{"id":"https://openalex.org/W2968459863","doi":"https://doi.org/10.1093/bioinformatics/btz640","title":"Alternating EM algorithm for a bilinear model in isoform quantification from RNA-seq data","display_name":"Alternating EM algorithm for a bilinear model in isoform quantification from RNA-seq data","publication_year":2019,"publication_date":"2019-08-09","ids":{"openalex":"https://openalex.org/W2968459863","doi":"https://doi.org/10.1093/bioinformatics/btz640","mag":"2968459863","pmid":"https://pubmed.ncbi.nlm.nih.gov/31400221"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz640","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz640","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"hybrid","oa_url":"https://doi.org/10.1093/bioinformatics/btz640","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5071209116","display_name":"Wenjiang Deng","orcid":"https://orcid.org/0000-0003-1834-3354"},"institutions":[{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Wenjiang Deng","raw_affiliation_strings":["Department of Medical Epidemiology and Biostatistics , Karolinska Institutet, Stockholm 17177, Sweden"],"affiliations":[{"raw_affiliation_string":"Department of Medical Epidemiology and Biostatistics , Karolinska Institutet, Stockholm 17177, Sweden","institution_ids":["https://openalex.org/I28166907"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017433903","display_name":"Tian Mou","orcid":"https://orcid.org/0000-0001-7707-8760"},"institutions":[{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Tian Mou","raw_affiliation_strings":["Department of Medical Epidemiology and Biostatistics , Karolinska Institutet, Stockholm 17177, Sweden"],"affiliations":[{"raw_affiliation_string":"Department of Medical Epidemiology and Biostatistics , Karolinska Institutet, Stockholm 17177, Sweden","institution_ids":["https://openalex.org/I28166907"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085014608","display_name":"Krishna R. Kalari","orcid":"https://orcid.org/0000-0001-8944-8378"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Krishna R Kalari","raw_affiliation_strings":["Department of Health Sciences Research , MN 55905, USA"],"affiliations":[{"raw_affiliation_string":"Department of Health Sciences Research , MN 55905, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109335158","display_name":"Nifang Niu","orcid":null},"institutions":[{"id":"https://openalex.org/I2802423016","display_name":"WinnMed","ror":"https://ror.org/02s47w807","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2802423016"]},{"id":"https://openalex.org/I1330342723","display_name":"Mayo Clinic","ror":"https://ror.org/02qp3tb03","country_code":"US","type":"funder","lineage":["https://openalex.org/I1330342723"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nifang Niu","raw_affiliation_strings":["Department of Molecular Pharmacology and Experimental Therapeutics , Mayo Clinic, Rochester, MN 55905, USA"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Pharmacology and Experimental Therapeutics , Mayo Clinic, Rochester, MN 55905, USA","institution_ids":["https://openalex.org/I1330342723","https://openalex.org/I2802423016"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069578729","display_name":"Liewei Wang","orcid":"https://orcid.org/0000-0003-3818-8531"},"institutions":[{"id":"https://openalex.org/I1330342723","display_name":"Mayo Clinic","ror":"https://ror.org/02qp3tb03","country_code":"US","type":"funder","lineage":["https://openalex.org/I1330342723"]},{"id":"https://openalex.org/I2802423016","display_name":"WinnMed","ror":"https://ror.org/02s47w807","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2802423016"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Liewei Wang","raw_affiliation_strings":["Department of Molecular Pharmacology and Experimental Therapeutics , Mayo Clinic, Rochester, MN 55905, USA"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Pharmacology and Experimental Therapeutics , Mayo Clinic, Rochester, MN 55905, USA","institution_ids":["https://openalex.org/I1330342723","https://openalex.org/I2802423016"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012606625","display_name":"Yudi Pawitan","orcid":"https://orcid.org/0000-0003-0324-7052"},"institutions":[{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]}],"countries":["SE"],"is_corresponding":true,"raw_author_name":"Yudi Pawitan","raw_affiliation_strings":["Department of Medical Epidemiology and Biostatistics , Karolinska Institutet, Stockholm 17177, Sweden"],"affiliations":[{"raw_affiliation_string":"Department of Medical Epidemiology and Biostatistics , Karolinska Institutet, Stockholm 17177, Sweden","institution_ids":["https://openalex.org/I28166907"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046377219","display_name":"Trung Nghia Vu","orcid":"https://orcid.org/0000-0001-7945-5750"},"institutions":[{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]}],"countries":["SE"],"is_corresponding":true,"raw_author_name":"Trung Nghia Vu","raw_affiliation_strings":["Department of Medical Epidemiology and Biostatistics , Karolinska Institutet, Stockholm 17177, Sweden"],"affiliations":[{"raw_affiliation_string":"Department of Medical Epidemiology and Biostatistics , Karolinska Institutet, Stockholm 