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Kinoshita Kengo  木下 賢吾

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KINOSHITA Kengo  木下 賢吾

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Researcher Number 60332293
Other IDs
External Links
Affiliation (Current) 2025: 東北大学, 情報科学研究科, 教授
2025: 東北大学, 東北メディカル・メガバンク機構, 教授
Affiliation (based on the past Project Information) *help 2022 – 2024: 東北大学, 情報科学研究科, 教授
2021 – 2023: 東北大学, 東北メディカル・メガバンク機構, 教授
2012 – 2018: 東北大学, 情報科学研究科, 教授
2016 – 2017: 東北大学, 大学院情報科学研究科, 教授
2014: 東北大学, 大学院情報科学研究科, 教授 … More
2009 – 2011: The University of Tokyo, 大学院・情報科学研究科, 教授
2006 – 2008: The University of Tokyo, 医科学研究所, 准教授
2004 – 2006: 東京大学, 医科学研究所, 助教授
2003: 横浜市立大学, 大学院・総合理学研究科, 助手
2001 – 2002: 横浜市立大学, 総合理学研究科, 助手
2001: Yokohama City University, Graduate School of Integrated Science, Instructor, 大学院・総合理学研究科, 助手
2000: 理化学研究所, ゲノム科学総合研究センター, 研究員 Less
Review Section/Research Field
Principal Investigator
Life / Health / Medical informatics / Biophysics / Complex systems / Biological Sciences / Applied genomics / Biophysics
Except Principal Investigator
Biological Sciences / 基礎ゲノム科学 / Basic Section 52010:General internal medicine-related / Basic Section 49020:Human pathology-related … More / Medium-sized Section 55:Surgery of the organs maintaining homeostasis and related fields / System genome science / Soft computing / Biophysics / Complex systems / Biophysics Less
Keywords
Principal Investigator
バイオインフォマティクス / タンパク質間相互作用 / タンパク質立体構造 / 変異 / ゲノム変異 / レアバリアント / 蛋白質立体構造 / 遺伝子共発現 / 静電ポテンシャル / リガンド結合部位 … More / 分子表面 / 立体構造 / 遺伝子発現量 / 生命情報 / 発現量変化 / 発現量 / ゲノム / ヒトゲノム / 蛋白質立体構構造 / 変異の意味づけ / ヒトタンパク質 / ホモロジーモデリング / 低頻度変異 / ネットワーククラスタリング / 遺伝子共発現ネットワーク / 相互作用ネットワーク / クラスター解析 / 種間比較 / 統合ネットワーク / 蛋白質間相互作用 / ブラウニアン動力学 / 膜タンパク質 / 生命情報科学 / 多階層シミュレーション / 分子動力学法 / 構造モデリング / イオンチャネル / ドッキングシュミレーション / シグナル伝達 / トランスポーター / 分子間相互作用 / 蛋白質 / トランスポートゾーム / タンパク質問相互作用 / 共発現 / 膜分子輸送複合体 / DNAマイクロアレイ / トランスポートソーム / 膜輸送複合体 / 立体構造-機能相関 / 立体構造・機能相関 / 機能部位予測 / X線結晶構造解析 / タンパク質 / データベース / モノヌクレオチド結合タンパク / 構造機能相関 / タンパク質の機能 … More
Except Principal Investigator
データベース / バイオインフォマティクス / 蛋白質 / 生物物理 / プロテオーム / 分子動力学 / 分子シミュレーション / 東北メディカル・メガバンク / 遺伝解析 / 脳MRI / UKバイオバンク / ToMMo / 遺伝 / 生活習慣病 / 加齢 / 脳 / MRI / 国際共同研究 / 分子標的 / がん関連線維芽細胞 / 膵管内腫瘍 / 化学療法 / ゲノム / オルガノイド / 胆道がん / 膵臓がん / 分子動力学シミュレーション / 構造生物学 / ナトリウムチャネル / 局所麻酔薬 / ゲノム進化 / 共発現データベース / シロイヌナズナ / ネットワーク生物学 / 遺伝子共発現 / 率的情報処理 / 確率的情報処理 / 情報統計力学 / 統計数学 / 機械学習 / 数理工学 / muscle-specific expression / in situ hybridization / model building / Markov chain / promoters / ascidians / ゲノム配列解析 / シスエレメント / モチーフ抽出 / 組織特異的プロモーター / 組織特異的発現 / モチーフ / カタユウレイボヤ / 筋肉特異的発現 / ハイブリダイゼーション / モデル化 / マルコフ連鎖 / プロモーター / ホヤ / myoglobin / Fermi resonance / mode coupling / vibrational reluxation / anharmonic vibration / proteins / ミオグロビンL / フレルミ共鳴 / 非線型振動 / ミオグロビン / フェルミ共鳴 / モードカップリング / 振動緩和 / 非線形振動 / 生物学 / 薬物動態学 / 代謝 / 全身循環 / 薬物動態 / 不整脈 / 心臓 / 生物物理学 / 生理学 / システム生物学 / 蛋白質間相互作用 / 生体分子 / 蛋白質の構造・機能予測 / ClassPPI / 蛋白質の会合表面 / 結晶水 / 原子占有率 / クリスタルパッキング / 会合表面間平均距離 / 会合空間体積 / ホモ二量体 / 溶媒接触表面積 / 蛋白質会合表面 / ドッキング計算 / 蛋白質ループ構造 / 構造アンサンブル予測 / 相互作用 / 生体生命情報学 / 立体構造 / 分子認識 / モノヌクレオチド / 構造機能相関 Less
  • Research Projects

    (20 results)
  • Research Products

    (176 results)
  • Co-Researchers

    (52 People)
  •  International research using big data for lifestyle disease, brain aging and genetic background

    • Principal Investigator
      鈴木 秀明
    • Project Period (FY)
      2023 – 2025
    • Research Category
      Grant-in-Aid for Scientific Research (C)
    • Review Section
      Basic Section 52010:General internal medicine-related
    • Research Institution
      Tohoku University
  •  Elucidation of the mechanism of intractability of pancreatobiliary cancers using patients-derived organoids

    • Principal Investigator
      古川 徹
    • Project Period (FY)
      2022 – 2025
    • Research Category
      Grant-in-Aid for Scientific Research (B)
    • Review Section
      Basic Section 49020:Human pathology-related
    • Research Institution
      Tohoku University
  •  Development of Adverse Events-free Local Anesthetics in Cryo-EM Structural Determination of Sodium Channels

    • Principal Investigator
      Yamauchi Masanori
    • Project Period (FY)
      2021 – 2023
    • Research Category
      Grant-in-Aid for Challenging Research (Exploratory)
    • Review Section
      Medium-sized Section 55:Surgery of the organs maintaining homeostasis and related fields
    • Research Institution
      Tohoku University
  •  Feasibility study of an evaluation of the impact of rare variants on gene expressionPrincipal Investigator

    • Principal Investigator
      Kinoshita Kengo
    • Project Period (FY)
      2016 – 2018
    • Research Category
      Grant-in-Aid for Challenging Exploratory Research
    • Research Field
      Life / Health / Medical informatics
    • Research Institution
      Tohoku University
  •  Construction of analyses basis for understanding rare variants using protein structural informationPrincipal Investigator

    • Principal Investigator
      Kinoshita Kengo
    • Project Period (FY)
      2015 – 2017
    • Research Category
      Grant-in-Aid for Scientific Research (B)
    • Research Field
      Life / Health / Medical informatics
    • Research Institution
      Tohoku University
  •  Analysis of cell-cell communication using comparison of gene co-expression for different tissues

    • Principal Investigator
      Obayashi Takeshi
    • Project Period (FY)
      2015 – 2017
    • Research Category
      Grant-in-Aid for Young Scientists (B)
    • Research Field
      System genome science
    • Research Institution
      Tohoku University
  •  Design Theory of Probabilistic Computational Models for Community Detections based on Non-Additive Volume and Entropy

    • Principal Investigator
      TANAKA Kazuyuki
    • Project Period (FY)
      2013 – 2016
    • Research Category
      Grant-in-Aid for Scientific Research (B)
    • Research Field
      Soft computing
    • Research Institution
      Tohoku University
  •  Development and analyses of integrated networks for cellular function predictionsPrincipal Investigator

    • Principal Investigator
      KENGO Kinoshita
    • Project Period (FY)
      2012 – 2014
    • Research Category
      Grant-in-Aid for Scientific Research (C)
    • Research Field
      Biophysics
    • Research Institution
      Tohoku University
  •  Establishment of Integrative Multi-level Systems Biology and its Applications

    • Principal Investigator
      KURACHI YOSHIHISA
    • Project Period (FY)
      2010 – 2015
    • Research Category
      Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
    • Review Section
      Complex systems
    • Research Institution
      Osaka University
  •  Development of new simulation methods at the molecular layerPrincipal Investigator

    • Principal Investigator
      KENGO Kinoshita
    • Project Period (FY)
      2010 – 2014
    • Research Category
      Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
    • Review Section
      Complex systems
    • Research Institution
      Tohoku University
  •  Structural Interactome Studies from Computational and Bioinformatics Approaches

