{"id":"https://openalex.org/W2157780603","doi":"https://doi.org/10.1093/bioinformatics/btu757","title":"WemIQ: an accurate and robust isoform quantification method for RNA-seq data","display_name":"WemIQ: an accurate and robust isoform quantification method for RNA-seq data","publication_year":2014,"publication_date":"2014-11-19","ids":{"openalex":"https://openalex.org/W2157780603","doi":"https://doi.org/10.1093/bioinformatics/btu757","mag":"2157780603","pmid":"https://pubmed.ncbi.nlm.nih.gov/25406327"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btu757","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu757","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/6/878/49011093/bioinformatics_31_6_878.pdf","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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/31/6/878/49011093/bioinformatics_31_6_878.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5073219155","display_name":"Jing Zhang","orcid":"https://orcid.org/0000-0002-0171-0683"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jing Zhang","raw_affiliation_strings":["1 Ming Hsieh Department of Electrical Engineering, University of Southern California, Los Angeles, CA 90089, USA and 2Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA"],"affiliations":[{"raw_affiliation_string":"1 Ming Hsieh Department of Electrical Engineering, University of Southern California, Los Angeles, CA 90089, USA and 2Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA","institution_ids":["https://openalex.org/I1174212"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001082656","display_name":"C.\u2010C. Jay Kuo","orcid":"https://orcid.org/0000-0001-9474-5035"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"C.-C. Jay Kuo","raw_affiliation_strings":["1 Ming Hsieh Department of Electrical Engineering, University of Southern California, Los Angeles, CA 90089, USA and 2Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA"],"affiliations":[{"raw_affiliation_string":"1 Ming Hsieh Department of Electrical Engineering, University of Southern California, Los Angeles, CA 90089, USA and 2Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA","institution_ids":["https://openalex.org/I1174212"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100334551","display_name":"Liang Chen","orcid":"https://orcid.org/0000-0001-6374-112X"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Liang Chen","raw_affiliation_strings":["1 Ming Hsieh Department of Electrical Engineering, University of Southern California, Los Angeles, CA 90089, USA and 2Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA"],"affiliations":[{"raw_affiliation_string":"1 Ming Hsieh Department of Electrical Engineering, University of Southern California, Los Angeles, CA 90089, USA and 2Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA","institution_ids":["https://openalex.org/I1174212"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5073219155"],"corresponding_institution_ids":["https://openalex.org/I1174212"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.5686,"has_fulltext":true,"cited_by_count":26,"citation_normalized_percentile":{"value":0.83117157,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"31","issue":"6","first_page":"878","last_page":"885"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9986000061035156,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9986000061035156,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.998199999332428,"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":0.9954000115394592,"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":0.6451500058174133},{"id":"https://openalex.org/keywords/gene-isoform","display_name":"Gene isoform","score":0.5696618556976318},{"id":"https://openalex.org/keywords/deconvolution","display_name":"Deconvolution","score":0.5686242580413818},{"id":"https://openalex.org/keywords/undersampling","display_name":"Undersampling","score":0.5280885100364685},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4993093013763428},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4961172044277191},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.4599449038505554},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.395550012588501},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2798759937286377},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.25561630725860596},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.23954975605010986},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.2052806317806244},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.18831464648246765},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13625985383987427}],"concepts":[{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.6451500058174133},{"id":"https://openalex.org/C53345823","wikidata":"https://www.wikidata.org/wiki/Q5531554","display_name":"Gene