Matthew N. Bernstein

Monkeybread identifies cellular niches in spatial transcriptomics data, revealing immunogenic and tolerogenic macrophage populations in melanoma tumors.

SpatialCorr identifies gene sets with spatially varying correlation structure in spatial transcriptomics data, revealing insights not found with existing methods.

The paper tests two models of beta cell dedifferentiation in diabetes using lineage tracing and RNA-seq in mice, showing dedifferentiation is not a reversal of development but varies by diabetes type.

CHARTS provides a web tool to analyze and compare tumor subpopulations across public scRNA-seq cancer datasets.

CellO is a machine learning tool for hierarchically classifying human cell types using the Cell Ontology, achieving competitive performance with a comprehensive training dataset and interpretable models.

MetaSRA normalizes SRA sample metadata using a schema inspired by ENCODE, enabling better analysis of biological relationships across diverse samples.