GENAS: a database system for nucleic acid sequence analysis. - Satoru Kuhara; Fumihiro Matsuo; Syoichi Futamura; Atsushi Fujita; Takeshi Shinohara; Toshihisa Takagi; Yoshiyuki Sakaki (Nucleic Acids Res., 1984)

A deductive database system PACADE for analyzing 3-D and secondary structures of protein. - Kenji Satou; Emiko Furuichi; Kyoko Takiguchi; Toshihisa Takagi; Satoru Kuhara (Comput. Appl. Biosci., 1993)

A Machine Discovery from Amino Acid Sequences by Decision Trees over Regular Patterns. - Setsuo Arikawa; Satoru Miyano; Ayumi Shinohara; Satoru Kuhara; Yasuhito Mukouchi; Takeshi Shinohara (New Gener. Comput., 1993)

Application of a Deductive Database System PACADE toward Discovery of Clusters of Similar Structures in Proteins. - Kenji Satou; Emiko Furuichi; Kyoko Takiguchi; Satoru Kuhara; Toshihisa Takagi (HICSS (5), 1994)

Development of an integrated Database for Genome Mapping and Nucleotide Sequences. - Takahiko Suzuki; Toshihisa Takagi; Satoru Kuhara; Minoru Kanehisa (HICSS (5), 1994)

BONSAI Garden: Parallel Knowledge Discovery System for Amino Acid Sequences. - Takayoshi Shoudai; Michael Lappe; Satoru Miyano; Ayumi Shinohara; Takeo Okazaki; Setsuo Arikawa; Tomoyuki Uchida; Shinichi Shimozono; Takeshi Shinohara; Satoru Kuhara (ISMB, 1995)

Data Classification Component in a Deductive Database System and Its Application to Protein Structural Analysis. - Akio Nishikawa; Kenji Satou; Emiko Furuichi; Satoru Kuhara; Kazuo Ushijima (IEICE Trans. Inf. Syst., 1995)

Extraction of Substructures of Proteins Essential to their Biological Functions by a Data Mining Technique. - Kenji Satou; Toshihide Ono; Yoshihisa Yamamura; Emiko Furuichi; Satoru Kuhara; Toshihisa Takagi (ISMB, 1997)

Application of a deductive database system to search for topological and similar three-dimensional structures in protein. - Y. Tsukamoto; Kyoko Takiguchi; Kenji Satou; Emiko Furuichi; Toshihisa Takagi; Satoru Kuhara (Comput. Appl. Biosci., 1997)

Identification of Gene Regulatory Networks by Strategic Gene Disruptions and Gene Overexpressions. - Tatsuya Akutsu; Satoru Kuhara; Osamu Maruyama; Satoru Miyano (SODA, 1998)

Identification of Genetic Networks from a Small Number of Gene Expression Patterns Under the Boolean Network Model. - Tatsuya Akutsu; Satoru Miyano; Satoru Kuhara (Pacific Symposium on Biocomputing, 1999)

Use of Bonsai Decision Trees for the Identification of Potential MHC Class I Peptide Epitope Motifs. - Christopher J. Savoie; Nobuhiro Kamikawaji; Takehiko Sasazuki; Satoru Kuhara (Pacific Symposium on Biocomputing, 1999)

The hydrophobic cores of proteins predicted by wavelet analysis. - Hideki Hirakawa; S. Muta; Satoru Kuhara (Bioinform., 1999)

A Simple Greedy Algorithm for Finding Functional Relations: Efficient Implementation and Average Case Anaylsis. - Tatsuya Akutsu; Satoru Miyano; Satoru Kuhara (Discovery Science, 2000)

Inferring qualitative relations in genetic networks and metabolic pathways. - Tatsuya Akutsu; Satoru Miyano; Satoru Kuhara (Bioinform., 2000)

Algorithms for Identifying Boolean Networks and Related Biological Networks Based on Matrix Multiplication and Fingerprint Function. - Tatsuya Akutsu; Satoru Miyano; Satoru Kuhara (J. Comput. Biol., 2000)

Learning Conformation Rules. - Osamu Maruyama; Takayoshi Shoudai; Emiko Furuichi; Satoru Kuhara; Satoru Miyano (Discovery Science, 2001)

Fast algorithm for extracting multiple unordered short motifs using bit operations. - Osamu Maruyama; Hideo Bannai; Yoshinori Tamada; Satoru Kuhara; Satoru Miyano (Inf. Sci., 2002)

Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection. - Yoshinori Tamada; SunYong Kim; Hideo Bannai; Seiya Imoto; Kousuke Tashiro; Satoru Kuhara; Satoru Miyano (ECCB, 2003)

Bayesian Network and Nonparametric Heteroscedastic Regression for Nonlinear Modeling of Genetic Network. - Seiya Imoto; SunYong Kim; Takao Goto; Sachiyo Aburatani; Kousuke Tashiro; Satoru Kuhara; Satoru Miyano (J. Bioinform. Comput. Biol., 2003)

