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Systems genomics towards system-level understanding of life

Research Project

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
Project Status Completed (Fiscal Year 2009)
Budget Amount *help
¥483,600,000 (Direct Cost: ¥483,600,000)
Fiscal Year 2009: ¥94,500,000 (Direct Cost: ¥94,500,000)
Fiscal Year 2008: ¥94,500,000 (Direct Cost: ¥94,500,000)
Fiscal Year 2007: ¥94,800,000 (Direct Cost: ¥94,800,000)
Fiscal Year 2006: ¥93,700,000 (Direct Cost: ¥93,700,000)
Fiscal Year 2005: ¥102,600,000 (Direct Cost: ¥102,600,000)
Fiscal Year 2004: ¥3,500,000 (Direct Cost: ¥3,500,000)
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.

Report

(7 results)
  • 2009 Annual Research Report   Final Research Report ( PDF )
  • 2008 Annual Research Report
  • 2007 Annual Research Report
  • 2006 Annual Research Report
  • 2005 Annual Research Report
  • 2004 Annual Research Report
  • Research Products

    (170 results)

All 2010 2009 2008 2007 2006 2005 2004 Other

All Journal Article (131 results) (of which Peer Reviewed: 61 results) Presentation (17 results) Book (10 results) Remarks (12 results)

  • [Journal Article] Figure classification in biomedical literature to elucidate disease mechanisms, based on pathways2010

    • Author(s)
      Ishii, N.
    • Journal Title

      Artificial Intelligence in Medicine ((印刷中)掲載確定)

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [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: 1000402-1000402

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Rapid Pathway Evolution Facilitated by Horizontal Gene Transfers across Prokaryotic Lineages2009

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

      PLoS Genetics 5(3)

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Classifying biomedical figures using combination of bag of keypoints and bag of keywords2009

    • Author(s)
      Koike, A.
    • Journal Title

      Proc. of 2nd Int. Workshop on Intell. Inform. in Biol. and Med 1(印刷中)(掲載確定)

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Differential binding profiles of StpA in wild-type and has mutantcells : a comparative analysis of cooperative partners by chromatin immunoprecipitation-microarray analysis2009

    • Author(s)
      Uyar, E.
    • Journal Title

      J Bacteriol 191

      Pages: 2388-2391

    • Related Report
      2008 Annual Research Report
    • 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

    • Related Report
      2009 Final Research Report
    • 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

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Figure Classification in Biomedical Literature towards Figure Mining2008

    • Author(s)
      Ishii, N.
    • Journal Title

      2008 IEEE International Conference on Bioinformatics and Biomedicine

      Pages: 263-269

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The functional analysis of YabA, which interacts with DnaA and regulates initiation of chromosome replication in Bacillus subtils2008

    • Author(s)
      Cho, E.
    • Journal Title

      Genes Genet Sys 83

      Pages: 111-125

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Metabolomics approach for determining growth-specific metabolites based on Fourier transform ion cyclotron resonance mass spectrometry2008

    • Author(s)
      Takahashi, H.
    • Journal Title

      Anal Bioanal Chem 391

      Pages: 2769-2782

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The genome of the moss Physcomitrella patens reveals evolutionary insights into the conquest of land by plants.2008

    • Author(s)
      Rensing, S, A. (Fujiyama, A., Kohara, Y., Sugano, S.)
    • Journal Title

      Science 319(5859)

      Pages: 64-69

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Familial cases presenting very early onset autosomal dominant Alzheimer's disease with I143T in presenilin-1 gene: Implication for genotype-phenotype correlation.2008

    • Author(s)
      Arai, N. (Tsuji, S.)
    • Journal Title

      Neurogenetics (印刷中)

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Development of high-throughput microarray-based resequencing system for neurological disorders and its application to molecular genetics of amyotrophic lateral sclerosis.2008

    • Author(s)
      Takahashi, Y. (Tsuji, S.)
    • Journal Title

      Arch Neurol. (印刷中)

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Total deletion and a missense mutation of ITPR1 in Japanese SCA15 families.2008

    • Author(s)
      Hara, K. (Tsuji, S.)
    • Journal Title

      Neurol. (印刷中)

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Discrimination between stable and dynamic components of proteincomplexes by means of quantitative proteomics.2008

    • Author(s)
      Kito, K. (Ito, T.)
    • Journal Title

      Proteomics (印刷中)

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] DBTSS:database of transcription start sites, progress report 2008.2008

    • Author(s)
      Wakaguri, H. (Sugano, S.)
    • Journal Title

      Nucleic Acids Res. 36

      Pages: 97-100

    • Related Report
      2007 Annual Research Report
    • 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)

    • Related Report
      2009 Final Research Report
    • 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

    • Related Report
      2009 Final Research Report
    • 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: 55-55

