생물정보학 세미나 공지

서울대학교 생물정보연구소 및 생물정보학 협동과정 공동 주최로 특별 세미나를 아래와 같이 열고자 하오니, 많은 참여 바랍니다.

일시: 2011년 11월 23일 17:00

연사: 윤성로 교수(고려대학교)

장소: 25동 411호

주제:

HiTRACE: high-throughput robust analysis for capillary electrophoresis

Abstract:

Capillary electrophoresis (CE) of nucleic acids is a workhorse technology underlying high-throughput genome analysis and large-scale chemical mapping for nucleic acid structural inference. Despite the wide availability of CE-based instruments, there remain challenges in leveraging their full power for quantitative analysis of RNA and DNA structure, thermodynamics and kinetics. In particular, the slow rate and poor automation of available analysis tools have bottlenecked a new generation of studies involving hundreds of CE profiles per experiment. We propose a computational method called high-throughput robust analysis for capillary electrophoresis (HiTRACE) to automate the key tasks in large-scale nucleic acid CE analysis, including the profile alignment that has heretofore been a rate-limiting step in the highest throughput experiments. We illustrate the application of HiTRACE on 13 datasets representing 4 different RNAs, 3 chemical modification strategies and up to 480 single mutant variants; the largest datasets each include 87 360 bands. By applying a series of robust dynamic programming algorithms, HiTRACE outperforms prior tools in terms of alignment and fitting quality, as assessed by measures including the correlation between quantified band intensities between replicate datasets. Furthermore, while the smallest of these datasets required 7.10 h of manual intervention using prior approaches, HiTRACE quantitation of even the largest datasets herein was achieved in 3.12 min. The HiTRACE method, therefore, resolves a critical barrier to the efficient and accurate analysis of nucleic acid structure in experiments involving tens of thousands of electrophoretic bands.

Bio:

Dr. Sungroh Yoon is an assistant professor of electrical engineering and of Samsung IT convergence at Korea University, Seoul Korea. He received the Ph.D. and M.S. degrees in electrical engineering from Stanford University and the B.S. degree in electrical engineering from Seoul National University. Prior to joining Korea University, Prof. Yoon held research positions at Intel Corporation, Santa Clara, USA and Stanford University. His research interests include biocomputation, RNA engineering and hardware acceleration. Dr. Yoon is a Senior Member of IEEE.

서울대학교 생물정보연구소

자연과학대학 생물정보학 협동과정 공동주최