웹기반 유전체 분석시스템 개발

박기정(Kiejung Park),서화정(Hwajung Seo),태홍석(Hongseok Tae),김기봉(Ki-Bong Kim),남혜원(Hyeweon Nam),이대상(Daesang Lee) 한국정보과학회 2003 정보과학회지 Vol.21 No.6

[유전체학과 생물정보 사업]

박기정(Kiejung Park) 한국정보과학회 2005 정보과학회지 Vol.23 No.5

Analysis of unmapped regions associated with long deletions in Korean whole genome sequences based on short read data

Lee, Yuna,Park, Kiejung,Koh, Insong Korea Genome Organization 2019 Genomics & informatics Vol.17 No.4

While studies aimed at detecting and analyzing indels or single nucleotide polymorphisms within human genomic sequences have been actively conducted, studies on detecting long insertions/deletions are not easy to orchestrate. For the last 10 years, the availability of long read data of human genomes from PacBio or Nanopore platforms has increased, which makes it easier to detect long insertions/deletions. However, because long read data have a critical disadvantage due to their relatively high cost, many next generation sequencing data are produced mainly by short read sequencing machines. Here, we constructed programs to detect so-called unmapped regions (UMRs, where no reads are mapped on the reference genome), scanned 40 Korean genomes to select UMR long deletion candidates, and compared the candidates with the long deletion break points within the genomes available from the 1000 Genomes Project (1KGP). An average of about 36,000 UMRs were found in the 40 Korean genomes tested, 284 UMRs were common across the 40 genomes, and a total of 37,943 UMRs were found. Compared with the 74,045 break points provided by the 1KGP, 30,698 UMRs overlapped. As the number of compared samples increased from 1 to 40, the number of UMRs that overlapped with the break points also increased. This eventually reached a peak of 80.9% of the total UMRs found in this study. As the total number of overlapped UMRs could probably grow to encompass 74,045 break points with the inclusion of more Korean genomes, this approach could be practically useful for studies on long deletions utilizing short read data.

An ensemble correlation-based gene selection algorithm for cancer classification with gene expression data.

Piao, Yongjun,Piao, Minghao,Park, Kiejung,Ryu, Keun Ho Oxford University Press 2012 Bioinformatics Vol.28 No.24

<P>Gene selection for cancer classification is one of the most important topics in the biomedical field. However, microarray data pose a severe challenge for computational techniques. We need dimension reduction techniques that identify a small set of genes to achieve better learning performance. From the perspective of machine learning, the selection of genes can be considered to be a feature selection problem that aims to find a small subset of features that has the most discriminative information for the target.</P>

Z-curve : A computer Program Calculating DNA Helical Axis Coordinates for three-dimensional Graphic Presentation of Curvature

Lee, Sang Soo,Park, Kiejung,Kang, Changwon Korean Society of Molecular Biology 1999 Molecules and cells Vol.9 No.4

Molecular characterization of positively selected genes contributing aquatic adaptation in marine mammals

Roh Yoo-Rim,Yim Hyung-Soon,Park Kiejung,Lee Jung-Hyun 한국유전학회 2024 Genes & Genomics Vol.46 No.7

