Rui Yamaguchi

According to our database, Rui Yamaguchi authored at least 59 papers between 2005 and 2022.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of three.

2022

Uncovering Molecular Mechanisms of Drug Resistance via Network-Constrained Common Structure Identification.

Heewon Park, Rui Yamaguchi, Seiya Imoto, Satoru Miyano

J. Comput. Biol., 2022

Machine learning methods for protein-protein binding affinity prediction in protein design.

Zhongliang Guo, Rui Yamaguchi

Frontiers Bioinform., 2022

Identification of bacteriophage genome sequences with representation learning.

Zeheng Bai, Yao-zhong Zhang, Satoru Miyano, Rui Yamaguchi, Kosuke Fujimoto, Satoshi Uematsu, Seiya Imoto

Bioinform., 2022

2021

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

Yao-Zhong Zhang, Seiya Imoto, Satoru Miyano, Rui Yamaguchi

PLoS Comput. Biol., 2021

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

Hiroki Konishi, Rui Yamaguchi, Kiyoshi Yamaguchi, Yoichi Furukawa, Seiya Imoto

Bioinform., 2021

On the application of BERT models for nanopore methylation detection.

Yao-Zhong Zhang, Kiyoshi Yamaguchi, Sera Hatakeyama, Yoichi Furukawa, Satoru Miyano, Rui Yamaguchi, Seiya Imoto

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021

2020

Nanopore basecalling from a perspective of instance segmentation.

Yao-zhong Zhang, Arda Akdemir, Georg Tremmel, Seiya Imoto, Satoru Miyano, Tetsuo Shibuya, Rui Yamaguchi

BMC Bioinform., April, 2020

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

Takanori Hasegawa, Rui Yamaguchi, Atsushi Niida, Satoru Miyano, Seiya Imoto

J. Frankl. Inst., 2020

Linear Tensor Projection Revealing Nonlinearity.

Koji Maruhashi, Heewon Park, Rui Yamaguchi, Satoru Miyano

CoRR, 2020

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

Takanori Hasegawa, Shuto Hayashi, Eigo Shimizu, Shinichi Mizuno, Atsushi Niida, Rui Yamaguchi, Satoru Miyano, Hidewaki Nakagawa, Seiya Imoto

Bioinform., 2020

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

Takuya Moriyama, Seiya Imoto, Satoru Miyano, Rui Yamaguchi

Proceedings of the Mathematical and Computational Oncology, 2020

2019

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

Shuto Hayashi, Takuya Moriyama, Rui Yamaguchi, Shinichi Mizuno, Mitsuhiro Komura, Satoru Miyano, Hidewaki Nakagawa, Seiya Imoto

J. Comput. Biol., 2019

Capturing the differences between humoral immunity in the normal and tumor environments from repertoire-seq of B-cell receptors using supervised machine learning.

Hiroki Konishi, Daisuke Komura, Hiroto Katoh, Shinichiro Atsumi, Hirotomo Koda, Asami Yamamoto, Yasuyuki Seto, Masashi Fukayama, Rui Yamaguchi, Seiya Imoto, Shumpei Ishikawa

BMC Bioinform., 2019

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

Satoshi Ito, Masaaki Yadome, Tatsuo Nishiki, Shigeru Ishiduki, Hikaru Inoue, Rui Yamaguchi, Satoru Miyano

BMC Bioinform., 2019

A Bayesian model integration for mutation calling through data partitioning.

Takuya Moriyama, Seiya Imoto, Shuto Hayashi, Yuichi Shiraishi, Satoru Miyano, Rui Yamaguchi

Bioinform., 2019

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

Takuya Moriyama, Seiya Imoto, Satoru Miyano, Rui Yamaguchi

Proceedings of the Mathematical and Computational Oncology - First International Symposium, 2019

2018

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

Satoshi Ito, Masaaki Yadome, Tatsuo Nishiki, Shigeru Ishiduki, Hikaru Inoue, Rui Yamaguchi, Satoru Miyano

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018

2017

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

Yao-Zhong Zhang, Seiya Imoto, Satoru Miyano, Rui Yamaguchi

Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine, 2017

2016

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

Tetsuhiro Yoshino, Kotoe Katayama, Yuko Horiba, Kaori Munakata, Rui Yamaguchi, Seiya Imoto, Satoru Miyano, Hideki Mima, Kenji Watanabe

BMC Medical Informatics Decis. Mak., 2016

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

Takanori Hasegawa, Atsushi Niida, Tomoya Mori, Teppei Shimamura, Rui Yamaguchi, Satoru Miyano, Tatsuya Akutsu, Seiya Imoto