    • Principal Investigator
      NAKAMURA Haruki
    • Project Period (FY)
      2008 – 2010
    • Research Category
      Grant-in-Aid for Scientific Research (B)
    • Research Field
      Biophysics
    • Research Institution
      Osaka University
  •  構造プロテオミクスに基づく蛋白質間相互作用の解析と予測

    • Principal Investigator
      NAKAMURA Haruki
    • Project Period (FY)
      2005
    • Research Category
      Grant-in-Aid for Scientific Research on Priority Areas
    • Review Section
      Biological Sciences
    • Research Institution
      Osaka University
  •  Construction and analyses of interaction network for transportsomeusing structural informationPrincipal Investigator

    • Principal Investigator
      KINOSHITA Kengo
    • Project Period (FY)
      2005 – 2009
    • Research Category
      Grant-in-Aid for Scientific Research on Priority Areas
    • Review Section
      Biological Sciences
    • Research Institution
      The University of Tokyo
  •  蛋白質の立体構造に基づく分子会合表面特性の解析

    • Principal Investigator
      前田 美紀
    • Project Period (FY)
      2005 – 2007
    • Research Category
      Grant-in-Aid for Exploratory Research
    • Research Field
      基礎ゲノム科学
    • Research Institution
      National Institute of Agrobiological Sciences
  •  Construction of a computational model for the transcriptional regulatory regions in Ciona intestinalis and its experimental verification

    • Principal Investigator
      NAKAI Kenta
    • Project Period (FY)
      2005 – 2006
    • Research Category
      Grant-in-Aid for Scientific Research (B)
    • Research Field
      基礎ゲノム科学
    • Research Institution
      The University of Tokyo
  •  蛋白質分子表面の形状と物性の類似性検索による機能予測法の開発Principal Investigator

    • Principal Investigator
      木下 賢吾
    • Project Period (FY)
      2003 – 2005
    • Research Category
      Grant-in-Aid for Young Scientists (B)
    • Research Field
      Applied genomics
    • Research Institution
      The University of Tokyo
      Yokohama City University
  •  蛋白質化学機能の立体構造からの第一原理的予測法の開発

    • Principal Investigator
      池口 満徳
    • Project Period (FY)
      2001
    • Research Category
      Grant-in-Aid for Scientific Research on Priority Areas (C)
    • Review Section
      Biological Sciences
    • Research Institution
      Yokohama City University
  •  モノヌクレオチド結合タンパク質の機能データベースの構築と構造機能相関の解析Principal Investigator

    • Principal Investigator
      木下 賢吾
    • Project Period (FY)
      2001 – 2002
    • Research Category
      Grant-in-Aid for Young Scientists (B)
    • Research Field
      Biophysics
    • Research Institution
      Yokohama City University
  •  蛋白質化学機能の立体構造からの第一原理的予測法の開発

    • Principal Investigator
      池口 満徳
    • Project Period (FY)
      2000
    • Research Category
      Grant-in-Aid for Scientific Research on Priority Areas (C)
    • Review Section
      Biological Sciences
    • Research Institution
      The University of Tokyo
  •  Energy Transfer in a Protein Molecule: From Chemical Reaction to Structural Change

    • Principal Investigator
      KIDERA Akinori
    • Project Period (FY)
      1999 – 2001
    • Research Category
      Grant-in-Aid for Scientific Research (B)
    • Research Field
      Biophysics
    • Research Institution
      Yokohama City University
      Kyoto University

All 2024 2023 2022 2018 2017 2016 2015 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005 2004 Other

All Journal Article Presentation Book Patent

  • [Book] 計算科学4巻計算と生命2012

    • Author(s)
      木下賢吾
    • Publisher
      岩波書店
    • Data Source
      KAKENHI-PLANNED-22136005
  • [Book] Protein function prediction for omics era (chapter 11)2011

    • Author(s)
      K Kinoshita, T Obayashi
    • Publisher
      Springer Verlag
    • Data Source
      KAKENHI-PLANNED-22136005
  • [Book] トランスポートソームの世界2011

    • Author(s)
      木下賢吾(金井好克、竹島浩、森泰生、久保義弘編)
    • Publisher
      京都廣川書店
    • Data Source
      KAKENHI-PLANNED-22136005
  • [Book] COXPRESdb:共発現データに基づいた機能関連遺伝子の探索(遺伝子医学MOOK)2011

    • Author(s)
      大林武、木下賢吾
    • Publisher
      メディカルドゥ
    • Data Source
      KAKENHI-PLANNED-22136005
  • [Book] タンパク質の立体構造入門(基礎から構造バイオインフォマティクスヘ)4章と6.3(節藤博幸編)2010

    • Author(s)
      木下賢吾
    • Publisher
      講談社
    • Data Source
      KAKENHI-PLANNED-22136005
  • [Book] Prediction of proetin structures, functions and interactions2009

    • Author(s)
      K Kinoshita, H Kono, K Yura
    • Publisher
      Wiley and Sons
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Book] Prediction of molecular interactions from 3D-structures : from small ligands to large protein complexes2009

    • Author(s)
      Kinoshita, H Kono, K Yura
    • Publisher
      Wiley and Sons(in press)
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Book] 立体構造からのタンパク質機能予測:現状と展望、遺伝子医学MOOK2009

    • Author(s)
      木下賢吾
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Book] Prediction of proetin structures, functions and interactions(第7章: Prediction of molecular interactions from 3D-structures : from small ligands to large protein complexes)2009

    • Author(s)
      K Kinoshita, H Kono, K Yura
    • Total Pages
      287
    • Publisher
      Wiley and Sons
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Book] ペプチジルプロリルイソメラーゼの構造・機能相関、蛋白質核酸酵素2009

    • Author(s)
      伊倉貞吉、木下賢吾、伊藤暢聡
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Book] タンパク質の機能部位の予測、実験医学増刊号(バイオインフォマティクスツールの開発と生命研究への応用の最前線)2008

    • Author(s)
      木下賢吾
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Book] Prediction of molecular interactions from 3D-structures: from small ligands to large protein complexes2008

    • Author(s)
      K Kinoshita, H Kono, K Yura Janusz Bujnicki ed
    • Publisher
      Wiley and Sons
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Book] Prediction of molecular interactions from 3D-structures : from small ligandsto large protein complexes2008

    • Author(s)
      Kengo Kinoshita
    • Publisher
      Wiley and Sons
    • Data Source
      KAKENHI-PROJECT-20370061
  • [Book] Prediction of molecular interactions from 3D-structures : from small ligands to large protein complexes(Janusz Bujnicki ed.)2008

    • Author(s)
      K. Kinoshita, H. Kono, K. Yura
    • Publisher
      Wiley & Sons
    • Data Source
      KAKENHI-PROJECT-20370061
  • [Book] タンパク質間相互作用に関するデータベースの構築、生体の科学2007

    • Author(s)
      木下賢吾
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] Gene Rearrangement and Expression of PRKACA and PRKACB Govern Morphobiology of Pancreatobiliary Oncocytic Neoplasms2024

    • Author(s)
      Itoh T, Omori Y, Seino M, Hirose K, Date F, Ono Y, Mizukami Y, Aoki S, Ishida M, Mizuma M, Morikawa T, Higuchi R, Honda G, Okamura Y, Kinoshita K, Unno M, Furukawa T.
    • Journal Title

      Modern Pathology

      Volume: 37 Issue: 1 Pages: 100358-100358

    • DOI

      10.1016/j.modpat.2023.100358

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-22KK0282, KAKENHI-PROJECT-22KK0125, KAKENHI-PROJECT-22K08858, KAKENHI-PROJECT-23K06759, KAKENHI-PROJECT-21H02996, KAKENHI-PROJECT-23K24101
  • [Journal Article] ATTED-II in 2018: A Plant Coexpression Database based on Investigation of Statistical Property of the Mutual Rank Index.2018

    • Author(s)
      Obayashi T, Aoki Y, Tadaka S, Kagaya Y, Kinoshita K.
    • Journal Title

      Plant Cell Physiology

      Volume: 59 Issue: 1 Pages: e3-e3

    • DOI

      10.1093/pcp/pcx191

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PROJECT-15K18464, KAKENHI-PROJECT-15K20863
  • [Journal Article] Matataki: an ultrafast mRNA quantification method for large-scale reanalysis of RNA-Seq data2018

    • Author(s)
      Okamura Yasunobu、Kinoshita Kengo
    • Journal Title

      BMC Bioinformatics

      Volume: 19 Issue: 1

    • DOI

      10.1186/s12859-018-2279-y

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PROJECT-16K12519
  • [Journal Article] New tools and functions in data-out activities at Protein Data Bank Japan (PDBj)2017

    • Author(s)
      Kinjo Akira R.、Bekker Gert-Jan、Wako Hiroshi、Endo Shigeru、Tsuchiya Yuko、Sato Hiromu、Nishi Hafumi、Kinoshita Kengo、Suzuki Hirofumi、Kawabata Takeshi、Yokochi Masashi、Iwata Takeshi、Kobayashi Naohiro、Fujiwara Toshimichi、Kurisu Genji、Nakamura Haruki
    • Journal Title

