{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,19]],"date-time":"2026-06-19T19:10:37Z","timestamp":1781896237275,"version":"3.54.5"},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2017,2,27]],"date-time":"2017-02-27T00:00:00Z","timestamp":1488153600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Pomona College","award":["52007555"],"award-info":[{"award-number":["52007555"]}]},{"DOI":"10.13039\/100006793","name":"Harvey Mudd College","doi-asserted-by":"publisher","award":["52007544"],"award-info":[{"award-number":["52007544"]}],"id":[{"id":"10.13039\/100006793","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000011","name":"Howard Hughes Medical Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000011","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,9,28]]},"DOI":"10.1093\/bib\/bbx008","type":"journal-article","created":{"date-parts":[[2017,1,30]],"date-time":"2017-01-30T13:24:04Z","timestamp":1485782644000},"page":"776-792","source":"Crossref","is-referenced-by-count":312,"title":["Selecting between-sample RNA-Seq normalization methods from the perspective of their assumptions"],"prefix":"10.1093","volume":"19","author":[{"given":"Ciaran","family":"Evans","sequence":"first","affiliation":[{"name":"Department of Statistics, Baker Hall, Carnegie Mellon University, Pittsburgh, PA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Johanna","family":"Hardin","sequence":"additional","affiliation":[{"name":"Pomona College"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel M","family":"Stoebel","sequence":"additional","affiliation":[{"name":"Harvey Mudd College"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2017,2,27]]},"reference":[{"issue":"7","key":"key\n\t\t\t\t20180928112234_bbx008-B1","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1038\/nmeth0708-585","article-title":"The beginning of the end for microarrays?","volume":"5","author":"Shendure","year":"2008","journal-title":"Nat Methods"},{"issue":"12","key":"key\n\t\t\t\t20180928112234_bbx008-B2","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1186\/gb-2010-11-12-220","article-title":"From RNA-seq reads to differential expression results","volume":"11","author":"Oshlack","year":"2010","journal-title":"Genome Biol"},{"issue":"1","key":"key\n\t\t\t\t20180928112234_bbx008-B3","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nrg2484","article-title":"RNA-Seq: a revolutionary tool for transcriptomics","volume":"10","author":"Wang","year":"2009","journal-title":"Nat Rev Genet"},{"issue":"1","key":"key\n\t\t\t\t20180928112234_bbx008-B4","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1093\/bfgp\/elr041","article-title":"Differential expression - the next generation and beyond","volume":"11","author":"Auer","year":"2012","journal-title":"Brief Funct Genomics"},{"issue":"1","key":"key\n\t\t\t\t20180928112234_bbx008-B5","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1745-6150-4-14","article-title":"Transcript length bias in RNA-seq data confounds systems biology","volume":"4","author":"Oshlack","year":"2009","journal-title":"Biol Direct"},{"issue":"1","key":"key\n\t\t\t\t20180928112234_bbx008-B6","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2105-12-480","article-title":"GC-content normalization for RNA-Seq data","volume":"12","author":"Risso","year":"2011","journal-title":"BMC Bioinformatics"},{"issue":"3","key":"key\n\t\t\t\t20180928112234_bbx008-B7","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2010-11-3-r25","article-title":"A scaling normalization method for differential expression analysis of RNA-seq data","volume":"11","author":"Robinson","year":"2010","journal-title":"Genome Biol"},{"issue":"1","key":"key\n\t\t\t\t20180928112234_bbx008-B8","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2164-12-293","article-title":"RNA-seq: technical variability and sampling","volume":"12","author":"McIntyre","year":"2011","journal-title":"BMC Genomics"},{"issue":"6","key":"key\n\t\t\t\t20180928112234_bbx008-B9","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1093\/bib\/bbs046","article-title":"A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis","volume":"14","author":"Dillies","year":"2013","journal-title":"Brief Bioinform"},{"issue":"1","key":"key\n\t\t\t\t20180928112234_bbx008-B10","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2105-11-94","article-title":"Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments","volume":"11","author":"Bullard","year":"2010","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"key\n\t\t\t\t20180928112234_bbx008-B11","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1748-7188-7-5","article-title":"A normalization strategy for comparing tag count data","volume":"7","author":"Kadota","year":"2012","journal-title":"Algorithms Mol