Rui Yamaguchi

Publication Activity (10 Years)

Years Active: 2005-2022
Publications (10 Years): 22

Top Topics

Supervised Machine Learning

Simulation Models

Data Assimilation

Gene Regulatory Networks

Top Venues

J. Comput. Biol.

Publications

Heewon Park, Rui Yamaguchi, Seiya Imoto, Satoru Miyano
Uncovering Molecular Mechanisms of Drug Resistance via Network-Constrained Common Structure Identification. J. Comput. Biol. 29 (3) (2022)
Zeheng Bai, Yao-zhong Zhang, Satoru Miyano, Rui Yamaguchi, Kosuke Fujimoto, Satoshi Uematsu, Seiya Imoto
Identification of bacteriophage genome sequences with representation learning. Bioinform. 38 (18) (2022)
Zhongliang Guo, Rui Yamaguchi
Machine learning methods for protein-protein binding affinity prediction in protein design. Frontiers Bioinform. 2 (2022)
Yao-Zhong Zhang, Kiyoshi Yamaguchi, Sera Hatakeyama, Yoichi Furukawa, Satoru Miyano, Rui Yamaguchi, Seiya Imoto
On the application of BERT models for nanopore methylation detection. BIBM (2021)
Hiroki Konishi, Rui Yamaguchi, Kiyoshi Yamaguchi, Yoichi Furukawa, Seiya Imoto
Halcyon: an accurate basecaller exploiting an encoder-decoder model with monotonic attention. Bioinform. 37 (9) (2021)
Yao-Zhong Zhang, Seiya Imoto, Satoru Miyano, Rui Yamaguchi
Enhancing breakpoint resolution with deep segmentation model: A general refinement method for read-depth based structural variant callers. PLoS Comput. Biol. 17 (10) (2021)
Takanori Hasegawa, Rui Yamaguchi, Atsushi Niida, Satoru Miyano, Seiya Imoto
Ensemble smoothers for inference of hidden states and parameters in combinatorial regulatory model. J. Frankl. Inst. 357 (5) (2020)
Takuya Moriyama, Seiya Imoto, Satoru Miyano, Rui Yamaguchi
Theoretical Foundation of the Performance of Phylogeny-Based Somatic Variant Detection. ISMCO (2020)
Yao-zhong Zhang, Arda Akdemir, Georg Tremmel, Seiya Imoto, Satoru Miyano, Tetsuo Shibuya, Rui Yamaguchi
Nanopore basecalling from a perspective of instance segmentation. BMC Bioinform. (3) (2020)
Takanori Hasegawa, Shuto Hayashi, Eigo Shimizu, Shinichi Mizuno, Atsushi Niida, Rui Yamaguchi, Satoru Miyano, Hidewaki Nakagawa, Seiya Imoto
Neoantimon: a multifunctional R package for identification of tumor-specific neoantigens. Bioinform. 36 (18) (2020)
Koji Maruhashi, Heewon Park, Rui Yamaguchi, Satoru Miyano
Linear Tensor Projection Revealing Nonlinearity. CoRR (2020)
Satoshi Ito, Masaaki Yadome, Tatsuo Nishiki, Shigeru Ishiduki, Hikaru Inoue, Rui Yamaguchi, Satoru Miyano
Virtual Grid Engine: a simulated grid engine environment for large-scale supercomputers. BMC Bioinform. (16) (2019)
Takuya Moriyama, Seiya Imoto, Shuto Hayashi, Yuichi Shiraishi, Satoru Miyano, Rui Yamaguchi
A Bayesian model integration for mutation calling through data partitioning. Bioinform. 35 (21) (2019)
Shuto Hayashi, Takuya Moriyama, Rui Yamaguchi, Shinichi Mizuno, Mitsuhiro Komura, Satoru Miyano, Hidewaki Nakagawa, Seiya Imoto
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. 26 (9) (2019)