    • Related Report
      2009 Final Research Report
    • 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

    • Related Report
      2009 Final Research Report
    • 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: 197-197

    • Related Report
      2009 Final Research Report
    • 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

    • Related Report
      2009 Final Research Report
    • 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

    • Related Report
      2009 Final Research Report
    • 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

    • Related Report
      2009 Final Research Report
    • 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

    • Related Report
      2009 Final Research Report
    • 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: 13-13

    • Related Report
      2009 Final Research Report
    • 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: 230-239

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] OReFiL: an online resource finder for life sciences2007

    • Author(s)
      Yamamoto, Y. (Takagi, T.)
    • Journal Title

      BMC Bioinformatics 8

      Pages: 287-287

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes2007

    • Author(s)
      Kurokawa, K. (Takagi, T.)
    • Journal Title

      DNA Research 14(4)

      Pages: 169-181

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Intrinsic promoter activities of primary DNA sequences in the human genome2007

    • Author(s)
      Sakakibara, Y. (Takagi, T.)
    • Journal Title

      DNA Research 14(2)

      Pages: 71-77

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Biomedical knowledge navigation by literature clustering2007

    • Author(s)
      Yamamoto, Y. (Takagi, T.)
    • Journal Title

      Journal of Biomedical Informatics 40(2)

      Pages: 114-130

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Knowledge discovery based on an implicit and explicit conceptual network2007

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

      Journal of the American Society for Information Science and Technology 58(1)

      Pages: 51-65

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The medaka draft genome and insights into vertebrate genome evolution.2007

    • Author(s)
      Kasahara, M. (Fujiyama, A., Kohara, Y.)
    • Journal Title

      Nature 447

      Pages: 714-719

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] UTGB/medaka: genomic resource database for medaka biology.2007

    • Author(s)
      Ahsan, B. (Fujiyama, A.)
    • Journal Title

      Nucleic Acids Res. (印刷中)

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Sox9b/sox9a2-EGFP transgenic medaka reveals the morphological reorganization of the gonads and a common precursor of both the female and male supporting cells.2007

    • Author(s)
      Nakamura, S. (Fujiyama, A.)
    • Journal Title

      Mol Reprod Dev. (印刷中)

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Asian Origin for the Worldwide-Spread Mutational Event in Machado-Joseph Disease.2007

    • Author(s)
      Martins, S. (Tsuji, S.)
    • Journal Title

      Arch Neurol. Oct;64(10)

      Pages: 1502-1508

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Retrotransposon Silencing by DNA Methylation can Drive Mammalian Genomic Imprinting.2007

    • Author(s)
      Suzuki, S. (Kohara, Y.)
    • Journal Title

      PLos Genetics 3,No.4

      Pages: 55-55

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] RUNX regulates stem cell proliferation and differentiation: Insights from studies of C. elegans.2007

    • Author(s)
      Kagoshima, H. (Kohara, Y.)
    • Journal Title

      J Cell Biochem. Apr 1;100(5)

      Pages: 1119-1130

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The C. elegans CBFb homologue BRO-1 interacts with the Runx factor, RNT-1, to promote stem cell proliferation and self-renewal.2007

    • Author(s)
      Kagoshima, H.(Kohara, Y.)
    • Journal Title

      Development 134

      Pages: 3905-3915

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Proteomic analysis of in vivo 14-3-3 interactions in the yeast Saccharomyces cerevisiae.2007

    • Author(s)
      Kakiuchi, K. (Ito, T.)
    • Journal Title

      Biochemistry 46

      Pages: 7781-7792

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structure and function of the PB1 domain, a protein interactionmodule conserved in animals, fungi, amoebas, and plants.2007

    • Author(s)
      Sumimoto, H.(Ito, T.)
    • Journal Title

      Science's STKE 007

      Pages: 6-6

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Distribution of stable DnaA-binding sites on the Bacillus subtilisgenome Detected using a modified ChIP-chip method.2007

    • Author(s)
      Ishikawa, S. (Ogasawara, N.)
    • Journal Title

      DNA Res. 14

      Pages: 155-168

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The entire organization of transcription units on the Bacillus subtilis genome.2007

    • Author(s)
      Kobayashi, H. (Ogasawara, N.)
    • Journal Title

      BMC Genomics 8

      Pages: 197-197

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Isolation and characterization of a dominant negative mutant of Bacillus subtilis GTP-binding Protein, YlqF, essential for biogenesis and maintenance of the 50S ribosomal subunit.2007

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

      J Biol Chem. 282

      Pages: 25270-25277

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Functional gene screening system identified TRPV4 as a regulator of chondrogenic differentiation.2007

