Asai Kiyoshi 浅井潔

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ASAI Kiyoshi 浅井潔

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Researcher Number	30356357
Other IDs
External Links
Affiliation (Current)	2025: 東京大学, 大学院新領域創成科学研究科, 教授 2025: 国立研究開発法人産業技術総合研究所, 情報・人間工学領域, 招聘研究員
Affiliation (based on the past Project Information) *help	2021 – 2024: 東京大学, 大学院新領域創成科学研究科, 教授 2015 – 2019: 東京大学, 大学院新領域創成科学研究科, 教授 2012 – 2015: 東京大学, 新領域創成科学研究科, 教授 2010 – 2011: 東京大学, 大学院・新領域創成科学研究科, 教授 2009: 東京大学, 新学術領域創成科学研究科, 教授 2003 – 2009: 東京大学, 新領域創成科学研究科, 教授 2002: 産業技術総合研究所, 生命情報科学研究センター, 主任研究員
Review Section/Research Field	Principal Investigator Medium-sized Section 62:Applied informatics and related fields / System genome science / Life / Health / Medical informatics / Bioinformatics/Life informatics Except Principal Investigator Biological Sciences / Life / Health / Medical informatics
Keywords	Principal Investigator RNA２次構造 / 翻訳効率 / RNA修飾塩基 / 修飾塩基 / RNA2次構造 / バイオインフォマティクス / 配列設計 / mRNA翻訳 / エピトランスクリプトーム解析 / エピとランスクリプトーム解析 … More / ＲＮＡ2次構造 / エヒトランスプリクトーム / エネルギーパラメタ / 分子動力学 / エピトランスクリプトーム / RNA立体構造 / RNA・タンパク質相互作用 / 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-RNA相互作用 / 確率モデル / マイクロRNA / snoRNA / RNA / 機能性RNA … More Except Principal Investigator ゲノム / メタゲノム / エピゲノム / バイオインフォマティクス / リシーケンシング / 次世代DNAシーケンサー / スーパーコンピュータ / 空間的オミックス解析 / RNA解析 / ゲノム・メタゲノム / 次世代シーケンサー / シングルセル解析 / オミックス解析 / ゲノムアノテーション / ゲノム多型 / ゲノムアッセンブル / スーパーコンピューター / メタゲノム解析 / 1細胞解析 / RNA-Seq / 新規ゲノム配列決定 / 配列検索 / データベース検索 / 暗号 / 化合物 / プライバシー / 準同型暗号 / 配列アラインメント / PPDM / 隠れマルコフモデル / アラインメント / 化合物検索 / プライバシー保護 / machine learning / stochastic model / gene finding / sequence analysis / bioinformatics / ソフトウェア / アルゴリズム / コンピュータ / アノテーション / 遺伝子 / ヒト / データマイニング / 認識アルゴリズム / 学習アルゴリズム / 統計推定 / 生物配列解析 / ゲノム生物学 / カーネル法 / 機械学習 / 確率モデル / 遺伝子発見 / 配列解析 / 次世代DNAシーケンサ / インフォームドコンセント / GWAS / 個人ゲノム / de novo配列決定 / ChIP-seq / RNA-seq / スコア行列 / 2次構造 / 構造的アライメント / 非コードRNA / 分子進化距離 / シンテニーブロック / 次世代シークエンサー / アセンブリ / 機能性RNA / 2次構造予測 / ゲノム再編成 / マルチプルアライメント / 比較ゲノム Less

化学修飾を含むmRNA配列設計の基盤技術Principal Investigator
- Principal Investigator
  
  浅井潔
- Project Period (FY)
  2024 – 2027
- Research Category
  
  Grant-in-Aid for Scientific Research (A)
- Review Section
  
  Medium-sized Section 62:Applied informatics and related fields
- Research Institution
  The University of Tokyo
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
修飾塩基を持つRNAの情報解析基盤技術の開発Principal Investigator
- Principal Investigator
  
  浅井潔
- Project Period (FY)
  2021 – 2023
- Research Category
  
  Grant-in-Aid for Scientific Research (A)
- Review Section
  
  Medium-sized Section 62:Applied informatics and related fields
- Research Institution
  The University of Tokyo
RNA informatics for epi-transcriptome analysisPrincipal Investigator
- 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
Platform for Advanced Genome Science
- Principal Investigator
  
  KOHARA Yuji
- Project Period (FY)
  2016 – 2021
- Research Category
  
  Grant-in-Aid for Scientific Research on Innovative Areas ― Platforms for Advanced Technologies and Research Resources
- Research Institution
  National Institute of Genetics
Comprehensive prediction of RNA-protein interactinosPrincipal Investigator
- 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 application
- 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
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
Exhaustive prediction of microRNAs, snoRNAs and their targetsPrincipal Investigator
- Principal Investigator
  
  ASAI Kiyoshi
- Project Period (FY)
  2010 – 2012
- Research Category
  
  Grant-in-Aid for Scientific Research (A)
- Research Field
  
  Bioinformatics/Life informatics
- Research Institution
  The University of Tokyo
Development of computational methods for comparing a large scale multiple genome sequences
- Principal Investigator
  
  SAKAKIBARA Yasubumi
- Project Period (FY)
  2005 – 2009
- Research Category
  
  Grant-in-Aid for Scientific Research on Priority Areas
- Review Section
  
  Biological Sciences
- Research Institution
  Keio University
Modeling and prediction of genome sequence information by using information representation models
- Principal Investigator
  
  YADA Tetsushi
- Project Period (FY)
  2000 – 2004
- Research Category
  
  Grant-in-Aid for Scientific Research on Priority Areas
- Review Section
  
  Biological Sciences
- Research Institution
  Kyoto University
  The University of Tokyo
  The Institute of Physical and Chemical Research

[Book] Encyclopedia of Bioinformatics and Computational Biology2018
- Author(s)
  Junichi Iwakiri, Kiyoshi Asai
- Total Pages
  3284
- Publisher
  Elsevier
- Data Source
  KAKENHI-PROJECT-16H06279
[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
[Book] 統計科学のフロンティア9生物配列の統計 : 核酸・タンパクから情報を読む2003
- Author(s)
  岸野洋久, 浅井潔
- Total Pages
  264
- Publisher
  岩波書店
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-12208010
[Journal Article] The history of ancient Japanese dogs revealed by mitogenomes2024
- Author(s)
  Xiayire Xiaokaiti, Takao Sato, Kenji Kasai, Kenichi Machida, Kyomi Yamazaki, Naomitsu Yamaji, Hiroki Kikuchi, Jun Gojobori1, Hitomi Hongo, Yohey Terai, Takashi Gakuhari
- Journal Title
  
  Anthropological Science
  
  Volume: 132 Issue: 1 Pages: 1-11
- DOI
  10.1537/ase.230617
- ISSN
  0918-7960, 1348-8570
- Language
  English
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-20H05819, KAKENHI-PLANNED-20H05822, KAKENHI-PLANNED-23H04846, KAKENHI-PROJECT-22H04925, KAKENHI-PROJECT-21H04358, KAKENHI-PROJECT-23K22009
[Journal Article] Claspin is Required for Growth Recovery from Serum Starvation through Regulating the PI3K-PDK1-mTOR Pathway in Mammalian Cells2023
- Author(s)
  Yang Chi-Chun、Masai Hisao
- Journal Title
  
  Molecular and Cellular Biology
  
  Volume: 43 Issue: 1 Pages: 1-21
- DOI
  10.1080/10985549.2022.2160598
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20KK0157, KAKENHI-PROJECT-22H04922, KAKENHI-PROJECT-22H04925, KAKENHI-PROJECT-20K21410, KAKENHI-PUBLICLY-21H00264, KAKENHI-PUBLICLY-22H04707, KAKENHI-PROJECT-20H00463
[Journal Article] Water-Soluble Gd(III)-Porphyrin Complexes Capable of Both Photosensitization and Relaxation Enhancement2023
- Author(s)
  Nemeth Tamas、Yoshizawa-Sugata Naoko、Pallier Agnes、Tajima Youichi、Ma Yue、Toth Eva、Masai Hisao、Yamakoshi Yoko
- Journal Title
  
  Chemical Biomedical Imaging
  
  Volume: 1 Issue: 2 Pages: 157-167
- DOI
  10.1021/cbmi.3c00007
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-20KK0157, KAKENHI-PUBLICLY-22H04707, KAKENHI-PROJECT-22H04922, KAKENHI-PROJECT-22H04925
[Journal Article] Cell fusion upregulates PD-L1 expression for evasion from immunosurveillance2023
- Author(s)
  Tajima Youichi、Shibasaki Futoshi、Masai Hisao
- Journal Title
  
  Cancer Gene Therapy
  
  Volume: 31 Issue: 1 Pages: 158-173
- DOI
  10.1038/s41417-023-00693-0
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20KK0157, KAKENHI-PUBLICLY-22H04707, KAKENHI-PROJECT-22H04922, KAKENHI-PROJECT-22H04925
[Journal Article] Histone Modification Analysis of Low-Mappability Regions2023
- Author(s)
  Naoko Yoshizawa-Sugata , Hisao Masai
- Journal Title
  
  Methods Mol Biol
  
  Volume: 2519 Pages: 163-185
- DOI
  10.1007/978-1-0716-2433-3_18
- ISBN
  9781071624326, 9781071624333
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-22H04922, KAKENHI-PROJECT-22H04925, KAKENHI-PROJECT-20K21410, KAKENHI-PUBLICLY-21H00264, KAKENHI-PROJECT-20KK0157, KAKENHI-PUBLICLY-22H04707
[Journal Article] Aberrant association of chromatin with nuclear periphery induced by Rif1 leads to mitotic defect2023
- Author(s)
  Kanoh Yutaka、Ueno Masaru、Hayano Motoshi、Kudo Satomi、Masai Hisao
- Journal Title
  
  Life Science Alliance
  
  Volume: 6 Issue: 4 Pages: e202201603-e202201603
- DOI
  10.26508/lsa.202201603
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20KK0157, KAKENHI-PROJECT-22H04922, KAKENHI-PROJECT-22H04925, KAKENHI-PROJECT-20K21410, KAKENHI-PUBLICLY-21H00264, KAKENHI-PUBLICLY-22H04707, KAKENHI-PROJECT-20H00463
[Journal Article] Cdc7 kinase is required for postnatal brain development2023
- Author(s)
  Hori Karin、Yamazaki Satoshi、Ohtaka‐Maruyama Chiaki、Ono Tomio、Iguchi Tomohiro、Masai Hisao
- Journal Title
  
