Basic Information

Affiliated programs (koza)

• Graduate School of Informatics, 知能情報学専攻 生命システム情報学, 教授

Academic Degree

• 工学博士(東京大学)

Academic Resume (Graduate Schools)

• 東京大学, 大学院工学系研究科情報工学専攻博士課程, 修了
• 東京大学, 大学院工学系研究科航空学専門課程修士課程, 修了

Academic Resume (Undergraduate School/Majors)

• 東京大学, 工学部航空学科, 卒業

High School

• High School

  栃木県立宇都宮高等学校

Research History

• From Oct. 2001, To Present

  Kyoto University, Institute for Chemical Research Bioinformatics Center, 教授
• From Apr. 1996, To Sep. 2001

  The University of Tokyo, The Institute of Medical Science Human Genome Center, 助教授
• From Apr. 1994, To Mar. 1996

  Gunma University, 工学部 情報工学科, 助教授
• From Apr. 1989, To Mar. 1994

  通商産業省工業技術院機械技術研究所, 研究員

Profile

• Profile

  [略歴]
  1989年3月 東京大学大学院工学系研究科情報工学専攻博士課程修了（工学博士）
  1989年4月～1994年3月 通商産業省工業技術院機械技術研究所研究員
  1994年4月～1996年3月 群馬大学工学部情報工学科助教授
  1996年4月～2001年9月 東京大学医科学研究所ヒトゲノム解析センター助教授
  2001年2月～2001年8月 カリフォルニア大学バークレー校客員研究員
  2001年11月～2003年3月 京都大学大学院情報学研究科知能情報学専攻併任教授
  2001年11月～2003年3月 京都大学大学院情報学研究科知能情報学専攻併任教授
  2001年10月～ 京都大学化学研究所バイオインフォマティクスセンター教授
  2020年4月～ 国立情報学研究所客員教授

  
  

  [研究分野]
  バイオインフォマティクス、離散アルゴリズム、複雑ネットワーク、ニューラルネットワーク

  
  

   

  
  

   

Language of Instruction

• English

ID,URL

• J-Global ID

  201401096521596568

• External link

  http://www.bic.kyoto-u.ac.jp/takutsu/members/takutsu/japanese.html

Website(s) (URL(s))

• http://www.bic.kyoto-u.ac.jp/takutsu/members/takutsu/japanese.html

researchmap URL

• https://researchmap.jp/7000008292

Research

Research Topics, Overview of the research

• Research Topics

  Bioinformatics, Complex Networks, Discrete Algorithms

• Overview of the research

  We study mathematical models and algorithms for analyzing biological sequences, structures, networks, and systems.

Research Areas

• Informatics, Intelligent informatics, Complex Networks
• Informatics, Information theory, Discrete Algorithms
• Informatics, Biological, health, and medical informatics, Bioinformatics

Papers

• 21aTP-11 Relationship between structure and arowth temperature in prokaryotic metabolic networks

  Takemoto Kazuhiro; Naoher Jose C.; Akutsu Tatsuya

  Meeting Abstracts of the Physical Society of Japan, 2007

  
• iAMPCN: a deep-learning approach for identifying antimicrobial peptides and their functional activities.

  Jing Xu; Fuyi Li; Chen Li; Xudong Guo; Cornelia Landersdorfer; Hsin-Hui Shen; Anton Y Peleg; Jian Li; Seiya Imoto; Jianhua Yao; Tatsuya Akutsu; Jiangning Song

  Briefings in bioinformatics, 20 Jul. 2023

  
• AQDnet: Deep Neural Network for Protein-Ligand Docking Simulation.

  Koji Shiota; Akira Suma; Hiroyuki Ogawa; Takuya Yamaguchi; Akio Iida; Takahiro Hata; Mutsuyoshi Matsushita; Tatsuya Akutsu; Masaru Tateno

  ACS omega, 04 Jul. 2023

  
• PFresGO: an attention mechanism-based deep-learning approach for protein annotation by integrating gene ontology inter-relationships.

  Tong Pan; Chen Li; Yue Bi; Zhikang Wang; Robin B Gasser; Anthony W Purcell; Tatsuya Akutsu; Geoffrey I Webb; Seiya Imoto; Jiangning Song

  Bioinformatics (Oxford, England), 01 Mar. 2023

  
• ResNetKhib: a novel cell type-specific tool for predicting lysine 2-hydroxyisobutylation sites via transfer learning.

  Xiaoti Jia; Pei Zhao; Fuyi Li; Zhaohui Qin; Haoran Ren; Junzhou Li; Chunbo Miao; Quanzhi Zhao; Tatsuya Akutsu; Gensheng Dou; Zhen Chen; Jiangning Song

  Briefings Bioinform., Mar. 2023

  
• Densest subgraph-based methods for protein-protein interaction hot spot prediction.

  Ruiming Li; Jung-Yu Lee 0001; Jinn-Moon Yang; Tatsuya Akutsu

  BMC Bioinformatics, 2022

  
• A Method for Molecular Design Based on Linear Regression and Integer Programming

  Jianshen Zhu; Naveed A. Azam; Kazuya Haraguchi; Liang Zhao; Hiroshi Nagamochi; Tatsuya Akutsu

  2022 12th International Conference on Bioscience, Biochemistry and Bioinformatics, 07 Jan. 2022

  
• eSPRESSO: topological clustering of single-cell transcriptomics data to reveal informative genes for spatio–temporal architectures of cells

  Tomoya Mori; Toshiro Takase; Kuan-Chun Lan; Junko Yamane; Cantas Alev; Azuma Kimura; Kenji Osafune; Jun K. Yamashita; Tatsuya Akutsu; Hiroaki Kitano; Wataru Fujibuchi

  BMC Bioinformatics, 15 Jun. 2023

  
• On the complexity of tree edit distance with variables

  Tatsuya Akutsu; Tomoya Mori; Naotoshi Nakamura; Satoshi Kozawa; Yuhei Ueno; Thomas N Sato

  33rd International Symposium on Algorithms and Computation (ISAAC 2022), Dec. 2022, Peer-reviewed

  
• Analyses and Algorithms for Predecessor and Control Problems for Boolean Networks of Bounded Indegree

  Akutsu Tatsuya; Hayashida Morihiro; Zhang Shu-Qin; Ching Wai-Ki; Ng Michael K.

  Information and Media Technologies, 2009

  
• A new approach to the design of acyclic chemical compounds using skeleton trees and integer linear programming

  Fan Zhang; Jianshen Zhu; Rachaya Chiewvanichakorn; Aleksandar Shurbevski; Hiroshi Nagamochi; Tatsuya Akutsu

  Applied Intelligence, 25 Mar. 2022

  
• バイオインフォマティクスにおける基本アルゴリズム

  Akutsu, Tatsuya; Yamanishi, Yoshihiro

  物性研究, 20 Oct. 2003

  
• MSNet-4mC: Learning effective multi-scale representations for identifying DNA N4-methylcytosine sites.

  Chunting Liu; Jiangning Song; Hiroyuki Ogata; Tatsuya Akutsu

  Bioinformatics (Oxford, England), 07 Oct. 2022

  
• An FVS-Based Approach to Attractor Detection in Asynchronous Random Boolean Networks.

  Trinh Van Giang; Tatsuya Akutsu; Kunihiko Hiraishi

  IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2022

  
• Adjustive Linear Regression and Its Application to the Inverse QSAR.

  Jianshen Zhu; Kazuya Haraguchi; Hiroshi Nagamochi; Tatsuya Akutsu

  Proceedings of the 15th International Joint Conference on Biomedical Engineering Systems and Technologies(BIOINFORMATICS), 2022

  
• PROST: AlphaFold2-aware Sequence-Based Predictor to Estimate Protein Stability Changes upon Missense Mutations.

  Shahid Iqbal; Fang Ge; Fuyi Li; Tatsuya Akutsu; Yuanting Zheng; Robin B. Gasser; Dong-Jun Yu; Geoffrey I. Webb; Jiangning Song

  Journal of Chemical Information and Modeling, 2022

  
• 1P-279 A mathematical model for apoptosis mechanism under oxidative stress(The 46th Annual Meeting of the Biophysical Society of Japan)

  Mouri Kazunari; Nacher Jose C.; Akutsu Tatsuya

  Seibutsu Butsuri, 2008

  
• Optimizing substitution matrices by separating score distributions.

  Yuichiro Hourai; Tatsuya Akutsu; Yutaka Akiyama

  Bioinformatics (Oxford, England), 12 Apr. 2004

  
• Point matching under non-uniform distortions

  Tatsuya Akutsu; Kyotetsu Kanaya; Akira Ohyama; Asao Fujiyama

  Discrete Applied Mathematics, 01 Apr. 2003, Peer-reviewed

  
• Statistical Significance of Tree Similarity Scores

  Aoki Kiyoko F.; Yamaguchi Atsuko; Okuno Yasushi; Akutsu Tatsuya; Ueda Nobuhisa; Kanehisa Minoru; Mamitsuka Hiroshi

  GI, 2003

  
• DP Algorithms for RNA Secondary Structure Prediction with Pseudoknots

  Akutsu Tatsuya

  GI, 1997

  
• Enhancement of the "PROTEIX" Database System for Three-Dimensional Protein Structures

  Akutsu Tatsuya; Hyakutake Toshio

  GI, 1994

  
• iFeatureOmega: an integrative platform for engineering, visualization and analysis of features from molecular sequences, structural and ligand data sets.

  Zhen Chen; Xuhan Liu; Pei Zhao; Chen Li; Yanan Wang; Fuyi Li; Tatsuya Akutsu; Chris Bain; Robin B Gasser; Junzhou Li; Zuoren Yang; Xin Gao; Lukasz Kurgan; Jiangning Song

  Nucleic acids research, 07 May 2022

  
• Comparison of the Representational Power of Random Forests, Binary Decision Diagrams, and Neural Networks.

  So Kumano; Tatsuya Akutsu

  Neural Computation, 23 Mar. 2022

  
• Identifying miRNA-Gene Common and Specific Regulatory Modules for Cancer Subtyping by a High-Order Graph Matching Model.

  Jiazhou Chen; Guoqiang Han; Aodan Xu; Tatsuya Akutsu; Hongmin Cai

  IEEE ACM Trans. Comput. Biol. Bioinform., 2023

  
• Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction.

  Meng Zhang; Cangzhi Jia; Fuyi Li; Chen Li; Yan Zhu; Tatsuya Akutsu; Geoffrey I Webb; Quan Zou; Lachlan J M Coin; Jiangning Song

  Briefings in bioinformatics, 10 Mar. 2022

  
• A novel graph convolutional neural network for predicting interaction sites on protein kinase inhibitors in phosphorylation.

  Feiqi Wang; Yun-Ti Chen; Jinn-Moon Yang; Tatsuya Akutsu

  Scientific reports, 07 Jan. 2022

  
• Identification of periodic attractors in Boolean networks using a priori information.

  Ulrike Münzner; Tomoya Mori; Marcus Krantz; Edda Klipp; Tatsuya Akutsu

  PLoS computational biology, Jan. 2022

  
• Attractor detection and enumeration algorithms for Boolean networks.

  Tomoya Mori; Tatsuya Akutsu

  Computational and structural biotechnology journal, 2022

  
• Systematic Characterization of Lysine Post-translational Modification Sites Using MUscADEL.

  Zhen Chen; Xuhan Liu; Fuyi Li; Chen Li; Tatiana Marquez-Lago; André Leier; Geoffrey I Webb; Dakang Xu; Tatsuya Akutsu; Jiangning Song

  Methods in molecular biology (Clifton, N.J.), 2022

  
• Knowledge-based system for computer-aided drug design.

  Einoshin Suzuki; Tatsuya Akutsu; Setsuo Ohsuga

  Knowledge Based Systems, 1993

  
• Logic-based approach to expert systems in chemistry.

  Tatsuya Akutsu; Einoshin Suzuki; Setsuo Ohsuga

  Knowledge Based Systems, 1991

  
• Mathematical Models and Data Analyses of Structures of Biological Networks

  AKUTSU Tatsuya; NACHER DIEZ Jose Carlos

  Seibutsu Butsuri, 25 Mar. 2007

  
• Algorithms for Computing an Optimal Protein Threading with Profiles and Distance Restraints

  Akutsu Tatsuya; Hayashida Morihiro; Tomita Etsuji; Suzuki Jun'ichi; Horimoto Katsuhisa

  GI, 2003

  
• Protein Structure Alignment Using a Graph Matching Technique

  Akutsu Tatsuya

  GI, 1995

  
• On Pattern Matching Methods for Three Dimensional Protein Structures

  Akutsu Tatsuya

  GI, 1993

  
• PROTEIX: An Interactive Database System for Three Dimensional Protein Structures

  Akutsu Tatsuya

  GI, 1993

  
• Protein Structure Analysis Using Continuous Density Hidden Markov Models

  Hayashida Morihiro; Ueda Nobuhisa; Horimoto Katsuhisa; Akutsu Tatsuya

  GI, 2002

  
• Algorithms for Inferring Genetic Networks

  AKUTSU Tatsuya

  Seibutsu Butsuri, 01 Dec. 1999

  
• 3I0924 Exploring Feature Extraction Method for Time Series Data Obtained by Molecular Dynamics Simulation(3I Protein: Measurement & Analysis 1,The 49th Annual Meeting of the Biophysical Society of Japan)

  Kamada Mayumi; Toda Mikito; Hayashida Morihiro; Robertazzi Arturo; Knapp Ernst Walter; Akutsu Tatsuya

  Seibutsu Butsuri, 2011

  
• An Inverse QSAR Method Based on Linear Regression and Integer Programming

  Jianshen Zhu; Naveed Ahmed Azam; Kazuya Haraguchi; Liang Zhao; Hiroshi Nagamochi; Tatsuya Akutsu

  Frontiers in Bioscience-Landmark, 10 Jun. 2022, Peer-reviewed, Last author

  
• Molecular Design Based on Artificial Neural Networks, Integer Programming and Grid Neighbor Search

  Naveed Ahmed Azam; Jianshen Zhu; Kazuya Haraguchi; Liang Zhao; Hiroshi Nagamochi; Tatsuya Akutsu

  2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 09 Dec. 2021

  
• 機械学習QSARの整数計画法に基づく逆解析法

  Hiroshi NAGAMOCHI; Jianshen ZHU; Naveed Ahmed AZAM; Kazuya HARAGUCHI; Liang ZHAO; Tatsuya AKUTSU

  Journal of Computer Chemistry, Japan, 2021

  
• Message from the Editor-in-Chief

  Akutsu Tatsuya

  IPSJ Transactions on Bioinformatics, 2009

  
• Probabilistic Critical Controllability Analysis of Protein Interaction Networks Integrating Normal Brain Ageing Gene Expression Profiles.