    • Author(s)
      Muramatsu, S. (Sugano, S.)
    • Journal Title

      J Biol Chem. 282

      Pages: 32158-32167

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Distinct class of putative "non-conserved"promoters in humans: Comparative studies of alternative promoters of human and mouse genes.2007

    • Author(s)
      Tsuritani, K. (Sugano, S.)
    • Journal Title

      Genome Res. 17

      Pages: 1005-1014

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Intrinsic Promoter Activities of Primary DNA Sequences in the Human Genome.2007

    • Author(s)
      Sakakibara, Y.(Sugano, S.)
    • Journal Title

      DNA Res. 14

      Pages: 71-77

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Knowledge discovery based on an implicit and explicit conceptual network.2007

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

      Journal of the American Society for Information Sciences 58(1)

      Pages: 51-65

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Biomedical knowledge navigation by literature clustering.2007

    • Author(s)
      Yamamoto, Y., (Takagi, T.)
    • Journal Title

      Journal of Biomedical Informatics 40(2)

      Pages: 114-130

    • Related Report
      2006 Annual Research Report
  • [Journal Article] The ELT-2 GATA-Factor and the Global Regulation of Transcription in the C. elegans Intestine.2007

    • Author(s)
      J.D.McGhee., (Kohara, Y.)
    • Journal Title

      Developmental Biology 302

      Pages: 627-645

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Axial patterning in cephalochordates and the evolution of the organizer.2007

    • Author(s)
      Yu, J-K., (Kohara, Y.)
    • Journal Title

      Nature 445

      Pages: 613-617

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Gene organization of the liverwort Y chromosome reveals distinct sex chromosome evolution in a haploid system.2007

    • Author(s)
      Yamato, K., (Kohara, Y.)
    • Journal Title

      Proceedings of the National Academy of Sciences 104

      Pages: 6472-6477

    • Related Report
      2006 Annual Research Report
  • [Journal Article] RUNX regulates stem cell proliferation and differentiation : Insights from studies of C. elegans.2007

    • Author(s)
      Kagoshima H., (Kohara, Y.)
    • Journal Title

      Journal of Cellular Biochemistry 100(5)

      Pages: 1119-1130

    • Related Report
      2006 Annual Research Report
  • [Journal Article] SAGE analysis of early oogenesis in the silkworm, Bombyxmori.2007

    • Author(s)
      Funaguma S., (Sugano, S.)
    • Journal Title

      Insect Biochemistry and Molecular Biology 37(2)

      Pages: 147-154

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Comparasite : a database for comparative study of transcriptomes of parasites defined by full-length cDNAs.2007

    • Author(s)
      Watanabe J., (Sugano, S.)
    • Journal Title

      Nucleic Acids Research 35:D

      Pages: 431-438

    • Related Report
      2006 Annual Research Report
  • [Journal Article] H-DBAS : Alternative splicing database of completely sequenced and manually annotated full-length cDNAs based on H-Invitational.2007

    • Author(s)
      Takeda, JI., (Sugano, S.)
    • Journal Title

      Nucleic Acids Research 35(1):D

      Pages: 104-109

    • Related Report
      2006 Annual Research Report
  • [Journal Article] A synthetic protein approach toward accurate mass spectrometric quantification of component stoichiometry of multiprotein complexes.2007

    • Author(s)
      Kito, K., (Ito, T.)
    • Journal Title

      Journal of Proteome Research 6

      Pages: 792-800

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Methods for protein-protein interaction analysis. in Introduction to Systems Biology (Ed. Choi, S.).2007

    • Author(s)
      Kito, K., (Ito, T.)
    • Journal Title

      Humana Press

      Pages: 160-182

    • Related Report
      2006 Annual Research Report
  • [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

    • Related Report
      2009 Final Research Report
    • 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

    • Related Report
      2009 Final Research Report
    • 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

    • Related Report
      2009 Final Research Report
    • 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

    • Related Report
      2009 Final Research Report
    • 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

    • Related Report
      2009 Final Research Report
    • 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

    • Related Report
      2009 Final Research Report
    • 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

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] MetaGene : prokaryotic gene finding from environmental genome shotgun sequences.2006

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

      Nucleic Acids Research 34(19)

      Pages: 5623-5630

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Improving the performance of an SVM-based method for predicting protein-protein interactions.2006

    • Author(s)
      Dohkan, S., (Takagi, T.)
    • Journal Title

      In Silico Biology 6

      Pages: 48-48

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Human chromosome 11 DNA sequence and analysis including novel gene identification.2006

    • Author(s)
      Taylor, T., (Fujiyama, A.)
    • Journal Title

      Nature 440

      Pages: 497-500

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Has the chimpanzee Y chromosome been sequenced?2006

    • Author(s)
      Kuroki, Y., (Fujiyama, A.)
    • Journal Title

      Nature Genetics 38

      Pages: 854-855

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Neuronal atrophy and synaptic alteration in a mouse model of dentatorubral-pallidoluysian atrophy.2006

