田村 武幸

Last Update: 2019/06/17 16:19:36

Print

Name(Kanji/Kana/Abecedarium Latinum)
田村 武幸/タムラ タケユキ/Tamura, Takeyuki
Primary Affiliation(Org1/Job title)
Institute for Chemical Research (ICR)/Associate Professor
Affiliated programs (koza)
Org1 Job title
Graduate Schools Informatics Associate Professor
Academic Organizations You are Affiliated to in Japan
Organization name(Japanese) Organization name(English)
日本バイオインフォマティクス学会
情報処理学会
電子情報通信学会
Academic Organizations Overaseas You are Affiliated to
Organization name Country
International Society for Computational Biology
Academic Degree
Field(Japanese) Field(English) University(Japanese) University(English) Method
修士(情報学) 京都大学
博士(情報学) 京都大学
Graduate School
University(Japanese) University(English) Faculty(Japanese) Faculty(English) Major(Japanese) Major(English) Degree
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
Undergraduate School / Major(s)
University(Japanese) University(English) Faculty(Japanese) Faculty(English) Major(s)(Japanese) Major(s)(English) Degree
京都大学 工学部情報学科 卒業
High School
Highschool Kana
東大寺学園高校
Work Experience
Period Organization(Japanese) Organization(English) Job title(Japanese) Job title(English)
2006/04/01-2007/11/30 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 Bioinformatics Center, Institute for Chemical Research, Kyoto University 博士研究員 Postdoctoral Fellow
2007/12/01-2017/09/30 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 Bioinformatics Center, Institute for Chemical Research, Kyoto University 助教 Assistant Professor
2017/10/01- 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 Bioinformatics Center, Institute for Chemical Research, Kyoto University 准教授 Associate Professor
Personal Profile
(Japanese)
2006年京都大学大学院情報学研究科 博士課程修了。 京都大学博士(情報学)。2006年4月より京都大学 化学研究所附属バイオインフォマティクスセンター にて博士研究員。2007年12月より助教、2017年10月より准教授。 専門はバイオインフォマティクスのアルゴリズム。 主に代謝ネットワークや遺伝子制御ネットワークの制御や 設計に関するアルゴリズムの研究を行っている。
(English)
Takeyuki Tamura received B.E., M.E. and Ph.D. degrees in informatics from Kyoto University, Japan, in 2001, 2003, and 2006, respectively. He joined Bioinformatics Center, Institute for Chemical Research, Kyoto University as a postdoctoral fellow in April, 2006. He worked as an assistant professor from December 2007 to September 2017. From October 2017, he works as an associate professor. His research interests are bioinformatics and the theory of combinatorial optimization for graphs and networks. The current research topics include control and design of metabolic networks and gene regulatory networks.
Personal Website(s) (URL(s))
URL
http://sunflower.kuicr.kyoto-u.ac.jp/~tamura/
http://rdb.kuicr.kyoto-u.ac.jp/researchers/view/tamura+takeyuki
ORCID ID
https://orcid.org/0000-0003-1596-901X
researchmap URL
https://researchmap.jp/read0123955
Research Topics
(Japanese)
バイオインフォマティクスのアルゴリズム理論
(English)
Algorithms for Bioinformatics
Overview of the research
(Japanese)
代謝ネットワークや遺伝子制御ネットワークの設計と制御に関するアルゴリズム
(English)
Algorithms for design and control of metabolic networks and gene regulatory networks
Fields of research (key words)
Key words(Japanese) Key words(English)
バイオインフォマティクス bioinformatics
アルゴリズム algorithm
代謝ネットワーク metabolic network
遺伝子制御ネットワーク gene regulatory network
Published Papers
Author Author(Japanese) Author(English) Title Title(Japanese) Title(English) Bibliography Bibliography(Japanese) Bibliography(English) Publication date Refereed paper Language Publishing type Disclose
Tamura T Tamura T Tamura T Grid-based computational methods for the design of constraint-based parsimonious chemical reaction networks to simulate metabolite production: GridProd. Grid-based computational methods for the design of constraint-based parsimonious chemical reaction networks to simulate metabolite production: GridProd. Grid-based computational methods for the design of constraint-based parsimonious chemical reaction networks to simulate metabolite production: GridProd. BMC bioinformatics, 19, 1, 325 BMC bioinformatics, 19, 1, 325 BMC bioinformatics, 19, 1, 325 2018/09/14 Refereed English Research paper(scientific journal) Disclose to all
Bao Y, Marini S, Tamura T, Kamada M, Maegawa S, Hosokawa H, Song J, Akutsu T Bao Y, Marini S, Tamura T, Kamada M, Maegawa S, Hosokawa H, Song J, Akutsu T Bao Y, Marini S, Tamura T, Kamada M, Maegawa S, Hosokawa H, Song J, Akutsu T Toward more accurate prediction of caspase cleavage sites: a comprehensive review of current methods, tools and features. Toward more accurate prediction of caspase cleavage sites: a comprehensive review of current methods, tools and features. Toward more accurate prediction of caspase cleavage sites: a comprehensive review of current methods, tools and features. Briefings in bioinformatics Briefings in bioinformatics Briefings in bioinformatics 2018/05 Refereed English Research paper(scientific journal) Disclose to all
Takeyuki Tamura, Wei Lu, Jiangning Song, Tatsuya Akutsu Takeyuki Tamura, Wei Lu, Jiangning song, Tatsuya Akutsu Takeyuki Tamura, Wei Lu, Jiangning Song, Tatsuya Akutsu Computing Minimum Reaction Modifications in a Boolean Metabolic Network. Computing Minimum Reaction Modifications in a Boolean Metabolic Network. Computing Minimum Reaction Modifications in a Boolean Metabolic Network. IEEE/ACM Trans. Comput. Biology Bioinform., 15, 6, 1853-1862 IEEE/ACM Trans. Comput. Biology Bioinform., 15, 6, 1853-1862 IEEE/ACM Trans. Comput. Biology Bioinform., 15, 6, 1853-1862 2018 Refereed English Research paper(scientific journal) Disclose to all
Tatsuya Akutsu,Colin de la Higuera,Takeyuki Tamura Tatsuya Akutsu,Colin de la Higuera,Takeyuki Tamura Tatsuya Akutsu,Colin de la Higuera,Takeyuki Tamura A Simple Linear-Time Algorithm for Computing the Centroid and Canonical Form of a Plane Graph and Its Applications. A Simple Linear-Time Algorithm for Computing the Centroid and Canonical Form of a Plane Graph and Its Applications. A Simple Linear-Time Algorithm for Computing the Centroid and Canonical Form of a Plane Graph and Its Applications. Annual Symposium on Combinatorial Pattern Matching, CPM 2018, July 2-4, 2018 - Qingdao, China, 10:1-10:12 Annual Symposium on Combinatorial Pattern Matching, CPM 2018, July 2-4, 2018 - Qingdao, China, 10:1-10:12 Annual Symposium on Combinatorial Pattern Matching, CPM 2018, July 2-4, 2018 - Qingdao, China, 10:1-10:12 2018 Refereed English Research paper(international conference proceedings) Disclose to all
Tatsuya Akutsu,Jesper Jansson,Ruiming Li,Atsuhiro Takasu,Takeyuki Tamura Tatsuya Akutsu,Jesper Jansson,Ruiming Li,Atsuhiro Takasu,Takeyuki Tamura Tatsuya Akutsu,Jesper Jansson,Ruiming Li,Atsuhiro Takasu,Takeyuki Tamura New and Improved Algorithms for Unordered Tree Inclusion. New and Improved Algorithms for Unordered Tree Inclusion. New and Improved Algorithms for Unordered Tree Inclusion. 29th International Symposium on Algorithms and Computation, ISAAC 2018, December 16-19, 2018, Jiaoxi, Yilan, Taiwan, 27:1-27:12 29th International Symposium on Algorithms and Computation, ISAAC 2018, December 16-19, 2018, Jiaoxi, Yilan, Taiwan, 27:1-27:12 29th International Symposium on Algorithms and Computation, ISAAC 2018, December 16-19, 2018, Jiaoxi, Yilan, Taiwan, 27:1-27:12 2018 Refereed Disclose to all