  Genes to Cells
  
  Volume: 28 Issue: 10 Pages: 679-693
- DOI
  10.1111/gtc.13059
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20KK0157, KAKENHI-PUBLICLY-22H04707, KAKENHI-PROJECT-22H04922, KAKENHI-PROJECT-22H04925
[Journal Article] Condensed but liquid-like domain organization of active chromatin regions in living human cells2023
- Author(s)
  Nozaki Tadasu、Shinkai Soya、Ide Satoru、Higashi Koichi、Tamura Sachiko、Shimazoe Masa A.、Nakagawa Masaki、Suzuki Yutaka、Okada Yasushi、Sasai Masaki、Onami Shuichi、Kurokawa Ken、Iida Shiori、Maeshima Kazuhiro
- Journal Title
  
  Science Advances
  
  Volume: 9 Issue: 14 Pages: 1-19
- DOI
  10.1126/sciadv.adf1488
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PUBLICLY-21H05763, KAKENHI-PROJECT-23K21326, KAKENHI-PROJECT-23KJ0996, KAKENHI-PUBLICLY-23H04297, KAKENHI-PROJECT-22H04925, KAKENHI-PROJECT-22H00406
[Journal Article] Claspin-Dependent and -Independent Chk1 Activation by a Panel of Biological Stresses2023
- Author(s)
  Hsiao Hao-Wen、Yang Chi-Chun、Masai Hisao
- Journal Title
  
  Biomolecules
  
  Volume: 13 Issue: 1 Pages: 125-125
- DOI
  10.3390/biom13010125
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20KK0157, KAKENHI-PROJECT-22H04922, KAKENHI-PROJECT-22H04925, KAKENHI-PROJECT-20K21410, KAKENHI-PUBLICLY-21H00264, KAKENHI-PUBLICLY-22H04707, KAKENHI-PROJECT-20H00463
[Journal Article] Claustrum mediates bidirectional and reversible control of stress-induced anxiety responses.2022
- Author(s)
  Niu M, Kasai A, Tanuma M, Seiriki K, Igarashi H, Kuwaki T, Nagayasu K, Miyaji K, Ueno H, Tanabe W, Seo K, Yokoyama R, Ohkubo J, Ago Y, Hayashida M, Inoue KI, Takada M, Yamaguchi S, Nakazawa T, Kaneko S, Okuno H, Yamanaka A, Hashimoto H.
- Journal Title
  
  Science Advances
  
  Volume: 8 Issue: 11
- DOI
  10.1126/sciadv.abi6375
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20H03556, KAKENHI-PROJECT-19H05467, KAKENHI-PUBLICLY-20H05062, KAKENHI-PROJECT-19H03328, KAKENHI-PROJECT-19H03335, KAKENHI-PROJECT-20J20247, KAKENHI-PROJECT-16H06279, KAKENHI-PROJECT-20K07064, KAKENHI-PROJECT-22K19378, KAKENHI-PROJECT-20H03391, KAKENHI-PUBLICLY-21H00200, KAKENHI-PROJECT-20H00492
[Journal Article] QRNAstruct: a method for extracting secondary structural features of RNA via regression with biological activity2022
- Author(s)
  Terai Goro、Asai Kiyoshi
- Journal Title
  
  Nucleic Acids Research
  
  Volume: na Issue: 13 Pages: e73-e73
- DOI
  10.1093/nar/gkac220
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-21K15075, KAKENHI-PROJECT-16H06279, KAKENHI-PROJECT-21H04912
[Journal Article] PBSIM3: a simulator for all types of PacBio and ONT long reads2022
- Author(s)
  Yukiteru Ono、Michiaki Hamada、Kiyoshi Asai
- Journal Title
  
  NAR Genomics and Bioinformatics
  
  Volume: 4 Issue: 4
- DOI
  10.1093/nargab/lqac092
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-22H04925
[Journal Article] Replicon hypothesis revisited2022
- Author(s)
  Masai Hisao
- Journal Title
  
  Biochemical and Biophysical Research Communications
  
  Volume: 633 Pages: 77-80
- DOI
  10.1016/j.bbrc.2022.09.060
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20KK0157, KAKENHI-PROJECT-22H04922, KAKENHI-PROJECT-22H04925, KAKENHI-PROJECT-20K21410, KAKENHI-PUBLICLY-21H00264, KAKENHI-PUBLICLY-22H04707, KAKENHI-PROJECT-20H00463
[Journal Article] DDX41 coordinates RNA splicing and transcriptional elongation to prevent DNA replication stress in hematopoietic cells2022
- Author(s)
  Satoru Shinriki;Mayumi Hirayama;Akiko Nagamachi;Akihiko Yokoyama;Takeshi Kawamura;Akinori Kanai;Hidehiko Kawai;Junichi Iwakiri;Rin Liu;Manabu Maeshiro;Saruul Tungalag;Masayoshi Tasaki;Mitsuharu Ueda;Kazuhito Tomizawa;Naoyuki Kataoka;Takashi Ideue;Yutaka Suzuki;Kiyoshi Asai;Tokio Tani;Toshiya Inaba;Hirotaka Matsui
- Journal Title
  
  Leukemia
  
  Volume: 36 Issue: 11 Pages: 2605-2620
- DOI
  10.1038/s41375-022-01708-9
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K06174, KAKENHI-PROJECT-21K08395, KAKENHI-PROJECT-21K08419, KAKENHI-PROJECT-21K12239, KAKENHI-PROJECT-22K10195, KAKENHI-PROJECT-22K12375, KAKENHI-PROJECT-22K20997, KAKENHI-PROJECT-22KK0119, KAKENHI-PROJECT-22H04925, KAKENHI-PROJECT-21H02948, KAKENHI-PROJECT-20K12041, KAKENHI-PROJECT-23K24368
[Journal Article] Remarkable improvement in detection of readthrough downstream-of-gene transcripts by semi-extractable RNA-sequencing2022
- Author(s)
  Iwakiri Junichi、Tanaka Kumiko、Chujo Takeshi、Takakuwa Hiro、Yamazaki Tomohiro、Terai Goro、Asai Kiyoshi、Hirose Tetsuro
- Journal Title
  
  RNA
  
  Volume: 29 Issue: 2 Pages: 170-177
- DOI
  10.1261/rna.079469.122
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22K19293, KAKENHI-PLANNED-21H05276, KAKENHI-PROJECT-22H04925, KAKENHI-PROJECT-20H00448, KAKENHI-PROJECT-20K12041, KAKENHI-PUBLICLY-21H00253, KAKENHI-PROJECT-23K23809
[Journal Article] TT-pocket/HIRAN: binding to 3′-terminus of DNA for recognition and processing of stalled replication forks2022
- Author(s)
  Masai Hisao
- Journal Title
  
  The Journal of Biochemistry
  
  Volume: 172 Issue: 2 Pages: 57-60
- DOI
  10.1093/jb/mvac042
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20KK0157, KAKENHI-PROJECT-22H04922, KAKENHI-PROJECT-22H04925, KAKENHI-PROJECT-20K21410, KAKENHI-PUBLICLY-21H00264, KAKENHI-PUBLICLY-22H04707, KAKENHI-PROJECT-20H00463
[Journal Article] Discovery of AS-0141, a Potent and Selective Inhibitor of CDC7 Kinase for the Treatment of Solid Cancers2021
- Author(s)
  Irie Takayuki、Asami Tokiko、Sawa Ayako、Uno Yuko、Taniyama Chika、Funakoshi Yoko、Masai Hisao、Sawa Masaaki
- Journal Title
  
  Journal of Medicinal Chemistry
  
  Volume: 64 Issue: 19 Pages: 14153-14164
- DOI
  10.1021/acs.jmedchem.1c01319
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PUBLICLY-20H05399, KAKENHI-PUBLICLY-21H00264, KAKENHI-PROJECT-20K21410, KAKENHI-PROJECT-20KK0157, KAKENHI-PROJECT-16H06276, KAKENHI-PROJECT-16H06279, KAKENHI-PROJECT-20H00463
[Journal Article] m6A modification of HSATIII lncRNAs regulates temperature‐dependent splicing2021
- Author(s)
  Ninomiya Kensuke、Iwakiri Junichi、Aly Mahmoud Khamis、Sakaguchi Yuriko、Adachi Shungo、Natsume Tohru、Terai Goro、Asai Kiyoshi、Suzuki Tsutomu、Hirose Tetsuro
- Journal Title
  
  The EMBO Journal
  
  Volume: 40 Issue: 15
- DOI
  10.15252/embj.2021107976
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19K06478, KAKENHI-PUBLICLY-20H05377, KAKENHI-PLANNED-21H05276, KAKENHI-PROJECT-20H00448, KAKENHI-PROJECT-20K12041, KAKENHI-PROJECT-16H06279, KAKENHI-PROJECT-18H05272
[Journal Article] A stem cell marker KLF5 regulates CCAT1 via three-dimensional genome structure in colorectal cancer cells2021
- Author(s)
  Takeda Takashi、Yokoyama Yuhki、Takahashi Hidekazu、Okuzaki Daisuke、Asai Kaho、Itakura Hiroaki、Miyoshi Norikatsu、Kobayashi Shogo、Uemura Mamoru、Fujita Toshitsugu、Ueno Hiroo、Mori Masaki、Doki Yuichiro、Fujii Hodaka、Eguchi Hidetoshi、Yamamoto Hirofumi
- Journal Title
  
  British Journal of Cancer
  
  Volume: 126 Issue: 1 Pages: 109-119
- DOI
  10.1038/s41416-021-01579-4
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20K09056, KAKENHI-PROJECT-16H06279
[Journal Article] Regulation of HP1 protein by phosphorylation during transcriptional repression and cell cycle2021
- Author(s)
  Oki Masaya、Masai Hisao
- Journal Title
  
