Stuart A. Lee

The paper identifies a fibroblast state called STIF that drives YAP-dependent regenerative programs and (pre)malignancy through mechanotransduction in response to tissue injury.

The paper introduces tidyomics, an ecosystem bridging Bioconductor and tidy R to streamline omic analysis using data from the Human Cell Atlas.

The paper introduces matchRanges, a tool for generating covariate-matched null genomic ranges to facilitate comparative genomic analyses.

bootRanges generates null genomic ranges for hypothesis testing, improving reliability by preserving genomic correlation structure through block bootstrap methods.

The paper demonstrates that intron reads from RNA-seq are informative and introduces methods to analyze them for transcriptional changes and intron retention.

The paper introduces plyranges, an R/Bioconductor package that simplifies genomic data analysis by providing a grammar of genomic data transformation based on the GRanges data structure.

The paper develops isoRelate, an IBD analysis method for haploid pathogens, identifies selection signals and population structure in Plasmodium falciparum data.