  Eimi Yamaguchi; Tatsuya Akutsu; Jose C Nacher

  International journal of molecular sciences, 13 Sep. 2021, Peer-reviewed

  
• On the Compressive Power of Boolean Threshold Autoencoders.

  Avraham A. Melkman; Sini Guo; Wai-Ki Ching; Pengyu Liu 0002; Tatsuya Akutsu

  IEEE Trans. Neural Networks Learn. Syst., Feb. 2023, Peer-reviewed, Last author, Corresponding author

  
• An Inverse QSAR Method Based on Decision Tree and Integer Programming.

  Kouki Tanaka; Jianshen Zhu; Naveed Ahmed Azam; Kazuya Haraguchi; Liang Zhao 0013; Hiroshi Nagamochi; Tatsuya Akutsu

  Proc. 17th International Conference on Intelligent Computing Theories and Application, Aug. 2021, Peer-reviewed

  
• Codependency and mutual exclusivity for gene community detection from sparse single-cell transcriptome data.

  Natsu Nakajima; Tomoatsu Hayashi; Katsunori Fujiki; Katsuhiko Shirahige; Tetsu Akiyama; Tatsuya Akutsu; Ryuichiro Nakato

  Nucleic acids research, 22 Jul. 2021, Peer-reviewed

  
• An Improved Integer Programming Formulation for Inferring Chemical Compounds with Prescribed Topological Structures.

  Jianshen Zhu; Naveed Ahmed Azam; Kazuya Haraguchi; Liang Zhao 0013; Hiroshi Nagamochi; Tatsuya Akutsu

  Proc. 34th International Conference on Industrial, Engineering and Other Applications of Applied Intelligent Systems, Jul. 2021, Peer-reviewed

  
• iLearnPlus: a comprehensive and automated machine-learning platform for nucleic acid and protein sequence analysis, prediction and visualization.

  Zhen Chen; Pei Zhao; Chen Li; Fuyi Li; Dongxu Xiang; Yong-Zi Chen; Tatsuya Akutsu; Roger J Daly; Geoffrey I Webb; Quanzhi Zhao; Lukasz Kurgan; Jiangning Song

  Nucleic acids research, 04 Jun. 2021, Peer-reviewed

  
• Uncovering and classifying the role of driven nodes in control of complex networks.

  Yuma Shinzawa; Tatsuya Akutsu; Jose C Nacher

  Scientific reports, 05 May 2021, Peer-reviewed, Corresponding author

  
• Inhibitory neurons exhibit high controlling ability in the cortical microconnectome.

  Motoki Kajiwara; Ritsuki Nomura; Felix Goetze; Masanori Kawabata; Yoshikazu Isomura; Tatsuya Akutsu; Masanori Shimono

  PLoS computational biology, Apr. 2021, Peer-reviewed

  
• An Inverse QSAR Method Based on a Two-Layered Model and Integer Programming.

  Yu Shi; Jianshen Zhu; Naveed Ahmed Azam; Kazuya Haraguchi; Liang Zhao; Hiroshi Nagamochi; Tatsuya Akutsu

  International journal of molecular sciences, 11 Mar. 2021, Peer-reviewed

  
• On the Distribution of Successor States in Boolean Threshold Networks.

  Sini Guo; Pengyu Liu 0002; Wai-Ki Ching; Tatsuya Akutsu

  IEEE Transactions on Neural Networks and Learning Systems, 2022, Peer-reviewed, Last author, Corresponding author

  
• Databases for Protein-Protein Interactions.

  Natsu Nakajima; Tatsuya Akutsu; Ryuichiro Nakato

  Methods in molecular biology (Clifton, N.J.), 2021, Peer-reviewed, Invited

  
• A Novel Method for Inferring Chemical Compounds With Prescribed Topological Substructures Based on Integer Programming.

  Jianshen Zhu; Naveed Ahmed Azam; Fan Zhang; Aleksandar Shurbevski; Kazuya Haraguchi; Liang Zhao 0013; Hiroshi Nagamochi; Tatsuya Akutsu

  IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2022, Peer-reviewed, Last author, Corresponding author

  
• Anthem: a user customised tool for fast and accurate prediction of binding between peptides and HLA class I molecules.

  Shutao Mei; Fuyi Li; Dongxu Xiang; Rochelle Ayala; Pouya Faridi; Geoffrey I Webb; Patricia T. Illing; Jamie Rossjohn; Tatsuya Akutsu; Nathan P. Croft; Anthony W. Purcell; Jiangning Song

  Briefings Bioinform., 2021, Peer-reviewed

  
• New and improved algorithms for unordered tree inclusion.

  Tatsuya Akutsu; Jesper Jansson; Ruiming Li; Atsuhiro Takasu; Takeyuki Tamura

  Theor. Comput. Sci., 2021, Peer-reviewed, Lead author, Corresponding author

  
• DeepVF: a deep learning-based hybrid framework for identifying virulence factors using the stacking strategy.

  Ruopeng Xie; Jiahui Li; Jiawei Wang; Wei Dai; André Leier; Tatiana T. Marquez-Lago; Tatsuya Akutsu; Trevor Lithgow; Jiangning Song; Yanju Zhang

  Briefings Bioinform., 2021, Peer-reviewed

  
• Discrimination of attractors with noisy nodes in Boolean networks.

  Xiaoqing Cheng; Wai-Ki Ching; Sini Guo; Tatsuya Akutsu

  Autom., 2021, Peer-reviewed, Last author, Corresponding author

  
• A novel method for inference of acyclic chemical compounds with bounded branch-height based on artificial neural networks and integer programming.

  Naveed Ahmed Azam; Jianshen Zhu; Yanming Sun; Yu Shi; Aleksandar Shurbevski; Liang Zhao 0013; Hiroshi Nagamochi; Tatsuya Akutsu

  Algorithms Mol. Biol., 2021, Peer-reviewed, Last author, Corresponding author

  
• Weighted minimum feedback vertex sets and implementation in human cancer genes detection.

  Ruiming Li; Chun-Yu Lin; Weifeng Guo; Tatsuya Akutsu

  BMC Bioinform., 2021, Peer-reviewed, Last author, Corresponding author

  
• ReCGBM: a gradient boosting-based method for predicting human dicer cleavage sites.

  Pengyu Liu; Jiangning Song; Chun-Yu Lin; Tatsuya Akutsu

  BMC Bioinform., 2021, Peer-reviewed, Last author, Corresponding author

  
• A New Integer Linear Programming Formulation to the Inverse QSAR/QSPR for Acyclic Chemical Compounds Using Skeleton Trees.

  Fan Zhang; Jianshen Zhu; Rachaya Chiewvanichakorn; Aleksandar Shurbevski; Hiroshi Nagamochi; Tatsuya Akutsu

  Proc. 33rd International Conference on Industrial, Engineering and Other Applications of Applied Intelligent Systems (IEA/AIE 2020), Sep. 2020, Peer-reviewed, Last author

  
• Comprehensive review and assessment of computational methods for predicting RNA post-transcriptional modification sites from RNA sequences.

  Zhen Chen 0009; Pei Zhao; Fuyi Li; Yanan Wang; Alexander Ian Smith; Geoffrey I. Webb; Tatsuya Akutsu; Abdelkader Baggag; Halima Bensmail; Jiangning Song

  Briefings Bioinform., Sep. 2020, Peer-reviewed

  
• Network control principles for identifying personalized driver genes in cancer.

  Weifeng Guo; Shaowu Zhang 0001; Tao Zeng; Tatsuya Akutsu; Luonan Chen

  Briefings Bioinform., Sep. 2020, Peer-reviewed

  
• Comparison of pseudoknotted RNA secondary structures by topological centroid identification and tree edit distance

  Wang F; Akutsu T; Mori T

  Journal of Computational Biology, Sep. 2020, Peer-reviewed

  
• A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide-binding prediction.

  Shutao Mei; Fuyi Li; André Leier; Tatiana T. Marquez-Lago; Kailin Giam; Nathan P. Croft; Tatsuya Akutsu; Alexander Ian Smith; Jian Li; Jamie Rossjohn; Anthony W. Purcell; Jiangning Song

  Briefings Bioinform., Jul. 2020, Peer-reviewed

  
• Extracting boolean and probabilistic rules from trained neural networks.

  Pengyu Liu; Avraham A. Melkman; Tatsuya Akutsu

  Neural Networks, Jun. 2020, Peer-reviewed, Last author, Corresponding author

  
• iLearn : an integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data.

  Zhen Chen 0009; Pei Zhao; Fuyi Li; Tatiana T. Marquez-Lago; André Leier; Jerico Nico De Leon Revote; Yan Zhu; David R. Powell; Tatsuya Akutsu; Geoffrey I. Webb; Kuo-Chen Chou; Alexander Ian Smith; Roger J. Daly; Jian Li 0052; Jiangning Song

  Briefings Bioinform., May 2020, Peer-reviewed

  
• Procleave: Predicting Protease-specific Substrate Cleavage Sites by Combining Sequence and Structural Information.

  Fuyi Li; André Leier; Quanzhong Liu; Yanan Wang; Dongxu Xiang; Tatsuya Akutsu; Geoffrey I. Webb; Alexander Ian Smith; Tatiana T. Marquez-Lago; Jian Li 0052; Jiangning Song

  Genom. Proteom. Bioinform., Feb. 2020, Peer-reviewed

  
• A Novel Method for the Inverse QSAR/QSPR based on Artificial Neural Networks and Mixed Integer Linear Programming with Guaranteed Admissibility

  Naveed Azam; Rachaya Chiewvanichakorn; Fan Zhang; Aleksandar Shurbevski; Hiroshi Nagamochi; Tatsuya Akutsu

  Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies, Feb. 2020, Peer-reviewed, Last author

  
• DeepCleave: a deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites.

  Fuyi Li; Jinxiang Chen; André Leier; Tatiana T. Marquez-Lago; Quanzhong Liu; Yanze Wang; Jerico Nico De Leon Revote; Alexander Ian Smith; Tatsuya Akutsu; Geoffrey I. Webb; Lukasz A. Kurgan; Jiangning Song

  Bioinform., Feb. 2020, Peer-reviewed

  
• PeNGaRoo, a combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins.

  Yanju Zhang; Sha Yu; Ruopeng Xie; Jiahui Li; André Leier; Tatiana T. Marquez-Lago; Tatsuya Akutsu; Alexander Ian Smith; Zongyuan Ge; Jiawei Wang; Trevor Lithgow; Jiangning Song

  Bioinform., Feb. 2020, Peer-reviewed

  
• A Method for the Inverse QSAR/QSPR Based on Artificial Neural Networks and Mixed Integer Linear Programming

  Rachaya Chiewvanichakorn; Chenxi Wang; Zhe Zhang; Aleksandar Shurbevski; Hiroshi Nagamochi; Tatsuya Akutsu

  Proceedings of the 2020 10th International Conference on Bioscience, Biochemistry and Bioinformatics, 19 Jan. 2020, Peer-reviewed, Last author

  
• An Overview of Bioinformatics Methods for Analyzing Autism Spectrum Disorders.

  Shogo Nakashima; Jose C Nacher; Jiangning Song; Tatsuya Akutsu

  Current pharmaceutical design, 2020, Peer-reviewed, Last author, Corresponding author

  
• Improved Hardness of Maximum Common Subgraph Problems on Labeled Graphs of Bounded Treewidth and Bounded Degree.

  Tatsuya Akutsu; Avraham A. Melkman; Takeyuki Tamura

  Int. J. Found. Comput. Sci., 2020, Peer-reviewed

  
• A Novel Method for Inference of Chemical Compounds of Cycle Index Two with Desired Properties Based on Artificial Neural Networks and Integer Programming.

  Jianshen Zhu; Chenxi Wang; Aleksandar Shurbevski; Hiroshi Nagamochi; Tatsuya Akutsu

  Algorithms, 2020, Peer-reviewed

  
• Circulating Exosomal miRNA Profiles Predict the Occurrence and Recurrence of Hepatocellular Carcinoma in Patients with Direct-Acting Antiviral-Induced Sustained Viral Response.

  Saori Itami-Matsumoto; Michiyo Hayakawa; Sawako Uchida-Kobayashi; Masaru Enomoto; Akihiro Tamori; Kazuyuki Mizuno; Hidenori Toyoda; Takeyuki Tamura; Tatsuya Akutsu; Takahiro Ochiya; Norifumi Kawada; Yoshiki Murakami

  Biomedicines, 03 Nov. 2019, Peer-reviewed

  
• Identification of the Structure of a Probabilistic Boolean Network From Samples Including Frequencies of Outcomes.

  Akutsu T; Melkman AA

  IEEE transactions on neural networks and learning systems, Aug. 2019, Peer-reviewed

  
• Convolutional neural network approach to lung cancer classification integrating protein interaction network and gene expression profiles.

  Matsubara T; Ochiai T; Hayashida M; Akutsu T; Nacher JC

  Journal of bioinformatics and computational biology, Jun. 2019, Peer-reviewed

  
• Deep learning with evolutionary and genomic profiles for identifying cancer subtypes.

  Lin CY; Ruan P; Li R; Yang JM; See S; Song J; Akutsu T

  Journal of bioinformatics and computational biology, Jun. 2019, Peer-reviewed

  
• Probabilistic controllability approach to metabolic fluxes in normal and cancer tissues.

  Schwartz JM; Otokuni H; Akutsu T; Nacher JC

  Nature communications, Jun. 2019, Peer-reviewed

  
• On the number of driver nodes for controlling a Boolean network when the targets are restricted to attractors.

  Hou W; Ruan P; Ching WK; Akutsu T

  Journal of theoretical biology, Feb. 2019, Peer-reviewed

  
• Network controllability analysis of intracellular signalling reveals viruses are actively controlling molecular systems.