Background Marine mammals, which have evolved independently into three distinct lineages, share common physiological features that contribute to their adaptation to the marine environment. Objective To identify positively selected genes (PSGs) for adaptation to the marine environment using available genomic data from three taxonomic orders: cetaceans, pinnipeds, and sirenians. Methods Based on the genomes within each group of Artiodactyla, Carnivora and Afrotheria, we performed selection analysis using the branch-site model in CODEML. Results Based on the branch-site model, 460, 614, and 359 PSGs were predicted for the cetaceans, pinnipeds, and sirenians, respectively. Functional enrichment analysis indicated that genes associated with hemostasis were positively selected across all lineages of marine mammals. We observed positive selection signals for the hemostasis and coagulation-related genes plasminogen activator, urokinase (PLAU), multimerin 1 (MMRN1), gamma-glutamyl carboxylase (GGCX), and platelet endothelial aggregation receptor 1 (PEAR1). Additionally, we found out that the sodium voltage-gated channel alpha subunit 9 (SCN9A), serine/arginine repetitive matrix 4 (SRRM4), and Ki-ras-induced actin-interacting protein (KRAP) are under positive selection pressure and are associated with cognition, neurite outgrowth, and IP3-mediated Ca2 + release, respectively. Conclusion This study will contribute to our understanding of the adaptive evolution of marine mammals by providing information on a group of candidate genes that are predicted to influence adaptation to aquatic environments, as well as their functional characteristics. Background Marine mammals, which have evolved independently into three distinct lineages, share common physiological features that contribute to their adaptation to the marine environment. Objective To identify positively selected genes (PSGs) for adaptation to the marine environment using available genomic data from three taxonomic orders: cetaceans, pinnipeds, and sirenians. Methods Based on the genomes within each group of Artiodactyla, Carnivora and Afrotheria, we performed selection analysis using the branch-site model in CODEML. Results Based on the branch-site model, 460, 614, and 359 PSGs were predicted for the cetaceans, pinnipeds, and sirenians, respectively. Functional enrichment analysis indicated that genes associated with hemostasis were positively selected across all lineages of marine mammals. We observed positive selection signals for the hemostasis and coagulation-related genes plasminogen activator, urokinase (PLAU), multimerin 1 (MMRN1), gamma-glutamyl carboxylase (GGCX), and platelet endothelial aggregation receptor 1 (PEAR1). Additionally, we found out that the sodium voltage-gated channel alpha subunit 9 (SCN9A), serine/arginine repetitive matrix 4 (SRRM4), and Ki-ras-induced actin-interacting protein (KRAP) are under positive selection pressure and are associated with cognition, neurite outgrowth, and IP3-mediated Ca2 + release, respectively. Conclusion This study will contribute to our understanding of the adaptive evolution of marine mammals by providing information on a group of candidate genes that are predicted to influence adaptation to aquatic environments, as well as their functional characteristics.

흰 DNA 의 총 쐐기 각도를 계산하는 컴퓨터 프로그램

이상수,강창원,박기정 ( Sang Soo Lee,Kiejung Park,Chang Won Kang ) 생화학분자생물학회 1991 BMB Reports Vol.24 No.6

A computer program for calculation of total wedge angles to reveal DNA curvature was developed. The calculation is essentially based on the wedge model and uses recently updated values of roll and tilt wedge angles and twist angles between the nearest neighbor base pairs. When the wedge angles of the individual neighboring base pairs are summed along a long DNA sequence, three dimension vectorial summations were employed. Thus, a major improvement in this calculation is to eliminate the earlier approximation of two dimension vectorial summation of roll and tilt wedge angles. The 33 DNA sequences of periodic repetition that have previously been reported to have a bent structure were analyzed with this computer program and the magnitude of gel retardation was found to be correlated with the accumulated wedge angle. Thus, the gel retardation patterns of permuted DNA fragments can be predicted with this computer program analysis. This program also correctly reveals the bending locus of pT181 replication origin sequence which does not contain any periodic poly(A) tracts.

의존성 반영 분해모델에 의한 유전자의 핵심 프로모터 영역 예측

김기봉(Ki-Bong Kim),박기정(Kiejung Park),공은배(Eun Bae Kong) 한국정보과학회 2003 정보과학회논문지 : 소프트웨어 및 응용 Vol.30 No.3·4

