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2009 Fiscal Year Final Research Report

Systems genomics towards system-level understanding of life

Research Project

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Project/Area Number 16063101
Research Category

Grant-in-Aid for Scientific Research on Priority Areas

Allocation TypeSingle-year Grants
Review Section Biological Sciences
Research InstitutionThe University of Tokyo

Principal Investigator

TAKAGI Toshihisa  The University of Tokyo, 大学院・新領域創成科学研究科, 教授 (30110836)

Co-Investigator(Kenkyū-buntansha) ITOH Takashi  東京大学, 大学院・新領域創成科学研究科, 教授 (90201326)
OGASAWARA Naotake  奈良先端科学技術大学院大学, 情報科学研究科, 教授 (10110553)
FUJIYAMA ASAO  国立情報学研究所, 情報学プリンシプル研究系, 教授 (60142311)
TSUJI Shoji  東京大学, 医学部附属病院, 教授 (70150612)
KOHARA Yuji  国立遺伝学研究所, 生物遺伝資源情報総合センター, 教授 (70135292)
SUGANO Sumio  東京大学, 大学院・新領域創成科学研究科, 教授 (60162848)
KUHARA Satoru  九州大学, 大学院・農学研究院, 教授 (00153320)
HAYASHI Tetsuya  宮崎大学, フロンティア科学実験総合センター, 教授 (10173014)
KATOH Kazuto  京都大学, 人文科学研究所, 准教授 (10202011)
Project Period (FY) 2004 – 2009
Keywords生命システム / ゲノム機能解析 / 生命シミュレーション / バイオインフォマティクス / 遺伝子ネットワーク / 表現型解析 / ゲノムオントロジー / システム生物学
Research Abstract

The steering group promoted the cooperation among four different research groups in Systems Genomics, one of the four research areas of the new genome reseach project. We also performed a variety of activities to manage the whole research area(that is, not only Systems Genomics but other three areas; Comparative Genomics, Applied Genomics, and Comprehensive Genomics) organically and smoothly, so that they can promote their research effectively as an entire research area.

  • Research Products

    (37 results)

All 2009 2008 2007 2006 2005 2004 Other

All Journal Article (27 results) (of which Peer Reviewed: 27 results) Presentation (2 results) Book (2 results) Remarks (6 results)

  • [Journal Article] Rapid pathway evolution facilitated by horizontal gene transfers across prokaryotic lineages2009

    • Author(s)
      Iwasaki, W., Takagi, T.
    • Journal Title

      PLoS Genetics 5(3)

      Pages: 1000402

    • Peer Reviewed
  • [Journal Article] The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants2008

    • Author(s)
      Rensing, SA., Lang, D., Zimmer, AD., Terry, A., Salamov, A., Shapiro, H., Nishiyama, T., Perroud, PF., Lindquist, EA., Kamisugi, Y., Tanahashi, T., Sakakibara, K., Fujita, T., Oishi, K.,Shin-I, T., Kuroki, Y., Toyoda, A., Suzuki, Y., Hashimoto, S., Yamaguchi, K., Sugano, S., Kohara, Y., Fujiyama, A., Anterola, A., Aoki, S., Ashton, N., Barbazuk, WB., Barker, E., Bennetzen, JL., Blankenship, R., Cho, SH., Dutcher, SK., Estelle, M., Fawcett, JA., Gundlach, H., Hanada, K., Heyl, A., Hicks, KA., Hughes, J., Lohr, M., Mayer, K., Melkozernov, A., Murata, T., Nelson, DR., Pils, B., Prigge, M., Reiss, B., Renner, T., Rombauts, S., Rushton, PJ., Sanderfoot, A., Schween, G., Shiu, SH., Stueber, K., Theodoulou, FL., Tu, H., Van de Peer Y., Verrier, PJ., Waters, E., Wood, A., Yang, L., Cove, D., Cuming, AC., Hasebe, M., Lucas, S., Mishler, BD., Reski, R., Grigoriev, IV., Quatrano, RS., Boore, JL.
    • Journal Title

