Rui Yamaguchi

62 papers C 5Journal 40Unranked 17
YearRankTypeTitle / Venue / Authors
2025 J jnl
DAG Learning from Zero-Inflated Count Data Using Continuous Optimization.
CoRR
Noriaki Sato, Marco Scutari, Shuichi Kawano, Rui Yamaguchi, Seiya Imoto
2025 J jnl
Practical Causal Evaluation Metrics for Biological Networks.
CoRR
Noriaki Sato, Marco Scutari, Shuichi Kawano, Rui Yamaguchi, Seiya Imoto
2025 J jnl
RVINN: a flexible modeling for inferring dynamic transcriptional and post-transcriptional regulation using physics-informed neural networks.
Bioinform.
Osamu Muto, Zhongliang Guo, Rui Yamaguchi
2022 J jnl
Identification of bacteriophage genome sequences with representation learning.
Bioinform.
Zeheng Bai, Yao-Zhong Zhang, Satoru Miyano, Rui Yamaguchi, Kosuke Fujimoto, Satoshi Uematsu, Seiya Imoto
2022 J jnl
Machine learning methods for protein-protein binding affinity prediction in protein design.
Frontiers Bioinform.
Zhongliang Guo, Rui Yamaguchi
2022 J jnl
Uncovering Molecular Mechanisms of Drug Resistance via Network-Constrained Common Structure Identification.
J. Comput. Biol.
Heewon Park, Rui Yamaguchi, Seiya Imoto, Satoru Miyano
2021 J jnl
Enhancing breakpoint resolution with deep segmentation model: A general refinement method for read-depth based structural variant callers.
PLoS Comput. Biol.
Yao-Zhong Zhang, Seiya Imoto, Satoru Miyano, Rui Yamaguchi
2021 J jnl
Halcyon: an accurate basecaller exploiting an encoder-decoder model with monotonic attention.
Bioinform.
Hiroki Konishi, Rui Yamaguchi, Kiyoshi Yamaguchi, Yoichi Furukawa, Seiya Imoto
2021 — conf
On the application of BERT models for nanopore methylation detection.
BIBM
Yao-Zhong Zhang, Kiyoshi Yamaguchi, Sera Hatakeyama, Yoichi Furukawa, Satoru Miyano, Rui Yamaguchi, Seiya Imoto
2020 J jnl
Ensemble smoothers for inference of hidden states and parameters in combinatorial regulatory model.
J. Frankl. Inst.
Takanori Hasegawa, Rui Yamaguchi, Atsushi Niida, Satoru Miyano, Seiya Imoto
2020 J jnl
Linear Tensor Projection Revealing Nonlinearity.
CoRR
Koji Maruhashi, Heewon Park, Rui Yamaguchi, Satoru Miyano
2020 J jnl
Nanopore basecalling from a perspective of instance segmentation.
BMC Bioinform.
Yao-Zhong Zhang, Arda Akdemir, Georg Tremmel, Seiya Imoto, Satoru Miyano, Tetsuo Shibuya, Rui Yamaguchi
2020 J jnl
Neoantimon: a multifunctional R package for identification of tumor-specific neoantigens.
Bioinform.
Takanori Hasegawa, Shuto Hayashi, Eigo Shimizu, Shinichi Mizuno, Atsushi Niida, Rui Yamaguchi, Satoru Miyano, Hidewaki Nakagawa, Seiya Imoto
2020 — conf
Theoretical Foundation of the Performance of Phylogeny-Based Somatic Variant Detection.
ISMCO
Takuya Moriyama, Seiya Imoto, Satoru Miyano, Rui Yamaguchi
2019 J jnl
A Bayesian model integration for mutation calling through data partitioning.
Bioinform.
Takuya Moriyama, Seiya Imoto, Shuto Hayashi, Yuichi Shiraishi, Satoru Miyano, Rui Yamaguchi
2019 J jnl
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.
Shuto Hayashi, Takuya Moriyama, Rui Yamaguchi, Shinichi Mizuno, Mitsuhiro Komura, Satoru Miyano, Hidewaki Nakagawa, Seiya Imoto
2019 — conf
Accurate and Flexible Bayesian Mutation Call from Multi-regional Tumor Samples.
