{"id":"https://openalex.org/W2119691317","doi":"https://doi.org/10.1142/s0219720015420019","title":"Estimation of isoform expression in RNA-seq data using a hierarchical Bayesian model","display_name":"Estimation of isoform expression in RNA-seq data using a hierarchical Bayesian model","publication_year":2015,"publication_date":"2015-08-12","ids":{"openalex":"https://openalex.org/W2119691317","doi":"https://doi.org/10.1142/s0219720015420019","mag":"2119691317","pmid":"https://pubmed.ncbi.nlm.nih.gov/26388142"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720015420019","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720015420019","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","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/A5008573424","display_name":"Zengmiao Wang","orcid":"https://orcid.org/0000-0001-6954-6069"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zengmiao Wang","raw_affiliation_strings":["Center for Quantitative Biology, Peking University, Beijing 100871, P. R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Quantitative Biology, Peking University, Beijing 100871, P. R. China","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100669834","display_name":"Jun Wang","orcid":"https://orcid.org/0000-0002-2742-3041"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jun Wang","raw_affiliation_strings":["Center for Quantitative Biology, Peking University, Beijing 100871, P. R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Quantitative Biology, Peking University, Beijing 100871, P. R. China","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020098960","display_name":"Changjing Wu","orcid":null},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Changjing Wu","raw_affiliation_strings":["School of Mathematical Sciences, Peking University, Beijing 100871, P. R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematical Sciences, Peking University, Beijing 100871, P. R. China","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101690048","display_name":"Minghua Deng","orcid":"https://orcid.org/0000-0002-2411-9650"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Minghua Deng","raw_affiliation_strings":["Center for Quantitative Biology, Peking University, Beijing 100871, P. R. China","Center for Statistical Science, Peking University, Beijing 100871, P. R. China","LMAM, School of Mathematical Sciences, Peking University, Beijing 100871, P. R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Quantitative Biology, Peking University, Beijing 100871, P. R. China","institution_ids":["https://openalex.org/I20231570"]},{"raw_affiliation_string":"Center for Statistical Science, Peking University, Beijing 100871, P. R. China","institution_ids":["https://openalex.org/I20231570"]},{"raw_affiliation_string":"LMAM, School of Mathematical Sciences, Peking University, Beijing 100871, P. R. China","institution_ids":["https://openalex.org/I20231570"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I20231570"],"apc_list":null,"apc_paid":null,"fwci":0.3496,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.61562146,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"13","issue":"06","first_page":"1542001","last_page":"1542001"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9987000226974487,"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"}},"topics":[{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9987000226974487,"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"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9983999729156494,"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":0.9973000288009644,"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/expression","display_name":"Expression (computer science)","score":0.6803358793258667},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.6101645231246948},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.586648166179657},{"id":"https://openalex.org/keywords/gene-isoform","display_name":"Gene isoform","score":0.5706741213798523},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5554166436195374},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.5426232814788818},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4837372601032257},{"id":"https://openalex.org/keywords/focus","display_name":"Focus (optics)","score":0.45237410068511963},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3908270597457886},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.3741982579231262},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.35902127623558044},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2990858256816864},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.28989696502685547},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.2860157787799835},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.19434809684753418}],"concepts":[{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.6803358793258667},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.6101645231246948},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.586648166179657},{"id":"https://openalex.org/C53345823","wikidata":"https://www.wikidata.org/wiki/Q5531554","display_name":"Gene