  Ravindran V; Nacher JC; Akutsu T; Ishitsuka M; Osadcenco A; Sunitha V; Bagler G; Schwartz JM; Robertson DL

  Scientific reports, Feb. 2019, Peer-reviewed

  
• Optimal string clustering based on a Laplace-like mixture and EM algorithm on a set of strings.

  Array,Morihiro Hayashida; Tatsuya Akutsu

  J. Comput. Syst. Sci., 2019, Peer-reviewed

  
• Systematic analysis and prediction of type IV secreted effector proteins by machine learning approaches.

  Jiawei Wang; Bingjiao Yang; Yi An; Tatiana T. Marquez-Lago; André Leier; Jonathan Wilksch; Qingyang Hong; Yang Zhang 0010; Morihiro Hayashida; Tatsuya Akutsu; Geoffrey I. Webb; Richard A. Strugnell; Jiangning Song; Trevor Lithgow

  Briefings Bioinform., 2019, Peer-reviewed

  
• iProt-Sub: a comprehensive package for accurately mapping and predicting protease-specific substrates and cleavage sites.

  Jiangning Song; Yanan Wang; Fuyi Li; Tatsuya Akutsu; Neil D. Rawlings; Geoffrey I. Webb; Kuo-Chen Chou

  Briefings Bioinform., 2019, Peer-reviewed

  
• Bastion3: a two-layer ensemble predictor of type III secreted effectors.

  Jiawei Wang; Jiahui Li; Bingjiao Yang; Ruopeng Xie; Tatiana T. Marquez-Lago; André Leier; Morihiro Hayashida; Tatsuya Akutsu; Yanju Zhang; Kuo-Chen Chou; Joel Selkrig; Tieli Zhou; Jiangning Song; Trevor Lithgow

  Bioinform., 2019, Peer-reviewed

  
• Causalcall: Nanopore Basecalling Using a Temporal Convolutional Network.

  Jingwen Zeng; Hongmin Cai; Hong Peng; Haiyan Wang; Yue Zhang; Tatsuya Akutsu

  Frontiers in genetics, 2019, Peer-reviewed

  
• Large-scale comparative assessment of computational predictors for lysine post-translational modification sites.

  Zhen Chen; Xuhan Liu; Fuyi Li; Chen Li 0021; Tatiana T. Marquez-Lago; André Leier; Tatsuya Akutsu; Geoffrey I. Webb; Dakang Xu; Alexander Ian Smith; Lei Li 0013; Kuo-Chen Chou; Jiangning Song

  Briefings Bioinform., 2019, Peer-reviewed

  
• Computational analysis and prediction of lysine malonylation sites by exploiting informative features in an integrative machine-learning framework.

  Yanju Zhang; Ruopeng Xie; Jiawei Wang; André Leier; Tatiana T. Marquez-Lago; Tatsuya Akutsu; Geoffrey I. Webb; Kuo-Chen Chou; Jiangning Song

  Briefings Bioinform., 2019, Peer-reviewed

  
• Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods.

  Fuyi Li; Yanan Wang; Chen Li 0021; Tatiana T. Marquez-Lago; André Leier; Neil D. Rawlings; Gholamreza Haffari; Jerico Nico De Leon Revote; Tatsuya Akutsu; Kuo-Chen Chou; Anthony W. Purcell; Robert N. Pike; Geoffrey I. Webb; Alexander Ian Smith; Trevor Lithgow; Roger J. Daly; James C. Whisstock; Jiangning Song

  Briefings Bioinform., 2019, Peer-reviewed

  
• Toward more accurate prediction of caspase cleavage sites: a comprehensive review of current methods, tools and features.

  Yu Bao; Simone Marini; Takeyuki Tamura; Mayumi Kamada; Shingo Maegawa; Hiroshi Hosokawa; Jiangning Song; Tatsuya Akutsu

  Briefings Bioinform., 2019, Peer-reviewed

  
• Resource Cut, a New Bounding Procedure to Algorithms for Enumerating Tree-Like Chemical Graphs.

  Nishiyama Y; Shurbevski A; Nagamochi H; Akutsu T

  IEEE/ACM transactions on computational biology and bioinformatics, Jan. 2019, Peer-reviewed

  
• Protease target prediction via matrix factorization.

  Simone Marini; Francesca Vitali; Sara Rampazzi; Andrea Demartini; Tatsuya Akutsu

  Bioinform., 2019, Peer-reviewed

  
• Controllability Methods for Identifying Associations Between Critical Control ncRNAs and Human Diseases.

  Nacher JC; Akutsu T

  Methods in molecular biology (Clifton, N.J.), 2019, Peer-reviewed

  
• Finding and analysing the minimum set of driver nodes required to control multilayer networks.

  Nacher JC; Ishitsuka M; Miyazaki S; Akutsu T

  Scientific reports, Jan. 2019, Peer-reviewed

  
• Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome.

  Li F; Li C; Marquez-Lago TT; Leier A; Akutsu T; Purcell AW; Ian Smith A; Lithgow T; Daly RJ; Song J; Chou KC

  Bioinformatics (Oxford, England), Dec. 2018, Peer-reviewed

  
• Computing Minimum Reaction Modifications in a Boolean Metabolic Network.

  Tamura T; Lu W; Song J; Akutsu T

  IEEE/ACM transactions on computational biology and bioinformatics, Nov. 2018, Peer-reviewed

  
• A simple linear-time algorithm for computing the centroid and canonical form of a plane graph and its applications

  Tatsuya Akutsu; Colin De La Higuera; Takeyuki Tamura

  Leibniz International Proceedings in Informatics, LIPIcs, 01 May 2018, Peer-reviewed

  
• Enumerating chemical mono-block 3-augmented trees with two junctions

  Yuui Tamura; Hiroshi Nagamochi; Aleksandar Shurbevski; Tatsuya Akutsu

  ACM International Conference Proceeding Series, 18 Jan. 2018, Peer-reviewed

  
• New and Improved Algorithms for Unordered Tree Inclusion.

  Tatsuya Akutsu; Jesper Jansson,Ruiming Li; Atsuhiro Takasu; Takeyuki Tamura

  29th International Symposium on Algorithms and Computation, ISAAC 2018, December 16-19, 2018, Jiaoxi, Yilan, Taiwan, 2018, Peer-reviewed

  
• New Algorithms for Unordered Tree Inclusion.

  Tatsuya Akutsu; Jesper Jansson; Ruiming Li; Atsuhiro Takasu; Takeyuki Tamura

  CoRR, 2017

  
• On Observability of Attractors in Boolean Networks

  Yushan Qiu; Xiaoqing Cheng; Wai-Ki Ching; Hao Jiang; Tatsuya Akutsu

  PROCEEDINGS 2015 IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE, 2015, Peer-reviewed

  
• Analysis of critical and redundant nodes in controlling directed and undirected complex networks using dominating sets

  Jose C. Nacher; Tatsuya Akutsu

  Journal of Complex Networks, 2014, Peer-reviewed

  
• Network completion for static gene expression data

  Natsu Nakajima; Tatsuya Akutsu

  Advances in Bioinformatics, 2014, Peer-reviewed

  
• A polynomial-time algorithm for computing the maximum common connected edge subgraph of outerplanar graphs of bounded Degree

  Tatsuya Akutsu; Takeyuki Tamura

  Algorithms, 2013, Peer-reviewed

  
• On the complexity of finding a largest common subtree of bounded degree

  Tatsuya Akutsu; Takeyuki Tamura; Avraham A. Melkman; Atsuhiro Takasu

  Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2013, Peer-reviewed

  
• On the degree distribution of projected networks mapped from bipartite networks

  J. C. Nacher; T. Akutsu

  Physica A: Statistical Mechanics and its Applications, 01 Nov. 2011, Peer-reviewed

  
• The role of internal duplication in the evolution of multi-domain proteins

  J. C. Nacher; M. Hayashida; T. Akutsu

  BIOSYSTEMS, Aug. 2010, Peer-reviewed

  
• Prediction of protein folding rates from structural topology and complex network properties

  Jiangning Song; Kazuhiro Takemoto; Hongbin Shen; Hao Tan; M. Michael Gromiha; Tatsuya Akutsu

  IPSJ Transactions on Bioinformatics, 2010, Peer-reviewed

  
• Finding minimum reaction cuts of metabolic networks under a Boolean model using integer programming and feedback vertex sets

  Tamura T; Takemoto K; Akutsu, T

  International Journal of Knowledge Discovery in Bioinformatics, Jan. 2010, Peer-reviewed

  
• A mathematical model for generating bipartite graphs and its application to protein networks

  J. C. Nacher; T. Ochiai; M. Hayashida; T. Akutsu

  JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL, Dec. 2009, Peer-reviewed

  
• Distribution and enumeration of attractors in probabilistic Boolean networks

  M. Hayashida; T. Tamura; T. Akutsu; W. -K. Ching; Y. Cong

  IET SYSTEMS BIOLOGY, Nov. 2009, Peer-reviewed

  
• Algorithms for singleton attractor detection in planar and nonplanar AND/OR Boolean networks

  Takeyuki Tamura; Tatsuya Akutsu

  Mathematics in Computer Science, Mar. 2009, Peer-reviewed

  
• Emergence of scale-free distribution in protein-protein interaction networks based on random selection of interacting domain pairs

  J. C. Nacher; M. Hayashida; T. Akutsu

  BIOSYSTEMS, Feb. 2009, Peer-reviewed

  
• Detecting a Singleton Attractor in a Boolean Network Utilizing SAT Algorithms

  Takeyuki Tamura; Tatsuya Akutsu

  IEICE TRANSACTIONS ON FUNDAMENTALS OF ELECTRONICS COMMUNICATIONS AND COMPUTER SCIENCES, Feb. 2009, Peer-reviewed

  
• Domain-based prediction and analysis of protein-protein interactions

  Tatsuya Akutsu; Morihiro Hayashida

  Biological Data Mining in Protein Interaction Networks, 2009, Peer-reviewed

  
• Integer programming-based methods for attractor detection and control of boolean networks

  Tatsuya Akutsu; Morihiro Hayashida; Takeyuki Tamura

  Proceedings of the IEEE Conference on Decision and Control, 2009, Peer-reviewed

  
• A Clustering Method for Analysis of Sequence Similarity Networks of Proteins Using Maximal Components of Graphs

  HAYASHIDA Morihiro; AKUTSU Tatsuya; NAGAMOCHI Hiroshi

  情報処理学会論文誌, 15 Mar. 2008, Peer-reviewed

  
• Integer programming-based approach to allocation of reporter genes for cell array analysis.

  Morihiro Hayashida; Fuyan Sun; Sachiyo Aburatani; Katsuhisa Horimoto; Tatsuya Akutsu

  International journal of bioinformatics research and applications, 2008

  
• Integer programming-based approach to allocation of reporter genes for cell array analysis.

  Morihiro Hayashida; Fuyan Sun; Sachiyo Aburatani; Katsuhisa Horimoto; Tatsuya Akutsu

  Int. J. Bioinform. Res. Appl., 2008

  
• Algorithms and complexity analyses for control of singleton attractors in Boolean networks

  Takeyuki Tamura; Morihiro Hayashida; Tatsuya Akutsu; Shu-Qin Zhang; Wai-Ki Ching

  Eurasip Journal on Bioinformatics and Systems Biology, 2008, Peer-reviewed

  
• Emergence of the self-similar property in gene expression dynamics

  T. Ochiai; J. C. Nacher; T. Akutsu

  Physica A: Statistical Mechanics and its Applications, 15 Aug. 2007, Peer-reviewed

  
• Algorithms for finding small attractors in boolean networks

  Shu-Qin Zhang; Morihiro Hayashida; Tatsuya Akutsu; Wai-Ki Ching; Michael K. Ng

  Eurasip Journal on Bioinformatics and Systems Biology, 2007, Peer-reviewed

  
• Sensitivity of the power-law exponent in gene expression distribution to mRNA decay rate

  J. C. Nacher; T. Akutsu

  Physics Letters, Section A: General, Atomic and Solid State Physics, 18 Dec. 2006, Peer-reviewed

  
• Protein domain networks: Scale-free mixing of positive and negative exponents

  JC Nacher; M Hayashida; T Akutsu

  PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS, Jul. 2006, Peer-reviewed

  
• Selecting informative genes for cancer classification using gene expression data

  Tatsuya Akutsu; Satoru Miyano

  Computational and Statistical Approaches to Genomics, 2006, Peer-reviewed

  
• Protein threading with profiles and distance constraints using clique based algorithms

  Bahadur K.C. Dukka; Etsuji Tomita; Jun'ichi Suzuki; Katsuhisa Horimoto; Tatsuya Akutsu

  Journal of Bioinformatics and Computational Biology, 2006, Peer-reviewed

  
• The role of log-normal dynamics in the evolution of biochemical pathways

  J. C. Nacher; T. Ochiai; T. Yamada; M. Kanehisa; T. Akutsu

  BioSystems, Jan. 2006, Peer-reviewed

  
• 原核生物の代謝ネットワークにおける 構造の乱雑さと生育温度の関係

  竹本和広; ホセ・C・ナチェル; 阿久津達也

  日本ソフトウェア科学会研究会資料, 2006, Peer-reviewed

  
• A novel representation of protein sequences for prediction of subcellular location using support vector machines

  Setsuro Matsuda; Jean-Philippe Vert; Hiroto Saigo; Nobuhisa Ueda; Hiroyuki Toh; Tatsuya Akutsu

  Protein Science, Nov. 2005, Peer-reviewed

  
• On the relation between fluctuation and scaling-law in gene expression time series from yeast to human

  J. C. Nacher; T. Ochiai; T. Akutsu

  Modern Physics Letters B, 20 Oct. 2005, Peer-reviewed

  
• On construction of stochastic genetic networks based on gene expression sequences

  Wai-Ki Ching; Michael M. Ng; Eric S. Fung; Tatsuya Akutsu

  International Journal of Neural Systems, Aug. 2005, Peer-reviewed

  
• A probabilistic model for mining labeled ordered trees: Capturing patterns in carbohydrate sugar chains

