Satoru Miyano
Orcid: 0000-0002-1753-6616Affiliations:
- University of Tokyo, Human Genome Center, Japan
- Kyushu University, Japan (former)
According to our database1,
Satoru Miyano
authored at least 239 papers
between 1980 and 2024.
Collaborative distances:
Collaborative distances:
Timeline
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Online presence:
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on zbmath.org
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on orcid.org
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on id.loc.gov
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on dl.acm.org
On csauthors.net:
Bibliography
2024
Network-Constrained Eigen-Single-Cell Profile Estimation for Uncovering Crucial Immunogene Regulatory Systems in Human Bone Marrow.
J. Comput. Biol., 2024
Proceedings of the 14th International Conference on Bioscience, 2024
2023
Gene Regulatory Network-Classifier: Gene Regulatory Network-Based Classifier and Its Applications to Gastric Cancer Drug (5-Fluorouracil) Marker Identification.
J. Comput. Biol., February, 2023
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2023
2022
Uncovering Molecular Mechanisms of Drug Resistance via Network-Constrained Common Structure Identification.
J. Comput. Biol., 2022
PredictiveNetwork: predictive gene network estimation with application to gastric cancer drug response-predictive network analysis.
BMC Bioinform., 2022
Bioinform., 2022
Bioinform., 2022
2021
Enhancing breakpoint resolution with deep segmentation model: A general refinement method for read-depth based structural variant callers.
PLoS Comput. Biol., 2021
High-speed parameter search of dynamic biological pathways from time-course transcriptomic profiles using high-level Petri net.
Biosyst., 2021
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021
2020
BMC Bioinform., April, 2020
Ensemble smoothers for inference of hidden states and parameters in combinatorial regulatory model.
J. Frankl. Inst., 2020
Neoantimon: a multifunctional R package for identification of tumor-specific neoantigens.
Bioinform., 2020
Theoretical Foundation of the Performance of Phylogeny-Based Somatic Variant Detection.
Proceedings of the Mathematical and Computational Oncology, 2020
2019
J. Comput. Biol., 2019
ALPHLARD-NT: Bayesian Method for Human Leukocyte Antigen Genotyping and Mutation Calling through Simultaneous Analysis of Normal and Tumor Whole-Genome Sequence Data.
J. Comput. Biol., 2019
Virtual Grid Engine: a simulated grid engine environment for large-scale supercomputers.
BMC Bioinform., 2019
Bioinform., 2019
Proceedings of the Mathematical and Computational Oncology - First International Symposium, 2019
2018
Adaptive NetworkProfiler for Identifying Cancer Characteristic-Specific Gene Regulatory Networks.
J. Comput. Biol., 2018
Virtual Grid Engine: Accelerating thousands of omics sample analyses using large-scale supercomputers.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018
2017
A Novel Adaptive Penalized Logistic Regression for Uncovering Biomarker Associated with Anti-Cancer Drug Sensitivity.
IEEE ACM Trans. Comput. Biol. Bioinform., 2017
J. Open Source Softw., 2017
Interaction-Based Feature Selection for Uncovering Cancer Driver Genes Through Copy Number-Driven Expression Level.
J. Comput. Biol., 2017
GIMLET: Identifying Biological Modulators in Context-Specific Gene Regulation Using Local Energy Statistics.
Proceedings of the Computational Intelligence Methods for Bioinformatics and Biostatistics, 2017
Proceedings of the Computational Intelligence Methods for Bioinformatics and Biostatistics, 2017
Reconstruction of high read-depth signals from low-depth whole genome sequencing data using deep learning.
Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine, 2017
2016
Proceedings of the Modeling in Systems Biology, The Petri Net Approach, 2016
A Case Study of HFPN Simulation: Finding Essential Roles of Ror Gene in the Interaction of Feedback Loops in Mammalian Circadian Clock.
Proceedings of the Modeling in Systems Biology, The Petri Net Approach, 2016
Predicting Japanese Kampo formulas by analyzing database of medical records: a preliminary observational study.