isoform","level":3,"score":0.5706741213798523},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5554166436195374},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.5426232814788818},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4837372601032257},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.45237410068511963},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3908270597457886},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.3741982579231262},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.35902127623558044},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2990858256816864},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.28989696502685547},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.2860157787799835},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19434809684753418},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"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":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000502","qualifier_name":"physiology","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":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011565","descriptor_name":"Psoriasis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011565","descriptor_name":"Psoriasis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011565","descriptor_name":"Psoriasis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","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":"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":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1142/s0219720015420019","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720015420019","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:26388142","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26388142","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":"Journal of bioinformatics and computational biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.6499999761581421,"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320324787","display_name":"Peking University","ror":"https://ror.org/02v51f717"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":35,"referenced_works":["https://openalex.org/W68436435","https://openalex.org/W1966799302","https://openalex.org/W1981509058","https://openalex.org/W2004419591","https://openalex.org/W2010637767","https://openalex.org/W2011920499","https://openalex.org/W2012036024","https://openalex.org/W2017728350","https://openalex.org/W2023621259","https://openalex.org/W2039525134","https://openalex.org/W2053057991","https://openalex.org/W2063530272","https://openalex.org/W2088669732","https://openalex.org/W2094492214","https://openalex.org/W2094792719","https://openalex.org/W2097065948","https://openalex.org/W2097860373","https://openalex.org/W2100448568","https://openalex.org/W2102619694","https://openalex.org/W2107432039","https://openalex.org/W2108871359","https://openalex.org/W2114104545","https://openalex.org/W2116868464","https://openalex.org/W2124482810","https://openalex.org/W2130494035","https://openalex.org/W2138773756","https://openalex.org/W2144141220","https://openalex.org/W2148499186","https://openalex.org/W2148931855","https://openalex.org/W2154431984","https://openalex.org/W2156631105","https://openalex.org/W2157780603","https://openalex.org/W2316306194","https://openalex.org/W4241482563","https://openalex.org/W4247420482"],"related_works":["https://openalex.org/W1540936366","https://openalex.org/W2079625624","https://openalex.org/W2004254765","https://openalex.org/W2126407448","https://openalex.org/W2125691904","https://openalex.org/W200174347","https://openalex.org/W2048132363","https://openalex.org/W2953122964","https://openalex.org/W1971262350","https://openalex.org/W3002447856"],"abstract_inverted_index":{"Estimation":[0],"of":[1,48,55,61,68,90,150],"gene":[2,95,122],"or":[3],"isoform":[4,86,113,124,145],"expression":[5,18,35,51,96,114,125,146],"is":[6,154],"a":[7,79,98,116,129,137],"fundamental":[8],"step":[9],"in":[10,71,128],"many":[11],"transcriptome":[12],"analysis":[13],"tasks,":[14],"such":[15],"as":[16,97],"differential":[17],"analysis,":[19],"eQTL":[20],"(or":[21],"sQTL)":[22],"studies,":[23],"and":[24,44,65,106,123,132,164],"biological":[25],"network":[26],"construction.":[27],"RNA-seq":[28,72,167],"technology":[29],"enables":[30],"us":[31,135],"to":[32,84],"monitor":[33],"the":[34,46,53,66,91,151],"on":[36],"genome-wide":[37],"scale":[38],"at":[39,52,176],"single":[40],"base":[41],"pair":[42],"resolution":[43],"offers":[45],"possibility":[47],"accurately":[49],"measuring":[50],"level":[54],"isoform.":[56],"However,":[57],"challenges":[58],"remain":[59],"because":[60],"non-uniform":[62],"read":[63],"sampling":[64],"presence":[67],"various":[69],"biases":[70],"data.":[73],"In":[74,119],"this":[75,120],"paper,":[76],"we":[77,100],"present":[78],"novel":[80],"hierarchical":[81],"Bayesian":[82],"method":[83,153],"estimate":[85],"expression.":[87],"While":[88],"most":[89],"existing":[92],"methods":[93],"treat":[94],"by-product,":[99],"incorporate":[101],"it":[102,133],"into":[103],"our":[104],"model":[105],"explicitly":[107],"describe":[108],"its":[109],"relationship":[110],"with":[111,160],"corresponding":[112],"using":[115,156],"Multinomial":[117],"distribution.":[118],"way,":[121],"are":[126,174],"included":[127],"unified":[130],"framework":[131],"helps":[134],"achieve":[136],"better":[138],"performance":[139],"over":[140],"other":[141],"state-of-the-art":[142],"algorithms":[143],"for":[144],"estimation.":[147],"The":[148,172],"effectiveness":[149],"proposed":[152],"demonstrated":[155],"both":[157],"simulated":[158],"data":[159],"known":[161],"ground":[162],"truth":[163],"two":[165],"real":[166],"datasets":[168],"from":[169],"MAQC":[170],"project.":[171],"codes":[173],"available":[175],"http://www.math.pku.edu.cn/teachers/dengmh/GIExp/.":[177]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
