{"id":"https://openalex.org/W2406985637","doi":"https://doi.org/10.1109/tcbb.2015.2480068","title":"Proteomic Evidence for In-Frame and Out-of-Frame Alternatively Spliced Isoforms in Human and Mouse","display_name":"Proteomic Evidence for In-Frame and Out-of-Frame Alternatively Spliced Isoforms in Human and Mouse","publication_year":2015,"publication_date":"2015-09-18","ids":{"openalex":"https://openalex.org/W2406985637","doi":"https://doi.org/10.1109/tcbb.2015.2480068","mag":"2406985637","pmid":"https://pubmed.ncbi.nlm.nih.gov/26394435"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2015.2480068","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2015.2480068","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5034779707","display_name":"Rodrigo Fernandes Ramalho","orcid":"https://orcid.org/0000-0002-5844-6422"},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rodrigo F. Ramalho","raw_affiliation_strings":["Department of Biology, Indiana University, Bloomington, IN"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Indiana University, Bloomington, IN","institution_ids":["https://openalex.org/I4210119109"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041639230","display_name":"Sujun Li","orcid":"https://orcid.org/0000-0001-5233-2005"},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sujun Li","raw_affiliation_strings":["Department of Computer Science and Informatics, Indiana University, Bloomington, IN"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Informatics, Indiana University, Bloomington, IN","institution_ids":["https://openalex.org/I4210119109"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051324698","display_name":"Predrag Radivojac","orcid":"https://orcid.org/0000-0002-6769-0793"},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Predrag Radivojac","raw_affiliation_strings":["Department of Computer Science and Informatics, Indiana University, Bloomington, IN"],"raw_orcid":"https://orcid.org/0000-0002-6769-0793","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Informatics, Indiana University, Bloomington, IN","institution_ids":["https://openalex.org/I4210119109"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5038671526","display_name":"Matthew W. Hahn","orcid":"https://orcid.org/0000-0002-5731-8808"},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matthew W. Hahn","raw_affiliation_strings":["Department of Computer Science and Informatics, Indiana University, Bloomington, IN"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Informatics, Indiana University, Bloomington, IN","institution_ids":["https://openalex.org/I4210119109"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I4210119109"],"apc_list":null,"apc_paid":null,"fwci":0.2956,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.63077429,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"15","issue":"4","first_page":"1284","last_page":"1289"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"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":0.9998000264167786,"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":0.9994000196456909,"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/exon","display_name":"Exon","score":0.9031887054443359},{"id":"https://openalex.org/keywords/open-reading-frame","display_name":"Open reading frame","score":0.7392220497131348},{"id":"https://openalex.org/keywords/alternative-splicing","display_name":"Alternative splicing","score":0.6858811974525452},{"id":"https://openalex.org/keywords/translation","display_name":"Translation (biology)","score":0.6624506711959839},{"id":"https://openalex.org/keywords/frame","display_name":"Frame (networking)","score":0.6176176071166992},{"id":"https://openalex.org/keywords/reading-frame","display_name":"Reading frame","score":0.6015960574150085},{"id":"https://openalex.org/keywords/rna-splicing","display_name":"RNA splicing","score":0.5634007453918457},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5540032386779785},{"id":"https://openalex.org/keywords/gene-isoform","display_name":"Gene isoform","score":0.5324180126190186},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5300043821334839},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4443071782588959},{"id":"https://openalex.org/keywords/messenger-rna","display_name":"Messenger RNA","score":0.4361993670463562},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.41090887784957886},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.35975003242492676},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.14294129610061646},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.09845951199531555}],"concepts":[{"id":"https://openalex.org/C36823959","wikidata":"https://www.wikidata.org/wiki/Q373027","display_name":"Exon","level":3,"score":0.9031887054443359},{"id":"https://openalex.org/C47289529","wikidata":"https://www.wikidata.org/wiki/Q908550","display_name":"Open reading frame","level":4,"score":0.7392220497131348},{"id":"https://openalex.org/C194583182","wikidata":"https://www.wikidata.org/wiki/Q21114084","display_name":"Alternative splicing","level":4,"score":0.6858811974525452},{"id":"https://openalex.org/C149364088","wikidata":"https://www.wikidata.org/wiki/Q185917","display_name":"Translation (biology)","level":4,"score":0.6624506711959839},{"id":"https://openalex.org/C126042441","wikidata":"https://www.wikidata.org/wiki/Q1324888","display_name":"Frame (networking)","level":2,"score":0.6176176071166992},{"id":"https://openalex.org/C166253671","wikidata":"https://www.wikidata.org/wiki/Q923372","display_name":"Reading frame","level":5,"score":0.6015960574150085},{"id":"https://openalex.org/C54458228","wikidata":"https://www.wikidata.org/wiki/Q237218","display_name":"RNA