https://openalex.org/W2135699773","https://openalex.org/W2141165889","https://openalex.org/W2141458291","https://openalex.org/W2147461734","https://openalex.org/W2152200681","https://openalex.org/W2152360905","https://openalex.org/W2154318594","https://openalex.org/W2154431984","https://openalex.org/W2156909104","https://openalex.org/W2158020463","https://openalex.org/W2161661150","https://openalex.org/W2162907639","https://openalex.org/W2166010828","https://openalex.org/W2166810745","https://openalex.org/W2167629040","https://openalex.org/W2169049403","https://openalex.org/W2170551349","https://openalex.org/W2171184528","https://openalex.org/W2171437346","https://openalex.org/W2292856761","https://openalex.org/W4233550359","https://openalex.org/W6600987510","https://openalex.org/W6604553253","https://openalex.org/W6683033130"],"related_works":["https://openalex.org/W2904939684","https://openalex.org/W2081598294","https://openalex.org/W2012312817","https://openalex.org/W2090969926","https://openalex.org/W4385462331","https://openalex.org/W2066028486","https://openalex.org/W2084464671","https://openalex.org/W2056672569","https://openalex.org/W2009697542","https://openalex.org/W2053656597"],"abstract_inverted_index":{"Integrating":[0],"large-scale":[1],"functional":[2,40,171],"genomic":[3,30,198],"data":[4,62,154],"has":[5,16],"significantly":[6],"accelerated":[7],"our":[8,78,106],"understanding":[9],"of":[10,24,84,96,129,195],"gene":[11,27,86,99,124,131],"functions.":[12],"However,":[13],"no":[14],"algorithm":[15,79,107],"been":[17],"developed":[18,54],"to":[19,67,113,123,143,185,203,222],"differentiate":[20,68,188],"functions":[21,69,112,189],"for":[22,70,173,190],"isoforms":[23,140,152],"the":[25,46,64,81,92,98,116,137,150,168,174,183,217],"same":[26],"using":[28,153,197],"high-throughput":[29],"data.":[31,199],"This":[32],"is":[33,108,182,201],"because":[34],"standard":[35],"supervised":[36],"learning":[37],"requires":[38],"'ground-truth'":[39],"annotations,":[41],"which":[42],"are":[43,141],"lacking":[44],"at":[45,63,91,97],"isoform":[47,93,170],"level.":[48,100],"To":[49],"address":[50],"this":[51],"challenge,":[52],"we":[53,103,165],"a":[55,75,85],"generic":[56,180],"framework":[57,181],"that":[58,105],"interrogates":[59],"public":[60],"RNA-seq":[61],"transcript":[65],"level":[66,94],"alternatively":[71,191,212],"spliced":[72,192,213],"isoforms.":[73],"For":[74],"specific":[76],"function,":[77],"identifies":[80],"'responsible'":[82,151],"isoform(s)":[83],"and":[87,121,127,147,162,177,187,208,215],"generates":[88],"classifying":[89],"models":[90],"instead":[95,194],"Through":[101],"cross-validation,":[102],"demonstrated":[104],"effective":[109],"in":[110,136],"assigning":[111],"genes,":[114,196],"especially":[115],"ones":[117],"with":[118,211],"multiple":[119],"isoforms,":[120,193,214],"robust":[122],"expression":[125],"levels":[126],"removal":[128],"homologous":[130],"pairs.":[132],"We":[133],"identified":[134],"genes":[135,175],"mouse":[138],"whose":[139],"predicted":[142,169],"have":[144],"disparate":[145],"functionalities":[146],"experimentally":[148],"validated":[149,167],"from":[155],"mammary":[156],"tissue.":[157],"With":[158],"protein":[159],"structure":[160],"modeling":[161],"experimental":[163],"evidence,":[164],"further":[166],"differences":[172],"Cdkn2a":[176],"Anxa6.":[178],"Our":[179],"first":[184],"predict":[186],"It":[200],"extendable":[202],"any":[204],"base":[205],"machine":[206],"learner":[207],"other":[209],"species":[210],"shifts":[216],"current":[218],"gene-centered":[219],"function":[220],"prediction":[221],"isoform-level":[223],"predictions.":[224]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":13},{"year":2020,"cited_by_count":13},{"year":2019,"cited_by_count":7},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":14},{"year":2014,"cited_by_count":9}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}