2004 Fiscal Year Final Research Report Summary
Knowledge Discovery from Genome Databases
| Project/Area Number |
12208003
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| Research Category |
Grant-in-Aid for Scientific Research on Priority Areas
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| Allocation Type | Single-year Grants |
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| Review Section |
Biological Sciences
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| Research Institution | University of Tokyo |
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Principal Investigator |
MORISHITA Shinichi University of Tokyo, Professor, 大学院新領域創成科学研究科, 教授 (90292854)
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| Co-Investigator(Kenkyū-buntansha) |
GOTOH Osamu Kyoto University, Professor, 大学院・情報学研究科, 教授 (40142111)
DOI Koichiro University of Tokyo, Research Associate, 大学院情報理工学系研究科, 科学技術振興特任教員 (10345126)
SESE Jun University of Tokyo, Research Associate, 大学院情報理工学系研究科, 科学技術振興特任教員 (40361539)
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| Project Period (FY) |
2000 – 2004
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| Keywords | Bioinformatics / Genome Sequencing / siRNA / Transcription Start Site Analysis / Comparative Genomics / Phenome / Image Processing of Micrographs / 顕微鏡画像解析 |
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| Research Abstract |
The elucidation of genomic sequences is ongoing. We have developed a number of algorithms for processing large-scale genomic sequences efficiently in order for deriving new insights into biological process. The major outcomes of these research activities are summarized as follows:
1. Research and development of designing highly specific genomic PCR primers and its application to the analysis of Chimpanzee Y chromosome.
2. Research and development of designing siRNA sequences to knockdown genes of interest specifically without affecting off-target genes. The results have been available through the WWW at http://designmai.jp/, which has been widely used.
3. Research and development of software programs for analyzing 5'SAGE tag information. Since 5'SAGE tags provide transcription start site information, we utilized 5'SAGE tags to predict gene coding regions in genomic sequences.
4. Research and development of software programs for assembling whole genome shotgun sequence fragments. The software was used to produce draft genome sequences for medaka fish and silkworm.
5. Research and development of efficient algorithms for comparing large-scale genomic sequences.
6. Elucidation of vertebrate genome evolution using the genomes of medaka, Tetraodon, zebrafish, humans, and chicken, which yielded novel scenario of vertebrate genome evolution.
7. Research and development of algorithms for extracting repetitive sequences from a genome. This software is effective in detecting novel repeat sequences, and we have used it to uncover 128 repeat sequences from the medaka genome.
8. Research and development of new data mining algorithm that combines the ideas of clustering and classification., and its application to the analysis of gene expression data.
9. Research and development of novel algorithm for predicting protein coding regions.
10. Research of image processing software for micrographs of fruitfly wings to study genes of controlling cell proliferation.
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[Journal Article] The Genome Sequence of Silkworm, Bombyx mori2004
Author(s)
Kazuei Mita, Masahiro Kasahara, Shin Sasaki, Yukinobu Nagayasu, Tomoyuki Yamada, Hiroyuki Kanamori, Nobukazu Namiki, Masanari Kitagawa, Hidetoshi Yamashita, Yuji Yasukochi, Keiko Kadono-Okuda, KimikoYamamoto, Masahiro Ajimura, Gopalapillai Ravikumar, Michihiko Shimomura, Yoshiaki Nagamura, Tadasu Shin-i, Hiroaki Abe, Toru Shimada, Shinichi Morishita, Takuji Sasaki
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Journal Title
DNA RESEARCH 11
Pages: 27-35
Description
「研究成果報告書概要(和文)」より
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[Journal Article] The Genome Sequence of Silkworm2004
Author(s)
Kazuei Mita, Masahiro Kasahara, Shin Sasaki, Yukinobu Nagayasu, Tomoyuki Yamada, Hiroyuki Kanamori, Nobukazu Namiki, Masanari Kitagawa, Hidetoshi Yamashita, Yuji Yasukochi, Keiko Kadono-Okuda, Kimiko Yamamoto, Masahiro Ajimura, Gopalapillai Ravikumar, Michihiko Shimomura, Yoshiaki Nagamura, Tadasu Shin-i, Hiroaki Abe, Toru Shimada, Shinichi Morishita, Takuji Sasaki.
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Journal Title
Bombyx mori. DNA RESEARCH Vol.11, No.1
Pages: 27-35
Description
「研究成果報告書概要(欧文)」より
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[Journal Article] KDD Cup 2001 Report2002
Author(s)
Jie Cheng, Christos Hatzis, Hisashi Hayashi, Mark-A. Krogel, Shinichi Morishita, David Page, Jun Sese
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Journal Title
ACM SIGKDD Explorations 3
Pages: 47-64
Description
「研究成果報告書概要(和文)」より
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[Journal Article] KDD Cup 2001 Report.2002
Author(s)
Jie Cheng, Christos Hatzis, Hisashi Hayashi, Mark-A. Krogel, Shinichi Morishita, David Page, Jun Sese
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Journal Title
ACM SIGKDD Explorations Volume 3, Issue 2
Pages: 47-64
Description
「研究成果報告書概要(欧文)」より
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