Seiya Imoto

134 papers B 1C 9Misc 7Journal 82Unranked 34
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
Gene behaviors-based network enrichment analysis and its application to reveal immune disease pathways enriched with COVID-19 severity-specific gene networks.
Bioinform.
Heewon Park, Seiya Imoto, Satory Miyano
2025 J jnl
Histo-Genomic Knowledge Association for Cancer Prognosis From Histopathology Whole Slide Images.
IEEE Trans. Medical Imaging
Zhikang Wang, Yumeng Zhang, Yingxue Xu, Seiya Imoto, Hao Chen, Jiangning Song
2025 J jnl
PharaCon: a new framework for identifying bacteriophages via conditional representation learning.
Bioinform.
Zeheng Bai, Yao-Zhong Zhang, Yuxuan Pang, Seiya Imoto
2025 J jnl
Powerful gene network enrichment analysis and its application to severe COVID-19 gene network.
Briefings Bioinform.
Heewon Park, Seiya Imoto, Satoru Miyano
2025 J jnl
Practical Causal Evaluation Metrics for Biological Networks.
CoRR
Noriaki Sato, Marco Scutari, Shuichi Kawano, Rui Yamaguchi, Seiya Imoto
2025 J jnl
STForte: tissue context-specific encoding and consistency-aware spatial imputation for spatially resolved transcriptomics.
Briefings Bioinform.
Yuxuan Pang, Chunxuan Wang, Yao-Zhong Zhang, Zhuo Wang, Seiya Imoto, Tzong-Yi Lee
2024 J jnl
Deep learning approaches for non-coding genetic variant effect prediction: current progress and future prospects.
Briefings Bioinform.
Xiaoyu Wang, Fuyi Li, Yiwen Zhang, Seiya Imoto, Hsin-Hui Shen, Shanshan Li, Yuming Guo, Jian Yang, Jiangning Song
2024 J jnl
Dual-stream multi-dependency graph neural network enables precise cancer survival analysis.
Medical Image Anal.
Zhikang Wang, Jiani Ma, Qian Gao, Chris Bain, Seiya Imoto, Pietro Liò, Hongmin Cai, Hao Chen, Jiangning Song
2024 J jnl
Histo-Genomic Knowledge Distillation For Cancer Prognosis From Histopathology Whole Slide Images.
CoRR
Zhikang Wang, Yumeng Zhang, Yingxue Xu, Seiya Imoto, Hao Chen, Jiangning Song
2023 J jnl
Gene Regulatory Network-Classifier: Gene Regulatory Network-Based Classifier and Its Applications to Gastric Cancer Drug (5-Fluorouracil) Marker Identification.
J. Comput. Biol.
Heewon Park, Seiya Imoto, Satoru Miyano
2023 — conf
Imputing time-series microbiome abundance profiles with diffusion model.
BIBM
Misato Seki, Yao-Zhong Zhang, Seiya Imoto
2023 J jnl
Investigation of the BERT model on nucleotide sequences with non-standard pre-training and evaluation of different k-mer embeddings.
Bioinform.
Yao-Zhong Zhang, Zeheng Bai, Seiya Imoto
2023 J jnl
PFresGO: an attention mechanism-based deep-learning approach for protein annotation by integrating gene ontology inter-relationships.
Bioinform.
Tong Pan, Chen Li, Yue Bi, Zhikang Wang, Robin B. Gasser, Anthony W. Purcell, Tatsuya Akutsu, Geoffrey I. Webb, Seiya Imoto, Jiangning Song
2023 J jnl
Surformer: An interpretable pattern-perceptive survival transformer for cancer survival prediction from histopathology whole slide images.
Comput. Methods Programs Biomed.
Zhikang Wang, Qian Gao, Xiaoping Yi, Xinyu Zhang, Yiwen Zhang, Daokun Zhang, Pietro Liò, Chris Bain, Richard Bassed, Shanshan Li, Yuming Guo, Seiya Imoto, Jianhua Yao, Roger J. Daly, Jiangning Song
2023 J jnl
Targeting tumor heterogeneity: multiplex-detection-based multiple instance learning for whole slide image classification.
Bioinform.
Zhikang Wang, Yue Bi, Tong Pan, Xiaoyu Wang, Chris Bain, Richard Bassed, Seiya Imoto, Jianhua Yao, Roger J. Daly, Jiangning Song
2023 J jnl
Zero-shot-capable identification of phage-host relationships with whole-genome sequence representation by contrastive learning.
Briefings Bioinform.
