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HAMADA MICHIAKI  浜田 道昭

… Alternative Names

HAMADA Michiaki  浜田 道昭

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Researcher Number 00596538
Other IDs
  • ORCIDhttps://orcid.org/0000-0001-9466-1034
Affiliation (Current) 2022: 早稲田大学, 理工学術院, 教授
2022: 国立研究開発法人産業技術総合研究所, 生命工学領域, 招聘研究員
Affiliation (based on the past Project Information) *help 2016 – 2022: 早稲田大学, 理工学術院, 教授
2013 – 2016: 早稲田大学, 理工学術院, 准教授
2013: 東京大学, 新領域創成科学研究科, 特任准教授
2012: 東京大学, 大学院・新領域創成科学研究科, 特任准教授
Review Section/Research Field
Principal Investigator
Life / Health / Medical informatics / Bioinformatics/Life informatics / Applied informatics and related fields / Biological Sciences / Medium-sized Section 62:Applied informatics and related fields
Except Principal Investigator
Life / Health / Medical informatics / System genome science / Complex Systems Disease Theory / Medium-sized Section 63:Environmental analyses and evaluation and related fields
Keywords
Principal Investigator
lncRNA / 長鎖ノンコーディングRNA / リピート要素 / トランスポゾン / RNA / 機械学習 / 隠れマルコフモデル / クロマチン / バイオインフォマティクス / lncRNA-RNA相互作用 … More / RNA結合タンパク質 / 2次構造予測 / 修飾塩基 / 学習モデル / 確率モデル / 半教師有り学習 / 2次構造 / 半教師有学習 / 2次構造予測 / 機能性RNA / 分子シミュレーション / 2次構造 / プライバシー保護 / 化合物検索 / アラインメント / PPDM / 配列アラインメント / 準同型暗号 / プライバシー / ゲノム / 化合物 / 暗号 / データベース検索 / 配列検索 / R-loop / 相互作用 / ランダムフォレスト / RNA-DNA相互作用 / RNAクロマチン相互作用 / ヒストンバリアント / クロマチン状態 / エピジェネティクス / ヒストン修飾 / ノンコーディングRNA / RNA修飾 / RNA構造 / 深層学習 / 機能エレメント / RNA相互作用 / 機能推定 / リボソーム / m6A / 大規模実験情報 / 進化 … More
Except Principal Investigator
RNA2次構造 / RNA2次構造 / バイオインフォマティクス / RNA-タンパク質相互作用 / ドッキング計算 / RNAタンパク質相互作用 / RNA・タンパク質相互作用 / RNA立体構造 / 次世代DNAシーケンサー / RNA-seq / ChIP-seq / de novo配列決定 / 個人ゲノム / リシーケンシング / GWAS / インフォームドコンセント / 次世代DNAシーケンサ / 修飾塩基 / エピトランスクリプトーム / 分子動力学 / エネルギーパラメタ / エヒトランスプリクトーム / RNA2次構造 / エピとランスクリプトーム解析 / エピトランスクリプトーム解析 / RNA / ネットワーク / 環境医科学 / 環境脳科学 / トランスレーショナルリサーチ / トランスレーショナル・リサーチ / ゲノム / メタゲノム / オミックス解析 / シングルセル解析 Less
  • Research Projects

    (12 results)
  • Research Products

    (179 results)
  • Co-Researchers

    (111 People)
  •  Platform for Advanced Genome Science

    • Principal Investigator
      黒川 顕
    • Project Period (FY)
      2022 – 2027
    • Research Category
      Grant-in-Aid for Transformative Research Areas (platforms for Advanced Technologies and Research Resources)
    • Research Institution
      National Institute of Genetics
  •  リピート要素のde novo発見に基づく長鎖ノンコーディングRNAの機能の解明Principal Investigator

    • Principal Investigator
      浜田 道昭
    • Project Period (FY)
      2020 – 2022
    • Research Category
      Grant-in-Aid for Scientific Research (A)
    • Review Section
      Medium-sized Section 62:Applied informatics and related fields
    • Research Institution
      Waseda University
  •  発達期ダイオキシンと老年期の高次認知機能低下の関係性解明

    • Principal Investigator
      掛山 正心
    • Project Period (FY)
      2019 – 2021
    • Research Category
      Grant-in-Aid for Scientific Research (A)
    • Review Section
      Medium-sized Section 63:Environmental analyses and evaluation and related fields
    • Research Institution
      Waseda University
  •  Development of strategy to design anticancer drug based on ceRNA network

    • Principal Investigator
      秋光 信佳
    • Project Period (FY)
      2018 – 2021
    • Research Category
      Grant-in-Aid for Scientific Research (B)
    • Research Field
      Complex Systems Disease Theory
    • Research Institution
      The University of Tokyo
  •  RNA-クロマチン相互作用予測と応用Principal Investigator

    • Principal Investigator
      浜田 道昭
    • Project Period (FY)
      2017 – 2022
    • Research Category
      Grant-in-Aid for Challenging Research (Exploratory)
    • Research Field
      Applied informatics and related fields
    • Research Institution
      Waseda University
  •  ヒストンバリアントに基づくクロマチンの機能の推定Principal Investigator

    • Principal Investigator
      浜田 道昭
    • Project Period (FY)
      2016 – 2017
    • Research Category
      Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
    • Review Section
      Biological Sciences
    • Research Institution
      Waseda University
  •  RNA informatics for epi-transcriptome analysis

    • Principal Investigator
      Asai Kiyoshi
    • Project Period (FY)
      2016 – 2018
    • Research Category
      Grant-in-Aid for Scientific Research (A)
    • Research Field
      System genome science
    • Research Institution
      The University of Tokyo
  •  機能エレメントと深層学習に基づく長鎖ノンコーディングRNAの機能分類Principal Investigator

    • Principal Investigator
      浜田 道昭
    • Project Period (FY)
      2016 – 2019
    • Research Category
      Grant-in-Aid for Young Scientists (A)
    • Research Field
      Life / Health / Medical informatics
    • Research Institution
      Waseda University
  •  Comprehensive prediction of RNA-protein interactinos

    • Principal Investigator
      Asai Kiyoshi
    • Project Period (FY)
      2013 – 2015
    • Research Category
      Grant-in-Aid for Scientific Research (A)
    • Research Field
      Life / Health / Medical informatics
    • Research Institution
      The University of Tokyo
  •  Development of basic technology for privacy-preserving bioinformatics and its applicationPrincipal Investigator

    • Principal Investigator
      Hamada Michiaki
    • Project Period (FY)
      2013 – 2015
    • Research Category
      Grant-in-Aid for Challenging Exploratory Research
    • Research Field
      Life / Health / Medical informatics
    • Research Institution
      Waseda University
      The University of Tokyo
  •  Research on structure predictions of RNA with modified nucleotiedsPrincipal Investigator

    • Principal Investigator
      Hamada Michiaki
    • Project Period (FY)
      2012 – 2015
    • Research Category
      Grant-in-Aid for Young Scientists (A)
    • Research Field
      Bioinformatics/Life informatics
    • Research Institution
      Waseda University
      The University of Tokyo
  •  Platform of large scale and high quality genomics and bioinformatics: Towards the advancement of genome sciences in academia

    • Principal Investigator
      KOHARA Yuji
    • Project Period (FY)
      2010 – 2015
    • Research Category
      Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
    • Research Institution
      National Institute of Genetics

All 2022 2021 2020 2019 2018 2017 2016 2015 2014 2013 2012 2011 2010 Other

All Journal Article Presentation Book

  • [Book] よくわかるバイオインフォマティクス入門2018

    • Author(s)
      藤 博幸、岩部 直之、川端 猛、浜田 道昭、門田 幸二、須山 幹太、光山 統泰、黒川 顕、森 宙史、東 光一、吉沢 明康、片山 俊明
    • Total Pages
      208
    • Publisher
      講談社
    • ISBN
      4065138213
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Book] よくわかるバイオインフォマティクス入門2018

    • Author(s)
      藤 博幸、岩部 直之、川端 猛、浜田 道昭、門田 幸二、須山 幹太、光山 統泰、黒川 顕、森 宙史、東 光一、吉沢 明康、片山 俊明
    • Total Pages
      208
    • Publisher
      講談社
    • ISBN
      4065138213
    • Data Source
      KAKENHI-PUBLICLY-16H01318
  • [Book] よくわかるバイオインフォマティクス入門2018

    • Author(s)
      藤 博幸、岩部 直之、川端 猛、浜田 道昭、門田 幸二、須山 幹太、光山 統泰、黒川 顕、森 宙史、東 光一、吉沢 明康、片山 俊明
    • Total Pages
      208
    • Publisher
      講談社
    • ISBN
      4065138213
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Book] 生命情報処理における機械学習2016

    • Author(s)
      瀬々潤、浜田道昭
    • Total Pages
      130
    • Publisher
      講談社
    • Data Source
      KAKENHI-PROJECT-24680031
  • [Book] 生命情報処理における機械学習2016

    • Author(s)
      瀬々潤、浜田道昭
    • Publisher
      講談社
    • Data Source
      KAKENHI-PROJECT-25540131
  • [Book] 生命情報処理における機械学習~多重検定と推定量設計~2015