Comput. Stat. Data Anal., 2016

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

Takuya Moriyama, Yuichi Shiraishi, Kenichi Chiba, Rui Yamaguchi, Seiya Imoto, Satoru Miyano

Proceedings of the Bioinformatics Research and Applications - 12th International Symposium, 2016

2015

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

Takanori Hasegawa, Tomoya Mori, Rui Yamaguchi, Teppei Shimamura, Satoru Miyano, Seiya Imoto, Tatsuya Akutsu

BMC Syst. Biol., 2015

2014

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

Takanori Hasegawa, Tomoya Mori, Rui Yamaguchi, Seiya Imoto, Satoru Miyano, Tatsuya Akutsu

J. Comput. Biol., 2014

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

Takanori Hasegawa, Masao Nagasaki, Rui Yamaguchi, Seiya Imoto, Satoru Miyano

Biosyst., 2014

Parameter estimation in multi-compartment SIR model.

Masaya M. Saito, Seiya Imoto, Rui Yamaguchi, Satoru Miyano, Tomoyuki Higuchi

Proceedings of the 17th International Conference on Information Fusion, 2014

2013

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

Mitsunori Kayano, Seiya Imoto, Rui Yamaguchi, Satoru Miyano

J. Comput. Biol., 2013

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

Masaya M. Saito, Seiya Imoto, Rui Yamaguchi, Satoru Miyano, Tomoyuki Higuchi

Proceedings of the 16th International Conference on Information Fusion, 2013

2012

Identifying Gene Pathways Associated with Cancer Characteristics via Sparse Statistical Methods.

Shuichi Kawano, Teppei Shimamura, Atsushi Niida, Seiya Imoto, Rui Yamaguchi, Masao Nagasaki, Ryo Yoshida, Cristin G. Print, Satoru Miyano

IEEE ACM Trans. Comput. Biol. Bioinform., 2012

Connection between traditional medicine and disease.

Kotoe Katayama, Rui Yamaguchi, Seiya Imoto, Keiko Matsuura, Kenji Watanabe

SIGHIT Rec., 2012

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

Ritsuko Onuki, Ryo Yamada, Rui Yamaguchi, Minoru Kanehisa, Tetsuo Shibuya

J. Comput. Biol., 2012

Computational gene network analysis reveals TNF-induced angiogenesis.

Kentaro Ogami, Rui Yamaguchi, Seiya Imoto, Yoshinori Tamada, Hiromitsu Araki, Cristin G. Print, Satoru Miyano

BMC Syst. Biol., 2012

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

Kaname Kojima, Seiya Imoto, Rui Yamaguchi, André Fujita, Mai Yamauchi, Noriko Gotoh, Satoru Miyano

BMC Genom., 2012

Identifiability of local transmissibility parameters in agent-based pandemic simulation.

Masaya M. Saito, Seiya Imoto, Rui Yamaguchi, Satoru Miyano, Tomoyuki Higuchi

Proceedings of the 15th International Conference on Information Fusion, 2012

Analysis of questionnaire for traditional medical and develop decision support system.

Kotoe Katayama, Seiya Imoto, Kenji Watanabe, Rui Yamaguchi, Keiko Matsuura, Satoru Miyano

Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2012

2011

Inferring Contagion in Regulatory Networks.

André Fujita, João Ricardo Sato, Marcos Angelo Almeida Demasi, Rui Yamaguchi, Teppei Shimamura, Carlos Eduardo Ferreira, Mari Cleide Sogayar, Satoru Miyano

IEEE ACM Trans. Comput. Biol. Bioinform., 2011

Clustering for Visual Analogue Scale Data in Symbolic Data Analysis.

Kotoe Katayama, Rui Yamaguchi, Seiya Imoto, Keiko Matsuura, Kenji Watanabe, Satoru Miyano

Proceedings of the Complex Adaptive Systems 2011 Conference, 2011

Transform of visual analogue scale data and their clustering.

Kotoe Katayama, Rui Yamaguchi, Seiya Imoto, Keiko Matsuura, Kenji Watanabe, Satoru Miyano

Int. J. Knowl. Eng. Soft Data Paradigms, 2011

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

Yoshinori Tamada, Rui Yamaguchi, Seiya Imoto, Osamu Hirose, Ryo Yoshida, Masao Nagasaki, Satoru Miyano

Bioinform., 2011

Comprehensive Pharmacogenomic Pathway Screening by Data Assimilation.

