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


田村 武幸 (たむら たけゆき)

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 協力講座)
助教
京都大学博士(情報学)
URL:http://sunflower.kuicr.kyoto-u.ac.jp/~tamura/
E-mail: tamura at kuicr.kyoto-u.ac.jp
Tel: 0774-38-3020
Fax: 0774-38-3022

研究・教育歴
    2001. 3 京都大学工学部情報学科卒業
    2003. 3 京都大学大学院情報学研究科修士課程修了
    2006. 3 京都大学大学院情報学研究科博士後期課程修了
    2006. 3 京都大学博士(情報学)
    2006. 4 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博士研究員
    2007.12 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助教
専門分野
    バイオインフォマティクスのアルゴリズム理論
主な研究テーマ
  1. 計算量理論と生化学に基づく生体ネットワーク解析手法の開発
  2. ブーリアンモデルによる遺伝子制御ネットワークや代謝ネットワークの数理モデル化と解析
  3. 最大共通部分グラフを見つけるアルゴリズム
主な論文・著書
  1. Takeyuki Tamura*, Wei Lu, Jiangning Song, and Tatsuya Akutsu (* corresponding author), Computing Minimum Reaction Modifications in a Boolean Metabolic Network, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
  2. Wenpin Hou, Takeyuki Tamura, Wai-Ki. Ching and Tatsuya Akutsu, Finding and analyzing the minimum set of driver nodes in control of Boolean networks, Advances in Complex Systems, 19, 1650006 (32 pages), 2016.
  3. Tomoya Mori, Atsuhiro Takasu, Jesper Jansson, Jaewook Hwang, Takeyuki Tamura, and Tatsuya Akutsu, Similar Subtree Search Using Extended Tree Inclusion, IEEE Transactions on Knowledge and Data Engineering, Vol. 27, 3360-3373, 2015.
  4. Takeyuki Tamura, Wei Lu, and Tatsuya Akutsu, Computational Methods for Modification of Metabolic Networks (invited mini review paper), Computational and Structural Biotechnology Journal, Volume 13, 376-381, 2015.  
  5. Wei Lu, Takeyuki Tamura*, Jiangning Song, and Tatsuya Akutsu, (* joint first author, and corresponding author), Computing smallest intervention strategies for multiple metabolic networks in a Boolean model, Journal of Computational Biology, 22(2), 85-110, 2015.
  6. Tatsuya Akutsu, Takeyuki Tamura, Avraham A. Melkman, and Atsuhiro Takasu, On the complexity of finding a largest common subtree of bounded degree, Theoretical Computer Science, 590, 2-16, 2015.
  7. Chia-Jung Chang, Takeyuki Tamura*, Kun-Mao Chao and Tatsuya Akutsu, (* corresponding author), A fixed-parameter algorithm for detecting a singleton attractor in an AND/OR Boolean network with bounded treewidth, IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences, E98-A(1), 384-390, 2015.
  8. Rikiya Takeuchi, Takeyuki Tamura, Toru Nakayashiki, Yuichirou Tanaka, Ai Muto, Barry L Wanner and Hirotada Mori, Colony-live --a high-throughput method for measuring microbial colony growth kinetics-- reveals diverse growth effects of gene knockouts in Escherichia coli, BMC Microbiology, 14:171, doi:10.1186/1471-2180-14-171, 2014.
  9. Wei Lu, Takeyuki Tamura*#, Jiangning Song, Tatsuya Akutsu#, (* joint first author, # corresponding aurhors), Integer Programming-based Method for Designing Synthetic Metabolic Networks by Minimum Reaction Insertion in a Boolean Model, PLoS ONE 9(3): e92637. doi:10.1371/journal.pone.0092637, 2014.
  10. Yushan Qiu, Takeyuki Tamura, Wai-Ki Ching, and Tatsuya Akutsu, On control of singleton attractors in multiple Boolean networks: integer programming-based method, BMC Systems Biology, 8 (Suppl for APBC2014):S1:S7, 2014.
  11. Takeyuki Tamura and Tatsuya Akutsu, Theory and method of completion for a Boolean regulatory network using observed data, Biological Data Mining and Its Applications in Healthcare, World Scientific, pp.123-146, 2014.
  12. Tatsuya Akutsu, Takeyuki Tamura*, Daiji Fukagawa, Atsuhiro Takasu, (* corresponding author), Efficient exponential-time algorithms for edit distance between unordered trees, (Preliminary version has appeared in CPM 2012), Journal of Discrete Algorithms, Vol.25, pp.75-93, 2014.