      Science 319(5859)

      Pages: 64-69

    • Peer Reviewed
  • [Journal Article] Development of a high-throughput microarray-based resequencing system for neurological disorders and its application to molecular genetics of amyotrophic lateral sclerosis2008

    • Author(s)
      Takahashi, Y., Seki, N., Ishiura, H., Mitsui, J., Matsukawa, T., Kishino, A., Onodera, O., Aoki, M., Shimozawa, N., Murayama, S., Itoyama, Y., Suzuki, Y., Sobue, G., Nishizawa, M., Goto, J., Tsuji, S.
    • Journal Title

      Arch Neurol 65(10)

      Pages: 1326-1332

    • Peer Reviewed
  • [Journal Article] Reconstruction of highly heterogeneous gene-content evolution across the three domains of life2007

    • Author(s)
      Iwasaki, W., Takagi, T.
    • Journal Title

      Bioinformatics 23(13)

      Pages: i230-239

    • Peer Reviewed
  • [Journal Article] The medaka draft genome and insights into vertebrate genome evolution2007

    • Author(s)
      Kasahara, M., Naruse, K., Sasaki, S., Nakatani, Y., Qu, W., Ahsan, B., Yamada, T., Nagayasu, Y., Doi, K., Kasai, Y., Jindo, T., Kobayashi, D., Shimada, A., Toyoda, A., Kuroki, Y., Fujiyama, A., Sasaki, T., Shimizu, A., Asakawa, S., Shimizu, N., Hashimoto, S., Yang, J., Lee, Y., Matsushima, K., Sugano, S., Sakaizumi, M., Narita, T., Ohishi, K., Haga, S., Ohta, F., Nomoto, H., Nogata, K., Morishita, T., Endo, T., Shin-I, T., Takeda, H., Morishita, S., Kohara, Y.
    • Journal Title

      Nature 447(7145)

      Pages: 714-719

    • Peer Reviewed
  • [Journal Article] Retrotransposon silencing by DNA methylation can drive mammalian genomic imprinting2007

    • Author(s)
      Suzuki, S., Ono, R., Narita, T., Pask, AJ., Shaw, G., Wang, C., Kohda, T., Alsop, AE., Marshall, Graves, JA., Kohara, Y., Ishino, F., Renfree, MB., Kaneko-Ishino, T.
    • Journal Title

      PLoS Genet. 3(4)

      Pages: 55

    • Peer Reviewed
  • [Journal Article] The C. elegans CBFbeta homologue BRO-1 interacts with the Runx factor, RNT-1, to promote stem cell proliferation and self-renewal2007

    • Author(s)
      Kagoshima, H., Nimmo, R., Saad, N., Tanaka, J., Miwa, Y., Mitani, S., Kohara, Y., Woollard, A.
    • Journal Title

      Development 134(21)

      Pages: 3905-3915

    • Peer Reviewed
  • [Journal Article] The entire organization of transcription units on the Bacillus subtilis genome2007

    • Author(s)
      Kobayashi, H., Akitomi, J., Fujii, N., Kobayashi, K., Altaf-Ul-Amin, M., Kurokawa, K., Ogasawara, N., Kanaya, S.
    • Journal Title

      BMC Genomics 8

      Pages: 197

    • Peer Reviewed
  • [Journal Article] Distinct class of putative "non-conserved" promoters in humans: comparative studies of alternative promoters of human and mouse genes2007

    • Author(s)
      Tsuritani, K., Irie, T., Yamashita, R., Sakakibara, Y., Wakaguri, H., Kanai, A., Mizushima-Sugano, J., Sugano, S., Nakai, K., Suzuki, Y.
    • Journal Title

      Genome Res. 17(7)

      Pages: 1005-1014

    • Peer Reviewed
  • [Journal Article] Axial patterning in cephalochordates and the evolution of the organizer2007

