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Functional classification of long noncoding RNAs based on functional elements and deep learning

Research Project

Project/Area Number 16H05879
Research Category

Grant-in-Aid for Young Scientists (A)

Allocation TypeSingle-year Grants
Research Field Life / Health / Medical informatics
Research InstitutionWaseda University

Principal Investigator

Hamada Michiaki  早稲田大学, 理工学術院, 教授 (00596538)

Project Period (FY) 2016-04-01 – 2020-03-31
Project Status Completed (Fiscal Year 2021)
Budget Amount *help
¥23,400,000 (Direct Cost: ¥18,000,000、Indirect Cost: ¥5,400,000)
Fiscal Year 2019: ¥6,890,000 (Direct Cost: ¥5,300,000、Indirect Cost: ¥1,590,000)
Fiscal Year 2018: ¥7,020,000 (Direct Cost: ¥5,400,000、Indirect Cost: ¥1,620,000)
Fiscal Year 2017: ¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Fiscal Year 2016: ¥5,590,000 (Direct Cost: ¥4,300,000、Indirect Cost: ¥1,290,000)
KeywordslncRNA / ノンコーディングRNA / RNA修飾 / RNA構造 / リピート要素 / 深層学習 / 長鎖ノンコーディングRNA / 機能エレメント / RNA結合タンパク質 / RNA相互作用 / バイオインフォマティクス / トランスポゾン / 機能推定 / lncRNA-RNA相互作用 / リボソーム / 機械学習 / m6A / 大規模実験情報 / 進化
Outline of Final Research Achievements

To elucidate the function of long non-coding RNAs (lncRNAs), which are not translated into proteins but have their own functions, we have conducted many studies from an informatics perspective, focusing on "functional elements" such as RNA sequences, structures, modifications, and interactions with biological macromolecules. For example, we attempted to elucidate the functions of lncRNAs by clarifying that repeat sequences, which were thought to be junk, contribute to the tissue-specific expression of lncRNAs and to their interactions with proteins and DNA. Through these efforts, we have established information infrastructure technology that contributes to the classification of lncRNA functions, and have made it widely available to the public.

Academic Significance and Societal Importance of the Research Achievements

現在機能のわかっていないlncRNAの中には,がんや神経変性疾患などの重篤な疾患と関連するものが存在すると考えられている.今回開発した技術や解析結果により,今後lncRNAと疾患との関連性が明らかになった暁には,RNAをターゲットにした医学・薬学研究などに発展する可能性が高い.

Report

(5 results)
  • 2021 Final Research Report ( PDF )
  • 2019 Annual Research Report
  • 2018 Annual Research Report
  • 2017 Annual Research Report
  • 2016 Annual Research Report
  • Research Products

    (76 results)

All 2022 2021 2020 2019 2018 2017

All Journal Article (28 results) (of which Int'l Joint Research: 2 results,  Peer Reviewed: 28 results,  Open Access: 21 results,  Acknowledgement Compliant: 1 results) Presentation (47 results) (of which Int'l Joint Research: 1 results,  Invited: 6 results) Book (1 results)

  • [Journal Article] Prediction of RNA-protein interactions using a nucleotide language model2022

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

      Bioinformatics Advances

      Volume: 2 Issue: 1

    • DOI

      10.1093/bioadv/vbac023

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [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 Issue: 2 Pages: 378-387

    • DOI

      10.1038/s41390-022-01999-9

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [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

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [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 & Genetic Systems

      Volume: 96 Issue: 1 Pages: 1-11

    • DOI

      10.1266/ggs.20-00012

    • NAID

      130008035886

    • ISSN
      1341-7568, 1880-5779
    • Year and Date
      2021-02-01
    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [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 Issue: 1 Pages: 554-554

    • DOI

      10.1186/s12859-021-04430-y

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [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 Issue: 1 Pages: 730-730

    • DOI

      10.1186/s12864-021-08038-7

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [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 Issue: 4

    • DOI

      10.1093/nargab/lqab093

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [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 Issue: 3

    • DOI

      10.1093/nargab/lqab055

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [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 Issue: Supplement_1 Pages: i16-i24

    • DOI

      10.1093/bioinformatics/btab287

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [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 Issue: 8 Pages: 4005-4005

    • DOI

      10.3390/ijms22084005

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [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 Issue: 1

    • DOI

      10.1093/nargab/lqab021

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [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

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Association analysis of repetitive elements and R-loop formation across species2021

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

      Mobile DNA

      Volume: 12 Issue: 1 Pages: 3-3

    • DOI

      10.1186/s13100-021-00231-5

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Detection and Characterization of Ribosome-Associated Long Noncoding RNAs2020

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

      Methods in Molecular Biology

      Volume: 2254 Pages: 179-194

    • DOI

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

    • ISBN
      9781071611579, 9781071611586
    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Targeting the TR4 nuclear receptor-mediated lncTASR/AXL signaling with Tretinoin increases the Sunitnib 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 Issue: 3 Pages: 530-545

    • DOI

      10.1038/s41388-019-0962-8

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Identification of RNA biomarkers for chemical safety screening in neural cells derived from mouse embryonic stem cells using RNA deep sequencing analysis.2019

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

      Biochem Biophys Res Commun.

      Volume: 512 Issue: 4 Pages: 641-646

    • DOI

      10.1016/j.bbrc.2018.11.141

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] LncRRIsearch: a web server for lncRNA-RNA interaction prediction integrated with tissue-specific expression and subcellular localization data2019

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

      Front. Genet.