Xiaoqing Cheng,Takeyuki Tamura,Wai-Ki Ching,Tatsuya Akutsu Xiaoqing Cheng,Takeyuki Tamura,Wai-Ki Ching,Tatsuya Akutsu Xiaoqing Cheng,Takeyuki Tamura,Wai-Ki Ching,Tatsuya Akutsu Discrimination of singleton and periodic attractors in Boolean networks. Discrimination of singleton and periodic attractors in Boolean networks. Discrimination of singleton and periodic attractors in Boolean networks. Automatica, 84, 205-213 Automatica, 84, 205-213 Automatica, 84, 205-213 2017/10 Refereed English Research paper(scientific journal) Disclose to all
Tatsuya Akutsu,Array,Atsuhiro Takasu,Takeyuki Tamura Tatsuya Akutsu,Array,Atsuhiro Takasu,Takeyuki Tamura Tatsuya Akutsu,Array,Atsuhiro Takasu,Takeyuki Tamura On the parameterized complexity of associative and commutative unification. On the parameterized complexity of associative and commutative unification. On the parameterized complexity of associative and commutative unification. Theor. Comput. Sci., 660, 57-74 Theor. Comput. Sci., 660, 57-74 Theor. Comput. Sci., 660, 57-74 2017/01/17 Refereed English Research paper(scientific journal) Disclose to all
Wenpin Hou,Takeyuki Tamura,Wai-Ki Ching,Tatsuya Akutsu Wenpin Hou,Takeyuki Tamura,Wai-Ki Ching,Tatsuya Akutsu Wenpin Hou,Takeyuki Tamura,Wai-Ki Ching,Tatsuya Akutsu Finding and Analyzing the Minimum Set of Driver Nodes in control of Boolean Networks. Finding and Analyzing the Minimum Set of Driver Nodes in control of Boolean Networks. Finding and Analyzing the Minimum Set of Driver Nodes in control of Boolean Networks. Advances in Complex Systems, 19, 3, 1-32 Advances in Complex Systems, 19, 3, 1-32 Advances in Complex Systems, 19, 3, 1-32 2016 Refereed English Research paper(scientific journal) Disclose to all
Takeyuki Tamura,Tatsuya Akutsu,Chun-Yu Lin,Jinn-Moon Yang Takeyuki Tamura,Tatsuya Akutsu,Chun-Yu Lin,Jinn-Moon Yang Takeyuki Tamura,Tatsuya Akutsu,Chun-Yu Lin,Jinn-Moon Yang Finding Influential Genes Using Gene Expression Data and Boolean Models of Metabolic Networks. Finding Influential Genes Using Gene Expression Data and Boolean Models of Metabolic Networks. Finding Influential Genes Using Gene Expression Data and Boolean Models of Metabolic Networks. 16th IEEE International Conference on Bioinformatics and Bioengineering, BIBE 2016, Taichung, Taiwan, October 31 - November 2, 2016, 2016, BIBE, 63-63 16th IEEE International Conference on Bioinformatics and Bioengineering, BIBE 2016, Taichung, Taiwan, October 31 - November 2, 2016, 2016, BIBE, 63-63 16th IEEE International Conference on Bioinformatics and Bioengineering, BIBE 2016, Taichung, Taiwan, October 31 - November 2, 2016, 2016, BIBE, 63-63 2016 Refereed English Research paper(scientific journal) Disclose to all
Tomoya Mori,Atsuhiro Takasu,Array,Jaewook Hwang,Takeyuki Tamura,Tatsuya Akutsu Tomoya Mori,Atsuhiro Takasu,Array,Jaewook Hwang,Takeyuki Tamura,Tatsuya Akutsu Tomoya Mori,Atsuhiro Takasu,Array,Jaewook Hwang,Takeyuki Tamura,Tatsuya Akutsu Similar subtree search using extended tree inclusion. Similar subtree search using extended tree inclusion. Similar subtree search using extended tree inclusion. 32nd IEEE International Conference on Data Engineering, ICDE 2016, Helsinki, Finland, May 16-20, 2016, 1558-1559 32nd IEEE International Conference on Data Engineering, ICDE 2016, Helsinki, Finland, May 16-20, 2016, 1558-1559 32nd IEEE International Conference on Data Engineering, ICDE 2016, Helsinki, Finland, May 16-20, 2016, 1558-1559 2016 Refereed English Research paper(international conference proceedings) Disclose to all
Tomoya Mori,Atsuhiro Takasu,Array,Jaewook Hwang,Takeyuki Tamura,Tatsuya Akutsu Tomoya Mori,Atsuhiro Takasu,Array,Jaewook Hwang,Takeyuki Tamura,Tatsuya Akutsu Tomoya Mori,Atsuhiro Takasu,Array,Jaewook Hwang,Takeyuki Tamura,Tatsuya Akutsu Similar Subtree Search Using Extended Tree Inclusion. Similar Subtree Search Using Extended Tree Inclusion. Similar Subtree Search Using Extended Tree Inclusion. IEEE Trans. Knowl. Data Eng., 27, 12, 3360-3373 IEEE Trans. Knowl. Data Eng., 27, 12, 3360-3373 IEEE Trans. Knowl. Data Eng., 27, 12, 3360-3373 2015/12 Refereed English Research paper(scientific journal) Disclose to all
Wei Lu*, Takeyuki Tamura*, Jiangning Song, and Tatsuya Akutsu, (* joint first authors) Wei Lu*, Takeyuki Tamura*, Jiangning Song, and Tatsuya Akutsu, (* joint first authors) Wei Lu*, Takeyuki Tamura*, Jiangning Song, and Tatsuya Akutsu, (* joint first authors) Computing smallest intervention strategies for multiple metabolic networks in a Boolean model Computing smallest intervention strategies for multiple metabolic networks in a Boolean model Computing smallest intervention strategies for multiple metabolic networks in a Boolean model Journal of Computational Biology, 22, 2, 85-110 Journal of Computational Biology, 22, 2, 85-110 Journal of Computational Biology, 22, 2, 85-110 2015/02 Refereed English Research paper(scientific journal) Disclose to all
Chia-Jung Chang, Takeyuki Tamura, Kun-Mao Chao and Tatsuya Akutsu Chia-Jung Chang, Takeyuki Tamura, Kun-Mao Chao and Tatsuya Akutsu Chia-Jung Chang, Takeyuki Tamura, Kun-Mao Chao and Tatsuya Akutsu A fixed-parameter algorithm for detecting a singleton attractor in an AND/OR Boolean network with bounded treewidth A fixed-parameter algorithm for detecting a singleton attractor in an AND/OR Boolean network with bounded treewidth A fixed-parameter algorithm for detecting a singleton attractor in an AND/OR Boolean network with bounded treewidth IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences, E98.A, 1, 384-390 IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences, E98.A, 1, 384-390 IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences, E98.A, 1, 384-390 2015/01 Refereed English Research paper(scientific journal) Disclose to all
Tatsuya Akutsu,Takeyuki Tamura,Avraham A. Melkman,Atsuhiro Takasu Tatsuya Akutsu,Takeyuki Tamura,Avraham A. Melkman,Atsuhiro Takasu Tatsuya Akutsu,Takeyuki Tamura,Avraham A. Melkman,Atsuhiro Takasu On the complexity of finding a largest common subtree of bounded degree. On the complexity of finding a largest common subtree of bounded degree. On the complexity of finding a largest common subtree of bounded degree. Theor. Comput. Sci., 590, 2-16 Theor. Comput. Sci., 590, 2-16 Theor. Comput. Sci., 590, 2-16 2015 Refereed English Research paper(scientific journal) Disclose to all
Tamura T, Lu W, Akutsu T Tamura T, Lu W, Akutsu T Tamura T, Lu W, Akutsu T Computational Methods for Modification of Metabolic Networks. Computational Methods for Modification of Metabolic Networks. Computational Methods for Modification of Metabolic Networks. Computational and structural biotechnology journal, 13, 376-381 Computational and structural biotechnology journal, 13, 376-381 Computational and structural biotechnology journal, 13, 376-381 2015 Refereed English Research paper(scientific journal) Disclose to all