ISMCO
Takuya Moriyama, Seiya Imoto, Satoru Miyano, Rui Yamaguchi
2019 J jnl
Capturing the differences between humoral immunity in the normal and tumor environments from repertoire-seq of B-cell receptors using supervised machine learning.
BMC Bioinform.
Hiroki Konishi, Daisuke Komura, Hiroto Katoh, Shinichiro Atsumi, Hirotomo Koda, Asami Yamamoto, Yasuyuki Seto, Masashi Fukayama, Rui Yamaguchi, Seiya Imoto, Shumpei Ishikawa
2019 J jnl
Virtual Grid Engine: a simulated grid engine environment for large-scale supercomputers.
BMC Bioinform.
Satoshi Ito, Masaaki Yadome, Tatsuo Nishiki, Shigeru Ishiduki, Hikaru Inoue, Rui Yamaguchi, Satoru Miyano
2018 — conf
Virtual Grid Engine: Accelerating thousands of omics sample analyses using large-scale supercomputers.
BIBM
Satoshi Ito, Masaaki Yadome, Tatsuo Nishiki, Shigeru Ishiduki, Hikaru Inoue, Rui Yamaguchi, Satoru Miyano
2017 — conf
Reconstruction of high read-depth signals from low-depth whole genome sequencing data using deep learning.
BIBM
Yao-Zhong Zhang, Seiya Imoto, Satoru Miyano, Rui Yamaguchi
2016 J jnl
A likelihood-free filtering method via approximate Bayesian computation in evaluating biological simulation models.
Comput. Stat. Data Anal.
Takanori Hasegawa, Atsushi Niida, Tomoya Mori, Teppei Shimamura, Rui Yamaguchi, Satoru Miyano, Tatsuya Akutsu, Seiya Imoto
2016 — conf
OVarCall: Bayesian Mutation Calling Method Utilizing Overlapping Paired-End Reads.
ISBRA
Takuya Moriyama, Yuichi Shiraishi, Kenichi Chiba, Rui Yamaguchi, Seiya Imoto, Satoru Miyano
2016 J jnl
Predicting Japanese Kampo formulas by analyzing database of medical records: a preliminary observational study.
BMC Medical Informatics Decis. Mak.
Tetsuhiro Yoshino, Kotoe Katayama, Yuko Horiba, Kaori Munakata, Rui Yamaguchi, Seiya Imoto, Satoru Miyano, Hideki Mima, Kenji Watanabe
2015 J jnl
Genomic data assimilation using a higher moment filtering technique for restoration of gene regulatory networks.
BMC Syst. Biol.
Takanori Hasegawa, Tomoya Mori, Rui Yamaguchi, Teppei Shimamura, Satoru Miyano, Seiya Imoto, Tatsuya Akutsu
2014 J jnl
An Efficient Data Assimilation Schema for Restoration and Extension of Gene Regulatory Networks Using Time-Course Observation Data.
J. Comput. Biol.
Takanori Hasegawa, Tomoya Mori, Rui Yamaguchi, Seiya Imoto, Satoru Miyano, Tatsuya Akutsu
2014 J jnl
An efficient method of exploring simulation models by assimilating literature and biological observational data.
Biosyst.
Takanori Hasegawa, Masao Nagasaki, Rui Yamaguchi, Seiya Imoto, Satoru Miyano
2014 C conf
Parameter estimation in multi-compartment SIR model.
FUSION
Masaya M. Saito, Seiya Imoto, Rui Yamaguchi, Satoru Miyano, Tomoyuki Higuchi
2013 C conf
Estimation of abrupt changes in sentinel observation data of influenza epidemics in Japan.
FUSION
Masaya M. Saito, Seiya Imoto, Rui Yamaguchi, Satoru Miyano, Tomoyuki Higuchi
2013 J jnl
Multi-omics Approach for Estimating Metabolic Networks Using Low-Order Partial Correlations.
J. Comput. Biol.
Mitsunori Kayano, Seiya Imoto, Rui Yamaguchi, Satoru Miyano
2012 — conf
Analysis of questionnaire for traditional medical and develop decision support system.
