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ORCIDRui Yamaguchi
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2020 – today
- 2022
[j36]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): 4264-4270 (2022)- [j35]Zhongliang Guo, Rui Yamaguchi:
Machine learning methods for protein-protein binding affinity prediction in protein design. Frontiers Bioinform. 2 (2022) - [j34]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): 257-275 (2022) - 2021
- [j33]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): 1211-1217 (2021) - [j32]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) - [c22]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: 320-327 - 2020
- [j31]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): 4813-4816 (2020) - [j30]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. 21-S(3): 136 (2020) - [j29]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): 2916-2933 (2020) - [c21]Takuya Moriyama, Seiya Imoto, Satoru Miyano, Rui Yamaguchi:
Theoretical Foundation of the Performance of Phylogeny-Based Somatic Variant Detection. ISMCO 2020: 87-101 - [i1]Koji Maruhashi, Heewon Park, Rui Yamaguchi, Satoru Miyano:
Linear Tensor Projection Revealing Nonlinearity. CoRR abs/2007.03912 (2020)
2010 – 2019
- 2019
- [j28]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): 4247-4254 (2019) - [j27]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): 267:1-267:11 (2019) - [j26]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. 20-S(16): 591:1-591:10 (2019) - [j25]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): 923-937 (2019) - [c20]Takuya Moriyama, Seiya Imoto, Satoru Miyano, Rui Yamaguchi:
Accurate and Flexible Bayesian Mutation Call from Multi-regional Tumor Samples. ISMCO 2019: 47-61 - 2018
- [c19]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: 387-392 - 2017
- [c18]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: 1227-1232 - 2016
- [j24]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: 63-74 (2016) - [j23]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: 118 (2016) - [c17]Takuya Moriyama, Yuichi Shiraishi, Kenichi Chiba, Rui Yamaguchi, Seiya Imoto, Satoru Miyano:
OVarCall: Bayesian Mutation Calling Method Utilizing Overlapping Paired-End Reads. ISBRA 2016: 40-51 - 2015
- [j22]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: 14 (2015) - 2014
- [j21]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: 54-66 (2014) - [j20]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): 785-798 (2014) - [c16]Masaya M. Saito, Seiya Imoto, Rui Yamaguchi, Satoru Miyano, Tomoyuki Higuchi:
Parameter estimation in multi-compartment SIR model. FUSION 2014: 1-5 - 2013
- [j19]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): 571-582 (2013) - [c15]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: 1385-1390 - 2012
- [j18]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): S6 (2012) - [j17]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): S12 (2012) - [j16]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): 55-67 (2012) - [j15]Kotoe Katayama, Rui Yamaguchi, Seiya Imoto, Keiko Matsuura, Kenji Watanabe:
Connection between traditional medicine and disease. SIGHIT Rec. 2(1): 21 (2012) - [j14]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): 966-972 (2012) - [c14]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: 762-763 - [c13]Masaya M. Saito, Seiya Imoto, Rui Yamaguchi, Satoru Miyano, Tomoyuki Higuchi:
Identifiability of local transmissibility parameters in agent-based pandemic simulation. FUSION 2012: 2466-2471 - 2011
- [j13]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): 1172-1173 (2011) - [j12]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): 143-151 (2011) - [j11]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): 570-576 (2011) - [c12]Masaya M. Saito, Seiya Imoto, Rui Yamaguchi, Satoru Miyano, Tomoyuki Higuchi:
Parallel Agent-Based Simulator for Influenza Pandemic. AAMAS Workshops 2011: 361-370 - [c11]Masaya M. Saito, Seiya Imoto, Rui Yamaguchi, Satoru Miyano, Tomoyuki Higuchi:
Estimation of macroscopic parameter in agent-based pandemic simulation. FUSION 2011: 1-6 - [c10]Takanori Hasegawa, Rui Yamaguchi, Masao Nagasaki, Seiya Imoto, Satoru Miyano:
Poster: Comprehensive pharmacogenomic pathway screening by data assimilation. ICCABS 2011: 246 - [c9]Takanori Hasegawa, Rui Yamaguchi, Masao Nagasaki, Seiya Imoto, Satoru Miyano:
Comprehensive Pharmacogenomic Pathway Screening by Data Assimilation. ISBRA 2011: 160-171 - [c8]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: 370-374 - 2010
- [j10]Teppei Shimamura, Seiya Imoto, Rui Yamaguchi, Masao Nagasaki, Satoru Miyano:
Inferring dynamic gene networks under varying conditions for transcriptomic network comparison. Bioinform. 26(8): 1064-1072 (2010) - [j9]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): 3090-3097 (2010) - [c7]Tomoya Higashigaki, Kaname Kojima, Rui Yamaguchi, Masato Inoue, Seiya Imoto, Satoru Miyano:
Identifying Hidden Confounders in Gene Networks by Bayesian Networks. BIBE 2010: 168-173 - [c6]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: 253-258 - [c5]Teppei Shimamura, Seiya Imoto, Atsushi Niida, Masao Nagasaki, Rui Yamaguchi, Satoru Miyano:
Network profiling analysis for generating modulator-dependent gene networks. BIBM Workshops 2010: 836
2000 – 2009
- 2009
- [j8]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: 41 (2009) - [j7]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): 131-153 (2009) - [c4]Satoru Miyano, Rui Yamaguchi, Yoshinori Tamada, Masao Nagasaki, Seiya Imoto:
Gene Networks Viewed through Two Models. BICoB 2009: 54-66 - 2008
- [j6]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): 932-942 (2008) - [j5]Ryo Yoshida, Masao Nagasaki, Rui Yamaguchi, Seiya Imoto, Satoru Miyano, Tomoyuki Higuchi:
Bayesian learning of biological pathways on genomic data assimilation. Bioinform. 24(22): 2592-2601 (2008) - [j4]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: 106 (2008) - [c3]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: 940-946 - 2007
- [j3]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: 39 (2007) - [j2]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): 37-46 (2007) - [c2]Pramod K. Gupta, Ryo Yoshida, Seiya Imoto, Rui Yamaguchi, Satoru Miyano:
Statistical Absolute Evaluation of Gene Ontology Terms with Gene Expression Data. ISBRA 2007: 146-157 - 2006
- [j1]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): 77-87 (2006) - 2005
- [c1]Rui Yamaguchi, Satoru Yamashita, Tomoyuki Higuchi:
Estimating Gene Networks with cDNA Microarray Data Using State-Space Models. ICCSA (3) 2005: 381-388
Coauthor Index
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