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Dae-Soo Kim

Bio: Dae-Soo Kim is an academic researcher from Korea Research Institute of Bioscience and Biotechnology. The author has contributed to research in topics: Gene & Genome. The author has an hindex of 21, co-authored 115 publications receiving 1988 citations. Previous affiliations of Dae-Soo Kim include Korea University of Science and Technology & Chungnam National University.


Papers
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Journal ArticleDOI
TL;DR: The first Korean individual genome sequence (SJK) and analysis results indicate that the overall genetic differences among individuals from closely related ethnic groups may be significant and constructing reference genomes for minor socio-ethnic groups will be useful for massive individual genome sequencing.
Abstract: We present the first Korean individual genome sequence (SJK) and analysis results. The diploid genome of a Korean male was sequenced to 28.95-fold redundancy using the Illumina paired-end sequencing method. SJK covered 99.9% of the NCBI human reference genome. We identified 420,083 novel single nucleotide polymorphisms (SNPs) that are not in the dbSNP database. Despite a close similarity, significant differences were observed between the Chinese genome (YH), the only other Asian genome available, and SJK: (1) 39.87% (1,371,239 out of 3,439,107) SNPs were SJK-specific (49.51% against Venter's, 46.94% against Watson's, and 44.17% against the Yoruba genomes); (2) 99.5% (22,495 out of 22,605) of short indels (< 4 bp) discovered on the same loci had the same size and type as YH; and (3) 11.3% (331 out of 2920) deletion structural variants were SJK-specific. Even after attempting to map unmapped reads of SJK to unanchored NCBI scaffolds, HGSV, and available personal genomes, there were still 5.77% SJK reads that could not be mapped. All these findings indicate that the overall genetic differences among individuals from closely related ethnic groups may be significant. Hence, constructing reference genomes for minor socio-ethnic groups will be useful for massive individual genome sequencing.

332 citations

Journal ArticleDOI
TL;DR: It appears that polyploidy and chromosomal diploidization are ongoing processes that collectively stabilize the B. rapa genome and facilitate its evolution.
Abstract: Brassica rapa is one of the most economically important vegetable crops worldwide. Owing to its agronomic importance and phylogenetic position, B. rapa provides a crucial reference to understand polyploidy-related crop genome evolution. The high degree of sequence identity and remarkably conserved genome structure between Arabidopsis and Brassica genomes enables comparative tiling sequencing using Arabidopsis sequences as references to select the counterpart regions in B. rapa, which is a strong challenge of structural and comparative crop genomics. We assembled 65.8 megabase-pairs of non-redundant euchromatic sequence of B. rapa and compared this sequence to the Arabidopsis genome to investigate chromosomal relationships, macrosynteny blocks, and microsynteny within blocks. The triplicated B. rapa genome contains only approximately twice the number of genes as in Arabidopsis because of genome shrinkage. Genome comparisons suggest that B. rapa has a distinct organization of ancestral genome blocks as a result of recent whole genome triplication followed by a unique diploidization process. A lack of the most recent whole genome duplication (3R) event in the B. rapa genome, atypical of other Brassica genomes, may account for the emergence of B. rapa from the Brassica progenitor around 8 million years ago. This work demonstrates the potential of using comparative tiling sequencing for genome analysis of crop species. Based on a comparative analysis of the B. rapa sequences and the Arabidopsis genome, it appears that polyploidy and chromosomal diploidization are ongoing processes that collectively stabilize the B. rapa genome and facilitate its evolution.

201 citations

Journal ArticleDOI
TL;DR: A novel human pluripotent stem cell-derived hepatocyte-like liver organoid that is critically advanced in terms of its generation method, functional performance, and application technologies is provided.

147 citations

Journal ArticleDOI
TL;DR: Reconstruction of the common ancestral Y chromosome reflects the dynamic changes in genomes in the 5–6 million years since speciation and confirmed the accelerated evolutionary rate of the Y chromosome.
Abstract: The mammalian Y chromosome has unique characteristics compared with the autosomes or X chromosomes. Here we report the finished sequence of the chimpanzee Y chromosome (PTRY), including 271 kb of the Y-specific pseudoautosomal region 1 and 12.7 Mb of the male-specific region of the Y chromosome. Greater sequence divergence between the human Y chromosome (HSAY) and PTRY (1.78%) than between their respective whole genomes (1.23%) confirmed the accelerated evolutionary rate of the Y chromosome. Each of the 19 PTRY protein-coding genes analyzed had at least one nonsynonymous substitution, and 11 genes had higher nonsynonymous substitution rates than synonymous ones, suggesting relaxation of selective constraint, positive selection or both. We also identified lineage-specific changes, including deletion of a 200-kb fragment from the pericentromeric region of HSAY, expansion of young Alu families in HSAY and accumulation of young L1 elements and long terminal repeat retrotransposons in PTRY. Reconstruction of the common ancestral Y chromosome reflects the dynamic changes in our genomes in the 5-6 million years since speciation.