    • Author(s)
      Sakai, K., (Tsuij, S.)
    • Journal Title

      Brain 129(PT 9)

      Pages: 2353-2362

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Functional dissection of YabA, a negative regulator of DNA replication initiation in Bacillus subtilis.2006

    • Author(s)
      Noirot-Gros, M., (Ogasawara, N.)
    • Journal Title

      Proceedings of the National Academy of Sciences 103

      Pages: 2368-2378

    • Related Report
      2006 Annual Research Report
  • [Journal Article] The GTP-binding Protein YlqF Participates in the Late Step of 50 S Ribosomal Subunit Assembly in Bacillus subtilis.2006

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

      Journal of Biological Chemistry 281

      Pages: 8110-8117

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Bacillus subtilis EzrA and FtsL synergistically regulate FtsZ ring dynamics during cell division.2006

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

      Microbiology 152

      Pages: 1129-1141

    • Related Report
      2006 Annual Research Report
  • [Journal Article] A new FtsZ-interacting protein, YlmF, complements the activity of FtsA during progression of cell division in Bacillus subtilis.2006

    • Author(s)
      Ishikawa, S., (Ogasawara, N.)
    • Journal Title

      Molecular Microbiology 60

      Pages: 1364-1380

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Escherichia coli histone-like protein H-NS preferentially binds to horizontally acquired DNA in association with RNA polymerase.2006

    • Author(s)
      Oshima, T., (Ogasawara, N.)
    • Journal Title

      DNA Research 13

      Pages: 141-153

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Transcriptome analyses of human genes and applications for proteome analyses.2006

    • Author(s)
      Suzuki Y., (Sugano, S.)
    • Journal Title

      Current Protein and Peptide Science 7

      Pages: 147-163

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Relationship between retinoic acid receptor alpha gene expression and growth-inhibitory effect of all-trans retinoic acid on canine tumor cells.2006

    • Author(s)
      Miyajima N., (Sugano, S.)
    • Journal Title

      J Vet Intern Med 20

      Pages: 348-354

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Diverse DNA methylation statuses at alternative promoters of human genes in various tissues.2006

    • Author(s)
      Cheong, J., (Sugano, S.)
    • Journal Title

      DNA Research 13

      Pages: 155-167

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs.2006

    • Author(s)
      Takeda, J., (Sugano, S.)
    • Journal Title

      Nucleic Acids Research 34

      Pages: 3917-3928

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Common inheritance of chromosome Ia associated with clonal expansion of Toxoplasma gondii.2006

    • Author(s)
      Khan, A., (Sugano, S.)
    • Journal Title

      Genome Research 16

      Pages: 1119-1125

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Activation of genes for growth factor and cytokine pathways late in chondrogenic differentiation of ATDC5 cells.2006

    • Author(s)
      Osawa, A., (Sugano, S.)
    • Journal Title

      Genomics 88(1)

      Pages: 52-64

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Deletion of angiotensin-converting enzyme 2 accelerates pressure overload-induced cardiac dysfunction by increasing local angiotensin II.2006

    • Author(s)
      Yamamoto, K., (Sugano, S.)
    • Journal Title

      Hypertension 47

      Pages: 718-726

    • Related Report
      2006 Annual Research Report
  • [Journal Article] A large-scale full-length cDNA analysis to explore the budding yeast transcriptome.2006

    • Author(s)
      Miura, F., (Ito, T.)
    • Journal Title

      Proceedings of the National Academy of Sciences USA 103

      Pages: 17846-17851

    • Related Report
      2006 Annual Research Report
  • [Journal Article] A novel Cdc42-interacting domain of the yeast polarity establishment protein Bem1 : implications for modulation of mating pheromone signaling.2006

    • Author(s)
      Yamaguchi, Y., (Ito, T.)
    • Journal Title

      Journal of Biological Chemistry 282

      Pages: 29-38

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Event Ontology : A Pathway-Centric Ontology for Biological Processes.2006

    • Author(s)
      Kushida, T.
    • Journal Title

      Pacific Symposium on Biocomputing 11

      Pages: 152-163

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Comparative analysis of chimpanzee and human Y chromosomes unveils complex evolutionary pathway.2006

    • Author(s)
      Kuroki, Y.
    • Journal Title

      Nature Genetics 38

      Pages: 158-167

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Functional dissection of YabA, a negative regulator of DNA replication initiation in Bacillus subtilis.2006

    • Author(s)
      Noirot-Gros, M.
    • Journal Title

      Proc Natl Acad Sci USA 103

      Pages: 2368-2373

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Diversification of transcriptional modulation : Large-scale identification and characterization of putative alternative promoters of human genes.2006

