京都大学化学研究所研究者情報   [ English | Japanese ]


阿久津 達也(あくつ たつや )

バイオインフォマティクスセンター 数理生物情報
(情報学研究科 知能情報学専攻 協力講座)
教授
工学博士
URL:http://www.bic.kyoto-u.ac.jp/takutsu/index_J.html
E-mail: takutsu @ kuicr.kyoto-u.ac.jp
Tel: 0774-38-3015
Fax: 0774-38-3022

研究・教育歴
    1989.3 東京大学大学院工学系研究科博士課程修了
    1989.3 東京大学工学博士
    1989.4〜1994.3 通商産業省工業技術院機械技術研究所研究員
    1994.4〜1996.3 群馬大学工学部助教授
    1996.4〜2001.9 東京大学医科学研究所ヒトゲノム解析センター助教授
    2001.10〜 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教授
専門分野
    数理生物情報学、バイオインフォマティクス、離散アルゴリズム
主な研究テーマ
  1. スケールフリーネットワーク
  2. タンパク質およびRNA高次構造解析
  3. 化学情報解析
主な論文・著書
  1. 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]
  2. Takemoto K, Akutsu T, Analysis of the effect of degree correlation on the size of minimum dominating sets in complex networks PLoS ONE 11, [e0157868:1]-[e0157868:11] (2016)  [pubmed]
  3. 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)
  4. 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)
  5. Nacher JC, Akutsu T., Structurally robust control of complex networks. Phys Rev E Stat Nonlin Soft Matter Phys 91, 012826 (2015)  [pubmed]
  6. 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)
  7. 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)
  8. 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]
  9. Nacher JC, Akutsu T., Structural controllability of unidirectional bipartite networks. Scientific Reports 3, 1647 (2013)  [pubmed]
  10. 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)
  11. 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)
  12. 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]
  13. 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)
  14. Akutsu T, Fukagawa D, Jansson J, Sadakane K., Inferring a graph from path frequency. Discrete Applied Mathematics 160, 1416-1428 (2012)
  15. 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)
  16. 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]
  17. Nacher JC, Akutsu T., On the degree distribution of projected networks mapped from bipartite networks. Physica A 390, 4636-4651 (2011)
  18. 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]
  19. 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]
  20. 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)
  21. 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)
  22. Akutsu T, A bisection algorithm for grammar-based compression of ordered trees Information Processing Letters 110, 815-820 (2010)
  23. Akutsu T, Fukagawa D, Takasu A, Approximating tree edit distance through string edit distance Algorithmica 57, 325-348 (2010)
  24. Akutsu T, Tamura T, Horimoto K, Completing networks using observed data Lecture Notes in Artificial Intelligence 5809, 126-140 (2009).
  25. Kato Y, Akutsu T, H Seki, A grammatical approach to RNA-RNA interaction prediction Pattern Recognition 42, 531-538 (2009)
  26. 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]
  27. Akutsu T., A relation between edit distance for ordered trees and edit distance for Euler strings Information Processing Letters 100, 105-109 (2006)
  28. 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]
  29. 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]
  30. Nacher JC, Ueda N, Kanehisa M, Akutsu T., Flexible construction of hierarchical scale-free networks with general exponent Physical Review E 71, 036132 (2005).
  31. 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]
  32. Akutsu T, Efficient extraction of mapping rules of atoms from enzymatic reaction data Journal of Computational Biology 11, 449-462 (2004)  [pubmed]
  33. 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)
  34. Akutsu T, Miyano S, Kuhara S, Inferring qualitative relations in genetic networks and metabolic pathways Bioinformatics 16, 727-734 (2000)
  35. Akutsu T, Dynamic programming algorithms for RNA secondary prediction with pseudoknots Discrete Applied Mathematics 104, 45-62 (2000)


Update: Jul 18,2017