Selected publications

1. 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. (Accepted 24 February 2022)
2. 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
3. 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
4. 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
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
6. 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
7. 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
8. Pal B, Chen Y, Bert A, Hu Y, Beck T, Sheridan JM, Shi W, Satterley K, Jamieson P, Goodall GJ, Lindeman GJ, Smyth GK, and Visvader JE. Integration of microRNA signatures of distinct mammary epithelial cell types with their gene expression and epigenetic portraits. Breast Cancer Research 2015, 17, 85. PMID: 26080807
9. 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
10. 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

# denotes equal first author