Biomedical Engineering

Departmental Seminar Series: Sharon Aviran, Postdoctoral Fellow, UC Berkeley

“Modeling and High-­‐throughput Analysis of RNA Structure Mapping Experiments”

I will present SHAPE-Seq, a high throughput assay that quantifies structural information at nucleotide resolution for mixtures of RNAs. SHAPE-Seq combines a novel chemistry with next-generation sequencing of its products.  Following sequencing, we use a fully automated signal processing pipeline to extract the desired structural information. In this talk, I will focus on SHAPE-Seq’s analysis methodology, which relies on a novel probabilistic model of the experiment, adjoined by maximum-likelihood-based statistical inference. I will then present a higher-resolution model of the experiment, which can be used to inform and improve computational RNA secondary structure prediction.

Faculty candidate.

When: Thursday, February 14, 3013 4:10 PM

Where: 1005 GBSF