One-Way Weak-Stack-Counter Automata. - Satoru Miyano (J. Comput. Syst. Sci., 1980)

A Hierarchy Theorem for Multihead Stack-Counter Automata. - Satoru Miyano (Acta Informatica, 1982)

Two-Way Deterministic Multi-Weak-Counter Machines. - Satoru Miyano (Theor. Comput. Sci., 1982)

Remarks on Multihead Pushdown Automata and Multihead Stack Automata. - Satoru Miyano (J. Comput. Syst. Sci., 1983)

Remarks on Two-Way Automata with Weak-Counters. - Satoru Miyano (Inf. Process. Lett., 1984)

Alternating Finite Automata on omega-Words. - Satoru Miyano; Takeshi Hayashi 004 (Theor. Comput. Sci., 1984)

The Lexicographically First Maximal Subgraph Problems: P-Completeness and NC Algorithms. - Satoru Miyano (ICALP, 1987)

Parallel Complexity and P-Complete Problems. - Satoru Miyano (FGCS, 1988)

Δ2p-Complete Lexicographically First Maximal Subgraph Problems. - Satoru Miyano (MFCS, 1988)

A Parallelizable Lexicographically First Maximal Edge-Induced Subgraph Problem. - Satoru Miyano (Inf. Process. Lett., 1988)

The Lexicographically First Maximum Subgraph Problems: P-Completeness and NC Algorithms. - Satoru Miyano (Math. Syst. Theory, 1989)

Teachability in Computational Learning. - Ayumi Shinohara; Satoru Miyano (ALT, 1990)

Analogy is NP-hard. - Shinji Furuya; Satoru Miyano (ALT, 1991)

Which classes of elementary formal systems are polynomial-time learnable. - Satoru Miyano; Ayumi Shinohara; Takeshi Shinohara (ALT, 1991)

More About Learning Elementary Formal Systems. - Setsuo Arikawa; Takeshi Shinohara; Satoru Miyano; Ayumi Shinohara (Nonmonotonic and Inductive Logic, 1991)

Delta_2^P-Complete Lexicographically First Maximal Subgraph Problems. - Satoru Miyano (Theor. Comput. Sci., 1991)

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)

Machine Learning and Discovery for Bloinformatics: Introduction. - Satoru Miyano; Ayumi Shinohara (HICSS (5), 1994)

Algorithmic Problems Arising from Genome Informatics (Abstract). - Satoru Miyano (ISAAC, 1995)

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)

Graph Inference from a Walk for TRees of Bounded Degree 3 is NP-Complete. - Osamu Maruyama; Satoru Miyano (MFCS, 1995)

Learning Theory Toward Genome Informatics. - Satoru Miyano (IEICE Trans. Inf. Syst., 1995)

Complexity of Finding Alphabet Indexing. - Shinichi Shimozono; Satoru Miyano (IEICE Trans. Inf. Syst., 1995)

Parallel Algorithms for Refutation Tree Problem on Formal Graph Systems. - Tomoyuki Uchida; Takayoshi Shoudai; Satoru Miyano (IEICE Trans. Inf. Syst., 1995)

Using Maximal Independent Sets to Solve Problems in Parallel. - Takayoshi Shoudai; Satoru Miyano (Theor. Comput. Sci., 1995)

Genome Informatics: New Frontiers of Computer Science and Biosciences. - Satoru Miyano (CODAS, 1996)

Extracting Best Consensus Motifs from Positive and Negative Examples. - Erika Tateishi; Osamu Maruyama; Satoru Miyano (STACS, 1996)

Inferring a Tree from Walks. - Osamu Maruyama; Satoru Miyano (Theor. Comput. Sci., 1996)

An Approximation Algorithm for the Minimum Common Supertree Problem. - Atsuko Yamaguchi; Koji Nakano; Satoru Miyano (Nord. J. Comput., 1997)

Toward Genomic Hypothesis Creator: View Designer for Discovery. - Osamu Maruyama; Tomoyuki Uchida; Takayoshi Shoudai; Satoru Miyano (Discovery Science, 1998)

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

A Definition of Discovery in Terms of Generalized Descriptional Complexity. - Hideo Bannai; Satoru Miyano (Discovery Science, 1999)

Designing Views in HypothesisCreator: System for Assisting in Discovery. - Osamu Maruyama; Tomoyuki Uchida; Kim Lan Sim; Satoru Miyano (Discovery Science, 1999)

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)

Foreword. - Ying Xu; Satoru Miyano; Tom Head (J. Comb. Optim., 1999)

On the Approximation of Protein Threading. - Tatsuya Akutsu; Satoru Miyano (Theor. Comput. Sci., 1999)

Foreword: Genome Informatics. - Satoru Miyano (Theor. Comput. Sci., 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)

Polynomial-time Learning of Elementary Formal Systems. - Satoru Miyano; Ayumi Shinohara; Takeshi Shinohara (New Gener. Comput., 2000)

VML: A View Modeling Language for Computational Knowledge Discovery. - Hideo Bannai; Yoshinori Tamada; Osamu Maruyama; Satoru Miyano (Discovery Science, 2001)

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

Views: Fundamental Building Blocks in the Process of Knowledge Discovery. - Hideo Bannai; Yoshinori Tamada; Osamu Maruyama; Kenta Nakai; Satoru Miyano (FLAIRS, 2001)

ProDDO: a database of disordered proteins from the Protein Data Bank (PDB). - Kim Lan Sim; Tomoyuki Uchida; Satoru Miyano (Bioinform., 2001)

HypothesisCreator: Concepts for Accelerating the Computational Knowledge Discovery Process. - Hideo Bannai; Yoshinori Tamada; Osamu Maruyama; Satoru Miyano (Electron. Trans. Artif. Intell., 2001)

Challenges for Intelligent Systems in Biology. - Russ B. Altman; Alfonso Valencia; Satoru Miyano; Shoba Ranganathan (IEEE Intell. Syst., 2001)

On the Complexity of Deriving Position Specific Score Matrices from Examples. - Tatsuya Akutsu; Hideo Bannai; Satoru Miyano; Sascha Ott (CPM, 2002)