      Protein Science

      Volume: 27 Issue: 1 Pages: 95-102

    • DOI

      10.1002/pro.3273

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PROJECT-16K00407, KAKENHI-PROJECT-15H02773
  • [Journal Article] IBiSA_Tools: A Computational Toolkit for Ion-Binding State Analysis in Molecular Dynamics Trajectories of Ion Channels2016

    • Author(s)
      Kota Kasahara and Kengo Kinoshita
    • Journal Title

      Plos One

      Volume: 11 Issue: 12 Pages: e0167524-e0167524

    • DOI

      10.1371/journal.pone.0167524

    • Peer Reviewed / Acknowledgement Compliant / Open Access
    • Data Source
      KAKENHI-PROJECT-15H02773, KAKENHI-PROJECT-16K18526
  • [Journal Article] Structural characterization of single nucleotide variants at ligand binding sites and enzyme active sites of human proteins2016

    • Author(s)
      Kazunori D. Yamada, Hafumi Nishi, Junichi Nakata, Kengo Kinoshita
    • Journal Title

      Biophysics and Physicobiology

      Volume: 印刷中

    • NAID

      130005165370

    • Peer Reviewed / Acknowledgement Compliant / Open Access
    • Data Source
      KAKENHI-PROJECT-15H02773
  • [Journal Article] Distribution of single nucleotide variants on protein-protein interaction sites and its relation to minor allele frequency2016

    • Author(s)
      Hafumi Nishi, Junichi Nakata, and Kengo Kinoshita
    • Journal Title

      Protein Science

      Volume: 25 Issue: 2 Pages: 316-321

    • DOI

      10.1002/pro.2845

    • Peer Reviewed / Acknowledgement Compliant / Open Access
    • Data Source
      KAKENHI-PROJECT-15H02773
  • [Journal Article] ALCOdb: Gene Coexpression Database for Microalgae.2016

    • Author(s)
      Aoki Y, Okamura Y, Ohta H, Kinoshita K, Obayashi T.
    • Journal Title

      Plant Cell Physiology

      Volume: 57 Issue: 1 Pages: e3-e3

    • DOI

      10.1093/pcp/pcv190

    • Peer Reviewed / Acknowledgement Compliant / Open Access
    • Data Source
      KAKENHI-PROJECT-15K18464, KAKENHI-PROJECT-15K20863, KAKENHI-ORGANIZER-24114001, KAKENHI-PLANNED-24114005
  • [Journal Article] ATTED-II in 2016: a plant coexpression database towards lineage-specific coexpression.2016

    • Author(s)
      Aoki Y, Okamura Y, Tadaka S, Kinoshita K, Obayashi T.
    • Journal Title

      Plant Cell Physiology

      Volume: 57 Issue: 1 Pages: e5-e5

    • DOI

      10.1093/pcp/pcv165

    • Peer Reviewed / Acknowledgement Compliant / Open Access
    • Data Source
      KAKENHI-PROJECT-15K18464, KAKENHI-PROJECT-15K20863, KAKENHI-ORGANIZER-24114001, KAKENHI-PLANNED-24114005
  • [Journal Article] Discrepancies between human DNA, mRNA and protein reference sequences and their relation to single nucleotide variants in the human population2016

    • Author(s)
      Matsuyuki Shirota and Kengo Kinoshita
    • Journal Title

      Database

      Volume: 1 Pages: 1-15

    • DOI

      10.1093/database/baw124

    • Peer Reviewed / Acknowledgement Compliant / Open Access
    • Data Source
      KAKENHI-PROJECT-15H02773
  • [Journal Article] NCMine: Core-peripheral based functional module detection using near-clique mining2016

    • Author(s)
      Shu Tadaka and Kengo Kinoshita
    • Journal Title

      Bioinformatics

      Volume: 32 Issue: 22 Pages: 3454-3460

    • DOI

      10.1093/bioinformatics/btw488

    • Peer Reviewed / Acknowledgement Compliant / Open Access
    • Data Source
      KAKENHI-PROJECT-15H02773
  • [Journal Article] NLDB: a database for 3D protein-ligand interactions in enzymatic reactions2016

    • Author(s)
      Yoichi Murakami, Satoshi Omori, and Kengo Kinoshita
    • Journal Title

      J Struct Funct Genomics

      Volume: 17 Issue: 4 Pages: 101-110

    • DOI

      10.1007/s10969-016-9206-0

    • Peer Reviewed / Acknowledgement Compliant / Open Access
    • Data Source
      KAKENHI-PROJECT-15H02773, KAKENHI-PROJECT-26870045
  • [Journal Article] Okamura Y, Aoki Y, Obayashi T, Tadaka S, Ito S1, Narise T, Kinoshita K.2015

    • Author(s)
      Okamura Y, Aoki Y, Obayashi T, Tadaka S, Ito S1, Narise T, Kinoshita K.
    • Journal Title

      Nucleic Acid Res

      Volume: 43 Issue: D1 Pages: D82-D86

    • DOI

      10.1093/nar/gku1163

    • Peer Reviewed / Acknowledgement Compliant / Open Access
    • Data Source
      KAKENHI-PLANNED-22136005, KAKENHI-ORGANIZER-24114001, KAKENHI-PLANNED-24114005, KAKENHI-PROJECT-24570176
  • [Journal Article] Comparison of gene coexpression profiles and construction of conserved gene networks to find functional modules.2015

    • Author(s)
      Okamura Y, Obayashi T, Kinoshita K.
    • Journal Title

      PLoS One

      Volume: 10 Issue: 7 Pages: e0132039-e0132039

    • DOI

      10.1371/journal.pone.0132039

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PROJECT-15K18464, KAKENHI-ORGANIZER-24114001, KAKENHI-PLANNED-24114005
  • [Journal Article] GIANT: pattern analysis of molecular interactions in 3D structures of protein-small ligand complexes2014

    • Author(s)
      Kasahara K and Kinoshita K
    • Journal Title

      BMC Bioinformatics

      Volume: 15 Issue: 1 Pages: 12-12

    • DOI

      10.1186/1471-2105-15-12

    • Peer Reviewed / Open Access
    • Data Source
      KAKENHI-PLANNED-22136005, KAKENHI-PROJECT-15H02773
  • [Journal Article] COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals.2013

    • Author(s)
      Obayashi T, Okamura Y, Ito S, Tadaka S, Motoike IN, Kinoshita K
    • Journal Title

      Nucleic Acids Res

      Volume: 41(Database Issue) Issue: D1 Pages: 1014-1020

    • DOI

      10.1093/nar/gks1014

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-24570176, KAKENHI-ORGANIZER-24114001, KAKENHI-PLANNED-24114005
  • [Journal Article] Analyses of the general rule on residue pair frequencies in local amino acid sequences of soluble ordered proteins2013

    • Author(s)
      Shirota M and Kinoshita K.
    • Journal Title

      Protein Science

      Volume: in press Issue: 6 Pages: 725-733

    • DOI

      10.1002/pro.2255

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-24570176
  • [Journal Article] ATTED-II in 2014: Evaluation of Gene Coexpression in Agriculturally Important Plants2013

    • Author(s)
      Takeshi Obayashi, Yasunobu Okamura, Satoshi Ito, Shu Tadaka, Yuichi Aoki, Matsuyuki Shirota and Kengo Kinoshita
    • Journal Title

      Plant Cell Physiology

      Volume: 55 Issue: 1 Pages: e6-e6

    • DOI

      10.1093/pcp/pct178

    • Peer Reviewed
    • Data Source
      KAKENHI-PLANNED-22136005, KAKENHI-ORGANIZER-24114001, KAKENHI-PLANNED-24114005, KAKENHI-PROJECT-24570176
  • [Journal Article] Analyses of the general rule on residue pair frequencies in local amino acid sequences of soluble, ordered proteins2013

    • Author(s)
      Shirota M, Kinoshita K
    • Journal Title

      Protein Science

      Volume: 22 Issue: 11 Pages: 725-733

    • DOI

      10.1002/pro.225

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-24570176
  • [Journal Article] COXPRESdb : a database to compare gene coexpression in seven model animals.2011

    • Author(s)
      T.Obayashi, K.Kinoshita
    • Journal Title

      Nucl.Acids Res. 39

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-20370061
  • [Journal Article] Absolute quality evaluation of protein model structures using statistical potentials with respect to the native and reference states.2011

    • Author(s)
      M.Shirota, T.Ishida, K.Kinoshita
    • Journal Title

      PROTEINS 79

      Pages: 1550-1563

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-20370061
  • [Journal Article] Absolute quality evaluation of protein model structures using statistical potentials with respect to the native and reference states2011

    • Author(s)
      M Shirota, T Ishida, K Kinoshita
    • Journal Title

      Proteins

      Volume: 79 Issue: 5 Pages: 1550-1563

    • DOI

      10.1002/prot.22982

    • Peer Reviewed
    • Data Source
      KAKENHI-PLANNED-22136005
  • [Journal Article] Community-wide assessment of protein-interface modeling suggests improvements to design methodology2011

