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Shimizu Kana  清水 佳奈

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SHIMIZU Kana  清水 佳奈

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Researcher Number 60367050
Other IDs
Affiliation (Current) 2025: 早稲田大学, 理工学術院, 教授
Affiliation (based on the past Project Information) *help 2019 – 2024: 早稲田大学, 理工学術院, 教授
2015 – 2016: 早稲田大学, 理工学術院, 准教授
2015: 国立研究開発法人産業技術総合研究所, その他部局等, 研究員
2015: 国立研究開発法人産業技術総合研究所, 創薬基盤研究部門, 主任研究員
2014: 独立行政法人産業技術総合研究所, ゲノム情報研究センター, 主任研究員 … More
2014: 独立行政法人産業技術総合研究所, 創薬基盤研究部門, 研究員
2014: 産業技術総合研究所, ゲノム情報研究センター, 主任研究員
2013: 独立行政法人産業技術総合研究所, ゲノム情報研究センター, 研究員
2010 – 2011: 独立行政法人産業技術総合研究所, 生命情報工学研究センター, 研究員 Less
Review Section/Research Field
Principal Investigator
Medium-sized Section 62:Applied informatics and related fields / Basic Section 62010:Life, health and medical informatics-related / Life / Health / Medical informatics / Bioinformatics/Life informatics
Except Principal Investigator
Broad Section J / Medium-sized Section 60:Information science, computer engineering, and related fields / Life / Health / Medical informatics / Bioinformatics/Life informatics
Keywords
Principal Investigator
アルゴリズム / 秘密計算 / プライバシ保護 / 個人ゲノム / 参照ゲノム / データ合成 / ヒトゲノム / color de Bruijn graph / 参照ゲノム配列 / プライバシ保護データマイニング … More / ゲノム情報解析 / 秘匿計算 / SGX / GWAS / 秘匿検索 / 決定木 / ゲノム配列計算 / 機械学習 / TEE / 暗号プロトコル / 秘密分散 / ゲノム配列検索 / Structural variation / Alignment free / 次世代シークエンスデータ / パターン / ゲノム配列 / アラインメントフリー / 次世代シークエンサー / 最小全域木 / ギガシークエンスデーター / 編集距離 / 類似配列検索 / ショートリード / ギガシークエンサー / ゲノム … More
Except Principal Investigator
簡潔データ構造 / 秘匿計算 / 学習 / 配列検索 / データベース検索 / 暗号 / 化合物 / ゲノム / 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 / データベース / 低分子化合物 / 低分子医薬品 / 機能部位 / 基質結合部位 / タンパク質 Less
  • Research Projects

    (8 results)
  • Research Products

    (43 results)
  • Co-Researchers

    (12 People)
  •  Development of efficient and secure data structure for reference genomePrincipal Investigator

    • Principal Investigator
      清水 佳奈
    • Project Period (FY)
      2023 – 2025
    • Research Category
      Grant-in-Aid for Challenging Research (Exploratory)
    • Review Section
      Medium-sized Section 62:Applied informatics and related fields
    • Research Institution
      Waseda University
  •  圧縮秘匿計算による大規模データ処理

    • Principal Investigator
      定兼 邦彦
    • Project Period (FY)
      2021 – 2024
    • Research Category
      Grant-in-Aid for Scientific Research (A)
    • Review Section
      Medium-sized Section 60:Information science, computer engineering, and related fields
    • Research Institution
      The University of Tokyo
  •  Big Data Processing with Compressed Secure Computation

    • Principal Investigator
      定兼 邦彦
    • Project Period (FY)
      2021 – 2025
    • Research Category
      Grant-in-Aid for Scientific Research (S)
    • Review Section
      Broad Section J
    • Research Institution
      The University of Tokyo
  •  Development of privacy-preserving technology for genome information analysisPrincipal Investigator

    • Principal Investigator
      Shimizu Kana
    • Project Period (FY)
      2019 – 2022
    • Research Category
      Grant-in-Aid for Scientific Research (C)
    • Review Section
      Basic Section 62010:Life, health and medical informatics-related
    • Research Institution
      Waseda University
  •  De novo approach to find differentially appearing genome sequence patterns from the two NGS datasets.Principal Investigator

