Akutsu Tatsuya 阿久津達也

… Alternative Names

AKUTSU Tatsuya 阿久津達也

阿久津達也アクツタツヤ

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Researcher Number	90261859
Other IDs
External Links
Affiliation (Current)	2025: 京都大学, 化学研究所, 教授
Affiliation (based on the past Project Information) *help	2001 – 2024: 京都大学, 化学研究所, 教授 2007: Kyoto University, 京都大学・化学研究所, 教授 1997 – 2000: 東京大学, 医科学研究所, 助教授 1995: 群馬大学, 工学部, 助教授
Review Section/Research Field	Principal Investigator Life / Health / Medical informatics / Medium-sized Section 61:Human informatics and related fields / Sensitivity informatics/Soft computing / Bioinformatics/Life informatics / 計算機科学 / Basic Section 62010:Life, health and medical informatics-related / Medium-sized Section 62:Applied informatics and related fields / Soft computing / Intelligent informatics / Intelligent informatics / Biological Sciences … More Except Principal Investigator … More Biological Sciences / Intelligent informatics / Bioinformatics/Life informatics Less
Keywords	Principal Investigator ブーリアンネットワーク / 特徴ベクトル / カーネル法 / 遺伝子ネットワーク / 木構造 / 化学構造 / ケモインフォマティクス / バイオインフォマティクス / ニューラルネットワーク / 編集距離 … More / グラフアルゴリズム / 生物情報ネットワーク / スケールフリーネットワーク / 代謝ネットワーク / アルゴリズム / パターンマッチング / ReLU関数 / 自己符号化器 / 深層学習 / 整数計画法 / 逆問題 / モチーフ抽出 / 最大共通部分点集合 / サポートベクタマシン / 最小支配集合 / 構造的可制御性 / 構造列挙 / オイラー文字列 / 外平面的グラフ / 立体異性体 / タンパク質立体構造 / グラフ理論 / サポートベクターマシン / 遺伝子発現 / 電気泳動 / 遺伝子進化 / 遺伝子変異 / 遺伝子発現量 / タンパク質相互作用ネットワーク / 汎がんモジュール / Machine learning, / Data fusion / Protein cleavage / bioinformatics / data fution / protease / caspase / 離散原像問題 / 多層ネットワーク / 定常状態制御 / 生体ネットワーク / 生成AI / subcellular location prediction / chemical structure / support vector machine / kernel method / Euler string / edit distance / triangle inequality / sequence alignment / 糖鎖 / 位置特異的スコア行列 / フランス / 国際情報交換 / タンパク質細胞内局在部位予測 / グラフカーネル / タンパク質配列 / クラスタリング / 平面的グラフ / 細胞内局在部位予測 / 三角不等式 / 配列アラインメント / Local alignment / Position specific score matrix / Kernel method / Algorithms / Sequence motif / Pattern matching / Bioinformatics / ローカルサーチ / 相対エントロピー / GIBBSサンプリング / 構造アライメント / スポットマッチング / 最大クリーク / 近似マッチング / 合同性判定 / 点集合 / ホモロジー検索 / ローカルアライメント / 局所アライメント / 位置依存スコア行列 / 配列モチーフ / ロバストネス / 複雑ネットワーク / グラフ列挙 / ヶモインフォマティクス / Canalyzing関数 / NP完全 / アトラクター / 制御 / 確率ブーリアンネットワーク / 線形離散時間システム / 代謝流束解析 / 制御理論 / 複雑生体ネットワーク / 構造比較 / ベンゼン環 / 異性体 / 画像圧縮 / Eulerツアー / グラフ構造 / 無順序木 / データ圧縮 / 生体構造 / 文字列圧縮 / 発生 / 文脈自由文法 / 複雑系 / 文法圧縮 / グラフ文法 / L-system / 外平面グラフ / 光学異性体 / 構造活性相関 / RNA二次構造 / 動的計画法 / 列挙アルゴリズム / 遺伝子間相互作用 / べき乗則 / システム生物学 / 概日リズム / ネットワーク定常状態 / オペロン / 遺伝子発現データ / 神経細胞 / 形態形成 / 緑膿菌 / 進化動力学モデル / スケールフリー / 大規模進化動力学モデル / タンパク質ドメイン / タンパク質相互作用 / DNAマイクロアレイ / 幾何マッチング / 計算幾何学 … More Except Principal Investigator データベース / アルゴリズム / 遺伝子ネットワーク / Bioinformatics / siRNA / バイオインフォマティクス / ゲノム情報 / ゲノム / データマイニング / 知識発見 / 学習 / Database / 分子間相互作用 / タンパク質立体構造予測 / simulation / pathway modeling / protein-RNA interaction prediction / protein-protein interaction / gene network / protein network / パスウェイシミュレーション / マイクロアレイ解析 / タンパク質相互作用 / シミュレーション / パスウェイモデリング / タンパク質-RNA相互作用予測 / タンパク質相互作用情報 / タンパク質ネットワーク / Computational learning / Systems biology / Hybrid Petri net / Microarray / Boolean network / Qualitative network / Knowledge discovery / Gene network / ブーリアンネットワーク / システムバイオロジー / ハイブリッドペトリネット / マイクロアレイ / ブーリンアンネットワーク / 質的ネットワーク / Network topology / GRID / Reaction network / Molecular interaction / Algorithm / Ontology / マイクロアレイ発現データ / 知識抽出 / ゲノムデータベース / 相関ルール発見手法 / リンク情報 / アミノ酸配列類似度データ / 経路探索 / 相関クラスタ / グラフ比較 / 酵素反応 / 分子生物学データベース / グリッドコンピューティング / タンパク質間相互作用予測 / 文献からの知識抽出 / 統合データベース / グラフトポロジー / 糖鎖構造データベース / 化合物構造比較 / ネットワークトポロジー / グリッド / 反応ネットワーク / オントロジー / Image Processing of Micrographs / Phenome / Comparative Genomics / Transcription Start Site Analysis / Genome Sequencing / アミノ酸モチーフ / アラインメント / ヒトゲノム / オリゴマ設計 / DNAチップ / ゲノム解析ソフトウエア / ゲノム配列解読 / 遺伝子発現量解析 / RNAi / ゲノムアノテーション / 遺伝子予測 / 顕微鏡画像解析 / フェノーム / 表現型 / 比較ゲノム / 転写開始点 / ゲノム解読 / genome / entropy / computational complexity / data mining / pattern matching algorithm / knowledge discovery / learning / binary decision diagram / データマインイング / 情報量 / 計算量 / パターンマッチングアルゴリズム / 二分決定グラフ / Genetic diseases / Pathway / Molecular interactions / Network / Protein structure prediction / Gene function prediction / Genome analysis / 配列解析 / 遺伝子疾患 / パスウェイ / ネットワーク / 遺伝子機能予測 / ゲノム解析 / fault-tolerant / synchronization / communication / device / semi-conductor / computer / algorithm / distribution / parallel / デバイスシミュレーション / 遺伝情報解析 / AND-EXOR論理式 / VLSIレイアウト / 耐故障性 / 並列・分散アルゴリズム / 並列オペレーティングシステム / 並列・分散処理 / 同期 / 通信 / デバイス / 半導体 / 計算機 / 分散 / 並列 Less

Cell-type Specific Control Methods Using Single Cell Gene Expression DataPrincipal Investigator
- Principal Investigator
  
  阿久津達也
- Project Period (FY)
  2023 – 2025
- Research Category
  
  Grant-in-Aid for JSPS Fellows
- Review Section
  
  Basic Section 62010:Life, health and medical informatics-related
- Research Institution
  Kyoto University
Analysis and Control of Steady States of Multiple Biological NetworksPrincipal Investigator
- Principal Investigator
  
  阿久津達也
- Project Period (FY)
  2022 – 2024
- Research Category
  
  Grant-in-Aid for Challenging Research (Exploratory)
- Review Section
  
  Medium-sized Section 62:Applied informatics and related fields
- Research Institution
  Kyoto University
Advanced Studies and Developments on Discrete Preimage ProblemsPrincipal Investigator
- Principal Investigator
  
  阿久津達也
- Project Period (FY)
  2022 – 2026
- Research Category
  
  Grant-in-Aid for Scientific Research (A)
- Review Section
  
  Medium-sized Section 61:Human informatics and related fields
- Research Institution
  Kyoto University
Analysis and Applications of Discrete Preimage ProblemsPrincipal Investigator
- Principal Investigator
  
  Akutsu Tatauya
- Project Period (FY)
  2018 – 2022
- Research Category
  
  Grant-in-Aid for Scientific Research (A)
- Review Section
  
  Medium-sized Section 61:Human informatics and related fields
- Research Institution
  Kyoto University
Pan-cancer module and network analysis for identifying dominating subnetworks across hu man cancersPrincipal Investigator
- Principal Investigator
  
  阿久津達也
- Project Period (FY)
  2017 – 2019
- Research Category
  
  Grant-in-Aid for JSPS Fellows
- Research Field
  
  Life / Health / Medical informatics
- Research Institution
  Kyoto University
データ融合によるタンパク質切断解析および疾患との関連性発見Principal Investigator
- Principal Investigator
  
  阿久津達也
- Project Period (FY)
  2015 – 2016
- Research Category
  
  Grant-in-Aid for JSPS Fellows
- Research Field
  
  Life / Health / Medical informatics
- Research Institution
  Kyoto University
An Approach to Novel Structure Design by Combining Discrete Methods and Statistical MethodsPrincipal Investigator
- Principal Investigator
  
  AKUTSU Tatsuya
- Project Period (FY)
  2014 – 2018
- Research Category
  
  Grant-in-Aid for Scientific Research (A)
- Research Field
  
  Intelligent informatics
- Research Institution
  Kyoto University
Structurally Robust Control of Complex NetworksPrincipal Investigator
- Principal Investigator
  
  Akutsu Tatsuya
- Project Period (FY)
  2014 – 2017
- Research Category
  
  Grant-in-Aid for Challenging Exploratory Research
- Research Field
  
  Soft computing
- Research Institution
  Kyoto University
An Approach to Novel Structural Design by Combining Discrete Methods and Kernel MethodsPrincipal Investigator
- Principal Investigator
  
  AKUTSU Tatsuya
- Project Period (FY)
  2010 – 2014
- Research Category
  
  Grant-in-Aid for Scientific Research (A)
- Research Field
  
  Intelligent informatics
- Research Institution
  Kyoto University
Discrete Model-Based Methods for Control of Complex BiologicalSyetemsPrincipal Investigator
- Principal Investigator
  
  AKUTSU Tatsuya
- Project Period (FY)
  2010 – 2012
- Research Category
  
  Grant-in-Aid for Challenging Exploratory Research
- Research Field
  
  Sensitivity informatics/Soft computing
- Research Institution
  Kyoto University
New Methods for Designing Chemical Structures Using Graph Theory and Kernel MethodsPrincipal Investigator
- Principal Investigator
  
  AKUTSU Tatsuya
- Project Period (FY)
  2007 – 2009
- Research Category
  
  Grant-in-Aid for Scientific Research (A)
- Research Field
  
  Bioinformatics/Life informatics
- Research Institution
  Kyoto University
複雑生体構造のデータ圧縮を通じた発生原理の解明Principal Investigator
- Principal Investigator
  
  阿久津達也
- Project Period (FY)
  2007 – 2009
- Research Category
  
  Grant-in-Aid for Challenging Exploratory Research
- Research Field
  
  Sensitivity informatics/Soft computing
- Research Institution
  Kyoto University
Analysis of Structure and Dynamics of Biological Information NetworksPrincipal Investigator
- Principal Investigator
  
  AKUTSU Tatsuya
- Project Period (FY)
  2005 – 2009
- Research Category
  
  Grant-in-Aid for Scientific Research on Priority Areas
- Review Section
  
  Biological Sciences
- Research Institution
  Kyoto University
Pattern Matching Methods for Structured Data in BioinformaticsPrincipal Investigator
- Principal Investigator
  
  AKUTSU Tatsuya
- Project Period (FY)
  2004 – 2006
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Research Field
  
  Bioinformatics/Life informatics
- Research Institution
  Kyoto University
Information Scientific Foundations of Knowledge Discovery from Proteome Data
- Principal Investigator
  
  MIYANO Satoru
- Project Period (FY)
  2003 – 2005
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Research Field
  
  Bioinformatics/Life informatics
- Research Institution
  The University of Tokyo
Algorithms for Extraction of Common Patterns from Data in BioinformaticsPrincipal Investigator
- Principal Investigator
  
  AKUTSU Tatsuya
- Project Period (FY)
  2001 – 2003
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Research Field
  
  計算機科学
- Research Institution
  Kyoto University
Knowledge Discovery from Genome Databases
- Principal Investigator
  
  MORISHITA Shinichi
- Project Period (FY)
  2000 – 2004
- Research Category
  
  Grant-in-Aid for Scientific Research on Priority Areas
- Review Section
  
  Biological Sciences
- Research Institution
  University of Tokyo
Construction and Retrieval of Highly Integrated Biological Databases
- Principal Investigator
  
  GOTO Susumu
- Project Period (FY)
  2000 – 2004
- Research Category
  
  Grant-in-Aid for Scientific Research on Priority Areas
- Review Section
  
  Biological Sciences
- Research Institution
  Kyoto University
Foundations of Computational Knowledge Discovery from cDNA Microarray Data
- Principal Investigator
  
  MIYANO Satoru
- Project Period (FY)
  2000 – 2002
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Research Field
  
  Intelligent informatics
- Research Institution
  The University of Tokyo
非線形の歪みに対応可能な幾何図形のマッチング・アルゴリズムPrincipal Investigator
- Principal Investigator
  
  阿久津達也
- Project Period (FY)
  1998 – 1999
- Research Category
  
  Grant-in-Aid for Encouragement of Young Scientists (A)
- Research Field
  
  計算機科学
- Research Institution
  The University of Tokyo
Development of Data Mining System Using Binary Decision Diagrams for Knowledge Representation
- Principal Investigator
  
  MIYANO Satoru
- Project Period (FY)
  1997 – 1999
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Research Field
  
  Intelligent informatics
- Research Institution
  The University of Tokyo
Biological Knowledge Based on Genome Information
- Principal Investigator
  
  KANEHISA Minoru
- Project Period (FY)
  1996 – 2000
- Research Category
  
  Grant-in-Aid for Scientific Research on Priority Areas (A)
- Research Institution
  KYOTO UNIVERSITY
Parallel and Distributed Computing and its Applications
- Principal Investigator
  
  IGARASHI Yoshihide
- Project Period (FY)
  1995 – 1996
- Research Category
  
  Grant-in-Aid for international Scientific Research
- Research Institution
  Gunma University, Faculty of Engineering

[Book] 複雑ネットワークと制御理論2023
- Author(s)
  阿久津達也、ホセ・ナチェル
- Total Pages
  216
- Publisher
  森北出版
- ISBN
  9784627818811
- Data Source
  KAKENHI-PROJECT-22K19830
[Book] バイオインフォマティクス, Python による実践レシピ2020
- Author(s)
  Antao,T.　(著）、阿久津　達也、竹本和広　(訳）
- Total Pages
  320
- Publisher
  朝倉書店
- ISBN
  9784254122541
- Data Source
  KAKENHI-PROJECT-18H04113
[Book] Algorithms for Analysis, Inference, and Control of Boolean Networks2018
- Author(s)
  Tatsuya Akutsu
- Total Pages
  228
- Publisher
  World Scientific
- ISBN
  9789813233423
- Data Source
  KAKENHI-PROJECT-26540125
[Book] バイオインフォマティクスの数理とアルゴリズム2007
- Author(s)
  阿久津達也
- Total Pages
  223
- Publisher
  共立出版
- Data Source
  KAKENHI-PROJECT-17017019
[Book] バイオインフォマティクスの数理とアルゴリズム2007
- Author(s)
  阿久津達也
- Total Pages
  223
- Publisher
  共立出版
- Data Source
  KAKENHI-PROJECT-17017019
[Book] バイオインフォマティクス-配列データ解析と構造予測-2007
- Author(s)
  丸山修、阿久津達也
- Total Pages
  190
- Publisher
  朝倉書店
- Data Source
  KAKENHI-PROJECT-17017019
[Book] 朝倉書店2007
- Author(s)
  丸山修, 阿久津達也
- Total Pages
  190
- Publisher
  バイオインフォマティクス-配列データ解析と構造予測-
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-16300092
[Book] バイオインフォマティクスの数理とアルゴリズム2007
- Author(s)
  阿久津達也
- Total Pages
  223
- Publisher
  共立出版
- Data Source
  KAKENHI-PROJECT-16300092
[Book] 共立出版2007
- Author(s)
  阿久津達也
- Total Pages
  223
- Publisher
  バイオインフォマティクスの数理とアルゴリズム
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-16300092
[Book] 遺伝子発現情報解析のための数理モデルとアルゴリズム2003
- Author(s)
  阿久津達也
- Total Pages
  36
- Publisher
  (財)国際高等研究所
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-13680394
[Journal Article] DiCleave: a deep learning model for predicting human Dicer cleavage sites2024
- Author(s)
  Mu Lixuan、Song Jiangning、Akutsu Tatsuya、Mori Tomoya
- Journal Title
  
  BMC Bioinformatics
  
  Volume: 25 Issue: 1 Pages: 13-13
- DOI
  10.1186/s12859-024-05638-4
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K19830, KAKENHI-PROJECT-22H00532
[Journal Article] Measuring criticality in control of complex biological networks2024
- Author(s)
  Someya Wataru、Akutsu Tatsuya、Schwartz Jean-Marc、Nacher Jose C.
- Journal Title
  
  npj Systems Biology and Applications
  
  Volume: 10(1) Issue: 1 Pages: 9-9
- DOI
  10.1038/s41540-024-00333-9
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K19830, KAKENHI-PROJECT-22H00532
[Journal Article] Multi-shelled ECIF: improved extended connectivity interaction features for accurate binding affinity prediction2023
- Author(s)
  Shiota Koji、Akutsu Tatsuya
- Journal Title
  
  Bioinformatics Advances
  
  Volume: 3(1) Issue: 1
- DOI
  10.1093/bioadv/vbad155
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-22K19830, KAKENHI-PROJECT-22H00532
[Journal Article] eSPRESSO: topological clustering of single-cell transcriptomics data to reveal informative genes for spatio-temporal architectures of cells2023
- Author(s)
  Mori Tomoya、Takase Toshiro、Lan Kuan-Chun、Yamane Junko、Alev Cantas、Kimura Azuma、Osafune Kenji、Yamashita Jun K.、Akutsu Tatsuya、Kitano Hiroaki、Fujibuchi Wataru
- Journal Title
  
  BMC Bioinformatics
  
  Volume: 24 Issue: 1 Pages: 252-252
- DOI
  10.1186/s12859-023-05355-4
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-22K19830, KAKENHI-PROJECT-22H00532
[Journal Article] Common Attractors in Multiple Boolean Networks2023
- Author(s)
  Cao Yu、Pi Wenya、Lin Chun-Yu、M?nzner Ulrike、Ohtomo Masahiro、Akutsu Tatsuya
- Journal Title
  
  IEEE/ACM Transactions on Computational Biology and Bioinformatics
  
  Volume: 20 Issue: 5 Pages: 2862-2873
- DOI
  10.1109/tcbb.2023.3268795
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K19830
[Journal Article] Identification of periodic attractors in Boolean networks using a priori information2022
- Author(s)
  Munzner Ulrike、Mori Tomoya、Krantz Marcus、Klipp Edda、Akutsu Tatsuya
- Journal Title
  
  PLOS Computational Biology
  
  Volume: 18 Issue: 1 Pages: e1009702-e1009702
- DOI
  10.1371/journal.pcbi.1009702
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H04113
[Journal Article] A novel graph convolutional neural network for predicting interaction sites on protein kinase inhibitors in phosphorylation2022
- Author(s)
  Wang Feiqi、Chen Yun-Ti、Yang Jinn-Moon、Akutsu Tatsuya
- Journal Title
  