  The Journal of Biochemistry
  
  Volume: － Issue: 6 Pages: 629-632
- DOI
  10.1093/jb/mvab040
- NAID
  40022686976
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-17H01418, KAKENHI-PUBLICLY-21H00264, KAKENHI-PROJECT-20K21410, KAKENHI-PROJECT-20KK0157, KAKENHI-PROJECT-16H06276, KAKENHI-PROJECT-16H06279, KAKENHI-PROJECT-20H00463
[Journal Article] Loss of full-length DNA replication regulator Rif1 in two-cell embryos is associated with zygotic transcriptional activation2021
- Author(s)
  Yoshizawa-Sugata Naoko、Yamazaki Satoshi、Mita-Yoshida Kaoru、Ono Tomio、Nishito Yasumasa、Masai Hisao
- Journal Title
  
  Journal of Biological Chemistry
  
  Volume: 297 Issue: 6 Pages: 101367-101367
- DOI
  10.1016/j.jbc.2021.101367
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PUBLICLY-20H05399, KAKENHI-PUBLICLY-21H00264, KAKENHI-PROJECT-20K21410, KAKENHI-PROJECT-20KK0157, KAKENHI-PROJECT-16H06276, KAKENHI-PROJECT-16H06279, KAKENHI-PROJECT-20H00463
[Journal Article] ConsAlifold : considering RNA structural alignments improves prediction accuracy of RNA consensus secondary structures2021
- Author(s)
  Masaki Tagashira, Kiyoshi Asai
- Journal Title
  
  Bioinformatics
  
  Volume: 38 Issue: 3 Pages: 710-719
- DOI
  10.1093/bioinformatics/btab738
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-16H06279, KAKENHI-PROJECT-21H04912
[Journal Article] Scent test using Caenorhabditis elegans to screen for early-stage pancreatic cancer2021
- Author(s)
  Asai Ayumu、Konno Masamitsu、Ozaki Miyuki、Kawamoto Koichi、Chijimatsu Ryota、Kondo Nobuaki、Hirotsu Takaaki、Ishii Hideshi
- Journal Title
  
  Oncotarget
  
  Volume: 12 Issue: 17 Pages: 1687-1696
- DOI
  10.18632/oncotarget.28035
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-18KK0251, KAKENHI-PROJECT-20H00541, KAKENHI-PROJECT-21K19526, KAKENHI-PROJECT-20K18053, KAKENHI-PROJECT-16H06276, KAKENHI-PROJECT-16H06279
[Journal Article] Single-molecule RNA sequencing for simultaneous detection of m6A and 5mC2021
- Author(s)
  Ohshiro Takahito、Konno Masamitsu、Asai Ayumu、Komoto Yuki、Yamagata Akira、Doki Yuichiro、Eguchi Hidetoshi、Ofusa Ken、Taniguchi Masateru、Ishii Hideshi
- Journal Title
  
  Scientific Reports
  
  Volume: 11 Issue: 1 Pages: 19304-19304
- DOI
  10.1038/s41598-021-98805-z
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-19K07688, KAKENHI-PROJECT-20K16414, KAKENHI-PROJECT-18KK0251, KAKENHI-PROJECT-19H00852, KAKENHI-PROJECT-20H00541, KAKENHI-PROJECT-21K19526, KAKENHI-PROJECT-16H06279, KAKENHI-PROJECT-23K21064
[Journal Article] Free-Energy Calculation of Ribonucleic Inosines and Its Application to Nearest-Neighbor Parameters2020
- Author(s)
  Sakuraba Shun、Iwakiri Junichi、Hamada Michiaki、Kameda Tomoshi、Tsuji Genichiro、Kimura Yasuaki、Abe Hiroshi、Asai Kiyoshi
- Journal Title
  
  Journal of Chemical Theory and Computation
  
  Volume: 16 Issue: 9 Pages: 5923-5935
- DOI
  10.1021/acs.jctc.0c00270
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20K12041, KAKENHI-PUBLICLY-19H05410, KAKENHI-PROJECT-16H06279
[Journal Article] Exchange of endogenous and heterogeneous yeast terminators in Pichia pastoris to tune mRNA stability and gene expression2020
- Author(s)
  Ito Yoichiro、Terai Goro、Ishigami Misa、Hashiba Noriko、Nakamura Yasuyuki、Bamba Takahiro、Kumokita Ryota、Hasunuma Tomohisa、Asai Kiyoshi、Ishii Jun、Kondo Akihiko
- Journal Title
  
  Nucleic Acids Research
  
  Volume: 48 Issue: 22 Pages: 13000-13012
- DOI
  10.1093/nar/gkaa1066
- NAID
  120006954873
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-19K15734, KAKENHI-PROJECT-16H06279
[Journal Article] Finding the Direct Optimal RNA Barrier Energy and Improving Pathways with an Arbitrary Energy Model2020
- Author(s)
  Hiroki Takizawa, Junichi Iwakiri, Goro Terai and Kiyoshi Asai
- Journal Title
  
  Bioinformatics
  
  Volume: 36 Issue: Supplement_1 Pages: i227-i235
- DOI
  10.1093/bioinformatics/btaa469
- Description
  in press
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-16H06279, KAKENHI-PROJECT-20K12041
[Journal Article] COVID-19 Drug Discovery Using Intensive Approaches2020
- Author(s)
  Asai Ayumu、Konno Masamitsu、Ozaki Miyuki、Otsuka Chihiro、Vecchione Andrea、Arai Takahiro、Kitagawa Toru、Ofusa Ken、Yabumoto Masami、Hirotsu Takaaki、Taniguchi Masateru、Eguchi Hidetoshi、Doki Yuichiro、Ishii Hideshi
- Journal Title
  
  International Journal of Molecular Sciences
  
  Volume: 21 Issue: 8 Pages: 2839-2839
- DOI
  10.3390/ijms21082839
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-20K16414, KAKENHI-PROJECT-18KK0251, KAKENHI-PROJECT-19H00852, KAKENHI-PROJECT-19K22658, KAKENHI-PROJECT-16H06279
[Journal Article] Improving the prediction accuracy of protein abundance in Escherichia coli using mRNA accessibility2020
- Author(s)
  Terai Goro、Asai Kiyoshi
- Journal Title
  
  Nucleic Acids Research
  
  Volume: 48 Issue: 14 Pages: e81-e81
- DOI
  10.1093/nar/gkaa481
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-18K18145, KAKENHI-PROJECT-16H06279
[Journal Article] State-of-the-Art Technology of Model Organisms for Current Human Medicine2020
- Author(s)
  Konno Masamitsu、Asai Ayumu、Kitagawa Toru、Yabumoto Masami、Ofusa Ken、Arai Takahiro、Hirotsu Takaaki、Doki Yuichiro、Eguchi Hidetoshi、Ishii Hideshi
- Journal Title
  
  Diagnostics
  
  Volume: 10 Issue: 6 Pages: 392-392
- DOI
  10.3390/diagnostics10060392
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20K16414, KAKENHI-PROJECT-18KK0251, KAKENHI-PROJECT-19K22658, KAKENHI-PROJECT-16H06279
[Journal Article] Immuno-Surgical Management of Pancreatic Cancer with Analysis of Cancer Exosomes2020
- Author(s)
  Takeda Yu、Kobayashi Shogo、Kitakaze Masatoshi、Yamada Daisaku、Akita Hirofumi、Asai Ayumu、Konno Masamitsu、Arai Takahiro、Kitagawa Toru、Ofusa Ken、Yabumoto Masami、Hirotsu Takaaki、Vecchione Andrea、Taniguchi Masateru、Doki Yuichiro、Eguchi Hidetoshi、Ishii Hideshi
- Journal Title
  
  Cells
  
  Volume: 9 Issue: 7 Pages: 1645-1645
- DOI
  10.3390/cells9071645
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19K07688, KAKENHI-PROJECT-20K16414, KAKENHI-PROJECT-18KK0251, KAKENHI-PROJECT-19H00852, KAKENHI-PROJECT-18K08704, KAKENHI-PROJECT-19K22658, KAKENHI-PROJECT-16H06279
[Journal Article] Hereditary pancreatitis model by blastocyst complementation in mouse2020
- Author(s)
  Asai Ayumu、Konno Masamitsu、Kawamoto Koichi、Isotani Ayako、Mori Masaki、Eguchi Hidetoshi、Doki Yuichiro、Arai Takahiro、Ishii Hideshi
- Journal Title
  
  Oncotarget
  
  Volume: 11 Issue: 22 Pages: 2061-2073
- DOI
  10.18632/oncotarget.27595
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-19K07688, KAKENHI-PROJECT-20K16414, KAKENHI-PROJECT-18KK0251, KAKENHI-PROJECT-19K22658, KAKENHI-PROJECT-16H06276, KAKENHI-PROJECT-16H06279
[Journal Article] PBSIM2 : a simulator for long-read sequencers with a novel generative model of quality scores2020
- Author(s)
  Yukiteru Ono, Kiyoshi Asai, Michiaki Hamada
- Journal Title
  
  Bioinformatics
  
  Volume: 37 Issue: 5 Pages: 589-595
- DOI
  10.1093/bioinformatics/btaa835
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-16H06279
[Journal Article] RintC: fast and accuracy-aware decomposition of distributions of RNA secondary structures with extended logsumexp2020
- Author(s)
  Hiroki Takizawa, Junichi Iwakiri, Kiyoshi Asai
- Journal Title
  
  BMC Bioinformatics
  
  Volume: 21 Issue: 1 Pages: 210-210
- DOI
  10.1186/s12859-020-3535-5
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-16H02484, KAKENHI-PROJECT-20K12041, KAKENHI-PROJECT-16H06279
[Journal Article] Heterogeneous fluid-like movements of chromatin and their implications to transcription2020
- Author(s)
  Ashwin SS, Maeshima K, Sasai M
- Journal Title
  
  Biophysical Reviews
  
  Volume: 12 Issue: 2 Pages: 461-468
- DOI
  10.1007/s12551-020-00675-8
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-19H01860, KAKENHI-PUBLICLY-19H05258, KAKENHI-PUBLICLY-19H05273, KAKENHI-PROJECT-16H06279
[Journal Article] One-carbon metabolism for cancer diagnostic and therapeutic approaches2020
- Author(s)
  Asai Ayumu、Konno Masamitsu、Koseki Jun、Taniguchi Masateru、Vecchione Andrea、Ishii Hideshi
- Journal Title
  