Rikiya Takeuchi, Takeyuki Tamura, Toru Nakayashiki, Yuichirou Tanaka, Ai Muto, Barry L. Wanner, and Hirotada Mori Rikiya Takeuchi, Takeyuki Tamura, Toru Nakayashiki, Yuichirou Tanaka, Ai Muto, Barry L. Wanner, and Hirotada Mori Rikiya Takeuchi, Takeyuki Tamura, Toru Nakayashiki, Yuichirou Tanaka, Ai Muto, Barry L. Wanner, and Hirotada Mori Colony-live --a high-throughput method for measuring microbial colony growth kinetics-- reveals diverse growth effects of gene knockouts in Escherichia coli Colony-live --a high-throughput method for measuring microbial colony growth kinetics-- reveals diverse growth effects of gene knockouts in Escherichia coli Colony-live --a high-throughput method for measuring microbial colony growth kinetics-- reveals diverse growth effects of gene knockouts in Escherichia coli BMC Microbiology, 14, 1, 171 BMC Microbiology, 14, 1, 171 BMC Microbiology, 14, 1, 171 2014/06 Refereed English Research paper(scientific journal) Disclose to all
Wei Lu*, Takeyuki Tamura*, Jiangning Song, and Tatsuya Akutsu, (* joint first authors) Wei Lu*, Takeyuki Tamura*, Jiangning Song, and Tatsuya Akutsu, (* joint first authors) Wei Lu*, Takeyuki Tamura*, Jiangning Song, and Tatsuya Akutsu, (* joint first authors) Integer Programming-based Method for Designing Synthetic Metabolic Networks by Minimum Reaction Insertion in a Boolean Model Integer Programming-based Method for Designing Synthetic Metabolic Networks by Minimum Reaction Insertion in a Boolean Model Integer Programming-based Method for Designing Synthetic Metabolic Networks by Minimum Reaction Insertion in a Boolean Model PLoS ONE, 9, 3, e92637 PLoS ONE, 9, 3, e92637 PLoS ONE, 9, 3, e92637 2014/03 Refereed English Research paper(scientific journal) Disclose to all
Yushan Qiu, Takeyuki Tamura, Wai-Ki Ching, and Tatsuya Akutsu Yushan Qiu, Takeyuki Tamura, Wai-Ki Ching, and Tatsuya Akutsu Yushan Qiu, Takeyuki Tamura, Wai-Ki Ching, and Tatsuya Akutsu On control of singleton attractors in multiple Boolean networks: integer programming-based method On control of singleton attractors in multiple Boolean networks: integer programming-based method On control of singleton attractors in multiple Boolean networks: integer programming-based method BMC Systems Biology, 8, S1:S7, S7 BMC Systems Biology, 8, S1:S7, S7 BMC Systems Biology, 8, S1:S7, S7 2014/01 Refereed English Research paper(scientific journal) Disclose to all
T. Akutsu; T. Tamura; D. Fukagawa; A. Takasu Tatsuya Akutsu,Takeyuki Tamura,Daiji Fukagawa,Atsuhiro Takasu T. Akutsu; T. Tamura; D. Fukagawa; A. Takasu Efficient exponential-time algorithms for edit distance between unordered trees Efficient exponential-time algorithms for edit distance between unordered trees. Efficient exponential-time algorithms for edit distance between unordered trees Journal of Discrete Algorithms, 25, 79-93 J. Discrete Algorithms, 25, 79-93 Journal of Discrete Algorithms, 25, 79-93 2014 Refereed English Disclose to all
Tatsuya Akutsu,Jesper Jansson,Atsuhiro Takasu,Takeyuki Tamura Tatsuya Akutsu,Jesper Jansson,Atsuhiro Takasu,Takeyuki Tamura Tatsuya Akutsu,Jesper Jansson,Atsuhiro Takasu,Takeyuki Tamura On the Parameterized Complexity of Associative and Commutative Unification. On the Parameterized Complexity of Associative and Commutative Unification. On the Parameterized Complexity of Associative and Commutative Unification. Parameterized and Exact Computation - 9th International Symposium, IPEC 2014, Wroclaw, Poland, September 10-12, 2014. Revised Selected Papers, 8894, 15-27 Parameterized and Exact Computation - 9th International Symposium, IPEC 2014, Wroclaw, Poland, September 10-12, 2014. Revised Selected Papers, 8894, 15-27 Parameterized and Exact Computation - 9th International Symposium, IPEC 2014, Wroclaw, Poland, September 10-12, 2014. Revised Selected Papers, 8894, 15-27 2014 Refereed English Research paper(international conference proceedings) Disclose to all
H. Jiang; T. Tamura; W.-K. Ching; T. Akutsu Hao Jiang,Takeyuki Tamura,Wai-Ki Ching,Tatsuya Akutsu H. Jiang; T. Tamura; W.-K. Ching; T. Akutsu On the complexity of inference and completion of boolean networks from given singleton attractors On the Complexity of Inference and Completion of Boolean Networks from Given Singleton Attractors. On the complexity of inference and completion of boolean networks from given singleton attractors IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences, E96-A, 11, 2265-2274 IEICE Transactions, E96-A, 11, 2265-2274 IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences, E96-A, 11, 2265-2274 2013/11 Refereed English Disclose to all
Y. Zhao; T. Tamura; T. Akutsu; J.-P. Vert Yang Zhao,Takeyuki Tamura,Tatsuya Akutsu,Jean-Philippe Vert Y. Zhao; T. Tamura; T. Akutsu; J.-P. Vert Flux balance impact degree: A new definition of impact degree to properly treat reversible reactions in metabolic networks Flux balance impact degree: a new definition of impact degree to properly treat reversible reactions in metabolic networks. Flux balance impact degree: A new definition of impact degree to properly treat reversible reactions in metabolic networks Bioinformatics, 29, 17, 2178-2185 Bioinformatics, 29, 17, 2178-2185 Bioinformatics, 29, 17, 2178-2185 2013/09 Refereed English Disclose to all
T. Akutsu; T. Tamura Tatsuya Akutsu,Takeyuki Tamura T. Akutsu; T. Tamura A polynomial-time algorithm for computing the maximum common connected edge subgraph of outerplanar graphs of bounded Degree A Polynomial-Time Algorithm for Computing the Maximum Common Connected Edge Subgraph of Outerplanar Graphs of Bounded Degree. A polynomial-time algorithm for computing the maximum common connected edge subgraph of outerplanar graphs of bounded Degree Algorithms, 6, 1, 119-135 Algorithms, 6, 1, 119-135 Algorithms, 6, 1, 119-135 2013 Refereed English Disclose to all
Tatsuya Akutsu,Takeyuki Tamura,Atsuhiro Takasu Tatsuya Akutsu,Takeyuki Tamura,Atsuhiro Takasu Tatsuya Akutsu,Takeyuki Tamura,Atsuhiro Takasu On the Parameterized Complexity of Associative and Commutative Unification. On the Parameterized Complexity of Associative and Commutative Unification. On the Parameterized Complexity of Associative and Commutative Unification. CoRR, abs/1310.0919 CoRR, abs/1310.0919 CoRR, abs/1310.0919 2013 Disclose to all
X. Chen; T. Akutsu; T. Tamura; W.-K. Ching Xi Chen,Tatsuya Akutsu,Takeyuki Tamura,Wai-Ki Ching X. Chen; T. Akutsu; T. Tamura; W.-K. Ching Finding optimal control policy in probabilistic Boolean Networks with hard constraints by using integer programming and dynamic programming Finding optimal control policy in probabilistic Boolean Networks with hard constraints by using integer programming and dynamic programming. Finding optimal control policy in probabilistic Boolean Networks with hard constraints by using integer programming and dynamic programming International Journal of Data Mining and Bioinformatics, 7, 3, 322-343 IJDMB, 7, 3, 322-343 International Journal of Data Mining and Bioinformatics, 7, 3, 322-343 2013 Refereed English Disclose to all
T. Akutsu; T. Tamura; A.A. Melkman; A. Takasu Tatsuya Akutsu,Takeyuki Tamura,Avraham A. Melkman,Atsuhiro Takasu T. Akutsu; T. Tamura; A.A. Melkman; A. Takasu On the complexity of finding a largest common subtree of bounded degree On the Complexity of Finding a Largest Common Subtree of Bounded Degree. On the complexity of finding a largest common subtree of bounded degree Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 8070, 4-15 Fundamentals of Computation Theory - 19th International Symposium, FCT 2013, Liverpool, UK, August 19-21, 2013. Proceedings, 8070, 4-15 Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 8070, 4-15 2013 Refereed English Disclose to all