    • Author(s)
      瀬々潤、浜田道昭
    • Total Pages
      192
    • Publisher
      講談社サイエンティフィック
    • Data Source
      KAKENHI-PROJECT-221S0002
  • [Book] RNA structural alignments, part II: non-Sankoff approaches for structural alignments N.J.: Clifton, RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods, Methods in molecular biology.2014

    • Author(s)
      Kiyoshi Asai, Michiaki Hamada
    • Total Pages
      11
    • Publisher
      Springer
    • Data Source
      KAKENHI-PROJECT-25240044
  • [Journal Article] HT-SELEX-based identification of binding pre-miRNA hairpin-motif for small molecules2022

    • Author(s)
      Mukherjee Sanjukta、Murata Asako、Ishida Ryoga、Sugai Ayako、Dohno Chikara、Hamada Michiaki、Krishna Sudhir、Nakatani Kazuhiko
    • Journal Title

      Molecular Therapy - Nucleic Acids

      Volume: 27 Pages: 165-174

    • DOI

      10.1016/j.omtn.2021.11.021

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PROJECT-16H05879, KAKENHI-PROJECT-18K05355, KAKENHI-PROJECT-19K22254, KAKENHI-PROJECT-17K20032
  • [Journal Article] G0S2 regulates innate immunity in Kawasaki disease via lncRNA HSD11B1-AS12022

    • Author(s)
      Okabe Mako、Takarada Shinya、Miyao Nariaki、Nakaoka Hideyuki、Ibuki Keijiro、Ozawa Sayaka、Watanabe Kazuhiro、Tsuji Harue、Hashimoto Ikuo、Hatasaki Kiyoshi、Hayakawa Shotaro、Hamaguchi Yu、Hamada Michiaki、Ichida Fukiko、Hirono Keiichi
    • Journal Title

      Pediatric Research

      Volume: 15 Pages: 1-10

    • DOI

      10.1038/s41390-022-01999-9

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PROJECT-16H05879, KAKENHI-PROJECT-18K07785, KAKENHI-PROJECT-17K20032
  • [Journal Article] Prediction of RNA?protein interactions using a nucleotide language model2022

    • Author(s)
      Yamada Keisuke、Hamada Michiaki
    • Journal Title

      Bioinformatics Advances

      Volume: 2

    • DOI

      10.1093/bioadv/vbac023

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-16H05879, KAKENHI-PROJECT-17K20032
  • [Journal Article] Detection and Characterization of Ribosome-Associated Long Noncoding RNAs2021

    • Author(s)
      Zeng Chao、Hamada Michiaki
    • Journal Title

      Method in Molecular Biology

      Volume: 2254 Pages: 179-194

    • DOI

      10.1007/978-1-0716-1158-6_11

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-20K15784, KAKENHI-PROJECT-16H05879, KAKENHI-PROJECT-17K20032
  • [Journal Article] Umibato: estimation of time-varying microbial interaction using continuous-time regression hidden Markov model2021

    • Author(s)
      Hosoda Shion、Fukunaga Tsukasa、Hamada Michiaki
    • Journal Title

      Bioinformatics

      Volume: 37

    • DOI

      10.1093/bioinformatics/btab287

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-16H05879, KAKENHI-PROJECT-19J20117, KAKENHI-PROJECT-17K20032
  • [Journal Article] Identification of m6A-Associated RNA Binding Proteins Using an Integrative Computational Framework2021

    • Author(s)
      Zhang Yiqian、Hamada Michiaki
    • Journal Title

      Frontiers in Genetics

      Volume: 12 Pages: 625797-625797

    • DOI

      10.3389/fgene.2021.625797

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-16H05879, KAKENHI-PROJECT-17K20032
  • [Journal Article] Binding patterns of RNA-binding proteins to repeat-derived RNA sequences reveal putative functional RNA elements2021

    • Author(s)
      Onoguchi Masahiro、Zeng Chao、Matsumaru Ayako、Hamada Michiaki
    • Journal Title

      NAR Genomics and Bioinformatics

      Volume: 3

    • DOI

      10.1093/nargab/lqab055

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PROJECT-16H05879, KAKENHI-PROJECT-21K06133, KAKENHI-PROJECT-17K20032, KAKENHI-PROJECT-20K15784
  • [Journal Article] Association analysis of repetitive elements and R-loop formation across species2021

    • Author(s)
      Chao Zeng, Masahiro Onoguchi, Michiaki Hamada
    • Journal Title

      Mobile DNA

      Volume: 12 Pages: 3-3

    • DOI

      10.1186/s13100-021-00231-5

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PROJECT-20K15784, KAKENHI-PROJECT-16H06279, KAKENHI-PROJECT-16H05879, KAKENHI-PROJECT-17K20032
  • [Journal Article] Possible roles for the hominoid-specific DSCR4 gene in human cells2021

    • Author(s)
      Saber Morteza M.、Karimiavargani Marziyeh、Uzawa Takanori、Hettiarachchi Nilmini、Hamada Michiaki、Ito Yoshihiro、Saitou Naruya
    • Journal Title

      Genes Genet. Syst.

      Volume: 96 Issue: 1 Pages: 1-11

    • DOI

      10.1266/ggs.20-00012

    • NAID

      130008035886

    • ISSN
      1341-7568, 1880-5779
    • Language
      English
    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-16H05879, KAKENHI-PROJECT-17K20032
  • [Journal Article] Multi-resBind: a residual network-based multi-label classifier for in vivo RNA binding prediction and preference visualization2021

    • Author(s)
      Zhao Shitao、Hamada Michiaki
    • Journal Title

      BMC Bioinformatics

      Volume: 22 Pages: 554-554

    • DOI

      10.1186/s12859-021-04430-y

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-16H05879, KAKENHI-PROJECT-17K20032
  • [Journal Article] Jonckheere?Terpstra?Kendall-based non-parametric analysis of temporal differential gene expression2021

    • Author(s)
      Iuchi Hitoshi、Hamada Michiaki
    • Journal Title

      NAR Genomics and Bioinformatics

      Volume: 3

    • DOI

      10.1093/nargab/lqab021

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-16H05879, KAKENHI-PROJECT-17K20032
  • [Journal Article] Clone decomposition based on mutation signatures provides novel insights into mutational processes2021

    • Author(s)
      Matsutani Taro、Hamada Michiaki
    • Journal Title

      NAR Genomics and Bioinformatics

      Volume: 3

    • DOI

      10.1093/nargab/lqab093

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PROJECT-16H05879, KAKENHI-PROJECT-20J20016, KAKENHI-PROJECT-17K20032
  • [Journal Article] Long Non-Coding RNA CRNDE Is Involved in Resistance to EGFR Tyrosine Kinase Inhibitor in EGFR-Mutant Lung Cancer via eIF4A3/MUC1/EGFR Signaling2021

    • Author(s)
      Takahashi Satoshi、Noro Rintaro、Seike Masahiro、Zeng Chao、Matsumoto Masaru、Yoshikawa Akiko、Nakamichi Shinji、Sugano Teppei、Hirao Mariko、Matsuda Kuniko、Hamada Michiaki、Gemma Akihiko
    • Journal Title

      International Journal of Molecular Sciences

      Volume: 22 Pages: 4005-4005

    • DOI

      10.3390/ijms22084005

    • Peer Reviewed / Open Access / Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-20K15784, KAKENHI-PROJECT-16H05879, KAKENHI-PROJECT-17K20032, KAKENHI-PROJECT-20K17200, KAKENHI-PROJECT-17KK0177
  • [Journal Article] Impact of human gene annotations on RNA-seq differential expression analysis2021

    • Author(s)
      Hamaguchi Yu、Zeng Chao、Hamada Michiaki
    • Journal Title

      BMC Genomics

      Volume: 22 Pages: 730-730

    • DOI

      10.1186/s12864-021-08038-7

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PROJECT-16H05879, KAKENHI-PROJECT-17K20032, KAKENHI-PROJECT-20K15784
  • [Journal Article] Targeting the TR4 nuclear receptor-mediated lncTASR/AXL signaling with tretinoin increases the sunitinib sensitivity to better suppress the RCC progression2020

    • Author(s)
      Hangchuan Shi, Yin Sun, Miao He, Xiong Yang, Michiaki Hamada, Tsukasa Fukunaga, Xiaoping Zhang and Chawnshang Chang.
    • Journal Title

      Oncogene

      Volume: 39 Pages: 530-545

    • DOI

      10.1038/s41388-019-0962-8

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PUBLICLY-17H05605, KAKENHI-PROJECT-16H05879
  • [Journal Article] Identification of RNA biomarkers for chemical safety screening in neural cells derived from mouse embryonic stem cells using RNA deep sequencing analysis2019

    • Author(s)
      ani H, Matsutani T, Aoki H, Nakamura K, Hamaguchi Y, Nakazato T, Hamada M.
    • Journal Title

      Biochemical and Biophysical Research Communications

      Volume: 512 Pages: 641-646

    • DOI

      10.1016/j.bbrc.2018.11.141

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PROJECT-17K14525, KAKENHI-PROJECT-15K01829, KAKENHI-PROJECT-16H05879
  • [Journal Article] Estimating energy parameters for RNA secondary structure predictions using both experimental and computational data2019

