{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,22]],"date-time":"2026-01-22T19:41:12Z","timestamp":1769110872876,"version":"3.49.0"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2021,12,2]],"date-time":"2021-12-02T00:00:00Z","timestamp":1638403200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Swedish Research Council (VR) and the Swedish Foundation for Strategic Research"},{"name":"Swedish National Infrastructure for Computing"},{"DOI":"10.13039\/501100004359","name":"Swedish Research Council","doi-asserted-by":"publisher","award":["2018-05973"],"award-info":[{"award-number":["2018-05973"]}],"id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,2,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>RNA expression at isoform level is biologically more informative than at gene level and can potentially reveal cellular subsets and corresponding biomarkers that are not visible at gene level. However, due to the strong 3\u02b9 bias sequencing protocol, mRNA quantification for high-throughput single-cell RNA sequencing such as Chromium Single Cell 3\u02b9 10\u00d7 Genomics is currently performed at the gene level.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We have developed an isoform-level quantification method for high-throughput single-cell RNA sequencing by exploiting the concepts of transcription clusters and isoform paralogs. The method, called Scasa, compares well in simulations against competing approaches including Alevin, Cellranger, Kallisto, Salmon, Terminus and STARsolo at both isoform- and gene-level expression. The reanalysis of a CITE-Seq dataset with isoform-based Scasa reveals a subgroup of CD14 monocytes missed by gene-based methods.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Implementation of Scasa including source code, documentation, tutorials and test data supporting this study is available at Github: https:\/\/github.com\/eudoraleer\/scasa and Zenodo: https:\/\/doi.org\/10.5281\/zenodo.5712503.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab807","type":"journal-article","created":{"date-parts":[[2021,11,25]],"date-time":"2021-11-25T20:17:58Z","timestamp":1637871478000},"page":"1287-1294","source":"Crossref","is-referenced-by-count":20,"title":["Isoform-level quantification for single-cell RNA sequencing"],"prefix":"10.1093","volume":"38","author":[{"given":"Lu","family":"Pan","sequence":"first","affiliation":[{"name":"Department of Medical Epidemiology and Biostatistics, Karolinska Institutet , 17177 Stockholm, Sweden"}]},{"given":"Huy Q","family":"Dinh","sequence":"additional","affiliation":[{"name":"McArdle Laboratory for Cancer Research, Department of Oncology, School of Medicine and Public Health, University of Wisconsin\u2014Madison , Madison, WI 53705-227, USA"},{"name":"Department of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin\u2014Madison , Madison, WI 53726, USA"}]},{"given":"Yudi","family":"Pawitan","sequence":"additional","affiliation":[{"name":"Department of Medical Epidemiology and Biostatistics, Karolinska Institutet , 17177 Stockholm, Sweden"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7945-5750","authenticated-orcid":false,"given":"Trung Nghia","family":"Vu","sequence":"additional","affiliation":[{"name":"Department of Medical Epidemiology and Biostatistics, Karolinska Institutet , 17177 Stockholm, Sweden"}]}],"member":"286","published-online":{"date-parts":[[2021,12,2]]},"reference":[{"key":"2023020108541658800_btab807-B1","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1038\/nbt.3519","article-title":"Near-optimal probabilistic RNA-seq quantification","volume":"34","author":"Bray","year":"2016","journal-title":"Nat. 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