Speaker: Hosna Jabbari
Title: RNA Secondary Structure Prediction including Pseudoknots

Abstract: 
Algorithms for prediction of RNA secondary structure - the set of base pairs 
that form when an RNA molecule folds - are valuable to biologists who aim to 
understand RNA structure and function. Improving the accuracy and efficiency 
of prediction methods is an ongoing challenge, particularly for pseudoknotted 
secondary structures, in which base pairs overlap. This challenge is 
biologically important, since pseudoknotted structures play essential roles in 
functions of many RNA molecules, such as splicing and ribosomal frameshifting. 
State-of-the-art methods, which are based on free energy minimization, have 
high run-time complexity (typically Theta(n^5) or worse), and can handle only
limited types of pseudoknotted structures. In this talk I present my join work 
with Dr. Anne Condon and Shelly Zhao, in which we developed a new approach for 
prediction of pseduoknotted structures. Using a two-phase energy minimization 
we can predict pseudoknotted secondary structures in O(n^3) time, matching the
complexity of the best algorithms for pseudoknot-free secondary structure 
prediction via energy minimization.