Inferring Gene Regulatory Networks from Time-Ordered Gene Expression Data Using Differential Equations. - Michiel J. L. de Hoon; Seiya Imoto; Satoru Miyano (Discovery Science, 2002)

Toward Drawing an Atlas of Hypothesis Classes: Approximating a Hypothesis via Another Hypothesis Model. - Osamu Maruyama; Takayoshi Shoudai; Satoru Miyano (Discovery Science, 2002)

Foundations of Designing Computational Knowledge Discovery Processes. - Yoshinori Tamada; Hideo Bannai; Osamu Maruyama; Satoru Miyano (Progress in Discovery Science, 2002)

Estimation of Genetic Networks and Functional Structures Between Genes by Using Bayesian Networks and Nonparametric Regression. - Seiya Imoto; Takao Goto; Satoru Miyano (Pacific Symposium on Biocomputing, 2002)

Extensive feature detection of N-terminal protein sorting signals. - Hideo Bannai; Yoshinori Tamada; Osamu Maruyama; Kenta Nakai; Satoru Miyano (Bioinform., 2002)

Statistical analysis of a small set of time-ordered gene expression data using linear splines. - Michiel J. L. de Hoon; Seiya Imoto; Satoru Miyano (Bioinform., 2002)

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

Towards Biopathway Modeling and Simulation. - Hiroshi Matsuno; Sachie Fujita; Atsushi Doi; Masao Nagasaki; Satoru Miyano (ICATPN, 2003)

Dynamic Bayesian Network and Nonparametric Regression for Nonlinear Modeling of Gene Networks from Time Series Gene Expression Data. - SunYong Kim; Seiya Imoto; Satoru Miyano (CMSB, 2003)

Inference, Modeling and Simulation of Gene Networks. - Satoru Miyano (CMSB, 2003)

Recreating Biopathway Databases towards Simulation. - Masao Nagasaki; Atsushi Doi; Hiroshi Matsuno; Satoru Miyano (CMSB, 2003)

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)

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 (Pacific Symposium on Biocomputing, 2003)

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 (Pacific Symposium on Biocomputing, 2003)

Intrasplicing - Analysis of Long Intron Sequences. - Sascha Ott; Yoshinori Tamada; Hideo Bannai; Kenta Nakai; Satoru Miyano (Pacific Symposium on Biocomputing, 2003)

Inferring gene networks from time series microarray data using dynamic Bayesian networks. - SunYong Kim; Seiya Imoto; Satoru Miyano (Briefings Bioinform., 2003)

Biopathways representation and simulation on hybrid functional Petri net. - Hiroshi Matsuno; Yukiko Tanaka; Hitoshi Aoshima; Atsushi Doi; Mika Matsui; Satoru Miyano (Silico Biol., 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)

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)

Integrating Biopathway Databases for Large-scale Modeling and Simulation. - Masao Nagasaki; Atsushi Doi; Hiroshi Matsuno; Satoru Miyano (APBC, 2004)

Case-Control Study of Binary Disease Trait Considering Interactions between SNPs and Environmental Effects using Logistic Regression. - Reiichiro Nakamichi; Seiya Imoto; Satoru Miyano (BIBE, 2004)

Residual Bootstrapping and Median Filtering for Robust Estimation of Gene Networks from Microarray Data. - Seiya Imoto; Tomoyuki Higuchi; SunYong Kim; Euna Jeong; Satoru Miyano (CMSB, 2004)

Finding Optimal Pairs of Cooperative and Competing Patterns with Bounded Distance. - Shunsuke Inenaga; Hideo Bannai; Heikki Hyyrö; Ayumi Shinohara; Masayuki Takeda; Kenta Nakai; Satoru Miyano (Discovery Science, 2004)

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 (ISMB/ECCB (Supplement of Bioinformatics), 2004)

Functional Data Analysis of the Dynamics of Gene Regulatory Networks. - Tomohiro Ando; Seiya Imoto; Satoru Miyano (KELSI, 2004)

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 (Pacific Symposium on Biocomputing, 2004)

Using Protein-Protein Interactions for Refining Gene Networks Estimated from Microarray Data by Bayesian Networks. - Naoki Nariai; SunYong Kim; Seiya Imoto; Satoru Miyano (Pacific Symposium on Biocomputing, 2004)

Finding Optimal Models for Small Gene Networks. - Sascha Ott; Seiya Imoto; Satoru Miyano (Pacific Symposium on Biocomputing, 2004)

Finding Optimal Pairs of Patterns. - Hideo Bannai; Heikki Hyyrö; Ayumi Shinohara; Masayuki Takeda; Kenta Nakai; Satoru Miyano (WABI, 2004)

Constructing biological pathway models with hybrid functional Petri net. - Atsushi Doi; Sachie Fujita; Hiroshi Matsuno; Masao Nagasaki; Satoru Miyano (Silico Biol., 2004)

Efficiently Finding Regulatory Elements Using Correlation with Gene Expression. - Hideo Bannai; Shunsuke Inenaga; Ayumi Shinohara; Masayuki Takeda; Satoru Miyano (J. Bioinform. Comput. Biol., 2004)

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)

Simulated Cell Division Processes of the Xenopus Cell Cycle Pathway by Genomic Object Net. - Mika Matsui; Sachie Fujita; Shunichi Suzuki; Hiroshi Matsuno; Satoru Miyano (J. Integr. Bioinform., 2004)

An O(N2) Algorithm for Discovering Optimal Boolean Pattern Pairs. - Hideo Bannai; Heikki Hyyrö; Ayumi Shinohara; Masayuki Takeda; Kenta Nakai; Satoru Miyano (IEEE ACM Trans. Comput. Biol. Bioinform., 2004)

Estimating gene regulatory networks and protein-protein interactions of Saccharomyces cerevisiae from multiple genome-wide data. - Naoki Nariai; Yoshinori Tamada; Seiya Imoto; Satoru Miyano (ECCB/JBI, 2005)