Takanori Hasegawa, Rui Yamaguchi, Masao Nagasaki, Seiya Imoto, Satoru Miyano

Proceedings of the Bioinformatics Research and Applications - 7th International Symposium, 2011

Poster: Comprehensive pharmacogenomic pathway screening by data assimilation.

Takanori Hasegawa, Rui Yamaguchi, Masao Nagasaki, Seiya Imoto, Satoru Miyano

Proceedings of the IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, 2011

Estimation of macroscopic parameter in agent-based pandemic simulation.

Masaya M. Saito, Seiya Imoto, Rui Yamaguchi, Satoru Miyano, Tomoyuki Higuchi

Proceedings of the 14th International Conference on Information Fusion, 2011

Parallel Agent-Based Simulator for Influenza Pandemic.

Masaya M. Saito, Seiya Imoto, Rui Yamaguchi, Satoru Miyano, Tomoyuki Higuchi

Proceedings of the Advanced Agent Technology, 2011

2010

Inferring dynamic gene networks under varying conditions for transcriptomic network comparison.

Teppei Shimamura, Seiya Imoto, Rui Yamaguchi, Masao Nagasaki, Satoru Miyano

Bioinform., 2010

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

Atsushi Niida, Seiya Imoto, Rui Yamaguchi, Masao Nagasaki, André Fujita, Teppei Shimamura, Satoru Miyano

Bioinform., 2010

Network profiling analysis for generating modulator-dependent gene networks.

Teppei Shimamura, Seiya Imoto, Atsushi Niida, Masao Nagasaki, Rui Yamaguchi, Satoru Miyano

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.

Shuichi Kawano, Teppei Shimamura, Atsushi Niida, Seiya Imoto, Rui Yamaguchi, Masao Nagasaki, Ryo Yoshida, Cristin G. Print, Satoru Miyano

Proceedings of the 2010 IEEE International Conference on Bioinformatics and Biomedicine, 2010

Identifying Hidden Confounders in Gene Networks by Bayesian Networks.

Tomoya Higashigaki, Kaname Kojima, Rui Yamaguchi, Masato Inoue, Seiya Imoto, Satoru Miyano

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.

Rui Yamaguchi, Seiya Imoto, Satoru Miyano

J. Comput. Sci. Technol., 2009

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

Teppei Shimamura, Seiya Imoto, Rui Yamaguchi, André Fujita, Masao Nagasaki, Satoru Miyano

BMC Syst. Biol., 2009

Gene Networks Viewed through Two Models.

Satoru Miyano, Rui Yamaguchi, Yoshinori Tamada, Masao Nagasaki, Seiya Imoto

Proceedings of the Bioinformatics and Computational Biology, 2009

2008

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

André Fujita, Luciana Rodrigues Gomes, João Ricardo Sato, Rui Yamaguchi, Carlos E. Thomaz, Mari Cleide Sogayar, Satoru Miyano

BMC Syst. Biol., 2008

Bayesian learning of biological pathways on genomic data assimilation.

Ryo Yoshida, Masao Nagasaki, Rui Yamaguchi, Seiya Imoto, Satoru Miyano, Tomoyuki Higuchi

Bioinform., 2008

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

Osamu Hirose, Ryo Yoshida, Seiya Imoto, Rui Yamaguchi, Tomoyuki Higuchi, Stephen D. Charnock-Jones, Cristin G. Print, Satoru Miyano

Bioinform., 2008

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

Osamu Hirose, Ryo Yoshida, Rui Yamaguchi, Seiya Imoto, Tomoyuki Higuchi, Satoru Miyano

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.

Rui Yamaguchi, Ryo Yoshida, Seiya Imoto, Tomoyuki Higuchi, Satoru Miyano

IEEE Signal Process. Mag., 2007

Modeling gene expression regulatory networks with the sparse vector autoregressive model.

André Fujita, João Ricardo Sato, Humberto Miguel Garay-Malpartida, Rui Yamaguchi, Satoru Miyano, Mari Cleide Sogayar, Carlos Eduardo Ferreira

BMC Syst. Biol., 2007

Statistical Absolute Evaluation of Gene Ontology Terms with Gene Expression Data.

Pramod K. Gupta, Ryo Yoshida, Seiya Imoto, Rui Yamaguchi, Satoru Miyano

Proceedings of the Bioinformatics Research and Applications, Third International Symposium, 2007

2006

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

Rui Yamaguchi, Tomoyuki Higuchi

Int. J. Data Min. Bioinform., 2006

2005

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

Rui Yamaguchi, Satoru Yamashita, Tomoyuki Higuchi

Proceedings of the Computational Science and Its Applications, 2005