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Tamura, Takeyuki

Institute for Chemical Research (ICR) Associate Professor

Tamura, Takeyuki
list
    Last Updated :2022/06/27

    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, 准教授

    Professional Memberships

    • 情報処理学会
    • 電子情報通信学会
    • 日本バイオインフォマティクス学会
    • NPOバイオインフォマティクス・ジャパン

    Academic Degree

    • 修士(情報学)(京都大学)
    • 博士(情報学)(京都大学)

    Academic Resume (Graduate Schools)

    • 京都大学, 大学院情報学研究科修士課程通信情報システム専攻, 修了
    • 京都大学, 大学院情報学研究科博士後期課程通信情報システム専攻, 修了

    Academic Resume (Undergraduate School/Majors)

    • 京都大学, 工学部情報学科, 卒業

    High School

    • High School

      東大寺学園高校

    Research History

    • From Oct. 2017, To Present
      Kyoto University, Institute for Chemical Research, 准教授
    • From Dec. 2007, To Sep. 2017
      Kyoto University, Institute for Chemical Research, 助教
    • From Apr. 2006, To Nov. 2007
      Kyoto University, Institute for Chemical Research

    Language of Instruction

    • English

    ID,URL

    Website(s) (URL(s))

    researchmap URL

    list
      Last Updated :2022/06/27

      Research

      Research Topics, Overview of the research

      • Research Topics

        Mathematical metabolic engineering
      • Overview of the research

        Algorithms for design and control of metabolic networks and gene regulatory networks

      Research Interests

      • バイオインフォマティクス
      • アルゴリズム
      • 代謝ネットワーク
      • 遺伝子ネットワーク
      • ブーリアンモデル
      • FBAモデル

      Research Areas

      • Informatics, Information theory
      • Informatics, Biological, health, and medical informatics
      • Informatics, Intelligent informatics