Yao-Zhong Zhang, Yunjie Liu, Zeheng Bai, Kosuke Fujimoto, Satoshi Uematsu, Seiya Imoto
2023 J jnl
iAMPCN: a deep-learning approach for identifying antimicrobial peptides and their functional activities.
Briefings Bioinform.
Jing Xu, Fuyi Li, Chen Li, Xudong Guo, Cornelia B. Landersdorfer, Hsin-Hui Shen, Anton Y. Peleg, Jian Li, Seiya Imoto, Jianhua Yao, Tatsuya Akutsu, Jiangning Song
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
Improvement of the Japanese healthcare data system for the effective management of patients with COVID-19: A national survey.
Int. J. Medical Informatics
Kohei Takeshita, Hiroyuki Takao, Seiya Imoto, Yuichi Murayama
2022 J jnl
Multiplex-detection Based Multiple Instance Learning Network for Whole Slide Image Classification.
CoRR
Zhikang Wang, Yue Bi, Tong Pan, Xiaoyu Wang, Chris Bain, Richard Bassed, Seiya Imoto, Jianhua Yao, Jiangning Song
2022 J jnl
PredictiveNetwork: predictive gene network estimation with application to gastric cancer drug response-predictive network analysis.
BMC Bioinform.
Heewon Park, Seiya Imoto, Satoru Miyano
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 — conf
Discovering microbe functionality in human disease with a gene-ontology-aware model.
BIBM
Yunjie Liu, Yaozhong Zhang, Seiya Imoto
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
HEAL: an automated deep learning framework for cancer histopathology image analysis.
Bioinform.
Yanan Wang, Nicolas Coudray, Yun Zhao, Fuyi Li, Changyuan Hu, Yao-Zhong Zhang, Seiya Imoto, Aristotelis Tsirigos, Geoffrey I. Webb, Roger J. Daly, Jiangning Song
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
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
Robust Sample-Specific Stability Selection with Effective Error Control.
J. Comput. Biol.
Heewon Park, Makoto Yamada, Seiya Imoto, Satoru Miyano
2018 J jnl
Adaptive NetworkProfiler for Identifying Cancer Characteristic-Specific Gene Regulatory Networks.
J. Comput. Biol.
Heewon Park, Teppei Shimamura, Seiya Imoto, Satoru Miyano
2017 J jnl
A Novel Adaptive Penalized Logistic Regression for Uncovering Biomarker Associated with Anti-Cancer Drug Sensitivity.
IEEE ACM Trans. Comput. Biol. Bioinform.
Heewon Park, Yuichi Shiraishi, Seiya Imoto, Satoru Miyano
2017 J jnl
Interaction-Based Feature Selection for Uncovering Cancer Driver Genes Through Copy Number-Driven Expression Level.
J. Comput. Biol.
Heewon Park, Atsushi Niida, Seiya Imoto, 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 J jnl
Binary contingency table method for analysing gene mutation in cancer genome.
Int. J. Bioinform. Res. Appl.
Emi Ayada, Takanori Hasegawa, Atsushi Niida, Satoru Miyano, 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
2016 J jnl
Protein Fold Recognition Using Genetic Algorithm Optimized Voting Scheme and Profile Bigram.
J. Softw.
Harsh Saini, Gaurav Raicar, Sunil Pranit Lal, Abdollah Dehzangi, Seiya Imoto, Alok Sharma
2015 — conf
Binary Contingency Table Method for Analyzing Gene Mutation in Cancer Genome.
ISBRA
Emi Ayada, Atsushi Niida, Takanori Hasegawa, Satoru Miyano, Seiya Imoto
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
2015 J jnl
Genomon ITDetector: a tool for somatic internal tandem duplication detection from cancer genome sequencing data.
Bioinform.
Kenichi Chiba, Yuichi Shiraishi, Yasunobu Nagata, Kenichi Yoshida, Seiya Imoto, Seishi Ogawa, Satoru Miyano
2015 J jnl
Sparse Overlapping Group Lasso for Integrative Multi-Omics Analysis.
J. Comput. Biol.
Heewon Park, Atsushi Niida, Satoru Miyano, Seiya Imoto
2014 J jnl
A feature selection method using fixed-point algorithm for DNA microarray gene expression data.
Int. J. Knowl. Based Intell. Eng. Syst.
Alok Sharma, Kuldip K. Paliwal, Seiya Imoto, Satoru Miyano, Vandana Sharma, Rajeshkannan Ananthanarayanan
2014 J jnl
A feature selection method using improved regularized linear discriminant analysis.