BMC Medical Informatics Decis. Mak., 2016
Int. J. Bioinform. Res. Appl., 2016
A likelihood-free filtering method via approximate Bayesian computation in evaluating biological simulation models.
Comput. Stat. Data Anal., 2016
Bioinform., 2016
Proceedings of the Bioinformatics Research and Applications - 12th International Symposium, 2016
2015
J. Comput. Biol., 2015
Genomic data assimilation using a higher moment filtering technique for restoration of gene regulatory networks.
BMC Syst. Biol., 2015
BMC Genom., 2015
Genomon ITDetector: a tool for somatic internal tandem duplication detection from cancer genome sequencing data.
Bioinform., 2015
Proceedings of the Bioinformatics Research and Applications - 11th International Symposium, 2015
Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 2015
2014
Mach. Vis. Appl., 2014
A feature selection method using fixed-point algorithm for DNA microarray gene expression data.
Int. J. Knowl. Based Intell. Eng. Syst., 2014
An Efficient Data Assimilation Schema for Restoration and Extension of Gene Regulatory Networks Using Time-Course Observation Data.
J. Comput. Biol., 2014
An efficient method of exploring simulation models by assimilating literature and biological observational data.
Biosyst., 2014
CSML2SBML: A novel tool for converting quantitative biological pathway models from CSML into SBML.
Biosyst., 2014
HapMuC: somatic mutation calling using heterozygous germ line variants near candidate mutations.
Bioinform., 2014
Proceedings of the 17th International Conference on Information Fusion, 2014
2013
Int. J. Mach. Learn. Cybern., 2013
Multi-omics Approach for Estimating Metabolic Networks Using Low-Order Partial Correlations.
J. Comput. Biol., 2013
A strategy to select suitable physicochemical attributes of amino acids for protein fold recognition.
BMC Bioinform., 2013
Bioinform., 2013
Proceedings of the Advances in Bioinformatics and Computational Biology, 2013
Estimation of abrupt changes in sentinel observation data of influenza epidemics in Japan.
Proceedings of the 16th International Conference on Information Fusion, 2013
2012
IEEE ACM Trans. Comput. Biol. Bioinform., 2012
Identifying Gene Pathways Associated with Cancer Characteristics via Sparse Statistical Methods.
IEEE ACM Trans. Comput. Biol. Bioinform., 2012
Int. J. Mach. Learn. Cybern., 2012
J. Bioinform. Comput. Biol., 2012
BMC Syst. Biol., 2012
BMC Syst. Biol., 2012
Identifying regulational alterations in gene regulatory networks by state space representation of vector autoregressive models and variational annealing.
BMC Genom., 2012
ChopSticks: High-resolution analysis of homozygous deletions by exploiting concordant read pairs.
BMC Bioinform., 2012
Bioinform., 2012
Identifiability of local transmissibility parameters in agent-based pandemic simulation.
Proceedings of the 15th International Conference on Information Fusion, 2012
Analysis of questionnaire for traditional medical and develop decision support system.
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2012
2011
Estimating Genome-Wide Gene Networks Using Nonparametric Bayesian Network Models on Massively Parallel Computers.
IEEE ACM Trans. Comput. Biol. Bioinform., 2011
IEEE ACM Trans. Comput. Biol. Bioinform., 2011
High Performance Hybrid Functional Petri Net Simulations of Biological Pathway Models on CUDA.
IEEE ACM Trans. Comput. Biol. Bioinform., 2011
Proceedings of the Complex Adaptive Systems 2011 Conference, 2011
Nat. Comput., 2011
J. Mach. Learn. Res., 2011
2D-Qsar for 450 types of amino acid induction peptides with a novel substructure pair descriptor having wider scope.
J. Cheminformatics, 2011
INTRODUCTION - The First IEEE Conference on Healthcare Informatics, Imaging, and Systems biology HISB'11.
J. Bioinform. Comput. Biol., 2011
Int. J. Knowl. Eng. Soft Data Paradigms, 2011
ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information.
