Takeyuki Tamura

Publication Activity (10 Years)

Years Active: 2004-2023
Publications (10 Years): 22

Top Topics

Boolean Networks

Metabolic Networks

Top Venues

IEEE ACM Trans. Comput. Biol. Bioinform.

Theor. Comput. Sci.

J. Comput. Biol.

Publications

Takeyuki Tamura
Trimming Gene Deletion Strategies for Growth-Coupled Production in Constraint-Based Metabolic Networks: TrimGdel. IEEE ACM Trans. Comput. Biol. Bioinform. 20 (2) (2023)
Takeyuki Tamura, Ai Muto-fujita, Yukako Tohsato, Tomoyuki Kosaka
Gene Deletion Algorithms for Minimum Reaction Network Design by Mixed-Integer Linear Programming for Metabolite Production in Constraint-Based Models: gDel_minRN. J. Comput. Biol. 30 (5) (2023)
Takeyuki Tamura
MetNetComp: Database for Minimal and Maximal Gene-Deletion Strategies for Growth-Coupled Production of Genome-Scale Metabolic Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 20 (6) (2023)
Tatsuya Akutsu, Jesper Jansson, Ruiming Li, Atsuhiro Takasu, Takeyuki Tamura
New and improved algorithms for unordered tree inclusion. Theor. Comput. Sci. 883 (2021)
Yier Ma, Takeyuki Tamura
Dynamic Solution Space Division-Based Methods for Calculating Reaction Deletion Strategies for Constraint-Based Metabolic Networks for Substance Production: DynCubeProd. Frontiers Bioinform. 1 (2021)
Takeyuki Tamura
L1 Norm Minimal Mode-Based Methods for Listing Reaction Network Designs for Metabolite Production. IEICE Trans. Inf. Syst. (5) (2021)
Tatsuya Akutsu, Avraham A. Melkman, Takeyuki Tamura
Improved Hardness of Maximum Common Subgraph Problems on Labeled Graphs of Bounded Treewidth and Bounded Degree. Int. J. Found. Comput. Sci. 31 (2) (2020)
Yu Bao, Simone Marini, Takeyuki Tamura, Mayumi Kamada, Shingo Maegawa, Hiroshi Hosokawa, Jiangning Song, Tatsuya Akutsu
Toward more accurate prediction of caspase cleavage sites: a comprehensive review of current methods, tools and features. Briefings Bioinform. 20 (5) (2019)
Tatsuya Akutsu, Jesper Jansson, Ruiming Li, Atsuhiro Takasu, Takeyuki Tamura
New and Improved Algorithms for Unordered Tree Inclusion. ISAAC (2018)
Takeyuki Tamura, Wei Lu, Jiangning Song, Tatsuya Akutsu
Computing Minimum Reaction Modifications in a Boolean Metabolic Network. IEEE ACM Trans. Comput. Biol. Bioinform. 15 (6) (2018)
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. CPM (2018)
Takeyuki Tamura
Grid-based computational methods for the design of constraint-based parsimonious chemical reaction networks to simulate metabolite production: GridProd. BMC Bioinform. 19 (1) (2018)
Xiaoqing Cheng, Takeyuki Tamura, Wai-Ki Ching, Tatsuya Akutsu
Discrimination of singleton and periodic attractors in Boolean networks. Autom. 84 (2017)
Tatsuya Akutsu, Jesper Jansson, Atsuhiro Takasu, Takeyuki Tamura
On the parameterized complexity of associative and commutative unification. Theor. Comput. Sci. 660 (2017)
Tatsuya Akutsu, Jesper Jansson, Ruiming Li, Atsuhiro Takasu, Takeyuki Tamura
New Algorithms for Unordered Tree Inclusion. CoRR (2017)
Wenpin Hou, Takeyuki Tamura, Wai-Ki Ching, Tatsuya Akutsu
Finding and Analyzing the Minimum Set of Driver Nodes in control of Boolean Networks. Adv. Complex Syst. 19 (3) (2016)
Tomoya Mori, Atsuhiro Takasu, Jesper Jansson, Jaewook Hwang, Takeyuki Tamura, Tatsuya Akutsu
Similar subtree search using extended tree inclusion. ICDE (2016)
Takeyuki Tamura, Tatsuya Akutsu, Chun-Yu Lin, Jinn-Moon Yang
Finding Influential Genes Using Gene Expression Data and Boolean Models of Metabolic Networks. BIBE (2016)
Wei Lu, Takeyuki Tamura, Jiangning Song, Tatsuya Akutsu
Computing Smallest Intervention Strategies for Multiple Metabolic Networks in a Boolean Model. J. Comput. Biol. 22 (2) (2015)
Chia-Jung Chang, Takeyuki Tamura, Kun-Mao Chao, Tatsuya Akutsu
