• KIPS Transactions on Computer and Communication Systems
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• v.2 no.2
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• pp.67-74
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• 2013

Approximate string matching problems have been studied in diverse fields. Recently, fast approximate string matching algorithms are being used to reduce the time and costs for the next generation sequencing. To measure the amounts of errors between two strings, we use a distance function such as the edit distance. Given two strings X(|X| = m) and Y(|Y| = n) over an alphabet ${\Sigma}$, the edit distance between X and Y is the minimum number of edit operations to convert X into Y. The edit distance between X and Y can be computed using the well-known dynamic programming technique in O(mn) time and space. The edit distance also can be computed using the Four-Russians' algorithm whose preprocessing step runs in $O((3{\mid}{\Sigma}{\mid})^{2t}t^2)$ time and $O((3{\mid}{\Sigma}{\mid})^{2t}t)$ space and the computation step runs in O(mn/t) time and O(mn) space where t represents the size of the block. In this paper, we present a parallelized version of the computation step of the Four-Russians' algorithm. Our algorithm computes the edit distance between X and Y in O(m+n) time using m/t threads. Then we implemented both the sequential version and our parallelized version of the Four-Russians' algorithm using CUDA to compare the execution times. When t = 1 and t = 2, our algorithm runs about 10 times and 3 times faster than the sequential algorithm, respectively.

• Journal of the Korean Society for Environmental Technology
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• v.19 no.6
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• pp.550-555
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• 2018

International Maritime Organization (IMO) is one of the most effective organizations in evolving international law for the protection and conservation of the marine environment. The IMO, MARPOL(Marine Pollution) 73/78 contains six Annexes that provide an overarching framework for the objectives of the international marine pollution. Annex IV was regulated by 64 th resolution in 2012 to control sea pollution from sewage. In 2014 large-scale wastewater treatment and nutrient removal device was developed with a grant from the Ministry of Oceans and Fisheries. A combined new process of Sequence Batch Reactor (SBR) and Membrane Bioreactor(MBR) was developed to overcome the pollution caused by shipboard sewage. In the present study, shipboard sewage wastewater was treated by mixing and aeration cycle in the newly developed SBR process. Furthermore, during analysis by NGS technique(Macrogen Co., Ltd.), dominant species of bacteria were found in the aeration tank of the Bench-scale wastewater treatment facility. Bacteroidetes and Gammaproteobacteria accounted for 27.1 % of the aerobicbacteria and 16.8 % of the anaerobicbacteria, respectively. Microorganisms play a vital role in shipboard wastewater treatment. A further detailed study is required to understand the precise role of the microorganisms in the wastewater treatment.

• Korean Journal of Ichthyology
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• v.33 no.4
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• pp.217-225
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• 2021

The family Platycephalidae is a taxonomic group of economically important demersal flathead fishes that predominantly occupy tropical or temperate estuaries and coastal environments of the Indo-Pacific oceans and the Mediterranean Sea. In this study, we for the first time analyzed the complete mitochondrial genome (mitogenome) of the flathead Platycephalus cultellatus Richardson, 1846 from Vietnam by Next Generation Sequencing method. Its mitogenome was 16,641 bp in total length, comprising 13 protein-coding genes (PCGs), two ribosomal RNA genes, and 22 transfer RNA genes. The gene composition and order of the mitogenome were identical to those of typical vertebrates. The phylogenetic trees were reconstructed based on the concatenated nucleotide sequence matrix of 13 PCGs and the partial sequence of a DNA barcoding marker, cox1 in order to determine its molecular phylogenetic position among the order Scorpaeniformes. The phylogenetic result revealed that P. cultellatus formed a monophyletic group with species belonging to the same family and consistently clustered with one nominal species, P. indicus, and two Platycephalus sp. specimens. Besides, the cox1 tree confirmed the taxonomic validity of our specimen by forming a monophyletic clade with its conspecific specimens. The mitogenome of P. cultellatus analyzed in this study will contribute valuable information for further study on taxonomy and phylogeny of flatheads.

• Journal of Marine Life Science
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• v.8 no.2
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• pp.93-103
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• 2023

eDNA, an abbreviation for environmental DNA, means DNA derived from organisms inhabiting in a specific environment. The utilization of eDNA extracted from environmental samples allows for efficient and accurate monitoring of organisms inhabiting the respective environment. Specifically, eDNA obtained from seawater samples can be used to analyze marine biodiversity. After collecting seawater samples and extracting eDNA, metagenome analysis enables the taxonomic and diversity analysis among marine organisms inhabiting the sampled area. This review proposed an overall process of marine biodiversity analysis by utilizing eDNA from seawater. Currently, the application of eDNA for analyzing marine biodiversity in domestic setting is not yet widespread. This review can contribute to establishment of marine eDNA research methods in Korea, providing valuable assistance in standardizing the use of eDNA in marine biodiversity studies.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.65 no.4
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• pp.386-398
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• 2020

Wheat is one of the world's top three crops and is an important staple crop, accounting for 20% of the nutrient calories consumed by the world's population. However, due to its complex heterogeneous hexaploid chromosomes and vast genome of approximately 16 Gb, compared to those of other crops, molecular biology and biotechnology studies on wheat are lacking. In recent years, wheat genome analysis has been performed using the latest next-generation sequencing technology so that useful genes can be easily obtained, and wheat biotechnology research is accelerating in various fields. In this review, wheat transformation, an indispensable technique for developing new functional biotech wheat by revealing the function of wheat genes, is described in detail. In addition, the latest research results for overcoming plant diseases, abiotic stresses, and wheat-related diseases that are difficult to solve by classical breeding through wheat transformation and biotechnology are described.