    • Author(s)
      Shimpei Nishida, Shun Sakuraba, Kiyoshi Asai, and Michiaki Hamada
    • Journal Title

      IEEE/ACM transactions on computational biology and bioinformatics

      Volume: - Pages: 1645-1655

    • DOI

      10.1109/tcbb.2018.2813388

    • Description
      in press
    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-16H06279, KAKENHI-PROJECT-16H05879, KAKENHI-PROJECT-16H02484
  • [Journal Article] Stromal fibroblasts induce metastatic tumor cell clusters via epithelial-mesenchymal plasticity.2019

    • Author(s)
      Matsumura Y, Daigo Y, Takano A, Orimo A, et. al.
    • Journal Title

      Life Sci Alliance

      Volume: 2(4):e201900425. Issue: 4 Pages: 1-24

    • DOI

      10.26508/lsa.201900425

    • Description
      in press
    • Peer Reviewed / Open Access / Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-17K10652, KAKENHI-PROJECT-18K06198, KAKENHI-PROJECT-18K07207, KAKENHI-PROJECT-18K08798, KAKENHI-PROJECT-19K07884, KAKENHI-PROJECT-18K19656, KAKENHI-PROJECT-18H02695, KAKENHI-PROJECT-19H03559, KAKENHI-PROJECT-18K19483, KAKENHI-PROJECT-19K21278, KAKENHI-PROJECT-16H05879, KAKENHI-PROJECT-16H06277
  • [Journal Article] LncRRIsearch : a web server for IncRNA-RNA interaction prediction integrated with tissue-specific expression and subcellular localization data2019

    • Author(s)
      Tsukasa Fukunaga, Junichi Iwakiri, Yukiteru Ono, Michiaki Hamada
    • Journal Title

      Frontiers in Genetics

      Volume: - Pages: 462-462

    • DOI

      10.3389/fgene.2019.00462

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PROJECT-17K20032, KAKENHI-PROJECT-16K16143, KAKENHI-PUBLICLY-17H05605, KAKENHI-PROJECT-16H05879, KAKENHI-PROJECT-16H06279
  • [Journal Article] Discovering novel mutation signatures by latent Dirichlet allocation with variational Bayes inference2019

    • Author(s)
      Taro Matsutani, Yuki Ueno, Tsukasa Fukunaga, Michiaki Hamada
    • Journal Title

      Bioinformatics

      Volume: 35 Issue: 22 Pages: 4543-4552

    • DOI

      10.1093/bioinformatics/btz266

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-16H05879, KAKENHI-PROJECT-16H06279
  • [Journal Article] Computational approaches for alternative and transient secondary structures of ribonucleic acids2019

    • Author(s)
      Fukunaga Tsukasa、Hamada Michiaki
    • Journal Title

      Briefings in Functional Genomics

      Volume: -

    • DOI

      10.1093/bfgp/ely042

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17K20032, KAKENHI-PUBLICLY-16H01318, KAKENHI-PROJECT-16H05879
  • [Journal Article] Identification of transposable elements contributing to tissue-specific expression of long non-coding RNAs2018

    • Author(s)
      Takashi Chishima, Junichi Iwakiri, Michiaki Hamada
    • Journal Title

      Genes

      Volume: 9 Issue: 1 Pages: 23-23

    • DOI

      10.3390/genes9010023

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PROJECT-16K16143, KAKENHI-PROJECT-16H06279, KAKENHI-PROJECT-16H02484, KAKENHI-PROJECT-16H05879
  • [Journal Article] Full Access A Novel Method for Assessing the Statistical Significance of RNA-RNA Interactions Between Two Long RNAs2018

    • Author(s)
      Fukunaga Tsukasa、Hamada Michiaki
    • Journal Title

      Journal of Computational Biology

      Volume: 25 Pages: 976-986

    • DOI

      10.1089/cmb.2017.0260

    • Peer Reviewed
    • Data Source
      KAKENHI-PUBLICLY-16H01318, KAKENHI-PUBLICLY-17H05605, KAKENHI-PROJECT-16H05879
  • [Journal Article] DeepM6ASeq: prediction and characterization of m6A-containing sequences using deep learning2018

    • Author(s)
      Zhang Yiqian、Hamada Michiaki
    • Journal Title

      BMC Bioinformatics

      Volume: 19 Pages: 524-524

    • DOI

      10.1186/s12859-018-2516-4

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Journal Article] Identifying sequence features that drive ribosomal association for lncRNA2018

    • Author(s)
      Zeng Chao、Hamada Michiaki
    • Journal Title

      BMC Genomics

      Volume: 19 Pages: 906-906

    • DOI

      10.1186/s12864-018-5275-8

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Journal Article] Beyond similarity assessment: selecting the optimal model for sequence alignment via the Factorized Asymptotic Bayesian algorithm2017

    • Author(s)
      Takeda Taikai、Hamada Michiaki
    • Journal Title

      Bioinformatics

      Volume: 34 Pages: 576-584

    • DOI

      10.1093/bioinformatics/btx643

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Journal Article] RIblast: an ultrafast RNA-RNA interaction prediction system based on a seed-and-extension approach2017

    • Author(s)
      Tsukasa Fukunaga and Michiaki Hamada
    • Journal Title

      Bioinformatics

      Volume: 印刷中 Pages: 2666-2674

    • DOI

      10.1093/bioinformatics/btx287

    • Peer Reviewed / Acknowledgement Compliant / Open Access
    • Data Source
      KAKENHI-PROJECT-16J00129, KAKENHI-PROJECT-16H05879
  • [Journal Article] Training alignment parameters for arbitrary sequencers with LAST-TRAIN.2017

    • Author(s)
      Michiaki Hamada, Yukiteru Ono, Kiyoshi Asai, Martin CFrith.
    • Journal Title

      Bioinformatics

      Volume: 33 Issue: 6 Pages: 926-928

    • DOI

      10.1093/bioinformatics/btw742

    • Peer Reviewed / Acknowledgement Compliant / Open Access / Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-26700030, KAKENHI-PROJECT-16H06279, KAKENHI-PROJECT-16H02484
  • [Journal Article] Computational prediction of lncRNA-mRNA interactions by integrating tissue2017

    • Author(s)
      Junichi Iwakiri, Goro Terai, Michiaki Hamada
    • Journal Title

      Biology Direct

      Volume: 12 Pages: 15-15

    • DOI

      10.1186/s13062-017-0183-4

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PROJECT-16K16143, KAKENHI-PROJECT-16H02484, KAKENHI-PROJECT-16H05879, KAKENHI-PROJECT-16H06279
  • [Journal Article] Comprehensive prediction of lncRNA-RNA interactions in human transcriptome2016

    • Author(s)
      Goro Terai#, Junichi Iwakiri#, Tomoshi Kameda, Michiaki Hamada*, Kiyoshi Asai*
    • Journal Title

      BMC Genomics

      Volume: 17 Pages: 12-12

    • DOI

      10.1186/s12864-015-2307-5

    • Peer Reviewed / Acknowledgement Compliant / Open Access
    • Data Source
      KAKENHI-PROJECT-24680031, KAKENHI-PROJECT-25240044
  • [Journal Article] Rtools : a web server for various secondary structural analyses on single RNA sequences.2016

    • Author(s)
      Michiaki Hamada, Yukiteru Ono, Hisanori Kiryu, Kengo Sato, Yuki Kato, Tsukasa Fukunaga, Ryota Mori, Kiyoshi Asai.
    • Journal Title

      Nucleic Acids Res

      Volume: 44

    • DOI

      10.1093/nar/gkw337

    • NAID

      120006346257

    • Peer Reviewed / Acknowledgement Compliant / Open Access / Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-13J06668, KAKENHI-PROJECT-24680031, KAKENHI-PROJECT-25240044, KAKENHI-PROJECT-25330348, KAKENHI-PROJECT-25870190, KAKENHI-PROJECT-15K00401, KAKENHI-PROJECT-16H06279
  • [Journal Article] Bioinformatics tools for lncRNA research2016

    • Author(s)
      Junichi Iwakiri, Michiaki Hamada, Kiyoshi Asai
    • Journal Title

      Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms

      Volume: 1859(1) Pages: 23-30

    • DOI

      10.1016/j.bbagrm.2015.07.014

    • Peer Reviewed / Acknowledgement Compliant / Open Access
    • Data Source
      KAKENHI-PROJECT-221S0002, KAKENHI-PROJECT-24680031, KAKENHI-PROJECT-25240044
  • [Journal Article] 長鎖ノンコーディングRNAのためのバイオインフォマティクス2016

    • Author(s)
      岩切淳一、浜田道昭
    • Journal Title

      生物物理

      Volume: 未定

    • NAID

      130005165637

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-24680031
  • [Journal Article] Improved Aocuracy in RNA-Protein Rigid Body Docking by Incorporating Force Field for Molecular Dynamics Simulation into the Scoring Function.2016

    • Author(s)
      Junichi Iwakiri, Michiaki Hamada, Kiyoshi Asai, Tomoshi Kameda.
    • Journal Title

