서울대학교 생물정보학 협동과정 주최로 세미나를 아래와 같이 열고자 하오니, 많은 참여 바랍니다.

 

일시: 2017년 11월 23일 목요일 오전 11시

연사: 박상철 (서울대학교 보건대학원)

장소: 서울대학교 25동 411호

 

Title : Large-scale genomic studies on species characteristics and species boundaries

 

Abstract : Due to the accumulation of genome sequences, the main interest of bacterial genomics has shifted from data generation to data analysis. In order to capture the characteristics of species and identify the genomic species boundary, this study applied numerous genomes to pan-genome analysis. The characteristics of the pan-genomes in seven species were investigated. A more than 27,000 genomes belonging to Streptococcus pneumoniae, Staphylococcus aureus subsp. aureus, Salmonella enterica subsp. enterica, Escherichia coli and Shigella, Mycobacterium tuberculosis complex, Pseudomonas aeruginosa, Acinetobacter baumannii, were collected and used to construct the pan-genome after filtering low quality genomes and confirming taxonomic information. The results from the pan-genome revealed that each species has different genetic content, and species boundaries from an evolutionary point of view. In this process, we also proved that the estimation method for deciding open property is no longer provide a clear solution. By applying a large number of genomic data, we were able to gain insights to broaden our understanding of bacterial species.

 

Education / Personal Held

2017.9- Postdoctoral researcher in Graduate School of Public Health, Seoul National University

2010.9-2017.8 Ph.D. in Interdisciplinary Program in Bioinformatics, Seoul National University

2006.3-2010.8 B.S. in Biological Sciences, Seoul National University

 

Selected Publications

1. Lee I*, Kim YO, ParkS-C, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. International journal of systematic and evolutionary microbiology. 2016;66(2):1100-3.

 

2. Kim M*, ParkS-C*, Baek I, Chun J. Large-scale evaluation of experimentally determined DNA G+ C contents with whole genome sequences of prokaryotes. Systematic and applied microbiology. 2015;38(2):79-83.

 

3. Jeon Y-S*, ParkS-C, Lim J, Chun J, Kim B-S. Improved pipeline for reducing erroneous identification by 16S rRNA sequences using the Illumina MiSeq platform. Journal of Microbiology. 2015;53(1):60-9.

 

4. Baek I*, Seo B, Lee I, Lee K, ParkS-C, Yi H, Chun J. Burkholderia megalochromosomata sp. nov., isolated from grassland soil. International journal of systematic and evolutionary microbiology. 2015;65(3):959-64.

 

5. Kim M*, Oh H-S, ParkS-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. International journal of systematic and evolutionary microbiology. 2014;64(2):346-51.

 

6. Jeon Y-S*, Lee K, ParkS-C, Kim B-S, Cho Y-J, Ha S-M, Chun J. EzEditor: a versatile sequence alignment editor for both rRNA-and protein-coding genes. International journal of systematic and evolutionary microbiology. 2014;64(2):689-91.

 

7. Lee K*, ParkS-C, Yi H, Chun J. Flavobacteriumlimnosediminis sp. nov., isolated from sediment of a freshwater lake. International journal of systematic and evolutionary microbiology. 2013;63(12):4784-9.

 

8. Yi H*, Cho Y-J, Yoon S-H, ParkS-C, Chun J. Comparative genomics of Neisseria weaveri clarifies the taxonomy of this species and identifies genetic determinants that may be associated with virulence. FEMS microbiology letters. 2012;328(2):100-5.

 

9. Kim O-S*, Cho Y-J, Lee K, Yoon S-H, Kim M, Na H, ParkS-C, Jeon Y-S, Lee J-H, Yi H, Won S, Chun J. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. International journal of systematic and evolutionary microbiology. 2012;62(3):716-21.

 

 

서울대학교 생물정보학 협동과정 주최