• Proceedings of the Korean Vacuum Society Conference
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• 2013.08a
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• pp.92.1-92.1
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• 2013

Molecular electronics has been the subject of intese research for many years because of the fundamental interest in molecular charge transport and potential applications, such as (bio)nanosensors and molecular memory devices. Molecular electronics requires a method for making reliable eletrical contacts to singlemolecules. To date, several approaches have been reported: scanning-probe microscopy, mechanical break junctions, nano patterning, and direct deposition of electrode on a self-assembled monolayers. However, most methods are laborious and difficult for large-scale application and more importantly, cannot control the number of moleucles in the junction. Recently, DNA has been used as a template for metallic nanostructures (e.g., Ag, Pd, and Au nanowires) through DNA metallization process. Furthermore, oligodeoxynucleotides have been tethered to organic molecules by using conventional organic reactions. Collectively, these techniques should provide an efficient route toward reliable and reproducible molecular electronic devices with large-scale fabrication. Therefore, I will present a paradigm for the fabrication of moleuclar electronic devices by using micrometer-sized DNA-singe organic molecule and DNA triblock structures.

• Journal of Korea Society of Industrial Information Systems
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• v.15 no.1
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• pp.37-46
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• 2010

A Suffix Tree is an efficient data structure that exposes the internal structure of a string and allows efficient solutions to a wide range of complex string problems, in particular, in the area of computational biology. However, as the biological information explodes, it is impossible to construct the suffix trees in main memory. We should find an efficient technique to construct the trees in a secondary storage. In this paper, we present a method for constructing a suffix tree in a disk for large set of DNA strings using new index scheme. We also show a typical application example with a suffix tree in the disk.

• Genomics & Informatics
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• v.3 no.1
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• pp.1-7
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• 2005

Case-control studies are widely used for disease gene mapping using individual genotyping data. However, analyses of large samples are often impractical due to the expense of individual genotyping. The use of DNA pooling can significantly reduce the number of genotyping reactions required; hence reducing the cost of large-scale case-control association studies. Here, we discuss the design and analysis of DNA pooling genetic association studies.

• Journal of Microbiology and Biotechnology
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• v.31 no.12
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• pp.1722-1731
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• 2021

The genus Streptomyces is intensively studied due to its excellent ability to produce secondary metabolites with diverse bioactivities. In particular, adequate precursors of secondary metabolites as well as sophisticated post modification systems make some high-yield industrial strains of Streptomyces the promising chassis for the heterologous production of natural products. However, lack of efficient genetic tools for the manipulation of industrial strains, especially the episomal vector independent tools suitable for large DNA fragment deletion, makes it difficult to remold the metabolic pathways and streamline the genomes in these strains. In this respect, we developed an efficient deletion system independent of the episomal vector for large DNA fragment deletion. Based on this system, four large segments of DNA, ranging in length from 10 kb to 200 kb, were knocked out successfully from three industrial Streptomyces strains without any marker left. Notably, compared to the classical deletion system used in Streptomyces, this deletion system takes about 25% less time in our cases. This work provides a very effective tool for further genetic engineering of the industrial Streptomyces.

• The KIPS Transactions:PartD
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• v.17D no.3
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• pp.175-184
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• 2010

Experiments and research on genes have become very convenient by using DNA chips, which provide large amounts of data from various experiments. The data provided by the DNA chips could be represented as a two dimensional matrix, in which one axis represents genes and the other represents samples. By performing an efficient and good quality clustering on such data, the classification work which follows could be more efficient and accurate. In this paper, we use a bio-inspired algorithm called the Particle Swarm Optimization algorithm to propose an efficient clustering mechanism for large amounts of DNA chip data, and show through experimental results that the clustering technique using the PSO algorithm provides a faster yet good quality result compared with other existing clustering solutions.

• Journal of Internet Computing and Services
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• v.19 no.2
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• pp.1-7
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• 2018

Due to advances in DNA sequencing technologies, its medical value continues to grow. However, once genome data leaked, it cannot be revoked, and disclosure of personal genome information impacts a large group of individuals. Therefore, secure techniques for managing genomic big data should be developed. We first propose a privacy-preserving inner product protocol for large data sets using the homomorphic encryption of Gentry et al., and then we introduce an efficient privacy-preserving DNA matching protocol based on the proposed protocol. Our efficient protocol satisfies the requirements of correctness, confidentiality, and privacy.