    • Author(s)
      Kimura., K.
    • Journal Title

      Genome Res 16

      Pages: 55-65

    • Related Report
      2005 Annual Research Report
  • [Journal Article] DBTSS : Database of Human Transcription Start Sites, Progress Report 2006.2006

    • Author(s)
      Yamashita, R
    • Journal Title

      Nucl.Acids Res 34

    • Related Report
      2005 Annual Research Report
  • [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

    • Related Report
      2009 Final Research Report
    • 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

    • Related Report
      2009 Final Research Report
    • 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

    • Related Report
      2009 Final Research Report
    • 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

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] ALICE : An Algorithm to Extract Abbreviations from MEDLINE.2005

    • Author(s)
      Ao, H.
    • Journal Title

      J Am Med Inform Assoc 12(5)

      Pages: 576-586

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Reassembly and interfacing neural models registered on biological model databases.2005

    • Author(s)
      Ohtake, M.
    • Journal Title

      Genome Informatics Workshop

      Pages: 76-85

    • Related Report
      2005 Annual Research Report
  • [Journal Article] A Sentence Classification System for Multi-document Summarization in the Biomedical Domain.2005

    • Author(s)
      Yamamoto, Y.
    • Journal Title

      In the Proc.Of International Workshop on Biomedical Data Engineering -

      Pages: 90-95

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Automatic Extraction of Gene/protein Biological Functions from Biomedical Text.2005

    • Author(s)
      Koike, A.
    • Journal Title

      Bioinformatics 21

      Pages: 1227-1236

    • Related Report
      2005 Annual Research Report
  • [Journal Article] DNA sequence and analysis of human chromosome 18.2005

    • Author(s)
      Nusbaum, C.
    • Journal Title

      Nature 437

      Pages: 551-555

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Hagfish leukocytes express a paired receptor family with a variable domain resembling those of antigen receptors.2005

    • Author(s)
      Suzuki, T.
    • Journal Title

      J.Immunol 174

      Pages: 2885-2891

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Interference of CREB-dependent transcriptional activation by expanded polyglutamine stretches-Augmentation of transcriptional activation as a potential therapeutic strategy for polyglutamine diseases.2005

    • Author(s)
      Shimohata, M.
    • Journal Title

      J Neurochem 93

      Pages: 654-663

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Polyglutamine represses cAMP-responsive-element-mediated transcription without aggregate formation.2005

    • Author(s)
      Takahashi, T
    • Journal Title

      Neuroreport 16(3)

      Pages: 295-299

    • Related Report
      2005 Annual Research Report
  • [Journal Article] The C. elegans RUNX transcription factor MAB-2/RNT-1 is required for asymmetrical cell division of the T blast cell.2005

    • Author(s)
      KAGOSHIMA, H.
    • Journal Title

      Developmental Biology 287

      Pages: 262-273

    • Related Report
      2005 Annual Research Report
  • [Journal Article] nfi-1 affects behavior and life-span in C. elegans but is not essential for-DNA replication or survival.2005

    • Author(s)
      Lazakovitch, E.
    • Journal Title

      BMC Developmental Biology 5

      Pages: 24-24

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Synergistic regulation of competence development in Bacillus subtilis by two Rap-Phr systems.2005

    • Author(s)
      Bongiorni, C.
    • Journal Title

      J Bacteriol 187

      Pages: 4353-4361

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Bacillus subtlis YabA is involved in determining the timing and synchrony of replication initiation.2005

    • Author(s)
      Hayashi, M.
    • Journal Title

      FEMS Microbiol Lett 247

      Pages: 73-79

    • Related Report
      2005 Annual Research Report
  • [Journal Article] 5'SAGE :5'-end Serial Analysis of Gene Expression database.2005

    • Author(s)
      Kasai, Y.
    • Journal Title

      Nucleic Acids Research 33

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Substitution Rate and Structural Divergence of 5'UTR Evolution : Comparative Analysis Between Human and Cynomolgus Monkey cDNAs.2005

    • Author(s)
      Osada, N.
    • Journal Title

      Mol Biol Evol 22

      Pages: 1976-1982

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Identification and characterization of a canine highly similar to retinoic acid receptor alpha.2005

    • Author(s)
      Miyajima, N.
    • Journal Title

      DNA Seq 16

      Pages: 7-15

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Cyclopedic protein expression analysis of cultured canine mammary gland adeno carcinoma cells from six tumours.2005

    • Author(s)
      Nakagawa, T.
    • Journal Title

      Res Vet Sci 80

      Pages: 317-323

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Cell surface labeling and mass spectrometry reveal diversity of cell-surface markers and signaling molecules expressed in undifferentiated mouse embryonic stem cells.2005