Tomoya Mori,Takeyuki Tamura,Daiji Fukagawa,Atsuhiro Takasu,Etsuji Tomita,Tatsuya Akutsu Tomoya Mori,Takeyuki Tamura,Daiji Fukagawa,Atsuhiro Takasu,Etsuji Tomita,Tatsuya Akutsu Tomoya Mori,Takeyuki Tamura,Daiji Fukagawa,Atsuhiro Takasu,Etsuji Tomita,Tatsuya Akutsu A Clique-Based Method Using Dynamic Programming for Computing Edit Distance Between Unordered Trees. A Clique-Based Method Using Dynamic Programming for Computing Edit Distance Between Unordered Trees. A Clique-Based Method Using Dynamic Programming for Computing Edit Distance Between Unordered Trees. Journal of Computational Biology, 19, 10, 1089-1104 Journal of Computational Biology, 19, 10, 1089-1104 Journal of Computational Biology, 19, 10, 1089-1104 2012/10 Refereed English Disclose to all
T. Akutsu; S. Kosub; A.A. Melkman; T. Tamura Akutsu T, Kosub S, Melkman AA, Tamura T T. Akutsu; S. Kosub; A.A. Melkman; T. Tamura Finding a periodic attractor of a Boolean network Finding a periodic attractor of a Boolean network. Finding a periodic attractor of a Boolean network IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9, 5, 1410-1421 IEEE/ACM transactions on computational biology and bioinformatics, 9, 5, 1410-1421 IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9, 5, 1410-1421 2012/09 Refereed English Disclose to all
Tatsuya Akutsu,Sven Kosub,Avraham A. Melkman,Takeyuki Tamura Tatsuya Akutsu,Sven Kosub,Avraham A. Melkman,Takeyuki Tamura Tatsuya Akutsu,Sven Kosub,Avraham A. Melkman,Takeyuki Tamura Finding a Periodic Attractor of a Boolean Network. Finding a Periodic Attractor of a Boolean Network. Finding a Periodic Attractor of a Boolean Network. IEEE/ACM Trans. Comput. Biology Bioinform., 9, 5, 1410-1421 IEEE/ACM Trans. Comput. Biology Bioinform., 9, 5, 1410-1421 IEEE/ACM Trans. Comput. Biology Bioinform., 9, 5, 1410-1421 2012 Refereed Disclose to all
T. Akutsu; T. Tamura; D. Fukagawa; A. Takasu Tatsuya Akutsu,Takeyuki Tamura,Daiji Fukagawa,Atsuhiro Takasu T. Akutsu; T. Tamura; D. Fukagawa; A. Takasu Efficient exponential time algorithms for edit distance between unordered trees Efficient Exponential Time Algorithms for Edit Distance between Unordered Trees. Efficient exponential time algorithms for edit distance between unordered trees Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 7354, 360-372 Combinatorial Pattern Matching - 23rd Annual Symposium, CPM 2012, Helsinki, Finland, July 3-5, 2012. Proceedings, 7354, 360-372 Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 7354, 360-372 2012 Refereed English Disclose to all
Tatsuya Akutsu,Takeyuki Tamura Tatsuya Akutsu,Takeyuki Tamura Tatsuya Akutsu,Takeyuki Tamura On the Complexity of the Maximum Common Subgraph Problem for Partial k-Trees of Bounded Degree. On the Complexity of the Maximum Common Subgraph Problem for Partial k-Trees of Bounded Degree. On the Complexity of the Maximum Common Subgraph Problem for Partial k-Trees of Bounded Degree. Algorithms and Computation - 23rd International Symposium, ISAAC 2012, Taipei, Taiwan, December 19-21, 2012. Proceedings, 146-155 Algorithms and Computation - 23rd International Symposium, ISAAC 2012, Taipei, Taiwan, December 19-21, 2012. Proceedings, 146-155 Algorithms and Computation - 23rd International Symposium, ISAAC 2012, Taipei, Taiwan, December 19-21, 2012. Proceedings, 146-155 2012 Refereed Disclose to all
T. Akutsu; T. Tamura Tatsuya Akutsu,Takeyuki Tamura T. Akutsu; T. Tamura A polynomial-time algorithm for computing the maximum common subgraph of outerplanar graphs of bounded degree A Polynomial-Time Algorithm for Computing the Maximum Common Subgraph of Outerplanar Graphs of Bounded Degree. A polynomial-time algorithm for computing the maximum common subgraph of outerplanar graphs of bounded degree Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 7464 LNCS, 76-87 Mathematical Foundations of Computer Science 2012 - 37th International Symposium, MFCS 2012, Bratislava, Slovakia, August 27-31, 2012. Proceedings, 7464 LNCS, 76-87 Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 7464 LNCS, 76-87 2012 Refereed English Disclose to all
T. Akutsu; M. Hayashida; T. Tamura Tatsuya Akutsu,Morihiro Hayashida,Takeyuki Tamura T. Akutsu; M. Hayashida; T. Tamura Finding conserved regions in protein structures using support vector machines and structure alignment Finding Conserved Regions in Protein Structures Using Support Vector Machines and Structure Alignment. Finding conserved regions in protein structures using support vector machines and structure alignment Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 7632, 233-242 Pattern Recognition in Bioinformatics - 7th IAPR International Conference, PRIB 2012, Tokyo, Japan, November 8-10, 2012. Proceedings, 7632, 233-242 Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 7632, 233-242 2012 Refereed English Disclose to all
Tatsuya Akutsu,Yang Zhao,Morihiro Hayashida,Takeyuki Tamura Tatsuya Akutsu,Yang Zhao,Morihiro Hayashida,Takeyuki Tamura Tatsuya Akutsu,Yang Zhao,Morihiro Hayashida,Takeyuki Tamura Integer Programming-Based Approach to Attractor Detection and Control of Boolean Networks. Integer Programming-Based Approach to Attractor Detection and Control of Boolean Networks. Integer Programming-Based Approach to Attractor Detection and Control of Boolean Networks. IEICE Transactions, E95-D, 12, 2960-2970 IEICE Transactions, E95-D, 12, 2960-2970 IEICE Transactions, E95-D, 12, 2960-2970 2012 Refereed Disclose to all
Tatsuya Akutsu,Avraham A. Melkman,Takeyuki Tamura Tatsuya Akutsu,Avraham A. Melkman,Takeyuki Tamura Tatsuya Akutsu,Avraham A. Melkman,Takeyuki Tamura Singleton and 2-periodic attractors of sign-definite Boolean networks. Singleton and 2-periodic attractors of sign-definite Boolean networks. Singleton and 2-periodic attractors of sign-definite Boolean networks. Inf. Process. Lett., 112, 1-2, 35-38 Inf. Process. Lett., 112, 1-2, 35-38 Inf. Process. Lett., 112, 1-2, 35-38 2012 Refereed Disclose to all
N. Nakajima; T. Tamura; Y. Yamanishi; K. Horimoto; T. Akutsu Nakajima N, Tamura T, Yamanishi Y, Horimoto K, Akutsu T N. Nakajima; T. Tamura; Y. Yamanishi; K. Horimoto; T. Akutsu Network completion using dynamic programming and least-squares fitting Network completion using dynamic programming and least-squares fitting. Network completion using dynamic programming and least-squares fitting The Scientific World Journal, 2012, 957620 TheScientificWorldJournal, 2012, 957620 The Scientific World Journal, 2012, 957620 2012 Refereed English Disclose to all
Daiji Fukagawa,Takeyuki Tamura,Atsuhiro Takasu,Etsuji Tomita,Tatsuya Akutsu Daiji Fukagawa,Takeyuki Tamura,Atsuhiro Takasu,Etsuji Tomita,Tatsuya Akutsu Daiji Fukagawa,Takeyuki Tamura,Atsuhiro Takasu,Etsuji Tomita,Tatsuya Akutsu A clique-based method for the edit distance between unordered trees and its application to analysis of glycan structures. A clique-based method for the edit distance between unordered trees and its application to analysis of glycan structures. A clique-based method for the edit distance between unordered trees and its application to analysis of glycan structures. BMC Bioinformatics, 12, S-1, S13 BMC Bioinformatics, 12, S-1, S13 BMC Bioinformatics, 12, S-1, S13 2011 Refereed Disclose to all