    • Author(s)
      SJ Fleishman, TA Whitehead, EM Strauch, JE Com, S Qin, HX Zhou, JC Mitchell, ON Demerdash, M Takeda-Shitaka, G Terashi, IH Moal, X Li, PA Bates, M Zacharias, H Park, JS Ko, H Lee, C Seok, T Bourquard, J Bernauer, A Poupon, J Aze, S Soner, SK Ovali, P Ozbek, NB Tal, T Haliloglu, H Hwang, T Vreven, BG Pierce, Z Weng, L Perez-Cano, C Pons, J Fernandez-Recio, F Jiang, F Yang, X Gong, L Cao, X Xu, B Liu, P Wang, C Li, C Wang, CH Robert, M Guharoy, S Liu, Y Huang, L Li, D Guo, Y Chen, Y Xiao, N London, Z Itzhaki, O Schucler-Furman, Y Inbar, V Potapov, M Cohen, G Schreiber, Y Tsuchiya, E Kanamori, DM Standley, H Nakamura, K Kinoshita, CM Driggers, RG Hall, JL Morgan, VL Hsu, J Zhan, Y Yang, Y Zhou, PL Kastritis, AM Bonvin, W Zhang, CJ Camacho, KP Kilambi, A Sircar, JJ Gray, M Ohue, N Uchikoga, Y Matsuzaki, T Ishida, Y Akiyama, R Khashan, S Bush, D Fouches, A Tropsha, J Esquivel-Rodriguez, D Kihara, PB Stranges, R Jacak, B Kuhlman, SY Huang, X Zou, SJ Wodak, J Janin, D Baker
    • Journal Title

      Journal of Molecular Biology

      Volume: volume414 Pages: 289-382

    • Peer Reviewed
    • Data Source
      KAKENHI-PLANNED-22136005
  • [Journal Article] Assessing the utility of gene co-expression stability in combination with correlation in the analysis of protein-protein interaction networks2011

    • Author(s)
      A Patil, K Nakai, K Kinoshita
    • Journal Title

      BMC genomics

      Volume: 12 Issue: Suppl 3 Pages: S19-S19

    • DOI

      10.1186/1471-2164-12-s3-s19

    • Peer Reviewed
    • Data Source
      KAKENHI-PLANNED-22136005
  • [Journal Article] COXPRESdb : a database to compare gene coexpression in seven model animals2011

    • Author(s)
      T Obayashi, K Kinoshita
    • Journal Title

      Nucleic Acids Res

      Volume: 39

    • Peer Reviewed
    • Data Source
      KAKENHI-PLANNED-22136005
  • [Journal Article] Domain distribution and intrinsic disorder in hubs in the human protein-protein interaction network.2010

    • Author(s)
      A.Patil, K.Kinoshita, H.Nakamura
    • Journal Title

      Protein Science 19

      Pages: 1461-1468

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-20370061
  • [Journal Article] Ligand-binding site prediction of proteins based on known fragment-fragment interactions2010

    • Author(s)
      K Kasahara, K Kinoshita, T Takagi
    • Journal Title

      Bioinformatics

      Volume: 26 Pages: 1493-1499

    • Peer Reviewed
    • Data Source
      KAKENHI-PLANNED-22136005
  • [Journal Article] Inhibition of TRPC6 Channel Activity contributes to the Anti-hypertrophic Effects of Natriuretic Peptides-guanylyl cyclase-A signaling in the heart2010

    • Author(s)
      Hideyuki Kinoshita, Koichiro Kuwahara, Motohiro Nishida, Jian Zhong, Xianglu Rong, Shigeki Kiyonaka, Yoshihiro Kuwabara, Hitoshi Kurose, Ryuji Inoue, Yasuo Mori, Yuhao Li, Yasuaki Nakagawa, Masao Murakami, Masaki Harada, Shinji Yasuno, Satoru Usami, Masataka Fujiwara, Yuko Yamada, Takeya Minami, Kenji Ueshima, Eric N.Olson, Kazuwa Nakao
    • Journal Title

      Circulation Research

      Volume: 106(12) Pages: 1849-1860

    • Peer Reviewed
    • Data Source
      KAKENHI-ORGANIZER-22136001
  • [Journal Article] Coexpression landscape in ATTED-II : usage of gene list and gene network for various types of pathways2010

    • Author(s)
      T Obayashi, K Kinoshita
    • Journal Title

      J.Plant Res. (in press)

    • NAID

      10027218882

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] Structural properties of hubs in protein-protein interaction networks.2010

    • Author(s)
      A.Patil, K.Kinoshita, H.Nakamura
    • Journal Title

      Int.J.Mol.Sci. 11

      Pages: 1930-1943

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-20370061
  • [Journal Article] Development of new indices to evaluate protein-protein interfaces : Assembling space volume, assembling space distance, global shape descriptor.2009

    • Author(s)
      Maeda MH and Kinoshita K
    • Journal Title

      J. Mol. Graph. Modell.

      Volume: 27 Issue: 6 Pages: 706-711

    • DOI

      10.1016/j.jmgm.2008.11.002

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17651108
  • [Journal Article] ATTED-II provides coexpressed gene networks for Arabidopsis2009

    • Author(s)
      T Obayashi, S Hayashi, M Saeki, H Ohta and K Kinoshita
    • Journal Title

      Nucleic Acids Res 37

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] Rank of correlation coefficient as a comparable measure for biological significance of gene coexpression2009

    • Author(s)
      T Obayashi, K Kinoshita
    • Journal Title

      DNA research 16,5

      Pages: 249-260

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] Analyses on hydrophobic characteristics and attractive effects induced by the different reference states in all-atom-distance-dependent potentials2009

    • Author(s)
      M Shirota, T Ishida, K Kinoshita
    • Journal Title

      Protein Sci. 18

      Pages: 1906-1915

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] PiSite : a database of protein interaction sites using multiple binding states in the PDB2009

    • Author(s)
      M Higurashi, T Ishida, and K Kinoshita
    • Journal Title

      Nucleic Acids Res 37

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] ATTED-II provides coexpressed gene networks for Arabidopsis2009

    • Author(s)
      T Obayashi, S Hayashi, M Saeki, H Ohta, K Kinoshita
    • Journal Title

      Nucleic Acids Res 37

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] Analyses on hydrophobic characteristics and attractive effects induced by the different reference states in all-atom-distance-dependent potentials2009

    • Author(s)
      M Shirota, T Ishida, K Kinoshita
    • Journal Title

      Protein Sci 18,9

      Pages: 1906-1915

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] Classification of hetero-dimer interfaces using docking models and construction of scoring functions for the complex structure prediction2009

    • Author(s)
      Y Tsuchiya, E Kanamori, H Nakamura, K Kinoshita
    • Journal Title

      Adv. Appl. Bioinfo. Chem 2,1

      Pages: 79-100

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] Classification of hetero-dimer interfaces using docking models and construction of scoring functions for the complex structure prediction2009

    • Author(s)
      Y Tsuchiya, E Kanamori, H Nakamura, K Kinoshita
    • Journal Title

      Adv.Appl.Bioinfo.Chem. 2

      Pages: 79-100

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis2009

    • Author(s)
      K Kinoshita, T Obayashi
    • Journal Title

      Bioinformatics 25,20

      Pages: 2677-2684

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] Classification of heterodimer interfaces using docking models and construction of scoring functions for the complex structure prediction.2009

    • Author(s)
      Y.Tsuchiya, E.Kanamori, H.Nakamura, K.Kinoshita
    • Journal Title

      Adv.Appl.Bioinfo.Chem. 2

      Pages: 79-10

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-20370061
  • [Journal Article] Development of new indices to evaluate protein-protein interfaces: Assembling space volume, assembling space distance, and global shape descriptor2009

    • Author(s)
      M Maeda, K Kinoshita
    • Journal Title

      J. Mol. Graph. Mod 27,6

      Pages: 706-711

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis2009

    • Author(s)
      K Kinoshita T Obayashi
    • Journal Title

      Bioinformatics 25

      Pages: 2677-2684

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] PiSite: a database of protein interaction sites using multiple binding states in the PDB2009

    • Author(s)
      M Higurashi, T Ishida, K Kinoshita
    • Journal Title

      Nucleic Acids Res 37

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] ATTED-II provides coexpressed gene networks for Arabidopsis.2009

    • Author(s)
      T.Obayashi, S.Hayashi, M.Saeki, H.Ohta, K.Kinoshita
    • Journal Title

      Nucl.Acids Res. 37

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-20370061
  • [Journal Article] Rank of correlation coefficient as a comparable measure for biological significance of gene coexpression2009

    • Author(s)
      T Obayashi, K Kinoshita
    • Journal Title

      DNA research 16

      Pages: 249-260

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] Effects of surfacetovolume ratio of proteins on hydrophilic residues, decrease in occurrence and increase in buried fraction2008

    • Author(s)
      M Shirota, T Ishida, and K Kinoshita
    • Journal Title

      Protein Sci 17

      Pages: 1596-1602

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] Identification of transient hub proteins and genthe possible structural basis for their multiple interactions2008

    • Author(s)
      M Higurashi, T Ishida and K Kinoshita
    • Journal Title

      Protein Sci 17

      Pages: 72-78

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] Effects of surface-to-volume ratio of proteins on hydrophilic residues, decrease in occurrence and increase in buried fraction2008

