{"id":"https://openalex.org/W2950830085","doi":"https://doi.org/10.1093/bioinformatics/btz453","title":"DECENT: differential expression with capture efficiency adjustmeNT for single-cell RNA-seq data","display_name":"DECENT: differential expression with capture efficiency adjustmeNT for single-cell RNA-seq data","publication_year":2019,"publication_date":"2019-06-06","ids":{"openalex":"https://openalex.org/W2950830085","doi":"https://doi.org/10.1093/bioinformatics/btz453","mag":"2950830085","pmid":"https://pubmed.ncbi.nlm.nih.gov/31197307"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz453","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz453","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/24/5155/31797930/btz453.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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://academic.oup.com/bioinformatics/article-pdf/35/24/5155/31797930/btz453.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5001464530","display_name":"Chengzhong Ye","orcid":"https://orcid.org/0000-0002-5710-1078"},"institutions":[{"id":"https://openalex.org/I196021976","display_name":"Walter and Eliza Hall Institute of Medical Research","ror":"https://ror.org/01b6kha49","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I196021976"]},{"id":"https://openalex.org/I165779595","display_name":"University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["AU","CN"],"is_corresponding":false,"raw_author_name":"Chengzhong Ye","raw_affiliation_strings":["Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research , Parkville, VIC, Australia","Department of Medical Biology, The University of Melbourne , Parkville, VIC, Australia","School of Medicine, Tsinghua University, Haidian District , Beijing, China"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research , Parkville, VIC, Australia","institution_ids":["https://openalex.org/I196021976"]},{"raw_affiliation_string":"Department of Medical Biology, The University of Melbourne , Parkville, VIC, Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"School of Medicine, Tsinghua University, Haidian District , Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001135422","display_name":"Terence P. Speed","orcid":"https://orcid.org/0000-0002-5403-7998"},"institutions":[{"id":"https://openalex.org/I196021976","display_name":"Walter and Eliza Hall Institute of Medical Research","ror":"https://ror.org/01b6kha49","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I196021976"]},{"id":"https://openalex.org/I165779595","display_name":"University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Terence P Speed","raw_affiliation_strings":["Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research , Parkville, VIC, Australia","Department of Mathematics and Statistics, The University of Melbourne , Parkville, VIC, Australia"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research , Parkville, VIC, Australia","institution_ids":["https://openalex.org/I196021976"]},{"raw_affiliation_string":"Department of Mathematics and Statistics, The University of Melbourne , Parkville, VIC, Australia","institution_ids":["https://openalex.org/I165779595"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006817516","display_name":"Agus Salim","orcid":"https://orcid.org/0000-0003-3999-7701"},"institutions":[{"id":"https://openalex.org/I142471025","display_name":"Baker Heart and Diabetes Institute","ror":"https://ror.org/03rke0285","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I142471025"]},{"id":"https://openalex.org/I196829312","display_name":"La Trobe University","ror":"https://ror.org/01rxfrp27","country_code":"AU","type":"education","lineage":["https://openalex.org/I196829312"]},{"id":"https://openalex.org/I196021976","display_name":"Walter and Eliza Hall Institute of Medical Research","ror":"https://ror.org/01b6kha49","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I196021976"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Agus Salim","raw_affiliation_strings":["Baker Heart and Diabetes Institute , Melbourne, VIC, Australia","Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research , Parkville, VIC, Australia","Department of Mathematics and Statistics, La Trobe University , Bundoora, VIC, Australia"],"affiliations":[{"raw_affiliation_string":"Baker Heart and Diabetes Institute , Melbourne, VIC, Australia","institution_ids":["https://openalex.org/I142471025"]},{"raw_affiliation_string":"Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research , Parkville, VIC, Australia","institution_ids":["https://openalex.org/I196021976"]},{"raw_affiliation_string":"Department of Mathematics and Statistics, La Trobe University , Bundoora, VIC, Australia","institution_ids":["https://openalex.org/I196829312"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5006817516"],"corresponding_institution_ids":["https://openalex.org/I142471025","https://openalex.org/I196021976","https://openalex.org/I196829312"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.7406,"has_fulltext":true,"cited_by_count":61,"citation_normalized_percentile":{"value":0.91236079,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"35","issue":"24","first_page":"5155","last_page":"5162"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9998999834060669,"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":0.9998999834060669,"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/T10773","display_name":"Extracellular vesicles in disease","score":0.9864000082015991,"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/T10031","display_name":"T-cell and B-cell Immunology","score":0.9021999835968018,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/dropout","display_name":"Dropout (neural networks)","score":0.765655517578125},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7036200761795044},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.6409223079681396},{"id":"https://openalex.org/keywords/sensitivity","display_name":"Sensitivity (control systems)","score":0.6007614731788635},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.4917810261249542},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4873962998390198},{"id":"https://openalex.org/keywords/differential","display_name":"Differential (mechanical