Takeyuki Tamura,Yang Cong,Tatsuya Akutsu,Wai-Ki Ching Takeyuki Tamura,Yang Cong,Tatsuya Akutsu,Wai-Ki Ching Takeyuki Tamura,Yang Cong,Tatsuya Akutsu,Wai-Ki Ching An Efficient Method of Computing Impact Degrees for Multiple Reactions in Metabolic Networks with Cycles. An Efficient Method of Computing Impact Degrees for Multiple Reactions in Metabolic Networks with Cycles. An Efficient Method of Computing Impact Degrees for Multiple Reactions in Metabolic Networks with Cycles. IEICE Transactions, 94-D, 12, 2393-2399 IEICE Transactions, 94-D, 12, 2393-2399 IEICE Transactions, 94-D, 12, 2393-2399 2011 Refereed Disclose to all
Tatsuya Akutsu,Avraham A. Melkman,Takeyuki Tamura,Masaki Yamamoto 0001 Tatsuya Akutsu,Avraham A. Melkman,Takeyuki Tamura,Masaki Yamamoto 0001 Tatsuya Akutsu,Avraham A. Melkman,Takeyuki Tamura,Masaki Yamamoto 0001 Determining a Singleton Attractor of a Boolean Network with Nested Canalyzing Functions. Determining a Singleton Attractor of a Boolean Network with Nested Canalyzing Functions. Determining a Singleton Attractor of a Boolean Network with Nested Canalyzing Functions. Journal of Computational Biology, 18, 10, 1275-1290 Journal of Computational Biology, 18, 10, 1275-1290 Journal of Computational Biology, 18, 10, 1275-1290 2011 Refereed Disclose to all
Tatsuya Akutsu,Daiji Fukagawa,Atsuhiro Takasu,Takeyuki Tamura Tatsuya Akutsu,Daiji Fukagawa,Atsuhiro Takasu,Takeyuki Tamura Tatsuya Akutsu,Daiji Fukagawa,Atsuhiro Takasu,Takeyuki Tamura Exact algorithms for computing the tree edit distance between unordered trees. Exact algorithms for computing the tree edit distance between unordered trees. Exact algorithms for computing the tree edit distance between unordered trees. Theor. Comput. Sci., 412, 4-5, 352-364 Theor. Comput. Sci., 412, 4-5, 352-364 Theor. Comput. Sci., 412, 4-5, 352-364 2011 Refereed Disclose to all
Takeyuki Tamura,Tatsuya Akutsu Takeyuki Tamura,Tatsuya Akutsu Takeyuki Tamura,Tatsuya Akutsu Exact Algorithms for Finding a Minimum Reaction Cut under a Boolean Model of Metabolic Networks. Exact Algorithms for Finding a Minimum Reaction Cut under a Boolean Model of Metabolic Networks. Exact Algorithms for Finding a Minimum Reaction Cut under a Boolean Model of Metabolic Networks. IEICE Transactions, 93-A, 8, 1497-1507 IEICE Transactions, 93-A, 8, 1497-1507 IEICE Transactions, 93-A, 8, 1497-1507 2010 Refereed Disclose to all
Takeyuki Tamura,Kazuhiro Takemoto,Tatsuya Akutsu Takeyuki Tamura,Kazuhiro Takemoto,Tatsuya Akutsu Takeyuki Tamura,Kazuhiro Takemoto,Tatsuya Akutsu Finding Minimum Reaction Cuts of Metabolic Networks Under a Boolean Model Using Integer Programming and Feedback Vertex Sets. Finding Minimum Reaction Cuts of Metabolic Networks Under a Boolean Model Using Integer Programming and Feedback Vertex Sets. Finding Minimum Reaction Cuts of Metabolic Networks Under a Boolean Model Using Integer Programming and Feedback Vertex Sets. IJKDB, 1, 1, 14-31 IJKDB, 1, 1, 14-31 IJKDB, 1, 1, 14-31 2010 Refereed Disclose to all
Avraham A. Melkman,Takeyuki Tamura,Tatsuya Akutsu Avraham A. Melkman,Takeyuki Tamura,Tatsuya Akutsu Avraham A. Melkman,Takeyuki Tamura,Tatsuya Akutsu Determining a singleton attractor of an AND/OR Boolean network in O(1.587n) time. Determining a singleton attractor of an AND/OR Boolean network in O(1.587n) time. Determining a singleton attractor of an AND/OR Boolean network in O(1.587n) time. Inf. Process. Lett., 110, 14-15, 565-569 Inf. Process. Lett., 110, 14-15, 565-569 Inf. Process. Lett., 110, 14-15, 565-569 2010 Refereed Disclose to all
Tatsuya Akutsu,Takeyuki Tamura Tatsuya Akutsu,Takeyuki Tamura Tatsuya Akutsu,Takeyuki Tamura On Finding a Fixed Point in a Boolean Network with Maximum Indegree 2. On Finding a Fixed Point in a Boolean Network with Maximum Indegree 2. On Finding a Fixed Point in a Boolean Network with Maximum Indegree 2. IEICE Transactions, 92-A, 8, 1771-1778 IEICE Transactions, 92-A, 8, 1771-1778 IEICE Transactions, 92-A, 8, 1771-1778 2009/08 Refereed Disclose to all
Takeyuki Tamura,Tatsuya Akutsu Takeyuki Tamura,Tatsuya Akutsu Takeyuki Tamura,Tatsuya Akutsu Detecting a Singleton Attractor in a Boolean Network Utilizing SAT Algorithms. Detecting a Singleton Attractor in a Boolean Network Utilizing SAT Algorithms. Detecting a Singleton Attractor in a Boolean Network Utilizing SAT Algorithms. IEICE Transactions, 92-A, 2, 493-501 IEICE Transactions, 92-A, 2, 493-501 IEICE Transactions, 92-A, 2, 493-501 2009 Refereed Disclose to all
T. Tamura; T. Akutsu Takeyuki Tamura,Tatsuya Akutsu T. Tamura; T. Akutsu Algorithms for singleton attractor detection in planar and nonplanar AND/OR Boolean networks Algorithms for Singleton Attractor Detection in Planar and Nonplanar AND/OR Boolean Networks. Algorithms for singleton attractor detection in planar and nonplanar AND/OR Boolean networks Mathematics in Computer Science, 2, 3, 401-420 Mathematics in Computer Science, 2, 3, 401-420 Mathematics in Computer Science, 2, 3, 401-420 2009 Refereed English Disclose to all
T. Tamura; H. Ito Tamura Takeyuki, Ito Hiro T. Tamura; H. Ito Inferring pedigree graphs from genetic distances Inferring pedigree graphs from genetic distances Inferring pedigree graphs from genetic distances IEICE Transactions on Information and Systems, E91D, 2, 162-169 IEICE TRANSACTIONS ON INFORMATION AND SYSTEMS, E91D, 2, 162-169 IEICE Transactions on Information and Systems, E91D, 2, 162-169 2008/02 Refereed Disclose to all
T. Akutsu; M. Hayashida; T. Tamura Akutsu Tatsuya, Hayashida Morihiro, Tamura Takeyuki T. Akutsu; M. Hayashida; T. Tamura Algorithms for inference, analysis and control of Boolean networks Algorithms for inference, analysis and control of Boolean networks Algorithms for inference, analysis and control of Boolean networks Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 5147, 1-15 ALGEBRAIC BIOLOGY, PROCEEDINGS, 5147, 1-15 Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 5147, 1-15 2008 Refereed Disclose to all
T. Tmura; T. Akutsu Tamura Takeyuki, Akutsu Tatsuya T. Tmura; T. Akutsu Approximation algorithms for optimal RNA secondary structures common to multiple sequences Approximation algorithms for optimal RNA secondary structures common to multiple sequences Approximation algorithms for optimal RNA secondary structures common to multiple sequences IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences, E90A, 5, 917-923 IEICE TRANSACTIONS ON FUNDAMENTALS OF ELECTRONICS COMMUNICATIONS AND COMPUTER SCIENCES, E90A, 5, 917-923 IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences, E90A, 5, 917-923 2007/05 Refereed Disclose to all
H. Ito; K. Iwama; T. Tamura Ito Hiro, Iwama Kazuo, Takeyuki Tamura H. Ito; K. Iwama; T. Tamura Efficient methods for determining DNA probe orders Efficient methods for determining DNA probe orders Efficient methods for determining DNA probe orders IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences, E89A, 5, 1292-1298 IEICE TRANSACTIONS ON FUNDAMENTALS OF ELECTRONICS COMMUNICATIONS AND COMPUTER SCIENCES, E89A, 5, 1292-1298 IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences, E89A, 5, 1292-1298 2006/05 Refereed Disclose to all