    • Principal Investigator
      Kana Shimizu
    • Project Period (FY)
      2014 – 2016
    • Research Category
      Grant-in-Aid for Challenging Exploratory Research
    • Research Field
      Life / Health / Medical informatics
    • Research Institution
      Waseda University
      National Institute of Advanced Industrial Science and Technology
  •  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
  •  Development of ultra-fast comparison method of protein local structures towards the prediction of ligand-binding sites

    • Principal Investigator
      TOMII KENTARO
    • Project Period (FY)
      2011 – 2014
    • Research Category
      Grant-in-Aid for Scientific Research (C)
    • Research Field
      Bioinformatics/Life informatics
    • Research Institution
      National Institute of Advanced Industrial Science and Technology
  •  Developing fast algorithm for analyzing Giga-sequence dataPrincipal Investigator

    • Principal Investigator
      SHIMIZU Kana
    • Project Period (FY)
      2010 – 2011
    • Research Category
      Grant-in-Aid for Young Scientists (B)
    • Research Field
      Bioinformatics/Life informatics
    • Research Institution
      National Institute of Advanced Industrial Science and Technology

All 2024 2023 2022 2021 2020 2019 2016 2015 2014 2013 2012 2011 2010

All Journal Article Presentation Patent

  • [Journal Article] Efficient Privacy Preserving Range Query Using Segment Tree2024

    • Author(s)
      Shirotake Shusuke、Shimizu Kana
    • Journal Title

      Proceedings of 58th Annual Conference on Information Sciences and Systems (CISS)

      Volume: - Pages: 1-6

    • DOI

      10.1109/ciss59072.2024.10480202

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-23K18515, KAKENHI-PROJECT-21H05052
  • [Journal Article] Private Evaluation of a Decision Tree based on Secret Sharing2023

    • Author(s)
      Mohammad Nabil Ahmed, Kana Shimizu
    • Journal Title

      Information Security and Cryptology - ICISC 2022, 25th International Conference, ICISC 2022, Seoul, South Korea, November 30–December 2, 2022, Revised Selected Papers

      Volume: 13849 Pages: 186-209

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-21H05052
  • [Journal Article] Private Evaluation of a Decision Tree Based on Secret Sharing2023

    • Author(s)
      Ahmed Mohammad Nabil、Shimizu Kana
    • Journal Title

      Lecture Notes in Computer Science

      Volume: 13849 Pages: 171-194

    • DOI

      10.1007/978-3-031-29371-9_9

    • ISBN
      9783031293702, 9783031293719
    • Data Source
      KAKENHI-PROJECT-19K12209
  • [Journal Article] Efficient privacy-preserving variable-length substring match for genome sequence2022

    • Author(s)
      Nakagawa Yoshiki、Ohata Satsuya、Shimizu Kana
    • Journal Title

      Algorithms for Molecular Biology

      Volume: 17 Issue: 1 Pages: 1-22

    • DOI

      10.1186/s13015-022-00211-1

    • Data Source
      KAKENHI-PROJECT-19K12209
  • [Journal Article] Efficient Privacy-Preserving Variable-Length Substring Match for Genome Sequence2021

    • Author(s)
      Nakagawa, Yoshiki ; Ohata, Satsuya ; Shimizu, Kana
    • Journal Title

      21st International Workshop on Algorithms in Bioinformatics (WABI 2021)

      Volume: 201

    • Peer Reviewed / Open Access / Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-19K12209
  • [Journal Article] Efficient Privacy-Preserving Variable-Length Substring Match for Genome Sequence2021

    • Author(s)
      Yoshiki Nakagawa, Satsuya Ohata, Kana Shimizu
    • Journal Title

      Proceedings of WABI

      Volume: LIPIcs 201

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PROJECT-21H05052
  • [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] 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] PDB-scale Analysis of Known and Putative Ligand-binding Sites with Structural Sketches2012

    • Author(s)
      J. Ito, Y. Tabei, K. Shimizu, K. Tomii and K. Tsuda
    • Journal Title

      Proteins

      Volume: 80 Issue: 3 Pages: 747-763

    • DOI

      10.1002/prot.23232

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-21680025, KAKENHI-PROJECT-23500374
  • [Journal Article] PoSSuM: a Database of Similar Protein-Ligand Binding and Putative Pockets2012