Use of Gene Networks for Identifying and Validating Drug Targets. - Seiya Imoto; Christopher J. Savoie; Sachiyo Aburatani; SunYong Kim; Kousuke Tashiro; Satoru Kuhara; Satoru Miyano (J. Bioinform. Comput. Biol., 2003)

Deduction of a gene regulatory relationship framework from gene expression data by the application of graphical Gaussian modeling. - Sachiyo Aburatani; Satoru Kuhara; Hiroyuki Toh; Katsuhisa Horimoto (Signal Process., 2003)

Identification of genetic networks by strategic gene disruptions and gene overexpressions under a boolean model. - Tatsuya Akutsu; Satoru Kuhara; Osamu Maruyama; Satoru Miyano (Theor. Comput. Sci., 2003)

A simple greedy algorithm for finding functional relations: efficient implementation and average case analysis. - Tatsuya Akutsu; Satoru Miyano; Satoru Kuhara (Theor. Comput. Sci., 2003)

Combining Microarrays and Biological Knowledge for Estimating Gene Networks via Bayesian Networks. - Seiya Imoto; Tomoyuki Higuchi; Takao Goto; Kousuke Tashiro; Satoru Kuhara; Satoru Miyano (J. Bioinform. Comput. Biol., 2004)

An Integrated Comprehensive Workbench for Inferring Genetic Networks: voyagene. - Yukihiro Maki; Yoriko Takahashi; Yuji Arikawa; Shoji Watanabe; Ken Aoshima; Yukihiro Eguchi; Takanori Ueda; Sachiyo Aburatani; Satoru Kuhara; Masahiro Okamoto (J. Bioinform. Comput. Biol., 2004)

Reconstructing phylogenetic trees of prokaryote genomes by randomly sampling oligopeptides. - Osamu Maruyama; Akiko Matsuda; Satoru Kuhara (Int. J. Bioinform. Res. Appl., 2005)

Multiclass Molecular Cancer Classification by Kernel Subspace Methods with Effective Kernel Parameter Selection. - Satoshi Niijima; Satoru Kuhara (J. Bioinform. Comput. Biol., 2005)

Computational Strategy for Discovering Druggable Gene Networks from Genome-Wide RNA Expression Profiles. - Seiya Imoto; Yoshinori Tamada; Hiromitsu Araki; Kaori Yasuda; Cristin G. Print; Stephen D. Charnock-Jones; Deborah Sanders; Christopher J. Savoie; Kousuke Tashiro; Satoru Kuhara; Satoru Miyano (Pacific Symposium on Biocomputing, 2006)

Recursive gene selection based on maximum margin criterion: a comparison with SVM-RFE. - Satoshi Niijima; Satoru Kuhara (BMC Bioinform., 2006)

Gene subset selection in kernel-induced feature space. - Satoshi Niijima; Satoru Kuhara (Pattern Recognit. Lett., 2006)

Evaluating Protein Sequence Signatures Inferred from Protein-Protein Interaction Data by Gene Ontology Annotations. - Osamu Maruyama; Hideki Hirakawa; Takao Iwayanagi; Yoshiko Ishida; Shizu Takeda; Jun Otomo; Satoru Kuhara (BIBM, 2008)

Unraveling Dynamic Activities of Autocrine Pathways that Control Drug-Response Transcriptome Networks. - Yoshinori Tamada; Hiromitsu Araki; Seiya Imoto; Masao Nagasaki; Atsushi Doi; Yukiko Nakanishi; Yuki Tomiyasu; Kaori Yasuda; Ben Dunmore; Deborah Sanders; Sally Humphreys; Cristin G. Print; et al. (Pacific Symposium on Biocomputing, 2009)

An Extension Approach for Neural Networks by Introducing a Nearest Neighbor Algorithm in Relative Coordinates. - Hirofumi Suzaki; Satoru Kuhara (J. Adv. Comput. Intell. Intell. Informatics, 2010)

hERGAPDbase: a database documenting hERG channel inhibitory potentials and APD-prolongation activities of chemical compounds. - Haretsugu Hishigaki; Satoru Kuhara (Database J. Biol. Databases Curation, 2011)

Infrequent, Unexpected, and Contrast Pattern Discovery from Bacterial Genomes by Genome-wide Comparative Analysis. - Daisuke Ikeda; Osamu Maruyama; Satoru Kuhara (BIOINFORMATICS, 2013)

The Purity Measure for genomic Regions leads to Horizontally Transferred genes. - Yuta Taniguchi; Yasuhiro Yamada; Osamu Maruyama; Satoru Kuhara; Daisuke Ikeda (J. Bioinform. Comput. Biol., 2013)

A novel method for gathering and prioritizing disease candidate genes based on construction of a set of disease-related MeSH(R) terms. - Toshihide Ono; Satoru Kuhara (BMC Bioinform., 2014)