Imperfectness of Data for STS-Based Physical Mapping. - Hiro Ito; Kazuo Iwama; Takeyuki Tamura (IFIP TCS, 2004)

Efficient Methods for Determining DNA Probe Orders. - Hiro Ito; Kazuo Iwama; Takeyuki Tamura (IEICE Trans. Fundam. Electron. Commun. Comput. Sci., 2006)

An O(1.787n)-Time Algorithm for Detecting a Singleton Attractor in a Boolean Network Consisting of AND/OR Nodes. - Takeyuki Tamura; Tatsuya Akutsu (FCT, 2007)

Subcellular location prediction of proteins using support vector machines with alignment of block sequences utilizing amino acid composition. - Takeyuki Tamura; Tatsuya Akutsu (BMC Bioinform., 2007)

Approximation Algorithms for Optimal RNA Secondary Structures Common to Multiple Sequences. - Takeyuki Tamura; Tatsuya Akutsu (IEICE Trans. Fundam. Electron. Commun. Comput. Sci., 2007)

Algorithms for Inference, Analysis and Control of Boolean Networks. - Tatsuya Akutsu; Morihiro Hayashida; Takeyuki Tamura (AB, 2008)

An Improved Algorithm for Detecting a Singleton Attractor in a Boolean Network Consisting of AND/OR Nodes. - Takeyuki Tamura; Tatsuya Akutsu (AB, 2008)

Algorithms and Complexity Analyses for Control of Singleton Attractors in Boolean Networks. - Morihiro Hayashida; Takeyuki Tamura; Tatsuya Akutsu; Shuqin Zhang; Wai-Ki Ching (EURASIP J. Bioinform. Syst. Biol., 2008)

Inferring Pedigree Graphs from Genetic Distances. - Takeyuki Tamura; Hiro Ito (IEICE Trans. Inf. Syst., 2008)

Completing Networks Using Observed Data. - Tatsuya Akutsu; Takeyuki Tamura; Katsuhisa Horimoto (ALT, 2009)

Integer programming-based methods for attractor detection and control of boolean networks. - Tatsuya Akutsu; Morihiro Hayashida; Takeyuki Tamura (CDC, 2009)

Efficient computation of impact degrees for multiple reactions in metabolic networks with cycles. - Yang Cong; Takeyuki Tamura; Tatsuya Akutsu; Wai-Ki Ching (DTMBIO, 2009)

Measuring Structural Robustness of Metabolic Networks under a Boolean Model Using Integer Programming and Feedback Vertex Sets. - Takeyuki Tamura; Kazuhiro Takemoto; Tatsuya Akutsu (CISIS, 2009)

On Finding a Fixed Point in a Boolean Network with Maximum Indegree 2. - Tatsuya Akutsu; Takeyuki Tamura (IEICE Trans. Fundam. Electron. Commun. Comput. Sci., 2009)

Detecting a Singleton Attractor in a Boolean Network Utilizing SAT Algorithms. - Takeyuki Tamura; Tatsuya Akutsu (IEICE Trans. Fundam. Electron. Commun. Comput. Sci., 2009)

Algorithms for Singleton Attractor Detection in Planar and Nonplanar AND/OR Boolean Networks. - Takeyuki Tamura; Tatsuya Akutsu (Math. Comput. Sci., 2009)

Exact Algorithms for Finding a Minimum Reaction Cut under a Boolean Model of Metabolic Networks. - Takeyuki Tamura; Tatsuya Akutsu (IEICE Trans. Fundam. Electron. Commun. Comput. Sci., 2010)

Finding Minimum Reaction Cuts of Metabolic Networks Under a Boolean Model Using Integer Programming and Feedback Vertex Sets. - Takeyuki Tamura; Kazuhiro Takemoto; Tatsuya Akutsu (Int. J. Knowl. Discov. Bioinform., 2010)

Determining a singleton attractor of an AND/OR Boolean network in O(1.587n) time. - Avraham A. Melkman; Takeyuki Tamura; Tatsuya Akutsu (Inf. Process. Lett., 2010)

An Improved Clique-Based Method for Computing Edit Distance between Unordered Trees and Its Application to Comparison of Glycan Structures. - Tatsuya Akutsu; Tomoya Mori; Takeyuki Tamura; Daiji Fukagawa; Atsuhiro Takasu; Etsuji Tomita (CISIS, 2011)

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 Bioinform., 2011)

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 Trans. Inf. Syst., 2011)

Determining a Singleton Attractor of a Boolean Network with Nested Canalyzing Functions. - Tatsuya Akutsu; Avraham A. Melkman; Takeyuki Tamura; Masaki Yamamoto 001 (J. Comput. Biol., 2011)

Exact algorithms for computing the tree edit distance between unordered trees. - Tatsuya Akutsu; Daiji Fukagawa; Atsuhiro Takasu; Takeyuki Tamura (Theor. Comput. Sci., 2011)

On the Complexity of the Maximum Common Subgraph Problem for Partial k-Trees of Bounded Degree. - Tatsuya Akutsu; Takeyuki Tamura (ISAAC, 2012)

A Polynomial-Time Algorithm for Computing the Maximum Common Subgraph of Outerplanar Graphs of Bounded Degree. - Tatsuya Akutsu; Takeyuki Tamura (MFCS, 2012)

