| 2014 | FUSION | Parameter estimation in multi-compartment SIR model. | Masaya M. Saito, Seiya Imoto, Rui Yamaguchi, Satoru Miyano, Tomoyuki Higuchi |
| 2013 | FUSION | Estimation of abrupt changes in sentinel observation data of influenza epidemics in Japan. | Masaya M. Saito, Seiya Imoto, Rui Yamaguchi, Satoru Miyano, Tomoyuki Higuchi |
| 2012 | FUSION | Identifiability of local transmissibility parameters in agent-based pandemic simulation. | Masaya M. Saito, Seiya Imoto, Rui Yamaguchi, Satoru Miyano, Tomoyuki Higuchi |
| 2011 | FUSION | Estimation of macroscopic parameter in agent-based pandemic simulation. | Masaya M. Saito, Seiya Imoto, Rui Yamaguchi, Satoru Miyano, Tomoyuki Higuchi |
| 2010 | BIBE | Identifying Hidden Confounders in Gene Networks by Bayesian Networks. | Tomoya Higashigaki, Kaname Kojima, Rui Yamaguchi, Masato Inoue, Seiya Imoto, Satoru Miyano |
| 2009 | CISIS | Computational Predictions for Functional Proteins Working after Cleaved in Apoptotic Pathway. | Chigusa Miyakawa, Manabu Sugii, Hiroshi Matsuno, Satoru Miyano |
| 2009 | DIS | Better Decomposition Heuristics for the Maximum-Weight Connected Graph Problem Using Betweenness Centrality. | Takanori Yamamoto, Hideo Bannai, Masao Nagasaki, Satoru Miyano |
| 2009 | PSB | Parameter Estimation of In Silico Biological Pathways with Particle Filtering Towards a Petascale Computing. | Kazuyuki Nakamura, Ryo Yoshida, Masao Nagasaki, Satoru Miyano, Tomoyuki Higuchi |
| 2009 | PSB | 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, Stephen D. Charnock-Jones, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano |
| 2008 | APBC | Preface. | Alvis Brazma, Satoru Miyano, Tatsuya Akutsu |
| 2007 | BIBE | A Structure Learning Algorithm for Inference of Gene Networks from Microarray Gene Expression Data Using Bayesian Networks. | Kazuyuki Numata, Seiya Imoto, Satoru Miyano |
| 2007 | BIBE | Computational Genome-Wide Discovery of Aberrant Splice Variations with Exon Expression Profiles. | Ryo Yoshida, Kazuyuki Numata, Seiya Imoto, Masao Nagasaki, Atsushi Doi, Kazuko Ueno, Satoru Miyano |
| 2006 | PSB | 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 |
| 2005 | APBC | A new regulatory interaction suggested by simulations for circadian genetic control mechanism in mammals. | Hiroshi Matsuno, Shin-Ichi T. Inouye, Yasuki Okitsu, Yasushi Fujii, Satoru Miyano |
| 2005 | ECCB | Estimating gene regulatory networks and protein-protein interactions of | Naoki Nariai, Yoshinori Tamada, Seiya Imoto, Satoru Miyano |
| 2005 | ICCSA | Estimating Gene Networks from Expression Data and Binding Location Data via Boolean Networks. | Osamu Hirose, Naoki Nariai, Yoshinori Tamada, Hideo Bannai, Seiya Imoto, Satoru Miyano |
| 2005 | PSB | Bayesian Joint Prediction of Associated Transcription Factors in Bacillus subtilis. | Yuko Makita, Michiel J. L. de Hoon, Naotake Ogasawara, Satoru Miyano, Kenta Nakai |
| 2004 | APBC | Integrating Biopathway Databases for Large-scale Modeling and Simulation. | Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno, Satoru Miyano |
| 2004 | BIBE | Case-Control Study of Binary Disease Trait Considering Interactions between SNPs and Environmental Effects using Logistic Regression. | Reiichiro Nakamichi, Seiya Imoto, Satoru Miyano |
| 2004 | DIS | Finding Optimal Pairs of Cooperative and Competing Patterns with Bounded Distance. | Shunsuke Inenaga, Hideo Bannai, Heikki Hyyr, Ayumi Shinohara, Masayuki Takeda, Kenta Nakai, Satoru Miyano |
| 2004 | ISMB | Predicting gene regulation by sigma factors in Bacillus subtilis from genome-wide data. | Michiel J. L. de Hoon, Yuko Makita, Seiya Imoto, Kazuo Kobayashi, Naotake Ogasawara, Kenta Nakai, Satoru Miyano |
| 2004 | PSB | Predicting the Operon Structure of Bacillus subtilis Using Operon Length, Intergene Distance, and Gene Expression Information. | Michiel J. L. de Hoon, Seiya Imoto, Kazuo Kobayashi, Naotake Ogasawara, Satoru Miyano |
| 2004 | PSB | Using Protein-Protein Interactions for Refining Gene Networks Estimated from Microarray Data by Bayesian Networks. | Naoki Nariai, SunYong Kim, Seiya Imoto, Satoru Miyano |
| 2004 | PSB | Finding Optimal Models for Small Gene Networks. | Sascha Ott, Seiya Imoto, Satoru Miyano |
