• Proceedings of the Korean Information Science Society Conference
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• 2003.10b
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• pp.775-777
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• 2003

miRNA(microRNA)는 길이가 약 22nt 정도 되는 작은 ncRNA로서 유전자 작용을 조절하는데 중요한 역할을 하는 것으로 알려져 있다. 다이서(dicer)에 의해 성숙한 miRNA(mature miRNA)를 계산학적(computational)방법으로 학습하여 인간 miRNA의 구조를 예측하였다. miRNA에 관한 구체적인 기작은 아직 확실히 밝혀지지 않았기 때문에 서열 기반과 구조 기반 모두를 포함 하는 모델을 구현 하였으며 ambiguity code를 씀으로써 정보의 손실을 최소화 하도록 하였다. miRNA와 비슷한 구조를 가진 인간 EST로부터 데이터를 무작위 추출하여 실제 인간 miRNA 데이터와 비교함으로써 학습된 결과의 성능을 평가하였다.

• Journal of Science and Technology Studies
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• v.17 no.1
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• pp.71-115
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• 2017

In 1953, theoretical physicist George Gamow attempted to explain the process of protein synthesis by hypothesizing that the base sequence of DNA encodes a protein's amino acid sequence and, in response, proposed the nucleic acid-protein information transfer model, which he dubbed the "diamond code." After expressing interest in discussing the daring hypothesis, contemporary biologists, including James Watson, Francis Crick, Sydney Brenner, and Gunther Stent, were soon invited to join the RNA Tie Club, an informal research group that would also count biologists and various researchers in physics, mathematics, and computer engineering among its members. In examining the club's formation, growth, and decline in multidisciplinary research on deciphering the genetic code in the 1950s, this paper first investigates whether Gamow's idiosyncratic approach could be adopted as a collaborative research forum among contemporary biologists. Second, it explores how the RNA Tie Club's research agenda could have been expanded to other relevant research topics needing multidisciplinary approach? Third, it asks why and how the RNA Tie Club dissolved in the late 1950s. In answering those questions, this paper shows that analyses on the intersymbol correlation of the overlapping code functioned to integrate diverse approaches, including sequence decoding and statistical analysis, in research on the genetic code. As those analyses reveal, the peculiar approaches of the RNA Tie Club could be regarded as a useful method for biological research. The paper also concludes that the RNA Tie Club dissolved in the late 1950s due to the disappearance of the collaborative research agenda when the overlapping code hypothesis was abandoned.

• The Journal of the Institute of Internet, Broadcasting and Communication
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• v.16 no.6
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• pp.135-140
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• 2016

In this paper, we analyze the [UC;AG] code which is genetic information standard DNA code, with 64 trigram. DNA which contains human genetic information, is a shape of adding three billion pairs of four bases which are A(adenine), C(cytosine), G(guanine) and T(thymine) to phosphoric acid and glucose. We present standard DNA code to 64 trigram which is $64{\times}4$ matrix with Kronecker product. This $64{\times}4$ matrix has double helix duplex property, and we can get the $4{\times}4$ matrix RNA code by removing the duplex of it. We present the DNA double helix to matrices and analysis the trigram array code of genetic information and the examples of it are presented in example 5, 6.

• The Journal of the Institute of Internet, Broadcasting and Communication
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• v.16 no.3
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• pp.203-211
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• 2016

The genetic code is a key to bio-informatics and to a science of biological self-organizing on the whole. Modern science faces the necessity of understanding and systematically explaining mysterious features of ensembles of molecular structures of the genetic code. This paper is devoted to symmetrical analysis for genetic systems. Mathematical theories of noise-immunity coding and discrete signal processing are based on Jacket matrix methods of representation and analysis of information. Both of the RNA and Jacket Matrix property also have the Element(Block) - wise Inverse Matrices. These matrix methods, which are connected closely with relations of symmetry, are borrowed for a matrix analysis of ensembles of molecular elements of the genetic code. This method is presented for its simplicity and the clarity with which it decomposes a Jacket Matrix in terms of the genetic RNA Codon.

• Korean Journal of Microbiology
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• v.30 no.3
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• pp.177-180
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• 1992

Among 120 U. maydis strains isolated in Korea 14 different strains containing specific viral dsRNA segments were analyzed for the distribution of dsRNA and the production of toxin protein. Several distinctive dsRNA patterns were identified, 9 cases of P type with typical H, M and L ds RNA and one case of non-P-type, the frequency of a specific isolate was decreased with increasing number of dsRNA segments. The presence of dsRNA had no effect on the cultural or morphological phenotype of the host. Two isolates containing P type dsRNA segments appeared to produce toxin protein (killer strains) which inhibited the growth of 4 isolates (sensitive strain) with different susceptibility. Two killer strains contain unique M dsRNA segment which may code for toxin protein. However, the presence of toxin-sensitive strains among dsRNA-free isolates was similar to that of ds RNA containing strains.

