Allan F. McRae

This study identifies genetic regulators of transcriptomic rhythmicity using GTEx data and links them to phenotypes in the Pan-UK Biobank.

The paper identifies seven sex-dependent differentially methylated positions in ALS blood samples, suggesting sex-specific biological mechanisms in the disease.

The paper identifies age-stable and age-variable DNA co-methylation modules in whole-blood data from over 7,500 individuals, showing most modules remain stable with aging while a small subset undergoes reorganisation.

This study conducts an epigenome-wide association study (EWAS) meta-analysis of wellbeing using DNA methylation data, finding no significant methylation sites but suggesting the need for larger studies.

This paper benchmarks parameters for TWAS signature-matching to prioritize drug candidates using GWAS data and CMap, showing sensitivity to cell line choice and proposing a best-practice framework.

The paper identifies 219 pleiotropic conflict regions in the human genome using GWAS data, showing antagonistic variants are enriched for intermediate allele frequency SNPs and under positive/balancing selection.

The paper maps cis- and trans-eQTLs in blood samples to infer gene regulatory networks and prioritize trait-relevant pathways.

The paper uses deconvolution on bulk RNA-seq data to identify cell type proportions and expression signatures linked to endometrial function and disease in women with and without endometriosis.

The paper identifies USP18 as a negative regulator of interferon response at a lupus risk locus through trans-eQTL analysis in lymphoblastoid cell lines.

This study determines updated GWAS significance thresholds for large cohorts, finding that a stricter p-value threshold reduces false positives in studies including rare variants.

The paper identifies sex-associated DNA methylation differences in ALS using a large-scale epigenome-wide association study and links them to survival outcomes.

The paper introduces a method to compress genetic data using autoencoders that leverage linkage disequilibrium structure, achieving high reconstruction accuracy while reducing data size.

The paper identifies tissue-informative DNA methylation sites in ALS using targeted sequencing and machine learning, showing accurate prediction of disease status and progression.

This study examines the genetic and phenotypic links between neonatal C3 and C4 protein concentrations and psychiatric and autoimmune disorders, finding no strong causal associations with mental disorders but evidence of lower autoimmune risk with higher C4 levels.

This study investigates the function of the ALS risk variant GGNBP2 in Drosophila motor neurons, showing it regulates autophagy and synaptic development.

The paper calculates DNA methylation correlations across body fat traits using genome-wide data to identify shared associations and sex-specific differences.

The paper evaluates normalization methods for DNA methylation data to improve BMI prediction across cohorts when projecting new data onto a reference panel.

The paper performs RNA-seq analysis of skeletal muscle in ALS patients and controls to identify differentially expressed genes and isoform switches associated with motor neuron disease.

This study identifies rare genetic variants associated with extreme DNA methylation levels and shows their impact on gene expression in healthy ageing populations.

The paper analyzes endometrial DNA methylation and genetic variants to identify mQTLs and their association with endometriosis risk and menstrual cycle phases.

This study evaluates how biological and statistical properties of CpGs affect epigenetic predictions for eighteen traits, showing that CpG methylation QTL status and beta-value distribution influence prediction accuracy.

The paper develops epigenetic scores (EpiScores) for plasma proteins to predict disease risk, finding 137 associations with incident morbidities independent of known factors.

The paper investigates a genotype by sex interaction in Ankylosing Spondylitis risk, showing it is driven by HLA-B rather than MICA variation.

The paper identifies genetic variants influencing DNA methylation in blood and shows their associations with complex traits and diseases, but finds limited direct causality.

The paper develops a DNA methylation-based proxy for interleukin-6 and finds it correlates with age and cognitive functioning better than serum IL-6.

The paper develops an epigenetic CRP score to assess chronic inflammation and its link to cognitive ability, finding it more consistently associated with cognition than serum CRP across two cohorts.

This study predicts promoter-anchored chromatin interactions using DNA methylation QTL data from a human cohort, finding overlaps with experimental data and associations with complex traits.

This study identifies genetic and epigenetic factors associated with inflammatory protein levels in older adults using GWAS and EWAS with a Bayesian framework.

This study identifies DNA methylation loci associated with age-by-sex interactions in a cohort of 2,586 individuals, finding most significant loci are X-linked and linked to disease-related genes.

The paper reports epigenome-wide meta-analyses of blood DNA methylation with subcortical brain volumes, identifying significant associations with hippocampal volume and potential biological mechanisms.