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Soonjae Kwon

Bio: Soonjae Kwon is an academic researcher from Seoul National University. The author has contributed to research in topics: Intercalation (chemistry) & Genome. The author has an hindex of 3, co-authored 5 publications receiving 4827 citations.

Papers
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Journal ArticleDOI
TL;DR: An integrated database, called EzBioCloud, that holds the taxonomic hierarchy of the Bacteria and Archaea, which is represented by quality-controlled 16S rRNA gene and genome sequences, with accompanying bioinformatics tools.
Abstract: The recent advent of DNA sequencing technologies facilitates the use of genome sequencing data that provide means for more informative and precise classification and identification of members of the Bacteria and Archaea. Because the current species definition is based on the comparison of genome sequences between type and other strains in a given species, building a genome database with correct taxonomic information is of paramount need to enhance our efforts in exploring prokaryotic diversity and discovering novel species as well as for routine identifications. Here we introduce an integrated database, called EzBioCloud, that holds the taxonomic hierarchy of the Bacteria and Archaea, which is represented by quality-controlled 16S rRNA gene and genome sequences. Whole-genome assemblies in the NCBI Assembly Database were screened for low quality and subjected to a composite identification bioinformatics pipeline that employs gene-based searches followed by the calculation of average nucleotide identity. As a result, the database is made of 61 700 species/phylotypes, including 13 132 with validly published names, and 62 362 whole-genome assemblies that were identified taxonomically at the genus, species and subspecies levels. Genomic properties, such as genome size and DNA G+C content, and the occurrence in human microbiome data were calculated for each genus or higher taxa. This united database of taxonomy, 16S rRNA gene and genome sequences, with accompanying bioinformatics tools, should accelerate genome-based classification and identification of members of the Bacteria and Archaea. The database and related search tools are available at www.ezbiocloud.net/.

5,027 citations

Journal ArticleDOI
TL;DR: ANI calculation can be greatly sped up by the OrthoANIu method without losing accuracy, and when genomes that are larger than 7 Mbp were analysed, the run-times of ANIm and Orthoaniu were shorter than that of ANIb by 53- and 22-fold, respectively.
Abstract: Average nucleotide identity (ANI) is a category of computational analysis that can be used to define species boundaries of Archaea and Bacteria. Calculating ANI usually involves the fragmentation of genome sequences, followed by nucleotide sequence search, alignment, and identity calculation. The original algorithm to calculate ANI used the BLAST program as its search engine. An improved ANI algorithm, called OrthoANI, was developed to accommodate the concept of orthology. Here, we compared four algorithms to compute ANI, namely ANIb (ANI algorithm using BLAST), ANIm (ANI using MUMmer), OrthoANIb (OrthoANI using BLAST) and OrthoANIu (OrthoANI using USEARCH) using >100,000 pairs of genomes with various genome sizes. By comparing values to the ANIb that is considered a standard, OrthoANIb and OrthoANIu exhibited good correlation in the whole range of ANI values. ANIm showed poor correlation for ANI of <90%. ANIm and OrthoANIu runs faster than ANIb by an order of magnitude. When genomes that are larger than 7 Mbp were analysed, the run-times of ANIm and OrthoANIu were shorter than that of ANIb by 53- and 22-fold, respectively. In conclusion, ANI calculation can be greatly sped up by the OrthoANIu method without losing accuracy. A web-service that can be used to calculate OrthoANIu between a pair of genome sequences is available at http://www.ezbiocloud.net/tools/ani . For large-scale calculation and integration in bioinformatics pipelines, a standalone JAVA program is available for download at http://www.ezbiocloud.net/tools/orthoaniu .