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 (ICCSA (3), 2005)

Bayesian Joint Prediction of Associated Transcription Factors in Bacillus subtilis. - Yuko Makita; Michiel J. L. de Hoon; Naotake Ogasawara; Satoru Miyano; Kenta Nakai (Pacific Symposium on Biocomputing, 2005)

Superiority of network motifs over optimal networks and an application to the revelation of gene network evolution. - Sascha Ott; Annika Hansen; SunYong Kim; Satoru Miyano (Bioinform., 2005)

Utilizing Evolutionary Information and Gene Expression Data for Estimating Gene Networks with Bayesian Network Models. - Yoshinori Tamada; Hideo Bannai; Seiya Imoto; Toshiaki Katayama; Minoru Kanehisa; Satoru Miyano (J. Bioinform. Comput. Biol., 2005)

Prediction of Transcriptional Terminators in Bacillus subtilis and Related Species. - Michiel J. L. de Hoon; Yuko Makita; Kenta Nakai; Satoru Miyano (PLoS Comput. Biol., 2005)

Machine Learning Prediction of Amino Acid Patterns in Protein N-myristoylation. - Ryo Okada; Manabu Sugii; Hiroshi Matsuno; Satoru Miyano (PRIB, 2006)

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)

ArrayCluster: an analytic tool for clustering, data visualization and module finder on gene expression profiles. - Ryo Yoshida; Tomoyuki Higuchi; Seiya Imoto; Satoru Miyano (Bioinform., 2006)

Petri Net Based Descriptions for Systematic Understanding of Biological Pathways. - Hiroshi Matsuno; Chen Li 007; Satoru Miyano (IEICE Trans. Fundam. Electron. Commun. Comput. Sci., 2006)

Statistical Model Selection Method to Analyze Combinatorial Effects of Snps and Environmental Factors for Binary Disease. - Reiichiro Nakamichi; Seiya Imoto; Satoru Miyano (Int. J. Artif. Intell. Tools, 2006)

Simulation-Based Validation of the p53 Transcriptional Activity with Hybrid Functional Petri Net. - Atsushi Doi; Masao Nagasaki; Hiroshi Matsuno; Satoru Miyano (Silico Biol., 2006)

Structural Modeling and Analysis of Signaling Pathways Based on Petri Nets. - Chen Li 007; Shunichi Suzuki; Qi-Wei Ge; Mitsuru Nakata; Hiroshi Matsuno; Satoru Miyano (J. Bioinform. Comput. Biol., 2006)

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 (J. Bioinform. Comput. Biol., 2006)

Preface: Special RECOMB 2005 Issue. - Satoru Miyano (J. Comput. Biol., 2006)

A Weighted Profile Based Method for Protein-RNA Interacting Residue Prediction. - Euna Jeong; Satoru Miyano (Trans. Comp. Sys. Biology, 2006)

A Structure Learning Algorithm for Inference of Gene Networks from Microarray Gene Expression Data Using Bayesian Networks. - Kazuyuki Numata; Seiya Imoto; Satoru Miyano (BIBE, 2007)

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 (BIBE, 2007)

Statistical Absolute Evaluation of Gene Ontology Terms with Gene Expression Data. - Pramod K. Gupta; Ryo Yoshida; Seiya Imoto; Rui Yamaguchi; Satoru Miyano (ISBRA, 2007)

An efficient grid layout algorithm for biological networks utilizing various biological attributes. - Kaname Kojima; Masao Nagasaki; Euna Jeong; Mitsuru Kato; Satoru Miyano (BMC Bioinform., 2007)

AYUMS: an algorithm for completely automatic quantitation based on LC-MS/MS proteome data and its application to the analysis of signal transduction. - Ayumu Saito; Masao Nagasaki; Masaaki Oyama; Hiroko Kozuka-Hata; Kentaro Semba; Sumio Sugano; Tadashi Yamamoto; Satoru Miyano (BMC Bioinform., 2007)

Modeling gene expression regulatory networks with the sparse vector autoregressive model. - André Fujita; João Ricardo Sato; Humberto Miguel Garay-Malpartida; Rui Yamaguchi; Satoru Miyano; Mari Cleide Sogayar; Carlos Eduardo Ferreira (BMC Syst. Biol., 2007)

On the complexity of deriving position specific score matrices from positive and negative sequences. - Tatsuya Akutsu; Hideo Bannai; Satoru Miyano; Sascha Ott (Discret. Appl. Math., 2007)

Cell System Ontology: Representation for Modeling, Visualizing, and Simulating Biological Pathways. - Euna Jeong; Masao Nagasaki; Ayumu Saito; Satoru Miyano (Silico Biol., 2007)

Finding module-based gene networks with state-space models - Mining high-dimensional and short time-course gene expression data. - Rui Yamaguchi; Ryo Yoshida; Seiya Imoto; Tomoyuki Higuchi; Satoru Miyano (IEEE Signal Process. Mag., 2007)

Preface. - Alvis Brazma; Satoru Miyano; Tatsuya Akutsu (APBC, 2008)

Analyzing Time Course Gene Expression Data with Biological and Technical Replicates to Estimate Gene Networks by State Space Models. - Osamu Hirose; Ryo Yoshida; Rui Yamaguchi; Seiya Imoto; Tomoyuki Higuchi; Satoru Miyano (Asia International Conference on Modelling and Simulation, 2008)

Partial Order-Based Bayesian Network Learning Algorithm for Estimating Gene Networks. - Kazuyuki Numata; Seiya Imoto; Satoru Miyano (BIBM, 2008)

An Algorithm to Estimate Delay Times in Petri Net Models of Signaling Pathways with Experimental Data. - Kanji Hioka; Yoshimasa Miwa; Chen Li 007; Qi-Wei Ge; Hiroshi Matsuno; Satoru Miyano (BIONETICS, 2008)

Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models. - Osamu Hirose; Ryo Yoshida; Seiya Imoto; Rui Yamaguchi; Tomoyuki Higuchi; Stephen D. Charnock-Jones; Cristin G. Print; Satoru Miyano (Bioinform., 2008)

