Faculty Information, Institute for Chemical Research, Kyoto University   [ English | Japanese ]

AKUTSU, Tatsuya

Bioinformatics Center - Mathematical Bioinformatics -
(Laboratory in the School of Informatics)
Dr. Engineering
E-mail: takutsu @ kuicr.kyoto-u.ac.jp
Tel: 0774-38-3015
Fax: 0774-38-3022

Academic career
    1989.3 Graduated from Dr. Course, University of Tokyo
    1989.3 D. Eng., University of Tokyo
    1989.4-1994.3 Researcher, Mechanical Engineering Laboratory, AIST, MITI
    1994.4-1996.3 Associate Professor, Gunma University
    1996.4-2001.9 Associate Professor, University of Tokyo, Institute of Medical Science
    2001.10 - Professor, Kyoto University, Institute for Chemical Research, Bioinformatics Center
Research field
    Bioinformatics, Discrete Algorithms
Current research
  1. Algorithms for DNA/Protein Sequence Analysis
  2. Algorithms for Protein Structure Analysis
  3. Algorithms for Chemical Structure/Reaction Analysis
Selected publications
  1. Hou W, Ruan P, Ching WK, Akutsu T., On the number of driver nodes for controlling a Boolean network when the targets are restricted to attractors. J Theor Biol 463, 1-11 (2019)  [pubmed]
  2. Akutsu T, Algorithms for Analysis, Inference, and Control of Boolean Networks World Scientific (2018)
  3. Akutsu T, Jansson, J, Li R, Takasu A, Tamura T, New and improved algorithms for unordered tree inclusion Proc. 29th Int. Symp. Algorithms and Computation (2018)
  4. Melkman AA, Cheng X, Ching WK, Akutsu T, Identifying a probabilistic Boolean threshold network from samples IEEE Transactions on Neural Networks and Learning Systems 29, 869-881 (2018)
  5. Cheng X, Tamura T, Ching W-K, Akutsu T, Discrimination of singleton and periodic attractors in Boolean networks Automatica 84, 205-213 (2017)
  6. Akutsu T, Jansson J, Takasu A, Tamura T, On the parameterized complexity of associative and commutative unification Theoretical Computer Science 660, 57-74 (2017)
  7. Cheng X, Mori T, Qiu Y, Ching WK, Akutsu T, "Exact identification of the structure of a probabilistic Boolean network from samples IEEE/ACM Transactions on Computational Biology and Bioinformatics 13, 1545-5963 (2016)  [pubmed]
  8. Mori T, Takasu A, Jansson J, Hwang J, Tamura T, Akutsu T., Similar subtree search using extended tree inclusion. IEEE Transactions on Knowledge and Data Engineering 27, 3360-3373 (2015)
  9. Akutsu T. Tamura T, Melkman AA, Takasu A., On the complexity of finding a largest common subtree of bounded degree. Theoretical Computer Science 590, 2-16 (2015)
  10. Nacher JC, Akutsu T., Structurally robust control of complex networks. Phys Rev E Stat Nonlin Soft Matter Phys 91, 012826 (2015)  [pubmed]
  11. Nacher JC, Akutsu T, Analysis of critical and redundant nodes in controlling directed and undirected complex networks using dominating sets Journal of Complex Networks 2, 394-412 (2014)
  12. Akutsu T, Tamura T, Fukagawa D, Takasu A, Efficient exponential-time algorithms for edit distance between unordered trees Journal of Discrete Algorithms 25, 79-93 (2014)
  13. Zhao Y, Tamura T, Akutsu T, Vert JP., Flux balance impact degree: a new definition of impact degree to properly treat reversible reactions in metabolic networks. Bioinformatics 29, 2178-85 (2013)  [pubmed]
  14. Nacher JC, Akutsu T., Structural controllability of unidirectional bipartite networks. Scientific Reports 3, 1647 (2013)  [pubmed]
  15. Akutsu T, Tamura T., A polynomial-time algorithm for computing the maximum common connected edge subgraph of outerplanar graphs of bounded degree. Algorithms 6, 119-135 (2013)
  16. Akutsu T, Fukagawa D, Halldorsson MM, Takasu A, Tanaka K., Approximation and parameterized algorithms for common subtrees and edit distance between unordered trees. Theoretical Computer Science 470, 10-22 (2013)
  17. Akutsu T, Kosub S, Melkman AA, Tamura T., Finding a periodic attractor of a Boolean network. IEEE/ACM Transactions on Computational Biology and Bioinformatics 9, 1410-21 (2012)  [pubmed]
