John W. Hickey

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.

A free Meta Quest virtual reality app harmonizes CODEX, Visium, Xenium, volumetric immunofluorescence and electron microscopy data from 5 organs into 4 scale levels using the Human Reference Atlas.

This paper introduces NanoSTAMP, a spatially resolved in vivo screening platform for barcoded LNPs, linking formulation to cell-type uptake and tissue responses.

MORPHE synthesizes biologically faithful tissue architecture from spatial-omics data, enabling reconstruction and extension of tissue context beyond experimental limitations.

This study evaluates segmentation models on live microscopy and spatial-omics data, finding that no single model consistently outperforms others across all datasets.

This paper identifies age-related impairment in systemic mRNA translation as a barrier to mRNA vaccine efficacy and develops an LNP formulation to restore transgene expression and T cell immunity in aged hosts.

MINGL quantifies tissue organization by modeling cell memberships across hierarchical units, detecting interfaces, gradients, and heterogeneity in spatial-omic datasets.

SPACEc provides a Python workflow for analyzing multiplexed imaging data with interactive tools for image processing, segmentation, and spatial analysis.

Fluid-Squid enables customizable, cost-effective multiplexed imaging of cells and tissues through automated fluidics and barcoding strategies.

FUSION is a web-based tool that integrates spatial -omics data with histology to analyze tissue states and identify spatial linkages between molecular and histopathologic features.

The paper analyzes endothelial cell environments across organs using spatially resolved omics data and provides an interactive tool for visualizing cell distances and neighborhoods.

This paper develops ACTIVATE, a hydrogel-based platform that enhances tumor control by synergizing adoptive and endogenous immunity through localized cytokine delivery and T-cell activation.

This study identifies immune cell changes and gene expression patterns in Barrett's esophagus progression to cancer using spatial and multi-omic analyses.

The paper identifies spatial immune patterns in Merkel cell carcinoma linked to viral status and patient outcomes.

MONTAGE identifies spatially resolved functional enrichment gradients in tumor microenvironments by analyzing spatial communities and their clinical relevance.

The paper examines TIL expansion in glioblastoma by analyzing spatial organization and myeloid context, finding that TIL+ tumors have distinct immune interactions and vascular niches.

This paper describes the construction and usage of the Human Reference Atlas (HRA) v2.0, which integrates multiscale data across 36 organs and provides tools for analysis and visualization.

The paper develops a nanofiber-hydrogel composite incorporating mRNA lipid nanoparticles to create a local immunostimulatory niche for cancer immunotherapy, showing enhanced immune responses with a single dose.

SEraster reduces computational resource needs for spatial omics analysis by aggregating cell data into spatial pixels, enabling efficient analysis of large datasets.

The paper integrates multiplexed imaging and multiscale modeling to show that T cell phenotype influences tumor phenotype conversion, critical for therapeutic efficacy.

The paper evaluates five algorithms for segmenting functional tissue units in kidney and colon tissues using histological stains, comparing their accuracy and generalizability.

The paper introduces MaxFuse, a method for integrating spatial and single-cell omics data with weak linkage, demonstrating its effectiveness in consolidating proteomic, transcriptomic, and epigenomic information.

STELLAR annotates spatially resolved single-cell data using geometric deep learning, discovering cell types and states while transferring annotations across tissues and donors.

The paper maps cell organization and function across human intestine regions using single nuclear RNA and open chromatin assays, revealing distinct cell neighborhoods and regulatory differences.