Çubuk H, Jin X, Phipson B, Marsh JA, Rubin AF. Variant scoring tools for deep mutational scanning. Molecular Systems Biology. 2025;:10.1038/s44320-025-00137-x
Urban RQ, Keerthikumar S, Clark A, Wang H, Phipson B, Bakshi A, Ryan A, Thorne H, Taylor RA, Lawrence MG, Risbridger GP, Toivanen R, Goode DL. Single‐cell transcriptomics redefines focal neuroendocrine differentiation as a distinct prostate cancer pathology. Molecular Oncology. 2025;:10.1002/1878-0261.70099
Bhuva DD, Tan CW, Salim A, Marceaux C, Pickering MA, Chen J, Kharbanda M, Jin X, Liu N, Feher K, Putri G, Tilley WD, Hickey TE, Asselin-Labat M-L, Phipson B, Davis MJ. Library size confounds biology in spatial transcriptomics data. Genome Biology. 2024;25(1):10.1186/s13059-024-03241-7
Putri GH, Howitt G, Marsh-Wakefield F, Ashhurst TM, Phipson B. SuperCellCyto: enabling efficient analysis of large scale cytometry datasets. Genome Biology. 2024;25(1):10.1186/s13059-024-03229-3
Tan CW, Chen J, Liu N, Bhuva DD, Blick T, Monkman J, Cooper C, Kharbanda M, Feher K, Phipson B, Killingbeck EE, Pan L, Kim Y, Liang Y, Nam A, Leon M, Souza-Fonseca-Guimaraes P, Nagashima S, Martins APC, Machado-Souza C, de Noronha L, Tang B, Short K, Fraser J, Belz GT, Souza-Fonseca-Guimaraes F, Kulasinghe A, Davis MJ. In situ single-cell profiling sheds light on IFI27 localisation during SARS-CoV-2 infection. EBioMedicine. 2024;101:10.1016/j.ebiom.2024.105016
Homan CC, Drazer MW, Yu K, Lawrence DM, Feng J, Arriola-Martinez L, Pozsgai MJ, McNeely KE, Ha T, Venugopal P, Arts P, King-Smith SL, Cheah J, Armstrong M, Wang P, Bödör C, Cantor AB, Cazzola M, Degelman E, DiNardo CD, Duployez N, Favier R, Fröhling S, Rio-Machin A, Klco JM, Krämer A, Kurokawa M, Lee J, Malcovati L, Morgan NV, Natsoulis G, Owen C, Patel KP, Preudhomme C, Raslova H, Rienhoff H, Ripperger T, Schulte R, Tawana K, Velloso E, Yan B, Kim E, Sood R, Program NCS, Hsu AP, Holland SM, Phillips K, Poplawski NK, Babic M, Wei AH, Forsyth C, Fan HM, Lewis ID, Cooney J, Susman R, Fox LC, Blombery P, Singhal D, Hiwase D, Phipson B, Schreiber AW, Hahn CN, Scott HS, Liu P, Godley LA, Brown AL. Somatic mutational landscape of hereditary hematopoietic malignancies caused by germ line RUNX1, GATA2, and DDX41 variants. Blood Advances. 2023;7(20):10.1182/bloodadvances.2023010045
Kueh AJ, Bergamasco MI, Quaglieri A, Phipson B, Li-Wai-Suen CSN, Lönnstedt IM, Hu Y, Feng Z-P, Woodruff C, May RE, Wilcox S, Garnham AL, Snyder MP, Smyth GK, Speed TP, Thomas T, Voss AK. Stem cell plasticity, acetylation of H3K14, and de novo gene activation rely on KAT7. Cell Reports. 2023;42(1):10.1016/j.celrep.2022.111980
Phipson B, Sim CB, Porrello ER, Hewitt AW, Powell J, Oshlack A. propeller: testing for differences in cell type proportions in single cell data. Bioinformatics. 2022;38(20):10.1093/bioinformatics/btac582
Mehdiabadi NR, Sim CB, Phipson B, Kalathur RKR, Sun Y, Vivien CJ, Huurne MT, Piers AT, Hudson JE, Oshlack A, Weintraub RG, Konstantinov IE, Palpant NJ, Elliott DA, Porrello ER. Defining the Fetal Gene Program at Single-Cell Resolution in Pediatric Dilated Cardiomyopathy. Circulation. 2022;146(14):10.1161/circulationaha.121.057763
Maksimovic J, Oshlack A, Phipson B. Gene set enrichment analysis for genome-wide DNA methylation data. Genome Biology. 2021;22(1):10.1186/s13059-021-02388-x