BMC Bioinform., 2011
Ontology-based instance data validation for high-quality curated biological pathways.
BMC Bioinform., 2011
SiGN-SSM: open source parallel software for estimating gene networks with state space models.
Bioinform., 2011
A rank-based statistical test for measuring synergistic effects between two gene sets.
Bioinform., 2011
Bioinform., 2011
Bioinform., 2011
Proceedings of the Bioinformatics Research and Applications - 7th International Symposium, 2011
Proceedings of the IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, 2011
Proceedings of the 14th International Conference on Information Fusion, 2011
Proceedings of the Advanced Agent Technology, 2011
Proceedings of the Handbook of Statistical Bioinformatics., 2011
2010
Optimal Search on Clustered Structural Constraint for Learning Bayesian Network Structure.
J. Mach. Learn. Res., 2010
J. Bioinform. Comput. Biol., 2010
Silico Biol., 2010
On Determining Firing Delay Time of Transitions for Petri Net Based Signaling Pathways by Introducing Stochastic Decision Rules.
Silico Biol., 2010
Delay Time Determination for the Timed Petri Net Model of a Signaling Pathway Based on Its Structural Information.
IEICE Trans. Fundam. Electron. Commun. Comput. Sci., 2010
Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram.
BMC Syst. Biol., 2010
An efficient biological pathway layout algorithm combining grid-layout and spring embedder for complicated cellular location information.
BMC Bioinform., 2010
The systems approach to the prespore-specific activation of sigma factor SigF in Bacillus subtilis.
Biosyst., 2010
Inferring dynamic gene networks under varying conditions for transcriptomic network comparison.
Bioinform., 2010
Model-free unsupervised gene set screening based on information enrichment in expression profiles.
Bioinform., 2010
DA 1.0: parameter estimation of biological pathways using data assimilation approach.
Bioinform., 2010
A fast and robust statistical test based on likelihood ratio with Bartlett correction to identify Granger causality between gene sets.
Bioinform., 2010
Granger Causality in Systems Biology: Modeling Gene Networks in Time Series Microarray Data Using Vector Autoregressive Models.
Proceedings of the Advances in Bioinformatics and Computational Biology, 2010
Searching Optimal Bayesian Network Structure on Constraint Search Space: Super-Structure Approach.
Proceedings of the New Frontiers in Artificial Intelligence, 2010
Proceedings of the 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2010
Discovering functional gene pathways associated with cancer heterogeneity via sparse supervised learning.
Proceedings of the 2010 IEEE International Conference on Bioinformatics and Biomedicine, 2010
Proceedings of the 10th IEEE International Conference on Bioinformatics and Bioengineering, 2010
2009
Network-Based Predictions and Simulations by Biological State Space Models: Search for Drug Mode of Action.
J. Comput. Sci. Technol., 2009
Comparing Pearson, Spearman and Hoeffding's d Measure for Gene Expression Association Analysis.
J. Bioinform. Comput. Biol., 2009
Recursive regularization for inferring gene networks from time-course gene expression profiles.
BMC Syst. Biol., 2009
Simulation-based model checking approach to cell fate specification during Caenorhabditis elegans vulval development by hybrid functional Petri net with extension.
BMC Syst. Biol., 2009
BFL: a node and edge betweenness based fast layout algorithm for large scale networks.
BMC Bioinform., 2009
BMC Bioinform., 2009
Unraveling Dynamic Activities of Autocrine Pathways that Control Drug-Response Transcriptome Networks.
Proceedings of the Biocomputing 2009: Proceedings of the Pacific Symposium, 2009
Parameter Estimation of In Silico Biological Pathways with Particle Filtering Towards a Petascale Computing.
Proceedings of the Biocomputing 2009: Proceedings of the Pacific Symposium, 2009
Better Decomposition Heuristics for the Maximum-Weight Connected Graph Problem Using Betweenness Centrality.
Proceedings of the Discovery Science, 12th International Conference, 2009
Computational Predictions for Functional Proteins Working after Cleaved in Apoptotic Pathway.