  Nobuhisa Ueda; Kiyoko F. Aoki-Kinoshita; Atsuko Yamaguchi; Tatsuya Akutsu; Hiroshi Mamitsuka

  IEEE Transactions on Knowledge and Data Engineering, Aug. 2005, Peer-reviewed

  
• Graph kernels for molecular structure-activity relationship analysis with support vector machines

  Pierre Mahé; Nobuhisa Ueda; Tatsuya Akutsu; Jean-Luc Perret; Jean-Philippe Vert

  Journal of Chemical Information and Modeling, Jul. 2005, Peer-reviewed

  
• A stochastic approach to multi-gene expression dynamics

  T. Ochiai; J. C. Nacher; T. Akutsu

  Physics Letters, Section A: General, Atomic and Solid State Physics, 16 May 2005, Peer-reviewed

  
• Fast and accurate database homology search using upper bounds of local alignment scores

  Masumi Itoh; Susumu Goto; Tatsuya Akutsu; Minoru Kanehisa

  Bioinformatics, 01 Apr. 2005, Peer-reviewed

  
• Two complementary representations of a scale-free network

  J. C. Nacher; T. Yamada; S. Goto; M. Kanehisa; T. Akutsu

  Physica A: Statistical Mechanics and its Applications, 01 Apr. 2005, Peer-reviewed

  
• A score matrix to reveal the hidden links in glycans

  KF Aoki; H Mamitsuka; T Akutsu; M Kanehisa

  BIOINFORMATICS, Apr. 2005, Peer-reviewed

  
• Flexible construction of hierarchical scale-free networks with general exponent

  J. C. Nacher; N. Ueda; M. Kanehisa; T. Akutsu

  Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, Mar. 2005, Peer-reviewed

  
• Performance analysis of a greedy algorithm for inferring Boolean functions

  D Fukagawa; T Akutsu

  INFORMATION PROCESSING LETTERS, Jan. 2005, Peer-reviewed

  
• Clustering under the line graph transformation: Application to reaction network

  Jose C. Nacher; Nobuhisa Ueda; Takuji Yamada; Minoru Kanehisa; Tatsuya Akutsu

  BMC Bioinformatics, 24 Dec. 2004, Peer-reviewed

  
• A constructive approach to gene expression dynamics

  T. Ochiai; J. C. Nacher; T. Akutsu

  Physics Letters, Section A: General, Atomic and Solid State Physics, 27 Sep. 2004, Peer-reviewed

  
• Protein homology detection using string alignment kernels

  Hiroto Saigo; Jean-Philippe Vert; Nobuhisa Ueda; Tatsuya Akutsu

  Bioinformatics, 22 Jul. 2004, Peer-reviewed

  
• KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains

  KF Aoki; A Yamaguchi; N Ueda; T Akutsu; H Mamitsuka; S Goto; M Kanehisa

  NUCLEIC ACIDS RESEARCH, Jul. 2004, Peer-reviewed

  
• Optimizing substitution matrices by separating score distributions.

  Yuichiro Hourai; Tatsuya Akutsu; Yutaka Akiyama

  Bioinform., 2004

  
• Managing and analyzing carbohydrate data

  Kiyoko F. Aoki; Nobuhisa Ueda; Atsuko Yamaguchi; Tatsuya Akutsu; Minoru Kanehisa; Hiroshi Mamitsuka

  SIGMOD Record, 2004, Peer-reviewed

  
• Identification of genetic networks by strategic gene disruptions and gene overexpressions under a boolean model

  T Akutsu; S Kuhara; O Maruyama; S Miyano

  THEORETICAL COMPUTER SCIENCE, Apr. 2003, Peer-reviewed

  
• Inferring qualitative relations in genetic networks and metabolic pathways

  Tatsuya Akutsu; Satoru Miyano; Satoru Kuhara

  Bioinformatics, 2000, Peer-reviewed

  
• On the approximation of protein threading

  Tatsuya Akutsu; Satoru Miyano

  Theoretical Computer Science, 17 Jan. 1999, Peer-reviewed

  
• Distribution of Distances and Triangles in Point Sets and Its Application to Largest Common Point Set Problems

  Tatsuya Akutsu; Hisao Tamaki; Takeshi Tokuyama

  Proc. 13th ACM Symposium on Computational Geometry, Jun. 1997, Peer-reviewed

  
• Protein structure alignment using dynamic programming and iterative improvement

  T Akutsu

  IEICE TRANSACTIONS ON INFORMATION AND SYSTEMS, Dec. 1996, Peer-reviewed

  
• On PAC learnability of functional dependencies

  Tatsuya Akutsu; Atsuhiro Takasu

  New Generation Computing, Dec. 1994, Peer-reviewed

  

Misc.

• タンパク質間相互作用ネットワークにおける相互作用ドメイン対の確率的選択に基づくべき乗分布のモデル化

  NACHER J.C.; HAYASHIDA Morihiro; AKUTSU Tatsuya

  IPSJ SIG technical reports, 10 Dec. 2008

  
• Analysis of non-coding RNA-protein interaction network and its controllability features

  香々見 春菜; 阿久津 達也; ナチェル ホセ

  IPSJ SIG technical reports, 11 Dec. 2014

  
• Conservation law and Stability in Competitive Systems : Restoration phenomena from external perturbation (Theory of Biomathematics and Its Applications IX)

  Uechi Lisa; Akutsu Tatsuya

  RIMS Kokyuroku, Oct. 2013

  
• Markov property on Gene Expression Dynamics

  OCHIAI T.; NACHER J. C.; AKUTSU T.

  IEICE technical report. Nonlinear problems, 06 Sep. 2004

  
• On Approximation Algorithms for Minimum Multiset Covering Problem

  YAGIURA Yutaka; SHIMOZONO Shinichi; AKUTSU Tatsuya

  IEICE technical report. Theoretical foundations of Computing, 09 Nov. 2001

  
• Matching of Spots in Two Dimensional Electrophoresis Images : Point Matching Under Non-uniform Distortion

  AKUTSU Tatsuya; KANAYA Kyotetsu; OHYAMA Akira; FUJIYAMA Asao

  Technical report of IEICE. PRMU, 04 May 2000

  
• Editor's Introductrion to "New Trends of Bioinformatic" ("New Trends of Bioinformatic")

  AKUTSU Tatsuya; ASOGAWA Minoru; KONAGAYA Akihiko; Tatsuya Akutsu; Minoru Asogawa; Akihiko Konagaya

  人工知能学会誌 = Journal of Japanese Society for Artificial Intelligence, 01 Jan. 2000

  
• Fast Identification of Boolean Networks

  AKUTSU Tatsuya; MIYANO Satoru; KUHARA Satoru

  IPSJ SIG Notes, 27 Jan. 1999

  
• A Parallel Algorithm for Determining the Congruence of Point Sets in Three-Dimensions

  AKUTSU Tatsuya

  IEICE transactions on information and systems, 25 Apr. 1995

  
• Representation of a 3D Protein Structure Using a Sequence of Line Segments

  AKUTSU Tatsuya; TASHIMO Hiroshi

  IPSJ SIG Notes, 07 Feb. 1995

  
• A linear time pattern matching algorithm between a string and a tree

  AKUTSU Tatsuya

  Proceedings of the 4th Annual Symposium on Combinatorial Pattern Matching, Padova, Italy, 1993, 1993

  
• A linear time pattern matching algorithm between a string and a tree

  AKUTSU Tatsuya

  Proc. CPM'93, 1993

  
• Efficient Determination of Cluster Boundaries for Gene Expression Data Using Hierarchical Clustering (テーマ:特集「宇宙とAI」および一般)

  Moesa Harry Amri; K. C. Dukka Bahadur; 阿久津 達也

  人工知能基本問題研究会, 15 Jul. 2005

  
• Secondary Structure Prediction of Interacting RNAs: A Grammatical Approach

  Kato Yuki; Akutsu Tatsuya; Seki Hiroyuki

  IPSJ SIG technical reports, 21 Dec. 2007

  
• 1001 SIG Nights : An Overview of Special Interest Group on Bioinformatics (SIGBIO)

  AKUTSU Tatsuya

  IPSJ Magazine, 15 Dec. 2007

  
• RNA Secondary Structure Prediction Based on Formal Grammars

  KATO Yuki; SEKI Hiroyuki; AKUTSU Tatsuya

  IEICE technical report, 20 Nov. 2007

  
• Self-similarity symmetry in gene expression dynamics

  OCHIAI T.; NACHER J. C.; AKUTSU T.

  IPSJ SIG technical reports, 25 Jul. 2005

  
• Inference of Nonlinear Biological Systems from Time Series Data Using Linear Programming

  Akutsu Tatsuya; Miyano Satoru; Kuhara Satoru

  IPSJ SIG Notes, 25 Nov. 1999

  
• Hardness Results on Gapless Local Multiple Sequence Alignment

  AKUTSU Tatsuya

  IPSJ SIG Notes, 14 May 1999

  
• Geometric Pattern Matching Algorithms for Protein Structure Comparison

  AKUTSU Tatsuya

  IPSJ Magazine, 15 Oct. 1996

  
• Learning Score Function for Protein Threading Using Linear Programming

  TASHIMO Hiroshi; AKUTSU Tatsuya

  IPSJ SIG Notes, 26 Jul. 1996

  
• An O (n2) Time Algorithm for Computing a Canonical Form of a Chemical Structure Which Has a Planar Graph Structure

  AKUTSU Tatsuya

  IPSJ Journal, 15 Dec. 1992

  
• An Approximate Learning Algorithm for Functional Dependencies

  高須 淳宏; 阿久津 達也

  全国大会講演論文集, 27 Sep. 1993

  
• Optimizing amino acid substitution matrices with local alignment kernels

  SAIGO Hiroto; VERT Jean-Philippe; AKUTSU Tatsuya

  IPSJ SIG Notes, 17 Mar. 2006

  
• Inferring a Chemical Structure from a Feature Vector Based on Frequency of Labeled Paths and Small Fragments

  AKUTSU Tatsuya; FUKAGAWA Daiji

  IPSJ SIG technical reports, 10 Feb. 2006

  
• Algorithm for finding optimal degenerate patterns with an application to transcription factor binding sites consensus identification.

  SHINOZAKI Daisuke; AKUTSU Tatsuya; MARUYAMA Osamu

  IPSJ SIG Notes, 19 Sep. 2003

  
• Editor's Message

  Akutsu T

  情報処理学会論文誌数理モデル化と応用（TOM）, 15 May 2003

  
• On the Complexity of Deriving Position Specific Score Matrices

  AKUTSU Tatsuya; BANNAI Hideo; MIYANO Satoru; OTT Sascha

  IPSJ SIG Notes, 24 Jan. 2002

  
• Genome Informatics:Computational Problems in Bioinformatics

  AKUTSU Tatsuya

  IPSJ Magazine, 15 Jan. 2002

  
• Algorithms for Identifying Boolean Networks Based on Matrix Multiplication and Fingerprint Function

  AKUTSU Tatsuya; MIYANO Satoru; KUHARA Satoru

  IPSJ SIG Notes, 08 Nov. 1999

  
• Approximation and Exact Algorithms for Global Free - Energy Minimization of RNA Secondary Structures

  AKUTSU Tatsuya

  IPSJ SIG Notes, 20 May 1998

  
• On the Complexity of Learning Score Functions for Problems in Molecular Biology

  AKUTSU Tatsuya; YAGIURA Mutsunori

  IPSJ SIG Notes, 16 May 1997

  
• Distribution of Distances and Triangles in a Point Set and Algorithms for Computing the Largest Common Point Set

  AKUTSU Tatsuya; TAMAKI Hisao; TOKUYAMA Takeshi

  IPSJ SIG Notes, 23 Jan. 1997

  
• On the Approximation of Protein Threading

  AKUTSU Tatsuya

  IPSJ SIG Notes, 29 May 1996

  
• Approximating Minimum Keys and Optimal Substructure Screens

  AKUTSU Tatsuya; BAO Feng

  IPSJ SIG Notes, 21 Sep. 1995

  
• A Randomized Algorithm for Computing Largest Common Point Sets

  AKUTSU Tatsuya

  IPSJ SIG Notes, 20 Jul. 1995

  
• On the Editing Distance between Two - Dimensional Arrays

  AKUTSU Tatsuya

  IPSJ SIG Notes, 17 Mar. 1995

  
• Approximate String Matching with Variable length Don't Cares

  AKUTSU Tatsuya

  IPSJ SIG Notes, 23 Jan. 1995

  
• Substructure Search and Alignment Algorithms for Three - Dimensional Protein Structures

  Akutsu Tatsuya

  IPSJ SIG Notes, 21 Sep. 1994

  
• ON DETERMINING THE CONGRUITY OF POINT SETS IN HIGHER DIMENSIONS

  Akutsu Tatsuya

  IPSJ SIG Notes, 17 Mar. 1994

  
• APPROXIMATE STRING MATCHING WITH DON'T CARE CHARACTERS

  Akutsu Tatsuya

  IPSJ SIG Notes, 01 Oct. 1993

  
• ON APPROXIMABILITY OF THE LARGEST COMMON POINT SET OF MULTIPLE POINT SETS

  Akutsu Tatsuya

  IPSJ SIG Notes, 28 May 1993

  
• A Simple Proof of a Tight Bound of the Sum of Smaller Endpoint Degree over Edges of Graphs and Its Applications to Geometric Problems

  阿久津 達也; 青木 保一; 長谷川 進; 今井 浩; 徳山 豪

  情報処理学会研究報告アルゴリズム（AL）, 22 Jul. 1991

  
• Algorithms for Point Set Matching with κ-Differences

  AKUTSU Tatsuya

  IEICE technical report. Theoretical foundations of Computing, 15 Apr. 2004

  
• Computational Methods for Analyzing Metabolic and Genetic Networks

  AKUTSU Tatsuya

  Systems, control and information, 15 Mar. 2004

  
• A 2-Phase Algorithm for Enumerating Tree-like Chemical Graphs Satisfying Given Upper and Lower Bounds

