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Events for September 21, 2012
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Improving RNA secondary structure prediction
Fri, Sep 21, 2012 @ 10:30 AM - 11:30 PM
Ming Hsieh Department of Electrical and Computer Engineering
Conferences, Lectures, & Seminars
Speaker: Michelle (Shel) Swensen, Postdoctoral Research Associate
Talk Title: Improving RNA secondary structure prediction
Abstract: RNA folding is one of the fundamental open problems in computational molecular biology. Thermodynamic optimization approaches, which find structures with minimum free energy (MFE), remain the most widely used RNA secondary structure prediction methods. Though these predictions do not always match known structures, the expectation is that structures with a lower free energy are more likely to contain native base pairings, even when the predicted MFE structure itself is not correct.
In this talk I will discuss two avenues for improving structural prediction in a thermodynamic framework: considering large sets of probable structures and augmenting thermodynamic models with additional experimental data.
The Boltzmann distribution specifies that the probability of RNA secondary structure is proportional to an exponential of the negative of its free energy. We present a novel combinatorial method for identifying patterns in structural elements across a Boltzmann sample. Our approach is based on classifying structures according to features chosen from well-defined structural units called helix classes. We show that this combinatorial profiling is straightforward, stable and surprisingly comprehensive.
Data from recently emerging high-throughput structure probing technologies, such as the SHAPE method, have been used in the framework of thermodynamic optimization to predict RNA secondary structure. Via stochastic simulations, we investigate the factors influencing the accuracy of SHAPE data-directed predictions as well as the potential of auxiliary data to further improve prediction accuracy.
Biography: Shel Swenson's training and research interest position her at the intersection of mathematics, computer science, and biology, where she utilizes discrete mathematics to answer questions in molecular and evolutionary biology. Her dissertation, completed under the advisement of Tandy Warnow at The University of Texas at Austin, developed methods for estimating large-scale evolutionary histories. Dr. Swenson is currently a postdoctoral fellow in the School of Mathematics at the Georgia Institute of Technology where she collaborates with Christine Heitsch and her students on problems in mathematical and computational biology.
Host: Professor Viktor K. Prasanna
Location: Hughes Aircraft Electrical Engineering Center (EEB) - 248
Audiences: Everyone Is Invited
Contact: Janice Thompson
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Integrated Systems Seminar Series (Cancelled)
Fri, Sep 21, 2012 @ 03:00 PM - 04:30 PM
Ming Hsieh Department of Electrical and Computer Engineering
Conferences, Lectures, & Seminars
Speaker: Prof. Amir Mortazawi, University of Michigan
Talk Title: Frequency Agile Circuits Based on Thin Film Ferroelectrics
Abstract: This talk concentrates on the development of frequency agile circuits based on thin film ferroelectrics. Central to this effort is the use of barium strontium titanate (BST) which is a low loss, high dielectric constant and non-linear dielectric material. The electric field dependence of BST permittivity allows fabrication of tunable RF and microwave devices and components. Applications of BST based varactors for the design of adaptive matching circuits and linearized power amplifiers will be discussed. Another important characteristic of such materials is their dc electric field induced piezoelectric and electrostrictive effects. These properties can be utilized to design intrinsically switchable film bulk acoustic wave resonators (FBARs) and FBAR filters. By eliminating the switching devices used in conventional filter banks, ferroelectric based filters provide reduced size and power consumption necessary for the design of low power multi-standard radios. Recent results on the development of intrinsically switchable resonators and filters will be presented.
Biography: Prof. Amir Mortazawi received the Ph.D. degree in electrical engineering from The University of Texas at Austin, in 1990.
He is a currently a Professor of electrical engineering with The University of Michigan at Ann Arbor. His research interests include millimeter-wave circuits, phased arrays, power amplifiers, ferroelectric thin film based devices and frequency-agile microwave circuits.
Prof. Mortazawi was the Editor-in-Chief of the IEEE TRANSACTIONS ON MICROWAVE THEORY AND TECHNIQUES from 2006-2010. He is a member of the IEEE Microwave Theory and Techniques Society (IEEE MTT-S) Administrative Committee (AdCom). He also served as Associate Editor for the IEEE TRANSACTIONS ON ANTENNAS AND PROPAGATION (1998â2001), IEEE TRANSACTIONS ON MICROWAVE THEORY AND TECHNIQUES (2005). Mortazawi is a Fellow of IEEE.
Host: Prof. Hossein Hashemi, Prof. Mahta Moghaddam, Prof. Mike Chen
More Info: http://mhi.usc.edu/activities/integrated-systems/
Location: Hughes Aircraft Electrical Engineering Center (EEB) - 248
Audiences: Everyone Is Invited
Contact: Hossein Hashemi
Event Link: http://mhi.usc.edu/activities/integrated-systems/
