Nightingale R, Reehorst CM, Vukelic N, Papadopoulos N, Liao Y, Guleria S, Bell C, Vaillant F, Paul S, Luk IY, Dhillon AS, Jenkins LJ, Morrow RJ, Jackling FC, Chand AL, Chisanga D, Chen Y, Williams DS, Anderson RL, Ellis S, Meikle PJ, Shi W, Visvader JE, Pal B, Mariadason JM. Ehf controls mammary alveolar lineage differentiation and is a putative suppressor of breast tumorigenesis. Developmental Cell. 2024;:10.1016/j.devcel.2024.04.022
Altman JE, Walker CJ, Zboril EK, Hairr NS, Myrick RK, Boyd DC, Koblenski JE, Puchalapalli M, Hu B, Dozmorov MG, Chen X, Chen Y, Perou CM, Lehmann BD, Visvader JE, Olex AL, Harrell JC. Abstract 1750: Decoding breast cancer: Unraveling subtype and model differences through multi-model single-cell RNA sequencing data integration. Cancer Research. 2024;84(6_Supplement):10.1158/1538-7445.am2024-1750
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
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
Cheng J, Smyth GK, Chen Y. Unraveling the timeline of gene expression: A pseudotemporal trajectory analysis of single-cell RNA sequencing data. F1000Research. 2023;12:10.12688/f1000research.134078.2
Chan WF, Coughlan HD, Chen Y, Keenan CR, Smyth GK, Perkins AC, Johanson TM, Allan RS. Activation of stably silenced genes by recruitment of a synthetic de-methylating module. Nature Communications. 2022;13(1):10.1038/s41467-022-33181-4
El-Saafin F, Bergamasco MI, Chen Y, May RE, Esakky P, Hediyeh-zadeh S, Dixon M, Wilcox S, Davis MJ, Strasser A, Smyth GK, Thomas T, Voss AK. Loss of TAF8 causes TFIID dysfunction and p53-mediated apoptotic neuronal cell death. Cell Death & Differentiation. 2022;29(5):10.1038/s41418-022-00982-5
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
