Rui Yamaguchi

发表

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

Satoru Miyano, Yuichi Shiraishi, Seiya Imoto, 2017, IEEE transactions on nanobioscience.

Identifying Hidden Confounders in Gene Networks by Bayesian Networks

Masato Inoue, Satoru Miyano, Seiya Imoto, 2010, 2010 IEEE International Conference on BioInformatics and BioEngineering.

Data science and precision health care.

Rui Yamaguchi, Seiya Imoto, Takanori Hasegawa, 2020, Nutrition reviews.

Parallel agent-based simulator for influenza pandemic

Satoru Miyano, Tomoyuki Higuchi, Seiya Imoto, 2011, AAMAS'11.

Ensemble smoothers for inference of hidden states and parameters in combinatorial regulatory model

Satoru Miyano, Atsushi Niida, Rui Yamaguchi, 2020, J. Frankl. Inst..

Additional file 1 of Sequence-specific bias correction for RNA-seq data using recurrent neural networks

Satoru Miyano, Seiya Imoto, Rui Yamaguchi, 2017 .

An Efficient Data Assimilation Schema for Restoration and Extension of Gene Regulatory Networks Using Time-Course Observation Data

Satoru Miyano, Tatsuya Akutsu, Tomoya Mori, 2014, J. Comput. Biol..

Discovering functional gene pathways associated with cancer heterogeneity via sparse supervised learning

Masao Nagasaki, Satoru Miyano, Teppei Shimamura, 2010, 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Estimation of macroscopic parameter in agent-based pandemic simulation

Satoru Miyano, Tomoyuki Higuchi, Seiya Imoto, 2011, 14th International Conference on Information Fusion.

Predicting Japanese Kampo formulas by analyzing database of medical records: a preliminary observational study

Hideki Mima, Satoru Miyano, Kenji Watanabe, 2016, BMC Medical Informatics and Decision Making.

Nanopore basecalling from a perspective of instance segmentation

Satoru Miyano, Tetsuo Shibuya, Rui Yamaguchi, 2020, BMC Bioinformatics.

Estimating Gene Networks with cDNA Microarray Data Using State-Space Models

Tomoyuki Higuchi, Rui Yamaguchi, Satoru Yamashita, 2005, ICCSA.

Gene Networks Viewed through Two Models

Masao Nagasaki, Satoru Miyano, Seiya Imoto, 2009, BICoB.

Genomic data assimilation using a higher moment filtering technique for restoration of gene regulatory networks

Satoru Miyano, Tatsuya Akutsu, Teppei Shimamura, 2015, BMC Systems Biology.

Poster: Comprehensive pharmacogenomic pathway screening by data assimilation

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

Parameter estimation in multi-compartment SIR model

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

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..

Nanopore basecalling from a perspective of instance segmentation

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

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).

PREDICTING DIFFERENCES IN GENE REGULATORY SYSTEMS BY STATE SPACE MODELS

Masao Nagasaki, Satoru Miyano, Teppei Shimamura, 2008 .

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.

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.

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..

Comprehensive Pharmacogenomic Pathway Screening by Data Assimilation

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

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.

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.

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.

Collocation-based sparse estimation for constructing dynamic gene networks.

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

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.

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

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

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.

Cost-effective length and timing of school closure during an influenza pandemic depend on the severity

Seiya Imoto, Rui Yamaguchi, Shinji Nakaoka, 2013, Theoretical Biology and Medical Modelling.

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.

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

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

Connection between traditional medicine and disease

Kenji Watanabe, Seiya Imoto, Rui Yamaguchi, 2012, SIGH.

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..

Population Model-Based Inter-Diplotype Similarity Measure for Accurate Diplotype Clustering

Tetsuo Shibuya, Ryo Yamada, Minoru Kanehisa, 2012, J. Comput. Biol..

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

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

Statistical Absolute Evaluation of Gene Ontology Terms with Gene Expression Data

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

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

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

Inferring Contagion in Regulatory Networks

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

Halcyon: an accurate basecaller exploiting an encoder–decoder model with monotonic attention

Rui Yamaguchi, Seiya Imoto, Hiroki Konishi, 2020, Bioinform..

Computational gene network analysis reveals TNF-induced angiogenesis

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

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 .

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..

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

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

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..

Genomic Signal Processing

Yufei Huang, Xiaodong Cai, Seungchan Kim, 2012, IEEE Signal Processing Magazine.

Global gene network exploration based on explainable artificial intelligence approach

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

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.

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).

State-space approach with the maximum likelihood principle to identify the system generating time-course gene expression data of yeast

Tomoyuki Higuchi, Rui Yamaguchi, T. Higuchi, 2006, Int. J. Data Min. Bioinform..

A Bayesian model integration for mutation calling through data partitioning

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

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).

Transform of visual analogue scale data and their clustering

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

Modeling gene expression regulatory networks with the sparse vector autoregressive model

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

Inferring dynamic gene networks under varying conditions for transcriptomic network comparison

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

Clustering for Visual Analogue Scale Data in Symbolic Data Analysis

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

Symbolic hierarchical clustering for visual analogue scale data

Satoru Miyano, Kenji Watanabe, Seiya Imoto, 2011 .

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

Satoru Miyano, Teppei Shimamura, Seiya Imoto, 2007 .

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

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

Application of state-space model with skew-t measurement noise to blood test value prediction

Seiya Imoto, Rui Yamaguchi, Takanori Hasegawa, 2021 .

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

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

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.

Prediction of blood test values under different lifestyle scenarios using time-series electronic health record

Seiya Imoto, Rui Yamaguchi, Takanori Hasegawa, 2020, PloS one.

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.

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.

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.

Metagenomic analysis of bacterial species in tongue microbiome of current and never smokers

Seiya Imoto, Rui Yamaguchi, Takanori Hasegawa, 2020, npj Biofilms and Microbiomes.

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.

Predicting differences in gene regulatory systems by state space models.

Masao Nagasaki, Satoru Miyano, Teppei Shimamura, 2008, 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 .

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

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

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.