Hiroki Konishi, Daisuke Komura, Hiroto Katoh, Shinichiro Atsumi, Hirotomo Koda, Asami Yamamoto, Yasuyuki Seto, Masashi Fukayama, Rui Yamaguchi, Seiya Imoto, Shumpei Ishikawa
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. 20 (1) (2019)
Takuya Moriyama, Seiya Imoto, Satoru Miyano, Rui Yamaguchi
Accurate and Flexible Bayesian Mutation Call from Multi-regional Tumor Samples. ISMCO (2019)
Satoshi Ito, Masaaki Yadome, Tatsuo Nishiki, Shigeru Ishiduki, Hikaru Inoue, Rui Yamaguchi, Satoru Miyano
Virtual Grid Engine: Accelerating thousands of omics sample analyses using large-scale supercomputers. BIBM (2018)
Yao-Zhong Zhang, Seiya Imoto, Satoru Miyano, Rui Yamaguchi
Reconstruction of high read-depth signals from low-depth whole genome sequencing data using deep learning. BIBM (2017)
Takuya Moriyama, Yuichi Shiraishi, Kenichi Chiba, Rui Yamaguchi, Seiya Imoto, Satoru Miyano
OVarCall: Bayesian Mutation Calling Method Utilizing Overlapping Paired-End Reads. ISBRA (2016)
Tetsuhiro Yoshino, Kotoe Katayama, Yuko Horiba, Kaori Munakata, Rui Yamaguchi, Seiya Imoto, Satoru Miyano, Hideki Mima, Kenji Watanabe
Predicting Japanese Kampo formulas by analyzing database of medical records: a preliminary observational study. BMC Medical Informatics Decis. Mak. 16 (2016)
Takanori Hasegawa, Atsushi Niida, Tomoya Mori, Teppei Shimamura, Rui Yamaguchi, Satoru Miyano, Tatsuya Akutsu, Seiya Imoto
A likelihood-free filtering method via approximate Bayesian computation in evaluating biological simulation models. Comput. Stat. Data Anal. 94 (2016)
Takanori Hasegawa, Tomoya Mori, Rui Yamaguchi, Teppei Shimamura, Satoru Miyano, Seiya Imoto, Tatsuya Akutsu
Genomic data assimilation using a higher moment filtering technique for restoration of gene regulatory networks. BMC Syst. Biol. 9 (2015)
Takanori Hasegawa, Masao Nagasaki, Rui Yamaguchi, Seiya Imoto, Satoru Miyano
An efficient method of exploring simulation models by assimilating literature and biological observational data. Biosyst. 121 (2014)
Takanori Hasegawa, Tomoya Mori, Rui Yamaguchi, Seiya Imoto, Satoru Miyano, Tatsuya Akutsu
An Efficient Data Assimilation Schema for Restoration and Extension of Gene Regulatory Networks Using Time-Course Observation Data. J. Comput. Biol. 21 (11) (2014)
Masaya M. Saito, Seiya Imoto, Rui Yamaguchi, Satoru Miyano, Tomoyuki Higuchi
Parameter estimation in multi-compartment SIR model. FUSION (2014)
Masaya M. Saito, Seiya Imoto, Rui Yamaguchi, Satoru Miyano, Tomoyuki Higuchi
Estimation of abrupt changes in sentinel observation data of influenza epidemics in Japan. FUSION (2013)
Mitsunori Kayano, Seiya Imoto, Rui Yamaguchi, Satoru Miyano
Multi-omics Approach for Estimating Metabolic Networks Using Low-Order Partial Correlations. J. Comput. Biol. 20 (8) (2013)
Kotoe Katayama, Rui Yamaguchi, Seiya Imoto, Keiko Matsuura, Kenji Watanabe
Connection between traditional medicine and disease. SIGHIT Rec. 2 (1) (2012)
Kaname Kojima, Seiya Imoto, Rui Yamaguchi, André Fujita, Mai Yamauchi, Noriko Gotoh, Satoru Miyano
