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The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote.
Liao Y, Smyth GK, Shi W. Liao Y, et al. Nucleic Acids Res. 2013 May 1;41(10):e108. doi: 10.1093/nar/gkt214. Epub 2013 Apr 4. Nucleic Acids Res. 2013. PMID: 23558742 Free PMC article.
Illumina WG-6 BeadChip strips should be normalized separately.
Shi W, Banerjee A, Ritchie ME, Gerondakis S, Smyth GK. Shi W, et al. BMC Bioinformatics. 2009 Nov 11;10:372. doi: 10.1186/1471-2105-10-372. BMC Bioinformatics. 2009. PMID: 19903361 Free PMC article.
Estimating the proportion of microarray probes expressed in an RNA sample.
Shi W, de Graaf CA, Kinkel SA, Achtman AH, Baldwin T, Schofield L, Scott HS, Hilton DJ, Smyth GK. Shi W, et al. Nucleic Acids Res. 2010 Apr;38(7):2168-76. doi: 10.1093/nar/gkp1204. Epub 2010 Jan 7. Nucleic Acids Res. 2010. PMID: 20056656 Free PMC article.
BeadArray expression analysis using bioconductor.
Ritchie ME, Dunning MJ, Smith ML, Shi W, Lynch AG. Ritchie ME, et al. PLoS Comput Biol. 2011 Dec;7(12):e1002276. doi: 10.1371/journal.pcbi.1002276. Epub 2011 Dec 1. PLoS Comput Biol. 2011. PMID: 22144879 Free PMC article.
limma powers differential expression analyses for RNA-sequencing and microarray studies.
Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK. Ritchie ME, et al. Nucleic Acids Res. 2015 Apr 20;43(7):e47. doi: 10.1093/nar/gkv007. Epub 2015 Jan 20. Nucleic Acids Res. 2015. PMID: 25605792 Free PMC article.
Blimp-1 controls plasma cell function through the regulation of immunoglobulin secretion and the unfolded protein response.
Tellier J, Shi W, Minnich M, Liao Y, Crawford S, Smyth GK, Kallies A, Busslinger M, Nutt SL. Tellier J, et al. Nat Immunol. 2016 Mar;17(3):323-30. doi: 10.1038/ni.3348. Epub 2016 Jan 18. Nat Immunol. 2016. PMID: 26779600 Free PMC article.
Haemopedia RNA-seq: a database of gene expression during haematopoiesis in mice and humans.
Choi J, Baldwin TM, Wong M, Bolden JE, Fairfax KA, Lucas EC, Cole R, Biben C, Morgan C, Ramsay KA, Ng AP, Kauppi M, Corcoran LM, Shi W, Wilson N, Wilson MJ, Alexander WS, Hilton DJ, de Graaf CA. Choi J, et al. Nucleic Acids Res. 2019 Jan 8;47(D1):D780-D785. doi: 10.1093/nar/gky1020. Nucleic Acids Res. 2019. PMID: 30395284 Free PMC article.
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