Mach. Vis. Appl.
Alok Sharma, Kuldip K. Paliwal, Seiya Imoto, Satoru Miyano
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 J jnl
HapMuC: somatic mutation calling using heterozygous germ line variants near candidate mutations.
Bioinform.
Naoto Usuyama, Yuichi Shiraishi, Yusuke Sato, Haruki Kume, Yukio Homma, Seishi Ogawa, Satoru Miyano, Seiya Imoto
2014 C conf
Parameter estimation in multi-compartment SIR model.
FUSION
Masaya M. Saito, Seiya Imoto, Rui Yamaguchi, Satoru Miyano, Tomoyuki Higuchi
2013 J jnl
A strategy to select suitable physicochemical attributes of amino acids for protein fold recognition.
BMC Bioinform.
Alok Sharma, Kuldip K. Paliwal, Abdollah Dehzangi, James G. Lyons, Seiya Imoto, Satoru Miyano
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
2013 — conf
Multilayer Cluster Heat Map Visualizing Biological Tensor Data.
BSB
Atsushi Niida, Georg Tremmel, Seiya Imoto, Satoru Miyano
2013 J jnl
Principal component analysis using QR decomposition.
Int. J. Mach. Learn. Cybern.
Alok Sharma, Kuldip K. Paliwal, Seiya Imoto, Satoru Miyano
2012 J jnl
A Top-r Feature Selection Algorithm for Microarray Gene Expression Data.
IEEE ACM Trans. Comput. Biol. Bioinform.
Alok Sharma, Seiya Imoto, Satoru Miyano
2012 J jnl
A between-Class Overlapping Filter-Based Method for transcriptome Data Analysis.
J. Bioinform. Comput. Biol.
Alok Sharma, Seiya Imoto, 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
Null space based feature selection method for gene expression data.
Int. J. Mach. Learn. Cybern.
Alok Sharma, Seiya Imoto, Satoru Miyano, Vandana Sharma
2012 J jnl
Statistical model-based testing to evaluate the recurrence of genomic aberrations.
Bioinform.
Atsushi Niida, Seiya Imoto, Teppei Shimamura, Satoru Miyano
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 — ch.
Computational Drug Target Pathway Discovery: A Bayesian Network Approach.
Handbook of Statistical Bioinformatics
Seiya Imoto, Yoshinori Tamada, Hiromitsu Araki, Satoru Miyano
2011 J jnl
Estimating Genome-Wide Gene Networks Using Nonparametric Bayesian Network Models on Massively Parallel Computers.
IEEE ACM Trans. Comput. Biol. Bioinform.
Yoshinori Tamada, Seiya Imoto, Hiromitsu Araki, Masao Nagasaki, Cristin G. Print, Stephen D. Charnock-Jones, Satoru Miyano
2011 J jnl
Estimating exogenous variables in data with more variables than observations.
Neural Networks
Yasuhiro Sogawa, Shohei Shimizu, Teppei Shimamura, Aapo Hyvärinen, Takashi Washio, Seiya Imoto
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 — conf
Parallel Agent-Based Simulator for Influenza Pandemic.
AAMAS Workshops
Masaya M. Saito, Seiya Imoto, Rui Yamaguchi, Satoru Miyano, Tomoyuki Higuchi
2011 J jnl
Parallel Algorithm for Learning Optimal Bayesian Network Structure.
J. Mach. Learn. Res.
Yoshinori Tamada, Seiya Imoto, Satoru Miyano
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 — conf
Discovery of Exogenous Variables in Data with More Variables Than Observations.
ICANN (1)
Yasuhiro Sogawa, Shohei Shimizu, Aapo Hyvärinen, Takashi Washio, Teppei Shimamura, Seiya Imoto
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
2010 J jnl
Optimal Search on Clustered Structural Constraint for Learning Bayesian Network Structure.
J. Mach. Learn. Res.
Kaname Kojima, Eric Perrier, Seiya Imoto, Satoru Miyano
2010 — conf
Searching Optimal Bayesian Network Structure on Constraint Search Space: Super-Structure Approach.
JSAI-isAI Workshops
Seiya Imoto, Kaname Kojima, Eric Perrier, Yoshinori Tamada, Satoru Miyano
2009 — conf
Gene Networks Viewed through Two Models.
BICoB
Satoru Miyano, Rui Yamaguchi, Yoshinori Tamada, Masao Nagasaki, Seiya Imoto
2009 J jnl
Gene set-based module discovery in the breast cancer transcriptome.
BMC Bioinform.