Proceedings of the 2009 International Conference on Complex, 2009
Proceedings of the Bioinformatics and Computational Biology, 2009
Computational Biology 13, Springer, ISBN: 978-1-84882-022-7, 2009
2008
J. Bioinform. Comput. Biol., 2008
BMC Syst. Biol., 2008
Multivariate gene expression analysis reveals functional connectivity changes between normal/tumoral prostates.
BMC Syst. Biol., 2008
BMC Bioinform., 2008
Bioinform., 2008
Bioinform., 2008
Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models.
Bioinform., 2008
An Algorithm to Estimate Delay Times in Petri Net Models of Signaling Pathways with Experimental Data.
Proceedings of the 3rd International ICST Conference on Bio-Inspired Models of Network, 2008
Partial Order-Based Bayesian Network Learning Algorithm for Estimating Gene Networks.
Proceedings of the 2008 IEEE International Conference on Bioinformatics and Biomedicine, 2008
Analyzing Time Course Gene Expression Data with Biological and Technical Replicates to Estimate Gene Networks by State Space Models.
Proceedings of the Second Asia International Conference on Modelling and Simulation, 2008
2007
Finding module-based gene networks with state-space models - Mining high-dimensional and short time-course gene expression data.
IEEE Signal Process. Mag., 2007
Cell System Ontology: Representation for Modeling, Visualizing, and Simulating Biological Pathways.
Silico Biol., 2007
On the complexity of deriving position specific score matrices from positive and negative sequences.
Discret. Appl. Math., 2007
Modeling gene expression regulatory networks with the sparse vector autoregressive model.
BMC Syst. Biol., 2007
AYUMS: an algorithm for completely automatic quantitation based on LC-MS/MS proteome data and its application to the analysis of signal transduction.
BMC Bioinform., 2007
An efficient grid layout algorithm for biological networks utilizing various biological attributes.
BMC Bioinform., 2007
Proceedings of the Bioinformatics Research and Applications, Third International Symposium, 2007
Computational Genome-Wide Discovery of Aberrant Splice Variations with Exon Expression Profiles.
Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, 2007
A Structure Learning Algorithm for Inference of Gene Networks from Microarray Gene Expression Data Using Bayesian Networks.
Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, 2007
2006
Trans. Comp. Sys. Biology, 2006
A New Regulatory Interaction Suggested by Simulations for Circadian Genetic Control Mechanism in Mammals.
J. Bioinform. Comput. Biol., 2006
J. Bioinform. Comput. Biol., 2006
Simulation-Based Validation of the p53 Transcriptional Activity with Hybrid Functional Petri Net.
Silico Biol., 2006
Statistical Model Selection Method to Analyze Combinatorial Effects of Snps and Environmental Factors for Binary Disease.
Int. J. Artif. Intell. Tools, 2006
IEICE Trans. Fundam. Electron. Commun. Comput. Sci., 2006
ArrayCluster: an analytic tool for clustering, data visualization and module finder on gene expression profiles.
Bioinform., 2006
Computational Strategy for Discovering Druggable Gene Networks from Genome-Wide RNA Expression Profiles.
Proceedings of the Biocomputing 2006, 2006
Proceedings of the Pattern Recognition in Bioinformatics, International Workshop, 2006
2005
Prediction of Transcriptional Terminators in <i>Bacillus subtilis</i> and Related Species.
PLoS Comput. Biol., 2005
Utilizing Evolutionary Information and Gene Expression Data for Estimating Gene Networks with Bayesian Network Models.
J. Bioinform. Comput. Biol., 2005
Superiority of network motifs over optimal networks and an application to the revelation of gene network evolution.
Bioinform., 2005
Proceedings of the Biocomputing 2005, 2005
Estimating Gene Networks from Expression Data and Binding Location Data via Boolean Networks.
Proceedings of the Computational Science and Its Applications, 2005
Estimating gene regulatory networks and protein-protein interactions of <i>Saccharomyces cerevisiae</i> from multiple genome-wide data.