Fast grid layout algorithm for biological networks with sweep calculation. - Kaname Kojima; Masao Nagasaki; Satoru Miyano (Bioinform., 2008)

Bayesian learning of biological pathways on genomic data assimilation. - Ryo Yoshida; Masao Nagasaki; Rui Yamaguchi; Seiya Imoto; Satoru Miyano; Tomoyuki Higuchi (Bioinform., 2008)

ExonMiner: Web service for analysis of GeneChip Exon array data. - Kazuyuki Numata; Ryo Yoshida; Masao Nagasaki; Ayumu Saito; Seiya Imoto; Satoru Miyano (BMC Bioinform., 2008)

Multivariate gene expression analysis reveals functional connectivity changes between normal/tumoral prostates. - André Fujita; Luciana Rodrigues Gomes; João Ricardo Sato; Rui Yamaguchi; Carlos E. Thomaz; Mari Cleide Sogayar; Satoru Miyano (BMC Syst. Biol., 2008)

Systematic reconstruction of TRANSPATH data into Cell System Markup Language. - Masao Nagasaki; Ayumu Saito; Chen Li 007; Euna Jeong; Satoru Miyano (BMC Syst. Biol., 2008)

Modeling Nonlinear Gene Regulatory Networks from Time Series Gene Expression Data. - André Fujita; João Ricardo Sato; Humberto Miguel Garay-Malpartida; Mari Cleide Sogayar; Carlos Eduardo Ferreira; Satoru Miyano (J. Bioinform. Comput. Biol., 2008)

Foundations of Systems Biology - Using Cell Illustrator® and Pathway Databases. - Masao Nagasaki; Ayumu Saito; Atsushi Doi; Hiroshi Matsuno; Satoru Miyano (Springer, 2009)

Gene Networks Viewed through Two Models. - Satoru Miyano; Rui Yamaguchi; Yoshinori Tamada; Masao Nagasaki; Seiya Imoto (BICoB, 2009)

Computational Predictions for Functional Proteins Working after Cleaved in Apoptotic Pathway. - Chigusa Miyakawa; Manabu Sugii; Hiroshi Matsuno; Satoru Miyano (CISIS, 2009)

Better Decomposition Heuristics for the Maximum-Weight Connected Graph Problem Using Betweenness Centrality. - Takanori Yamamoto; Hideo Bannai; Masao Nagasaki; Satoru Miyano (Discovery Science, 2009)

Parameter Estimation of In Silico Biological Pathways with Particle Filtering Towards a Petascale Computing. - Kazuyuki Nakamura; Ryo Yoshida; Masao Nagasaki; Satoru Miyano; Tomoyuki Higuchi (Pacific Symposium on Biocomputing, 2009)

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)

The impact of measurement errors in the identification of regulatory networks. - André Fujita; Alexandre Galvão Patriota; João Ricardo Sato; Satoru Miyano (BMC Bioinform., 2009)

BFL: a node and edge betweenness based fast layout algorithm for large scale networks. - Tatsunori B. Hashimoto; Masao Nagasaki; Kaname Kojima; Satoru Miyano (BMC Bioinform., 2009)

Simulation-based model checking approach to cell fate specification during Caenorhabditis elegans vulval development by hybrid functional Petri net with extension. - Chen Li 007; Masao Nagasaki; Kazuko Ueno; Satoru Miyano (BMC Syst. Biol., 2009)

Recursive regularization for inferring gene networks from time-course gene expression profiles. - Teppei Shimamura; Seiya Imoto; Rui Yamaguchi; André Fujita; Masao Nagasaki; Satoru Miyano (BMC Syst. Biol., 2009)

Comparing Pearson, Spearman and Hoeffding's d Measure for Gene Expression Association Analysis. - André Fujita; João Ricardo Sato; Marcos Angelo Almeida Demasi; Mari Cleide Sogayar; Carlos Eduardo Ferreira; Satoru Miyano (J. Bioinform. Comput. Biol., 2009)

Network-Based Predictions and Simulations by Biological State Space Models: Search for Drug Mode of Action. - Rui Yamaguchi; Seiya Imoto; Satoru Miyano (J. Comput. Sci. Technol., 2009)

Identifying Hidden Confounders in Gene Networks by Bayesian Networks. - Tomoya Higashigaki; Kaname Kojima; Rui Yamaguchi; Masato Inoue; Seiya Imoto; Satoru Miyano (BIBE, 2010)

Discovering functional gene pathways associated with cancer heterogeneity via sparse supervised learning. - Shuichi Kawano; Teppei Shimamura; Atsushi Niida; Seiya Imoto; Rui Yamaguchi; Masao Nagasaki; Ryo Yoshida; Cristin G. Print; Satoru Miyano (BIBM, 2010)

Network profiling analysis for generating modulator-dependent gene networks. - Teppei Shimamura; Seiya Imoto; Atsushi Niida; Masao Nagasaki; Rui Yamaguchi; Satoru Miyano (BIBM Workshops, 2010)

Searching Optimal Bayesian Network Structure on Constraint Search Space: Super-Structure Approach. - Seiya Imoto; Kaname Kojima; Eric Perrier; Yoshinori Tamada; Satoru Miyano (JSAI-isAI Workshops, 2010)

Granger Causality in Systems Biology: Modeling Gene Networks in Time Series Microarray Data Using Vector Autoregressive Models. - André Fujita; Patricia Severino; João Ricardo Sato; Satoru Miyano (BSB, 2010)

A fast and robust statistical test based on likelihood ratio with Bartlett correction to identify Granger causality between gene sets. - André Fujita; Kaname Kojima; Alexandre Galvão Patriota; João Ricardo Sato; Patricia Severino; Satoru Miyano (Bioinform., 2010)

DA 1.0: parameter estimation of biological pathways using data assimilation approach. - Chuan Hock Koh; Masao Nagasaki; Ayumu Saito; Limsoon Wong; Satoru Miyano (Bioinform., 2010)

