Farhan Ameen

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.

This study creates a spatiotemporal atlas of mouse gastrulation and early organogenesis using spatial transcriptomics and scRNA-seq, revealing gene expression dynamics and mesodermal fate decisions.

BIDCell improves subcellular spatial transcriptomics segmentation by combining self-supervised learning with biologically informed loss functions, outperforming existing methods across multiple tissue types.