Jason L. Stein

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.

The paper re-engineers an abandoned MATLAB-based image analysis toolkit into a sustainable, FAIR-compliant Nextflow workflow for light-sheet microscopy.

This paper maps genetic, proteomic, and metabolomic effects along human white-matter tracts using UK Biobank data, revealing localized associations with neurodegenerative and psychiatric traits.

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.

This study uses single-nucleus multi-omics to analyze the developing Down syndrome neocortex, identifying dysregulated molecular and gene-regulatory mechanisms affecting neurogenesis and cell specification.

This paper introduces CBSS, a framework for analyzing structural connectomes across multiple cohorts, showing its reliability and utility in cross-cohort diffusion MRI studies.

The paper exposes human neural progenitors to valproic acid and lithium, identifying gene by treatment interactions linked to psychiatric disorder risk and folate metabolism.

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.

This paper introduces RVGA, a framework for efficient genome-wide association analysis in imaging genetics, identifying novel loci and genetic correlations in brain structures using UK Biobank data.

The paper identifies rare protein-coding variants associated with multi-organ MRI traits using exome-wide association analysis in the UK Biobank.

The paper introduces a multi-camera array scanner (MCAS) that significantly reduces imaging time for organoids, enabling faster and more consistent analysis of growth and responses to treatments.

This paper introduces a method to classify gene-by-treatment interactions using Bayesian model selection and applies it to molecular count phenotypes with a software package.

The paper links early cell cycle gene expression in cortical organoids to interindividual variability in infant brain growth trajectories.

This study shows that human cortical organoids generated across multiple sites using a harmonized protocol consistently produce similar cell types and structures, though with some site-specific differences in size and stress markers.

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.

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

The paper investigates the genetic impact of the X-chromosome and sex differences in the human brain, identifying 72 genome-wide significant trait-locus pairs linked to brain-related disorders.

The paper constructs a cross-ancestry, cell-type-informed gene regulatory atlas of the developing human brain, identifying genetic regulation and linking it to neuropsychiatric disorders.

The paper identifies context-specific genetic effects on gene regulation in neural progenitors by stimulating the Wnt pathway and analyzing chromatin accessibility and gene expression.

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.

The paper identifies a genetic locus on chr3p21.1 associated with lithium-induced neural progenitor proliferation and links it to bipolar disorder risk through the gene GNL3.

The paper identifies genetic variations in human gained enhancers that explain heritability of specific brain sulcal morphologies in the UK Biobank.

The paper identifies 60 genetic loci associated with brain ventricular and subcortical shape features using shape measures from over 45,000 UK Biobank and ABCD study subjects.

The paper identifies cell-type-specific causal gene regulatory networks in human neurogenesis by analyzing mediation between chromatin accessibility and gene expression.

This study identifies common genetic variants influencing intrinsic brain networks using rsfMRI data from 44,190 individuals, finding associations with cognitive and clinical traits.

The paper investigates phenotypic and genetic links between heart and brain using MRI data from 40,000 UK Biobank subjects, finding strong correlations and shared genetic influences.

The paper infers cell-type specific imprinted regulatory elements and genes during human neuronal differentiation using allelic bias analysis in chromatin accessibility and gene expression.

This study identifies genetic loci associated with functional brain networks and areas using large-scale fMRI data, linking them to cognitive traits and brain disorders.

This study identifies common genetic variants influencing white matter microstructure using dMRI data from 42,919 individuals, revealing genetic links to neuropsychiatric disorders and other traits.

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