  Cancer Letters
  
  Volume: 470 Pages: 141-148
- DOI
  10.1016/j.canlet.2019.11.023
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19K07688, KAKENHI-PROJECT-17H04282, KAKENHI-PROJECT-18K16355, KAKENHI-PROJECT-18K16356, KAKENHI-PROJECT-18KK0251, KAKENHI-PROJECT-19K22658, KAKENHI-PROJECT-16H06279
[Journal Article] Theoretical analyses and experimental validation of the effects caused by the fluorinated substituent modification of DNA2020
- Author(s)
  Koseki Jun、Konno Masamitsu、Asai Ayumu、Horie Naohiro、Tsunekuni Kenta、Kawamoto Koichi、Obika Satoshi、Doki Yuichiro、Mori Masaki、Ishii Hideshi
- Journal Title
  
  Scientific Reports
  
  Volume: 10 Issue: 1 Pages: 1138-1138
- DOI
  10.1038/s41598-020-57899-7
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-17H04282, KAKENHI-PROJECT-18K16355, KAKENHI-PROJECT-18K16356, KAKENHI-PROJECT-19K07688, KAKENHI-PROJECT-18KK0251, KAKENHI-PROJECT-19K22658, KAKENHI-PROJECT-16H06279
[Journal Article] Convolutional Neural Network Can Recognize Drug Resistance of Single Cancer Cells2020
- Author(s)
  Yanagisawa Kiminori、Toratani Masayasu、Asai Ayumu、Konno Masamitsu、Niioka Hirohiko、Mizushima Tsunekazu、Satoh Taroh、Miyake Jun、Ogawa Kazuhiko、Vecchione Andrea、Doki Yuichiro、Eguchi Hidetoshi、Ishii Hideshi
- Journal Title
  
  International Journal of Molecular Sciences
  
  Volume: 21 Issue: 9 Pages: 3166-3166
- DOI
  10.3390/ijms21093166
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19K07688, KAKENHI-PROJECT-19K09172, KAKENHI-PROJECT-20K16414, KAKENHI-PROJECT-18KK0251, KAKENHI-PROJECT-19K22658, KAKENHI-PROJECT-16H06279
[Journal Article] Direct Analysis of Incorporation of an Anticancer Drug into DNA at Single-Molecule Resolution2019
- Author(s)
  Ohshiro Takahito、Komoto Yuuki、Konno Masamitsu、Koseki Jun、Asai Ayumu、Ishii Hideshi、Taniguchi Masateru
- Journal Title
  
  Scientific Reports
  
  Volume: 9 Issue: 1 Pages: 3886-3886
- DOI
  10.1038/s41598-019-40504-x
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-18K16356, KAKENHI-PROJECT-18KK0251, KAKENHI-PROJECT-26220603, KAKENHI-PROJECT-17H04282, KAKENHI-PROJECT-17K19698, KAKENHI-PROJECT-16H06279, KAKENHI-PROJECT-19H00852, KAKENHI-PROJECT-18K16355
[Journal Article] A robust model for quantitative prediction of the silencing efficacy of wild-type and A-to-I edited miRNAs2019
- Author(s)
  Tian Shen、Terai Goro、Kobayashi Yoshiaki、Kimura Yasuaki、Abe Hiroshi、Asai Kiyoshi、Ui-Tei Kumiko
- Journal Title
  
  RNA Biology
  
  Volume: 17 Issue: 2 Pages: 264-280
- DOI
  10.1080/15476286.2019.1678364
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PUBLICLY-18H04398, KAKENHI-PROJECT-16H02484, KAKENHI-PROJECT-16H06279
[Journal Article] LncRNA ‐dependent nuclear stress bodies promote intron retention through SR protein phosphorylation2019
- Author(s)
  Ninomiya Kensuke、Adachi Shungo、Natsume Tohru、Iwakiri Junichi、Terai Goro、Asai Kiyoshi、Hirose Tetsuro
- Journal Title
  
  The EMBO Journal
  
  Volume: 39 Issue: 3
- DOI
  10.15252/embj.2019102729
- NAID
  120006876293
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-19K06478, KAKENHI-PROJECT-19K22374, KAKENHI-PROJECT-17H03630, KAKENHI-PROJECT-16K16143, KAKENHI-PROJECT-16H06279
[Journal Article] Single nucleosome imaging reveals loose genome chromatin networks via active RNA polymerase II2019
- Author(s)
  R Nagashima, K Hibino, SS Ashwin, M Babokhov, S Fujishiro, R Imai, T Nozaki, S Tamura, T Tani, H Kimura, M Shribak, MT Kanemaki, M Sasai, K Maeshima
- Journal Title
  
  Journal of Cell Biology
  
  Volume: 218 Issue: 5 Pages: 1511-1530
- DOI
  10.1083/jcb.201811090
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16H02217, KAKENHI-PROJECT-16J07205, KAKENHI-PROJECT-16H06279, KAKENHI-PROJECT-18K19962
[Journal Article] Distinct methylation levels of mature microRNAs in gastrointestinal cancers2019
- Author(s)
  Konno Masamitsu、Koseki Jun、Asai Ayumu、Yamagata Akira、Shimamura Teppei、Motooka Daisuke、Okuzaki Daisuke、Kawamoto Koichi、Mizushima Tsunekazu、Eguchi Hidetoshi、Takiguchi Shuji、Satoh Taroh、Mimori Koshi、Ochiya Takahiro、Doki Yuichiro、Ofusa Ken、Mori Masaki、Ishii Hideshi
- Journal Title
  
  Nature Communications
  
  Volume: 10 Issue: 1 Pages: 3888-3888
- DOI
  10.1038/s41467-019-11826-1
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-18K08617, KAKENHI-PROJECT-18K08704, KAKENHI-PROJECT-19K07688, KAKENHI-PROJECT-19K09172, KAKENHI-PROJECT-19K22658, KAKENHI-PROJECT-18KK0251, KAKENHI-PUBLICLY-18H04798, KAKENHI-PUBLICLY-19H05210, KAKENHI-PROJECT-15H05791, KAKENHI-PROJECT-17H04282, KAKENHI-PROJECT-19H03715, KAKENHI-PROJECT-18K16355, KAKENHI-PROJECT-18K16356, KAKENHI-PROJECT-16H06276, KAKENHI-PROJECT-16H06279
[Journal Article] Mitochondrial pyruvate carrier 1 expression controls cancer epithelial‐mesenchymal transition and radioresistance2019
- Author(s)
  Takaoka Yuji、Konno Masamitsu、Koseki Jun、Colvin Hugh、Asai Ayumu、Tamari Keisuke、Satoh Taroh、Mori Masaki、Doki Yuichiro、Ogawa Kazuhiko、Ishii Hideshi
- Journal Title
  
  Cancer Science
  
  Volume: 110 Issue: 4 Pages: 1331-1339
- DOI
  10.1111/cas.13980
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-18K16355, KAKENHI-PROJECT-18K16356, KAKENHI-PROJECT-18KK0251, KAKENHI-PROJECT-17H04282, KAKENHI-PROJECT-17K19698, KAKENHI-PROJECT-18K15633, KAKENHI-PROJECT-16H06276, KAKENHI-PROJECT-16H06279
[Journal Article] Organization of fast and slow chromatin revealed by single-nucleosome dynamics.2019
- Author(s)
  Ashwin, S.S., Nozaki, T., Maeshima, K., Sasai, M.
- Journal Title
  
  Proc Natl Acad Sci USA
  
  Volume: 116 Issue: 40 Pages: 19939-19944
- DOI
  10.1073/pnas.1907342116
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PUBLICLY-19H05273, KAKENHI-PROJECT-19H01860, KAKENHI-PROJECT-16H06279, KAKENHI-PUBLICLY-19H05258
[Journal Article] Polyamine flux suppresses histone lysine demethylases and enhances ID1 expression in cancer stem cells2018
- Author(s)
  Tamari K, KonnoM , Asai A, Koseki J, Hayashi K, Kawamoto K, Murai N, Matsufuji S, Isohashi F, Satoh T, Gotoh N, Tanaka S, Doki Y, Mori M, Ogawa K, Ishii H.
- Journal Title
  
  Cell Death Discovery
  
  Volume: 4 Issue: 104 Pages: 104-104
- DOI
  10.1038/s41420-018-0117-7
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-18K19575, KAKENHI-PROJECT-18K16355, KAKENHI-PROJECT-18K16356, KAKENHI-PROJECT-18KK0251, KAKENHI-PROJECT-16H02670, KAKENHI-PROJECT-17H04282, KAKENHI-PROJECT-18H02679, KAKENHI-PROJECT-16K10393, KAKENHI-PROJECT-17K19587, KAKENHI-PROJECT-17K19698, KAKENHI-PROJECT-16H06276, KAKENHI-PROJECT-16H06279
[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
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16H06279, KAKENHI-PROJECT-16H05879, KAKENHI-PROJECT-16H02484
[Journal Article] Combining probabilistic alignments with read pair information improves accuracy of split-alignments2018
- Author(s)
  Anish M S Shrestha, Naruki Yoshikawa, Kiyoshi Asai
- Journal Title
  
  Bioinformatics
  
  Volume: 34 Issue: 21 Pages: 3631-3637
- DOI
  10.1093/bioinformatics/bty398
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-16H06279
[Journal Article] Capturing alternative secondary structures of RNA by decomposition of base-pairing probabilities2018
- Author(s)
  Hagio Taichi、Sakuraba Shun、Iwakiri Junichi、Mori Ryota、Asai Kiyoshi
- Journal Title
  
  BMC Bioinformatics
  
  Volume: 19 Issue: Suppl 1 Pages: 38-38
- DOI
  10.1186/s12859-018-2018-4
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-16K16143, KAKENHI-PROJECT-16K17778, KAKENHI-PROJECT-16H06279, KAKENHI-PROJECT-16H02484
[Journal Article] A Convolutional Neural Network Uses Microscopic Images to Differentiate between Mouse and Human Cell Lines and Their Radioresistant Clones2018
- Author(s)
  Toratani Masayasu、Konno Masamitsu、Asai Ayumu、Koseki Jun、Kawamoto Koichi、Tamari Keisuke、Li Zhihao、Sakai Daisuke、Kudo Toshihiro、Satoh Taroh、Sato Katsutoshi、Motooka Daisuke、Okuzaki Daisuke、Doki Yuichiro、Mori Masaki、Ogawa Kazuhiko、Ishii Hideshi
- Journal Title
  
