Satoru Miyano

Masao Nagasaki, Satoru Miyano, Seiya Imoto, 2011, 2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences (ICCABS).

Dynamic Bayesian Network and Nonparametric Regression for Nonlinear Modeling of Gene Networks from Time Series Gene Expression Data

Satoru Miyano, Seiya Imoto, SunYong Kim, 2003, CMSB.

The C Clustering Library

Satoru Miyano, Michiel J. L. de Hoon, Seiya Imoto, 2005 .

HAKKE: Automatic Predictor Generator for Sequences

Ayumi Shinohara, Satoru Miyano, Takayoshi Shoudai, 1995 .

A PAC-Learning Algorithm for Conformation Rules and its Experiments

Satoru Miyano, Satoru Kuhara, Emiko Furuichi, 1996 .

CSML2SBML: A novel tool for converting quantitative biological pathway models from CSML into SBML

Masao Nagasaki, Satoru Miyano, Chen Li, 2014, Biosyst..

Toward Genomic Hypothesis Creator: View Designer for Discovery

Satoru Miyano, Takayoshi Shoudai, Tomoyuki Uchida, 1998, Discovery Science.

More About Learning Elementary Formal Systems

Satoru Miyano, Setsuo Arikawa, Takeshi Shinohara, 1991, Nonmonotonic and Inductive Logic.

Finding alphabet indexing for decision trees over regular patterns: an approach to bioinformatical knowledge acquisition

Ayumi Shinohara, Satoru Miyano, Setsuo Arikawa, 1993, [1993] Proceedings of the Twenty-sixth Hawaii International Conference on System Sciences.

Parameter estimation in multi-compartment SIR model

Satoru Miyano, Tomoyuki Higuchi, Seiya Imoto, 2014, 17th International Conference on Information Fusion (FUSION).

A Simple Greedy Algorithm for Finding Functional Relations: Efficient Implementation and Average Case Anaylsis

Satoru Miyano, Tatsuya Akutsu, Satoru Kuhara, 2000, Discovery Science.

A Structure Learning Algorithm for Inference of Gene Networks from Microarray Gene Expression Data Using Bayesian Networks

Satoru Miyano, Seiya Imoto, Kazuyuki Numata, 2007, 2007 IEEE 7th International Symposium on BioInformatics and BioEngineering.

Strategy of finding optimal number of features on gene expression data

Satoru Miyano, Alokanand Sharma, Chuan Hock Koh, 2011 .

Combining Microarrays and Biological Knowledge for Estimating Gene Networks via Bayesian Networks

Satoru Miyano, Tomoyuki Higuchi, Satoru Kuhara, 2004, J. Bioinform. Comput. Biol..

Adaptive NetworkProfiler for Identifying Cancer Characteristic-Specific Gene Regulatory Networks

Satoru Miyano, Teppei Shimamura, Heewon Park, 2018, J. Comput. Biol..

Finding Sparse Gene Networks

Ayumi Shinohara, Satoru Miyano, Masayuki Takeda, 2000 .

Cell Illustrator 4.0: A Computational Platform for Systems Biology

Masao Nagasaki, Satoru Miyano, Chen Li, 2010, Silico Biol..

Superiority of network motifs over optimal networks and an application to the revelation of gene network evolution

Satoru Miyano, Sascha Ott, SunYong Kim, 2005, Bioinform..

Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models

Satoru Miyano, Tomoyuki Higuchi, Rui Yamaguchi, 2008, Bioinform..

High Performance Hybrid Functional Petri Net Simulations of Biological Pathway Models on CUDA

Masao Nagasaki, Satoru Miyano, Georgios Chalkidis, 2011, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Development of Genomic Object Net Builder for Supporting XML Design for Visualization

Hironori Kitakaze, Hiroshi Matsuno, Satoru Miyano, 2002 .

Nanopore basecalling from a perspective of instance segmentation

Satoru Miyano, Tetsuo Shibuya, Rui Yamaguchi, 2019, BMC Bioinformatics.

A feature selection method using fixed-point algorithm for DNA microarray gene expression data

Kuldip K. Paliwal, Satoru Miyano, Alok Sharma, 2014, Int. J. Knowl. Based Intell. Eng. Syst..

A between-Class Overlapping Filter-Based Method for transcriptome Data Analysis

Satoru Miyano, Alok Sharma, Seiya Imoto, 2012, J. Bioinform. Comput. Biol..

Dynamic Bayesian network and nonparametric regression for nonlinear modeling of gene networks from time series gene expression data.

Satoru Miyano, Seiya Imoto, Sun Yong Kim, 2004 .

Accurate and Flexible Bayesian Mutation Call from Multi-regional Tumor Samples

Satoru Miyano, Takuya Moriyama, Rui Yamaguchi, 2019, ISMCO.

Analyzing Time Course Gene Expression Data with Biological and Technical Replicates to Estimate Gene Networks by State Space Models

Satoru Miyano, Tomoyuki Higuchi, Seiya Imoto, 2008, 2008 Second Asia International Conference on Modelling & Simulation (AMS).

A List of P-Complete Problems

Satoru Miyano, Shuji Shiraishi, Takayoshi Shoudai, 1989 .

An efficient biological pathway layout algorithm combining grid-layout and spring embedder for complicated cellular location information

Masao Nagasaki, Satoru Miyano, Kaname Kojima, 2010, BMC Bioinformatics.

Experiments by BONSAI Garden

Satoru Miyano, Takayoshi Shoudai, Naohiro Furukawa, 1995 .

Proceedings of the 6th Asia-Pacific Bioinformatics Conference, APBC 2008, 14-17 January 2008, Kyoto, Japan

Satoru Miyano, Tatsuya Akutsu, Alvis Brazma, 2008, APBC.

Online model checking approach based parameter estimation to a neuronal fate decision simulation model in Caenorhabditis elegans with hybrid functional Petri net with extension.

Masao Nagasaki, Satoru Miyano, Chen Li, 2011, Molecular bioSystems.

PREDICTING DIFFERENCES IN GENE REGULATORY SYSTEMS BY STATE SPACE MODELS

Masao Nagasaki, Satoru Miyano, Teppei Shimamura, 2008 .

Delay Time Estimation for Petri Net Models of Signaling Pathways Based on Experimental Data

Hiroshi Matsuno, Satoru Miyano, Yoshimasa Miwa, 2008 .

Preface

Satoru Miyano, Tatsuya Akutsu, Alvis Brazma, 2008, APBC.

O(log*n) Time Parallel Algorithm for Computing Bounded Degree Maximal Subgraphs

Satoru Miyano, Tomoyuki Uchida, S. Miyano, 1991 .

A strategy to select suitable physicochemical attributes of amino acids for protein fold recognition

Kuldip K. Paliwal, Satoru Miyano, James G. Lyons, 2013, BMC Bioinformatics.

ViewDesigner: A Tool for Designing Viewscopes in Discovery System HypothesisCreator

Satoru Miyano, Satoshi Matsumoto, Osamu Maruyama, 1999 .

Estimation of Genetic Networks and Functional Structures Between Genes by Using Bayesian Networks and Nonparametric Regression

Satoru Miyano, Seiya Imoto, Takao Goto, 2001, Pacific Symposium on Biocomputing.

Enhancing breakpoint resolution with deep segmentation model: A general refinement method for read-depth based structural variant callers

Satoru Miyano, Seiya Imoto, Rui Yamaguchi, 2019, bioRxiv.

XML Pathway File Conversion between Genomic Object Net and SBML

Hironori Kitakaze, Hiroshi Matsuno, Satoru Miyano, 2002 .

Functional Data Analysis of the Dynamics of Gene Regulatory Networks

Satoru Miyano, Seiya Imoto, Tomohiro Ando, 2004, KELSI.

CSO validator: improving manual curation workflow for biological pathways

Masao Nagasaki, Satoru Miyano, Ayumu Saito, 2011, Bioinform..