      J. Chem Theory Comput.

      Volume: 12(9) Issue: 9 Pages: 4688-4697

    • DOI

      10.1021/acs.jctc.6b00254

    • Peer Reviewed / Acknowledgement Compliant
    • Data Source
      KAKENHI-PROJECT-25240044, KAKENHI-PROJECT-16H06279
  • [Journal Article] A semi-supervised learning approach for RNA secondary structure prediction.2015

    • Author(s)
      Haruka Yonemoto, Kiyoshi Asai, Michiaki Hamada
    • Journal Title

      Computational biology and chemistry

      Volume: 未定 Pages: 72-79

    • DOI

      10.1016/j.compbiolchem.2015.02.002

    • Peer Reviewed / Acknowledgement Compliant
    • Data Source
      KAKENHI-PROJECT-24680031, KAKENHI-PROJECT-221S0002, KAKENHI-PROJECT-25240044
  • [Journal Article] Learning chromatin states with factorized information criteria.2015

    • Author(s)
      Michiaki Hamada, Yukiteru Ono, Ryohei Fujimaki, Kiyoshi Asai
    • Journal Title

      Bioinformatics

      Volume: 未定 Pages: 2426-2433

    • DOI

      10.1093/bioinformatics/btv163

    • Peer Reviewed / Acknowledgement Compliant / Open Access
    • Data Source
      KAKENHI-PROJECT-24680031, KAKENHI-PROJECT-221S0002
  • [Journal Article] Privacy-preserving search for chemical compound databases2015

    • Author(s)
      Kana Shimizu, Koji Nuida, Hiromi Arai, Shigeo Mitsunari, Nuttapong Attrapadung, Michiaki Hamada, Koji Tsuda, Takatsugu Hirokawa, Jun Sakuma, Goichiro Hanaoka, Kiyoshi Asai
    • Journal Title

      BMC Bioinformatics

      Volume: 16(Suppl 18):S6 Pages: 1-14

    • DOI

      10.1186/1471-2105-16-s18-s6

    • NAID

      120007128511

    • Peer Reviewed / Acknowledgement Compliant / Open Access
    • Data Source
      KAKENHI-PLANNED-24106010, KAKENHI-PROJECT-25540131
  • [Journal Article] Efficient calculation of exact probability distributions of integer features on RNA secondary structures2014

    • Author(s)
      Mori R, Hamada M, Asai K
    • Journal Title

      BMC Genomics

      Volume: 15

    • DOI

      10.1186/1471-2164-15-s10-s6

    • Peer Reviewed / Acknowledgement Compliant / Open Access
    • Data Source
      KAKENHI-PROJECT-13J06668, KAKENHI-PROJECT-221S0002, KAKENHI-PROJECT-25240044
  • [Journal Article] Reference-free prediction of rearrangement breakpoint reads2014

    • Author(s)
      Edward Wijaya, Kana Shimizu, Kiyoshi Asai, Michiaki Hamada
    • Journal Title

      Bioinformatics

      Volume: 30(18) Pages: 2559-2567

    • DOI

      10.1093/bioinformatics/btu360

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PROJECT-26540159, KAKENHI-PROJECT-221S0002
  • [Journal Article] Fighting against uncertainty: An essential issue in bioinformatics2014

    • Author(s)
      Michiaki Hamada
    • Journal Title

      Briefings in Bionformatics

      Volume: 未定

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-24680031
  • [Journal Article] PBSIM: PacBio reads simulator--toward accurate genome assembly.2013

    • Author(s)
      Yukiteru Ono, Kiyoshi Asai, Michiaki Hamada
    • Journal Title

      Bioinformatics

      Volume: 29 Pages: 119-121

    • DOI

      10.1093/bioinformatics/bts649

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-221S0002
  • [Journal Article] Analysis of base-pairing probabilities of RNA molecules involved in protein-RNA2013

    • Author(s)
      Junichi Iwakiri, Tomoshi Kameda, Kiyoshi Asai, Michiaki Hamada
    • Journal Title

      Bioinformatics

      Volume: 29 Pages: 2524-2528

    • DOI

      10.1093/bioinformatics/btt453

    • Peer Reviewed / Acknowledgement Compliant
    • Data Source
      KAKENHI-PROJECT-22240031, KAKENHI-PROJECT-24680031, KAKENHI-PROJECT-25240044, KAKENHI-PROJECT-221S0002
  • [Journal Article] PBSIM: PacBio reads simulator--toward accurate genome assembly2013

    • Author(s)
      Yukiteru Ono, Kiyoshi Asai, Michiaki Hamada
    • Journal Title

      Bioinformatics

      Volume: 29 Pages: 119-121

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-24680031
  • [Journal Article] Draft assembly of the Symbiodinium minutum nuclear genome reveals dinoflagellate gene structure.2013

    • Author(s)
      Shoguchi1, E., Shinzato, C., Kawashima, T., Gyoja, F., et al.
    • Journal Title

      Curr Biol.

      Volume: 23 Pages: 1399-1408

    • DOI

      10.1016/j.cub.2013.05.062

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-24241071, KAKENHI-PUBLICLY-25128712, KAKENHI-PROJECT-221S0002
  • [Journal Article] CentroidAlign-Web: a fast and accurate multiple aligner for long non-coding RNAs2013

    • Author(s)
      Haruka Yonemoto, Kiyoshi Asai, Michiaki Hamada
    • Journal Title

      Int. J. Mol. Sci.

      Volume: 14 Pages: 6144-6156

    • DOI

      10.3390/ijms14036144

    • Peer Reviewed / Acknowledgement Compliant
    • Data Source
      KAKENHI-PROJECT-22240031, KAKENHI-PROJECT-24680031, KAKENHI-PROJECT-25240044, KAKENHI-PROJECT-221S0002
  • [Journal Article] Direct updating of an RNA base-pairing probability matrix with marginal probability constraints2012

    • Author(s)
      Michiaki Hamada
    • Journal Title

      Journal of Computational Biology

      Volume: 19 Pages: 1265-1276

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-24680031
  • [Journal Article] A classification of bioinformatics algorithms from the viewpoint of maximizing expected accuracy (MEA).2012

    • Author(s)
      Michiaki Hamada, Kiyoshi Asai
    • Journal Title

      J. Comput Biol

      Volume: 19 Pages: 532-549

    • DOI

      10.1089/cmb.2011.0197

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-22240031, KAKENHI-PROJECT-221S0002
  • [Journal Article] Generalized centroid estimators in bioinformatics2011

    • Author(s)
      Michiaki Hamada, Hisanori Kiryu, Wataru Iwasaki, Kiyoshi Asai
    • Journal Title

      PLoS One

      Volume: 6

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-221S0002
  • [Journal Article] Probabilistic alignments with quality scores : an application to short-read mapping toward accurate SNP/indel detection2011

    • Author(s)
      Michiaki Hamada, Edward Wijaya, Martin C Frith, Kiyoshi Asai
    • Journal Title

      Bioinformatics

      Volume: 27 Pages: 3085-3092

    • DOI

      10.1093/bioinformatics/btr537

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-221S0002
  • [Journal Article] Improving the accuracy of predicting secondary structure for aligned RNA sequences2011

    • Author(s)
      Michiaki Hamada, Kengo Sato, Kiyoshi Asai
    • Journal Title

      Nucleic Acids Research

      Volume: 39 Pages: 393-402

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-221S0002
  • [Journal Article] Prediction of RNA secondary structure by maximizing pseudo-expected accuracy2010

    • Author(s)
      Michiaki Hamada, Kengo Sato, Kiyoshi Asai
    • Journal Title

      BMC Bioinformatics

      Volume: 11 Pages: 586-586

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-221S0002
  • [Presentation] RNA情報学の最前線2022

    • Author(s)
      浜田 道昭(早大/CBBD-OIL)
    • Organizer
      生命情報科学勉強会
    • Invited
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] The analysis of mutational signatures for understanding carcinogenesis considering temporal heterogeneity2022

    • Author(s)
      Shiina NAITO(早大), Taro Matsutani(早大/CBBD-OIL), Michiaki HAMADA(早大/CBBD-OIL)
    • Organizer
      Tokyo Bioinformatics Meeting 第5回研究会
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] レファレンスフリーな発現変動解析ツールの比較2022

    • Author(s)
      吉次なぎ(TIRI/早大)、浜口 悠(早大)、曽超(早大/CBBD-OIL)、浜田道昭(早大/CBBD-OIL)
    • Organizer
      RNAフロンティアミーティング
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] The analysis of mutational signatures for understanding carcinogenesis considering temporal heterogeneity2022

    • Author(s)
      Shiina NAITO(早大), Taro Matsutani(早大/CBBD-OIL), Michiaki HAMADA(早大/CBBD-OIL)
    • Organizer
      Tokyo Bioinformatics Meeting 第5回研究会
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] AIアプタマー創薬プロジェクト2022

    • Author(s)
      浜田 道昭(早大/CBBD-OIL)
    • Organizer
      日本医科大学・早稲田大学合同シンポジウム
    • Invited
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] 二次構造情報を考慮したアプタマー生成モデル2022

