{"id":"https://openalex.org/W2152559563","doi":"https://doi.org/10.1093/bioinformatics/btt381","title":"TIGAR: transcript isoform abundance estimation method with gapped alignment of RNA-Seq data by variational Bayesian inference","display_name":"TIGAR: transcript isoform abundance estimation method with gapped alignment of RNA-Seq data by variational Bayesian inference","publication_year":2013,"publication_date":"2013-07-02","ids":{"openalex":"https://openalex.org/W2152559563","doi":"https://doi.org/10.1093/bioinformatics/btt381","mag":"2152559563","pmid":"https://pubmed.ncbi.nlm.nih.gov/23821651"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt381","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt381","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5082629535","display_name":"Naoki Nariai","orcid":null},"institutions":[{"id":"https://openalex.org/I10091056","display_name":"Kanazawa University","ror":"https://ror.org/02hwp6a56","country_code":"JP","type":"education","lineage":["https://openalex.org/I10091056"]},{"id":"https://openalex.org/I201537933","display_name":"Tohoku University","ror":"https://ror.org/01dq60k83","country_code":"JP","type":"education","lineage":["https://openalex.org/I201537933"]},{"id":"https://openalex.org/I4210136366","display_name":"Tohoku Medical Megabank Organization","ror":"https://ror.org/03zzyap02","country_code":"JP","type":"healthcare","lineage":["https://openalex.org/I4210136366"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Naoki Nariai","raw_affiliation_strings":["1 Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan and 2Faculty of Electrical and Computer Engineering, Institute of Science and Engineering, Kanazawa University, Kakuma, Kanazawa, Ishikawa, 920-1192, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan and 2Faculty of Electrical and Computer Engineering, Institute of Science and Engineering, Kanazawa University, Kakuma, Kanazawa, Ishikawa, 920-1192, Japan","institution_ids":["https://openalex.org/I4210136366","https://openalex.org/I201537933","https://openalex.org/I10091056"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072391173","display_name":"Osamu Hirose","orcid":"https://orcid.org/0000-0002-8077-8589"},"institutions":[{"id":"https://openalex.org/I10091056","display_name":"Kanazawa University","ror":"https://ror.org/02hwp6a56","country_code":"JP","type":"education","lineage":["https://openalex.org/I10091056"]},{"id":"https://openalex.org/I201537933","display_name":"Tohoku University","ror":"https://ror.org/01dq60k83","country_code":"JP","type":"education","lineage":["https://openalex.org/I201537933"]},{"id":"https://openalex.org/I4210136366","display_name":"Tohoku Medical Megabank Organization","ror":"https://ror.org/03zzyap02","country_code":"JP","type":"healthcare","lineage":["https://openalex.org/I4210136366"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Osamu Hirose","raw_affiliation_strings":["1 Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan and 2Faculty of Electrical and Computer Engineering, Institute of Science and Engineering, Kanazawa University, Kakuma, Kanazawa, Ishikawa, 920-1192, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan and 2Faculty of Electrical and Computer Engineering, Institute of Science and Engineering, Kanazawa University, Kakuma, Kanazawa, Ishikawa, 920-1192, Japan","institution_ids":["https://openalex.org/I4210136366","https://openalex.org/I201537933","https://openalex.org/I10091056"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101893270","display_name":"Kaname Kojima","orcid":"https://orcid.org/0000-0001-5713-2483"},"institutions":[{"id":"https://openalex.org/I10091056","display_name":"Kanazawa University","ror":"https://ror.org/02hwp6a56","country_code":"JP","type":"education","lineage":["https://openalex.org/I10091056"]},{"id":"https://openalex.org/I201537933","display_name":"Tohoku University","ror":"https://ror.org/01dq60k83","country_code":"JP","type":"education","lineage":["https://openalex.org/I201537933"]},{"id":"https://openalex.org/I4210136366","display_name":"Tohoku Medical Megabank Organization","ror":"https://ror.org/03zzyap02","country_code":"JP","type":"healthcare","lineage":["https://openalex.org/I4210136366"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kaname Kojima","raw_affiliation_strings":["1 Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan and 2Faculty of Electrical and Computer Engineering, Institute of Science and Engineering, Kanazawa University, Kakuma, Kanazawa, Ishikawa, 920-1192, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan and 2Faculty of Electrical and Computer Engineering, Institute of Science and Engineering, Kanazawa University, Kakuma, Kanazawa, Ishikawa, 920-1192, Japan","institution_ids":["https://openalex.org/I4210136366","https://openalex.org/I201537933","https://openalex.org/I10091056"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025220924","display_name":"Masao Nagasaki","orcid":"https://orcid.org/0000-0002-4292-8785"},"institutions":[{"id":"https://openalex.org/I10091056","display_name":"Kanazawa