Alan J. Simmons

The paper develops an optimized multimodal imaging workflow that preserves tissue integrity and enables comprehensive profiling of morphology, collagen, cell populations, N-glycans, and extracellular matrix peptides from a single tissue section.

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 study shows MYT1 and ST18 regulate human beta-cell survival and insulin secretion under normal and stress conditions, with their genes enriched for T2D-risk loci.

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

The paper shows that Myt3 translation is deregulated in β-cells under obesity-induced stress, leading to β-cell dysfunction and glucose intolerance.

The paper shows that chromatin accessibility and DNA demethylation occur at different times during enhancer regulation, with methylation states predicting chromatin dynamics using machine learning.

This study shows Atf4 protects beta-cell function under high glucose but worsens beta-cell failure when combined with free fatty acids.

The paper identifies a pathobiont-epithelial IDO1 pathway that drives region-specific susceptibility to inflammatory bowel disease in the ascending colon.

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.

The paper identifies a novel epithelial cell type, LND, in Crohn's disease that is associated with immune dysregulation and disease activity.

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

The paper develops contamination-focused metrics and software to optimize scRNA-seq experiments by reducing ambient contamination through experimental adjustments.

Petagraph integrates biomolecular data into a unified knowledge graph using UMLS ontologies to enable efficient multi-omics analysis across multiple datasets.

This study shows SCLC cells exist in a continuum of plastic states rather than discrete subtypes, with gene expression patterns linked to cancer hallmarks and potential therapeutic targets.

The paper identifies shared and species-specific enteric neuron subtypes in humans and mice using transcriptional profiling and in situ visualization.

The paper develops a translation model to identify integrin signaling in anti-TNF-resistant Crohn’s disease and validates it using single-cell RNA sequencing.

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

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.