Justin Martin O'Sullivan

This study uses Mendelian randomization with spatial gene networks to identify causal genes and shared/distinct drivers of risk for melanoma, BCC, and SCC.

The paper develops a model to estimate infant gut microbiome age using metagenomic data, finding conserved microbial succession patterns across diverse human populations.

The paper identifies melanoma-specific mutation hotspots in non-coding regions that affect gene expression and suggest novel candidate driver genes.

The paper benchmarks nanopore sequencing performance and validates a rapid genomics pipeline for clinical use in New Zealand.

The paper identifies infection-dependent changes in lung-specific gene expression and chromatin remodelling associated with SARS-CoV-2 risk variants.

This study identifies causal genes and genetic loci linking autism to co-occurring traits using Mendelian Randomisation and eQTL integration.

This study identifies genetic variants and genes associated with COPD and co-occurring traits by integrating multi-omics data and gene regulatory networks.

The paper identifies 123 genomic variants that regulate RAD21 expression, both locally and distantly, and links them to cancer-related genes and Sp2 transcription factor binding sites.

This paper uses local Bayesian regressions to identify genomic regions with significant genetic covariance between chronic kidney disease and hyperuricemia, finding both novel and previously reported shared loci.

The paper introduces a method to estimate rDNA copy number using modal coverage and applies it to yeast isolates, finding population-level variation in copy numbers.

This study identifies gene regulatory networks influenced by Parkinson's disease risk SNPs using eQTL and chromosomal conformation data across multiple tissues.

The paper uses machine learning to identify six genetic variants and tissue-specific eQTL effects linked to Parkinson's disease risk.

The paper constructs a liver-specific gene regulatory network to identify genetic links between NAFLD and co-occurring conditions, revealing shared regulatory mechanisms.

This study identifies shared genetic mechanisms across 18 autoimmune diseases by integrating chromatin contact, expression quantitative trait loci, and protein-protein interaction data.

The paper identifies ASD-associated SNPs in fetal and adult cortex tissues and links them to regulatory processes and pathways, highlighting differences in their impact across developmental stages.

This study identifies 33 genes and 62 pathways impacted by GWAS SNPs associated with psychiatric disorders and cognitive functioning, revealing shared regulatory mechanisms despite no common SNPs or eQTLs.

The paper identifies transcriptional connections and functional links between cohesin genes and disease-relevant pathways, showing their intolerance to expression variation.

The paper identifies shared regulatory pathways between grip strength and neuromuscular disorders using eQTL and Hi-C data, revealing common drug targets and biological mechanisms.

The paper identifies regulatory elements within the ACE2 locus that control host gene expression, suggesting they may contribute to a pro-viral environment for SARS-CoV-2.

This study integrates chromatin interactions and genetic data to identify SNP-gene-metabolite associations across multiple tissues.

This paper identifies 15 novel serum urate loci and links them to 44 genes, revealing new molecular mechanisms of urate control through genomic and eQTL analysis.

This study shows TNF-α induces different cell cycle gene responses in promyelocytic and granulocytic HL-60/S4 cells, with promyelocytes showing upregulation and granulocytes downregulation, and granulocytes shifting towards a macrophage-like transcriptome.

The paper uses Hi-C and RNA-seq to identify and compare structural variants in HL-60 and HL-60/S4 cell lines, finding novel SVs and differences in their stability.

The paper identifies genetic drivers of multimorbidities by analyzing chromatin interactions and eQTL data to uncover regulatory interactions across multiple phenotypes.

The paper shows that neutrophil migration through small pores disrupts inactive chromatin organization, as revealed by transcriptomic and Hi-C analyses.

This study identifies immune regulatory networks influenced by T1D-associated genetic variants using 3D genome organization and gene expression data.

This study shows that cohesin is essential for zygotic genome activation in zebrafish by redistributing to active genes and influencing chromosome architecture.

The paper identifies novel hematopoietic enhancers regulating Runx1 expression using DNA contact maps in mouse hematopoietic progenitor cells.

The paper identifies genetic variants associated with post-term birth in Northern Finland cohorts and links some to gene expression changes.