Ritchie, ME, Phipson, B, Wu, D, Hu, Y, Law, CW, Shi, W, and Smyth, GK (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Research 43, e47. PMID: 25605792
Lun, ATL and Smyth, GK (2014). De novo detection of differentially bound regions for ChIP-seq data using peaks and windows: controlling error rates correctly. Nucleic Acids Research 42, e95. PMID: 24852250
Law, CW, Chen, Y, Shi, W, and Smyth, GK. Voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biology 2014. 15, R29. PMID: 24485249
Wu, D, Smyth, GK. Camera: a competitive gene set test accounting for inter-gene correlation. Nucleic Acids Research 2012. 40, e133. PMID: 22638577
McCarthy, DJ, Chen, Y, Smyth, GK. Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Research 2012. 40, 4288-4297. PMID: 22287627
Wu, D, Lim, E, François Vaillant, F, Asselin-Labat, M-L, Visvader, JE, and Smyth, GK. ROAST: rotation gene set tests for complex microarray experiments. Bioinformatics 2010. 26, 2176-2182. PMID: 20610611
Robinson, M, McCarthy, DJ, Smyth, GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010. 26, 139-140. PMID: 19910308
Robinson, MD, and Smyth, GK. Moderated statistical tests for assessing differences in tag abundance. Bioinformatics 2007. 23, 2881-2887. PMID: 17881408
Smyth, G. K., Michaud, J., and Scott, H. Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics 2005. 21(9), 2067-2075. PMID: 15657102
Smyth, G. K. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology 2004. 3, No. 1, Article 3. PMID: 16646809