Minna Unelma Kaikkonen

This paper develops an in vitro system that mimics osteochondrogenic differentiation of smooth muscle cells and intimal vascular calcification, showing distinct transcriptional states compared to standard calcification assays.

The paper develops a computational framework using optimal transport to analyze macrophage state transitions in atherosclerosis, identifying origin-dependent plasticity mechanisms and shared regulatory circuits in inflammation and fibrosis.

This study identifies METTL7A as a mechanosensitive methyltransferase that regulates internal m7G methylation in endothelial cells, protecting against atherosclerosis through stabilization of anti-inflammatory transcripts.

Smooth muscle foam cells in early-to-intermediate human coronary plaques map to fibromyocytes, express CFH and SERPINE1 unlike macrophage foam cells, and show matrix, coagulation and angiogenesis programs.

This paper shows that nuclear speckles regulate viral and host mRNA processing and export during HSV-1 infection, with viral transcripts uniquely relying on speckles for export.

This study shows that the nucleus softens during herpesvirus infection due to reduced outward forces and low biomolecular density in the viral replication compartment.

This study examines miRNA distribution and function in nuclear and cytoplasmic compartments of human endothelial cells under hypoxia, revealing nuclear-specific roles in cell proliferation and inflammation.

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

The paper identifies causal genetic mechanisms at CAD GWAS loci using CRISPR screens and chromatin analysis, revealing enhancer-gene links and ancestry/sex-specific risk factors.

The paper introduces ambimux, a method to estimate and demultiplex ambient molecule contamination in single-cell RNA+ATAC multiome data, improving the detection of biologically meaningful signals.

This study identifies 59 novel genome-wide significant loci shared between coronary artery disease and aortic aneurysms through joint meta-analysis and functional characterization.

The paper integrates single-cell omics with biobank data to show SREBF1 risk variants affect adipocyte gene expression in trans, impacting abdominal obesity.

QClus improves snRNA-seq data quality by filtering droplets in challenging samples, achieving high quality across multiple datasets and metrics.

The paper uses single-nuclei RNA-seq and spatial transcriptomics to analyze gene expression changes in the right atrium of patients with ischemic heart disease, revealing inflammatory microvascular dysfunction and altered tissue composition.

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 evaluates isomiR expression differences across conditions and shows their impact on miRNA-seq quantification, highlighting the need for isomiR-aware analysis.

The paper shows that ciRS-7 and miR-7 regulate ischemia-induced neuronal death through glutamatergic signaling in mice.

This study shows how herpesvirus infection alters mitochondrial structure and metabolism during infection progression.

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

The paper analyzes multi-omic data from two pig heart xenografts in human decedents to identify immune and metabolic responses associated with rejection and injury.

The paper identifies functional non-coding SNPs in human endothelial cells that influence vascular traits by affecting transcriptional regulation and chromatin states.

The paper identifies eQTLs and sQTLs in human aortic SMCs that colocalize with CAD GWAS loci, highlighting splicing regulation as a mechanism for CAD risk.

The paper shows isomiRs significantly affect differential expression analysis and highlights the need to consider them instead of relying solely on reference miRNA sequences.

This study identifies disease-specific gene expression and protein secretion patterns in olfactory mucosa cells from Alzheimer's patients, revealing potential diagnostic and mechanistic insights.

The paper identifies Essrg as a necessary factor for Sox8-mediated M cell differentiation, regulated by PRC2 during intestinal M cell development.