      Papers

      • Dynamic Solution Space Division-Based Methods for Calculating Reaction Deletion Strategies for Constraint-Based Metabolic Networks for Substance Production: DynCubeProd
        Yier Ma; Takeyuki Tamura
        Frontiers in Bioinformatics, 13 Aug. 2021, Peer-reviewed, Last author, Corresponding author
      • 有用物質生産のための代謝ネットワーク設計
        田村武幸
        JSBi Bioinformatics Review, May 2021, Peer-reviewed, Invited, Lead author, Last author, Corresponding author
      • New and improved algorithms for unordered tree inclusion.
        Tatsuya Akutsu; Jesper Jansson; Ruiming Li; Atsuhiro Takasu; Takeyuki Tamura
        Theor. Comput. Sci., 2021, Peer-reviewed
      • Efficient Reaction Deletion Algorithms for Redesign of Constraint-based Metabolic Networks for Metabolite Production with Weak Coupling
        Takeyuki Tamura
        IPSJ Transactions on Bioinformatics, 2021, Peer-reviewed, Lead author, Last author, Corresponding author
      • L1 Norm Minimal Mode-Based Methods for Listing Reaction Network Designs for Metabolite Production.
        Takeyuki Tamura
        IEICE Trans. Inf. Syst., 2021, Peer-reviewed, Lead author, 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
      • 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
      • 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
      • 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, 2018, Peer-reviewed
      • Computing Minimum Reaction Modifications in a Boolean Metabolic Network.
        Takeyuki Tamura; Wei Lu; Jiangning Song; Tatsuya Akutsu
        IEEE ACM Trans. Comput. Biol. Bioinform., 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
      • Grid-based computational methods for the design of constraint-based parsimonious chemical reaction networks to simulate metabolite production: GridProd.
        Takeyuki Tamura
        BMC Bioinform., 2018, Peer-reviewed, Lead author, Last author, Corresponding author
      • Discrimination of singleton and periodic attractors in Boolean networks.
        Xiaoqing Cheng; Takeyuki Tamura; Wai-Ki Ching; Tatsuya Akutsu
        Autom., 2017, Peer-reviewed
      • On the parameterized complexity of associative and commutative unification.
        Tatsuya Akutsu; Jesper Jansson; Atsuhiro Takasu; Takeyuki Tamura
        Theor. Comput. Sci., 2017, Peer-reviewed
      • Similar subtree search using extended tree inclusion.
        Tomoya Mori; Atsuhiro Takasu; Jesper Jansson; Jaewook Hwang; Takeyuki Tamura; Tatsuya Akutsu
        2016 32ND IEEE INTERNATIONAL CONFERENCE ON DATA ENGINEERING (ICDE), 2016, Peer-reviewed
      • Finding Influential Genes Using Gene Expression Data and Boolean Models of Metabolic Networks.
        Takeyuki Tamura; Tatsuya Akutsu; Chun-Yu Lin; Jinn-Moon Yang
        2016 IEEE 16TH INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOENGINEERING (BIBE), 2016, Peer-reviewed
      • Finding and Analyzing the Minimum Set of Driver Nodes in control of Boolean Networks.
        Wenpin Hou; Takeyuki Tamura; Wai-Ki Ching; Tatsuya Akutsu
        Adv. Complex Syst., 2016, Peer-reviewed
      • Computational Methods for Modification of Metabolic Networks
        Takeyuki Tamura; Wei Lu; Tatsuya Akutsu
        COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, 2015, Peer-reviewed
      • Similar Subtree Search Using Extended Tree Inclusion.
        Tomoya Mori; Atsuhiro Takasu; Jesper Jansson; Jaewook Hwang; Takeyuki Tamura; Tatsuya Akutsu
        IEEE Trans. Knowl. Data Eng., 2015, Peer-reviewed
      • On the complexity of finding a largest common subtree of bounded degree.
        Tatsuya Akutsu; Takeyuki Tamura; Avraham A. Melkman; Atsuhiro Takasu
        Theor. Comput. Sci., 2015, Peer-reviewed
      • Computing Smallest Intervention Strategies for Multiple Metabolic Networks in a Boolean Model.
        Wei Lu; Takeyuki Tamura; Jiangning Song; Tatsuya Akutsu
        J. Comput. Biol., 2015, Peer-reviewed
      • A Fixed-Parameter Algorithm for Detecting a Singleton Attractor in an AND/OR Boolean Network with Bounded Treewidth.
        Chia-Jung Chang; Takeyuki Tamura; Kun-Mao Chao; Tatsuya Akutsu
        IEICE Trans. Fundam. Electron. Commun. Comput. Sci., 2015, Peer-reviewed
