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上田, 佐藤
階層隠れマルコフモデルに対する簡単な訓練アルゴリズム
電子情報通信学会論文誌, vol. 85-D-I, no. 6
98 99 00 01 02 03F 03S 04 05 06 07
Tatsuya Akutsu, Satoru Miyano, Satoru Kuhara
A simple greedy algorithm for finding functional relations:efficient implementation and average case analysis
Theoretical Computer Science, 292, 481-495
98 99 00 01 02 03F 03S 04 05 06 07
Tatsuya Akutsu, Kyotetsu Kanaya, Akira Ohyama, Asao Fujiyama
Point matching under non-uniform distortions
Discrete Applied Mathematics, 127, 5-21
Tatsuya Akutsu, Satoru Kuhara, Osamu Maruyama, Satoru Miyano
Identification of genetic networks by strategic gene disruptionsand gene overexpressions under a boolean model
Theoretical Computer Science, 298, 235-251
Daisuke Shinozaki, Tatsuya Akutsu, Osamu Maruyama
Finding optimal degenerated patterns in DNA sequences
Bioinformatics, 19, ii206-ii214
Morihiro Hayashida, Nobuhisa Ueda, Tatauya Akutsu
Inferring strengths of protein-protein interactions fromexperimental data using linear programming
Bioinformatics, 19, ii58-ii65
98 99 00 01 02 03 04F 04S 05 06 07
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98 99 00 01 02 03 04F 04S 05 06 07
Tatsuya Akutsu
Efficient extraction of mapping rules of atoms from enzymatic reaction data
Journal of Computational Biology, 11, 449-462
Hiroto Saigo, Jean-Philippe Vert, Nobuhisa Ueda, Tatsuya Akutsu
Protein homology detection using string alignment kernels
Bioinformatics, 20, 1682-1689
Kiyoko Aoki, Atsuko Yamaguchi, Nobuhisa Ueda, Tatsuya Akutsu, Hiroshi Mamitsuka, Susumu Goto, Minoru Kanehisa
KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains
Nucleic Acids Research, 32, w267-w272
Kiyoko Aoki, Nobuhisa Ueda, Atsuko Yamaguchi, Minoru Kanehisa, Tatsuya Akutsu, Hiroshi Mamitsuka
of a new probabilistic model for recognizing complex patterns in glycans
Bioinformatics, 20, i6-i14
Tomoshiro Ochiai, Jose Carlos Nacher, Tatsuya Akutsu
A constructive approach to gene expression dynamics
Physics Letters A, 330, 313-321
Jose Carlos Nacher, Nobuhisa Ueda, Takuji Yamada, Minoru Kanehisa, Tatsuya Akutsu
Clustering under the line graph transformation: application to reaction network
BMC Bioinformatics, 5, 207
98 99 00 01 02 03 04 05F 05S 06 07
Daiji Fukagawa, Tatsuya Akutsu
Performance analysis of a greedy algorithm for inferring Boolean functions
Information Processing Letters, 93, 7-12
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, 83-90
98 99 00 01 02 03 04 05F 05S 06 07
Jose Carlos Nacher, Takuji Yamada, Susumo Goto, Minoru Kanehisa, Tatsuya Akutsu
Two complementary representations of a scale-free network
Physica A,, 349, 349-363
Dukka Bahadur K.C., Etsuji Tomita, Jun'ichi Suzuki, Tatsuya Akutsu
Protein side-chain packing problem: a maximum edge-weight clique algorithmic approach
Journal of Bioinformatics and Computational Biology, 3, 103-126
Masumi Itoh, Susumu Goto, Tatsuya Akutsu, Minoru Kanehisa
Fast and accurate database homology search using upper bounds of local alignment scores
Bioinformatics, 21, 912-921
Jose Carlos Nacher, Nobuhisa Ueda, Minoru Kanehisa, Tatsuya Akutsu
Flexible construction of hierarchical scale-free networks with general exponent
Physical Review E, 71, 036132
Kiyoko Aoki, Hiroshi Mamitsuka, Tatsuya Akutsu, Minoru Kenehisa
A score matrix to reveal the hidden links in glycans
Bioinformatics, 21, 1457-1463
Nobuhisa Ueda, Kiyoko Aoki, Atsuko Yamaguchi, Tatsuya Akutsu, Hiroshi Mamitsuka
A probabilistic model for mining labeled ordered trees: capturing patterns in carbohydrate sugar chains
IEEE Transactions on Knowledge and Data Engineering, 17, 1051-1064
