Nicholas J. Eagles

Multi-omic spatial mapping of the human habenula defines the molecular and anatomical organization of medial and lateral subregions

This study maps the spatiomolecular organization of the human habenula using multi-omic approaches, identifying molecular signatures and spatial domains linked to psychiatric disorders.

Molecular impact of nicotine and smoking exposure on the developing and adult mouse brain

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.

Spatiomolecular mapping reveals anatomical organization of heterogeneous cell types in the human nucleus accumbens

This study creates a spatiomolecular atlas of the human nucleus accumbens using spatial transcriptomics and single-nucleus RNA sequencing, revealing spatial gradients and conserved features across species.

Transcriptional response to chronic long-access fentanyl self-administration in rat habenula and amygdala

This study identifies transcriptomic changes in rat habenula and amygdala after chronic fentanyl self-administration, linking them to human cell types and risk genes for addiction.

Mapping spatially organized molecular and genetic signatures of schizophrenia across multiple scales in human prefrontal cortex

This study maps molecular and genetic signatures of schizophrenia in human prefrontal cortex across spatial scales, revealing altered BDNF-TrkB signaling and inhibitory circuit dysfunction.

APOE E4 Alzheimer's Risk Converges on an Oligodendrocyte Subtype in the Human Entorhinal Cortex

The paper investigates how APOE genotype affects gene expression in the human entorhinal cortex, identifying an oligodendrocyte subtype as a potential mediator of Alzheimer's disease risk.

Transcriptomic analysis of the human habenula in schizophrenia

The paper performs transcriptomic analysis of the human habenula and identifies molecular changes associated with schizophrenia risk and illness state.

An integrated single-nucleus and spatial transcriptomics atlas reveals the molecular landscape of the human hippocampus

The paper integrates single-nucleus and spatial transcriptomics data to map the molecular landscape of the human hippocampus, identifying cell types and spatial domains.

Benchmark of cellular deconvolution methods using a multi-assay reference dataset from postmortem human prefrontal cortex

The paper benchmarks cellular deconvolution methods using a multi-assay dataset from human prefrontal cortex, finding Bisque and hspe to be the most accurate.

Integrating gene expression and imaging data across Visium capture areas with visiumStitched

The paper introduces visiumStitched, a tool for stitching Visium spatial transcriptomics data across multiple capture areas, enabling seamless analysis without data loss.

Stimulation of locus coeruleus inputs to the frontal cortex in mice induces cell type-specific expression of the Apoe gene

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.

Massively parallel characterization of psychiatric disorder-associated and cell-type-specific regulatory elements in the developing human cortex

The paper identifies 46,802 enhancers and 164 psychiatric disorder variants with regulatory effects in the developing cortex and organoids using massively parallel reporter assays and deep learning.

Integrated single cell and unsupervised spatial transcriptomic analysis defines molecular anatomy of the human dorsolateral prefrontal cortex

The paper generates a molecular neuroanatomical map of the human prefrontal cortex using spatial transcriptomics and single nucleus RNA-sequencing, revealing novel spatial domains and cell-cell interactions linked to psychiatric disorders.

Influence of Alzheimer's disease related neuropathology on local microenvironment gene expression in the human inferior temporal cortex

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

BiocMAP: A Bioconductor-friendly, GPU-Accelerated Pipeline for Bisulfite-Sequencing Data

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

Genetic and environmental contributions to ancestry differences in gene expression in the human brain

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.

Performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments

Samui is a web-based tool for visualizing and annotating spatially-resolved transcriptomics data, enabling fast exploration of large images and their features.

Electrophysiological measures from human iPSC-derived neurons are associated with schizophrenia clinical status and predict individual cognitive performance

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

Investigating trait variability of gene co-expression network architecture in brain by manipulating genomic signatures of schizophrenia risk

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

SPEAQeasy: a Scalable Pipeline for Expression Analysis and Quantification for R/Bioconductor-powered RNA-seq analyses

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

Widespread methylation quantitative trait loci and their role in schizophrenia risk

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

Characterizing the dynamic and functional DNA methylation landscape in the developing human cortex

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