Here are some of the software products to come out of my research:


Explore cellular niches in single-cell resolution spatial transcriptomics data.


Identify gene sets with spatially varying correlation structure.


Cell type classification of single-cell RNA-seq data against the Cell Ontology.

CellO Viewer

Explore cell type-specific gene expression signatures across the Cell Ontology.

MetaSRA Website

Search for public RNA-seq data within the Sequence Read Archive using biomedical ontologies.

MetaSRA Pipeline

Standardize biomedical metadata that are encoded as key-value pairs.


Characterize and compare tumor subpopulations across public single-cell RNA-seq data.

Series Finder & Case-Control Finder

Build structured datasets of RNA-seq data from the Sequence Read Archive.