Cheng J, Jin X, Smyth GK, Chen Y. Benchmarking cell type annotation methods for 10x Xenium spatial transcriptomics data. BMC Bioinformatics. 2025;26:10.1186/s12859-025-06044-0
2025;
Ang CH, Arandjelovic P, Cheng J, Yang J, Guo F, Yu Y, Nelameham S, Whitehead L, Li J, Silver DL, Barker N, Visvader JE, Chow PKH, Smyth GK, Chen Y, Virshup DM, Fu NY. Self-maintenance of zonal hepatocytes during adult homeostasis and their complex plasticity upon distinct liver injuries. Cell Reports. 2024;44(1):10.1016/j.celrep.2024.115093
Dawson CA, Milevskiy MJG, Capaldo BD, Yip RKH, Song X, Vaillant F, Prokopuk L, Jackling FC, Smyth GK, Chen Y, Lindeman GJ, Visvader JE. Hormone-responsive progenitors have a unique identity and exhibit high motility during mammary morphogenesis. Cell Reports. 2024;43(12):10.1016/j.celrep.2024.115073
Altman JE, Olex AL, Zboril EK, Walker CJ, Boyd DC, Myrick RK, Hairr NS, Koblinski JE, Puchalapalli M, Hu B, Dozmorov MG, Chen XS, Chen Y, Perou CM, Lehmann BD, Visvader JE, Harrell JC. Single‐cell transcriptional atlas of human breast cancers and model systems. Clinical and Translational Medicine. 2024;14(10):10.1002/ctm2.70044
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;59(15):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
