Caramia F, Speed TP, Shen H, Haupt Y, Haupt S. Establishing the Link between X-Chromosome Aberrations and TP53 Status, with Breast Cancer Patient Outcomes. Cells. 2023;12(18):10.3390/cells12182245
Mangiola S, Roth-Schulze AJ, Trussart M, Zozaya-Valdés E, Ma M, Gao Z, Rubin AF, Speed TP, Shim H, Papenfuss AT. sccomp: Robust differential composition and variability analysis for single-cell data. Proceedings of the National Academy of Sciences of the United States of America. 2023;120(33):10.1073/pnas.2203828120
Gurun B, Horton W, Murugan D, Zhu B, Leyshock P, Kumar S, Byrne KT, Vonderheide RH, Margolin AA, Mori M, Spellman PT, Coussens LM, Speed TP. An open protocol for modeling T Cell Clonotype repertoires using TCRβ CDR3 sequences. BMC Genomics. 2023;24(1):10.1186/s12864-023-09424-z
Brown LC, Luen SJ, Molania R, Caramia F, Savas P, VanGeelen C, Chic N, Fleming GF, Kammler R, Colleoni M, Viale G, Speed TP, Regan MM, Francis PA, Loi S. Evaluation of PAM50 intrinsic subtypes and risk of recurrence (ROR) scores in premenopausal women with early-stage HR+ breast cancer: A secondary analysis of the SOFT trial.Journal of Clinical Oncology. 2023;41(16_suppl):10.1200/jco.2023.41.16_suppl.504
Feng Y, Yang T, Zhu J, Li M, Doyle M, Ozcoban V, Bass GT, Pizzolla A, Cain L, Weng S, Pasam A, Kocovski N, Huang Y-K, Keam SP, Speed TP, Neeson PJ, Pearson RB, Sandhu S, Goode DL, Trigos AS. Spatial analysis with SPIAT and spaSim to characterize and simulate tissue microenvironments. Nature Communications. 2023;14(1):10.1038/s41467-023-37822-0
Weeden CE, Gayevskiy V, Marceaux C, Batey D, Tan T, Yokote K, Ribera NT, Clatch A, Christo S, Teh CE, Mitchell AJ, Trussart M, Rankin L, Obers A, McDonald JA, Sutherland KD, Sharma VJ, Starkey G, D’Costa R, Antippa P, Leong T, Steinfort D, Irving L, Swanton C, Gordon CL, Mackay LK, Speed TP, Gray DHD, Asselin-Labat M-L. Early immune pressure initiated by tissue-resident memory T cells sculpts tumor evolution in non-small cell lung cancer. Cancer Cell. 2023;41(5):10.1016/j.ccell.2023.03.019
Luen SJ, Viale G, Nik-Zainal S, Savas P, Kammler R, Dell’Orto P, Biasi O, Degasperi A, Brown LC, Láng I, MacGrogan G, Tondini C, Bellet M, Villa F, Bernardo A, Ciruelos E, Karlsson P, Neven P, Climent M, Müller B, Jochum W, Bonnefoi H, Martino S, Davidson NE, Geyer C, Chia SK, Ingle JN, Coleman R, Solbach C, Thürlimann B, Colleoni M, Coates AS, Goldhirsch A, Fleming GF, Francis PA, Speed TP, Regan MM, Loi S. Genomic characterisation of hormone receptor-positive breast cancer arising in very young women. Annals of Oncology. 2023;34(4):10.1016/j.annonc.2023.01.009
Virassamy B, Caramia F, Savas P, Sant S, Wang J, Christo SN, Byrne A, Clarke K, Brown E, Teo ZL, von Scheidt B, Freestone D, Gandolfo LC, Weber K, Teply-Szymanski J, Li R, Luen SJ, Denkert C, Loibl S, Lucas O, Swanton C, Speed TP, Darcy PK, Neeson PJ, Mackay LK, Loi S. Intratumoral CD8+ T cells with a tissue-resident memory phenotype mediate local immunity and immune checkpoint responses in breast cancer. Cancer Cell. 2023;41(3):10.1016/j.ccell.2023.01.004
Lönnstedt IM, Speed TP. Remove unwanted variation retrieves unknown experimental designs. Scandinavian Journal of Statistics. 2023;50(1):10.1111/sjos.12633
Gurun B, Horton W, Murugan D, Zhu B, Leyshock P, Kumar S, Byrne KT, Vonderheide RH, Margolin AA, Mori M, Spellman PT, Coussens LM, Speed TP. An open protocol for modeling T Cell Clonotype repertoires using TCRβ CDR3 sequences. 2023;:10.21203/rs.3.rs-2140339/v1
