• Molecules and Cells
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• v.27 no.3
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• pp.271-277
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• 2009

Proteins interact with each other within a cell, and those interactions give rise to the biological function and dynamical behavior of cellular systems. Generally, the protein interactions are temporal, spatial, or condition dependent in a specific cell, where only a small part of interactions usually take place under certain conditions. Recently, although a large amount of protein interaction data have been collected by high-throughput technologies, the interactions are recorded or summarized under various or different conditions and therefore cannot be directly used to identify signaling pathways or active networks, which are believed to work in specific cells under specific conditions. However, protein interactions activated under specific conditions may give hints to the biological process underlying corresponding phenotypes. In particular, responsive functional modules consist of protein interactions activated under specific conditions can provide insight into the mechanism underlying biological systems, e.g. protein interaction subnetworks found for certain diseases rather than normal conditions may help to discover potential biomarkers. From computational viewpoint, identifying responsive functional modules can be formulated as an optimization problem. Therefore, efficient computational methods for extracting responsive functional modules are strongly demanded due to the NP-hard nature of such a combinatorial problem. In this review, we first report recent advances in development of computational methods for extracting responsive functional modules or active pathways from protein interaction network and microarray data. Then from computational aspect, we discuss remaining obstacles and perspectives for this attractive and challenging topic in the area of systems biology.

• 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.

• Journal of the Korea Convergence Society
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• v.9 no.9
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• pp.47-52
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• 2018

Wi-Fi enabled Internet of Things (IoTs) had a substantial impact on society, economy and industry. However wireless connectivity technologies in unlicensed band such as Wi-Fi are vulnerable to interferences. They also face difficulty providing wireless connectivity over long range in dense networks due to the dynamically changed interference effect and asymmetric interference conditions. In this paper, robust acknowledgement transmission scheme is proposed for long range IoTs. According to the proposed scheme, it is possible to control the transmission rate of the transmission success rate of the response frame by adjusting the transmission rate of the response frame when the interference is present asymmetrically. It is also possible to use higher data rate when high quality link is guaranteed. The evaluation results demonstrated the proposed scheme improves the aggregate throughput by at most 9 Mbps when 20 MHz bandwidth transmission mode was adopted.

• Journal of the Institute of Electronics Engineers of Korea TC
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• v.46 no.12
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• pp.117-124
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• 2009

In this paper, we have developed communication modules for ubiquitous transportation sensor network (u-TSN). The developed module can be used for intelligent transportation services. The developed systems are based on IEEE 802.11a and IEEE 802.11g technologies for vehicle and infrastructure systems, respectively. We have found that the throughput for the developed systems is at maximum around 15 Mbps. It is reduced to 10 Mbps at a long distance and high speed condition. The performance is enough to support traffic control services in dense traffic condition.

• Journal of Plant Biotechnology
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• v.37 no.2
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• pp.196-204
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• 2010

With the completion of genome sequencing of several organisms, attention has been focused to determine the function and functional network of proteins by proteome analysis. The recent techniques of proteomics have been advanced quickly so that the high-throughput and systematic analyses of cellular proteins are enabled in combination with bioinformatics tools. Furthermore, the development of proteomic techniques helps to elucidate the functions of proteins under stress or diseased condition, resulting in the discovery of biomarkers responsible for the biological stimuli. Ultimate goal of proteomics orients toward the entire proteome of life, subcellular localization, biochemical activities, and their regulation. Comprehensive analysis strategies of proteomics can be classified as three categories: (i) protein separation by 2-dimensional gel electrophoresis (2-DE) or liquid chromatography (LC), (ii) protein identification by either Edman sequencing or mass spectrometry (MS), and (iii) quanitation of proteome. Currently MS-based proteomics turns shiftly from qualitative proteome analysis by 2-DE or 2D-LC coupled with off-line matrix assisted laser desorption ionization (MALDI) and on-line electrospray ionization (ESI) MS, respectively, to quantitative proteome analysis. Some new techniques which include top-down mass spectrometry and tandem affinity purification have emerged. The in vitro quantitative proteomic techniques include differential gel electrophoresis with fluorescence dyes, protein-labeling tagging with isotope-coded affinity tag, and peptide-labeling tagging with isobaric tags for relative and absolute quantitation. In addition, stable isotope labeled amino acid can be in vivo labeled into live culture cells through metabolic incorporation. MS-based proteomics extends to detect the phosphopeptide mapping of biologically crucial protein known as one of post-translational modification. These complementary proteomic techniques contribute to not only the understanding of basic biological function but also the application to the applied sciences for industry.

• KSII Transactions on Internet and Information Systems (TIIS)
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• v.4 no.6
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• pp.1063-1079
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• 2010

Vehicle ad hoc networks (VANET) are one of the most important technologies to provide various ITS services. While VANET requires rapid and reliable transmission, packet transmission in VANET is unstable because of high mobility. Many routing protocols have been proposed and assessed to improve the efficiency of VANET. However, topology-based routing protocols generate heavy overhead and long delay, and position-based routing protocols have frequent packet loss due to inaccurate node position. In this paper, we propose a position-based routing repair algorithm to improve the efficiency of VANET. This algorithm is proposed based on the premise that AODV (-PGB) can be used effectively in VANET, if the discovery, maintenance and repair mechanism of AODV is optimized for the features of VANET. The main focus of this algorithm is that the relay node can determine whether its alternative node exits and judge whether the routing path is disconnected. If the relay node is about to swerve from the routing path in a multi-hop network, the node recognizes the possibility of path loss based on a defined critical domain. The node then transmits a handover packet to the next hop node, alternative nodes and previous node. The next node repairs the alternative path before path loss occurs to maintain connectivity and provide seamless service. We simulated protocols using both the ideal traffic model and the realistic traffic model to assess the proposed algorithm. The result shows that the protocols that include the proposed algorithm have fewer path losses, lower overhead, shorter delay and higher data throughput compared with other protocols in VANET.