다수의 미생물 유전체 프로젝트들이 완료되면서 엄청난 양의 유전체 핵산 염기서열 데이타들이 양산되고 있다. 이러한 상황에서 전산 기법을 이용하여 유전체 DNA 염기서열 상에서 유전자의 프로모터 영역을 규명하는 문제는 최근에 상당한 연구의 관심대상으로 떠오르고 있다. 본 논문에서는 전사조절의 핵심 역할을 하는 -10 영역과 전사개시 부위를 포함한 원핵생물의 핵심 프로모터 영역에 대한 의존성 반영 분해모델 (Dependency-Reflecting Decomposition Model)을 제안한다. 이 모델은 인접한 위치에 존재하는 핵산 염기들 사이의 의존성뿐만 아니라 인접하지 않은 위치의 핵산 염기들간의 의존성까지 고려함으로써 핵산 염기서열 상에 내포되어있는 중요한 생물학적 의존성들을 함축하고 있다. DRDM 모델은 우수한 성능평가 결과를 보였으며, 미생물 유전체 Contig들 상에서 임의의 유전자 프로모터를 예측하는데 효과적으로 이용될 수 있다. A lot of microbial genome projects have been completed to pour the enormous amount of genomic sequence data. In this context, the problem of identifying promoters in genomic DNA sequences by computational methods has attracted considerable research attention in recent years. In this paper, we propose a new model of prokaryotic core promoter region including the -10 region and transcription initiation site, that is, Dependency-Reflecting Decomposition Model (DRDM), which captures the most significant biological dependencies between positions (allowing for non-adjacent as well as adjacent dependencies). DRDM showed a good result of performance test and it will be employed effectively in predicting promoters in long microbial genomic Contigs.

리드 시퀀싱 시뮬레이터 비교 분석

탁해성 ( Haesung Tak ),이상민 ( Sang-min Lee ),박기정 ( Kiejung Park ),이도훈 ( Dohoon Lee ),조환규 ( Hwan-gue Cho ) 한국정보처리학회 2013 한국정보처리학회 학술대회논문집 Vol.20 No.2

차세대 유전자 서열 시퀀싱 기법이 등장함에 따라 참조 유전자 서열로부터 리드를 생성하는 시퀀서의 기술이 다양화 되었다. 이전 시퀀싱 방식에 비해 비용 및 시간 측면에서 효율성이 증대 되었으나, 매핑도구의 검증을 위해서 다양한 생물학적 특이성을 반영하거나 비용이 소요되지 않는 방법을 연구하는 과정에서 리드 시퀀싱 시뮬레이터가 개발되었다. 본 논문에서는 현재 사용되고 있는 리드 시퀀싱 시뮬레이터에서 반영된 시퀀싱 기법을 분석하고 시뮬레이터의 기능적 특성을 분석하고자 한다. 이는 시뮬레이터 개발에 필요한 기능 설계 및 생물학적 특성을 반영하는데 활용하고자 한다.

BLAST/FASTA를 활용한 미생물 유전체 비교용 도구의 개발

태홍석,이대상,박완,박기정,Tae, Hongseok,Lee, Daesang,Park, Wan,Park, Kiejung 한국미생물학회 2002 미생물학회지 Vol.38 No.4

미생물 유전체 프로젝트의 결과인 유전체 서열에 대해, 비교 유전체 분석을 수행할 수 있는 분석 도구인 GComp를 개발하였다. 이 도구는 국부 상동성 계산을 BLAST나 FASTA를 사용하여 수행한 후에 그 결과를 받아들여, 상동성을 보이는 부분을 분석하고 위치 파악 및 연결한 뒤, 두 유전체간의 상동성 정도를 일목요연하게 보여줄 수 있는 테이블과 파일들을 생성한다. 한편. 그 결과를 그래픽으로 표시하고 전체를 살펴볼 수 있는 인터페이스 기능을 구현하였다. 시험 데이터로 기존의 미생물 유전체 서열을 상대로 분석하면서, 유전체 서열의 핵산 및 단백질 수준에서의 비교분석 결과를 통해 두 유전체에 대한 비교 정보를 효과적으로 확인할 수 있었고, 보다 다양한 분석을 위한 도구 개발의 기준을 설정할 수 있었다. We have developed GComp as an analysis tool for microbial genome comparison. This tool exploits BLAST or FASTA as a preprocessing program for local alignments to detect homologous regions, parses the homology search results, and generates tables and files to show homology relationship between two genomes at a glance. The interface for graphical representation of the comparative genomic analysis has been also implemented. Our test cases shows that the program can be useful in practice for intuitive and quantitative comparison of microbial genome sequence pairs as well as self-genome analysis. A few additional features have been devised and designed, which will be added in the further development.