Identifying regulational alterations in gene regulatory networks by state space representation of vector autoregressive models and variational annealing. BMC Genom. 13 (S-1) (2012)
Ritsuko Onuki, Ryo Yamada, Rui Yamaguchi, Minoru Kanehisa, Tetsuo Shibuya
Population Model-Based Inter-Diplotype Similarity Measure for Accurate Diplotype Clustering. J. Comput. Biol. 19 (1) (2012)
Shuichi Kawano, Teppei Shimamura, Atsushi Niida, Seiya Imoto, Rui Yamaguchi, Masao Nagasaki, Ryo Yoshida, Cristin G. Print, Satoru Miyano
Identifying Gene Pathways Associated with Cancer Characteristics via Sparse Statistical Methods. IEEE ACM Trans. Comput. Biol. Bioinform. 9 (4) (2012)
Kentaro Ogami, Rui Yamaguchi, Seiya Imoto, Yoshinori Tamada, Hiromitsu Araki, Cristin G. Print, Satoru Miyano
Computational gene network analysis reveals TNF-induced angiogenesis. BMC Syst. Biol. 6 (S-2) (2012)
Masaya M. Saito, Seiya Imoto, Rui Yamaguchi, Satoru Miyano, Tomoyuki Higuchi
Identifiability of local transmissibility parameters in agent-based pandemic simulation. FUSION (2012)
Kotoe Katayama, Seiya Imoto, Kenji Watanabe, Rui Yamaguchi, Keiko Matsuura, Satoru Miyano
Analysis of questionnaire for traditional medical and develop decision support system. BIBM Workshops (2012)
Kotoe Katayama, Rui Yamaguchi, Seiya Imoto, Keiko Matsuura, Kenji Watanabe, Satoru Miyano
Clustering for Visual Analogue Scale Data in Symbolic Data Analysis. Complex Adaptive Systems (2011)
Kotoe Katayama, Rui Yamaguchi, Seiya Imoto, Keiko Matsuura, Kenji Watanabe, Satoru Miyano
Transform of visual analogue scale data and their clustering. Int. J. Knowl. Eng. Soft Data Paradigms 3 (2) (2011)
Masaya M. Saito, Seiya Imoto, Rui Yamaguchi, Satoru Miyano, Tomoyuki Higuchi
Estimation of macroscopic parameter in agent-based pandemic simulation. FUSION (2011)
Masaya M. Saito, Seiya Imoto, Rui Yamaguchi, Satoru Miyano, Tomoyuki Higuchi
Parallel Agent-Based Simulator for Influenza Pandemic. AAMAS Workshops (2011)
Yoshinori Tamada, Rui Yamaguchi, Seiya Imoto, Osamu Hirose, Ryo Yoshida, Masao Nagasaki, Satoru Miyano
SiGN-SSM: open source parallel software for estimating gene networks with state space models. Bioinform. 27 (8) (2011)
André Fujita, João Ricardo Sato, Marcos Angelo Almeida Demasi, Rui Yamaguchi, Teppei Shimamura, Carlos Eduardo Ferreira, Mari Cleide Sogayar, Satoru Miyano
Inferring Contagion in Regulatory Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 8 (2) (2011)
Takanori Hasegawa, Rui Yamaguchi, Masao Nagasaki, Seiya Imoto, Satoru Miyano
Comprehensive Pharmacogenomic Pathway Screening by Data Assimilation. ISBRA (2011)
Takanori Hasegawa, Rui Yamaguchi, Masao Nagasaki, Seiya Imoto, Satoru Miyano
Poster: Comprehensive pharmacogenomic pathway screening by data assimilation. ICCABS (2011)
Teppei Shimamura, Seiya Imoto, Rui Yamaguchi, Masao Nagasaki, Satoru Miyano
Inferring dynamic gene networks under varying conditions for transcriptomic network comparison. Bioinform. 26 (8) (2010)
Tomoya Higashigaki, Kaname Kojima, Rui Yamaguchi, Masato Inoue, Seiya Imoto, Satoru Miyano
