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Note: Links lead to the DBLP on the Web. Tatsuya Akutsu Tatsuya Akutsu, Morihiro Hayashida , Wai-Ki Ching , Michael K. Ng : On the Complexity of Finding Control Strategies for Boolean Networks. APBC 2006 : 99-108 Hiroto Saigo , Jean-Philippe Vert , Tatsuya Akutsu: Optimizing amino acid substitution matrices with a local alignment kernel. BMC Bioinformatics 7 : 246 (2006) Bahadur K. C. Dukka , Etsuji Tomita , Jun'ichi Suzuki , Katsuhisa Horimoto , Tatsuya Akutsu: Protein Threading with Profiles and Distance Constraints Using Clique Based Algorithms. J. Bioinformatics and Computational Biology 4 (1): 19-42 (2006) Dukka Bahadur , Etsuji Tomita , Jun'ichi Suzuki , Katsuhisa Horimoto , Tatsuya Akutsu: Clique-based algorithms for protein threading with profiles and constraints. APBC 2005 : 51-64 Tatsuya Akutsu, Daiji Fukagawa : Inferring a Graph from Path Frequency. CPM 2005 : 371-382 Masumi Itoh , Susumu Goto , Tatsuya Akutsu, Minoru Kanehisa : Fast and accurate database homology search using upper bounds of local alignment scores. Bioinformatics 21 (7): 912-921 (2005) Kiyoko F. Aoki , Hiroshi Mamitsuka , Tatsuya Akutsu, Minoru Kanehisa : A score matrix to reveal the hidden links in glycans. Bioinformatics 21 (8): 1457-1463 (2005) Nobuhisa Ueda , Kiyoko F. Aoki-Kinoshita , Atsuko Yamaguchi , Tatsuya Akutsu, Hiroshi Mamitsuka : A Probabilistic Model for Mining Labeled Ordered Trees: Capturing Patterns in Carbohydrate Sugar Chains. IEEE Trans. Knowl. Data Eng. 17 (8): 1051-1064 (2005) Daiji Fukagawa , Tatsuya Akutsu: Performance analysis of a greedy algorithm for inferring Boolean functions. Inf. Process. Lett. 93 (1): 7-12 (2005) Wai-Ki Ching , Michael M. Ng , Eric S. Fung , Tatsuya Akutsu: On construction of stochastic genetic networks based on gene expression sequences. Int. J. Neural Syst. 15 (4): 297-310 (2005) K. C. Dukka Bahadur , Etsuji Tomita , Jun'ichi Suzuki , Tatsuya Akutsu: Protein Side-chain Packing Problem: a Maximum Edge-weight Clique Algorithmic Approach. J. Bioinformatics and Computational Biology 3 (1): 103-126 (2005) Dukka Bahadur , Tatsuya Akutsu, Etsuji Tomita , Tomokazu Seki : Protein Side-chain Packing Problem: A Maximum Edge-weight Clique Algorithmic Approach. APBC 2004 : 191-200 Tatsuya Akutsu, Morihiro Hayashida , Etsuji Tomita , Jun'ichi Suzuki , Katsuhisa Horimoto : Protein Threading with Profiles and Constraints. BIBE 2004 : 537-544 Tatsuya Akutsu: Algorithms for Point Set Matching with k-Differences. COCOON 2004 : 249-258 Pierre Mahé , Nobuhisa Ueda , Tatsuya Akutsu, Jean-Luc Perret , Jean-Philippe Vert : Extensions of marginalized graph kernels. ICML 2004 Daiji Fukagawa , Tatsuya Akutsu: Fast Algorithms for Comparison of Similar Unordered Trees. ISAAC 2004 : 452-463 Kiyoko F. Aoki , Nobuhisa Ueda , Atsuko Yamaguchi , Minoru Kanehisa , Tatsuya Akutsu, Hiroshi Mamitsuka : Application of a new probabilistic model for recognizing complex patterns in glycans. ISMB/ECCB (Supplement of Bioinformatics) 2004 : 6-14 Jose C. Nacher , Nobuhisa Ueda , Takuji Yamada , Minoru Kanehisa , Tatsuya Akutsu: Clustering under the line graph transformation: application to reaction network. BMC Bioinformatics 5 : 207 (2004) Hiroto Saigo , Jean-Philippe Vert , Nobuhisa Ueda , Tatsuya Akutsu: Protein homology detection using string alignment kernels. Bioinformatics 20 (11): 1682-1689 (2004) Yuichiro Hourai , Tatsuya Akutsu, Yutaka Akiyama : Optimizing substitution matrices by separating score distributions. Bioinformatics 20 (6): 863-873 (2004) Tatsuya Akutsu: Efficient Extraction of Mapping Rules of Atoms from Enzymatic Reaction Data. Journal of Computational Biology 11 (2/3): 449-462 (2004) Kiyoko F. 