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, 1438. PMID: 27508061
2. Chen Y, Pal B, Visvader JE, Smyth GK. Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR. F1000Research 2017, 6, 2055. PMID: 29333247
3. 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: 24485249. #Joint first.
4. Pal B#, Chen Y#, Vaillant F#, Capaldo BD, Joyce R, Song X, Bryant VL, Penington JS, Di Stefano L, Ribera NT, Wilcox S, Mann GB, kConFab, Papenfuss AT, Lindeman GJ, Smyth GK*, Visvader JE*. A single cell RNA atlas of human breast spanning normal, preneoplastic and tumorigenic states. EMBO Journal 2021, 40(11), e3107333. PMID: 33950524. #Joint first.
5. Pal B#, Chen Y#, Vaillant F#, Jamieson P, Gordon L, Rios AC, Wilcox S, Fu N, Liu KH, Jackling FC, Davis MJ, Lindeman GJ, Smyth GK*, Visvader JE*. Construction of developmental lineage relationships in the mouse mammary gland by single-cell RNA profiling. Nature Communications 2017, 8(1), 1627. PMID: 29158510. #Joint first.
6. 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
7. Chen Y, Lun ATL, Smyth GK (2014). Differential expression analysis of complex RNA-seq experiments using edgeR. Statistical Analysis of Next Generation Sequence Data, Somnath Datta and Daniel S Nettleton (eds), Springer, New York, pages 51-74.
8. Pal B#, Chen Y#, Milevskiy MJG#, Vaillant F, Prokopuk L, Dawson C, Capaldo BD, Song X, Jackling F, Timpson P, Lindeman GJ, Smyth GK*, Visvader JE*. Single cell transcriptome atlas of mouse mammary epithelial cells across development. Breast Cancer Research. 2021. 23(1), 69. PMID: 34187545. #Joint first.
9. 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. https://doi.org/10.1038/s41597-022-01236-2.
10. Weeden CE, Chen Y, Ma SB, Hu Y, Ramm G, Sutherland KD, Smyth GK, Asselin-Labat ML (2017). Lung basal stem cells rapidly repair DNA damage using the error-prone non-homologous end-joining pathway. PLOS Biology 2017, 15(1), e2000731. PMID: 28125611.