  Scientific Reports
  
  Volume: 12 Issue: 1 Pages: 229-229
- DOI
  10.1038/s41598-021-04230-7
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H04113
[Journal Article] A Method for Molecular Design Based on Linear Regression and Integer Programming2022
- Author(s)
  Zhu Jianshen、Azam Naveed A.、Haraguchi Kazuya、Zhao Liang、Nagamochi Hiroshi、Akutsu Tatsuya
- Journal Title
  
  Proc. 12th International Conference on Bioscience, Biochemistry and Bioinformatics
  
  Volume: N/A Pages: 21-28
- DOI
  10.1145/3510427.3510431
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-18H04113
[Journal Article] Adjustive Linear Regression and Its Application to the Inverse QSAR2022
- Author(s)
  Zhu Jianshen、Haraguchi Kazuya、Nagamochi Hiroshi、Akutsu Tatsuya
- Journal Title
  
  Proc. 15th International Joint Conference on Biomedical Engineering Systems and Technologies - BIOINFORMATICS
  
  Volume: N/A Pages: 144-151
- DOI
  10.5220/0010853700003123
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-18H04113
[Journal Article] On the Complexity of Tree Edit Distance with Variables2022
- Author(s)
  Tatsuya Akutsu, Tomoya Mori, Naotoshi Nakamura, Satoshi Kozawa, Yuhei Ueno, Thomas N. Sato
- Journal Title
  
  Proceedings of 33rd International Symposium on Algorithms and Computation
  
  Volume: LIPIcs 248
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-22K19830
[Journal Article] MSNet-4mC: learning effective multi-scale representations for identifying DNA N4-methylcytosine sites2022
- Author(s)
  Liu Chunting、Song Jiangning、Ogata Hiroyuki、Akutsu Tatsuya
- Journal Title
  
  Bioinformatics
  
  Volume: 38 Issue: 23 Pages: 5160-5167
- DOI
  10.1093/bioinformatics/btac671
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22H00532
[Journal Article] Densest subgraph-based methods for protein-protein interaction hot spot prediction2022
- Author(s)
  Li Ruiming、Lee Jung-Yu、Yang Jinn-Moon、Akutsu Tatsuya
- Journal Title
  
  BMC Bioinformatics
  
  Volume: 23 Issue: 1
- DOI
  10.1186/s12859-022-04996-1
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22H00532
[Journal Article] An Improved Integer Programming Formulation for Inferring Chemical Compounds with Prescribed Topological Structures2021
- Author(s)
  Zhu Jianshen、Azam Naveed Ahmed、Haraguchi Kazuya、Zhao Liang、Nagamochi Hiroshi、Akutsu Tatsuya
- Journal Title
  
  Lecture Notes in Computer Science
  
  Volume: 12798 Pages: 197-209
- DOI
  10.1007/978-3-030-79457-6_17
- ISBN
  9783030794569, 9783030794576
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-18H04113
[Journal Article] Molecular Design Based on Artificial Neural Networks, Integer Programming and Grid Neighbor Search2021
- Author(s)
  Azam Naveed Ahmed、Zhu Jianshen、Haraguchi Kazuya、Zhao Liang、Nagamochi Hiroshi、Akutsu Tatsuya
- Journal Title
  
  Proc. 2021 IEEE International Conference on Bioinformatics and Biomedicine
  
  Volume: N/A Pages: 360-363
- DOI
  10.1109/bibm52615.2021.9669710
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-18H04113
[Journal Article] A novel method for inference of acyclic chemical compounds with bounded branch-height based on artificial neural networks and integer programming2021
- Author(s)
  Azam Naveed Ahmed、Zhu Jianshen、Sun Yanming、Shi Yu、Shurbevski Aleksandar、Zhao Liang、Nagamochi Hiroshi、Akutsu Tatsuya
- Journal Title
  
  Algorithms for Molecular Biology
  
  Volume: 16 Issue: 1 Pages: 18-18
- DOI
  10.1186/s13015-021-00197-2
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-18H04113, KAKENHI-PROJECT-20K11691
[Journal Article] Probabilistic Critical Controllability Analysis of Protein Interaction Networks Integrating Normal Brain Ageing Gene Expression Profiles2021
- Author(s)
  Yamaguchi Eimi、Akutsu Tatsuya、Nacher Jose C.
- Journal Title
  
  International Journal of Molecular Sciences
  
  Volume: 22 Issue: 18 Pages: 9891-9891
- DOI
  10.3390/ijms22189891
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-18H04113, KAKENHI-PROJECT-18K11535
[Journal Article] Discrimination of attractors with noisy nodes in Boolean networks2021
- Author(s)
  Cheng Xiaoqing、Ching Wai-Ki、Guo Sini、Akutsu Tatsuya
- Journal Title
  
  Automatica
  
  Volume: 130 Pages: 109630-109630
- DOI
  10.1016/j.automatica.2021.109630
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H04113
[Journal Article] Uncovering and classifying the role of driven nodes in control of complex networks2021
- Author(s)
  Yuma Shinzawa, Tatsuya Akutsu and Jose C. Nacher
- Journal Title
  
  Scientific Reports
  
  Volume: 11 Issue: 1 Pages: 9627-9627
- DOI
  10.1038/s41598-021-88295-4
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-18K11535, KAKENHI-PROJECT-18H04113
[Journal Article] An Inverse QSAR Method Based on a Two-Layered Model and Integer Programming2021
- Author(s)
  Shi Yu、Zhu Jianshen、Azam Naveed Ahmed、Haraguchi Kazuya、Zhao Liang、Nagamochi Hiroshi、Akutsu Tatsuya
- Journal Title
  
  International Journal of Molecular Sciences
  
  Volume: 22 Issue: 6 Pages: 2847-2847
- DOI
  10.3390/ijms22062847
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-20K04978, KAKENHI-PROJECT-20K11691, KAKENHI-PROJECT-18J23484, KAKENHI-PROJECT-18H04113
[Journal Article] ReCGBM: a gradient boosting-based method for predicting human dicer cleavage sites2021
- Author(s)
  Liu Pengyu、Song Jiangning、Lin Chun-Yu、Akutsu Tatsuya
- Journal Title
  
  BMC Bioinformatics
  
  Volume: 22 Issue: 1 Pages: 63-63
- DOI
  10.1186/s12859-021-03993-0
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H04113
[Journal Article] An Inverse QSAR Method Based on Decision Tree and Integer Programming2021
- Author(s)
  Tanaka Kouki、Zhu Jianshen、Azam Naveed Ahmed、Haraguchi Kazuya、Zhao Liang、Nagamochi Hiroshi、Akutsu Tatsuya
- Journal Title
  
  Lecture Notes in Computer Science
  
  Volume: 12837 Pages: 628-644
- DOI
  10.1007/978-3-030-84529-2_53
- ISBN
  9783030845285, 9783030845292
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-18H04113
[Journal Article] 機械学習QSARの整数計画法に基づく逆解析法2021
- Author(s)
  NAGAMOCHI Hiroshi、ZHU Jianshen、AZAM Naveed Ahmed、HARAGUCHI Kazuya、ZHAO Liang、AKUTSU Tatsuya
- Journal Title
  
  J. Comput. Chem. Jpn.
  
  Volume: 20 Issue: 3 Pages: 106-111
- DOI
  10.2477/jccj.2021-0030
- NAID
  130008130265
- ISSN
  1347-1767, 1347-3824
- Language
  English
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-18H04113, KAKENHI-PROJECT-20K11691
[Journal Article] Weighted minimum feedback vertex sets and implementation in human cancer genes detection2021
- Author(s)
  Li Ruiming、Lin Chun-Yu、Guo Wei-Feng、Akutsu Tatsuya
- Journal Title
  
  BMC Bioinformatics
  
  Volume: 22 Issue: 1 Pages: 143-143
- DOI
  10.1186/s12859-021-04062-2
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H04113
[Journal Article] A New Integer Linear Programming Formulation to the Inverse QSAR/QSPR for Acyclic Chemical Compounds Using Skeleton Trees2020
- Author(s)
  Zhang Fan、Zhu Jianshen、Chiewvanichakorn Rachaya、Shurbevski Aleksandar、Nagamochi Hiroshi、Akutsu Tatsuya
- Journal Title
  
  Lecture Notes in Computer Science
  
  Volume: 12114 Pages: 433-444
- DOI
  10.1007/978-3-030-55789-8_38
- NAID
  120006893967
- ISBN
  9783030557881, 9783030557898
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-18H04113
[Journal Article] Extracting boolean and probabilistic rules from trained neural networks2020
- Author(s)
  Liu Pengyu、Melkman Avraham A.、Akutsu Tatsuya
- Journal Title
  
  Neural Networks
  
  Volume: 126 Pages: 300-311
- DOI
  10.1016/j.neunet.2020.03.024
- NAID
  120006936364
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H04113
[Journal Article] A novel method for inference of chemical compounds of cycle index two with desired properties based on artificial neural networks and integer programming2020
- Author(s)
  Jianshen Zhu, Chenxi Wang, Aleksandar Shurbevski, Hiroshi Nagamochi,Tatsuya Akutsu
- Journal Title
  
  Algorithms
  
  Volume: 13 Issue: 5 Pages: 124-124
- DOI
  10.3390/a13050124
- NAID
  120006993972
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20K11691, KAKENHI-PROJECT-18H04113
[Journal Article] Comparison of Pseudoknotted RNA Secondary Structures by Topological Centroid Identification and Tree Edit Distance2020
- Author(s)
  Wang Feiqi、Akutsu Tatsuya、Mori Tomoya
- Journal Title
  
  Journal of Computational Biology
  
  Volume: 27 Issue: 9 Pages: 1443-1451
- DOI
  10.1089/cmb.2019.0512
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-18H04113
[Journal Article] Probabilistic controllability approach to metabolic fluxes in normal and cancer tissues2019
- Author(s)
  Jean-Marc Schwartz, Hiroaki Otokuni, Tatsuya Akutsu and Jose C. Nacher
- Journal Title
  
  Nature Communications
  
  Volume: 10 Issue: 1 Pages: 2725-2725
- DOI
  10.1038/s41467-019-10616-z
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18K11535, KAKENHI-PROJECT-18H04113
[Journal Article] On the Number of Driver Nodes for Controlling a Boolean Network when the Targets are Restricted to Attractors2019
- Author(s)
  Wenpin Hou, Peying Ruan, Wai-Ki. Ching, Tatsuya Akutsu
- Journal Title
  
  Journal of Theoretical Biolog
  
  Volume: 463 Pages: 1-11
- DOI
  10.1016/j.jtbi.2018.12.012
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H04113
[Journal Article] Deep learning with evolutionary and genomic profiles for identifying cancer subtypes2019
- Author(s)
  C-Y. Lin, P. Ruan, R. Li, J-M. Yang, S. See, J. Song, T. Akutsu
- Journal Title
  
  Journal of Bioinformatics and Computational Biology
  
  Volume: 17 Issue: 03 Pages: 1940005-1940005
- DOI
  10.1142/s0219720019400055
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H04113, KAKENHI-PROJECT-17F17353
[Journal Article] Identification of the structure of a probabilistic Boolean network from samples including frequencies of outcomes2019
- Author(s)
  T. Akutsu, A. A. Melkman
- Journal Title
  
  IEEE Transactions on Neural Networks and Learning Systems
  
  Volume: 30 Issue: 8 Pages: 2383-2396
- DOI
  10.1109/tnnls.2018.2884454
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H04113
[Journal Article] Resource Cut, a New Bounding Procedure to Algorithms for Enumerating Tree-Like Chemical Graphs2019
- Author(s)
  Yuhei Nishiyama, Aleksandar Shurbevski , Hiroshi Nagamochi, Tatsuya Akutsu
- Journal Title
  
  IEEE/ACM Transactions on Computational Biology and Bioinformatics
  
  Volume: 16 Issue: 1 Pages: 77-90
- DOI
  10.1109/tcbb.2018.2832061
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-18H04113, KAKENHI-PROJECT-17K00014
[Journal Article] Convolutional neural network approach to lung cancer classification integrating protein interaction network and gene expression profiles2019
- Author(s)
  Teppei Matsubara, Tomoshiro Ochiai, Morihiro Hayashida, Tatsuya Akutsu and Jose C. Nacher
- Journal Title
  
  Journal of Bioinformatics and Computational Biology
  
  Volume: 17 Issue: 03 Pages: 1940007-1940007
- DOI
  10.1142/s0219720019400079
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-18K11535, KAKENHI-PROJECT-18H04113, KAKENHI-PROJECT-15K01200, KAKENHI-PROJECT-16K00392
[Journal Article] Deep Learning with Evolutionary and Genomic Profiles for Identifying Cancer Subtypes2018
- Author(s)
  Lin, C. Y., Ruan, P. Y., Li, R. M., Yang, J. M., See S., and Akutsu, T.
- Journal Title
  
  Proc. IEEE 18th International Conference on BioInformatics and BioEngineering
  
  Volume: N/A Pages: 147-150
- DOI
  10.1109/bibe.2018.00035
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-17F17353
[Journal Article] PROSPERous: high-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracy2018
- Author(s)
  J. Song, F. Li, A. Leier, T. T. Marquez-Lago. T. Akutsu, G. Haffari, K-C. Chou, G. I. Webb and R. N. Pike
- Journal Title
  
  Bioinformatics
  
  Volume: 34 Issue: 4 Pages: 684-687
- DOI
  10.1093/bioinformatics/btx670
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-26240034
[Journal Article] Identifying a Probabilistic Boolean Threshold Network From Samples2018
- Author(s)
  Avraham A. Melkman, Xiaoqing Cheng, Wai-Ki Ching, Tatsuya Akutsu
- Journal Title
  
  IEEE Transactions on Neural Networks and Learning Systems
  
  Volume: 29 Issue: 4 Pages: 869-881
- DOI
  10.1109/tnnls.2017.2648039
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H04113
[Journal Article] Euler string-based compression of tree-structured data and its application to analysis of RNAs2018
- Author(s)
  L. Liu, T. Mori, Y. Zhao, M. Hayashida and T. Akutsu
- Journal Title
  
  Current Bioinformatics
  
  Volume: 13 Issue: 1 Pages: 25-33
- DOI
  10.2174/1574893611666160608102231
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-26240034, KAKENHI-PROJECT-16KT0020
[Journal Article] Improving prediction of heterodimeric protein complexes using combination with pairwise kernel2018
- Author(s)
  Ruan Peiying、Hayashida Morihiro、Akutsu Tatsuya、Vert Jean-Philippe
- Journal Title
  
  BMC Bioinformatics
  
  Volume: 19 Issue: S1 Pages: 39-39
- DOI
  10.1186/s12859-018-2017-5
- NAID
  120006537092
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16K00392, KAKENHI-PROJECT-26240034, KAKENHI-PROJECT-16KT0020
[Journal Article] Enumerating Substituted Benzene Isomers of Tree-Like Chemical Graphs2018
- Author(s)
  J. Li, H. Nagamochi, T. Akutsu
- Journal Title
  
  IEEE/ACM Trans. Comput. Biology Bioinform.
  
  Volume: 15(2) Issue: 2 Pages: 633-646
- DOI
  10.1109/tcbb.2016.2628888
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17K00014, KAKENHI-PROJECT-18H04113
[Journal Article] PREvaIL, an integrative approach for inferring catalytic residues using sequence, structural, and network features in a machine-learning framework2018
- Author(s)
  J. Song, F. Li, K. Takemoto, G. HaHaffari, T. Akutsu, K-C. Chou, and G. I. Webb
- Journal Title
  
  Journal of Theoretical Biology
  
  Volume: 443 Pages: 125-137
- DOI
  10.1016/j.jtbi.2018.01.023
- NAID
  120007026466
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-26240034, KAKENHI-PROJECT-17H04703
[Journal Article] Determining the minimum number of protein-protein interactions required to support known protein complexes2018
- Author(s)
  Natsu Nakajima, Morihiro Hayashida, Jesper Jansson, Osamu Maruyama, Tatsuya Akutsu
- Journal Title
  
  PLOS ONE
  
  Volume: 13 Issue: 4 Pages: e0195545-e0195545
- DOI
  10.1371/journal.pone.0195545
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16K00392, KAKENHI-PROJECT-17K00407, KAKENHI-PROJECT-18H04113, KAKENHI-PROJECT-16KT0020
[Journal Article] On the parameterized complexity of associative and commutative unification2017
- Author(s)
  T. Akutsu, J. Jansson, A. Takasu, T. Tamura
- Journal Title
  
  Theoretical Computer Science
  
  Volume: 660 Pages: 57-74
- DOI
  10.1016/j.tcs.2016.11.026
- NAID
  120006537095
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PROJECT-26240034, KAKENHI-PROJECT-16K00391
[Journal Article] Discrimination of singleton and periodic attractors in Boolean networks2017
- Author(s)
  Cheng Xiaoqing、Tamura Takeyuki、Ching Wai-Ki、Akutsu Tatsuya
- Journal Title
  
  Automatica
  
  Volume: 84 Pages: 205-213
- DOI
  10.1016/j.automatica.2017.07.012
- NAID
  120006542020
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16K00391, KAKENHI-PROJECT-26240034, KAKENHI-PROJECT-26540125
[Journal Article] Critical controllability analysis of directed biological networks using efficient graph reduction2017
- Author(s)
  M. Ishitsuka1, T. Akutsu, J. C. Nacher
- Journal Title
  
  Scientific Reports
  
  Volume: 7 Issue: 1 Pages: 14361-14361
- DOI
  10.1038/s41598-017-14334-8
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-26240034, KAKENHI-PROJECT-25330351, KAKENHI-PROJECT-26540125
[Journal Article] Averaged n-dependence estimators for positive unlabeled learning2017
- Author(s)
  F. Li, J. Song, C. Li, T. Akutsu and Y. Zhang
- Journal Title
  
  ICIC Express Letters, Part B: Applications
  
  Volume: 8 Pages: 1287-1297
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-26240034
[Journal Article] An accessibility-incorporated method for accurate prediction of RNA-RNA interactions from sequence data2017
- Author(s)
  Y. Kato, T. Mori, K. Sato, S. Maegawa, H. Hosokawa, T. Akutsu
- Journal Title
  
  Bioinformatics
  
  Volume: 33 Issue: 2 Pages: 202-209
- DOI
  10.1093/bioinformatics/btw603
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-26240034, KAKENHI-PROJECT-25330348, KAKENHI-PROJECT-15K00401
[Journal Article] SecretEPDB: a comprehensive web-based resource for secreted effector proteins of the bacterial types III, IV and VI secretion systems2017
- Author(s)
  Y. An, J. Wang, J. Song, C. Li, J. Revote, T. Naderer, M. Hayashida, T. Akutsu, Y. Zhang, G. I. Webb, T. Lithgow
- Journal Title
  
  Scientific Reports
  
  Volume: 7 Issue: 1 Pages: 41031-41031
- DOI
  10.1038/srep41031
- NAID
  120005997781
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-26240034, KAKENHI-PROJECT-16KT0020
[Journal Article] hosphoPredict: A bioinformatics tool for prediction of human kinase-specific phosphorylation substrates and sites by integrating heterogeneous feature selection2017
- Author(s)
  J. Song, H. Wang, J. Wang, A, Leier, T. Marquez-Lago, B. Yang, Z. Zhang, T. Akutsu, G. I. Webb and R. J. Daly
- Journal Title
  
  Scientific Reports
  
  Volume: 7 Issue: 1
- DOI
  10.1038/s41598-017-07199-4
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-26240034
[Journal Article] LBSizeCleav: improved support vector machine (SVM)-based prediction of Dicer cleavage sites using loop/bulge length2016
- Author(s)
  Y. Bao, M. Hayashida, T. Akutsu
- Journal Title
  
  BMC Bioinformatics
  
  Volume: 17 Issue: 1 Pages: 487-487
- DOI
  10.1186/s12859-016-1353-6
- NAID
  120005973378
- Peer Reviewed / Acknowledgement Compliant / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-26240034, KAKENHI-PROJECT-16KT0020, KAKENHI-PROJECT-16K00392
[Journal Article] Complex network-based approaches to biomarker discovery2016
- Author(s)
  Hayashida, M. and Akutsu, T.
- Journal Title
  