Atsushi Niida, Andrew D. Smith, Seiya Imoto, Hiroyuki Aburatani, Michael Q. Zhang, Tetsu Akiyama
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
2009 Misc conf
Unraveling Dynamic Activities of Autocrine Pathways that Control Drug-Response Transcriptome Networks.
Pacific Symposium on Biocomputing
Yoshinori Tamada, Hiromitsu Araki, Seiya Imoto, Masao Nagasaki, Atsushi Doi, Yukiko Nakanishi, Yuki Tomiyasu, Kaori Yasuda, Ben Dunmore, Deborah Sanders, Sally Humphreys, Cristin G. Print, Stephen D. Charnock-Jones, Kousuke Tashiro, Satoru Kuhara, 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
ExonMiner: Web service for analysis of GeneChip Exon array data.
BMC Bioinform.
Kazuyuki Numata, Ryo Yoshida, Masao Nagasaki, Ayumu Saito, Seiya Imoto, Satoru Miyano
2008 J jnl
Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells.
BMC Bioinform.
Atsushi Niida, Andrew D. Smith, Seiya Imoto, Shuichi Tsutsumi, Hiroyuki Aburatani, Michael Q. Zhang, Tetsu Akiyama
2008 — conf
Partial Order-Based Bayesian Network Learning Algorithm for Estimating Gene Networks.
BIBM
Kazuyuki Numata, Seiya Imoto, 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 C conf
A Structure Learning Algorithm for Inference of Gene Networks from Microarray Gene Expression Data Using Bayesian Networks.
BIBE
Kazuyuki Numata, Seiya Imoto, Satoru Miyano
2007 C conf
Computational Genome-Wide Discovery of Aberrant Splice Variations with Exon Expression Profiles.
BIBE
Ryo Yoshida, Kazuyuki Numata, Seiya Imoto, Masao Nagasaki, Atsushi Doi, Kazuko Ueno, Satoru Miyano
2007 — conf
DIGDAG, a First Algorithm to Mine Closed Frequent Embedded Sub-DAGs.
MLG
Alexandre Termier, Yoshinori Tamada, Kazuyuki Numata, Seiya Imoto, Takashi Washio, Tomoyuki Higuchi
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 — 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
ArrayCluster: an analytic tool for clustering, data visualization and module finder on gene expression profiles.
Bioinform.
Ryo Yoshida, Tomoyuki Higuchi, Seiya Imoto, Satoru Miyano
2006 Misc conf
Computational Strategy for Discovering Druggable Gene Networks from Genome-Wide RNA Expression Profiles.
Pacific Symposium on Biocomputing
Seiya Imoto, Yoshinori Tamada, Hiromitsu Araki, Kaori Yasuda, Cristin G. Print, Stephen D. Charnock-Jones, Deborah Sanders, Christopher J. Savoie, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano
2006 J jnl
Statistical Model Selection Method to Analyze Combinatorial Effects of Snps and Environmental Factors for Binary Disease.
Int. J. Artif. Intell. Tools
Reiichiro Nakamichi, Seiya Imoto, Satoru Miyano
2005 — conf
A Penalized Likelihood Estimation on Transcriptional Module-Based Clustering.
ICCSA (3)
Ryo Yoshida, Seiya Imoto, Tomoyuki Higuchi
2005 — conf
Estimating Gene Networks from Expression Data and Binding Location Data via Boolean Networks.
ICCSA (3)
Osamu Hirose, Naoki Nariai, Yoshinori Tamada, Hideo Bannai, Seiya Imoto, Satoru Miyano
2005 — conf
Estimating Time-Dependent Gene Networks from Time Series Microarray Data by Dynamic Linear Models with Markov Switching.
CSB
Ryo Yoshida, Seiya Imoto, Tomoyuki Higuchi
2005 — conf
Estimating gene regulatory networks and protein-protein interactions of
ECCB/JBI
Naoki Nariai, Yoshinori Tamada, Seiya Imoto, Satoru Miyano
2005 J jnl
Utilizing Evolutionary Information and Gene Expression Data for Estimating Gene Networks with Bayesian Network Models.
J. Bioinform. Comput. Biol.
Yoshinori Tamada, Hideo Bannai, Seiya Imoto, Toshiaki Katayama, Minoru Kanehisa, Satoru Miyano
2004 — conf
A Mixed Factors Model for Dimension Reduction and Extraction of a Group Structure in Gene Expression Data.
CSB
Ryo Yoshida, Tomoyuki Higuchi, Seiya Imoto
2004 C conf
Case-Control Study of Binary Disease Trait Considering Interactions between SNPs and Environmental Effects using Logistic Regression.
