• Genomics & Informatics
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• v.11 no.1
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• pp.2-6
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• 2013

Until recently, since the Human Genome Project, the general view has been that the majority of the human genome is composed of junk DNA and has little or no selective advantage to the organism. Now we know that this conclusion is an oversimplification. In April 2003, the National Human Genome Research Institute (NHGRI) launched an international research consortium called Encyclopedia of DNA Elements (ENCODE) to uncover non-coding functional elements in the human genome. The result of this project has identified a set of new DNA regulatory elements, based on novel relationships among chromatin accessibility, histone modifications, nucleosome positioning, DNA methylation, transcription, and the occupancy of sequence-specific factors. The project gives us new insights into the organization and regulation of the human genome and epigenome. Here, we sought to summarize particular aspects of the ENCODE project and highlight the features and data that have recently been released. At the end of this review, we have summarized a case study we conducted using the ENCODE epigenome data.

• Genomics & Informatics
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• v.11 no.2
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• pp.60-67
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• 2013

A decade-long project, led by several international research groups, called the Encyclopedia of DNA Elements (ENCODE), recently released an unprecedented amount of data. The ambitious project covers transcriptome, cistrome, epigenome, and interactome data from more than 1,600 sets of experiments in human. To make use of this valuable resource, it is important to understand the information it represents and the techniques that were used to generate these data. In this review, we introduce the data that ENCODE generated, summarize the observations from the data analysis, and revisit a computational approach that ENCODE used to predict gene expression, with a focus on the human transcriptome and its association with chromatin modifications.

• KOGO NEWS
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• v.3 no.1
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• pp.6.1-6.1
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• 2003

• Microbiology and Biotechnology Letters
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• v.50 no.1
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• pp.63-70
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• 2022

Two small cryptic plasmids, pHG1 and pHG2, were isolated from Levilactobacillus zymae (formerly Lactobacillus zymae) GU240 and characterized. pHG1 is 1,814 bp in size with a GC content of 37.4% and contains two open reading frames. orf1 can potentially encode a protein of 101 amino acids (aa) with 99% identity with the copy number control protein of Lacticaseibacillus paracasei. orf2 can potentially encode a protein of 230 aa with 99% identity with a replication protein from multiple species. Six inverted repeats (IR I-VI) and six direct repeats (DR I-VI) were found in pHG1. pHG2 is 2,864 bp in size, with a GC content of 39.6%. pHG2 has two orfs. orf1 might encode a protein with 99% identity with the TrsL transmembrane protein. orf2 might encode a protein with 99% identity with plasmid recombination proteins from lactic acid bacteria. Both pHG1 and pHG2 may be useful as frames for constructing lactic acid bacteria-Escherichia coli shuttle vectors.

• Phonetics and Speech Sciences
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• v.1 no.4
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• pp.17-27
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• 2009

Despite many studies on the production and perception of L2 phonemes, studies on how such phonemes are encoded lexically remain scarce. The aim of this study is to examine whether L2 learners have a perceptual problem with L2 suprasegmentals which are not present in their L1, or if they are able to perceive but not able to encode them in their lexicon. Specifically, Korean learners were tested to see if they could discriminate the vowel length differences in Japanese at the psychoacoustic level through a simple AX discrimination task. Then, a speeded lexical decision task with high phonetic variability was conducted to see whether they could use such contrasts lexically. The results showed that Korean learners of Japanese have no difficulties in discriminating Japanese vowel length contrast, but they are unable to encode such contrast in their phonological representation, even with long L2 exposure.

• Proceedings of the IEEK Conference
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• 2003.11a
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• pp.45-48
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• 2003

In general, speech coding methods are classified into the following three categories: the waveform coding, the source coding and the hybrid coding. Fast speaking is possible to encode with a few information compared with slow speaking rate. In case of speaking rate, low frequency band is more important than high frequency band while listening. Speech vocoding technique is developing to way with low bit rate and complexity and high sound quality. the CELP type of vocoder support very good sound quality with low bit rate but these vocoders don't consider about the speaking rate. When we consider speaking rate and encode the frame depending on the speaking rate, the bit rate is able to reduce the bit rate than the conventional vocoder. We propose the technique to estimate the speaking rate and applied PSOLA technique in case of the frame of slow speaking rate. As a result of simulation bit rate can be reduced about 300 bps.

• Genomics & Informatics
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• v.16 no.3
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• pp.65-70
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• 2018

The non-coding DNA in eukaryotic genomes encodes a language which programs chromatin accessibility, transcription factor binding, and various other activities. The objective of this short report was to determine the impact of primary DNA sequence on the epigenomic landscape across 200-base pair genomic units by integrating nine publicly available ChromHMM Browser Extensible Data files of the Encyclopedia of DNA Elements (ENCODE) project. The nucleotide frequency profiles of nine chromatin annotations with the units of 200 bp were analyzed and integrative Markov chains were built to detect the Markov properties of the DNA sequences in some of the active chromatin states of different ChromHMM regions. Our aim was to identify the possible relationship between DNA sequences and the newly built chromatin states based on the integrated ChromHMM datasets of different cells and tissue types.

• Proceedings of the Korea Information Processing Society Conference
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• 2013.11a
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• pp.768-770
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• 2013

We propose a symmetric key based cryptography algorithm to encode and decode the text data with limited length using 3-dimensional magic square matrix. To encode the plain text message, input text will be translated into an index of the number stored in the key matrix. Then, Caesar's shift with pre-defined constant value is fabricated to finalize an encryption algorithm. In decode process, Caesar's shift is applied first, and the generated key matrix is used with 2D magic squares to replace the index numbers in ciphertext to restore an original text.

• Proceedings of the Korean Society of Applied Pharmacology
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• 1993.11a
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• pp.39-40
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• 1993

Hepatitis B virus (HBV)is a member of the Hepadna virus family whose members share a characteristic virion structure and genome size, around 3.2kb in a paritially double-stranded form. The genome of HBV contains four overlapping open reading frames designated as P(polymerase). C(core), S(surface antigen)and X. The X gene has potential to encode 154 amino acids protein.

• Proceedings of the IEEK Conference
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• 2002.07a
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• pp.50-53
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• 2002

There are increasing needs to deliver the multimedia streaming over heterogeneous networks. When considering network environments and equipment accessed by user, delivery of video streaming must be scalable. There are many kinds of scalable video coding: spatial, temporal, SNR, and hybrid. The SNR scalable and spatial resolution, but different SNR quality with respect to layers. The 1-layer SNR scalable encoder produces SNR scalable video streams with ease. But, there is drift problem. Modified 1-layer approach does not have this problem but coding inefficiency, and is not MPEG-compliant. The present MPEG-compliant 2-layer encoder comes out to reduce coding rate. But it still use only base layer to encode whole layer. In this paper, we propose adaptive MPEG-compliant 2-layer encoder. Using linear combination algorithm, encoder use 1 motion vector to encode the sequences efficiently. By dong this, we can achieve the coding efficiency of SNR scalable coding.