A Modified Prony Algorithm for Fitting Functions Defined by Difference Equations. - Michael R. Osborne; Gordon K. Smyth (SIAM J. Sci. Comput., 1991)

A Modified Prony Algorithm for Exponential Function Fitting. - Michael R. Osborne; Gordon K. Smyth (SIAM J. Sci. Comput., 1995)

Partitioned algorithms for maximum likelihood and other non-linear estimation. - Gordon K. Smyth (Stat. Comput., 1996)

Employing Symmetry Constraints for Improved Frequency Estimation by Eigenanalysis Methods. - Gordon K. Smyth (Technometrics, 2000)

An Improved Saddlepoint Approximation Based on the Negative Binomial Distribution for the General Birth Process. - Gordon K. Smyth; Heather M. Podlich (Comput. Stat., 2002)

limmaGUI: A graphical user interface for linear modeling of microarray data. - James M. Wettenhall; Gordon K. Smyth (Bioinform., 2004)

Semi-parametric extended Poisson process models for count data. - Heather M. Podlich; Malcolm J. Faddy; Gordon K. Smyth (Stat. Comput., 2004)

A systematic approach for comprehensive T-cell epitope discovery using peptide libraries. - Tim Beißbarth; Jason A. Tye-Din; Gordon K. Smyth; Terence P. Speed; Robert P. Anderson (ISMB (Supplement of Bioinformatics), 2005)

Use of within-array replicate spots for assessing differential expression in microarray experiments. - Gordon K. Smyth; Joëlle Michaud; Hamish S. Scott (Bioinform., 2005)

Series evaluation of Tweedie exponential dispersion model densities. - Peter K. Dunn; Gordon K. Smyth (Stat. Comput., 2005)

affylmGUI: a graphical user interface for linear modeling of single channel microarray data. - James M. Wettenhall; Ken M. Simpson; Keith Satterley; Gordon K. Smyth (Bioinform., 2006)

Statistical analysis of an RNA titration series evaluates microarray precision and sensitivity on a whole-array basis. - Andrew J. Holloway; Alicia Oshlack; Dileepa S. Diyagama; David D. L. Bowtell; Gordon K. Smyth (BMC Bioinform., 2006)

Empirical array quality weights in the analysis of microarray data. - Matthew E. Ritchie; Dileepa S. Diyagama; Jody Neilson; Ryan van Laar; Alexander Dobrovic; Andrew J. Holloway; Gordon K. Smyth (BMC Bioinform., 2006)

Using DNA microarrays to study gene expression in closely related species. - Alicia Oshlack; Adrien E. Chabot; Gordon K. Smyth; Yoav Gilad (Bioinform., 2007)

A comparison of background correction methods for two-colour microarrays. - Matthew E. Ritchie; Jeremy David Silver; Alicia Oshlack; Melissa Holmes; Dileepa S. Diyagama; Andrew J. Holloway; Gordon K. Smyth (Bioinform., 2007)

Moderated statistical tests for assessing differences in tag abundance. - Mark D. Robinson; Gordon K. Smyth (Bioinform., 2007)

Evaluation of Tweedie exponential dispersion model densities by Fourier inversion. - Peter K. Dunn; Gordon K. Smyth (Stat. Comput., 2008)

Testing significance relative to a fold-change threshold is a TREAT. - Davis J. McCarthy; Gordon K. Smyth (Bioinform., 2009)

Illumina WG-6 BeadChip strips should be normalized separately. - Wei Shi; Ashish Banerjee; Matthew E. Ritchie; Steve Gerondakis; Gordon K. Smyth (BMC Bioinform., 2009)

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. - Mark D. Robinson; Davis J. McCarthy; Gordon K. Smyth (Bioinform., 2010)

ROAST: rotation gene set tests for complex microarray experiments. - Di Wu; Elgene Lim; François Vaillant; Marie-Liesse Asselin-Labat; Jane E. Visvader; Gordon K. Smyth (Bioinform., 2010)

Separate-channel analysis of two-channel microarrays: recovering inter-spot information. - Gordon K. Smyth; Naomi S. Altman (BMC Bioinform., 2013)

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. - Yang Liao; Gordon K. Smyth; Wei Shi (Bioinform., 2014)

diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data. - Aaron T. L. Lun; Gordon K. Smyth (BMC Bioinform., 2015)

It's DE-licious: A Recipe for Differential Expression Analyses of RNA-seq Experiments Using Quasi-Likelihood Methods in edgeR. - Aaron T. L. Lun; Yunshun Chen; Gordon K. Smyth (Statistical Genomics, 2016)

From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline. - Yunshun Chen; Aaron T. L. Lun; Gordon K. Smyth (F1000Research, 2016)

statmod: Probability Calculations for the Inverse Gaussian Distribution. - Göknur Giner; Gordon K. Smyth (R J., 2016)

Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR. - Yunshun Chen; Bhupinder Pal; Jane E. Visvader; Gordon K. Smyth (F1000Research, 2017)

Neither random nor censored: estimating intensity-dependent probabilities for missing values in label-free proteomics. - Mengbo Li; Gordon K. Smyth (Bioinform., 2023)

Benchmarking cell type annotation methods for 10x Xenium spatial transcriptomics data. - Jinming Cheng; Xinyi Jin; Gordon K. Smyth; Yunshun Chen (BMC Bioinform., 2025)