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Chapter and Conference Paper
A Search Ant and Labor Ant Algorithm for Clustering Data
In 1990, Deneubourg et al. [1] developed the first ant clustering algorithm based on mimicking corpse piling process of ants. In his algorithm, an ant picks up and drops the data items based on the similarity ...
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Article
Open AccessTowards realistic benchmarks for multiple alignments of non-coding sequences
With the continued development of new computational tools for multiple sequence alignment, it is necessary today to develop benchmarks that aid the selection of the most effective tools. Simulation-based bench...
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Chapter and Conference Paper
PSAR: Measuring Multiple Sequence Alignment Reliability by Probabilistic Sampling
Multiple sequence alignment (MSA), which is of fundamental importance for comparative genomics, is a difficult problem and error-prone. Therefore, it is essential to measure the reliability of the alignments a...
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Article
Open AccessThe yak genome and adaptation to life at high altitude
Jianquan Liu and colleagues report the draft genome sequence of the domestic yak, Bos grunniens. Their comparative analyses with low-altitude cattle provide insights into high-altitude adaptation in the yak.
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Article
Open AccessAnalyses of pig genomes provide insight into porcine demography and evolution
For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and...
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Article
Open AccessDraft genome sequence of the Tibetan antelope
The Tibetan antelope (Pantholops hodgsonii) is endemic to the extremely inhospitable high-altitude environment of the Qinghai-Tibetan Plateau, a region that has a low partial pressure of oxygen and high ultraviol...
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Article
The North Korean Factor in East Asian Regional Security
This paper first examines briefly the current security environment in East Asia and then identifies the North Korean factor in regional security. It later reviews the implications of this factor in a broader c...
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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 ...
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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
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
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
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
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
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 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
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 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
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 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
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 ...