    • Author(s)
      M Shirota, T Ishida, K Kinoshita
    • Journal Title

      Protein Sci 17,9

      Pages: 1596-1602

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] COXPRESdb: a database of coexpressed gene networks in mammals2008

    • Author(s)
      T Obayashi, S Hayashi, M Shibaoka, M Saeki, H Ohta, K Kinoshita
    • Journal Title

      Nucleic Acids Res 36

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] A cavity with an appropriate size is the basis of the PPIase activity2008

    • Author(s)
      T Ikura, K Kinoshita, and N Ito
    • Journal Title

      PEDS (in press)

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] Prediction of disordered protein regions based on meta-approach2008

    • Author(s)
      T Ishida, K Kinoshita
    • Journal Title

      Bioinformatics 24,11

      Pages: 1344-1348

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] Weak correlation between sequence conservation in promoter regions and protein-coding regions of human-mouse orthologous gene pairs2008

    • Author(s)
      H Chiba, R Yamashita, K Kinoshita, and K Nakai
    • Journal Title

      BMC Genomics 9

      Pages: 152-152

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] Discrimination between biological interfaces and crystal-packing contacts2008

    • Author(s)
      Y Tsuchiya, H Nakamura, K Kinoshita
    • Journal Title

      Adv. Appl. Bioinfo. Chem 1,1

      Pages: 99-113

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] A novel strategy to search concerted transcription factor activities using gene expression profile and genomic data2008

    • Author(s)
      Y Hatanaka, M Nagasaki, R Yamaguchi, T Obayashi, K Numata, S Imoto, T Shimamura, K Kinoshita, K Nakai, S Miyano
    • Journal Title

      Genome Informatics 21

      Pages: 101-103

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] COXPRESdb: a database of coexpressed gene networks in mammals2008

    • Author(s)
      T Obayashi, S Hayashi, M Shibaoka, M Saeki, H Ohta and K Kinoshita
    • Journal Title

      Nucleic Acids Res 36

      Pages: 77-82

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] Discrimination between biological interfaces and crystalpacking contacts2008

    • Author(s)
      Y Tsuchiya, H Nakamura and K Kinoshita
    • Journal Title

      Compt Biol Chem 1

      Pages: 99-113

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] A cavity with an appropriate size is the basis of the PPIase activity2008

    • Author(s)
      T Ikura, K Kinoshita, N Ito
    • Journal Title

      Protein Eng Des Sel 21,2

      Pages: 83-89

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] Discrimination between biological interfaces and crystal-packing contacts.2008

    • Author(s)
      Y.Tsuchiya, H.Nakamura, K.Kinoshita
    • Journal Title

      Comput.Biol.Chem. 1

      Pages: 99-113

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-20370061
  • [Journal Article] Identification of transient hub proteins and the possible structural basis for their multiple interactions2008

    • Author(s)
      M Higurashi, T Ishida, K Kinoshita
    • Journal Title

      Protein Sci 17,1

      Pages: 72-78

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] Mutational analysis of block and facilitation of HERG current by a class III anti-arrhythmic agent, nifekalant2007

    • Author(s)
      Y Hosaka, M Iwata, N Kamiya, M Yamada, K Kinoshita, Y Fukunishi, K Tsujimae, H Hibino, Y Aizawa, A Inanobe, H Nakamura and Y Kurachi
    • Journal Title

      Channels 1

      Pages: 198-208

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] Docking of protein molecular surfaces with evolutionary trace analysis2007

    • Author(s)
      E Kanamori, Y Murakami, Y Tsuchiya, DM Standley, H Nakamura, K Kinoshita
    • Journal Title

      Proteins 69,4

      Pages: 832-838

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] Mutational analysis of block and facilitation of HERG current by a class III anti-arrhythmic agent, nifekalant2007

    • Author(s)
      Y Hosaka, M Iwata, N Kamiya, M Yamada, K Kinoshita, Y Fukunishi, K Tsujimae, H Hibino, Y Aizawa, A Inanobe, H Nakamura, Y Kurachi
    • Journal Title

      Channels 1,1

      Pages: 198-208

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] タンパク質間相互作用に関するデータベースの構築2007

    • Author(s)
      木下賢吾
    • Journal Title

      生体の科学 58

      Pages: 334-337

    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis2007

    • Author(s)
      Takeshi Obayashi, Kengo Kinoshita, Kenta Nakai, Masayuki Shibaoka, Shinpei Hayashi, Motoshi Saeki, Daisuke Shibata, Kazuki Saito, Hiroyuki Ohta
    • Journal Title

      Nuc Acid Rec 35

    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape2007

    • Author(s)
      K Kinoshita, Y Murakami and H Nakamura
    • Journal Title

      Nucleic Acids Res 35

      Pages: 398-402

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] Probabilistic alignment detects remote homology in a pair of protein sequences without homologous sequence information2007

    • Author(s)
      R Koike, K Kinoshita and A Kidera
    • Journal Title

      Proteins 66

      Pages: 655-663

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis2007

    • Author(s)
      T Obayashi, K Kinoshita, K Nakai, M Shibaoka, S Hayashi, M Saeki, D Shibata, K Saito, H Ohta
    • Journal Title

      Nucleic Acids Res 35

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis2007

    • Author(s)
      T Obayashi, K Kinoshita, K Nakai, M Shibaoka, S Hayashi, M Saeki, D Shibata, K Saito and H Ohta
    • Journal Title

      Nucleic Acids Res 35

      Pages: 863-869

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] PrDOS: prediction of disordered protein regions from amino acid sequence2007

    • Author(s)
      T Ishida, K Kinoshita
    • Journal Title

      Nucleic Acids Res 35

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape2007

    • Author(s)
      K Kinoshita, Y Murakami, H Nakamura
    • Journal Title

      Nucleic Acids Res 35

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] Docking of protein molecular surfaces with evolutionary trace analysis2007

    • Author(s)
      E Kanamori, Y Murakami, Y Tsuchiya, DM Standley, H Nakamura and K Kinoshita
    • Journal Title

      Proteins 69

      Pages: 832-838

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] Probablistic alignment detects remote homology in a pair of protein sequences without homologous sequence information2007

    • Author(s)
      Ryotaro Koike, Kengo Kinoshita, Akinori Kidera,
    • Journal Title

      Proteins 66,

      Pages: 655-663

    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] PrDOS: prediction of disordered protein regions from amino acid sequence2007

    • Author(s)
      T Ishida and K Kinoshita
    • Journal Title

      Nucleic Acids Res 35

      Pages: 460-464

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] Analyses of homo-oligomer interfaces of proteins from the complementarity of molecular surface, electrostatic potential and hydrophobicity2006

    • Author(s)
      Y Tsuchiya, K Kinoshita, H Nakamura
    • Journal Title

      Protein Eng Des Sel 19,9

      Pages: 421-429

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] DBTGR:a database of tunicate promoters and their regulatory elements2006

    • Author(s)
      Sierro, N., Kusakabe, T., Park, K.-J., Yamashita, R., Kinoshita, K., Nakai, K.
    • Journal Title

      Nucl.Acids Res. 34

    • Description
      「研究成果報告書概要(和文)」より
    • Data Source
      KAKENHI-PROJECT-17310114
  • [Journal Article] Pre BI: Prediction of biological interfaces of proteins in crystals2006

    • Author(s)
      Yuko Tsuchiya, Kengo Kinoshita, Nobutoshi Ito, Haruki Nakamura,
    • Journal Title

      Nuc Acid Res, 34

    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] Analysis of the three- dimensional structure of the "C-X-G-X-C" motif in the CMGCC and CAGYC regions of alpha- and beta-subunits of human chorionic gonadotropin : Importance of Glycine Residue (G) in the Motif in beta-subunit2006

    • Author(s)
      Kinoshita, K., Kusunoki, M., Miyai, K.
    • Journal Title

      Endocrine J. 53

      Pages: 51-58

    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] PreBI: prediction of biological interfaces of proteins in crystals2006

    • Author(s)
      Y Tsuchiya, K Kinoshita, N Ito, H Nakamura
    • Journal Title

      Nucleic Acids Res 34

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] Analysis of homo-oligomer interfaces of proteins from the complementarity of molecular surface, electrostatic potential and hydrophobicity2006

    • Author(s)
      Yuko Tsuchiya, Kengo Kinoshita, Haruki Nakamura
    • Journal Title

      Protein Eng Des Sel. 19

      Pages: 421-429

    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] DBTGR : a database of tunicate promoters and their regulatory elements.2006

    • Author(s)
      Sierro, N., Kusakabe, T., Park, K.-J., Yamashita, R., Kinoshita, K., Nakai, K.
    • Journal Title

      Nuci. Acids Res. 34

    • Description
      「研究成果報告書概要(欧文)」より
    • Data Source
      KAKENHI-PROJECT-17310114
  • [Journal Article] eF-siteを利用した機能部位の予測2006

    • Author(s)
      木下賢吾
    • Journal Title

      バイオテクノロジージャーナル 6

      Pages: 444-447

    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] Identification of the ligand binding sites on the molecular surface of proteins2005

    • Author(s)
      Kinoshita, K., Nakamura, H.
    • Journal Title

      Protein Sci. 14

      Pages: 711-718

    • Data Source
      KAKENHI-PROJECT-15710150
  • [Journal Article] プロテインインフォマティクスによるタンパク質の機能推定2005

