Simon Cameron Biddie

Identifying severe COVID-19 risk variants modulating enhancer reporter activity in lung cells

The paper identifies severe COVID-19 risk variants that modulate enhancer activity in lung cells using functional assays and deep learning.

Benchmarking tissue- and cell type-of-origin deconvolution in cell-free transcriptomics

This study benchmarks deconvolution methods for inferring tissue and cell type-of-origin from plasma cfRNA, showing method and reference variability impact performance.

Contribution of dominant and recessive model effects to the genetic architecture of Idiopathic Pulmonary Fibrosis

This study performs GWAS of IPF using dominant and recessive models, identifying five new genome-wide significant signals and genes, including PMF1 and EPN3, and observing increased PMF1 expression in IPF patients.

Disease-associated genetic variants can cause mutations in tissue-specific protein isoforms

The paper shows that disease-associated variants in alternative protein isoforms can cause structural mutations, emphasizing the need to consider tissue-specific expression and full-length transcripts in variant interpretation.

A structure-guided approach to non-coding variant evaluation for transcription factor binding using AlphaFold 3

This paper evaluates non-coding variants' impact on TF binding using AlphaFold 3 and FoldX, showing structural modeling can provide interpretable insights despite lower accuracy than sequence-based methods.

DNA-binding factor footprints and enhancer RNAs identify functional non-coding genetic variants

The paper identifies functional non-coding genetic variants by combining DNase footprints and enhancer RNAs, introducing a framework called FINDER to prioritize variants for functional validation.