{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,27]],"date-time":"2026-04-27T20:10:22Z","timestamp":1777320622617,"version":"3.51.4"},"reference-count":24,"publisher":"Springer Science and Business Media LLC","issue":"S4","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2017,3]]},"DOI":"10.1186\/s12859-017-1526-y","type":"journal-article","created":{"date-parts":[[2017,3,22]],"date-time":"2017-03-22T06:24:20Z","timestamp":1490163860000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":57,"title":["Comprehensive evaluation of RNA-seq quantification methods for linearity"],"prefix":"10.1186","volume":"18","author":[{"given":"Haijing","family":"Jin","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ying-Wooi","family":"Wan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhandong","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2017,3,22]]},"reference":[{"issue":"1","key":"1526_CR1","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nrg2484","volume":"10","author":"Z Wang","year":"2009","unstructured":"Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nature reviews Genetics. 2009; 10(1):57\u201363. doi: 10.1038\/nrg2484 .","journal-title":"Nature reviews Genetics"},{"key":"1526_CR2","doi-asserted-by":"crossref","unstructured":"Zhao S, Fung-Leung WP, Bittner A, Ngo K, Liu X. Comparison of RNA-Seq and microarray in transcriptome profiling of activated T cells. PLoS ONE. 2014; 9(1). doi: 10.1371\/journal.pone.0078644 .","DOI":"10.1371\/journal.pone.0078644"},{"issue":"1","key":"1526_CR3","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1186\/s13059-016-0940-1","volume":"17","author":"M Teng","year":"2016","unstructured":"Teng M, Love MI, Davis CA, Djebali S, Dobin A, Graveley BR, Li S, Mason CE, Olson S, Pervouchine D, Sloan CA, Wei X, Zhan L, Irizarry RA. A benchmark for RNA-seq quantification pipelines. Genome Biol. 2016; 17(1):74. doi: 10.1186\/s13059-016-0940-1 .","journal-title":"Genome Biol"},{"issue":"1","key":"1526_CR4","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1186\/s13059-016-0881-8","volume":"17","author":"A Conesa","year":"2016","unstructured":"Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, Szcze\u015bniak MW, Gaffney DJ, Elo LL, Zhang X, Mortazavi A. A survey of best practices for RNA-seq data analysis. Genome Biol. 2016; 17(1):13. doi: 10.1186\/s13059-016-0881-8 .","journal-title":"Genome Biol"},{"issue":"1","key":"1526_CR5","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","volume":"26","author":"MD Robinson","year":"2009","unstructured":"Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2009; 26(1):139\u201340. doi: 10.1093\/bioinformatics\/btp616 .","journal-title":"Bioinformatics"},{"issue":"11","key":"1526_CR6","doi-asserted-by":"crossref","first-page":"5054","DOI":"10.1093\/nar\/gkw448","volume":"44","author":"PL Germain","year":"2016","unstructured":"Germain PL, Vitriolo A, Adamo A, Laise P, Das V, Testa G. RNAontheBENCH: Computational and empirical resources for benchmarking RNAseq quantification and differential expression methods. Nucleic Acids Res. 2016; 44(11):5054\u201367. doi: 10.1093\/nar\/gkw448 .","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"1526_CR7","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1186\/s13059-015-0702-5","volume":"16","author":"A Kanitz","year":"2015","unstructured":"Kanitz A, Gypas F, Gruber AJ, Gruber AR, Martin G, Zavolan M. Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data. Genome Biol. 2015; 16(1):150. doi: 10.1186\/s13059-015-0702-5 .","journal-title":"Genome Biol"},{"key":"1526_CR8","doi-asserted-by":"crossref","unstructured":"Chandramohan R, Wu PY, Phan JH, Wang MD. Benchmarking RNA-Seq quantification tools. In: Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society. EMBS: 2013. p. 647\u201350. doi: 10.1109\/EMBC.2013.6609583 .","DOI":"10.1109\/EMBC.2013.6609583"},{"key":"1526_CR9","doi-asserted-by":"crossref","unstructured":"Fonseca NA, Marioni J, Brazma A. RNA-Seq gene profiling - a systematic empirical comparison. PLoS ONE. 2014;9(9). doi: 10.1371\/journal.pone.0107026 .","DOI":"10.1371\/journal.pone.0107026"},{"key":"1526_CR10","doi-asserted-by":"crossref","unstructured":"Mohammadi S, Zuckerman N, Goldsmith A, Grama A. A critical survey of deconvolution methods for separating cell-types in complex tissues. arXiv: arXiv:1510.04583 [cs.CE]. doi: 10.1109\/JPROC.2016.2607121 .","DOI":"10.1109\/JPROC.2016.2607121"},{"issue":"2014","key":"1526_CR11","first-page":"1","volume":"12","author":"AM Newman","year":"2015","unstructured":"Newman AM, Liu CL, Green MR, Gentles AJ, Feng W, Xu Y, Hoang CD, Diehn M, Alizadeh AA. Robust enumeration of cell subsets from tissue expression profiles. Nat Methods. 2015; 12(2014):1\u201310. doi: 10.1038\/nmeth.3337 .","journal-title":"Nat Methods"},{"key":"1526_CR12","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1186\/1471-2105-14-89","volume":"14","author":"Y Zhong","year":"2013","unstructured":"Zhong Y, Wan YW, Pang K, Chow LML, Liu Z. Digital sorting of complex tissues for cell type-specific gene expression profiles. BMC Bioinforma. 2013; 14:89. doi: 10.1186\/1471-2105-14-89 .","journal-title":"BMC Bioinforma"},{"issue":"5","key":"1526_CR13","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1038\/nmeth.3809","volume":"13","author":"E Rahmani","year":"2016","unstructured":"Rahmani E, Zaitlen N, Baran Y, Eng C, Hu D, Galanter J, Oh S, Burchard EG, Eskin E, Zou J, Halperin E. Sparse PCA corrects for cell type heterogeneity in epigenome-wide association studies. Nat Methods. 2016; 13(5):443\u20135. doi: 10.1038\/nmeth.3809 .","journal-title":"Nat Methods"},{"issue":"5","key":"1526_CR14","doi-asserted-by":"crossref","first-page":"682","DOI":"10.1093\/bioinformatics\/btt566","volume":"30","author":"DA Liebner","year":"2014","unstructured":"Liebner DA, Huang K, Parvin JD. MMAD: microarray microdissection with analysis of differences is a computational tool for deconvoluting cell type-specific contributions from tissue samples. Bioinformatics. 2014; 30(5):682\u20139. doi: 10.1093\/bioinformatics\/btt566 .","journal-title":"Bioinformatics"},{"key":"1526_CR15","doi-asserted-by":"crossref","unstructured":"Abbas AR, Wolslegel K, Seshasayee D, Modrusan Z, Clark HF. Deconvolution of blood microarray data identifies cellular activation patterns in systemic lupus erythematosus. PLoS ONE. 2009;4(7). doi: 10.1371\/journal.pone.0006098 . arXiv:1506.03733v1 .","DOI":"10.1371\/journal.pone.0006098"},{"key":"1526_CR16","doi-asserted-by":"crossref","unstructured":"Gong T, Hartmann N, Kohane IS, Brinkmann V, Staedtler F, Letzkus M, Bongiovanni S, Szustakowski JD. Optimal deconvolution of transcriptional profiling data using quadratic programming with application to complex clinical blood samples. PLoS ONE. 2011;6(11). doi: 10.1371\/journal.pone.0027156 .","DOI":"10.1371\/journal.pone.0027156"},{"issue":"4","key":"1526_CR17","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1038\/nmeth.1439","volume":"7","author":"SS Shen-Orr","year":"2010","unstructured":"Shen-Orr SS, Tibshirani R, Khatri P, Bodian DL, Staedtler F, Perry NM, Hastie T, Sarwal MM, Davis MM, Butte AJ. Cell type-specific gene expression differences in complex tissues. Nat Methods. 2010; 7(4):287\u20139. doi: 10.1038\/nmeth.1439 .","journal-title":"Nat Methods"},{"issue":"1","key":"1526_CR18","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1038\/nmeth.1830","volume":"9","author":"Y Zhong","year":"2012","unstructured":"Zhong Y, Liu Z. Gene expression deconvolution in linear space. Nat Meth. 2012; 9(1):8\u20139. doi: 10.1038\/nmeth.1830 .","journal-title":"Nat Meth"},{"issue":"9","key":"1526_CR19","doi-asserted-by":"crossref","first-page":"903","DOI":"10.1038\/nbt.2957","volume":"32","author":"Z Su","year":"2014","unstructured":"Su Z, \u0141abaj PP, Li SS, Thierry-Mieg J, Thierry-Mieg D, Shi W, Wang C, Schroth GP, Setterquist