| 2009 |
|---|
| 97 | EE | Yuki Kato,
Tatsuya Akutsu,
Hiroyuki Seki:
A grammatical approach to RNA-RNA interaction prediction.
Pattern Recognition 42(4): 531-538 (2009) |
| 2008 |
|---|
| 96 | | Alvis Brazma,
Satoru Miyano,
Tatsuya Akutsu:
Proceedings of the 6th Asia-Pacific Bioinformatics Conference, APBC 2008, 14-17 January 2008, Kyoto, Japan
Imperial College Press 2008 |
| 95 | EE | Tatsuya Akutsu,
Morihiro Hayashida,
Takeyuki Tamura:
Algorithms for Inference, Analysis and Control of Boolean Networks.
AB 2008: 1-15 |
| 94 | EE | Takeyuki Tamura,
Tatsuya Akutsu:
An Improved Algorithm for Detecting a Singleton Attractor in a Boolean Network Consisting of AND/OR Nodes.
AB 2008: 216-229 |
| 93 | EE | Morihiro Hayashida,
Tatsuya Akutsu:
Image Compression-based Approach to Measuring the Similarity of Protein Structures.
APBC 2008: 221-230 |
| 92 | EE | Alvis Brazma,
Satoru Miyano,
Tatsuya Akutsu:
Preface.
APBC 2008 |
| 91 | EE | Yuki Kato,
Tatsuya Akutsu,
Hiroyuki Seki:
Prediction of Protein Beta-Sheets: Dynamic Programming versus Grammatical Approach.
PRIB 2008: 66-77 |
| 90 | EE | Tatsuya Akutsu:
Bioinformatics.
Wiley Encyclopedia of Computer Science and Engineering 2008 |
| 89 | EE | Jiangning Song,
Hao Tan,
Kazuhiro Takemoto,
Tatsuya Akutsu:
HSEpred: predict half-sphere exposure from protein sequences.
Bioinformatics 24(13): 1489-1497 (2008) |
| 88 | EE | Morihiro Hayashida,
Fuyan Sun,
Sachiyo Aburatani,
Katsuhisa Horimoto,
Tatsuya Akutsu:
Integer programming-based approach to allocation of reporter genes for cell array analysis.
IJBRA 4(4): 385-399 (2008) |
| 87 | EE | Tatsuya Akutsu,
Daiji Fukagawa,
Atsuhiro Takasu:
Improved approximation of the largest common subtree of two unordered trees of bounded height.
Inf. Process. Lett. 109(2): 165-170 (2008) |
| 2007 |
|---|
| 86 | EE | Tatsuya Akutsu,
Daiji Fukagawa:
Inferring a Chemical Structure from a Feature Vector Based on Frequency of Labeled Paths and Small Fragments.
APBC 2007: 165-174 |
| 85 | EE | Morihiro Hayashida,
Tatsuya Akutsu,
Hiroshi Nagamochi:
A Novel Clustering Method for Analysis of Biological Networks using Maximal Components of Graphs.
APBC 2007: 257-266 |
| 84 | EE | Takeyuki Tamura,
Tatsuya Akutsu:
An O(1.787n)-Time Algorithm for Detecting a Singleton Attractor in a Boolean Network Consisting of AND/OR Nodes.
FCT 2007: 494-505 |
| 83 | EE | Atsuhiro Takasu,
Daiji Fukagawa,
Tatsuya Akutsu:
Statistical Learning Algorithm for Tree Similarity.
ICDM 2007: 667-672 |
| 82 | EE | Jiexun Wang,
Liang Zhao,
Hiroshi Nagamochi,
Tatsuya Akutsu:
An Efficient Algorithm for Generating Colored Outerplanar Graphs.
TAMC 2007: 573-583 |
| 81 | EE | Jose C. Nacher,
Morihiro Hayashida,
Tatsuya Akutsu:
Topological aspects of protein networks.
Emergent Intelligence of Networked Agents 2007: 147-158 |
| 80 | EE | Wai-Ki Ching,
Shuqin Zhang,
Michael K. Ng,
Tatsuya Akutsu:
An approximation method for solving the steady-state probability distribution of probabilistic Boolean networks.