      • Colony-live -a high-throughput method for measuring microbial colony growth kinetics- reveals diverse growth effects of gene knockouts in Escherichia coli
        Rikiya Takeuchi; Takeyuki Tamura; Toru Nakayashiki; Yuichirou Tanaka; Ai Muto; Barry L. Wanner; Hirotada Mori
        BMC MICROBIOLOGY, Jun. 2014, Peer-reviewed
      • Integer Programming-Based Method for Designing Synthetic Metabolic Networks by Minimum Reaction Insertion in a Boolean Model
        Wei Lu; Takeyuki Tamura; Jiangning Song; Tatsuya Akutsu
        PLOS ONE, Mar. 2014, Peer-reviewed
      • Efficient exponential-time algorithms for edit distance between unordered trees.
        Tatsuya Akutsu; Takeyuki Tamura; Daiji Fukagawa; Atsuhiro Takasu
        J. Discrete Algorithms, 2014, Peer-reviewed
      • On the Parameterized Complexity of Associative and Commutative Unification
        Tatsuya Akutsu; Jesper Jansson; Atsuhiro Takasu; Takeyuki Tamura
        PARAMETERIZED AND EXACT COMPUTATION, IPEC 2014, 2014
      • On the Parameterized Complexity of Associative and Commutative Unification.
        Tatsuya Akutsu; Jesper Jansson; Atsuhiro Takasu; Takeyuki Tamura
        PARAMETERIZED AND EXACT COMPUTATION, IPEC 2014, 2014, Peer-reviewed
      • On control of singleton attractors in multiple Boolean networks: integer programming-based method.
        Yushan Qiu; Takeyuki Tamura; Wai-Ki Ching; Tatsuya Akutsu
        BMC Syst. Biol., 2014, Peer-reviewed
      • On the Complexity of Inference and Completion of Boolean Networks from Given Singleton Attractors
        Hao Jiang; Takeyuki Tamura; Wai-Ki Ching; Tatsuya Akutsu
        IEICE TRANSACTIONS ON FUNDAMENTALS OF ELECTRONICS COMMUNICATIONS AND COMPUTER SCIENCES, Nov. 2013, Peer-reviewed
      • Theoretical estimation of metabolic network robustness against multiple reaction knockouts using branching process approximation
        Kazuhiro Takemoto; Takeyuki Tamura; Tatsuya Akutsu
        Physica A: Statistical Mechanics and its Applications, 01 Nov. 2013, Peer-reviewed
      • Flux balance impact degree: a new definition of impact degree to properly treat reversible reactions in metabolic networks
        Yang Zhao; Takeyuki Tamura; Tatsuya Akutsu; Jean-Philippe Vert
        BIOINFORMATICS, Sep. 2013, 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
      • Finding optimal control policy in probabilistic Boolean Networks with hard constraints by using integer programming and dynamic programming
        Xi Chen; Tatsuya Akutsu; Takeyuki Tamura; Wai-Ki Ching
        INTERNATIONAL JOURNAL OF DATA MINING AND BIOINFORMATICS, 2013, Peer-reviewed
      • Integer Programming-Based Approach to Attractor Detection and Control of Boolean Networks
        Tatsuya Akutsu; Yang Zhao; Morihiro Hayashida; Takeyuki Tamura
        IEICE TRANSACTIONS ON INFORMATION AND SYSTEMS, Dec. 2012, Peer-reviewed
      • Integer Programming-Based Approach to Attractor Detection and Control of Boolean Networks
        Tatsuya Akutsu; Yang Zhao; Morihiro Hayashida; Takeyuki Tamura
        IEICE TRANSACTIONS ON INFORMATION AND SYSTEMS, Dec. 2012, Peer-reviewed
      • A Clique-Based Method Using Dynamic Programming for Computing Edit Distance Between Unordered Trees
        Tomoya Mori; Takeyuki Tamura; Daiji Fukagawa; Atsuhiro Takasu; Etsuji Tomita; Tatsuya Akutsu
        JOURNAL OF COMPUTATIONAL BIOLOGY, Oct. 2012, Peer-reviewed
      • Finding a Periodic Attractor of a Boolean Network
        Tatsuya Akutsu; Sven Kosub; Avraham A. Melkman; Takeyuki Tamura
        IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, Sep. 2012, Peer-reviewed
      • Finding a Periodic Attractor of a Boolean Network
        Tatsuya Akutsu; Sven Kosub; Avraham A. Melkman; Takeyuki Tamura
        IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, Sep. 2012, Peer-reviewed
      • Singleton and 2-periodic attractors of sign-definite Boolean networks
        Tatsuya Akutsu; Avraham A. Melkman; Takeyuki Tamura
        INFORMATION PROCESSING LETTERS, Jan. 2012, Peer-reviewed
      • Analysis of the impact degree distribution in metabolic networks using branching process approximation
        Kazuhiro Takemoto; Takeyuki Tamura; Yang Cong; Wai-Ki Ching; Jean-Philippe Vert; Tatsuya Akutsu
        PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS, Jan. 2012, Peer-reviewed