    • Author(s)
      木下賢吾
    • Journal Title

      日本結晶学会誌 47

      Pages: 341-347

    • NAID

      10018280602

    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] PreDs : a server for predicting dsDNA-binding site on protein molecular surfaces2005

    • Author(s)
      Tsuchiya, Y., Kinoshita, K, Nakamura, H.
    • Journal Title

      Bioinformatics 21

      Pages: 1721-1723

    • Data Source
      KAKENHI-PROJECT-15710150
  • [Journal Article] Identification of the ligand binding sites on the molecular surface of proteins2005

    • Author(s)
      Kinoshita K, Nakamura H
    • Journal Title

      Protein Science 14

      Pages: 711-718

    • Data Source
      KAKENHI-PROJECT-15710150
  • [Journal Article] P-cats : prediction of catalytic residues in proteins from their tertiary structures2005

    • Author(s)
      Kinoshita, K., Ota, M.
    • Journal Title

      Bioinformatics 21

      Pages: 3570-3571

    • Data Source
      KAKENHI-PROJECT-15710150
  • [Journal Article] PreDs : a server for predicting dsDNA-binding site on protein molecular surfaces.2005

    • Author(s)
      Tsuchiya Y, Kinoshita K, Nakamura H
    • Journal Title

      Bioinformatics (In press)

    • Data Source
      KAKENHI-PROJECT-15710150
  • [Journal Article] Structure-based prediction of DNA-binding sites on proteins using the empirical preference of electrostatic potential and the shape of molecular surfaces2004

    • Author(s)
      Tsuchiya Y, Kinoshita K, Nakamura H
    • Journal Title

      Proteins : Struct.Funct.Bioinformatics 55

      Pages: 885-894

    • Data Source
      KAKENHI-PROJECT-15710150
  • [Journal Article] タンパク質の表面物性の類似性にもとづく機能予測2004

    • Author(s)
      木下賢吾
    • Journal Title

      生物物理 44

      Pages: 150-154

    • Data Source
      KAKENHI-PROJECT-15710150
  • [Journal Article] タンパク質の機能部位の予測

    • Author(s)
      木下賢吾
    • Journal Title

      実験医学増刊号(バイオインフォマティクスツールの開発と生命研究への応用の最前線) (印刷中)

    • Data Source
      KAKENHI-PROJECT-17081003
  • [Journal Article] Protein Structure Databases with new web services for structural biology and biomedical research

    • Author(s)
      S Daron, A Kinjo, K Kinoshita, H Nakamura
    • Journal Title

      Brief. Bioinform (in press)

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Patent] 免疫沈降用の内部標準分子および免疫沈降方法2015

    • Inventor(s)
      五十嵐和彦、落合恭子、中山啓子、木下賢吾、舟山亮ら7名
    • Industrial Property Rights Holder
      五十嵐和彦、落合恭子、中山啓子、木下賢吾、舟山亮ら7名
    • Industrial Property Rights Type
      特許
    • Industrial Property Number
      2015-035734
    • Filing Date
      2015-02-25
    • Data Source
      KAKENHI-PROJECT-24570176
  • [Presentation] 高異型度PanIN/膵上皮内癌・小径膵癌の分子進化モデル2024

    • Author(s)
      伊藤泰斗、大森優子、小野裕介、高橋賢治、岡村容伸、木下賢吾、正宗淳、海野倫明、水上裕輔、古川徹
    • Organizer
      第113回日本病理学会総会
    • Data Source
      KAKENHI-PROJECT-23K24101
  • [Presentation] Exploring the growth morphology and mucus secretion mechanism of IPMN using patients-derived organoids and comprehensive genome analysis.2023

    • Author(s)
      Shiihara M, Takahashi K, Ishikawa T, Omori Y, Hirose K, Nakagawa K, Mizuma M, Ohtsuka H, Motoi F, Unno M, Okamura Y, Kinoshita K, Furukawa T.
    • Organizer
      A Joint International Conference Pancreas 2023
    • Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-23K24101
  • [Presentation] Characteristics of growth and mucus secretion of patient-derived organoids may substantiate invasive phenotypes of IPMN.2022

    • Author(s)
      Shiihara M, Ishikawa T, Yoshida T, Omori Y, Hirose K, Morikawa T, Nakagawa K, Mizuma M, Otsuka H, Motoi F, Unno M, Okamura Y, Kinoshita K, Furukawa T.
    • Organizer
      International Association of Pancreatology and Japan Pancreas Society Meeting 2022
    • Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-23K24101
  • [Presentation] 東北における大規模コホート構築とゲノム・オミックス解析戦略2018

    • Author(s)
      木下賢吾
    • Organizer
      シンポジウム「理論生物物理学の現在と未来」
    • Data Source
      KAKENHI-PROJECT-16K12519
  • [Presentation] A revised coexpression calculation procedure in ATTED-II version 9 with batch-normalization and bagging methods.2018

    • Author(s)
      Takeshi Obayashi, Yuichi Aoki and Kengo Kinoshita
    • Organizer
      the 59th Annual Meeting of the Japanese Society of Plant Physiologists
    • Data Source
      KAKENHI-PROJECT-15K18464
  • [Presentation] ChIP-Seqデータのクラスタリングによる実験条件・解析手法に起因するバイアスの可視化2017

    • Author(s)
      安澤隼人, 木下賢吾
    • Organizer
      NGS現場の会第五回研究会
    • Data Source
      KAKENHI-PROJECT-16K12519
  • [Presentation] Sample Alignment of Different Species toward Species-Specific Coexpression Analyses2017

    • Author(s)
      Takeshi Obayashi, Yuichi Aoki, Shu Tadaka, Yasunobu Okamura, Kengo Kinoshita
    • Organizer
      the 58th Annual Meeting of the Japanese Society of Plant Physiologists
    • Data Source
      KAKENHI-PROJECT-15K18464
  • [Presentation] A Challenge to Understand Functional Impacts of Rare Variants Using Protein Structural Information2017

    • Author(s)
      Kengo Kinoshita
    • Organizer
      2nd Karolinska-Tohoku Joint Symposium on Medical Sciences
    • Invited / Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-15H02773
  • [Presentation] 薬物によるKir1.1チャネル阻害の基盤.2016

    • Author(s)
      古谷和春, 半田健一郎, 村上洋一, 木下賢吾, 倉智嘉久.
    • Organizer
      第89回日本薬理学会年会
    • Place of Presentation
      パシフィコ横浜(横浜市)
    • Year and Date
      2016-03-10
    • Data Source
      KAKENHI-ORGANIZER-22136001
  • [Presentation] Model based discrimination method of ChIPed data from control data in ChIP-seq experiment dataset2016

    • Author(s)
      Hayato Anzawa and Kengo Kinoshita
    • Organizer
      第5回 生命医薬情報学連合大会
    • Place of Presentation
      東京国際交流館プラザ平成(東京都江東区)
    • Year and Date
      2016-09-29
    • Data Source
      KAKENHI-PROJECT-16K12519
  • [Presentation] Distribution of human single nucleotide variants at protein functional sites and its relation to minor allele frequency2016

    • Author(s)
      Hafumi Nishi, Kazunori D Yamada, Junichi Nakata, Kengo Kinoshita
    • Organizer
      Gordon Conference
    • Place of Presentation
      South Hadley, MA, USA.
    • Year and Date
      2016-06-13
    • Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-15H02773
  • [Presentation] Development and application of a simple yet flexible framework for construction of gene-pair relationship database2016

    • Author(s)
      Shu Tadaka and Kengo KInoshita
    • Organizer
      生命医薬情報学連合大会
    • Place of Presentation
      東京国際交流プラザ平成(東京都江東区)
    • Year and Date
      2016-09-29
    • Data Source
      KAKENHI-PROJECT-15H02773
  • [Presentation] Impact of Evolutionary Age on Gene Coexpression Network and Gene Functional Relationship2016

    • Author(s)
      Yuichi Aoki, Takeshi Obayashi, Kengo Kinoshita
    • Organizer
      第39回 日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜(神奈川県横浜市)
    • Year and Date
      2016-12-01
    • Invited
    • Data Source
      KAKENHI-PROJECT-15K18464
  • [Presentation] Gene age determines the fundamental structure of the gene coexpression network.2016

    • Author(s)
      Yuichi Aoki, Takeshi Obayashi, Kengo Kinoshita
    • Organizer
      Intelligent Systems for Molecular Biology 2016
    • Place of Presentation
      Orlando, Florida, U.S.A
    • Year and Date
      2016-07-11
    • Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-15K18464
  • [Presentation] Meta-analysis of gene coexpression in ATTED-II toward species-specific coexpression analyses2016

    • Author(s)
      大林武,青木裕一,岡村容伸,田高周,木下賢吾
    • Organizer
      日本植物生理学会年会
    • Place of Presentation
      岩手大学(岩手)
    • Year and Date
      2016-03-17
    • Data Source
      KAKENHI-PROJECT-15K18464
  • [Presentation] Kir1.1チャネルにおける小分子結合部位の構造活性相関解析.2016