  Biomarkers in Medicine
  
  Volume: 10 Issue: 6 Pages: 621-632
- DOI
  10.2217/bmm-2015-0047
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16KT0020, KAKENHI-PROJECT-26540125
[Journal Article] Finding influential genes using gene expression data and Boolean models of metabolic networks2016
- Author(s)
  T. Tamura, C-Y. Lin, J-M. Yang, T. Akutsu
- Journal Title
  
  Proc. IEEE 16th International Conference on Bioinformatics and Bioengineering
  
  Volume: - Pages: 57-63
- DOI
  10.1109/bibe.2016.25
- Peer Reviewed / Acknowledgement Compliant / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-26240034, KAKENHI-PROJECT-26540125
[Journal Article] Analysis of the effect of degree correlation on the size of minimum dominating sets in complex networks2016
- Author(s)
  Takemoto K, Akutsu T
- Journal Title
  
  PLoS ONE
  
  Volume: 11 Issue: 6 Pages: e0157868-e0157868
- DOI
  10.1371/journal.pone.0157868
- NAID
  120005819482
- Peer Reviewed / Acknowledgement Compliant / Open Access
- Data Source
  KAKENHI-PROJECT-25700030, KAKENHI-PROJECT-26540125
[Journal Article] Maximum margin classifier working in a set of strings2016
- Author(s)
  H. Koyano, M. Hayashida, T. Akutsu
- Journal Title
  
  Proceedings of the Royal Society A
  
  Volume: 472 Issue: 2187 Pages: 20150551-20150551
- DOI
  10.1098/rspa.2015.0551
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PROJECT-26240034, KAKENHI-PROJECT-26610037, KAKENHI-PROJECT-16KT0020
[Journal Article] Minimum dominating set-based Methods for Analyzing Biological Networks2016
- Author(s)
  J.C. Nacher and T. Akutsu
- Journal Title
  
  Methods
  
  Volume: 印刷中 Pages: 57-63
- DOI
  10.1016/j.ymeth.2015.12.017
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PROJECT-25330351, KAKENHI-PROJECT-26540125
[Journal Article] Critical controllability in proteome-wide protein interaction network integrating transcriptome2016
- Author(s)
  M. Ishitsuka, T. Akutsu and J.C. Nacher
- Journal Title
  
  Scientific Reports
  
  Volume: 6 Issue: 1 Pages: 1-14
- DOI
  10.1038/srep23541
- Peer Reviewed / Acknowledgement Compliant / Open Access
- Data Source
  KAKENHI-PROJECT-25330351, KAKENHI-PROJECT-26540125
[Journal Article] Enumerating naphthalene isomers of tree-like chemical graphs2016
- Author(s)
  F. He, A. Hanai, H. Nagamochi, T. Akutsu
- Journal Title
  
  Proc. 9th International Joint Conference on Biomedical Engineering Systems and Technologies
  
  Volume: 3 Pages: 258-265
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PROJECT-26240034
[Journal Article] Finding and analyzing the minimum set of driver nodes in control of Boolean networks2016
- Author(s)
  Wenpin Hou, Takeyuki Tamura, Wai-Ki. Ching and Tatsuya Akutsu
- Journal Title
  
  Advances in Complex Systems
  
  Volume: 19 Issue: 03 Pages: 1650006-1650006
- DOI
  10.1142/s0219525916500065
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16K00391, KAKENHI-PROJECT-26540125
[Journal Article] Enumeration method for tree-like chemical compounds with benzene rings and naphthalene rings by breadth-first search order2016
- Author(s)
  J. Jindalertudomdee, M. Hayashida, Y. Zhao, T. Akutsu
- Journal Title
  
  BMC Bioinformatics
  
  Volume: 17 Issue: 1 Pages: 113-113
- DOI
  10.1186/s12859-016-0962-4
- NAID
  120005822781
- Peer Reviewed / Acknowledgement Compliant / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-26240034, KAKENHI-PROJECT-24500361, KAKENHI-PROJECT-16KT0020
[Journal Article] Enumeration method for structural isomers containing user-defined structures based on breadth-first search approach2016
- Author(s)
  J. Jindalertudomdee, M. Hayashida, T. Akutsu
- Journal Title
  
  Journal of Computational Biology
  
  Volume: 23 Issue: 8 Pages: 625-640
- DOI
  10.1089/cmb.2016.0056
- Peer Reviewed / Acknowledgement Compliant / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-26240034, KAKENHI-PROJECT-16KT0020
[Journal Article] Complex network-based approaches to biomarker discovery2016
- Author(s)
  M. Hayashida, T. Akutsu
- Journal Title
  
  Biomarkers in Medicine
  
  Volume: 10 Pages: 621-632
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PROJECT-26240034
[Journal Article] Exact identification of the structure of a probabilistic Boolean network from samples2016
- Author(s)
  X. Cheng, T. Mori, Y. Qiu, W-K. Ching, T. Akutsu
- Journal Title
  
  IEEE/ACM Transactions on Computational Biology and Bioinformatics
  
  Volume: 13 Issue: 6 Pages: 1107-1116
- DOI
  10.1109/tcbb.2015.2505310
- NAID
  120006863512
- Peer Reviewed / Acknowledgement Compliant / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-26540125
[Journal Article] Host-pathogen protein interaction prediction based on local topology structures of a protein interaction network2016
- Author(s)
  J. Jindalertudomdee, M. Hayashida, J. Song, T. Akutsu
- Journal Title
  
  Proc. IEEE 16th International Conference on Bioinformatics and Bioengineering
  
  Volume: - Pages: 7-12
- DOI
  10.1109/bibe.2016.26
- Peer Reviewed / Acknowledgement Compliant / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-26240034
[Journal Article] On the complexity of finding a largest common subtree of bounded degree2015
- Author(s)
  T. Akutsu, T. Tamura, A.A. Melkman, A. Takasu
- Journal Title
  
  Theoretical Computer Science
  
  Volume: 590 Pages: 2-16
- DOI
  10.1016/j.tcs.2014.10.012
- NAID
  120005689204
- Peer Reviewed / Acknowledgement Compliant / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-26240034, KAKENHI-PROJECT-25730005
[Journal Article] Grammar-based compression approach to extraction of common rules among multiple trees of glycans and RNAs2015
- Author(s)
  Y. Zhao, M. Hayashida, Y. Cao, J. Hwang, T. Akutsu
- Journal Title
  
  BMC Bioinformatics
  
  Volume: 16 Issue: 1 Pages: 128-128
- DOI
  10.1186/s12859-015-0558-4
- NAID
  120005749951
- Peer Reviewed / Acknowledgement Compliant / Open Access
- Data Source
  KAKENHI-PROJECT-26240034, KAKENHI-PROJECT-24500361
[Journal Article] Similar subtree search using extended tree inclusion2015
- Author(s)
  T. Mori, A. Takasu, J. Jansson, J. Hwang, T. Tamura, T. Akutsu
- Journal Title
  
  IEEE Transactions on Knowledge and Data Engineering
  
  Volume: 27 Issue: 12 Pages: 3360-3373
- DOI
  10.1109/tkde.2015.2457922
- Peer Reviewed / Acknowledgement Compliant / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-26240034, KAKENHI-PROJECT-25730005, KAKENHI-PROJECT-15H02789
[Journal Article] Determining associations between human diseases and non-coding RNAs with critical roles in network control2015
- Author(s)
  H. Kagami, T. Akutsu, S. Maegawa, H. Hosokawa, J. C. Nacher
- Journal Title
  
  Scientific Reports
  
  Volume: 5 Issue: 1 Pages: 14577-14577
- DOI
  10.1038/srep14577
- NAID
  120005818233
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-26540125, KAKENHI-PROJECT-26240034
[Journal Article] Computing smallest intervention strategies for multiple metabolic networks in a boolean model.2015
- Author(s)
  Lu, W., Tamura, T., Song, J. & Akutsu, T.
- Journal Title
  
  Journal of computational biology
  
  Volume: 22 Issue: 2 Pages: 85-110
- DOI
  10.1089/cmb.2014.0274
- NAID
  120005657917
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-25250028, KAKENHI-PROJECT-25730005, KAKENHI-PROJECT-26240034, KAKENHI-PROJECT-26540125
[Journal Article] Structurally Robust Control of Complex Networks2015
- Author(s)
  J.C. Nacher and T. Akutsu
- Journal Title
  
  Physical Review E
  
  Volume: 91 Issue: 1 Pages: 0128261-19
- DOI
  10.1103/physreve.91.012826
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PROJECT-25330351, KAKENHI-PROJECT-26540125
[Journal Article] Computational methods for modification of metabolic networks2015
- Author(s)
  T. Tamura, W. Liu, T. Akutsu
- Journal Title
  
  Computational and Structural Biotechnology Journal
  
  Volume: 12 Pages: 376-381
- DOI
  10.1016/j.csbj.2015.05.004
- NAID
  120005712915
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-26540125, KAKENHI-PROJECT-26240034, KAKENHI-PROJECT-25730005, KAKENHI-PROJECT-25250028
[Journal Article] A Fixed-Parameter Algorithm for Detecting a Singleton Attractor in an AND/OR Boolean Network with Bounded Treewidth2015
- Author(s)
  Chia-Jung Chang, Takeyuki Tamura, Kun-Mao Chao and Tatsuya Akutsu
- Journal Title
  
  IEICE Trans. Fundamentals
  
  Volume: E98.A Issue: 1 Pages: 384-390
- DOI
  10.1587/transfun.E98.A.384
- NAID
  130004770922
- ISSN
  0916-8508, 1745-1337
- Language
  English
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PROJECT-25730005, KAKENHI-PROJECT-26540125
[Journal Article] Matrix Network: A New Data Structure for Efficient Enumeration of Microstates of a Genetic Regulatory Network2015
- Author(s)
  X. Cong, T. Akutsu
- Journal Title
  
  Journal of Information Processing
  
  Volume: 23 Issue: 6 Pages: 804-813
- DOI
  10.2197/ipsjjip.23.804
- NAID
  130005109167
- ISSN
  1882-6652
- Language
  English
- Peer Reviewed / Acknowledgement Compliant / Open Access
- Data Source
  KAKENHI-PROJECT-26540125, KAKENHI-PROJECT-26240034
[Journal Article] Parallelization of enumerating tree-like chemical compounds by breadth-first search order2015
- Author(s)
  M. Hayashida, J. Jindalertudomdee, Y. Zhao, T. Akutsu
- Journal Title
  
  BMC Medical Genomics
  
  Volume: 8 (Suppl 2) Issue: S2
- DOI
  10.1186/1755-8794-8-s2-s15
- NAID
  120005947140
- Peer Reviewed / Acknowledgement Compliant / Open Access
- Data Source
  KAKENHI-PROJECT-26240034, KAKENHI-PROJECT-24500361
[Journal Article] Proteome Compression via Protein Domain Compositions2014
- Author(s)
  Hayashida, M., Ruan, P., Akutsu, T.
- Journal Title
  
  Methods
  
  Volume: 67 Issue: 3 Pages: 380-385
- DOI
  10.1016/j.ymeth.2014.01.012
- NAID
  120005466444
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PROJECT-24500361, KAKENHI-PROJECT-26240034
[Journal Article] Analysis of critical and redundant nodes in controlling directed and undirected complex networks using dominating sets2014
- Author(s)
  J.C. Nacher and T. Akutsu
- Journal Title
  
  Journal of Complex Networks
  
  Volume: 2 Issue: 4 Pages: 394-412
- DOI
  10.1093/comnet/cnu029
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PROJECT-25330351, KAKENHI-PROJECT-26540125
[Journal Article] Efficient Enumeration of Monocyclic Chemical Graphs with Given Path Frequencies2014
- Author(s)
  Masaki Suzuki, Hiroshi Nagamochi, Tatsuya Akutsu
- Journal Title
  
  Journal of Cheminformatics
  
  Volume: 6 Issue: 1 Pages: 31-31
- DOI
  10.1186/1758-2946-6-31
- NAID
  120005456003
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-26240034
[Journal Article] Prediction of heterotrimeric protein complexes by two-phase learning using neighboring kernels2014
- Author(s)
  Peiying Ruan, Morihiro Hayashida, Osamu Maruyama, Tatsuya Akutsu
- Journal Title
  
  BMC Bioinformatics
  
  Volume: 15
- NAID
  120005372925
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22240009
[Journal Article] Prediction of Protein-protein Interaction Strength Using Domain Features with Supervised Regression2014
- Author(s)
  Kamada, M., Sakuma, Y., Hayashida, M., Akutsu, T.
- Journal Title
  
  The Scientific World Journal
  
  Volume: 2014 Pages: 240673-240673
- DOI
  10.1155/2014/240673
- NAID
  120005462601
- Peer Reviewed / Acknowledgement Compliant / Open Access
- Data Source
  KAKENHI-PROJECT-24500361, KAKENHI-PROJECT-26240034
[Journal Article] Approximation and parameterized algorithms for common subtrees and edit distance between unordered trees2013
- Author(s)
  Tatsuya Akutsu, Daiji Fukagawa, Magnus M. Halldorsson, Atsuhiro Takasu, Keisuke Tanaka
- Journal Title
  
  Theoretical Computer Science
  
  Volume: 470 Pages: 10-22
- DOI
  10.1016/j.tcs.2012.11.017
- NAID
  120005241356
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22240009, KAKENHI-PROJECT-23500010, KAKENHI-PROJECT-24240001
[Journal Article] Breadth-first search approach to enumeration of tree-like chemical compounds2013
- Author(s)
  Y. Zhao, M. Hayashida, J. Jindalertudomdee, H. Nagamochi and T. Akutsu
- Journal Title
  
  Journal of Bioinformatics and Computational Biology
  
  Volume: 11 Issue: 06 Pages: 1143007-1143007
- DOI
  10.1142/s0219720013430075
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-13J02920, KAKENHI-PROJECT-22240009
[Journal Article] Prediction of protein-RNA residue-base contacts using two-dimensional conditional random field with the lasso2013
- Author(s)
  Morihiro Hayashida, Mayumi Kamada, Jiangning Song, Tatsuya Akutsu
- Journal Title
  
  BMC Systems Biology
  
  Volume: 7
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22240009
[Journal Article] Prediction of heterodimeric protein complexes from weighted protein-protein interaction networks using novel features and kernel functions2013
- Author(s)
  Peiying Ruan, Morihiro Hayashida, Osamu Maruyama, Tatsuya Akutsu
- Journal Title
  
  PLoS ONE
  
  Volume: 8 Issue: 6 Pages: e65265-e65265
- DOI
  10.1371/journal.pone.0065265
- NAID
  120005296009
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22240009, KAKENHI-PROJECT-24500361
[Journal Article] A polynomial-time algorithm for computing the maximum common connected edge subgraph of outerplanar graphs of bounded degree2013
- Author(s)
  Tatsuya Akutsu, Takeyuki Tamura
- Journal Title
  
  Algorithms
  
  Volume: 6 Issue: 1 Pages: 119-135
- DOI
  10.3390/a6010119
- NAID
  120005243648
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22240009, KAKENHI-PROJECT-23700017
[Journal Article] Flux balance impact degree : a new definition of impact degree to properly treat reversible reactions in metabolic networks2013
- Author(s)
  Y. Zhao, T. Tamura, T. Akutsu and J-P. Vert
- Journal Title
  
  Bioinformatics
  
  Volume: 29 Issue: 17 Pages: 2178-2185
- DOI
  10.1093/bioinformatics/btt364
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-13J02920, KAKENHI-PROJECT-22240009
[Journal Article] Comparison and enumeration of chemical graphs2013
- Author(s)
  Tatsuya Akutsu, Hiroshi Nagamochi
- Journal Title
  
  Computational and Structural Biotechnology Journal
  
  Volume: 5 Issue: 6 Pages: e201302004-e201302004
- DOI
  10.5936/csbj.201302004
- NAID
  120005243649
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22240009
[Journal Article] Analysis of the impact degree distribution in metabolic networks using branching process approximation2012
- Author(s)
  K. Takemoto, T. Tamura, Y. Cong,W-K. Ching, J-P. Vert, T. Akutsu
- Journal Title
  
  Physica A
  
  Volume: 391 Issue: 1-2 Pages: 379-397
- DOI
  10.1016/j.physa.2011.08.011
- NAID
  120003497116
- Data Source
  KAKENHI-PROJECT-22650045
[Journal Article] Protein complex prediction via improved verification methods using constrained domain-domain matching2012
- Author(s)
  Zhao, Y., Hayashida, M., Nacher, J. C., Nagamochi, H. and Akutsu, T
- Journal Title
  
  International Journal of Bioinformatics Research and Applications
  
  Volume: vol. 8 Issue: 3/4 Pages: 210-227
- DOI
  10.1504/ijbra.2012.048970
- NAID
  120005243442
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-21700323, KAKENHI-PROJECT-22240009
[Journal Article] Two-level support vector regression approach for protein backbone torsion angle prediction from primary sequences2012
- Author(s)
  J.Song, H.Tan, M.Wang, G.I.Webb, T.Akutsu
- Journal Title
  
  PLoS ONE
  
  Volume: 7 Issue: 2 Pages: e30361-e30361
- DOI
  10.1371/journal.pone.0030361
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22240009
[Journal Article] A Clique-Based Method Using Dynamic Programming for Computing Edit Distance Between Unordered Trees2012
- Author(s)
  Tomoya Mori, Takeyuki Tamura, Daiji Fukagawa, Atsuhiro Takasu, Etsuji Tomita, Tatsuya Akutsu
- Journal Title
  
  Journal of Computational Biology
  
  Volume: 19(10) Issue: 10 Pages: 1089-1104
- DOI
  10.1089/cmb.2012.0133
- NAID
  120004920413
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-21700178, KAKENHI-PROJECT-22240009, KAKENHI-PROJECT-23700017
[Journal Article] Dominating scale-free networks with variable scaling exponent: Heterogeneous networks are notdifficult to control2012
- Author(s)
  J. C. Nacher, T. Akutsu
- Journal Title
  
  New Journal of Physics
  
  Volume: 14 Issue: 7 Pages: 73005-73005
- DOI
  10.1088/1367-2630/14/7/073005
- NAID
  120004419126
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22650045
[Journal Article] Network completion using dynamic programming and least-squares fitting2012
- Author(s)
  N. Nakajima, T. Tamura, Y. Yamanishi, K. Horimoto, T. Akutsu
- Journal Title
  
  The Scientific World Journal
  
  Volume: 2012 Pages: 957620-957620
- DOI
  10.1100/2012/957620
- NAID
  120005054551
- Data Source
  KAKENHI-PROJECT-22650045, KAKENHI-PROJECT-23700017
[Journal Article] Singleton and 2-periodic attractors of sign-definite Boolean networks2012
- Author(s)
  T. Akutsu, A. A. Melkman, T. Tamura
- Journal Title
  
  Information Processing Letters
  
  Volume: 112 Issue: 1-2 Pages: 35-38
- DOI
  10.1016/j.ipl.2011.10.002
- Data Source
  KAKENHI-PROJECT-22650045, KAKENHI-PROJECT-23700017
[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] Finding a periodic attractor of a Boolean network2012
- Author(s)
  T. Akutsu, S. Kosub, A. A. Melkman, T.Tamura
- Journal Title
  
  IEEE/ACM Transactions on Computational Biology and Bioinformatics
  
  Volume: 9 Issue: 5 Pages: 1410-1421
- DOI
  10.1109/tcbb.2012.87
- NAID
  120004873985
- Data Source
  KAKENHI-PROJECT-22650045, KAKENHI-PROJECT-23700017
[Journal Article] Inferring a graph from path frequency2012
- Author(s)
  Tatsuya Akutsu, Daiji Fukagawa, Jesper Jansson, Kunihiko Sadakane
- Journal Title
  
  Discrete Applied Mathematics
  
  Volume: 160 Issue: 10-11 Pages: 1416-1428
- DOI
  10.1016/j.dam.2012.02.002
- NAID
  120004057190
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22240009, KAKENHI-PROJECT-23240002
[Journal Article] Integer Programming-Based Approach to Attractor Detection and Control of Boolean Networks2012
- Author(s)
  T. Akutsu, Y. Zhao, M. Hayashida, T.Tamura
- Journal Title
  
  IEICE Trans. Inf. & Syst.
  