  Cancer Research
  
  Volume: 78 Issue: 23 Pages: 6703-6707
- DOI
  10.1158/0008-5472.can-18-0653
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-18K08617, KAKENHI-PROJECT-18K16355, KAKENHI-PROJECT-18K16356, KAKENHI-PROJECT-18KK0251, KAKENHI-PROJECT-17H04282, KAKENHI-PROJECT-17K19698, KAKENHI-PROJECT-16H06279
[Journal Article] Poly(ethylene glycol)ーpoly(lysine) block copolymerーubenimex conjugate targets aminopeptidase N and exerts an antitumor effect in hepatocellular carcinoma stem cells2018
- Author(s)
  Toshiyama, R., Konno, M., Eguchi, H., Takemoto, H., Noda, T., Asai, A., Koseki, J., Haraguchi, N., Ueda, Y. Matsushita, K., Asukai, K., Ohashi, T., Iwagami, Y., Yamada, D., Sakai, D., Asaoka, T., Kudo, T., Kawamoto, K., Gotoh, K., Kobayashi, S., Satoh, T., Doki, Y., Nishiyama, N., Mori, M., Ishii, H.
- Journal Title
  
  Oncogene
  
  Volume: 38 Issue: 2 Pages: 244-260
- DOI
  10.1038/s41388-018-0406-x
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-18K16355, KAKENHI-PROJECT-18K16356, KAKENHI-PROJECT-18KK0251, KAKENHI-PROJECT-18H04163, KAKENHI-PROJECT-17H04282, KAKENHI-PROJECT-16F16058, KAKENHI-PROJECT-17K19698, KAKENHI-PROJECT-16H06276, KAKENHI-PROJECT-16H06279
[Journal Article] Training alignment parameters for arbitrary sequencers with LAST-TRAIN2017
- Author(s)
  Hamada M, Ono Y, Asai K, Frith MC
- 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] 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 Issue: S1 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 sequences2016
- Author(s)
  Hamada Michiaki, Ono Yukiteru, Kiryu Hisanori, Sato Kengo, Kato Yuki, Fukunaga Tsukasa, Mori Ryota, Asai Kiyosh
- Journal Title
  
  Nucleic Acids Research
  
  Volume: 44 Issue: W1 Pages: W302-W307
- DOI
  10.1093/nar/gkw337
- 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] Improved Accuracy in RNA-Protein Rigid Body Docking by Incorporating Force Field for Molecular Dynamics Simulation into the Scoring Function2016
- Author(s)
  Junichi Iwakiri, Michiaki Hamada, Kiyoshi Asai, and Tomoshi Kameda
- Journal Title
  
  J. Chem. Theory Comput
  
  Volume: 12(9) Issue: 9 Pages: 4688-5697
- 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 prediction2015
- 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 criteria2015
- Author(s)
  Michiaki Hamada, Yukiteru Ono, Ryohei Fujimaki, Kiyoshi Asai
- Journal Title
  
  Bioinformatics
  
  Volume: 未定 Issue: 15 Pages: 2426-2433
- DOI
  10.1093/bioinformatics/btv163
- Peer Reviewed / Acknowledgement Compliant / Open Access
- Data Source
  KAKENHI-PROJECT-24680031, KAKENHI-PROJECT-221S0002
[Journal Article] Bioinformatics tools for lncRNA research.2015
- Author(s)
  Junichi Iwakiri, Michiaki Hamada, Kiyoshi Asai
- Journal Title
  
  Biochimica et biophysica acta (BBA) Gene Regulatory Mechanisms
  
  Volume: 1859(1) Issue: 1 Pages: 23-30
- DOI
  10.1016/j.bbagrm.2015.07.014
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-221S0002, KAKENHI-PROJECT-24680031, KAKENHI-PROJECT-25240044
[Journal Article] Predicting RNA Duplex Dimerization Free-Energy Changes upon Mutations Using Molecular Dynamics Simulations2015
- Author(s)
  Shun Sakuraba, Kiyoshi Asai, Tomoshi Kameda
- Journal Title
  
  he journal of physical chemistry letters
  
  Volume: 6(21) Issue: 21 Pages: 4341-4358
- DOI
  10.1021/acs.jpclett.5b01984
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PROJECT-25240044
[Journal Article] Hybrid De Novo Genome Assembly Using MiSeq and SOLiD Short Read Data.2015
- Author(s)
  Tsutomu Ikegami, Toyohiro Inatsugi, Isao Kojima, Myco Umemura, Hiroko Hagiwara, Masayuki Machida, Kiyoshi Asai
- Journal Title
  
  PLoS ONE
  
  Volume: 10(4) Issue: 4 Pages: e0126289-e0126289
- DOI
  10.1371/journal.pone.0126289
- Peer Reviewed / Open Access
- Data Source
  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 Issue: S18 Pages: 1-14
- DOI
  10.1186/1471-2105-16-s18-s6
- NAID
  120007128511
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PLANNED-24106010, KAKENHI-PROJECT-25540131
[Journal Article] Direct binding of Ataxin-2 to distinct elements in 3' UTRs promotes mRNA stability and protein expression.2014
- Author(s)
  Yokoshi, M., Li, Q., Yamamoto, M., Okada, H., Suzuki, Y., and Kawahara, Y.
- Journal Title
  
  Molecular cell
  
  Volume: 55 Issue: 2 Pages: 186-198
- DOI
  10.1016/j.molcel.2014.05.022
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-14J01452, KAKENHI-PUBLICLY-25110719, KAKENHI-PROJECT-25293201, KAKENHI-PROJECT-25670419, KAKENHI-PROJECT-221S0002
[Journal Article] CapR : revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data2014
- Author(s)
  Tsukasa Fukunaga, Haruka Ozaki, Goro Terai, Kiyoshi Asai, Wataru Iwasaki and Hisanori Kiryu
- Journal Title
  
  Genome Biology
  
  Volume: 15 Issue: 1
- DOI
  10.1186/gb-2014-15-1-r16
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-22240031, KAKENHI-PROJECT-23710231, KAKENHI-PUBLICLY-25134701, KAKENHI-PROJECT-25240044, KAKENHI-PROJECT-25870190
[Journal Article] Efficient calculation of exact probability distributions of integer features on RNA secondary structures.2014
- Author(s)
  Mori R, Hamada M, Asai K
- Journal Title
  
  BMC genomics
  
  Volume: 15 Issue: S10
- 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) Issue: 18 Pages: 2559-2567
- DOI
  10.1093/bioinformatics/btu360
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-26540159, 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 Issue: 1 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-RNA interactions2013
- Author(s)
  Junichi Iwakiri, Tomoshi Kameda, Kiyoshi Asai, Michiaki Hamada
- Journal Title
  
  Bioinformatics
  
  Volume: 29 Issue: 20 Pages: 2524-2528
- DOI
  10.1093/bioinformatics/btt453
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22240031, KAKENHI-PROJECT-24680031, KAKENHI-PROJECT-25240044, 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
  
  International journal of molecular sciences
  
  Volume: 14 Issue: 3 Pages: 6144-6156
- DOI
  10.3390/ijms14036144
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22240031, KAKENHI-PROJECT-24680031, KAKENHI-PROJECT-25240044, KAKENHI-PROJECT-221S0002
[Journal Article] RecountDB : a database of mapped and count corrected transcribed sequences2012
- Author(s)
  Edward Wijaya, Martin C Frith, Kiyoshi Asai, Paul Horton
- Journal Title
  
  Nucleic Acids Research
  
  Volume: 40 Issue: D1 Pages: D1089-D1092
- DOI
  10.1093/nar/gkr1172
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-221S0002
[Journal Article] Rchange : Algorithms for computing the energy changes of RNA secondary structures in response to base mutations2012
- Author(s)
  Hisanori Kiryu and Kiyoshi Asai
- Journal Title
  
  Bioinformatics
  
  Volume: 28(8) Issue: 8 Pages: 1093-1101
- DOI
  10.1093/bioinformatics/bts097
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-21700330, KAKENHI-PROJECT-22240031
[Journal Article] Rtips : fast and accurate tools for RNA 2D structure prediction using integer programming2012
- Author(s)
  Yuki Kato, Kengo Sato, Kiyoshi Asai, Tatsuya Akutsu
- Journal Title
  
  Nucleic Acids Res
  
  Volume: 40 Issue: W1 Pages: W29-W34
- DOI
  10.1093/nar/gks412
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22240031, KAKENHI-PROJECT-23650153, KAKENHI-PROJECT-24700296
[Journal Article] Prediction of Conserved Precursors of miRNAs and Their Mature Forms by Integrating Position-Specific Structural Features2012
- Author(s)
  Goro Terai, Hiroaki Okida, Kiyoshi Asai, Toutai Mituyama
- Journal Title
  
  PLoS One
  
  Volume: 7 Issue: 9 Pages: e44314-e44314
- DOI
  10.1371/journal.pone.0044314
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22240031
[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 Issue: 5 Pages: 532-549
- DOI
  10.1089/cmb.2011.0197
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22240031, KAKENHI-PROJECT-221S0002
[Journal Article] DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition2012
- Author(s)
  Kengo Sato, Yuki Kato, Tatsuya Akutsu, Kiyoshi Asai, Yasubumi Sakakibara
- Journal Title
  
  Bioinformatics
  
  Volume: 28 Issue: 24 Pages: 3218-3224
- DOI
  10.1093/bioinformatics/bts612
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22240009, KAKENHI-PROJECT-22240031, KAKENHI-PROJECT-23241066, KAKENHI-PROJECT-23650153, KAKENHI-PROJECT-24700296, KAKENHI-PROJECT-221S0002
[Journal Article] Transformations for the compression of FASTQ quality scores of next-generation sequencing data2012
- Author(s)
  Raymond Wan, Vo Ngoc Anh, Kiyoshi Asai
- Journal Title
  
  Bioinformatics
  
  Volume: 28 Issue: 5 Pages: 628-635
- DOI
  10.1093/bioinformatics/btr689
- Peer Reviewed
- Data Source
  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(2) Issue: 2 Pages: e16450-e16450
- DOI
  10.1371/journal.pone.0016450
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-21700330, KAKENHI-PROJECT-22240031
[Journal Article] A detailed investigation of accessibilities around target sites of siRNAs and miRNAs2011
- Author(s)
  Hisanori Kiryu, Goro Terai, Osamu Imamura, Hiroyuki Yoneyama, Kenji Suzuki, Kiyoshi Asai
- Journal Title
  
