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Yamashita Riu  山下 理宇

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YAMASHITA Riu  山下 理宇

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Researcher Number 10401259
Other IDs
Affiliation (Current) 2020: 国立研究開発法人国立がん研究センター, 先端医療開発センター, ユニット長
Affiliation (based on the past Project Information) *help 2013 – 2017: 東北大学, 東北メディカル・メガバンク機構, 准教授
2009 – 2010: The University of Tokyo, 医科学研究所, 特任助教
2006 – 2007: 東京大学, 医科学研究所, 特任助教
2006: University of Tokyo, Institute of Medical Science, Researcher
2006: 東京大学, 医科学研究所, 特任助手
2006: The University of Tokyo, Institute of Medical Science, Human Genome Center, Assistant Professor
Review Section/Research Field
Principal Investigator
Bioinformatics/Life informatics / ゲノム情報科学 / Life / Health / Medical informatics
Except Principal Investigator
基礎ゲノム科学 / Genome biology
Keywords
Principal Investigator
データベース / 転写制御 / 転写開始点 / プロモータ / DBTSS / 選択的プロモータ / バイオインフォマティックス / シスエレメント / 発現解析 / ゲノム … More / 次世代シークエンサー / 大規模データ / 比較ゲノム / トランスクリプトーム / 翻訳制御 / non-coding RNA / 翻訳調節 / short peptide / 翻訳 / Ribosomal profiling / モチーフ / 国際情報交換 … More
Except Principal Investigator
寄生原虫 / マラリア / トキソプラズマ / 比較ゲノム / 発現遺伝子 / 発現制御 / 全長cDNA / 遺伝子発現制御 / 全長cDNAライブラリ / マラリア原虫 / トキソプラズマ原虫 / parasitic protozoa / malaria / toxoplasma / comparative genomics / gene expression / expression mechanism / ホヤ / プロモーター / マルコフ連鎖 / モデル化 / ハイブリダイゼーション / 筋肉特異的発現 / カタユウレイボヤ / バイオインフォマティクス / モチーフ / 組織特異的発現 / 組織特異的プロモーター / モチーフ抽出 / データベース / シスエレメント / ゲノム配列解析 / ascidians / promoters / Markov chain / model building / in situ hybridization / muscle-specific expression / 多層オーミクス解析 / シングルセル解析 / 単一細胞解析 / 次世代シークエンス / 多層オーミクス / 細胞多様性 / ゲノム / がん多様性 / マルチオミクス解析 / ガン細胞 Less
  • Research Projects

    (6 results)
  • Research Products

    (47 results)
  • Co-Researchers

    (13 People)
  •  Mutli-Omics single cell analysis

    • Principal Investigator
      Suzuki Yutaka
    • Project Period (FY)
      2015 – 2017
    • Research Category
      Grant-in-Aid for Scientific Research (B)
    • Research Field
      Genome biology
    • Research Institution
      The University of Tokyo
  •  Detection of translational signal in RNAsPrincipal Investigator

    • Principal Investigator
      YAMASHITA Riu
    • Project Period (FY)
      2013 – 2014
    • Research Category
      Grant-in-Aid for Challenging Exploratory Research
    • Research Field
      Life / Health / Medical informatics
    • Research Institution
      Tohoku University
  •  Transcriptional regulation analysis and construction of database based on massive 5'-EST sequencesPrincipal Investigator

    • Principal Investigator
      YAMASHITA Riu
    • Project Period (FY)
      2009 – 2010
    • Research Category
      Grant-in-Aid for Young Scientists (B)
    • Research Field
      ゲノム情報科学
    • Research Institution
      The University of Tokyo
  •  転写開始点データベースDBTSSの拡張とプロモータ解析Principal Investigator

    • Principal Investigator
      山下 理宇
    • Project Period (FY)
      2006 – 2007
    • Research Category
      Grant-in-Aid for Young Scientists (B)
    • Research Field
      Bioinformatics/Life informatics
    • Research Institution
      The University of Tokyo
  •  Construction of a computational model for the transcriptional regulatory regions in Ciona intestinalis and its experimental verification

    • Principal Investigator
      NAKAI Kenta
    • Project Period (FY)
      2005 – 2006
    • Research Category
      Grant-in-Aid for Scientific Research (B)
    • Research Field
      基礎ゲノム科学
    • Research Institution
      The University of Tokyo
  •  Comparative genomics of gene expression mechanisms of parasitic protozoa using full-length cDNA