    • Author(s)
      Akiya MICHISHITA(早大), Shunsuke SUMI(早大/京大) Natsuki IWANO(早大), Michiaki HAMADA(早大/CBBD-OIL)
    • Organizer
      Tokyo Bioinformatics Meeting 第5回研究会
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] Classification of antibiotic resistance mechanisms considering the interaction of distal sequences2022

    • Author(s)
      Kanami Yagimoto(早大),Shion HOSODA(早大/CBBD-OIL),Michiaki HAMADA(早大/CBBD-OIL)
    • Organizer
      Tokyo Bioinformatics Meeting 第5回研究会
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] Estimation of Stability of State transition of Human gut microbiota using Hidden Markov Model2022

    • Author(s)
      YOKOYAMA Gentaro(早大), HOSODA Shion(早大/CBBD-OIL), FUKUNAGA Tsukasa(早大), HAMADA Michiaki(早大/CBBD-OIL)
    • Organizer
      Tokyo Bioinformatics Meeting 第5回研究会
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] ゲノム社会とバイオインフォマティクス2022

    • Author(s)
      浜田 道昭(早大/CBBD-OIL)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Invited
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] ヒトのエンハンサーと遺伝子相互作用や転写制御に影響する、方向性のある転写因子DNA結合配列の解析法の開発2022

    • Author(s)
      大里直樹(早大)、浜田 道昭(早大/CBBD-OIL)
    • Organizer
      第67回バイオ情報学研究会
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] The function of transposons as cell-type specific gene regulatory regions in the adult mouse brain2022

    • Author(s)
      Kotaro Sekine(早大), Masahiro Onoguchi(早大/CBBD-OIL), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      Tokyo Bioinformatics Meeting 第5回研究会
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] ヒトのエンハンサーと遺伝子相互作用や転写制御に影響する、方向性のある転写因子DNA結合配列の解析法の開発2022

    • Author(s)
      大里直樹(早大)、浜田 道昭(早大/CBBD-OIL)
    • Organizer
      第68回バイオ情報学研究会
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] 二次構造情報を考慮したアプタマー生成モデル2022

    • Author(s)
      Akiya MICHISHITA(早大), Shunsuke SUMI(早大/京大) Natsuki IWANO(早大), Michiaki HAMADA(早大/CBBD-OIL)
    • Organizer
      Tokyo Bioinformatics Meeting 第5回研究会
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] 深層学習の予測結果に寄与する因子の大規模な解析に伴うノイズの影響の低減2022

    • Author(s)
      大里直樹(早大)、浜田 道昭(早大/CBBD-OIL)
    • Organizer
      第24回情報論的学習理論ワークショップ
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] 深層学習の予測結果に寄与する因子の大規模な解析に伴うノイズの影響の低減2022

    • Author(s)
      大里直樹(早大)、浜田 道昭(早大/CBBD-OIL)
    • Organizer
      第24回情報論的学習理論ワークショップ
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] A novel fast pipeline for RNA homology search considering secondary structure2022

    • Author(s)
      Kento Kubo(早大), Tsukasa Fukunaga(早大), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      Tokyo Bioinformatics Meeting 第5回研究会
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] RNA情報学の最前線2022

    • Author(s)
      浜田 道昭(早大/CBBD-OIL)
    • Organizer
      生命情報科学勉強会
    • Invited
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] AIアプタマー創薬「アプタマー研究の最前線」2022

    • Author(s)
      浜田 道昭(早大/CBBD-OIL)
    • Organizer
      分子生物学会ワークショップ1PWS1-09
    • Invited
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] De novo repeat detection using inexact seed2022

    • Author(s)
      Atsushi Takeda(早大/CBBD-OIL), Yuta Imazu(東大), Daisuke Nonaka(東大), Tsukasa Fukunaga(早大), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      Tokyo Bioinformatics Meeting 第5回研究会
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] ヒトのエンハンサーと遺伝子相互作用や転写制御に影響する、方向性のある転写因子DNA結合配列の解析法の開発2022

    • Author(s)
      大里直樹(早大)、浜田 道昭(早大/CBBD-OIL)
    • Organizer
      第68回バイオ情報学研究会
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] A novel fast pipeline for RNA homology search considering secondary structure2022

    • Author(s)
      Kento Kubo(早大), Tsukasa Fukunaga(早大), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      Tokyo Bioinformatics Meeting 第5回研究会
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] Classification of antibiotic resistance mechanisms considering the interaction of distal sequences2022

    • Author(s)
      Kanami Yagimoto(早大),Shion HOSODA(早大/CBBD-OIL),Michiaki HAMADA(早大/CBBD-OIL)
    • Organizer
      Tokyo Bioinformatics Meeting 第5回研究会
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] レファレンスフリーな発現変動解析ツールの比較2022

    • Author(s)
      吉次なぎ(TIRI/早大)、浜口 悠(早大)、曽超(早大/CBBD-OIL)、浜田道昭(早大/CBBD-OIL)
    • Organizer
      RNAフロンティアミーティング
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] The function of transposons as cell-type specific gene regulatory regions in the adult mouse brain2022

    • Author(s)
      Kotaro Sekine(早大), Masahiro Onoguchi(早大/CBBD-OIL), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      Tokyo Bioinformatics Meeting 第5回研究会
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] AIアプタマー創薬「アプタマー研究の最前線」2022

    • Author(s)
      浜田 道昭(早大/CBBD-OIL)
    • Organizer
      分子生物学会ワークショップ1PWS1-09
    • Invited
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] AIアプタマー創薬プロジェクト2022

    • Author(s)
      浜田 道昭(早大/CBBD-OIL)
    • Organizer
      日本医科大学・早稲田大学合同シンポジウム
    • Invited
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] 深層学習を用いた、ヒトのエンハンサー・遺伝子相互作用に影響する転写因子の解析2022

    • Author(s)
      大里直樹(早大)、浜田 道昭(早大/CBBD-OIL)
    • Organizer
      「データ駆動・AI駆動を中心としたデジタルトランスフォーメーションによる生命科学研究の革新[バイオDX]」 キックオフシンポジウム「バイオDXの最前線」
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] ゲノム社会とバイオインフォマティクス2022

    • Author(s)
      浜田 道昭(早大/CBBD-OIL)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Invited
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] 深層学習を用いた、ヒトのエンハンサー・遺伝子相互作用に影響する転写因子の解析2022

    • Author(s)
      大里直樹(早大)、浜田 道昭(早大/CBBD-OIL)
    • Organizer
      「データ駆動・AI駆動を中心としたデジタルトランスフォーメーションによる生命科学研究の革新[バイオDX]」 キックオフシンポジウム「バイオDXの最前線」
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] ヒトのエンハンサーと遺伝子相互作用や転写制御に影響する、方向性のある転写因子DNA結合配列の解析法の開発2022

    • Author(s)
      大里直樹(早大)、浜田 道昭(早大/CBBD-OIL)
    • Organizer
      第44回日本分子生物学会年会
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] De novo repeat detection using inexact seed2022

    • Author(s)
      Atsushi Takeda(早大/CBBD-OIL), Yuta Imazu(東大), Daisuke Nonaka(東大), Tsukasa Fukunaga(早大), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      Tokyo Bioinformatics Meeting 第5回研究会
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] ヒトのエンハンサーと遺伝子相互作用や転写制御に影響する、方向性のある転写因子DNA結合配列の解析法の開発2022

    • Author(s)
      大里直樹(早大)、浜田 道昭(早大/CBBD-OIL)
    • Organizer
      第67回バイオ情報学研究会
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] Estimation of Stability of State transition of Human gut microbiota using Hidden Markov Model2022

    • Author(s)
      YOKOYAMA Gentaro(早大), HOSODA Shion(早大/CBBD-OIL), FUKUNAGA Tsukasa(早大), HAMADA Michiaki(早大/CBBD-OIL)
    • Organizer
      Tokyo Bioinformatics Meeting 第5回研究会
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] ヒトのエンハンサーと遺伝子相互作用や転写制御に影響する、方向性のある転写因子DNA結合配列の解析法の開発2022

    • Author(s)
      大里直樹(早大)、浜田 道昭(早大/CBBD-OIL)
    • Organizer
      第44回日本分子生物学会年会
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] Relationship between abnormal retrotransposition and development of schizophrenia in neurons2021

    • Author(s)
      Miyako Ishihara(早大), Kotaro Sekine(早大), Masahiro Onoguchi(早大/CBBD-OIL), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      第44回日本神経科学大会・CJK第1回国際会議
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] 変異アレル頻度を考慮したヒトがんゲノムの変異シグネチャー解析2021

    • Author(s)
      Taro Matsutani(早大/CBBD-OIL), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] 変異アレル頻度を考慮したヒトがんゲノムの変異シグネチャー解析2021

    • Author(s)
      Taro Matsutani(早大/CBBD-OIL), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] 隠れマルコフモデルを用いたヒト腸内細菌叢の個人内エンテロタイプ遷移の推定2021

    • Author(s)
      横山 源太朗(早大)、細田 至温(早大/CBBD-OIL)、福永 津嵩(早大/東大)、浜田 道昭(早大/CBBD-OIL)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] 細菌叢データにおける系統樹に基づいた回帰のためのベイジアンモデルの提案2021