• International Journal of Computer Science & Network Security
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• v.21 no.8
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• pp.196-202
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• 2021

DNA sequencing provides fundamental data in genomics, bioinformatics, biology and many other research areas. With the emergent evolution in DNA sequencing technology, a massive amount of genomic data is produced every day, mainly DNA sequences, craving for more storage and bandwidth. Unfortunately, managing, analyzing and specifically storing these large amounts of data become a major scientific challenge for bioinformatics. Those large volumes of data also require a fast transmission, effective storage, superior functionality and provision of quick access to any record. Data storage costs have a considerable proportion of total cost in the formation and analysis of DNA sequences. In particular, there is a need of highly control of disk storage capacity of DNA sequences but the standard compression techniques unsuccessful to compress these sequences. Several specialized techniques were introduced for this purpose. Therefore, to overcome all these above challenges, lossless compression techniques have become necessary. In this paper, it is described a new DNA compression mechanism of pattern matching extended Compression algorithm that read the input sequence as segments and find the matching pattern and store it in a permanent or temporary table based on number of bases. The remaining unmatched sequence is been converted into the binary form and then it is been grouped into binary bits i.e. of seven bits and gain these bits are been converted into an ASCII form. Finally, the proposed algorithm dynamically calculates the compression ratio. Thus the results show that pattern matching extended Compression algorithm outperforms cutting-edge compressors and proves its efficiency in terms of compression ratio regardless of the file size of the data.

• Korean Journal of Biological Psychiatry
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• v.7 no.2
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• pp.123-130
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• 2000

The development of inexpensive high throughput methods to identify individual DNA sequences is important to the future growth of medical genetics. This has become increasingly apparent as psychiatric geneticists focus more attention on the molecular basis of complex multifactorial diseases at which most of psychiatric disease is estimated. Furthermore, candidate gene approaches used in identifying disease associated genes necessitate screening large sequence blocks for changes tracking with the disease state. Even after such genes are isolated, large scale mutational analysis will often be needed for risk assessment studies to define the likely medical consequences of carrying a mutated gene. This review provide basic knowledge of up-to-date technology, cDNA microarray which enables above mentioned various research themes.

• Proceedings of the Korean Society of Applied Pharmacology
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• 1994.04a
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• pp.267-267
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• 1994

In order to obtain insight into the mechanism by which DNA containing a thymine photo-dimer is recognized by the excision repair enzyme, T$_4$ endonuclease V, we have taken NMR study of this protein and its complex with oligonucleotides. The conformations of five different DNA duplexes DNA I : d(GCGGATGGCG).d(CGCCTACCGC), DNA II d(GCGGTTGGCG) .d(CGCCAACCGC), DNA III : d(GCGGT ^ TGGCG) .d(CGCCAACCGC), DNA IV d(GCGGGCGGCG).d(CGCCCGCCGC) and DNA V d(GCGGCCGGCG) . d(CGCCGGCCGC) were studied by $^1$H NMR. The NMR spectra of these five DNA duplexes in the absence of the enzyme clearly show that the formation of a thymine dimer within the DNA induces only a minor distortion in the structure, and that the overall structure of B type DNA is retained. The photo-dimer formation is found to cause a large change in chemical shifts at the GC7 base pair, which is located at the 3'-side of the thymine dimer, accompanied by the major conformational change at the thymine dimer site. The binding of a mutant T$_4$ endonuclease V (E23Q), which is unable to digest DNA containing a thymine dimer, to the DNA duplex d(GCGGT ^ TGGCG)ㆍd(CGCCAACCGC) causes a large down-field shift in the imino proton resonance of GC7. Therefore, this position is thought to be either the crucial point of the interaction wi th T$_4$ endonuclease V, or the si to of a conformational change in the DNA caused by the binding of T$_4$ endonuclease V. Usually, it is very difficult to assign NMR peaks in DNA * protein complex because of severe peak overlaps. In order to overcome these peak overlaps, we used a method of deuterium incorporation.

• Proceedings of the Korean Vacuum Society Conference
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• 2016.02a
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• pp.375.1-375.1
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• 2016

Polymerase chain reaction (PCR) has revolutionized genetics and become one of the most popular techniques in modern biological and medical sciences. It can be used not only as an in vitro DNA amplification method but also used in many bioassay applications. The PCR can be used to exponentially produce a large number of DNA copies from a small quantity of DNA molecules in a few hours. However, as unwanted DNA fragments are also often manufactured, the amplification efficiency of PCR is decreased. To overcome this limitation, several nanomaterials have been employed to increase the specificity of the PCR reaction. Recently, graphene has attracted a great interest for its excellent electron transfer, thermal and biocompatibility. Especially, gold nanoparticle-coated graphene oxide (GO/AuNPs) led to enhance electron and thermal transfer rate and low-charge transfer resistance. Therefore, we report the development of a demonstration for the PCR efficiency using a large-scale production of the GO and combination of gold nanoparticles. Because a thermal conductivity is an important factor for improving the PCR efficiency in different DNA polymerases and different size samples. When PCR use GO/AuNPs, the result of transmission electron microscopy and real-time quantitative PCR (qPCR) showed an enhanced PCR efficiency. We have demonstrated that GO/AuNPs would be simply outperformed for enhancing the specificity and efficiency of DNA amplification procedure.