  Volume: E95.D Issue: 12 Pages: 2960-2970
- DOI
  10.1587/transinf.E95.D.2960
- NAID
  10031161464
- ISSN
  0916-8532, 1745-1361
- Language
  English
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22650045, KAKENHI-PROJECT-23700017
[Journal Article] On the degree distribution of projected networks mappedfrom bipartite networks2011
- Author(s)
  J. C. Nacher, T. Akutsu
- Journal Title
  
  Physica A
  
  Volume: 390 Issue: 23-24 Pages: 4636-4651
- DOI
  10.1016/j.physa.2011.06.073
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22650045, KAKENHI-PROJECT-23700352
[Journal Article] Determining a singletonattractor of a Boolean network with nested canalyzing functions2011
- Author(s)
  T. Akutsu, A. A. Melkman, T. Tamura, M. Yamamoto
- Journal Title
  
  Journal of Computational Biology
  
  Volume: 18 Issue: 10 Pages: 1275-1290
- DOI
  10.1089/cmb.2010.0281
- NAID
  120003517916
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22650045
[Journal Article] Using binding profiles to predict RNA binding sites of target RNAs2011
- Author(s)
  U.Poolsap, Y.Kato, K.Sato, T.Akutsu
- Journal Title
  
  Tournal of Bioinformatics and Computational Biology
  
  Volume: 9 Issue: 06 Pages: 697-713
- DOI
  10.1142/s0219720011005628
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22240009, KAKENHI-PROJECT-22700305, KAKENHI-PROJECT-22700313, KAKENHI-PROJECT-23650153
[Journal Article] Efficient enumeration of stereoisomers of outerplanar chemical graphs using dynamic programming2011
- Author(s)
  T.Imada, S.Ota, H.Nagamochi, T.Akutsu
- Journal Title
  
  Journal of Chemical Information and Modeling
  
  Volume: 51 Issue: 11 Pages: 2788-2807
- DOI
  10.1021/ci200084b
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22240009
[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] Efficient enumeration of stereoisomers of tree structured molecules using dynamic programming2011
- Author(s)
  T.Imada, S.Ota, H.Nagamochi, T.Akutsu
- Journal Title
  
  Journal of Mathematical Chemistry
  
  Volume: 49 Pages: 910-970
- NAID
  120003001339
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22240009
[Journal Article] Kernel Methods for Chemical Compounds: From Classification to Design2011
- Author(s)
  T.Akutsu, H.Nagamochi
- Journal Title
  
  IEICE Trans. Inf. & Syst.
  
  Volume: E94-D Issue: 10 Pages: 1846-1853
- DOI
  10.1587/transinf.E94.D.1846
- NAID
  10030193064
- ISSN
  0916-8532, 1745-1361
- Language
  English
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22240009
[Journal Article] An Efficient Method of Computing Impact Degrees for Multiple Reactions in Metabolic Networks with Cycles2011
- Author(s)
  T. Tamura, Y. Cong, T. Akutsu, W-K. Ching
- Journal Title
  
  IEICE Trans. Inf. & Syst.
  
  Volume: E94-D Issue: 12 Pages: 2393-2399
- DOI
  10.1587/transinf.E94.D.2393
- NAID
  10030538036
- ISSN
  0916-8532, 1745-1361
- Language
  English
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22650045, KAKENHI-PROJECT-23700017
[Journal Article] Conditional random field approach to prediction of protein-protein interactions using domain information2011
- Author(s)
  Hayashida, M., Kamada, M., Song, J. and Akutsu, T
- Journal Title
  
  BMC Systems Biology
  
  Volume: vol. 5, Suppl. 1 Issue: Suppl 1 Pages: S8-S8
- DOI
  10.1186/1752-0509-5-s1-s8
- NAID
  120003238942
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-21700323, KAKENHI-PROJECT-22240009
[Journal Article] Enumerating tree-like chemical graphs with given upper and lower bounds on path frequencies2011
- Author(s)
  M.Shimizu, H.Nagamochi, T.Akutsu
- Journal Title
  
  BMC Bioinformatics
  
  Volume: 12 Issue: S14
- DOI
  10.1186/1471-2105-12-s14-s3
- NAID
  120004770232
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22240009
[Journal Article] Cascleave : towards more accurate prediction of caspase substrate cleavage sites2010
- Author(s)
  J.Song, H.Tan, H.Shen, K.Mahmood, S.E.Boyd, G.I.Webb, T.Akutsu, J.C.Whisstock
- Journal Title
  
  Bioinfornatics 26
  
  Pages: 752-760
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19200022
[Journal Article] RactIP : fast and accurate prediction of RNA-RNA interaction using integer programming2010
- Author(s)
  Y.Kato, K.Sato, M.Hamada, Y.Watanabe, K.Asai, T.Akutsu
- Journal Title
  
  Bioinformatics
  
  Volume: 26
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22240009
[Journal Article] Approximating tree edit distance through string edit distance2010
- Author(s)
  T.Akutsu, D.Fukagawa, A.Takasu
- Journal Title
  
  Algorithmica 57
  
  Pages: 325-348
- NAID
  120002141662
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19650053
[Journal Article] Compound analysis via graph kernels incorporating chirality2010
- Author(s)
  J.B.Brown, T.Urata, T.Tamura, M.A.Arai, T.Kawabata, T.Akutsu
- Journal Title
  
  Journal of Bioinformatics and Computational Biology
  
  Volume: 8(Suppl.1) Pages: 63-81
- NAID
  120002709552
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22240009
[Journal Article] Branch-and-bound algorithms forenumerating treelike chemical graphswith given path frequency usingdetachment-cut2010
- Author(s)
  Y.Ishida, Y.Kato, L.Zhao, H.Nagamochi, T.Akutsu
- Journal Title
  
  Journal of ChemicalInformation and Modeling 50
  
  Pages: 934-946
- Data Source
  KAKENHI-PROJECT-19200022
[Journal Article] Tree edit distance problems : algorithms and applications to bioinformatics2010
- Author(s)
  T.Akutsu
- Journal Title
  
  IEICE Transactions on Information and Systems E93-D
  
  Pages: 208-218
- NAID
  10026813476
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19650053
[Journal Article] Integer programming-based method for grammar-based tree compression and its application to pattern extraction of glycan tree structures2010
- Author(s)
  Y.Zhao, M.Hayashida, T.Akutsu
- Journal Title
  
  BMC Bioinformatics
  
  Volume: 11(Suppl.11)
- NAID
  120002723148
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22240009
[Journal Article] Exact algorithms for finding a minimum reaction cut under a Boolean model of metabolic networks2010
- Author(s)
  T. Tamura and T. Akutsu
- Journal Title
  
  IEICE Trans. Fundamentals
  
  Volume: E93-A Pages: 1497-1507
- NAID
  10027367933
- Data Source
  KAKENHI-PROJECT-22650045
[Journal Article] Exact algorithms for finding a minimum reaction cut under a Boolean model of metabolic networks2010
- Author(s)
  T.Tamura, T.Akutsu
- Journal Title
  
  IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences
  
  Volume: E93-A Pages: 1497-1507
- NAID
  10027367933
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22650045
[Journal Article] A bisection algorithm for grammar-based compression of ordered trees2010
- Author(s)
  T.Akutsu
- Journal Title
  
  Information Processing Letters
  
  Volume: 110 Pages: 815-820
- NAID
  120002949715
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22240009
[Journal Article] Branch-and-bound algorithms for enumerating treelike chemical graphs with given path frequency using detachment-cut2010
- Author(s)
  Y.Ishisa, Y.Kato, L.Zhao, H.Nagamochi, T.Akutsu
- Journal Title
  
  Journal of Chemical Information and Modeling 50(採録決定)
  
  Pages: 834-946
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19200022
[Journal Article] Determining a singleton attractor of an AND/OR Boolean network in O(1.587^n) time2010
- Author(s)
  A. A. Melkman, T. Tamura and T. Akutsu
- Journal Title
  
  Information Processing Letters
  
  Volume: 110 Issue: 14-15 Pages: 565-569
- DOI
  10.1016/j.ipl.2010.05.001
- Data Source
  KAKENHI-PROJECT-22650045
[Journal Article] Comparing biological networks via graph compression2010
- Author(s)
  M.Hayashida, T.Akutsu
- Journal Title
  
  BMC Systems Biology
  
  Volume: 4(Suppl.2)
- NAID
  120002561281
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22240009
[Journal Article] A mathematical model for the detection mechanism of DNA double-strand breaks depending on autophosphorylation of ATM2009
- Author(s)
  K.Mouri, J.C.Nacher, T.Akutsu
- Journal Title
  
  PLoS ONE
  
  Volume: 4
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17017019
[Journal Article] Constant factor approximation of edit distance of bounded height unordered trees2009
- Author(s)
  D.Fukagawa, T.Akutsu, A.Takasu
- Journal Title
  
  Lecture Notes in Computer Science 5721
  
  Pages: 7-17
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19650053
[Journal Article] Enumerating stereoisomers of tree structured molecules using dynamic programming2009
- Author(s)
  T.Imada, S.Ota, H.Nagamochi, T.Akutsu
- Journal Title
  
  Lecture Notes in Computer Science 5878
  
  Pages: 14-23
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19200022
[Journal Article] Comparing biological networks via graph compression2009
- Author(s)
  M.Hayashida, T.Akutsu
- Journal Title
  
  Lecture Notes in Operations Research 11
  
  Pages: 168-176
- NAID
  120002561281
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19650053
[Journal Article] Distribution and enumeration of attractors in probabilistic Boolean networks2009
- Author(s)
  M.Hayashida, T.Tamura, T.Akutsu, W-K.Ching, Y.Cong
- Journal Title
  
  IET Systems Biology
  
  Volume: 3 Pages: 465-474
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17017019
[Journal Article] A grammatical approach to RNA-RNA interaction prediction2009
- Author(s)
  Y.Kato, T.Akutsu, H.Seki
- Journal Title
  
  Pattern Recognition 42
  
  Pages: 531-538
- Data Source
  KAKENHI-PROJECT-19200022
[Journal Article] Detecting a singleton attractor in a Boolean network utilizing SAT algorithms2009
- Author(s)
  T. Tamura and T. Akutsu
- Journal Title
  
  IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences E92-A
  
  Pages: 493-501
- NAID
  10026855697
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17017019
[Journal Article] Finding minimum reaction cuts of metabolic networks under a Boolean model using integer programming and feedback vertex sets2009
- Author(s)
  T.Tamura, K.Takemoto, T.Akutsu
- Journal Title
  
  International Journal of Knowledge Discovery in Bioinformatics
  
  Volume: 1 Pages: 14-31
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17017019
[Journal Article] Algorithms for singleton attractor detection in planar and nonplanar AND/OR Boolean networks2009
- Author(s)
  T.Tamura, T.Akutsu
- Journal Title
  
  Mathematics in Computer Science
  
  Volume: 2 Pages: 401-420
- NAID
  120001921981
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17017019
[Journal Article] Dynamic programming algorithms and grammatical modeling for protein beta-sheet prediction2009
- Author(s)
  Y.Kato, T.Akutsu, H.Seki
- Journal Title
  
  Journal of Computational Biology 16
  
  Pages: 945-957
- Data Source
  KAKENHI-PROJECT-19200022
[Journal Article] Prodepth : predict residue depth by support vector regression approach from sequences only2009
- Author(s)
  J.Song, H.Tan, K.Mamhood, R.H.P Law, A.M.Buckle, G.I.Webb, T.Akutsu, J.C.Whisstock
- Journal Title
  
  PLoS ONE 4
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19200022
[Journal Article] Optimal control policy for probabilistic Boolean networks with hard constraints2009
- Author(s)
  W-K. Ching, S-Q. Zhang, Y. Jiao, T. Akutsu, N-K. Tsing and A.S. Wong
- Journal Title
  
  IET Systems Biology 3
  
  Pages: 90-99
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17017019
[Journal Article] Enumerating stereoisomers of tree structured molecules using dynamic programming2009
- Author(s)
  T. Imada, S. Ota, H. Nagamochi, T. Akutsu
- Journal Title
  
  Lecture Notes in Computer Science No. 5878
  
  Pages: 14-23
- Data Source
  KAKENHI-PROJECT-19200022
[Journal Article] Identification of novel DNA repair proteins via primary sequence2009
- Author(s)
  J. B. Brown, T. Akutsu
- Journal Title
  
  BMC Bioinformatics 10
  
  Pages: 25-25
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19200022
[Journal Article] Prediction of RNA secondary structure with pseudoknots using integer programming2009
- Author(s)
  U. Poolsap, Y. Kato, T. Akutsu
- Journal Title
  
  BMC Bioinformatics 10
- NAID
  110006595413
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19200022
[Journal Article] Emergence of scale-free distribution in protein-protein interaction networks based on random selection of interacting domain pairs2009
- Author(s)
  J. C. Nacher, M. Hayashida and T. Akutsu
- Journal Title
  
  BioSystems 95
  
  Pages: 155-159
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17017019
[Journal Article] Emergence of scale-free distribution in protein-protein interaction networks based on random selection of interacting domain pairs2009
- Author(s)
  Nacher, J.C., Hayashida, M., Akutsu, T.
- Journal Title
  
  Bio Systems 95
  
  Pages: 155-159
- Data Source
  KAKENHI-PROJECT-17017019
[Journal Article] A mathematical model for generating bipartite graphs and its application to protein networks2009
- Author(s)
  J.C.Nacher, T.Ochiai, M.Hayashida, T.Akutsu
- Journal Title
  
  Journal of Physics A : Mathematical and Theoretical
  
  Volume: 42
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17017019
[Journal Article] Enumerating stereoisomers oftree structured molecules usingdynamic programming2009
- Author(s)
  T.Imada, S.Ota, H.Nagamochi, T.Akutsu
- Journal Title
  
  Lecture Notes inComputer Science 5878
  
  Pages: 14-23
- Data Source
  KAKENHI-PROJECT-19200022
[Journal Article] A grammatical approach to RNA-RNA interaction prediction2009
- Author(s)
  Y. Kato, T. Akutsu, H. Seki
- Journal Title
  
  Pattern Recognition 42
  
  Pages: 531-538
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19200022
[Journal Article] A clustering method for analysis of sequence similarity networks of proteins using maximal components of graphs2008
- Author(s)
  M.Hayashida, T.Akutsu, H.Nagamochi
- Journal Title
  
  IPSJ Transactions on Bioinformatics 49-Sig 5
  
  Pages: 15-24
- NAID
  110006684906
- Data Source
  KAKENHI-PROJECT-19200022
[Journal Article] Analyses and algorithms for predecessor and control problems for Boolean networks of bounded indegree2008
- Author(s)
  T. Akutsu, M. Hayashida, S-Q. Zhang, W-K. Ching and M. K. Ng
- Journal Title
  
  IPST Transactions on Bioinformatics 1
  
  Pages: 23-34
- NAID
  130000120676
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17017019
[Journal Article] Enumerating tree-like chemical graphs with given path frequency2008
- Author(s)
  H. Fujiwara, J. Wang, L. Zhao, H. Nagamochi, T. Akutsu
- Journal Title
  
  Journal of Chemical Information and Modeling Vol. 48
  
  Pages: 1345-1357
- Data Source
  KAKENHI-PROJECT-19200022
[Journal Article] Algorithms and complexity analyses for control of singleton attractors in Boolean networks2008
- Author(s)
  M. Hayashida, T. Tamura, T. Akutsu. S-Q. Zhang and W-K. Ching
- Journal Title
  
  EURASIP Journal on Bioinformatics and Systems Biology 2008
- NAID
  120004754352
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17017019
[Journal Article] Enumerating tree-like chemical graphs with given path frequency2008
- Author(s)
  H.Fujiwara, J.Wang, L.Zhao, H.Nagamochi, T.Akutsu
- Journal Title
  
  Journal of Chemical Information and Modeling 48
  
  Pages: 1345-1357
- Data Source
  KAKENHI-PROJECT-19200022
[Journal Article] Origin of structural difference in metabolic networks with respect to temperature2008
- Author(s)
  K. Takemoto and T. Akutsu
- Journal Title
  
  BMC Syslems Biology 2
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17017019
[Journal Article] Improved approximation of the largest common subtree of two unordered trees of bounded height2008
- Author(s)
  T. Akutsu, D. Fukagawa, A. Takasu
- Journal Title
  
  Information Processing Letters 109
  
  Pages: 165-170
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19650053
[Journal Article] Enumerating tree-like chemical graphs with given path frequency2008
- Author(s)
  H. Fujiwara, J. Wang, L. Zhao, H. Nagamochi, T. Akutsu
- Journal Title
  
  Journal of Chemical Information and Modeling 48
  
  Pages: 1345-1357
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19200022
[Journal Article] HSEpred : predict half-sphere exposure from protein sequences2008
- Author(s)
  J. Song, H. Tan, K. Takemoto, T. Akutsu
- Journal Title
  
  Bioinformatics 24
  
  Pages: 1489-1497
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19200022
[Journal Article] 遺伝子制御ネットワークの離散モデルと制御2008
- Author(s)
  阿久津達也
- Journal Title
  
  計測と制御 47
  
  Pages: 664-669
- Data Source
  KAKENHI-PROJECT-17017019
[Journal Article] Image compression-based approach to measuring the similarity of protein structures2008
- Author(s)
  M. Hayashida and T. Akutsu
- Journal Title
  
  Proceedings of the 6th Asia-Pacific Bioinformatics Conference
  
  Pages: 221-230
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19650053
[Journal Article] A grammatical approach to RNA-RNA interaction prediction2008
- Author(s)
  Y. Kato, T. Akutsu, H. Seki
- Journal Title
  
  Pattern Recognition Vol. 42
  
  Pages: 531-538
- Data Source
  KAKENHI-PROJECT-19200022
[Journal Article] Integer programming-based approach to allocation of reporter genes for cell array analysis2008
- Author(s)
  M. Hayashida, F. Sun, S. Aburatani, K. Horimoto and T. Akutsu
- Journal Title
  
  International Journal of Bioinformatics Research and Applications 4
  
  Pages: 385-399
- NAID
  110006402728
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17017019
[Journal Article] A clustering method for analysis of sequence similarity networks of proteins using maximal components of graphs2008
- Author(s)
  M. Hayashida, T. Akutsu and H. Nagamochi
- Journal Title
  
  IPSJ Transactions on Bioinformatics 49-Sig5
  
  Pages: 15-24
- NAID
  110006684906
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19200022
[Journal Article] An approximation method for solving the steady-state probability distribution of probabilistic Boolean networks2007
- Author(s)
  Ching, W-K., Zhang, S-Q., Ng, M. K., and Akutsu, T.
- Journal Title
  
  Bioinformatics 23
  
  Pages: 1511-1518
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17017019
[Journal Article] On the complexity of deriving position specific score matrices from positive and negative sequences2007
- Author(s)
  T. Akutsu, H. Bannai, S. Miyano, S. Ott
- Journal Title
  
  Discrete Applied Mathematics 155
  
  Pages: 676-685
- Description
  「研究成果報告書概要(和文)」より
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] On the complexity of deriving position specific score matrices from positive and negative sequences2007
- Author(s)
  T., Akutsu, H., Bannai, S., Miyano, S., Ott
- Journal Title
  
  Discrete Applied Mathematics 155
  
  Pages: 676-685
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] Emergence of the self-similar property in gene expression dynamics2007
- Author(s)
  Ochiai, T., Nacher, J. C., and Akutsu, T.
- Journal Title
  
  Physica A 382
  
  Pages: 739-752
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17017019
[Journal Article] Subcellular location prediction of proteins using support vector machines with alignment of block sequences utilizing amino acid composition2007
- Author(s)
  T. Tamura and T. Akutsu
- Journal Title
  