    • Author(s)
      Yu, JK., Satou, Y., Holland, ND., Shin-I, T., Kohara, Y., Satoh, N., Bronner-Fraser, M., Holland, LZ.
    • Journal Title

      Nature 445(7128)

      Pages: 613-617

    • Peer Reviewed
  • [Journal Article] Gene organization of the liverwort Y chromosome reveals distinct sex chromosome evolution in a haploid system2007

    • Author(s)
      Yamato, KT., Ishizaki, K., Fujisawa, M., Okada, S., Nakayama, S., Fujishita, M., Bando, H., Yodoya, K., Hayashi, K., Bando, T., Hasumi, A., Nishio, T., Sakata, R., Yamamoto, M., Yamaki, A., Kajikawa, M., Yamano, T., Nishide, T., Choi, SH., Shimizu-Ueda, Y., Hanajiri, T., Sakaida, M., Kono, K., Takenaka, M., Yamaoka, S., Kuriyama, C., Kohzu, Y., Nishida, H., Brennicke, A., Shin-I, T., Kohara, Y., Kohchi, T., Fukuzawa, H., Ohyama, K.
    • Journal Title

      Proc. Natl. Acad. Sci. 104(15)

      Pages: 6472-6477

    • Peer Reviewed
  • [Journal Article] a database for comparative study of transcriptomes of parasites defined by full-length cDNAs2007

    • Author(s)
      Watanabe, J., Wakaguri, H., Sasaki, M., Suzuki, Y., Sugano, S.
    • Journal Title

      Nucleic Acids Res. 35

      Pages: 431-438

    • Peer Reviewed
  • [Journal Article] Rate of evolution in brain-expressed genes in humans and other primates2007

    • Author(s)
      Wang, HY., Chien, HC., Osada, N., Hashimoto, K., Sugano, S., Gojobori, T., Chou, CK., Tsai, SF., Wu, CI., Shen, CK.
    • Journal Title

      PLoS Biol. 5(2)

      Pages: 13

    • Peer Reviewed
  • [Journal Article] MetaGene: prokaryotic gene finding from environmental genome shotgun sequences2006

    • Author(s)
      Noguchi, H., Park, J., Takagi, T.
    • Journal Title

      Nucleic Acids Res. 34(19)

      Pages: 5623-5630

    • Peer Reviewed
  • [Journal Article] Human chromosome 11 DNA sequence and analysis including novel gene identification2006

    • Author(s)
      Taylor, TD., Noguchi, H., Totoki, Y., Toyoda, A., Kuroki, Y., Dewar, K., Lloyd,C., Itoh, T., Takeda, T., Kim, DW., She, X., Barlow, KF., Bloom, T., Bruford, E., Chang, JL., Cuomo, CA., Eichler, E., FitzGerald, MG., Jaffe, DB., LaButti, K., Nicol, R., Park, HS., Seaman, C., Sougnez, C., Yang, X., Zimmer, AR., Zody, MC., Birren, BW., Nusbaum, C., Fujiyama, A., Hattori, M., Rogers, J., Lander, ES., Sakaki, Y.
    • Journal Title

      Nature 440(7083)

      Pages: 497-500

    • Peer Reviewed
  • [Journal Article] Bacillus subtilis EzrA and FtsL synergistically regulate FtsZ ring dynamics during cell division2006

    • Author(s)
      Kawai, Y., Ogasawara, N.
    • Journal Title

      Microbiology 152(Pt4)

      Pages: 1129-1141

    • Peer Reviewed
  • [Journal Article] A large-scale full-length cDNA analysis to explore the budding yeast transcriptome2006

    • Author(s)
      Miura, F., Kawaguchi, N., Sese, J., Toyoda, A., Hattori, M., Morishita, S., Ito, T
    • Journal Title

      Proc. Natl. Acad. Sci. 103(47)