Biol"},{"issue":"1","key":"key\n\t\t\t\t20180928112234_bbx008-B12","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12859-015-0778-7","article-title":"Comparing the normalization methods for the differential analysis of Illumina high-throughput RNA-Seq data","volume":"16","author":"Li","year":"2015","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"key\n\t\t\t\t20180928112234_bbx008-B13","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12864-015-2353-z","article-title":"Comparison of normalization and differential expression analyses using RNA-Seq data from 726 individual Drosophila melanogaster","volume":"17","author":"Lin","year":"2016","journal-title":"BMC Genomics"},{"issue":"6","key":"key\n\t\t\t\t20180928112234_bbx008-B14","doi-asserted-by":"crossref","first-page":"e25849","DOI":"10.4161\/cib.25849","article-title":"Comparison of normalization methods for differential gene expression analysis in RNA-Seq experiments: a matter of relative size of studied transcriptomes","volume":"6","author":"Maza","year":"2013","journal-title":"Commun Integr Biol"},{"issue":"9","key":"key\n\t\t\t\t20180928112234_bbx008-B15","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/gb-2013-14-9-r95","article-title":"Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data","volume":"14","author":"Rapaport","year":"2013","journal-title":"Genome Biol"},{"key":"key\n\t\t\t\t20180928112234_bbx008-B16","doi-asserted-by":"crossref","first-page":"621690","DOI":"10.1155\/2015\/621690","article-title":"The impact of normalization methods on RNA-seq data analysis","volume":"2015","author":"Zyprych-Walczak","year":"2015","journal-title":"BioMed Res Int"},{"key":"key\n\t\t\t\t20180928112234_bbx008-B17","author":"Athanasiadou","year":"2016"},{"issue":"4","key":"key\n\t\t\t\t20180928112234_bbx008-B18","doi-asserted-by":"crossref","first-page":"396","DOI":"10.1101\/gad.233221.113","article-title":"Nucleosome loss leads to global transcriptional up-regulation and genomic instability during yeast aging","volume":"28","author":"Hu","year":"2014","journal-title":"Genes Dev"},{"issue":"1","key":"key\n\t\t\t\t20180928112234_bbx008-B19","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1016\/j.cell.2012.08.026","article-title":"Transcriptional amplification in tumor cells with elevated c-Myc","volume":"151","author":"Lin","year":"2012","journal-title":"Cell"},{"issue":"1","key":"key\n\t\t\t\t20180928112234_bbx008-B20","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1016\/j.cell.2012.08.033","article-title":"c-Myc is a universal amplifier of expressed genes in lymphocytes and embryonic stem cells","volume":"151","author":"Nie","year":"2012","journal-title":"Cell"},{"issue":"5","key":"key\n\t\t\t\t20180928112234_bbx008-B21","doi-asserted-by":"crossref","first-page":"662","DOI":"10.1128\/MCB.00970-14","article-title":"The overlooked fact: fundamental need for spike-in controls for virtually all genome-wide analyses","volume":"36","author":"Chen","year":"2015","journal-title":"Mol Cell Biol"},{"issue":"3","key":"key\n\t\t\t\t20180928112234_bbx008-B22","doi-asserted-by":"crossref","first-page":"476","DOI":"10.1016\/j.cell.2012.10.012","article-title":"Revisiting global gene expression analysis","volume":"151","author":"Lov\u00e9n","year":"2012","journal-title":"Cell"},{"issue":"1","key":"key\n\t\t\t\t20180928112234_bbx008-B23","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1007\/s00412-014-0496-3","article-title":"Variation in transcriptome size: are we getting the message?","volume":"124","author":"Coate","year":"2015","journal-title":"Chromosoma"},{"issue":"10","key":"key\n\t\t\t\t20180928112234_bbx008-B24","doi-asserted-by":"crossref","first-page":"R106","DOI":"10.1186\/gb-2010-11-10-r106","article-title":"Differential expression analysis for sequence count data","volume":"11","author":"Anders","year":"2010","journal-title":"Genome Biol"},{"key":"key\n\t\t\t\t20180928112234_bbx008-B25","author":"Pachter","year":"2011"},{"issue":"7","key":"key\n\t\t\t\t20180928112234_bbx008-B26","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1038\/nmeth.1226","article-title":"Mapping and quantifying mammalian transcriptomes by RNA-Seq","volume":"5","author":"Mortazavi","year":"2008","journal-title":"Nat Methods"},{"issue":"5","key":"key\n\t\t\t\t20180928112234_bbx008-B27","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1038\/nbt.1621","article-title":"Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isofrom switching during cell differentiation","volume":"28","author":"Trapnell","year":"2010","journal-title":"Nat Biotechnol"},{"issue":"2","key":"key\n\t\t\t\t20180928112234_bbx008-B28","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1093\/bioinformatics\/19.2.185","article-title":"A comparison of normalization methods for high density oligonucleotide array data based on variance and