• Genomics & Informatics
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• v.3 no.4
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• pp.149-153
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• 2005

Asthma is an inflammatory airways disease characterized by bronchial hyperresponsiveness and airways obstruction, which results from a complex interaction of genetic and environmental factors. Interleukin (IL)-13 and IL-4 are important in IgE synthesis and allergic inflammation, therefore genes encoding IL-13 and IL-4 are candidates for predisposition to asthma. In the present study, we screened single-nucleotide polymorphisms (SNPs) in IL-13 and IL-4 and examined whether they are risk factors for asthma. We resequenced all exons and the promoter region in 12 asthma patients and 12 normal controls, and identified 18 SNPs including 2 novel SNPs. The linkage disequilibrium(LD) pattern was evaluated with 16 common SNPs, and haplotypes were also estimated within the block. Although IL-13 and IL-4 are localized within 27 kb on chromosome 5q31 and share many biological profiles, this region was partitioned into 2 blocks. One SNP and three SNPs were determined as haplotype-taggingSNPs (htSNPs) within IL-13 and IL-4 haplotype-block, respectively. No significant associations were observed between any of the SNPs or haplotypes and development of asthma in small number of Korean subjects. However, the genetic variants of IL-13 and IL-4 would provide valuable strategies for the genotyping studies in large population.

• BMB Reports
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• v.49 no.12
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• pp.653-654
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• 2016

The human reference genome, maintained by the Genome Reference Consortium, is conceivably the most complete genome assembly ever, since its first construction. It has continually been improved by incorporating corrections made to the previous assemblies, thanks to various technological advances. Many currently-ongoing population sequencing projects have been based on this reference genome, heightening hopes of the development of useful medical applications of genomic information, thanks to the recent maturation of high-throughput sequencing technologies. However, just one reference genome does not fit all the populations across the globe, because of the large diversity in genomic structures and technical limitations inherent to short read sequencing methods. The recent success in de novo construction of the highly contiguous Asian diploid genome AK1, by combining single molecule technologies with routine sequencing data without resorting to traditional clone-by-clone sequencing and physical mapping, reveals the nature of genomic structure variation by detecting thousands of novel structural variations and by finally filling in some of the prior gaps which had persistently remained in the current human reference genome. Now it is expected that the AK1 genome, soon to be paired with more upcoming de novo assembled genomes, will provide a chance to explore what it is really like to use ancestry-specific reference genomes instead of hg19/hg38 for population genomics. This is a major step towards the furthering of genetically-based precision medicine.

• Microbiology and Biotechnology Letters
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• v.46 no.3
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• pp.300-312
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• 2018

Whole-genome sequencing of the wood-rotting fungus, Flammulina fennae, was carried out to identify carbohydrate-active enzymes (CAZymes). De novo genome assembly (31 kmer) of short reads by next-generation sequencing revealed a total genome length of 32,423,623 base pairs (39% GC). A total of 11,591 gene models in the assembled genome sequence of F. fennae were predicted by ab initio gene prediction using the AUGUSTUS tool. In a genome-wide comparison, 6,715 orthologous groups shared at least one gene with F. fennae and 10,667 (92%) of 11,591 genes for F. fennae proteins had orthologs among the Dikarya. Additionally, F. fennae contained 23 species-specific genes, of which 16 were paralogous. CAZyme identification and annotation revealed 513 CAZymes, including 82 auxiliary activities, 220 glycoside hydrolases, 85 glycosyltransferases, 20 polysaccharide lyases, 57 carbohydrate esterases, and 45 carbohydrate binding-modules in the F. fennae genome. The genome information of F. fennae increases the understanding of this basidiomycete fungus. CAZyme gene information will be useful for detailed studies of lignocellulosic biomass degradation for biotechnological and industrial applications.

• Microbiology and Biotechnology Letters
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• v.52 no.2
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• pp.163-178
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• 2024

Pan-genome analysis is used to interpret genome heterogeneity and diversification of bacterial species. Here, we present pan-genome analysis of 22 strains of Enterococcus mundtii. The GenBank file of E. mundtii strains that have been isolated from different sources i.e., human fecal matter, soil, leaf, dairy products, and insects was downloaded from National Center for Biotechnology Information (NCBI) database and analyzed using BPGA-1.3.0 (Bacterial Pan Genome Analysis) pipeline. Out of a total, 4503 gene families, 1843 belongs to the core genes whereas 1,762 gene families represent the accessory genes and 898 gene families depict the unique genes among all the selected genomes. Majority of the core genes belongs to the categories of Metabolism (37.83%) and Information storage & processing (29.84%) whereas unique genes belongs to the category of Information storage & processing (48.08%). Further, accessory genes are almost equally present in both functional categories i.e. Information storage & processing and Metabolism (34.34% and 32.27% respectively). Further, subset analysis on the basis of the origin of isolates exhibits presence and absence of exclusive gene families. The observation suggests that even closely related strains of a species show extensive disparity in genome owing to their ability to adapt to a specific environment.

• Journal of Microbiology and Biotechnology
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• v.14 no.5
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• pp.1081-1085
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• 2004

Genome research has become very popular in most nations. In order to enhance the efficiency of collaboration among genome research groups, ways to store and share data, communicate with each other, be guided through right research strategies, and to easily use well-established databases. In addition, since techniques and softwares for genome research groups are well established, a similar research road map could commonly be applied. In this study, we developed a web-based work place for effective genome research, named 'BioPlace.' From the beginning of writing a proposal, research members can work on the same environment with convenient aid to share files or data. BioPlace provides various ways of collaboration methods among genome researchers. The BioPlace system supports two types of workplaces, namely 'Personal Workspace' and 'Team Workspace.' For each BioPlace user, a Persona] Workspace is provided, while a Team Workspace is provided for each group with the same purpose. In addition, BioPlace provides a 'General Research Road Map' for genome research, and several Korean user interfaces for BLAST, PDB, and Primer3. We expect that BioPlace may facilitate collaboration of genome research among the experienced scientists and help beginners in many different ways as well.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.83-85
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• 2000

A lot of microbial genome sequencing projects is being done in many genome centers around the world, since the first genome, Haemophilus influenzae, was sequenced in 1995. The deluge of microbial genome sequence data demands new and highly automatic data flow system in order for genome researchers to manage and analyze their own bulky sequence data from low-level to high-level. In such an aspect, we developed the automatic data management system for microbial genome projects, which consists mainly of local database, analysis programs, and user-friendly interface. We designed and implemented the local database for large-scale sequencing projects, which makes systematic and consistent data management and retrieval possible and is tightly coupled with analysis programs and web-based user interface, That is, parsing and storage of the results of analysis programs in local database is possible and user can retrieve the data in any level of data process by means of web-based graphical user interface. Contig assembly, homology search, and ORF prediction, which are essential in genome projects, make analysis programs in our system. All but Contig assembly program are open as public domain. These programs are connected with each other by means of a lot of utility programs. As a result, this system will maximize the efficiency in cost and time in genome research.

• Proceedings of the Korean Society of Potoscience Conference
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• 2005.06a
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• pp.119-119
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• 2005

• Proceedings of the Korean Society of Plant Biotechnology Conference
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• 2003.04a
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• pp.122-122
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• 2003

• Proceedings of the Korean Society of Plant Biotechnology Conference
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• 2003.04a
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• pp.126-126
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• 2003

• Proceedings of the Korean Society of Plant Biotechnology Conference
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• 2005.11a
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• pp.192-192
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• 2005