  BMC Bioinformatics 8
  
  Pages: 466-466
- NAID
  120004754353
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19200022
[Journal Article] Correlation between structure and temperature in prokaryotic metabolic networks2007
- Author(s)
  Takemoto, K., Nacher, J. C., and Akutsu, T.
- Journal Title
  
  BMC Bioinformatics 8(論文番号)
  
  Pages: 303-303
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17017019
[Journal Article] A novel clustering method for analysis of biological networks using maximal components of graphs2007
- Author(s)
  M.Hayashida, T.Akutsu, H.Nagamochi
- Journal Title
  
  Proc. 5th Asia Pasific Bioinformatics Conference
  
  Pages: 257-266
- NAID
  110004823195
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] Recent progress on the analysis of power-law features in complex cellular networks2007
- Author(s)
  Nacher, J. C., and Akutsu, T.
- Journal Title
  
  Cell Biochemistry and Biophysics 49
  
  Pages: 37-47
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17017019
[Journal Article] A novel clustering method for analysis of biological networks using maximal components of graphs2007
- Author(s)
  M., Hayashida, T., Akutsu, H., Nagamochi
- Journal Title
  
  Proc. 5th Asia-Pacific Bioinformatics Conference (APBC 2007)
  
  Pages: 257-266
- NAID
  110004823195
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] A novel clustering method for analysis of biological networks using maximal components of graphs2007
- Author(s)
  M. Hayashida, T. Akutsu, H. Nagamochi
- Journal Title
  
  Proc. 5th Asia-Pacific Bioinformatics Conference(APBC 2007)
  
  Pages: 257-266
- NAID
  110004823195
- Description
  「研究成果報告書概要(和文)」より
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] Inferring a chemical structure from a feature vector based on frequency of labeled paths and small fragments2007
- Author(s)
  T., Akutsu, D., Fukagawa
- Journal Title
  
  Proc. 5th Asia-Pacific Bioinformatics Conference (APBC 2007)
  
  Pages: 165-174
- NAID
  110004710250
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] Algorithms for finding small attractors in Boolean networks2007
- Author(s)
  Zhang, M-Q., Hayashida, M., Akutsu, T., Ching, W-K., and Ng, M. K.
- Journal Title
  
  EURASIP Journal on Bioinformatics and Systems Biology 2007(論文番号)
  
  Pages: 20180-20180
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17017019
[Journal Article] Inferring a chemical structure from a feature vector based on frequency of labeled paths and small fragments2007
- Author(s)
  T. Akutsu, D. Fukagawa
- Journal Title
  
  Proc. 5th Asia-Pacific Bioinformatics Conference(APBC 2007)
  
  Pages: 165-174
- NAID
  110004710250
- Description
  「研究成果報告書概要(和文)」より
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] Control of Boolean networks: hardness results and algorithms for tree structured networks2007
- Author(s)
  Akutsu, T., Hayashida, M., Ching, W-K., Ng, M.K.
- Journal Title
  
  Journal of Theoretical Biology 24
  
  Pages: 670-679
- Data Source
  KAKENHI-PROJECT-17017019
[Journal Article] Algorithms for point set matching with k-differences2006
- Author(s)
  T. Akutsu
- Journal Title
  
  International Journal of Foundations of Computer Science 17
  
  Pages: 903-917
- Description
  「研究成果報告書概要(和文)」より
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] Optimizing amino acid substitution matrices with a local alignment kernel2006
- Author(s)
  H. Saigo, J-P. Vert, T. Akutsu
- Journal Title
  
  BMG Bioinformatics 7
  
  Pages: 246-246
- NAID
  110004687501
- Description
  「研究成果報告書概要(和文)」より
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] Approximating tree edit distance through string edit distance2006
- Author(s)
  T.Akutsu, D.Fukagawa, A.Takasu
- Journal Title
  
  Lecture Notes in Computer Science 4288
  
  Pages: 90-99
- NAID
  120002141662
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] Algorithms for point set matching with k-differences2006
- Author(s)
  T.Akutsu
- Journal Title
  
  International Journal of Foundations of Computer Science 17
  
  Pages: 903-917
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] A relation between edit distance for ordered trees and edit distance for Euler strings2006
- Author(s)
  T.Akutsu
- Journal Title
  
  Information Processing Letters 100
  
  Pages: 105-109
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] Approximating tree edit distance through string edit distance2006
- Author(s)
  T., Akutsu, D., Fukagawa, A., Takasu
- Journal Title
  
  Proc. 17th International Symposium on Algorithms and Computation (ISAAC 2006), Lecture Notes in Computer Science 4288
  
  Pages: 90-99
- NAID
  120002141662
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] Optimizing amino acid substitution matrices with a local alignment kernel2006
- Author(s)
  H., Saigo, J-P., Vert, T., Akutsu
- Journal Title
  
  BMC Bioinformatics 7
  
  Pages: 246-246
- NAID
  110004687501
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] Fast algorithms for comparison of similar unordered trees2006
- Author(s)
  D., Fukagawa, T., Akutsu
- Journal Title
  
  International Journal of Foundations of Computer Science 17
  
  Pages: 703-729
- NAID
  110003178860
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] Fast algorithms for comparison of similar unordered trees2006
- Author(s)
  D. Fukagawa, T. Akutsu
- Journal Title
  
  International Journal of Foundations of Computer Science 17
  
  Pages: 703-729
- NAID
  110003178860
- Description
  「研究成果報告書概要(和文)」より
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] Approximating tree edit distance through string edit distance2006
- Author(s)
  T. Akutsu, D. Fukagawa, A. Takasu
- Journal Title
  
  Proc. 17th International Symposium on Algorithms and Computation(ISAAC 2006), Lecture Notes in Computer Science 4288
  
  Pages: 90-99
- NAID
  120002141662
- Description
  「研究成果報告書概要(和文)」より
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] Protein domain networks : scale-free mixing of positive and negative exponents2006
- Author(s)
  Nacher, J.C., Hayashida, M., Akutsu, T.
- Journal Title
  
  Physica A 367
  
  Pages: 538-552
- Data Source
  KAKENHI-PROJECT-17017019
[Journal Article] A relation between edit distance for ordered trees and edit distance for Euler strings2006
- Author(s)
  T. Akutsu
- Journal Title
  
  Information Processing Letters 100
  
  Pages: 105-109
- Description
  「研究成果報告書概要(和文)」より
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] Algorithms for point set matching with k-differences2006
- Author(s)
  T., Akutsu
- Journal Title
  
  International Journal of Foundations of Computer Science 17
  
  Pages: 903-917
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] A relation between edit distance for ordered trees and edit distance for Euler strings2006
- Author(s)
  T., Akutsu
- Journal Title
  
  Information Processing Letters 100
  
  Pages: 105-109
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] Identification of metabolic units induced by environmental signals2006
- Author(s)
  Nacher, J.C., Schwartz, J.M., Kanehisa, M., Akutsu, T.
- Journal Title
  
  Bioinformatics 22
- Data Source
  KAKENHI-PROJECT-17017019
[Journal Article] Optimizing amino acid substitution matrices with a local alignment kernel2006
- Author(s)
  H.Saigo, J-P.Vert, T.Akutsu
- Journal Title
  
  BMC Bioinformatics 7
  
  Pages: 246-246
- NAID
  110004687501
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] A stochastic approach to multi-gene expression dynamics2005
- Author(s)
  Ochiai, T.Nacher, J.C., Akutsu, T.
- Journal Title
  
  Physics Letters A 839
  
  Pages: 1-9
- Data Source
  KAKENHI-PROJECT-17017019
[Journal Article] Graph kernels for molecular structure-activity relationship analysis with support vector machines2005
- Author(s)
  P.Mahe, N.Ueda, T.Akutsu, J-L.Perret J-P.Vert
- Journal Title
  
  Journal of Chemical Information and Modeling 45
  
  Pages: 939-951
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] A novel representation of protein sequences for prediction of subcellular location using support vector machines2005
- Author(s)
  S. Matsuda, J-P. Vert, H. Saigo, N. Ueda, H. Toh, T. Akutsu
- Journal Title
  
  Protein Science 14
  
  Pages: 2804-2813
- Description
  「研究成果報告書概要(和文)」より
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] Flexible construction of hierarchical scale-free networks with general exponent2005
- Author(s)
  Nacher, J.C., Ueda, N., Kanehisa, M., Akutsu, T.
- Journal Title
  
  Physical Review E, 71
  
  Pages: 36132-36132
- Data Source
  KAKENHI-PROJECT-17017019
[Journal Article] Fast and accurate database homology search using upper bounds of local alignment scores2005
- Author(s)
  M. Itoh, S. Goto, T. Akutsu, M. Kanehisa
- Journal Title
  
  Bioinformatics 21
  
  Pages: 912-921
- Description
  「研究成果報告書概要(和文)」より
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] A novel representation of protein sequences for prediction of subcellular location using support vector machines2005
- Author(s)
  S., Matsuda, J-P., Vert, H., Saigo, N., Ueda, H., Toh, T.,Akutsu
- Journal Title
  
  Protein Science 14
  
  Pages: 2804-2813
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] Fast and accurate database homology search using upper bounds of local alignment2005
- Author(s)
  Itoh, M., Goto, S., Akutsu, T., Kanehisa, M.
- Journal Title
  
  Bioinformatics 21
  
  Pages: 912-921
- Data Source
  KAKENHI-PROJECT-12208007
[Journal Article] Two complementary representations of a scale-free network2005
- Author(s)
  Nacher, J.C., Yamada, T., Goto, S., Kanehisa, M., Akutsu, T.
- Journal Title
  
  Physica A 349
  
  Pages: 349-363
- Data Source
  KAKENHI-PROJECT-12208007
[Journal Article] Graph kernels for molecular structure-activity relationship analysis with support vector machines2005
- Author(s)
  P. Mahe, T. Akutsu, J-L. Perret, J-P. Vert
- Journal Title
  
  Journal of Chemical Information and Modeling 45
  
  Pages: 939-951
- Description
  「研究成果報告書概要(和文)」より
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] Fast and accurate database homology search using upper bounds of local alignment scores2005
- Author(s)
  M., Itoh, S., Goto, T.,Akutsu, M., Kanehisa
- Journal Title
  
  Bioinformatics 21
  
  Pages: 912-921
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] A novel representation of protein sequences for prediction of subcellular location using support vector machines2005
- Author(s)
  S.Matsuda, J-P.Vert, H.Saigo, N.Ueda, H.Toh, T.Akutsu
- Journal Title
  
  Protein Science 14
  
  Pages: 2804-2813
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] Graph kernels for molecular structure-activity relationship analysis with support vector machines2005
- Author(s)
  P., Mahe, T., Akutsu,J-L., Perret, J-P., Vert
- Journal Title
  
  Journal of Chemical Information and Modeling 45
  
  Pages: 939-951
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] Inferring a graph from path frequency2005
- Author(s)
  T.Akutsu, D.Fukagawa
- Journal Title
  
  Lecture Notes in Computer Science 3537
  
  Pages: 371-382
- NAID
  120004057190
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] Inferring a graph from path frequency2005
- Author(s)
  T. Akutsu, D. Fukagawa
- Journal Title
  
  Proc. 16th Annual Symposium on Combinatorial Pattern Matching(CPM 2005), Lecture Notes in Computer Science 3537
  
  Pages: 371-382
- NAID
  120004057190
- Description
  「研究成果報告書概要(和文)」より
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] On the relation between fluctuations and scaling-law in gene expression series from yeast to human2005
- Author(s)
  Nacher, J.C., Ochiai, T., Akutsu, T.
- Journal Title
  
  Modern Physics Letters B 19
  
  Pages: 1169-1177
- Data Source
  KAKENHI-PROJECT-17017019
[Journal Article] Fast and accurate database homology search using upper bounds of local alignment scores2005
- Author(s)
  M.Itoh, S.Goto, T.Akutsu, M.Kanehisa
- Journal Title
  
  Bioinformatics 21
  
  Pages: 912-921
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] Inferring a graph from path frequency2005
- Author(s)
  T., Akutsu, D., Fukagawa
- Journal Title
  
  Proc. 16th Annual Symposium on Combinatorial Pattern Matching (CPM 2005), Lecture Notes in Computer Science 3537
  
  Pages: 371-382
- NAID
  120004057190
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] Algorithms for point set matching with k-differences2004
- Author(s)
  T., Akutsu
- Journal Title
  
  Proc. 10th Int. Computing and Combinatorics Conference (COCOON 2004), Lecture Notes in Computer Science 3106
  
  Pages: 249-258
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] Algorithms for point set matching with k-differences2004
- Author(s)
  T. Akutsu
- Journal Title
  
  Proc. 10th Int. Computing and Combinatorics Conference(COCOON 2004), Lecture Notes in Computer Science 3106
  
  Pages: 249-258
- Description
  「研究成果報告書概要(和文)」より
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] KCaM (KEGG Carbohydrate Matcher) : a software tool for analyzing the structures of carbohydrate sugar chains2004
- Author(s)
  K.F.Aoki, A.Yamaguchi, N.Ueda, T.Akutsu, et al.
- Journal Title
  
  Nucleic Acids Research 32
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] KCaM(KEGG Carbohydrate Matcher):a software tool for analyzing the structures of carbohydrate sugar chains2004
- Author(s)
  K. F. Aoki, A. Yamaguchi, N. Ueda, T. Akutsu, H. Mamitsuka, S. Goto, M. Kanehisa
- Journal Title
  
  Nucleic Acids Research 32
- Description
  「研究成果報告書概要(和文)」より
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] Extensions of marginalized graph kernels2004
- Author(s)
  P. Mahe, N. Ueda, T. Akutsu, J-L. Perret, J-P. Vert
- Journal Title
  
  Proc. 21st Int. Conf. Machine Learning(ICML 2004)
  
  Pages: 552-559
- Description
  「研究成果報告書概要(和文)」より
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] Algorithms for point set matching with k-differences2004
- Author(s)
  T.Akutsu
- Journal Title
  
  Lecture Notes in Computer Science 3106
  
  Pages: 249-258
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-13680394
[Journal Article] Efficient extraction of mapping rules of atoms from enzymatic reaction data2004
- Author(s)
  T., Akutsu
- Journal Title
  
  Journal of Computational Biology 11
  
  Pages: 449-462
- NAID
  10011887302
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] Efficient extraction of mapping rules of atoms from enzymaticreaction data2004
- Author(s)
  T.Akutsu
- Journal Title
  
  Journal of Computational Biology 11
  
  Pages: 449-462
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] A simple method for inferring strengths of protein-protein interactions2004
- Author(s)
  Hayashida, M., Ueda, N., Akutsu, T.
- Journal Title
  
  Genome Informatics 15・1
  
  Pages: 56-68
- NAID
  130003812081
- Data Source
  KAKENHI-PROJECT-15300099
[Journal Article] A Simple Method for Inferring Strengths of Protein-Protein Interactions2004
- Author(s)
  Hayashida, M., Ueda, N., Akutsu, T
- Journal Title
  
  Genome Informatics 15(1)
  
  Pages: 56-68
- NAID
  130003812081
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-15300099
[Journal Article] Extensions of marginalized graph kernels2004
- Author(s)
  P., Mahe, N., Ueda, T., Akutsu,J-L., Perret, J-P., Vert
- Journal Title
  
  Proc. 21st Int. Conf. Machine Learning (ICML 2004)
  
  Pages: 552-559
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] Fast algorithms for comparison of similar unordered trees2004
- Author(s)
  D. Fukagawa, T. Akutsu
- Journal Title
  
  Proc. 15th Int. Symp. Algorithms and Computation(ISAAC 2004), Lecture Notes in Computer Science 3341
  
  Pages: 452-463
- NAID
  110003178860
- Description
  「研究成果報告書概要(和文)」より
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] Extensions of marginalized graph kernels2004
- Author(s)
  P.Mahe, N.Ueda, T.Akutsu, J-L.Perret, J-P.Vert
- Journal Title
  
  Proc.21st Int.Conf.Machine Learning(ICML 2004)
  
  Pages: 552-559
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] Protein homology detection using string alignment kernels2004
- Author(s)
  H.Saigo, J-P.Vert, N.Ueda, T.Akutsu
- Journal Title
  
  Bioinformatics 20
  
  Pages: 1682-1689
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-13680394
[Journal Article] Fast algorithms for comparison of similar unordered trees2004
- Author(s)
  D., Fukagawa, T.,Akutsu
- Journal Title
  
  Proc. 15th IM. Symp. Algorithms and Computation (ISAAC 2004), Lecture Notes in Computer Science 3341
  
  Pages: 452-463
- NAID
  110003178860
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] A Simple Method for Inferring Strengths of Protein-Protein Interactions.2004
- Author(s)
  Hayashida, M., Ueda, N., Akutsu, T.
- Journal Title
  
  Genome Informatics 15(1)
  
  Pages: 56-68
- NAID
  130003812081
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-15300099
[Journal Article] Fast algorithms for comparison of similar unordered trees2004
- Author(s)
  D.Fukagawa, T.Akutsu
- Journal Title
  
  Lecture Notes in Computer Science 3341
  
  Pages: 452-463
- NAID
  110003178860
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] KCaM (KEGG Carbohydrate Matcher) : a software tool for analyzing the structures of carbohydrate sugar chains2004
- Author(s)
  K.F., Aoki, A., Yamaguchi, N., Ueda, T., Akutsu, H., Mamitsuka, S., Goto, M., Kanehisa
- Journal Title
  
  Nucleic Acids Research 32
  
  Pages: 267-272
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] Efficient extraction of mapping rules of atoms from enzymatic reaction data2004
- Author(s)
  T. Akutsu
- Journal Title
  
  Journal of Computational Biology 11
  
  Pages: 449-462
- NAID
  10011887302
- Description
  「研究成果報告書概要(和文)」より
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] Algorithms for point set matching with k-differences2004
- Author(s)
  T.Akutsu
- Journal Title
  
  Lecture Notes in Computer Science 3106
  
  Pages: 249-258
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] Identification of genetic networks by strategic gene disruptions and gene overexpressions under a boolean model2003
- Author(s)
  T.Akutsu, S.Kuhara, O.Maruyama, S.Miyano
- Journal Title
  
  Theoretical Computer Science 298
  
  Pages: 235-251
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-13680394
[Journal Article] Point matching under non-uniform distortions2003
- Author(s)
  T.Akutsu, K.Kanaya, A.Ohyama, A.Fujiyama
- Journal Title
  
  Discrete Applied Mathematics 127
  
  Pages: 5-21
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-13680394
[Journal Article] Finding optimal degenerated patterns in DNA sequences2003
- Author(s)
  D.Shinozaki, T.Akutsu, O.Maruyama
- Journal Title
  
  Bioinformatics 19
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-13680394
[Journal Article] A simple greedy algorithm for finding functional relations : efficient implementation and average case analysis2003
- Author(s)
  T.Akutsu, S.Miyano, S.Kuhara
- Journal Title
  
  Theoretical Computer Science 292
  
  Pages: 481-495
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-13680394
[Journal Article] Inferring strengths of protein-protein interactions from experimental data using linear programming2003
- Author(s)
  M.Hayashida, N.Ueda, T.Akutsu
- Journal Title
  
  Bioinformatics 19
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-13680394
[Journal Article] Point matching under non-uniform distortions and protein side chain packing based on an efficient maximum clique algorithm2002
- Author(s)
  K.C.D.Bahadur, T.Akutsu, E.Tomita, T.Seki, A.Fujiyama
- Journal Title
  
  Genome Informatics 13
  
  Pages: 143-152
- NAID
  130003997148
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-13680394
[Journal Article] Inferring a union of halfspaces from examples2002
- Author(s)
  T.Akutsu, S.Ott
- Journal Title
  
  Lecture Notes in Computer Science 2387
  
  Pages: 117-126
- NAID
  110002812493
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-13680394
[Journal Article] On the complexity of deriving position specific score matrices from examples2002
- Author(s)
  T.Akutsu, H.Bannai, S.Miyano, S.Ott
- Journal Title
  