      • Finding Conserved Regions in Protein Structures Using Support Vector Machines and Structure Alignment
        Tatsuya Akutsu; Morihiro Hayashida; Takeyuki Tamura
        PATTERN RECOGNITION IN BIOINFORMATICS, 2012, Peer-reviewed
      • A Polynomial-Time Algorithm for Computing the Maximum Common Subgraph of Outerplanar Graphs of Bounded Degree
        Tatsuya Akutsu; Takeyuki Tamura
        MATHEMATICAL FOUNDATIONS OF COMPUTER SCIENCE 2012, 2012, Peer-reviewed
      • Efficient exponential time algorithms for edit distance between unordered trees
        Tatsuya Akutsu; Takeyuki Tamura; Daiji Fukagawa; Atsuhiro Takasu
        Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2012, Peer-reviewed
      • Network Completion Using Dynamic Programming and Least-Squares Fitting
        Natsu Nakajima; Takeyuki Tamura; Yoshihiro Yamanishi; Katsuhisa Horimoto; Tatsuya Akutsu
        SCIENTIFIC WORLD JOURNAL, 2012, Peer-reviewed
      • On the Complexity of the Maximum Common Subgraph Problem for Partial k-Trees of Bounded Degree
        Tatsuya Akutsu; Takeyuki Tamura
        ALGORITHMS AND COMPUTATION, ISAAC 2012, 2012, Peer-reviewed
      • Singleton and 2-periodic attractors of sign-definite Boolean networks
        Tatsuya Akutsu; Avraham A. Melkman; Takeyuki Tamura
        INFORMATION PROCESSING LETTERS, Jan. 2012, Peer-reviewed
      • An Efficient Method of Computing Impact Degrees for Multiple Reactions in Metabolic Networks with Cycles
        Takeyuki Tamura; Yang Cong; Tatsuya Akutsu; Wai-Ki Ching
        IEICE TRANSACTIONS ON INFORMATION AND SYSTEMS, Dec. 2011, Peer-reviewed
      • Determining a Singleton Attractor of a Boolean Network with Nested Canalyzing Functions
        Tatsuya Akutsu; Avraham A. Melkman; Takeyuki Tamura; Masaki Yamamoto
        JOURNAL OF COMPUTATIONAL BIOLOGY, Oct. 2011, Peer-reviewed
      • Determining a Singleton Attractor of a Boolean Network with Nested Canalyzing Functions
        Tatsuya Akutsu; Avraham A. Melkman; Takeyuki Tamura; Masaki Yamamoto
        JOURNAL OF COMPUTATIONAL BIOLOGY, Oct. 2011, Peer-reviewed
      • A clique-based method for the edit distance between unordered trees and its application to analysis of glycan structures
        Daiji Fukagawa; Takeyuki Tamura; Atsuhiro Takasu; Etsuji Tomita; Tatsuya Akutsu
        BMC BIOINFORMATICS, Feb. 2011, Peer-reviewed
      • Exact algorithms for computing the tree edit distance between unordered trees
        Tatsuya Akutsu; Daiji Fukagawa; Atsuhiro Takasu; Takeyuki Tamura
        THEORETICAL COMPUTER SCIENCE, Feb. 2011, Peer-reviewed
      • Exact algorithms for computing the tree edit distance between unordered trees
        Tatsuya Akutsu; Daiji Fukagawa; Atsuhiro Takasu; Takeyuki Tamura
        THEORETICAL COMPUTER SCIENCE, Feb. 2011, Peer-reviewed
      • A clique-based method for the edit distance between unordered trees and its application to analysis of glycan structures
        Daiji Fukagawa; Takeyuki Tamura; Atsuhiro Takasu; Etsuji Tomita; Tatsuya Akutsu
        BMC BIOINFORMATICS, Feb. 2011, Peer-reviewed
      • COMPOUND ANALYSIS VIA GRAPH KERNELS INCORPORATING CHIRALITY
        J. B. Brown; Takashi Urata; Takeyuki Tamura; Midori A. Arai; Takeo Kawabata; Tatsuya Akutsu
        JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, Dec. 2010, Peer-reviewed
      • Exact Algorithms for Finding a Minimum Reaction Cut under a Boolean Model of Metabolic Networks
        Takeyuki Tamura; Tatsuya Akutsu
        IEICE TRANSACTIONS ON FUNDAMENTALS OF ELECTRONICS COMMUNICATIONS AND COMPUTER SCIENCES, Aug. 2010, Peer-reviewed
      • Determining a singleton attractor of an AND/OR Boolean network in O(1.587(n)) time
        Avraham A. Melkman; Takeyuki Tamura; Tatsuya Akutsu
        INFORMATION PROCESSING LETTERS, Jul. 2010, Peer-reviewed
      • Determining a singleton attractor of an AND/OR Boolean network in O(1.587(n)) time
        Avraham A. Melkman; Takeyuki Tamura; Tatsuya Akutsu
        INFORMATION PROCESSING LETTERS, Jul. 2010, Peer-reviewed
      • Finding Minimum Reaction Cuts of Metabolic Networks Under a Boolean Model Using Integer Programming and Feedback Vertex Sets.
        Takeyuki Tamura; Kazuhiro Takemoto; Tatsuya Akutsu
        IJKDB, 2010, Peer-reviewed