University","ror":"https://ror.org/02hwp6a56","country_code":"JP","type":"education","lineage":["https://openalex.org/I10091056"]},{"id":"https://openalex.org/I201537933","display_name":"Tohoku University","ror":"https://ror.org/01dq60k83","country_code":"JP","type":"education","lineage":["https://openalex.org/I201537933"]},{"id":"https://openalex.org/I4210136366","display_name":"Tohoku Medical Megabank Organization","ror":"https://ror.org/03zzyap02","country_code":"JP","type":"healthcare","lineage":["https://openalex.org/I4210136366"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Masao Nagasaki","raw_affiliation_strings":["1 Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan and 2Faculty of Electrical and Computer Engineering, Institute of Science and Engineering, Kanazawa University, Kakuma, Kanazawa, Ishikawa, 920-1192, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan and 2Faculty of Electrical and Computer Engineering, Institute of Science and Engineering, Kanazawa University, Kakuma, Kanazawa, Ishikawa, 920-1192, Japan","institution_ids":["https://openalex.org/I4210136366","https://openalex.org/I201537933","https://openalex.org/I10091056"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5082629535"],"corresponding_institution_ids":["https://openalex.org/I10091056","https://openalex.org/I201537933","https://openalex.org/I4210136366"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.8884,"has_fulltext":false,"cited_by_count":42,"citation_normalized_percentile":{"value":0.94364886,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"29","issue":"18","first_page":"2292","last_page":"2299"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.4101000130176544,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.4101000130176544,"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":0.25209999084472656,"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":0.09399999678134918,"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/rna-seq","display_name":"RNA-Seq","score":0.6327716112136841},{"id":"https://openalex.org/keywords/gene-isoform","display_name":"Gene isoform","score":0.6050989627838135},{"id":"https://openalex.org/keywords/alternative-splicing","display_name":"Alternative splicing","score":0.5448442101478577},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5341343879699707},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5012631416320801},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.48984047770500183},{"id":"https://openalex.org/keywords/focus","display_name":"Focus (optics)","score":0.46060875058174133},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.4601150155067444},{"id":"https://openalex.org/keywords/rna-splicing","display_name":"RNA splicing","score":0.44175249338150024},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.43130603432655334},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.41684046387672424},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.401145875453949},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.37144163250923157},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.23102495074272156},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.22293666005134583},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.20335116982460022},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.18523338437080383},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.07742366194725037}],"concepts":[{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.6327716112136841},{"id":"https://openalex.org/C53345823","wikidata":"https://www.wikidata.org/wiki/Q5531554","display_name":"Gene isoform","level":3,"score":0.6050989627838135},{"id":"https://openalex.org/C194583182","wikidata":"https://www.wikidata.org/wiki/Q21114084","display_name":"Alternative splicing","level":4,"score":0.5448442101478577},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5341343879699707},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5012631416320801},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.48984047770500183},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.46060875058174133},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.4601150155067444},{"id":"https://openalex.org/C54458228","wikidata":"https://www.wikidata.org/wiki/Q237218","display_name":"RNA splicing","level":4,"score":0.44175249338150024},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.43130603432655334},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.41684046387672424},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.401145875453949},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.37144163250923157},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.23102495074272156},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.22293666005134583},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20335116982460022},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.18523338437080383},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.07742366194725037},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.0}],"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":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","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":false},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":null,"qualifier_name":null,"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":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059368","descriptor_name":"RNA