  Lecture Notes in Computer Science 2373
  
  Pages: 168-177
- NAID
  110002812473
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-13680394
[Journal Article] A local search algorithm for local multiple alignment : special case analysis and application to cancer classification2001
- Author(s)
  T.Akutsu
- Journal Title
  
  Proc. 2001 Int.Conf. Parallel and Distributed Processing Techniques and Applications
  
  Pages: 1284-1290
- NAID
  110002936539
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-13680394
[Journal Article] Local multiple alignment of numerical sequences : detection of subtle motifs from protein sequences and structures2001
- Author(s)
  T.Akutsu, K.Horimoto
- Journal Title
  
  Genome Informatics 12
  
  Pages: 83-92
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-13680394
[Journal Article] A local search algorithm for local multiple alignment : special case analysis and application to cancer classification2001
- Author(s)
  T.Akutsu
- Journal Title
  
  Proc.2001 International Conference on Parallel and Distributed Processing Techniques and Applications
  
  Pages: 1284-1290
- NAID
  110002936539
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-13680394
[Journal Article] Local multiple alignment of numerical sequences : detection of subtlemotifs from protein sequences and structures2001
- Author(s)
  T.Akutsu, K.Horimoto
- Journal Title
  
  Genome Informatics 12
  
  Pages: 83-92
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-13680394
[Journal Article] On the complexity of deriving position specific score matrices from positive and negative sequences
- Author(s)
  T.Akutsu, H.Bannai, S.Miyano, S.Ott
- Journal Title
  
  Discrete Applied Mathematics (In press)
- Data Source
  KAKENHI-PROJECT-16300092
[Journal Article] Branch-and-bound algorithms for enumerating treelike chemical graphs with given path frequency using detachment-cut
- Author(s)
  Y. Ishida, Y. Kato, L. Zhao, H. Nagamochi, T. Akutsu
- Journal Title
  