splicing","level":4,"score":0.5634007453918457},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5540032386779785},{"id":"https://openalex.org/C53345823","wikidata":"https://www.wikidata.org/wiki/Q5531554","display_name":"Gene isoform","level":3,"score":0.5324180126190186},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5300043821334839},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4443071782588959},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.4361993670463562},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.41090887784957886},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.35975003242492676},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.14294129610061646},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.09845951199531555},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0}],"mesh":[{"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":"D005091","descriptor_name":"Exons","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":false},{"descriptor_ui":"D005091","descriptor_name":"Exons","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":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016364","descriptor_name":"Reading Frames","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016364","descriptor_name":"Reading Frames","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016364","descriptor_name":"Reading Frames","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","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":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","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":2,"locations":[{"id":"doi:10.1109/tcbb.2015.2480068","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2015.2480068","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26394435","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26394435","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education","score":0.8500000238418579}],"awards":[{"id":"https://openalex.org/G1759869059","display_name":null,"funder_award_id":"R01 GM103725","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2839081034","display_name":null,"funder_award_id":"R01 GM103725-04","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306151","display_name":"Alfred P. Sloan Foundation","ror":"https://ror.org/052csg198"},{"id":"https://openalex.org/F4320321091","display_name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior","ror":"https://ror.org/00x0ma614"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":34,"referenced_works":["https://openalex.org/W1418224","https://openalex.org/W1967205151","https://openalex.org/W1971846931","https://openalex.org/W1980599684","https://openalex.org/W1990994379","https://openalex.org/W1991703748","https://openalex.org/W2006368030","https://openalex.org/W2006943116","https://openalex.org/W2012827002","https://openalex.org/W2026771976","https://openalex.org/W2037139598","https://openalex.org/W2046872827","https://openalex.org/W2064036807","https://openalex.org/W2081410039","https://openalex.org/W2092756750","https://openalex.org/W2096057003","https://openalex.org/W2099030066","https://openalex.org/W2108141237","https://openalex.org/W2110871180","https://openalex.org/W2112226798","https://openalex.org/W2113381588","https://openalex.org/W2118416745","https://openalex.org/W2132352688","https://openalex.org/W2145070407","https://openalex.org/W2147075791","https://openalex.org/W2147640998","https://openalex.org/W2147652847","https://openalex.org/W2151100808","https://openalex.org/W2151462466","https://openalex.org/W2155804510","https://openalex.org/W2156052197","https://openalex.org/W2157115023","https://openalex.org/W2158463967","https://openalex.org/W2161811833"],"related_works":["https://openalex.org/W2904939684","https://openalex.org/W2321791250","https://openalex.org/W4213427798","https://openalex.org/W2081598294","https://openalex.org/W2012312817","https://openalex.org/W2056672569","https://openalex.org/W2090969926","https://openalex.org/W4385462331","https://openalex.org/W2564462691","https://openalex.org/W2023199111"],"abstract_inverted_index":{"In":[0],"order":[1],"to":[2,34,127],"find":[3],"evidence":[4],"for":[5],"translation":[6,122],"of":[7,37,51,71,80,88,103],"alternatively":[8],"spliced":[9],"transcripts,":[10],"especially":[11],"those":[12],"that":[13,117],"result":[14],"in":[15,18,76],"a":[16,31],"change":[17],"reading":[19,84],"frame,":[20],"we":[21,67],"collected":[22],"exon-skipping":[23,73],"cases":[24],"previously":[25],"found":[26,75],"by":[27],"RNA-Seq":[28],"and":[29,46,64,97,108,120],"applied":[30],"computational":[32],"approach":[33],"screen":[35],"millions":[36],"mass":[38],"spectra.":[39],"These":[40],"spectra":[41],"came":[42],"from":[43],"seven":[44],"human":[45],"six":[47],"mouse":[48],"tissues,":[49],"five":[50],"which":[52],"are":[53],"the":[54,57,101],"same":[55],"between":[56,95],"two":[58],"organisms:":[59],"liver,":[60],"kidney,":[61],"lung,":[62],"heart,":[63],"brain.":[65],"Overall,":[66],"detected":[68,91],"4":[69],"percent":[70],"all":[72],"events":[74],"RNA-seq":[77],"data,":[78],"regardless":[79],"their":[81],"effect":[82],"on":[83],"frame.":[85],"The":[86],"fraction":[87,102],"alternative":[89,105],"isoforms":[90],"did":[92],"not":[93],"differ":[94],"out-of-frame":[96,121],"in-frame":[98,119],"events.":[99],"Moreover,":[100],"identified":[104],"exon-exon":[106],"junctions":[107,110],"constitutive":[109],"were":[111],"similar.":[112],"Together,":[113],"our":[114],"results":[115],"suggest":[116],"both":[118],"may":[123],"be":[124],"actively":[125],"used":[126],"regulate":[128],"protein":[129],"activity":[130],"or":[131],"localization.":[132]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