  13. Tatsuya Akutsu, Takeyuki Tamura, Avraham A. Melkman and Atsuhiro Takasu, On the complexity of finding a largest common subtree of bounded degree, Proc. 19th Int. Symp. Fundamentals of Computation Theory (FCT 2013), Lecture Notes in Bioinformatics 8070, 4-15, 2013.
  14. Hao Jiang, Takeyuki Tamura, Wai-Ki Ching and Tatsuya Akutsu, On the complexity of inference and completion of Boolean networks from given singleton attractors, IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences, Vol.E96-A, No.11, pp. 2265-2274, 2013.
  15. Kazuhiro Takemoto, Takeyuki Tamura and Tatsuya Akutsu, Theoretical estimation of metabolic network robustness against multiple reaction knockouts using branching process approximation, Physica A, Vol. 392, pp. 5525--5535, 2013.
  16. Yang Zhao, Takeyuki Tamura, Tatsuya Akutsu and Jean-Philippe Vert, Flux balance impact degree: A new definition of impact degree to properly treat reversible reactions in metabolic networks, Bioinformatics, Vol. 29(17), pp. 2178--2185, 2013.
  17. Tatsuya Akutsu and Takeyuki Tamura, A polynomial-time algorithm for computing the maximum common connected edge subgraph of outerplanar graphs of bounded degree, Algorithms, Vol.6, pp.119-135, 2013.
  18. Xi Chen, Tatsuya Akutsu, Takeyuki Tamura and Wai-Ki Ching, Finding optimal control policy in probabilistic Boolean networks with hard constraints by using integer programming and dynamic programming(Preliminary version has appeared in BIBM 2010), International Journal of Data Mining and Bioinformatics, Vol.7, No.3, pp.321-343, 2013.  
  19. Tatsuya Akutsu and Takeyuki Tamura, On the complexity of the maximum common subgraph problem for partial k-trees of bounded degree, Proc. 23rd International Symposium on Algorithms and Computation (ISAAC 2012), pp.146--155, 2012.
  20. Tatsuya Akutsu and Takeyuki Tamura, A polynomial-time algorithm for computing the maximum common subgraph of outerplanar graphs of bounded degree, Proc. 37th International Symposium on Mathematical Foundations of Computer Science (MFCS 2012), pp.76--87, 2012.
  21. Natsu Nakajima, Takeyuki Tamura, Yoshihiro Yamanishi, Katsuhisa Horimoto, Tatsuya Akutsu, Network completion using dynamic programming and least-squares fitting, The Scientific World Journal, Vol. 2012, Article ID 957620, 8 pages, 2012.
  22. Tatsuya Akutsu, Yang Zhao, Morihiro Hayashida, Takeyuki Tamura, Integer programming-based approach to attractor detection and control of Boolean networks (Preliminary version has appeared in CDC/CCC 2009), IEICE Transactions on Information and Systems, Vol.E95-D, No.12, pp.2960-2970, 2012.
  23. Tomoya Mori, Takeyuki Tamura, Daiji Fukagawa, Atsuhiro Takasu, Etsuji Tomita and Tatsuya Akutsu, A clique-based method using dynamic programming for computing edit distance between unordered trees, Journal of Computational Biology, 19(10): 1089-1104, 2012.
  24. Tatsuya Akutsu, Sven Kosub, Avraham A. Melkman and Takeyuki Tamura, Finding a periodic attractor of a Boolean network, IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 9, pp,1410--1421, 2012.
  25. Tatsuya Akutsu, Avraham A. Melkman and Takeyuki Tamura, Singleton and 2-periodic attractors of sign-definite Boolean networks, Information Processing Letters, Vol.112, Issues 1-2, pp.35--38, 2012.
  26. Kazuhiro Takemoto, Takeyuki Tamura, Yang Cong, Wai-Ki Ching, Jean-Philippe Vert and Tatsuya Akutsu, Analysis of the impact degree distribution in metabolic networks using branching process approximation, Physica A, 391, 379, 17pages, 2012.
  27. Takeyuki Tamura*, Yang Cong, Tatsuya Akutsu and Wai-Ki Ching, (* corresponding author), An Efficient Method of Computing Impact Degrees for Multiple Reactions in Metabolic Networks with Cycles, IEICE Transactions on Information and Systems, Vol.E94-D, No.12 pp.2393-2399, 2011.