    • Author(s)
      J. Ito, Y. Tabei, K. Shimizu, K. Tsuda and K. Tomii
    • Journal Title

      Nucleic Acids Research

      Volume: 40 Issue: D1 Pages: D541-D548

    • DOI

      10.1093/nar/gkr1130

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-21680025, KAKENHI-PROJECT-23500374
  • [Journal Article] SlideSort : All Pairs Similarity Search for Short Reads2011

    • Author(s)
      Kana Shimizu, Koji Tsuda
    • Journal Title

      Bioinformatics

      Volume: 27(4) Pages: 464-470

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-22700319
  • [Journal Article] SlideSort: All Pairs Similarity Search for Short Reads2011

    • Author(s)
      K. Shimizu and K. Tsuda
    • Journal Title

      Bioinformatics

      Volume: 27 Issue: 4 Pages: 464-470

    • DOI

      10.1093/bioinformatics/btq677

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-21680025, KAKENHI-PROJECT-22700319
  • [Patent] 配列解析装置、配列解析方法およびコンピュータプログラム2010

    • Inventor(s)
      清水佳奈, 津田宏治
    • Industrial Property Rights Holder
      清水佳奈, 津田宏治
    • Industrial Property Number
      2010-156342
    • Filing Date
      2010-07-09
    • Data Source
      KAKENHI-PROJECT-22700319
  • [Patent] 配列解析装置,配列解析方法およびコンピュータプログラム2010

    • Inventor(s)
      清水佳奈,津田宏治
    • Industrial Property Rights Holder
      産業技術総合研究所
    • Filing Date
      2010-07-09
    • Data Source
      KAKENHI-PROJECT-22700319
  • [Presentation] 勾配クリッピングを用いたプライバシ保護ヒトゲノム合成2024

    • Author(s)
      橋本康平, 清水佳奈
    • Organizer
      情報処理学会バイオ情報学研究会(BIO)
    • Data Source
      KAKENHI-PROJECT-23K18515
  • [Presentation] 文法圧縮アルゴリズムを用いた colored de Bruijn graph の効率化2024

    • Author(s)
      岩月悠真, 清水佳奈
    • Organizer
      情報処理学会バイオ情報学研究会(BIO)
    • Data Source
      KAKENHI-PROJECT-23K18515
  • [Presentation] Function Secret Sharing を用いた秘匿全文検索2024

    • Author(s)
      内山智貴,清水佳奈
    • Organizer
      暗号と情報セキュリティシンポジウム(SCIS2024)
    • Data Source
      KAKENHI-PROJECT-21H05052
  • [Presentation] 生命情報を安全に活用するプライバシ保護データマイニング2023

    • Author(s)
      清水佳奈
    • Organizer
      バイオメディカル・ファジィ・システム学会第36回年次大会
    • Invited
    • Data Source
      KAKENHI-PROJECT-21H05052
  • [Presentation] 生命情報を安全に活用するプライバシ保護データマイニング2023

    • Author(s)
      清水佳奈
    • Organizer
      バイオメディカル・ファジィ・システム学会第36回年次大会
    • Invited
    • Data Source
      KAKENHI-PROJECT-23K18515
  • [Presentation] Private Evaluation of a Decision Tree Based on Secret Sharing2022

    • Author(s)
      Ahmed Mohammad Nabil、Shimizu Kana
    • Organizer
      ICISC 2022
    • Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-19K12209
  • [Presentation] Intel SGXを用いた個人ゲノム情報解析システム2020

    • Author(s)
      岩田大輝 清水佳奈
    • Organizer
      2020年暗号と情報セキュリティシンポジウム(SCIS2020)
    • Data Source
      KAKENHI-PROJECT-19K12209
  • [Presentation] Novel reference-free detection of somatic structural variant based on graph-aware index2020

    • Author(s)
      Taiki Yamada, Kenichi Chiba, Keisuke Kataoka, Yuichi Shiraishi and Kana Shimizu
    • Organizer
      IIBMP 2020
    • Data Source
      KAKENHI-PROJECT-19K12209
  • [Presentation] 生体情報セキュリティ2019

