Takeyuki Tamura

Summary

Affiliation: Kyoto University
Country: Japan

Publications

  1. ncbi request reprint Analysis and prediction of nutritional requirements using structural properties of metabolic networks and support vector machines
    Takeyuki Tamura
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    Genome Inform 22:176-90. 2010
  2. ncbi request reprint Integer programming-based method for completing signaling pathways and its application to analysis of colorectal cancer
    Takeyuki Tamura
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    Genome Inform 24:193-203. 2010
  3. pmc A clique-based method for the edit distance between unordered trees and its application to analysis of glycan structures
    Daiji Fukagawa
    Faculty of Culture and Information Science, Doshisha University, Kyoto 610 0394, Japan
    BMC Bioinformatics 12:S13. 2011
  4. pmc Subcellular location prediction of proteins using support vector machines with alignment of block sequences utilizing amino acid composition
    Takeyuki Tamura
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611 0011, Japan
    BMC Bioinformatics 8:466. 2007
  5. ncbi request reprint A dynamic programming algorithm to predict synthesis processes of tree-structured compounds with graph grammar
    Yang Zhao
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611 0011, Japan
    Genome Inform 24:218-29. 2010
  6. pmc Network completion using dynamic programming and least-squares fitting
    Natsu Nakajima
    Bioinformatics Center, Institute for Chemical Research, Kyoto University Gokasho, Uji, Kyoto 611 0011, Japan
    ScientificWorldJournal 2012:957620. 2012
  7. ncbi request reprint Finding a periodic attractor of a Boolean network
    Tatsuya Akutsu
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan
    IEEE/ACM Trans Comput Biol Bioinform 9:1410-21. 2012
  8. doi request reprint Determining a singleton attractor of a boolean network with nested canalyzing functions
    Tatsuya Akutsu
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyot, Japan
    J Comput Biol 18:1275-90. 2011
  9. pmc Flux balance impact degree: a new definition of impact degree to properly treat reversible reactions in metabolic networks
    Yang Zhao
    Bioinformatics Center, Kyoto University, Kyoto, Japan, Centre for Computational Biology, Mines ParisTech, 35 rue Saint Honore, Fontainebleau, France
    Bioinformatics 29:2178-85. 2013
  10. ncbi request reprint Compound analysis via graph kernels incorporating chirality
    J B Brown
    Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan
    J Bioinform Comput Biol 8:63-81. 2010

Collaborators

Detail Information

Publications12

  1. ncbi request reprint Analysis and prediction of nutritional requirements using structural properties of metabolic networks and support vector machines
    Takeyuki Tamura
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    Genome Inform 22:176-90. 2010
    ..Furthermore, we study which properties are influential to the nutritional requirements...
  2. ncbi request reprint Integer programming-based method for completing signaling pathways and its application to analysis of colorectal cancer
    Takeyuki Tamura
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    Genome Inform 24:193-203. 2010
    ..In this paper, we develop an integer programming-based method for inferring such changes by using gene expression data. We test our method on its ability to reconstruct the pathway of colorectal cancer in the KEGG database...
  3. pmc A clique-based method for the edit distance between unordered trees and its application to analysis of glycan structures
    Daiji Fukagawa
    Faculty of Culture and Information Science, Doshisha University, Kyoto 610 0394, Japan
    BMC Bioinformatics 12:S13. 2011
    ..However, it is known that computation of the edit distance for rooted unordered trees is NP-hard. Furthermore, there is almost no available software tool that can compute the exact edit distance for unordered trees...
  4. pmc Subcellular location prediction of proteins using support vector machines with alignment of block sequences utilizing amino acid composition
    Takeyuki Tamura
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611 0011, Japan
    BMC Bioinformatics 8:466. 2007
    ..Since existing predictors are based on various heuristics, it is important to develop a simple method with high prediction accuracies...
  5. ncbi request reprint A dynamic programming algorithm to predict synthesis processes of tree-structured compounds with graph grammar
    Yang Zhao
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611 0011, Japan
    Genome Inform 24:218-29. 2010
    ..In order to represent rules corresponding to chemical reactions, we employ a subclass of NLC (Node Label Controlled) grammars. We also give some computational results on this algorithm...
  6. pmc Network completion using dynamic programming and least-squares fitting
    Natsu Nakajima
    Bioinformatics Center, Institute for Chemical Research, Kyoto University Gokasho, Uji, Kyoto 611 0011, Japan
    ScientificWorldJournal 2012:957620. 2012
    ..We also perform computational experiments using both artificially generated and real gene expression time series data...
  7. ncbi request reprint Finding a periodic attractor of a Boolean network
    Tatsuya Akutsu
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan
    IEEE/ACM Trans Comput Biol Bioinform 9:1410-21. 2012
    ..For finding an attractor of a fixed period of a BN consisting of n nested canalyzing functions and having constant treewidth w, we present an O(n(2p(w+1))poly(n)) time algorithm...
  8. doi request reprint Determining a singleton attractor of a boolean network with nested canalyzing functions
    Tatsuya Akutsu
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyot, Japan
    J Comput Biol 18:1275-90. 2011
    ..Finally, we present an o(2(n)) time algorithm for bounded degree BNs consisting of canalyzing functions...
  9. pmc Flux balance impact degree: a new definition of impact degree to properly treat reversible reactions in metabolic networks
    Yang Zhao
    Bioinformatics Center, Kyoto University, Kyoto, Japan, Centre for Computational Biology, Mines ParisTech, 35 rue Saint Honore, Fontainebleau, France
    Bioinformatics 29:2178-85. 2013
    ..While several approaches have been proposed for that purpose, they are computationally too intensive to analyze large networks, and do not properly handle reversible reactions...
  10. ncbi request reprint Compound analysis via graph kernels incorporating chirality
    J B Brown
    Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan
    J Bioinform Comput Biol 8:63-81. 2010
    ....
  11. pmc A clique-based method using dynamic programming for computing edit distance between unordered trees
    Tomoya Mori
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, Japan
    J Comput Biol 19:1089-104. 2012
    ..For large tree-structures, the improved method is much faster than the previous method. In particular, for hard instances, the improved method achieved more than 100 times speed-up...
  12. pmc Integer programming-based method for designing synthetic metabolic networks by Minimum Reaction Insertion in a Boolean model
    Wei Lu
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, Japan
    PLoS ONE 9:e92637. 2014
    ..A theoretical analysis of MRI is also conducted, and the NP-completeness of MRI is proved in the Boolean model. Our developed software is available at "http://sunflower.kuicr.kyoto-u.ac.jp/~rogi/minRect/minRect.html." ..