Du MRM, Wang C, Law CW, Amann-Zalcenstein D, Anttila CJA, Ling L, Hickey PF, Sargeant CJ, Chen Y, Ioannidis LJ, Rajasekhar P, Yip RKH, Rogers KL, Hansen DS, Bowden R, Ritchie ME. Benchmarking spatial transcriptomics technologies with the multi-sample SpatialBenchVisium dataset. Genome Biology. 2025;26(1):10.1186/s13059-025-03543-4
Chin HS, Cheng J, Hsu SH, Lum GG, Zaldivia MT, Nelameham S, Guo F, Mallavarapu K, Jackling FC, Yang J, Tan JSL, Sampath P, Barker N, Smyth GK, Lindeman GJ, Strasser A, Visvader JE, Chen Y, Chen T, Fu NY. MCL‑1 safeguards activated hair follicle stem cells to enable adult hair regeneration. Nature Communications. 2025;16(1):10.1038/s41467-025-58150-5
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. 2025;44(1):10.1016/j.celrep.2024.115093
Cheng J, Jin X, Smyth GK, Chen Y. Benchmarking cell type annotation methods for 10x Xenium spatial transcriptomics data. BMC Bioinformatics. 2025;26(1):10.1186/s12859-025-06044-0
Chen Y, Chen L, Lun ATL, Baldoni PL, Smyth GK. edgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets. Nucleic Acids Research. 2025;53(2):10.1093/nar/gkaf018
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