• Korean Journal of Microbiology
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• v.51 no.4
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• pp.347-354
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• 2015

Soybean is well known to be originated from Korea and far-east Asian countries, and studies of many root nodule bacteria associated with soybean have mainly-focused on nitrogen fixation, but much less study was carried out on bacterial community in the rhizosphere of soybean. In this study, we analyzed the bacterial community in rhizosphere of Korean soybean, Daepungkong using the pyrosequencing method based on the 16S rRNA gene to characterize the change of the rhizosphere community structure according to the growth stages of soybeans and to elucidate bacterial core community in rhizosphere of soybean. Our results revealed that bacterial community of rhizosphere soil differed from that of bulk soil and was composed of a total of 21 bacterial phyla. The predominant phylum in the rhizosphere of soybean was Proteobacteria (36.6-42.5%) and followed by Acidobacteria (8.6-9.4%), Bacteroidetes (6.1-10.9%), Actinobacteria (6.4-9.8%), and Firmicutes (5.7-6.3%). The bacterial core community in soybean rhizosphere was mainly composed of the operational taxonomic units (OTUs) belonging to the phylum Proteobacteria throughout all growth stages. The OTU00006 belonged to the genus Bradyrhizobium had the highest abundance and Steroidobacter, Streptomyces, Devosia were followed. These results show that bacterial core community in soybean rhizosphere was mainly composed of OTUs associated with plant growth promotion and nutrient cycles.

• Korean Journal of Medicinal Crop Science
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• v.22 no.5
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• pp.339-348
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• 2014

The transcriptomes of four ginseng accessions such as Cheonryang (Korean ginseng cultivar), Yunpoong (Korean ginseng cultivar), G03080 (breeding line of Korean ginseng), and P. quinquefolius (American ginseng) was characterized. As a result of sequencing, total lengths of the reads in each sample were 156.42 Mb (Cheonryang cultivar), 161.95 Mb (Yunpoong cultivar), 165.07 Mb (G03080 breeding line), and 166.48 Mb (P. quinquefolius). Using a BLAST search against the Phytozome databases with an arbitrary expectation value of 1E-10, over 20,000 unigenes were functionally annotated and classified using DAVID software, and were found in response to external stress in the G03080 breeding line, as well as in the Cheonryang cultivar, which was associated with the ion binding term. Finally, unigenes related to transmembrane transporter activity were observed in Cheonryang and P. quinquefolius, which involves controlling osmotic pressure and turgor pressure within the cell. The expression patterns were analyzed to identify dehydrin family genes that were abundantly detected in the Cheonryang cultivar and the G03080 breeding line. In addition, the Yunpoong cultivar and P. quinquefolius accession had higher expression of heat shock proteins expressed in Ricinus communis. These results will be a valuable resource for understanding the structure and function of the ginseng transcriptomes.

• The Journal of the Korea Contents Association
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• v.19 no.3
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• pp.365-374
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• 2019

Unlike benign tumors, malignant tumors are capable of metastasis, easy to relapse, poor survival, and low quality of life. In Korea, here is a tendency to treat the tumors collectively according to the General Principles of Cancer Chemotherapy(GPCC) of the Health Insurance Review & Assessment Service (HIRA). But recently, companion diagnostics(CDx) is recommended rather than unilateral medication because biomarker-based molecular diagnostics is possible to predict the drug response of patients before drug treatment. Not only domestic but also overseas Food and Drug Administratio (FDA) recommends the development of the CDx system at the stage of drug development to ensure the responsiveness and safety of medicines. In this study, I focused on the necessity of CDx development direction as well as CDx development status through literature review. Furthermore I also discussed CDx types according to the molecular diagnostic technology such as immunohistochemistry (IHC), polymerase chain reaction (PCR), in situ hybridization (ISH), and next-generation sequencing (NGS) not only in the approved CDx but also in the developing one by US FDA. And I suggested the technology issue of CDx development process such as a selection of molecular diagnostics at the time of release, a clear understanding of the CDx mechanism, and a convergence of drug with CDx development. The necessity of social insurance system also was proposed for CDx development.

• Journal of Life Science
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• v.32 no.5
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• pp.391-410
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• 2022

Human microbiota is a community of microorganisms, including bacteria, fungi, and viruses, that inhabit various locations of the body, such as the gut, oral, and skin. Along with the development of metabolomic analysis and next-generation sequencing techniques for 16S ribosomal RNA, it has become possible to analyze the population for subtypes of microbiota, and with these techniques, it has been demonstrated that bacterial microbiota are involved in the metabolic and immunological processes of the hosts. While specific bacteria of microbiota, called commensal bacteria, positively affect hosts by producing essential nutrients and protecting hosts against other pathogenic microorganisms, dysbiosis, an abnormal microbiota composition, disrupts homeostasis and thereby has a detrimental effect on the development and progression of various types of diseases. Recently, several studies have reported that oral and gut bacteria of microbiota are involved in the carcinogenesis of gastrointestinal tumors and the therapeutic effects of anticancer therapy, such as radiation, chemotherapy, targeted therapy, and immunotherapy. Studying the complex relationships (bacterial microbiota-cancer-immunity) and microbiota-related carcinogenic mechanisms can provide important clues for understanding cancer and developing new cancer treatments. This review provides a summary of current studies focused on how bacterial microbiota affect gastrointestinal cancer and anticancer therapy and discusses compelling possibilities for using microbiota as a combinatorial therapy to improve the therapeutic effects of existing anticancer treatments.