RA, Thompson JF, Jones WD, Xiao W, Xu W, Jensen RV, Kelly R, Xu J, Conesa A, Furlanello C, Gao HH, Hong H, Jafari N, Letovsky S, Liao Y, Lu F, Oakeley EJ, Peng Z, Praul CA, Santoyo-Lopez J, Scherer A, Shi T, Smyth GK, Staedtler F, Sykacek P, Tan XX, Thompson EA, Vandesompele J, Wang MD, Wang JJJ, Wolfinger RD, Zavadil J, Auerbach SS, Bao W, Binder H, Blomquist T, Brilliant MH, Bushel PR, Cai W, Catalano JG, Chang CW, Chen T, Chen G, Chen R, Chierici M, Chu TM, Clevert DA, Deng Y, Derti A, Devanarayan V, Dong Z, Dopazo J, Du T, Fang H, Fang Y, Fasold M, Fernandez A, Fischer M, Furi\u00f3-Tari P, Fuscoe JC, Caimet F, Gaj S, Gandara J, Gao HH, Ge W, Gondo Y, Gong B, Gong M, Gong Z, Green B, Guo C, Guo L-WL, Guo L-WL, Hadfield J, Hellemans J, Hochreiter S, Jia M, Jian M, Johnson CD, Kay S, Kleinjans J, Lababidi S, Levy S, Li QZ, Li L, Li P, Li Y, Li H, Li J, Li SS, Lin SM, L\u00f3pez FJ, Lu X, Luo H, Ma X, Meehan J, Megherbi DB, Mei N, Mu B, Ning B, Pandey A, P\u00e9rez-Florido J, Perkins RG, Peters R, Phan JH, Pirooznia M, Qian F, Qing T, Rainbow L, Rocca-Serra P, Sambourg L, Sansone SA, Schwartz S, Shah R, Shen J, Smith TM, Stegle O, Stralis-Pavese N, Stupka E, Suzuki Y, Szkotnicki LT, Tinning M, Tu B, van Delft J, Vela-Boza A, Venturini E, Walker SJ, Wan L, Wang W, Wang JJJ, Wang JJJ, Wieben ED, Willey JC, Wu PY, Xuan J, Yang Y, Ye Z, Yin Y, Yu Y, Yuan YC, Zhang J, Zhang KK, Zhang WW, Zhang WW, Zhang Y, Zhao C, Zheng Y, Zhou Y, Zumbo P, Tong W, Kreil DP, Mason CE, Shi L. A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. Nat Biotechnol. 2014; 32(9):903\u201314. doi: 10.1038\/nbt.2957 . NIHMS150003 .","journal-title":"Nat Biotechnol"},{"issue":"4","key":"1526_CR20","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1186\/gb-2013-14-4-r36","volume":"14","author":"D Kim","year":"2013","unstructured":"Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013; 14(4):36. doi: 10.1186\/gb-2013-14-4-r36 .","journal-title":"Genome Biol"},{"issue":"2","key":"1526_CR21","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","volume":"31","author":"S Anders","year":"2015","unstructured":"Anders S, Pyl PT, Huber W. HTSeq-A Python framework to work with high-throughput sequencing data. Bioinformatics. 2015; 31(2):166\u20139. doi: 10.1093\/bioinformatics\/btu638 .","journal-title":"Bioinformatics"},{"issue":"5","key":"1526_CR22","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1038\/nbt.1621","volume":"28","author":"C Trapnell","year":"2010","unstructured":"Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010; 28(5):511\u20135. doi: 10.1038\/nbt.1621 . 171 .","journal-title":"Nat Biotechnol"},{"issue":"5","key":"1526_CR23","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1038\/nbt.3519","volume":"34","author":"NL Bray","year":"2016","unstructured":"Bray NL, Pimentel H, Melsted P, Pachter L. Near-optimal probabilistic RNA-seq quantification. Nat Biotechnol. 2016; 34(5):525\u20137. doi: 10.1038\/nbt.3519 . http:\/\/arxiv.org\/abs\/1505.02710.","journal-title":"Nat Biotechnol"},{"key":"1526_CR24","doi-asserted-by":"crossref","unstructured":"Patro R, Duggal G, Kingsford C. Salmon: accurate, versatile and ultrafast quantification from RNA-seq data using lightweight-alignment. bioRxiv. 2015:021592. doi: 10.1101\/021592 . http:\/\/arxiv.org\/abs\/1505.02710.","DOI":"10.1101\/021592"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-017-1526-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,9,19]],"date-time":"2019-09-19T22:16:27Z","timestamp":1568931387000},"score":1,"resource":{"primary":{"URL":"http:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-017-1526-y"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,3]]},"references-count":24,"journal-issue":{"issue":"S4","published-print":{"date-parts":[[2017,3]]}},"alternative-id":["1526"],"URL":"https:\/\/doi.org\/10.1186\/s12859-017-1526-y","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,3]]},"article-number":"117"}}