Proceedings of the ECCB/JBI'05 Proceedings, Fourth European Conference on Computational Biology/Sixth Meeting of the Spanish Bioinformatics Network (Jornadas de BioInformática), Palacio de Congresos, Madrid, Spain, September 28, 2005
2004
IEEE ACM Trans. Comput. Biol. Bioinform., 2004
Simulated Cell Division Processes of the Xenopus Cell Cycle Pathway by Genomic Object Net.
J. Integr. Bioinform., 2004
Combining Microarrays and Biological Knowledge for Estimating Gene Networks via Bayesian Networks.
J. Bioinform. Comput. Biol., 2004
J. Bioinform. Comput. Biol., 2004
Silico Biol., 2004
Proceedings of the Algorithms in Bioinformatics, 4th International Workshop, 2004
Proceedings of the Biocomputing 2004, 2004
Using Protein-Protein Interactions for Refining Gene Networks Estimated from Microarray Data by Bayesian Networks.
Proceedings of the Biocomputing 2004, 2004
Predicting the Operon Structure of Bacillus subtilis Using Operon Length, Intergene Distance, and Gene Expression Information.
Proceedings of the Biocomputing 2004, 2004
Proceedings of the Knowledge Exploration in Life Science Informatics, 2004
Predicting gene regulation by sigma factors in Bacillus subtilis from genome-wide data.
Proceedings of the Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, 2004
Proceedings of the Discovery Science, 7th International Conference, 2004
Residual Bootstrapping and Median Filtering for Robust Estimation of Gene Networks from Microarray Data.
Proceedings of the Computational Methods in Systems Biology, International Conference, 2004
Case-Control Study of Binary Disease Trait Considering Interactions between SNPs and Environmental Effects using Logistic Regression.
Proceedings of the 4th IEEE International Symposium on BioInformatics and BioEngineering (BIBE 2004), 2004
Proceedings of the Second Asia-Pacific Bioinformatics Conference (APBC 2004), 2004
2003
A simple greedy algorithm for finding functional relations: efficient implementation and average case analysis.
Theor. Comput. Sci., 2003
Identification of genetic networks by strategic gene disruptions and gene overexpressions under a boolean model.
Theor. Comput. Sci., 2003
J. Bioinform. Comput. Biol., 2003
Bayesian Network and Nonparametric Heteroscedastic Regression for Nonlinear Modeling of Genetic Network.
J. Bioinform. Comput. Biol., 2003
Silico Biol., 2003
Inferring gene networks from time series microarray data using dynamic Bayesian networks.
Briefings Bioinform., 2003
Proceedings of the 8th Pacific Symposium on Biocomputing, 2003
Boundary Formation by Notch Signaling in Drosophila Multicellular Systems: Experimental Observations and Gene Network Modeling by Genomic Object Net.
Proceedings of the 8th Pacific Symposium on Biocomputing, 2003
Inferring Gene Regulatory Networks from Time-Ordered Gene Expression Data of Bacillus Subtilis Using Differential Equations.
Proceedings of the 8th Pacific Symposium on Biocomputing, 2003
Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection.
Proceedings of the European Conference on Computational Biology (ECCB 2003), 2003
Proceedings of the Computational Methods in Systems Biology, First International Workshop, 2003
Proceedings of the Computational Methods in Systems Biology, First International Workshop, 2003
Dynamic Bayesian Network and Nonparametric Regression for Nonlinear Modeling of Gene Networks from Time Series Gene Expression Data.
Proceedings of the Computational Methods in Systems Biology, First International Workshop, 2003
Proceedings of the Applications and Theory of Petri Nets 2003, 2003
2002
Inf. Sci., 2002
Statistical analysis of a small set of time-ordered gene expression data using linear splines.
Bioinform., 2002
Estimation of Genetic Networks and Functional Structures Between Genes by Using Bayesian Networks and Nonparametric Regression.