  Journal of Chemical Information and Modeling (in press)
- Data Source
  KAKENHI-PROJECT-19200022
[Presentation] On the Number of Nodes in Autoencoders with Linear Threshold Activation Functions and Random Forests2024
- Author(s)
  Tatsuya Akutsu
- Organizer
  Prediction Science Seminar (Riken)
- Invited
- Data Source
  KAKENHI-PROJECT-22H00532
[Presentation] A Simple and Efficient Method for Target Control Based on the Path Cover Problem2023
- Author(s)
  Someya Wataru, Akutsu Tatsuya, Nacher Jose
- Organizer
  The 12th International Conference on Complex Networks and their Applications
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K19830
[Presentation] Predicting Aqueous Solubility Based on Multiple Linear Regression and Graph Theoretic Features2023
- Author(s)
  Muniba Batool, Naveed Ahmed Azam, Jianshen Zhu, Kazuya Haraguchi, Liang Zhao and Tatsuya Akutsu
- Organizer
  The 6th Conference on Emerging Materials and Processes
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22H00532
[Presentation] ランダムフォレストとMILPを用いた化合物推定法2023
- Author(s)
  武智將平, 朱見深, アザムナビードアフマド, 原口和也, 趙亮, 阿久津達也
- Organizer
  2023年日本オペレーションズ・リサーチ学会秋季研究発表会
- Data Source
  KAKENHI-PROJECT-22H00532
[Presentation] A Deep Learning-Based Approach for Identifying DNA N4-Methylcytosine Sites2023
- Author(s)
  Liu Chunting、Song Jiangning、Ogata Hiroyuki、Akutsu Tatsuya
- Organizer
  2023 13th International Conference on Bioscience, Biochemistry and Bioinformatics
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22H00532
[Presentation] Graph Theoretic Approaches to Analysis of Biological Networks2023
- Author(s)
  Akutsu Tatsuya
- Organizer
  2023 13th International Conference on Biomedical Engineering and Technology (ICBET 2023)
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K19830
[Presentation] A Method for Molecular Design Based on Linear Regression and Integer Programming2022
- Author(s)
  Zhu Jianshen、Azam Naveed A.、Haraguchi Kazuya、Zhao Liang、Nagamochi Hiroshi、Akutsu Tatsuya
- Organizer
  12th International Conference on Bioscience, Biochemistry and Bioinformatics
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H04113
[Presentation] 生体ネットワークの推定と制御のための数理とアルゴリズム2022
- Author(s)
  阿久津達也
- Organizer
  2022年日本バイオインフォマティクス学会年会
- Invited
- Data Source
  KAKENHI-PROJECT-22K19830
[Presentation] Network-based Approaches to Identification of Important Genes and Proteins2022
- Author(s)
  Tatsuya Akutsu
- Organizer
  2022 10th International Conference on Bioinformatics and Computational Biology
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K19830
[Presentation] Adjustive Linear Regression and Its Application to the Inverse QSAR2022
- Author(s)
  Zhu Jianshen、Haraguchi Kazuya、Nagamochi Hiroshi、Akutsu Tatsuya
- Organizer
  15th International Joint Conference on Biomedical Engineering Systems and Technologies - BIOINFORMATICS
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H04113
[Presentation] Network-based Approaches to Identification of Important Genes and Proteins2022
- Author(s)
  Tatsuya Akutsu
- Organizer
  2022 10th International Conference on Bioinformatics and Computational Biology
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22H00532
[Presentation] On the Compressive Power of Boolean Threshold Autoencoders2021
- Author(s)
  Tatsuya Akutsu
- Organizer
  The 1st Online Conference on Algorithms
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H04113
[Presentation] Control and Observation of Boolean Networks when Targets are Restricted to Attractors2021
- Author(s)
  Tatsuya Akutsu
- Organizer
  Modeling and Control of Boolean Dynamical Systems (Workshop in European Control Conference 2021)
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H04113
[Presentation] An Inverse QSAR Method Based on Decision Tree and Integer Programming2021
- Author(s)
  Tanaka Kouki、Zhu Jianshen、Azam Naveed Ahmed、Haraguchi Kazuya、Zhao Liang、Nagamochi Hiroshi、Akutsu Tatsuya
- Organizer
  17th International Conference on Intelligent Computing
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H04113
[Presentation] Graph Theoretic Approaches to Analysis and Control of Biological Networks2021
- Author(s)
  Tatsuya Akutsu
- Organizer
  2021 IEEE the 9th International Conference on Bioinformatics and Computational Biology
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H04113
[Presentation] An Improved Integer Programming Formulation for Inferring Chemical Compounds with Prescribed Topological Structures2021
- Author(s)
  Zhu Jianshen、Azam Naveed Ahmed、Haraguchi Kazuya、Zhao Liang、Nagamochi Hiroshi、Akutsu Tatsuya
- Organizer
  34th International Conference on Industrial, Engineering and Other Applications of Applied Intelligent Systems
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H04113
[Presentation] 機械学習QSARの整数計画法に基づく逆解析法2021
- Author(s)
  NAGAMOCHI Hiroshi、ZHU Jianshen、AZAM Naveed Ahmed、HARAGUCHI Kazuya、ZHAO Liang、AKUTSU Tatsuya
- Organizer
  日本コンピュータ化学会2021年春季年会
- Data Source
  KAKENHI-PROJECT-18H04113
[Presentation] Molecular Design Based on Artificial Neural Networks, Integer Programming and Grid Neighbor Search2021
- Author(s)
  Azam Naveed Ahmed、Zhu Jianshen、Haraguchi Kazuya、Zhao Liang、Nagamochi Hiroshi、Akutsu Tatsuya
- Organizer
  2021 IEEE International Conference on Bioinformatics and Biomedicine
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H04113
[Presentation] A New Integer Linear Programming Formulation to the Inverse QSAR/QSPR for Acyclic Chemical Compounds Using Skeleton Trees2020
- Author(s)
  F. Zhang, J. Jianshen, R. Chiewvanichakorn , A. Shurbevski, H. Nagamochi, T. Akutsu
- Organizer
  33rd International Conference on Industrial, Engineering and Other Applications of Applied Intelligent Systems (IEA/AIE 2020)
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H04113
[Presentation] A method for the inverse QSAR/QSPR based on artificial neural networks and mixed integer linear programming2020
- Author(s)
  R. Chiewvanichakorn, C. Wang, Z. Zhan, A. Shurbevski, H. Nagamochi, T. Akutsu
- Organizer
  12th International Conference on Bioscience, Biochemistry and Bioinformatics
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H04113
[Presentation] A novel method for the inverse QSAR/QSPR based on artificial neural networks and mixed integer linear programming with guaranteed admissibility2020
- Author(s)
  N. A. Azam, R. Chiewvanichakorn, F. Zhang, A. Shurbevski, H. Nagamochi, T. Akutsu
- Organizer
  13th International Joint Conference on Biomedical Engineering Systems and Technologies
- Data Source
  KAKENHI-PROJECT-18H04113
[Presentation] A novel method for the inverse QSAR/QSPR to monocyclic chemical compounds based on artificial neural networks and integer programming2020
- Author(s)
  R. Ito, N. A. Azam, C. Wang, A. Shurbevski, H. Nagamochi, T. Akutsu
- Organizer
  21st International Conference on Bioinformatics & Computational Biology
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H04113
[Presentation] A method for the inverse QSAR/QSPR based on artificial neural networks and mixed integer linear programming2019
- Author(s)
  R. Chiewvanichakorn, C. Wang, Z. Zhan, A. Shurbevski, H. Nagamochi, T. Akutsu
- Organizer
  第123回MPS・第58回BIO合同研究発表会
- Data Source
  KAKENHI-PROJECT-18H04113
[Presentation] Graph theoretic approaches to controllability of biological networks2019
- Author(s)
  T. Akutsu
- Organizer
  Workshop on Bioinformatics and Data Analysis
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H04113
[Presentation] Integration and Analysis of Heterogeneous Biological Data via Convolutional Neural Networks and Matrix Factorization2019
- Author(s)
  Tatsuya Akutsu
- Organizer
  9th International Conference on Bioscience, Biochemistry and Bioinformatics
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H04113
[Presentation] A Mixed Integer Linear Programming Formulation to Artificial Neural Networks2019
- Author(s)
  Tatsuya Akutsu, Hiroshi Nagamochi
- Organizer
  2nd International Conference on Information Science and System
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H04113
[Presentation] 細胞種情報解析における数理モデル概説2019
- Author(s)
  阿久津達也
- Organizer
  第１回　幹細胞情報学イニシアティブ研究会
- Invited
- Data Source
  KAKENHI-PROJECT-18H04113
[Presentation] Grammar-based compression for directed and undirected generalized series-parallel graphs using integer linear programming2018
- Author(s)
  M. Hayashida, H. Koyano, T. Akutsu:
- Organizer
  The 11th International Joint Conference on Biomedical Engineering Systems and Technologies
- Data Source
  KAKENHI-PROJECT-26240034
[Presentation] Deep Learning with Evolutionary and Genomic Profiles for Identifying Cancer Subtypes2018
- Author(s)
  Chun-Yu Lin, Ruiming Li, Tatsuya. Akutsu, Peiyng Ruan, Simon Sea, Jinn-Moon. Yang
- Organizer
  International Workshop on Cancer Bioinformatics and Intelligent Medicine 2018
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H04113
[Presentation] ncRNA-disease association prediction based on sequence information and tripartite network2018
- Author(s)
  T. Mori, H. Ngouv, M. Hayashida, T. Akutsu and J. Nacher
- Organizer
  The Sixteenth Asia Pacific Bioinformatics Conference
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-26240034
[Presentation] Convolutional Neural Network Approach to Lung Cancer Classification Integrating Protein Interaction Network and Gene Expression Profiles2018
- Author(s)
  Teppei Matsubara, Jose C. Nacher, Tomoshiro Ochiai, Morihiro Hayashida, Tatsuya Akutsu
- Organizer
  International Workshop on Cancer Bioinformatics and Intelligent Medicine 2018
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H04113
[Presentation] New and Improved Algorithms for Unordered Tree Inclusion2018
- Author(s)
  Tatsuya Akutsu, Jesper Jansson, Ruiming Li, Atsuhiro Takasu, Takeyuki Tamura
- Organizer
  29th International Symposium on Algorithms and Computation
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H04113
[Presentation] Resource cut, a new bounding procedure to algorithms for Enumerating tree-like chemical graphs2018
- Author(s)
  Y. Nishiyama, A. Shurbevski, H. Nagamochi and T. Akutsu
- Organizer
  The Sixteenth Asia Pacific Bioinformatics Conference
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-26240034
[Presentation] Algorithms for Analysis and Control of Boolean Networks2018
- Author(s)
  Tatsuya Akutsu
- Organizer
  5th International Conference on Algorithms for Computational Biology
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H04113
[Presentation] Deep Learning with Evolutionary and Genomic Profiles for Identifying Cancer Subtypes2018
- Author(s)
  Lin, C. Y., Ruan, P. Y., Li, R. M., Yang, J. M., See S., and Akutsu, T.
- Organizer
  IEEE 18th International Conference on BioInformatics and BioEngineering
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-17F17353
[Presentation] Pan-cancer module network analysis for identifying dominating networks across human cancers2018
- Author(s)
  Lin, C. Y., Yang, J. M., and Akutsu, T.
- Organizer
  The 7th joint Conference on Informatics In Biology, Medicine and Pharmacology
- Data Source
  KAKENHI-PROJECT-17F17353
[Presentation] Enumerating chemical mono-block 3-augmented trees with two junctions2018
- Author(s)
  Y. Tamura, A. Shurbevski, H. Nagamochi, and T. Akutsu
- Organizer
  The 8th International Conference on Bioscience, Biochemistry and Bioinformatics
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-26240034
[Presentation] 最小支配集合に基づく有向生体ネットワーク解析のための高速アルゴリズム2017
- Author(s)
  石塚雅之, 阿久津達也, ナチェルホセ
- Organizer
  情報処理学会第113回MPS・第50回BIO合同研究発表会
- Data Source
  KAKENHI-PROJECT-26540125
[Presentation] On the minimum number of genes required for discriminating steady states under a Boolean model2017
- Author(s)
  X. Cheng, T. Tamura, W-K. Ching, T. Akutsu
- Organizer
  情報処理学会第51回バイオ情報学研究会
- Data Source
  KAKENHI-PROJECT-26540125
[Presentation] 最小支配集合に基づく有向生体ネットワーク解析のための高速アルゴリズム2017
- Author(s)
  石塚雅之, 阿久津達也, ナチェルホセ
- Organizer
  情報処理学会第113回MPS・第50回BIO合同研究発表会
- Data Source
  KAKENHI-PROJECT-26240034
[Presentation] The 28th International Conference on Genome Informatics2017
- Author(s)
  P. Ruan, M. Hayashida, T. Akutsu and J-P. Vert
- Organizer
  Improving prediction of heterodimeric protein complexes using combination with pairwise kernel
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-26240034
[Presentation] On exact identification of the structure of a probabilistic Boolean threshold network from samples2017
- Author(s)
  A. A. Melkman, X. Cheng, W-K. Ching, T. Akutsu
- Organizer
  情報処理学会第113回MPS・第50回BIO合同研究発表会
- Data Source
  KAKENHI-PROJECT-26540125
[Presentation] A short review of methods for Caspase cleavage site prediction2017
- Author(s)
  B. Yu、M. Simone、T. Takeyuki、K. Mayumi、M. Shingo、H. Hiroshi、S. Jiangning、T. Akutsu
- Organizer
  情報処理学会第51回バイオ情報学研究会
- Data Source
  KAKENHI-PROJECT-26240034
[Presentation] Data Fusion for cleavage target prediction2016
- Author(s)
  S.Marini, A. Demartini, F. Vitali, R. Bellazzi, T. Akutsu
- Organizer
  Bioinformatics Italian Society National Congress
- Place of Presentation
  University of Salerno, Italy
- Year and Date
  2016-06-15
- Data Source
  KAKENHI-PROJECT-15F15788
[Presentation] Extensions and Applications of the Minimum Dominating Set-Based Approach to Controllability of Complex Networks2016
- Author(s)
  T. Akutsu
- Organizer
  Controlling Complex Networks (Satellite Symposium of International School and Conference on Network Science)
- Place of Presentation
  韓国・ソウル・K-Hotel
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-26540125
[Presentation] Minimum Dominating Set-based Approaches for Analyzing and Controlling Biological Networks2016
- Author(s)
  T. Akutsu
- Organizer
  第26回日本数理生物学会大会
- Place of Presentation
  九州大学伊都キャンパス
- Invited
- Data Source
  KAKENHI-PROJECT-26540125
[Presentation] Minimum Dominating Set-based Approaches for Analyzing and Controlling Biological Networks2016
- Author(s)
  T. Tamura, C-Y. Lin, J-M. Yang, T. Akutsu
- Organizer
  IEEE 16th International Conference on Bioinformatics and Bioengineering
- Place of Presentation
  台湾・台中・Sprendor Hotel
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-26240034
[Presentation] Finding Influential Genes Using Gene Expression Data and Boolean Models of Metabolic Networks2016
- Author(s)
  T. Tamura, C-Y. Lin, J-M. Yang, T. Akutsu
- Organizer
  IEEE 16th International Conference on Bioinformatics and Bioengineering
- Place of Presentation
  台湾・台中・Splendor Hotel
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-26540125
[Presentation] Host-pathogen protein interaction prediction based on local topology structures of a protein interaction network2016
- Author(s)
  J. Jindalertudomdee, M. Hayashida, J. Song, T. Akutsu
- Organizer
  IEEE 16th International Conference on Bioinformatics and Bioengineering
- Place of Presentation
  台湾・台中・Sprendor Hotel
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-26240034
[Presentation] Minimum Dominating Set-Based Approaches for Controlling and Analyzing Biological Networks2016
- Author(s)
  T. Akutsu
- Organizer
  Controlling Complex Network Systems in Biology (Workshop)
- Place of Presentation
  理研和光キャンパス
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-26540125
[Presentation] Minimum Dominating Set-based Approaches for Analyzing and Controlling Biological Networks2016
- Author(s)
  T. Akutsu
- Organizer
  2016 Biotech and Pharmaceutical Service Platform - Biological Network Analysis Conference
- Place of Presentation
  台湾・国立交通大学
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-26540125
[Presentation] On the efficient identification of proteins with control roles in large networks2015
- Author(s)
  M. Ishitsuka, T. Akutsu, J. C. Nacher
- Organizer
  生命医薬情報学連合大会2015年大会
- Place of Presentation
  京都大学宇治キャンパス
- Year and Date
  2015-10-29
- Data Source
  KAKENHI-PROJECT-26240034
[Presentation] Minimum Dominating Set-based Approaches for Analyzing and Controlling Biological Networks2015
- Author(s)
  T. Akutsu
- Organizer
  9th Asian Biophysics Association Symposium
- Place of Presentation
  Shangyu International Hotel, China
- Year and Date
  2015-05-09
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-26540125
[Presentation] Prediction of ncRNA-disease association based on sequence expression and tripartite network2015
- Author(s)
  H. Ngouv, M. Hayashida, J.C. Nacher, T. Akutsu
- Organizer
  生命医薬情報学連合大会2015年大会
- Place of Presentation
  京都大学宇治キャンパス
- Year and Date
  2015-10-29
- Data Source
  KAKENHI-PROJECT-26240034
[Presentation] Integer programming-based method for designing synthetic metabolic networks by Minimum Reaction Insertion in a Boolean Model2015
- Author(s)
  W. Lu, T. Tamura, J. Song, T. Akutsu
- Organizer
  情報処理学会　バイオ情報学研究会
- Place of Presentation
  慶応義塾大学
- Year and Date
  2015-09-12
- Data Source
  KAKENHI-PROJECT-26240034
[Presentation] Minimum Dominating Set-based Approach to Analysis and Control of Biological Networks2015
- Author(s)
  T. Akutsu
- Organizer
  The Protein Network Workshop
- Place of Presentation
  Institute for Mathematical Sciences, NUS, Singapore
- Year and Date
  2015-06-08
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-26540125
[Presentation] non-coding RNA-タンパク質相互作用ネットワークとその制御性の特徴分析2014
- Author(s)
  香々見春菜, 阿久津達也, ホセ・ナチェル
- Organizer
  情報処理学会バイオ情報学研究会
- Place of Presentation
  産業技術総合研究所臨海副都心センター別館
- Year and Date
  2014-12-18
- Data Source
  KAKENHI-PROJECT-26540125
[Presentation] Prediction of heterotrimeric protein complexes by two-phase learning using neighboring kernels2014
- Author(s)
  Peiying Ruan, Morihiro Hayashida, Osamu Maruyama, Tatsuya Akutsu
- Organizer
  The 20th Asia Pacific Bioinformatics Conference
- Place of Presentation
  Fudan University, Shanghai, China
- Data Source
  KAKENHI-PROJECT-22240009
[Presentation] ブーリアントネットワークにおけるアトラクターの検出、観測、制御2014
- Author(s)
  阿久津達也
- Organizer
  日本バイオインフォマティクス学会　生命システム理論研究会
- Place of Presentation
  京都大学 iPS細胞研究所
- Year and Date
  2014-11-18
- Invited
- Data Source
  KAKENHI-PROJECT-26540125
[Presentation] 代謝ネットワークの頑健性解析と化学グラフの比較と列挙2014
- Author(s)
  阿久津達也
- Organizer
  第27期CAMM(コンピュータによる材料開発・物質設計を考える会）本例会
- Place of Presentation
  アイビーホール, 東京
- Invited
- Data Source
  KAKENHI-PROJECT-22240009
[Presentation] ベンゼン環を持つ木状化学構造の幅優先探索による列挙手法2013
- Author(s)
  Jira Jindalertudomdee, 林田守広, 阿久津達也
- Organizer
  第３６回情報化学討論会
- Place of Presentation
  筑波大学
- Data Source
  KAKENHI-PROJECT-22240009
[Presentation] Breadth first search approach to enumeration of tree-like chemical compounds2013
- Author(s)
  Yang Zhao, Morihiro Hayashida, Jira Jindalertudomdee, Hiroshi Nagamochi, Tatsuya Akutsu
- Organizer
  The 24th International Conference on Genome Informatics
- Place of Presentation
  Matrix, Biopolis, Singapore
- Data Source
  KAKENHI-PROJECT-22240009
[Presentation] On the complexity of the maximum common subgraph problem for partial k-trees of bounded degree2012
- Author(s)
  Takeyuki Tamura, Tatsuya Akutsu
- Organizer
  23rd International Symposium on Algorithms and Computation
- Place of Presentation
  National Taiwan University, Taipei, Taiwan
- Data Source
  KAKENHI-PROJECT-22240009
[Presentation] 遺伝子ネットワークと代謝ネットワークの離散数理モデルとその制御2012
- Author(s)
  阿久津達也
- Organizer
  2012年電子情報通信学会総合大会
- Place of Presentation
  岡山大学
- Year and Date
  2012-03-22
- Data Source
  KAKENHI-PROJECT-22650045
[Presentation] 遺伝子ネットワークと代謝ネットワークの離散数理モデルとその制御2012
- Author(s)
  阿久津達也
- Organizer
  2012年電子情報通信学会総合大会
- Place of Presentation
  岡山大学(招待講演)
- Year and Date
  2012-03-22
- Data Source
  KAKENHI-PROJECT-22650045
[Presentation] パス頻度の上下限制約を満たす木状化合物の二段階列挙法2012
- Author(s)
  鈴木政喜, 永持仁, 阿久津達也
- Organizer
  情報処理学会・第28回バイオ情報学研究会
- Place of Presentation
  東北大学
- Year and Date
  2012-03-29
- Data Source
  KAKENHI-PROJECT-22240009
[Presentation] 上下限パス頻度に基づいた環構造を一つ持つ化合物の列挙法2012
- Author(s)
  鈴木政喜, 永持仁, 阿久津達也
- Organizer
  第３５回情報化学討論会
- Place of Presentation
  広島大学
- Data Source
  KAKENHI-PROJECT-22240009
[Presentation] Enumerating chemical graphs of 1-tree structure from given upper and lower bounds on path frequencies2012
- Author(s)
  Masaki Suzuki, Hiroshi Nagamochi, Tatsuya Akutsu
- Organizer
  23rd International Conference on Genome Informatics
- Place of Presentation
  National Cheng Kung University, Tainan, Taiwan
- Data Source
  KAKENHI-PROJECT-22240009
[Presentation] A polynomial-time algorithm for computing the maximum common subgraph of outerplanar graphs of bounded degree2012
- Author(s)
  Takeyuki Tamura, Tatsuya Akutsu
- Organizer
  37th International Symposium on Mathematical Foundations of Computer Science
- Place of Presentation
  Hotel Sorea Regia, Bratislava, Slovakia
- Data Source
  KAKENHI-PROJECT-22240009
[Presentation] Integer programming method for completing ortholog-based gene-protein-reaction network by gene essentiality2012
- Author(s)
  Takeyuki Tamura, Tatsuya Akutsu
- Organizer
  23rd International Conference on Genome Informatics
- Place of Presentation
  National Cheng Kung University, Tainan, Taiwan
- Data Source
  KAKENHI-PROJECT-22650045
[Presentation] Controlling bipartite networks with power-law degree distributions using dominating sets2012
- Author(s)
  Jose C. Nacher, Tatsuya Akutsu
- Organizer
  International Conference on Systems Medicine (SYSMED 2012)
- Place of Presentation
  Carton House Hotel & Conference Centre, Dublin, Ireland
- Data Source
  KAKENHI-PROJECT-22650045
[Presentation] Analysis on controlling complex networks based on dominating sets2012
- Author(s)
  Jose C. Nacher, Tatsuya Akutsu
- Organizer
  International Conference on Mathematical Modeling in Physical Sciences, IC-MSQUARE
- Place of Presentation
  Budapest, Hungary
- Data Source
  KAKENHI-PROJECT-22650045
[Presentation] ブーリアンネットワークとスケールフリーネットワークの制御2012
- Author(s)
  阿久津達也
- Organizer
  計測自動制御学会関西支部物理と情報をつなぐ次世代システム制御研究会
- Place of Presentation
  京都大学
- Year and Date
  2012-10-13
- Data Source
  KAKENHI-PROJECT-22650045
[Presentation] Analyzing metabolic networks using Boolean models2011
- Author(s)
  T.Akutsu
- Organizer
  The International Conference on Computational and Systems Biology 2011
- Place of Presentation
  Great Tang Hotel Shanghai, China(招待講演)
- Year and Date
  2011-10-15
- Data Source
  KAKENHI-PROJECT-22650045
[Presentation] An improved clique-based method for computing edit distance between unordered2011
- Author(s)
  T.Akutsu, T.Mori, T.Tamura, D.Fukagawa, A.Takasu, E.
- Organizer
  The 4th International Workshop on Intelligent Informatics in Biology and Medicine
- Place of Presentation
  Korean Bible University, Seol, Korea
- Year and Date
  2011-06-30
- Data Source
  KAKENHI-PROJECT-22240009
[Presentation] Analyzing metabolic networks using Boolean models2011
- Author(s)
  T. Akutsu
- Organizer
  Modeling andAnalysis in the Life Sciences: A ReaDiLab Conference in Tokyo
- Place of Presentation
  東京大学
- Year and Date
  2011-11-28
- Data Source
  KAKENHI-PROJECT-22650045
[Presentation] Enumerating tree-like chemical graphs with given upper and lower bounds on path frequencies2011
- Author(s)
  M.Shimizu, H.Nagamochi, T.Akutsu
- Organizer
  The 22nd International Conference on Genome Informatics
- Place of Presentation
  Haeundae Grand Hotel, Busan, Korea
- Year and Date
  2011-12-05
- Data Source
  KAKENHI-PROJECT-22240009
[Presentation] Analyzing metabolic networks using Boolean models2011
- Author(s)
  T. Akutsu
- Organizer
  The International Conference on Computational and Systems Biology 2011
- Place of Presentation
  Great Tang Hotel Shanghai, China
- Year and Date
  2011-10-15
- Data Source
  KAKENHI-PROJECT-22650045
[Presentation] Analyzing metabolic networks using Boolean models2011
- Author(s)
  T.Akutsu
- Organizer
  Modeling and Analysis in the Life Sciences : A ReaDiLab Conference in Tokyo
- Place of Presentation
  東京大学大学院数理科学研究科(招待講演)
- Year and Date
  2011-11-28
- Data Source
  KAKENHI-PROJECT-22650045
[Presentation] Inference and enumeration of chemical structures from feature vectors2011
- Author(s)
  T.Akutsu
- Organizer
  IPAM Workshop II : Optimization, Search and Graph-Theoretical Algorithms for Chemical Compound Space
- Place of Presentation
  ULCA, LA, USA
- Year and Date
  2011-04-15
- Data Source
  KAKENHI-PROJECT-22240009
[Presentation] 上下限付きパス頻度に基づく木状化合物の列挙2011
- Author(s)
  清水雅章, 永持仁, 阿久津達也
- Organizer
  情報処理学会バイオ情報学研究会
- Place of Presentation
  京都大学化学研究所
- Year and Date
  2011-03-10
- Data Source
  KAKENHI-PROJECT-22240009
[Presentation] An improved clique-based method for computing edit distance between rooted unordered trees2011
- Author(s)
  森智弥, 田村武幸, 深川大路, 高須淳宏, 富田悦次, 阿久津達也
- Organizer
  情報処理学会・第26回バイオ情報学研究会
- Place of Presentation
  神戸大学
- Year and Date
  2011-09-13
- Data Source
  KAKENHI-PROJECT-22240009
[Presentation] Attractor detection and control of Boolean networks2011
- Author(s)
  T.Akutsu
- Organizer
  International Symposium on Symbolic Systems Biology
- Place of Presentation
  湘南国際村センター
- Year and Date
  2011-11-15
- Data Source
  KAKENHI-PROJECT-22650045
[Presentation] Control of Boolean networks and probabilistic Boolean networks2010
- Author(s)
  T.Akutsu
- Organizer
  2nd Symposium on Systems and Synthetic Biology
- Place of Presentation
  CBRC, Tokyo, Japan(招待講演)
- Year and Date
  2010-10-04
- Data Source
  KAKENHI-PROJECT-22650045
[Presentation] Integer programming-based method for grammar-based tree compression and its application to pattern extraction of glycantree structures2010
- Author(s)
  Y.Zhao, M.Hayashida, T.Akutsu
- Organizer
  The 21st International Conference on Genome Informatics
- Place of Presentation
  The First World Hotel, Hangzhou, China
- Year and Date
  2010-12-16
- Data Source
  KAKENHI-PROJECT-22240009
[Presentation] Algorithmic aspects of analysis and control of Boolean networks2010
- Author(s)
  T. Akutsu
- Organizer
  Every Spring School on Modelling Complex Biological Systems in the Context of Genomics
- Place of Presentation
  Evry, France
- Year and Date
  2010-05-04
- Data Source
  KAKENHI-PROJECT-22650045
[Presentation] Data compression-based approaches to analysis of biological networks2010
- Author(s)
  T.Akutsu
- Organizer
  The 4th International Conference on Computational Systems Biology
- Place of Presentation
  Suzhou University, Suzhou, China(招待講演)
- Year and Date
  2010-09-09
- Data Source
  KAKENHI-PROJECT-22240009
[Presentation] Algorithmic aspects of analysis and control of Boolean networks2010
- Author(s)
  T.Akutsu
- Organizer
  Every Spring School on Modelling Complex Biological Systems in the Context of Genomics
- Place of Presentation
  Evry, France(招待講演)
- Year and Date
  2010-05-04
- Data Source
  KAKENHI-PROJECT-22650045
[Presentation] Compound analysis via graph kernels incorporating chirality2010
- Author(s)
  J.B.Brown, T.Urata, T.Tamura, M.A.Arai, T.Kawabata, T.Akutsu
- Organizer
  The 21st International Conference on Genome Informatics
- Place of Presentation
  The First World Hotel, Hangzhou, China
- Year and Date
  2010-12-16
- Data Source
  KAKENHI-PROJECT-22240009
[Presentation] Control of Boolean networks and probabilistic Boolean networks2010
- Author(s)
  T. Akutsu
- Organizer
  2nd Symposium on Systems and Synthetic Biology
- Place of Presentation
  産業技術総合研究所CBRC, 東京
- Year and Date
  2010-10-04
- Data Source
  KAKENHI-PROJECT-22650045
[Presentation] Dynamic programming algorithms for RNA structure prediction with binding sites2010
- Author(s)
  U.Poolsap, Y.Kato, T.Akutsu
- Organizer
  Pacific Symposium on Biocomputing 2010(PSB 2010)
- Place of Presentation
  Fairmont Orchid, Hawaii, USA
- Year and Date
  2010-01-07
- Data Source
  KAKENHI-PROJECT-19200022
[Presentation] Mathematical models and computational methods for analysis of structures of biological networks2010
- Author(s)
  T.Akutsu
- Organizer
  The 2nd International Conference on Advanced Science and Technology
- Place of Presentation
  Seagaia, Miyazaki, Japan(招待講演)
- Year and Date
  2010-06-25
- Data Source
  KAKENHI-PROJECT-22240009
[Presentation] Finding optimal control policy in probabilistic Boolean networks with hard constraints by using integer programming and dynamic programming2010
- Author(s)
  X.Chen, T.Akutsu, T.Tamura, T., W-K.Ching
- Organizer
  IEEE International Conference on Bioinformatics and Biomedicine 2010
- Place of Presentation
  Hong Kong, China
- Year and Date
  2010-12-19
- Data Source
  KAKENHI-PROJECT-22650045
[Presentation] Integer programming-based methods for attractor detection and control of Boolean networks2009
- Author(s)
  T.Akutsu, M.Hayashida, T.Tamura
- Organizer
  The combined 48th IEEE Conference on Decision and Control and 28th Chinese Control Conference
- Place of Presentation
  Shanghai, China
- Year and Date
  2009-12-17
- Data Source
  KAKENHI-PROJECT-17017019
[Presentation] Enumerating stereoisomers of tree structured molecules using dynanic programming2009
- Author(s)
  T.Imada, S.Ota, H.Nagamochi, T.Akutsu
- Organizer
  20th International Symposium on Algorithms and Computation(ISAAC 2009)
- Place of Presentation
  Ala Moana Hotel, Hawaii, USA
- Year and Date
  2009-12-16
- Data Source
  KAKENHI-PROJECT-19200022
[Presentation] A bipartite graph based model of protein domain networks2009
- Author(s)
  J. Nacher, T. Ochiai, M. Havashida and T. Akutsu
- Organizer
  The First International Conference on Complex Sciences : Theory and Applications
- Place of Presentation
  Shanghai, China
- Year and Date
  2009-02-24
- Data Source
  KAKENHI-PROJECT-17017019
[Presentation] Comparing biological networks via graph compression2009
- Author(s)
  M.Hayashida, T.Akutsu
- Organizer
  3rd International Symposium on Optimization and Systems Biology
- Place of Presentation
  Zhangjiajie, China
- Year and Date
  2009-09-20
- Data Source
  KAKENHI-PROJECT-17017019
[Presentation] 木構造および化学構造に対する特徴ベクトル : 埋め込み、検索、構造推定2009
- Author(s)
  阿久津達也
- Organizer
  第12回情報論的学習理論ワークショップ
- Place of Presentation
  九州大学医学部百年講堂
- Year and Date
  2009-10-20
- Data Source
  KAKENHI-PROJECT-19200022
[Presentation] 木構造および化学構造に対する特徴ベクトル : 埋め込み、検索、構造推定2009
- Author(s)
  阿久津達也
- Organizer
  第12回情報論的学習理論ワークショップ
- Place of Presentation
  九州大学医学部百年講堂
- Year and Date
  2009-10-20
- Data Source
  KAKENHI-PROJECT-19650053
[Presentation] Enumerating stereoisomers of tree structured molecules using dynamic programming2009
- Author(s)
  T.Imada, S.Ota, H.Nagamochi, T.Akutsu
- Organizer
  20th International Symposium on Algorithms and Computation
- Place of Presentation
  Hawaii, USA
- Year and Date
  2009-12-16
- Data Source
  KAKENHI-PROJECT-19200022
[Presentation] 木の文法圧縮を行う分割型アルゴリズム2009
- Author(s)
  阿久津達也
- Organizer
  人工知能学会第77回人工知能基本問題研究会
- Place of Presentation
  北海道大学百年記念会館
- Year and Date
  2009-03-18
- Data Source
  KAKENHI-PROJECT-19650053
[Presentation] 木構造および化学構造に対する特徴ベクトル:埋め込み、検索、構造推定2009
- Author(s)
  阿久津達也
- Organizer
  第12回情報論的学習理論ワークショップ
- Place of Presentation
  九州大学(福岡)
- Year and Date
  2009-10-20
- Data Source
  KAKENHI-PROJECT-19200022
[Presentation] 無順序木の編集距離計算のための厳密アルゴリズム2009
- Author(s)
  阿久津達也, 深川大路, 高須淳宏, 田村武幸
- Organizer
  情報処理学会第129回アルゴリズム研究会
- Place of Presentation
  東芝科学館
- Year and Date
  2009-03-05
- Data Source
  KAKENHI-PROJECT-19650053
[Presentation] 化合物に対するカーネル法 : 分類から設計へ2009
- Author(s)
  阿久津達也
- Organizer
  第41回人工知能学会分子生物情報研究会
- Place of Presentation
  京都大学工学部10号館
- Year and Date
  2009-08-28
- Data Source
  KAKENHI-PROJECT-19200022
[Presentation] 木構造および化学構造に対する特徴ベクトル : 埋め込み、検索、構造推定2009
- Author(s)
  阿久津達也
- Organizer
  第12回情報論的学習理論ワークショップ
- Place of Presentation
  九州大学
- Year and Date
  2009-10-20
- Data Source
  KAKENHI-PROJECT-19200022
[Presentation] Measuring structural robustness of metabolic networks under a Boolean model using integer programming and feedback vertex2009
- Author(s)
  T. Tamura, K. Takemoto and T. Akutsu
- Organizer
  The 2nd International Workshop on Intelligent Informatics in Biology and Medicine
- Place of Presentation
  福岡工業大学
- Year and Date
  2009-03-19
- Data Source
  KAKENHI-PROJECT-17017019
[Presentation] Improved algorithms for enumerating tree-like chemical graphs with given path frequency2008
- Author(s)
  Y. Ishida, L. Zhao, H. Nagamochi, T. Akutsu
- Organizer
  The 19th Int. Conference on Genome Informatics
- Place of Presentation
  Gold Coast, Australia
- Year and Date
  2008-12-01
- Data Source
  KAKENHI-PROJECT-19200022
[Presentation] Structural Analysis of Biological Information Networks2008
- Author(s)
  Tatsuya Akutsu
- Organizer
  RERF Symposium on Bioinformatics
- Place of Presentation
  放射線影響研究所(広島)
- Year and Date
  2008-03-24
- Data Source
  KAKENHI-PROJECT-17017019
[Presentation] 列挙型アルゴリズムのバイオインフォマティクスへの応用2008
- Author(s)
  阿久津達也
- Organizer
  第7回情報科学技術フォーラム
- Place of Presentation
  慶応義塾大学(神奈川)
- Year and Date
  2008-09-02
- Data Source
  KAKENHI-PROJECT-19200022
[Presentation] Improved algorithms for enumerating tree-like chemical graphs with given path frequency2008
- Author(s)
  Y.Ishida, L.Zhao, H.Nagamochi, T.Akutsu
- Organizer
  The 19th Int.Conference on Genome Informatics
- Place of Presentation
  Gold Coast, Australia
- Year and Date
  2008-12-01
- Data Source
  KAKENHI-PROJECT-19200022
[Presentation] An improved algorithm for detecting a singleton attractor in a Boolean network consisting of AND/OR nodes2008
- Author(s)
  T. Tamura and T. Akutsu
- Organizer
  The 3rd International Conference on Algebraic Biology
- Place of Presentation
  Hagenberg, Austria
- Year and Date
  2008-07-31
- Data Source
  KAKENHI-PROJECT-17017019
[Presentation] Detection and enumeration of steady states in biological information networks2008
- Author(s)
  T. Akutsu
- Organizer
  Kyoto RIMS Workshop on Acceleration and Visualization of Computation for Enumeration Problems
- Place of Presentation
  京都大学数理解析研究所
- Year and Date
  2008-09-30
- Data Source
  KAKENHI-PROJECT-17017019
[Presentation] 不斉炭素原子を考慮した化合物に対するグラフカーネル法2008
- Author(s)
  浦田隆史, J.B.Brown, 田村武幸, 川端猛夫, 阿久津達也
- Organizer
  情報処理学会バイオ情報学研究会
- Place of Presentation
  九州大学(福岡)
- Year and Date
  2008-03-04
- Data Source
  KAKENHI-PROJECT-19200022
[Presentation] 列挙型アルゴリズムのバイオインフォマティクスヘの応用2008
- Author(s)
  阿久津達也
- Organizer
  第7回情報科学技術フォーラム
- Place of Presentation
  慶応義塾大学
- Year and Date
  2008-09-02
- Data Source
  KAKENHI-PROJECT-19200022
[Presentation] 遺伝子ネットワークの離散モデルとその制御2008
- Author(s)
  阿久津達也
- Organizer
  第2回SICE生物制御システム調査研究会
- Place of Presentation
  京都工芸繊維大学
- Year and Date
  2008-01-31
- Data Source
  KAKENHI-PROJECT-17017019
[Presentation] 木の編集距離の近似アルゴリズム2008
- Author(s)
  阿久津達也
- Organizer
  日本オペレーシヨンズ・リサーチ学会コンピュテーシヨン研究部会
- Place of Presentation
  京都大学
- Year and Date
  2008-12-04
- Data Source
  KAKENHI-PROJECT-19650053
[Presentation] Prediction of RNA secondary structure with pseudoknots using integer Drogramming2008
- Author(s)
  U. Poolsap, Y. Kato, T. Akutsu
- Organizer
  8th International Workshop on Bioinformatics, Systems Biology
- Place of Presentation
  Berlin, Germany
- Year and Date
  2008-06-08
- Data Source
  KAKENHI-PROJECT-19200022
[Presentation] 化合物に対するカーネル法 -分類から設計へ-2008
- Author(s)
  阿久津達也
- Organizer
  人工知能学会第71回人工知能基本問題研究会
- Place of Presentation
  北海道大学
- Year and Date
  2008-09-18
- Data Source
  KAKENHI-PROJECT-19200022
[Presentation] On distribution and enumeration of attractors in probabilistic Boolean networks2008
- Author(s)
  Akutsu, M Hayashida, T. Tamura and W-K Ching
- Organizer
  ReaDiLab : Mathematical Understanding of Complex Systems arising in Biology and Medicine
- Place of Presentation
  明治大学
- Year and Date
  2008-10-27
- Data Source
  KAKENHI-PROJECT-17017019
[Presentation] 酸化ストレス化におけるアポトーシス制御機構の数理的解明2008
- Author(s)
  毛利一成,J. C. Nacher,阿久津達也
- Organizer
  日本生物物理学会第46回年会
- Place of Presentation
  福岡国際会議場
- Year and Date
  2008-12-03
- Data Source
  KAKENHI-PROJECT-17017019
[Presentation] Algorithms for inference, analysis and control of Boolean networks2008
- Author(s)
  Akutsu, T., Hayashida, M., Tamura, T.
- Organizer
  The 3rd International Conference on Algebraic Biology
- Place of Presentation
  Hagenberg, Austria
- Year and Date
  2008-07-31
- Data Source
  KAKENHI-PROJECT-17017019
[Presentation] Prediction of protein beta-sheets : dynamic programming versus grammatical approach2008
- Author(s)
  Y. Kato, T. Akutsu, H. Seki
- Organizer
  3rd IAPR International Conference on Pattern Recognition in Bioinformatics
- Place of Presentation
  Melbourne, Australia
- Year and Date
  2008-10-15
- Data Source
  KAKENHI-PROJECT-19200022
[Presentation] Improved approximation of the largest common subtree of two unordered trees of bounded height2008
- Author(s)
  T. Akutsu, D. Fukagawa, A. Takasu
- Organizer
  電子情報通信学会コンピューテーション研究会
- Place of Presentation
  九州産業大学
- Year and Date
  2008-05-13
- Data Source
  KAKENHI-PROJECT-19650053
[Presentation] On distribution and enumeration of attractors in probabilistic Boolean networks2008
- Author(s)
  M. Hayashida, T. Tamura, T. Akutsu and W-K Ching
- Organizer
  The 2nd International Symposium on Optimization and Systems Biology
- Place of Presentation
  Lijiang, China
- Year and Date
  2008-11-01
- Data Source
  KAKENHI-PROJECT-17017019
[Presentation] Kernel-based approachs to classification and design of chemical compounds2008
- Author(s)
  T. Akutsu
- Organizer
  The 2nd Taiwan-Japan Young Researchers Conferenceon Computational and Systems Biology
- Place of Presentation
  産業技術総合研究所生命情報工学研究センター
- Year and Date
  2008-11-05
- Data Source
  KAKENHI-PROJECT-19200022
[Presentation] A graph kernel method incorporating chirality2007
- Author(s)
  T.Urata, J.B.Brown, T. Tamura, T.Kawabata, T. Akutsu
- Organizer
  日本バイオインフォマティクス学会年会
- Place of Presentation
  日本未来館(東京)
- Year and Date
  2007-12-19
- Data Source
  KAKENHI-PROJECT-19200022
[Presentation] 生育温度による代謝ネットワーク構造の差異2007
- Author(s)
  竹本和広, ホセ・C・ナチェル, 阿久津達也
- Organizer
  情報処理学会バイオ情報学研究会
- Place of Presentation
  はこだて未来大学
- Year and Date
  2007-09-13
- Data Source
  KAKENHI-PROJECT-17017019
[Presentation] Subcellular location prediction of proteins using support vector machines with alignment and amino acid composition2007
- Author(s)
  T., Tamura, T., Akutsu
- Organizer
  IPSJ, Special Interest Group on Bioinformatics
- Place of Presentation
  Osaka University
- Year and Date
  2007-03-05
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-16300092
[Presentation] Hardness results on local multiple alignment of biological sequences2007
- Author(s)
  T., Akutsu, H., Arimura, S.,Shimozono
- Organizer
  IPSJ, Special Interest Group on Bioinformatics
- Place of Presentation
  Osaka University
- Year and Date
  2007-03-05
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-16300092
[Presentation] アラインメントとアミノ酸構成比に基づいたサポートベクターマシンによるタンパク質の細胞内局在予測2007
- Author(s)
  田村武幸, 阿久津達也
- Organizer
  情報処理学会第8回バイオ情報学研究会
- Place of Presentation
  大阪大学
- Year and Date
  2007-03-05
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-16300092
[Presentation] 生物配列の局所マルチプルアラインメントの計算困難性2007
- Author(s)
  阿久津達也, 有村博紀, 下薗真一
- Organizer
  情報処理学会第8回バイオ情報学研究会
- Place of Presentation
  大阪大学
- Year and Date
  2007-03-05
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-16300092
[Presentation] An efficient algorithm for generating colored outerplanar graphs2007
- Author(s)
  W. Jiexun, Z. Liang, H. Nagamochi and T. Akutsu
- Organizer
  The 4th Annual Conference on Theory and Applications of Models of Computation
- Place of Presentation
  Shanghai, China
- Year and Date
  2007-05-25
- Data Source
  KAKENHI-PROJECT-19200022
[Presentation] A graph kernel method incorporating chirality2007
- Author(s)
  T. Urata, J. B. Brown, T. Tamura, T. Kawabata, T. Akutsu
- Organizer
  日本バイオインフォマティクス学会年会
- Place of Presentation
  日本未来館 (東京)
- Year and Date
  2007-12-18
- Data Source
  KAKENHI-PROJECT-19200022
[Presentation] Image compression-based approach to measuring the similarity of protein structures2007
- Author(s)
  M. Hayashida and T. Akutsu
- Organizer
  The Seventh Annual International Workshop on Bioinformatics and Systems Biology
- Place of Presentation
  東京大学医科学研究所
- Year and Date
  2007-07-31
- Data Source
  KAKENHI-PROJECT-19650053
[Presentation] Optimizing amino acid substitution matrices with local alignment kernels2006
- Author(s)
  H., Saigo, J-P., Vert, T., Akutsu
- Organizer
  IPSJ, Special Interest Group on Mathematical Modeling and Problem Solving
- Place of Presentation
  Toyooka, Hyogo
- Year and Date
  2006-03-17
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-16300092
[Presentation] Kernel-based approaches to classification and design of protein sequences and chemical compounds2006
- Author(s)
  T. Akutsu
- Organizer
  The First Japan-Taiwan Bilateral Symposium on Bioinformatics
- Place of Presentation
  東京大学
- Year and Date
  2006-03-13
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-16300092
[Presentation] Kernel-based approaches to classification and design of protein sequences and chemical compounds2006
- Author(s)
  T., Akutsu
- Organizer
  The First Japan-Taiwan Bilateral Symposium on Bioinformatics
- Place of Presentation
  The University of Tokyo
- Year and Date
  2006-03-13
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-16300092
[Presentation] Inferring a chemical structure from a feature vector based on frequency of labeled paths and small fragments2006
- Author(s)
  T., Akutsu, D., Fukagawa
- Organizer
  IPSJ, Special Interest Group on Bioinformatics
- Place of Presentation
  Hokkaido University
- Year and Date
  2006-02-10
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-16300092
[Presentation] 木の編集距離の文字列の編集距離による近似2006
- Author(s)
  阿久津達也, 深川大路, 高須淳宏
- Organizer
  電子情報通信学会コンピューテーション研究会
- Place of Presentation
  九州工業大学
- Year and Date
  2006-05-24
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-16300092
[Presentation] Enumerating tree-like chemical structures from feature vector2006
- Author(s)
  H., Fujiwara, Z., Liang, H., Nagamochi, T., Akutsu
- Organizer
  IPSJ, Special Interest Group on Bioinformatics
- Place of Presentation
  The University of Electro-Communications
- Year and Date
  2006-12-22
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-16300092
[Presentation] 特徴ベクトルからの化学構造の推定2006
- Author(s)
  阿久津達也, 深川大路
- Organizer
  情報処理学会第4回バイオ情報学研究会
- Place of Presentation
  北海道大学
- Year and Date
  2006-02-10
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-16300092
[Presentation] 局所アラインメントカーネルを用いたアミノ酸置換行列の最適化2006
- Author(s)
  西郷浩人, J-P. Vert, 阿久津達也
- Organizer
  情報処理学会第58回数理モデル化と問題解決研究会
- Place of Presentation
  兵庫県豊岡市
- Year and Date
  2006-03-17
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-16300092
[Presentation] Approximating tree edit distance through string edit distance2006
- Author(s)
  T., Akutsu, D., Fukagawa, A., Takasu
- Organizer
  IEICE, Technical Group on Computation
- Place of Presentation
  Kyushu Institute of Technology
- Year and Date
  2006-05-24
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-16300092
[Presentation] 特徴ベクトルに基づく木状の化学分子の列挙アルゴリズム2006
- Author(s)
  藤原大樹, 趙亮, 永持仁, 阿久津達也
- Organizer
  情報処理学会第7回バイオ情報学研究会
- Place of Presentation
  電気通信大学
- Year and Date
  2006-12-22
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-16300092
[Presentation] パス頻度ベクトルからのグラフ推定問題の困難性について2005
- Author(s)
  阿久津達也, 深川大路
- Organizer
  電子情報通信学会コンピューテーション研究会
- Place of Presentation
  関西学院大学
- Year and Date
  2005-04-18
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-16300092
[Presentation] Kernel-based approaches to classification and design of protein sequences and chemical compounds2005
- Author(s)
  T., Akutsu
- Organizer
  2005 International Joint Conference of InCoB(AASBi and KSBI)
- Place of Presentation
  Busan, Korea
- Year and Date
  2005-09-22
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-16300092
[Presentation] Kernel-based approaches to classification and design of protein sequences and chemical compounds2005
- Author(s)
  T. Akutsu
- Organizer
  2005 International Joint Conference of InCoB, AASBi and KSBI
- Place of Presentation
  Busan, Korea
- Year and Date
  2005-09-22
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-16300092
[Presentation] On the complexity of inferring a graph from path frequency2005
- Author(s)
  T., Akutsu, D., Fukagawa
- Organizer
  IEICE, Technical Group on Computation
- Place of Presentation
  Kwansei Gakuin University
- Year and Date
  2005-04-18
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-16300092
[Presentation] Algorithms for point set matching with k-differences2004
- Author(s)
  T., Akutsu
- Organizer
  IEICE, Technical Group on Computation
- Place of Presentation
  Kyoto University
- Year and Date
  2004-04-22
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-16300092
[Presentation] k個のミスマッチを許した点集合マッチング・アルゴリズム2004
- Author(s)
  阿久津達也
- Organizer
  電子情報通信学会コンピューテーション研究会
- Place of Presentation
  京都大学
- Year and Date
  2004-04-22
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-16300092
[Presentation] Fast algorithms for comparison of similar unordered trees2004
- Author(s)
  D., Fukagawa, T., Akutsu
- Organizer
  IEICE, Technical Group on Computation
- Place of Presentation
  Hokkaido University
- Year and Date
  2004-09-17
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-16300092
[Presentation] 類似度の高い無順序木の比較に対する高速アルゴリズム2004
- Author(s)
  深川大路, 阿久津達也
- Organizer
  電子情報通信学会コンピューテーション研究会
- Place of Presentation
  北海道大学
- Year and Date
  2004-09-17
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-16300092
[Presentation] Computing Smallest Intervention Strategies for Multiple Metabolic Networks in a Boolean Model
- Author(s)
  Wei Lu, Takeyuki Tamura, Jiangning Song, Tatsuya Akutsu
- Organizer
  14th International Workshop on Bioinformatics and Systems Biology
- Place of Presentation
  Humboldt University, Berlin, Germany
- Year and Date
  2014-07-20 – 2014-07-23
- Data Source
  KAKENHI-PROJECT-26240034
[Presentation] ナフタレン環を持つ木状化学構造の幅優先探索による列挙手法
- Author(s)
  Jindalertudomdee Jira, 林田守広, 趙楊, 阿久津達也
- Organizer
  第37回情報化学討論会
- Place of Presentation
  豊橋商工会議所
- Year and Date
  2014-11-27 – 2014-11-28
- Data Source
  KAKENHI-PROJECT-26240034
[Presentation] Parallelization of Enumerating Tree-like Chemical Compounds by Breadth-first Search Order
- Author(s)
  Morihiro Hayashida, Jira Jindalertudomdee, Yang Zhao, Tatsuya Akutsu
- Organizer
  The 8th International Conference on Systems Bioloy
- Place of Presentation
  Qingdao, China
- Year and Date
  2014-10-24 – 2014-10-27
- Data Source
  KAKENHI-PROJECT-26240034