    • Principal Investigator
      WATANABE Junichi
    • Project Period (FY)
      2004 – 2006
    • Research Category
      Grant-in-Aid for Scientific Research (B)
    • Research Field
      基礎ゲノム科学
    • Research Institution
      The University of Tokyo

All 2015 2014 2013 2011 2010 2009 2008 2007 2006 Other

All Journal Article Presentation

  • [Journal Article] DBTSS as an integrative platform for transcriptome, epigenome and genome sequence variation data. DNA methylation patterns.2015

    • Author(s)
      Suzuki A, Wakaguri H, Yamashita R, Kawano S, Tsuchihara K, Sugano S, Suzuki Y, Nakai K.
    • Journal Title

      Nucleic Acids Res

      Volume: 43 Pages: 1-5

    • DOI

      10.1093/nar/gku1080

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PROJECT-24300345, KAKENHI-PROJECT-25540129, KAKENHI-PROJECT-221S0002
  • [Journal Article] The Babesia bovis gene and promoter model: an update from full-length EST analysis.2014

    • Author(s)
      Yamagishi J, Wakaguri H, Yokoyama N, Yamashita R, Suzuki Y, Xuan X, Igarashi I.
    • Journal Title

      BMC Genomics.

      Volume: 15 Pages: 678-678

    • DOI

      10.1186/1471-2164-15-678

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PUBLICLY-25108501, KAKENHI-PROJECT-25540129, KAKENHI-PROJECT-25660235, KAKENHI-PROJECT-26257417
  • [Journal Article] miR-126-mediated control of cell fate in B cell-myeloid progenitors as a potential alternative to transcriptional factors.2013

    • Author(s)
      Okuyama K, Ikawa T, Gentner B, Hozumi K, Harnprasopwat R, Lu J, Yamashita R, Ha D, Toyoshima T, Chanda B, Kawamata T, Yokoyama K, Wang S, Ando K, Lodish HF, Tojo A, Kawamoto H, Kotani A
    • Journal Title

      Proc Natl Acad Sci U S A

      Volume: 110 Pages: 13410-13415

    • DOI

      10.1073/pnas.1220710110

    • Peer Reviewed
    • Data Source
      KAKENHI-PLANNED-22118004, KAKENHI-PROJECT-23591373, KAKENHI-PROJECT-24249057, KAKENHI-PROJECT-24689042, KAKENHI-PUBLICLY-25118732, KAKENHI-PROJECT-25540129
  • [Journal Article] Predicting promoter activities of primary human DNA sequences.2011

    • Author(s)
      Irie T, Park SJ, Yamashita R, Seki M, Yada T, Sugano S, Nakai K, Suzuki Y.
    • Journal Title

      Nucleic Acids Res.

    • Data Source
      KAKENHI-PROJECT-21710210
  • [Journal Article] Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis2011

    • Author(s)
      Yamashita R., et al
    • Journal Title

      Genome Research

      Volume: 21 Pages: 775-789

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-21710210
  • [Journal Article] Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis.2011

    • Author(s)
      Yamashita R, Sathira NP, Kanai A, Tanimoto K, Arauchi T, Tanaka Y, Hashimoto SI, Sugano S, Nakai K, Suzuki Y.
    • Journal Title

      Genome Res.

    • Data Source
      KAKENHI-PROJECT-21710210
  • [Journal Article] Effects of Alu elements on global nucleosome positioning in the human genome.2010

    • Author(s)
      Tanaka Y, Yamashita R, Suzuki Y, Nakai K.
    • Journal Title

      BMC Genomics. 11

      Pages: 309-309

    • Data Source
      KAKENHI-PROJECT-21710210
  • [Journal Article] Characterization of Transcription Start Sites of Putative Non-coding RNAs by Multifaceted Use of Massively Paralleled Sequencer.2010

    • Author(s)
      Sathira N, Yamashita R, Tanimoto K, Kanai A, Arauchi T, Kanematsu S, Nakai K, Suzuki Y, Sugano S.
    • Journal Title

      DNA Res.

    • Data Source
      KAKENHI-PROJECT-21710210
  • [Journal Article] DBTSS provides a tissue specific dynamic view of Transcription Start Sites2010

    • Author(s)
      Riu Yamashita
    • Journal Title

      Nucl.Acids Res 36

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-21710210
  • [Journal Article] DBTSS provides a tissue specific dynamic view of Transcription Start Sites.2009

    • Author(s)
      Yamashita R, Wakaguri H, Sugano S, Suzuki Y, Nakai K.
    • Journal Title

      Nucleic Acids Res.