  Masaki Suzuki; Hiroshi Nagamochi; Tatsuya Akutsu

  IPSJ SIG technical reports, 21 Mar. 2012

  
• Prediction of protein residue contacts using discriminative random field

  Mayumi Kamada; Morihiro Hayashida; Jiangning Song; Tatsuya Akutsu

  研究報告バイオ情報学（BIO）, 24 Nov. 2011

  
• Prediction of protein residue contacts using discriminative random field

  Mayumi Kamada; Morihiro Hayashida; Jiangning Song; Tatsuya Akutsu

  研究報告数理モデル化と問題解決（MPS）, 24 Nov. 2011

  
• Integer Programming and Dynamic Programming-based Methods of Optimizing Control Policy in Probabilistic Boolean Networks with Hard Constraints

  Xi Chen; Tatsuya Akutsu; Takeyuki Tamura; Wai-KiChing

  研究報告バイオ情報学（BIO）, 03 Mar. 2011

  
• A Fast Method for Inferring Strengths of Protein-Protein Interactions and a Hardness Result

  HAYASHIDA Morihiro; UEDA Nobuhisa; AKUTSU Tatsuya

  The Transactions of the Institute of Electronics, Information and Communication Engineers A, 01 Jan. 2005

  
• Knowledge Discovery in Bioinformatics

  Akutsu Tatsuya

  Proceedings of the Society Conference of IEICE, 29 Aug. 2001

  
• A Minimum Path Decomposition of the Hasse Diagram for Testing the Consistency of Functional Dependencies

  Takasu Atsuhiro; Akutsu Tatsuya

  IEICE transactions on information and systems, 25 Feb. 1993

  
• Algorithms for Identifying Gene Regulatory Networks

  Akutsu Tatsuya

  Proceedings of the Society Conference of IEICE, 07 Sep. 1998

  
• Prediction of Protein Folding Rates from Structural Topology and Complex Network Properties

  SONG JIANGNING; TAKEMOTO KAZUHIRO; SHEN HONGBIN; TAN HAO; GROMIHA M. MICHAEL; AKUTSU TATSUYA

  研究報告バイオ情報学（BIO）, 11 Jun. 2010

  
• A Quadsection Algorithm for Grammar-Based Image Compression (数理モデル化と問題解決(MPS) Vol.2010-MPS-78)

  HAYASHIDA MORIHIRO; RUAN PEIYING; AKUTSU TATSUYA

  情報処理学会研究報告, Jun. 2010

  
• A Quadsection Algorithm for Grammar-Based Image Compression

  HAYASHIDA MORIHIRO; RUAN PEIYING; AKUTSU TATSUYA

  研究報告数理モデル化と問題解決（MPS）, 14 May 2010

  
• Prediction of RNA Secondary Structures with Binding Sites Using Dynamic Programming Algorithm

  POOLSAP UNYANEE; KATO YUKI; AKUTSU TATSUYA

  研究報告バイオ情報学（BIO）, 18 May 2009

  
• A_007 Approximation Algorithms for Optimal RNA Secondary Structures Common to Multiple Sequences

  Tamura Takeyuki; Akutsu Tatsuya

  情報科学技術フォーラム一般講演論文集, 21 Aug. 2006

  
• Dynamic Programming and Clique Based Approaches for Protein Threading with Profiles and Constraints

  AKUTSU Tatsuya; HAYASHIDA Morihiro; BAHADUR K. C. Dukka; TOMITA Etsuji; SUZUKI Jun'ichi; HORIMOTO Katsuhisa

  IEICE Trans., A, 01 May 2006

  
• Detection and Enumeration of Steady States in Biological Information Networks (Acceleration and Visualization of Computation for Enumeration Problems)

  Akutsu Tatsuya

  RIMS Kokyuroku, Apr. 2009

  
• Efficient Computation of Impact Degrees for Multiple Reactions in Metabolic Networks with Cycles (バイオ情報学(BIO) Vol.2009-BIO-18)

  CONG YANG; TAMURA TAKEYUKI; AKUTSU TATSUYA

  情報処理学会研究報告, Oct. 2009

  
• Bioinformatics: An Overview.

  Tatsuya Akutsu

  情報の科学と技術, Jun. 2021, Invited, Lead author, Last author, Corresponding author

  
• Identifying gene co-expression networks and mutually exclusive gene sets from scRNA-seq data

  Natsu Nakajima; Tatsuya Akutsu; Ryuichiro Nakato

  細胞, Nov. 2020, Invited

  
• Analysis of Boolean Networks and Boolean Models of Metabolic Networks

  Tatsuya Akutsu

  Application of Omics, AI and Blockchain in Bioinformatics Research (Book Chapter), Nov. 2019, Invited, Lead author, Last author, Corresponding author

  
• On the minimum number of genes required for discriminating steady states under a Boolean model

  Cheng Xiaoqing; Tamura Takeyuki; Ching Wai-Ki; Akutsu Tatsuya

  情報処理学会第51回バイオ情報学研究会, Sep. 2017

  
• A short review of methods for Caspase cleavage site prediction.

  情報処理学会第51回バイオ情報学研究会, Sep. 2017

  
• 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

  石塚雅之; 阿久津達也; ナチェルホセ

  情報処理学会バイオ情報学研究会, Jun. 2017

  
• 数理と人工知能技術によるゲノム情報と化学情報の解析

  阿久津達也

  海洋化学研究, 12 Nov. 2016

  
• Exact Identification of the Structure of a Probabilistic Boolean Network from Samples

  Xiaoqing Cheng; Tomoya Mori; Yushan Qiu; Wai-Ki Ching; Tatsuya Akutsu

  IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, Nov. 2016

  
• Enumerating Naphthalene Isomers of Tree-like Chemical Graphs.

  Fei He; Akiyoshi Hanai; NAGAMOCHI Hiroshi; Tatsuya Akutsu

  BIOINFORMATICS, Feb. 2016, Peer-reviewed

  
• 文字列データの統計的クラスタリングのためのLaplace様混合モデルとEMアルゴリズムの理論

  小谷野仁; 林田守広; 阿久津達也

  日本応用数理学会年会講演予稿集(CD-ROM), 02 Sep. 2015

  
• 根付き順序木の圧縮における分割型文法とオイラー文字列との比較

  劉立偉; 森智弥; 趙楊; 林田守広; 阿久津達也

  電子情報通信学会技術研究報告, 16 Jun. 2015

  
• String Clustering Based on a Laplace-like Mixture and EM Algorithm on a Set of Strings

  小谷野仁; 林田守広; 阿久津達也

  電子情報通信学会技術研究報告, 16 Jun. 2015

  
• Network Completion for Static Gene Expression Data

  Natsu Nakajima; Tatsuya Akutsu

  IPSJ SIG technical reports, 13 Mar. 2015

  
• タンパク質ドメイン構成に基づくプロテオーム圧縮

  林田守広; 阮佩穎; 阿久津達也

  研究報告数理モデル化と問題解決（MPS）, 18 Sep. 2014

  
• A-008 On Observability of Steady States in a Boolean Network

  Akutsu Tatsuya; Tamura Takeyuki

  情報科学技術フォーラム講演論文集, 19 Aug. 2014

  
• Prediction of Heterotrimeric Protein Complexes by Two-phase Learning Using Neighboring Kernels

  RUAN PEIYING; HAYASHIDA MORIHIRO; MARUYAMA OSAMU; AKUTSU TATSUYA

  電子情報通信学会技術研究報告 = IEICE technical report : 信学技報, 25 Jun. 2014

  
• Maximum Margin Classifier Working in a Metric Space of Strings and Its Application to Protein Science

  KOYANO HITOSHI; HAYASHIDA MORIHIRO; AKUTSU TATSUYA

  電子情報通信学会技術研究報告 = IEICE technical report : 信学技報, 25 Jun. 2014

  
• Grammar-based Compression for Multiple Trees Using Integer Programming

  ZHAO YANG; HAYASHIDA MORIHIRO; CAO YUE; HWANG JAEWOOK; AKUTSU TATSUYA

  電子情報通信学会技術研究報告. IBISML, 情報論的学習理論と機械学習, 18 Jun. 2014

  
• Prediction of Heterotrimeric Protein Complexes by Two-phase Learning Using Neighboring Kernels

  Peiying Ruan; Morihiro Hayashida; Osamu Maruyama; Tatsuya Akutsu

  IPSJ SIG Notes, 18 Jun. 2014

  
• Prediction of Heterotrimeric Protein Complexes by Two-phase Learning Using Neighboring Kernels

  Peiying Ruan; Morihiro Hayashida; Osamu Maruyama; Tatsuya Akutsu

  IPSJ SIG technical reports, 18 Jun. 2014

  
• Grammar-based Compression for Multiple Trees Using Integer Programming

  Yang Zhao; Morihiro Hayashida; Yue Cao; Jaewook Hwang; Tatsuya Akutsu

  IPSJ SIG technical reports, 18 Jun. 2014

  
• Maximum Margin Classifier Working in a Metric Space of Strings and Its Application to Protein Science

  Hitoshi Koyano; Morihiro Hayashida; Tatsuya Akutsu

  IPSJ SIG Notes, 18 Jun. 2014

  
• Parallelization of Enumerating Tree-like Chemical Compounds by Breadth-first Search Order

  Morihiro Hayashida; Jira Jindalertudomdee; Yang Zhao; Tatsuya Akutsu

  IPSJ SIG Notes, 24 Feb. 2014

  
• Algorithms for Finding a Largest Common Subtree of Bounded Degree

  Tatsuya Akutsu; Takeyuki Tamura; Avraham A.Melkman; Atsuhiro Takasu

  IPSJ SIG Notes, 23 Jan. 2014

  
• Breadth-first Search Approach to Enumeration of Tree-like Chemical Compounds

  Yang Zhao; Morihiro Hayashida; Jira Jindalertudomdee; Hiroshi Nagamochi; Tatsuya Akutsu

  IPSJ SIG technical reports, 04 Dec. 2013

  
• Prediction of Heterodimeric Protein Complexes from Weighted Protein-Protein Interaction Networks Using Novel Features and Kernel Functions

  Peiying Ruan; Morihiro Hayashida; Osamu Maruyama; Tatsuya Akutsu

  IPSJ SIG technical reports, 04 Dec. 2013

  
• Breadth-first Search Approach to Enumeration of Tree-like Chemical Compounds

  Yang Zhao; Morihiro Hayashida; Jira Jindalertudomdee; Hiroshi Nagamochi; Tatsuya Akutsu

  IPSJ SIG Notes, 04 Dec. 2013

  
• A Dominating Set Approach to Structural Controllability of Unidirectional Bipartite Networks

  Jose C.Nacher; Tatsuya Akutsu

  IPSJ SIG Notes, 19 Sep. 2013

  
• Survival Analysis by Penalized Regression and Matrix Factorization

  Yeuntyng Lai; Morihiro Hayashida; Tatsuya Akutsu

  IPSJ SIG Notes, 19 Sep. 2013

  
• Inferring Strengths of Protein-Protein Interactions Using Support Vector Regression

  Yusuke Sakuma; Mayumi Kamada; Morihiro Hayashida; Tatsuya Akutsu

  IPSJ SIG Notes, 15 Jul. 2013

  
• Comparison and enumeration of chemical graphs

  Tatsuya Akutsu; Hiroshi Nagamochi

  Computational and Structural Biotechnology Journal, 2013

  
• BI-7-5 Discrete Models and Control of Genetic Networks and Metabolic Networks

  Akutsu Tatsuya

  Proceedings of the IEICE General Conference, 06 Mar. 2012

  
• Integer programming-based method for grammar-based compression of ordered and unordered trees (特集 「脳科学と知識処理」および一般)

  趙 楊; 林田 守広; 阿久津 達也

  人工知能基本問題研究会, 31 Jul. 2010

  
• 高さ制約付き無順序木の高速類似検索アルゴリズムについて

  深川大路; 阿久津達也; 高須淳宏; 安達淳

  情報処理学会全国大会講演論文集, 08 Mar. 2010

  
• 2K-1 A fast similarity search algortihm for unordered trees of bounded height

  FUKAGAWA Daiji; AKUTSU Tatsuya; TAKASU Atsuhiro; ADACHI Jun

  全国大会講演論文集, 08 Mar. 2010

  
• Approximating Edit Distance of Unordered Trees of Bounded Height

  FUKAGAWA Daiji; AKUTSU Tatsuya; TAKASU Atsuhiro

  IEICE technical report. Theoretical foundations of Computing, 22 Jun. 2009

  
• Statistical learning algorithm for tree similarity (特集「知識発見の諸科学への応用」および一般)

  高須 淳宏; 深川 大路; 阿久津 達也

  人工知能基本問題研究会, 17 Sep. 2008

  
• 確率モデルに基づく木の類似度のパラメータ学習について

  深川大路; 高須淳宏; 阿久津達也

  情報処理学会全国大会講演論文集, 13 Mar. 2008

  
• 2J-3 Learning Tree Similarity Based on a Statistical Model

  Fukagawa Daiji; Takasu Atsuhiro; Akutsu Tatsuya

  全国大会講演論文集, 13 Mar. 2008

  
• Recent progress on the analysis of power-law features in complex cellular networks

  J. C. Nacher; T. Akutsu

  Cell Biochemistry and Biophysics, Sep. 2007

  
• タンパク質間相互作用強度の計算機による予測法 (タンパク質間相互作用)

  林田 守広; 阿久津 達也

  生体の科学, Sep. 2007

  
• Enumerating tree-like chemical structures from feature vector

  H. Fujiwara; L. Zhao; Hiroshi Nagamochi; T. Akutsu; W. Jiexun

  2007 Korea-Japan Joint Workshop on Algorithms and Computation, pp. 48-55, 2007, Peer-reviewed

  
• A novel clustering method for analysis of biological networks using maximal components of graphs

  HAYASHIDA Morihiro; AKUTSU Tatsuya; NAGAMOCHI Hiroshi

  IPSJ SIG technical reports, 15 Sep. 2006

  
• Approximating Tree Edit Distance Through String Edit Distance

  AKUTSU Tatsuya; FUKAGAWA Daiji; TAKASU Atsuhiro

  IEICE technical report. Theoretical foundations of Computing, 17 May 2006

  
• Scale-free mixing in protein domain networks

  NACHER Jose C; HAYASHIDA Morihiro; AKUTSU Tatsuya

  IPSJ SIG technical reports, 10 Feb. 2006

  
• 生物情報ネットワークの構造およびダイナミクス解析 (ゲノムから生命システムへ) -- (ゲノムから情報科学)

  阿久津 達也; 落合 友四郎; Nacher Jose C.

