若手研究者インターナショナル・トレーニング・プログラム(ITP)
バイオインフォマティクスとシステムズバイオロジーの国際連携教育研究プログラム 応募書類

Name: Unyanee Poolsap
Title: Computational methods for predicting single and interacting RNA secondary structures
Institute: Bioinformatics Center, Institute for Chemical Research, Kyoto University
Partner institute of your choice：Department of Biology and Computer Science Program in
Bioinformatics Boston University
Duration of your choice: February 19 - May 18, 2010
Plan：
Background:
The research that I have been doing is RNA secondary structure analysis using themathematical methods and computational algorithms to model and predict RNA secondarystructures and RNA-RNA interaction structures.
In particular, the first project was RNA secondary structure prediction using integer
programming. The structure prediction problem is modeled as an optimization problem undersome constraints. Since the arbitrary structure is NP-hard for prediction, we constructed someconstraints to limit the scope of structures that our algorithm can predict. We proposed integer
programming model for prediction of RNA secondary structure with a subclass of pseudoknot. This
research was presented in The Seventh Asia Pacific Bioinformatics Conference (APBC2009) heldin Beijing, China. It was also published in BMC Bioinformatics, vol. 10, suppl. 1, Jan. 2009.
The ongoing project is RNA-RNA interaction prediction and target discovery. In this work, weincorporate binding site profile of an antisense RNA to reduce the computation time of RNA-RNA
interaction prediction. We use dynamic programming with binding site profile to predict secondary
structure and interaction site(s) of target RNA. We also apply our algorithm to search for target
RNA(s) of a given antisense RNA. The preliminary result has been published in Proceedings of The
15th Pacific Symposium on Biocomputing (PSB2010), page 98-107.
Research objectives:
The partner laboratory is Laboratory for Biocomputing and Informatics which belongs to theDepartment of Biology and Computer Science, Program in Bioinformatics, Boston University. The
group leader is Associate Professor Gary Benson. This lab mainly focuses on development ofalgorithms and software tools for detection and analysis of novel repeats and reverses patterns inDNA sequences. The project that I will be involving is a collaborative research on developing analgorithm for mapping sequencing data to the human genome. The algorithm will take shortfragments of DNA sequence from the sequencer machine as inputs. Since the input sequences
contain some errors in general, the algorithm should be able to handle some erroneous sequences
and map them to the human genome with reliability and effective computation time.

若手研究者インターナショナル・トレーニング・プログラム(ITP)
バイオインフォマティクスとシステムズバイオロジーの国際連携教育研究プログラム 応募書類

Plan (Continued)
Advantages that I expected to gain from participating ITP:z Have a chance to study sequence analysis in genome-wide scale, which could be used toimprove my recent research project. For example, enhance my algorithm so that it is able
to search for RNA binding site in genome-wide scale.
z Apply algorithms that I have been used to model RNA sequences (Integer programmingand Dynamic Programming) to the project that I will be participating in the partnerlaboratory.
z Improve my programming skillz Acquire experience of working in a collaborative project.
z Improve English skill in communicating with native speakers, giving presentations aswell as writing academic papers.