Greg C. Gibson

Single-Cell Transcriptomics of Multi-Site Cell Therapy in Osteoarthritis: Tissue-Specific Traits and Treatment Correlations

This study uses single-cell RNA sequencing to analyze cell therapy samples in osteoarthritis, identifying tissue-specific pathways and treatment correlations while highlighting challenges in patient heterogeneity.

Trans-eQTL mapping prioritises USP18 as a negative regulator of interferon response at a lupus risk locus

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

snATAC-Express infers Gene Expression from Prioritized Chromatin Accessibility Peaks using Machine Learning

The paper develops a machine learning pipeline to infer gene expression from chromatin accessibility peaks using single nuclear multi-omic data, finding that important peaks are enriched in GWAS variants for inflammatory bowel disease and lupus.

Aberrant Fibro-Adipogenic Progenitor Subpopulations Drive Volumetric Muscle Loss-Induced Fibrosis

This study identifies an aberrant FAP subpopulation in VML that drives fibrosis and presents potential targets for scarless muscle regeneration.

Haplotype rather than single causal variants effects contribute to regulatory gene expression associations in human myeloid cells

The paper validates the effects of SNPs on gene expression in myeloid cells and finds that haplotype effects, not single variants, explain many associations.

Dual exposure-by-polygenic score interactions highlight disparities across social groups in the proportion needed to benefit

The paper quantifies PGS-by-Exposure interactions for seven diseases and 75 exposures in the UK Biobank, finding 3.1% significant interactions and introducing the PNB metric to highlight disparities in benefit across social groups.

Acceleration of Large-Scale Single Cell Differential Gene Expression Analysis with FastDE

FastDE accelerates differential gene expression analysis in single-cell data by 50X, replicating age and gender effects on immune cell differentiation in PBMC atlases.

OTTERS: A powerful TWAS framework leveraging summary-level reference data

OTTERS is a TWAS framework that uses summary-level eQTL reference data to estimate eQTL weights and perform omnibus TWAS, showing improved power and applicability.

Methylation Quantitative Trait Loci are Largely Consistent across Disease States in Crohns disease

The paper identifies methylation quantitative trait loci (mQTLs) in blood and ileum samples from Crohn's disease patients and finds they are largely consistent across disease states and tissues.

TIGAR-V2: Efficient TWAS Tool with Nonparametric Bayesian eQTL Weights of 49 Tissue Types from GTEx V8

TIGAR-V2 improves TWAS efficiency by directly reading VCF files, enabling parallel computation, and reducing computation cost by up to 90%, while identifying risk genes for breast and ovarian cancer.

Stratification of Risk of Progression to Colectomy in Ulcerative Colitis using Measured and Predicted Gene Expression

The paper uses measured and predicted gene expression to identify ulcerative colitis patients at elevated risk of colectomy, showing both methods independently replicate in multiple datasets.

TreeMap: A Structured Approach to Fine Mapping of eQTL Variants

TreeMap identifies causal eQTL variants by accounting for multisite effects and linkage, showing improved accuracy and enabling genome-wide analysis of long-range eQTL.

The effect of X-linked dosage compensation on complex trait variation

The paper examines how X-linked dosage compensation affects genetic variation in complex traits, finding more genetic variation in males than females for X-linked loci.

TIGAR: An Improved Bayesian Tool for Transcriptomic Data Imputation Enhances Gene Mapping of Complex Traits

The paper introduces a Bayesian method for transcriptomic data imputation that improves gene mapping of complex traits by enhancing imputation accuracy and TWAS power over existing tools.

Profiling gene expression of the host response to a Plasmodium vivax irradiated sporozoite immunization and infectious challenge

This paper uses RNAseq to analyze gene expression in vaccinated and challenged individuals to identify transcriptional signatures associated with protection against Plasmodium vivax malaria.

The Medical Genome Reference Bank: Whole genomes and phenotype of 2,570 healthy elderly

The paper introduces the Medical Genome Reference Bank, a resource of whole genome sequences and phenotypes from 2,570 healthy elderly Australians, showing fewer disease-associated variants and age-related somatic changes linked to grip strength.

Widespread signatures of negative selection in the genetic architecture of human complex traits

The paper estimates the joint distribution of effect size and MAF for genetic variants in 28 complex traits and detects widespread negative selection signatures.

Constraints on eQTL fine mapping in the presence of multi-site local regulation of gene expression

This study shows that multi-site regulation of gene expression leads to biased eQTL fine mapping and highlights the need for joint multi-site analysis to improve accuracy.