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Article
Open AccessIdentification and characterization of structural variants related to meat quality in pigs using chromosome-level genome assemblies
Many studies have been performed to identify various genomic loci and genes associated with the meat quality in pigs. However, the full genetic architecture of the trait still remains unclear in part because o...
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Article
Open AccessA chromosome-level genome assembly of the Korean crossbred pig Nanchukmacdon (Sus scrofa)
As plentiful high-quality genome assemblies have been accumulated, reference-guided genome assembly can be a good approach to reconstruct a high-quality assembly. Here, we present a chromosome-level genome ass...
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Article
Open AccessmsPIPE: a pipeline for the analysis and visualization of whole-genome bisulfite sequencing data
DNA methylation is an important epigenetic modification that is known to regulate gene expression. Whole-genome bisulfite sequencing (WGBS) is a powerful method for studying cytosine methylation in a whole gen...
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Article
Open AccessComparative methylation and RNA-seq expression analysis in CpG context to identify genes involved in Backfat vs. Liver diversification in Nanchukmacdon Pig
DNA methylation and demethylation at CpG islands is one of the main regulatory factors that allow cells to respond to different stimuli. These regulatory mechanisms help in develo** tissue without affecting ...
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Article
Open AccessIntegration of multi-omics approaches for functional characterization of muscle related selective sweep genes in Nanchukmacdon
Pig as a food source serves daily dietary demand to a wide population around the world. Preference of meat depends on various factors with muscle play the central role. In this regards, selective breeding able...
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Article
Open AccessPopulation analysis of the Korean native duck using whole-genome sequencing data
Advances in next-generation sequencing technologies have provided an opportunity to perform population-level comparative genomic analysis to discover unique genomic characteristics of domesticated animals. Duc...
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Article
Open AccessTAMA: improved metagenomic sequence classification through meta-analysis
Microorganisms are important occupants of many different environments. Identifying the composition of microbes and estimating their abundance promote understanding of interactions of microbes in environmental ...
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Article
Markov chain Monte Carlo simulation of a Bayesian mixture model for gene network inference
Simultaneous measurement of gene expression level for thousands of genes contains the rich information about many different aspects of biological mechanisms. A major computational challenge is to find methods ...
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Article
Open AccessGMASS: a novel measure for genome assembly structural similarity
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 be...
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Article
Open AccessReconstruction of avian ancestral karyotypes reveals differences in the evolutionary history of macro- and microchromosomes
Reconstruction of ancestral karyotypes is critical for our understanding of genome evolution, allowing for the identification of the gross changes that shaped extant genomes. The identification of such changes...
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Article
Open AccessmySyntenyPortal: an application package to construct websites for synteny block analysis
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 s...
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Article
Application of metagenome analysis to characterize the molecular diversity and saxitoxin-producing potentials of a cyanobacterial community: a case study in the North Han River, Korea
A wide variety of cyanobacterial species that inhabit freshwater systems are known to produce diverse toxins and off-flavor compounds during the development of environmentally harmful blooms. However, cyanobac...
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Article
Open AccessFunctional and evolutionary analysis of Korean bob-tailed native dog using whole-genome sequencing data
Rapid and cost effective production of large-scale genome data through next-generation sequencing has enabled population-level studies of various organisms to identify their genotypic differences and phenotypi...
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Article
Open AccessDiversity, distribution, and significance of transposable elements in the genome of the only selfing hermaphroditic vertebrate Kryptolebias marmoratus
The Kryptolebias marmoratus is unique because it is the only self-fertilizing hermaphroditic vertebrate, known to date. It primarily reproduces by internal self-fertilization in a mixed ovary/testis gonad. Here, ...
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Article
Open AccessIdentification of disease comorbidity through hidden molecular mechanisms
Despite multiple diseases co-occur, their underlying common molecular mechanisms remain elusive. Identification of comorbid diseases by considering the interactions between molecular components is a key to und...
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Article
Correction: Corrigendum: Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax
Nature Communications 5: Article number: 3966 (2014); Published online: 3 June 2014; Updated: 12 Aug 2015. In Fig. 2 of this Article, the CLOCK protein sequence of the blind mole rat (Spalax) was inadvertently...
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Article
Effects of omics data combinations on in silico tumor-normal tissue classification
A disease can be characterized by various attributes such as genomic, epigenetic, and transcriptomic features beyond physiological symptoms. The accumulation of vast datasets allows us to investigate the relat...
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Article
Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax
The blind mole rat (BMR), Spalax galili, is an excellent model for studying mammalian adaptation to life underground and medical applications. The BMR spends its entire life underground, protecting itself from pr...
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Article
A clustering method for next-generation sequences of bacterial genomes through multiomics data map**
With various ‘omics’ data becoming available recently, new challenges and opportunities are provided for researches on the assembly of next-generation sequences. As an attempt to utilize novel opportunities, w...
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Article
Computational prediction of transcription factor binding sites based on an integrative approach incorporating genomic and epigenomic features
Transcription factor binding sites (TFBSs) are often predicted by sequence-based methods that use a position weight matrix or consensus sequences. However, the degeneracy of TFBSs makes the prediction of them ...