      • Exact algorithms for finding a minimum reaction cut under a Boolean model of metabolic networks
        Takeyuki Tamura; Tatsuya Akutsu
        IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences, 2010, 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
      • On Finding a Fixed Point in a Boolean Network with Maximum Indegree 2
        Tatsuya Akutsu; Takeyuki Tamura
        IEICE TRANSACTIONS ON FUNDAMENTALS OF ELECTRONICS COMMUNICATIONS AND COMPUTER SCIENCES, Aug. 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
      • 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
      • 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
      • Completing Networks Using Observed Data
        Tatsuya Akutsu; Takeyuki Tamura; Katsuhisa Horimoto
        ALGORITHMIC LEARNING THEORY, PROCEEDINGS, 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
      • Inferring pedigree graphs from genetic distances
        Takeyuki Tamura; Hiro Ito
        IEICE TRANSACTIONS ON INFORMATION AND SYSTEMS, Feb. 2008, Peer-reviewed
      • An improved algorithm for detecting a singleton attractor in a Boolean network consisting of AND/OR nodes
        Takeyuki Tamura; Tatsuya Akutsu
        Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2008, Peer-reviewed
      • Algorithms for inference, analysis and control of Boolean networks
        Tatsuya Akutsu; Morihiro Hayashida; Takeyuki Tamura
        ALGEBRAIC BIOLOGY, PROCEEDINGS, 2008, Peer-reviewed
      • 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
      • On Distribution and Enumeration of Attractors in Probabilistic Boolean Networks
        Moribiro Hayashida; Takeyuki Tamura; Tatsuya Akutsu; Wai-Ki Ching
        OPTIMIZATION AND SYSTEMS BIOLOGY, PROCEEDINGS, 2008, Peer-reviewed
      • Subcellular location prediction of proteins using support vector machines with alignment of block sequences utilizing amino acid composition
        Takeyuki Tamura; Tatsuya Akutsu
        BMC BIOINFORMATICS, Nov. 2007, Peer-reviewed
      • Approximation algorithms for optimal RNA secondary structures common to multiple sequences
        Takeyuki Tamura; Tatsuya Akutsu
        IEICE TRANSACTIONS ON FUNDAMENTALS OF ELECTRONICS COMMUNICATIONS AND COMPUTER SCIENCES, May 2007, Peer-reviewed
      • Efficient methods for determining DNA probe orders
        Hiro Ito; Kazuo Iwama; Tamura Takeyuki
        IEICE TRANSACTIONS ON FUNDAMENTALS OF ELECTRONICS COMMUNICATIONS AND COMPUTER SCIENCES, May 2006, Peer-reviewed
      • Determining a singleton attractor of an AND/OR Boolean network in O(1.587^n) time. Information Processing Letters, Vol. 110, pp. 565-569, 2010.
        Avraham Melkman; Takeyuki Tamura; Tatsuya Akutsu
        , ,, Peer-reviewed
      • Journal of Computational Biology, Determining a singleton attractor of a Boolean network with nested canalyzing functions, Vol. 18(0), pp. 1--16, 2011.
        Tatsuya Akutsu; Avraham. A. Melkman; Takeyuki Tamura; Masaki Yamamoto
        , ,, Peer-reviewed
      • An Efficient Method of Computing Impact Degrees for Multiple Reactions in Metabolic Networks with Cycles, IEICE Transactions on Information and Systems, Vol.E94-D, No.12 pp.2393-2399, 2011.
        Takeyuki Tamura; Yang Cong; Tatsuya Akutsu; Wai-Ki Ching
        , ,, Peer-reviewed
      • Finding optimal control policy in probabilistic Boolean networks with hard constraints by using integer programming and dynamic programming(Preliminary version has appeared in BIBM 2010), International Journal of Data Mining and Bioinformatics, in press.
        Xi Chen; Tatsuya Akutsu; Takeyuki Tamura; Wai-Ki Ching
        , ,, Peer-reviewed
      • On Distribution and Enumeration of Attractors in Probabilistic Boolean Networks,IET Systems Biology, Vol. 3, pp. 465-474, (Preliminary version has appeared in OSB 2008) 2009.
        Morihiro Hayashida; Takeyuki Tamura; Tatsuya Akutsu; Wai-Ki Ching; Yang Cong
        , ,, Peer-reviewed
      • Finding Minimum Reaction Cuts of Metabolic Networks Under a Boolean Model Using Integer Programming and Feedback Vertex Sets.International Journal of Knowledge Discovery in Bioinformatics, Vol 1, pp. 14-31, (Preliminary version has appeared in IIBM2009)20
        Takeyuki Tamura; Kazuhiro Takemoto; Tatsuya Akutsu
        , ,, Peer-reviewed

