Thomas M. Ashhurst

An open multimodal spatial resource integrating same-tissue transcriptomics, proteomics, and histology

The paper presents a workflow and dataset integrating spatial transcriptomics, proteomics, and histology on the same tissue section, along with an open-source tool for multimodal data analysis.

Developmental stage-dependent decoupling of molecular and phenotypic responses to heat in wheat grain

This study shows that heat stress at different developmental stages in wheat causes distinct molecular and phenotypic responses, with stronger effects on grain set and composition at the trinucleate stage.

Combining xenium in situ spatial transcriptomics and imaging mass cytometry on a single tissue section

This paper combines Xenium spatial transcriptomics and imaging mass cytometry on a single tissue section to analyze mRNA and protein at single-cell resolution, showing improved biological insights when integrating both data types.

The Changing Immune Landscape of Innate-like T Cells and Innate Cells Throughout Life

This study uses spectral flow cytometry to analyze age-related changes in innate and innate-like T cells, identifying age-associated phenotypic shifts in immune cell subsets.

Identifying the Minimal Number of Protein Markers for Cell Type Annotation Using MiniMarS

MiniMarS identifies the minimal number of protein markers for cell type annotation across multiple datasets and improves rare population identification.

SuperCellCyto: enabling efficient analysis of large scale cytometry datasets

SuperCellCyto efficiently analyzes large cytometry datasets by grouping similar cells into supercells, avoiding the need for random subsampling.

TrackSOM: mapping immune response dynamics through sequential clustering of time- and disease-course single-cell cytometry data

TrackSOM maps immune response dynamics through sequential clustering of time- and disease-course single-cell cytometry data, revealing heterogeneous immune cell populations and their functional evolution in West Nile Virus infection.