1. MIYANO Satoru (50128104)

# of Collaborated Projects: 6 results

# of Collaborated Products: 6 results
2. NAGAMOCHI Hiroshi (70202231)

# of Collaborated Projects: 5 results

# of Collaborated Products: 53 results
3. HAYASHIDA Morihiro (40402929)

# of Collaborated Projects: 4 results

# of Collaborated Products: 38 results
4. MARUYAMA Osamu (20282519)

# of Collaborated Projects: 3 results

# of Collaborated Products: 1 results
5. 細川浩 (90359779)

# of Collaborated Projects: 3 results

# of Collaborated Products: 1 results
6. GOTO Susumu (40263149)

# of Collaborated Projects: 2 results

# of Collaborated Products: 2 results
7. KAWABATA Takeo (50214680)

# of Collaborated Projects: 2 results

# of Collaborated Products: 5 results
8. KUHARA Satoru (00153320)

# of Collaborated Projects: 2 results

# of Collaborated Products: 0 results
9. MATSUDA Hideo (50183950)

# of Collaborated Projects: 2 results

# of Collaborated Products: 0 results
10. SHINOHARA Ayumi (00226151)

# of Collaborated Projects: 2 results

# of Collaborated Products: 0 results
11. UEDA Nobuhisa (80346048)

# of Collaborated Projects: 2 results

# of Collaborated Products: 12 results
12. MOCHIZUKI Atsushi (10304726)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
13. TOKITA Keiichirou (00263195)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
14. MAEGAWA shingo (30467401)

# of Collaborated Projects: 1 results

# of Collaborated Products: 1 results
15. IGARASHI Yoshihide (60006260)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
16. MOTEGI Kazuhiro (00251124)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
17. SHIRAISHI Yoichi (80261858)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
18. NISHITANI Yasuyuki (60198463)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
19. KANEHISA Minoru (70183275)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
20. TAKAGI Toshihisa (30110836)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
21. SHIMOZONO Shinichi (70243988)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
22. SHOUDAI Takayoshi (50226304)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
23. MORISHITA Shinichi (90292854)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
24. GOTOH Osamu (40142111)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
25. DOI Koichiro (10345126)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
26. SESE Jun (40361539)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
27. SATOU Kenji (10215783)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
28. HATTORI Masahiro (60372554)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
29. OKUNO Yasushi (20283666)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
30. MATSUNO Hiroshi (10181744)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
31. OHM Shinobu (20160046)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
32. IMOTO Seiya (10345027)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
33. BANNAI Hideo (20323644)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
34. 中井謙太 (60217643)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
35. 森浩禎 (90182203)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
36. 蓑島伸生 (90181966)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
37. 内田智之 (70264934)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
38. 西田友是 (10131690)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
39. 原口和也 (80453356)

# of Collaborated Projects: 1 results

# of Collaborated Products: 3 results
40. WILKINSON Tim

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
41. MCCANN Julie

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
42. MURRAY Kevin

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
43. DOWLING Geoff

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
44. OSMON Peter

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
45. 浅井潔

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
46. MARINI SIMONE

# of Collaborated Projects: 1 results

# of Collaborated Products: 2 results
47. LIN CHUN-YU

# of Collaborated Projects: 1 results

# of Collaborated Products: 9 results
48. SUN LIANGJIE

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
49. NACHER Jose

# of Collaborated Projects: 0 results

# of Collaborated Products: 7 results
50. FUKAGAWA Daiji

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
51. 田村武幸

# of Collaborated Projects: 0 results

# of Collaborated Products: 3 results
52. 竹本和広

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
53. Shurbevski A

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results

Akutsu Tatsuya 阿久津 達也

AKUTSU Tatsuya 阿久津 達也

阿久津 達也 アクツ タツヤ

Research Projects

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Co-Researchers

Cell-type Specific Control Methods Using Single Cell Gene Expression DataPrincipal Investigator

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Analysis and Control of Steady States of Multiple Biological NetworksPrincipal Investigator

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Advanced Studies and Developments on Discrete Preimage ProblemsPrincipal Investigator

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Analysis and Applications of Discrete Preimage ProblemsPrincipal Investigator

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Pan-cancer module and network analysis for identifying dominating subnetworks across hu man cancersPrincipal Investigator

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データ融合によるタンパク質切断解析および疾患との関連性発見Principal Investigator

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An Approach to Novel Structure Design by Combining Discrete Methods and Statistical MethodsPrincipal Investigator

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Structurally Robust Control of Complex NetworksPrincipal Investigator

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An Approach to Novel Structural Design by Combining Discrete Methods and Kernel MethodsPrincipal Investigator

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Discrete Model-Based Methods for Control of Complex BiologicalSyetemsPrincipal Investigator

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New Methods for Designing Chemical Structures Using Graph Theory and Kernel MethodsPrincipal Investigator

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複雑生体構造のデータ圧縮を通じた発生原理の解明Principal Investigator

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Analysis of Structure and Dynamics of Biological Information NetworksPrincipal Investigator

Principal Investigator

Akutsu Tatsuya 阿久津達也

AKUTSU Tatsuya 阿久津達也

阿久津達也アクツタツヤ