Bioinformatics 23(12): 1511-1518 (2007) |
| 79 | EE | 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(6-7): 676-685 (2007) |
| 78 | EE | Takeyuki Tamura,
Tatsuya Akutsu:
Approximation Algorithms for Optimal RNA Secondary Structures Common to Multiple Sequences.
IEICE Transactions 90-A(5): 917-923 (2007) |
| 77 | EE | Shuqin Zhang,
Wai-Ki Ching,
Michael K. Ng,
Tatsuya Akutsu:
Simulation study in Probabilistic Boolean Network models for genetic regulatory networks.
IJDMB 1(3): 217-240 (2007) |
| 2006 |
|---|
| 76 | EE | Tatsuya Akutsu,
Morihiro Hayashida,
Wai-Ki Ching,
Michael K. Ng:
On the Complexity of Finding Control Strategies for Boolean Networks.
APBC 2006: 99-108 |
| 75 | EE | Tatsuya Akutsu,
Daiji Fukagawa,
Atsuhiro Takasu:
Approximating Tree Edit Distance Through String Edit Distance.
ISAAC 2006: 90-99 |
| 74 | EE | Jose C. Nacher,
Jean-Marc Schwartz,
Minoru Kanehisa,
Tatsuya Akutsu:
Identification of metabolic units induced by environmental signals.
ISMB (Supplement of Bioinformatics) 2006: 375-383 |
| 73 | EE | Hiroto Saigo,
Jean-Philippe Vert,
Tatsuya Akutsu:
Optimizing amino acid substitution matrices with a local alignment kernel.
BMC Bioinformatics 7: 246 (2006) |
| 72 | EE | Tatsuya Akutsu,
Morihiro Hayashida,
Dukka Bahadur,
Etsuji Tomita,
Jun'ichi Suzuki,
Katsuhisa Horimoto:
Dynamic Programming and Clique Based Approaches for Protein Threading with Profiles and Constraints.
IEICE Transactions 89-A(5): 1215-1222 (2006) |
| 71 | EE | Tatsuya Akutsu:
A relation between edit distance for ordered trees and edit distance for Euler strings.
Inf. Process. Lett. 100(3): 105-109 (2006) |
| 70 | EE | Daiji Fukagawa,
Tatsuya Akutsu:
Fast Algorithms for Comparison of Similar Unordered Trees.
Int. J. Found. Comput. Sci. 17(3): 703-729 (2006) |
| 69 | EE | Tatsuya Akutsu:
Algorithms for Point Set Matching with K-differences.
Int. J. Found. Comput. Sci. 17(4): 903-918 (2006) |
| 68 | EE | K. C. Dukka Bahadur,
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) |
| 67 | EE | Michael K. Ng,
Shuqin Zhang,
Wai-Ki Ching,
Tatsuya Akutsu:
A Control Model for Markovian Genetic Regulatory Networks.
T. Comp. Sys. Biology: 36-48 (2006) |
| 2005 |
|---|
| 66 | EE | 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 |
| 65 | EE | Tatsuya Akutsu,
Daiji Fukagawa:
Inferring a Graph from Path Frequency.
CPM 2005: 371-382 |
| 64 | EE | Shuqin Zhang,
Michael K. Ng,
Wai-Ki Ching,
Tatsuya Akutsu:
A linear control model for gene intervention in a genetic regulatory network.
GrC 2005: 354-358 |
| 63 | EE | 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) |
| 62 | EE | 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) |
| 61 | EE | 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) |
| 60 | EE | Daiji Fukagawa,
Tatsuya Akutsu:
Performance analysis of a greedy algorithm for inferring Boolean functions.
Inf. Process. Lett. 93(1): 7-12 (2005) |
| 59 | EE | Wai-Ki Ching,
Michael K. 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) |
| 58 | EE | 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) |
| 57 | EE | Pierre Mahé,
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(4): 939-951 (2005) |
| 2004 |
|---|
| 56 | EE | Dukka Bahadur,
Tatsuya Akutsu,
Etsuji Tomita,
Tomokazu Seki:
Protein Side-chain Packing Problem: A Maximum Edge-weight Clique Algorithmic Approach.
