Katja Kaipio

The paper introduces an interactive workflow called Cyto for analyzing mass cytometry data, demonstrating its ability to capture immune cell sub-populations and tumor compositions in blood and ovarian cancer samples.

The paper identifies a stress-related transcriptional profile in ovarian cancer linked to chemotherapy resistance and poor survival, suggesting MEK1/2 inhibitors as a potential treatment.

PRISM recovers cell type specific expression profiles from composite RNA-seq data, improving patient response prediction compared to raw bulk data.

The paper presents a computational method to identify differentially methylated sites in heterogeneous tumor samples with varying cancer cell fractions, without needing normal controls or prior purity estimates.