R. Yamaguchi

S. Imoto, R. Yamaguchi, Eiichiro Uchino, 2020, Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association.

Comprehensive molecular characterization of mitochondrial genomes in human cancers

Nuno A. Fonseca, Gary D Bader, Benjamin J. Raphael, 2017, bioRxiv.

Genome-wide association studies and heritability analysis reveal the involvement of host genetics in the Japanese gut microbiota

S. Imoto, R. Yamaguchi, T. Odamaki, 2020, Communications Biology.

Genome-wide association studies and heritability analysis reveal the involvement of host genetics in the Japanese gut microbiota

S. Miyano, S. Imoto, R. Yamaguchi, 2020, Communications biology.

Author Correction: Pan-cancer analysis of whole genomes

Nuno A. Fonseca, Gary D Bader, Benjamin J. Raphael, 2023, Nature.

Circulating exosomal microRNA-203 is associated with metastasis possibly via inducing tumor-associated macrophages in colorectal cancer

S. Miyano, Takaaki Masuda, Taro Tobo, 2017, Oncotarget.

Sex differences in oncogenic mutational processes

Nuno A. Fonseca, Gary D Bader, Benjamin J. Raphael, 2019, Nature Communications.

Successful Clinical Sequencing by Molecular Tumor Board in an Elderly Patient With Refractory Sézary Syndrome.

S. Miyano, S. Imoto, R. Yamaguchi, 2020, JCO precision oncology.

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.

Estimation of macroscopic parameter in agent-based pandemic simulation

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

Reduced expression of APC-1B but not APC-1A by the deletion of promoter 1B is responsible for familial adenomatous polyposis

Y. Furukawa, S. Miyano, S. Imoto, 2016, Scientific Reports.

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.

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

Satoru Miyano, Teppei Shimamura, Seiya Imoto, 2007 .

Identifiability of local transmissibility parameters in agent-based pandemic simulation

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

Characterization of the T cell repertoire by deep T cell receptor sequencing in tissues and blood from patients with advanced colorectal cancer

Yusuke Nakamura, S. Miyano, S. Imoto, 2016, Oncology letters.

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

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

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.

Histological markers, sickle-shaped blood vessels, myxoid area, and infiltrating growth pattern help stratify the prognosis of patients with myxofibrosarcoma/undifferentiated sarcoma

Y. Miyagi, Y. Furukawa, S. Imoto, 2023, Scientific reports.

A microarray analysis of gnotobiotic mice indicating that microbial exposure during the neonatal period plays an essential role in immune system development

S. Miyano, S. Imoto, R. Yamaguchi, 2012, BMC Genomics.

Impact of salivary and pancreatic amylase gene copy numbers on diabetes, obesity, and functional profiles of microbiome in Northern Japanese population

S. Imoto, R. Yamaguchi, Noriaki Sato, 2021, Scientific Reports.

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

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

Nanopore basecalling from a perspective of instance segmentation

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

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.

Detection of APC mosaicism by next-generation sequencing in an FAP patient

Y. Furukawa, S. Sugano, Yutaka Suzuki, 2015, Journal of Human Genetics.

Sequence-specific bias correction for RNA-seq data using recurrent neural networks

S. Miyano, S. Imoto, Yao-zhong Zhang, 2017, BMC Genomics.

Comparison of gene expression profiles produced by CAGE, illumina microarray and real time RT-PCR.

Y. Hayashizaki, S. Miyano, T. Shimamura, 2010, Genome informatics. International Conference on Genome Informatics.

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.

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..

International society for gastrointestinal hereditary tumours—InSiGHT

Aung Ko Win, Y. Furukawa, S. Sugano, 2015, Familial Cancer.

Enhancement of Collective Immunity in Tokyo Metropolitan Area by Selective Vaccination against an Emerging Influenza Pandemic

Masaya M. Saito, T. Higuchi, S. Miyano, 2013, PloS one.

Forecasting Japan's Physician Shortage in 2035 as the First Full-Fledged Aged Society

S. Imoto, R. Yamaguchi, K. Imai, 2012, PloS one.

Bromodomain protein BRD8 regulates cell cycle progression in colorectal cancer cells through a TIP60-independent regulation of the pre-RC complex

Y. Furukawa, M. Oyama, S. Imoto, 2023, iScience.

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

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

Clustering for Visual Analogue Scale Data in Symbolic Data Analysis

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

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.

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.

On the application of BERT models for nanopore methylation detection

Y. Furukawa, S. Miyano, S. Imoto, 2021, bioRxiv.

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

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

A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns

Nuno A. Fonseca, Benjamin J. Raphael, Allison P. Heath, 2020, Nature Communications.

Inferring Contagion in Regulatory Networks

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

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

Masaya M. Saito, H. Nishiura, S. Imoto, 2014, Theoretical Biology and Medical Modelling.

Computational gene network analysis reveals TNF-induced angiogenesis

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

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.

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

S. Miyano, R. Yamaguchi, C. Thomaz, 2008 .

KMT2C expression and DNA homologous recombination repair factors in lung cancers with a high-grade fetal adenocarcinoma component

Y. Miyagi, Y. Furukawa, S. Imoto, 2023, Translational lung cancer research.

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

S. Miyano, K. Kumamoto, J. Yokota, 2012, Cancer research.

Antigen delivery targeted to tumor-associated macrophages overcomes tumor immune resistance

S. Miyano, S. Imoto, R. Yamaguchi, 2019, The Journal of clinical investigation.

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.

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).

Genomic Data Assimilation for a Hybrid Functional Petri Net Model of Circadian Rhythm with Time Course Gene Expression Data

T. Higuchi, S. Miyano, S. Imoto, 2006 .

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.

Inferring dynamic gene networks under varying conditions for transcriptomic network comparison

S. Miyano, S. Imoto, R. Yamaguchi, 2010, Bioinform..

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

S. Miyano, S. Imoto, R. Yamaguchi, 2009, BMC Systems Biology.

Development of an MSI-positive colon tumor with aberrant DNA methylation in a PPAP patient

Y. Furukawa, S. Miyano, S. Imoto, 2019, Journal of Human Genetics.

Linear Tensor Projection Revealing Nonlinearity pdf

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

A Bayesian model integration for mutation calling through data partitioning

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

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

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

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).

Identification of Bacteriophage Genome Pieces with Representation Learning

S. Imoto, Yao-zhong Zhang, R. Yamaguchi, 2022 .

Intra-bin structural variant segmentation for whole-genome sequencing data using U-net

S. Miyano, S. Imoto, Yao-zhong Zhang, 2019 .

Automatic sparse principal component analysis

S. Miyano, S. Imoto, R. Yamaguchi, 2020, Canadian Journal of Statistics.