bias","volume":"19","author":"Bolstad","year":"2003","journal-title":"Bioinformatics"},{"issue":"1","key":"key\n\t\t\t\t20180928112234_bbx008-B29","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: a Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2010","journal-title":"Bioinformatics"},{"issue":"3","key":"key\n\t\t\t\t20180928112234_bbx008-B30","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1093\/biostatistics\/kxr031","article-title":"Normalization, testing, and false discovery rate estimation for RNA-sequencing data","volume":"13","author":"Li","year":"2012","journal-title":"Biostatistics"},{"issue":"10","key":"key\n\t\t\t\t20180928112234_bbx008-B31","first-page":"569","article-title":"Human housekeeping genes, revisted","volume":"29","author":"Eisenberg","year":"2013","journal-title":"Hum Genet"},{"issue":"9","key":"key\n\t\t\t\t20180928112234_bbx008-B32","doi-asserted-by":"crossref","first-page":"1543","DOI":"10.1101\/gr.121095.111","article-title":"Synthetic spike-in standards for RNA-seq experiments","volume":"21","author":"Jiang","year":"2011","journal-title":"Genome Res"},{"issue":"9","key":"key\n\t\t\t\t20180928112234_bbx008-B33","doi-asserted-by":"crossref","first-page":"896","DOI":"10.1038\/nbt.2931","article-title":"Normalization of RNA-seq data using factor analysis of control genes or samples","volume":"32","author":"Risso","year":"2014","journal-title":"Nat Biotechnol"},{"issue":"2","key":"key\n\t\t\t\t20180928112234_bbx008-B34","doi-asserted-by":"crossref","first-page":"R29","DOI":"10.1186\/gb-2014-15-2-r29","article-title":"voom: precision weights unlock linear model analysis tools for RNA-seq read counts","volume":"15","author":"Law","year":"2014","journal-title":"Genome Biol"},{"issue":"12","key":"key\n\t\t\t\t20180928112234_bbx008-B35","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol"},{"issue":"1","key":"key\n\t\t\t\t20180928112234_bbx008-B36","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J R Stat Soc Series B Stat Methodol"},{"key":"key\n\t\t\t\t20180928112234_bbx008-B37","doi-asserted-by":"crossref","first-page":"903","DOI":"10.1038\/nbt.2957","article-title":"A comprehensive assessment of RNA-Seq accuracy, reproducibility and information content by the sequencing quality control consortium","volume":"32","author":"Su","year":"2014","journal-title":"Nat Biotechnol"},{"issue":"20","key":"key\n\t\t\t\t20180928112234_bbx008-B38","doi-asserted-by":"crossref","first-page":"2584","DOI":"10.1093\/bioinformatics\/bts497","article-title":"Systematic comparison of RNA-Seq normalization methods using measurement error models","volume":"28","author":"Sun","year":"2012","journal-title":"Bioinformatics"},{"issue":"2","key":"key\n\t\t\t\t20180928112234_bbx008-B39","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1101\/gr.217802","article-title":"Control genes and variability: absence of ubiquitous reference transcripts in diverse mammalian expression studies","volume":"12","author":"Lee","year":"2002","journal-title":"Genome Res"},{"issue":"1","key":"key\n\t\t\t\t20180928112234_bbx008-B40","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2164-7-64","article-title":"\u201cPer cell\u201d normalization method for mRNA measurement by quantitative PCR and microarrays","volume":"7","author":"Kanno","year":"2006","journal-title":"BMC Genomics"},{"issue":"2","key":"key\n\t\t\t\t20180928112234_bbx008-B41","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1007\/s11427-013-4437-9","article-title":"mRNA enrichment protocols determine the quantification characteristics of external RNA spike-in controls in RNA-Seq studies","volume":"56","author":"Qing","year":"2013","journal-title":"Sci China Life Sci"},{"issue":"1","key":"key\n\t\t\t\t20180928112234_bbx008-B42","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12864-015-2197-6","article-title":"Dormant non-culturable Mycobacterium tuberculosis retains stable low-abundant mRNA","volume":"16","author":"Ignatov","year":"2015","journal-title":"BMC Genomics"},{"key":"key\n\t\t\t\t20180928112234_bbx008-B43","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1038\/nbt.2450","article-title":"Differential analysis of gene regulation at transcript resolution with RNA-Seq","volume":"31","author":"Trapnell","year":"2013","journal-title":"Nat Biotechnol"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bib\/article-pdf\/19\/5\/776\/25861266\/bbx008.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,14]],"date-time":"2025-06-14T21:38:42Z","timestamp":1749937122000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/19\/5\/776\/3056951"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,2,27]]},"references-count":43,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2017,2,27]]},"published-print":{"date-parts":[[2018,9,28]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbx008","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,9]]},"published":{"date-parts":[[2017,2,27]]}}}