A5033232650- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- CRISPR and Genetic Engineering
- Genetic Mapping and Diversity in Plants and Animals
- Genetic and phenotypic traits in livestock
- Bioinformatics and Genomic Networks
- Protein Structure and Dynamics
- Microbial Metabolic Engineering and Bioproduction
- Machine Learning in Bioinformatics
- Microbial Community Ecology and Physiology
- Metabolomics and Mass Spectrometry Studies
- Genetic diversity and population structure
- Molecular Biology Techniques and Applications
- Genome Rearrangement Algorithms
- Cell Image Analysis Techniques
- Privacy-Preserving Technologies in Data
- Modular Robots and Swarm Intelligence
- Bacteriophages and microbial interactions
- Cancer Genomics and Diagnostics
- Animal Genetics and Reproduction
- Plant Virus Research Studies
- Diet and metabolism studies
- Genetics, Bioinformatics, and Biomedical Research
- Privacy, Security, and Data Protection
- Fungal and yeast genetics research
Konkuk University
2017-2025
Agency for Defense Development
2012
Abstract Background Many studies have been performed to identify various genomic loci and genes associated with the meat quality in pigs. However, full genetic architecture of trait still remains unclear part because lack accurate identification related structural variations (SVs) which resulted from shortage target breeds, limitations sequencing data, incompleteness genome assemblies. The recent generation a new pig breed superior quality, called Nanchukmacdon, its chromosome-level assembly...
Abstract As plentiful high-quality genome assemblies have been accumulated, reference-guided assembly can be a good approach to reconstruct assembly. Here, we present chromosome-level of the Korean crossbred pig called Nanchukmacdon (the NCMD assembly) using with short and long reads. The contains 20 scaffolds total size 2.38 Gbp (N50: 138.77 Mbp). Its BUSCO score is 93.1%, which comparable reference assembly, 20,588 protein-coding genes, 8,651 non-coding 996.14 Mbp repetitive elements are...
Proteins perform biological functions through cascading interactions with each other by forming protein complexes. As a result, among proteins, called protein-protein (PPIs) are not completely free from selection constraint during evolution. Therefore, the identification and analysis of PPI changes evolution can give us new insight into functions. Although many algorithms, databases websites have been developed to help study PPIs, most them limited visualize structure features PPIs in chosen...
Recent advancements in sequencing and genome assembly technologies have led to rapid generation of high-quality assemblies for various species breeds. Despite the importance as minipigs an animal model biomedical research, construction still lags behind other pig To address this problem, we constructed a chromosome-level Korean minipig (KMP) utilizing multiple different types reads reference genomes. The KMP included 19 sequences with total length 2.52 Gb N50 137 Mb. Comparative analyses...
Currently, diverse minipigs have acquired a common dwarfism phenotype through independent artificial selections. Characterizing the population and genetic diversity in is important to unveil mechanisms regulating their body sizes effects of selections on those mechanisms. However, full understanding for phenotypic consequences still lag behind. Here, using whole genome sequencing data 41 pig breeds, including eight minipigs, we identified large genomic minipig compared other populations...
Thanks to the recent advancements in next-generation sequencing (NGS) technologies, large amount of genomic data, which are short DNA sequences known as reads, has been accumulating. Diverse assemblers have developed generate high quality de novo assemblies using NGS but their output is very different because algorithmic differences. However, there not properly structured measures show similarity or difference assemblies.We a new measure, called GMASS score, for comparing two genome terms...
Metagenomic assembly using high-throughput sequencing data is a powerful method to construct microbial genomes in environmental samples without cultivation. However, metagenomic assembly, especially when only short reads are available, complex and challenging task because mixed of multiple microorganisms constitute the metagenome. Although long read technologies have been developed begun be used for many studies performed based on generation requires higher cost than reads.In this study, we...
Advances in sequencing technologies have facilitated large-scale comparative genomics based on whole genome sequencing. Constructing and investigating conserved genomic regions among multiple species (called synteny blocks) are essential the genomics. However, they require significant amounts of computational resources time addition to bioinformatics skills. Many web interfaces been developed make such tasks easier. these cannot be customized for users who want use their own set sequences or...
Abstract Background Alzheimer's disease (AD), the most prevalent form of dementia, affects 6.5 million Americans and over 50 people globally. Clinical, genetic, phenotypic studies dementia provide some insights observed progressive neurodegenerative processes, however, mechanisms underlying AD onset remain enigmatic. Aims This paper examines late‐onset dementia‐related cognitive impairment utilizing neuroimaging‐genetics biomarker associations. Materials Methods The participants, ages 65–85,...
Microorganisms are important occupants of many different environments. Identifying the composition microbes and estimating their abundance promote understanding interactions in environmental samples. To understand environments more deeply, microorganisms samples has been studied using metagenomes, which collections genomes microorganisms. Although tools have developed for taxonomy analysis based on algorithms, variability outputs existing from same input metagenome datasets is main obstacle...
Rapid and cost effective production of large-scale genome data through next-generation sequencing has enabled population-level studies various organisms to identify their genotypic differences phenotypic consequences. This is also used study indigenous animals with historical economical values, although they are less studied than model organisms. The objective this was perform functional evolutionary analysis Korean bob-tailed native dog Donggyeong distinct tail agility phenotype using...
Background Genomic data have become major resources to understand complex mechanisms at fine-scale temporal and spatial resolution in functional evolutionary genetic studies, including human diseases, such as cancers. Recently, a large number of whole genomes evolving populations yeast (Saccharomyces cerevisiae W303 strain) were sequenced time-dependent manner identify patterns. For this type study, chromosome-level sequence assembly the strain or population time zero is required compare...
Deep learning has been applied for solving many biological problems, and it shown outstanding performance. Applying deep in research requires knowledge of theories programming skills, but researchers have developed diverse platforms to allow users build models without programming. Despite these efforts, is still difficult biologists use because limitations the existing platforms. Therefore, a new platform necessary that can solve challenges biologists. To alleviate this situation, we...
Researchers using various of statistical data want to obtain microdata for a detailed analysis. Institutes need provide after masking processes sensitive data. Many researchers have used the proportion unique identity measurement disclosure risk. We proposed new risk that considers case all identities are same or similar. As an application example, we compare newly and existing 10667 in 'Korea Household Income Expenditure Survey 2010'.
Abstract INTER‐Species Protein Interaction Analysis (INTERSPIA) is a web application for identifying diverse patterns of protein‐protein interactions (PPIs) in different species. Given set proteins interest to the user, INTERSPIA first discovers additional that are functionally associated with input as well or common PPIs among multiple species through server‐side pipeline. Second, it visualizes dynamics via an easy‐to‐use interface. This article contains basic protocol describing how...
Constructing accurate microbial genome assemblies is necessary to understand genetic diversity in genomes and its functional consequences. However, it still remains as a challenging task especially when only short-read sequencing technologies are used. Here, we present new read-clustering algorithm, called RBRC, for improving de novo assembly, by accurately estimating read proximity using multiple reference genomes. The performance of RBRC was confirmed simulation-based evaluation terms...