On the Complexity of Deriving Position Specific Score Matrices from Examples

Satoru Miyano, Tatsuya Akutsu, Hideo Bannai, 2002, CPM.

Bayesian learning of biological pathways on genomic data assimilation

Masao Nagasaki, Satoru Miyano, Tomoyuki Higuchi, 2008, Bioinform..

Gene set differential analysis of time course expression profiles via sparse estimation in functional logistic model with application to time-dependent biomarker detection.

Satoru Miyano, Seiya Imoto, Rui Yamaguchi, 2016, Biostatistics.

Estimating Genome-Wide Gene Networks Using Nonparametric Bayesian Network Models on Massively Parallel Computers

Masao Nagasaki, Satoru Miyano, Seiya Imoto, 2011, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

On Determining Firing Delay Time of Transitions for Petri Net Based Signaling Pathways by Introducing Stochastic Decision Rules

Hiroshi Matsuno, Satoru Miyano, Yoshimasa Miwa, 2010, Silico Biol..

Inferring Gene Regulatory Networks from Time-Ordered Gene Expression Data of Bacillus Subtilis Using Differential Equations

Satoru Miyano, Seiya Imoto, Michiel J. L. de Hoon, 2002, Pacific Symposium on Biocomputing.

Combining Gene Expression Data with DNA Sequence Information for Estimating Gene Networks Using Bayesian Network Model

Sun Yong Kim, Satoru Miyano, Hideo Bannai, 2003 .

Modeling and Simulation of Fission Yeast Cell Cycle on Hybrid Functional Petri Net

Hiroshi Matsuno, Satoru Miyano, Mika Matsui, 2004 .

Inference, Modeling and Simulation of Gene Networks

Satoru Miyano, 2003, CMSB.

The Lexicographically First Maximal Subgraph Problems: P-Completeness and NC Algorithms

Satoru Miyano, S. Miyano, 1987, International Colloquium on Automata, Languages and Programming.

Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram

Masao Nagasaki, Satoru Miyano, Chen Li, 2010, BMC Systems Biology.

A filter based feature selection algorithm using null space of covariance matrix for DNA microarray gene expression data

Satoru Miyano, Alok Sharma, Seiya Imoto, 2012 .

Interaction-Based Feature Selection for Uncovering Cancer Driver Genes Through Copy Number-Driven Expression Level

Satoru Miyano, Heewon Park, Atsushi Niida, 2017, J. Comput. Biol..

Recreating Biopathway Databases towards Simulation

Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno, 2003, CMSB.

Identification of genetic networks by strategic gene disruptions and gene overexpressions under a boolean model

Satoru Miyano, Tatsuya Akutsu, Satoru Kuhara, 2003, Theor. Comput. Sci..

INTRODUCTION - The First IEEE Conference on Healthcare Informatics, Imaging, and Systems biology HISB'11

Satoru Miyano, Xue-Wen Chen, 2011, J. Bioinform. Comput. Biol..

Knowledge Acquisition from Amino Acid Sequences by Decision Trees and Indexing

Ayumi Shinohara, Satoru Miyano, Setsuo Arikawa, 1992 .

Machine Learning and Discovery for Bloinformatics: Introduction

Ayumi Shinohara, Satoru Miyano, S. Miyano, 1994, HICSS.

Genetic algorithm for an optimized weighted voting scheme incorporating k-separated bigram transition probabilities to improve protein fold recognition

Kuldip K. Paliwal, Satoru Miyano, Abdollah Dehzangi, 2014, Asia-Pacific World Congress on Computer Science and Engineering.

Conversion from BioPAX to CSO for system dynamics and visualization of biological pathway.

Masao Nagasaki, Satoru Miyano, Euna Jeong, 2007, Genome informatics. International Conference on Genome Informatics.

Genomic Object Net: XML Visualization of Simulation Results from Biological Modeling on Hybrid Functional Petri Net

Atsushi Doi, Hiroshi Matsuno, Satoru Miyano, 2001 .

Residual Bootstrapping and Median Filtering for Robust Estimation of Gene Networks from Microarray Data

Satoru Miyano, Tomoyuki Higuchi, Seiya Imoto, 2004, CMSB.

A likelihood-free filtering method via approximate Bayesian computation in evaluating biological simulation models

Satoru Miyano, Tatsuya Akutsu, Teppei Shimamura, 2016, Comput. Stat. Data Anal..

Mining Binary Diagram Rules

Satoru Miyano, Takayoshi Shoudai, Osamu Maruyama, 1996 .

Computational Modeling of Biological Processes with Petri Net-Based Architecture

Masao Nagasaki, Hiroshi Matsuno, Satoru Miyano, 2005 .

Bootstrap Analysis of Gene Networks Based on Bayesian Networks and Nonparametric Regression

Sun Yong Kim, Satoru Miyano, Satoru Kuhara, 2002 .

Bayesian Network and Nonparametric Heteroscedastic Regression for Nonlinear Modeling of Genetic Network

Satoru Miyano, Satoru Kuhara, Seiya Imoto, 2003, J. Bioinform. Comput. Biol..

Comprehensive Pharmacogenomic Pathway Screening by Data Assimilation

Masao Nagasaki, Satoru Miyano, Seiya Imoto, 2011, ISBRA.

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

Jun Yu, Chen Hong, Ken Chen, 2020, Nature.

Parallel Complexity and P-Complete Problems

Satoru Miyano, 1988, FGCS.

HAKKE: A Multi-Strategy Prediction System for Sequences

Satoru Miyano, Satoshi Matsumoto, Naohiro Furukawa, 1996 .

Constructing biological pathway models with hybrid functional petri nets.

Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno, 2011, Studies in health technology and informatics.

Recursive regularization for inferring gene networks from time-course gene expression profiles

Masao Nagasaki, Satoru Miyano, Teppei Shimamura, 2009, BMC Systems Biology.

Linear Tensor Projection Revealing Nonlinearity pdf

Satoru Miyano, Rui Yamaguchi, Koji Maruhashi, 2020, ArXiv.

A state space representation of VAR models with sparse learning for dynamic gene networks.

Masao Nagasaki, Satoru Miyano, Teppei Shimamura, 2010, Genome informatics. International Conference on Genome Informatics.

Protein Dynamics Observations of Lambda Phage by Hybrid Petri Net

Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno, 1999 .

Hybrid Functional Petri Net with Extension for Dynamic Pathway Modeling

Masao Nagasaki, Hiroshi Matsuno, Satoru Miyano, 2016, Modeling in Systems Biology, The Petri Net Approach.

A Weighted Profile Based Method for Protein-RNA Interacting Residue Prediction

Satoru Miyano, Euna Jeong, S. Miyano, 2006, Trans. Comp. Sys. Biology.

Simulated Cell Division Processes of the Xenopus Cell Cycle Pathway by Genomic Object Net

Hiroshi Matsuno, Satoru Miyano, Mika Matsui, 2004, J. Integr. Bioinform..

GIMLET: Identifying Biological Modulators in Context-Specific Gene Regulation Using Local Energy Statistics

Satoru Miyano, Yusuke Matsui, Satoshi Ito, 2017, CIBB.

Estimation of abrupt changes in sentinel observation data of influenza epidemics in Japan

Satoru Miyano, Tomoyuki Higuchi, Seiya Imoto, 2013, Proceedings of the 16th International Conference on Information Fusion.

HapMuC: somatic mutation calling using heterozygous germ line variants near candidate mutations

Yusuke Sato, Satoru Miyano, Yuichi Shiraishi, 2014, Bioinform..

Inferring the global structure of chromosomes from structural variations

Satoru Miyano, Tomohiro Yasuda, Tomohiro Yasuda, 2015, BMC Genomics.

An Approximation Algorithm for the Minimum Common Supertree Problem

Satoru Miyano, Koji Nakano, Atsuko Yamaguchi, 1997, Nord. J. Comput..

Introduction to bioinformatics. 6. For knowledge discovery from the biological information data.

Satoru Miyano, S. Miyano, 1998 .

