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


林田 守広 (はやしだ もりひろ )

バイオインフォマティクスセンター 数理生物情報
(京都大学大学院 協力講座)
助教
博士(情報学)
URL:http://sunflower.kuicr.kyoto-u.ac.jp/morihiro/
E-mail: morihiro@kuicr.kyoto-u.ac.jp
Tel: 0774-38-3020
Fax: 0774-38-3022

研究・教育歴
    2005.3 京都大学大学院情報学研究科博士課程修了
    2005.3 京都大学博士(情報学)
    2005.4 京都大学化学研究所 特任助手
    2006.1 京都大学化学研究所 助手
    2007.4 京都大学化学研究所 助教
専門分野
    バイオインフォマティクス
主な研究テーマ
主な論文・著書
  1. Jindalertudomdee J, Hayashida M, Akutsu T, Enumeration Method for Structural Isomers Containing User-Defined Structures Based on Breadth-First Search Approach J Comput Biol 23(8), 625-640 (2016)  [pubmed]
  2. Koyano H, Hayashida M, Akutsu T, Maximum margin classifier working in a set of strings Proc Math Phys Eng Sci 472(2187), 20150551 (2016)  [pubmed]
  3. Jindalertudomdee J, Hayashida M, Zhao Y, Akutsu T, Enumeration method for tree-like chemical compounds with benzene rings and naphthalene rings by breadth-first search order BMC Bioinformatics 17, 113 (2016)  [pubmed]
  4. Li C, Ching Han Chang C, Nagel J, Porebski BT, Hayashida M, Akutsu T, Song J, Buckle AM, Critical evaluation of in silico methods for prediction of coiled-coil domains in proteins Brief Bioinform 17(2), 270-282 (2016)  [pubmed]
  5. Hayashida M, Jindalertudomdee J, Zhao Y, Akutsu T, Parallelization of enumerating tree-like chemical compounds by breadth-first search order BMC Med Genomics 8(Suppl 2), S15 (2015)  [pubmed]
  6. Zhao Y, Hayashida M, Cao Y, Hwang J, Akutsu T, Grammar-based compression approach to extraction of common rules among multiple trees of glycans and RNAs BMC Bioinformatics 16, 128 (2015)  [pubmed]
  7. Kamada M, Sakuma Y, Hayashida M, Akutsu T, Prediction of protein-protein interaction strength using domain features with supervised regression. ScientificWorldJournal 2014, 240673 (2014)  [pubmed]
  8. Hayashida M, Ruan P, Akutsu T., Proteome compression via protein domain compositions. Methods 67, 380-5 (2014)  [pubmed]
  9. Ruan P, Hayashida M, Maruyama O, Akutsu T., Prediction of heterotrimeric protein complexes by two-phase learning using neighboring kernels. BMC Bioinformatics 15 Suppl 2, S6 (2014)  [pubmed]
  10. Zhao Y, Hayashida M, Jindalertudomdee J, Nagamochi H, Akutsu T., Breadth-first search approach to enumeration of tree-like chemical compounds. J Bioinform Comput Biol 11, 1343007 (2013)  [pubmed]
  11. Hayashida M, Kamada M, Song J, Akutsu T., Prediction of protein-RNA residue-base contacts using two-dimensional conditional random field with the lasso. BMC Syst Biol 7 Suppl 2, S15 (2013)  [pubmed]
  12. Ruan P, Hayashida M, Maruyama O, Akutsu T., Prediction of heterodimeric protein complexes from weighted protein-protein interaction networks using novel features and kernel functions. PLoS One 8, e65265 (2013)  [pubmed]
  13. Lai Y, Hayashida M, Akutsu T., Survival analysis by penalized regression and matrix factorization. ScientificWorldJournal 2013, 632030 (2013)  [pubmed]
  14. Akutsu, T.; Zhao, Y.; Hayashida, M.; Tamura, T., Integer programming-based approach to attractor detection and control of Boolean networks IEICE TRANS. INF. & SYST. E95-D, 2960-2970 (2012)
  15. Zhao Y, Hayashida M, Nacher JC, Nagamochi H, Akutsu T., Protein complex prediction via improved verification methods using constrained domain-domain matching. Int J Bioinform Res Appl 8, 210-27 (2012)  [pubmed]
  16. Hayashida, M.; Ruan, P.; Akutsu, T., A quadsection algorithm for grammar-based image compression Integrated Computer-Aided Engineering 19, 23-38 (2012)
  17. Hayashida, M.; Akutsu, T, Measuring the similarity of protein structures using image compression algorithms IEICE Transactions on Information and Systems E94-D, 2468-2478 (2011)
