Yamashita Riu 山下理宇

… Alternative Names

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 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

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

Yamashita Riu 山下 理宇

YAMASHITA Riu 山下 理宇

Research Projects

Research Products

Co-Researchers

Mutli-Omics single cell analysis

Principal Investigator

Project Period (FY)

Research Category

Research Field

Research Institution

Detection of translational signal in RNAsPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Research Field

Research Institution

Transcriptional regulation analysis and construction of database based on massive 5'-EST sequencesPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Research Field

Research Institution

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

Project Period (FY)

Research Category

Research Field

Research Institution

Construction of a computational model for the transcriptional regulatory regions in Ciona intestinalis and its experimental verification

Principal Investigator

Project Period (FY)

Research Category

Research Field

Research Institution

Comparative genomics of gene expression mechanisms of parasitic protozoa using full-length cDNA

Principal Investigator

Project Period (FY)

Research Category

Research Field

Research Institution

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

Author(s)

Journal Title

DOI

Data Source

[Journal Article] The Babesia bovis gene and promoter model: an update from full-length EST analysis.2014

Author(s)

Journal Title

DOI

Data Source

[Journal Article] miR-126-mediated control of cell fate in B cell-myeloid progenitors as a potential alternative to transcriptional factors.2013

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Predicting promoter activities of primary human DNA sequences.2011

Author(s)

Journal Title

Data Source

[Journal Article] Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis2011

Author(s)

Journal Title

Data Source

[Journal Article] Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis.2011

Author(s)

Journal Title

Data Source

[Journal Article] Effects of Alu elements on global nucleosome positioning in the human genome.2010

Author(s)

Journal Title

Data Source

[Journal Article] Characterization of Transcription Start Sites of Putative Non-coding RNAs by Multifaceted Use of Massively Paralleled Sequencer.2010

Author(s)

Journal Title

Data Source

[Journal Article] DBTSS provides a tissue specific dynamic view of Transcription Start Sites2010

Author(s)

Journal Title

Data Source

Yamashita Riu 山下理宇

YAMASHITA Riu 山下理宇