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December 2014

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ECE Colloquium - Prof. Sharon Aviran, UC Davis

Speaker Prof. Sharon Aviran, UC Davis
Title ECE Colloquium (ECE 500): "Deciphering RNA structure from experiments and probabilistic models"
Date: 4/24/2014
Time: 4:00 pm
Location: 151 Everitt Lab
ECE Faculty Host: Prof. Olgica Milenkovic
Sponsor: ECE ILLINOIS
Event Type: Seminars
 

Abstract:

 New regulatory roles continue to emerge for both natural and engineered RNAs, many of which have specific structures essential to their function. This highlights a growing need to develop technologies that enable rapid and accurate characterization of structural features within complex RNA populations. Yet, available techniques that are reliable are vastly limited by technological constraints, while the accuracy of popular computational methods is generally poor. These limitations pose a major barrier to comprehensive determination of structure from sequence.

Recently, numerous novel high-throughput approaches to RNA structure determination have emerged, which facilitate parallel measurements of high-resolution structural information for a multitude of distinct RNAs. One of these techniques, SHAPE-Seq, was the first to couple a chemistry-based approach to structure determination with next-generation sequencing of its products. Following sequencing, an algorithmic pipeline recovers the desired information from noisy experimental data, representing a new approach to rapid, consistent, and automated analysis of this new wealth of structural data. In this talk, I will describe SHAPE-Seq and its analysis methodology, which relies on a novel probabilistic model of this emerging family of techniques. I will also discuss recent breakthroughs in experimental structure characterization along with some of the informatics challenges (and opportunities) they introduce. 

Bio:

Sharon Aviran is an Assistant Professor of Biomedical Engineering and a member of the Genome Center at UC Davis. Her current research interests are at the intersection of genomics, statistical inference, and structural biology, focusing on developing computational methods for high-throughput analysis of RNA molecular dynamics. Before joining UC Davis in 2014, she was a postdoctoral researcher at the Center for Computational Biology and the Bioengineering Department at UC Berkeley, where she worked with Professors Lior Pachter, Adam Arkin, and David Schaffer. Professor Aviran pursued her Ph.D. studies in Electrical Engineering at UCSD, specializing in signal processing for communications systems and in information theory, and was awarded the 2006 Sheldon Schultz Prize for Excellence in Graduate Student Research. She was a Calit2 Fellow at UCSD and a Celera/TCS Postdoctoral Innovation Fellow at UC Berkeley and received an NIH K99/R00 award in 2012 for her research on computatio  nal methodology for RNA genomics.