• Journal of Microbiology and Biotechnology
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• 제16권6호
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• pp.832-848
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• 2006

Systems biology has recently become an important research paradigm that is anticipated to decipher the metabolic, regulatory, and signaling networks of complex living organisms on the whole organism level. Thus, various research outputs are being generated, along with the development of many tools and resources for systems biology research. Accordingly, this review provides a comprehensive summary of the current resources and tools for systems biology research that will hopefully be helpful to researchers involved in this field. The resources are categorized into the following five groups: genome information and analysis, transcriptome and proteome databases, metabolic profiling and metabolic control analysis, metabolic and regulatory information, and software for computational systems biology. A summary table and some future perspectives are also provided.

• Journal of Biosystems Engineering
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• 제43권1호
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• pp.45-58
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• 2018

Background: Metabolic modeling has been an essential tool in metabolic reconstruction, which has dramatically advanced in the last decades as a part of systems biology. At present, the protocol for metabolic reconstruction has been systematically established, and it provides the basis for the analysis of complex systems, which has been limited in the past. Therefore, metabolic reconstruction can be adapted to analyze agricultural systems whose metabolic data has been accumulated recently. Purpose: The aim of this review is to suggest the suitability of metabolic modeling for understanding agricultural metabolic data and to encourage the potential use of this modeling in the field of agriculture. Review: We reviewed the procedure of metabolic reconstruction using computational modeling with applicable strategies and software tools. Additionally, we presented the initial attempts of metabolic reconstruction in the field of agriculture and proposed further applications.

• Biotechnology and Bioprocess Engineering:BBE
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• 제10권5호
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• pp.425-431
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• 2005

The systems-level analysis of microbes with myriad of heterologous data generated by omics technologies has been applied to improve our understanding of cellular function and physiology and consequently to enhance production of various bioproducts. At the heart of this revolution resides in silico genome-scale metabolic model, In order to fully exploit the power of genome-scale model, a systematic approach employing user-friendly software is required. Metabolic flux analysis of genome-scale metabolic network is becoming widely employed to quantify the flux distribution and validate model-driven hypotheses. Here we describe the development of an upgraded MetaFluxNet which allows (1) construction of metabolic models connected to metabolic databases, (2) calculation of fluxes by metabolic flux analysis, (3) comparative flux analysis with flux-profile visualization, (4) the use of metabolic flux analysis markup language to enable models to be exchanged efficiently, and (5) the exporting of data from constraints-based flux analysis into various formats. MetaFluxNet also allows cellular physiology to be predicted and strategies for strain improvement to be developed from genome-based information on flux distributions. This integrated software environment promises to enhance our understanding on metabolic network at a whole organism level and to establish novel strategies for improving the properties of organisms for various biotechnological applications.

• 한국생물공학회:학술대회논문집
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• 한국생물공학회 2005년도 생물공학의 동향(XVII)
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• pp.634-634
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• 2005

• 한국미생물학회:학술대회논문집
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• 한국미생물학회 2009년도 International Meeting of the Microbiological Society of Korea
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• pp.135-136
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• 2009

• Korean Chemical Engineering Research
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• 제45권6호
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• pp.529-535
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• 2007

최근 DNA microarray, 2-D gel, MS/MS 등 다양한 high-throughput 기술의 발달에 힘입어 생명체의 복잡한 대사특성을 종합적으로 분석하려는 시도가 이루어지고 있으며, 이를 시스템 생물학이라 칭하고 있다. 특히 근래에 들어 고유가 등 산업환경의 변화에 따라 미생물의 대사특성을 개량하여 다양한 화학물질들을 생물학적으로 생산하려는 연구가 최근 많은 관심을 얻고 있으며, 이를 위하여 다양한 시스템 생물학 혹은 시스템 생물공학 연구가 수행되어져 왔다. 본 총설에서는 시스템 생물공학 연구에 대한 소개 및 사용되는 여러 연구전략들을 소개하고, 이러한 시스템 생물공학 연구들이 실제 대사산물 생산균주의 개량에 어떻게 적용되었는지 살펴보고자 한다.

• 한국생물공학회:학술대회논문집
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• 한국생물공학회 2005년도 생물공학의 동향(XVII)
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• pp.692-693
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• 2005

• Biotechnology and Bioprocess Engineering:BBE
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• 제10권5호
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• pp.462-469
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• 2005

A top-down approach is known to be a useful and effective technique for the design and analysis of metabolic systems. In this Study, we have constructed a grouped metabolic network for Lactococcus lactis under aerobic conditions using grouped enzyme kinetics. To test the usefulness of grouping work, a non-grouped system and grouped systems were compared quantitatively with each other. Here, grouped Systems were designed as two groups according to the extent of grouping. The overall simulated flux values in grouped and non-grouped models had pretty similar distribution trends, but the details on flux ratio at the pyruvate branch point showed a little difference. This result indicates that our grouping technique can be used as a good model for complicated metabolic networks, however, for detailed analysis of metabolic network, a more robust mechanism Should be considered. In addition to the data for the pyruvate branch point analysis, Some major flux control coefficients were obtained in this research.

• 한국생물공학회:학술대회논문집
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• 한국생물공학회 2005년도 생물공학의 동향(XVI)
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• pp.11-11
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• 2005

• Journal of Microbiology and Biotechnology
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• 제16권7호
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• pp.1139-1143
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• 2006

Various techniques and strategies have been developed for the identification of intracellular metabolic conditions, and among them, isotope balance-based flux analysis with gas chromatography/mass spectrometry (GC/ MS) has recently become popular. Even though isotope balance-based flux analysis allows a more accurate estimation of intracellular fluxes, its application has been restricted to relatively small metabolic systems because of the limited number of measurable metabolites. In this paper, a strategy for incorporating isotope balance-based flux data obtained for a small network into metabolic flux analysis was examined as a feasible alternative allowing more accurate quantification of intracellular flux distribution in a large metabolic system. To impose GC/MS based data into a large metabolic network and obtain optimum flux distribution profile, data reconciliation procedure was applied. As a result, metabolic flux values of 308 intracellular reactions could be estimated from 29 GC/ MS based fluxes with higher accuracy.