  Bioinformatics
  
  Volume: 27 Issue: 13 Pages: 1788-1797
- DOI
  10.1093/bioinformatics/btr276
- Peer Reviewed
- Data Source
  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] CentroidHomfold-LAST : accurateprediction of RNA secondary structure using automatically collected homologous sequences2011
- Author(s)
  Michiaki Hamada, Koichiro Yamada, Kengo Sato, Martin C Frith, Kiyoshi Asai
- Journal Title
  
  Nucleic Acids Research
  
  Volume: 39
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22240031
[Journal Article] CentroidHomfold-LAST : accurate prediction of RNA secondary structure using automatically collected homologous sequences2011
- Author(s)
  Michiaki Hamada, Koichiro Yamada, Kengo Sato, Martin C Frith, Kiyoshi Asai
- Journal Title
  
  Nucleic Acids Res
  
  Volume: 39 Issue: suppl_2 Pages: W100-W106
- DOI
  10.1093/nar/gkr290
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22240031, KAKENHI-PROJECT-22700305
[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 Issue: 22 Pages: 3085-3092
- DOI
  10.1093/bioinformatics/btr537
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-221S0002
[Journal Article] A detailed investigation of accessibilities around target sites of siRNAs and miRNAs2011
- Author(s)
  Hisanori Kiryu, Goro Terai, Osamu Imamura, Hiroyuki Yoneyama, Kenji Suzuki, and Kiyoshi Asai
- Journal Title
  
  Bioinformatics
  
  Volume: 27 Pages: 1788-1797
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22240031
[Journal Article] On algorithms for computing thermodynamic entropy of RNA secondary structures2011
- Author(s)
  Hisanori Kiryu, Goro Terai, Osamu Imamura, Hiroyuki Yoneyama, Kenji Suzuki, Kiyoshi Asai
- Journal Title
  
  Bioinformatics
  
  Volume: 27 Pages: 1788-1797
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22240031
[Journal Article] Antagonistic RNA aptamer specific to a heterodimeric form of human interleukin-17A/F2011
- Author(s)
  Hironori Adachi, Akira Ishiguro, Michiaki Hamada, Eri Sakota, Kiyoshi Asai, Yoshikazu Nakamura
- Journal Title
  
  Biochimie
  
  Volume: 93 Issue: 7 Pages: 1081-1088
- DOI
  10.1016/j.biochi.2011.04.003
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22240031
[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] IPknot : fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming2011
- Author(s)
  K.Sato, Y.Kato, M.Hamada, T.Akutsu, K.Asai
- Journal Title
  
  Bioinformatics
  
  Volume: 27 Issue: 13 Pages: i85-i93
- DOI
  10.1093/bioinformatics/btr215
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22240009, KAKENHI-PROJECT-22240031, KAKENHI-PROJECT-22700305, KAKENHI-PROJECT-22700313, KAKENHI-PROJECT-23650153
[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 Res
  
  Volume: 39 Issue: 2 Pages: 393-402
- DOI
  10.1093/nar/gkq792
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22240031
[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 Issue: 1 Pages: 586-586
- DOI
  10.1186/1471-2105-11-586
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22240031
[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
[Journal Article] A non-parametric Bayesian approach for predicting RNA secondary structures2010
- Author(s)
  Kengo Sato, Michiaki Hamada, Toutai Mituyama, Kiyoshi Asai, Yasufumi Sakakibara
- Journal Title
  
  Journal of Bioinformatics and Computational Biology
  
  Volume: 8 Issue: 04 Pages: 727-742
- DOI
  10.1142/s0219720010004926
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22240031
[Journal Article] RactIP : fast and accurate prediction of RNA-RNA interaction using integer programming2010
- Author(s)
  Yuki Kato, Kengo Sato, Michiaki Hamada, Yoshihide Watanabe, Kiyoshi Asai, Tatsuya Akutsu
- Journal Title
  
  Bioinformatics
  
  Volume: 26 Issue: 18 Pages: i460-i466
- DOI
  10.1093/bioinformatics/btq372
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22240031
[Journal Article] Discovery of short pseudogenes derived from messenger RNAs2010
- Author(s)
  Goro Terai, Aya Yoshizawa, Hiroaki Okida, Kiyoshi Asai, Toutai Mituyama
- Journal Title
  
  Nucleic Acids Res
  
  Volume: 38 Issue: 4 Pages: 1163-1171
- DOI
  10.1093/nar/gkp1098
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22240031
[Journal Article] A local multiple alignment method for detection of non-coding RNA sequences2009
- Author(s)
  Tabei, Y., Asai, K.
- Journal Title
  
  Bioinformatics 25(12)
  
  Pages: 1498-1505
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] A regulatory circuit for piwi by the large Maf gene traffic jam in Drosophila2009
- Author(s)
  Saito, K., Inagaki, S., Mituyama, T., Kawamura, Y, Ono, Y., Sakota, E., Kotani, H., Asai, K., Siomi, H., Siomi, M.C
- Journal Title
  
  Nature 461(7268)
  
  Pages: 1296-1299
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] CentroidAlign : Fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score2009
- Author(s)
  Hamada, M., Sato, K., Kiryu, H., Mituyama, T., Asai, K.
- Journal Title
  
  Bioinformatics 25(24)
  
  Pages: 3236-3243
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Prediction of RNA secondary structure by combining homologous sequence information2009
- Author(s)
  Hamada, M., Sato, K., Kiryu, H., Mituyama, T., Asai, K.
- Journal Title
  
  Bioinformatics 25(12)
  
  Pages: 330-338
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] CENTROIDFOLD: a web server for RNA secondary structure prediction2009
- Author(s)
  Sato, K., Hamada, M., Asai, K., Mituyama, T.
- Journal Title
  
  Nucleic Acids Res. 37(Web Server issue)
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] CentroidAlign: Fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score2009
- Author(s)
  Hamada, M., Sato, K., Kiryu, H., Mituyama, T., Asai, K.
- Journal Title
  
  Bioinformatics (Advance Access)
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] A local multiple alignment method for detection of non-coding RNA sequences2009
- Author(s)
  Tabei. Y., Asai. K.
- Journal Title
  
  Bioinformatics 25(12)
  
  Pages: 1498-1505
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Prediction of RNA secondary structure using generalized centro id estimators2009
- Author(s)
  Hamada, M., Kiryu, H, Sato, K, Mituvama. T., and Asai K
- Journal Title
  
  Bioinformatics 25
  
  Pages: 465-473
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] CENTROIDFOLD : a web server for RNA secondary structure prediction2009
- Author(s)
  Sato, K., Hamada, M., Asai, K., Mituyama, T.
- Journal Title
  
  Nucleic Acids Res. 37(Web server issue)
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] A regulatory circuit for piwi by the large Maf gene traffic jam in Drosophila2009
- Author(s)
  Saito, K., Inagaki, S., Mituyama, T., Kawamura, Y., Ono, Y., Sakota, E., Kotani, H., Asai, K., Siomi, H., Siomi, M.C.
- Journal Title
  
  Nature 461(7268)
  
  Pages: 1296-1299
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Transcripts of unknown function in multiple-signaling pathways involved in human stem cell differentiation2009
- Author(s)
  Kikuchi, K., Fukuda, M., Ito, T., Inoue, M., Yokoi, T., Chiku, S., Mitsuyama, T., Asai, K., Hirose, T., Aizawa, Y.
- Journal Title
  
  Nucleic Acids Res. 35(15)
  
  Pages: 4987-5000
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Expansion of signaling genes for adaptive immune system evolution in early vertebrates2008
- Author(s)
  Okada, K,, amd Asai, K
- Journal Title
  
  BMC Genomics 9
  
  Pages: 218-218
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] A fast structural multiple alignment method for long RNA sequences2008
- Author(s)
  Tabei, Y., Kiryu, H., Kin, T., Asai, K.
- Journal Title
  
  BMC Bioinformatics 9
  
  Pages: 33-33
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Retention of genes involved in the adenohypophysis-mediated en docrine system in early vertebrates2008
- Author(s)
  Okada, K, and Asai, K.
- Journal Title
  
  Gene 412
  
  Pages: 71-83
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Software. ncrna. org: web servers for analyses of RNA sequences2008
- Author(s)
  Asai, K, Kiryu, H, Hamada, M, Tabei, Y, Sato, K, Matsui, H, Sakakibara, Y, Terai, G,, Mituyama, T.
- Journal Title
  
  Nucleic Acids Res. 36
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Directed acyclic graph kernels for structural RNA analysis2008
- Author(s)
  K Sato, T. Mituyama, K Asai, and Y. Sakakibara
- Journal Title
  
  BMC Bioinformatics 9
  
  Pages: 318-318
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Characterization of endogenous human Argonautes and their miRNA partners in RNA silencing2008
- Author(s)
  Azuma-Mukai, A, Oguri, H, Mituyama, T, Qian, Z. R, Asai, K, Siomi, H,, Siomi, M.C.
- Journal Title
  
  PNAS 105(23)
  
  Pages: 7964-7969
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells2008
- Author(s)
  Kawamura, Y, Saito, K, Kin, T, Ono, Y, Asai, K, Sunohara, T, Okada, T. N, Siomi, M. C,, Siomi, H.
- Journal Title
  
  Nature 453(7196)
  
  Pages: 793-797
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Expansion of signaling genes for adaptive immune system evolut ion in early vertebrates2008
- Author(s)
  Okada K, and Asai K
- Journal Title
  
  BMC Genomics 9
  
  Pages: 218-218
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Prediction of RNA secondary structure using generalized centroid estimators2008
- Author(s)
  Hamada, M., Kiryu, H., Sato, K., Mituyama, T., Asai, K.
- Journal Title
  
  Bioinformatics 25(4)
  
  Pages: 465-73
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Retention of genes involved in the adenohypophysis-mediated endocrine system in early vertebrates2008
- Author(s)
  Okada, K., Asai, K.
- Journal Title
  
  Gene 412(1-2)
  
  Pages: 71-83
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Software.ncrna.org : web servers for analyses of RNA sequences2008
- Author(s)
  Asai, K, Kiryu, H, Hamada., M., Tabei, Y., Sato, K, Matsui, H., Sakakibara, Y., Terai, G., and Mituyama. T.
- Journal Title
  
