The Chinese University of Hong Kong
Department of Computer Science and Engineering
Division of Biomedical Engineering

Joint CSE-BME Seminar

Title: Gene-centric functional analysis of NGS data
Date: December 20, 2016 (Tuesday)
Time: 11:00 a.m. - 12:00 n.n.
Venue: Room 121, 1/F, Ho Sin-hang Engineering Building,
The Chinese University of Hong Kong,
Shatin, N.T.
Speaker: Prof. Yanni Sun
Associate Professor
Department of Computer Science and Engineering
Michigan State University, USA



Next generation sequencing (NGS) technologies produce vast amount of sequencing data for answering fundamental biological and medical questions. They have been widely applied to transcriptomic sequencing, metagenomic sequencing, genome sequencing etc.

However, in contrast to the rapid accumulation of NGS data, data analysis methods and tools that can take full advantage of this sequencing power seriously lag. In particular, metagenomic sequencing, which sequences the DNA contents of microbes from natural habitats directly without cultivation, can stretch the limits of computational resources. For example, complicated metagenomic data such as those sequenced from soil, a gram of which can contain 4 petabase pairs (1x10^15 bps) of DNA. The sheer size and complicated composition of metagenomic data pose great challenges for existing tools, which either fail to run on available hardware resources or only identify highly abundant species but miss rare ones.

In this talk, I will present our recent work on designing targeted gene assembly algorithms and tools for annotation and analysis of functional elements in NGS data. Particularly I will focus on two projects. The first one is to apply the gene-centric framework for characterizing CRISPRs in metagenomic data. The second project is about improving homology search sensitivity of PacBio data by correcting frameshift errors.



Yanni Sun is an Associate Professor in the Department of Computer Science and Engineering at Michigan State University, USA. She received the B.S. and M.S. degrees from Xi'an JiaoTong University (China), both in Computer Science. She received the Ph.D. degree in Computer Science from Washington University in Saint Louis, USA in 2008. She works in bioinformatics and computational biology. In particular, her recent research interests include sequence analysis, next-generation sequencing data analysis, protein domain annotation, and noncoding RNA annotation. She was a recipient of NSF CAREER Award in 2010.


Enquiries: Miss Ricola Lo at tel 3943 8440

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