    • Author(s)
      Shion Hosoda(早大/CBBD-OIL), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] Prediction of RNA-Protein Interactions Using a Nucleotide Language Model2021

    • Author(s)
      Keisuke Yamada(早大), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      第22回日本RNA学会年会
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] 深層学習を用いたRNAアクセシビリティ予測の高速化2021

    • Author(s)
      Kaisei Hara(早大), Natsuki Iwano(早大), Tsukasa Fukunaga(早大/東大), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] ヒトのエンハンサーと遺伝子相互作用や転写制御に影響する、方向性のある転写因子DNA結合配列の発見2021

    • Author(s)
      大里 直樹(早大)、浜田 道昭(早大/CBBD-OIL)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] 細菌叢データにおける系統樹に基づいた回帰のためのベイジアンモデルの提案2021

    • Author(s)
      Shion Hosoda(早大/CBBD-OIL), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] Umibato: estimation of time-varying microbial interaction using continuous-time regression hidden Markov model2021

    • Author(s)
      Shion Hosoda(早大/CBBD-OIL; 筆頭), Tsukasa Fukunaga(早大/東大), Michiaki Hamada(早大/CBBD-OIL; C.A.)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] 脳における細胞種特異的なDNA結合モチーフとしての転移因子の機能2021

    • Author(s)
      Kotaro Sekine(早大), Masahiro Onoguchi(早大/CBBD-OIL), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] The function of transposons as regulatory DNA elements in excitatory neurons2021

    • Author(s)
      Kotaro Sekine(早大), Masahiro Onoguchi(早大/CBBD-OIL), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      第44回日本神経科学大会・CJK第1回国際会議
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] ヒト遺伝子アノテーションがRNA-seq解析に与える影響の評価2021

    • Author(s)
      Yu Hamaguchi(早大), Chao Zeng(早大/CBBD-OIL), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] E.coli K-12 MG1655株の機能未知遺伝子群y-omeの特徴解析及びその機能予測可能性の検証2021

    • Author(s)
      Hitoshi Iuchi(早大/CBBD-OIL), Michiaki Hamada(早大/CBBD-OIL), Tsukasa Fukunaga(早大)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] Binding patterns of RNA binding proteins to repeat-derived RNA sequences reveal putative functional RNA elements2021

    • Author(s)
      Masahiro Onoguchi(早大/CBBD-OIL; 筆頭),Chao Zeng(早大/CBBD-OIL), Ayako Matsumaru, Michiaki Hamada(早大/CBBD-OIL; C.A.)
    • Organizer
      Keystone Symposia: Non-Coding RNAs: Biology and Applications
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] 転写因子結合部位として働く反復配列の発見とその機能の解明2021

    • Author(s)
      Ryo Niwa(早大), Chao Zeng(早大/CBBD-OIL), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] Searching for Repeat-derived Functional Elements in RNAs2021

    • Author(s)
      Chao Zeng(早大/CBBD-OIL), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      第22回日本RNA学会年会
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] Prediction of RNA-Protein Interactions Using a Nucleotide Language Model2021

    • Author(s)
      Keisuke Yamada(早大), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      第22回日本RNA学会年会
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] Searching for Repeat-derived Functional Elements in RNAs2021

    • Author(s)
      Chao Zeng(早大/CBBD-OIL), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      第22回日本RNA学会年会
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] 液-液相分離の現象に着目したエンハンサーRNAの機能解析2021

    • Author(s)
      Arisa Nozaki(早大), Masahiro Onoguchi(早大/CBBD-OIL), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] Binding Patterns of RNA Binding Proteins To Repeat-Derived RNA Sequences Reveal Putative Functional RNA Elements2021

    • Author(s)
      Masahiro Onoguchi(早大/CBBD-OIL; 筆頭),Chao Zeng(早大/CBBD-OIL), Ayako Matsumaru, Michiaki Hamada(早大/CBBD-OIL; C.A.)
    • Organizer
      第22回日本RNA学会年会
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] リピート配列由来の機能エレメントの探索2021

    • Author(s)
      曽 超(早大/CBBD-OIL)、浜田 道昭i(早大/CBBD-OIL)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] 転写因子結合部位として働く反復配列の発見とその機能の解明2021

    • Author(s)
      Ryo Niwa(早大), Chao Zeng(早大/CBBD-OIL), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] De Novo Repeat Detection using Inexact Seed2021

    • Author(s)
      Atsushi Takeda(早大), Daisuke Nonaka(東大), Yuta Imazu(東大), Tsukasa Fukunaga(早大), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] 変異クラスに依存しない階層ベイズモデルに基づくがんゲノムのIndelシグネチャー決定2021

    • Author(s)
      Taro Matsutani(早大/CBBD-OIL), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] IS-divergenceを用いた非負値行列因子分解による変異シグネチャ抽出ツールの改善2021

    • Author(s)
      Risa Akita(早大), Taro Matsutani(早大/CBBD-OIL), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] 脳における細胞種特異的なDNA結合モチーフとしての転移因子の機能2021

    • Author(s)
      Kotaro Sekine(早大), Masahiro Onoguchi(早大/CBBD-OIL), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] Binding Patterns of RNA Binding Proteins To Repeat-Derived RNA Sequences Reveal Putative Functional RNA Elements2021

    • Author(s)
      Masahiro Onoguchi(早大/CBBD-OIL; 筆頭),Chao Zeng(早大/CBBD-OIL), Ayako Matsumaru, Michiaki Hamada(早大/CBBD-OIL; C.A.)
    • Organizer
      第22回日本RNA学会年会
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] The function of transposons as regulatory DNA elements in excitatory neurons2021

    • Author(s)
      Kotaro Sekine(早大), Masahiro Onoguchi(早大/CBBD-OIL), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      第44回日本神経科学大会・CJK第1回国際会議
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] ニューロンにおける転移因子の転移異常と統合失調症発症の関係2021

    • Author(s)
      Miyako Ishihara(早大), Kotaro Sekine(早大), Masahiro Onoguchi(早大/CBBD-OIL), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] 塩基対確率に基づくRNA二次構造検索ツールの開発2021

    • Author(s)
      Chisato Yuki(早大), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] Umibato: estimation of time-varying microbial interaction using continuous-time regression hidden Markov model2021

    • Author(s)
      Shion Hosoda(早大/CBBD-OIL; 筆頭), Tsukasa Fukunaga(早大/東大), Michiaki Hamada(早大/CBBD-OIL; C.A.)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] Relationship between abnormal retrotransposition and development of schizophrenia in neurons2021

    • Author(s)
      Miyako Ishihara(早大), Kotaro Sekine(早大), Masahiro Onoguchi(早大/CBBD-OIL), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      第44回日本神経科学大会・CJK第1回国際会議
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] ニューロンにおける転移因子の転移異常と統合失調症発症の関係2021

    • Author(s)
      Miyako Ishihara(早大), Kotaro Sekine(早大), Masahiro Onoguchi(早大/CBBD-OIL), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] LDAを使用した微生物-代謝物相互作用の推定,2021

    • Author(s)
      Risa Maemura(早大), Shion Hosoda(早大/CBBD-OIL), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] 変異クラスに依存しない階層ベイズモデルに基づくがんゲノムのIndelシグネチャー決定2021

    • Author(s)
      Taro Matsutani(早大/CBBD-OIL), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] A variational autoencoder with profile hidden Markov model for generative aptamer discovery2021

    • Author(s)
      Natsuki Iwano(早大), Tatsuo Adachi, Kazuteru Aoki, Yoshikazu Nakamura and Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] LDAを使用した微生物-代謝物相互作用の推定,2021

    • Author(s)
      Risa Maemura(早大), Shion Hosoda(早大/CBBD-OIL), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] De Novo Repeat Detection using Inexact Seed2021

    • Author(s)
      Atsushi Takeda(早大), Daisuke Nonaka(東大), Yuta Imazu(東大), Tsukasa Fukunaga(早大), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] ヒトのエンハンサーと遺伝子相互作用や転写制御に影響する、方向性のある転写因子DNA結合配列の発見2021

    • Author(s)
      大里 直樹(早大)、浜田 道昭(早大/CBBD-OIL)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] IS-divergenceを用いた非負値行列因子分解による変異シグネチャ抽出ツールの改善2021

    • Author(s)
      Risa Akita(早大), Taro Matsutani(早大/CBBD-OIL), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] 液-液相分離の現象に着目したエンハンサーRNAの機能解析2021

    • Author(s)
      Arisa Nozaki(早大), Masahiro Onoguchi(早大/CBBD-OIL), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] 隠れマルコフモデルを用いたヒト腸内細菌叢の個人内エンテロタイプ遷移の推定2021

    • Author(s)
      横山 源太朗(早大)、細田 至温(早大/CBBD-OIL)、福永 津嵩(早大/東大)、浜田 道昭(早大/CBBD-OIL)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] リピート配列由来の機能エレメントの探索2021

    • Author(s)
      曽 超(早大/CBBD-OIL)、浜田 道昭i(早大/CBBD-OIL)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] E.coli K-12 MG1655株の機能未知遺伝子群y-omeの特徴解析及びその機能予測可能性の検証2021