      Misc.

      • 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
      • 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
      • Mathematical model and analysis of biological networks on Boolean model
        田村 武幸
        京都大学化学研究所スーパーコンピュータシステム研究成果報告書, 2017
      • 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
      • 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
      • A-002 A Fixed-Parameter Algorithm for Detecting a Singleton Attractor in an AND/OR Boolean Network with Bounded Treewidth
        Akutsu Tatsuya; Tamura Takeyuki
        情報科学技術フォーラム講演論文集, 20 Aug. 2013
      • Efficient Exponential Time Algorithms for Edit Distance between Unordered Trees
        AKUTSU Tatsuya; TAMURA Takeyuki; FUKAGAWA Daiji; TAKASU Atsuhiro
        IEICE technical report. Theoretical foundations of Computing, 14 Jun. 2012
      • An Improved Clique-Based Method for Computing Edit Distance between Rooted Unordered Trees
        Tomoya Mori; Takeyuki Tamura; Daiji Fukagawa; Atsuhiro Takasu; Etsuji Tomita; Tatsuya Akutsu
        IPSJ SIG technical reports, 06 Sep. 2011
      • A clique-based method for the edit distance between unordered trees (特集 「脳科学と知識処理」および一般)
        Daiji Fukagawa; Takeyuki Tamura; Atsuhiro Takasu; Etsuji Tomita; Tatsuya Akutsu
        SIG-FPAI, 31 Jul. 2010
      • Exact Algorithms for Computing Tree Edit Distance between Unordered Trees
        Tatsuya Akutsu; Daiji Fukagawa; Atsuhiro Takasu; Takeyuki Tamura
        IPSJ SIG Notes, 26 Feb. 2010
      • Analyzing Boolean Networks by Using Integer Programming
        AKUTSU Tatsuya; HAYASHIDA Morihiro; TAMURA Takeyuki
        IEICE technical report, 30 Jul. 2009
      • Probabilistic Boolean Network Attractor Identification and a Relationship to Attractor Distribution in Boolean Networks
        HAYASHIDA Morihiro; TAMURA Takeyuki; AKUTSU Tatsuya; CHING Wai-Ki; CONG Yang
        IPSJ SIG technical reports, 26 Feb. 2009

