Light directed spatial omics


This is the research area I am working on as a postdoctoral research fellow.  Cells have molecules called RNA and one of their crucial functions is to carry information from genes stored in DNA to make proteins. The set of all RNA in a cell is called its transcriptome and typically contains several thousand RNAs. Information of the transcriptome can give us a variety of information including what type of cell it is, if the cell is functioning properly, or what genes are activated under stimuli. Combined with information of where that cell is positioned in relation to others in a tissue can now start to help us understand how the tissue functions from a ground-up approach. There are two classes of methods that perform such spatial omics measurements: imaging-based, which has high resolution but is selective in the transcriptome, and sequencing-based, which has lower resolution but can measure the transcriptome unbiased. I am developing a method to combine the two approaches to use light and sequencing to bridge the gap between them to have high-resolution and unbiased measurements. The hope is that high-quality characterization of molecules in tissues can help us understand them better!


Multiplexed optical barcoding and sequencing for spatial omics

A Venkatramani*, D Ciftci*, L Cohen, C Li, K Pham, X Zhuang

BioRxiv (2024)