%0 Generic %A Isaeva, Olga %D 2025 %T Data underlying the PhD thesis: Computational approaches to dissect immunotherapy response in breast cancer %U %R 10.4121/1881e4a5-55ff-4b51-984b-3d9a2dda1821.v1 %K breast cancer %K covid-19 %K immunotherapy %K lobular breast cancer %K checkpoint inhibitors %K bioinformatics %K RNA-Seq %K WES %K TNBC %K tumor immunology %X

Code underlying the publications described in the thesis. The dataset includes the Python 3, R and bash scripts for bioinformatic analyses included in the following research papers:

1) Nederlof, I., Isaeva, O.I., de Graaf, M. et al. Neoadjuvant nivolumab or nivolumab plus ipilimumab in early-stage triple-negative breast cancer: a phase 2 adaptive trial. Nat Med 30, 3223–3235 (2024). https://doi.org/10.1038/s41591-024-03249-3

2) Voorwerk, L., Isaeva, O.I., Horlings, H.M. et al. PD-L1 blockade in combination with carboplatin as immune induction in metastatic lobular breast cancer: the GELATO trial. Nat Cancer 4, 535–549 (2023). https://doi.org/10.1038/s43018-023-00542-x

3) Gangaev, A., Ketelaars, S.L.C., Isaeva, O.I. et al. Identification and characterization of a SARS-CoV-2 specific CD8+ T cell response with immunodominant features. Nat Commun 12, 2593 (2021). https://doi.org/10.1038/s41467-021-22811-y

%I 4TU.ResearchData