Proceedings of the 7th Pacific Symposium on Biocomputing, 2002
Proceedings of the Progress in Discovery Science, 2002
Toward Drawing an Atlas of Hypothesis Classes: Approximating a Hypothesis via Another Hypothesis Model.
Proceedings of the Discovery Science, 5th International Conference, 2002
Inferring Gene Regulatory Networks from Time-Ordered Gene Expression Data Using Differential Equations.
Proceedings of the Discovery Science, 5th International Conference, 2002
Proceedings of the Combinatorial Pattern Matching, 13th Annual Symposium, 2002
2001
HypothesisCreator: Concepts for Accelerating the Computational Knowledge Discovery Process.
Electron. Trans. Artif. Intell., 2001
Bioinform., 2001
Proceedings of the Fourteenth International Florida Artificial Intelligence Research Society Conference, 2001
Proceedings of the Discovery Science, 4th International Conference, DS 2001, Washington, 2001
Proceedings of the Discovery Science, 4th International Conference, DS 2001, Washington, 2001
2000
Algorithms for Identifying Boolean Networks and Related Biological Networks Based on Matrix Multiplication and Fingerprint Function.
J. Comput. Biol., 2000
Bioinform., 2000
A Simple Greedy Algorithm for Finding Functional Relations: Efficient Implementation and Average Case Anaylsis.
Proceedings of the Discovery Science, 2000
1999
Identification of Genetic Networks from a Small Number of Gene Expression Patterns Under the Boolean Network Model.
Proceedings of the 4th Pacific Symposium on Biocomputing, 1999
Proceedings of the Discovery Science, 1999
Proceedings of the Discovery Science, 1999
1998
Identification of Gene Regulatory Networks by Strategic Gene Disruptions and Gene Overexpressions.
Proceedings of the Ninth Annual ACM-SIAM Symposium on Discrete Algorithms, 1998
Proceedings of the Discovery Science, 1998
1997
An Approximation Algorithm for the Minimum Common Supertree Problem.
Nord. J. Comput., 1997
1996
Proceedings of the STACS 96, 1996
Genome Informatics: New Frontiers of Computer Science and Biosciences.
Proceedings of the International Symposium on Cooperative Database Systems for Advanced Applications, 1996
1995
Theor. Comput. Sci., 1995
IEICE Trans. Inf. Syst., 1995
Proceedings of the Mathematical Foundations of Computer Science 1995, 1995
Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology, 1995
Proceedings of the Algorithms and Computation, 6th International Symposium, 1995
1994
Machine Learning and Discovery for Bloinformatics: Introduction.
Proceedings of the 27th Annual Hawaii International Conference on System Sciences (HICSS-27), 1994
1993
A Machine Discovery from Amino Acid Sequences by Decision Trees over Regular Patterns.
New Gener. Comput., 1993
1991
Theor. Comput. Sci., 1991
Proceedings of the Nonmonotonic and Inductive Logic, 1991
Which classes of elementary formal systems are polynomial-time learnable.
Proceedings of the Algorithmic Learning Theory, 2nd International Workshop, 1991
Analogy is NP-hard.
Proceedings of the Algorithmic Learning Theory, 2nd International Workshop, 1991
1990
Teachability in Computational Learning.
Proceedings of the Algorithmic Learning Theory, First International Workshop, 1990
1989
The Lexicographically First Maximum Subgraph Problems: P-Completeness and NC Algorithms.
Math. Syst. Theory, 1989
1988
Inf. Process. Lett., 1988
Δ<sub>2</sub><sup>p</sup>-Complete Lexicographically First Maximal Subgraph Problems.
Proceedings of the Mathematical Foundations of Computer Science 1988, 1988
Parallel Complexity and P-Complete Problems.
Proceedings of the International Conference on Fifth Generation Computer Systems, 1988
1987
The Lexicographically First Maximal Subgraph Problems: P-Completeness and NC Algorithms.
Proceedings of the Automata, Languages and Programming, 14th International Colloquium, 1987
1984
1983
J. Comput. Syst. Sci., 1983
1982
1980