    • Data Source
      KAKENHI-PROJECT-21710210
  • [Journal Article] Comprehensive detection of human terminal oligo-pyrimidine (TOP) gene and analysis of their characteristics.2008

    • Author(s)
      Yamashita R. et al
    • Journal Title

      Nucleic Acids Research 36(11)

      Pages: 3707-15

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-18700286
  • [Journal Article] DBTGR:a database of tunicate promoters and their regulatory elements2006

    • Author(s)
      Sierro, N., Kusakabe, T., Park, K.-J., Yamashita, R., Kinoshita, K., Nakai, K.
    • Journal Title

      Nucl.Acids Res. 34

    • Description
      「研究成果報告書概要(和文)」より
    • Data Source
      KAKENHI-PROJECT-17310114
  • [Journal Article] DBTGR : a database of tunicate promoters and their regulatory elements.2006

    • Author(s)
      Sierro, N., Kusakabe, T., Park, K.-J., Yamashita, R., Kinoshita, K., Nakai, K.
    • Journal Title

      Nuci. Acids Res. 34

    • Description
      「研究成果報告書概要(欧文)」より
    • Data Source
      KAKENHI-PROJECT-17310114
  • [Journal Article] RANK signaling induces interferon-stimulated genes in the fetal thymic stroma.

    • Author(s)
      Ohshima D, Qin J, Konnno H, Hirosawa A, Shiraishi T, Yanai H, Shimo Y, Akiyama N, Yamashita R, Nakai K.Inoue J.
    • Journal Title

      BBRC. in press.

    • Data Source
      KAKENHI-PROJECT-21710210
  • [Presentation] transcriptional research to translational research2015

    • Author(s)
      Riu Yamashita et al
    • Organizer
      第一回translational research meeting
    • Place of Presentation
      東京都港区 東京大学医科学研究所
    • Year and Date
      2015-03-13
    • Data Source
      KAKENHI-PROJECT-25540129
  • [Presentation] 潜在的に翻訳されるRNAとそのデータベース2014

    • Author(s)
      山下理宇
    • Organizer
      SIG-BIO研究会
    • Place of Presentation
      北陸先端大学
    • Data Source
      KAKENHI-PROJECT-25540129
  • [Presentation] Potential translation in RNA sequences2013

    • Author(s)
      Riu yamashita
    • Organizer
      生命医薬情報学連合大会
    • Place of Presentation
      タワーホール船堀
    • Data Source
      KAKENHI-PROJECT-25540129
  • [Presentation] 翻訳に着目したnon-coding RNAとcoding RNA2013

    • Author(s)
      山下理宇
    • Organizer
      NGS現場の会
    • Place of Presentation
      神戸国際会議場
    • Data Source
      KAKENHI-PROJECT-25540129
  • [Presentation] An Application of DBTSS (Database of transcription start sites) for transcriptional regulation analysis2011

    • Author(s)
      Riu Yamashita, et al
    • Organizer
      Towards Comprehensive Understanding of Immune Dynamism
    • Place of Presentation
      大阪 阪急ホテル
    • Year and Date
      2011-03-01
    • Data Source
      KAKENHI-PROJECT-21710210
  • [Presentation] A Database of Transcription Start Sites (DBTSS) for transcriptional regulation and its application2011

    • Author(s)
      Riu Yamashita
    • Organizer
      Pathogen genome analysis with next generation sequence technologies
    • Place of Presentation
      北海道大学
    • Year and Date
      2011-02-21
    • Data Source
      KAKENHI-PROJECT-21710210
  • [Presentation] 転写制御機構解明のためのデータベースDBTSSの構築とその利用2011

    • Author(s)
      山下理宇
    • Organizer
      卓越した若手研究者の自立促進プログラム成果発表会
    • Place of Presentation
      東京大学医科学研究所、東京、
    • Year and Date
      2011-03-30
    • Data Source
      KAKENHI-PROJECT-21710210
  • [Presentation] Introduction and application of DBTSS (Database of Transcription Start Sites) for Transcriptional regulation analysis2011

    • Author(s)
      Riu Yamashita, et al.
    • Organizer
      BioSoft 1011.
    • Place of Presentation
      Beijing, China.
    • Data Source
      KAKENHI-PROJECT-21710210
  • [Presentation] 転写制御機構解明のためのデータベースDBTSSの構築とその利用2011