APBC 2004: 191-200 |
| 55 | EE | Tatsuya Akutsu,
Morihiro Hayashida,
Etsuji Tomita,
Jun'ichi Suzuki,
Katsuhisa Horimoto:
Protein Threading with Profiles and Constraints.
BIBE 2004: 537-544 |
| 54 | EE | Tatsuya Akutsu:
Algorithms for Point Set Matching with k-Differences.
COCOON 2004: 249-258 |
| 53 | EE | Pierre Mahé,
Nobuhisa Ueda,
Tatsuya Akutsu,
Jean-Luc Perret,
Jean-Philippe Vert:
Extensions of marginalized graph kernels.
ICML 2004 |
| 52 | EE | Daiji Fukagawa,
Tatsuya Akutsu:
Fast Algorithms for Comparison of Similar Unordered Trees.
ISAAC 2004: 452-463 |
| 51 | EE | 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 |
| 50 | EE | 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) |
| 49 | EE | Hiroto Saigo,
Jean-Philippe Vert,
Nobuhisa Ueda,
Tatsuya Akutsu:
Protein homology detection using string alignment kernels.
Bioinformatics 20(11): 1682-1689 (2004) |
| 48 | EE | Yuichiro Hourai,
Tatsuya Akutsu,
Yutaka Akiyama:
Optimizing substitution matrices by separating score distributions.
Bioinformatics 20(6): 863-873 (2004) |
| 47 | EE | Tatsuya Akutsu:
Efficient Extraction of Mapping Rules of Atoms from Enzymatic Reaction Data.
Journal of Computational Biology 11(2/3): 449-462 (2004) |
| 46 | | 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) |
| 45 | EE | 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) |
| 2003 |
|---|
| 44 | EE | Tatsuya Akutsu:
Computational and Statistical Methods in Bioinformatics.
Active Mining 2003: 11-33 |
| 43 | EE | Daiji Fukagawa,
Tatsuya Akutsu:
Performance Analysis of a Greedy Algorithm for Inferring Boolean Functions.
Discovery Science 2003: 114-127 |
| 42 | | Daisuke Shinozaki,
Tatsuya Akutsu,
Osamu Maruyama:
Finding optimal degenerate patterns in DNA sequences.
ECCB 2003: 206-214 |
| 41 | | Morihiro Hayashida,
Nobuhisa Ueda,
Tatsuya Akutsu:
Inferring strengths of protein-protein interactions from experimental data using linear programming.
ECCB 2003: 58-65 |
| 40 | EE | Tatsuya Akutsu:
Efficient extraction of mapping rules of atoms from enzymatic reaction data.
RECOMB 2003: 1-8 |
| 39 | | Tatsuya Akutsu,
Kyotetsu Kanaya,
Akira Ohyama,
Asao Fujiyama:
Point matching under non-uniform distortions.
Discrete Applied Mathematics 127(1): 5-21 (2003) |
| 38 | EE | 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) |
| 37 | | 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) |
| 2002 |
|---|
| 36 | EE | Tatsuya Akutsu,
Sascha Ott:
Inferring a Union of Halfspaces from Examples.
COCOON 2002: 117-126 |
| 35 | EE | Tatsuya Akutsu,
Hideo Bannai,
Satoru Miyano,
Sascha Ott:
On the Complexity of Deriving Position Specific Score Matrices from Examples.
CPM 2002: 168-177 |
| 2000 |
|---|
| 34 | EE | 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 |
| 33 | EE | Tatsuya Akutsu,
Hiroki Arimura,
Shinichi Shimozono:
On approximation algorithms for local multiple alignment.
RECOMB 2000: 1-7 |
| 32 | EE | 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 |
| 31 | | Tatsuya Akutsu,
Satoru Miyano,
Satoru Kuhara:
Inferring qualitative relations in genetic networks and metabolic pathways.
Bioinformatics 16(8): 727-734 (2000) |
| 30 | | Tatsuya Akutsu:
Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots.
Discrete Applied Mathematics 104(1-3): 45-62 (2000) |
| 29 | | 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) |
| 28 | EE | 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) |
| 1999 |
|---|
| 27 | EE | 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 |
| 26 | EE | 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 |
| 25 | | 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) |
| 24 | EE | Tatsuya Akutsu,
Satoru Miyano:
On the Approximation of Protein Threading.
