• Microbiology and Biotechnology Letters
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• v.26 no.1
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• pp.23-33
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• 1998

The entire sequence of a 4,214,810 bp genome of the Bacillus subtilis 168 has been determined by an international project, and the completion has been announced on July 19, 1997. For the sequencing project an international consortium was established and 25 European, 7 Japanese laboratories, 2 biotechnology companies, and our laboratory participated in the project. Within this framework we determined the complete nucleotide sequence of a 53,289 bp fragment upstream of the odhA gene (181 $^{\circ}$) of the B. subtilis 168 chromosome. On the basis of the published DNA sequences of the B. subtilis sspC and odhA genes, we obtained genomic fragments by plasmid rescue and long-range PCR. The sequenced fragment contains 56 putative open reading frames (designated yojA-yolI and 9 known genes (sspC, cge cluster, orfE5, orfRMl and odhA), in which we found many interesting features. In addition, the entire nucleotide sequence of a 53,289 bp region enabled us to revise the current genetic map of this region.

• Toxicological Research
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• v.17
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• pp.241-249
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• 2001

Toxicology is under challenge from several new trends in science and technology, namely computer, the Internet, genome projects, genomic technologies, and combinatorial chemistry. These new trends will drastically change research style of toxicology. In addition to conventional uni cellular tests and animal tests using rodents, computer simulation, DNA chips (microarrays), in vivo tests using simple model organisms such as nematodesor flies become important routine screening tests. How to arrange these tests in tiers will become a new problem. Endocrine disruptors hypothesis is a good example for this kind of futuristic approach. Computer, particularly the Internet, is also enabling toxicologists and regulatory experts to collaborate more closely. The IPCS (International Program for Chemical Safety) which is ajoint project of WHO, ILO and UNEP, is a well-known international collaborative research for chemical risk assessments. The GINC project of IPCS is an effort to utilize the Internet for such collaborations. Some efforts were also made to establish regional collaboration network in East Asia under this project.

• Interdisciplinary Bio Central
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• v.3 no.1
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• pp.2.1-2.4
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• 2011

Arabidopsis is well-known to the world's plant research community as a model plant. Many significant resources and innovative research tools, as well as large bodies of genomic information, have been created and shared by the research community, partly explaining why so many researchers use this small plant for their research. The genome sequence of Arabidopsis was fully characterized by the end of the $20^{th}$ century. Soon afterwards, the Arabidopsis research community began a 10-year international project on the functional genomics of the species. In 2001, at the beginning of the project, the RIKEN BioResource Center (BRC) started its Arabidopsis resource project. The following year, the National BioResource Project was launched, funded by the Japanese government, and the RIKEN BRC was chosen as a core facility for Arabidopsis resource. Seeds of RIKEN Arabidopsis transposon-tagged mutant lines, activation-tagged lines, full-length cDNA over-expresser lines, and natural accessions, as well as RIKEN Arabidopsis full-length cDNA clones and T87 cells, are preserved at RIKEN BRC and distributed around the world. The major resources provided to the research community have been full-length cDNA clones and insertion mutants that are suitable for use in reverse-genetics studies. This paper provides an overview of the Arabidopsis resources made available by RIKEN BRC and examples of research that has been done by users and developers of these resources.

• BMB Reports
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• v.37 no.1
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• pp.107-113
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• 2004

Since the completion of the genome project of the nematode C. elegans in 1998, functional genomic approaches have been applied to elucidate the gene and protein networks in this model organism. The recent completion of the whole genome of C. briggsae, a close sister species of C. elegans, now makes it possible to employ the comparative genomic approaches for identifying regulatory mechanisms that are conserved in these species and to make more precise annotation of the predicted genes. RNA interference (RNAi) screenings in C. elegans have been performed to screen the whole genome for the genes whose mutations give rise to specific phenotypes of interest. RNAi screens can also be used to identify genes that act genetically together with a gene of interest. Microarray experiments have been very useful in identifying genes that exhibit co-regulated expression profiles in given genetic or environmental conditions. Proteomic approaches also can be applied to the nematode, just as in other species whose genomes are known. With all these functional genomic tools, genetics will still remain an important tool for gene function studies in the post genome era. New breakthroughs in C. elegans biology, such as establishing a feasible gene knockout method, immortalized cell lines, or identifying viruses that can be used as vectors for introducing exogenous gene constructs into the worms, will augment the usage of this small organism for genome-wide biology.

• KIPS Transactions on Software and Data Engineering
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• v.2 no.2
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• pp.97-106
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• 2013

Since human genome project finished, the cost for human genome analysis has decreased very rapidly. This results in the sharp increase of human genome data to be analyzed. As the need for fast analysis of very large bio data such as human genome increases, non IT researchers such as biologists should be able to execute fast and effectively many kinds of bio applications, which have a variety of characteristics, under HPC environment. To accomplish this purpose, a biologist need to define a sequence of bio applications as workflow easily because generally bio applications should be combined and executed in some order. This bio workflow should be executed in the form of distributed and parallel computing by allocating computing resources efficiently under HPC cluster system. Through this kind of job, we can expect better performance and fast response time of very large bio data analysis. This paper proposes a workflow-based data analysis system specialized for bio applications. Using this system, non-IT scientists and researchers can analyze very large bio data easily under HPC environment.