Tomoshiro Ochiai, Jose Carlos Nacher, Tatsuya Akutsu
A stochastic approach to multi-gene expression dynamics
Physics Letters A, 339, 1-9
Pierre Mahe, Nobuhisa Ueda, Tatsuya Akutsu, Jean-Luc Perret, Jean-Philippe Vert
Graph kernels for molecular structure-activity relationship analysis with support vector machines
Journal of Chemical Information and Modeling, 45, 939-951
Wai-Ki Ching, Michael K. Ng, Eric S. Fung, Tatsuya Akutsu
On construction of stochastic genetic networks based on gene expression sequences
International Journal of Neural Systems, 15, 297-310
Jose Carlos Nacher, Tomoshiro Ochiai, Tatsuya Akutsu
On the relation between fluctuations and scaling-law in gene expression time series from yeast to human
Modern Physics Letters B, 19, 1169-1177
Setsuro Matsuda, Jean-Philippe Vert, Hiroto Saigo, Nobuhisa Ueda, Hiroyuki Toh, Tatsuya Akutsu
A novel representation of protein sequences for prediction of subcellular location using support vector machines
Protein Science, 14, 2804-2813
98 99 00 01 02 03 04 05 06F 06S 07
Jose Carlos Nacher, Tomoshiro Ochiai, Takuji Yamada, Minoru Kanehisa , Tatsuya Akutsu
The role of log-normal dynamics in the evolution of biochemical pathways
BioSystems, 83, 26-37
Tatsuya Akutsu, Morihiro Hayashida, Dukka Bahadur K.C., Etsuji Tomita, Jun'ichi Suzuki, Katsuhisa Horimoto
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
98 99 00 01 02 03 04 05 06F 06S 07
Dukka Bahadur K.C., Etsuji Tomita, Jun'ichi Suzuki, Katsuhisa Horimoto, Tatsuya Akutsu
Protein threading with profiles and distance constraints using clique based algorithms
Journal of Bioinformatics and Computational Biology, 4, 19-42
Hiroto Saigo, Jean-Philippe Vert, Tatsuya Akutsu
Optimizing amino acid substitution matrices with a local alignment kernel
BMC Bioinformatics, 7, 246
Jose Carlos Nacher, Morihiro Hayashida, Tatsuya Akutsu
Protein domain networks: Scale-free mixing of positive and negative exponents
Physica A, 367, 538-552
Daiji Fukagawa, Tatsuya Akutsu
Fast algorithms for comparison of similar unordered trees
International Journal of Foundations of Computer Science, 17, 703-729
Tatsuya Akutsu
Algorithms for point set matching with k-differences
International Journal of Foundations of Computer Science, 17, 903-917
Jose Carlos Nacher, Jean-Marc Schwartz, Minoru Kanehisa, Tatsuya Akutsu
Identification of metabolic units induced by environmental signals
Bioinformatics, 22, e375-e383
Michael K. Ng, Shuqin Zhang, Wai-Ki Ching, Tatsuya Akutsu
A control model for Markovian genetic regulatory networks
Transactions on Computational Systems Biology, V, 36-48
Tatsuya Akutsu
A relation between edit distance for ordered trees and edit distance for Euler strings
Information Processing Letters, 100, 105-109
Jose Carlos Nacher, Tatsuya Akutsu
Sensitivity of the power-law exponent in gene expression distribution to mRNA decay rate
Physics Letters A, 360, 174-178
98 99 00 01 02 03 04 05 06 07F 07S
Shuqin Zhang, Wai-Ki Ching, Michael K. Ng, Tatsuya Akutsu
Simulation study in Probabilistic Boolean Network models for genetic regulatory networks
International Journal of Data Mining and Bioinformatics, 1, 217-240
Tatsuya Akutsu, Morihiro Hayashida, Wai-Ki Ching, Michael K. Ng
Control of Boolean networks: Hardness results and algorithms for tree structured networks
Journal of Theoretical Biology, 244, 670-679
98 99 00 01 02 03 04 05 06 07F 07S
Tatsuya Akutsu, Hideo Bannai, Satoru Miyano, Sascha Ott
On the complexity of deriving position specific score matrices from positive and negative sequences
Discrete Applied Mathematics, 155, 676-685