Jeffrey R. Moffitt

This study shows that early hematopoietic fate decisions are not strongly influenced by bone marrow niche identity, as fate-shaping signals are redundantly provided across niches.

The paper presents the Human Gut Cell Atlas v1.0, a unified reference of gut cell diversity, revealing how tissue structure influences cellular composition and enabling disease and organoid analysis.

This paper introduces an RNA-aware preservation method, RIPIN, that improves spatial transcriptomics data quality by inhibiting RNase activity across human and mouse tissues.

The paper shows that CD4 T cell memory is enhanced when antigens are presented by intestinal epithelial cells rather than bacterial proteins.

This paper creates a gut transcriptomics atlas using MERFISH to show how microbiota influences cell types, spatial organization, and molecular responses in the murine gut.

The paper investigates pathogen-specific sickness states by analyzing immune and neural responses across multiple scales in various inflammatory models.

This paper constructs a human dorsal root ganglion reference atlas, identifying 22 neuronal subtypes and 10 non-neuronal cell types, and reveals functional differences between human and mouse DRG neurons.

This study optimizes MERFISH protocols to improve RNA imaging performance in cell culture and tissue samples.

The paper uses multi-generational imaging to study essential genes in E. coli, revealing new mechanisms behind growth laws and identifying unknown gene functions.

This study introduces BCR-MERFISH to profile plasma cell clonality in situ using image-based single-cell transcriptomics, revealing microbiota-dependent changes and spatial distribution patterns in mice.

This paper introduces bacterial-MERFISH, a method to profile bacterial transcriptomes spatially, and applies it to study E. coli and B. thetaiotaomicron under different conditions.

The paper uses spatial transcriptomics to map cell types and their spatial organization in healthy and fibrotic human liver, identifying changes in hepatocyte populations during fibrosis.

The paper introduces a method to identify spatially variable genes by projecting spatial transcriptomics data onto morphologically relevant curves, improving detection accuracy and biological interpretation.

Polaris provides a deep learning-based pipeline for analyzing spatial transcriptomics data, improving spot detection and gene expression quantification.

The paper uses spatial transcriptomics to study complement system development in the brain, revealing distinct roles of the classical and alternative pathways.

This study maps the molecular, cellular, and circuit organization of the prefrontal cortex and identifies a cell type involved in chronic pain pathogenesis.

The paper performs spatial transcriptomic profiling of the mouse retina to uncover its laminar organization and generates a comprehensive spatial single cell reference atlas.

The paper introduces a high-throughput screening method to identify genetic variants with desired phenotypes by imaging barcoded mutants in individual cells.