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

• IEEE
• 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

• J-Global ID

  200901077727906267

• Researcher number

  00437261

• External link

  http://sunflower.kuicr.kyoto-u.ac.jp/~tamura/

Website(s) (URL(s))

• http://sunflower.kuicr.kyoto-u.ac.jp/~tamura/
• http://rdb.kuicr.kyoto-u.ac.jp/researchers/view/tamura+takeyuki

researchmap URL

• https://researchmap.jp/takeyuki-tamura

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

• Mathematical metabolic engineering
• Bioinformatics
• Algorithms
• Metabolic networks
• Genetic networks
• Boolean model
• Flux balance analysis model

Research Areas

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

Papers

• MetNetComp: Database for minimal and maximal gene-deletion strategies for growth-coupled production of genome-scale metabolic networks

  Takeyuki Tamura

  IEEE/ACM Transactions on Computational Biology and Bioinformatics (early access version)), Sep. 2023, Peer-reviewed, Lead author, Last author, Corresponding author

  
• Gene Deletion Algorithms for Minimum Reaction Network Design by Mixed-Integer Linear Programming for Metabolite Production in Constraint-Based Models: gDel_minRN

  Takeyuki Tamura; Ai Muto-fujita; Yukako Tohsato; Tomoyuki Kosaka

  Journal of Computational Biology, 01 May 2023, Peer-reviewed, Lead author, Corresponding author

  
• Trimming gene deletion strategies for growth-coupled production in constraint-based metabolic networks: TrimGdel.

  Takeyuki Tamura

  IEEE/ACM transactions on computational biology and bioinformatics, 01 Mar. 2023, Peer-reviewed, Lead author, Last author, Corresponding author

  
• 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.

• Inferring Pedigrees from Genetic Distances

  TAMURA Takeyuki; ITO Hiro; IWAMA Kazuo

  IEICE technical report. Theoretical foundations of Computing, 21 Jan. 2005

  
• Completing networks using observed data (特集 「知見の創出を目指した情報技術」および一般)

  阿久津 達也; 田村 武幸; 堀本 勝久

  人工知能基本問題研究会, 27 Jan. 2010

  
• Graph Kernels for Compounds Incorporating Chirality

  URATA Takashi; BROWN J. B.; TAMURA Takeyuki; KAWABATA Takeo; AKUTSU Tatsuya

  IPSJ SIG technical reports, 04 Mar. 2008

  
• An Improved Algorithm for Detecting a Singleton Attractor in a Boolean Network Consisting of AND/OR Nodes

  TAMURA Takeyuki; AKUTSU Tatsuya

  IPSJ SIG Notes, 21 Sep. 2007

  
• An O(1.787^n)-time Algorithm for Detecting a Singleton Attractor in a Boolean Network Consisting of AND/OR Nodes

  TAMURA Takeyuki; AKUTSU Tatsuya

  IEICE technical report, 25 May 2007

  
• Subcellular Location Prediction of Proteins Using Support Vector Machines with Alignment and Amino Acid Composition

  TAMURA Takeyuki; AKUTSU Tatsuya

  IPSJ SIG technical reports, 05 Mar. 2007

  
• Measuring Structural Robustness of Metabolic Networks Using Integer Programming and Feedback Vertex Sets

  TAMURA Takeyuki; TAKEMOTO Kazuhiro; AKUTSU Tatsuya

  IPSJ SIG technical reports, 11 Sep. 2008

  
• Minimum Sets of Fragments for Fixing Probe Sequences for DNA Strands

  TAMURA Takeyuki; ITO Hiro; IWAMA Kazuo

  IEICE technical report. Theoretical foundations of Computing, 11 Mar. 2003

  
• 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

  
• LA-3 Minimum Fragments for Deciding Probe Sequences for DNA Strands

  Tamura Takeyuki; Tsuchida Daisuke; Ito Hiro; Iwama Kazuo

  情報技術レターズ, 13 Sep. 2002

  
• Algorithm for Finding Minimum Reaction Cut of Metabolic Network

  TAMURA Takeyuki; TAKEMOTO Kazuhiro; AKUTSU Tatsuya

  IEICE technical report, 09 Oct. 2009

  
• Efficient Computation of Impact Degrees for Multiple Reactions in Metabolic Networks with Cycles

  CONG YANG; TAMURA TAKEYUKI; AKUTSU TATSUYA; CHING WAI-KI

  研究報告バイオ情報学（BIO）, 10 Sep. 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

  
• 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

• 精密発酵のための数理代謝工学とデータベース開発

  田村 武幸

  第五回細胞農業会議, 29 Aug. 2023, Invited

  
• Trimming gene deletion strategies for growth-coupled production in constraint-based metabolic networks: TrimGdel

  田村武幸

  IIBMP2022, 15 Sep. 2022

  
• 数理代謝工学による細胞の最適化

  田村武幸

  第四回細胞農業会議, 29 Aug. 2022

  
• 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

• 微生物を活用した有用物質の製造技術

  監修; 蓮沼,誠久, Contributor, 有用物質を効率的に生産する代謝ネットワークの設計アルゴリズム（pp.53-58）

  シーエムシー出版, May 2023

  Find Kyoto University's collection of books :

  
• バイオプロセスを用いた有用性物質生産技術

  田村武幸, Contributor, 第3章3 バイオインフォマティクスを活用した物質生産の効率化

  技術情報協会, Nov. 2022

  
• バイオサイエンスとインダストリー（Ｂ＆Ｉ）

  田村武幸, Contributor, バイオの窓: AIによる代謝ネットワークの設計

  バイオインダストリー協会, Sep. 2022

  
• 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;有用物質生産;増殖連動生産;アルゴリズム;混合整数線形計画法;制約モデル;反応削除問題;遺伝子削除問題;線形計画問題;増殖連動型生産;流束均衡解析;生育結合

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-20H04242/
• 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. 2020, 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

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-16K00391/
• 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

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-16H02485/
• 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. 2016, 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

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-25730005/
• 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

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-25250028/
• Analysis of gene regulatory networks in Boolean models

  Grant-in-Aid for Young Scientists (B)

  Kyoto University

  Takeyuki TAMURA

  From 01 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

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-23700017/

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

Education

Teaching subject(s)

• 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

  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

Administration

Faculty management (title, position)

• From 01 Apr. 2023, To 31 Mar. 2024

  化学研究所総務・教務委員会
• 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

Academic, Social Contribution

Committee Memberships

• From Apr. 2022, To Present

  月刊バイオインダストリー編集委員, バイオインダストリー協会
• 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