• BMB Reports
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• v.45 no.1
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• pp.44-46
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• 2012

Recent advances in high-throughput genotyping technologies have enabled us to conduct a genome-wide association study (GWAS) on a large cohort. However, analyzing millions of single nucleotide polymorphisms (SNPs) is still a difficult task for researchers conducting a GWAS. Several difficulties such as compatibilities and dependencies are often encountered by researchers using analytical tools, during the installation of software. This is a huge obstacle to any research institute without computing facilities and specialists. Therefore, a proper research environment is an urgent need for researchers working on GWAS. We developed BioSMACK to provide a research environment for GWAS that requires no configuration and is easy to use. BioSMACK is based on the Ubuntu Live CD that offers a complete Linux-based operating system environment without installation. Moreover, we provide users with a GWAS manual consisting of a series of guidelines for GWAS and useful examples. BioSMACK is freely available at http://ksnp.cdc.go.kr/biosmack.

• Genomics & Informatics
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• v.12 no.4
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• pp.187-194
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• 2014

Metabolic syndrome (METS) is a disorder of energy utilization and storage and increases the risk of developing cardiovascular disease and diabetes. To identify the genetic risk factors of METS, we carried out a genome-wide association study (GWAS) for 2,657 cases and 5,917 controls in Korean populations. As a result, we could identify 2 single nucleotide polymorphisms (SNPs) with genome-wide significance level p-values (< $5{\times}10^{-8}$), 8 SNPs with genome-wide suggestive p-values ($5{\times}10^{-8}{\leq}$ p < $1{\times}10^{-5}$), and 2 SNPs of more functional variants with borderline p-values ($5{\times}10^{-5}{\leq}$ p < $1{\times}10^{-4}$). On the other hand, the multiple correction criteria of conventional GWASs exclude false-positive loci, but simultaneously, they discard many true-positive loci. To reconsider the discarded true-positive loci, we attempted to include the functional variants (nonsynonymous SNPs [nsSNPs] and expression quantitative trait loci [eQTL]) among the top 5,000 SNPs based on the proportion of phenotypic variance explained by genotypic variance. In total, 159 eQTLs and 18 nsSNPs were presented in the top 5,000 SNPs. Although they should be replicated in other independent populations, 6 eQTLs and 2 nsSNP loci were located in the molecular pathways of LPL, APOA5, and CHRM2, which were the significant or suggestive loci in the METS GWAS. Conclusively, our approach using the conventional GWAS, reconsidering functional variants and pathway-based interpretation, suggests a useful method to understand the GWAS results of complex traits and can be expanded in other genomewide association studies.

• Molecules and Cells
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• v.37 no.5
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• pp.372-382
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• 2014

In this study, the chloroplast (cp) genome sequences from three early diverged leptosporangiate ferns were completed and analyzed in order to understand the evolution of the genome of the fern lineages. The complete cp genome sequence of Osmunda cinnamomea (Osmundales) was 142,812 base pairs (bp). The cp genome structure was similar to that of eusporangiate ferns. The gene/intron losses that frequently occurred in the cp genome of leptosporangiate ferns were not found in the cp genome of O. cinnamomea. In addition, putative RNA editing sites in the cp genome were rare in O. cinnamomea, even though the sites were frequently predicted to be present in leptosporangiate ferns. The complete cp genome sequence of Diplopterygium glaucum (Gleicheniales) was 151,007 bp and has a 9.7 kb inversion between the trnL-CAA and trnV-GCA genes when compared to O. cinnamomea. Several repeated sequences were detected around the inversion break points. The complete cp genome sequence of Lygodium japonicum (Schizaeales) was 157,142 bp and a deletion of the rpoC1 intron was detected. This intron loss was shared by all of the studied species of the genus Lygodium. The GC contents and the effective numbers of codons (ENCs) in ferns varied significantly when compared to seed plants. The ENC values of the early diverged leptosporangiate ferns showed intermediate levels between eusporangiate and core leptosporangiate ferns. However, our phylogenetic tree based on all of the cp gene sequences clearly indicated that the cp genome similarity between O. cinnamomea (Osmundales) and eusporangiate ferns are symplesiomorphies, rather than synapomorphies. Therefore, our data is in agreement with the view that Osmundales is a distinct early diverged lineage in the leptosporangiate ferns.

