• Journal of Genetic Medicine
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• v.20 no.1
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• pp.1-5
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• 2023

Until now, rare disease studies have mainly been carried out by detecting simple variants such as single nucleotide substitutions and short insertions and deletions in protein-coding regions of disease-associated gene panels using diagnostic next-generation sequencing in association with patient phenotypes. However, several recent studies reported that the detection rate hardly exceeds 50% even when whole-exome sequencing is applied. Therefore, the necessity of introducing whole-genome sequencing is emerging to discover more diverse genomic variants and examine their association with rare diseases. When no diagnosis is provided by whole-genome sequencing, additional omics techniques such as RNA-seq also can be considered to further interrogate causal variants. This paper will introduce a description of these multi-omics techniques and their applications in rare disease studies.

• Development and Reproduction
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• v.27 no.1
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• pp.9-24
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• 2023

The advancement in high-throughput sequencing (HTS) technology has revolutionized the field of biology, including genomics, epigenomics, transcriptomics, and metagenomics. This technology has become a crucial tool in many areas of research, allowing scientists to generate vast amounts of genetic data at a much faster pace than traditional methods. With this increased speed and scale of data generation, researchers can now address critical questions and gain new insights into the inner workings of living organisms, as well as the underlying causes of various diseases. Although the first HTS technology have been introduced about two decades ago, it can still be challenging for those new to the field to understand and use effectively. This review aims to provide a comprehensive overview of commonly used HTS technologies these days and their applications in terms of genome sequencing, transcriptome, DNA methylation, DNA-protein interaction, chromatin accessibility, three-dimensional genome organization, and microbiome.

• 제어로봇시스템학회:학술대회논문집
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• 2005.06a
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• pp.1118-1122
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• 2005

In order to keep production balance at a mixed-model assembly line and a painting line, large WIP(Work- In-Process) inventories are required between two lines. To increase the efficiency of line handling through reducing the inventories under this circumstance, this paper concerns with a sequencing problem for a mixed-model assembly line that includes a painting line where the uncertain elements regarding the defective products exist. Then, we formulate a new type of the sequencing problem minimizing the line stoppage time and the idle time with forecasting the supply time of the products from the painting line. Finally, we examine the effectiveness of the proposed sequencing through computer simulations.

• Proceedings of the Korean Institute of Intelligent Systems Conference
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• 1998.06a
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• pp.640-645
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• 1998

A Sequencing problem is one to find an ordered sequence of some entities which maximizes (or minimize) some objective function. This paper introduces an new type of sequencing problems, named a Sequencing problem with fuzzy preference relation is previded for the evaluation of the quality of sequences, It presents how such a problem can be formulated in the point of objective function. In addition, it proposes a genetic algorithm applicable to such a sequencing problem.

• Journal of Sensor Science and Technology
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• v.21 no.5
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• pp.359-366
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• 2012

Nanopore DNA sequencing is an emerging and promising technique that can potentially realize the goal of a low-cost and high-throughput method for analyzing human genome. Especially, solid-state nanopores have relatively high mechanical stability, simple surface modification, and facile fabrication process without the need for labeling or amplification of PCR (polymerized chain reaction) in DNA sequencing. For these advantages of solid-sate nanopores, the use of solid-state nanopores has been extensively considered for developing a next generation DNA sequencing technology. Solid-state nanopore sequencing technique can determine and count charged molecules such as single-stranded DNA, double-stranded DNA, or RNA when they are driven to pass through a membrane nanopore between two electrolytes of cis-trans chambers with applied bias voltage by measuring the ionic current which varies due to the existence of the charged particles in the nanopore. Recently, many researchers have suggested that nanopore-based sensors can be competitive with other third-generation DNA sequencing technologies, and may be able to rapidly and reliably sequence the human genome for under $1,000.

• Genomics & Informatics
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• v.13 no.2
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• pp.31-39
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• 2015

Sequencing depth, which is directly related to the cost and time required for the generation, processing, and maintenance of next-generation sequencing data, is an important factor in the practical utilization of such data in clinical fields. Unfortunately, identifying an exome sequencing depth adequate for clinical use is a challenge that has not been addressed extensively. Here, we investigate the effect of exome sequencing depth on the discovery of sequence variants for clinical use. Toward this, we sequenced ten germ-line blood samples from breast cancer patients on the Illumina platform GAII(x) at a high depth of ${\sim}200{\times}$. We observed that most function-related diverse variants in the human exonic regions could be detected at a sequencing depth of $120{\times}$. Furthermore, investigation using a diagnostic gene set showed that the number of clinical variants identified using exome sequencing reached a plateau at an average sequencing depth of about $120{\times}$. Moreover, the phenomena were consistent across the breast cancer samples.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.19
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• pp.8035-8040
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• 2014

Gastric cancer is the second after lung cause of cancer-related mortality in the world. Early detection and treatment can lead to a long survival time. Recently microarrays and next generation sequencing (NGS) have become very useful tools of comprehensive research into gastric cancer, facilitating the identification of treatment targets and personalized treatments. However, there are numerous challenges from cancer target discovery to practical clinical benefits. Although there are many biomarkers and target agents, only a minority of patients are tested and treated accordingly. Microarray technology with maturity was established more than 10 years ago, and has been widely used in the study of functional genomics, systems biology, and genomes in medicine. Second generation sequencing technology is more recent, but development is very fast, and it has been applied to the genome, including sequencing and epigenetics and many aspects of functional genomics. Here we review insights gained from these studies regarding the technology of microarray and NGS, how to elucidate the molecular basis of gastric cancer and identify potential therapeutic targets, and how to analyse candidate genes. We also discuss the challenges and future directions of such efforts.

• Korean Journal of Clinical Laboratory Science
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• v.44 no.4
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• pp.167-177
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• 2012

Next-Generation Sequencing (NGS) is a term that means post-Sanger sequencing methods with high-throughput sequencing technologies. NGS parallelizes the sequencing process, producing thousands or millions of sequences at once. The latest NGS technologies use even single DNA molecule as a template and measures the DNA sequence directly via measuring electronic signals from the extension or degradation of DNA. NGS is making big impacts on biomedical research, molecular diagnosis and personalized medicine. The hospitals are rapidly adopting the use of NGS to help to patients understand treatment with sequencing data. As NGS equipments are getting smaller and affordable, many hospitals are in the process of setting up NGS platforms. In this review, the progress of NGS technology development and action mechanisms of representative NGS equipments of each generation were discussed. The key technological advances in the commercialized platforms were presented. As NGS platforms are a great concern in the healthcare area, the latest trend in the use of NGS and the prospect of NGS in the future in diagnosis and personalized medicine were also discussed.

• BT NEWS
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• v.12 no.2
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• pp.20-25
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• 2005

• Journal of Korean Institute of Industrial Engineers
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• v.27 no.3
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• pp.315-327
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• 2001

This paper considers the problem of operation sequencing in nonlinear process planning, which is the problem of selecting and sequencing operations required to produce a part with the objective of minimizing the sum of operation processing costs and machine, setup and tool change costs. Main constraints are the precedence relations among operations. The problem can be decomposed into two subproblems: operation selection and operation sequencing. We suggest four simulated annealing algorithms, which solve the two subproblems iteratively until a good solution is obtained. Here, the operation selection problem can be solved using a shortest path algorithm. Application of the algorithms is illustrated using an example. Also, to show the performances of the suggested algorithms, computational experiments were done on randomly generated test problems and the results are reported. In particular, one of the suggested algorithms outperforms an existing simulated annealing algorithm.