A5004980827- Microbial Metabolic Engineering and Bioproduction
- Bacterial Genetics and Biotechnology
- Bacteriophages and microbial interactions
- Genomics and Phylogenetic Studies
- Biofuel production and bioconversion
- Viral Infectious Diseases and Gene Expression in Insects
- Gene expression and cancer classification
- Cancer Research and Treatments
- Bioinformatics and Genomic Networks
- Biopolymer Synthesis and Applications
- Probiotics and Fermented Foods
- RNA and protein synthesis mechanisms
- Mechanical Behavior of Composites
- Gene Regulatory Network Analysis
- Evolution and Genetic Dynamics
- Fiber-reinforced polymer composites
- CRISPR and Genetic Engineering
- Protein Structure and Dynamics
- Enzyme Catalysis and Immobilization
- Molecular Biology Techniques and Applications
- Advanced biosensing and bioanalysis techniques
- Aquaculture Nutrition and Growth
- Microbial Community Ecology and Physiology
- Microbial Metabolites in Food Biotechnology
- Polyamine Metabolism and Applications
Konkuk University
2017-2024
Konkuk University Medical Center
2023
Kumoh National Institute of Technology
2012-2021
Kookmin University
2016
Korea Institute of Nuclear Safety
2015
Korea Research Institute of Bioscience and Biotechnology
2005-2014
Bio-Medical Science (South Korea)
2014
Institute for Systems Biology
2011-2013
Kyungsung University
2011
Chungnam National University
2009
Elucidation of a genotype-phenotype relationship is critical to understand an organism at the whole-system level. Here, we demonstrate that comparative analyses multi-omics data combined with computational modeling approach provide framework for elucidating phenotypic characteristics organisms whose genomes are sequenced.We present comprehensive analysis genome-wide measurements incorporating multifaceted holistic - genome, transcriptome, proteome, and phenome determine differences between...
Pathogenicity is a complex multifactorial process confounded by the concerted activity of genetic regions associated with virulence and/or resistance determinants. islands (PAIs) and (REIs) are key to evolution pathogens appear play complimentary roles in bacterial infection. While PAIs promote disease development, REIs give fitness advantage host against multiple antimicrobial agents. The Island Database (PAIDB, http://www.paidb.re.kr) has been only database dedicated providing...
Abstract Combined transcriptome and proteome analysis was carried out to understand metabolic physiological changes of Escherichia coli during the high cell density cultivation (HCDC). The expression genes TCA cycle enzymes, NADH dehydrogenase ATPase, up‐regulated exponential fed‐batch period down‐regulated afterward. However, most involved in glycolysis pentose phosphate pathway at stationary phase. amino acid biosynthesis as increased, which seems be major reason for reduced specific...
Pathogenicity islands (PAIs) are genetic elements whose products essential to the process of disease development. They have been horizontally (laterally) transferred from other microbes and important in evolution pathogenesis. In this study, a comprehensive database search engines specialized for PAIs were established. The pathogenicity island (PAIDB) is relational all reported potential PAI regions which predicted by method that combines feature-based analysis similarity-based analysis....
ABSTRACT Hydrogenotrophic methanogenic Archaea are defined by an H 2 requirement for growth. Despite this requirement, many hydrogenotrophs also capable of growth with formate as electron donor methanogenesis. While certain responses these organisms to hydrogen availability have been characterized, starvation not reported. Here we report that during continuous culture Methanococcus maripaludis under nutrient conditions, yields relative methane production decreased markedly either excess or...
Escherichia coli BL21(DE3) has long served as a model organism for scientific research, well workhorse biotechnology. Here we present the most current genome annotation of E. based on transcriptome structure strain that was determined first time. The annotated using multiple automated pipelines and compared to closely related strain, K-12. High-resolution tiling array data from several different stages cell growth in rich minimal media were analyzed characterize provide supporting evidence...
Bifidobacterium animalis subsp. lactis is a probiotic bacterium that naturally inhabits the guts of most mammals, including humans. Here we report complete genome sequence B. AD011 was isolated from an infant fecal sample. Biological functions encoded in single circular chromosome 1,933,695 bp, smallest among completely sequenced bifidobacterial genomes, are suggestive their functions, such as utilization bifidogenic factors and variety glycosidic enzymes biosynthesis polysaccharides.
