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7,015 results
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featureCounts: an efficient general purpose program for assigning sequence reads to genomic features.
Liao Y, Smyth GK, Shi W. Liao Y, et al. Among authors: shi w. Bioinformatics. 2014 Apr 1;30(7):923-30. doi: 10.1093/bioinformatics/btt656. Epub 2013 Nov 13. Bioinformatics. 2014. PMID: 24227677
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.
Optimizing the noise versus bias trade-off for Illumina whole genome expression BeadChips.
Shi W, Oshlack A, Smyth GK. Shi W, et al. Nucleic Acids Res. 2010 Dec;38(22):e204. doi: 10.1093/nar/gkq871. Epub 2010 Oct 6. Nucleic Acids Res. 2010. PMID: 20929874 Free PMC article.
BeadArray expression analysis using bioconductor.
Ritchie ME, Dunning MJ, Smith ML, Shi W, Lynch AG. Ritchie ME, et al. Among authors: shi w. 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.
Global changes in the mammary epigenome are induced by hormonal cues and coordinated by Ezh2.
Pal B, Bouras T, Shi W, Vaillant F, Sheridan JM, Fu N, Breslin K, Jiang K, Ritchie ME, Young M, Lindeman GJ, Smyth GK, Visvader JE. Pal B, et al. Among authors: shi w. Cell Rep. 2013 Feb 21;3(2):411-26. doi: 10.1016/j.celrep.2012.12.020. Epub 2013 Jan 31. Cell Rep. 2013. PMID: 23375371
The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote.
Liao Y, Smyth GK, Shi W. Liao Y, et al. Among authors: shi w. 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.
Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures.
Munro SA, Lund SP, Pine PS, Binder H, Clevert DA, Conesa A, Dopazo J, Fasold M, Hochreiter S, Hong H, Jafari N, Kreil DP, Łabaj PP, Li S, Liao Y, Lin SM, Meehan J, Mason CE, Santoyo-Lopez J, Setterquist RA, Shi L, Shi W, Smyth GK, Stralis-Pavese N, Su Z, Tong W, Wang C, Wang J, Xu J, Ye Z, Yang Y, Yu Y, Salit M. Munro SA, et al. Among authors: shi l, shi w. Nat Commun. 2014 Sep 25;5:5125. doi: 10.1038/ncomms6125. Nat Commun. 2014. PMID: 25254650
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. Among authors: shi w. 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.
Whole transcriptome analysis for T cell receptor-affinity and IRF4-regulated clonal expansion of T cells.
Shi W, Man K, Smyth GK, Nutt SL, Kallies A. Shi W, et al. Genom Data. 2014 Nov 1;2:396-8. doi: 10.1016/j.gdata.2014.10.019. eCollection 2014 Dec. Genom Data. 2014. PMID: 26484137 Free PMC article.
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