BIBM Workshops
Kotoe Katayama, Seiya Imoto, Kenji Watanabe, Rui Yamaguchi, Keiko Matsuura, Satoru Miyano
2012 J jnl
Computational gene network analysis reveals TNF-induced angiogenesis.
BMC Syst. Biol.
Kentaro Ogami, Rui Yamaguchi, Seiya Imoto, Yoshinori Tamada, Hiromitsu Araki, Cristin G. Print, Satoru Miyano
2012 J jnl
Connection between traditional medicine and disease.
SIGHIT Rec.
Kotoe Katayama, Rui Yamaguchi, Seiya Imoto, Keiko Matsuura, Kenji Watanabe
2012 C conf
Identifiability of local transmissibility parameters in agent-based pandemic simulation.
FUSION
Masaya M. Saito, Seiya Imoto, Rui Yamaguchi, Satoru Miyano, Tomoyuki Higuchi
2012 J jnl
Identifying Gene Pathways Associated with Cancer Characteristics via Sparse Statistical Methods.
IEEE ACM Trans. Comput. Biol. Bioinform.
Shuichi Kawano, Teppei Shimamura, Atsushi Niida, Seiya Imoto, Rui Yamaguchi, Masao Nagasaki, Ryo Yoshida, Cristin G. Print, Satoru Miyano
2012 J jnl
Identifying regulational alterations in gene regulatory networks by state space representation of vector autoregressive models and variational annealing.
BMC Genom.
Kaname Kojima, Seiya Imoto, Rui Yamaguchi, André Fujita, Mai Yamauchi, Noriko Gotoh, Satoru Miyano
2012 J jnl
Population Model-Based Inter-Diplotype Similarity Measure for Accurate Diplotype Clustering.
J. Comput. Biol.
Ritsuko Onuki, Ryo Yamada, Rui Yamaguchi, Minoru Kanehisa, Tetsuo Shibuya
2011 — conf
Clustering for Visual Analogue Scale Data in Symbolic Data Analysis.
Complex Adaptive Systems
Kotoe Katayama, Rui Yamaguchi, Seiya Imoto, Keiko Matsuura, Kenji Watanabe, Satoru Miyano
2011 — conf
Comprehensive Pharmacogenomic Pathway Screening by Data Assimilation.
ISBRA
Takanori Hasegawa, Rui Yamaguchi, Masao Nagasaki, Seiya Imoto, Satoru Miyano
2011 C conf
Estimation of macroscopic parameter in agent-based pandemic simulation.
FUSION
Masaya M. Saito, Seiya Imoto, Rui Yamaguchi, Satoru Miyano, Tomoyuki Higuchi
2011 J jnl
Inferring Contagion in Regulatory Networks.
IEEE ACM Trans. Comput. Biol. Bioinform.
André Fujita, João Ricardo Sato, Marcos Angelo Almeida Demasi, Rui Yamaguchi, Teppei Shimamura, Carlos Eduardo Ferreira, Mari Cleide Sogayar, Satoru Miyano
2011 — conf
Parallel Agent-Based Simulator for Influenza Pandemic.
AAMAS Workshops
Masaya M. Saito, Seiya Imoto, Rui Yamaguchi, Satoru Miyano, Tomoyuki Higuchi
2011 — conf
Poster: Comprehensive pharmacogenomic pathway screening by data assimilation.
ICCABS
Takanori Hasegawa, Rui Yamaguchi, Masao Nagasaki, Seiya Imoto, Satoru Miyano
2011 J jnl
SiGN-SSM: open source parallel software for estimating gene networks with state space models.
Bioinform.
Yoshinori Tamada, Rui Yamaguchi, Seiya Imoto, Osamu Hirose, Ryo Yoshida, Masao Nagasaki, Satoru Miyano
2011 J jnl
Transform of visual analogue scale data and their clustering.
Int. J. Knowl. Eng. Soft Data Paradigms
Kotoe Katayama, Rui Yamaguchi, Seiya Imoto, Keiko Matsuura, Kenji Watanabe, Satoru Miyano
2010 — conf
Discovering functional gene pathways associated with cancer heterogeneity via sparse supervised learning.
BIBM
Shuichi Kawano, Teppei Shimamura, Atsushi Niida, Seiya Imoto, Rui Yamaguchi, Masao Nagasaki, Ryo Yoshida, Cristin G. Print, Satoru Miyano
2010 C conf
Identifying Hidden Confounders in Gene Networks by Bayesian Networks.
