Merja Heinäniemi

CyStainer imputes markers in high-parameter cytometry data without shared markers, outperforming existing methods in panel merging and dataset integration.

This paper develops a subspace one-class classification framework for proteomics-driven anomaly detection using healthy reference data to identify disease patterns across multiple conditions.

The paper analyzes subclonal gene dosage effects in cancer using DNTR-seq, finding additive and compensatory transcriptional impacts and identifying transient clonality in ovarian and soft tissue sarcomas.

The paper identifies immune-related transcriptional changes in adipose-derived fibroblasts in obesity-associated atherosclerosis using single-cell RNA sequencing and spatial transcriptomics.

This study identifies H1-0 as a mediator of ETV6::RUNX1-induced quiescence in BCP-ALL preleukemic cells and suggests HDACi treatment as a potential therapeutic approach.

The paper identifies a CAD risk SNP rs880890 in an endothelial enhancer that reduces CALCRL expression by impairing HSF binding under shear stress.

The paper compares three scRNA-seq methods for ex vivo drug screening in ALL cells, finding consistent transcriptional responses to fludarabine despite method-specific differences.

The paper quantifies and integrates miRNA gene expression in single-cell studies, revealing age- and disease-related miRNA regulation in immune cells.

The paper introduces a semi-supervised generative model for single-cell data using CITE-seq protein counts to improve gene expression analysis.