device)","score":0.478512167930603},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.4669343829154968},{"id":"https://openalex.org/keywords/spike","display_name":"Spike (software development)","score":0.437588095664978},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3319936990737915},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.08563092350959778}],"concepts":[{"id":"https://openalex.org/C2776145597","wikidata":"https://www.wikidata.org/wiki/Q25339462","display_name":"Dropout (neural networks)","level":2,"score":0.765655517578125},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7036200761795044},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.6409223079681396},{"id":"https://openalex.org/C21200559","wikidata":"https://www.wikidata.org/wiki/Q7451068","display_name":"Sensitivity (control systems)","level":2,"score":0.6007614731788635},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.4917810261249542},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4873962998390198},{"id":"https://openalex.org/C93226319","wikidata":"https://www.wikidata.org/wiki/Q193137","display_name":"Differential (mechanical device)","level":2,"score":0.478512167930603},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.4669343829154968},{"id":"https://openalex.org/C2781390188","wikidata":"https://www.wikidata.org/wiki/Q25203449","display_name":"Spike (software development)","level":2,"score":0.437588095664978},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3319936990737915},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.08563092350959778},{"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/C24326235","wikidata":"https://www.wikidata.org/wiki/Q126095","display_name":"Electronic engineering","level":1,"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/C146978453","wikidata":"https://www.wikidata.org/wiki/Q3798668","display_name":"Aerospace engineering","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"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/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","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}],"mesh":[{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","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":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":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":"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},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btz453","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz453","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/24/5155/31797930/btz453.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31197307","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31197307","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:jupiter.its.unimelb.edu.au:11343/247479","is_oa":true,"landing_page_url":"http://hdl.handle.net/11343/247479","pdf_url":"http://hdl.handle.net/11343/247479","source":{"id":"https://openalex.org/S4377196259","display_name":"Minerva Access (University of Melbourne)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I165779595","host_organization_name":"The University of Melbourne","host_organization_lineage":["https://openalex.org/I165779595"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"},{"id":"pmh:oai:europepmc.org:5915407","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6954660","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btz453","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz453","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/24/5155/31797930/btz453.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","score":0.4399999976158142,"id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320334705","display_name":"National Health and Medical Research Council","ror":"https://ror.org/011kf5r70"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2950830085.pdf","grobid_xml":"https://content.openalex.org/works/W2950830085.grobid-xml"},"referenced_works_count":46,"referenced_works":["https://openalex.org/W1580018887","https://openalex.org/W1967327758","https://openalex.org/W1979283544","https://openalex.org/W1981641790","https://openalex.org/W1984883254","https://openalex.org/W2009458183","https://openalex.org/W2025828346","https://openalex.org/W2084942072","https://openalex.org/W2102212449","https://openalex.org/W2107018762","https://openalex.org/W2112562104","https://openalex.org/W2121690903","https://openalex.org/W2130116522","https://openalex.org/W2135937351","https://openalex.org/W2139838862","https://openalex.org/W2145416275","https://openalex.org/W2179438025","https://openalex.org/W2190545194","https://openalex.org/W2343956310","https://openalex.org/W2555892463","https://openalex.org/W2591733518","https://openalex.org/W2598326928","https://openalex.org/W2605611918","https://openalex.org/W2608558240","https://openalex.org/W2747877289","https://openalex.org/W2757764553","https://openalex.org/W2760824708","https://openalex.org/W2771918070","https://openalex.org/W2779910850","https://openalex.org/W2783644856","https://openalex.org/W2788908087","https://openalex.org/W2801949492","https://openalex.org/W2805619986","https://openalex.org/W2805888371","https://openalex.org/W2809205318","https://openalex.org/W2949086748","https://openalex.org/W2950541340","https://openalex.org/W2951217100","https://openalex.org/W2951506174","https://openalex.org/W2951638683","https://openalex.org/W2951890476","https://openalex.org/W2952027905","https://openalex.org/W2952383043","https://openalex.org/W2952595146","https://openalex.org/W4256266823","https://openalex.org/W6746499259"],"related_works":["https://openalex.org/W4206721050","https://openalex.org/W2765947158","https://openalex.org/W2012842278","https://openalex.org/W4313036973","https://openalex.org/W2889453578","https://openalex.org/W4200201589","https://openalex.org/W4210643267","https://openalex.org/W4200297168","https://openalex.org/W2347219288","https://openalex.org/W2898932805"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":12},{"year":2023,"cited_by_count":12},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":11},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":2}],"updated_date":"2026-03-10T16:38:18.471706","created_date":"2025-10-10T00:00:00"}