Model-free unsupervised gene set screening based on information enrichment in expression profiles. - Atsushi Niida; Seiya Imoto; Rui Yamaguchi; Masao Nagasaki; André Fujita; Teppei Shimamura; Satoru Miyano (Bioinform., 2010)

Inferring dynamic gene networks under varying conditions for transcriptomic network comparison. - Teppei Shimamura; Seiya Imoto; Rui Yamaguchi; Masao Nagasaki; Satoru Miyano (Bioinform., 2010)

The systems approach to the prespore-specific activation of sigma factor SigF in Bacillus subtilis. - Jin Hwan Do; Masao Nagasaki; Satoru Miyano (Biosyst., 2010)

An efficient biological pathway layout algorithm combining grid-layout and spring embedder for complicated cellular location information. - Kaname Kojima; Masao Nagasaki; Satoru Miyano (BMC Bioinform., 2010)

Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram. - Chen Li 007; Masao Nagasaki; Ayumu Saito; Satoru Miyano (BMC Syst. Biol., 2010)

Delay Time Determination for the Timed Petri Net Model of a Signaling Pathway Based on Its Structural Information. - Yoshimasa Miwa; Yuki Murakami; Qi-Wei Ge; Chen Li 007; Hiroshi Matsuno; Satoru Miyano (IEICE Trans. Fundam. Electron. Commun. Comput. Sci., 2010)

On Determining Firing Delay Time of Transitions for Petri Net Based Signaling Pathways by Introducing Stochastic Decision Rules. - Yoshimasa Miwa; Chen Li 007; Qi-Wei Ge; Hiroshi Matsuno; Satoru Miyano (Silico Biol., 2010)

Cell Illustrator 4.0: A Computational Platform for Systems Biology. - Masao Nagasaki; Ayumu Saito; Euna Jeong; Chen Li 007; Kaname Kojima; Emi Ikeda; Satoru Miyano (Silico Biol., 2010)

Identification of Granger Causality between Gene Sets. - André Fujita; João Ricardo Sato; Kaname Kojima; Luciana Rodrigues Gomes; Masao Nagasaki; Mari Cleide Sogayar; Satoru Miyano (J. Bioinform. Comput. Biol., 2010)

Optimal Search on Clustered Structural Constraint for Learning Bayesian Network Structure. - Kaname Kojima; Eric Perrier; Seiya Imoto; Satoru Miyano (J. Mach. Learn. Res., 2010)

Computational Drug Target Pathway Discovery: A Bayesian Network Approach. - Seiya Imoto; Yoshinori Tamada; Hiromitsu Araki; Satoru Miyano (Handbook of Statistical Bioinformatics, 2011)

Parallel Agent-Based Simulator for Influenza Pandemic. - Masaya M. Saito; Seiya Imoto; Rui Yamaguchi; Satoru Miyano; Tomoyuki Higuchi (AAMAS Workshops, 2011)

Estimation of macroscopic parameter in agent-based pandemic simulation. - Masaya M. Saito; Seiya Imoto; Rui Yamaguchi; Satoru Miyano; Tomoyuki Higuchi (FUSION, 2011)

Poster: Comprehensive pharmacogenomic pathway screening by data assimilation. - Takanori Hasegawa; Rui Yamaguchi; Masao Nagasaki; Seiya Imoto; Satoru Miyano (ICCABS, 2011)

Comprehensive Pharmacogenomic Pathway Screening by Data Assimilation. - Takanori Hasegawa; Rui Yamaguchi; Masao Nagasaki; Seiya Imoto; Satoru Miyano (ISBRA, 2011)

CSO validator: improving manual curation workflow for biological pathways. - Euna Jeong; Masao Nagasaki; Emi Ikeda; Yayoi Sekiya; Ayumu Saito; Satoru Miyano (Bioinform., 2011)

MIRACH: efficient model checker for quantitative biological pathway models. - Chuan Hock Koh; Masao Nagasaki; Ayumu Saito; Chen Li 007; Limsoon Wong; Satoru Miyano (Bioinform., 2011)

Systems biology model repository for macrophage pathway simulation. - Masao Nagasaki; Ayumu Saito; André Fujita; Georg Tremmel; Kazuko Ueno; Emi Ikeda; Euna Jeong; Satoru Miyano (Bioinform., 2011)

A rank-based statistical test for measuring synergistic effects between two gene sets. - Yuichi Shiraishi; Mariko Okada-Hatakeyama; Satoru Miyano (Bioinform., 2011)

SiGN-SSM: open source parallel software for estimating gene networks with state space models. - Yoshinori Tamada; Rui Yamaguchi; Seiya Imoto; Osamu Hirose; Ryo Yoshida; Masao Nagasaki; Satoru Miyano (Bioinform., 2011)

Ontology-based instance data validation for high-quality curated biological pathways. - Euna Jeong; Masao Nagasaki; Kazuko Ueno; Satoru Miyano (BMC Bioinform., 2011)

ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information. - Shin Suzuki; Tomohiro Yasuda; Yuichi Shiraishi; Satoru Miyano; Masao Nagasaki (BMC Bioinform., 2011)

Transform of visual analogue scale data and their clustering. - Kotoe Katayama; Rui Yamaguchi; Seiya Imoto; Keiko Matsuura; Kenji Watanabe; Satoru Miyano (Int. J. Knowl. Eng. Soft Data Paradigms, 2011)

INTRODUCTION - The First IEEE Conference on Healthcare Informatics, Imaging, and Systems biology HISB'11. - Xue-Wen Chen; Satoru Miyano (J. Bioinform. Comput. Biol., 2011)

2D-Qsar for 450 types of amino acid induction peptides with a novel substructure pair descriptor having wider scope. - Tsutomu Osoda; Satoru Miyano (J. Cheminformatics, 2011)

Parallel Algorithm for Learning Optimal Bayesian Network Structure. - Yoshinori Tamada; Seiya Imoto; Satoru Miyano (J. Mach. Learn. Res., 2011)

Hybrid Petri net based modeling for biological pathway simulation. - Hiroshi Matsuno; Masao Nagasaki; Satoru Miyano (Nat. Comput., 2011)

