tumor-immunology

Re-analysis of the Dean et al. 2024 (Nat Commun) Kaede NK-cell tumour-entry dataset with a CD160 signature overlay

CRC immunoepigenomics integrating methylation-derived immune deconvolution, LINE-1, CIMP, ATM methylation, environmental context, and statistical modeling.

Spatial transcriptomics investigation of immune-program colocalization, multicellular niches, and tissue organization in breast cancer using 10x Visium.

Re-analysis of the Borcherding et al. 2024 (Nature Immunology) pan-cancer tumour-infiltrating NK-cell reference

Preprocessing and analysis of a renal cell carcinoma (RCC) spatial transcriptomics dataset

Reproducible analyses for tumor-cell TNFR1 loss and CAR-T functional fitness: bulk RNA-seq, targeted single-cell mRNA profiling, DepMap and exploratory immunotherapy cohorts.

Re-analysis of the Sade-Feldman et al. 2018 (Cell) melanoma tumour-infiltrating lymphocyte scRNA-seq dataset

Re-analysis of the Cillo et al. 2020 (Immunity) human HNSCC immune scRNA-seq dataset

CMS4 CRC single-cell immune-state analysis integrating Seurat, Harmony, Azimuth, pseudobulk DESeq2, pathway GSEA, and African ancestry.

Re-analysis of the Nieto et al. 2021 pan-cancer Tumour Immune Cell Atlas (CD226/DNAM signature scoring)

Re-analysis of the Abdelfattah et al. 2022 (Nat Commun) human glioma immune scRNA-seq atlas (GSE182109)

Scientific framework and immunological rationale for individualized brain tumor immunotherapy protocols.

Re-analysis of the Tang et al. 2023 (Cell) pan-cancer NK-cell atlas with CD160/DGAT signature scoring

Identifying and marking T-Cells capable of resisting exhaustion and fighting against tumors - Colorectal Cancer.

Immune-compartment secretory and regulatory programmes distinguishing checkpoint response in melanoma - single-cell and bulk RNA-seq analysis