BIBE
Reiichiro Nakamichi, Seiya Imoto, Satoru Miyano
2004 J jnl
Combining Microarrays and Biological Knowledge for Estimating Gene Networks via Bayesian Networks.
J. Bioinform. Comput. Biol.
Seiya Imoto, Tomoyuki Higuchi, Takao Goto, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano
2004 Misc conf
Finding Optimal Models for Small Gene Networks.
Pacific Symposium on Biocomputing
Sascha Ott, Seiya Imoto, Satoru Miyano
2004 — conf
Functional Data Analysis of the Dynamics of Gene Regulatory Networks.
KELSI
Tomohiro Ando, Seiya Imoto, Satoru Miyano
2004 — conf
Predicting gene regulation by sigma factors in Bacillus subtilis from genome-wide data.
ISMB/ECCB (Supplement of Bioinformatics)
Michiel J. L. de Hoon, Yuko Makita, Seiya Imoto, Kazuo Kobayashi, Naotake Ogasawara, Kenta Nakai, Satoru Miyano
2004 Misc conf
Predicting the Operon Structure of Bacillus subtilis Using Operon Length, Intergene Distance, and Gene Expression Information.
Pacific Symposium on Biocomputing
Michiel J. L. de Hoon, Seiya Imoto, Kazuo Kobayashi, Naotake Ogasawara, Satoru Miyano
2004 — conf
Residual Bootstrapping and Median Filtering for Robust Estimation of Gene Networks from Microarray Data.
CMSB
Seiya Imoto, Tomoyuki Higuchi, Sunyong Kim, Euna Jeong, Satoru Miyano
2004 Misc conf
Using Protein-Protein Interactions for Refining Gene Networks Estimated from Microarray Data by Bayesian Networks.
Pacific Symposium on Biocomputing
Naoki Nariai, Sunyong Kim, Seiya Imoto, Satoru Miyano
2003 J jnl
Bayesian Network and Nonparametric Heteroscedastic Regression for Nonlinear Modeling of Genetic Network.
J. Bioinform. Comput. Biol.
Seiya Imoto, Sunyong Kim, Takao Goto, Sachiyo Aburatani, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano
2003 — conf
Combining Microarrays and Biological Knowledge for Estimating Gene Networks via Bayesian Networks.
CSB
Seiya Imoto, Tomoyuki Higuchi, Takao Goto, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano
2003 — conf
Dynamic Bayesian Network and Nonparametric Regression for Nonlinear Modeling of Gene Networks from Time Series Gene Expression Data.
CMSB
Sunyong Kim, Seiya Imoto, Satoru Miyano
2003 C conf
Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection.
ECCB
Yoshinori Tamada, Sunyong Kim, Hideo Bannai, Seiya Imoto, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano
2003 Misc conf
Inferring Gene Regulatory Networks from Time-Ordered Gene Expression Data of Bacillus Subtilis Using Differential Equations.
Pacific Symposium on Biocomputing
Michiel J. L. de Hoon, Seiya Imoto, Kazuo Kobayashi, Naotake Ogasawara, Satoru Miyano
2003 J jnl
Inferring gene networks from time series microarray data using dynamic Bayesian networks.
Briefings Bioinform.
Sunyong Kim, Seiya Imoto, Satoru Miyano
2003 J jnl
Use of Gene Networks for Identifying and Validating Drug Targets.
J. Bioinform. Comput. Biol.
Seiya Imoto, Christopher J. Savoie, Sachiyo Aburatani, Sunyong Kim, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano
2002 — conf
Bayesian Network and Nonparametric Heteroscedastic Regression for Nonlinear Modeling of Genetic Network.
CSB
Seiya Imoto, Sunyong Kim, Takao Goto, Sachiyo Aburatani, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano
2002 Misc conf
Estimation of Genetic Networks and Functional Structures Between Genes by Using Bayesian Networks and Nonparametric Regression.
Pacific Symposium on Biocomputing
Seiya Imoto, Takao Goto, Satoru Miyano
2002 B conf
Inferring Gene Regulatory Networks from Time-Ordered Gene Expression Data Using Differential Equations.
Discovery Science
Michiel J. L. de Hoon, Seiya Imoto, Satoru Miyano
2002 J jnl
Statistical analysis of a small set of time-ordered gene expression data using linear splines.
Bioinform.
Michiel J. L. de Hoon, Seiya Imoto, Satoru Miyano