      Pages: 17846-17851

    • Peer Reviewed
  • [Journal Article] Comparative analysis of chimpanzee and human Y chromosomes unveils complex evolutionary pathway2006

    • Author(s)
      Kuroki, Y., Toyoda, A., Noguchi, H., Taylor, TD, Itoh, T., Kim, DS, Kim, DW, Choi, SH, Kim, IC, Choi, HH, Kim, YS, Satta, Y, Saitouk N., Yamada, T., Morishita, S., Hattori, M., Sakaki, Y., Park, HS, Fujiyama, A.
    • Journal Title

      Nat. Genet. 38(2)

      Pages: 158-167

    • Peer Reviewed
  • [Journal Article] Functional dissection of YabA, a negative regulator of DNA replication initiation in Bacillus subtilis2006

    • Author(s)
      Noirot-Gros, MF., Velten, M., Yoshimura, M., McGovern, S., Morimoto, T., Ehrlich, SD., Ogasawara, N., Polard, P., Noirot, P.
    • Journal Title

      Proc. Natl. Acad. Sci 103(7)

      Pages: 2368-2373

    • Peer Reviewed
  • [Journal Article] Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes2006

    • Author(s)
      Kimura, K., Wakamatsu, A., Suzuki, Y., Ota, T., Nishikawa, T., Yamashita, R., Yamamoto, J., Sekine, M., Tsuritani, K., Wakaguri, H., Ishii, S., Sugiyama, T., Saito, K., Isono, Y., Irie, R., Kushida, N., Yoneyama, T., Otsuka, R., Kanda, K., Yokoi, T., Kondo, H., Wagatsuma, M., Murakawa, K., Ishida, S., Ishibashi, T., Takahashi-Fujii, A., Tanase, T., Nagai, K., Kikuchi, H., Nakai, K., Isogai, T., Sugano, S.
    • Journal Title

      Genome Res. 16(1)

      Pages: 55-65

    • Peer Reviewed
  • [Journal Article] DNA sequence and analysis of human chromosome 182005

    • Author(s)
      Nusbaum, C., Zody, MC., Borowsky, ML., Kamal, M., Kodira, CD., Taylor, TD., Whittaker, CA., Chang, JL., Cuomo, CA., Dewar, K., FitzGerald, MG., Yang, X., Abouelleil, A., Allen, NR., Anderson, S., Bloom,T., Bugalter, B., Butler, J., Cook, A., DeCaprio, D., Engels, R., Garber, M., Gnirke, A., Hafez, N., Hall, JL., Norman, CH., Itoh, T., Jaffe, DB., Kuroki, Y., Lehoczky, J., Lui, A., Macdonald, P., Mauceli, E., Mikkelsen, TS., Naylor, JW., Nicol, R., Nguyen, C., Noguchi, H., O'Leary, SB., O'Neill, K., Piqani, B., Smith, CL., Talamas, JA., Topham, K., Totoki, Y., Toyoda, A., Wain, HM., Young, SK., Zeng, Q., Zimmer, AR., Fujiyama, A., Hattori, M., Birren, BW., Sakaki, Y., Lander, ES.
    • Journal Title

      Nature 437(7058)

      Pages: 551-555

    • Peer Reviewed
  • [Journal Article] 5'SAGE: 5'-end serial analysis of gene expression database2005

    • Author(s)
      Kasai, Y., Hashimoto, S., Yamada, T., Sese, J., Sugano, S., Matsushima, K., Morishita, S.
    • Journal Title

      Nucleic Acids Res. 33

      Pages: 550-552

    • Peer Reviewed
  • [Journal Article] A novel strategy to design highly specific PCR primers based on the stability and uniqueness of 3'-end subsequences2005

    • Author(s)
      Miura, F., Uematsu, C., Sakaki, Y., Ito, T.
    • Journal Title

      Bioinformatics 21(24)

      Pages: 4363-4370

    • Peer Reviewed
  • [Journal Article] Automatic extraction of gene/protein biological functions from biomedical text2005