A Fixed-Parameter Algorithm for Detecting a Singleton Attractor in an AND/OR Boolean Network with Bounded Treewidth. IEICE Trans. Fundam. Electron. Commun. Comput. Sci. (1) (2015)
Tomoya Mori, Atsuhiro Takasu, Jesper Jansson, Jaewook Hwang, Takeyuki Tamura, Tatsuya Akutsu
Similar Subtree Search Using Extended Tree Inclusion. IEEE Trans. Knowl. Data Eng. 27 (12) (2015)
Tatsuya Akutsu, Takeyuki Tamura, Avraham A. Melkman, Atsuhiro Takasu
On the complexity of finding a largest common subtree of bounded degree. Theor. Comput. Sci. 590 (2015)
Tatsuya Akutsu, Jesper Jansson, Atsuhiro Takasu, Takeyuki Tamura
On the Parameterized Complexity of Associative and Commutative Unification. IPEC (2014)
Yushan Qiu, Takeyuki Tamura, Wai-Ki Ching, Tatsuya Akutsu
On control of singleton attractors in multiple Boolean networks: integer programming-based method. BMC Syst. Biol. 8 (S-1) (2014)
Tatsuya Akutsu, Takeyuki Tamura, Daiji Fukagawa, Atsuhiro Takasu
Efficient exponential-time algorithms for edit distance between unordered trees. J. Discrete Algorithms 25 (2014)
Tatsuya Akutsu, Takeyuki Tamura
A Polynomial-Time Algorithm for Computing the Maximum Common Connected Edge Subgraph of Outerplanar Graphs of Bounded Degree. Algorithms 6 (1) (2013)
Tatsuya Akutsu, Takeyuki Tamura, Atsuhiro Takasu
On the Parameterized Complexity of Associative and Commutative Unification. CoRR (2013)
Tatsuya Akutsu, Takeyuki Tamura, Avraham A. Melkman, Atsuhiro Takasu
On the Complexity of Finding a Largest Common Subtree of Bounded Degree. FCT (2013)
Yang Zhao, Takeyuki Tamura, Tatsuya Akutsu, Jean-Philippe Vert
Flux balance impact degree: a new definition of impact degree to properly treat reversible reactions in metabolic networks. Bioinform. 29 (17) (2013)
Xi Chen, Tatsuya Akutsu, Takeyuki Tamura, Wai-Ki Ching
Finding optimal control policy in probabilistic Boolean Networks with hard constraints by using integer programming and dynamic programming. Int. J. Data Min. Bioinform. 7 (3) (2013)
Hao Jiang, Takeyuki Tamura, Wai-Ki Ching, Tatsuya Akutsu
On the Complexity of Inference and Completion of Boolean Networks from Given Singleton Attractors. IEICE Trans. Fundam. Electron. Commun. Comput. Sci. (11) (2013)
Tatsuya Akutsu, Avraham A. Melkman, Takeyuki Tamura
Singleton and 2-periodic attractors of sign-definite Boolean networks. Inf. Process. Lett. 112 (1-2) (2012)
Tatsuya Akutsu, Yang Zhao, Morihiro Hayashida, Takeyuki Tamura
Integer Programming-Based Approach to Attractor Detection and Control of Boolean Networks. IEICE Trans. Inf. Syst. (12) (2012)
Tatsuya Akutsu, Morihiro Hayashida, Takeyuki Tamura
Finding Conserved Regions in Protein Structures Using Support Vector Machines and Structure Alignment. PRIB (2012)
Tatsuya Akutsu, Takeyuki Tamura
On the Complexity of the Maximum Common Subgraph Problem for Partial k-Trees of Bounded Degree. ISAAC (2012)
Tatsuya Akutsu, Takeyuki Tamura, Daiji Fukagawa, Atsuhiro Takasu
Efficient Exponential Time Algorithms for Edit Distance between Unordered Trees. CPM (2012)
Tatsuya Akutsu, Sven Kosub, Avraham A. Melkman, Takeyuki Tamura
Finding a Periodic Attractor of a Boolean Network. IEEE ACM Trans. Comput. Biol. Bioinform. 9 (5) (2012)
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. J. Comput. Biol. 19 (10) (2012)
Tatsuya Akutsu, Takeyuki Tamura
A Polynomial-Time Algorithm for Computing the Maximum Common Subgraph of Outerplanar Graphs of Bounded Degree. MFCS (2012)
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. BMC Bioinform. 12 (S-1) (2011)
Takeyuki Tamura, Yang Cong, Tatsuya Akutsu, Wai-Ki Ching
An Efficient Method of Computing Impact Degrees for Multiple Reactions in Metabolic Networks with Cycles. IEICE Trans. Inf. Syst. (12) (2011)
Tatsuya Akutsu, Daiji Fukagawa, Atsuhiro Takasu, Takeyuki Tamura