      Volume: - Pages: 462-462

    • DOI

      10.3389/fgene.2019.00462

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Stromal fibroblasts induce metastatic tumor cell clusters via epithelial-mesenchymal plasticity.2019

    • Author(s)
      Matsumura Y, Ito Y, Mezawa Y, Sulidan K, Daigo Y, Hiraga T, Mogushi K, Wali N, Suzuki H, Itoh T, Miyagi Y, Yokose T, Shimizu S, Takano A, Terao Y, Saeki H, Ozawa M, Abe M, Takeda S, Okumura K, Habu S, Hino O, Takeda K, Hamada M, Orimo A.
    • Journal Title

      Life Sci Alliance

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

    • DOI

      10.26508/lsa.201900425

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Discovering novel mutation signatures by latent Dirichlet allocation with variational Bayes inference2019

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

      Bioinformatics

      Volume: 35 Issue: 22 Pages: 4543-4552

    • DOI

      10.1093/bioinformatics/btz266

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [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: - Issue: 3 Pages: 182-191

    • DOI

      10.1093/bfgp/ely042

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Identifying sequence features that drive ribosomal association for lncRNA2018

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

      BMC Genomics

      Volume: 19 Issue: S10 Pages: 906-906

    • DOI

      10.1186/s12864-018-5275-8

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [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 Issue: S19 Pages: 524-524

    • DOI

      10.1186/s12859-018-2516-4

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Estimating energy parameters for RNA secondary structure predictions using both experimental and computational data2018

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

      IEEE/ACM Transactions on Computational Biology and Bioinformatics

      Volume: - Issue: 5 Pages: 1645-1655

    • DOI

      10.1109/tcbb.2018.2813388

    • Description
      in press
    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 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 Issue: 9 Pages: 976-986

    • DOI

      10.1089/cmb.2017.0260

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Identification of Transposable Elements Contributing to Tissue-Specific Expression of Long Non-Coding RNAs2018

    • Author(s)
      Chishima Takafumi、Iwakiri Junichi、Hamada Michiaki
    • Journal Title

      Genes

      Volume: 9 Issue: 1 Pages: 23-23

    • DOI

      10.3390/genes9010023

    • Related Report
      2017 Annual Research Report 2016 Annual Research Report
    • Peer Reviewed / Open Access
  • [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 Issue: 4 Pages: 576-584

    • DOI

      10.1093/bioinformatics/btx643

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Computational prediction of lncRNA-mRNA interactions by integrating tissue specificity in human transcriptome2017

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

      Biology Direct

      Volume: 12 Issue: 1 Pages: 15-15

    • DOI

      10.1186/s13062-017-0183-4

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] RIblast: An ultrafast RNA-RNA interaction prediction system based on a seed-and-extension approach.2017

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

      Bioinformatics

      Volume: 印刷中 Issue: 17 Pages: 2666-2674

    • DOI

      10.1093/bioinformatics/btx287

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [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
    • Related Report
      2019 Annual Research Report
  • [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
    • Related Report
      2019 Annual Research Report
  • [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
    • Related Report
      2019 Annual Research Report
  • [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
    • Related Report
      2019 Annual Research Report
  • [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
    • Related Report
      2019 Annual Research Report
  • [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
    • Related Report
      2019 Annual Research Report
  • [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
    • Related Report
      2019 Annual Research Report
  • [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
    • Related Report
      2019 Annual Research Report
  • [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
    • Related Report
      2019 Annual Research Report
  • [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」
    • Related Report
      2019 Annual Research Report
  • [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
    • Related Report
      2019 Annual Research Report
  • [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
    • Related Report
      2019 Annual Research Report
  • [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
    • Related Report
      2019 Annual Research Report
    • Invited
  • [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
    • Related Report
      2019 Annual Research Report
    • Invited
  • [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)
    • Related Report
      2019 Annual Research Report
    • Invited
  • [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
    • Related Report
      2019 Annual Research Report
    • Invited
  • [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
    • Related Report
      2019 Annual Research Report
  • [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
    • Related Report
      2019 Annual Research Report
  • [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
    • Related Report
      2019 Annual Research Report
  • [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
    • Related Report
      2019 Annual Research Report
  • [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
    • Related Report
      2019 Annual Research Report
  • [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)
    • Related Report
      2019 Annual Research Report
  • [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)
    • Related Report
      2019 Annual Research Report
  • [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)
    • Related Report
      2019 Annual Research Report
  • [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)
    • Related Report
      2019 Annual Research Report
  • [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)
    • Related Report
      2019 Annual Research Report
  • [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)
    • Related Report
      2019 Annual Research Report
  • [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)
    • Related Report
      2019 Annual Research Report
  • [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)
    • Related Report
      2019 Annual Research Report
  • [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)
    • Related Report
      2019 Annual Research Report
  • [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)
    • Related Report
      2019 Annual Research Report
  • [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)
    • Related Report
      2019 Annual Research Report
  • [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)
    • Related Report
      2019 Annual Research Report
  • [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)
    • Related Report
      2019 Annual Research Report
  • [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)
    • Related Report
      2019 Annual Research Report
  • [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)
    • Related Report
      2019 Annual Research Report
  • [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)
    • Related Report
      2019 Annual Research Report
  • [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)
    • Related Report
      2019 Annual Research Report
  • [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)
    • Related Report
      2019 Annual Research Report
  • [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)
    • Related Report
      2019 Annual Research Report
  • [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
    • Related Report
      2019 Annual Research Report
  • [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
    • Related Report
      2019 Annual Research Report
  • [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)
    • Related Report
      2019 Annual Research Report
  • [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)
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [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
    • Related Report
      2016 Annual Research Report
    • Invited
  • [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
    • Related Report
      2016 Annual Research Report
    • Invited
  • [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)
    • Related Report
      2016 Annual Research Report
  • [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
    • Related Report
      2017 Annual Research Report

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Published: 2016-04-21   Modified: 2023-01-30  

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