  18. Nacher JC, Akutsu T., Dominating scale-free networks with variable scaling exponent: Heterogeneous networks are not difficult to control. New Journal of Physics 14, [073005:1-073005:24] (2012)
  19. Akutsu T, Fukagawa D, Jansson J, Sadakane K., Inferring a graph from path frequency. Discrete Applied Mathematics 160, 1416-1428 (2012)
  20. Shimizu M, Nagamochi H, Akutsu T., Enumerating tree-like chemical graphs with given upper and lower bounds on path frequencies. BMC Bioinformatics 12 Suppl 14, [S3:1-S3:9] (2011)
  21. Imada T, Ota S, Nagamochi H, Akutsu T., Efficient enumeration of stereoisomers of outerplanar chemical graphs using dynamic programming. Journal of Chemical Information and Modeling 51, 2788-2807 (2011)  [pubmed]
  22. Nacher JC, Akutsu T., On the degree distribution of projected networks mapped from bipartite networks. Physica A 390, 4636-4651 (2011)
  23. Sato K, Kato Y, Hamada M, Akutsu T, Asai K., IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming. Bioinformatics 27, i85-93 (2011)  [pubmed]
  24. Akutsu T, Melkman AA, Tamura T, Yamamoto M., Determining a singleton attractor of a boolean network with nested canalyzing functions. Journal of Computational Biology 18, 1275-90 (2011)  [pubmed]
  25. Akutsu T, Fukagawa D, Takasu A, Tamura T, Exact algorithms for computing tree edit distance between unordered trees Theoretical Computer Science 421, 352-364 (2011)
  26. Brown JB, Urata T, Tamura T, Arai MA, Kawabata T, Akutsu T, Compound analysis via graph kernels incorporating chirality Journal of Bioinformatics and Computational Biology 8, Suppl 1, 53-81 (2010)
  27. Akutsu T, A bisection algorithm for grammar-based compression of ordered trees Information Processing Letters 110, 815-820 (2010)
  28. Akutsu T, Fukagawa D, Takasu A, Approximating tree edit distance through string edit distance Algorithmica 57, 325-348 (2010)
  29. Akutsu T, Tamura T, Horimoto K, Completing networks using observed data Lecture Notes in Artificial Intelligence 5809, 126-140 (2009).
  30. Kato Y, Akutsu T, H Seki, A grammatical approach to RNA-RNA interaction prediction Pattern Recognition 42, 531-538 (2009)
  31. Akutsu T, Hayashida M, Ching WK, Ng MK., Control of Boolean networks: hardness results and algorithms for tree structured networks. Journal Theoretical Biology 244, 670-679 (2007).  [pubmed]
  32. Akutsu T., A relation between edit distance for ordered trees and edit distance for Euler strings Information Processing Letters 100, 105-109 (2006)
  33. Mahe P, Ueda N, Akutsu T, Perret JL, Vert JP., Graph kernels for molecular structure-activity relationship analysis with support vector machines. Journal of Chemcal Information and Modeling 45, 939-951 (2005)  [pubmed]
  34. Itoh M, Goto S, Akutsu T, Kanehisa M., Fast and accurate database homology search using upper bounds of local alignment scores Bioinformatics 21, 912-921 (2005).  [pubmed]
  35. Nacher JC, Ueda N, Kanehisa M, Akutsu T., Flexible construction of hierarchical scale-free networks with general exponent Physical Review E 71, 036132 (2005).
  36. Aoki K F, Yamaguchi A, Ueda N, Akutsu T, Mamitsuka H, Goto S, Kanehisa, M, KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains Nucleic Acids Research 32, w267-w272 (2004)  [pubmed]
  37. Akutsu T, Efficient extraction of mapping rules of atoms from enzymatic reaction data Journal of Computational Biology 11, 449-462 (2004)  [pubmed]
  38. Akutsu T, Kuhara S, Maruyama O, Miyano S, Identification of genetic networks by strategic gene disruptions and gene overexpressions under a boolean model Theoretical Computer Science 298, 235-251 (2003)
  39. Akutsu T, Miyano S, Kuhara S, Inferring qualitative relations in genetic networks and metabolic pathways Bioinformatics 16, 727-734 (2000)
  40. Akutsu T, Dynamic programming algorithms for RNA secondary prediction with pseudoknots Discrete Applied Mathematics 104, 45-62 (2000)

Update: Jun 21,2019