    • Author(s)
      古谷和春, 半田健一郎, 村上洋一, 木下賢吾, 倉智嘉久.
    • Organizer
      第93回日本生理学会大会
    • Place of Presentation
      札幌コンベンションセンター(札幌市)
    • Year and Date
      2016-03-24
    • Data Source
      KAKENHI-ORGANIZER-22136001
  • [Presentation] Prediction of biological and biochemical functions of uncharacterized genes2015

    • Author(s)
      Kengo Kinoshita
    • Organizer
      Data Science in Life Science and Engineering Collaboration and Symposium
    • Place of Presentation
      Case western university, USA
    • Year and Date
      2015-07-30
    • Invited / Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-15H02773
  • [Presentation] ヒトゲノム一塩基変異のタンパク質間相互作用面上での分布2015

    • Author(s)
      西羽美、中田純一、木下賢吾
    • Organizer
      第15回日本蛋白質科学会
    • Place of Presentation
      あわぎんホール、徳島県
    • Year and Date
      2015-06-25
    • Data Source
      KAKENHI-PROJECT-15H02773
  • [Presentation] Molecular basis of Kir1.1 channel block2015

    • Author(s)
      Kenichiro Handa, Kazuharu Furutani, Yoichi Murakami, Kengo Kinoshita, Yoshihisa Kurachi
    • Organizer
      新学術領域研究「多階層生体機能学」最終成果報告会
    • Place of Presentation
      大阪大学中之島センター(大阪市)
    • Year and Date
      2015-03-05
    • Data Source
      KAKENHI-ORGANIZER-22136001
  • [Presentation] Distribution of single nucleotide variants on protein-protein interaction sites2015

    • Author(s)
      Hafumi Nishi, Junichi Nakata, Kengo Kinoshita
    • Organizer
      3Dsig2015, 23rd Annual International Conference on Intelligent Systems for Molecular Biology
    • Place of Presentation
      Dublin, Ireland
    • Year and Date
      2015-07-13
    • Int'l Joint Research
    • Data Source
      KAKENHI-PROJECT-15H02773
  • [Presentation] DEG.js : Streaming web-based differential expression genes analysis tool for RNA-seq2014

    • Author(s)
      岡村容伸,大林武,木下賢吾
    • Organizer
      生命情報科学若手の会 第6回研究会
    • Place of Presentation
      愛知県岡崎市
    • Year and Date
      2014-10-30
    • Data Source
      KAKENHI-PROJECT-24570176
  • [Presentation] ゲノム情報解析の現状と課題2014

    • Author(s)
      木下賢吾
    • Organizer
      次世代PGSフォーラム設立記念シンポジウム
    • Place of Presentation
      品川プリンスホテル
    • Year and Date
      2014-12-04
    • Invited
    • Data Source
      KAKENHI-PLANNED-22136005
  • [Presentation] 大規模ゲノム解析研究に必要なスパコン環境の構築2014

    • Author(s)
      木下賢吾
    • Organizer
      バイオスーパーコンピューティング東北
    • Place of Presentation
      東北大学
    • Year and Date
      2014-06-02
    • Invited
    • Data Source
      KAKENHI-PLANNED-22136005
  • [Presentation] Development of descriptors of protein-ligand binding sites with genetic algorithm2013

    • Author(s)
      Kohei Nakamura, Kasahara Kota, Matsuyuki Shirota, Kengo Kinoshita
    • Organizer
      第2回 生命医薬情報学連合大会
    • Place of Presentation
      東京
    • Data Source
      KAKENHI-PLANNED-22136005
  • [Presentation] 蛋白質低分子結合部位の予測に向けた結合部位多様性の解析2012

    • Author(s)
      木下賢吾
    • Organizer
      化学工学会第44回秋季大会
    • Place of Presentation
      仙台
    • Year and Date
      2012-09-21
    • Invited
    • Data Source
      KAKENHI-PLANNED-22136005
  • [Presentation] 次世代生命科学研究に必要な計算機インフラについて2012

    • Author(s)
      木下賢吾
    • Organizer
      データ駆動型生命情報科学の挑戦
    • Place of Presentation
      仙台
    • Year and Date
      2012-05-10
    • Invited
    • Data Source
      KAKENHI-PLANNED-22136005
  • [Presentation] Illuminating the background and capabilities of statistical potentials of protein structures2011

    • Author(s)
      M Shirota, K Kinoshita
    • Organizer
      The 11th KIAS Conference on Protein Structure and Function
    • Place of Presentation
      Korea Institute for Advanced Study, Seoul, Korea(招待講演)
    • Year and Date
      2011-10-08
    • Data Source
      KAKENHI-PLANNED-22136005
  • [Presentation] Seeing in silico is believing, Brief introduction and some recent topics in bioinformatics2011

    • Author(s)
      K Kinoshita
    • Organizer
      The 12^<th>, RIES-Hokudai International Symposium
    • Place of Presentation
      Chateraise Gateaux Kingdom Sapporo(招待講演)
    • Year and Date
      2011-11-22
    • Data Source
      KAKENHI-PLANNED-22136005
  • [Presentation] Estimation of native-like state of protein structure using statistical potentials for protein structure prediction2010

    • Author(s)
      木下賢吾
    • Organizer
      第48回生物物理学会年会
    • Place of Presentation
      東北大学、仙台
    • Year and Date
      2010-09-22
    • Data Source
      KAKENHI-PROJECT-20370061
  • [Presentation] Application of distance dependent statistical pair potentials of protein folding to the evaluation of protein-protein interaction : Commonalities and differences between folding and docking.2010

    • Author(s)
      M. Shirota, K. Kasahara, Y. Tsuchiya, K. Kinoshita
    • Organizer
      MPI 2010
    • Place of Presentation
      Lawrence(USA)
    • Data Source
      KAKENHI-PROJECT-20370061
  • [Presentation] Relationship between physics and information science in statistical potentials of protein structures.2010

    • Author(s)
      M. Shirota, T. Ishida, K. Kinoshita
    • Organizer
      AYRCOB 2010
    • Place of Presentation
      Tainan(Taiwan)
    • Data Source
      KAKENHI-PROJECT-20370061
  • [Presentation] ヒトゲノム構造・機能アノテーションデータベースSAHGの構築2010

    • Author(s)
      木下賢吾
    • Organizer
      第10回日本蛋白質科学会年会
    • Place of Presentation
      札幌コンベンションセンター・札幌
    • Year and Date
      2010-06-18
    • Data Source
      KAKENHI-PROJECT-20370061
  • [Presentation] Conservation of protein-ligand interactions : a data-mining of the PDB by using Gaussian mixture model2010

    • Author(s)
      木下賢吾
    • Organizer
      第48回生物物理学会年会
    • Place of Presentation
      東北大学、仙台
    • Year and Date
      2010-09-20
    • Data Source
      KAKENHI-PROJECT-20370061
  • [Presentation] 蛋白質立体構造と複合体構造の評価関数の共通点と相違点2010

    • Author(s)
      木下賢吾
    • Organizer
      第10回日本蛋白質科学会年会
    • Place of Presentation
      札幌コンベンションセンター・札幌
    • Year and Date
      2010-06-16
    • Data Source
      KAKENHI-PROJECT-20370061
  • [Presentation] タンパク質-低分子化合物フラグメント間相互作用情報を利用した結合部位・結合構造の予測2010

    • Author(s)
      木下賢吾
    • Organizer
      第10回日本蛋白質科学会年会
    • Place of Presentation
      札幌コンベンションセンター・札幌
    • Year and Date
      2010-06-17
    • Data Source
      KAKENHI-PROJECT-20370061
  • [Presentation] 機能未知タンパク質の機能推定法の開発2009

    • Author(s)
      木下賢吾
    • Organizer
      第82回日本生化学大会
    • Place of Presentation
      神戸ポートピアアイランド
    • Year and Date
      2009-10-21
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Presentation] Web services for function prediction of proteins2009

    • Author(s)
      Kengo Kinoshita
    • Organizer
      Bioinfo2009
    • Place of Presentation
      韓国・釜山
    • Data Source
      KAKENHI-PROJECT-20370061
  • [Presentation] Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis2009

    • Author(s)
      K Kinoshita
    • Organizer
      Bioinformatics beyond omics data analyses
    • Place of Presentation
      Ochanomizu University
    • Year and Date
      2009-12-04
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Presentation] Web services for function prediction of proteins2009

    • Author(s)
      K Kinoshita
    • Organizer
      Bioinfo2009
    • Place of Presentation
      The Haeundae Grand Hotel, Busan, Korea
    • Year and Date
      2009-11-04
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Presentation] 基準振動に基づく蛋白質複合体界面の動的構造の解析2009

    • Author(s)
      木下賢吾
    • Organizer
      第9回日本蛋白質科学会年会
    • Place of Presentation
      熊本全日空ホテルニュースカイ、能本
    • Year and Date
      2009-05-21
    • Data Source
      KAKENHI-PROJECT-20370061
  • [Presentation] 蛋白質の会合形状を表す記述子 : Glocal shape descriptor(GS10)2009

    • Author(s)
      前田美紀, 木下賢吾
    • Organizer
      日本薬学会第129年会
    • Place of Presentation
      北里大学薬学部
    • Year and Date
      2009-03-27
    • Data Source
      KAKENHI-PROJECT-17651108
  • [Presentation] COXPRESdb : gene coexpression database for Human, mouse and rat2009