    • Author(s)
      清水佳奈
    • Organizer
      第58回 日本生体医工学会大会
    • Data Source
      KAKENHI-PROJECT-19K12209
  • [Presentation] Towards Privacy-preserving Biomedical Knowledge Integration2019

    • Author(s)
      Kana Shimizu
    • Organizer
      JAPAN - NORDIC WORKSHOP ON DIGITAL HEALTH FOR HEALTHY LONGEVITY
    • Data Source
      KAKENHI-PROJECT-19K12209
  • [Presentation] 属性ベース暗号とIntel SGXを用いた堅牢かつ柔軟なアクセス制御を実現するデータ分析プラットフォームの構築2019

    • Author(s)
      岩田大輝 清水佳奈
    • Organizer
      情報処理学会 第58回バイオ情報学研究会
    • Data Source
      KAKENHI-PROJECT-19K12209
  • [Presentation] 秘密分散に基づく秘匿全文検索2019

    • Author(s)
      中川 佳貴 大畑 幸矢 清水 佳奈
    • Organizer
      コンピュータセキュリティシンポジウム2019(CSS2019)
    • Data Source
      KAKENHI-PROJECT-19K12209
  • [Presentation] Privacy-preserving Search for Sharing Genetic Variants2019

    • Author(s)
      Masanobu Jimbo, Nobutaka Mitsuhashi, Shigeo Mitsunari, Shin Kawano, Toshiaki Katayama, Kiyoshi Asai, Kana Shimizu
    • Organizer
      The 27th International Conference on Intelligent Systems for Molecular Biology and the 19 th European Conference on Computational Biology (ISMB/ECCB 2019)
    • Data Source
      KAKENHI-PROJECT-19K12209
  • [Presentation] BV-SGX: 生命情報解析向け仮想マシンを搭載したSGXクラウド2019

    • Author(s)
      櫻井碧 清水佳奈
    • Organizer
      情報処理学会 第58回バイオ情報学研究会
    • Data Source
      KAKENHI-PROJECT-19K12209
  • [Presentation] Privacy-preserving genome sequence search2016

    • Author(s)
      Kana Shimizu
    • Organizer
      2016 International Workshop on Spatial and Temporal Modeling from Statistical, Machine Learning and Engineering perspectives (STM2016)
    • Place of Presentation
      東京
    • Year and Date
      2016-06-23
    • Invited
    • Data Source
      KAKENHI-PROJECT-26540159
  • [Presentation] SlideSort for comparative NGS data and privacy preserving search for sensitive data2016

    • Author(s)
      Kana Shimizu
    • Organizer
      RDF Summit 2016
    • Place of Presentation
      東北大学
    • Year and Date
      2016-02-19
    • Data Source
      KAKENHI-PROJECT-26540159
  • [Presentation] 参照ゲノムをなるべく用いない解析 / ゲノム秘匿検索2015

    • Author(s)
      清水 佳奈
    • Organizer
      NGS現場の会 第四回研究会
    • Place of Presentation
      つくば国際会議場
    • Year and Date
      2015-07-02
    • Data Source
      KAKENHI-PROJECT-26540159
  • [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] PoSSuM: a database for predicting protein-ligand Interactions2012

    • Author(s)
      K. Tomii, J. Ito, Y. Tabei, K. Shimizu, K. Tsuda
    • Organizer
      生命医薬情報学連合大会(2012年日本バイオインフォマティクス学会年会 情報計算化学生物学会(CBI学会)年次大会 オミックス医療研究会年会)
    • Place of Presentation
      タワーホール船堀(東京都)
    • Data Source
      KAKENHI-PROJECT-23500374
  • [Presentation] PoSSuM: a database for searching similar pairs of known and potential ligand-binding sites in proteins2012

    • Author(s)
      J. Ito, Y. Tabei, K. Shimizu, K. Tsuda, K. Tomii
    • Organizer
      第50回日本生物物理学会年会
    • Place of Presentation
      名古屋大学
    • Data Source
      KAKENHI-PROJECT-23500374
  • [Presentation] PoSSuM: a database of known and potential ligand-binding sites in proteins2012

    • Author(s)
      J. Ito, Y. Tabei, K. Shimizu, K. Tsuda, K. Tomii
    • Organizer
      Bioinformatics 2012, SocBiN
    • Place of Presentation
      Stockholm, Sweden
    • Data Source
      KAKENHI-PROJECT-23500374
  • [Presentation] Fast and exact algorithm for Next Generation Sequencing data analysis2011

