Clarence Mah
I’m a bioinformatics scientist exploring the intersection of spatial genomics, ML/AI, and cell biology. I am currently a Postdoctoral Researcher in the Yeo Lab at UC San Diego, recently graduated from the UC San Diego Bioinformatics & Systems Biology PhD Program, co-advised by Dr. Gene Yeo and Dr. Hannah Carter. During my PhD, I created bento-tools, an open-source Python toolkit that unifies novel machine learning algorithms and statistics for studying RNA and cell biology. Outside of the lab, I enjoy spending time with my dog in sunny San Diego, CA at my favorite coffee shops and breweries.
Sessions
This goal of this workshop is to demonstrate how spatial transcriptomics data can be used to extract subcellular insights about cell biology, primarily emphasizing analysis with Bento – a package in the Scverse ecosystem – that utilizes the SpatialData framework enabling interoperability with Scanpy and Squidpy. The workshop will briefly introduce motivations and applications of spatial transcriptomics technologies for subcellular measurements. Then we will walk through how Bento models single-molecule resolution data, computes spatial features, and finally how they are utilized for functional analysis i.e. annotating subcellular spatial patterns and domains, modeling gene colocalization, and measuring cell morphology. We will conclude with a short Q&A session for more open-ended discussion.