    • Author(s)
      Nunomura, K.
    • Journal Title

      Mol Cell Proteomics 4

      Pages: 1968-1976

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Signal Sequence and Keyword Trap in silico for Selection of Full-Length Human cDNAs Encoding Secretion or Membrane Proteins from Oligo-Capped cDNA Libraries.2005

    • Author(s)
      Otsuki, T.
    • Journal Title

      DNA Res 12

      Pages: 117-126

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Centaurin-alpha 1 is a PI3K dependent activator of ERK1/2 map kinases.2005

    • Author(s)
      Hayashi H
    • Journal Title

      J Biol Chem 281

      Pages: 1332-1337

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue specificity.2005

    • Author(s)
      Yamashita, R
    • Journal Title

      Gene 350

      Pages: 129-136

    • Related Report
      2005 Annual Research Report
  • [Journal Article] A novel strategy to design highly specific PCR primers based on the stability and uniqueness of 3'-end subsequences.2005

    • Author(s)
      Miura, F.
    • Journal Title

      Bioinformatics 21(24)

      Pages: 4363-4370

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Automatic extraction of gene/protein biological functions from Biomedical text.2005

    • Author(s)
      Koike, A.
    • Journal Title

      Bioinformatics (印刷中)

    • Related Report
      2004 Annual Research Report
  • [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

    • Related Report
      2009 Final Research Report
    • 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

    • Related Report
      2009 Final Research Report
    • 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

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] SPI : A tool for incorporating gene expression data into a four-dimensional database of C.elegans embryogenesis.2004

    • Author(s)
      Yohei Minakuchi
    • Journal Title

      Bioinformatics 20

      Pages: 1097-1109

    • Related Report
      2004 Annual Research Report
  • [Journal Article] A comprehensive analysis of allelic methylation status of CpG is lands on human chromosome 21q.2004

    • Author(s)
      Yamada, Y.
    • Journal Title

      Genome Research 14

      Pages: 247-266

    • Related Report
      2004 Annual Research Report
  • [Journal Article] 5'-end SAGE for the analysis of transcriptional start sites.2004

    • Author(s)
      Hashimoto, SI.
    • Journal Title

      Nature Biotechnology 22

      Pages: 1146-1149

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Systematic analysis of SigD-regulated genes in Bacillus subtilis by DNA microarray and Northern blotting analyses.2004

    • Author(s)
      Serizawa, M.
    • Journal Title

      Gene 329

      Pages: 125-136

    • Related Report
      2004 Annual Research Report
  • [Journal Article] DNA sequence and comparative analysis of chimpanzee chromosome 22.2004

    • Author(s)
      H.Watanabe
    • Journal Title

      Nature 429

      Pages: 382-388

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Intrinsic promoter activities of primary DNA sequences in the human genome.

    • Author(s)
      Sakakibara, Y., (Takagi, T.)
    • Journal Title

      DNA Research (印刷中)

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Sox9b/sox9a2-EGFP transgenic medaka reveals the morphological reorganization of the gonads and a common precursor of both the female and male supporting cells.

    • Author(s)
      Nakamura, S., (Fujiyama, A.)
    • Journal Title

      Molecular Reproduction and Development (印刷中)

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Multiplex families with multiple system atrophy Arch.

    • Author(s)
      Hara, K., (Tsuij, S.)
    • Journal Title

      The Journal of Comparative Neurology (印刷中)

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Rate of Evolution in Brain-Expressed Genes in Humans and Other Primates.

    • Author(s)
      Wang, HY., (Sugano, S.)
    • Journal Title

      PLoS Biology (印刷中)

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Knowledge discovery based on an implicit and explicit conceptual network.

    • Author(s)
      Koike, A.
    • Journal Title

      J Am Soc Info Sci Tech (印刷中)

    • Related Report
      2005 Annual Research Report
  • [Journal Article] The GTP-binding protein, YlgF, participates in the late step of 50S ribosomal subunit assembly in Bacillus subtilis.

    • Author(s)
      Matsuo, Y.
    • Journal Title

      J Biol Chem (印刷中)

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Bacillus subtilis EzrA abd FtsL synergistically regulate FtsZ ring dynamics during cell division.

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

      Microbiol (印刷中)

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Transcriptional activators in yeast.

