Joel E. Kleinman

The paper re-analyzes RNA sequencing data comparing gene expression in living and postmortem human brain tissue, finding that living samples had lower quality, and questions the validity of previous conclusions about postmortem studies.

The paper uses spatial proteogenomics to analyze gene expression changes in Alzheimer's disease brains linked to amyloid-beta and tau pathology.

The paper identifies a striatal gene set linked to schizophrenia risk that predicts in vivo dopamine synthesis and striatal activation in neurotypical and patient cohorts.

The paper examines how genetic ancestry influences gene expression and DNA methylation in admixed African/Black Americans, showing environmental and genetic factors affect brain disease risk.

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 characterizes the molecular landscape of the human locus coeruleus using spatially-resolved transcriptomics and single-nucleus RNA-sequencing, providing a publicly accessible resource.

SUFI automates spectral unmixing of fluorescent multiplex images in mouse and postmortem human brain tissues, improving accuracy over manual methods and existing software.

VistoSeg processes high-resolution Visium/Visium-IF images to integrate image-derived metrics with spatial gene expression data for spatial transcriptomics analysis.

The paper identifies sex differences in schizophrenia across three brain regions using RNA-seq and genotypes, finding sex-specific genes, eQTLs, and transcriptional features.

The paper identifies differentially expressed genes in PTSD and MDD across brain regions, highlighting shared and unique transcriptional patterns and immune-related pathways.

This study characterizes TAF1 expression variation in XDP female carriers and human brain ontogeny, identifying age- and region-specific patterns that may explain neostriatum vulnerability in XDP.

The paper uses ventral forebrain organoids from schizophrenia patients and controls to show accelerated maturation of inhibitory neurons and shared gene expression patterns with postmortem brain tissue.

The paper uses snRNA-seq to analyze five human brain regions, identifies novel neuronal subpopulations, and links them to psychiatric and substance use risks.

The paper shows that incorporating cell size parameters improves deconvolution of brain RNA-seq data, but using external cell size estimates can introduce bias.

The paper manipulates genomic risk signatures for schizophrenia in brain co-expression networks to explore their impact on gene connectivity and variability.

The paper identifies transcriptomic differences in human pluripotent stem cells that correlate with retinoic acid response and neural fate bias.

The paper maps spatial gene expression in the human dorsolateral prefrontal cortex using spatial transcriptomics and identifies layer-specific gene expression patterns linked to neuropsychiatric disorders.

The paper investigates how psychiatric disease and aging affect FKBP5 expression in the human brain, identifying supragranular neurons as key targets.

The paper compares gene expression in the prefrontal cortex between individuals who died from acute opioid intoxication and controls, finding NPAS4 is downregulated and associated with opioid use.

This study examines DNA methylation in brain tissue from opioid users and controls, finding a significant association between opioid use and phenotypic age but no genome-wide significant CpG sites.

The paper identifies widespread genetic influences on DNA methylation in the human brain and links schizophrenia GWAS variants to epigenetic changes.

This paper shows that primed human pluripotent stem cells can differentiate to trophoblast stem cells without becoming naive, using specific signaling conditions and revealing a transcriptional network involving BMP5/7 and GATA3.

This study identifies DNA methylation differences in the nucleus accumbens of smokers versus nonsmokers, revealing both shared and tissue-specific CpGs associated with smoking.

The paper characterizes dynamic DNA methylation patterns in the prenatal human cortex, identifying loci associated with gene expression, enhancer states, and psychiatric disorder genes.

The paper uses hiPSC transcriptomics to study neuronal differentiation and maturation across multiple conditions and develops a tool to estimate neuronal maturity.

The paper uses long-read sequencing to uncover the complex splicing profile of the CACNA1C gene in human brain, identifying numerous novel exons and transcripts with potential functional implications.

This study characterizes DNA methylation changes in human neurons across development, identifies distinct methylation patterns, and links them to heritable brain-related phenotypes.

The paper identifies regional differences in gene expression and regulation in hippocampus and dorsolateral prefrontal cortex across development and in schizophrenia using RNA-seq data from 900 samples.

The paper identifies a gene co-expression module enriched for schizophrenia risk genes and shows its association with treatment response in schizophrenia patients.