Derek E. Wildman

DNA Methylation as a Mediator of Cardiovascular Disease Risk in Relation to PTSD Severity: Identification of Potential Epigenetic Biomarkers.

The paper investigates DNA methylation mediation between PTSD severity and cardiovascular disease risk, identifying six CpGs as potential epigenetic biomarkers.

Time-varying mediation analysis for incomplete data with application to DNA methylation study for PTSD

The paper develops time-varying mediation analysis methods for DNA methylation data to study dynamic mediation effects of trauma on PTSD using the Detroit Neighborhood Health Study.

Miniaturized Workflow for Transcriptomic Profiling of Urinary Extracellular RNA during Pregnancy

The paper develops a scalable workflow for transcriptomic profiling of urinary exRNA during pregnancy, identifying differentially expressed exRNAs associated with pregnancy-related changes.

Differentially Expressed Heterogeneous Overdispersion Genes Testing for Count Data

The paper introduces DEHOGT, a method for detecting differentially expressed genes in RNA-seq data that accounts for overdispersion, and shows it outperforms DESeq and EdgeR on synthetic data and detects more DE genes in microglial cells under stress hormone treatments.

Multi-ancestry GWAS of major depression aids locus discovery, fine-mapping, gene prioritisation, and causal inference

This paper conducts a multi-ancestry GWAS of major depression, identifying 190 loci and 354 genes, with findings showing increased fine-mapping power and bidirectional BMI relationship in European ancestry samples.

Heterogeneous Mediation Analysis on Epigenomic PTSD and Traumatic Stress in a Predominantly African American Cohort

The paper develops a heterogeneous mediation analysis method to study DNA methylation's role in PTSD among African Americans, identifying subgroups and mediators linked to PTSD symptoms.

DNA methylation of Nuclear Factor of Activated T Cells 1 mediates the prospective relation between exposure to different traumatic event types and post-traumatic stress disorder

The paper examines how DNA methylation at NFATC1 CpG sites mediates the relationship between different trauma types and PTSD risk in a prospective study.

Psychosocial experiences modulate asthma-associated genes through gene-environment interactions

The paper identifies 174 asthma-associated genes regulated by psychosocial factors and 349 gene-environment interactions using RNA-sequencing and machine learning in children with asthma.

Neighborhood environment, social cohesion, and epigenetic aging

This study examines how neighborhood conditions relate to epigenetic aging using DNA methylation clocks in a sample of 158 individuals from the Detroit Neighborhood Health Study.

The Impact of Psychopathology, Social Adversity and Stress-relevant DNAm on Prospective Risk for Post-traumatic Stress: A Machine Learning Approach

The paper uses machine learning to identify factors predicting prospective risk of post-traumatic stress symptoms, finding that prior PTSS, loneliness, and a specific DNA methylation site are key predictors.

Computational performance and accuracy of Sentieon DNASeq variant calling workflow

This study compares the accuracy and performance of Sentieon DNASeq and GATK for single-sample variant calling, finding they are nearly identical in accuracy with Sentieon being faster and more scalable.

Methylomic profiles reveal sex-specific shifts in leukocyte composition associated with post-traumatic stress disorder

The paper identifies sex-specific changes in monocyte proportions in males with PTSD using methylomic data, showing no such changes in females.

DNA Methylation Explains a Subset of Placental Gene Expression Differences Based on Ancestry and Altitude

The paper examines how DNA methylation influences gene expression differences in placental tissue between Andean and European ancestry individuals at high and low altitudes, finding more methylation regulation in ancestry-related genes.

Performance benchmarking of GATK3.8 and GATK4

This study benchmarks GATK3.8 and GATK4 to evaluate performance improvements and cost trade-offs in genomic variant calling.

The Core Transcriptome Of Mammalian Placentas And The Divergence Of Expression With Placental Shape

The paper identifies 115 core genes expressed in all eutherian placentas and finds genes associated with placental shape and pre-eclampsia.