17177, Sweden","institution_ids":["https://openalex.org/I28166907"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5012606625","https://openalex.org/A5046377219"],"corresponding_institution_ids":["https://openalex.org/I28166907"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.5346,"has_fulltext":false,"cited_by_count":15,"citation_normalized_percentile":{"value":0.59562905,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"36","issue":"3","first_page":"805","last_page":"812"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9972000122070312,"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":0.9972000122070312,"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":0.9937999844551086,"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":0.9919999837875366,"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/computer-science","display_name":"Computer science","score":0.6841065883636475},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.6123279929161072},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.59839928150177},{"id":"https://openalex.org/keywords/bilinear-interpolation","display_name":"Bilinear interpolation","score":0.5259217023849487},{"id":"https://openalex.org/keywords/expectation\u2013maximization-algorithm","display_name":"Expectation\u2013maximization algorithm","score":0.5027251243591309},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.45638540387153625},{"id":"https://openalex.org/keywords/focus","display_name":"Focus (optics)","score":0.45183879137039185},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.4242151379585266},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.38478323817253113},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.19942796230316162},{"id":"https://openalex.org/keywords/maximum-likelihood","display_name":"Maximum likelihood","score":0.18826261162757874},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.12798869609832764}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6841065883636475},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.6123279929161072},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.59839928150177},{"id":"https://openalex.org/C205203396","wikidata":"https://www.wikidata.org/wiki/Q612143","display_name":"Bilinear interpolation","level":2,"score":0.5259217023849487},{"id":"https://openalex.org/C182081679","wikidata":"https://www.wikidata.org/wiki/Q1275153","display_name":"Expectation\u2013maximization algorithm","level":3,"score":0.5027251243591309},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.45638540387153625},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.45183879137039185},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.4242151379585266},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.38478323817253113},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.19942796230316162},{"id":"https://openalex.org/C49781872","wikidata":"https://www.wikidata.org/wiki/Q1045555","display_name":"Maximum likelihood","level":2,"score":0.18826261162757874},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.12798869609832764},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.0},{"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/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","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":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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"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":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btz640","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz640","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31400221","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31400221","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:pubmedcentral.nih.gov:9883676","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9883676","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btz640","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz640","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320322725","display_name":"China Scholarship Council","ror":"https://ror.org/04atp4p48"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W1988674564","https://openalex.org/W1998349282","https://openalex.org/W2008049885","https://openalex.org/W2015207840","https://openalex.org/W2018838463","https://openalex.org/W2032920995","https://openalex.org/W2055666215","https://openalex.org/W2064397275","https://openalex.org/W2065128082","https://openalex.org/W2097065948","https://openalex.org/W2100305481","https://openalex.org/W2100448568","https://openalex.org/W2102278945","https://openalex.org/W2107420975","https://openalex.org/W2112876600","https://openalex.org/W2138773756","https://openalex.org/W2141458291","https://openalex.org/W2152559563","https://openalex.org/W2154431984","https://openalex.org/W2158485828","https://openalex.org/W2169456326","https://openalex.org/W2171501288","https://openalex.org/W2323326409","https://openalex.org/W2339613031","https://openalex.org/W2592811885","https://openalex.org/W2743624002","https://openalex.org/W2952944477"],"related_works":["https://openalex.org/W2165589608","https://openalex.org/W3093557575","https://openalex.org/W3182767856","https://openalex.org/W2354231916","https://openalex.org/W2162140574","https://openalex.org/W2354073393","https://openalex.org/W2361009070","https://openalex.org/W2378988399","https://openalex.org/W1983356840","https://openalex.org/W4250600009"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