    • Author(s)
      Titz, B.
    • Journal Title

      Nucleic Acids Res (印刷中)

    • Related Report
      2005 Annual Research Report
  • [Presentation] Biomedical figure search using combination of bag of keypoints and bag of words2009

    • Author(s)
      Koike, A.
    • Organizer
      The 20th International Conference on Genome Informatics
    • Place of Presentation
      パシフィコ横浜(神奈川)
    • Year and Date
      2009-12-15
    • Related Report
      2009 Annual Research Report
  • [Presentation] Classification of neuroimaging figures toward automatic figure annotation system2009

    • Author(s)
      Ishii, N.
    • Organizer
      The 20th International Conference on Genome Informatics
    • Place of Presentation
      パシフィコ横浜(神奈川)
    • Year and Date
      2009-12-14
    • Related Report
      2009 Annual Research Report
  • [Presentation] 生命科学研究者のための統合文献情報管理システム2009

    • Author(s)
      岩崎渉
    • Organizer
      第32回日本分子生物学会
    • Place of Presentation
      パシフィコ横浜(神奈川)
    • Year and Date
      2009-12-10
    • Related Report
      2009 Annual Research Report
  • [Presentation] 既知複合体立体構造データベースを利用したタンパク質一リガンド相互作用パターンの解析と結合様式予測手法の開発2009

    • Author(s)
      笠原浩太
    • Organizer
      日本薬学会第129年会
    • Place of Presentation
      京都
    • Year and Date
      2009-03-27
    • Related Report
      2008 Annual Research Report
  • [Presentation] 枯草菌染色体のDnaA結合配列の機能2009

    • Author(s)
      奥村元
    • Organizer
      第3回日本ゲノム微生物学会年会
    • Year and Date
      2009-03-07
    • Related Report
      2008 Annual Research Report
  • [Presentation] Control of RNA polymerase dynamics by GreA in B. subtilis2009

    • Author(s)
      楠屋陽子
    • Organizer
      第3回日本ゲノム微生物学会年会
    • Place of Presentation
      東京
    • Year and Date
      2009-03-06
    • Related Report
      2008 Annual Research Report
  • [Presentation] Effective multi-scale graph navigation system powered by fast and biologically meaningful hierarchical clustering2009

    • Author(s)
      Praneenararat, T.
    • Organizer
      The 20th International Conference on Genome Informatics
    • Place of Presentation
      パシフィコ横浜(神奈川)
    • Related Report
      2009 Annual Research Report
  • [Presentation] 既知複合体立体構造の知識に基づいたタンパク質-リガンド結合様式予測手法の開発2008

    • Author(s)
      笠原浩太
    • Organizer
      第31回情報化学討論会
    • Place of Presentation
      東京
    • Year and Date
      2008-11-13
    • Related Report
      2008 Annual Research Report
  • [Presentation] Distribution of RNA polymerase on the Bacillus subtilis genome2008

    • Author(s)
      Ogasawara, N.
    • Organizer
      GENOMES 2008, Functional Genomics of Microorganisms
    • Place of Presentation
      Paris, France
    • Year and Date
      2008-04-09
    • Related Report
      2008 Annual Research Report
  • [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
    • Related Report
      2009 Final Research Report
  • [Presentation] Unexpected complexity of the budding yeast transcriptome: Yeast as a potential model organism for ncRNA research.2007

    • Author(s)
      Ito, T.
    • Organizer
      The 7th International Workshop on Advanced Genomics
    • Place of Presentation
      Tokyo
    • Year and Date
      2007-11-28
    • Related Report
      2007 Annual Research Report
  • [Presentation] デュアルベイト逆2ハイブリッドシステムとPCS-MSによるタンパク質間相互作用の機能解析2007

    • Author(s)
      伊藤隆司
    • Organizer
      日本ヒトプロテオーム機構第5回大会
    • Place of Presentation
      東京
    • Year and Date
      2007-07-30
    • Related Report
      2007 Annual Research Report
  • [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
    • Related Report
      2009 Final Research Report
  • [Presentation] Distribution of Transcription Elongatio Factor NusA and GreA in Bacillus subtilis.2007

    • Author(s)
      Kusuya, Y.(Ogasawara, N.)
    • Organizer
      4th Conference on Functional. Genomics of Gram-Positive Microorganisms
    • Place of Presentation
      Pisa, Italy.
    • Year and Date
      2007-06-25
    • Related Report
      2007 Annual Research Report
  • [Presentation] Regulation of initiation of replication of the Bacillus subtilis genomeby DnaA and YabA.2007

    • Author(s)
      Cho, E.(Ogasawara, N.)
    • Organizer
      4th Conference on Functional Genomics of Gram-Positive Microorganisms
    • Place of Presentation
      Pisa, Italy.
    • Year and Date
      2007-06-25
    • Related Report
      2007 Annual Research Report
  • [Presentation] In vivo dynamics of the Bacillus subtilis RNA polymerase on the Genome.2007

    • Author(s)
      Ishikawa, S.(Ogasawara, N.)
    • Organizer
      4th Conference on Functional Genomics of Gram-Positive Microorganisms
    • Place of Presentation
      Pisa, Italy.
    • Year and Date
      2007-06-24
    • Related Report
      2007 Annual Research Report
  • [Presentation] Y2H and MS approaches for annotating protein interactions and modifications, Interactome Mapping Project for Human and Model Organisms.2007