Clustering for Visual Analogue Scale Data in Symbolic Data Analysis. - Kotoe Katayama; Rui Yamaguchi; Seiya Imoto; Keiko Matsuura; Kenji Watanabe; Satoru Miyano (Complex Adaptive Systems, 2011)

High Performance Hybrid Functional Petri Net Simulations of Biological Pathway Models on CUDA. - Georgios Chalkidis; Masao Nagasaki; Satoru Miyano (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

Inferring Contagion in Regulatory Networks. - André Fujita; João Ricardo Sato; Marcos Angelo Almeida Demasi; Rui Yamaguchi; Teppei Shimamura; Carlos Eduardo Ferreira; Mari Cleide Sogayar; Satoru Miyano (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

Estimating Genome-Wide Gene Networks Using Nonparametric Bayesian Network Models on Massively Parallel Computers. - Yoshinori Tamada; Seiya Imoto; Hiromitsu Araki; Masao Nagasaki; Cristin G. Print; Stephen D. Charnock-Jones; Satoru Miyano (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

Analysis of questionnaire for traditional medical and develop decision support system. - Kotoe Katayama; Seiya Imoto; Kenji Watanabe; Rui Yamaguchi; Keiko Matsuura; Satoru Miyano (BIBM Workshops, 2012)

Identifiability of local transmissibility parameters in agent-based pandemic simulation. - Masaya M. Saito; Seiya Imoto; Rui Yamaguchi; Satoru Miyano; Tomoyuki Higuchi (FUSION, 2012)

IRView: a database and viewer for protein interacting regions. - Shigeo Fujimori; Naoya Hirai; Kazuyo Masuoka; Tomohiro Oshikubo; Tatsuhiro Yamashita; Takanori Washio; Ayumu Saito; Masao Nagasaki; Satoru Miyano; Etsuko Miyamoto-Sato (Bioinform., 2012)

Statistical model-based testing to evaluate the recurrence of genomic aberrations. - Atsushi Niida; Seiya Imoto; Teppei Shimamura; Satoru Miyano (Bioinform., 2012)

ChopSticks: High-resolution analysis of homozygous deletions by exploiting concordant read pairs. - Tomohiro Yasuda; Shin Suzuki; Masao Nagasaki; Satoru Miyano (BMC Bioinform., 2012)

Identifying regulational alterations in gene regulatory networks by state space representation of vector autoregressive models and variational annealing. - Kaname Kojima; Seiya Imoto; Rui Yamaguchi; André Fujita; Mai Yamauchi; Noriko Gotoh; Satoru Miyano (BMC Genom., 2012)

Functional clustering of time series gene expression data by Granger causality. - André Fujita; Patricia Severino; Kaname Kojima; João Ricardo Sato; Alexandre Galvão Patriota; Satoru Miyano (BMC Syst. Biol., 2012)

Computational gene network analysis reveals TNF-induced angiogenesis. - Kentaro Ogami; Rui Yamaguchi; Seiya Imoto; Yoshinori Tamada; Hiromitsu Araki; Cristin G. Print; Satoru Miyano (BMC Syst. Biol., 2012)

A between-Class Overlapping Filter-Based Method for transcriptome Data Analysis. - Alok Sharma; Seiya Imoto; Satoru Miyano (J. Bioinform. Comput. Biol., 2012)

Null space based feature selection method for gene expression data. - Alok Sharma; Seiya Imoto; Satoru Miyano; Vandana Sharma (Int. J. Mach. Learn. Cybern., 2012)

Identifying Gene Pathways Associated with Cancer Characteristics via Sparse Statistical Methods. - Shuichi Kawano; Teppei Shimamura; Atsushi Niida; Seiya Imoto; Rui Yamaguchi; Masao Nagasaki; Ryo Yoshida; Cristin G. Print; Satoru Miyano (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

A Top-r Feature Selection Algorithm for Microarray Gene Expression Data. - Alok Sharma; Seiya Imoto; Satoru Miyano (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Estimation of abrupt changes in sentinel observation data of influenza epidemics in Japan. - Masaya M. Saito; Seiya Imoto; Rui Yamaguchi; Satoru Miyano; Tomoyuki Higuchi (FUSION, 2013)

Multilayer Cluster Heat Map Visualizing Biological Tensor Data. - Atsushi Niida; Georg Tremmel; Seiya Imoto; Satoru Miyano (BSB, 2013)

XiP: a computational environment to create, extend and share workflows. - Masao Nagasaki; André Fujita; Yayoi Sekiya; Ayumu Saito; Emi Ikeda; Chen Li 007; Satoru Miyano (Bioinform., 2013)

A strategy to select suitable physicochemical attributes of amino acids for protein fold recognition. - Alok Sharma; Kuldip K. Paliwal; Abdollah Dehzangi; James G. Lyons; Seiya Imoto; Satoru Miyano (BMC Bioinform., 2013)

Multi-omics Approach for Estimating Metabolic Networks Using Low-Order Partial Correlations. - Mitsunori Kayano; Seiya Imoto; Rui Yamaguchi; Satoru Miyano (J. Comput. Biol., 2013)

Principal component analysis using QR decomposition. - Alok Sharma; Kuldip K. Paliwal; Seiya Imoto; Satoru Miyano (Int. J. Mach. Learn. Cybern., 2013)

Parameter estimation in multi-compartment SIR model. - Masaya M. Saito; Seiya Imoto; Rui Yamaguchi; Satoru Miyano; Tomoyuki Higuchi (FUSION, 2014)

HapMuC: somatic mutation calling using heterozygous germ line variants near candidate mutations. - Naoto Usuyama; Yuichi Shiraishi; Yusuke Sato; Haruki Kume; Yukio Homma; Seishi Ogawa; Satoru Miyano; Seiya Imoto (Bioinform., 2014)

CSML2SBML: A novel tool for converting quantitative biological pathway models from CSML into SBML. - Chen Li 007; Masao Nagasaki; Emi Ikeda; Yayoi Sekiya; Satoru Miyano (Biosyst., 2014)