• Genomics & Informatics
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• v.10 no.1
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• pp.65-67
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• 2012

We have discovered copy number variations (CNVs) in 3,578 Korean individuals with the Affymetrix Genome-Wide SNP array 5.0, and 4,003 copy number variation regions (CNVRs) were defined in a previous study. To explore the details of the variants easily in related studies, we built a database, cataloging the CNVs and related information. This system helps researchers browsing these variants with gene and structure variant annotations. Users can easily find specific regions with search options and verify them from system-integrated genome browsers with annotations.

• BMB Reports
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• v.37 no.1
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• pp.75-82
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• 2004

Recent years saw a dramatic increase in genomic and proteomic data in public archives. Now with the complete genome sequences of human and other species in hand, detailed analyses of the genome sequences will undoubtedly improve our understanding of biological systems and at the same time require sophisticated bioinformatic tools. Here we review what computational challenges are ahead and what are the new exciting developments in this exciting field.

• 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.

• Asian-Australasian Journal of Animal Sciences
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• v.29 no.7
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• pp.938-943
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• 2016

Development of body hair is an important physiological and cellular process that leads to better adaption in tropical environments for dairy cattle. Various studies suggested a major gene and, more recently, associated genes for hairy locus in dairy cattle. Main aim of this study was to i) employ a variant of the discordant sib pair model, in which half sibs from the same sires are randomly sampled using their affection statues, ii) use various single marker regression approaches, and iii) use whole genome regression approaches to dissect genetic architecture of the hairy gene in the cattle. Whole and single genome regression approaches detected strong genomic signals from Chromosome 23. Although there is a major gene effect on hairy phenotype sourced from chromosome 23: whole genome regression approach also suggested polygenic component related with other parts of the genome. Such a result could not be obtained by any of the single marker approaches.

• Biotechnology and Bioprocess Engineering:BBE
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• v.5 no.3
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• pp.159-163
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• 2000

The genome sequencing project has generated and will contitute to generate enormous amounts of sequence data. Since the first complete genome sequence of bacterium Haemophilus in fluenzae was published in 1995, the complete genome sequences of 2 eukaryotic and about 22 prokaryotic organisms have detemined. Given this everincreasing amounts of sequence information, new strategies are necessary to efficiently pursue the phase of the geome project- the elucidation of gene expression patterns and gene product function on a whole genome scale. In order to assign functional information to the genome sequence, DNA chip technology was developed to efficienfly identify the differential expression pattern of indepondent biogical samples. DNA chip provides a new tool for genome expreesion analysis that may revolutionize revolutionize many aspects of human kife including mew surg discovery and human disease diagnostics.

• Animal cells and systems
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• v.12 no.3
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• pp.117-125
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• 2008

One of the interesting trends in genome research is the study about epigenetic modification above single gene level. Epigenetics refers study about heritable change in the genome, which accompany modification in DNA or Chromatin besides DNA sequence alteration. We used to have the idea that the coding potential of the genome lies within the arrangement of the four bases A, T, G, C; However, additional information that affects phenotype is stored in the distribution of the modified base 5-methylcytosine. This form of information storage is flexible enough to be adapted for different somatic cell types, yet is stable enough to be retained during mitosis and/or meiosis. Epigenetic modification is a modification of the genome, as opposed to being part of the genome, so is known as "epigenetics"(Greek for "upon" genetics). This modification could be methylation on Cytosine base or post translational modification on histone protein(methylation, acetylation, phosphorylation, Sumoylation)($Dimitrijevi\hat{E}$ et al 2005). In this review, we would like to focus on the relationship of DNA methylation and cancer.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2006.02a
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• pp.125-126
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• 2006

NimbleGen has developed strategies to use its high-density oligonucleotide microarray platform (385,000 probes per array) to map both promoter binding sites and copy number variation at very high-resolution in the human genome. Here we describe a genome-wide map of active promoters determined by experimentally locating the sites of transcription imitation complex binding throughout the human genome using microarrays combined with chromatin immunoprecipitation. This map defines 10,567 active promoters corresponding to 6,763 known genes and at least 1,196 un-annotated transcriptional units. Microarray-based comparative genomic hybridisation (CGH) is animportant research tool for investigating chromosomal aberrations frequently associated with complex diseases such as cancer, neuropsychiatric disorders, and congenital developmental disorders. NimbleGen array CGH is an ultra-high resolution (0.5-50 Kb) oligo array platform that can be used to detect amplifications and deletions and map the associated breakpoints on the whole-genome level or with custom fine-tiling arrays. For whole-genome array CGH, probes are tiled through genic and intergenic regions with a median probe spacing of 6 Kb, which provides a comprehensive, unbiased analysis of the genome.