isoform","level":3,"score":0.5696618556976318},{"id":"https://openalex.org/C174576160","wikidata":"https://www.wikidata.org/wiki/Q1183700","display_name":"Deconvolution","level":2,"score":0.5686242580413818},{"id":"https://openalex.org/C136536468","wikidata":"https://www.wikidata.org/wiki/Q1225894","display_name":"Undersampling","level":2,"score":0.5280885100364685},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4993093013763428},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4961172044277191},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.4599449038505554},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.395550012588501},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2798759937286377},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.25561630725860596},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.23954975605010986},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.2052806317806244},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.18831464648246765},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13625985383987427},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005091","descriptor_name":"Exons","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005091","descriptor_name":"Exons","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005091","descriptor_name":"Exons","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":null,"qualifier_name":null,"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}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btu757","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu757","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/6/878/49011093/bioinformatics_31_6_878.pdf","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:25406327","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25406327","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:escholarship.org:ark:/13030/qt5r97r2vp","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/5r97r2vp","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, vol 31, iss 6","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:4380033","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4380033","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":"doi:10.1093/bioinformatics/btu757","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu757","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/6/878/49011093/bioinformatics_31_6_878.pdf","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"},"sustainable_development_goals":[{"score":0.4099999964237213,"display_name":"Reduced inequalities","id":"https://metadata.un.org/sdg/10"}],"awards":[{"id":"https://openalex.org/G3611247453","display_name":null,"funder_award_id":"R01GM","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4723392868","display_name":null,"funder_award_id":"R01GM097230","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":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2157780603.pdf","grobid_xml":"https://content.openalex.org/works/W2157780603.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W1975714281","https://openalex.org/W1981509058","https://openalex.org/W1984708728","https://openalex.org/W1999574084","https://openalex.org/W2004419591","https://openalex.org/W2006330642","https://openalex.org/W2010637767","https://openalex.org/W2011920499","https://openalex.org/W2013340095","https://openalex.org/W2023621259","https://openalex.org/W2031874858","https://openalex.org/W2053057991","https://openalex.org/W2063530272","https://openalex.org/W2089465951","https://openalex.org/W2094492214","https://openalex.org/W2097065948","https://openalex.org/W2098849734","https://openalex.org/W2102813686","https://openalex.org/W2105776281","https://openalex.org/W2105875994","https://openalex.org/W2107420975","https://openalex.org/W2110768394","https://openalex.org/W2117688129","https://openalex.org/W2122789575","https://openalex.org/W2124985265","https://openalex.org/W2129916363","https://openalex.org/W2138443081","https://openalex.org/W2138773756","https://openalex.org/W2141458291","https://openalex.org/W2144141220","https://openalex.org/W2147087089","https://openalex.org/W2154431984","https://openalex.org/W2154537630","https://openalex.org/W2797829469"],"related_works":["https://openalex.org/W2109073422","https://openalex.org/W2887783772","https://openalex.org/W2101754595","https://openalex.org/W4249381695","https://openalex.org/W2534887053","https://openalex.org/W2026172757","https://openalex.org/W2080076470","https://openalex.org/W4389292014","https://openalex.org/W2394059563","https://openalex.org/W2017942469"],"abstract_inverted_index":{"We":[0],"present":[1],"a":[2,18,44],"weighted-log-likelihood":[3],"expectation":[4,20],"maximization":[5,21],"method":[6],"on":[7,51],"isoform":[8,63],"quantification":[9,61],"(WemIQ).":[10],"WemIQ":[11,57,100],"integrates":[12],"an":[13],"effective":[14],"bias":[15,53,107],"removal":[16],"with":[17],"weighted":[19],"(EM)":[22],"algorithm":[23],"to":[24,105],"distribute":[25],"reads":[26,39],"among":[27],"isoforms":[28],"efficiently.":[29],"The":[30],"weight":[31],"represents":[32],"the":[33,52,60,70,89,95,103],"oversampling":[34],"or":[35],"undersampling":[36],"of":[37,62,92],"sequence":[38],"and":[40,55,64,83,113],"is":[41,86],"estimated":[42],"through":[43],"generalized":[45],"Poisson":[46],"model":[47],"without":[48],"any":[49],"presumption":[50],"sources":[54],"formats.":[56],"significantly":[58],"improves":[59],"gene":[65],"expression":[66,78,117],"as":[67,69],"well":[68],"derived":[71],"exon":[72],"inclusion":[73],"rates.":[74],"It":[75],"provides":[76,102],"robust":[77],"estimates":[79],"across":[80],"different":[81],"laboratories":[82],"protocols,":[84],"which":[85],"valuable":[87],"for":[88],"integrative":[90],"analysis":[91],"RNA-seq.":[93],"For":[94],"recent":[96],"single-cell":[97],"RNA-seq":[98],"data,":[99],"also":[101],"opportunity":[104],"distinguish":[106],"heterogeneity":[108,112],"from":[109],"true":[110],"biological":[111],"uncovers":[114],"smaller":[115],"cell-to-cell":[116],"variability.":[118]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":7},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":4}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}