Identifying Hidden Confounders in Gene Networks by Bayesian Networks. BIBE (2010)
Teppei Shimamura, Seiya Imoto, Atsushi Niida, Masao Nagasaki, Rui Yamaguchi, Satoru Miyano
Network profiling analysis for generating modulator-dependent gene networks. BIBM Workshops (2010)
Shuichi Kawano, Teppei Shimamura, Atsushi Niida, Seiya Imoto, Rui Yamaguchi, Masao Nagasaki, Ryo Yoshida, Cristin G. Print, Satoru Miyano
Discovering functional gene pathways associated with cancer heterogeneity via sparse supervised learning. BIBM (2010)
Atsushi Niida, Seiya Imoto, Rui Yamaguchi, Masao Nagasaki, André Fujita, Teppei Shimamura, Satoru Miyano
Model-free unsupervised gene set screening based on information enrichment in expression profiles. Bioinform. 26 (24) (2010)
Rui Yamaguchi, Seiya Imoto, Satoru Miyano
Network-Based Predictions and Simulations by Biological State Space Models: Search for Drug Mode of Action. J. Comput. Sci. Technol. 25 (1) (2009)
Satoru Miyano, Rui Yamaguchi, Yoshinori Tamada, Masao Nagasaki, Seiya Imoto
Gene Networks Viewed through Two Models. BICoB (2009)
Teppei Shimamura, Seiya Imoto, Rui Yamaguchi, André Fujita, Masao Nagasaki, Satoru Miyano
Recursive regularization for inferring gene networks from time-course gene expression profiles. BMC Syst. Biol. 3 (2009)
Ryo Yoshida, Masao Nagasaki, Rui Yamaguchi, Seiya Imoto, Satoru Miyano, Tomoyuki Higuchi
Bayesian learning of biological pathways on genomic data assimilation. Bioinform. 24 (22) (2008)
André Fujita, Luciana Rodrigues Gomes, João Ricardo Sato, Rui Yamaguchi, Carlos E. Thomaz, Mari Cleide Sogayar, Satoru Miyano
Multivariate gene expression analysis reveals functional connectivity changes between normal/tumoral prostates. BMC Syst. Biol. 2 (2008)
Osamu Hirose, Ryo Yoshida, Rui Yamaguchi, Seiya Imoto, Tomoyuki Higuchi, Satoru Miyano
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 (2008)
Osamu Hirose, Ryo Yoshida, Seiya Imoto, Rui Yamaguchi, Tomoyuki Higuchi, Stephen D. Charnock-Jones, Cristin G. Print, Satoru Miyano
Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models. Bioinform. 24 (7) (2008)
Pramod K. Gupta, Ryo Yoshida, Seiya Imoto, Rui Yamaguchi, Satoru Miyano
Statistical Absolute Evaluation of Gene Ontology Terms with Gene Expression Data. ISBRA (2007)
André Fujita, João Ricardo Sato, Humberto Miguel Garay-Malpartida, Rui Yamaguchi, Satoru Miyano, Mari Cleide Sogayar, Carlos Eduardo Ferreira
Modeling gene expression regulatory networks with the sparse vector autoregressive model. BMC Syst. Biol. 1 (2007)
Rui Yamaguchi, Ryo Yoshida, Seiya Imoto, Tomoyuki Higuchi, Satoru Miyano
Finding module-based gene networks with state-space models - Mining high-dimensional and short time-course gene expression data. IEEE Signal Process. Mag. 24 (1) (2007)
Rui Yamaguchi, Tomoyuki Higuchi
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. 1 (1) (2006)
Rui Yamaguchi, Satoru Yamashita, Tomoyuki Higuchi
Estimating Gene Networks with cDNA Microarray Data Using State-Space Models. ICCSA (3) (2005)