  Nucleic Acids Research 36
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Rfold: An exact algorithm for computing local base pairing probabilities2008
- Author(s)
  Kiryu, H., Kin, T., and Asai, K.
- Journal Title
  
  Bioinformatics 24・3
  
  Pages: 367-373
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Rfold: An exact algorithm for computing local base pairing probabilities2008
- Author(s)
  Kiryu, H., Kin, T., Asai, K.
- Journal Title
  
  Bioinformatics 24(3)
  
  Pages: 367-373
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Directed acyclic graph kernels for structural RNA analysis2008
- Author(s)
  Sato, K., Mituyama, T., Asai, K., Sakakibara, Y.
- Journal Title
  
  BMC Bioinformatics 9
  
  Pages: 318-318
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] A fast structural multiple alignment method for long RNA sequences2008
- Author(s)
  Tabei, Y, Kiryu, H., Kin, T., and Asai, K.
- Journal Title
  
  BMC Bioim^2ormatics 9
  
  Pages: 33-33
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Stem kernels for KNA sequence analyses2007
- Author(s)
  Sakakibara, Y., Ogawa, N・, Popendorf, K., Asai, K., and K. Sato
- Journal Title
  
  Journal of Bioinformatics and Computational Biology 5・6
  
  Pages: 1103-1122
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Stem kernels for RNA sequence analyses2007
- Author(s)
  Sakakibara, Y., Ogawa, N., Popendorf, K., Asai, K., K. Sato
- Journal Title
  
  Journal of Bioinformatics and Computational Biology 5(6)
  
  Pages: 1103-1122
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Robust prediction of consensus secondary structures using averaged base pairing probability matrices2007
- Author(s)
  Kiryu, H., Kin, T., Asai, K.
- Journal Title
  
  Bioinformatics 23(13)
  
  Pages: 1588-1598
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] miRRim: A novel system to find conserved miRNAs with high sensitivity and specificity2007
- Author(s)
  Terai, G., Komori, T., Asai, K., Kin, T.
- Journal Title
  
  RNA 13
  
  Pages: 2081-2090
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Murlet: A practical multiple alignment tool for structural RNA sequences2007
- Author(s)
  Kiryu, H., Tabei, Y., Kin T., Asai, K.
- Journal Title
  
  Bioinformatics 23(13)
  
  Pages: 1588-1598
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Murlet:A practical multiple alignment tool for structural RNA sequences2007
- Author(s)
  Kiryu, H., Tabei, Kin, T., and Asai, K.
- Journal Title
  
  Bioinformatics 23・13
  
  Pages: 1588-1598
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Stem Kernels for RNA Sequence Analyses2007
- Author(s)
  Sakakibara, Y., Asai, K., Sato, K.
- Journal Title
  
  Proc. 1st International Conference on Bioinformatics Research and Development
  
  Pages: 278-291
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] miRRim: A novel system to find miRNAs with hight sensitivity and spe cificity2007
- Author(s)
  Terai, G, Komori, T., Asai, K., and Kin, T.
- Journal Title
  
  RNA 13
  
  Pages: 2081-2090
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Robust prediction of consensus secondary structures using averaged base pairing probability matrices2006
- Author(s)
  Kiryu, H., Kin, T., Asai, K.
- Journal Title
  
  Bioinformatics, Advance Access
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Mining frequence stem patterns from unaligned RNA sequences2006
- Author(s)
  Hamada, M., Tsuda, K., Kudo, T., Kin, T., Asai, K.
- Journal Title
  
  Bioinformatics 22・20
  
  Pages: 2480-2487
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments2006
- Author(s)
  Tabei, Y., Tsuda, K., Kin, T., Asai, K.
- Journal Title
  
  Bioinformatics 22(14)
  
  Pages: 1723-1729
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] SCARNA : fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments2006
- Author(s)
  Tabei, Y., Tsuda, K., Kin, T., Asai, K.
- Journal Title
  
  Bioinformatics 22・14
  
  Pages: 1723-1729
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Mining frequent stem patterns from unaligned RNA sequences2006
- Author(s)
  Hamada, M., Tsuda, K., Kudo, T., Kin, T., Asai, K.
- Journal Title
  
  Bioinformatics 22(20)
  
  Pages: 2480-2487
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Genome sequencing and analysis of Aspergillus oryzae2005
- Author(s)
  Machida M, Asai K, Sano M, Tanaka T, Kumagai T, Terai G, Kusumoto K, Arima T, Akita O, Kashiwagi Y, et al.
- Journal Title
  
  Nature 438(7071)
  
  Pages: 1057-1161
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Extracting relations between promoter sequences and their strengths from microarray data2005
- Author(s)
  Hisanori Kiryu, Taku Oshima, Kiyoshi Asai
- Journal Title
  
  Bioinformatics 21
  
  Pages: 1062-1068
- Data Source
  KAKENHI-PROJECT-12208010
[Journal Article] Genome sequencing and analysis of Aspergillus oryzae2005
- Author(s)
  Machida M., Asai K., et al.
- Journal Title
  
  Nature 438
  
  Pages: 1157-1161
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-12208010
[Journal Article] Extracting relations between promoter sequences and their strengths from microarray data2005
- Author(s)
  Kiryu, H., Oshima, T., Asai, K.
- Journal Title
  
  Bioinformatics 21
  
  Pages: 1062-1068
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-12208010
[Journal Article] Genome sequencing and analysis of Aspergillus oryzae2005
- Author(s)
  Machida, M., Asai, K.et al.
- Journal Title
  
  Nature 438・7071
  
  Pages: 1057-1161
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Minimizing the Cross Validation Error to Mix Kernel Matrices of Heterogeneous Biological Data2004
- Author(s)
  Tsuda, K., Uda, S., Kin, T., Asai, K.
- Journal Title
  
  Neural Processing Letters 19
  
  Pages: 63-72
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-12208010
[Journal Article] Statistics for Biological Sequences2003
- Author(s)
  Kishino, H., Asai, K.
- Journal Title
  
  Iwanami Publisher
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-12208010
[Journal Article] Modeling Splicing Sites with Pairwise Correlations2002
- Author(s)
  Arita, M., Tsuda, K., Asai, K.
- Journal Title
  
  Bioinformatics 18
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-12208010
[Journal Article] Marginalized Kernels for RNA Sequence Data Analysis2002
- Author(s)
  Kin, T., Tsuda K., Asai, K.
- Journal Title
  
  Proc. of Genome Informatics Workshop 2002
  
  Pages: 112-122
- NAID
  130003997145
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-12208010
[Journal Article] Marginalized kernels for biological sequences2002
- Author(s)
  Tsuda, K., Kin, T., Asai, K.
- Journal Title
  
  Bioinformatics 18
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-12208010
[Journal Article] Marginalized Kernels for RNA Sequence Data Analysis2002
- Author(s)
  Kin, T., Tsuda K., Asai, K.
- Journal Title
  
  In Proc. of Genome Informatics Workshop 2002
  
  Pages: 112-122
- NAID
  130003997145
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-12208010
[Journal Article] Selective integration of multiple biological data for supervised network inference
- Author(s)
  Tsuyoshi Kato, Koji Tsuda, Kiyoshi Asai
- Journal Title
  
  Bioinformatics (in press)
- Data Source
  KAKENHI-PROJECT-12208010
[Journal Article] Accurate extraction of functional associations between proteins based on common interaction partners and common domains
- Author(s)
  Kinya Okada, Shig_ehiko Kanaya, Kiyoshi Asai
- Journal Title
  
