Oleh Krupa

Massively parallel assessment of gene regulatory activity at human cortical structure associated variants

The paper assesses regulatory activity of cortical structure-associated variants using MPRA in human neural progenitor cells, identifying 918 variants with regulatory potential and showing condition-dependent effects.

Chd8 haploinsufficiency leads to molecular layer heterotopias and age-dependent cortical expansion

This study identifies molecular layer heterotopias and age-dependent cortical expansion in Chd8 haploinsufficient mice, linking them to neuronal migration defects and autism-related brain overgrowth.

CellPheno: A High-throughput Computational Platform for Quantifying Cellular Resolution Whole Brain Microscopy Images

CellPheno is a 3D nuclei segmentation tool for whole-brain microscopy that enables efficient morphometry and co-localization analysis across multiple cell types in mouse brains.

Genetics of cell-type-specific post-transcriptional gene regulation during human neurogenesis

The paper identifies cell-type-specific genetic regulation of RNA-editing and alternative polyadenylation in human neural progenitors and neurons, linking these to brain-related traits.

Systematic investigation of allelic regulatory activity of schizophrenia-associated common variants

The paper uses MPRA to identify functional regulatory variants associated with schizophrenia and shows they differ from eQTLs in genomic location and regulatory impact.

MicroRNA-eQTLs in the developing human neocortex link miR-4707-3p expression to brain size

The paper identifies miRNA-eQTLs in human neocortical tissue, linking miR-4707-3p expression to brain size and educational attainment through colocalization with GWAS data.

Segmentor: A tool for manual refinement of 3D microscopy annotations

Segmentor is a tool for manual refinement of 3D microscopy annotations, improving efficiency without sacrificing accuracy.

Cell-type specific effects of genetic variation on chromatin accessibility during human neuronal differentiation

The paper identifies cell-type specific effects of genetic variation on chromatin accessibility during human neuronal differentiation and links these to regulatory mechanisms of neuropsychiatric disorder risk variants.

Genetic effects on brain traits impact cell-type specific gene regulation during neurogenesis

The paper identifies cell-type specific regulatory mechanisms in human neural progenitors and their neuronal progeny that influence brain-relevant traits, revealing loci not detected in bulk tissue.

NuMorph: tools for cellular phenotyping in tissue cleared whole brain images

NuMorph quantifies nuclei and nuclear markers in cleared mouse brain images, revealing gene deletion effects on cell-type distribution and brain morphology in two mouse models.