  18. Hayashida M, Kamada M, Song J, Akutsu T., Conditional random field approach to prediction of protein-protein interactions using domain information. BMC Syst Biol 5 Suppl 1, S8 (2011)  [pubmed]
  19. Zhao Y, Hayashida M, Akutsu T., Integer programming-based method for grammar-based tree compression and its application to pattern extraction of glycan tree structures. BMC Bioinformatics 11 Suppl 11, S4 (2010)  [pubmed]
  20. Hayashida M, Akutsu T., Comparing biological networks via graph compression. BMC Syst Biol 4 Suppl 2, S13 (2010)  [pubmed]
  21. Nacher JC, Hayashida M, Akutsu T., The role of internal duplication in the evolution of multi-domain proteins. Biosystems 101, 127-35 (2010)  [pubmed]
  22. Hayashida M, Tamura T, Akutsu T, Ching WK, Cong Y., Distribution and enumeration of attractors in probabilistic Boolean networks. IET Syst Biol 3, 465-74 (2009)  [pubmed]
  23. Nacher JC, Ochiai T, Hayashida M, Akutsu T, A mathematical model for generating bipartite graphs and its application to protein networks Journal of Physics A: Mathematical and Theoretical 42, 485005 (2009)
  24. Nacher JC, Hayashida M, Akutsu T., Emergence of scale-free distribution in protein-protein interaction networks based on random selection of interacting domain pairs. Biosystems 95, 155-9 (2009)  [pubmed]
  25. Hayashida M, Sun F, Aburatani S, Horimoto K, Akutsu T., Integer programming-based approach to allocation of reporter genes for cell array analysis. Int J Bioinform Res Appl 4, 385-99 (2008)  [pubmed]
  26. Hayashida M, Tamura T, Akutsu T, Zhang SQ, Ching WK., Algorithms and complexity analyses for control of singleton attractors in Boolean networks. EURASIP J Bioinform Syst Biol 521407 (2008)  [pubmed]
  27. Morihiro Hayashida, Tatsuya Akutsu and Hiroshi Nagamochi , A clustering method for analysis of sequence similarity networks of proteins using maximal components of graphs IPSJ Transactions on Bioinformatics 49, 15-24 (2008)
  28. Jose C. Nacher, Morihiro Hayashida, Tatsuya Akutsu, Topological aspects of protein networks Studies in Computational Intelligence 56, 147-158 (2007)
  29. Zhang SQ, Hayashida M, Akutsu T, Ching WK, Ng MK., Algorithms for finding small attractors in Boolean networks. EURASIP J Bioinform Syst Biol 20180 (2007)  [pubmed]
  30. Akutsu T, Hayashida M, Ching WK, Ng MK., Control of Boolean networks: hardness results and algorithms for tree structured networks. J Theor Biol 244, 670-9 (2007)  [pubmed]
  31. Hayashida M, Ueda N, Akutsu T., Inferring strengths of protein-protein interactions from experimental data using linear programming. Bioinformatics 19 Suppl 2, II58-II65 (2003)  [pubmed]
  32. Hayashida M, Ueda N, Akutsu T., A simple method for inferring strengths of protein-protein interactions. Genome Inform Ser Workshop Genome Inform 15, 56-68 (2004)  [pubmed]
  33. 林田 守広, 上田 展久, 阿久津 達也, タンパク質間相互作用強度予測の高速化と困難性 電子情報通信学会論文誌 J88-A (1), 83-90 (2005)
  34. Nacher J.C., Hayashida M., Akutsu T., Protein domain networks: Scale-free mixing of positive and negative exponents Physica A 367, 538-552 (2006)
  35. Akutsu T, Hayashida M, Ching WK, Ng MK., Control of Boolean networks: hardness results and algorithms for tree structured networks. J Theor Biol 244, 670-9 (2007)  [pubmed]
  36. Akutsu T., Hayashida M., Bahadur D.K.C., Tomita E., Suzuki J., Horimoto K. , Dynamic programming and clique based approaches for protein threading with profiles and constraints IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences E89-A, 1215-1222 (2006)
  37. Sato I., Hayashida M., Kai F., Sato Y., Ikeuchi K. , Fast image synthesis of virtual objects in a real scene with natural shadings Systems and Computers in Japan 36, 102-111 (2005)
  38. 佐藤 いまり, 林田 守広, 甲斐 郁代, 佐藤 洋一, 池内 克史 , 実光源環境下での画像生成:基礎画像の線形和による高速レンダリング手法 電子情報通信学会論文誌 J84-DII (8), 1864-1872 (2001)


Update: Nov 08,2016