Robert J. Coffey

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.

This paper develops COX-2-targeted nanobodies for enhanced endoscopic imaging of colorectal adenomas, showing tumor-specific accumulation in vivo.

This paper introduces LEVA, a label-free, high-resolution, tunable platform for EV adsorption and characterization, demonstrating its versatility with various EV sources and applications.

This study identifies CLDN18.2 as a diagnostic marker for Menetrier Disease and shows that Hedgehog signaling is upregulated and therapeutically targetable in the disease.

The paper introduces rPAL-seq, a method for profiling sialoglycoRNAs with low RNA input, revealing lineage-associated patterns and secreted glycoRNA profiles.

The paper uses clonal analysis to reveal species-specific differences in intestinal regeneration and stem cell dynamics in mice and humans.

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.

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.

This study identifies miR-100 and miR-125b as regulators of 3D growth and invasiveness in cancer cells, showing they can be transferred extracellularly to silence target genes in recipient cells.

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

This study investigates whether inhibiting EGFR/ErbB receptors protects against C. difficile toxin B, finding no protective effect.

This paper introduces NSC-seq, a direct sgRNA capture method for single-cell CRISPR screens using standard knockout libraries, and characterizes sgRNA expression in three whole-genome libraries.

This study shows that 5-FU treatment alters the export and base modifications of small RNAs in extracellular vesicles from colorectal cancer cells.

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.

This paper introduces a novel immunoassay for detecting EGFR and its activity state in plasma CD63-EVs from glioblastoma patients, achieving high sensitivity and specificity for early detection.

This study investigates the role of EGFR in mouse forebrain development through bulk and mosaic deletions, revealing region-specific effects on glial lineage formation.

The paper presents a pipeline for cell segmentation and quantification in complex tissue images using machine learning and deep learning methods.

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.

MCMICRO processes multiplexed tissue images into single-cell data, demonstrating its versatility across different tissues and imaging platforms.

This paper introduces sc-UniFrac, a framework to quantify compositional diversity in cell populations across single-cell transcriptome datasets, demonstrating its utility in various applications.