  蛋白質核酸酵素, Dec. 2005

  
• On the Complexity of Inferring a Graph from Path Frequency

  AKUTSU Tatsuya; FUKAGAWA Daiji

  電子情報通信学会技術研究報告. COMP, コンピュテーション, 11 Apr. 2005

  
• Profile Alignment with Constraints

  AKUTSU Tatsuya; HAYASHIDA Morihiro; TOMITA Etsuji; SUZUKI Jun'ichi; HORIMOTO Katsuhisa

  IEICE technical report. Theoretical foundations of Computing, 22 Jan. 2004

  
• Performance Analysis of a Greedy Algorithm for Inferring Boolean Functions

  FUKAGAWA Daiji; AKUTSU Tatsuya

  IEICE technical report. Theoretical foundations of Computing, 18 Apr. 2003

  

Presentations

• Graph Theoretic Approaches to Analysis of Biological Networks

  Tatsuya Akutsu

  2023 13th International Conference on Biomedical Engineering and Technology (ICBET 2023), 16 Jun. 2023, Invited

  
• On the Complexity of Tree Edit Distance with Variables

  Tatsuya Akutsu

  33rd International Symposium on Algorithms and Computation (ISAAC 2022), 19 Dec. 2022

  
• 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

  阿久津達也

  第11回生命医薬情報学連合退会, 15 Sep. 2022, Invited

  
• Network-based Approaches to Identification of Important Genes and Proteins

  Tatsuya Akutsu

  2022 10th International Conference on Bioinformatics and Computational Biology (ICBCB 2022), 14 May 2022, Invited

  
• On the Compressive Power of Boolean Threshold Autoencoders

  Tatsuya Akutsu

  The 1st Online Conference on Algorithms, 27 Sep. 2021, Invited

  
• Control and Observation of Boolean Networks when Targets are Restricted to Attractors

  Tatsuya Akutsu

  Modeling and Control of Boolean Dynamical Systems (Workshop in European Control Conference 2021), 29 Jun. 2021, Invited

  
• Graph Theoretic Approaches to Analysis and Control of Biological Networks

  Tatsuya Akutsu

  2021 IEEE the 9th International Conference on Bioinformatics and Computational Biology, 21 May 2021, Invited

  
• A New Integer Linear Programming Formulation to the Inverse QSAR/QSPR for Acyclic Chemical Compounds Using Skeleton Trees

  Fan Zhang; Jianshen Zhu; Rachaya Chiewvanichakorn; Aleksandar Shurbevski; Hiroshi Nagamochi; Tatsuya Akutsu

  33rd International Conference on Industrial, Engineering and Other Applications of Applied Intelligent Systems, 24 Sep. 2020

  
• A Novel Method for the Inverse QSAR/QSPR based on Artificial Neural Networks and Mixed Integer Linear Programming with Guaranteed Admissibility

  Naveed Ahmed AzamRachaya Chiewvanichakorn; Fan Zhang; Aleksandar Shurbevski; Hiroshi Nagamochi; Tatsuya Akutsu

  13th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2020), 24 Feb. 2020

  
• Breast cancer subtype by imbalanced omics data through a deep learning fusion model

  J. Zeng; H. Cai; T. Akutsu

  10th International Conference on Bioscience, Biochemistry and Bioinformatics (ICBBB 2020), 21 Jan. 2020

  
• Procleave: A Bioinformatic Approach for Protease-specific Substrate Cleavage Site Prediction by Combining Sequence and Structural Information

  Fuyi Li; Tatsuya Akutsu; Jian Li; Jiangning Song

  10h International Conference on Bioscience, Biochemistry and Bioinformatics (ICBBB2020), 21 Jan. 2020

  
• A method for the inverse QSAR/QSPR based on artificial neural networks and mixed integer linear programming

  R. ChiewvanichakornC. Wang; Z. Zhang; A. Shurbevski; H. Nagamochi; T. Akutsu

  10th International Conference on Bioscience, Biochemistry and Bioinformatics (ICBBB 2020), 20 Jan. 2020

  
• Boolean Network-Based Approaches towards Precisions Medicine

  Tatsuya Akutsu

  Workshop on Precision Network Medicine in the era of big data! (ICSB 2019), 31 Oct. 2019, Invited

  
• 生体ネットワーク制御の ための数理モデル

  阿久津 達也

  生命情報科学若手の会 第11回研究会, 19 Oct. 2019, Invited

  
• Boolean Network-based Approaches for Controlling Genetic Networks and Metabolic Networks

  Tatsuya Akutsu

  International Symposium on the Genetics of Industrial Microorganisms (GIM 2019), 09 Sep. 2019, Invited

  
• Python と Scikit-learn によるバイオインフォマティクスデータ解析

  阿久津 達也

  データサイエンススクール 2019 -京都大学データサイエンス教育公開ワークショップ-, 02 Aug. 2019, Invited

  
• Graph theoretic approaches to controllability of biological networks

  Tatsuya Akutsu

  Workshop on Bioinformatics and Data Analysis, 15 Jun. 2019, Invited

  
• A Method for Analyzing Single Cell Expression Data Based on PCA, Gaussian Mixture Model, and Kullback–Leibler Divergence

  Tatsuya Akutsu

  Japan-Germany International Workshop 2019-1 The Human Cell Type Authentication Initiative, 15 May 2019, Invited

  
• 細胞種情報解析における数理モデル概説

  阿久津 達也

  第1回 幹細胞情報学イニシアチブ研究会, 10 May 2019, Invited

  
• A mixed integer linear programming formulation to artificial neural networks

  Tatsuya Akutsu; Hiroshi Nagamochi

  2nd International Conference on Information Science and System, 17 Mar. 2019

  
• 確率ブーリアンネットワークの部分例の出現頻度からの同定可能性について

  阿久津 達也

  第109回人工知能基本問題研究会, 14 Mar. 2019

  
• バイオインフォマティクスにおけるデータサイエンス

  阿久津 達也

  Data Science Spring School 2019, 27 Feb. 2019

  
• Integration and Analysis of Heterogeneous Biological Data via Convolutional Neural Networks and Matrix Factorization

  Tatsuya Akutsu

  9th International Conference on Bioscience, Biochemistry and Bioinformatics, 08 Jan. 2019, Invited

  
• Algorithms for Analysis and Control of Boolean Networks

  阿久津 達也

  5th International Conference on Algorithms for Computational Biology, 25 Jun. 2018, Invited

  
• Minimum Dominating Set-based Approaches for Analyzing and Controlling Biological Networks

  Tatsuya Akutsu

  2016 Biotech and Pharmaceutical Service Platform - Biological Network Analysis Conference, 04 Nov. 2016

  
• Minimum Dominating Set-Based Approaches for Controlling and Analyzing Biological Networks

  Tatsuya Akutsu

  The 2016 (26th) Annual Meeting of the Japanese Society for Mathematical Biology, 07 Sep. 2016

  
• Minimum Dominating Set-Based Approaches for Controlling and Analyzing Biological Networks

  Tatsuya Akutsu

  Controlling Complex Network Systems in Biology (Workshop), 05 Sep. 2016

  
• Extensions and Applications of the Minimum Dominating Set-Based Approach to Controllability of Complex Networks

  Tatsuya Akutsu

  Controlling Complex Networks (Satellite Symposium of International School and Conference on Network Science), 30 May 2016

  

Books and Other Publications

• 複雑ネットワークと制御理論

  阿久津; 達也、ホセ・ナチェル, Joint work

  森北出版, Jun. 2023

  Find Kyoto University's collection of books :

  
• バイオインフォマティクス : Pythonによる実践レシピ

  阿久津, 達也; 竹本, 和広(共訳)

  朝倉書店, Aug. 2020

  Find Kyoto University's collection of books :

  
• Algorithms for Analysis, Inference, and Control of Boolean Networks

  Tatsuya Akutsu, Single work, 216 pages

  World Scientific, Apr. 2018, Not refereed

  
• Sequence alignment algorithms: Applications to glycans and trees and tree-like structures

  Akutsu T

  Handbook of Chemoinformatics Algorithms , , 363-381, 2010, Not refereed

  
• バイオインフォマティクス ー配列データ解析と構造予測ー

  阿久津 達也

  朝倉書店, May 2007, Not refereed

  
• バイオインフォマティクスの数理とアルゴリズム

  丸山 修; 阿久津 達也, Joint work

  共立出版, Feb. 2007, Not refereed

  
• バイオインフォマティクス ―確率モデルによる遺伝子配列解析ー

  阿久津 達也; 浅井 潔; 矢田 哲士, Joint translation

  Mar. 2001, Not refereed

  

Awards

• 15 Sep. 2023

  日本バイオインフォマティクス学会, 2022年度日本バイオインフォマティクス学会賞

  生体ネットワークの推定と制御に関する数理的・先駆的研究,, Japan, Japan society

  阿久津達也
• 05 Sep. 2014

  FIT（情報科学技術フォーラム）, FIT奨励賞
• 26 Oct. 2014

  InTech (Open Access Publisher),, Intech Award Diploma
• 18 Dec. 2014

  情報処理学会　バイオ情報学研究会, SIGBIO功労賞
• 16 Dec. 2009

  The 20th International Conference on Genome Informatics, 2009 Oxford Journals - JSBi Bioinformatics Prize (Best Poster Award)
• 2006

  情報処理学会　数理モデル化と問題解決研究会, SIGMPS功労賞
• 15 Dec. 2004

  15th International Conference on Genome Informatics, 2004 Oxford University Press Bioinformatics Prize (Best Poster Award)
• 03 Jun. 2016

  Information Processing Society of Japan, Fellow, Information Processing Society of Japan
• 25 Sep. 2020

  The 33th International Conference on Industrial, Engineering & Other Applications of Applied Intelligent Systems, Best Theory Paper Award

External funds: Kakenhi

• Analysis and Applications of Discrete Preimage Problems

  Grant-in-Aid for Scientific Research (A)

  Medium-sized Section 61:Human informatics and related fields

  Kyoto University

  阿久津 達也

  From 01 Apr. 2018, To 31 Mar. 2023, Project Closed

  逆問題;特徴ベクトル;グラフアルゴリズム;ニューラルネットワーク;バイオインフォマティクス;ケモインフォマティクス

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-18H04113/
• Pan-cancer module and network analysis for identifying dominating subnetworks across hu man cancers

  Grant-in-Aid for JSPS Fellows

  Kyoto University

  From 10 Nov. 2017, To 31 Mar. 2020, Project Closed

  汎がんモジュール;タンパク質相互作用ネットワーク;遺伝子発現量;遺伝子変異;遺伝子進化;深層学習;ブーリアンネットワーク

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-17F17353/
• 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

  Grant-in-Aid for JSPS Fellows

  Kyoto University

  From 09 Nov. 2015, To 31 Mar. 2017, Project Closed

  caspase;protease;data fution;bioinformatics;Protein cleavage;Data fusion;Machine learning,

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-15F15788/
• Structurally Robust Control of Complex Networks

  Grant-in-Aid for Challenging Exploratory Research

  Kyoto University

  Tatsuya Akutsu

  From 01 Apr. 2014, To 31 Mar. 2018, Project Closed

  複雑ネットワーク;スケールフリーネットワーク;ブーリアンネットワーク;遺伝子ネットワーク;最小支配集合;構造的可制御性;ロバストネス

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-26540125/
• An Approach to Novel Structure Design by Combining Discrete Methods and Statistical Methods

  Grant-in-Aid for Scientific Research (A)

  Kyoto University

  Tatsuya AKUTSU

  From 01 Apr. 2014, To 31 Mar. 2019, Project Closed

  ケモインフォマティクス;構造列挙;グラフアルゴリズム;カーネル法;生物情報ネットワーク;化学構造;特徴ベクトル;ヶモインフォマティクス;グラフ列挙

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-26240034/
• Discrete Model-Based Methods for Control of Complex BiologicalSyetems

  Grant-in-Aid for Challenging Exploratory Research

  Kyoto University

  Tatsuya AKUTSU

  From 01 Apr. 2010, To 31 Mar. 2013, Project Closed

  複雑生体ネットワーク;ブーリアンネットワーク;スケールフリーネットワーク;遺伝子ネットワーク;代謝ネットワーク;制御理論;構造的可制御性;代謝流束解析;線形離散時間システム;確率ブーリアンネットワーク;制御;アトラクター;NP完全;Canalyzing関数

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-22650045/
• An Approach to Novel Structural Design by Combining Discrete Methods and Kernel Methods

  Grant-in-Aid for Scientific Research (A)

  Kyoto University

  Tatsuya AKUTSU

  From 01 Apr. 2010, To 31 Mar. 2015, Project Closed

  特徴ベクトル;カーネル法;化学構造;グラフ理論;立体異性体;構造列挙;木構造;異性体;ベンゼン環;構造比較;外平面的グラフ

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-22240009/
• 複雑生体構造のデータ圧縮を通じた発生原理の解明

  Grant-in-Aid for Challenging Exploratory Research

  Kyoto University

  阿久津 達也

  From 01 Apr. 2007, To 31 Mar. 2010, Project Closed

  L-system;グラフ文法;文法圧縮;複雑系;代謝ネットワーク;木構造;文脈自由文法;発生;オイラー文字列;文字列圧縮;生体構造;データ圧縮;編集距離;無順序木;グラフ構造;Eulerツアー;画像圧縮;タンパク質立体構造

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-19650053/
• New Methods for Designing Chemical Structures Using Graph Theory and Kernel Methods

  Grant-in-Aid for Scientific Research (A)

  Kyoto University

  Tatsuya AKUTSU

  From 01 Apr. 2007, To 31 Mar. 2010, Project Closed

  カーネル法;グラフアルゴリズム;特徴ベクトル;サポートベクターマシン;列挙アルゴリズム;動的計画法;ケモインフォマティクス;グラフ理論;RNA二次構造;タンパク質立体構造;化学構造;立体異性体;木構造;外平面的グラフ;構造活性相関;光学異性体;外平面グラフ

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-19200022/
• Analysis of Structure and Dynamics of Biological Information Networks