Theor. Comput. Sci. 210(2): 261-275 (1999) |
| 1998 |
|---|
| 23 | EE | Tatsuya Akutsu,
Mutsunori Yagiura:
On the Complexity of Deriving Score Functions from Examples for Problems in Molecular Biology.
ICALP 1998: 832-843 |
| 22 | EE | Tatsuya Akutsu:
Approximation and Exact Algorithms for RNA Secondary Structure Prediction and Recognition of Stochastic Context-Free Languages.
ISAAC 1998: 337-346 |
| 21 | | Tatsuya Akutsu,
Satoru Kuhara,
Osamu Maruyama,
Satoru Miyano:
Identification of Gene Regulatory Networks by Strategic Gene Disruptions and Gene Overexpressions.
SODA 1998: 695-702 |
| 20 | | Tatsuya Akutsu:
On determining the congruence of point sets in d dimensions.
Comput. Geom. 9(4): 247-256 (1998) |
| 19 | EE | 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) |
| 1997 |
|---|
| 18 | EE | Tatsuya Akutsu,
Satoru Miyano:
On the approximation of protein threading.
RECOMB 1997: 3-8 |
| 17 | EE | 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 |
| 16 | | 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) |
| 1996 |
|---|
| 15 | | Tatsuya Akutsu,
Feng Bao:
Approximating Minimum Keys and Optimal Substructure Screens.
COCOON 1996: 290-299 |
| 1995 |
|---|
| 14 | EE | Tatsuya Akutsu,
Kentaro Onizuka,
Masato Ishikawa:
New hashing techniques and their application to a protein structure database system.
HICSS (5) 1995: 197-206 |
| 13 | EE | Tatsuya Akutsu:
Approximate String Matching with don't Care Characters.
Inf. Process. Lett. 55(5): 235-239 (1995) |
| 1994 |
|---|
| 12 | | Tatsuya Akutsu:
Approximate String Matching with Don't Care Characters.
CPM 1994: 240-249 |
| 11 | | Tatsuya Akutsu:
Efficient and Robust Three-Dimensional Pattern Matching Algorithms Using Hashing and Dynamic Programming Techniques.
HICSS (5) 1994: 225-234 |
| 10 | | Tatsuya Akutsu:
On Determining the Congruity of Point Sets in Higher Dimensions.
ISAAC 1994: 38-46 |
| 9 | | Tatsuya Akutsu,
Magnús M. Halldórsson:
On the Approximation of Largest Common Subtrees and Largest Common Point Sets.
ISAAC 1994: 405-413 |
| 8 | | Tatsuya Akutsu,
Atsuhiro Takasu:
On PAC Learnability of Functional Depencies.
New Generation Comput. 12(4): 359-374 (1994) |
| 1993 |
|---|
| 7 | | Tatsuya Akutsu:
A Linear Time Pattern Matching Algorithm Between a String and a Tree.
CPM 1993: 1-10 |
| 6 | EE | Einoshin Suzuki,
Tatsuya Akutsu,
Setsuo Ohsuga:
Knowledge-based system for computer-aided drug design.
Knowl.-Based Syst. 6(2): 114-126 (1993) |
| 1992 |
|---|
| 5 | | Tatsuya Akutsu,
Atsuhiro Takasu:
On PAC Learnability of Functional Dependencies.
ALT 1992: 229-239 |
| 4 | | Tatsuya Akutsu:
Algorithms for Determining the Geometrical Congruity in Two and Three Dimensions.
ISAAC 1992: 279-288 |
| 1991 |
|---|
| 3 | EE | 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) |
| 2 | EE | Tatsuya Akutsu,
Einoshin Suzuki,
Setsuo Ohsuga:
Logic-based approach to expert systems in chemistry.
Knowl.-Based Syst. 4(2): 103-116 (1991) |
| 1988 |
|---|
| 1 | | Tatsuya Akutsu,
Setsuo Ohsuga:
CHEMILOG - A Logic Programming Language/System for Chemical Information Processing.
FGCS 1988: 1176-1183 |