BIBE
Tomoya Higashigaki, Kaname Kojima, Rui Yamaguchi, Masato Inoue, Seiya Imoto, Satoru Miyano
2010 J jnl
Inferring dynamic gene networks under varying conditions for transcriptomic network comparison.
Bioinform.
Teppei Shimamura, Seiya Imoto, Rui Yamaguchi, Masao Nagasaki, Satoru Miyano
2010 J jnl
Model-free unsupervised gene set screening based on information enrichment in expression profiles.
Bioinform.
Atsushi Niida, Seiya Imoto, Rui Yamaguchi, Masao Nagasaki, André Fujita, Teppei Shimamura, Satoru Miyano
2010 — conf
Network profiling analysis for generating modulator-dependent gene networks.
BIBM Workshops
Teppei Shimamura, Seiya Imoto, Atsushi Niida, Masao Nagasaki, Rui Yamaguchi, Satoru Miyano
2009 — conf
Gene Networks Viewed through Two Models.
BICoB
Satoru Miyano, Rui Yamaguchi, Yoshinori Tamada, Masao Nagasaki, Seiya Imoto
2009 J jnl
Network-Based Predictions and Simulations by Biological State Space Models: Search for Drug Mode of Action.
J. Comput. Sci. Technol.
Rui Yamaguchi, Seiya Imoto, Satoru Miyano
2009 J jnl
Recursive regularization for inferring gene networks from time-course gene expression profiles.
BMC Syst. Biol.
Teppei Shimamura, Seiya Imoto, Rui Yamaguchi, André Fujita, Masao Nagasaki, Satoru Miyano
2008 — conf
Analyzing Time Course Gene Expression Data with Biological and Technical Replicates to Estimate Gene Networks by State Space Models.
Asia International Conference on Modelling and Simulation
Osamu Hirose, Ryo Yoshida, Rui Yamaguchi, Seiya Imoto, Tomoyuki Higuchi, Satoru Miyano
2008 J jnl
Bayesian learning of biological pathways on genomic data assimilation.
Bioinform.
Ryo Yoshida, Masao Nagasaki, Rui Yamaguchi, Seiya Imoto, Satoru Miyano, Tomoyuki Higuchi
2008 J jnl
Multivariate gene expression analysis reveals functional connectivity changes between normal/tumoral prostates.
BMC Syst. Biol.
André Fujita, Luciana Rodrigues Gomes, João Ricardo Sato, Rui Yamaguchi, Carlos E. Thomaz, Mari Cleide Sogayar, Satoru Miyano
2008 J jnl
Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models.
Bioinform.
Osamu Hirose, Ryo Yoshida, Seiya Imoto, Rui Yamaguchi, Tomoyuki Higuchi, Stephen D. Charnock-Jones, Cristin G. Print, Satoru Miyano
2007 J jnl
Finding module-based gene networks with state-space models - Mining high-dimensional and short time-course gene expression data.
IEEE Signal Process. Mag.
Rui Yamaguchi, Ryo Yoshida, Seiya Imoto, Tomoyuki Higuchi, Satoru Miyano
2007 J jnl
Modeling gene expression regulatory networks with the sparse vector autoregressive model.
BMC Syst. Biol.
André Fujita, João Ricardo Sato, Humberto Miguel Garay-Malpartida, Rui Yamaguchi, Satoru Miyano, Mari Cleide Sogayar, Carlos Eduardo Ferreira
2007 — conf
Statistical Absolute Evaluation of Gene Ontology Terms with Gene Expression Data.
ISBRA
Pramod K. Gupta, Ryo Yoshida, Seiya Imoto, Rui Yamaguchi, Satoru Miyano
2006 J jnl
State-space approach with the maximum likelihood principle to identify the system generating time-course gene expression data of yeast.
Int. J. Data Min. Bioinform.
Rui Yamaguchi, Tomoyuki Higuchi
2005 — conf
Estimating Gene Networks with cDNA Microarray Data Using State-Space Models.
ICCSA (3)
Rui Yamaguchi, Satoru Yamashita, Tomoyuki Higuchi