| 2004 | WABI | Finding Optimal Pairs of Patterns. | Hideo Bannai, Heikki Hyyr, Ayumi Shinohara, Masayuki Takeda, Kenta Nakai, Satoru Miyano |
| 2003 | ECCB | 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 |
| 2003 | PSB | Inferring Gene Regulatory Networks from Time-Ordered Gene Expression Data of Bacillus Subtilis Using Differential Equations. | Michiel J. L. de Hoon, Seiya Imoto, Kazuo Kobayashi, Naotake Ogasawara, Satoru Miyano |
| 2003 | PSB | Boundary Formation by Notch Signaling in Drosophila Multicellular Systems: Experimental Observations and Gene Network Modeling by Genomic Object Net. | Hiroshi Matsuno, Ryutaro Murakani, Rie Yamane, Naoyuki Yamasaki, Sachie Fujita, Haruka Yoshimori, Satoru Miyano |
| 2003 | PSB | Intrasplicing - Analysis of Long Intron Sequences. | Sascha Ott, Yoshinori Tamada, Hideo Bannai, Kenta Nakai, Satoru Miyano |
| 2002 | CPM | On the Complexity of Deriving Position Specific Score Matrices from Examples. | Tatsuya Akutsu, Hideo Bannai, Satoru Miyano, Sascha Ott |
| 2002 | DIS | Inferring Gene Regulatory Networks from Time-Ordered Gene Expression Data Using Differential Equations. | Michiel J. L. de Hoon, Seiya Imoto, Satoru Miyano |
| 2002 | DIS | Toward Drawing an Atlas of Hypothesis Classes: Approximating a Hypothesis via Another Hypothesis Model. | Osamu Maruyama, Takayoshi Shoudai, Satoru Miyano |
| 2002 | PSB | Estimation of Genetic Networks and Functional Structures Between Genes by Using Bayesian Networks and Nonparametric Regression. | Seiya Imoto, Takao Goto, Satoru Miyano |
| 2001 | DIS | VML: A View Modeling Language for Computational Knowledge Discovery. | Hideo Bannai, Yoshinori Tamada, Osamu Maruyama, Satoru Miyano |
| 2001 | DIS | Learning Conformation Rules. | Osamu Maruyama, Takayoshi Shoudai, Emiko Furuichi, Satoru Kuhara, Satoru Miyano |
| 2001 | FlAIRS | Views: Fundamental Building Blocks in the Process of Knowledge Discovery. | Hideo Bannai, Yoshinori Tamada, Osamu Maruyama, Kenta Nakai, Satoru Miyano |
| 2000 | DIS | A Simple Greedy Algorithm for Finding Functional Relations: Efficient Implementation and Average Case Anaylsis. | Tatsuya Akutsu, Satoru Miyano, Satoru Kuhara |
| 2000 | RECOMB | Algorithms for identifying Boolean networks and related biological networks based on matrix multiplication and fingerprint function. | Tatsuya Akutsu, Satoru Miyano, Satoru Kuhara |
| 1999 | DIS | A Definition of Discovery in Terms of Generalized Descriptional Complexity. | Hideo Bannai, Satoru Miyano |
| 1999 | DIS | Designing Views in HypothesisCreator: System for Assisting in Discovery. | Osamu Maruyama, Tomoyuki Uchida, Kim Lan Sim, Satoru Miyano |
| 1999 | PSB | Identification of Genetic Networks from a Small Number of Gene Expression Patterns Under the Boolean Network Model. | Tatsuya Akutsu, Satoru Miyano, Satoru Kuhara |
| 1998 | DIS | Toward Genomic Hypothesis Creator: View Designer for Discovery. | Osamu Maruyama, Tomoyuki Uchida, Takayoshi Shoudai, Satoru Miyano |
| 1998 | SODA | Identification of Gene Regulatory Networks by Strategic Gene Disruptions and Gene Overexpressions. | Tatsuya Akutsu, Satoru Kuhara, Osamu Maruyama, Satoru Miyano |
| 1997 | RECOMB | On the approximation of protein threading. | Tatsuya Akutsu, Satoru Miyano |
| 1996 | STACS | Extracting Best Consensus Motifs from Positive and Negative Examples. | Erika Tateishi, Osamu Maruyama, Satoru Miyano |
| 1995 | ISAAC | Algorithmic Problems Arising from Genome Informatics (Abstract). | Satoru Miyano |
| 1995 | ISMB | 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 |
| 1995 | MFCS | Graph Inference from a Walk for TRees of Bounded Degree 3 is NP-Complete. | Osamu Maruyama, Satoru Miyano |
| 1993 | ALT | Learning Theory Toward Genome Informatics. | Satoru Miyano |
| 1992 | MFCS | Inferring a Tree from Walks. | Osamu Maruyama, Satoru Miyano |
| 1991 | ALT | Analogy is NP-hard. | Shinji Furuya, Satoru Miyano |
| 1991 | ALT | Which classes of elementary formal systems are polynomial-time learnable. | Satoru Miyano, Ayumi Shinohara, Takeshi Shinohara |
| 1990 | ALT | Teachability in Computational Learning. | Ayumi Shinohara, Satoru Miyano |
| 1988 | MFCS | Δ | Satoru Miyano |
| 1987 | ICALP | The Lexicographically First Maximal Subgraph Problems: P-Completeness and NC Algorithms. | Satoru Miyano |