Estimating Gene Networks from Expression Data and Binding Location Data via Boolean Networks

Satoru Miyano, Hideo Bannai, Seiya Imoto, 2005, ICCSA.

Robust Sample-Specific Stability Selection with Effective Error Control

Satoru Miyano, Makoto Yamada, Heewon Park, 2019, J. Comput. Biol..

Combining microarrays and biological knowledge for estimating gene networks via Bayesian networks

Satoru Miyano, Tomoyuki Higuchi, Satoru Kuhara, 2003, Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003.

Identifying Gene Pathways Associated with Cancer Characteristics via Sparse Statistical Methods

Masao Nagasaki, Satoru Miyano, Teppei Shimamura, 2012, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Genomic Object Net in JAVA: A Platform for Biopathway Modeling and Simulation

Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno, 2002 .

Collocation-based sparse estimation for constructing dynamic gene networks.

Masao Nagasaki, Satoru Miyano, André Fujita, 2010, Genome informatics. International Conference on Genome Informatics.

Foreword: Genome Informatics

Satoru Miyano, S. Miyano, 1999, Theor. Comput. Sci..

Functional clustering of time series gene expression data by Granger causality

João Ricardo Sato, Satoru Miyano, Alexandre Galvão Patriota, 2012, BMC Systems Biology.

Inferring a Tree from Walks

Satoru Miyano, Osamu Maruyama, 1996, Theor. Comput. Sci..

A Novel Adaptive Penalized Logistic Regression for Uncovering Biomarker Associated with Anti-Cancer Drug Sensitivity

Satoru Miyano, Yuichi Shiraishi, Heewon Park, 2017, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Binary Contingency Table Method for Analyzing Gene Mutation in Cancer Genome

Satoru Miyano, Atsushi Niida, Seiya Imoto, 2015, ISBRA.

Genomic data assimilation for estimating hybrid functional Petri net from time-course gene expression data.

Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno, 2006, Genome informatics. International Conference on Genome Informatics.

SIGMA: A Text Database Management System

Akihiro Yamamoto, Makoto Haraguchi, Satoru Miyano, 1988 .

A new regulatory interaction suggested by simulations for circadian genetic control mechanism in mammals

Hiroshi Matsuno, Satoru Miyano, Shin-Ichi T. Inouye, 2006, APBC.

OVarCall: Bayesian Mutation Calling Method Utilizing Overlapping Paired-End Reads

Satoru Miyano, Yuichi Shiraishi, Seiya Imoto, 2016, IEEE Transactions on NanoBioscience.

Bayesian Joint Prediction of Associated Transcription Factors in Bacillus subtilis

Satoru Miyano, Kenta Nakai, Yuko Makita, 2005, Pacific Symposium on Biocomputing.

Views: Fundamental Building Blocks in the Process of Knowledge Discovery

Satoru Miyano, Kenta Nakai, Hideo Bannai, 2001, FLAIRS.

Finding Optimal Pairs of Cooperative and Competing Patterns with Bounded Distance

Ayumi Shinohara, Satoru Miyano, Kenta Nakai, 2004, Discovery Science.

Systematized approaches to complexity of subgraph problems

Satoru Miyano, S. Miyano, 1990 .

Butler enables rapid cloud-based analysis of thousands of human genomes

Robert L. Grossman, Oliver Hofmann, Roland Eils, 2020, Nature Biotechnology.

Preface: Special RECOMB 2005 Issue

Satoru Miyano, S. Miyano, 2006, J. Comput. Biol..

Network-Based Predictions and Simulations by Biological State Space Models: Search for Drug Mode of Action

Satoru Miyano, Seiya Imoto, Rui Yamaguchi, 2010, Journal of Computer Science and Technology.

Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection

Satoru Miyano, Hideo Bannai, Satoru Kuhara, 2003, ECCB.

Genomic Object Net: I. A platform for modelling and simulating biopathways.

Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno, 2003, Applied bioinformatics.

Sensitivity analysis of agent-based simulation utilizing massively parallel computation and interactive data visualization

Satoru Miyano, Atsushi Niida, Takanori Hasegawa, 2019, bioRxiv.

Identifying regulational alterations in gene regulatory networks by state space representation of vector autoregressive models and variational annealing

Satoru Miyano, Seiya Imoto, Rui Yamaguchi, 2012, BMC Genomics.

Sign: large-scale gene network estimation environment for high performance computing.

Masao Nagasaki, Satoru Miyano, Teppei Shimamura, 2011, Genome informatics. International Conference on Genome Informatics.

A tutorial to identify nonlinear associations in gene expression time series data.

Satoru Miyano, André Fujita, S. Miyano, 2014, Methods in molecular biology.

Algorithms and Computation : 7th International Symposium, ISAAC '96 Osaka, Japan, December 16-18, 1996 Proceedings

Hiroshi Nagamochi, Satoru Miyano, Subhash Suri, 1996 .

Multivariate gene expression analysis reveals functional connectivity changes between normal/tumoral prostates

Carlos E. Thomaz, João Ricardo Sato, Satoru Miyano, 2008, BMC Systems Biology.

Simulated Cell Division Processes of the Xenopus Cell Cycle Pathway by Genomic Object Net

Hiroshi Matsuno, Satoru Miyano, Mika Matsui, 2004, J. Integr. Bioinform..

Binary contingency table method for analysing gene mutation in cancer genome

Satoru Miyano, Atsushi Niida, Seiya Imoto, 2016, Int. J. Bioinform. Res. Appl..

Weighted lasso in graphical Gaussian modeling for large gene network estimation based on microarray data.

Satoru Miyano, Teppei Shimamura, Seiya Imoto, 2007, Genome informatics. International Conference on Genome Informatics.

An efficient method of exploring simulation models by assimilating literature and biological observational data

Masao Nagasaki, Satoru Miyano, Rui Yamaguchi, 2014, Biosyst..

A Foundation of Algorithmic Teaching

Ayumi Shinohara, Satoru Miyano, 宮野悟, 1989 .

Modelling and simulation of signal transductions in an apoptosis pathway by using timed Petri nets

Li Chen, Hiroshi Matsuno, Satoru Miyano, 2007, Journal of Biosciences.

2D-Qsar for 450 types of amino acid induction peptides with a novel substructure pair descriptor having wider scope

Satoru Miyano, Tsutomu Osoda, 2011, J. Cheminformatics.

Advances in Bioinformatics and Computational Biology, 5th Brazilian Symposium on Bioinformatics, BSB 2010, Rio de Janeiro, Brazil, August 31-September 3, 2010. Proceedings

Carlos Eduardo Ferreira, Satoru Miyano, Peter F. Stadler, 2010, BSB.

Granger Causality in Systems Biology: Modeling Gene Networks in Time Series Microarray Data Using Vector Autoregressive Models

João Ricardo Sato, Satoru Miyano, André Fujita, 2010, BSB.

Finding Optimal Pairs of Patterns

Ayumi Shinohara, Satoru Miyano, Kenta Nakai, 2004, WABI.

Null space based feature selection method for gene expression data

Satoru Miyano, Alok Sharma, Vandana Sharma, 2012, Int. J. Mach. Learn. Cybern..

Graph Inference from a Walk for TRees of Bounded Degree 3 is NP-Complete

Satoru Miyano, Osamu Maruyama, S. Miyano, 1994, MFCS.

Finding Optimal Models for Small Gene Networks

Satoru Miyano, Sascha Ott, Seiya Imoto, 2003 .

Hybrid Petri net based modeling for biological pathway simulation

Masao Nagasaki, Hiroshi Matsuno, Satoru Miyano, 2011, Natural Computing.

Algorithms for Identifying Boolean Networks and Related Biological Networks Based on Matrix Multiplication and Fingerprint Function

Satoru Miyano, Tatsuya Akutsu, Satoru Kuhara, 2000, J. Comput. Biol..

