{"id":"https://openalex.org/W2100448568","doi":"https://doi.org/10.1093/bioinformatics/btp113","title":"Statistical inferences for isoform expression in RNA-Seq","display_name":"Statistical inferences for isoform expression in RNA-Seq","publication_year":2009,"publication_date":"2009-02-25","ids":{"openalex":"https://openalex.org/W2100448568","doi":"https://doi.org/10.1093/bioinformatics/btp113","mag":"2100448568","pmid":"https://pubmed.ncbi.nlm.nih.gov/19244387"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp113","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp113","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":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2666817","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100779276","display_name":"Hui Jiang","orcid":"https://orcid.org/0000-0003-2718-9811"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Hui Jiang","raw_affiliation_strings":["1 Institute for Computational and Mathematical Engineering and 2Department of Statistics, Stanford University, Stanford, CA 94305, USA"],"affiliations":[{"raw_affiliation_string":"1 Institute for Computational and Mathematical Engineering and 2Department of Statistics, Stanford University, Stanford, CA 94305, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015401462","display_name":"Wing Hung Wong","orcid":"https://orcid.org/0000-0001-7466-2339"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wing Hung Wong","raw_affiliation_strings":["1 Institute for Computational and Mathematical Engineering and 2Department of Statistics, Stanford University, Stanford, CA 94305, USA"],"affiliations":[{"raw_affiliation_string":"1 Institute for Computational and Mathematical Engineering and 2Department of Statistics, Stanford University, Stanford, CA 94305, USA","institution_ids":["https://openalex.org/I97018004"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5100779276"],"corresponding_institution_ids":["https://openalex.org/I97018004"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":21.433,"has_fulltext":false,"cited_by_count":482,"citation_normalized_percentile":{"value":0.99711729,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"25","issue":"8","first_page":"1026","last_page":"1032"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.9994999766349792,"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":0.9994999766349792,"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":0.9980999827384949,"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9980000257492065,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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":0.6051534414291382},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5543496012687683},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5488489270210266},{"id":"https://openalex.org/keywords/gene-isoform","display_name":"Gene isoform","score":0.5325307846069336},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5249360203742981},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.5217926502227783},{"id":"https://openalex.org/keywords/statistical-inference","display_name":"Statistical inference","score":0.4135902523994446},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32775259017944336},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3193087577819824},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.22104918956756592},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.20368850231170654},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.190432608127594},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.18503329157829285},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.17870000004768372},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1612759828567505},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.148758202791214}],"concepts":[{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.6051534414291382},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5543496012687683},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5488489270210266},{"id":"https://openalex.org/C53345823","wikidata":"https://www.wikidata.org/wiki/Q5531554","display_name":"Gene isoform","level":3,"score":0.5325307846069336},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5249360203742981},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.5217926502227783},{"id":"https://openalex.org/C134261354","wikidata":"https://www.wikidata.org/wiki/Q938438","display_name":"Statistical inference","level":2,"score":0.4135902523994446},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32775259017944336},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3193087577819824},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.22104918956756592},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.20368850231170654},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.190432608127594},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.18503329157829285},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.17870000004768372},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1612759828567505},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.148758202791214},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"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":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btp113","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp113","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:19244387","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19244387","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.892.9857","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.892.9857","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/early/2009/02/25/bioinformatics.btp113.full.pdf","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:2666817","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2666817","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:2666817","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2666817","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},"sustainable_development_goals":[{"score":0.4699999988079071,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320306171","display_name":"California Institute for Regenerative Medicine","ror":"https://ror.org/033m8b439"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":18,"referenced_works":["https://openalex.org/W1460189015","https://openalex.org/W1967656072","https://openalex.org/W1984708728","https://openalex.org/W1986113553","https://openalex.org/W2011920499","https://openalex.org/W2047765648","https://openalex.org/W2067151470","https://openalex.org/W2069739265","https://openalex.org/W2089657469","https://openalex.org/W2097117811","https://openalex.org/W2097862362","https://openalex.org/W2105776281","https://openalex.org/W2118129991","https://openalex.org/W2121211805","https://openalex.org/W2154431984","https://openalex.org/W2155804510","https://openalex.org/W2168783124","https://openalex.org/W2740984310"],"related_works":["https://openalex.org/W1540936366","https://openalex.org/W2381031055","https://openalex.org/W2366070815","https://openalex.org/W3000984192","https://openalex.org/W137830373","https://openalex.org/W4286952477","https://openalex.org/W2134368299","https://openalex.org/W4321348134","https://openalex.org/W2103073163","https://openalex.org/W3017020030"],"abstract_inverted_index":{"The":[0,56,77],"development":[1],"of":[2,29,58,79],"RNA":[3],"sequencing":[4],"(RNA-Seq)":[5],"makes":[6],"it":[7],"possible":[8,116],"for":[9],"us":[10],"to":[11,48],"measure":[12],"transcription":[13],"at":[14],"an":[15],"unprecedented":[16],"precision":[17],"and":[18,27,36,91],"throughput.":[19],"However,":[20],"challenges":[21],"remain":[22],"in":[23,113],"understanding":[24],"the":[25,30,33,51,65,95,100],"source":[26],"distribution":[28,102],"reads,":[31],"modeling":[32],"transcript":[34],"abundance":[35],"developing":[37],"efficient":[38],"computational":[39],"methods.":[40,121],"In":[41],"this":[42],"article,":[43],"we":[44],"develop":[45],"a":[46,62,74,87],"method":[47],"deal":[49],"with":[50,68],"isoform":[52,82,110],"expression":[53,78,111],"estimation":[54],"problem.":[55],"count":[57],"reads":[59],"falling":[60],"into":[61],"locus":[63],"on":[64],"genome":[66],"annotated":[67],"multiple":[69],"isoforms":[70],"is":[71,83,115],"modeled":[72],"as":[73],"Poisson":[75],"variable.":[76],"each":[80],"individual":[81],"estimated":[84],"by":[85,103,117],"solving":[86],"convex":[88],"optimization":[89],"problem":[90],"statistical":[92,120],"inferences":[93],"about":[94],"parameters":[96],"are":[97],"obtained":[98],"from":[99],"posterior":[101],"importance":[104],"sampling.":[105],"Our":[106],"results":[107],"show":[108],"that":[109],"inference":[112],"RNA-Seq":[114],"employing":[118],"appropriate":[119]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":15},{"year":2021,"cited_by_count":17},{"year":2020,"cited_by_count":25},{"year":2019,"cited_by_count":20},{"year":2018,"cited_by_count":26},{"year":2017,"cited_by_count":20},{"year":2016,"cited_by_count":37},{"year":2015,"cited_by_count":43},{"year":2014,"cited_by_count":52},{"year":2013,"cited_by_count":48},{"year":2012,"cited_by_count":59}],"updated_date":"2026-04-15T08:11:43.952461","created_date":"2025-10-10T00:00:00"}