Exact algorithms for computing the tree edit distance between unordered trees. Theor. Comput. Sci. 412 (4-5) (2011)
Tatsuya Akutsu, Tomoya Mori, Takeyuki Tamura, Daiji Fukagawa, Atsuhiro Takasu, Etsuji Tomita
An Improved Clique-Based Method for Computing Edit Distance between Unordered Trees and Its Application to Comparison of Glycan Structures. CISIS (2011)
Tatsuya Akutsu, Avraham A. Melkman, Takeyuki Tamura, Masaki Yamamoto
Determining a Singleton Attractor of a Boolean Network with Nested Canalyzing Functions. J. Comput. Biol. 18 (10) (2011)
Takeyuki Tamura, Tatsuya Akutsu
Exact Algorithms for Finding a Minimum Reaction Cut under a Boolean Model of Metabolic Networks. IEICE Trans. Fundam. Electron. Commun. Comput. Sci. (8) (2010)
Takeyuki Tamura, Kazuhiro Takemoto, Tatsuya Akutsu
Finding Minimum Reaction Cuts of Metabolic Networks Under a Boolean Model Using Integer Programming and Feedback Vertex Sets. Int. J. Knowl. Discov. Bioinform. 1 (1) (2010)
Xi Chen, Tatsuya Akutsu, Takeyuki Tamura, Wai-Ki Ching
Finding optimal control policy in Probabilistic Boolean Networks with hard constraints by using integer programming and dynamic programming. BIBM (2010)
Avraham A. Melkman, Takeyuki Tamura, Tatsuya Akutsu
) time. Inf. Process. Lett. 110 (14-15) (2010)
Takeyuki Tamura, Kazuhiro Takemoto, Tatsuya Akutsu
Measuring Structural Robustness of Metabolic Networks under a Boolean Model Using Integer Programming and Feedback Vertex Sets. CISIS (2009)
Tatsuya Akutsu, Morihiro Hayashida, Takeyuki Tamura
Integer programming-based methods for attractor detection and control of boolean networks. CDC (2009)
Takeyuki Tamura, Tatsuya Akutsu
Detecting a Singleton Attractor in a Boolean Network Utilizing SAT Algorithms. IEICE Trans. Fundam. Electron. Commun. Comput. Sci. (2) (2009)
Tatsuya Akutsu, Takeyuki Tamura
On Finding a Fixed Point in a Boolean Network with Maximum Indegree 2. IEICE Trans. Fundam. Electron. Commun. Comput. Sci. (8) (2009)
Tatsuya Akutsu, Takeyuki Tamura, Katsuhisa Horimoto
Completing Networks Using Observed Data. ALT (2009)
Takeyuki Tamura, Tatsuya Akutsu
Algorithms for Singleton Attractor Detection in Planar and Nonplanar AND/OR Boolean Networks. Math. Comput. Sci. 2 (3) (2009)
Yang Cong, Takeyuki Tamura, Tatsuya Akutsu, Wai-Ki Ching
Efficient computation of impact degrees for multiple reactions in metabolic networks with cycles. DTMBIO (2009)
Takeyuki Tamura, Hiro Ito
Inferring Pedigree Graphs from Genetic Distances. IEICE Trans. Inf. Syst. (2) (2008)
Tatsuya Akutsu, Morihiro Hayashida, Takeyuki Tamura
Algorithms for Inference, Analysis and Control of Boolean Networks. AB (2008)
Morihiro Hayashida, Takeyuki Tamura, Tatsuya Akutsu, Shuqin Zhang, Wai-Ki Ching
Algorithms and Complexity Analyses for Control of Singleton Attractors in Boolean Networks. EURASIP J. Bioinform. Syst. Biol. 2008 (2008)
Takeyuki Tamura, Tatsuya Akutsu
An Improved Algorithm for Detecting a Singleton Attractor in a Boolean Network Consisting of AND/OR Nodes. AB (2008)
Takeyuki Tamura, Tatsuya Akutsu
Approximation Algorithms for Optimal RNA Secondary Structures Common to Multiple Sequences. IEICE Trans. Fundam. Electron. Commun. Comput. Sci. (5) (2007)
Takeyuki Tamura, Tatsuya Akutsu
)-Time Algorithm for Detecting a Singleton Attractor in a Boolean Network Consisting of AND/OR Nodes. FCT (2007)
Takeyuki Tamura, Tatsuya Akutsu
Subcellular location prediction of proteins using support vector machines with alignment of block sequences utilizing amino acid composition. BMC Bioinform. 8 (2007)
Hiro Ito, Kazuo Iwama, Takeyuki Tamura
Efficient Methods for Determining DNA Probe Orders. IEICE Trans. Fundam. Electron. Commun. Comput. Sci. (5) (2006)
Hiro Ito, Kazuo Iwama, Takeyuki Tamura
Imperfectness of Data for STS-Based Physical Mapping. IFIP TCS (2004)