VML: A View Modeling Language for Computational Knowledge Discovery

Satoru Miyano, Hideo Bannai, Osamu Maruyama, 2001, Discovery Science.

Computational Predictions for Functional Proteins Working after Cleaved in Apoptotic Pathway

Hiroshi Matsuno, Satoru Miyano, Manabu Sugii, 2009, 2009 International Conference on Complex, Intelligent and Software Intensive Systems.

Quality control and reproducibility in DNA microarray experiments.

Satoru Miyano, André Fujita, João R Sato, 2009, Genome informatics. International Conference on Genome Informatics.

Modeling Nonlinear Gene Regulatory Networks from Time Series Gene Expression Data

João Ricardo Sato, Carlos Eduardo Ferreira, Satoru Miyano, 2008, J. Bioinform. Comput. Biol..

Genomic Object Net: II. Modelling biopathways by hybrid functional Petri net with extension.

Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno, 2003, Applied bioinformatics.

GIMLET: Identifying Biological Modulators in Context-Specific Gene Regulation Using Local Energy Statistics

Satoru Miyano, Yusuke Matsui, Teppei Shimamura, 2017, bioRxiv.

Algorithmic Problems Arising from Genome Informatics (Abstract)

Satoru Miyano, 1995, ISAAC.

A versatile petri net based architecture for modeling and simulation of complex biological processes.

Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno, 2004, Genome informatics. International Conference on Genome Informatics.

On the Approximation of Protein Threading

Satoru Miyano, Tatsuya Akutsu, 1999, Theor. Comput. Sci..

Parallel Algorithms for Refutation Tree Problem on Formal Graph Systems

Satoru Miyano, Takayoshi Shoudai, Tomoyuki Uchida, 1995, IEICE Trans. Inf. Syst..

Gene Networks: Estimation, Modeling, and Simulation

Hiroshi Matsuno, Satoru Miyano, Seiya Imoto, 2014 .

RECOMB 2000 : proceedings of the Fourth annual international conference on computational molecular biology : April 8-11, 2000, Tokyo, Japan

Satoru Miyano, Ron Shamir, Sorin Istrail, 2000 .

The lexicographically first maximal subgraph problems:P-completeness andNC algorithms

Satoru Miyano, S. Miyano, 1987, Mathematical systems theory.

Challenges for Intelligent Systems in Biology

Satoru Miyano, Russ B. Altman, Alfonso Valencia, 2001, IEEE Intell. Syst..

Delta_2^P-Complete Lexicographically First Maximal Subgraph Problems

Satoru Miyano, 1991, Theor. Comput. Sci..

Utilizing Evolutionary Information and Gene Expression Data for Estimating Gene Networks with Bayesian Network Models

Satoru Miyano, Hideo Bannai, Seiya Imoto, 2005, J. Bioinform. Comput. Biol..

BONSAI Garden: Parallel Knowledge Discovery System for Amino Acid Sequences

Ayumi Shinohara, Satoru Miyano, Setsuo Arikawa, 1995, ISMB.

The systems approach to the prespore-specific activation of sigma factor SigF in Bacillus subtilis

Masao Nagasaki, Satoru Miyano, Jin Hwan Do, 2010, Biosyst..

Cell System Ontology: Representation for Modeling, Visualizing, and Simulating Biological Pathways

Masao Nagasaki, Satoru Miyano, Ayumu Saito, 2007, Silico Biol..

Genomon ITDetector: a tool for somatic internal tandem duplication detection from cancer genome sequencing data

Satoru Miyano, Yuichi Shiraishi, Kenichi Chiba, 2015, Bioinform..

Constructing biological pathway models with hybrid functional Petri net

Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno, 2004, Silico Biol..

Multi-omics Approach for Estimating Metabolic Networks Using Low-Order Partial Correlations

Satoru Miyano, Seiya Imoto, Rui Yamaguchi, 2013, J. Comput. Biol..

Simulation-based model checking approach to cell fate specification during Caenorhabditis elegans vulval development by hybrid functional Petri net with extension

Masao Nagasaki, Satoru Miyano, Chen Li, 2009, BMC Systems Biology.

Statistical Absolute Evaluation of Gene Ontology Terms with Gene Expression Data

Satoru Miyano, Seiya Imoto, Rui Yamaguchi, 2007, ISBRA.

Machine Learning Prediction of Amino Acid Patterns in Protein N-myristoylation

Hiroshi Matsuno, Satoru Miyano, Manabu Sugii, 2006, PRIB.

PRD: A protein–RNA interaction database

Satoru Miyano, Shigeo Fujimori, Katsuya Hino, 2012, Bioinformation.

A Parallel Algorithm for the Maximal Co-Hitting Set Problem

Satoru Miyano, Takayoshi Shoudai, 1992 .

BPE: Biopathway Executer for Large-Scale Biopathway Modeling and Simulation

Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno, 2003 .

ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information

Masao Nagasaki, Satoru Miyano, Yuichi Shiraishi, 2011, BMC Bioinformatics.

Polynomial-time learning of elementary formal systems

Ayumi Shinohara, Satoru Miyano, Takeshi Shinohara, 2000, New Generation Computing.

Toward Drawing an Atlas of Hypothesis Classes: Approximating a Hypothesis via Another Hypothesis Model

Satoru Miyano, Takayoshi Shoudai, Osamu Maruyama, 2002, Discovery Science.

Neoantimon: a multifunctional R package for identification of tumor-specific neoantigens

Satoru Miyano, Atsushi Niida, Rui Yamaguchi, 2020, Bioinform..

On the Complexity of Data Mining for Binary Decision Diagram Rules

Satoru Miyano, Takayoshi Shoudai, Osamu Maruyama, 1998 .

Efficiently Finding Regulatory Elements Using Correlation with Gene Expression

Ayumi Shinohara, Satoru Miyano, Hideo Bannai, 2004, J. Bioinform. Comput. Biol..

AYUMS: an algorithm for completely automatic quantitation based on LC-MS/MS proteome data and its application to the analysis of signal transduction

Masao Nagasaki, Satoru Miyano, Sumio Sugano, 2007, BMC Bioinform..

Better Decomposition Heuristics for the Maximum-Weight Connected Graph Problem Using Betweenness Centrality

Masao Nagasaki, Satoru Miyano, Hideo Bannai, 2009, Discovery Science.

Evaluation of N-myristoylation Prediction Tool using Machine Learning

Hiroshi Matsuno, Satoru Miyano, Manabu Sugii, 2008 .

Inferring Contagion in Regulatory Networks

João Ricardo Sato, Carlos Eduardo Ferreira, Satoru Miyano, 2011, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Learning Conformation Rules

Satoru Miyano, Takayoshi Shoudai, Satoru Kuhara, 2001, Discovery Science.

Proceedings of the Advances in bioinformatics and computational biology, and 5th Brazilian conference on Bioinformatics

Carlos Eduardo Ferreira, Satoru Miyano, Peter F. Stadler, 2010 .

Predicting gene regulation by sigma factors in Bacillus subtilis from genome-wide data

Satoru Miyano, Kenta Nakai, Seiya Imoto, 2004, ISMB/ECCB.

A Parallelizable Lexicographically First Maximal Edge-Induced Subgraph Problem

Satoru Miyano, 1988, Inf. Process. Lett..

Remarks on Multihead Pushdown Automata and Multihead Stack Automata

Satoru Miyano, S. Miyano, 1983, J. Comput. Syst. Sci..

GENE NETWORK INFERENCE AND BIOPATHWAY MODELING

Satoru Miyano, S. Miyano, 2004 .

Extracting Best Consensus Motifs from Positive and Negative Examples

Satoru Miyano, Osamu Maruyama, Erika Tateishi, 1996, STACS.

An Intelligent Tool for Selecting Abstracts in MEDLINE

Hiroshi Matsuno, Satoru Miyano, Miyako Tanaka, 1999 .

An Introduction to Time‐Varying Connectivity Estimation for Gene Regulatory Networks

João Ricardo Sato, Carlos Eduardo Ferreira, Satoru Miyano, 2010 .