114 citations

Journal ArticleDOI
TL;DR: The results clearly indicated the necessity of using different reference genes for normalization of expression levels between rhesus monkeys and humans in various tissues.
Abstract: The rhesus monkey (Macaca mulatta) is a valuable and widely used model animal for biomedical research. However, quantitative analyses of rhesus gene expression profiles under diverse experimental conditions are limited by a shortage of suitable internal controls for the normalization of mRNA levels. In this study, we used a systematic approach for the selection of potential reference genes in the rhesus monkey and compared their suitability to that of the corresponding genes in humans. Eight housekeeping genes (HKGs) (GAPDH, SDHA, ACTB, RPL13A, RPL32, UBA52, PGK1Y, and YWHAZ) from rhesus monkeys and humans were selected to test for normalization of expression levels in six different tissue types (brain, colon, kidney, liver, lung, and stomach). Their stability and suitability as reference genes were validated by geNorm, NormFinder and BestKeeper programs. Intriguingly, RPL13A and RPL32 were selected as ideal reference genes only in rhesus monkeys. The results clearly indicated the necessity of using different reference genes for normalization of expression levels between rhesus monkeys and humans in various tissues.

82 citations


Cited by
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TL;DR: A technical review of template preparation, sequencing and imaging, genome alignment and assembly approaches, and recent advances in current and near-term commercially available NGS instruments is presented.
Abstract: Demand has never been greater for revolutionary technologies that deliver fast, inexpensive and accurate genome information. This challenge has catalysed the development of next-generation sequencing (NGS) technologies. The inexpensive production of large volumes of sequence data is the primary advantage over conventional methods. Here, I present a technical review of template preparation, sequencing and imaging, genome alignment and assembly approaches, and recent advances in current and near-term commercially available NGS instruments. I also outline the broad range of applications for NGS technologies, in addition to providing guidelines for platform selection to address biological questions of interest.

7,023 citations

Journal ArticleDOI
TL;DR: A new greedy alignment algorithm is introduced with particularly good performance and it is shown that it computes the same alignment as does a certain dynamic programming algorithm, while executing over 10 times faster on appropriate data.
Abstract: For aligning DNA sequences that differ only by sequencing errors, or by equivalent errors from other sources, a greedy algorithm can be much faster than traditional dynamic programming approaches and yet produce an alignment that is guaranteed to be theoretically optimal. We introduce a new greedy alignment algorithm with particularly good performance and show that it computes the same alignment as does a certain dynamic programming algorithm, while executing over 10 times faster on appropriate data. An implementation of this algorithm is currently used in a program that assembles the UniGene database at the National Center for Biotechnology Information.

4,628 citations

Journal ArticleDOI
13 Jul 2011-Nature
TL;DR: A more detailed history of human population sizes between approximately ten thousand and a million years ago is presented, using the pairwise sequentially Markovian coalescent model applied to the complete diploid genome sequences of a Chinese male, a Korean male, three European individuals, and two Yoruba males.
Abstract: The history of human population size is important for understanding human evolution. Various studies have found evidence for a founder event (bottleneck) in East Asian and European populations, associated with the human dispersal out-of-Africa event around 60 thousand years (kyr) ago. However, these studies have had to assume simplified demographic models with few parameters, and they do not provide a precise date for the start and stop times of the bottleneck. Here, with fewer assumptions on population size changes, we present a more detailed history of human population sizes between approximately ten thousand and a million years ago, using the pairwise sequentially Markovian coalescent model applied to the complete diploid genome sequences of a Chinese male (YH), a Korean male (SJK), three European individuals (J. C. Venter, NA12891 and NA12878 (ref. 9)) and two Yoruba males (NA18507 (ref. 10) and NA19239). We infer that European and Chinese populations had very similar population-size histories before 10-20 kyr ago. Both populations experienced a severe bottleneck 10-60 kyr ago, whereas African populations experienced a milder bottleneck from which they recovered earlier. All three populations have an elevated effective population size between 60 and 250 kyr ago, possibly due to population substructure. We also infer that the differentiation of genetically modern humans may have started as early as 100-120 kyr ago, but considerable genetic exchanges may still have occurred until 20-40 kyr ago.