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 (Web-Server-Issue): 267-272 (2004) Kiyoko F. Aoki , Nobuhisa Ueda , Atsuko Yamaguchi , Tatsuya Akutsu, Minoru Kanehisa , Hiroshi Mamitsuka : Managing and Analyzing Carbohydrate Data. SIGMOD Record 33 (2): 33-38 (2004) Tatsuya Akutsu: Computational and Statistical Methods in Bioinformatics. Active Mining 2003 : 11-33 Daiji Fukagawa , Tatsuya Akutsu: Performance Analysis of a Greedy Algorithm for Inferring Boolean Functions. Discovery Science 2003 : 114-127 Daisuke Shinozaki , Tatsuya Akutsu, Osamu Maruyama : Finding optimal degenerate patterns in DNA sequences. ECCB 2003 : 206-214 Morihiro Hayashida , Nobuhisa Ueda , Tatsuya Akutsu: Inferring strengths of protein-protein interactions from experimental data using linear programming. ECCB 2003 : 58-65 Tatsuya Akutsu: Efficient extraction of mapping rules of atoms from enzymatic reaction data. RECOMB 2003 : 1-8 Tatsuya Akutsu, Kyotetsu Kanaya , Akira Ohyama , Asao Fujiyama : Point matching under non-uniform distortions. Discrete Applied Mathematics 127 (1): 5-21 (2003) Tatsuya Akutsu, Satoru Kuhara , Osamu Maruyama , Satoru Miyano : Identification of genetic networks by strategic gene disruptions and gene overexpressions under a boolean model. Theor. Comput. Sci. 1 (298): 235-251 (2003) Tatsuya Akutsu, Satoru Miyano , Satoru Kuhara : A simple greedy algorithm for finding functional relations: efficient implementation and average case analysis. Theor. Comput. Sci. 292 (2): 481-495 (2003) Tatsuya Akutsu, Sascha Ott : Inferring a Union of Halfspaces from Examples. COCOON 2002 : 117-126 Tatsuya Akutsu, Hideo Bannai , Satoru Miyano , Sascha Ott : On the Complexity of Deriving Position Specific Score Matrices from Examples. CPM 2002 : 168-177 Tatsuya Akutsu, Satoru Miyano , Satoru Kuhara : A Simple Greedy Algorithm for Finding Functional Relations: Efficient Implementation and Average Case Anaylsis. Discovery Science 2000 : 86-98 Tatsuya Akutsu, Hiroki Arimura , Shinichi Shimozono : On approximation algorithms for local multiple alignment. RECOMB 2000 : 1-7 Tatsuya Akutsu, Satoru Miyano , Satoru Kuhara : Algorithms for identifying Boolean networks and related biological networks based on matrix multiplication and fingerprint function. RECOMB 2000 : 8-14 Tatsuya Akutsu, Satoru Miyano , Satoru Kuhara : Inferring qualitative relations in genetic networks and metabolic pathways. Bioinformatics 16 (8): 727-734 (2000) Tatsuya Akutsu: Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots. Discrete Applied Mathematics 104 (1-3): 45-62 (2000) Tatsuya Akutsu, Satoru Miyano , Satoru Kuhara : Algorithms for Identifying Boolean Networks and Related Biological Networks Based on Matrix Multiplication and Fingerprint Function. Journal of Computational Biology 7 (3-4): 331-343 (2000) Tatsuya Akutsu, Magnús M. Halldórsson : On the approximation of largest common subtrees and largest common point sets. Theor. Comput. Sci. 233 (1-2): 33-50 (2000) Tatsuya Akutsu, Kyotetsu Kanaya , Akira Ohyama , Asao Fujiyama : Matching of Spots in 2D Electrophoresis Images. Point Matching Under Non-uniform Distortions. CPM 1999 : 212-222 Tatsuya Akutsu, Satoru Miyano , Satoru Kuhara : Identification of Genetic Networks from a Small Number of Gene Expression Patterns Under the Boolean Network Model. Pacific Symposium on Biocomputing 1999 : 17-28 Tatsuya Akutsu: Approximation and Exact Algorithms for RNA Secondary Structure Prediction and Recognition of Stochastic Context-free Languages. J. Comb. Optim. 