Fast algorithm for extracting multiple unordered short motifs using bit operations

Satoru Miyano, Hideo Bannai, Osamu Maruyama, 2002, Inf. Sci..

Computational gene network analysis reveals TNF-induced angiogenesis

Satoru Miyano, Seiya Imoto, Rui Yamaguchi, 2012, BMC Systems Biology.

Using Maximal Independent Sets to Solve Problems in Parallel

Satoru Miyano, Takayoshi Shoudai, 1995, Theor. Comput. Sci..

Inferring gene networks from time series microarray data using dynamic Bayesian networks

Satoru Miyano, Seiya Imoto, SunYong Kim, 2003, Briefings Bioinform..

DA 1.0: parameter estimation of biological pathways using data assimilation approach

Masao Nagasaki, Satoru Miyano, Limsoon Wong, 2010, Bioinform..

Bayesian Network Approach to Estimate Gene Networks

Satoru Miyano, Seiya Imoto, 2007 .

Alternating Finite Automata on omega-Words

Satoru Miyano, Takeshi Hayashi, Takeshi Hayashi, 1984, CAAP.

Inferring qualitative relations in genetic networks and metabolic pathways

Satoru Miyano, Tatsuya Akutsu, Satoru Kuhara, 2000, Bioinform..

Learning Theory Toward Genome Informatics

Satoru Miyano, 1995, IEICE Trans. Inf. Syst..

Virtual Grid Engine: a simulated grid engine environment for large-scale supercomputers

Satoru Miyano, Rui Yamaguchi, Satoshi Ito, 2019, BMC Bioinformatics.

Finding Gene Networks with

Satoru Miyano, Tomoyuki Higuchi, Seiya Imoto, 2007 .

Searching Optimal Bayesian Network Structure on Constraint Search Space: Super-Structure Approach

Satoru Miyano, Seiya Imoto, Eric Perrier, 2010, JSAI-isAI Workshops.

Theory of Parallel Algorithms

Satoru Miyano, S. Miyano, 1995 .

BONSAI Garden: Parallel Machine Discovery System for Sequences

Ayumi Shinohara, Satoru Miyano, Setsuo Arikawa, 1994 .

Pathway Simulation Software

Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno, 2009 .

Chapter 11 – Gene Networks: Estimation, Modeling, and Simulation

Satoru Miyano, Seiya Imoto, S. Miyano, 2006 .

Case-control study of binary disease trait considering interactions between SNPs and environmental effects using logistic regression

Satoru Miyano, Seiya Imoto, Reiichiro Nakamichi, 2004, Proceedings. Fourth IEEE Symposium on Bioinformatics and Bioengineering.

Estimation of nonlinear gene regulatory networks via L1 regularized NVAR from time series gene expression data.

Satoru Miyano, André Fujita, Teppei Shimamura, 2008, Genome informatics. International Conference on Genome Informatics.

ALPHLARD-NT: Bayesian Method for Human Leukocyte Antigen Genotyping and Mutation Calling through Simultaneous Analysis of Normal and Tumor Whole-Genome Sequence Data

Satoru Miyano, Seiya Imoto, Takuya Moriyama, 2019, J. Comput. Biol..

Computational Genome-Wide Discovery of Aberrant Splice Variations with Exon Expression Profiles

Masao Nagasaki, Atsushi Doi, Satoru Miyano, 2007, 2007 IEEE 7th International Symposium on BioInformatics and BioEngineering.

Genomic Hypothesis Creator

Satoru Miyano, Takayoshi Shoudai, Osamu Maruyama, 1998 .

Theoretical Foundation of the Performance of Phylogeny-Based Somatic Variant Detection

Satoru Miyano, Takuya Moriyama, Rui Yamaguchi, 2020, ISMCO.

A machine discovery from amino acid sequences by decision trees over regular patterns

Satoru Miyano, Setsuo Arikawa, Satoru Kuhara, 1993, New Generation Computing.

More Speed and More Pattern Variations for Knowledge Discovery System BONSAI

Ayumi Shinohara, Satoru Miyano, Hideo Bannai, 2001 .

A Visualization Tool for Gene Network Discovery-G.NET

Sun Yong Kim, Satoru Miyano, Seiya Imoto, 2002 .

MIRACH: efficient model checker for quantitative biological pathway models

Masao Nagasaki, Satoru Miyano, Limsoon Wong, 2011, Bioinform..

Distributed Client-Server System Architecture for High Performance Simulations on Genomic Object Net

Tomokazu Kono, Masao Nagasaki, Atsushi Doi, 2003 .

Δ2p-Complete Lexicographically First Maximal Subgraph Problems

Satoru Miyano, 1988, MFCS.

Predicting the Operon Structure of Bacillus subtilis Using Operon Length, Intergene Distance, and Gene Expression Information

Satoru Miyano, Seiya Imoto, Michiel J. L. de Hoon, 2003, Pacific Symposium on Biocomputing.

Enhancing breakpoint resolution with deep segmentation model: A general refinement method for read-depth based structural variant callers

Satoru Miyano, Rui Yamaguchi, Seiya Imoto, 2019, bioRxiv.

Identifiability of local transmissibility parameters in agent-based pandemic simulation

Satoru Miyano, Tomoyuki Higuchi, Seiya Imoto, 2012, 2012 15th International Conference on Information Fusion.

SiGN-SSM: open source parallel software for estimating gene networks with state space models

Masao Nagasaki, Satoru Miyano, Seiya Imoto, 2011, Bioinform..

Towards Biopathway Modeling and Simulation

Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno, 2003, ICATPN.

One-Way Weak-Stack-Counter Automata

Satoru Miyano, 1980, J. Comput. Syst. Sci..

Knowledge Acquisition from Amino Acid Sequences by Machine Learning System BONSAI

Ayumi Shinohara, Satoru Miyano, Setsuo Arikawa, 1992 .

Complexity of Finding Alphabet Indexing

Satoru Miyano, Shinichi Shimozono, 1995, IEICE Trans. Inf. Syst..

Intrasplicing - Analysis of Long Intron Sequences

Satoru Miyano, Kenta Nakai, Hideo Bannai, 2002, Pacific Symposium on Biocomputing.

Global gene network exploration based on explainable artificial intelligence approach

Satoru Miyano, Heewon Park, Rui Yamaguchi, 2020, PloS one.

Use of Gene Networks for Identifying and Validating Drug Targets

Satoru Miyano, Satoru Kuhara, Seiya Imoto, 2003, J. Bioinform. Comput. Biol..

Gene regulatory network clustering for graph layout based on microarray gene expression data.

Masao Nagasaki, Satoru Miyano, Seiya Imoto, 2010, Genome informatics. International Conference on Genome Informatics.

An Algorithm to Estimate Delay Times in Petri Net Models of Signaling Pathways with Experimental Data

Hiroshi Matsuno, Satoru Miyano, Yoshimasa Miwa, 2008, BIONETICS.

A hierarchy theorem for multihead stack-counter automata

Satoru Miyano, S. Miyano, 1982, Acta Informatica.

Design Aspects of Discovery Systems

Satoru Miyano, Osamu Maruyama, S. Miyano, 2000 .

Running Learning Systems in Parallel for Machine Discovery from Sequences

Ayumi Shinohara, Satoru Miyano, Setsuo Arikawa, 1993 .

Statistical model-based testing to evaluate the recurrence of genomic aberrations

Satoru Miyano, Teppei Shimamura, Atsushi Niida, 2012, Bioinform..

High performance computing of a fusion gene detection pipeline on the K computer

Satoru Miyano, Yuichi Shiraishi, Satoshi Ito, 2015, 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Identification of Genetic Networks from a Small Number of Gene Expression Patterns Under the Boolean Network Model

Satoru Miyano, Tatsuya Akutsu, Satoru Kuhara, 1998, Pacific Symposium on Biocomputing.

