세미나 안내
Microbial community analysis using next-generation sequencing data
작성자
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작성일
2019-06-18
조회
38
서울대학교 생물정보연구소 세미나를 아래와 같이 열고자 하오니, 많은 참여 바랍니다.
일시: 2019년 6월 19일(수)
연사: Yanni Sun (City Univesity of Hong Kong)
장소: 서울대학교 220동 625호 대회의실
Title: Microbial community analysis using next-generation sequencing data
Abstract
Known as the blueprint of life, the genomic sequence contains instructions for controlling a species’ growth, development, survival, and reproduction. Next-generation sequencing (NGS) technologies, which produce vast amount of sequencing data for various life forms, have provided tremendous information for tackling grand challenges from finding more effective treatment for human diseases to improving biofuel energy production. In particular, combined with modern molecular biology techniques, NGS allows scientists to sequence both culturable and unculturable microbes in human microbiota and natural environments at unprecedented depth and resolution. However, in contrast to the rapid accumulation of the microbial community data, data analysis methods and tools that can take full advantage of this sequencing power seriously lag. Thus, there is a pressing need to convert the BIG NGS data into knowledge.
Known as the blueprint of life, the genomic sequence contains instructions for controlling a species’ growth, development, survival, and reproduction. Next-generation sequencing (NGS) technologies, which produce vast amount of sequencing data for various life forms, have provided tremendous information for tackling grand challenges from finding more effective treatment for human diseases to improving biofuel energy production. In particular, combined with modern molecular biology techniques, NGS allows scientists to sequence both culturable and unculturable microbes in human microbiota and natural environments at unprecedented depth and resolution. However, in contrast to the rapid accumulation of the microbial community data, data analysis methods and tools that can take full advantage of this sequencing power seriously lag. Thus, there is a pressing need to convert the BIG NGS data into knowledge.
In this talk, I will present our recent work on composition and functional analysis for microbial community data. In particular, I will focus on characterization of the intra-host viral populations using NGS data. Many clinically important RNA viruses such as HIV, HCV, SARS-coV, Influenza have a high mutation rate during replication and thus form a population of related but different viral strains, which are referred to as quasispecies. Reconstruction of each strain sequence is highly important for development of clinic prevention and treatment. I will present our work on effective reconstruction of all haplotypes in quasispecies using NGS data.
In the second part of my talk, I will focus on metagenomic analysis using long reads. Long read sequencing technologies such as Single Molecule, Real-Time (SMRT) Sequencing have the potential to characterize complex microbial communities more accurately. However, their current applications are hampered by the high sequencing error rate. I will introduce our recently developed algorithm that incorporates hidden Markov models and alignment graph for error correction and sensitive homology search. By applying our algorithm to a human arm metagenomic data, we can clearly identify more protein homologs.
Bio
Yanni Sun is an Associate Professor in the Department of Electronics at City University of Hong Kong. Before she joined CityU in 2018, she was 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. She works in bioinformatics and computational biology. In particular, her recent research interests include sequence analysis, next-generation sequencing data analysis, metagenomics, protein domain annotation, and noncoding RNA annotation. She was a recipient of NSF CAREER Award in 2010.
Yanni Sun is an Associate Professor in the Department of Electronics at City University of Hong Kong. Before she joined CityU in 2018, she was 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. She works in bioinformatics and computational biology. In particular, her recent research interests include sequence analysis, next-generation sequencing data analysis, metagenomics, protein domain annotation, and noncoding RNA annotation. She was a recipient of NSF CAREER Award in 2010.
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