  Bioinformatics (in press)
- Data Source
  KAKENHI-PROJECT-12208010
[Patent] エピジェネティックスを標的とした新規医薬2020
- Inventor(s)
  石井秀始、今野雅允、小関準、浅井歩、目黒寛司、赤井周司、川野泰彦、布村一人
- Industrial Property Rights Holder
  大阪大学
- Industrial Property Rights Type
  特許
- Filing Date
  2020
- Overseas
- Data Source
  KAKENHI-PROJECT-16H06279
[Presentation] Elucidation of the molecular function of Qin in the germline piRNA pathway2023
- Author(s)
  Yurika Namba、Kazumichi M. Nishida、Yukiteru Ono、Yui Kuroda、Kiyoshi Asai、Mikiko C. Siomi
- Organizer
  第24回日本RNA学会年会
- Data Source
  KAKENHI-PROJECT-22H04925
[Presentation] From DNA replication to G-quadruplex: my long journey on science with my mentor, Ken-ichi Arai2023
- Author(s)
  Hisao Masai
- Organizer
  Cold Spring Harbor Meeting Asia on The Now and Future of RNA Therapeutics
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22H04925
[Presentation] Regulation of replication timing and DNA repair by nuclear membrane tethering of Rif12023
- Author(s)
  Hisao Masai、Tomohiro Iguchi、Sayuri Ito、Mikhiko Shibata、Naoko Kakusho、Rino Fukatsu、Asami Oji、Ichiro Hiratani、Hiroyuki Sasanuma
- Organizer
  The 14th International Symposium on DNA Damage Response & Human Disease (isDDRHD-2023)
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22H04925
[Presentation] Biological functions of G-quadruplexes in regulation of DNA replication2023
- Author(s)
  Hisao Masai
- Organizer
  50th International Symposium on Nucleic Acid Chemistry(ISNAC2023)
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22H04925
[Presentation] Regulation of replication timing and nuclear localization of chromatin by Fission yeast Rif1 protein2023
- Author(s)
  Hisao Masai、Yutaka Kanoh、Daisuke Kohda、Tomoko Sagi
- Organizer
  The 11th International Fission Yeast Meeting(POMBE2023)
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22H04925
[Presentation] G4 binding and oligomerization activities of fission yeast Rif1protein are required for long-range regulation of origin firing.2023
- Author(s)
  H. Masai、Y. Kanoh、D. Kohda、T. Sagi
- Organizer
  Cold Spring Harbor Asia Conference on YEAST AND LIFE SCIENCES
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22H04925
[Presentation] Transcription can drive DNA replication2023
- Author(s)
  Hisao Masai
- Organizer
  70 Years of DNA Double Helix: Celebration of Breakthroughs in Life Science
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22H04925
[Presentation] Association of Rif1 with nuclear membrane is essential for genome-wide replication timing regulation2023
- Author(s)
  Tomohiro Iguchi、Sayuri Ito、Naoko Kakusho、Rino Fukatsu、Kenji Moriyama、Asako Sawano、Asami Oji、Mikihiro Shibata、Atsushi Miyawaki、Ichiro Hiratani、Hiroyuki Sasanuma and Hisao Masai
- Organizer
  CSHL Meeting 2023 on Eukaryotic DNA Replication & Genome Maintenance
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22H04925
[Presentation] Roles of G4 binding and multimization of Rifl in S phase regulation in fission yeast cells.2021
- Author(s)
  Hisao Masai, Yutaka Kanoh, Kaho Takasawa, Daisuke Koida, Seiji Matsumoto
- Organizer
  Cold Spring Harbor Asia Conference YEAST AND LIFE SCIENCES
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16H06279
[Presentation] Mechanisms of membrane association of Rif1 and its role in replication timing regulation2021
- Author(s)
  Tomohiro Iguchi, Sayuri Ito, Naoko Kokusho, Yutaka Kanoh, Kaho, Takasawa, Kenji Moriyama, Hiroyuki Sasanuma, *Hisao Masai.
- Organizer
  Cold Spring Harbor Laboratory Meeting EUKARYOTIC DNA REPLICATION & GENOME MAINTENANCE
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16H06279
[Presentation] Association of Rifl with nuclear membrane is essential for genome-wide replication timing regulation2021
- Author(s)
  Tomohiro Iguchi, Sayuri Ito, Naoko Kakusho, Satoshi Yamazaki, Asami Oji, Rino Fukatsu, Ichiro Hiratani, Hiroyuki Sasanuma, *Hisao Masai
- Organizer
  第44回日本分子生物学会年会
- Invited
- Data Source
  KAKENHI-PROJECT-16H06279
[Presentation] Claspin is required for growth recovery from serum starvation through regulating the PI3K-PDK1-mTOR pathway.2021
- Author(s)
  Chi-Chun Yang, Hisao Masai
- Organizer
  Cold Spring Harbor Asia Conference, DNA METABOLISM, GENOMIC STABILITY & HUMAN DISEASE
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16H06279
[Presentation] PBSIM2 : simulator for long read sequencers with a novel generative model of quality scores2020
- Author(s)
  Yukiteru Ono, Kiyoshi Asai, Michiaki Hamada
- Organizer
  2020年日本バイオインフォマティクス学会年会・第9回生命医薬情報学連合大会(IIBMP2020)
- Data Source
  KAKENHI-PROJECT-16H06279
[Presentation] 大腸菌のタンパク質発現量予測のためのRNA2次構造特徴の抽出2020
- Author(s)
  寺井悟朗、浅井潔
- Organizer
  第43回日本分子生物学会年会
- Data Source
  KAKENHI-PROJECT-16H06279
[Presentation] Discovery of mRNA secondary structural features for the accurate prediction of protein abundance in Escherichia coli2020
- Author(s)
  Goro Terai, Kiyoshi Asai
- Organizer
  2020年日本バイオインフォマティクス学会年会・第9回生命医薬情報学連合大会(IIBMP2020)
- Data Source
  KAKENHI-PROJECT-16H06279
[Presentation] 核内ストレス体によるストレス回復期のスプライシング制御2018
- Author(s)
  二宮賢介, 足達俊吾, 夏目徹, 岩切淳一, 寺井悟朗, 浅井潔, 廣瀬哲郎
- Organizer
  第20回日本RNA学会年会
- Data Source
  KAKENHI-PROJECT-16H06279
[Presentation] 先進的RNA-seqのデータ解析を改善するマッピングパラメータ学習2018
- Author(s)
  岩切淳一, Martin C. Frith, 浜田道昭, 浅井潔
- Organizer
  第20回日本RNA学会年会
- Data Source
  KAKENHI-PROJECT-16H06279
[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] RNA配列設計のための情報解析技術2017
- Author(s)
  浅井潔
- Organizer
  日本核酸医薬学会第3回年会
- Data Source
  KAKENHI-PROJECT-16H06279
[Presentation] Capturing Alternative Secondary Structures of RNA by Decomposition of Base Pairing Probabilities2017
- Author(s)
  Taichi Hagio, Shun Sakuraba, Junichi Iwakiri, Ryota Mori and Kiyoshi Asai
- Organizer
  The 28th International Conference on Genome Informatics GIW/BIOINFO 2017
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16H02484
[Presentation] Capturing Alternative Secondary Structures of RNA by Decomposition of Base Pairing Probabilities2017
- Author(s)
  Taichi Hagio, Shun Sakuraba, Junichi Iwakiri, Ryota Mori, Kiyoshi Asai
- Organizer
  The 28th International conference on Genome Informatics
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16H06279
[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] Algorithms on Marginal Distributions of RNA Secondary Structures,2016
- Author(s)
  Kiyoshi Asai
- Organizer
  ALGO2016
- Place of Presentation
  Aarhus University, Denmark
- Year and Date
  2016-08-23
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16H06279
[Presentation] Algorithms on Marginal Distributions of RNA Secondary Structures2016
- Author(s)
  Kiyoshi Asai
- Organizer
  ALGO2016 & WABI2016
- Place of Presentation
  Aarhus University, Denmark
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-25240044
[Presentation] Algorithms for Marginal Probabilities on RNA Secondary Structures2016
- Author(s)
  Kiyoshi Asai
- Organizer
  ALGO2016 & WABI2016
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16H02484
[Presentation] Predicting RNA-RNA duplex dimerization energy from the molecular dynamics simulation2016
- Author(s)
  Shun Sakuraba, Tomoshi Kameda and Kiyoshi Asai
- Organizer
  RNA2016
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16H02484
[Presentation] RNA-RNA の相対結合自由エネルギー計算2016
- Author(s)
  桜庭俊, 浅井潔, 亀田倫史
- Organizer
  第19回理論化学討論会
- Data Source
  KAKENHI-PROJECT-16H02484
[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] 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,
- Organizer
  RNA2016
- Place of Presentation
  京都
- Year and Date
  2016-06-29
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16H06279
[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] 分子動力学法による核酸修飾塩基対の結合エネルギー予測2015
- Author(s)
  桜庭俊、亀田倫史、浅井潔
- 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] 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] 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] 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] 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] On algorithms for computing thermodynamic entropy of RNA secondary structures2011
- Author(s)
  Kiyoshi Asai
- Organizer
  CBI/JSBI2011合同大会
- Place of Presentation
  兵庫県神戸市神戸国際会議場(ポスター発表)
- Year and Date
  2011-11-09
- Data Source
  KAKENHI-PROJECT-22240031
[Presentation] Binary estimation problems in structural information analysis of RNA2011
- Author(s)
  Kiyoshi Asai
- Organizer
  The 16Th Annual Meeting of the RNA Society
- Place of Presentation
  京都府京都市国立京都国際会館
- Year and Date
  2011-06-15
- Data Source
  KAKENHI-PROJECT-22240031
[Presentation] Recent advances in structure prediction of RNA2011
- Author(s)
  Kiyoshi Asai
- Organizer
  第34回日本分子生物学会年会
- Place of Presentation
  神奈川県横浜市パシフィコ横浜(口頭発表)
- Year and Date
  2011-12-14
- Data Source
  KAKENHI-PROJECT-22240031
[Presentation] Algorithms for RNA sequence analysis2011
- Author(s)
  Kiyoshi Asai
- Organizer
  GIW2011
- Place of Presentation
  韓国、釜山、Haeundae Grand Hotel(招待講演)
- Year and Date
  2011-12-06
- Data Source
  KAKENHI-PROJECT-22240031
[Presentation] On algorithms for computing thermodynamic entropy of RNA secondary structures2011
- Author(s)
  Hisanori Kiryu and Kiyoshi Asai
- Organizer
  第34回日本分子生物学会年会
- Year and Date
  2011-12-14
- Data Source
  KAKENHI-PROJECT-22240031
[Presentation] A non-parametric Bayesian approach for predicting RNA secondary structures2009
- Author(s)
  Sato, K., Hamada, M., Mituyama, T., Asai, K., Sakakibara, Y.
- Organizer
  Proceedings of 9th Workshop on Algorithms in Bioinformatics (WABI 2009)
- Place of Presentation
  Philadelphia, USA
- Year and Date
  2009-09-12
- Data Source
  KAKENHI-PROJECT-17018029
[Presentation] A non-parametric Bayesian approach for predicting RNA secondarystructures2009
- Author(s)
  Sato, K., Hamada, M., Mituyama, T., Asai, K., Sakakibara, Y.
- Organizer
  Proceedings of 9th Workshop on Algorithms in Bioinformatics (WABI 2009)
- Place of Presentation
  フィラデルフィア,米国
- Year and Date
  2009-09-12
- Data Source
  KAKENHI-PROJECT-17018029
[Presentation] Stem Kernels for RNA Sequence Analyses2007
- Author(s)
  Sakakibara, Y., Asai, K., Sato, K.
- Organizer
  Proc. 1st International Conference on Bioinformatics Research and Development
- Place of Presentation
  Berlin, Germany
- Year and Date
  2007-03-13
- Data Source
  KAKENHI-PROJECT-17018029
[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] 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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Asai Kiyoshi 浅井 潔

ASAI Kiyoshi 浅井 潔

Research Projects

Research Products

Co-Researchers

化学修飾を含むmRNA配列設計の基盤技術Principal Investigator

Principal Investigator

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Review Section

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Platform for Advanced Genome Science

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修飾塩基を持つRNAの情報解析基盤技術の開発Principal Investigator

Principal Investigator

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RNA informatics for epi-transcriptome analysisPrincipal Investigator

Principal Investigator

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Platform for Advanced Genome Science

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Comprehensive prediction of RNA-protein interactinosPrincipal Investigator

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Development of basic technology for privacy-preserving bioinformatics and its application

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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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Exhaustive prediction of microRNAs, snoRNAs and their targetsPrincipal Investigator

Principal Investigator

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Development of computational methods for comparing a large scale multiple genome sequences

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Modeling and prediction of genome sequence information by using information representation models

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[Book] Encyclopedia of Bioinformatics and Computational Biology2018

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[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

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[Book] 統計科学のフロンティア9生物配列の統計 : 核酸・タンパクから情報を読む2003

Author(s)

Asai Kiyoshi 浅井潔

ASAI Kiyoshi 浅井潔