Multilayer Cluster Heat Map Visualizing Biological Tensor Data

Satoru Miyano, Atsushi Niida, Seiya Imoto, 2013, BSB.

Analysis of questionnaire for traditional medical and develop decision support system

Satoru Miyano, Kenji Watanabe, Seiya Imoto, 2012, 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops.

Automatic drawing of biological networks using cross cost and subcomponent data.

Masao Nagasaki, Atsushi Doi, Satoru Miyano, 2005, Genome informatics. International Conference on Genome Informatics.

Virtual Grid Engine: Accelerating thousands of omics sample analyses using large-scale supercomputers

Satoru Miyano, Satoshi Ito, Hikaru Inoue, 2018, 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, RECOMB 2000, Tokyo, Japan, April 8-11, 2000

Satoru Miyano, Ron Shamir, Sorin Istrail, 1997, Annual International Conference on Research in Computational Molecular Biology.

XiP: a computational environment to create, extend and share workflows

Masao Nagasaki, Satoru Miyano, Chen Li, 2013, Bioinform..

Optimal Search on Clustered Structural Constraint for Learning Bayesian Network Structure

Satoru Miyano, Seiya Imoto, Eric Perrier, 2010, J. Mach. Learn. Res..

A Bayesian model integration for mutation calling through data partitioning

Satoru Miyano, Yuichi Shiraishi, Seiya Imoto, 2019, Bioinform..

Enumeration of Likely Gene Networks and Network Motif Extraction for Large Gene Networks

Satoru Miyano, Sascha Ott, S. Miyano, 2003 .

A learning algorithm for elementary formal systems and its experiments on identification of transmembrane domains

Ayumi Shinohara, Satoru Miyano, Setsuo Arikawa, 1992, Proceedings of the Twenty-Fifth Hawaii International Conference on System Sciences.

Systems biology model repository for macrophage pathway simulation

Masao Nagasaki, Satoru Miyano, André Fujita, 2011, Bioinform..

A framework for generating interactive reports for cancer genome analysis

Satoru Miyano, Yuichi Shiraishi, Kenichi Chiba, 2017, bioRxiv.

Prediction of debacle points for robustness of biological pathways by using recurrent neural networks.

Hironori Kitakaze, Hiroshi Matsuno, Satoru Miyano, 2005, Genome informatics. International Conference on Genome Informatics.

Estimating gene regulatory networks and protein-protein interactions of Saccharomyces cerevisiae from multiple genome-wide data

Satoru Miyano, Seiya Imoto, Yoshinori Tamada, 2005, ECCB/JBI.

Genomic Object Net: Object Oriented Representation of Biological Systems

Atsushi Doi, Hiroshi Matsuno, Satoru Miyano, 2000 .

A Top-r Feature Selection Algorithm for Microarray Gene Expression Data

Satoru Miyano, Alok Sharma, Seiya Imoto, 2012, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Alphabet Indexing by Cluster Analysis

Satoru Miyano, Takeo Okazaki, Hideaki Nakakuni, 1994 .

Computational Platform for Systems Biology

Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno, 2009 .

INDEXING ALTERNATING FINITE AUTOMATA AND BINARY TREE LIKE CIRCUITS

Satoru Miyano, 宮野悟, S. Miyano, 1988 .

Revolutionizing Cancer Genomic Medicine by AI and Supercomputer with Big Data

Satoru Miyano, S. Miyano, 2018, 2018 IEEE Symposium on VLSI Technology.

Introduction of TOP500 supercomputers for bioinformaticians -Case study of GFK-

Satoru Miyano, Yuichi Shiraishi, Teppei Shimamura, 2015 .

Machine Discovery of a Negative Motif

Ayumi Shinohara, Satoru Miyano, Setsuo Arikawa, 1991 .

Boundary Formation by Notch Signaling in Drosophila Multicellular Systems: Experimental Observations and Gene Network Modeling by Genomic Object Net

Hiroshi Matsuno, Satoru Miyano, Sachie Fujita, 2002, Pacific Symposium on Biocomputing.

Genomic Object Net: Towards Biopathway Modeling and Simulation (BIOINFORMATICS CENTER - Pathway Engineering)

Satoru Miyano, S. Miyano, 2002 .

Statistical Model Selection Method to Analyze Combinatorial Effects of Snps and Environmental Factors for Binary Disease

Satoru Miyano, Seiya Imoto, Reiichiro Nakamichi, 2006, Int. J. Artif. Intell. Tools.

Systematic reconstruction of TRANSPATH data into Cell System Markup Language

Masao Nagasaki, Satoru Miyano, Chen Li, 2008, BMC Systems Biology.

Reconstruction of high read-depth signals from low-depth whole genome sequencing data using deep learning

Satoru Miyano, Seiya Imoto, Rui Yamaguchi, 2017, 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

phyC: Clustering cancer evolutionary trees

Satoru Miyano, Yusuke Matsui, Teppei Shimamura, 2016, bioRxiv.

Bayesian network and nonparametric heteroscedastic regression for nonlinear modeling of genetic network

Satoru Miyano, Satoru Kuhara, Seiya Imoto, 2003, Proceedings. IEEE Computer Society Bioinformatics Conference.

Integrating Biopathway Databases for Large-scale Modeling and Simulation

Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno, 2004, APBC.

Open source clustering software

Satoru Miyano, Seiya Imoto, J. Nolan, 2004 .

A Definition of Discovery in Terms of Generalized Descriptional Complexity

Satoru Miyano, Hideo Bannai, S. Miyano, 1999, Discovery Science.

Designing Views in HypothesisCreator: System for Assisting in Discovery

Satoru Miyano, Tomoyuki Uchida, Osamu Maruyama, 1999, Discovery Science.

A Case Study of HFPN Simulation: Finding Essential Roles of Ror Gene in the Interaction of Feedback Loops in Mammalian Circadian Clock

Hiroshi Matsuno, Satoru Miyano, Shin-Ichi T. Inouye, 2016, Modeling in Systems Biology, The Petri Net Approach.

Computational Strategy for Discovering Druggable Gene Networks from Genome-Wide RNA Expression Profiles

Deborah Sanders, Satoru Miyano, Satoru Kuhara, 2005, Pacific Symposium on Biocomputing.

Structural Modeling and Analysis of Signaling Pathways Based on Petri Nets

Hiroshi Matsuno, Satoru Miyano, Qi-Wei Ge, 2006, J. Bioinform. Comput. Biol..

Tumor Subclonal Progression Model for Cancer Hallmark Acquisition

Satoru Miyano, Yusuke Matsui, Teppei Shimamura, 2017, CIBB.

Special Issue on Surveys on Discovery Science

Satoru Miyano, S. Miyano, 2000 .

ArrayCluster: an analytic tool for clustering, data visualization and module finder on gene expression profiles

Satoru Miyano, Tomoyuki Higuchi, Seiya Imoto, 2006, Bioinform..

COMPUTATIONAL CHALLENGES FOR TOP-DOWN MODELING AND SIMULATION OF BIOLOGICAL PATHWAYS

Satoru Miyano, S. Miyano, 2008, RECOMB 2008.

Large-scale DNA Barcode Library Generation for Biomolecule Identification in High-throughput Screens

Satoru Miyano, Sumio Sugano, Paul Sheridan, 2017, Scientific Reports.

RECOVERY OF INCOMPLETE TABLES UNDER FUNCTIONAL DEPENDENCIES

Makoto Haraguchi, Satoru Miyano, S. Miyano, 1982 .

Transform of visual analogue scale data and their clustering

Satoru Miyano, Kenji Watanabe, Seiya Imoto, 2011, Int. J. Knowl. Eng. Soft Data Paradigms.

Partial Order-Based Bayesian Network Learning Algorithm for Estimating Gene Networks

Satoru Miyano, Seiya Imoto, Kazuyuki Numata, 2008, 2008 IEEE International Conference on Bioinformatics and Biomedicine.

