Anni Virtanen

FEATMAP: Targeted Correction of Acquisition Signatures Harmonizes Medical Foundation Model Embeddings and Enables Robust Task Generalization

FEATMAP corrects acquisition signatures in medical foundation model embeddings to improve cross-condition similarity and task generalization without retraining.

Spatio-Temporal Landscape of Whole-Genome DNA Methylation Patterns in Ovarian Cancer

This study maps the spatio-temporal DNA methylation patterns in ovarian cancer using longitudinal data from the DECIDER trial, showing early establishment of regulatory methylomes and their stability through treatment.

Single-cell spatial atlas of high-grade serous ovarian cancer unveils MHC class II as a key driver of spatial tumor ecosystems and clinical outcomes

Cyclic immunofluorescence of 265 high-grade serous ovarian carcinomas and random-forest feature ranking identify cancer-cell MHC-II as an adjusted predictor of longer survival marking immune-activated tumor-stroma hotspots.

Multi-Omics Analysis Reveals the Attenuation of the Interferon Pathway as a Driver of Chemo-Refractory Ovarian Cancer

The paper identifies reduced IFN-I pathway activity as a driver of chemo-refractory ovarian cancer using multi-omics analysis in a clinical trial cohort.

Multi-modal characterization of transcriptional programs that drive metastatic cascades to solid sites and ascites in ovarian cancer

The paper identifies nine transcriptional programs driving metastasis in ovarian cancer using multi-modal data from 350 tumor samples, highlighting intra-patient heterogeneity and therapeutic implications.

Tribus: Semi-automated discovery of cell identities and phenotypes from multiplexed imaging and proteomicdata

Tribus is a semi-automated tool for cell phenotyping from multiplexed imaging and proteomic data, achieving high accuracy and efficiency compared to existing methods.

Histolytics: A Panoptic Spatial Analysis Framework for Interpretable Histopathology

Histolytics provides a framework for interpretable spatial analysis of histopathology images, enabling high-resolution characterization of tissue structures and features.

Chemotherapy induces myeloid-driven spatial T-cell exhaustion in ovarian cancer

This study shows chemotherapy causes myeloid-driven spatial T-cell exhaustion in ovarian cancer by altering immune cell states and interactions, suggesting new immunotherapy approaches.

Patient-derived functional immuno-oncology platform identifies responders to ATR inhibitor and immunotherapy combinations in ovarian cancer

Deciphering Cancer Genomes with GenomeSpy: A Grammar-Based Visualization Toolkit

GenomeSpy is a grammar-based visualization toolkit for genomic data analysis that enables interactive exploration of large datasets, demonstrated on ovarian cancer samples.