Baldoni PL, Chen Y, Hediyeh-zadeh S, Liao Y, Dong X, Ritchie ME, Shi W, Smyth GK. Dividing out quantification uncertainty allows efficient assessment of differential transcript expression with edgeR. Nucleic Acids Research. 2024;52(3):10.1093/nar/gkad1167
Li M, Smyth GK. Neither random nor censored: estimating intensity-dependent probabilities for missing values in label-free proteomics. Bioinformatics. 2023;39(5):10.1093/bioinformatics/btad200
Chen Y, Pal B, Lindeman GJ, Visvader JE, Smyth GK. R code and downstream analysis objects for the scRNA-seq atlas of normal and tumorigenic human breast tissue. Scientific Data. 2022;9(1):10.1038/s41597-022-01236-2
Liao Y, Smyth GK, Shi W. The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads. Nucleic Acids Research. 2019;47(8):10.1093/nar/gkz114
Chen Y, Pal B, Visvader JE, Smyth GK. Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR. F1000Research. 2017;6:10.12688/f1000research.13196.1
Chen Y, Lun ATL, Smyth GK. From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline. F1000Research. 2016;5:10.12688/f1000research.8987.1
Phipson B, Lee S, Majewski IJ, Alexander WS, Smyth GK. Robust hyperparameter estimation protects against hypervariable genes and improves power to detect differential expression. The Annals of Applied Statistics. 2016;10(2):10.1214/16-aoas920
Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Research. 2015;43(7):10.1093/nar/gkv007
Lieschke E, Thomas AF, Kueh A, Atkin-Smith GK, Baldoni PL, La Marca JE, Young S, Huang AS, Ross AM, Whelan L, Kaloni D, Tai L, Smyth GK, Herold MJ, Hawkins ED, Strasser A, Kelly GL. Mouse models to investigate in situ cell fate decisions induced by p53. The EMBO Journal. 2024;:10.1038/s44318-024-00189-z
Bergamasco MI, Ranathunga N, Abeysekera W, Li-Wai-Suen CSN, Garnham AL, Willis SN, McRae HM, Yang Y, D’Amico A, Di Rago L, Wilcox S, Nutt SL, Alexander WS, Smyth GK, Voss AK, Thomas T. The histone acetyltransferase KAT6B is required for hematopoietic stem cell development and function. Stem Cell Reports. 2024;19(4):10.1016/j.stemcr.2024.02.005
Bergamasco MI, Vanyai HK, Garnham AL, Geoghegan ND, Vogel AP, Eccles S, Rogers KL, Smyth GK, Blewitt ME, Hannan AJ, Thomas T, Voss AK. Increasing histone acetylation improves sociability and restores learning and memory in KAT6B-haploinsufficient mice. Journal of Clinical Investigation. 2024;134(7):10.1172/jci167672
Keenan CR, Coughlan HD, Iannarella N, del Fierro AT, Keniry A, Johanson TM, Chan F, Garnham AL, Whitehead LW, Blewitt ME, Smyth GK, Allan RS. Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription. Genome Research. 2024;34(4):10.1101/gr.279119.124
Mah SYY, Vanyai HK, Li-Wai-Suen CSN, Garnham AL, Wynn J, Bergamasco MI, Malelang S, Wilcox S, Biben C, Smyth GK, Thomas T, Voss AK. ING4 and ING5 are essential for histone H3 lysine 14 acetylation and epicardial cell lineage development.Development. 2024;151(5):10.1242/dev.202617
Ashayeripanah M, Vega-Ramos J, Fernandez-Ruiz D, Valikhani S, Lun ATL, White JT, Young LJ, Yaftiyan A, Zhan Y, Wakim L, Caminschi I, Lahoud MH, Lew AM, Shortman K, Smyth GK, Heath WR, Mintern JD, Roquilly A, Villadangos JA. Systemic inflammatory response syndrome triggered by blood-borne pathogens induces prolonged dendritic cell paralysis and immunosuppression. Cell Reports. 2024;43(2):10.1016/j.celrep.2024.113754
Tellier J, Tarasova I, Nie J, Smillie CS, Fedele PL, Cao WHJ, Groom JR, Belz GT, Bhattacharya D, Smyth GK, Nutt SL. Unraveling the diversity and functions of tissue-resident plasma cells. Nature Immunology. 2024;25(2):10.1038/s41590-023-01712-w
Joyce R, Pascual R, Heitink L, Capaldo BD, Vaillant F, Christie M, Tsai M, Surgenor E, Anttila CJA, Rajasekhar P, Jackling FC, Trussart M, Milevskiy MJG, Song X, Li M, Teh CE, Gray DHD, Smyth GK, Chen Y, Lindeman GJ, Visvader JE. Identification of aberrant luminal progenitors and mTORC1 as a potential breast cancer prevention target in BRCA2 mutation carriers. Nature Cell Biology. 2024;26(1):10.1038/s41556-023-01315-5
Milevskiy MJG, Coughlan HD, Kane SR, Johanson TM, Kordafshari S, Chan F, Tsai M, Surgenor E, Wilcox S, Allan RS, Chen Y, Lindeman GJ, Smyth GK, Visvader JE. Three-dimensional genome architecture coordinates key regulators of lineage specification in mammary epithelial cells. Cell Genomics. 2023;3(11):10.1016/j.xgen.2023.100424
Dong X, Du MRM, Gouil Q, Tian L, Jabbari JS, Bowden R, Baldoni PL, Chen Y, Smyth GK, Amarasinghe SL, Law CW, Ritchie ME. Benchmarking long-read RNA-sequencing analysis tools using in silico mixtures. Nature Methods. 2023;20(11):10.1038/s41592-023-02026-3
