Robert J. Coffey

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.

Novel COX-2 Targeted Nanobodies for Molecular Endoscopic Imaging of Colorectal Adenomas

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

Light-induced Extracellular Vesicle Adsorption

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.

Catch and release of sialoglycoRNAs enables sequencing-based profiling across cellular and extracellular material

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

Unbiased recording of clonal potency reveals species-specific regulation of mammalian intestine

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

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.

Inhibition of EGFR/ErbB does not protect against C. difficile toxin B

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

Scalable single-cell pooled CRISPR screens with conventional knockout vector libraries

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.

5-Fluorouracil Treatment Represses Pseudouridine-Containing Small RNA Export into Extracellular Vesicles

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

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.

Bulk and Mosaic Deletions of Egfr Reveal Regionally Defined Gliogenesis in the Developing Mouse Forebrain

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

Machine and deep learning single-cell segmentation and quantification of multi-dimensional tissue images

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

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.

MCMICRO: A scalable, modular image-processing pipeline for multiplexed tissue imaging

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

Quantitative assessment of cell population diversity in single-cell landscapes

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.