      Presentations

      • Gene deletion algorithms for minimum reaction network design by mixed-integer linear programming for metabolite production in constraint-based models: gDel_minRN
        田村武幸
        第10回生命医薬情報学連合大会, 28 Sep. 2021
      • Efficient reaction deletion algorithms for redesign of constraint-based metabolic networks for metabolite production with weak coupling
        田村武幸
        情報処理学会バイオ情報学研究会, 11 Mar. 2021
      • 有用物質を生産する代謝ネットワーク設計の高速アルゴリズム
        田村武幸
        第9回生命医薬情報学連合大会(IIBMP2020), 02 Sep. 2020
      • 物質生産のための代謝コアネットワークの研究
        田村武幸
        01 Sep. 2020
      • Algorithms for analyzing and controlling Boolean networks as biological networks
        Takeyuki Tamura
        International workshop on Boolean networks, 09 Jan. 2020, Invited
      • Growth-coupled overproduction is theoretically possible for most metabolites in Saccharomyces cerevisiae under anaerobic condition
        Takeyuki Tamura
        The 20th international workshop in systems biology, 02 Nov. 2019
      • Integer linear programming-based methods for controlling Boolean metabolic networks
        Takeyuki Tamura
        Qualitative computational modeling for biological networks: A workshop in the 20th international workshop in systems biology, 31 Oct. 2019, Invited
      • Growth-coupled overproduction is theoretically possible for most metabolites in Saccharomyces cerevisiae under anaerobic condition
        田村 武幸
        生命医薬情報学連合大会2019, 10 Sep. 2019
      • 有用化合物を生産・増産する代謝ネットワークの設計
        田村 武幸
        生命医薬情報学連合大会2019, 09 Sep. 2019
      • Growth-coupled overproduction is theoretically possible for most metabolites in Saccharomyces cerevisiae under anaerobic conditions
        TAMURA Takeyuki
        Metabolic Pathway Analysis 2019, 14 Aug. 2019
      • Growth-coupled overproduction is theoretically possible for most metabolites in Saccharomyces cerevisiae under anaerobic conditions
        TAMURA Takeyuki
        Intelligent Systems for Molecular Biology 2019, 21 Jul. 2019
      • Growth-coupled overproduction is theoretically possible for most metabolites in Saccharomyces cerevisiae under anaerobic conditions
        TAMURA Takeyuki
        19th Annual International Workshop on Bioinformatics and Systems Biology, 18 Jul. 2019, Invited
      • Growth-coupled overproduction is theoretically possible for most metabolites in Saccharomyces cerevisiae under anaerobic conditions
        TAMURA Takeyuki
        情報処理学会バイオ情報学研究会, 19 Jun. 2019
      • Grid-based computational methods for the design of constraint-based parsimonious chemical reaction networks to simulate metabolite production: GridProd.
        TAMURA Takeyuki
        5th Conference on Constraint-Based Reconstruction and Analysis (COBRA2018), 14 Oct. 2018
      • Computational methods for design of metabolic networks for production of valuable compounds
        TAMURA Takeyuki
        生命医薬情報学連合大会, 20 Sep. 2018
      • 有用化合物を生産・増産する代謝ネットワークを設計するアルゴリズム
        田村 武幸
        情報処理学会バイオ情報学研究会, 18 Sep. 2018
      • 有用物質を生産・増産する準最適な代謝流束均衡モデルのデザイン
        田村 武幸
        第70回日本生物工学会大会, 06 Sep. 2018
      • Computing minimum reaction modification in a Boolean metabolic network
        TAMURA Takeyuki
        2016 Biotech and Pharmaceutical Service Platform - Biological Network Analysis Conference, 04 Nov. 2016, Invited
      • Computing Minimum Reaction Modifications in a Boolean Metabolic Network
        Takeyuki Tamura; Wei Lu; Jiangning Song; Tatsuya Akutsu
        GIW/InCoB2015, Sep. 2015
      • 遺伝子の破壊と導入による代謝への影響予測の数理モデル
        田村 武幸
        JSBi生命システム理論研究会 〜細胞状態の理論的解明に向けて〜, 18 Nov. 2014, Invited
      • On the parameterized complexity of associative and commutative unification
        Tatsuya Akutsu; Jesper Jansson; Atsuhiro Takasu; Takeyuki Tamura
        9th International Symposium on Parameterized and Exact Computation (IPEC 2014), Sep. 2014
      • On the complexity of finding a largest common subtree of bounded degree
        Tatsuya Akutsu; Takeyuki Tamura; Avraham A. Melkman; Atsuhiro Takasu
        19th Int. Symp. Fundamentals of Computation Theory (FCT 2013), 2013
      • Integer programming method for completing ortholog-based gene-protein-reaction network by gene essentiality
        Takeyuki Tamura; Tatsuya Akutsu
        The 23rd International Conference on Genome Informatics (GIW2012), Dec. 2012
      • On the complexity of the maximum common subgraph problem for partial k-trees of bounded degree
        Tatsuya Akutsu; Takeyuki Tamura
        23rd International Symposium on Algorithms and Computation (ISAAC 2012), Dec. 2012
      • Efficient exponential time algorithms for edit distance between unordered trees
        Tatsuya Akutsu; Takeyuki Tamura; Daiji Fukagawa; Atsuhiro Takasu
        23rd Annual Symposium on Combinatorial Pattern Matching (CPM 2012), Jul. 2012
      • A polynomial-time algorithm for computing the maximum common subgraph of outerplanar graphs of bounded degree
        Tatsuya Akutsu; Takeyuki Tamura
        37th International Symposium on Mathematical Foundations of Computer Science (MFCS 2012), 2012
      • Predicting essential genes via impact degree on metabolic networks
        International Symposium on Symbolic Systems Biology (ISSSB’11), 16 Nov. 2011, Shonan, Japan
      • Measuring structural robustness of metabolic networks under a Boolean model using integer programming and feedback vertex sets
        Takeyuki Tamura; Kazuhiro Takemoto; Tatsuya Akutsu
        2nd International Workshop on Intelligent Informatics in Biology and Medicine (IIBM2009), 2009
      • Completing networks using observed data
        Tatsuya Akutsu; Takeyuki Tamura; Katsuhisa Horimoto
        20th International Conference on Algorithmic Learning Theory (ALT 2009), 2009
      • An improved algorithm for detecting a singleton attractor in a Boolean network consisting of AND/OR nodes
        Takeyuki Tamura; Tatsuya Akutsu
        3rd International Conference on Algebraic Biology (AB2008), 2008
      • An O(1.787^n)-time algorithm for detecting a singleton attractor in a Boolean network consisting of AND/OR nodes
        Takeyuki Tamura; Tatsuya Akutsu
        16th International Symposium on Fundamentals of Computation Theory (FCT2007), 2007
      • Imperfectness of data for STS-based physical mapping
        Hiro Ito; Kazuo Iwama; Takeyuki Tamura
        IFIP World Computer Congress, 2004, 2004