  28. Tatsuya Akutsu, Avraham. A. Melkman, Takeyuki Tamura and Masaki Yamamoto, Journal of Computational Biology, Determining a singleton attractor of a Boolean network with nested canalyzing functions, Vol. 18(0), pp. 1--16, 2011.  
  29. Daiji Fukagawa, Takeyuki Tamura, Atsuhiro Takasu, Etsuji Tomita and Tatsuya Akutsu, A clique-based method for the edit distance between unordered trees and its application to analysis of glycan structures, BMC Bioinformatics (Suppl. for APBC 2011), 12, Suppl 1, S14 (9 pages), 2011.
  30. Tatsuya Akutsu, Daiji Fukagawa, Atsuhiro Takasu and Takeyuki Tamura, Exact algorithms for computing tree edit distance between unordered trees, Theoretical Computer Science, Vol. 421, pp. 352-364, 2011.
  31. J.B. Brown, Takashi Urata, Takeyuki Tamura, Midori A. Arai, Takeo Kawabata and Tatsuya Akutsu, Compound analysis via graph kernels incorporating chirality, Journal of Bioinformatics and Computational Biology (Suppl. for GIW 2010), Vol. 8, Suppl. 1, 63-81, 2010.
  32. Takeyuki Tamura* and Tatsuya Akustu, (* corresponding author), Exact algorithms for finding a minimum reaction cut under a Boolean model of metabolic networks, IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences, Vol. E93-A, pp. 1497-1507, 2010.
  33. Avraham Melkman, Takeyuki Tamura*, Tatsuya Akutsu, (* corresponding author) , Determining a singleton attractor of an AND/OR Boolean network in O(1.587^n) time. Information Processing Letters, Vol. 110, pp. 565-569, 2010.
  34. Takeyuki Tamura, Kazuhiro Takemoto and Tatsuya Akutsu, Finding Minimum Reaction Cuts of Metabolic Networks Under a Boolean Model Using Integer Programming and Feedback Vertex Sets. International Journal of Knowledge Discovery in Bioinformatics, Vol 1, pp. 14-31, (Preliminary version has appeared in IIBM2009) 2010.
  35. Morihiro Hayashida, Takeyuki Tamura, Tatsuya Akutsu, Wai-Ki Ching and Yang Cong, On Distribution and Enumeration of Attractors in Probabilistic Boolean Networks, IET Systems Biology, Vol. 3, pp. 465-474, (Preliminary version has appeared in OSB 2008) 2009.
  36. Tatsuya Akutsu and Takeyuki Tamura, On Finding a Fixed Point in a Boolean Network with Maximum Indegree 2, IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences, Vol.E92-A, No.8, pp.1771-1778, 2009.
  37. Takeyuki Tamura and Tatsuya Akustu, Algorithms for singleton attractor detection in planar and nonplanar AND/OR Boolean networks, Mathematics in Computer Science, Vol. 2, No. 3, pp. 401--420, (Preliminary version has appeared in AB 2008) 2009.
  38. Takeyuki Tamura and Tatsuya Akutsu, Detecting a Singleton Attractor in a Boolean Network Utilizing SAT Algorithms, IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences, Vol.E92-A No.2 pp.493--501, (Preliminary version has appeared in FCT 2007) 2009.
  39. Morihiro Hayashida, Takeyuki Tamura*, Tatsuya Akutsu, Shu-Qin Zhang and Wai-Ki Ching, (* joint first author), Algorithms and Complexity Analyses for Control of Singleton Attractors in Boolean Networks, EURASIP Journal on Bioinformatics and Systems Biology, 521407 (16pages), 2008.
  40. Takeyuki Tamura and Hiro Ito, Inferring Pedigree Graphs from Genetic Distances. IEICE Transactions on Information and Systems, Vol. E91-D, No. 2, pp. 162--169, 2008.
  41. Takeyuki Tamura* and Tatsuya Akutsu, (* corresponding author), Subcellular Location Prediction of Proteins Using Support Vector Machines with Alignment of Block Sequences Utilizing Amino Acid Composition. BMC Bioinformatics, Vol. 8, No. 466, 2007.
  42. Takeyuki Tamura and Tatsuya Akutsu, Approximation Algorithms for Optimal RNA Secondary Structures Common to Multiple Sequences, IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences, Vol. E-90A, No.5, pp.917--923, 2007.
  43. Hiro Ito*, Kazuo Iwama*, and Takeyuki Tamura* (Authors are in alphabetical order), Efficient Methods for Determining DNA Probe Orders, IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences, Vol. E89-A, No. 5, pp.1292--1298, 2006.


Update: Jul 18,2017