Andrew E. Jaffe

This study compares the molecular effects of prenatal nicotine exposure and maternal smoking during pregnancy on mouse brain development and adulthood, finding distinct gene expression changes in pups but not adults.

The paper stimulates locus coeruleus inputs to the frontal cortex in mice and finds cell type-specific Apoe gene expression, particularly in GABAergic neurons, with sex-dependent effects.

This study shows TCF4 mutations impair synaptic function in patient-derived cortical neurons by disrupting RIMBP2 expression, leading to deficits in synaptic transmission and network excitability.

This study investigates TrkB signaling in the lateral septum using RNA-seq, identifying gene expression changes linked to psychiatric and neurodegenerative disorders.

BiocMAP is a GPU-accelerated pipeline for WGBS data that reduces computational time and memory usage through efficient alignment and data representation.

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.

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

DeepMosaic detects mosaic single nucleotide variants without control samples using deep convolutional neural networks, achieving high accuracy and uncovering many variants missed by existing methods.

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

CaPTure is a scalable pipeline for analyzing calcium imaging data from cultured neurons, enabling high-throughput phenotypic discovery.

This study identifies the basolateral amygdala to lateral septum circuit as critical for regulating sociability in mice through BDNF-TrkB signaling.

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

spatialLIBD provides an R/Bioconductor package for interactive visualization of spatially-resolved transcriptomics data from the 10x Genomics Visium platform.

PACeR is a bioinformatic pipeline for analyzing chimeric RNA-seq data, providing tools for read processing, alignment, peak calling, and motif analysis.

The paper evaluates brain somatic mosaicism in the adult human to identify rules governing cellular distribution during embryogenesis.

The paper shows that Bdnf exon 1 expression is necessary for ECS-induced dendritic spine plasticity in piriform cortex neurons.

The paper identifies electrophysiological measures in hiPSC-derived neurons linked to schizophrenia diagnosis and cognitive performance.

recount3 provides uniformly processed RNA-seq data and tools for querying and analyzing large-scale human and mouse expression and splicing data.

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.

SPEAQeasy provides a user-friendly, scalable RNA-seq pipeline that simplifies data processing and connects to R/Bioconductor tools for downstream analysis.

The paper examines the developmental expression of genes related to voltage-gated cation channels and their association with psychiatric disorders, finding that gene expression patterns vary with age and disorder type.

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 introduces a machine learning method to detect somatic L1 insertions in human brain tissue, revealing their widespread distribution in neurons and glia and potential role in neuropsychiatric diseases.

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