Smyth, Gordon K.

<tt>edgeR</tt> : a Bioconductor package for differential expression analysis of digital gene expression data

Robinson, M. D., McCarthy, D. J., & Smyth, G. K. (2010) · Bioinformatics

Gene expression and cancer classificationGenomics and Phylogenetic Studies

Cited by 41,364

limma powers differential expression analyses for RNA-sequencing and microarray studies

Ritchie, M. E., Phipson, B., Wu, D., Hu, Y., Law, C. W., Shi, W., & Smyth, G. K. (2015) · Nucleic Acids Research

Gene expression and cancer classificationGenomics and Phylogenetic Studies

Cited by 40,458

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

Liao, Y., Smyth, G. K., & Shi, W. (2014) · Bioinformatics

Genomics and Phylogenetic StudiesGene expression and cancer classification

Cited by 27,219

Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments

Smyth, G. K. (2004) · Statistical Applications in Genetics and Molecular Biology

Gene expression and cancer classificationBioinformatics and Genomic Networks

Cited by 11,829

Gene ontology analysis for RNA-seq: accounting for selection bias

Young, M. D., Wakefield, M. J., Smyth, G. K., & Oshlack, A. (2010) · Genome Biology

Bioinformatics and Genomic NetworksGenomics and Phylogenetic Studies

Cited by 7,107

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

Law, C. W., Chen, Y., Shi, W., & Smyth, G. K. (2014) · Genome Biology

Gene expression and cancer classificationGenomics and Phylogenetic Studies

Cited by 6,155

limma: Linear Models for Microarray Data

Smyth, G. K. (2005) · Statistics for Biology and Health

Gene expression and cancer classificationBioinformatics and Genomic Networks

Cited by 5,796

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

McCarthy, D. J., Chen, Y., & Smyth, G. K. (2012) · Nucleic Acids Research

Gene expression and cancer classificationGenomics and Phylogenetic Studies

Cited by 5,195

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

Liao, Y., Smyth, G. K., & Shi, W. (2013) · Nucleic Acids Research

Genomics and Phylogenetic StudiesAlgorithms and Data Compression

Cited by 3,064

Generation of a functional mammary gland from a single stem cell

Shackleton, M., Vaillant, F., Simpson, K. J., Stingl, J., Smyth, G. K., Asselin-Labat, M.-L., Wu, L., Lindeman, G. J., & Visvader, J. E. (2006) · Nature

Cancer Cells and MetastasisMesenchymal stem cell research

Cited by 2,005

Normalization of cDNA microarray data

Smyth, G. K., & Speed, T. (2003) · Methods

Gene expression and cancer classificationGenomics and Phylogenetic Studies

Cited by 1,871

Aberrant luminal progenitors as the candidate target population for basal tumor development in BRCA1 mutation carriers

kConFab, Lim, E., Vaillant, F., Wu, D., Forrest, N. C., Pal, B., Hart, A. H., Asselin-Labat, M.-L., Gyorki, D. E., Ward, T., et al. (2009) · Nature Medicine

BRCA gene mutations in cancerCancer Cells and Metastasis

Cited by 1,492

Small-sample estimation of negative binomial dispersion, with applications to SAGE data

Robinson, M. D., & Smyth, G. K. (2007) · Biostatistics

Gene expression and cancer classificationStatistical Distribution Estimation and Applications

Cited by 1,073

A comparison of background correction methods for two-colour microarrays

Ritchie, M. E., Silver, J., Oshlack, A., Holmes, M., Diyagama, D., Holloway, A., & Smyth, G. K. (2007) · Bioinformatics

Gene expression and cancer classificationBioinformatics and Genomic Networks

Cited by 907

Moderated statistical tests for assessing differences in tag abundance

Robinson, M. D., & Smyth, G. K. (2007) · Bioinformatics

Gene expression and cancer classificationGenomics and Phylogenetic Studies

Cited by 856

Permutation P-values Should Never Be Zero: Calculating Exact P-values When Permutations Are Randomly Drawn

Phipson, B., & Smyth, G. K. (2010) · Statistical Applications in Genetics and Molecular Biology

Probability and Statistical ResearchBioinformatics and Genomic Networks

Cited by 712

Control of mammary stem cell function by steroid hormone signalling

Asselin-Labat, M.-L., Vaillant, F., Sheridan, J. M., Pal, B., Wu, D., Simpson, E. R., Yasuda, H., Smyth, G. K., Martin, T. J., Lindeman, G. J., et al. (2010) · Nature

Estrogen and related hormone effectsCancer Cells and Metastasis

Cited by 693

The transcription factors Blimp-1 and IRF4 jointly control the differentiation and function of effector regulatory T cells

Cretney, E., Xin, A., Shi, W., Minnich, M., Masson, F., Miasari, M., Belz, G. T., Smyth, G. K., Busslinger, M., Nutt, S. L., et al. (2011) · Nature Immunology

T-cell and B-cell ImmunologyPsoriasis: Treatment and Pathogenesis

Cited by 605

ROAST: rotation gene set tests for complex microarray experiments

Wu, D., Lim, E., Vaillant, F., Asselin-Labat, M.-L., Visvader, J. E., & Smyth, G. K. (2010) · Bioinformatics

Bioinformatics and Genomic NetworksGene expression and cancer classification

Cited by 560

Transcriptome analyses of mouse and human mammary cell subpopulations reveal multiple conserved genes and pathways

Lim, E., Wu, D., Pal, B., Bouras, T., Asselin-Labat, M.-L., Vaillant, F., Yagita, H., Lindeman, G. J., Smyth, G. K., & Visvader, J. E. (2010) · Breast Cancer Research

Cancer Cells and MetastasisBreast Cancer Treatment Studies

Cited by 440

Empirical array quality weights in the analysis of microarray data

Ritchie, M. E., Diyagama, D., Neilson, J., van Laar, R., Dobrovic, A., Holloway, A., & Smyth, G. K. (2006) · BMC Bioinformatics

Gene expression and cancer classificationBioinformatics and Genomic Networks

Cited by 312

Complementarity and redundancy of IL-22-producing innate lymphoid cells

Rankin, L. C., Girard-Madoux, M. J. H., Seillet, C., Mielke, L. A., Kerdiles, Y., Fenis, A., Wieduwild, E., Putoczki, T., Mondot, S., Lantz, O., et al. (2016) · Nature Immunology

IL-33, ST2, and ILC PathwaysT-cell and B-cell Immunology

Cited by 249

Optimizing the noise versus bias trade-off for Illumina Whole Genome Expression Beadchips

Shi, W., Oshlack, A., & Smyth, G. K. (2010) · Nucleic Acids Research

Gene expression and cancer classificationGenomics and Phylogenetic Studies

Cited by 225

Targeting histone acetylation dynamics and oncogenic transcription by catalytic P300/CBP inhibition

Hogg, S. J., Motorna, O., Cluse, L. A., Johanson, T. M., Coughlan, H. D., Raviram, R., Myers, R. M., Costacurta, M., Todorovski, I., Pijpers, L., et al. (2021) · Molecular Cell

Genomics and Chromatin DynamicsEpigenetics and DNA Methylation

Cited by 170