3 (2-3): 321-336 (1999) Tatsuya Akutsu, Satoru Miyano : On the Approximation of Protein Threading. Theor. Comput. Sci. 210 (2): 261-275 (1999) Tatsuya Akutsu, Mutsunori Yagiura : On the Complexity of Deriving Score Functions from Examples for Problems in Molecular Biology. ICALP 1998 : 832-843 Tatsuya Akutsu: Approximation and Exact Algorithms for RNA Secondary Structure Prediction and Recognition of Stochastic Context-Free Languages. ISAAC 1998 : 337-346 Tatsuya Akutsu, Satoru Kuhara , Osamu Maruyama , Satoru Miyano : Identification of Gene Regulatory Networks by Strategic Gene Disruptions and Gene Overexpressions. SODA 1998 : 695-702 Tatsuya Akutsu: On determining the congruence of point sets in d dimensions. Comput. Geom. 9 (4): 247-256 (1998) Tatsuya Akutsu, Hisao Tamaki , Takeshi Tokuyama : Distribution of Distances and Triangles in a Point Set and Algorithms for Computing the Largest Common Point Sets. Discrete & Computational Geometry 20 (3): 307-331 (1998) Tatsuya Akutsu, Satoru Miyano : On the approximation of protein threading. RECOMB 1997 : 3-8 Tatsuya Akutsu, Hisao Tamaki , Takeshi Tokuyama : Distribution of Distances and Triangles in a Point Set and Algorithms for Computing the Largest Common Point Sets. Symposium on Computational Geometry 1997 : 314-323 Tatsuya Akutsu, Kentaro Onizuka , Masato Ishikawa : Rapid protein fragment search using hash functions based on the Fourier transform. Computer Applications in the Biosciences 13 (4): 357-364 (1997) Tatsuya Akutsu, Feng Bao : Approximating Minimum Keys and Optimal Substructure Screens. COCOON 1996 : 290-299 Tatsuya Akutsu, Kentaro Onizuka , Masato Ishikawa : New hashing techniques and their application to a protein structure database system. HICSS (5) 1995 : 197-206 Tatsuya Akutsu: Approximate String Matching with don't Care Characters. Inf. Process. Lett. 55 (5): 235-239 (1995) Tatsuya Akutsu: Approximate String Matching with Don't Care Characters. CPM 1994 : 240-249 Tatsuya Akutsu: Efficient and Robust Three-Dimensional Pattern Matching Algorithms Using Hashing and Dynamic Programming Techniques. HICSS (5) 1994 : 225-234 Tatsuya Akutsu: On Determining the Congruity of Point Sets in Higher Dimensions. ISAAC 1994 : 38-46 Tatsuya Akutsu, Magnús M. Halldórsson : On the Approximation of Largest Common Subtrees and Largest Common Point Sets. ISAAC 1994 : 405-413 Tatsuya Akutsu, Atsuhiro Takasu : On PAC Learnability of Functional Depencies. New Generation Comput. 12 (4): 359-374 (1994) Tatsuya Akutsu: A Linear Time Pattern Matching Algorithm Between a String and a Tree. CPM 1993 : 1-10 Einoshin Suzuki , Tatsuya Akutsu, Setsuo Ohsuga : Knowledge-based system for computer-aided drug design. Knowl.-Based Syst. 6 (2): 114-126 (1993) Tatsuya Akutsu, Atsuhiro Takasu : On PAC Learnability of Functional Dependencies. ALT 1992 : 229-239 Tatsuya Akutsu: Algorithms for Determining the Geometrical Congruity in Two and Three Dimensions. ISAAC 1992 : 279-288 Tatsuya Akutsu: A new method of computer representation of stereochemistry. Transforming a stereochemical structure into a graph. Journal of Chemical Information and Computer Sciences 31 (3): 414-417 (1991) Tatsuya Akutsu, Einoshin Suzuki , Setsuo Ohsuga : Logic-based approach to expert systems in chemistry. Knowl.-Based Syst. 4 (2): 103-116 (1991) Tatsuya Akutsu, Setsuo Ohsuga : CHEMILOG - A Logic Programming Language/System for Chemical Information Processing. 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