    • Author(s)
      Hitoshi Iuchi(早大/CBBD-OIL), Michiaki Hamada(早大/CBBD-OIL), Tsukasa Fukunaga(早大)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] A variational autoencoder with profile hidden Markov model for generative aptamer discovery2021

    • Author(s)
      Natsuki Iwano(早大), Tatsuo Adachi, Kazuteru Aoki, Yoshikazu Nakamura and Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] Binding patterns of RNA binding proteins to repeat-derived RNA sequences reveal putative functional RNA elements2021

    • Author(s)
      Masahiro Onoguchi(早大/CBBD-OIL; 筆頭),Chao Zeng(早大/CBBD-OIL), Ayako Matsumaru, Michiaki Hamada(早大/CBBD-OIL; C.A.)
    • Organizer
      Keystone Symposia: Non-Coding RNAs: Biology and Applications
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] 塩基対確率に基づくRNA二次構造検索ツールの開発2021

    • Author(s)
      Chisato Yuki(早大), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] A novel fast pipeline for RNA homology search considering secondary structure with E-value calculation2021

    • Author(s)
      Kento Kubo(早大), Tsukasa Fukunaga(早大), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] A novel fast pipeline for RNA homology search considering secondary structure with E-value calculation2021

    • Author(s)
      Kento Kubo(早大), Tsukasa Fukunaga(早大), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] 深層学習を用いたRNAアクセシビリティ予測の高速化2021

    • Author(s)
      Kaisei Hara(早大), Natsuki Iwano(早大), Tsukasa Fukunaga(早大/東大), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] ヒト遺伝子アノテーションがRNA-seq解析に与える影響の評価2021

    • Author(s)
      Yu Hamaguchi(早大), Chao Zeng(早大/CBBD-OIL), Michiaki Hamada(早大/CBBD-OIL)
    • Organizer
      第10回生命医薬情報学連合大会(IIBMP2021)
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] Subcellular localization of lncRNAs is affected by Transposable Element (TE) derived sequences inside lncRNAs2018

    • Author(s)
      Takafumi Chishima and Michiaki Hamada
    • Organizer
      The Sixteenth Asia Pacific Bioinformatics Conference (APBC 2018)
    • Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] 生命科学と情報科学をつなぐバイオインフォマティクス研究2018

    • Author(s)
      浜田道昭
    • Organizer
      日本材料科学会 平成30年度学術講演大会
    • Invited
    • Data Source
      KAKENHI-PROJECT-17K20032
  • [Presentation] Estimating energy parameters for RNA secondary structure predictions using both experimental and computational data2017

    • Author(s)
      Shimpei Nishida, Shun Sakuraba, Kiyoshi Asai, Michiaki Hamada
    • Organizer
      The 28th International Conference on Genome Informatics GIW/BIOINFO 2017
    • Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-16H02484
  • [Presentation] 隠れ特徴モデル(LFM)によるヒストン修飾解析2017

    • Author(s)
      武田 悠希, 浜田 道昭
    • Organizer
      東京バイオインフォマティクスミーティング
    • Data Source
      KAKENHI-PUBLICLY-16H01318
  • [Presentation] 生命情報科学と私2017

    • Author(s)
      浜田道昭
    • Organizer
      第9回生命情報科学若手の会
    • Invited
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] Analysis of histone modifications using latent feature models2017

    • Author(s)
      Yuki Takeda and Michiaki Hamada
    • Organizer
      第6回生命医薬情報学連合大会(IIBMP 2017)
    • Data Source
      KAKENHI-PUBLICLY-16H01318
  • [Presentation] Identification of Transposable Elements which contribute to tissue specific expression of lncRNAs2017

    • Author(s)
      Takafumi Chishima, Junichi Iwakiri and Michiaki Hamada
    • Organizer
      第6回生命医薬情報学連合大会(IIBMP 2017)
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] 長鎖ノンコーディングRNA の機能の解明に向けたバイオインフォマティクス技術2017

    • Author(s)
      浜田道昭
    • Organizer
      EWE 三月会 11 月例会
    • Invited
    • Data Source
      KAKENHI-PROJECT-16H05879
  • [Presentation] Improved accuracy in RNA-protein rigid body docking by incorporating force eld for molecular dynamics simulation into the scoring function2016

    • Author(s)
      unichi Iwakiri, Michiaki Hamada, Kiyoshi Asai, Tomoshi Kameda
    • Organizer
      RNA2016
    • Place of Presentation
      京都国際会議場
    • Year and Date
      2016-06-29
    • Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-25240044
  • [Presentation] 疾患リスクの評価へ向けた加法準同型性暗号によるプライバシー保護HMMの実装と評価2016

    • Author(s)
      三品 気吹, 浜田道昭
    • Organizer
      情報処理学会 第108回MPS・第46回BIO合同研究発表会
    • Place of Presentation
      沖縄
    • Year and Date
      2016-07-04
    • Data Source
      KAKENHI-PROJECT-25540131
  • [Presentation] Comprehensive prediction of lncRNA–RNA interactions in human transcriptome2016

    • Author(s)
      Michiaki Hamada
    • Organizer
      APBC2016
    • Place of Presentation
      サンフランシスコ
    • Year and Date
      2016-01-12
    • Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-24680031
  • [Presentation] Rtools: a web server for various secondary structural analyses on single RNA sequences2016

    • Author(s)
      Michiaki Hamada, Yukiteru Ono, Hisanori Kiryu, Kengo Sato, Yuki Kato, Tsukasa Fukunaga, Ryota Mori, Kiyoshi Asai
    • Organizer
      RNA2016
    • Place of Presentation
      京都国際会議場
    • Year and Date
      2016-06-29
    • Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-25240044
  • [Presentation] ヒトトランスクリプトームにおける網羅的 lncRNA-RNA 相互作用予測2015

    • Author(s)
      寺井悟朗、岩切淳一、亀田倫史、浜田道昭、浅井潔
    • Organizer
      第17回日本RNA学会年会
    • Place of Presentation
      札幌パークホテル
    • Year and Date
      2015-07-15
    • Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-25240044
  • [Presentation] 全ゲノム変異解析のためのパイプラインの構築2015

    • Author(s)
      石井 公太郎,平野 智也,風間 裕介,浜田 道昭,小野 幸輝,阿部 知子
    • Organizer
      日本育種学会 第127回講演会
    • Place of Presentation
      玉川大学
    • Year and Date
      2015-03-20
    • Data Source
      KAKENHI-PROJECT-221S0002
  • [Presentation] 分子動力学計算を用いた蛋白質・RNA 複合体立体構㐀予測2015

    • Author(s)
      由良敬,岩切淳一,浜田道昭,浅井潔,亀田倫史
    • Organizer
      第17回日本RNA学会年会
    • Place of Presentation
      札幌パークホテル
    • Year and Date
      2015-07-15
    • Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-25240044
  • [Presentation] A semi-supervised learning approach for RNA secondary structure prediction2015

    • Author(s)
      浜田道昭
    • Organizer
      The 13-th Asia Pacific Bioinformatics Conference (APBC2015)
    • Place of Presentation
      台湾
    • Year and Date
      2015-01-21
    • Data Source
      KAKENHI-PROJECT-24680031
  • [Presentation] RNA 発現量を用いた組織特異的 lncRNA-mRNA 相互作用予測2015

    • Author(s)
      岩切淳一、寺井悟朗、亀田倫史、浅井潔 、浜田道昭
    • Organizer
      第17回日本RNA学会年会
    • Place of Presentation
      札幌パークホテル
    • Year and Date
      2015-07-15
    • Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-25240044
  • [Presentation] 分子動力学計算を用いたRNA・タンパク質複合体立体構造予測2015

    • Author(s)
      由良敬、岩切淳一、浜田道昭、浅井潔、亀田倫史
    • Organizer
      第17回日本RNA学会年会
    • Place of Presentation
      北海道札幌市 ホテルライフォート札幌
    • Year and Date
      2015-07-15
    • Data Source
      KAKENHI-PROJECT-25240044
  • [Presentation] RNA2次構造情報解析のための統合ウェブ2014

    • Author(s)
      浅井潔、浜田道昭、小野幸輝
    • Organizer
      第16回日本RNA学会年会
    • Place of Presentation
      愛知県名古屋市 ウインクあいち
    • Year and Date
      2014-07-23
    • Data Source
      KAKENHI-PROJECT-25240044
  • [Presentation] RNA-タンパク質相互作用予測法の開発2014

    • Author(s)
      岩切淳一、亀田倫史、浅井潔、浜田道昭
    • Organizer
      第16回日本RNA学会年会
    • Place of Presentation
      愛知県名古屋市 ウインクあいち
    • Year and Date
      2014-07-23
    • Data Source
      KAKENHI-PROJECT-25240044
  • [Presentation] Credibility Limitは推定二次構造の定量的な信頼度を示す2014

    • Author(s)
      森僚太、浜田道昭、浅井潔
    • Organizer
      第16回日本RNA学会年会
    • Place of Presentation
      愛知県名古屋市 ウインクあいち
    • Year and Date
      2014-07-23
    • Data Source
      KAKENHI-PROJECT-25240044
  • [Presentation] 分子動力学計算を用いたRNA・タンパク質複合体立体構造予測2014

