Hyun Uk Kim

Genome-scale metabolic models (GEMs) computationally describe gene-protein-reaction associations for entire metabolic genes in an organism, and can be simulated to predict metabolic fluxes for various systems-level metabolic studies. Since the first GEM for Haemophilus influenzae was reported in 1999, advances have been made to develop and simulate GEMs for an increasing number of organisms across bacteria, archaea, and eukarya. Here, we review current reconstructed GEMs and discuss their applic

Although the genomes of many microbial pathogens have been studied to help identify effective drug targets and novel drugs, such efforts have not yet reached full fruition. In this study, we report a systems biological approach that efficiently utilizes genomic information for drug targeting and discovery, and apply this approach to the opportunistic pathogen Vibrio vulnificus CMCP6. First, we partially re-sequenced and fully re-annotated the V. vulnificus CMCP6 genome, and accordingly reconstru

Recent advances in metabolic flux analysis including genome-scale constraints-based flux analysis and its applications in metabolic engineering are reviewed. Various computational aspects of constraints-based flux analysis including genome-scale stoichiometric models, additional constraints used for the improved accuracy, and several algorithms for identifying the target genes to be manipulated are described. Also, some of the successful applications of metabolic flux analysis in metabolic engin

Acinetobacter baumannii has emerged as a new clinical threat to human health, particularly to ill patients in the hospital environment. Current lack of effective clinical solutions to treat this pathogen urges us to carry out systems-level studies that could contribute to the development of an effective therapy. Here we report the development of a strategy for identifying drug targets by combined genome-scale metabolic network and essentiality analyses. First, a genome-scale metabolic network of

Whereas the autism prevalence rate has been very closely monitored in the United States, the same has not been observed in many other countries. This may be attributed to the fact that each culture views and defines autism differently. Using field notes and semi-structured interviews with family members with an individual with autism, teachers, and professionals in Canada, Nicaragua, and Korea, this paper illustrates how autism is socially differently constructed in these distinctively different

This Highlight examines current status of metabolic engineering and systems biology tools deployed for the optimal production of prokaryotic secondary metabolites.

The textile industry has caused severe water pollution by using many toxic chemicals for producing fabric dyes. In response to this problem, indigoidine has attracted attention as an alternative natural blue dye, but it is necessary to achieve a high-level production to compete with synthetic blue dyes. Here we report a metabolically engineered Corynebacterium glutamicum capable of producing indigoidine to a high concentration with high productivity. First, the blue-pigment indigoidine synthetas

Systems biology has greatly contributed toward the analysis and understanding of biological systems under various genotypic and environmental conditions on a much larger scale than ever before. One of the applications of systems biology can be seen in unraveling and understanding complicated human diseases where the primary causes for a disease are often not clear. The in silico genome-scale metabolic network models can be employed for the analysis of diseases and for the discovery of novel drug