Martha J. Shrubsole

Single-cell transcriptome-wide association analysis reveals epithelial cell-specific genetic susceptibility to colorectal cancer

The paper performs single-cell transcriptome-wide association analysis to identify cell-type-specific genetic susceptibility genes for colorectal cancer, finding 546 gene-cell-type associations and 347 candidate susceptibility genes.

Spatial atlas highlights contribution of C. difficile in early-stage colorectal cancer

The paper creates a spatial atlas of early-stage colorectal cancer tumors to identify bacterial niches and their impact on tumor transcriptomes, highlighting C. difficile's significant influence despite low abundance.

Differences in T-cell counts and neighborhood patterns in human colorectal adenomas and sessile serrated lesions

The paper compares T-cell counts and spatial patterns in colorectal adenomas and sessile serrated lesions, finding differences in T-cell infiltration and clustering by lesion type.

Genetically predicted gene expression effects on changes in red blood cell and plasma polyunsaturated fatty acids

This study uses GWAS and eQTL data to identify genetic effects on PUFA levels in RBCs and plasma, finding shared variants and differences in gene expression impacts.

Consensus tissue domain detection in spatial -omics data using MILWRM

The paper introduces MILWRM, a tool for detecting tissue domains in spatial-omics data, and demonstrates its application in human colonic polyps and mouse brain slices.

Temporal recording of mammalian development and precancer

The paper introduces NSC-seq, a CRISPR-based molecular clock to track temporal and clonal events in development and precancer, revealing polyancestral initiation in colonic precancers.

GammaGateR: semi-automated marker gating for single-cell multiplexed imaging

GammaGateR provides a semi-automated marker gating tool for multiplexed imaging data, improving consistency and reducing manual effort while revealing biological signals.

Molecular cartography uncovers evolutionary and microenvironmental dynamics in sporadic colorectal tumors

This study maps tumor evolution and microenvironment dynamics in colorectal cancer using spatial multi-omic data, identifying key genes associated with immune exclusion and prognosis.

Quantifying and correcting slide-to-slide variation in multiplexed immunofluorescence images

This paper quantifies slide-to-slide variation in multiplexed immunofluorescence data and introduces normalization methods to correct it, showing that dividing by slide mean and functional data registration perform best.

Dual indexed design of in-Drop single-cell RNA-seq libraries improves sequencing quality and throughput

The paper introduces a dual-indexed library design for scRNA-seq to improve sequencing quality and throughput on high-throughput sequencers.