Assembly of genes into operons is generally viewed as an important process during the continual adaptation microbes to changing environmental challenges. However, genome reorganization events that drive this are also roots instability for existing operons. We have determined there exists a statistically significant trend correlates proportion encoded in archaea their phylogenetic lineage. further characterized how deal with operon by mapping and comparing transcriptome architectures four...
Current understanding of heat shock response has been complicated by the fact that stress is inevitably accompanied changes in specific growth rates and stages. In this study, a chemostat culture was successfully performed to avoid physico-chemical biological accompany heatshock, which provided unique opportunity investigate full range cellular responses thermal stress, ranging from temporary adjustment phenotypic adaptation at multi-omics levels. Heat-responsive time-resolved transcriptome...
Pathogenicity islands (PAIs), distinct genomic segments of pathogens encoding virulence factors, represent a subgroup (GIs) that have been acquired by horizontal gene transfer event. Up to now, computational approaches for identifying PAIs focused on the detection regions which only differ from rest genome in their base composition and codon usage. These often lead identification islands, rather than PAIs.We present method detecting potential complete prokaryotic genomes combining sequence...
High-throughput growth phenotyping is receiving great attention for establishing the genotype–phenotype map of sequenced organisms owing to ready availability complete genome sequences. To date, microbial phenotypes have been investigated mostly by conventional method batch cultivation using test tubes, Erlenmeyer flasks, or recently available microwell plates. However, current methods are time- and labor-intensive often fail consider sophisticated environmental changes. The implementation...
Abstract Carbon source-dependent control of bacterial growth is fundamental to physiology and survival. However, pinpointing the metabolic steps important for cell challenging due complexity cellular networks. Here, elastic net model multilayer perception that integrated genome-wide gene-deletion data simulated flux distributions were constructed identify reactions beneficial or detrimental Escherichia coli grown on 30 different carbon sources. Both models outperformed traditional in silico...
Genome scale metabolic models (GEMs) and other constraint-based (CBMs) play a pivotal role in understanding biological phenotypes advancing research areas like engineering, human disease modelling, drug discovery, personalized medicine. Despite their growing application, significant challenge remains ensuring the reproducibility of GEMs, primarily due to inconsistent reporting inadequate model documentation results. Addressing this gap, we introduce FROG analysis, community driven initiative...
Methanogens catalyze the critical methane-producing step (called methanogenesis) in anaerobic decomposition of organic matter. Here, we present first predictive model global gene regulation methanogenesis a hydrogenotrophic methanogen, Methanococcus maripaludis . We generated comprehensive list genes (protein-coding and noncoding) for M. through integrated analysis transcriptome structure newly constructed Peptide Atlas. The environment gene-regulatory influence network (EGRIN) strain was...
Methylomonas sp. DH-1, newly isolated from the activated sludge of a brewery plant, has been used as promising biocatalytic platform for conversion methane to value-added chemicals. DH-1 can efficiently convert and propane into methanol acetone with specific productivity 4.31 0.14 mmol/g cell/h, highest values ever reported, respectively. Here, we present complete genome sequence which consists 4.86 Mb chromosome 278 kb plasmid. The existence set genes related one-carbon metabolism various...
Most inducible expression systems suffer from growth defects, leaky basal induction, and inhomogeneous levels within a host cell population. These difficulties are most prominent with the overproduction of membrane proteins that toxic to cells. Here, we developed an Escherichia coli system for protein production based on titrated mutant lac repressor (mLacI). Performance mLacI was evaluated in conjunction commonly used operator-based vectors using T7 or tac promoter. Remarkably, target gene...
Escherichia coli BL21(DE3) is an industrial model microbe for the mass-production of bioproducts such as biofuels, biorefineries, and recombinant proteins. However, despite its important role in scientific research biotechnological applications, a high-quality metabolic network engineering yet to be developed. Here, we present comprehensive E. BL21(DE3), named iHK1487, based on latest genome reannotation phenome analysis. The consists 1,164 unique metabolites, 2,701 reactions, 1,487 genes....