Dillon Lue will present his General Exam "Multimodal Single Cell Genomics Datasets for Identifying Cell Types and their Function" on Wednesday, May 8, 2024 at 1:30 PM in Icahn 280. Committee Members: Yuri Pritykin (advisor), Ben Raphael, Olga Troyanskaya Abstract: Recent advances in single-cell genomics enable the simultaneous measurement of RNA and another modality in the same cell, known as multimodal scRNA-seq. In this talk, I demonstrate how multimodal assays can enhance our understanding of T cell biology and inform scRNA-seq analysis. First, I will talk about the analysis of a multimodal scRNA-seq assay with a novel combination of modalities: barcoded lineage tracing, CRISPR perturbations, and RNA. This combination of modalities enables us to interrogate how CRISPR perturbations influence the transcriptional states in T cell clones. Next, I propose a new framework to benchmark scRNA-seq analysis by utilizing the second modality in multimodal datasets as ground truth. Due to the complex nature of scRNA-seq data, a multi-step procedure has emerged to map cells onto a low dimensional transcriptional manifold. This procedure has many user-defined choices that can influence biological results. Unlike existing benchmarks, this new framework introduces a ground truth for the context of continuous biological processes. Reading List: https://docs.google.com/document/d/12K-XVW5NfBQZ5MBXesUvJlqHBIoA9blOhI0CYHJn... Everyone is invited to attend the talk, and those faculty wishing to remain for the oral exam following are welcome to do so.