1,943 citations

Journal ArticleDOI
TL;DR: New data highlights include seven new genome assemblies, a Neandertal genome data portal, phenotype and disease association data, a human RNA editing track, and a zebrafish Conservation track.
Abstract: The University of California, Santa Cruz Genome Browser (http://genome.ucsc.edu) offers online access to a database of genomic sequence and annotation data for a wide variety of organisms. The Browser also has many tools for visualizing, comparing and analyzing both publicly available and user-generated genomic data sets, aligning sequences and uploading user data. Among the features released this year are a gene search tool and annotation track drag-reorder functionality as well as support for BAM and BigWig/BigBed file formats. New display enhancements include overlay of multiple wiggle tracks through use of transparent coloring, options for displaying transformed wiggle data, a ‘mean+whiskers’ windowing function for display of wiggle data at high zoom levels, and more color schemes for microarray data. New data highlights include seven new genome assemblies, a Neandertal genome data portal, phenotype and disease association data, a human RNA editing track, and a zebrafish Conservation track. We also describe updates to existing tracks.

1,818 citations

Journal ArticleDOI
Xiaowu Wang1, Hanzhong Wang, Jun Wang2, Jun Wang3, Jun Wang4, Rifei Sun, Jian Wu, Shengyi Liu, Yinqi Bai2, Jeong-Hwan Mun5, Ian Bancroft6, Feng Cheng, Sanwen Huang, Xixiang Li, Wei Hua, Junyi Wang2, Xiyin Wang7, Xiyin Wang8, Michael Freeling9, J. Chris Pires10, Andrew H. Paterson8, Boulos Chalhoub, Bo Wang2, Alice Hayward11, Alice Hayward12, Andrew G. Sharpe13, Beom-Seok Park5, Bernd Weisshaar14, Binghang Liu2, Bo Li2, Bo Liu, Chaobo Tong, Chi Song2, Chris Duran15, Chris Duran12, Chunfang Peng2, Geng Chunyu2, Chushin Koh13, Chuyu Lin2, David Edwards15, David Edwards12, Desheng Mu2, Di Shen, Eleni Soumpourou6, Fei Li, Fiona Fraser6, Gavin C. Conant10, Gilles Lassalle16, Graham J.W. King3, Guusje Bonnema17, Haibao Tang9, Haiping Wang, Harry Belcram, Heling Zhou2, Hideki Hirakawa, Hiroshi Abe, Hui Guo8, Hui Wang, Huizhe Jin8, Isobel A. P. Parkin18, Jacqueline Batley12, Jacqueline Batley11, Jeong-Sun Kim5, Jérémy Just, Jianwen Li2, Jiaohui Xu2, Jie Deng, Jin A Kim5, Jingping Li8, Jingyin Yu, Jinling Meng19, Jinpeng Wang7, Jiumeng Min2, Julie Poulain20, Katsunori Hatakeyama, Kui Wu2, Li Wang7, Lu Fang, Martin Trick6, Matthew G. Links18, Meixia Zhao, Mina Jin5, Nirala Ramchiary21, Nizar Drou22, Paul J. Berkman15, Paul J. Berkman12, Qingle Cai2, Quanfei Huang2, Ruiqiang Li2, Satoshi Tabata, Shifeng Cheng2, Shu Zhang2, Shujiang Zhang, Shunmou Huang, Shusei Sato, Silong Sun, Soo-Jin Kwon5, Su-Ryun Choi21, Tae-Ho Lee8, Wei Fan2, Xiang Zhao2, Xu Tan8, Xun Xu2, Yan Wang, Yang Qiu, Ye Yin2, Yingrui Li2, Yongchen Du, Yongcui Liao, Yong Pyo Lim21, Yoshihiro Narusaka, Yupeng Wang7, Zhenyi Wang7, Zhenyu Li2, Zhiwen Wang2, Zhiyong Xiong10, Zhonghua Zhang 
TL;DR: The annotation and analysis of the draft genome sequence of Brassica rapa accession Chiifu-401-42, a Chinese cabbage, and used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structural and functional evolution.
Abstract: We report the annotation and analysis of the draft genome sequence of Brassica rapa accession Chiifu-401-42, a Chinese cabbage. We modeled 41,174 protein coding genes in the B. rapa genome, which has undergone genome triplication. We used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structural and functional evolution. The extent of gene loss (fractionation) among triplicated genome segments varies, with one of the three copies consistently retaining a disproportionately large fraction of the genes expected to have been present in its ancestor. Variation in the number of members of gene families present in the genome may contribute to the remarkable morphological plasticity of Brassica species. The B. rapa genome sequence provides an important resource for studying the evolution of polyploid genomes and underpins the genetic improvement of Brassica oil and vegetable crops.

1,811 citations