  Grant-in-Aid for Scientific Research on Priority Areas

  Biological Sciences

  Kyoto University

  Tatsuya AKUTSU

  From 01 Apr. 2005, To 31 Mar. 2010, Project Closed

  遺伝子ネットワーク;代謝ネットワーク;タンパク質相互作用;スケールフリーネットワーク;タンパク質ドメイン;遺伝子発現;大規模進化動力学モデル;生物情報ネットワーク;スケールフリー;進化動力学モデル;緑膿菌;ブーリアンネットワーク;形態形成;神経細胞;遺伝子発現データ;オペロン;ネットワーク定常状態;概日リズム;バイオインフォマティクス;システム生物学;べき乗則;遺伝子間相互作用

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-17017019/
• Pattern Matching Methods for Structured Data in Bioinformatics

  Grant-in-Aid for Scientific Research (B)

  Kyoto University

  Tatsuya AKUTSU

  From 01 Apr. 2004, To 31 Mar. 2007, Project Closed

  配列アラインメント;三角不等式;編集距離;オイラー文字列;カーネル法;サポートベクタマシン;化学構造;細胞内局在部位予測;特徴ベクトル;木構造;平面的グラフ;クラスタリング;タンパク質配列;生物情報ネットワーク;グラフカーネル;アルゴリズム;タンパク質細胞内局在部位予測;サポートベクターマシン;パターンマッチング;モチーフ抽出;国際情報交換;フランス;位置特異的スコア行列;最大共通部分点集合;糖鎖, sequence alignment;triangle inequality;edit distance;Euler string;kernel method;support vector machine;chemical structure;subcellular location prediction

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-16300092/
• Information Scientific Foundations of Knowledge Discovery from Proteome Data

  Grant-in-Aid for Scientific Research (B)

  The University of Tokyo

  Satoru MIYANO

  From 01 Apr. 2003, To 31 Mar. 2006, Project Closed

  タンパク質ネットワーク;遺伝子ネットワーク;タンパク質相互作用情報;タンパク質-RNA相互作用予測;パスウェイモデリング;シミュレーション;タンパク質相互作用;マイクロアレイ解析;パスウェイシミュレーション, protein network;gene network;protein-protein interaction;protein-RNA interaction prediction;pathway modeling;simulation

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-15300099/
• Algorithms for Extraction of Common Patterns from Data in Bioinformatics

  Grant-in-Aid for Scientific Research (C)

  Kyoto University

  Tatsuya AKUTSU

  From 01 Apr. 2001, To 31 Mar. 2004, Project Closed

  バイオインフォマティクス;パターンマッチング;配列モチーフ;アルゴリズム;カーネル法;位置依存スコア行列;局所アライメント;サポートベクタマシン;ローカルアライメント;ホモロジー検索;点集合;合同性判定;最大共通部分点集合;近似マッチング;モチーフ抽出;最大クリーク;電気泳動;スポットマッチング;構造アライメント;GIBBSサンプリング;相対エントロピー;ローカルサーチ, Bioinformatics;Pattern matching;Sequence motif;Algorithms;Kernel method;Position specific score matrix;Local alignment

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-13680394/
• Foundations of Computational Knowledge Discovery from cDNA Microarray Data

  Grant-in-Aid for Scientific Research (B)

  The University of Tokyo

  Satoru MIYANO

  From 01 Apr. 2000, To 31 Mar. 2003, Project Closed

  遺伝子ネットワーク;知識発見;質的ネットワーク;ブーリンアンネットワーク;マイクロアレイ;ハイブリッドペトリネット;システムバイオロジー;学習;ブーリアンネットワーク, Gene network;Knowledge discovery;Qualitative network;Boolean network;Microarray;Hybrid Petri net;Systems biology;Computational learning

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-12480080/
• Construction and Retrieval of Highly Integrated Biological Databases

  Grant-in-Aid for Scientific Research on Priority Areas

  Biological Sciences

  Kyoto University

  Susumu GOTO

  From 01 Apr. 2000, To 31 Mar. 2005, Project Closed

  データベース;バイオインフォマティクス;オントロジー;アルゴリズム;分子間相互作用;反応ネットワーク;グリッド;ネットワークトポロジー;化合物構造比較;糖鎖構造データベース;グラフトポロジー;統合データベース;タンパク質立体構造予測;文献からの知識抽出;タンパク質間相互作用予測;グリッドコンピューティング;分子生物学データベース;酵素反応;グラフ比較;相関クラスタ;経路探索;アミノ酸配列類似度データ;リンク情報;相関ルール発見手法;ゲノムデータベース;知識抽出;マイクロアレイ発現データ, Database;Bioinformatics;Ontology;Algorithm;Molecular interaction;Reaction network;GRID;Network topology

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-12208007/
• Knowledge Discovery from Genome Databases

  Grant-in-Aid for Scientific Research on Priority Areas

  Biological Sciences

  University of Tokyo

  Shinichi MORISHITA

  From 01 Apr. 2000, To 31 Mar. 2005, Project Closed

  バイオインフォマティクス;ゲノム解読;siRNA;転写開始点;比較ゲノム;表現型;フェノーム;顕微鏡画像解析;遺伝子予測;ゲノムアノテーション;RNAi;遺伝子発現量解析;ゲノム配列解読;ゲノム解析ソフトウエア;DNAチップ;オリゴマ設計;ゲノム情報;アルゴリズム;データマイニング;ヒトゲノム;アラインメント;アミノ酸モチーフ;データベース;ゲノム, Bioinformatics;Genome Sequencing;siRNA;Transcription Start Site Analysis;Comparative Genomics;Phenome;Image Processing of Micrographs

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-12208003/
• 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

  Grant-in-Aid for Encouragement of Young Scientists (A)

  The University of Tokyo

  阿久津 達也

  From 01 Apr. 1998, To 31 Mar. 2000, Project Closed

  計算幾何学;パターンマッチング;幾何マッチング;アルゴリズム;電気泳動;DNAマイクロアレイ

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-10780171/
• Development of Data Mining System Using Binary Decision Diagrams for Knowledge Representation

  Grant-in-Aid for Scientific Research (B)

  The University of Tokyo

  Satoru MIYANO

  From 01 Apr. 1997, To 31 Mar. 2000, Project Closed

  二分決定グラフ;学習;知識発見;パターンマッチングアルゴリズム;データマイニング;計算量;情報量;ゲノム;データマインイング;ゲノム情報, binary decision diagram;learning;knowledge discovery;pattern matching algorithm;data mining;computational complexity;entropy;genome

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-09558032/
• Biological Knowledge Based on Genome Information

  Grant-in-Aid for Scientific Research on Priority Areas (A)

  KYOTO UNIVERSITY

  Minoru KANEHISA

  From 01 Apr. 1996, To 31 Mar. 2001, Project Closed

  ゲノム解析;遺伝子機能予測;タンパク質立体構造予測;データベース;ネットワーク;分子間相互作用;パスウェイ;遺伝子疾患;配列解析, Genome analysis;Gene function prediction;Protein structure prediction;Database;Network;Molecular interactions;Pathway;Genetic diseases

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-08283103/
• Parallel and Distributed Computing and its Applications

  Grant-in-Aid for international Scientific Research

  Gunma University, Faculty of Engineering

  Yoshihide IGARASHI

  From 01 Apr. 1995, To 31 Mar. 1997, Project Closed

  並列;分散;アルゴリズム;計算機;半導体;デバイス;通信;同期;並列・分散処理;並列オペレーティングシステム;並列・分散アルゴリズム;耐故障性;VLSIレイアウト;AND-EXOR論理式;遺伝情報解析;デバイスシミュレーション, parallel;distribution;algorithm;computer;semi-conductor;device;communication;synchronization;fault-tolerant

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-07045019/
• Advanced Studies and Developments on Discrete Preimage Problems

  Grant-in-Aid for Scientific Research (A)

  Medium-sized Section 61:Human informatics and related fields

  Kyoto University

  阿久津 達也

  From 01 Apr. 2022, To 31 Mar. 2027, Granted

  離散原像問題;ニューラルネットワーク;整数計画法;ケモインフォマティクス;バイオインフォマティクス

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-22H00532/
• Analysis and Control of Steady States of Multiple Biological Networks

  Grant-in-Aid for Challenging Research (Exploratory)

  Medium-sized Section 62:Applied informatics and related fields

  Kyoto University

  阿久津 達也

  From 30 Jun. 2022, To 31 Mar. 2025, Granted

  生体ネットワーク;定常状態制御;多層ネットワーク;遺伝子ネットワーク;ブーリアンネットワーク

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-22K19830/

Education

Teaching subject(s)

• From 01 Apr. 2023, To 31 Mar. 2024

  Introduction to Computational Systems Bioinformatics

  9119, Spring, Faculty of Engineering, 2
• From 01 Apr. 2023, To 31 Mar. 2024

  Bioinformatics, Adv.

  3179, Fall, Graduate School of Informatics, 2
• From 01 Apr. 2023, To 31 Mar. 2024

  Introduction to Bioinformatics

  3159, Spring, Graduate School of Informatics, 2
• From 01 Apr. 2022, To 31 Mar. 2023

  Seminar on Intelligence Science and Technology III

  3194, Fall, Graduate School of Informatics, 2
• From 01 Apr. 2022, To 31 Mar. 2023

  Seminar on Intelligence Science and Technology I

  3190, Spring, Graduate School of Informatics, 2
• From 01 Apr. 2022, To 31 Mar. 2023

  Seminar on Intelligence Science and Technology IV

  3196, Fall, Graduate School of Informatics, 2
• From 01 Apr. 2022, To 31 Mar. 2023

  Introduction to Bioinformatics

  3159, Spring, Graduate School of Informatics, 2
• From 01 Apr. 2022, To 31 Mar. 2023

  Seminar on Intelligence Science and Technology III

  3195, Fall, Graduate School of Informatics, 2
• From 01 Apr. 2022, To 31 Mar. 2023

  Seminar on Intelligence Science and Technology I

  3191, Spring, Graduate School of Informatics, 2
• From 01 Apr. 2022, To 31 Mar. 2023

  Seminar on Intelligence Science and Technology IV

  3197, Fall, Graduate School of Informatics, 2
• From 01 Apr. 2022, To 31 Mar. 2023

  Seminar on Intelligence Science and Technology II

  3193, Spring, Graduate School of Informatics, 2
• From 01 Apr. 2022, To 31 Mar. 2023

  Seminar on Intelligence Science and Technology II

  3192, Spring, Graduate School of Informatics, 2
• From 01 Apr. 2022, To 31 Mar. 2023

  Bioinformatics, Adv.

  3179, Fall, Graduate School of Informatics, 2
• From 01 Apr. 2022, To 31 Mar. 2023