Isoforms","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D059368","descriptor_name":"RNA Isoforms","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D059368","descriptor_name":"RNA Isoforms","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"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":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D059368","descriptor_name":"RNA Isoforms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btt381","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt381","pdf_url":null,"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:23821651","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23821651","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}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W1516111018","https://openalex.org/W1570770495","https://openalex.org/W1592076897","https://openalex.org/W1601795611","https://openalex.org/W1618600317","https://openalex.org/W1663973292","https://openalex.org/W1981509058","https://openalex.org/W1984268382","https://openalex.org/W1999574084","https://openalex.org/W2008906462","https://openalex.org/W2070564797","https://openalex.org/W2093253451","https://openalex.org/W2097065948","https://openalex.org/W2100305481","https://openalex.org/W2100448568","https://openalex.org/W2107564978","https://openalex.org/W2107903949","https://openalex.org/W2117608012","https://openalex.org/W2124097252","https://openalex.org/W2124715997","https://openalex.org/W2124985265","https://openalex.org/W2129495613","https://openalex.org/W2141458291","https://openalex.org/W2154431984","https://openalex.org/W2155804510","https://openalex.org/W2159730169","https://openalex.org/W2168175751","https://openalex.org/W4236354166","https://openalex.org/W6633833189","https://openalex.org/W6636504819"],"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":{"MOTIVATION:":[0],"Many":[1],"human":[2,166],"genes":[3],"express":[4],"multiple":[5],"transcript":[6,36,52,71,105,136],"isoforms":[7,53,106],"through":[8,111],"alternative":[9],"splicing,":[10],"which":[11],"greatly":[12],"increases":[13],"diversity":[14],"of":[15,30,35,83,104,146,152,165,184,190],"protein":[16],"function.":[17],"Although":[18],"RNA":[19],"sequencing":[20],"(RNA-Seq)":[21],"technologies":[22],"have":[23],"been":[24],"widely":[25],"used":[26],"in":[27,134],"measuring":[28],"amounts":[29],"transcribed":[31],"mRNA,":[32],"accurate":[33],"estimation":[34],"isoform":[37,72,137],"abundances":[38,73],"from":[39,74],"RNA-Seq":[40,75,163],"data":[41,164,202],"is":[42,118,193],"challenging":[43],"because":[44],"reads":[45,84],"often":[46],"map":[47],"to":[48,60,69,162],"more":[49,177],"than":[50,150,182],"one":[51],"or":[54,93],"paralogs":[55],"whose":[56],"sequences":[57,87],"are":[58,203],"similar":[59],"each":[61],"other.":[62],"RESULTS:":[63],"We":[64,157],"propose":[65],"a":[66,121],"statistical":[67],"method":[68,78,100,128,161,192],"estimate":[70],"data.":[76],"Our":[77],"can":[79],"handle":[80],"gapped":[81],"alignments":[82],"against":[85],"reference":[86],"so":[88],"that":[89,151,172],"it":[90],"allows":[91],"insertion":[92],"deletion":[94],"errors":[95],"within":[96],"reads.":[97],"The":[98],"proposed":[99],"optimizes":[101],"the":[102,130,141,153],"number":[103],"by":[107],"variational":[108],"Bayesian":[109],"inference":[110],"an":[112],"iterative":[113],"procedure,":[114],"and":[115,139,170],"its":[116,144],"convergence":[117,147],"guaranteed":[119],"under":[120],"stopping":[122],"criterion.":[123],"On":[124],"simulated":[125],"datasets,":[126],"our":[127,160,173,191],"outperformed":[129],"comparable":[131],"quantification":[132],"methods":[133],"inferring":[135],"abundances,":[138],"at":[140,195,205],"same":[142],"time":[143],"rate":[145],"was":[148,176],"faster":[149],"expectation":[154],"maximization":[155],"algorithm.":[156],"also":[158],"applied":[159],"cell":[167],"line":[168],"samples,":[169],"showed":[171],"prediction":[174],"result":[175],"consistent":[178],"among":[179],"technical":[180],"replicates":[181],"those":[183],"other":[185],"methods.":[186],"AVAILABILITY:":[187],"An":[188],"implementation":[189],"available":[194,204],"http://github.com/nariai/tigar":[196],"CONTACT:":[197],"nariai@megabank.tohoku.ac.jp":[198],"SUPPLEMENTARY":[199],"INFORMATION:":[200],"Supplementary":[201],"Bioinformatics":[206],"online.":[207]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":9},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":8},{"year":2013,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}