K. Takemoto; T. Tamura; T. Akutsu K. Takemoto; T. Tamura; T. Akutsu Theoretical estimation of metabolic network robustness against multiple reaction knockouts using branching process approximation Theoretical estimation of metabolic network robustness against multiple reaction knockouts using branching process approximation Physica A: Statistical Mechanics and its Applications, 392, 21, 5525-5535 , 392, 21, 5525-5535 Physica A: Statistical Mechanics and its Applications, 392, 21, 5525-5535 2013 Refereed English Disclose to all
T. Akutsu; Y. Zhao; M. Hayashida; T. Tamura T. Akutsu; Y. Zhao; M. Hayashida; T. Tamura Integer programming-based approach to attractor detection and control of boolean networks Integer programming-based approach to attractor detection and control of boolean networks IEICE Transactions on Information and Systems, E95D, 12, 2960-2970 , E95D, 12, 2960-2970 IEICE Transactions on Information and Systems, E95D, 12, 2960-2970 2012/12 Refereed English Disclose to all
T. Akutsu; A.A. Melkman; T. Tamura T. Akutsu; A.A. Melkman; T. Tamura Singleton and 2-periodic attractors of sign-definite Boolean networks Singleton and 2-periodic attractors of sign-definite Boolean networks Information Processing Letters, 112, 1-2, 35-38 , 112, 1-2, 35-38 Information Processing Letters, 112, 1-2, 35-38 2012/01/15 Refereed English Disclose to all
K. Takemoto; T. Tamura; Y. Cong; W.-K. Ching; J.-P. Vert; T. Akutsu K. Takemoto; T. Tamura; Y. Cong; W.-K. Ching; J.-P. Vert; T. Akutsu Analysis of the impact degree distribution in metabolic networks using branching process approximation Analysis of the impact degree distribution in metabolic networks using branching process approximation Physica A: Statistical Mechanics and its Applications, 391, 1-2, 379-387 , 391, 1-2, 379-387 Physica A: Statistical Mechanics and its Applications, 391, 1-2, 379-387 2012/01/01 Refereed English Disclose to all
T. Akutsu; A.A. Melkman; T. Tamura; M. Yamamoto T. Akutsu; A.A. Melkman; T. Tamura; M. Yamamoto Determining a singleton attractor of a Boolean network with nested canalyzing functions Determining a singleton attractor of a Boolean network with nested canalyzing functions Journal of Computational Biology, 18, 10, 1275-1290 , 18, 10, 1275-1290 Journal of Computational Biology, 18, 10, 1275-1290 2011/10 Refereed English Disclose to all
D. Fukagawa; T. Tamura; A. Takasu; E. Tomita; T. Akutsu D. Fukagawa; T. Tamura; A. Takasu; E. Tomita; T. Akutsu A clique-based method for the edit distance between unordered trees and its application to analysis of glycan structures A clique-based method for the edit distance between unordered trees and its application to analysis of glycan structures BMC Bioinformatics, 12 , 12 BMC Bioinformatics, 12 2011/02/15 Refereed English Disclose to all
T. Akutsu; D. Fukagawa; A. Takasu; T. Tamura T. Akutsu; D. Fukagawa; A. Takasu; T. Tamura Exact algorithms for computing the tree edit distance between unordered trees Exact algorithms for computing the tree edit distance between unordered trees Theoretical Computer Science, 412, 4-5, 352-364 , 412, 4-5, 352-364 Theoretical Computer Science, 412, 4-5, 352-364 2011/02/04 Refereed English Disclose to all
J.B. Brown; T. Urata; T. Tamura; M.A. Arai; T. Kawabata; T. Akutsu J.B. Brown; T. Urata; T. Tamura; M.A. Arai; T. Kawabata; T. Akutsu Compound analysis via graph kernels incorporating chirality Compound analysis via graph kernels incorporating chirality Journal of Bioinformatics and Computational Biology, 8, 63-81 , 8, 63-81 Journal of Bioinformatics and Computational Biology, 8, 63-81 2010/12 Refereed English Disclose to all
T. Tamura; T. Akutsu T. Tamura; T. Akutsu Exact algorithms for finding a minimum reaction cut under a Boolean model of metabolic networks Exact algorithms for finding a minimum reaction cut under a Boolean model of metabolic networks IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences, E93A, 8, 1497-1507 , E93A, 8, 1497-1507 IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences, E93A, 8, 1497-1507 2010/08 Refereed English Disclose to all
A.A. Melkman; T. Tamura; T. Akutsu A.A. Melkman; T. Tamura; T. Akutsu Determining a singleton attractor of an AND/OR Boolean network in O(1.587<sup>n</sup>) time Determining a singleton attractor of an AND/OR Boolean network in O(1.587<sup>n</sup>) time Information Processing Letters, 110, 14-15, 565-569 , 110, 14-15, 565-569 Information Processing Letters, 110, 14-15, 565-569 2010 Refereed English Disclose to all
M. Hayashida; T. Tamura; T. Akutsu; W.-K. Ching; Y. Cong M. Hayashida; T. Tamura; T. Akutsu; W.-K. Ching; Y. Cong Distribution and enumeration of attractors in probabilistic Boolean networks Distribution and enumeration of attractors in probabilistic Boolean networks IET Systems Biology, 3, 6, 465-474 , 3, 6, 465-474 IET Systems Biology, 3, 6, 465-474 2009/11 Refereed English Disclose to all
T. Tamura; T. Akutsu T. Tamura; T. Akutsu Detecting a singleton attractor in a Boolean network utilizing sat algorithms Detecting a singleton attractor in a Boolean network utilizing sat algorithms IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences, E92A, 2, 493-501 , E92A, 2, 493-501 IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences, E92A, 2, 493-501 2009/02 Refereed English Disclose to all
T. Akutsu; T. Tamura; K. Horimoto T. Akutsu; T. Tamura; K. Horimoto Completing networks using observed data Completing networks using observed data Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 5809 LNAI, 126-140 , 5809 LNAI, 126-140 Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 5809 LNAI, 126-140 2009 Refereed English Disclose to all
T. Tamura; M. Hayashida; T. Akutsu; S.-Q. Zhang; W.-K. Ching T. Tamura; M. Hayashida; T. Akutsu; S.-Q. Zhang; W.-K. Ching Algorithms and complexity analyses for control of singleton attractors in Boolean networks Algorithms and complexity analyses for control of singleton attractors in Boolean networks Eurasip Journal on Bioinformatics and Systems Biology, 2008 , 2008 Eurasip Journal on Bioinformatics and Systems Biology, 2008 2008 Refereed English Disclose to all
T. Tamura; T. Akutsu T. Tamura; T. Akutsu An improved algorithm for detecting a singleton attractor in a Boolean network consisting of AND/OR nodes An improved algorithm for detecting a singleton attractor in a Boolean network consisting of AND/OR nodes Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 5147 LNCS, 216-229 , 5147 LNCS, 216-229 Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 5147 LNCS, 216-229 2008 Refereed English Disclose to all
T. Tamura; T. Akutsu T. Tamura; T. Akutsu Subcellular location prediction of proteins using support vector machines with alignment of block sequences utilizing amino acid composition Subcellular location prediction of proteins using support vector machines with alignment of block sequences utilizing amino acid composition BMC Bioinformatics, 8 , 8 BMC Bioinformatics, 8 2007 Refereed English Disclose to all
Takeyuki Tamura, Kazuhiro Takemoto and Tatsuya Akutsu Takeyuki Tamura, Kazuhiro Takemoto and Tatsuya Akutsu 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 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 , , , , Refereed English Disclose to all