BFL: a node and edge betweenness based fast layout algorithm for large scale networks

Masao Nagasaki, Satoru Miyano, Kaname Kojima, 2009, BMC Bioinformatics.

Identification of gene regulatory networks by strategic gene disruptions and gene overexpressions

Satoru Miyano, Tatsuya Akutsu, Satoru Kuhara, 1998, SODA '98.

Ontology-based instance data validation for high-quality curated biological pathways

Masao Nagasaki, Satoru Miyano, Euna Jeong, 2011, BMC Bioinformatics.

The impact of measurement errors in the identification of regulatory networks

João Ricardo Sato, Satoru Miyano, Alexandre Galvão Patriota, 2009, BMC Bioinformatics.

Fast Grid Layout Algorithm for Biological Networks with Sweep Calculation

Masao Nagasaki, Satoru Miyano, Kaname Kojima, 2022 .

IRView: a database and viewer for protein interacting regions

Masao Nagasaki, Satoru Miyano, Ayumu Saito, 2012, Bioinform..

Starting Cell Illustrator

Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno, 2009 .

Modeling gene expression regulatory networks with the sparse vector autoregressive model

João Ricardo Sato, Carlos Eduardo Ferreira, Satoru Miyano, 2007, BMC Systems Biology.

A framework for generating interactive reports for cancer genome analysis

Satoru Miyano, Yuichi Shiraishi, Kenichi Chiba, 2017 .

Petri Net Based Descriptions for Systematic Understanding of Biological Pathways

Hiroshi Matsuno, Satoru Miyano, Chen Li, 2006, IEICE Trans. Fundam. Electron. Commun. Comput. Sci..

Inferring dynamic gene networks under varying conditions for transcriptomic network comparison

Masao Nagasaki, Satoru Miyano, Teppei Shimamura, 2010, Bioinform..

Performance improvement in protein N-myristoyl classification by BONSAI with insignificant indexing symbol.

Hiroshi Matsuno, Satoru Miyano, Manabu Sugii, 2007, Genome informatics. International Conference on Genome Informatics.

ExonMiner: Web service for analysis of GeneChip Exon array data

Masao Nagasaki, Satoru Miyano, Seiya Imoto, 2008, BMC Bioinformatics.

Clustering for Visual Analogue Scale Data in Symbolic Data Analysis

Satoru Miyano, Kenji Watanabe, Rui Yamaguchi, 2011, Complex Adaptive Systems.

Principal component analysis using QR decomposition

Kuldip K. Paliwal, Satoru Miyano, Alok Sharma, 2013, Int. J. Mach. Learn. Cybern..

A simple greedy algorithm for finding functional relations: efficient implementation and average case analysis

Satoru Miyano, Tatsuya Akutsu, Satoru Kuhara, 2003, Theor. Comput. Sci..

Symbolic hierarchical clustering for visual analogue scale data

Satoru Miyano, Kenji Watanabe, Seiya Imoto, 2011 .

Using Protein-Protein Interactions for Refining Gene Networks Estimated from Microarray Data by Bayesian Networks

Satoru Miyano, Seiya Imoto, Naoki Nariai, 2003, Pacific Symposium on Biocomputing.

TAKING A WALK ON A GRAPH

Satoru Miyano, Osamu Maruyama, S. Miyano, 1995 .

A feature selection method using improved regularized linear discriminant analysis

Kuldip K. Paliwal, Satoru Miyano, Alok Sharma, 2014, Machine Vision and Applications.

WEIGHTED LASSO IN GRAPHICAL GAUSSIAN MODELING FOR LARGE GENE NETWORK ESTIMATION BASED ON MICROARRAY DATA

Satoru Miyano, Teppei Shimamura, Seiya Imoto, 2007 .

ProDDO: a database of disordered proteins from the Protein Data Bank (PDB)

Satoru Miyano, Tomoyuki Uchida, Kim Lan Sim, 2001, Bioinform..

Model-free unsupervised gene set screening based on information enrichment in expression profiles

Masao Nagasaki, Satoru Miyano, Teppei Shimamura, 2010, Bioinform..

Dynamic Bayesian Network and Nonparametric Regression Model for Inferring Gene Networks

Sun Yong Kim, Satoru Miyano, Seiya Imoto, 2002 .

ChopSticks: High-resolution analysis of homozygous deletions by exploiting concordant read pairs

Masao Nagasaki, Satoru Miyano, Tomohiro Yasuda, 2012, BMC Bioinformatics.

An O(N2) Algorithm for Discovering Optimal Boolean Pattern Pairs

Ayumi Shinohara, Satoru Miyano, Kenta Nakai, 2004, IEEE ACM Trans. Comput. Biol. Bioinform..

Enhancing breakpoint resolution with deep segmentation model: A general refinement method for read-depth based structural variant callers

Satoru Miyano, Seiya Imoto, Rui Yamaguchi, 2021, PLoS Comput. Biol..

On the application of BERT models for nanopore methylation detection

Satoru Miyano, Seiya Imoto, Rui Yamaguchi, 2021, 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

High-speed parameter search of dynamic biological pathways from time-course transcriptomic profiles using high-level Petri net

Masao Nagasaki, Satoru Miyano, Keisuke Kuroyanagi, 2020, Biosyst..

Whole-genome sequencing and comprehensive variant analysis of a Japanese individual using massively parallel sequencing

Masao Nagasaki, Satoru Miyano, Yusuke Nakamura, 2010, Nature Genetics.

A Weighting Profile Method for Protein-RNA Interaction Prediction

Satoru Miyano, Euna Jeong, S. Miyano, 2005 .

Analysis of Questionnaire for Traditional Medicine and Development of Decision Support System

Satoru Miyano, Seiya Imoto, Rui Yamaguchi, 2014, Evidence-based complementary and alternative medicine : eCAM.

Integrated genetic and epigenetic analysis defines novel molecular subgroups in rhabdomyosarcoma

Satoru Miyano, Yuichi Shiraishi, Teppei Shimamura, 2015, Nature Communications.

Algorithmic Learning Theory with Elementary Formal Systems

Akihiro Yamamoto, Ayumi Shinohara, Satoru Miyano, 1992 .

Prediction of Residues in Protein-RNA Interaction Sites by Neural Networks

Satoru Miyano, Euna Jeong, I-Fang Chung, 2003 .

Acquired initiating mutations in early hematopoietic cells of CLL patients.

Satoru Miyano, Yuichi Shiraishi, Daniel Gautheret, 2014, Cancer discovery.

Cell fate simulation model of gustatory neurons with MicroRNAs double-negative feedback loop by hybrid functional Petri net with extension.

Masao Nagasaki, Satoru Miyano, Ayumu Saito, 2006, Genome informatics. International Conference on Genome Informatics.

D3M: Detection of differential distributions of methylation levels

Satoru Miyano, Masahiro Mizuta, Teppei Shimamura, 2015, bioRxiv.

Error tolerant model for incorporating biological knowledge with expression data in estimating gene networks

Satoru Miyano, Tomoyuki Higuchi, Seiya Imoto, 2006 .

Identifying drug active pathways from gene networks estimated by gene expression data.

Satoru Miyano, Seiya Imoto, Yoshinori Tamada, 2005, Genome informatics. International Conference on Genome Informatics.

Modeling and estimation of dynamic EGFR pathway by data assimilation approach using time series proteomic data.

Masao Nagasaki, Satoru Miyano, Tomoyuki Higuchi, 2006, Genome informatics. International Conference on Genome Informatics.

A comprehensive characterization of cis-acting splicing-associated variants in human cancer.

Satoru Miyano, Yuichi Shiraishi, Kenichi Chiba, 2018, Genome research.

Comprehensive analysis of indels in whole-genome microsatellite regions and microsatellite instability across 21 cancer types

Satoru Miyano, Yuichi Shiraishi, Seiya Imoto, 2018, bioRxiv.

Evaluation of Sequence Features from Intrinsically Disordered Regions for the Estimation of Protein Function

Satoru Miyano, Abdollah Dehzangi, Kenta Nakai, 2014, PloS one.