    • Author(s)
      Ito, T.
    • Organizer
      Cold Spring Harbor
    • Place of Presentation
      NY, USA
    • Year and Date
      2007-04-24
    • Related Report
      2007 Annual Research Report
  • [Book] 医学生物学分野におけるシソーラスとテキストマイニング技術の開発(実験医学増刊号Vol.26, No.7)2008

    • Author(s)
      小池麻子(高木利久)
    • Total Pages
      6
    • Publisher
      羊土社
    • Related Report
      2007 Annual Research Report
  • [Book] 実験医学2007

    • Author(s)
      渡邉日出海
    • Total Pages
      6
    • Publisher
      羊土社
    • Related Report
      2009 Final Research Report
  • [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
    • Related Report
      2009 Final Research Report
  • [Book] The Five Year Project for Genome Research in Japan: Genome Science 2004-2009(special issue, Bioinformatics in Japnan, (2007)11, 1030-1032)2007

    • Author(s)
      Fujiyama, A
    • Total Pages
      3
    • Publisher
      Asia Pacific Biotech News
    • Related Report
      2007 Annual Research Report
  • [Book] ヒトへの進化のゲノム基盤、ヒト・霊長類の比較ゲノム解析(「実験医学」25, 226-231)2007

    • Author(s)
      渡邉日出海(藤山秋佐夫)
    • Total Pages
      6
    • Publisher
      羊土社
    • Related Report
      2007 Annual Research Report
  • [Book] ヒトーチンプY染色体の常染色体よりも早い進化male-driven evolutionの可能性(「遺伝 別冊」No.20, 138-143)2007

    • Author(s)
      黒木陽子(藤山秋佐夫)
    • Total Pages
      6
    • Publisher
      裳華房
    • Related Report
      2007 Annual Research Report
  • [Book] ヒトと霊長類の比較ゲノム:近縁種との比較から見るヒトゲノムの特徴(「細胞工学別冊 比較ゲノム学から読み解く生命システム」pp43-49)2007

    • Author(s)
      黒木陽子(藤山秋佐夫)
    • Total Pages
      7
    • Publisher
      秀潤社
    • Related Report
      2007 Annual Research Report
  • [Book] Chapter 9 Methods for protein-protein interaction analysis (「Introduction to Systems Biology」542, pp160-182)2007

    • Author(s)
      Kito, K.(Ito, T)
    • Total Pages
      23
    • Publisher
      Humana Press
    • Related Report
      2007 Annual Research Report
  • [Book] Genome Informatics 2005.2005

    • Author(s)
      Edited by Takagi, T.et al.
    • Total Pages
      293
    • Publisher
      UNIVERSAL ACADEMY PRESS, INC
    • Related Report
      2005 Annual Research Report
  • [Book] 東京大学バイオインフォマティクス集中講義2004

    • Author(s)
      高木利久(監修)
    • Total Pages
      141
    • Publisher
      株式会社羊土社
    • Related Report
      2004 Annual Research Report
  • [Remarks] 特定領域ゲノム4領域ホームページ

    • URL

      http://www.genome-sci.jp

    • Related Report
      2009 Final Research Report
  • [Remarks] ゲノムひろば

    • URL

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

    • Related Report
      2009 Final Research Report
  • [Remarks] BioTermNet

    • URL

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

    • Related Report
      2009 Final Research Report
  • [Remarks] OReFiL

    • URL

      http://orefil.dbcls.jp/

    • Related Report
      2009 Final Research Report
  • [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/

    • Related Report
      2009 Final Research Report
  • [Remarks] UT Genome Browser for yeast

    • URL

      http://yeast.utgenome.org/

    • Related Report
      2009 Final Research Report
  • [Remarks] 特定領域ゲノム4領域ホームページ

    • URL

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

    • Related Report
      2009 Annual Research Report
  • [Remarks] ゲノムひろば

    • URL

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

    • Related Report
      2009 Annual Research Report
  • [Remarks] Takagi, T. BioTermNet:明示的/潜在的な概念間の関係性のネットワークの可視化

    • URL

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

    • Related Report
      2007 Annual Research Report
  • [Remarks] Takagi, T. OReFiL:インターネット上のデータベースやツールなどの検索システム

    • URL

      http://orefil.dbcls.jp/

    • Related Report
      2007 Annual Research Report
  • [Remarks] Ito, T.出芽酵母完全長cDNA解析プロジェクトホームページ

    • URL

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

    • Related Report
      2007 Annual Research Report
  • [Remarks] Ito, T. UT Genome Browser for yeast

    • URL

      http://yeast.utgenome.org/

    • Related Report
      2007 Annual Research Report

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Published: 2004-04-01   Modified: 2018-03-28  

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