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Do, Yoonkyung
DC-based Immune System & Immunotherapy (DISNI) Lab
Research Interests
  • Study on various subsets of dendritic cells and their immunological functions
  • Vaccine development by targeting pathogenic antigens to distinct DC subsets via anti-DC-subset-specific-receptor monoclonal antibodies
  • Characterization of roles of DCs in tumor microenvironment and tumor metastasis
  • Studies on role of DCs in neuro-related diseases
  • Study DCs in collaboration with Biotechnology or Engineering field

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Dropout alignment allows homology recognition and evolutionary analysis of rDNA intergenic spacers

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dc.contributor.author Ryu, Seongho ko
dc.contributor.author Do, Yoonkyung ko
dc.contributor.author Fitch, David H. A. ko
dc.contributor.author Kim, Won ko
dc.contributor.author Mishra, Bud ko
dc.date.available 2014-10-10T01:57:56Z -
dc.date.created 2014-10-08 ko
dc.date.issued 2008-04 -
dc.identifier.citation JOURNAL OF MOLECULAR EVOLUTION, v.66, no.4, pp.368 - 383 ko
dc.identifier.issn 0022-2844 ko
dc.identifier.uri https://scholarworks.unist.ac.kr/handle/201301/7054 -
dc.identifier.uri http://www.scopus.com/inward/record.url?partnerID=HzOxMe3b&scp=43149089345 ko
dc.description.abstract Subrepeats within the ribosomal gene (rDNA) intergenic spacer (IGS) play an important role in enhancing RNA polymerase I transcription. Despite this functional role and presumed selective constraint, there is surprisingly little sequence similarity among IGS subrepeats of different species. This sequence dissimilarity corresponds with the fast insertion-deletion (indel) rates observed in short mononucleotide microsatellites (here referred to as poly[N] runs, where N is any nucleotide), which are relatively abundant in rDNA IGS subrepeats. Some species have different types of IGS subrepeats that share species-specific poly(N) run patterns. This finding indicates that many IGS subrepeats within species share a common evolutionary history. Furthermore, by aligning sequences after modifying them by the dropout method, i.e., by disregarding poly(N) runs during the sequence aligning step, we sought to uncover evolutionarily shared similarities that fail to be recognized by current alignment programs. To ensure that the improved similarities in the computed alignments are not a chance artifact, we calibrated and corrected the IGS subrepeat sequences for the influence of repeat length and estimated the statistical significance of the alignments (in terms of a stringent p-value) obtained by the dropout method by comparing them to null models constructed using random sequence sets from the same genomes. We found that most diverse kinds of rDNA IGS subrepeats in one species must have been derived from a common ancestral subrepeat, and that it is possible to infer the evolutionary relationships among the IGS subrepeats of different species by comparative genomics methods based on dropout alignments. ko
dc.description.statementofresponsibility close -
dc.language ENG ko
dc.publisher SPRINGER ko
dc.subject Comparative genomics ko
dc.subject Dropout alignment method ko
dc.subject Homopolymeric runs ko
dc.subject Intergenic spacer ko
dc.subject Mononucleotide microsatellites ko
dc.subject Poly(N) ko
dc.subject Ribosomal DNA ko
dc.subject Subrepeat ko
dc.title Dropout alignment allows homology recognition and evolutionary analysis of rDNA intergenic spacers ko
dc.type ARTICLE ko
dc.identifier.scopusid 2-s2.0-43149089345 ko
dc.identifier.wosid 000255629900006 ko
dc.type.rims ART ko
dc.description.wostc 3 *
dc.description.scopustc 0 *
dc.date.tcdate 2015-05-06 *
dc.date.scptcdate 2014-10-08 *
dc.identifier.doi 10.1007/s00239-008-9090-8 ko
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