      Books and Other Publications

      • Biological Data Mining and Its Applications in Healthcare
        Takeyuki Tamura; Tatsuya Akutsu, Joint work, Theory and method of completion for a Boolean regulatory network using observed data
        World Scientific, Jan. 2014, Not refereed

      External funds: Kakenhi

      • Algorithms for metabolic network design for producing useful substances
        Grant-in-Aid for Scientific Research (B)
        Basic Section 61030:Intelligent informatics-related
        Kyoto University
        田村 武幸
        From 01 Apr. 2020, To 31 Mar. 2025, Granted
        代謝ネットワーク;制約モデル;増殖連動生産;アルゴリズム;混合整数線形計画法;増殖連動型生産;線形計画問題;流束均衡解析;有用物質生産;生育結合
      • Methods for controlling biological networks using mathematical models
        Grant-in-Aid for Scientific Research (C)
        Kyoto University
        Takeyuki Tamura
        From 01 Apr. 2016, To 31 Mar. 2019, Project Closed
        代謝ネットワーク;アルゴリズム;有用物質生産;流束均衡解析モデル;ブーリアンモデル;NP完全問題;流束均衡解析;数理モデル;反応削除戦略;生育結合;線形計画;ブーリアンネットワーク;遺伝子制御ネットワーク;NP完全;整数計画法;定常状態;unification問題;遺伝子ネットワーク;GPRネットワーク;整数線形計画法;細胞の制御;制御方法
      • Survival strategy of a cell; intra- and inter-species interaction analysis by barcode tchnology in Escherichia coli
        Grant-in-Aid for Scientific Research (A)
        Nara Institute of Science and Technology
        Hirotada Mori
        From 01 Apr. 2016, To 31 Mar. 2019, Project Closed
        大腸菌;分子バーコード;population dynamics;混合培養液;遺伝的相互作用;CRISPRi;必須遺伝子;網羅解析;混合培養;細胞生育;モデル化;シミュレーション;網羅的;ネットワーク;分子バーコード欠失株;population;deep sequencing;chemical genomics;相互作用ネットワーク;長期定常期;細胞死;lag;システム生物学;バーコード解析;細胞のモデル化;相互作用解析
      • Integrated mathematical model and analysis of Boolean biological network
        Grant-in-Aid for Young Scientists (B)
        Kyoto University
        Takeyuki Tamura
        From 01 Apr. 2013, To 31 Mar. 2017, Project Closed
        アルゴリズム;整数線形計画法;遺伝子制御ネットワーク;代謝ネットワーク;ブーリアンモデル;定常状態;制御;固定パラメータ;整数計画法;木幅;NP完全
      • Strategy of a cell to survive during a long term stationary phase before cell proliferation.
        Grant-in-Aid for Scientific Research (A)
        Nara Institute of Science and Technology
        Hirotada Mori
        From 01 Apr. 2013, To 31 Mar. 2016, Project Closed
        E. coli;bar-code;deletion collection;population dynamics;chemical genomics;stationary phase;deep sequencing;バーコード解析;大腸菌population変動解析;長期定常期;ケミカルバイオロジー;大腸菌;分子バーコード;一遺伝子欠失株;deep sequence;貞コピー可動型発現プラスミド;population変動;Multiplex解析;Chemical Genomics;二重欠失株;遺伝的ネットワーク;細胞内ネットワーク
      • Analysis of gene regulatory networks in Boolean models
        Grant-in-Aid for Young Scientists (B)
        Kyoto University
        Takeyuki TAMURA
        From 28 Apr. 2011, To 31 Mar. 2013, Project Closed
        遺伝子制御ネットワーク;ブーリアンモデル;定常状態;アルゴリズム;数理モデル;代謝ネットワーク;計算量理論;充足可能性問題;バイオインフォマティクス;整数計画法;動的計画法

      External funds: others

      • 生産困難化合物を生成するFBAモデルの代謝ネットワークの設計
        京都大学教育研究振興財団・研究活動推進助成
        From 01 Apr. 2019, To 31 Mar. 2020
        田村武幸
      list
        Last Updated :2022/06/27

        Education

        Teaching subject(s)

        • 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
          Bioinformatics, Adv.
          3179, Fall, Graduate School of Informatics, 2
        • From Apr. 2014, To Mar. 2015
          Introduction to Bioinformatics
          Spring, 情報学研究科
        • From Apr. 2015, To Mar. 2016
          Introduction to Bioinformatics
          Spring, 情報学研究科
        • From Apr. 2016, To Mar. 2017
          Introduction to Bioinformatics
          Spring, 情報学研究科
        • From Apr. 2016, To Mar. 2017
          Bioinformatics, Adv.
          Fall, 情報学研究科
        • From Apr. 2017, To Mar. 2018
          Introduction to Bioinformatics
          Spring, 情報学研究科
        • From Apr. 2017, To Mar. 2018
          Bioinformatics, Adv.
          Fall, 情報学研究科
        • 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 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 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
          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
        list
          Last Updated :2022/06/27

          Administration

          Faculty management (title, position)

          • From 01 Apr. 2013, To 31 Mar. 2014
            化学研究所講演委員会 委員
          • From 01 Apr. 2017, To 31 Mar. 2018
            化学研究所広報委員会 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
          • From 01 Apr. 2018, To 31 Mar. 2019
            化学研究所広報委員会 委員
          • 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
          • From 01 Apr. 2019, To 31 Mar. 2020
            化学研究所講演委員会 委員
          list
            Last Updated :2022/06/27

            Academic, Social Contribution

            Committee Memberships

            • From Apr. 2020, To Present
              専門委員, 電子情報通信学会コンピュテーション研究会
            • From Jan. 2019, To Present
              ICBBB Technical Program Committee
            • From Apr. 2019, To Mar. 2021
              理事, 日本バイオインフォマティクス学会
            • From Apr. 2018, To Mar. 2020
              専門委員, 情報処理学会アルゴリズム研究会

            Academic Contribution

            • 第9回生命医薬情報学連合大会ワークショップ「代謝ネットワークの解析と制御」オーガナイザー
              Planning, management, etc., Panel moderator
              田村武幸, From 02 Sep. 2020, To 02 Sep. 2020

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