Finding Conserved Regions in Protein Structures Using Support Vector Machines and Structure Alignment. - Tatsuya Akutsu; Morihiro Hayashida; Takeyuki Tamura (PRIB, 2012)

Integer Programming-Based Approach to Attractor Detection and Control of Boolean Networks. - Tatsuya Akutsu; Yang Zhao 018; Morihiro Hayashida; Takeyuki Tamura (IEICE Trans. Inf. Syst., 2012)

Singleton and 2-periodic attractors of sign-definite Boolean networks. - Tatsuya Akutsu; Avraham A. Melkman; Takeyuki Tamura (Inf. Process. Lett., 2012)

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 (J. Comput. Biol., 2012)

Finding a Periodic Attractor of a Boolean Network. - Tatsuya Akutsu; Sven Kosub; Avraham A. Melkman; Takeyuki Tamura (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

A Polynomial-Time Algorithm for Computing the Maximum Common Connected Edge Subgraph of Outerplanar Graphs of Bounded Degree. - Tatsuya Akutsu; Takeyuki Tamura (Algorithms, 2013)

Flux balance impact degree: a new definition of impact degree to properly treat reversible reactions in metabolic networks. - Yang Zhao 018; Takeyuki Tamura; Tatsuya Akutsu; Jean-Philippe Vert (Bioinform., 2013)

On the Parameterized Complexity of Associative and Commutative Unification. - Tatsuya Akutsu; Takeyuki Tamura; Atsuhiro Takasu (CoRR, 2013)

On the Complexity of Inference and Completion of Boolean Networks from Given Singleton Attractors. - Hao Jiang 009; Takeyuki Tamura; Wai-Ki Ching; Tatsuya Akutsu (IEICE Trans. Fundam. Electron. Commun. Comput. Sci., 2013)

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 (Int. J. Data Min. Bioinform., 2013)

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)

Efficient exponential-time algorithms for edit distance between unordered trees. - Tatsuya Akutsu; Takeyuki Tamura; Daiji Fukagawa; Atsuhiro Takasu (J. Discrete Algorithms, 2014)

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)

Computing Smallest Intervention Strategies for Multiple Metabolic Networks in a Boolean Model. - Wei Lu 027; Takeyuki Tamura; Jiangning Song; Tatsuya Akutsu (J. Comput. Biol., 2015)

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)

Similar Subtree Search Using Extended Tree Inclusion. - Tomoya Mori; Atsuhiro Takasu; Jesper Jansson 001; Jaewook Hwang; Takeyuki Tamura; Tatsuya Akutsu (IEEE Trans. Knowl. Data Eng., 2015)

Finding Influential Genes Using Gene Expression Data and Boolean Models of Metabolic Networks. - Takeyuki Tamura; Tatsuya Akutsu; Chun-Yu Lin 003; Jinn-Moon Yang (BIBE, 2016)

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)

Discrimination of singleton and periodic attractors in Boolean networks. - Xiaoqing Cheng; Takeyuki Tamura; Wai-Ki Ching; Tatsuya Akutsu (Autom., 2017)

New Algorithms for Unordered Tree Inclusion. - Tatsuya Akutsu; Jesper Jansson 001; Ruiming Li; Atsuhiro Takasu; Takeyuki Tamura (CoRR, 2017)

On the parameterized complexity of associative and commutative unification. - Tatsuya Akutsu; Jesper Jansson 001; Atsuhiro Takasu; Takeyuki Tamura (Theor. Comput. Sci., 2017)

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 (CPM, 2018)

Grid-based computational methods for the design of constraint-based parsimonious chemical reaction networks to simulate metabolite production: GridProd. - Takeyuki Tamura (BMC Bioinform., 2018)

Computing Minimum Reaction Modifications in a Boolean Metabolic Network. - Takeyuki Tamura; Wei Lu 027; Jiangning Song; Tatsuya Akutsu (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

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)

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)

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 Bioinform., 2021)

L1 Norm Minimal Mode-Based Methods for Listing Reaction Network Designs for Metabolite Production. - Takeyuki Tamura (IEICE Trans. Inf. Syst., 2021)

New and improved algorithms for unordered tree inclusion. - Tatsuya Akutsu; Jesper Jansson 001; Ruiming Li; Atsuhiro Takasu; Takeyuki Tamura (Theor. Comput. Sci., 2021)

Trimming Gene Deletion Strategies for Growth-Coupled Production in Constraint-Based Metabolic Networks: TrimGdel. - Takeyuki Tamura (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

MetNetComp: Database for Minimal and Maximal Gene-Deletion Strategies for Growth-Coupled Production of Genome-Scale Metabolic Networks. - Takeyuki Tamura (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

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 (J. Comput. Biol., 2023)

DBgDel: Database-Enhanced Gene Deletion Framework for Growth-Coupled Production in Genome-Scale Metabolic Models. - Ziwei Yang; Takeyuki Tamura (CoRR, 2024)

DeepGDel: Deep Learning-based Gene Deletion Prediction Framework for Growth-Coupled Production in Genome-Scale Metabolic Models. - Ziwei Yang; Takeyuki Tamura (CoRR, 2025)