• Korean Journal of Materials Research
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• v.19 no.4
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• pp.224-227
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• 2009

Nanofabrication is an essential process throughout industry. Technologies that produce general nanofabrication, such as e-beam lithography, dip-pen lithography, DUV lithography, immersion lithography, and laser interference lithography, have drawbacks including complicated processes, low throughput, and high costs, whereas nano-transfer printing (nTP) is inexpensive, simple, and can produce patterns on non-plane substrates and multilayer structures. In general nTP, the coherency of gold-deposited stamps is strengthened by using SAM treatment on substrates, so the gold patterns are transferred from stamps to substrates. However, it is hard to apply to transfer other metallic materials, and the existing nTP process requires a complicated surface treatment. Therefore, it is necessary to simplify the nTP technology to obtain an easy and simple method for fabricating metal patterns. In this paper, asnTP process with poly vinyl alcohol (PVA) mold was proposed without any chemical treatment. At first, a PVA mold was duplicated from the master mold. Then, a Mo layer, with a thickness of 20 nm, was deposited on the PVA mold. The Mo deposited PVA mold was put on the Si wafer substrate, and nTP process progressed. After the nTP process, the PVA mold was removed using DI water, and transferred Mo nano patterns were characterized by a Scanning electron micrograph (SEM) and Energy Dispersive spectroscopy (EDS).

• Microbiology and Biotechnology Letters
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• v.47 no.3
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• pp.441-448
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• 2019

This study was aimed at identifying the lower airway microbiota in patients with lung cancer (LC) using protected brush sampling. We enrolled 37 patients undergoing diagnostic bronchoscopy for suspected LC, 26 with LC and 11 with benign diseases. Protected brush specimens were obtained from the contralateral lung and the side of the tumor; these specimens were analyzed by 16S rRNA-based-next-generation sequencing. The results indicated that the biodiversity was not different between groups, and there were no significant differences between the proportion of microorganisms in the tumor and in the contralateral side of patients with LC. In patients with LC, there was a higher abundance of several microorganisms including Capnocytophaga, Haemophilus, Enterococcus, and Streptococcus; whereas, in individuals without LC, Bacteroides, Lactobacillus, or Methylobacterium were more abundant. Malignancy could be determined with an accuracy of 70% by isolating Enterococcus, Capnocytophaga, or Actinomyces. Microbispora indicated benignity with a sensitivity of 55%, specificity of 88%, and accuracy of 78%. Lower airway microbiota in patients with LC is fairly similar in both the tumor and contralateral sites. Endobronchial microbiota is different in patients with and without LC, and these differences may have a potential clinical value as diagnostic or prognostic biomarkers.

• Journal of Microbiology and Biotechnology
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• v.29 no.5
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• pp.794-808
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• 2019

Bacillus velezensis strain WRN014 was isolated from banana fields in Hainan, China. Bacillus velezensis is an important member of the plant growth-promoting rhizobacteria (PGPR) which can enhance plant growth and control soil-borne disease. The complete genome of Bacillus velezensis WRN014 was sequenced by combining Illumina Hiseq 2500 system and Pacific Biosciences SMRT high-throughput sequencing technologies. Then, the genome of Bacillus velezensis WRN014, together with 45 other completed genome sequences of the Bacillus velezensis strains, were comparatively studied. The genome of Bacillus velezensis WRN014 was 4,063,541bp in length and contained 4,062 coding sequences, 9 genomic islands and 13 gene clusters. The results of comparative genomic analysis provide evidence that (i) The 46 Bacillus velezensis strains formed 2 obviously closely related clades in phylogenetic trees. (ii) The pangenome in this study is open and is increasing with the addition of new sequenced genomes. (iii) Analysis of single nucleotide polymorphisms (SNPs) revealed local diversification of the 46 Bacillus velezensis genomes. Surprisingly, SNPs were not evenly distributed throughout the whole genome. (iv) Analysis of gene clusters revealed that rich gene clusters spread over Bacillus velezensis strains and some gene clusters are conserved in different strains. This study reveals that the strain WRN014 and other Bacillus velezensis strains have potential to be used as PGPR and biopesticide.

• Genomics & Informatics
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• v.21 no.1
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• pp.12.1-12.8
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• 2023

A wave of new technologies has created opportunities for the cost-effective generation of high-throughput profiles of biological systems, foreshadowing a "data-driven science" era. The large variety of data available from biological research is also a rich resource that can be used for innovative endeavors. However, we are facing considerable challenges in big data deposition, integration, and translation due to the complexity of biological data and its production at unprecedented exponential rates. To address these problems, in 2020, the Korean government officially announced a national strategy to collect and manage the biological data produced through national R&D fund allocations and provide the collected data to researchers. To this end, the Korea Bioinformation Center (KOBIC) developed a new biological data repository, the Korea BioData Station (K-BDS), for sharing data from individual researchers and research programs to create a data-driven biological study environment. The K-BDS is dedicated to providing free open access to a suite of featured data resources in support of worldwide activities in both academia and industry.