    • Author(s)
      山下理宇
    • Organizer
      卓越した若手研究者の自立促進プログラム成果発表会
    • Place of Presentation
      東京大学医科学研究所、東京
    • Year and Date
      2011-03-30
    • Data Source
      KAKENHI-PROJECT-21710210
  • [Presentation] An Application of DBTSS (Database of transcription start sites) for transcriptional regulation analysis2011

    • Author(s)
      Riu Yamashita, et al
    • Organizer
      International Symposium "Towards Comprehensive Understanding of Immune Dynamism"
    • Place of Presentation
      Osaka, Japan
    • Data Source
      KAKENHI-PROJECT-21710210
  • [Presentation] Introduction and application of DBTSS (Database of Transcription Start Sites) for Transcriptional regulation2011

    • Author(s)
      Riu Yamashita, et al
    • Organizer
      BioSoft 2011
    • Place of Presentation
      Beijing, China
    • Year and Date
      2011-03-23
    • Data Source
      KAKENHI-PROJECT-21710210
  • [Presentation] A Database of Transcription Start Sites (DBTSS) for transcriptional regulation and its application2011

    • Author(s)
      山下理宇
    • Organizer
      Pathogen genome analysis with next generation sequence technologies
    • Place of Presentation
      Sapporo
    • Year and Date
      2011-02-21
    • Data Source
      KAKENHI-PROJECT-21710210
  • [Presentation] Extension of Database of Transcription Start Sites (DBTSS) with a Large Number of Sequences and Analysis of Bi-directional Promoters2010

    • Author(s)
      Riu Yamashita, et al
    • Organizer
      Biocuration 2010
    • Place of Presentation
      Tokyo, Japan
    • Data Source
      KAKENHI-PROJECT-21710210
  • [Presentation] New features of DBTSS (DataBase of Transcription Start Sites) and promoter analysis.2010

    • Author(s)
      Riu Yamashita, et al
    • Organizer
      1st international conference on bioinformatics and systems biology
    • Place of Presentation
      India Jan.
    • Data Source
      KAKENHI-PROJECT-21710210
  • [Presentation] New features of DBTSS (DataBase of Transcription Start Sites)2010

    • Author(s)
      山下理宇, 他
    • Organizer
      分子生物学会
    • Place of Presentation
      神戸
    • Data Source
      KAKENHI-PROJECT-21710210
  • [Presentation] Extension of Database of Transcription Start Sites (DBTSS) with a Large Number of Sequences an2010

    • Author(s)
      Riu Yamashita, et al
    • Organizer
      Biocuration 2010
    • Place of Presentation
      Tokyo, Japan 東京国際交流会館
    • Data Source
      KAKENHI-PROJECT-21710210
  • [Presentation] ヒトのトランスクリプトーム解析2010

    • Author(s)
      山下理宇(鈴木穣代理)
    • Organizer
      第148回農林交流センターワークショップ次世代シーケンサーを利用したゲノム解析の実際
    • Place of Presentation
      筑波 農林水産先端技術研究所
    • Year and Date
      2010-09-09
    • Data Source
      KAKENHI-PROJECT-21710210
  • [Presentation] Analysis of bi-directional promoters based on a huge number of transcription start sites data2010

    • Author(s)
      Riu Yamashita, et al
    • Organizer
      JSBi学会年会
    • Place of Presentation
      Kyushu, Japan 九州大学
    • Data Source
      KAKENHI-PROJECT-21710210
  • [Presentation] New features of DBTSS(DataBase of Transcription Start Sites)and promoter analysis2010

    • Author(s)
      山下理宇, et al
    • Organizer
      1st international conference on bioinformatics and systems biology
    • Place of Presentation
      India(チェンナイ)
    • Year and Date
      2010-02-20
    • Data Source
      KAKENHI-PROJECT-21710210
  • [Presentation] New features of DBTSS (DataBase of Transcription Start Sites)2010

    • Author(s)
      山下理宇, 他
    • Organizer
      分子生物学会年会
    • Place of Presentation
      神戸 神戸ポートアイランド
    • Data Source
      KAKENHI-PROJECT-21710210
  • [Presentation] Extension of DBTSS with SOLEXA sequences and analysis of bi-directional promoters.2010

    • Author(s)
      Riu Yamashita, et al.
    • Organizer
      CBI学会年会
    • Place of Presentation
      東京
    • Data Source
      KAKENHI-PROJECT-21710210
  • [Presentation] ヒトのトランスクリプトーム解析2010

    • Author(s)
      山下理宇(鈴木穣 代理)
    • Organizer
      第148回農林交流センターワークショップ 次世代シーケンサーを利用したゲノム解析の実際理化学研究所
    • Place of Presentation
      筑波
    • Data Source
      KAKENHI-PROJECT-21710210
  • [Presentation] Analysis of bi-directional promoters based on a huge number of transcription start sites data2010

