Yannis Ntekas

PhD Candidate, Cornell University
PhD Advisor: Iwijn De Vlaminck
Spatial RNA-seq · Host-Microbiome · Non-coding RNA

I am building new tools for spatial biology that expand what this technology can capture and reveal. Spatial transcriptomics is a groundbreaking type of measurement that allows us to map phenotypes of cells in their native spatial location, reconstructing detailed spatial maps of cells—and, increasingly, their intentions. This approach holds great promise to revolutionize our understanding of biology and transform clinical pathology by enabling what is essentially a “biopsy on steroids,” where instead of relying on a few stains, we can extract rich, multilayered molecular information from a single tissue section.

My work focuses on expanding the capabilities of spatial transcriptomics beyond its current emphasis on protein-coding RNAs. I develop methods that allow the simultaneous spatial mapping of non-host and non-coding RNA molecules, including microbial transcripts and regulatory RNAs that are often missed by standard assays.

So far, I’ve applied these tools to map the host–microbiome interface—reconstructing spatial abundance of microbes alongside host cell types in the intestine—and to study the transcriptional architecture of reproductive tissues, where spatial cues are key to development and function.