1,977 citations

Journal ArticleDOI
Jin-Ho Choy1, Soonjae Kwon1, Seong Ju Hwang, Young-Il Kim1, Woo Lee1 
TL;DR: In this article, a systematic application of intercalation techniques to layered superconducting oxides enables us to open a new chapter in the development of nano-hybrid with various functions.
Abstract: A systematic application of intercalation techniques to layered superconducting oxides enables us to open a new chapter in the development of nano-hybrids with various functions. Recently we were successful in preparing a new series of inorganic-inorganic nano-hybrids, M-X-Bi 2 Sr 2 Ca m–1 Cu m O y (M=Hg, Ag, Au; X=Br, I; m=1-3) and organic-inorganic ones, R 2 HgI 4 -Bi 2 Sr 2 Ca m–1 Cu m O y (R=organic cation). Our synthetic strategies are based on (1) HSAB (hard-soft acid-base) interactions and (2) interlayer complexation concepts. Since the iodine species in IBi 2 Sr 2 Ca m–1 Cu m O y are stabilized as I3– (soft base) with a charge transfer between host and guest, soft Lewis acids like Ag + , Au + , and Hg 2+ can be further intercalated into the iodine layers inbetween the (Bi-O) double layers. On the other hand, new organic-inorganic nano-hybrids (R 2 HgI 4 -Bi 2 Sr 2 Ca m–1 Cu m O y ) have also been achieved through the intercalative complex-salt formation reaction between preintercalated HgI 2 molecules and R + I – salts in the interlayer space of Bi 2 Sr 2 Ca m–1 Cu m O y . Compared to the pure compounds the superconducting transition temperatures of the organic-salt intercalates are little changed even with a large basal increment upon intercalation, indicating a two-dimensional nature of the high-T c superconductivity. From the viewpoint of application, the intercalation of large organic molecules provides a new synthetic route to high-T c superconducting thin-film and nano-particles by separating superconducting blocks into isolated single sheets.

36 citations

Patent
23 Oct 2008
TL;DR: In this paper, a coprecipitant is added to the solution to form precipitation and heat treating the solution in which the precipitation is formed to synthesize zinc silicate (Zn 2 SiO 4 ).
Abstract: Provided are a method of preparing a zinc silicate-based phosphor and a zinc silicate-based phosphor prepared using the method. The method includes: (a) preparing a solution including a Zn precursor compound and a Si precursor compound; (b) adding a coprecipitant to the solution to form precipitation; and (c) heat treating the solution in which the precipitation is formed to synthesize zinc silicate (Zn 2 SiO 4 ), wherein a solvent of the solution including the Zn precursor compound and the Si precursor compound includes at least one selected from the group consisting of ethanol, methanol, 1-propanol, 2-propanol, 1-butanol, 2-butanol, 1-pentanol, 2-pentanol, 3-pentanol, 1-hexanol, and 1-heptanol, and hydrazine is used as the coprecipitant.

2 citations

Patent
08 May 2001
TL;DR: In this article, a superconducting colloid prepared by an exfoliating multi-layered superconductor, represented by the formula Bi2Sr2Cam-1CumO?2m+4+δ? is described.
Abstract: The present invention relates to a superconducting colloid prepared by an exfoliating multi-layered superconductor, represented by the formula Bi2Sr2Cam-1CumO?2m+4+δ? (wherein, m is 1, 2 or 3 and δ is a positive number greater than 0 and less than 1) in which a mercuric halide- organic complex is intercalated, a process thereof, a superconducting thin layer prepared using the above superconducting colloid, and a process thereof.

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TL;DR: In this article, a review of polymer-layered silicate nanocomposites is presented, where the polymer chains are sandwiched in between silicate layers and exfoliated layers are more or less uniformly dispersed in the polymer matrix.
Abstract: This review aims at reporting on very recent developments in syntheses, properties and (future) applications of polymer-layered silicate nanocomposites. This new type of materials, based on smectite clays usually rendered hydrophobic through ionic exchange of the sodium interlayer cation with an onium cation, may be prepared via various synthetic routes comprising exfoliation adsorption, in situ intercalative polymerization and melt intercalation. The whole range of polymer matrices is covered, i.e. thermoplastics, thermosets and elastomers. Two types of structure may be obtained, namely intercalated nanocomposites where the polymer chains are sandwiched in between silicate layers and exfoliated nanocomposites where the separated, individual silicate layers are more or less uniformly dispersed in the polymer matrix. This new family of materials exhibits enhanced properties at very low filler level, usually inferior to 5 wt.%, such as increased Young’s modulus and storage modulus, increase in thermal stability and gas barrier properties and good flame retardancy.