    • Author(s)
      Riu Yamashita, et al
    • Organizer
      JSBI学会年会
    • Place of Presentation
      Kyushu, Japan
    • Data Source
      KAKENHI-PROJECT-21710210
  • [Presentation] Extension of Database of Transcription Start Sites (DBTSS) with a Large Number of Sequences an2010

    • Author(s)
      Riu Yamashita, et al
    • Organizer
      CBI学会年会
    • Place of Presentation
      東京 学術総会センター一橋記念講堂
    • Data Source
      KAKENHI-PROJECT-21710210
  • [Presentation] 転写・翻訳制御のゲノムワイドな解析2009

    • Author(s)
      山下理宇
    • Organizer
      卓越した若手研究者の自立促進プログラム成果発表会
    • Place of Presentation
      東京
    • Year and Date
      2009-09-02
    • Data Source
      KAKENHI-PROJECT-21710210
  • [Presentation] New features of DBTSS (DataBase of Transcription Start Sites)2009

    • Author(s)
      山下理宇, 他
    • Organizer
      分子生物学会
    • Place of Presentation
      横浜
    • Data Source
      KAKENHI-PROJECT-21710210
  • [Presentation] New features of DBTSS(DataBase of Transcription Start Sites)2009

    • Author(s)
      山下理宇, 他
    • Organizer
      分子生物学会
    • Place of Presentation
      横浜
    • Year and Date
      2009-12-12
    • Data Source
      KAKENHI-PROJECT-21710210
  • [Presentation] 転写・翻訳制御のゲノムワイドな解析2009

    • Author(s)
      山下理宇
    • Organizer
      卓越した若手研究者の自立促進プログラム成果発表会
    • Place of Presentation
      東京大学、東京
    • Data Source
      KAKENHI-PROJECT-21710210
  • [Presentation] 大規模シークエンサーに基づくトランスクリプトーム解析2008

    • Author(s)
      山下理宇
    • Organizer
      分子生物学会
    • Place of Presentation
      神戸
    • Data Source
      KAKENHI-PROJECT-18700286
  • [Presentation] Analysis of Alternative Promoters Using a Huge Number of TSS Information.2007

    • Author(s)
      Riu Yamashita
    • Organizer
      JSBI学会年会
    • Place of Presentation
      Osaka, Japan
    • Data Source
      KAKENHI-PROJECT-18700286
  • [Presentation] New features of Database of transcriptional start sites (DBTSS)2007

    • Author(s)
      Riu Yamashita
    • Organizer
      JSBI学会年会
    • Place of Presentation
      Tokyo, Japan
    • Data Source
      KAKENHI-PROJECT-18700286
  • [Presentation] New features of Database of Transcriptional start sites (DBTSS)2007

    • Author(s)
      Riu Yamashita
    • Organizer
      Workshop on Advanced Genomics
    • Place of Presentation
      Tokyo, Japan
    • Data Source
      KAKENHI-PROJECT-18700286
  • [Presentation] 転写開始点データベースDBTSSのアップデート2007

    • Author(s)
      山下理宇
    • Organizer
      分子生物学会
    • Place of Presentation
      横浜
    • Data Source
      KAKENHI-PROJECT-18700286
  • 1.  SUZUKI Yutaka (40323646)
    # of Collaborated Projects: 2 results
    # of Collaborated Products: 1 results
  • 2.  WATANABE Junichi (20201189)
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 3.  SUGIMOTO Chihiro (90231373)
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 4.  NAKAI Kenta (60217643)
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 2 results
  • 5.  KUSAKABE Takehiro (40280862)
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 2 results
  • 6.  木下 賢吾 (60332293)
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 2 results
  • 7.  土原 一哉 (00415514)
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 1 results
  • 8.  河野 隆志 (80280783)
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 9.  IKAWA Tomokatsu
    # of Collaborated Projects: 0 results
    # of Collaborated Products: 1 results
  • 10.  河本 宏
    # of Collaborated Projects: 0 results
    # of Collaborated Products: 1 results
  • 11.  東條 有伸
    # of Collaborated Projects: 0 results
    # of Collaborated Products: 1 results
  • 12.  横山 直明
    # of Collaborated Projects: 0 results
    # of Collaborated Products: 1 results
  • 13.  菅野 純夫
    # of Collaborated Projects: 0 results
    # of Collaborated Products: 1 results

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