Morihiro Hayashida, Takeyuki Tamura, Tatsuya Akutsu, Wai-Ki Ching and Yang Cong Morihiro Hayashida, Takeyuki Tamura, Tatsuya Akutsu, Wai-Ki Ching and Yang Cong 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. 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. , , , , Refereed English Disclose to all
Xi Chen, Tatsuya Akutsu, Takeyuki Tamura and Wai-Ki Ching Xi Chen, Tatsuya Akutsu, Takeyuki Tamura and Wai-Ki Ching 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. 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. , , , , Refereed English Disclose to all
Takeyuki Tamura, Yang Cong, Tatsuya Akutsu and Wai-Ki Ching Takeyuki Tamura, Yang Cong, Tatsuya Akutsu and Wai-Ki Ching 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. 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. , , , , Refereed English Disclose to all
Tatsuya Akutsu, Avraham. A. Melkman, Takeyuki Tamura and Masaki Yamamoto Tatsuya Akutsu, Avraham. A. Melkman, Takeyuki Tamura and Masaki Yamamoto Journal of Computational Biology, Determining a singleton attractor of a Boolean network with nested canalyzing functions, Vol. 18(0), pp. 1--16, 2011. Journal of Computational Biology, Determining a singleton attractor of a Boolean network with nested canalyzing functions, Vol. 18(0), pp. 1--16, 2011. , , , , Refereed English Disclose to all
Avraham Melkman, Takeyuki Tamura, Tatsuya Akutsu, Avraham Melkman, Takeyuki Tamura, Tatsuya Akutsu, 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. 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. , , , , Refereed English Disclose to all

  • <<
  • >>
Title language:
Conference Activities & Talks
Title Title(Japanese) Title(English) Conference Conference(Japanese) Conference(English) Promotor Promotor(Japanese) Promotor(English) Date Language Assortment Disclose
Grid-based computational methods for the design of constraint-based parsimonious chemical reaction networks to simulate metabolite production: GridProd. Grid-based computational methods for the design of constraint-based parsimonious chemical reaction networks to simulate metabolite production: GridProd. Grid-based computational methods for the design of constraint-based parsimonious chemical reaction networks to simulate metabolite production: GridProd. 5th Conference on Constraint-Based Reconstruction and Analysis (COBRA2018) 5th Conference on Constraint-Based Reconstruction and Analysis (COBRA2018) 2018/10/14 English Poster presentation Disclose to all
Computational methods for design of metabolic networks for production of valuable compounds Computational methods for design of metabolic networks for production of valuable compounds Computational methods for design of metabolic networks for production of valuable compounds 生命医薬情報学連合大会 生命医薬情報学連合大会 2018/09/20 English Poster presentation Disclose to all
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 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 情報処理学会バイオ情報学研究会 情報処理学会バイオ情報学研究会 2018/09/18 Japanese Oral presentation(general) Disclose to all
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 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 第70回日本生物工学会大会 第70回日本生物工学会大会 2018/09/06 Japanese Oral presentation(general) Disclose to all
Computing minimum reaction modification in a Boolean metabolic network[Invited] Computing minimum reaction modification in a Boolean metabolic network [Invited] Computing minimum reaction modification in a Boolean metabolic network [Invited] 2016 Biotech and Pharmaceutical Service Platform - Biological Network Analysis Conference 2016 Biotech and Pharmaceutical Service Platform - Biological Network Analysis Conference 2016 Biotech and Pharmaceutical Service Platform - Biological Network Analysis Conference 2016/11/04 English Oral presentation(invited, special) Disclose to all
Computing Minimum Reaction Modifications in a Boolean Metabolic Network Computing Minimum Reaction Modifications in a Boolean Metabolic Network Computing Minimum Reaction Modifications in a Boolean Metabolic Network GIW/InCoB2015 GIW/InCoB2015 GIW/InCoB2015 2015/09 English Oral presentation(general) Disclose to all
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[Invited] 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 [Invited] 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〜 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〜 2014/11/18 Japanese Oral presentation(invited, special) Disclose to all
On the parameterized complexity of associative and commutative unification On the parameterized complexity of associative and commutative unification On the parameterized complexity of associative and commutative unification 9th International Symposium on Parameterized and Exact Computation (IPEC 2014) 9th International Symposium on Parameterized and Exact Computation (IPEC 2014) 9th International Symposium on Parameterized and Exact Computation (IPEC 2014) 2014/09 English Oral presentation(general) Disclose to all
On the complexity of finding a largest common subtree of bounded degree On the complexity of finding a largest common subtree of bounded degree On the complexity of finding a largest common subtree of bounded degree 19th Int. Symp. Fundamentals of Computation Theory (FCT 2013) 19th Int. Symp. Fundamentals of Computation Theory (FCT 2013) 19th Int. Symp. Fundamentals of Computation Theory (FCT 2013) 2013 English Oral presentation(general) Disclose to all
On the complexity of the maximum common subgraph problem for partial k-trees of bounded degree On the complexity of the maximum common subgraph problem for partial k-trees of bounded degree On the complexity of the maximum common subgraph problem for partial k-trees of bounded degree 23rd International Symposium on Algorithms and Computation (ISAAC 2012) 23rd International Symposium on Algorithms and Computation (ISAAC 2012) 23rd International Symposium on Algorithms and Computation (ISAAC 2012) 2012/12 English Oral presentation(general) Disclose to all
Integer programming method for completing ortholog-based gene-protein-reaction network by gene essentiality Integer programming method for completing ortholog-based gene-protein-reaction network by gene essentiality Integer programming method for completing ortholog-based gene-protein-reaction network by gene essentiality The 23rd International Conference on Genome Informatics (GIW2012) The 23rd International Conference on Genome Informatics (GIW2012) The 23rd International Conference on Genome Informatics (GIW2012) 2012/12 English Oral presentation(general) Disclose to all
Efficient exponential time algorithms for edit distance between unordered trees Efficient exponential time algorithms for edit distance between unordered trees Efficient exponential time algorithms for edit distance between unordered trees 23rd Annual Symposium on Combinatorial Pattern Matching (CPM 2012) 23rd Annual Symposium on Combinatorial Pattern Matching (CPM 2012) 23rd Annual Symposium on Combinatorial Pattern Matching (CPM 2012) 2012/07 English Oral presentation(general) Disclose to all