Aberrant PD-L1 expression through 3′-UTR disruption in multiple cancers

Satoru Miyano, Yuichi Shiraishi, Kenichi Chiba, 2016, Nature.

A novel meta-analysis approach of cancer transcriptomes reveals prevailing transcriptional networks in cancer cells.

Masao Nagasaki, Satoru Miyano, Atsushi Niida, 2010, Genome informatics. International Conference on Genome Informatics.

Clustering samples characterized by time course gene expression profiles using the mixture of state space models.

Satoru Miyano, Tomoyuki Higuchi, Seiya Imoto, 2007, Genome informatics. International Conference on Genome Informatics.

Recursive Random Lasso (RRLasso) for Identifying Anti-Cancer Drug Targets

Satoru Miyano, Seiya Imoto, Heewon Park, 2015, PloS one.

Bounded Degree Maximal Subgraph Problems are in NC

Satoru Miyano, Takayoshi Shoudai, 正代隆義, 1990 .

A Novel Network Profiling Analysis Reveals System Changes in Epithelial-Mesenchymal Transition

Masao Nagasaki, Satoru Miyano, Teppei Shimamura, 2011, PloS one.

Identification of genes upregulated in ALK-positive and EGFR/KRAS/ALK-negative lung adenocarcinomas.

Satoru Miyano, Rui Yamaguchi, Seiichiro Yamamoto, 2012, Cancer research.

Global implementation of genomic medicine: We are not alone

Satoru Miyano, Wasun Chantratita, Andres Metspalu, 2015, Science Translational Medicine.

Identification of activated transcription factors from microarray gene expression data of Kampo medicine-treated mice.

Masao Nagasaki, Satoru Miyano, Seiya Imoto, 2007, Genome informatics. International Conference on Genome Informatics.

An NC Algorithm for Computing a Maximal Independent Set in a Hypergraph of Bounded Valence

Satoru Miyano, 正代隆義, 宮野悟, 1993 .

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

Ken Chen, Mark Gerstein, Satoru Miyano, 2018, Nature Genetics.

Recurrent mutations in multiple components of the cohesin complex in myeloid neoplasms

Masao Nagasaki, Satoru Miyano, Yuichi Shiraishi, 2012, Nature Genetics.

Statistical Analysis of Hie (Cold Sensation) and Hiesho (Cold Disorder) in Kampo Clinic

Satoru Miyano, Seiya Imoto, Rui Yamaguchi, 2013, Evidence-based complementary and alternative medicine : eCAM.

Analysis of gene networks for drug target discovery and validation.

Satoru Miyano, Seiya Imoto, Yoshinori Tamada, 2007, Methods in molecular biology.

Predicting differences in gene regulatory systems by state space models.

Masao Nagasaki, Satoru Miyano, Teppei Shimamura, 2008, Genome informatics. International Conference on Genome Informatics.

Memory-Efficient Clustering Algorithms for Microarray Gene Expression Data

Satoru Miyano, Hideo Bannai, Seiya Imoto, 2005 .

FINITE TREE AUTOMATA ON INFINITE TREES

Satoru Miyano, Takeshi Hayashi, Takeshi Hayashi, 1985 .

ACTN1 mutations cause congenital macrothrombocytopenia.

Satoru Miyano, Yuichi Shiraishi, Ryoji Kobayashi, 2013, American journal of human genetics.

Comprehensive phosphoproteome analysis unravels the core signaling network that initiates the earliest synapse pathology in preclinical Alzheimer's disease brain.

Satoru Miyano, Seiya Imoto, Takeshi Iwatsubo, 2015, Human molecular genetics.

Transcriptional profiling of hematopoietic stem cells by high-throughput sequencing

Satoru Miyano, Hideo Bannai, Yoshimi Yashiro, 2009, International journal of hematology.

A statistical framework for genome-wide discovery of biomarker splice variations with GeneChip Human Exon 1.0 ST Arrays.

Masao Nagasaki, Atsushi Doi, Satoru Miyano, 2006, Genome informatics. International Conference on Genome Informatics.

91 FADS AND FALLACIES IN THE NAME OF SMALL-SAMPLE MICROARRAY CLASSIFICATION

Rabab K. Ward, Petar M. Djuric, Sergios Theodoridis, 2007 .

Gene Finding Using HAKKE System

Ayumi Shinohara, Satoru Miyano, Takayoshi Shoudai, 1997 .

Learning Elementary Formal Systems and an Application to Discovering Motifs in Proteins

Ayumi Shinohara, Satoru Miyano, 篠原武, 1991 .

Phosphoproteomics-Based Modeling Defines the Regulatory Mechanism Underlying Aberrant EGFR Signaling

Masao Nagasaki, Satoru Miyano, Sumio Sugano, 2010, PloS one.

Clonal evolution in myelodysplastic syndromes

Satoru Miyano, Yuichi Shiraishi, Martin Dugas, 2017, Nature Communications.

Simulation-Based Validation of the p53 Transcriptional Activity with Hybrid Functional Petri Net.

Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno, 2011, Studies in health technology and informatics.

Biopathways representation and simulation on hybrid functional petri net.

Atsushi Doi, Hiroshi Matsuno, Satoru Miyano, 2011, Studies in health technology and informatics.

Detection of differential distributions of methylation patterns

Satoru Miyano, Masahiro Mizuta, Teppei Shimamura, 2015 .

A simple model-based approach to inferring and visualizing cancer mutation signatures

Satoru Miyano, Yuichi Shiraishi, Matthew Stephens, 2015 .

Epidermal Growth Factor Receptor Tyrosine Kinase Defines Critical Prognostic Genes of Stage I Lung Adenocarcinoma

Masao Nagasaki, Satoru Miyano, Teppei Shimamura, 2012, PloS one.

Mutational landscape and clonal architecture in grade II and III gliomas

Satoru Miyano, Yuichi Shiraishi, Toshihiko Wakabayashi, 2015, Nature Genetics.

Inference of Gene Regulatory Networks Incorporating Multi-Source Biological Knowledge via a State Space Model with L1 Regularization

Masao Nagasaki, Satoru Miyano, Seiya Imoto, 2014, PloS one.

Gene Set-Based Module Discovery Decodes cis-Regulatory Codes Governing Diverse Gene Expression across Human Multiple Tissues

Masao Nagasaki, Satoru Miyano, Atsushi Niida, 2010, PloS one.

Analysis of PPARα-dependent and PPARα-independent transcript regulation following fenofibrate treatment of human endothelial cells

Masao Nagasaki, Atsushi Doi, Satoru Miyano, 2009, Angiogenesis.

Deep sequencing reveals stepwise mutation acquisition in paroxysmal nocturnal hemoglobinuria.

Satoru Miyano, Yuichi Shiraishi, Seishi Ogawa, 2014, The Journal of clinical investigation.

Integrated Multiregional Analysis Proposing a New Model of Colorectal Cancer Evolution

Satoru Miyano, Yuichi Shiraishi, Teppei Shimamura, 2016, PLoS genetics.

Gene expression and risk of leukemic transformation in myelodysplasia.

Satoru Miyano, Yuichi Shiraishi, Kenichi Chiba, 2017, Blood.

Robust Prediction of Anti-Cancer Drug Sensitivity and Sensitivity-Specific Biomarker

Satoru Miyano, Teppei Shimamura, Seiya Imoto, 2014, PloS one.

Approximating Minimum Common Supertrees for Complete k-Ary Trees

Satoru Miyano, Atsuko Yamaguchi, 宮野悟, 1993 .

A NOTE ON THE REGURALITY OF FUZZY LANGUAGES

Satoru Miyano, Sachio Hirokawa, S. Miyano, 1978 .

Kernel mixture survival models for identifying cancer subtypes, predicting patient's cancer types and survival probabilities.

Satoru Miyano, Seiya Imoto, Tomohiro Ando, 2004, Genome informatics. International Conference on Genome Informatics.