Stephen Pederson

This study identifies AP-2β as a key regulator of active enhancers in molecular apocrine breast cancer, linking its expression to cell identity and proliferation.

tadar reduces eQTL noise in bulk RNA-sequencing by accounting for differential allelic representation during differential expression analysis.

The paper introduces a method to identify eQTLs and improve transcriptome analysis by quantifying differential allelic representation in RNA-sequencing data.

The paper identifies a transient period of PRC2 activity in mouse and human oocytes that represses developmental genes, with conservation in human germline but loss during early embryonic development.

The paper investigates transcriptional regulation of autophagy by identifying differentially expressed genes and their association with neurodegenerative pathways in response to autophagy induction.

The paper identifies core and flanking DNA interactions in bHLH-PAS transcription factors that determine binding specificity and link to obesity.

This paper reviews methods for identifying functional interactions from Hi-C data by classifying approaches into three categories: domain discovery, statistical significance detection, and epigenomic integration.

The paper compares the effects of frameshift and frame-preserving mutations in zebrafish psen2 on gene expression in young adult brains, identifying distinct cellular pathways affected.

This study investigates the effects of a SORL1 mutation in zebrafish, identifying changes in mitochondrial and ribosome function without affecting APP-related proteins or mitochondrial content.

The paper investigates the molecular effects of SORL1 mutations in zebrafish, identifying both loss- and gain-of-function impacts on brain transcriptomes related to AD.

This paper introduces 3DFAACTS-SNP, a workflow that identifies T1D risk variants with regulatory mechanisms using Treg-specific epigenomic data, finding 36 candidate SNPs and 51 target genes.

The paper analyzes the transcriptome of zebrafish with a psen2 mutation to identify dominant effects on ribosome, mitochondrial, and anion transport functions.

The paper identifies IRE-containing genes and shows their expression changes are early markers of Alzheimer's disease in zebrafish, revealing species-specific differences in IRE transcript stability under iron dyshomeostasis.

This study uses a zebrafish model of familial Alzheimer’s disease to show accelerated brain aging and transcriptional inversion linked to glucocorticoid resistance and immune pathway changes before histopathology.

ngsReports manages and visualizes NGS QC reports in R, enabling analysis of FastQC and aligner outputs with heatmaps and interactive tools.

The paper analyzes transcriptomes of zebrafish with a familial Alzheimer's disease-like mutation in psen1, finding effects on mitochondrial ATP synthesis and ATP-dependent processes.

The paper analyzes the genome-wide impact of transposable elements on gene regulation, finding that Alu elements are associated with upregulated gene expression and contribute more to regulatory regions than ancient TEs.

This study uses RAD-Seq to discover SNPs in Australian Plutella species, revealing a cryptic species and population structure in diamondback moths.