Jaana Oikkonen

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.

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.

Multi-Omics Characterization of ctDNA Release Mechanisms in Ovarian Cancer

This study identifies molecular drivers of ctDNA variability in ovarian cancer by analyzing genomic and transcriptomic data from 118 patients, linking ctDNA levels to proliferation and immune activity.

SegmentQTL: Identifying genetic variants influencing molecular phenotypes in copy number-driven cancers

SegmentQTL improves molQTL analysis in copy number-driven cancers by incorporating breakpoint information to reduce false discoveries and refine associations.

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.

Analysis of single-cell RNA-seq data from ovarian cancer samples before and after chemotherapy links stress-related transcriptional profile withchemotherapy resistance

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.