    • Author(s)
      木下賢吾
    • Organizer
      XXXVI International congress of Physiological Sciences
    • Place of Presentation
      Kyoto International conference center
    • Year and Date
      2009-07-29
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Presentation] 基準振動に基づく蛋白質-蛋白質相互作用の動的解析2009

    • Author(s)
      木下賢吾
    • Organizer
      第47回日本生物物理学会年会
    • Place of Presentation
      アスティとくしま、徳島
    • Year and Date
      2009-10-31
    • Data Source
      KAKENHI-PROJECT-20370061
  • [Presentation] 類似性検索による遺伝子機能推定2009

    • Author(s)
      木下賢吾
    • Organizer
      情報処理学会アルゴリズム研究会・特別講演
    • Place of Presentation
      東京大学医科学研究所
    • Year and Date
      2009-05-11
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Presentation] 蛋白質インターフェースに関する新規な記述子2009

    • Author(s)
      前田美紀, 木下賢吾
    • Organizer
      第9回日本蛋白質科学会年会
    • Place of Presentation
      熊本全日空ホテルニュースカイ
    • Year and Date
      2009-05-22
    • Data Source
      KAKENHI-PROJECT-17651108
  • [Presentation] Classification of hetero-dimer interfaces and development of multiple scoring functions for complex structure predictions of proteins2009

    • Author(s)
      K Kinoshita
    • Organizer
      International symposium on multi-scale dynamics of protein complex formation and function
    • Place of Presentation
      Sanjo Conference Hall, The University of Tokyo
    • Year and Date
      2009-07-14
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Presentation] A new multi-dimensional index for gene coexpression and application to the large-scale data of Arabidopsis2009

    • Author(s)
      K Kinoshita
    • Organizer
      The 1299th Biological Symposium at National Institute of Genetics
    • Place of Presentation
      National Institute of Genomics
    • Year and Date
      2009-03-31
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Presentation] COXPRESdb: gene coexpression database for Human, mouse and rat2009

    • Author(s)
      K Kinoshita
    • Organizer
      XXXVI International congress of Physiological Sciences
    • Place of Presentation
      Kyoto
    • Year and Date
      2009-07-29
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Presentation] Coexpressed gene database for human, mouse, rat and Arabidopsis2008

    • Author(s)
      K Kinoshita
    • Organizer
      Japan-UK symposium on protein informatics toward interactome analysis
    • Place of Presentation
      Senri Life science center
    • Year and Date
      2008-09-01
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Presentation] Coexpressed gene database for human, mouse, rat and Arabidopsis2008

    • Author(s)
      K Kinoshita
    • Organizer
      Japan-UK symposium on protein informatics toward interactome analysis
    • Place of Presentation
      大阪・千里ライクサイエンスセンター
    • Year and Date
      2008-09-02
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Presentation] Ordered and Disordered Structure of Proteins2008

    • Author(s)
      木下賢吾
    • Organizer
      タンパク質研究の未来像
    • Place of Presentation
      東海大学
    • Year and Date
      2008-03-07
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Presentation] Prediction of protein-protein interaction using evolutionary trance method and molecular surface complementarity2007

    • Author(s)
      E Kanamori, Y Murakami, Y Tsuchiya, D Standley, K Kinoshita, H Nakamura
    • Organizer
      CAPRI evaluation meeting
    • Place of Presentation
      Canada
    • Year and Date
      2007-04-21
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Presentation] 蛋白質立体構造情報を利用した機能推定2007

    • Author(s)
      木下賢吾
    • Organizer
      第41回遺伝医学研究会
    • Place of Presentation
      東京女子医科大学
    • Year and Date
      2007-11-02
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Presentation] 蛋白質の配列・構造・機能相関の博物学2007

    • Author(s)
      木下賢吾
    • Organizer
      生物物理学会
    • Place of Presentation
      パシフィコ横浜
    • Year and Date
      2007-12-23
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Presentation] Prediction of protein-protein interaction using evolutionary trance method and molecular surface complementarity2007

    • Author(s)
      E Kanamori, Y Murakami, Y Tsuchiya, D Standley, K Kinoshita, H Nakamura
    • Organizer
      CAPRI evaluation meeting
    • Place of Presentation
      Toronto Canada
    • Year and Date
      2007-04-21
    • Data Source
      KAKENHI-PROJECT-17081003
  • [Presentation] Identification of functional modules in protein network by near-clique detection

    • Author(s)
      Shu Tadaka, Takeshi Obayashi, Kengo Kinoshita
    • Organizer
      情報処理学会第33回バイオ情報学研究会
    • Place of Presentation
      東北大学
    • Data Source
      KAKENHI-PROJECT-24570176
  • [Presentation] ゲノム解析による個別化予防に向けた情報科学の挑戦

    • Author(s)
      木下賢吾
    • Organizer
      生体医工学大会
    • Place of Presentation
      仙台国際センター
    • Year and Date
      2014-06-24 – 2014-06-26
    • Invited
    • Data Source
      KAKENHI-PLANNED-22136005
  • [Presentation] Analysis of the ion permeation mechanism of Kv1.2 using the molecular dynamics simulations of a single point mutant

    • Author(s)
      近藤寛子,城田松之,笠原浩太,齊藤俊幸,木下賢吾
    • Organizer
      第52回日本生物物理学会
    • Place of Presentation
      札幌コンベンションセンター
    • Year and Date
      2014-09-25 – 2014-09-27
    • Data Source
      KAKENHI-PLANNED-22136005
  • [Presentation] Behavior of potassium ions around the potassium channel in relation to permeation events

    • Author(s)
      Toshiyuki Saito, Kota Kasahara, Matsuyuki Shirota, Hiroko Kondo, Kengo Kinoshita
    • Organizer
      生物物理学会
    • Place of Presentation
      京都
    • Data Source
      KAKENHI-PLANNED-22136005
  • [Presentation] Prediction of the biological and biochemical functions of uncharacterized genes

    • Author(s)
      Kinoshita K
    • Organizer
      2014 Bilateral Workshop between Tohoku University & National Tsing Hua University
    • Place of Presentation
      宮城県松島市
    • Year and Date
      2014-11-21 – 2014-11-22
    • Invited
    • Data Source
      KAKENHI-PROJECT-24570176
  • [Presentation] Classify RNA-seq runs as origin organs or other features by using machine learning

    • Author(s)
      Okamura Y, Obayashi T, Kinoshita K
    • Organizer
      22st Annual International Conference on Intelligent Systems for Molecular Biology
    • Place of Presentation
      Boston, USA
    • Year and Date
      2014-07-13 – 2014-07-15
    • Data Source
      KAKENHI-PROJECT-24570176
  • [Presentation] Functional gene network prediction based on conservation of gene expression patterns

    • Author(s)
      Yasunobu Okamura, Takeshi Obayashi, Kengo Kinoshita
    • Organizer
      21st Annual International Conference on Intelligent Systems for Molecular Biology
    • Place of Presentation
      Berlin, Germany
    • Data Source
      KAKENHI-PROJECT-24570176
  • [Presentation] タンパク質機能解析に向けた立体構造情報の活用基盤の構築

    • Author(s)
      木下賢吾
    • Organizer
      第52回日本生物物理学会
    • Place of Presentation
      札幌コンベンションセンター
    • Year and Date
      2014-09-25 – 2014-09-27
    • Invited
    • Data Source
      KAKENHI-PLANNED-22136005
  • [Presentation] NCMine: a novel method for exploring clusters in biological networks

    • Author(s)
      Shu Tadaka, Takeshi Obayashi, Kengo Kinoshita
    • Organizer
      分子生物学会
    • Place of Presentation
      神戸
    • Data Source
      KAKENHI-PROJECT-24570176
  • [Presentation] Detection of functional modules in protein networks by near-clique extraction

    • Author(s)
      Tadaka S, Obayashi T, Kinoshita K
    • Organizer
      Genome Information Workshop 2014
    • Place of Presentation
      東京
    • Year and Date
      2014-12-15 – 2014-12-18
    • Data Source
      KAKENHI-PROJECT-24570176
  • [Presentation] In-Silico Approach to Predict the Biological and Biochemical Functions of Uncharacterized Genes.

    • Author(s)
      Kengo Kinoshita
    • Organizer
      NIH-Tohoku University-JSPS Symposium
    • Place of Presentation
      宮城
    • Invited
    • Data Source
      KAKENHI-PLANNED-22136005
  • [Presentation] 生命科学ビッグデータへの情報科学の挑戦

    • Author(s)
      木下賢吾
    • Organizer
      東北大学電気・情報東京フォーラム2013
    • Place of Presentation
      東京
    • Invited
    • Data Source
      KAKENHI-PLANNED-22136005
  • [Presentation] GO analysis of gene expression patterns comparison among organs and species

    • Author(s)
      Yasunobu Okamura, Takeshi Obayashi, Kengo Kinoshita
    • Organizer
      生命医薬情報学連合大会
    • Place of Presentation
      タワーホール船堀
    • Data Source
      KAKENHI-PROJECT-24570176
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