A polynomial-time algorithm for computing the maximum common subgraph of outerplanar graphs of bounded degree A polynomial-time algorithm for computing the maximum common subgraph of outerplanar graphs of bounded degree A polynomial-time algorithm for computing the maximum common subgraph of outerplanar graphs of bounded degree 37th International Symposium on Mathematical Foundations of Computer Science (MFCS 2012) 37th International Symposium on Mathematical Foundations of Computer Science (MFCS 2012) 37th International Symposium on Mathematical Foundations of Computer Science (MFCS 2012) 2012 English Oral presentation(general) Disclose to all
Completing networks using observed data Completing networks using observed data Completing networks using observed data 20th International Conference on Algorithmic Learning Theory (ALT 2009) 20th International Conference on Algorithmic Learning Theory (ALT 2009) 20th International Conference on Algorithmic Learning Theory (ALT 2009) 2009 English Oral presentation(general) Disclose to all
Measuring structural robustness of metabolic networks under a Boolean model using integer programming and feedback vertex sets Measuring structural robustness of metabolic networks under a Boolean model using integer programming and feedback vertex sets Measuring structural robustness of metabolic networks under a Boolean model using integer programming and feedback vertex sets 2nd International Workshop on Intelligent Informatics in Biology and Medicine (IIBM2009) 2nd International Workshop on Intelligent Informatics in Biology and Medicine (IIBM2009) 2nd International Workshop on Intelligent Informatics in Biology and Medicine (IIBM2009) 2009 English Oral presentation(general) Disclose to all
An improved algorithm for detecting a singleton attractor in a Boolean network consisting of AND/OR nodes An improved algorithm for detecting a singleton attractor in a Boolean network consisting of AND/OR nodes An improved algorithm for detecting a singleton attractor in a Boolean network consisting of AND/OR nodes 3rd International Conference on Algebraic Biology (AB2008) 3rd International Conference on Algebraic Biology (AB2008) 3rd International Conference on Algebraic Biology (AB2008) 2008 English Oral presentation(general) Disclose to all
An O(1.787^n)-time algorithm for detecting a singleton attractor in a Boolean network consisting of AND/OR nodes An O(1.787^n)-time algorithm for detecting a singleton attractor in a Boolean network consisting of AND/OR nodes An O(1.787^n)-time algorithm for detecting a singleton attractor in a Boolean network consisting of AND/OR nodes 16th International Symposium on Fundamentals of Computation Theory (FCT2007) 16th International Symposium on Fundamentals of Computation Theory (FCT2007) 16th International Symposium on Fundamentals of Computation Theory (FCT2007) 2007 English Oral presentation(general) Disclose to all
Imperfectness of data for STS-based physical mapping Imperfectness of data for STS-based physical mapping Imperfectness of data for STS-based physical mapping IFIP World Computer Congress, 2004 IFIP World Computer Congress, 2004 IFIP World Computer Congress, 2004 2004 English Oral presentation(general) Disclose to all
Predicting essential genes via impact degree on metabolic networks Predicting essential genes via impact degree on metabolic networks International Symposium on Symbolic Systems Biology (ISSSB’11) International Symposium on Symbolic Systems Biology (ISSSB’11) Shonan, Japan Shonan, Japan 2011/11/16 English Oral presentation(invited, special) Disclose to all

  • <<
  • >>
Title language:
Books etc
Author Author(Japanese) Author(English) Title Title(Japanese) Title(English) Publisher Publisher(Japanese) Publisher(English) Publication date Language Type Disclose
Takeyuki Tamura and Tatsuya Akutsu Takeyuki Tamura and Tatsuya Akutsu Takeyuki Tamura and Tatsuya Akutsu Biological Data Mining and Its Applications in Healthcare Biological Data Mining and Its Applications in Healthcare Biological Data Mining and Its Applications in Healthcare World Scientific World Scientific World Scientific 2014/01 Joint Work Disclose to all
Title language:
External funds: competitive funds and Grants-in-Aid for Scientific Research (Kakenhi)
Type Position Title(Japanese) Title(English) Period
若手研究(B) Representative ブーリアンモデルによる生体ネットワークの統合的な数理モデル化と解析 2013-2016
若手研究(B) Representative ブーリアンモデルによる遺伝子制御ネットワークの解析 Analysis of gene regulatory networks in Boolean models 2011/04/28-2014/03/31
基盤研究(A) Assignment 長期定常期から分裂再開までの細胞の生存戦略 2013/04/01-2016/03/31
若手研究(B) Representative ブーリアンモデルによる生体ネットワークの統合的な数理モデル化と解析 (平成27年度分) 2015/04/01-2016/03/31
基盤研究(C) Representative 数理モデルによる生体ネットワーク制御手法の開発 (平成28年度分) 2016/04/01-2017/03/31
基盤研究(C) Representative 数理モデルによる生体ネットワーク制御手法の開発 (平成29年度分) 2017/04/01-2018/03/31
基盤研究(A) Assignment 細胞の生存 - 自然界における大腸菌の場合 2016/04/01-2019/03/31
基盤研究(C) Representative 数理モデルによる生体ネットワーク制御手法の開発 (平成30年度分) 2018/04/01-2019/03/31
External funds: other than those above
System Main person Title(Japanese) Title(English) Period
京都大学教育研究振興財団・研究活動推進助成 田村武幸 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 2019/04/01-2020/03/31
Teaching subject(s)
Name(Japanese) Name(English) Term Department Period
生命情報学基礎論 Introduction to Bioinformatics 前期 情報学研究科 2014/04-2015/03
生命情報学基礎論 Introduction to Bioinformatics 前期 情報学研究科 2015/04-2016/03
生命情報学基礎論 Introduction to Bioinformatics 前期 情報学研究科 2016/04-2017/03
生命情報学特論 Bioinformatics, Adv. 後期 情報学研究科 2016/04-2017/03
生命情報学基礎論 Introduction to Bioinformatics 前期 情報学研究科 2017/04-2018/03
生命情報学特論 Bioinformatics, Adv. 後期 情報学研究科 2017/04-2018/03
生命情報学基礎論 Introduction to Bioinformatics 前期 情報学研究科 2018/04-2019/03
生命情報学特論 Bioinformatics, Adv. 後期 情報学研究科 2018/04-2019/03
生命情報学基礎論 Introduction to Bioinformatics 前期 情報学研究科 2019/04-2020/03
生命情報学特論 Bioinformatics, Adv. 後期 情報学研究科 2019/04-2020/03
Faculty management (title, position)
Title Period
化学研究所講演委員会委員 2013/04/01-2014/03/31
化学研究所広報委員会委員 2017/04/01-2018/03/31
化学研究所情報システム技術委員会委員 2017/04/01-2018/03/31
化学研究所広報委員会委員 2018/04/01-2019/03/31
化学研究所情報システム技術委員会委員 2018/04/01-2019/03/31
化学研究所講演委員会委員 2019/04/01-2020/03/31
Academic organizations (administrative history with title(s), position(s), etc.)
Organization name(Japanese) Organization name(English) Title(Japanese) Title(English) Period
日本バイオインフォマティクス学会 理事 2019/04/01-2021/03/31
Academic organizations (editor, editing team)
Organization name(Japanese) Organization name(English) Journal name(Japanese) Journal name(English) Title Period
Algorithms, special issue "Biological networks," 2016 guest editor -
Academic organizaions (other)
Organization name(Japanese) Organization name(English) Misc(Japanese) Misc(English) Period
第77回情報処理学会全国大会 実行委員 2015/03/-2015/03/
生命医薬情報学連合大会2015年大会 プログラム委員 2015/10/-2015/10/
生命医薬情報学連合大会2015年大会 実行委員 2015/10/-2015/10/
APBC2008 The 6th Asia Pacific Bioinformatics Conference (APBC2008) 組織委員 Organizing Committee 2008/01/14-2008/01/17
IBSB2010 The 10th Annual International Workshop on Bioinformatics and Systems Biology (IBSB2010) 組織委員 Organizing Committee 2010/07/26-2010/07/28
International Conference on Towards Mathematical Foundations of Complex Network Theory International Conference on Towards Mathematical Foundations of Complex Network Theory 組織委員 Organizing Committee 2012/09/14-2012/09/16
PRIB2014 Pattern Recognition in Bioinformatics 2014 プログラム委員 Program Committee 2014-2014