    • Author(s)
      由良敬、岩切淳一、浜田道昭、浅井潔、亀田倫史
    • Organizer
      第16回日本RNA学会年会
    • Place of Presentation
      愛知県名古屋市 ウインクあいち
    • Year and Date
      2014-07-23
    • Data Source
      KAKENHI-PROJECT-25240044
  • [Presentation] 2 次構造情報を基盤とした RNA バイオインフォマティクス技 術・ツールの最近の進展2013

    • Author(s)
      浜田道昭
    • Organizer
      第15回日本RNA学会
    • Place of Presentation
      愛媛県、ひめぎんホール
    • Data Source
      KAKENHI-PROJECT-24680031
  • [Presentation] Privacy-preserving search for a chemical compound database2013

    • Author(s)
      Kana Shimizu, Hiromi Arai, Koji Nuida, Michiaki Hamada, Koji Tsuda, Jun Sakuma, Takatsugu Hirokawa, Goichiro Hanaoka, Kiyoshi Asai,
    • Organizer
      ISMB/ECCB 2013
    • Place of Presentation
      ベルリン、ドイツ
    • Data Source
      KAKENHI-PROJECT-25540131
  • [Presentation] 次世代バイオインフォマティクス技術の研究開発2013

    • Author(s)
      浜田道昭
    • Organizer
      医薬会セミナー
    • Place of Presentation
      東京都、国立国際医療研究センター
    • Invited
    • Data Source
      KAKENHI-PROJECT-24680031
  • [Presentation] 次世代バイオインフォマティクス技術の研究開発2013

    • Author(s)
      浜田道昭
    • Organizer
      医薬会セミナー
    • Place of Presentation
      国立国際医療研究センター、東京都
    • Invited
    • Data Source
      KAKENHI-PROJECT-25540131
  • [Presentation] タンパク質-RNA相互作用におけるRNA2次構造認識機構:塩基対確率に基づく解析2013

    • Author(s)
      岩切 淳一,亀田 倫史,浅井 潔,浜田 道昭
    • Organizer
      第15回日本RNA学会年会
    • Place of Presentation
      愛媛県・県民文化会館・ひめぎんホール
    • Data Source
      KAKENHI-PROJECT-221S0002
  • [Presentation] Direct updating of an RNA base-pairing probability matrix with marginal Probability constraints2012

    • Author(s)
      Michiaki Hamada
    • Organizer
      BIW02012
    • Place of Presentation
      産総研臨海副都心センター(東京都)
    • Year and Date
      2012-11-01
    • Data Source
      KAKENHI-PROJECT-24680031
  • [Presentation] 分子動力学計算を用いた蛋白質・RNA 複合体立体構造予測

    • Author(s)
      由良 敬、岩切 淳一、浜田 道昭、浅井 潔、亀田 倫史
    • Organizer
      第16回日本RNA学会
    • Place of Presentation
      名古屋
    • Year and Date
      2014-07-23 – 2014-07-25
    • Data Source
      KAKENHI-PROJECT-25240044
  • [Presentation] RNA2次構造情報解析のための統合ウェブ

    • Author(s)
      浅井潔、浜田道昭、小野幸輝
    • Organizer
      第16回日本RNA学会
    • Place of Presentation
      名古屋
    • Year and Date
      2014-07-23 – 2014-07-25
    • Data Source
      KAKENHI-PROJECT-25240044
  • [Presentation] Prediction of joint RNA secondary structure by using their homologous sequence information

    • Author(s)
      Takashi Matsuda, Michiaki Hamada and Kiyoshi Asai
    • Organizer
      GIW/ISCB-Asia 2014
    • Place of Presentation
      東京
    • Year and Date
      2014-12-15 – 2014-12-17
    • Data Source
      KAKENHI-PROJECT-25240044
  • [Presentation] Pipeline for whole-genome analysis of heavy-ion-induced mutants

    • Author(s)
      Kotaro Ishii, Tomonari Hirano, Yusuke Kazama, Michiaki Hamada, Yukiteru Ono, Tomoko Abe
    • Organizer
      International Symposium on Genome Science
    • Place of Presentation
      東京 一橋講堂
    • Year and Date
      2015-01-20 – 2015-01-21
    • Data Source
      KAKENHI-PROJECT-221S0002
  • [Presentation] Credibility Limit は推定二次構造の定量的な信頼度を示す

    • Author(s)
      森 遼太、浜田 道昭、浅井 潔
    • Organizer
      第16回日本RNA学会
    • Place of Presentation
      名古屋
    • Year and Date
      2014-07-23 – 2014-07-25
    • Data Source
      KAKENHI-PROJECT-25240044
  • [Presentation] 分子動力学計算を用 いた蛋白質・RNA 複合体立体構造予測

    • Author(s)
      由良 敬、岩切 淳一、浜田 道昭、浅井 潔、亀田 倫史
    • Organizer
      第52回日本生物物理学会
    • Place of Presentation
      札幌
    • Year and Date
      2014-09-25 – 2014-09-27
    • Data Source
      KAKENHI-PROJECT-25240044
  • [Presentation] RNA-タンパク質相互作用予測手法の開発

    • Author(s)
      岩切淳一、亀田 倫史、浅井 潔、浜田 道昭
    • Organizer
      第16回日本RNA学会
    • Place of Presentation
      名古屋
    • Year and Date
      2014-07-23 – 2014-07-25
    • Data Source
      KAKENHI-PROJECT-25240044
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    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 65.  山田 拓司 (10437262)
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 66.  KURIYAMA Mariko
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 67.  ANZAI Yuichiro
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 68.  OKADA Kiyotaka
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 69.  SAKAKI Yoshiyuki
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 70.  TAKAKU Fumimaro
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 71.  TOYOSHIMA Kumao
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 72.  NAKAMURA Keiko
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 73.  HOTTA Yoshiki
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 74.  YONEZAWA Akinori
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 75.  YOSHIKAWA Hiroshi
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 76.  YOSHIDA Mitsuaki
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 77.  INOKO Hidetoshi
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 78.  TODA Tatsushi
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 79.  INAZAWA Johji
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 80.  GOJOBORI Takashi
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 81.  URUSHIHARA Hideko
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 82.  TAKEDA Hiroyuki
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 83.  SHIROISHI Toshihiko
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 84.  ITOH Takashi
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 85.  SATOH Noriyuki
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 1 results
  • 86.  MATSUDA Hideo
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 87.  GOTO Susumu
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 1 results
  • 88.  TSUDA Masataka
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 89.  AOKI Hiroshi
    # of Collaborated Projects: 0 results
    # of Collaborated Products: 1 results
  • 90.  MURATA Asako
    # of Collaborated Projects: 0 results
    # of Collaborated Products: 1 results
  • 91.  SATO Kengo
    # of Collaborated Projects: 0 results
    # of Collaborated Products: 2 results
  • 92.  KIRYU Hisanori
    # of Collaborated Projects: 0 results
    # of Collaborated Products: 1 results
  • 93.  KATO Yuki
    # of Collaborated Projects: 0 results
    # of Collaborated Products: 2 results
  • 94.  ONO Yukiteru
    # of Collaborated Projects: 0 results
    # of Collaborated Products: 1 results
  • 95.  MORI Ryota
    # of Collaborated Projects: 0 results
    # of Collaborated Products: 1 results
  • 96.  HIRONO Keiichi
    # of Collaborated Projects: 0 results
    # of Collaborated Products: 1 results
  • 97.  MOGUSHI Kaoru
    # of Collaborated Projects: 0 results
    # of Collaborated Products: 1 results
  • 98.  TAKANO Atsushi
    # of Collaborated Projects: 0 results
    # of Collaborated Products: 1 results
  • 99.  SHOGUCHI Eiichi
    # of Collaborated Projects: 0 results
    # of Collaborated Products: 2 results
  • 100.  SHINZATO Chuya
    # of Collaborated Projects: 0 results
    # of Collaborated Products: 1 results
  • 101.  谷 英典
    # of Collaborated Projects: 0 results
    # of Collaborated Products: 1 results
  • 102.  中谷 和彦
    # of Collaborated Projects: 0 results
    # of Collaborated Products: 1 results
  • 103.  市田 蕗子
    # of Collaborated Projects: 0 results
    # of Collaborated Products: 1 results
  • 104.  小澤 綾佳
    # of Collaborated Projects: 0 results
    # of Collaborated Products: 1 results
  • 105.  ワリ ナディラ
    # of Collaborated Projects: 0 results
    # of Collaborated Products: 1 results
  • 106.  折茂 彰
    # of Collaborated Projects: 0 results
    # of Collaborated Products: 1 results
  • 107.  醍醐 弥太郎
    # of Collaborated Projects: 0 results
    # of Collaborated Products: 1 results
  • 108.  平賀 徹
    # of Collaborated Projects: 0 results
    # of Collaborated Products: 1 results
  • 109.  竹田 和由
    # of Collaborated Projects: 0 results
    # of Collaborated Products: 1 results
  • 110.  伊藤 匠
    # of Collaborated Projects: 0 results
    # of Collaborated Products: 1 results
  • 111.  野呂 林太郎
    # of Collaborated Projects: 0 results
    # of Collaborated Products: 1 results

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