HAMADA MICHIAKI 浜田道昭

… Alternative Names

Researcher Number	00596538
Other IDs	https://orcid.org/0000-0001-9466-1034
Affiliation (Current)	2021: 早稲田大学, 理工学術院, 教授 2021: 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 – 2021: 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 / Complex Systems Disease Theory / System genome science / 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 / 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 / RNA結合タンパク質 / トランスポゾン … More Except Principal Investigator RNA２次構造 / RNA2次構造 / 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 / RNA / ネットワーク / 修飾塩基 / エピトランスクリプトーム / バイオインフォマティクス / 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 / 環境医科学 / 環境脳科学 / トランスレーショナルリサーチ Less

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
ceRNAネットワーク構造の解読を基盤とした、全く新しい抗がん剤開発戦略の開発
- Principal Investigator
  
  秋光信佳
- Project Period (FY)
  2018 – 2020
- 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 – 2020
- 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 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] 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] Training alignment parameters for arbitrary sequencers with last-train,2017
- Author(s)
  Michiaki Hamada, Yukiteru Ono, Kiyoshi Asai, Martin C, Frith
- 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-16H02484, KAKENHI-PROJECT-16H06279
[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] RIblast: an ultrafast RNA-RNA interaction prediction system based on a seed-and-extension approach2017
- Author(s)
  Fukunaga Tsukasa、Hamada Michiaki
- Journal Title
  
  Bioinformatics
  
  Volume: 33 Pages: 2666-2674
- DOI
  10.1093/bioinformatics/btx287
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-16H05879, KAKENHI-PROJECT-16J00129
[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
- 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 assembly2013
- 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] 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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90. SHINZATO Chuya

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91. 谷英典

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92. ワリナディラ

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93. 折茂彰

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94. 醍醐弥太郎

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95. 平賀徹

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96. 竹田和由

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
97. 伊藤匠

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results

HAMADA MICHIAKI 浜田 道昭

HAMADA Michiaki 浜田 道昭

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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

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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

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ceRNAネットワーク構造の解読を基盤とした、全く新しい抗がん剤開発戦略の開発

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RNA-クロマチン相互作用予測と応用Principal Investigator

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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

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RNA informatics for epi-transcriptome analysis

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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

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Comprehensive prediction of RNA-protein interactinos

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Development of basic technology for privacy-preserving bioinformatics and its applicationPrincipal Investigator

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Research on structure predictions of RNA with modified nucleotiedsPrincipal Investigator

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Platform of large scale and high quality genomics and bioinformatics: Towards the advancement of genome sciences in academia

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[Book] よくわかるバイオインフォマティクス入門2018

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[Book] よくわかるバイオインフォマティクス入門2018

Author(s)

Total Pages

Publisher

HAMADA MICHIAKI 浜田道昭

HAMADA Michiaki 浜田道昭