  Introduction to Computational Systems Bioinformatics

  9119, Spring, Faculty of Engineering, 2
• From Apr. 2011, To Mar. 2012

  Advanced Study in IST I

  Year-long, 情報学研究科
• From Apr. 2011, To Mar. 2012

  Advanced Study in IST II

  Year-long, 情報学研究科
• From Apr. 2011, To Mar. 2012

  知能情報学特殊研究１

  Year-long, 情報学研究科
• From Apr. 2011, To Mar. 2012

  知能情報学特殊研究２

  Year-long, 情報学研究科
• From Apr. 2011, To Mar. 2012

  生命情報学

  Fall, 工学部
• From Apr. 2011, To Mar. 2012

  知能情報学特別セミナー

  Year-long, 情報学研究科
• From Apr. 2011, To Mar. 2012

  生命情報学特別セミナー

  Fall, 情報学研究科
• From Apr. 2011, To Mar. 2012

  System Bioinformatics

  Fall, 全学共通科目
• From Apr. 2011, To Mar. 2012

  Introduction to Bioinformatics

  Spring, 全学共通科目
• From Apr. 2011, To Mar. 2012

  生命情報学基礎論

  Spring, 情報学研究科
• From Apr. 2012, To Mar. 2013

  Bioinformatics

  Fall, 全学共通科目
• From Apr. 2012, To Mar. 2013

  Introduction to Computational Systems Bioinformatics

  Fall, 工学部
• From Apr. 2012, To Mar. 2013

  Introduction to Bioinformatics

  Spring, 情報学研究科
• From Apr. 2012, To Mar. 2013

  Advanced Seminar on Gene Informatics

  Fall, 情報学研究科
• From Apr. 2012, To Mar. 2013

  Advanced Seminar on Intelligence Science and Technology

  Year-long, 情報学研究科
• From Apr. 2012, To Mar. 2013

  Advanced Study in Intelligence Science and Technology II

  Year-long, 情報学研究科
• From Apr. 2012, To Mar. 2013

  Advanced Study in Intelligence Science and Technology I

  Year-long, 情報学研究科
• From Apr. 2013, To Mar. 2014

  Introduction to Computational Systems Bioinformatics

  Fall, 工学部
• From Apr. 2013, To Mar. 2014

  Advanced Study in Intelligence Science and Technology I

  Year-long, 情報学研究科
• From Apr. 2013, To Mar. 2014

  Advanced Study in Intelligence Science and Technology I

  Spring, 情報学研究科
• From Apr. 2013, To Mar. 2014

  Advanced Study in Intelligence Science and Technology II

  Year-long, 情報学研究科
• From Apr. 2013, To Mar. 2014

  Introduction to Bioinformatics

  Spring, 情報学研究科
• From Apr. 2013, To Mar. 2014

  Advanced Seminar on Intelligence Science and Technology

  Year-long, 情報学研究科
• From Apr. 2013, To Mar. 2014

  Advanced Seminar on Gene Informatics

  Fall, 情報学研究科
• From Apr. 2013, To Mar. 2014

  Bioinformatics

  Fall, 全学共通科目
• From Apr. 2014, To Mar. 2015

  Introduction to Computational Systems Bioinformatics

  Fall, 工学部
• From Apr. 2014, To Mar. 2015

  Advanced Study in Intelligence Science and Technology I

  Year-long, 情報学研究科
• From Apr. 2014, To Mar. 2015

  Advanced Study in Intelligence Science and Technology I

  Year-long, 情報学研究科
• From Apr. 2014, To Mar. 2015

  Advanced Study in Intelligence Science and Technology II

  Year-long, 情報学研究科
• From Apr. 2014, To Mar. 2015

  Introduction to Bioinformatics

  Spring, 情報学研究科
• From Apr. 2014, To Mar. 2015

  Advanced Seminar on Intelligence Science and Technology

  Year-long, 情報学研究科
• From Apr. 2014, To Mar. 2015

  Advanced Seminar on Gene Informatics

  Fall, 情報学研究科
• From Apr. 2014, To Mar. 2015

  Bioinformatics

  Fall, 全学共通科目
• From Apr. 2014, To Mar. 2015

  Advanced Study in Intelligence Science and Technology I

  Year-long, 情報学研究科
• From Apr. 2014, To Mar. 2015

  Advanced Study in Intelligence Science and Technology II

  Year-long, 情報学研究科
• From Apr. 2015, To Mar. 2016

  Advanced Study in Intelligence Science and Technology I

  Year-long, 情報学研究科
• From Apr. 2015, To Mar. 2016

  Advanced Study in Intelligence Science and Technology II

  Year-long, 情報学研究科
• From Apr. 2015, To Mar. 2016

  Introduction to Computational Systems Bioinformatics

  Fall, 工学部
• From Apr. 2015, To Mar. 2016

  Introduction to Bioinformatics

  Spring, 情報学研究科
• From Apr. 2015, To Mar. 2016

  Advanced Seminar on Gene Informatics

  Fall, 情報学研究科
• From Apr. 2015, To Mar. 2016

  Advanced Seminar on Intelligence Science and Technology

  Year-long, 情報学研究科
• From Apr. 2015, To Mar. 2016

  Advanced Study in Intelligence Science and Technology II

  Spring, 情報学研究科
• From Apr. 2015, To Mar. 2016

  Advanced Study in Intelligence Science and Technology II

  Year-long, 情報学研究科
• From Apr. 2015, To Mar. 2016

  Advanced Study in Intelligence Science and Technology I

  Year-long, 情報学研究科
• From Apr. 2015, To Mar. 2016

  Advanced Study in Intelligence Science and Technology I

  Year-long, 情報学研究科
• From Apr. 2015, To Mar. 2016

  Introduction to Computational Science

  Fall, 全学共通科目
• From Apr. 2016, To Mar. 2017

  Advanced Study in Intelligence Science and Technology I

  Year-long, 情報学研究科
• From Apr. 2016, To Mar. 2017

  Advanced Study in Intelligence Science and Technology II

  Year-long, 情報学研究科
• From Apr. 2016, To Mar. 2017

  Introduction to Computational Systems Bioinformatics

  Fall, 工学部
• From Apr. 2016, To Mar. 2017

  Introduction to Bioinformatics

  Spring, 情報学研究科
• From Apr. 2016, To Mar. 2017

  Advanced Seminar on Gene Informatics

  Fall, 情報学研究科
• From Apr. 2016, To Mar. 2017

  Bioinformatics, Adv.

  Fall, 情報学研究科
• From Apr. 2016, To Mar. 2017

  Advanced Seminar on Intelligence Science and Technology

  Year-long, 情報学研究科
• From Apr. 2016, To Mar. 2017

  Advanced Study in Intelligence Science and Technology II

  Year-long, 情報学研究科
• From Apr. 2016, To Mar. 2017

  Advanced Study in Intelligence Science and Technology I

  Year-long, 情報学研究科
• From Apr. 2016, To Mar. 2017

  Advanced Study in Intelligence Science and Technology I

  Year-long, 情報学研究科
• From Apr. 2016, To Mar. 2017

  Introduction to Computational Science

  Fall, 全学共通科目
• From Apr. 2017, To Mar. 2018

  Advanced Study in Intelligence Science and Technology I

  Year-long, 情報学研究科
• From Apr. 2017, To Mar. 2018

  Advanced Study in Intelligence Science and Technology II

  Year-long, 情報学研究科
• From Apr. 2017, To Mar. 2018

  Introduction to Computational Systems Bioinformatics

  Fall, 工学部
• From Apr. 2017, To Mar. 2018

  Introduction to Bioinformatics

  Spring, 情報学研究科
• From Apr. 2017, To Mar. 2018

  Advanced Seminar on Gene Informatics

  Fall, 情報学研究科
• From Apr. 2017, To Mar. 2018

  Bioinformatics, Adv.

  Fall, 情報学研究科
• From Apr. 2017, To Mar. 2018

  Advanced Seminar on Intelligence Science and Technology

  Year-long, 情報学研究科
• From Apr. 2017, To Mar. 2018

  Advanced Study in Intelligence Science and Technology II

  Year-long, 情報学研究科
• From Apr. 2017, To Mar. 2018

  Advanced Study in Intelligence Science and Technology I

  Year-long, 情報学研究科
• From Apr. 2017, To Mar. 2018

  Introduction to Computational Science

  Spring, 全学共通科目
• From Apr. 2018, To Mar. 2019

  Introduction to Computational Systems Bioinformatics

  Spring, 工学部
• From Apr. 2018, To Mar. 2019

  Introduction to Bioinformatics

  Spring, 情報学研究科
• From Apr. 2018, To Mar. 2019

  Bioinformatics, Adv.

  Fall, 情報学研究科
• From Apr. 2019, To Mar. 2020

  Introduction to Computational Systems Bioinformatics

  Spring, 工学部
• From Apr. 2019, To Mar. 2020

  Introduction to Bioinformatics

  Spring, 情報学研究科
• From Apr. 2019, To Mar. 2020

  Bioinformatics, Adv.

  Fall, 情報学研究科
• From Apr. 2020, To Mar. 2021

  Introduction to Computational Systems Bioinformatics

  Spring, 工学部
• From Apr. 2020, To Mar. 2021

  Introduction to Bioinformatics

  Spring, 情報学研究科
• From Apr. 2020, To Mar. 2021

  Bioinformatics, Adv.

  Fall, 情報学研究科
• From Apr. 2021, To Mar. 2022

  Seminar on Intelligence Science and Technology III

  Fall, 情報学研究科
• From Apr. 2021, To Mar. 2022

  Seminar on Intelligence Science and Technology II

  Spring, 情報学研究科
• From Apr. 2021, To Mar. 2022

  Seminar on Intelligence Science and Technology I

  Spring, 情報学研究科
• From Apr. 2021, To Mar. 2022

  Seminar on Intelligence Science and Technology IV

  Fall, 情報学研究科
• From Apr. 2021, To Mar. 2022

  Introduction to Computational Systems Bioinformatics

  Spring, 工学部
• From Apr. 2021, To Mar. 2022

  Introduction to Bioinformatics

  Spring, 情報学研究科
• From Apr. 2021, To Mar. 2022

  Bioinformatics, Adv.

  Fall, 情報学研究科
• From Apr. 2021, To Mar. 2022

  Seminar on Intelligence Science and Technology III

  Fall, 情報学研究科
• From Apr. 2021, To Mar. 2022

  Seminar on Intelligence Science and Technology II

  Spring, 情報学研究科
• From Apr. 2021, To Mar. 2022

  Seminar on Intelligence Science and Technology I

  Spring, 情報学研究科
• From Apr. 2021, To Mar. 2022

  Seminar on Intelligence Science and Technology IV

  Fall, 情報学研究科

Participation in PhD Defense

• Treatment Effect Estimation from Small Observational Data

  HARADA SHONOSUKE, Graduate School of Informatics, Sub-chief Examiner

  23 Mar. 2023
• Analysis of Biological Networks by Graph Theory-based Methods

  LI RUIMING, Graduate School of Informatics, Chief Examiner

  23 Mar. 2023
• Algorithms for Stable Matching Problems toward Real-World Applications

  HAMADA KOKI, Graduate School of Informatics, Sub-chief Examiner

  23 Mar. 2022
• Predicting with Structured Data: Graphs, Ranks, and Time Series

  Jiuding Duan, Graduate School of Informatics, Sub-chief Examiner

  26 Jul. 2021
• Design of Computational Models for Analyzing Graph-Structured Biological Data

  WANG Feiqi, Graduate School of Informatics, Chief Examiner

  23 Mar. 2022
• Extracting Rules from Trained Machine Learning Models with Applications in Bioinformatics

  LIU PENGYU, Graduate School of Informatics, Chief Examiner

  24 May 2021

Part-time lecturer

• From 21 Sep. 2023, To 31 Mar. 2024

  バイオインフォマティクス特論、バイオインフォマティクス論

  期間中14回、1回　2時間, 関西大学
• From 01 Apr. 2023, To 30 Sep. 2023

  生命情報学

  前期15時間, 京都大学, 工学部
• From 01 Oct. 2023, To 31 Mar. 2024

  情報理工学特別講義

  後期18時間, 九州大学, 大学院システム情報科学府
• From 01 Apr. 2022, To 30 Sep. 2022

  生命情報学

  前期15時間, 工学部
• From 01 Apr. 2022, To 30 Jun. 2022

  生物情報ソフトウェア特論

  期間中12回、総時間数21時間, 東京大学, 大学院新領域創成科学研究科
• From 21 Sep. 2022, To 31 Mar. 2023

  バイオインフォマティクス特論、バイオインフォマティクス論

  期間中14回、1回　2時間, 関西大学
• From 01 Oct. 2022, To 31 Mar. 2023

  情報理工学特別講義

  期間中1回（3日間）、総時間数18時間, 九州大学, 大学院システム情報科学府

Administration

School management (title, position)

• From 01 Apr. 2013, To 31 Mar. 2015

  化学研究所附属バイオインフォマティクスセンター長
• From 01 Oct. 2014, To 31 Mar. 2018

  大学評価委員会点検・評価実行委員会 委員
• From 01 Apr. 2017, To 31 Mar. 2019

  化学研究所附属バイオインフォマティクスセンター長

Faculty management (title, position)

• From 01 Apr. 2023, To 31 Mar. 2024

  化学研究所自己点検評価委員会
• From 01 Apr. 2023, To 31 Mar. 2024

  化学研究所総務・教務委員会
• From 01 Apr. 2023, To 31 Mar. 2024

  化学研究所情報セキュリティ委員会
• From 01 Apr. 2023, To 31 Mar. 2024

  化学研究所ゲノムネット推進室運営委員会
• From 01 Apr. 2023, To 31 Mar. 2025

  情報環境整備委員会ソフトウェアライセンス専門委員会 委員
• From 01 Apr. 2023, To 31 Mar. 2025

  大学院生命科学研究科附属放射線生物研究センター運営委員会 委員
• From 01 Apr. 2022, To 31 Mar. 2024

  化学研究所ゲノムネット推進室運営委員会 委員
• From 01 Apr. 2022, To 31 Mar. 2023

  化学研究所情報セキュリティ委員会副委員長
• From 01 Apr. 2022, To 31 Mar. 2023

  化学研究所総務・教務委員会副委員長
• From 01 Apr. 2022, To 31 Mar. 2024

  情報環境機構基盤システム運用委員会委員
• From 01 Apr. 2006, To 31 Mar. 2008

  学術情報メディアセンター全国共同利用運営委員会 委員
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  化学研究所ゲノムネット推進室運営委員会 委員
• From 01 Apr. 2013, To 31 Mar. 2014

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• From 01 Apr. 2013, To 31 Mar. 2014

  化学研究所建物管理委員会 委員
• From 01 Apr. 2013, To 31 Mar. 2014

  化学研究所自己点検評価委員会 委員
• From 01 Apr. 2013, To 31 Mar. 2014

  化学研究所情報システム技術委員会 委員長
• From 01 Apr. 2013, To 31 Mar. 2014

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• From 01 Jul. 2013, To 30 Jun. 2015

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• From 01 Apr. 2014, To 31 Mar. 2015

  化学研究所運営委員会 委員
• From 01 Apr. 2014, To 31 Mar. 2015

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• From 01 Apr. 2014, To 31 Mar. 2015

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• From 01 Apr. 2014, To 31 Mar. 2015

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• From 01 Apr. 2014, To 31 Mar. 2016

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• From 01 Apr. 2015, To 31 Mar. 2017

  化学研究所ゲノムネット推進室運営委員会 委員
• From 01 Apr. 2015, To 31 Mar. 2016

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• From 01 Apr. 2015, To 31 Mar. 2016

  化学研究所情報システム技術委員会 委員長
• From 01 Apr. 2015, To 31 Mar. 2016

  化学研究所情報セキュリティ委員会 副委員長
• From 01 Jul. 2015, To 31 Mar. 2018

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  化学研究所情報システム技術委員会 委員長
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• From 01 Apr. 2017, To 31 Mar. 2019

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• From 01 Apr. 2017, To 31 Mar. 2018

  化学研究所運営委員会 委員
• From 01 Apr. 2017, To 31 Mar. 2018

  化学研究所建物管理委員会 委員
• From 01 Apr. 2017, To 31 Mar. 2018

  化学研究所自己点検評価委員会 委員
• From 01 Apr. 2017, To 31 Mar. 2018

  化学研究所情報システム技術委員会 委員長
• From 01 Apr. 2017, To 31 Mar. 2018

  化学研究所情報セキュリティ委員会 副委員長
• From 01 Apr. 2018, To 31 Mar. 2019

  化学研究所運営委員会 委員
• From 01 Apr. 2018, To 31 Mar. 2019

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• From 01 Apr. 2018, To 31 Mar. 2019

  化学研究所情報システム技術委員会 委員長
• From 01 Apr. 2018, To 31 Mar. 2019

  化学研究所情報セキュリティ委員会 副委員長
• From 01 Apr. 2019, To 31 Mar. 2020

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• From 01 Apr. 2019, To 31 Mar. 2020

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  化学研究所情報システム技術委員会 委員長
• From 01 Apr. 2019, To 31 Mar. 2020

  化学研究所情報セキュリティ委員会 副委員長
• From 01 Apr. 2020, To 31 Mar. 2022

  化学研究所ゲノムネット推進室運営委員会委員
• From 01 Apr. 2020, To 31 Mar. 2021

  化学研究所情報システム技術委員会委員長
• From 01 Apr. 2020, To 31 Mar. 2021

  化学研究所情報セキュリティ委員会副委員長
• From 01 Apr. 2021, To 31 Mar. 2022

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• From 01 Apr. 2021, To 31 Mar. 2022

  化学研究所情報セキュリティ委員会副委員長
• From 01 Apr. 2021, To 31 Mar. 2022

  化学研究所情報システム技術委員会委員長