5,901 citations

Journal ArticleDOI
TL;DR: FastANI is developed, a method to compute ANI using alignment-free approximate sequence mapping, and it is shown 95% ANI is an accurate threshold for demarcating prokaryotic species by analyzing about 90,000 proKaryotic genomes.
Abstract: A fundamental question in microbiology is whether there is continuum of genetic diversity among genomes, or clear species boundaries prevail instead. Whole-genome similarity metrics such as Average Nucleotide Identity (ANI) help address this question by facilitating high resolution taxonomic analysis of thousands of genomes from diverse phylogenetic lineages. To scale to available genomes and beyond, we present FastANI, a new method to estimate ANI using alignment-free approximate sequence mapping. FastANI is accurate for both finished and draft genomes, and is up to three orders of magnitude faster compared to alignment-based approaches. We leverage FastANI to compute pairwise ANI values among all prokaryotic genomes available in the NCBI database. Our results reveal clear genetic discontinuity, with 99.8% of the total 8 billion genome pairs analyzed conforming to >95% intra-species and <83% inter-species ANI values. This discontinuity is manifested with or without the most frequently sequenced species, and is robust to historic additions in the genome databases. Average Nucleotide Identity (ANI) is a robust and useful measure to gauge genetic relatedness between two genomes. Here, the authors develop FastANI, a method to compute ANI using alignment-free approximate sequence mapping, and show 95% ANI is an accurate threshold for demarcating prokaryotic species by analyzing about 90,000 prokaryotic genomes.

2,176 citations

Journal ArticleDOI
TL;DR: This work used a concatenated protein phylogeny as the basis for a bacterial taxonomy that conservatively removes polyphyletic groups and normalizes taxonomic ranks on the basis of relative evolutionary divergence.
Abstract: Taxonomy is an organizing principle of biology and is ideally based on evolutionary relationships among organisms. Development of a robust bacterial taxonomy has been hindered by an inability to obtain most bacteria in pure culture and, to a lesser extent, by the historical use of phenotypes to guide classification. Culture-independent sequencing technologies have matured sufficiently that a comprehensive genome-based taxonomy is now possible. We used a concatenated protein phylogeny as the basis for a bacterial taxonomy that conservatively removes polyphyletic groups and normalizes taxonomic ranks on the basis of relative evolutionary divergence. Under this approach, 58% of the 94,759 genomes comprising the Genome Taxonomy Database had changes to their existing taxonomy. This result includes the description of 99 phyla, including six major monophyletic units from the subdivision of the Proteobacteria, and amalgamation of the Candidate Phyla Radiation into a single phylum. Our taxonomy should enable improved classification of uncultured bacteria and provide a sound basis for ecological and evolutionary studies.

2,098 citations

Journal ArticleDOI
TL;DR: The minimal standards for the quality of genome sequences and how they can be applied for taxonomic purposes are described.
Abstract: Advancement of DNA sequencing technology allows the routine use of genome sequences in the various fields of microbiology. The information held in genome sequences proved to provide objective and reliable means in the taxonomy of prokaryotes. Here, we describe the minimal standards for the quality of genome sequences and how they can be applied for taxonomic purposes.

1,908 citations

Journal ArticleDOI
TL;DR: TYGS, the Type (Strain) Genome Server, a user-friendly high-throughput web server for genome-based prokaryote taxonomy and analysis connected to a large, continuously growing database of genomic, taxonomic and nomenclatural information.
Abstract: Microbial taxonomy is increasingly influenced by genome-based computational methods. Yet such analyses can be complex and require expert knowledge. Here we introduce TYGS, the Type (Strain) Genome Server, a user-friendly high-throughput web server for genome-based prokaryote taxonomy, connected to a large, continuously growing database of genomic, taxonomic and nomenclatural information. It infers genome-scale phylogenies and state-of-the-art estimates for species and subspecies boundaries from user-defined and automatically determined closest type genome sequences. TYGS also provides comprehensive access to nomenclature, synonymy and associated taxonomic literature. Clinically important examples demonstrate how TYGS can yield new insights into microbial classification, such as evidence for a species-level separation of previously proposed subspecies of Salmonella enterica. TYGS is an integrated approach for the classification of microbes that unlocks novel scientific approaches to microbiologists worldwide and is particularly helpful for the rapidly expanding field of genome-based taxonomic descriptions of new genera, species or subspecies.

1,202 citations