    • Author(s)
      Koike, A., Niwa, Y., Takagi, T.
    • Journal Title

      Bioinformatics 21(7)

      Pages: 227-1236

    • Peer Reviewed
  • [Journal Article] A comprehensive analysis of allelic methylation status of CpG islands on human chromosome 21q2004

    • Author(s)
      Yamada, Y., Watanabe, H., Miura, F., Soejima, H., Uchiyama, M., Iwasaka, T., Mukai, T., Sakaki, Y., Ito, T.
    • Journal Title

      Genome Res. 14(2)

      Pages: 247-266

    • Peer Reviewed
  • [Journal Article] 5'-end SAGE for the analysis of transcriptional start sites2004

    • Author(s)
      Hashimoto, S., Suzuki, Y., Kasai, Y., Morohoshi, K., Yamada, T., Sese, J., Morishita, S., Sugano, S., Matsushima, K.
    • Journal Title

      Nature Biotechnology 22(9)

      Pages: 1146-1149

    • Peer Reviewed
  • [Journal Article] DNA sequence and comparative analysis of chimpanzee chromosome 222004

    • Author(s)
      Watanabe, H., Fujiyama, A., Hattori, M., Taylor, TD, Toyoda, A., Kuroki, Y., Noguchi, H., BenKahla, A., Lehrach, H., Sudbrak, R., Kube, M., Taenzer, S., Galgoczy, P., Platzer, M., Scharfe, M., Nordsiek, G., Blocker, H., Hellmann, I., Khaitovich, P., Paabo, S., Reinhardt, R., Zheng, HJ, Zhang, XL, Zhu, GF, Wang, BF, Fu, G., Ren, SX, Zhao, GP, Chen, Z., Lee, YS, Cheong, JE, Choi, SH, Wu, KM, Liu, TT, Hsiao, KJ, Tsai, SF, Kim, CG, Oota, S., Kitano, T., Kohara,Y., Saitou, N., Park, HS, Wang, SY, Yaspo, ML, Sakaki, Y.
    • Journal Title

      Nature 429(6990)

      Pages: 82-388

    • Peer Reviewed
  • [Presentation] Unexpected complexity of the budding yeast transcriptome: Yeast as a potential model organism for ncRNA research2007

    • Author(s)
      Ito, T.
    • Organizer
      The 7th International Workshop on Advanced Genomics
    • Place of Presentation
      Tokyo
    • Year and Date
      2007-11-28
  • [Presentation] Distribution of transcription elongation factor NusA and GreA in Bacillus subtilis.2007

    • Author(s)
      Kusuya, Y.
    • Organizer
      4th Conference on Functional Genomics of Gram-Positive Microorganisms
    • Place of Presentation
      Pisa, Italy
    • Year and Date
      2007-06-25
  • [Book] 実験医学2007

    • Author(s)
      渡邉日出海
    • Total Pages
      6
    • Publisher
      羊土社
  • [Book] 細胞工学別冊比較ゲノム学から読み解く生命システム2007

    • Author(s)
      黒木陽子
    • Total Pages
      7
    • Publisher
      秀潤社
  • [Remarks] 特定領域ゲノム4領域ホームページ

    • URL

      http://www.genome-sci.jp

  • [Remarks] ゲノムひろば

    • URL

      http://hiroba.genome-sci.jp/

  • [Remarks] BioTermNet

    • URL

      http://btn.ontology.ims.u-tokyo.ac.jp/

  • [Remarks] OReFiL

    • URL

      http://orefil.dbcls.jp/

  • [Remarks] 出芽酵母完全長cDNA解析プロジェクトHP

    • URL

      http://itolab.cb.k.u-tokyo.ac.jp/GCap/

  • [Remarks] UT Genome Browser for yeast

    • URL

      http://yeast.utgenome.org/

URL: 

Published: 2011-06-18   Modified: 2018-02-07  

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