Academic career
| 1989.3 | Graduated from Dr. Course, University of Tokyo
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| 1989.3 | D. Eng., University of Tokyo
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| 1989.4-1994.3 | Researcher, Mechanical Engineering Laboratory, AIST, MITI
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| 1994.4-1996.3 | Associate Professor, Gunma University
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| 1996.4-2001.9 | Associate Professor, University of Tokyo, Institute of Medical Science
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| 2001.10 - | Professor, Kyoto University, Institute for Chemical Research, Bioinformatics Center |
Research field
Bioinformatics, Discrete Algorithms
Current research
- Algorithms for DNA/Protein Sequence Analysis
- Algorithms for Protein Structure Analysis
- Algorithms for Chemical Structure/Reaction Analysis
Selected publications
- 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]
- 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)
- Akutsu T, Fukagawa D, Jansson J, Sadakane K., Inferring a graph from path frequency. Discrete Applied Mathematics 160, 1416-1428 (2012)
- 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)
- 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]
- Nacher JC, Akutsu T., On the degree distribution of projected networks mapped from bipartite networks. Physica A 390, 4636-4651 (2011)
- 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]
- 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]
- 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)
- 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)
- Akutsu T, A bisection algorithm for grammar-based compression of ordered trees Information Processing Letters 110, 815-820 (2010)
- Akutsu T, Fukagawa D, Takasu A, Approximating tree edit distance through string edit distance Algorithmica 57, 325-348 (2010)
- Akutsu T, Tamura T, Horimoto K, Completing networks using observed data Lecture Notes in Artificial Intelligence 5809, 126-140 (2009).
- Kato Y, Akutsu T, H Seki, A grammatical approach to RNA-RNA interaction prediction Pattern Recognition 42, 531-538 (2009)
- Song J, Tan H, Takemoto K, Akutsu T., HSEpred: predict half-sphere exposure from protein sequences. Bioinformatics 24, 1489-97 (2008) [pubmed]
- Ching WK, Zhang S, Ng MK, Akutsu T., An approximation method for solving the steady-state probability distribution of probabilistic Boolean networks. Bioinformatics 23, 1511-1518 (2007). [pubmed]
- 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]
- Akutsu T., A relation between edit distance for ordered trees and edit distance for Euler strings Information Processing Letters 100, 105-109 (2006)
- Nacher JC, Hayashida M, Akutsu T., Protein domain networks: scale-free mixing of positive and negative exponents Physica A, 367, 538-552 (2006)
- Matsuda S, Vert JP, Saigo H, Ueda N, Toh H, Akutsu T., A novel representation of protein sequences for prediction of subcellular location using support vector machines. Protein Science 14, 2804-2813 (2005) [pubmed]
- 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]
- 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]
- Nacher JC, Ueda N, Kanehisa M, Akutsu T., Flexible construction of hierarchical scale-free networks with general exponent Physical Review E 71, 036132 (2005).
- 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]
- Akutsu T, Efficient extraction of mapping rules of atoms from enzymatic reaction data Journal of Computational Biology 11, 449-462 (2004) [pubmed]
- 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)
- Akutsu T, Miyano S, Kuhara S, Inferring qualitative relations in genetic networks and metabolic pathways Bioinformatics 16, 727-734 (2000)
- Akutsu T, Dynamic programming algorithms for RNA secondary prediction with pseudoknots Discrete Applied Mathematics 104, 45-62 (2000)
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