An efficient method of exploring simulation models by assimilating literature and biological observational data. - Takanori Hasegawa; Masao Nagasaki; Rui Yamaguchi; Seiya Imoto; Satoru Miyano (Biosyst., 2014)

An Efficient Data Assimilation Schema for Restoration and Extension of Gene Regulatory Networks Using Time-Course Observation Data. - Takanori Hasegawa; Tomoya Mori; Rui Yamaguchi; Seiya Imoto; Satoru Miyano; Tatsuya Akutsu (J. Comput. Biol., 2014)

A feature selection method using fixed-point algorithm for DNA microarray gene expression data. - Alok Sharma; Kuldip K. Paliwal; Seiya Imoto; Satoru Miyano; Vandana Sharma; Rajeshkannan Ananthanarayanan (Int. J. Knowl. Based Intell. Eng. Syst., 2014)

A feature selection method using improved regularized linear discriminant analysis. - Alok Sharma; Kuldip K. Paliwal; Seiya Imoto; Satoru Miyano (Mach. Vis. Appl., 2014)

High performance computing of a fusion gene detection pipeline on the K computer. - Satoshi Ito; Yuichi Shiraishi; Teppei Shimamura; Kenichi Chiba; Satoru Miyano (BIBM, 2015)

Binary Contingency Table Method for Analyzing Gene Mutation in Cancer Genome. - Emi Ayada; Atsushi Niida; Takanori Hasegawa; Satoru Miyano; Seiya Imoto (ISBRA, 2015)

Genomon ITDetector: a tool for somatic internal tandem duplication detection from cancer genome sequencing data. - Kenichi Chiba; Yuichi Shiraishi; Yasunobu Nagata; Kenichi Yoshida; Seiya Imoto; Seishi Ogawa; Satoru Miyano (Bioinform., 2015)

Inferring the global structure of chromosomes from structural variations. - Tomohiro Yasuda; Satoru Miyano (BMC Genom., 2015)

Genomic data assimilation using a higher moment filtering technique for restoration of gene regulatory networks. - Takanori Hasegawa; Tomoya Mori; Rui Yamaguchi; Teppei Shimamura; Satoru Miyano; Seiya Imoto; Tatsuya Akutsu (BMC Syst. Biol., 2015)

Sparse Overlapping Group Lasso for Integrative Multi-Omics Analysis. - Heewon Park; Atsushi Niida; Satoru Miyano; Seiya Imoto (J. Comput. Biol., 2015)

OVarCall: Bayesian Mutation Calling Method Utilizing Overlapping Paired-End Reads. - Takuya Moriyama; Yuichi Shiraishi; Kenichi Chiba; Rui Yamaguchi; Seiya Imoto; Satoru Miyano (ISBRA, 2016)

D3M: detection of differential distributions of methylation levels. - Yusuke Matsui; Masahiro Mizuta; Satoshi Ito; Satoru Miyano; Teppei Shimamura (Bioinform., 2016)

A likelihood-free filtering method via approximate Bayesian computation in evaluating biological simulation models. - Takanori Hasegawa; Atsushi Niida; Tomoya Mori; Teppei Shimamura; Rui Yamaguchi; Satoru Miyano; Tatsuya Akutsu; Seiya Imoto (Comput. Stat. Data Anal., 2016)

Binary contingency table method for analysing gene mutation in cancer genome. - Emi Ayada; Takanori Hasegawa; Atsushi Niida; Satoru Miyano; Seiya Imoto (Int. J. Bioinform. Res. Appl., 2016)

Predicting Japanese Kampo formulas by analyzing database of medical records: a preliminary observational study. - Tetsuhiro Yoshino; Kotoe Katayama; Yuko Horiba; Kaori Munakata; Rui Yamaguchi; Seiya Imoto; Satoru Miyano; Hideki Mima; Kenji Watanabe (BMC Medical Informatics Decis. Mak., 2016)

A Case Study of HFPN Simulation: Finding Essential Roles of Ror Gene in the Interaction of Feedback Loops in Mammalian Circadian Clock. - Natsumi Mitou; Hiroshi Matsuno; Satoru Miyano; Shin-Ichi T. Inouye (Modeling in Systems Biology, The Petri Net Approach, 2016)

Hybrid Functional Petri Net with Extension for Dynamic Pathway Modeling. - Ayumu Saito; Masao Nagasaki; Hiroshi Matsuno; Satoru Miyano (Modeling in Systems Biology, The Petri Net Approach, 2016)

Reconstruction of high read-depth signals from low-depth whole genome sequencing data using deep learning. - Yao-Zhong Zhang; Seiya Imoto; Satoru Miyano; Rui Yamaguchi (BIBM, 2017)

Tumor Subclonal Progression Model for Cancer Hallmark Acquisition. - Yusuke Matsui; Satoru Miyano; Teppei Shimamura (CIBB, 2017)

GIMLET: Identifying Biological Modulators in Context-Specific Gene Regulation Using Local Energy Statistics. - Teppei Shimamura; Yusuke Matsui; Taisuke Kajino; Satoshi Ito; Takashi Takahashi; Satoru Miyano (CIBB, 2017)

Interaction-Based Feature Selection for Uncovering Cancer Driver Genes Through Copy Number-Driven Expression Level. - Heewon Park; Atsushi Niida; Seiya Imoto; Satoru Miyano (J. Comput. Biol., 2017)

A framework for generating interactive reports for cancer genome analysis. - Ai Okada; Kenichi Chiba; Hiroko Tanaka; Satoru Miyano; Yuichi Shiraishi (J. Open Source Softw., 2017)

phyC: Clustering cancer evolutionary trees. - Yusuke Matsui; Atsushi Niida; Ryutaro Uchi; Koshi Mimori; Satoru Miyano; Teppei Shimamura (PLoS Comput. Biol., 2017)

A Novel Adaptive Penalized Logistic Regression for Uncovering Biomarker Associated with Anti-Cancer Drug Sensitivity. - Heewon Park; Yuichi Shiraishi; Seiya Imoto; Satoru Miyano (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

