Marieke E. Ijsselsteijn

The paper integrates single-cell data from CRC patients to identify immune subtypes and neutrophil phenotypes, revealing their spatial organization and tumor-induced changes.

GRIDGENE identifies tissue compartments using transcript density in spatial transcriptomics data, enabling analysis without cell segmentation.

The paper uses imaging mass cytometry to analyze granulomas in Mtb-infected non-human primates, finding that NK cell-macrophage interactions correlate with reduced tuberculosis pathology.

This study compares immunogenic features between undifferentiated soft tissue sarcoma and myxofibrosarcoma, finding differences in T cell and macrophage infiltration and their prognostic significance.

PENGUIN is a preprocessing tool for multiplexed spatial proteomics that normalizes signal-to-noise ratios and reduces noise without manual annotation or machine learning training.

The paper examines immune profiles in Lynch syndrome colorectal cancers across different MMR gene defects and finds no significant differences in immunogenic features.

The paper identifies iron-accumulating microglia in Alzheimer's brains, linking iron uptake to microglial activation and disease pathology.

quanTIseq estimates absolute fractions of ten immune cell types from bulk RNA-seq; across TCGA, CXCL9/CXCR3 expression, not mutational load, tracks CD8+ T cell infiltration.