Emily E. Burke

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.

Developmental profile of psychiatric risk associated with voltage-gated cation channel activity

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.

Dissecting transcriptomic signatures of neuronal differentiation and maturation using iPSCs

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

Divergent neuronal DNA methylation patterns across human cortical development: Critical periods and a unique role of CpH methylation

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

Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods

This study evaluates biases in small RNA sequencing methods, showing that UMIs improve accuracy and highlighting limitations in current miRNA and isomiR quantification.

Regional heterogeneity in gene expression, regulation and coherence in hippocampus and dorsolateral prefrontal cortex across development and in schizophrenia

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.

Characterizing the nuclear and cytoplasmic transcriptomes in developing and mature human cortex uncovers new insight into psychiatric disease gene regulation

The paper characterizes nuclear and cytoplasmic transcriptomes in human cortex development and finds increased nuclear retention in mature brain, linked to psychiatric disease gene regulation.

Defects of myelination are common pathophysiology in syndromic and idiopathic autism spectrum disorders

The paper compares mouse models of syndromic ASD with human ASD brain data to identify shared myelination and axon development disruptions across both syndromic and idiopathic ASD.