Virtual Grid Engine: Accelerating thousands of omics sample analyses using large-scale supercomputers. - Satoshi Ito; Masaaki Yadome; Tatsuo Nishiki; Shigeru Ishiduki; Hikaru Inoue; Rui Yamaguchi; Satoru Miyano (BIBM, 2018)

Adaptive NetworkProfiler for Identifying Cancer Characteristic-Specific Gene Regulatory Networks. - Heewon Park; Teppei Shimamura; Seiya Imoto; Satoru Miyano (J. Comput. Biol., 2018)

Accurate and Flexible Bayesian Mutation Call from Multi-regional Tumor Samples. - Takuya Moriyama; Seiya Imoto; Satoru Miyano; Rui Yamaguchi (ISMCO, 2019)

A Bayesian model integration for mutation calling through data partitioning. - Takuya Moriyama; Seiya Imoto; Shuto Hayashi; Yuichi Shiraishi; Satoru Miyano; Rui Yamaguchi (Bioinform., 2019)

Virtual Grid Engine: a simulated grid engine environment for large-scale supercomputers. - Satoshi Ito; Masaaki Yadome; Tatsuo Nishiki; Shigeru Ishiduki; Hikaru Inoue; Rui Yamaguchi; Satoru Miyano (BMC Bioinform., 2019)

ALPHLARD-NT: Bayesian Method for Human Leukocyte Antigen Genotyping and Mutation Calling through Simultaneous Analysis of Normal and Tumor Whole-Genome Sequence Data. - Shuto Hayashi; Takuya Moriyama; Rui Yamaguchi; Shinichi Mizuno; Mitsuhiro Komura; Satoru Miyano; Hidewaki Nakagawa; Seiya Imoto (J. Comput. Biol., 2019)

Robust Sample-Specific Stability Selection with Effective Error Control. - Heewon Park; Makoto Yamada; Seiya Imoto; Satoru Miyano (J. Comput. Biol., 2019)

Theoretical Foundation of the Performance of Phylogeny-Based Somatic Variant Detection. - Takuya Moriyama; Seiya Imoto; Satoru Miyano; Rui Yamaguchi (ISMCO, 2020)

Neoantimon: a multifunctional R package for identification of tumor-specific neoantigens. - Takanori Hasegawa; Shuto Hayashi; Eigo Shimizu; Shinichi Mizuno; Atsushi Niida; Rui Yamaguchi; Satoru Miyano; Hidewaki Nakagawa; Seiya Imoto (Bioinform., 2020)

Linear Tensor Projection Revealing Nonlinearity. - Koji Maruhashi; Heewon Park; Rui Yamaguchi; Satoru Miyano (CoRR, 2020)

Ensemble smoothers for inference of hidden states and parameters in combinatorial regulatory model. - Takanori Hasegawa; Rui Yamaguchi; Atsushi Niida; Satoru Miyano; Seiya Imoto (J. Frankl. Inst., 2020)

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. - Esther Rheinbay; Morten Muhlig Nielsen; Federico Abascal; Jeremiah Wala; Ofer Shapira; Grace Tiao; Henrik Hornshøj; Julian M. Hess; Randi Istrup Juul; Ziao Lin; Lars Feuerbach; Radhakrishnan Sabarinathan; et al. (Nat., 2020)

Nanopore basecalling from a perspective of instance segmentation. - Yao-zhong Zhang; Arda Akdemir; Georg Tremmel; Seiya Imoto; Satoru Miyano; Tetsuo Shibuya; Rui Yamaguchi (BMC Bioinform., 2020)

On the application of BERT models for nanopore methylation detection. - Yao-Zhong Zhang; Kiyoshi Yamaguchi; Sera Hatakeyama; Yoichi Furukawa; Satoru Miyano; Rui Yamaguchi; Seiya Imoto (BIBM, 2021)

High-speed parameter search of dynamic biological pathways from time-course transcriptomic profiles using high-level Petri net. - Chen Li 007; Jiale Qin; Keisuke Kuroyanagi; Lu Lu; Masao Nagasaki; Satoru Miyano (Biosyst., 2021)

Enhancing breakpoint resolution with deep segmentation model: A general refinement method for read-depth based structural variant callers. - Yao-Zhong Zhang; Seiya Imoto; Satoru Miyano; Rui Yamaguchi (PLoS Comput. Biol., 2021)

Identification of bacteriophage genome sequences with representation learning. - Zeheng Bai; Yao-zhong Zhang; Satoru Miyano; Rui Yamaguchi; Kosuke Fujimoto; Satoshi Uematsu; Seiya Imoto (Bioinform., 2022)

RoDiCE: robust differential protein co-expression analysis for cancer complexome. - Yusuke Matsui; Yuichi Abe; Kohei Uno; Satoru Miyano (Bioinform., 2022)

PredictiveNetwork: predictive gene network estimation with application to gastric cancer drug response-predictive network analysis. - Heewon Park; Seiya Imoto; Satoru Miyano (BMC Bioinform., 2022)

Uncovering Molecular Mechanisms of Drug Resistance via Network-Constrained Common Structure Identification. - Heewon Park; Rui Yamaguchi; Seiya Imoto; Satoru Miyano (J. Comput. Biol., 2022)

Acceleration of BAM I/O on distributed file systems. - Satoshi Ito; Satoru Miyano; Kenji Ono (BIBM, 2023)

Gene Regulatory Network-Classifier: Gene Regulatory Network-Based Classifier and Its Applications to Gastric Cancer Drug (5-Fluorouracil) Marker Identification. - Heewon Park; Seiya Imoto; Satoru Miyano (J. Comput. Biol., 2023)

Large-scaleWGS Analysis on the supercomputer Fugaku. - Satoshi Ito; Kenji Ono; Satoru Miyano (ICBBB, 2024)

Network-Constrained Eigen-Single-Cell Profile Estimation for Uncovering Crucial Immunogene Regulatory Systems in Human Bone Marrow. - Heewon Park; Satoru Miyano (J. Comput. Biol., 2024)