• Genomics & Informatics
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• v.12 no.3
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• pp.127-133
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• 2014

Gastritis is a major disease that has the potential to grow as gastric cancer. Gastric cancer is a very common cancer, and it is related to a very high mortality rate in Korea. This disease is known to have various reasons, including infection with Helicobacter pylori, dietary habits, tobacco, and alcohol. The incidence rate of gastritis has reported to differ between age, population, and gender. However, unlike other factors, there has been no analysis based on gender. So, we examined the high risk factors of gastritis in each gender in the Korean population by focusing on sex. We performed an analysis of 120 clinical characteristics and genome-wide association studies (GWAS) using 349,184 single-nucleotide polymorphisms from the results of Anseong and Ansan cohort study in the Korea Association Resource (KARE) project. As the result, we could not prove a strong relation with these factors and gastritis or gastric ulcer in the GWAS. However, we confirmed several already-known risk factors and also found some differences of clinical characteristics in each gender using logistic regression. As a result of the logistic regression, a relation with hyperlipidemia, coronary artery disease, myocardial infarction, hyperlipidemia therapy, hypotensive or antihypotensive drug, diastolic blood pressure, and gastritis was seen in males; the results of this study suggest that vascular disease has a potential association with gastritis in males.

• Genomics & Informatics
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• v.17 no.3
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• pp.29.1-29.8
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• 2019

The Wellcome Trust Case Control Consortium (WTCCC) study was a large genome-wide association study that aimed to identify common variants associated with seven diseases. That study combined two control datasets (58C and UK Blood Services) as shared controls. Prior to using the combined controls, the WTCCC performed analyses to show that the genomic content of the control datasets was not significantly different. Recently, the analysis of human leukocyte antigen (HLA) genes has become prevalent due to the development of HLA imputation technology. In this project, we extended the between-control homogeneity analysis of the WTCCC to HLA. We imputed HLA information in the WTCCC control dataset and showed that the HLA content was not significantly different between the two control datasets, suggesting that the combined controls can be used as controls for HLA fine-mapping analysis based on HLA imputation.

• Proceedings of the IEEK Conference
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• 2002.07c
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• pp.1788-1791
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• 2002

In the post-genome era. it is one of important research subject to Investigate the roles of the proteins in human body based on decoded genome information during Human Genome Project. In order to clarify them. it is necessary to analyze the structure of the protein crystals and their function. ' Crystallization is the beginning stage of protein structure determination process. There are some methods for structural analysis of the proteins, and general one is X-ray structural analysis method. In order to utilize this method for analyzing the protein crystal's structure, artificial protein crystallization is required. However, since artificial crystallizing work takes much time and manpower. the performance against its cost is still low. Therefore. we started to discuss to develop a supporting system for improving efficiency of the crystallization distinction procedure. In this paper, we examine to realize such supporting system for crystallization distinction using image-processing technique and report about our experimental result with many real protein solution images.

• Genomics & Informatics
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• v.20 no.1
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• pp.8.1-8.14
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• 2022

Despite the success of recent genome-wide association studies investigating longitudinal traits, a large fraction of overall heritability remains unexplained. This suggests that some of the missing heritability may be accounted for by gene-gene and gene-time/environment interactions. In this paper, we develop a Bayesian variable selection method for longitudinal genetic data based on mixed models. The method jointly models the main effects and interactions of all candidate genetic variants and non-genetic factors and has higher statistical power than previous approaches. To account for the within-subject dependence structure, we propose a grid-based approach that models only one fixed-dimensional covariance matrix, which is thus applicable to data where subjects have different numbers of time points. We provide the theoretical basis of our Bayesian method and then illustrate its performance using data from the 1000 Genome Project with various simulation settings. Several simulation studies show that our multivariate method increases the statistical power compared to the corresponding univariate method and can detect gene-time/ environment interactions well. We further evaluate our method with different numbers of individuals, variants, and causal variants, as well as different trait-heritability, and conclude that our method performs reasonably well with various simulation settings.

• Proceedings of the Korean Society of Plant Pathology Conference
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• 2003.10a
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• pp.80.2-81
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• 2003

Since hot peppers (Capsicum annuum L.) are getting reputation as an important source of vitamins, medicine and many other areas, consumption and cultivation is being increased in the world. In spite of this usefulness, so little attention has been given to the hot pepper plants. To date, less than 500 nucleotide sequences including redundancy has been identified in NCBI database. Therefore we started to EST sequencing project for initial characterization of the genome, because of the large genome size of hot pepper (2.7 3.3 ${\times}$ 109 bp), To date, a set of 10,000 non-redundant genes were identified by EST sequencing for microarray-based gene expression studies. At present, cDNA microarrays containing 4,685 unigene clones are used for hybridization labeled targets derived from pathogen infected and uninoculated leaf tissues. Monitoring of gene expression profiles of hot pepper interactions with soybean pustule pathogen (Xag；Xanthomonas axonopodis pv. glycine) will be presented.