    • Author(s)
      Kana Shimizu, Koji Tsuda
    • Organizer
      ISMB 2011 Highlights Track
    • Place of Presentation
      Vienna, Austria
    • Year and Date
      2011-07-18
    • Data Source
      KAKENHI-PROJECT-22700319
  • [Presentation] SlideSort : A fast and exact tool for finding all similar pairs from next-generation sequencing data2011

    • Author(s)
      Kana Shimizu, Koji Tsuda
    • Organizer
      RECOMB 2011
    • Place of Presentation
      Vancouver
    • Year and Date
      2011-03-29
    • Data Source
      KAKENHI-PROJECT-22700319
  • [Presentation] Pdb-wide discovery of similar ligand binding sites Using structural sketches2011

    • Author(s)
      J. Ito, Y. Tabei, K. Shimizu, K.Tomii, K. Tsuda
    • Organizer
      3DSIG 2011: The 7th Structural Bioinformatics and Computational Biophysics
    • Place of Presentation
      Austria Center Vienna (Austria)
    • Data Source
      KAKENHI-PROJECT-23500374
  • [Presentation] Structural Sketchを用いたタンパク質リガンド類似結合部位の高速列挙とそのデータベース構築2011

    • Author(s)
      伊東純一、田部井靖生、清水佳奈、富井健太郎、津田宏治
    • Organizer
      第11回日本蛋白質科学会年会
    • Place of Presentation
      ホテル阪急エキスポパーク (大阪府)
    • Data Source
      KAKENHI-PROJECT-23500374
  • [Presentation] A novel ultra-fast comparison method for known and potential ligand-binding sites of proteins2011

    • Author(s)
      K.Tomii, J. Ito, Y. Tabei, K. Shimizu, K. Tsuda
    • Organizer
      19th Annual International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational Biology
    • Place of Presentation
      Austria Center Vienna (Austria)
    • Data Source
      KAKENHI-PROJECT-23500374
  • [Presentation] Fast and exact algorithm for Next Generation Sequencing data analysis2011

    • Author(s)
      Kana Shimizu, Koji Tsuda
    • Organizer
      ISMB/ECCB 2011 Highlights Track
    • Place of Presentation
      Vienna
    • Year and Date
      2011-07-18
    • Data Source
      KAKENHI-PROJECT-22700319
  • [Presentation] SLIDESORT : All pairs similarity search for short reads2010

    • Author(s)
      Kana Shimizu, Koji Tsuda
    • Organizer
      2010年日本バイオインフォマティクス学会年会
    • Place of Presentation
      九州
    • Year and Date
      2010-12-15
    • Data Source
      KAKENHI-PROJECT-22700319
  • [Presentation] Developing an exact method to find similar pairs with small edit-distance2010

    • Author(s)
      Kana Shimizu, Koji Tsuda
    • Organizer
      ISMB 2010
    • Place of Presentation
      Boston
    • Year and Date
      2010-07-12
    • Data Source
      KAKENHI-PROJECT-22700319
  • 1.  TSUDA Koji (90357517)
    # of Collaborated Projects: 2 results
    # of Collaborated Products: 11 results
  • 2.  定兼 邦彦 (20323090)
    # of Collaborated Projects: 2 results
    # of Collaborated Products: 0 results
  • 3.  坂本 比呂志 (50315123)
    # of Collaborated Projects: 2 results
    # of Collaborated Products: 0 results
  • 4.  渋谷 哲朗 (60396893)
    # of Collaborated Projects: 2 results
    # of Collaborated Products: 0 results
  • 5.  申 吉浩 (60523587)
    # of Collaborated Projects: 2 results
    # of Collaborated Products: 0 results
  • 6.  TOMII KENTARO (40357570)
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 6 results
  • 7.  Hamada Michiaki (00596538)
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 1 results
  • 8.  Hanaoka Goichiro (30415731)
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 1 results
  • 9.  Frith Martin (40462832)
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 10.  Asai Kiyoshi (30356357)
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 1 results
  • 11.  神保 洸貴 (80966630)
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 results
  • 12.  ITO Junichi
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 6 results

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