• Journal of Microbiology
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• v.34 no.1
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• pp.61-67
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• 1996

Double-stranded RNA (dsRNA) viruses and single-stranded RNA(ssRNA) viruses were detected in a strain of Pleurotus mushroom cultivated in a farm. Those fungal virsus were purified in the pH 6.0 or pH 7.2 using CsCI or Cs$_{2}$SO$_{4}$ buoyant density centrifugation. Each viral particles were not completely separated at any trials. However, mushroom bacili-form virus contains a single major nucleic acid with 0.7 Kb ssRNA, which might code for 20 Kd viral capsid protein. The dsRNAs are encapsidatred into spherical-form viruses, whereas ssRNA viral genomes are encapsidated into two different sizes of bacili-form particles. A healthy-looking mushroom also contained some spherical-form viruses with dsRNAs. Laboratory strains of Pleurotus ostreatus and a cultivated strain of P. sajor-caju did not show any viral particles. Mushrooms with specific disease symptoms. however, contained at least four different sizes of spherical-form viruses. Thus, we concluded that a bacilli-form virus case a severe disease symptoms of adnormal on mushroom development.

• Genomics & Informatics
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• v.16 no.4
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• pp.36.1-36.3
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• 2018

Next generation sequencing (NGS), a high-throughput DNA sequencing technology, is widely used for molecular biological studies. In NGS, RNA-sequencing (RNA-Seq), which is a short-read massively parallel sequencing, is a major quantitative transcriptome tool for different transcriptome studies. To utilize the RNA-Seq data, various quantification and analysis methods have been developed to solve specific research goals, including identification of differentially expressed genes and detection of novel transcripts. Because of the accumulation of RNA-Seq data in the public databases, there is a demand for integrative analysis. However, the available RNA-Seq data are stored in different formats such as read count, transcripts per million, and fragments per kilobase million. This hinders the integrative analysis of the RNA-Seq data. To solve this problem, we have developed a web-based application using Shiny, COEX-seq (Convert a Variety of Measurements of Gene Expression in RNA-Seq) that easily converts data in a variety of measurement formats of gene expression used in most bioinformatic tools for RNA-Seq. It provides a workflow that includes loading data set, selecting measurement formats of gene expression, and identifying gene names. COEX-seq is freely available for academic purposes and can be run on Windows, Mac OS, and Linux operating systems. Source code, sample data sets, and supplementary documentation are available as well.

• Genomics & Informatics
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• v.18 no.3
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• pp.26.1-26.6
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• 2020

Single-cell RNA sequencing (scRNA-seq) has been widely applied to provide insights into the cell-by-cell expression difference in a given bulk sample. Accordingly, numerous analysis methods have been developed. As it involves simultaneous analyses of many cell and genes, efficiency of the methods is crucial. The conventional cell type annotation method is laborious and subjective. Here we propose a semi-automatic method that calculates a normalized score for each cell type based on user-supplied cell type-specific marker gene list. The method was applied to a publicly available scRNA-seq data of mouse cardiac non-myocyte cell pool. Annotating the 35 t-stochastic neighbor embedding clusters into 12 cell types was straightforward, and its accuracy was evaluated by constructing co-expression network for each cell type. Gene Ontology analysis was congruent with the annotated cell type and the corollary regulatory network analysis showed upstream transcription factors that have well supported literature evidences. The source code is available as an R script upon request.

• Journal of Engineering Education Research
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• v.21 no.1
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• pp.77-89
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• 2018

The chromosomes of all the world are the same in all 24 pairs, but the key, skin color and appearance are different. Also, it is the resistance of adult disease, diabetes, cancer. In 1953, Watson, Crick of Cambridge University experimentally discovered a DNA double helix structure, and in 1962, They laureates the Nobel Prize. In 1964, Temin, University of Wisconsin, USA, experimentally identified the ability to copy gene information from RNA to DNA and received the Nobel Prize in 1975. In this paper, we analyzed 24 pairs of DNA chromosomes using mathematical matrices based on the combination order sequence of four groups, and designed the Taegeuk pattern genetic code for the first time in the world. In the case of normal persons, the middle Yin-Yang taegeuk is designed as a block circulant Jacket matrix in DNA, and the left-right and upper-lower pairs of east-west and north-south rulings are designed as pair complementary matrices. If (C U: A G) chromosomes are unbalanced, that is, people with disease or inheritance become squashed squirming patterns. In 2017, Professor Michel Young was awarded a Nobel by presenting a biological clock and experimentally explained the bio-imbalance through a yellow fruit fly experiment.This study proved mathematical matrices for balanced and unbalanced RNA.

• BMB Reports
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• v.28 no.6
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• pp.494-498
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• 1995

Maize mitochondrial tRNAs for isoleucine have been isolated using a putative $tRNA^{Ile}$ gene probe which has been previously isolated and characterized. It contains the 5'-CAT anticodon which would normally recognize the AUG methionine codon. The nucleotide sequence of one of these tRNAs has been partially determined, and contains a modified nucleotide at the first position of the anticodon. This type of posttranscriptional modification event could change the specificity of amino acid acceptance of a tRNA, unlike that deduced from the corresponding gene. An aminoacylation experiment also demonstrated that these purified tRNAs have isoleucine acceptance activity but no methionine-accepting activity.